bluuebunny/crossref_metadata_2025 huggingface dataset:
High quality of SARS-CoV-2 molecular diagnostics in a diverse laboratory landscape through supported benchmark testing and External Quality Assessment
Authors: Sluimer John , van den Akker Willem M. R. , Goderski Gabriel , Swart Arno , van der Veer Bas , Cremer Jeroen , Chung Ngoc Hoa , Molenkamp Richard , Voermans Jolanda , Guldemeester Judith ,   Working Group SARS-CoV-2 Diagnostics The Netherlands, van der Eijk Annemiek , de Jong Menno D. , Mithoe Glen , Hermans Mirjam H. A. , de Beer Jessica L. , Wessels Els , von Wintersdorff Christian , Pas Suzan , Verweij Jaco J. , Melchers Willem J. G. , van de Bovenkamp Jeroen H. B. , Vahidnia Ali , Gard Lilli , Schuurman Rob , Wintermans Bas , Leversteijn-van Hall Maurine , Smits Paul , de Groot Theun , Deiman Birgit A. L. M. , Bart Aldert , van der Reijden Wil , Svraka-Latifovic Sanela , van der Zanden Adri G. M. , Thijsen Steven , Schubbert Rainer , Dreesens Lisa L. , van Duijn Gert , Ong David S. Y. , Oostra Monique , Bruisten Sylvia , van Trijp Marijke , Pettersson Annika , van Burgel Nathalie D. , Oudbier Joke , van der Linden Michael , van Rijn Michiel , Bos Martine P. , Rossen John , Schuurs Theo A. , Grosser Roger , Smit Pieter , Nijhuis Roel H. T. , Rozemeijer Wouter , van de Laar Thijs , Scheepers Theodoor M. M. , Smeets Leonard C. , Flipse Jacky , de Leeuw Bertie , Dijkman Remco , van Maarseveen Noortje , Koppelman Marco , Postma Bent , van Hannen Erik J. , Thai Khoa , Braun Kathrin , Schepers Raf J. F. , Henning Jana , van Hees Eva R. , Tacken Mirriam G. J. , Mol Jaqueline , Heddema Edou R. , Eggink Dirk , Presser Lance D. , Meijer Adam
Published: January 2024

A two-step strategy combining assisted benchmark testing (entry controls) and External Quality Assessments (EQAs) with blinded simulated clinical specimens to enhance and maintain the quality of nucleic acid amplification testing was developed. This strategy was successfully applied to 71 diagnostic laboratories in The Netherlands when upscaling the national diagnostic capacity during the SARS-CoV-2 pandemic. The availability of benchmark testing in combination with advice for improvement substantially enhanced the quality of the laboratory testing procedures for SARS-CoV-2 detection. The three subsequent EQA rounds demonstrated high quality testing with regard to specificity (99.6% correctly identified) and sensitivity (93.3% correctly identified). Even with the implementation of novel assays, changing workflows using diverse equipment and a high degree of assay heterogeneity, the overall high quality was maintained using this two-step strategy. We show that in contrast to the limited value of Cq value for absolute proxies of viral load, these Cq values can, in combination with metadata on strategies and techniques, provide valuable information for laboratories to improve their procedures. In conclusion, our two-step strategy (preparation phase followed by a series of EQAs) is a rapid and flexible system capable of scaling, improving, and maintaining high quality diagnostics even in a rapidly evolving (e.g. pandemic) situation.
Immunoinformatics-guided approach for designing a pan-proteome multi-epitope subunit vaccine against African swine fever virus
Authors: Simbulan Alea Maurice , Banico Edward C. , Sira Ella Mae Joy S. , Odchimar Nyzar Mabeth O. , Orosco Fredmoore L.
Published: January 2024

Despite being identified over a hundred years ago, there is still no commercially available vaccine for the highly contagious and deadly African swine fever virus (ASFV). This study used immunoinformatics for the rapid and inexpensive designing of a safe and effective multi-epitope subunit vaccine for ASFV. A total of 18,858 proteins from 100 well-annotated ASFV proteomes were screened using various computational tools to identify potential epitopes, or peptides capable of triggering an immune response in swine. Proteins from genotypes I and II were prioritized for their involvement in the recent global ASFV outbreaks. The screened epitopes exhibited promising qualities that positioned them as effective components of the ASFV vaccine. They demonstrated antigenicity, immunogenicity, and cytokine-inducing properties indicating their ability to induce potent immune responses. They have strong binding affinities to multiple swine allele receptors suggesting a high likelihood of yielding more amplified responses. Moreover, they were non-allergenic and non-toxic, a crucial prerequisite for ensuring safety and minimizing any potential adverse effects when the vaccine is processed within the host. Integrated with an immunogenic 50S ribosomal protein adjuvant and linkers, the epitopes formed a 364-amino acid multi-epitope subunit vaccine. The ASFV vaccine construct exhibited notable immunogenicity in immune simulation and molecular docking analyses, and stable profiles in secondary and tertiary structure assessments. Moreover, this study designed an optimized codon for efficient translation of the ASFV vaccine construct into the Escherichia coli K-12 expression system using the pET28a(+) vector. Overall, both sequence and structural evaluations suggested the potential of the ASFV vaccine construct as a candidate for controlling and eradicating outbreaks caused by the pathogen.
Multivalent next generation influenza virus vaccines protect against seasonal and pre-pandemic viruses
Authors: Uno Naoko , Ross Ted M.
Published: January 2024

