bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction of Emergency Preparedness Evaluation Index System of public for Major Emerging Infectious Diseases: A Delphi Study
Authors: Wei Wei , Liu Yubei , Zhou Na , Tian Min , Xie Longsheng , Watson Roger , Dai Fengling , Hu Weili , Chen Yanhua 
Published: January 2023

Abstract
Objective
To construct a scientific and comprehensive emergency preparedness evaluation index system of public for major emerging infectious diseases (MEIDs).
Methods
Based on the global national-level emergency preparedness index framework and a literature review, a preliminary index system was constructed. From June 2022 to September 2022, a panel of 20 experts from the fields of public health, infectious diseases, disease control, and psychology participated in the study. They rated the importance of pre-defined indicators using a five-point Likert scale. The index inclusion criteria were: mean scores of importance > 3.5, coefficient of variation < 2.5, and full mark rate > 20%. According to the feedback of each round of experts, the indicators of the index system were revised.
Results
After two rounds of expert consultation, the evaluation index system reached a consensus. The expert authority coefficient of consultation was 0.88 and 0.90. The Kendall’s coefficient of concordance of expert consultations was 0.294 and 0.322, respectively. The differences were statistically significant (P < 0.05). Finally, the emergency preparedness evaluation index system of public for major emerging infectious diseases was ultimately formed, including five first-level indicators, 20 second-level indicators and 53 third-level indicators.
Conclusion
The evaluation index system established by experts was reasonably scientific and could be used as a tool to evaluate the emergency preparedness of public for major emerging infectious diseases. At the same time, it could provide a reference for future education and training.
Comprehensive single-cell transcriptomic and proteomic analysis reveals NK cell exhaustion and unique tumor cell evolutionary trajectory in non-keratinizing nasopharyngeal carcinoma
Authors: Chen Cuimin , Wang Chun , Pang Ruifang , Liu Huanyu , Yin Weihua , Chen Jiakang , Tao Lili 
Published: January 2023

Abstract
Background

Nonkeratinizing nasopharyngeal carcinoma (NK-NPC) has a strong association with Epstein-Barr virus (EBV) infection. The role of NK cells and the tumor cell evolutionary trajectory in NK-NPC remain unclear. In this study, we aim to investigate the function of NK cell and the evolutionary trajectory of tumor cells in NK-NPC by single-cell transcriptomic analysis, proteomics and immunohistochemistry.

Methods

NK-NPC (n=3) and normal nasopharyngeal mucosa cases (n=3) were collected for proteomic analysis. Single-cell transcriptomic data of NK-NPC were obtained from Gene Expression Omnibus (GSE162025). Quality control, dimension reduction and clustering were based on Seurat software (v4.0.2) process and batch effects were removed by harmony (v0.1.1) software. Normal cells of nasopharyngeal mucosa and tumor cells of NK-NPC were identified using copykat software (v1.0.8). Cell-cell interactions were explored using CellChat software (v1.4.0). Tumor cell evolutionary trajectory analysis was performed using SCORPIUS software (v1.0.8). Protein and gene function enrichment analyses were performed using clusterProfiler software (v4.2.2).

Results

A total of 161 differentially expressed proteins were obtained between NK-NPC (n = 3) and normal nasopharyngeal mucosa (n = 3) by proteomics (log2 fold change>0.5 and P value <0.05). Most of proteins associated with the nature killer cell mediated cytotoxicity pathway were downregulated in the NK-NPC group. In single cell transcriptomics, we identified three NK cell subsets (NK1-3), among which NK cell exhaustion was identified in the NK3 subset with high ZNF683 expression (a signature of tissue-resident NK cell) in NK-NPC. Moreover, the trajectory analysis revealed that the evolutionary trajectory of NK-NPC tumor cells was associated with the status of EBV infection (active or latent). The analysis of cell-cell interactions uncovered a complex network of cellular interactions in NK-NPC.