Each year, new influenza virus vaccine formulations are generated to keep up with continuously circulating and mutating viral variants. A next-generation influenza virus vaccine would provide long-lasting, broadly-reactive immune protection against current and future influenza virus strains for both seasonal and pre-pandemic viruses. Next generation immunogens were designed using computationally optimized broadly reactive antigen (COBRA) methodology to protect against a broad range of strains over numerous seasons. Novel HA and NA amino acid sequences were derived from multilayered consensus sequence alignment for multiple subtypes of influenza. This multivalent formulation was hypothesized to elicit broadly protective immune responses against both seasonal and pre-pandemic influenza viruses. Mice were vaccinated with multivalent mixtures of HA and NA (H1, H2, H3, H5, H7, N1, N2) proteins. Multivalent COBRA vaccinations elicited antibodies that recognized a broad panel of strains and vaccinated mice were protected against viruses representing multiple subtypes. This is a promising candidate for a universal influenza vaccine that elicits protective immune responses against seasonal and pre-pandemic strains over multiple seasons.
Evolution of a plant sex chromosome driven by expanding pericentromeric recombination suppression
Authors: Filatov Dmitry A.
Published: January 2024

Recombination suppression around sex-determining gene(s) is a key step in evolution of sex chromosomes, but it is not well understood how it evolves. Recently evolved sex-linked regions offer an opportunity to understand the mechanisms of recombination cessation. This paper analyses such a region on Silene latifolia (Caryophyllaceae) sex chromosomes, where recombination was suppressed in the last 120 thousand years ("stratum 3"). Locating the boundaries of the stratum 3 in S. latifolia genome sequence revealed that this region is far larger than assumed previously—it is about 14 Mb long and includes 202 annotated genes. A gradient of X:Y divergence detected in the stratum 3, with divergence increasing proximally, indicates gradual recombination cessation, possibly caused by expansion of pericentromeric recombination suppression (PRS) into the pseudoautosomal region. Expansion of PRS was also the likely cause for the formation of the older stratum 2 on S. latifolia sex chromosomes. The role of PRS in sex chromosome evolution has been underappreciated, but it may be a significant factor, especially in the species with large chromosomes where PRS is often extensive.
Baseline imaging characteristics and early structural changes in macula on rhegmatogenous retinal detachment
Authors: Quarta Alberto , Gironi Matteo , Ruggeri Maria Ludovica , Aharrh-Gnama Agbeanda , Porreca Annamaria , D’Aloisio Rossella , Toto Lisa , Di Nicola Marta , Mastropasqua Rodolfo
Published: January 2024

Animal models have demonstrated that structural changes affect the macula during peripheral rhegmatogenous retinal detachment. This study aimed to assess photoreceptors, retinal and choriocapillaris perfusion in non-macula involving rhegmatogenous retinal detachment by analyzing en-face images from structural OCTA segmented at the ellipsoid zone (EZ) level, calculating (1) “normalized” reflectivity as a surrogate biomarker of photoreceptor damage (2) perfusion density (PD), vessel length density (VLD) and vessel diameter index (VDI) of superficial capillary plexus (SCP) and deep capillary plexus (DCP) (3) perfusion density of choriocapillaris (PDCC). Twenty-one eyes affected by macula-on rhegmatogenous retinal detachment (RRD) were enrolled at the University “G. d’Annunzio”, Chieti-Pescara. The fellow unaffected eye was used as control. The mean age at the onset of RRD was 60.09 ± 10.22 (range 34–83). Compared with fellow eyes, we found lower EZ “normalized” reflectivity in macula-on (0.42 ± 0.15 in fellow eyes and 0.31 ± 0.09 in macula on p = 0.004). The affected eye was also characterized by impaired perfusion in SCP (17.26 ± 3.34% in macula on and 20.56 ± 3.62% in the fellow eye p = 0.004) and CC (50.21 ± 6.20% in macula on the eye and 57.43 ± 6.20% in the fellow eye p = 0.004). Macula-on rhegmatogenous retinal detachment has subclinical changes in photoreceptors, SCP, and CC. Future longitudinal studies should evaluate if early changes could impact post-operative macular function.
Prediction of sentinel lymph node metastasis in breast cancer patients based on preoperative features: a deep machine learning approach
Authors: Shahriarirad Reza , Meshkati Yazd Seyed Mostafa , Fathian Ramin , Fallahi Mohammadmehdi , Ghadiani Zahra , Nafissi Nahid
Published: January 2024

Sentinel lymph node (SLN) biopsy is the standard surgical approach to detect lymph node metastasis in breast cancer. Machine learning is a novel tool that provides better accuracy for predicting positive SLN involvement in breast cancer patients. This study obtained data from 2890 surgical cases of breast cancer patients from two referral hospitals in Iran from 2000 to 2021. Patients whose SLN involvement status was identified were included in our study. The dataset consisted of preoperative features, including patient features, gestational factors, laboratory data, and tumoral features. In this study, TabNet, an end-to-end deep learning model, was proposed to predict SLN involvement in breast cancer patients. We compared the accuracy of our model with results from logistic regression analysis. A total of 1832 patients with an average age of 51 ± 12 years were included in our study, of which 697 (25.5%) had SLN involvement. On average, the TabNet model achieved an accuracy of 75%, precision of 81%, specificity of 70%, sensitivity of 87%, and AUC of 0.74, while the logistic model demonstrated an accuracy of 70%, precision of 73%, specificity of 65%, sensitivity of 79%, F1 score of 73%, and AUC of 0.70 in predicting the SLN involvement in patients. Vascular invasion, tumor size, core needle biopsy pathology, age, and FH had the most contributions to the TabNet model. The TabNet model outperformed the logistic regression model in all metrics, indicating that it is more effective in predicting SLN involvement in breast cancer patients based on preoperative data.
Investigating robust associations between functional connectivity based on graph theory and general intelligence
Authors: Metzen Dorothea , Stammen Christina , Fraenz Christoph , Schlüter Caroline , Johnson Wendy , Güntürkün Onur , DeYoung Colin G. , Genç Erhan
Published: January 2024

Previous research investigating relations between general intelligence and graph-theoretical properties of the brain’s intrinsic functional network has yielded contradictory results. A promising approach to tackle such mixed findings is multi-center analysis. For this study, we analyzed data from four independent data sets (total N > 2000) to identify robust associations amongst samples between g factor scores and global as well as node-specific graph metrics. On the global level, g showed no significant associations with global efficiency or small-world propensity in any sample, but significant positive associations with global clustering coefficient in two samples. On the node-specific level, elastic-net regressions for nodal efficiency and local clustering yielded no brain areas that exhibited consistent associations amongst data sets. Using the areas identified via elastic-net regression in one sample to predict g in other samples was not successful for local clustering and only led to one significant, one-way prediction across data sets for nodal efficiency. Thus, using conventional graph theoretical measures based on resting-state imaging did not result in replicable associations between functional connectivity and general intelligence.
Prognostic significance of pretreatment albumin–bilirubin (ALBI) grade and platelet–albumin–bilirubin (PALBI) grade in patients with small cell lung cancer
Authors: Kut Engin , Menekse Serkan
Published: January 2024

Small cell lung cancer (SCLC) is a common cancer among the world’s lung cancers. Despite advances in diagnosis and treatment, the prognosis is still poor. There is no effective biomarker other than stage in daily practice. However, in daily practice, patients may have different features and survival times even though they have the same stage. Previously, albumin–bilirubin (ALBI) grade, platelet–albumin–bilirubin (PALBI) grade were used to determine the prognosis of acute-chronic liver failure and acute upper gastrointestinal bleeding in liver cirrhosis. In subsequent studies, they were found to be associated with prognosis in hepatocellular carcinoma (HCC) and other solid cancers. However, the prognostic relationship between ALBI grade, PALBI grade, and SCLC is unknown. Therefore, we conducted this study to examine the relationship between ALBI grade and PALBI grade and prognosis in SCLC patients. Data of 138 patients with advanced SCLC at diagnosis between 2009 and 2020 were analyzed retrospectively. The results of the multivariate analysis were as follows: ALBI grade 1 vs 2, hazard ratio (HR) = 1.608, p = 0.002 for OS and HR = 1.575, p = 0.002 for PFS; ALBI grade 1 vs 3, HR = 2.035, p < 0.001 for OS and HR = 2.675, p < 0.001 for PFS; PALBI grade 1 vs 2, HR = 1.302, p = 0.006 for OS and HR = 1.674, p = 0.002 for PFS; and PALBI grade 1 vs 3, HR = 1.725, p < 0.001 for OS and HR = 2.675, p < 0.001 for PFS. In conclusion, the ALBI and PALBI grades were determined to be associated with the prognosis of SCLC, and they can be used as easy, inexpensive, and practical markers in determining the follow-up treatment and prognosis of SCLC patients.
Resolving acne with optimized adapalene microspongeal gel, in vivo and clinical evaluations
Authors: Yehia Rania M. , Teaima Mahmoud H. , Ragaie Maha H. , Elmazar Mohamed M. , Attia Dalia A. , El-Nabarawi Mohamed A.
Published: January 2024

In our pursuit of enhancing acne treatment while minimizing side effects, we developed tailored Adapalene microsponges (MS) optimized using a Box–Behnken design 33. The independent variables, Eudragit RS100 percentage in the polymer mixture, organic phase volume, and drug to polymer percentage, were explored. The optimized formulation exhibited remarkable characteristics, with a 98.3% ± 1.6 production yield, 97.3% ± 1.64 entrapment efficiency, and a particle size of 31.8 ± 1.1 µm. Notably, it achieved a 24 h cumulative drug release of 75.1% ± 1.4. To delve deeper into its efficacy, we evaluated the optimized microspongeal-gel in vitro, in vivo, and clinically. It demonstrated impressive retention in the pilosebaceous unit, a target for acne treatment. Comparative studies between our optimized Adapalene microspongeal gel and marketed Adapalene revealed superior performance. In vivo studies on Propionibacterium acnes-infected mice ears showed a remarkable 97% reduction in ear thickness, accompanied by a significant decrease in inflammatory signs and NF-κB levels, as confirmed by histopathological and histochemical examination. Moreover, in preliminary clinical evaluation, it demonstrated outstanding effectiveness in reducing comedonal lesions while causing fewer irritations. This not only indicates its potential for clinical application but also underscores its ability to enhance patient satisfaction, paving the way for future commercialization.
Interactive effects of long-term management of crop residue and phosphorus fertilization on wheat productivity and soil health in the rice–wheat
Authors: Gupta Rajeev Kumar , Sraw Paramjit Kaur , Kang Jasjit Singh , Kaur Jagroop , Sharma Vivek , Pathania Neemisha , Kalia Anu , Al-Ansari Nadhir , Alataway Abed , Dewidar Ahmed Z. , Mattar Mohamed A.
Published: January 2024