Conclusions

This study revealed that the NK cell exhaustion might be induced by upregulation of inhibitory receptors on the surface of NK cells in NK-NPC. Treatments for the reversal of NK cell exhaustion may be a promising strategy for NK-NPC. Meanwhile, we identified a unique evolutionary trajectory of tumor cells with active status of EBVinfection in NK-NPC for the first time. Our study may provide new immunotherapeutic targets and new sight of evolutionary trajectory involving tumor genesis, development and metastasis in NK-NPC.
Identification of targetable genomic profiling of breast cancer brain metastases identifies alterations and genomic signatures relevant to immune-checkpoint and PARP inhibitors
Authors: Palmieri Carlo , Giannoudis Athina , Sokol Ethan , Bhogal Talvinder , Ramkissoon Shakti , Razis Evangelia , Bartsch Rupert , Shaw Jacqui , McGregor Kimberly , Clark Allison , Huang Richard 
Published: January 2023

AbstractUnderstanding the genomic landscape of breast cancer brain metastases (BCBMs) is key to elucidating their cause and developing novel treatments. In this study, comprehensive genomic profiling was performed on 822 BCBMs, 11,988 local breast cancer (BC) biopsies and 15,516 non-central nervous system (N-CNS) metastases (all unpaired samples). Clinically-relevant genomic alterations were significantly enriched in BCBMs compared to local BCs and N-CNS metastases. Homologous recombination deficiency as measured byBRCA1/2alteration prevalence and loss-of-heterozygosity and immune checkpoint inhibitor (ICI) biomarkers [Tumour mutation burden (TMB)-High, Microsatellite instability (MSI)-High,PD-L1/L2)] were significantly more prevalent in BCBM than local BC and N-CNS. High PD-L1 protein expression was observed in ER-negative/HER2-negative BCBMs (48.3% vs 50.0% in local BCs, 21.4% in N-CNS). Collectively, our data highlights that a high proportion of BCBMs are potentially amenable to treatment with targeted therapeutic agents including PARP inhibitors and ICIs.
Epistatic interactions promote resistance against direct-acting antivirals targeting the HCV NS3 protein
Authors: Zhang Hang , Quadeer Ahmed Abdul , McKay Matthew 
Published: January 2023

Abstract
Direct-acting antiviral agents (DAAs) provide efficacious therapeutic treatments for chronic Hepatitis C virus (HCV) infection. However, emergence of drug resistance mutations (DRMs) can greatly affect treatment outcomes and impede virological cure. While multiple DRMs have been observed for all currently used DAAs, the evolutionary determinants of such mutations are not currently well understood. Here, by considering DAAs targeting the nonstructural 3 (NS3) protein of HCV, we present results suggesting that epistasis plays an important role in the evolution of DRMs. Using a sequence-based fitness landscape model that we validate using experimental data, we identify specific DRMs that are associated with strong epistatic interactions, and these are found to be enriched in multiple NS3-specific DAAs. We further demonstrate, using evolutionary modelling, that the identified DRMs involve compensatory mutational interactions that facilitate relatively easy escape from drug-induced selection pressures. Our results indicate that accounting for epistasis is important for designing future HCV NS3-targeting DAAs.
Assessment of the DASH-TOP Shared decision-making intervention using the decisional conflict scale: A mixed- method study
Authors: León‑García Montserrat , Humphries Brittany , Morales Pablo Roca , Gravholt Derek , Eckman Mark H. , Bates Shannon M. , Suárez Nataly R. Espinoza , Xie Feng , Alonso‑Coello Pablo , Perestelo‑Perez Lilisbeth 
Published: January 2023