In the context of degradation of soil health, environmental pollution, and yield stagnation in the rice–wheat system in the Indo-Gangetic Plains of South Asia, an experiment was established in split plot design to assess the long-term effect of crop residue management on productivity and phosphorus requirement of wheat in rice–wheat system. The experiment comprised of six crop residue management practices as the main treatment factor with three levels (0, 30 and 60 kg P2O5 ha–1) of phosphorus fertilizer as sub-treatments. Significant improvement in soil aggregation, bulk density, and infiltration rate was observed under residue management (retention/incorporation) treatments compared to residue removal or residue burning. Soil organic carbon (SOC), available nutrient content (N, P, and K), microbial count, and enzyme activities were also significantly higher in conservation tillage and residue-treated plots than without residue/burning treatments. The residue derived from both crops when was either retained/incorporated improved the soil organic carbon (0.80%) and resulted in a significant increase in SOC (73.9%) in the topsoil layer as compared to the conventional practice. The mean effect studies revealed that crop residue management practices and phosphorus levels significantly influenced wheat yield attributes and productivity. The higher grain yield of wheat was recorded in two treatments, i.e. the basal application of 60 kg P2O5 ha–1 without residue incorporation and the other with half the P-fertilizer (30 kg P2O5 ha–1) with rice residue only. The grain yield of wheat where the rice and wheat residue were either retained/incorporated without phosphorus application was at par with 30 and 60 kg P2O5ha–1. Phosphorus levels also significantly affected wheat productivity and available P content in the soil. Therefore, results suggested that crop residue retention following the conservation tillage approach improved the yield of wheat cultivated in the rice–wheat cropping system.
Early detection of liver injuries by the Serum enhanced binding test sensitive to albumin post-transcriptional modifications
Authors: El Balkhi Souleiman , Rahali Mohamad Ali , Lakis Roy , Sauvage François Ludovic , Martin Marving , Janaszkiewicz Angelika , Lawson Roland , Goncalves Ruben , Carrier Paul , Loustaud-Ratti Veronique , Guyot Anne , Marquet Pierre , Di Meo Florent , Saint-Marcoux Franck
Published: January 2024

Early and sensitive biomarkers of liver dysfunction and drug-induced liver injury (DILI) are still needed, both for patient care and drug development. We developed the Serum Enhanced Binding (SEB) test to reveal post-transcriptional modifications (PTMs) of human serum albumin resulting from hepatocyte dysfunctions and further evaluated its performance in an animal model. The SEB test consists in spiking serum ex-vivo with ligands having specific binding sites related to the most relevant albumin PTMs and measuring their unbound fraction. To explore the hypothesis that albumin PTMs occur early during liver injury and can also be detected by the SEB test, we induced hepatotoxicity in male albino Wistar rats by administering high daily doses of ethanol and CCl4 over several days. Blood was collected for characterization and quantification of albumin isoforms by high-resolution mass spectrometry, for classical biochemical analyses as well as to apply the SEB test. In the exposed rats, the appearance of albumin isoforms paralleled the positivity of the SEB test ligands and histological injuries. These were observed as early as D3 in the Ethanol and CCl4 groups, whereas the classical liver tests (ALT, AST, PAL) significantly increased only at D7. The behavior of several ligands was supported by structural and molecular simulation analysis. The SEB test and albumin isoforms revealed hepatocyte damage early, before the current biochemical biomarkers. The SEB test should be easier to implement in the clinics than albumin isoform profiling.
An intelligent LinkNet-34 model with EfficientNetB7 encoder for semantic segmentation of brain tumor
Authors: Sulaiman Adel , Anand Vatsala , Gupta Sheifali , Al Reshan Mana Saleh , Alshahrani Hani , Shaikh Asadullah , Elmagzoub M. A.
Published: January 2024

A brain tumor is an unnatural expansion of brain cells that can’t be stopped, making it one of the deadliest diseases of the nervous system. The brain tumor segmentation for its earlier diagnosis is a difficult task in the field of medical image analysis. Earlier, segmenting brain tumors was done manually by radiologists but that requires a lot of time and effort. Inspite of this, in the manual segmentation there was possibility of making mistakes due to human intervention. It has been proved that deep learning models can outperform human experts for the diagnosis of brain tumor in MRI images. These algorithms employ a huge number of MRI scans to learn the difficult patterns of brain tumors to segment them automatically and accurately. Here, an encoder-decoder based architecture with deep convolutional neural network is proposed for semantic segmentation of brain tumor in MRI images. The proposed method focuses on the image downsampling in the encoder part. For this, an intelligent LinkNet-34 model with EfficientNetB7 encoder based semantic segmentation model is proposed. The performance of LinkNet-34 model is compared with other three models namely FPN, U-Net, and PSPNet. Further, the performance of EfficientNetB7 used as encoder in LinkNet-34 model has been compared with three encoders namely ResNet34, MobileNet_V2, and ResNet50. After that, the proposed model is optimized using three different optimizers such as RMSProp, Adamax and Adam. The LinkNet-34 model has outperformed with EfficientNetB7 encoder using Adamax optimizer with the value of jaccard index as 0.89 and dice coefficient as 0.915.
Modeling of antibody responses to COVID-19 vaccination in patients with rheumatoid arthritis
Authors: Kim Yun Kyu , Choi Yunhee , Jung Ji In , Kim Ju Yeon , Kim Mi Hyeon , Curtis Jeffrey , Lee Eun Bong
Published: January 2024