Abstract
Background
Venous thromboembolism (VTE) in pregnancy is a major cause of maternal morbidity and death. The use of low-molecular-weight heparin (LMWH), despite being the standard of care to prevent VTE, comes with some challenges. Shared decision-making (SDM) interventions are recommended to support patients and clinicians in making preference-sensitive decisions. The quality of the SDM process has been widely assessed with the decisional conflict scale (DCS). Our aim is to report participants’ perspectives of each of the components of an SDM intervention (DASH-TOP) in relation to the different subscales of the DCS.
Methods
Design: A convergent, parallel, mixed-methods design.
Participants: The sample consisted of 22 health care professionals, students of an Applied Clinical Research in Health Sciences (ICACS) master program.
Intervention: We randomly divided the participants in three groups: Group 1 received one component (evidence -based information), Group 2 received two components (first component and value elicitation exercises), and Group 3 received all three components (the first two and a decision analysis recommendation) of the SDM intervention.
Analysis: For the quantitative strand, we used a non-parametric test to analyze the differences in the DCS subscales between the three groups. For the qualitative strand, we conducted a content analysis using the decisional conflict domains to deductively categorize the responses.
Results
Groups that received more intervention components experienced less conflict and better decision-making quality, although the differences between groups were not statistically significant. The decision analysis recommendation improved the efficacy with the decision-making process, however there are some challenges when implementing it in clinical practice. The uncertainty subscale showed a high decisional conflict for all three groups; contributing factors included low certainty of the evidence-based information provided and a perceived small effect of the drug to reduce the risk of a VTE event.
Conclusions
The DASH-TOP intervention reduced decisional conflict in the decision -making process, with decision analysis being the most effective component to improve the quality of the decision. There is a need for more implementation research to improve the delivery of SDM interventions in the clinical encounter.
Simultaneous preconcentration and determination of Cu(II), Ni(II), and Co(II) in food and environmental samples by the application of chelate adsorption on Amberlite XAD-1180
Authors: TOPUZ Berrin , ALTINIŞIK Ece Talya 
Published: January 2023

Abstract
A simultaneous preconcentration and determination procedure for solid phase extraction on AXAD-1180 as 2,6-dimethlmorpholinedithiocarbamate (DMMDTC) chelates and spectrophotometric determinations of Cu (II), Ni (II), and Co (II) in food and environmental samples is proposed in the present work. The effect of some SPE parameters, such as reagent amount, sample pH, eluent type, concentration, and volume, sample and eluent flow rate, and sample volume, on trace metal ion recovery (R%) for the method developed in the standard model solution medium was investigated. Cu(II), Ni(II), and Co(II) retained as DMMDTC complexes on Amberlite XAD-1180 were eluted with 10 mL of 1 M HNO3 (in acetone). Foreign ions were also studied individually on the recovery of trace metal ions using the developed method. Cu(II), Ni(II), and Co(II) ions were preconcentrated and separated from the sample using the developed SPE method, and their concentrations were simultaneously determined using the UV-VIS spectrophotometric method. The spectrophotometric determination was made by measuring the absorbance of colored chelates of metal ions complexed with DMMDTC in a surfactant medium (1% Triton X-100) at wavelengths of 460, 328, and 342 nm for Cu(II), Ni(II), and Co(II), respectively. To test the method's accuracy, certified reference materials (CRM 1204 waste water and TMDA-70.2 Ontario lake water) were analyzed using the proposed method, and metal recoveries were calculated to be between 97.1% and 100.7%. The proposed method worked well with the wheat flour sample. Wheat flour has Cu(II) and Ni(II) contents of 2,16 µgmL− 1 and 0,56 µgmL− 1, respectively.
Plant beneficial bacterium promotes plant growth by altering social networks of bacteria in the rhizosphere
Authors: Liu Yan , Xu Zhihui , Xun Weibing , Štefanič Polonca , Yang Tianjie , Miao Youzhi , Zhang Nan , Zhang Ruifu , Shen Qirong , Mulec Ines Mandic 
Published: January 2023

Abstract

Plant growth-promoting rhizobacteria (PGPR) represent a green solution to emerging food production challenges but the knowledge of their role in shaping phylogenetic and social relationships of bacterial rhizosphere community is lacking. We here address this gap in knowledge by following effects of Bacillus velezensis SQR9, the commercially important PGP rhizobacterium, on rhizosphere community focusing on Bacillus species. Results show that SQR9 dramatically shifts phylogenetic and social relationships in the rhizosphere enriching moderately related and swarming compatible Bacillus species with decreased carbon resource niche overlap. By combining Bacillus isolates from the SQR9 treated rhizosphere with SQR9 into multispecies consortia we confirm in hydroponic systems and soil experiments that relatedness-based sociality and competition for carbon resources represent fundamental knowledge for the intelligent design of efficient PGP consortia. The work contributes toward sustainable agriculture by providing the first insight in PGPR’s sociality effects in the rhizosphere and their importance for PGP consortia design.
Integrating Cybersecurity Concerns in Functional Safety Assurance of AI-Based Automotive Functions
Authors: Lami Giuseppe , Merola Francesco 
Published: January 2023

Abstract
Automated vehicles are characterized by intelligent functions (many developed using AI-based solutions), autonomy, and high connectivity with the external environment. The high connectivity of AV opens relevant cybersecurity issues due to many potential attack surfaces. Cybersecurity attacks' effects on AV may also determine severe risks in terms of functional safety due to vehicles' high automation and autonomy. Functional safety assurance of AV cannot be disjoint from the analysis and treatment of cybersecurity concerns. In this paper, we define a methodology called ISCA (Integrated Safety and Cybersecurity Assurance) aimed at integrating, in a systematic manner, cybersecurity concerns into the functional safety assurance process of AI-based functions of AV. The ISCA methodology focuses on the emerging scenario-based approach for testing AI-based vehicle functions and is based on creating variants of the scenarios used for functional safety testing. The variants are derived from the original scenarios modified by the effects of highly risky cyberattacks that can occur during the scenario execution. The risk assessment of cyberattacks is based on the fuzzy logic mechanism. ISCA represents a possible way to strengthen the scenario-based functional safety assurance of AI-based vehicle functions by integrating cybersecurity concerns.
Synchronized Oscillations of Carbon Nanotubes Dispersed in Solution
Authors: Fukumoto Makoto , Akai Ryunosuke , Yoshida Yume , Sakuma Shin-nosuke , Ono Hayato , Mori Rintaro , Sano Masahito 
Published: January 2023

Abstract
Although synchronized oscillations are found in a variety of systems and living organisms in nature, there has been no report on technologically important materials. We have observed by a fluorescence microscope that a large number of carbon nanotubes (CNTs) dispersed in an aqueous mixture of the surfactant and dye execute synchronized oscillations spontaneously. The movement was quantified to give a power spectrum, revealing a single, sharp synchronization peak at 20 Hz. It was found not to be affected nor created by external vibrations. The surfactant concentration dependence demonstrates that the Kuramoto model is applicable to describe the CNT synchronization. It is always associated with the power-law noise, indicating the presence of complex heterogeneous networks. These results suggest a highly cooperative form of the sparse CNT network connected with variable linkages.
Urine-derived bladder cancer organoids (urinoids) as tool for cancer longitudinal response monitoring and therapy adaptation
Authors: Viergever Bastiaan , Raats Daniëlle , Geurts Veerle , Mullenders Jasper , Jonges Trudy , Heijden Michiel (S.) Van der , Es Johan van , Kranenburg Onno , Meijer Richard 
Published: January 2023

Abstract
Bladder cancer is one of the most common cancer-types worldwide. Generally, research relies on invasive sampling strategies. Here, we generate bladder cancer organoids directly from urine (urinoids). In this project, we establish 12 urinoid-lines from 22 patients with non-muscle and muscle-invasive bladder tumors, with an efficiency of 55%. The histopathological features of the urinoids accurately resemble those of the original bladder tumors. Genetically there is a high concordance of single nucleotide polymorphisms (92.56%) and insertions and deletions (91.54%) between urinoids and original tumors. Furthermore, urinoids show sensitivity to bladder cancer drugs, similar to their tissue-derived organoid counterparts. Genetic analysis of longitudinally generated urinoids from one patient receiving systemic immunotherapy, identify alterations that may guide the choice for second-line therapy. Successful treatment adaptation was subsequently demonstrated in the urinoid-setting. Therefore, urinoids can advance precision medicine in bladder cancer as a non-invasive platform for tumor pathogenesis, longitudinal drug-response monitoring, and therapy adaptation.
A Novel Perspective for M-Polynomials to Compute Molecular Descriptors of Borophene Nanosheet
Authors: Xavier D. Antony , Ismail Rashad , Ghani Muhammad Usman , karamti Hanen , Baby Annmaria , Varghese Eddith Sarah , Nair Theertha 
Published: January 2023