To construct a model of the antibody response to COVID-19 vaccination in patients with rheumatoid arthritis (RA), and to identify clinical factors affecting the antibody response. A total of 779 serum samples were obtained from 550 COVID-19-naïve RA patients who were vaccinated against COVID-19. Antibody titers for the receptor binding domain (anti-RBD) and nucleocapsid (anti-N) were measured. The time from vaccination, and the log-transformed anti-RBD titer, were modeled using a fractional polynomial method. Clinical factors affecting antibody responses were analyzed by a regression model using generalized estimating equation. The anti-RBD titer peaked at about 2 weeks post-vaccination and decreased exponentially to 36.5% of the peak value after 2 months. Compared with the first vaccination, the 3rd or 4th vaccinations shifted the peaks of anti-RBD antibody response curves significantly upward (by 28-fold [4–195] and 32-fold [4–234], respectively). However, there was no significant shift in the peak from the 3rd vaccination to the 4th vaccination (p = 0.64). Multivariable analysis showed that sulfasalazine increased the vaccine response (by 1.49-fold [1.13–1.97]), but abatacept or JAK inhibitor decreased the vaccine response (by 0.13-fold [0.04–0.43] and 0.44-fold [0.26–0.74], respectively). Age was associated with lower ln [anti-RBD] values (coefficient: − 0.03 [− 0.04 to − 0.02]). In conclusion, the anti-RBD response of RA patients peaked at 2 weeks after COVID-19 vaccination, and then decreased exponentially, with the maximum peak increase observed after the 3rd vaccination. The antibody response was affected by age and the medications used to treat RA.
Enhanced convergence in p-bit based simulated annealing with partial deactivation for large-scale combinatorial optimization problems
Authors: Onizawa Naoya , Hanyu Takahiro
Published: January 2024

This article critically investigates the limitations of the simulated annealing algorithm using probabilistic bits (pSA) in solving large-scale combinatorial optimization problems. The study begins with an in-depth analysis of the pSA process, focusing on the issues resulting from unexpected oscillations among p-bits. These oscillations hinder the energy reduction of the Ising model and thus obstruct the successful execution of pSA in complex tasks. Through detailed simulations, we unravel the root cause of this energy stagnation, identifying the feedback mechanism inherent to the pSA operation as the primary contributor to these disruptive oscillations. To address this challenge, we propose two novel algorithms, time average pSA (TApSA) and stalled pSA (SpSA). These algorithms are designed based on partial deactivation of p-bits and are thoroughly tested using Python simulations on maximum cut benchmarks that are typical combinatorial optimization problems. On the 16 benchmarks from 800 to 5000 nodes, the proposed methods improve the normalized cut value from 0.8 to 98.4% on average in comparison with the conventional pSA.
Ab initio investigation of functionalization of titanium carbide Ti3C2 MXenes to tune the selective detection of lung cancer biomarkers
Authors: Alfalasi Wadha , Hussain Tanveer , Tit Nacir
Published: January 2024

Selected volatile organic compounds (VOCs), such as benzene (C6H6), cyclohexane (C6H12), isoprene (C5H8), cyclopropanone (C3H4O), propanol (C3H8O), and butyraldehyde butanal (C4H8O), in exhaled human breath can act as indicators or biomarkers of lung cancer diseases. Detection of such VOCs with low density would pave the way for an early diagnosis of the disease and thus early treatment and cure. In the present investigation, the density-functional theory (DFT) is applied to study the detection of the mentioned VOCs on Ti3C2TX MXenes, saturated with the functional groups Tx = O, F, S, and OH. For selectivity, comparative sensing of other interfering air molecules from exhaled breath, such as O2, N2, CO2, and H2O is further undertaken. Three functionalization (Tx = O, F, and S) are found promising for the selective detection of the studied VOCs, in particular Ti3C2O2 MXenes has shown distinct sensor response toward the C5H8, C6H6, C6H12, and C3H4O. The relatively strong physisorption ($${E}_{ads}\cong -0.45 to-0.65 {\text{eV}}$$

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-
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), triggered between VOC and MXene due to an enhancement of van der Waals interaction, is found responsible to affect the near Fermi level states, which in turn controls the conductivity and consequently the sensor response. Meanwhile, such intermediate-strength interactions remain moderate to yield small desorption recovery time (of order $$\tau \cong \mu {\text{s}}-{\text{ms}})$$

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using visible light at room temperature. Thus, Ti3C2O2 MXenes are found promising candidate material for reusable biosensor for the early diagnosis of lung cancer diseases through the VOC detection in exhaled breath.
Light-enhanced catalytic activity of stable and large gold nanoparticles in homocoupling reactions
Authors: Hou Jian , Lartey Jemima A. , Lee Chang Yeon , Kim Jun-Hyun
Published: January 2024

Validating the direct photocatalytic activity of colloidal plasmonic nanoparticles is challenging due to their limited stability and needed support materials that can often contribute to the chemical reactions. Stable gold nanoparticles (AuNPs) with tunable sizes are prepared across porous polymer particles without any chemical bonds where the resulting composite particles exhibit intense surface plasmon resonances (SPRs) in the visible region. These composite particles are then tested as photocatalysts under a broadband solar-simulated light source to examine the contribution degree of photothermal heating and SPR coming from the incorporated AuNPs in the C–C bond forming homocoupling reaction. Generally, the thermal and photothermal heating are the main driving force to increase the reactivity of relatively smaller AuNPs (~ 44 nm in diameter) with a narrower SPR band. However, the SPR-induced catalytic activity is much greater for the composite particles containing larger AuNPs (~ 87 nm in diameter) with a broader SPR. As the polymer particle matrix does not influence the catalytic activity (e.g., inducing charge delocalization and/or separation), the unique SPR role of the colloidal AuNPs in the catalytic reaction is assessable under light irradiation. This study experimentally demonstrates the possibility of evaluating the direct contribution of SPRs to photocatalytic chemical reactions.
A novel aging-associated lncRNA signature for predicting prognosis in osteosarcoma
Authors: He Yi , Huang Xiao , Ma Yajie , Yang Guohui , Cui Yuqing , Lv Xuefeng , Zhao Rongling , Jin Huifang , Tong Yalin , Zhang Xinyu , Li Jitian , Peng Mengle
Published: January 2024

Osteosarcoma (OS) is one of the most prevalent bone tumors in adolescents, and the correlation between aging and OS remains unclear. Currently, few accurate and reliable biomarkers have been determined for OS prognosis. To address this issue, we carried out a detailed bioinformatics analysis based on OS with data from the Cancer Genome Atlas data portal and Human Aging Genomic Resources database, as well as in vitro experiments. A total of 88 OS samples with gene expression profiles and corresponding clinical characteristics were obtained. Through univariate Cox regression analysis and survival analysis, 10 aging-associated survival lncRNAs (AASRs) were identified to be associated with the overall survival of OS patients. Based on the expression levels of the 10 AASRs, the OS patients were classified into two clusters (Cluster A and Cluster B). Cluster A had a worse prognosis, while Cluster B had a better prognosis. Then, 5 AASRs were ultimately included in the signature through least absolute shrinkage and selection operator-Cox regression analysis. Kaplan‒Meier survival analysis verified that the high-risk group exhibited a worse prognosis than the low-risk group. Furthermore, univariate and multivariate Cox regression analyses confirmed that the riskScore was an independent prognostic factor for OS patients. Subsequently, we discovered that the risk signature was correlated with the properties of the tumor microenvironment and immune cell infiltration. Specifically, there was a positive association between the risk model and naïve B cells, resting dendritic cells and gamma delta T cells, while it was negatively related to CD8+ T cells. Finally, in vitro experiments, we found that UNC5B-AS1 inhibited OS cells from undergoing cellular senescence and apoptosis, thereby promoting OS cells proliferation. In conclusion, we constructed and verified a 5 AASR-based signature, that exhibited excellent performance in evaluating the overall survival of OS patients. In addition, we found that UNC5B-AS1 might inhibit the senescence process, thus leading to the development and progression of OS. Our findings may provide novel insights into the treatment of OS patients.
Low urinary sodium-to-potassium ratio in the early phase following single-unit cord blood transplantation is a predictive factor for poor non-relapse mortality in adults
Authors: Takano Kosuke , Monna-Oiwa Maki , Isobe Masamichi , Kato Seiko , Takahashi Satoshi , Nannya Yasuhito , Konuma Takaaki
Published: January 2024

Although daily higher urinary sodium (Na) and potassium (K) excretion ratio is associated with the risk of cardiovascular disease in the general population, a low Na/K ratio is associated with renal dysfunction in critically ill patients. Thus, we retrospectively analyzed the impact of daily urinary Na and K excretion and their ratio on non-relapse mortality (NRM) and overall mortality in 172 adult single-unit cord blood transplantation (CBT) patients treated at our institution between 2007 and 2020. Multivariate analysis showed that a low urinary Na/K ratio at both 14 days (hazard ratio [HR], 4.82; 95% confidence interval [CI], 1.81–12.83; P = 0.001) and 28 days (HR, 4.47; 95% CI 1.32–15.12; P = 0.015) was significantly associated with higher NRM. Furthermore, a low urinary Na/K ratio at 28 days was significantly associated with higher overall mortality (HR, 2.38; 95% CI 1.15–4.91; P = 0.018). Patients with a low urinary Na/K ratio had decreased urine volume, more weight gain, experienced more grade III–IV acute graft-versus-host disease, and required corticosteroids by 28 days after CBT. These findings indicate that a low urinary Na/K ratio early after single-unit CBT is associated with poor NRM and survival in adults.
Mass spectra prediction with structural motif-based graph neural networks
Authors: Park Jiwon , Jo Jeonghee , Yoon Sungroh
Published: January 2024

Mass spectra, which are agglomerations of ionized fragments from targeted molecules, play a crucial role across various fields for the identification of molecular structures. A prevalent analysis method involves spectral library searches, where unknown spectra are cross-referenced with a database. The effectiveness of such search-based approaches, however, is restricted by the scope of the existing mass spectra database, underscoring the need to expand the database via mass spectra prediction. In this research, we propose the Motif-based Mass Spectrum prediction Network (MoMS-Net), a GNN-based architecture to predict the mass spectra pattern utilizing the structural motif information of the molecule. MoMS-Net considers both a molecule and its substructures as a graph form, which facilitates the incorporation of long-range dependencies while using less memory compared to the graph transformer model. We evaluated our model over various types of mass spectra and showed the validity and superiority over the conventional models.
Chaotic dynamics in X-ray free-electron lasers with an optical undulator
Authors: Abbasi E. , Jafari S.
Published: January 2024