Abstract
Nanomaterials feature exceptional, one-of-a-kind qualities that might be used in electronics, medicine, and other industries. Due to their unique photonic, electrical, catalytic, and magnetic capabilities as well as their use in helping immunotherapy, drug carriers, biosensors, electronic devices, etc., two dimensional materials are becoming considerably more important. Two-dimensional nanomaterials called borophene have a variety of intriguing characteristics. In the fields of chemistry, material science, nanotechnology, and condensed matter physics, they left an indelible impression thanks to their astounding physical and molecular characteristics. The concept of modelling the structure of a molecule or chemical network to a chemical graph and then quantitatively analysing the resulting graph with the aid of topological descriptors was a major advance in the fields of mathematics and chemistry. Topological descriptors are used in a wide range of fields, including chemistry, information technology, biology, quantitative structure-property relationships (QSPR), quantitative structure-activity relationships (QSAR), and many more. New descriptors that more closely connect with the structural characteristics of a chemical structure are being developed by researchers working on this idea. Finding a chemical graph's structural descriptors may be done in a variety of ways. It is discovered that the M-polynomial is a very versatile and quick method for computing the degree-based descriptors of chemical graphs or networks. The degree-based descriptors of the $\beta_{12}$-Borophene nanosheet are established in this study utilising the M-polynomial technique. At the conclusion, the numerical and graphical comparison based on the identified analytic expressions is also provided.
Are You Better Than Me? Social Comparisons in Carrion Crows (Corvus corone)
Authors: Federspiel Ira G. , Schmitt Vanessa , Schuster Richard , Rockenbach Courtney , Braun Anna , Loretto Matthias-Claudio , Michels Corinna , Fischer Julia , Mussweiler Thomas , Bugnyar Thomas 
Published: January 2023

Abstract
Comparing oneself to others is a key process in humans that allows individuals to gauge their performances and abilities and thus develop and calibrate their self-image. Very little is known about its evolutionary foundations. A key feature of social comparison is the sensitivity to other individuals’ performance. Recent studies on primates produced equivocal results, leading us to distinguish a ‘strong’ variant of the social comparison hypothesis formulated for humans from a ‘weak’ variant found in non-human primates. Here, we focus on animals that are distantly related to primates but renowned for their socio-cognitive skills, birds from the family Corvidae. We were interested in whether crows’ task performances were influenced i) by the presence of a conspecific co-actor performing the same discrimination task and ii) by the simulated acoustic cues of a putative co-actor performing better or worse than themselves. Crows reached a learning criterion quicker when tested simultaneously as compared to when tested alone, indicating a facilitating effect of social context. The performance of a putative co-actor influenced their performance: crows were better at discriminating familiar images when their co-actor was better than they were. Standard extremity, i.e., how pronounced the difference was between the performance of the subject and that of the co-actor, and category membership (i.e., affiliation status and sex), of the putative co-actors had no effect on their performance. Our findings are in line with the ‘weak’ variant of social comparison and indicate that elements of human social comparison can be found outside of primates.
The landscape of the long non-coding RNAs in developing mouse retinas
Authors: Yu Dongliang , Wu Yuqing , Zhu Leilei , Wang Yuying , Sheng Donglai , Zhao Xiaofeng , Liang Guoqing , Gan Lin 
Published: January 2023

Abstract
Background The long non-coding RNAs (lncRNAs) are critical regulators of diverse biological processes. Nevertheless, a global view of its expression and function in the mouse retina, a crucial model for neurogenesis study, still needs to be made available.
Results Herein, by integrating the established gene models and the result from ab initio prediction using short- and long-read sequencing, we characterized 4,523 lncRNA genes (MRLGs) in developing mouse retinas (from the embryonic day of 12.5 to the neonatal day of P28), which was so far the most comprehensive collection of retinal lncRNAs. Next, derived from transcriptomics analyses of different tissues and developing retinas, we found that the MRLGs were highly spatiotemporal specific in expression and played essential roles in regulating the genesis and function of mouse retinas. In addition, we investigated the expression of MRLGs in some mouse mutants and revealed that 97 intergenic MRLGs might be involved in regulating differentiation and development of retinal neurons through Math5, Isl1, Brn3b, NRL, Onecut1, or Onecut2 mediated pathways.
Conclusions In summary, this work significantly enhanced our knowledge of lncRNA genes in mouse retina development and provided valuable clues for future exploration of their biological roles.