In this work, the chaotic motions of relativistic electrons in X-ray free-electron lasers are investigated using an optical undulator in the presence of a magnetized ion-channel background. To miniaturize X-ray light sources, the optical undulator is a promising concept. The optical undulator provides higher optical gain than conventional magnetostatic undulators due to its micrometer wavelength. In addition, it reduces the required electron beam energy from several GeV to the multi-MeV range to produce X-ray pulses. The interaction of an optical undulator with an intense relativistic electron beam is a highly non-linear phenomenon that can lead to chaotic dynamics. At synchrotron radiation sources, the possibility of chaos control for X-ray FELs can be critical for certain classes of experimental studies. The equations of motion for a relativistic electron propagating through the optical undulator in the presence of a magnetized ion-channel can be derived from the Hamiltonian of the interaction region. Simulation results revealed that the intensity of the perturbation route from orderly behavior to chaos depends on the beam density, axial magnetic field strength, ion-channel density parameter, and pump laser undulator. Specific values of parameters were obtained for the transition from regular to chaotic paths. Bifurcation diagrams of the system were plotted to demonstrate the origin of chaos at a critical point, and Poincaré maps were created to distinguish between chaotic and orderly motions of electrons. The proposed new scheme can help to improve X-ray FELs, which have potential usages in basic sciences, medicine, and industry.
Peripheral neurotrophin levels during controlled crack/cocaine abstinence: a systematic review and meta-analysis
Authors: Morelos-Santana E. , Islas-Preciado D. , Alcalá-Lozano R. , González-Olvera J. , Estrada-Camarena E.
Published: January 2024

Cocaine/crack abstinence periods have higher risk of relapse. Abstinence as initial part of the recovery process is affected by learning and memory changes that could preserve the addictive cycle. To further understand how the interruption of cocaine/crack consumption affects neurotrophin level we performed the present systematic review and meta-analysis following the PRISMA statement (number CRD42019121643). The search formula was conducted in PubMed, Web of Science, Embase, ScienceDirect, and Google Scholar databases. The inclusion criterion was cocaine use disorder in 18 to 60-year-old people, measuring at least one neurotrophin in blood before and after a controlled abstinence period. Studies without pre-post design were excluded. Five investigations had nine different reports, four of them were subjected to a meta-analysis (n = 146). GRADE risk of bias method was followed. Individual studies reported increased peripheral brain derived neurotrophic factor (BDNF) after abstinence, evidence pooled by Hedge’s g showed no significant change in BDNF after abstinence. Relevant heterogeneity in the length of the abstinence period (12–32 days), last cocaine/crack consumption monitoring and blood processing were detected that could help to explain non-significant results. Further improved methods are suggested, and a potential BDNF augmentation hypothesis is proposed that, if true, would help to understand initial abstinence as a re-adaptation period influenced by neurotrophins such as the BDNF.
Assessment of refining efficiency during the refining cycle in a foundry degassing unit in industrial conditions
Authors: Socha Ladislav , Prášil Tomáš , Gryc Karel , Svizelova Jana , Saternus Mariola , Merder Tomasz , Pieprzyca Jacek , Nuska Petr
Published: January 2024

The article focuses on the issue of improving the efficiency of a Foundry Degassing Unit (FDU) via operational testing of aluminium alloys during casting at MOTOR JIKOV Slévárna a.s.. As part of the research, the efficiency of the refining process in the FDU was assessed. The main emphasis was placed on determining the moment of the greatest decrease in the hydrogen content in the melt and whether it is possible to shorten the refining cycle. The values of the Dichte Index were determined, on the basis of which the degassing curve was plotted and the progress of the melt degassing was assessed. To ensure the required quality of castings, the maximum allowable value of the Dichte Index ranged from 3 to 4%. During the process, the temperature drop during the refining cycle was also determined. The total temperature drop from pouring the melt into the ladle to the end of refining ranged from 26 to 32 °C, which is within the acceptable limits of the foundry. Based on the knowledge resulting from the operational experiments, recommendations were formulated to optimize the refining technology at the FDU for the MOTOR JIKOV Slévárna a.s. foundry.
Cryptographic triboelectric random number generator with gentle breezes of an entropy source
Authors: Kim Moon-Seok , Tcho Il-Woong , Choi Yang-Kyu
Published: January 2024

A wind-driven triboelectric nanogenerator (W-TENG) is a promising energy harvesting device due to its clean, ubiquitous and unexhausted properties. In addition, a W-TENG induces unpredictable chaotic outputs from wind flow that can serve as an entropy source for cryptography. This can be applied to a true random number generator (TRNG) for a secured system due to its inherent turbulent nature; thus, a W-TENG with a two-in-one structure can simultaneously generate both power and true random numbers. However, a previously reported W-TENG had one major drawback: a wind velocity of 10 m/s is required for stable energy harvesting by wind force. Thus, it is timely to demonstrate a W-TENG-based RNG whose operating condition is below 3 m/s, which is a gentle breeze similar to natural wind. In this study, we demonstrate a wind-driven cryptographic triboelectric random number generator (WCT-RNG) by using a W-TENG whose operating condition for wind speed is below 3 m/s by adopting a rear-fixed film structure instead of a conventional structure. The rear-fixed film refers to the fluttering film being freestanding on the front-side and fixed on the rear-side, where the front- and rear-sides are the wind inlet and outlet, respectively. The WCT-RNG enables the W-TENG to operate below a 3 m/s wind velocity. Because of this, the working time of the WCT-RNG is dramatically enhanced from only 8–42% at an average altitude above sea level. As the capability of operating at low wind speeds is significantly improved, a WCT-RNG becomes more useful and practical for generating both power and true random numbers in a single device. The device can thereby lead to the construction of a self-powered TRNG and secure communication for Internet of Things (IoT) devices in various environments, even under a gentle breeze. In this study, we explain the design of a WCT-RNG structure and also evaluate its randomness by using an NIST SP 800-22 B test suite with a reliability test.
Assessment of macular choroidal and retinal thickness: a cohort study in Tibetan healthy children
Authors: Yao Yao , Fu Jing , Liu Jiawen , Li Lei , Chen Weiwei , Meng Zhaojun
Published: January 2024

This research investigates the distribution, progressive changes, and contributing factors of macular choroidal and retinal thickness in Tibetan children utilizing swept-source optical coherence tomography (SS-OCT). The Lhasa childhood study recruited 1632 students from seven primary schools in Lhasa. These participants underwent OCT and ophthalmological evaluations, encompassing retinal and choroidal thickness measurements, refractive error, axial length (AL), and systemic examinations. The median age of the scholars was 8.57 ± 0.50 years with a median spherical equivalent (SE) of 0.19 ± 1.28D. Multivariate regression analysis revealed that thinner macular choroid thickness was correlated with lower value of SE, worse best-corrected visual acuity, higher mean arterial blood pressure (MABP) and boys, while retinal thickness was associated with better image quality and lower value of SE. The choroid and retina were significantly thinner in myopic children. SE was positively related to the thickness of all choroidal and full retinal subregions. In comparison to baseline data from 20 months prior, most regions of the full retina had significantly thinned. Choroidal thickness of Tibetan children is thinner than that of same-age children from other regions. Thinning of retina, the outer-sector GCC and GCIPL may be specified as a follow-up and prognostic indicator for myopia.
Phase-separated stretchable conductive nanocomposite to reduce contact resistance of skin electronics
Authors: Lee Hyunjin , Kim Hye Jin , Shin Yoonsoo , Kim Dae-Hyeong
Published: January 2024

Skin electronics, facilitating a high-quality interface between external devices and human skin for recording physiological and/or electrophysiological signals as well as delivering external electrical and/or mechanical energy into the human body, has shown significant progress. However, achieving mechanically conformal contact and electrically low contact resistance at the device-skin interface remains challenging. Here, we propose a material strategy to potentially address such an issue by using phase separation of silver nanowires and silver nanoparticles (Ag NWs and Ag NPs) within a stretchable conductive nanocomposite (NC). This phase-separated NC ensures low contact resistance and high conductivity, which are key requirements in skin electronics, while maintaining excellent mechanical contact with the skin. To achieve phase separation, we hydrophobically treated the surfaces of Ag NWs and Ag NPs. Then, as the NC solidified, the solvent contained in the NC was slowly evaporated to sufficiently precipitate Ag NPs within the NC. As a result, the phase-separated NC exhibited high conductivity (~ 18,535 S cm−1), excellent stretchability (~ 80%), and low contact resistance on both the top and bottom NC surfaces (average ~ 0.132 Ω). The phase-separated NC has enabled implementation of high performance skin-mounted devices, including strain sensors, electrophysiological sensors, and a wearable heater.
Ketosis prevents abdominal aortic aneurysm rupture through C–C chemokine receptor type 2 downregulation and enhanced extracellular matrix balance
Authors: Sastriques-Dunlop Sergio , Elizondo-Benedetto Santiago , Arif Batool , Meade Rodrigo , Zaghloul Mohamed S. , Luehmann Hannah , Heo Gyu S. , English Sean J. , Liu Yongjian , Zayed Mohamed A.
Published: January 2024

Abdominal aortic aneurysms (AAAs) are prevalent with aging, and AAA rupture is associated with increased mortality. There is currently no effective medical therapy to prevent AAA rupture. The monocyte chemoattractant protein (MCP-1)/C–C chemokine receptor type 2 (CCR2) axis critically regulates AAA inflammation, matrix-metalloproteinase (MMP) production, and extracellular matrix (ECM) stability. We therefore hypothesized that a diet intervention that can modulate CCR2 axis may therapeutically impact AAA risk of rupture. Since ketone bodies (KBs) can trigger repair mechanisms in response to inflammation, we evaluated whether systemic ketosis in vivo could reduce CCR2 and AAA progression. Male Sprague–Dawley rats underwent surgical AAA formation using porcine pancreatic elastase and received daily β-aminopropionitrile to promote AAA rupture. Rats with AAAs received either a standard diet, ketogenic diet (KD), or exogenous KBs (EKB). Rats receiving KD and EKB reached a state of ketosis and had significant reduction in AAA expansion and incidence of rupture. Ketosis also led to significantly reduced aortic CCR2 content, improved MMP balance, and reduced ECM degradation. Consistent with these findings, we also observed that Ccr2−/− mice have significantly reduced AAA expansion and rupture. In summary, this study demonstrates that CCR2 is essential for AAA expansion, and that its modulation with ketosis can reduce AAA pathology. This provides an impetus for future clinical studies that will evaluate the impact of ketosis on human AAA disease.