bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Variants of Concern Mutations on the Force-Stability of the SARS-CoV-2:ACE2 Interface and Virus Transmissibility
Authors: Bauer Magnus , Gruber Sophia , Hausch Adina , Melo Marcelo Cardoso dos Reis , Gomes Priscila , Nicolaus Thomas , Milles Lukas , Gaub Hermann , Bernardi Rafael , Lipfert Jan 
Published: January 2023

Abstract
Viruses mutate under a variety of selection pressures, allowing them to continuously adapt to their hosts. Mutations in SARS-CoV-2 have shown effective evasion of population immunity and increased affinity to host factors, in particular to the cellular receptor ACE2. However, in the dynamic environment of the respiratory tract forces act on the binding partners, which raises the question whether not only affinity, but also force-stability of the SARS-CoV-2:ACE2 bond, might be a selection factor for mutations. Here, we use magnetic tweezers (MT) to study the effect of amino acid substitutions in variants of concern (VOCs) on RBD:ACE2 bond kinetics with and without external load. We find higher affinity for all VOCs compared to wt, in good agreement with previous affinity measurements in bulk. In contrast, Alpha is the only VOC that shows significantly higher force stability compared to wt. Investigating the RBD:ACE2 interactions with molecular dynamics simulations, we are able to rationalize the mechanistic molecular origins of this increase in force-stability. Our study emphasizes the diversity of contributions to the assertiveness of variants and establishes force-stability as one of several factors for fitness. Understanding fitness-advantages opens the possibility for prediction of likely mutations allowing rapid adjustment of therapeutics, vaccination, and intervention measures.
Sharing of best practices from an emergency medical team deployment in Papua New Guinea: Piloting a community engagement workshop targeting COVID-19 vaccine uptake
Authors: Maddah Diana , Vadi Ramnath , Marmont Lizzi , Holden Jane , Pyanyo Fredah , Hallit Souheil 
Published: January 2023

Abstract
Objectives
COVID-19 tremendously affected Papua New Guinea in late 2021, which accompanied by a low vaccination rate (< 4%), lead to an International Emergency Medical Team (EMT) Request for Assistance. The study's aim was to assess the knowledge, skills and attitude of health-care workers (HCWs) before and after a workshop conducted by the UK EMT in developing best practices related to Risk Communication and Community Engagement (RCCE) integration within a COVID-19 emergency response.
Methods
A participatory workshop was piloted in Western Highland Province among 71 HCWs. Training of trainers’ approach was adopted to build the capacity of health workers in advocating for vaccines uptake. A perception survey was used at the baseline and at the end of the workshop to assess the knowledge, skills, and attitude of the participants towards COVID-19 vaccine acceptance.
Results
The healthcare professionals were not well equipped with accurate, scientific, and up-to-date information related to COVID-19 vaccines, which led to concern and fear among them. HCWs reported being a source of information for community members about COVID-19 vaccines. The paired t-test showed a significant increase in the knowledge, skills, and attitude of the participants toward COVID-19 vaccines after the workshop. Participants described being ready to engage community influencers and cascade training to further reach out to community groups
Discussion
Integrating RCCE within EMT deployments plays a crucial role in leveraging healthcare capabilities to influence community members and advocate for COVID-19 vaccines uptake; which will ultimately decrease morbidity and mortality.
A multicomponent intranasal adjuvant drives durable humoral, cellular, and mucosal immune responses to SARS-CoV-2 in young and aged mice.
Authors: Jangra Sonia , Landers Jeffrey , Laghlali Gabriel , Rathnasinghe Raveen , O'Konek Jessica , Janczak Katarzyna , Garcia-Sastre Adolfo , Baker James , Schotsaert Michael , Wong Pamela 
Published: January 2023

Abstract
Multiple FDA-approved SARS-CoV-2 vaccines provide excellent protection against severe disease. Despite this, immunity can wane relatively fast, particularly in the elderly and novel viral variants capable of evading infection- and vaccination-induced immunity continue to emerge. Intranasal (IN) vaccination more effectively induces mucosal immune responses than parenteral vaccines, which would improve protection and reduce viral transmission. Here, we developed a rationally designed IN adjuvant consisting of a combined nanoemulsion (NE)-based adjuvant and an RNA-based RIG-I agonist (IVT DI) to drive more robust, broadly protective antibody and T cell responses. We previously demonstrated this combination adjuvant (NE/IVT) potently induces protective immunity through synergistic activation of an array of innate receptors. We now demonstrate that NE/IVT with the SARS-CoV-2 receptor binding domain (RBD), induces robust and durable humoral, mucosal, and cellular immune responses of equivalent magnitude and quality in young and aged mice. This contrasted with the MF59-like intramuscular adjuvant, Addavax, which showed a marked decrease in immunogenicity with age. Robust antigen-specific IFNγ/IL-2/TNF-α was induced in both young and aged NE/IVT-immunized animals, which is significant as their reduced production is associated with suboptimal protective immunity in the elderly. These findings highlight the potential of adjuvanted mucosal vaccines for improving protection against COVID-19.
Effects of restructuring tilth layers on the occurrence of Verticillium wilt and the soil microbial community in a continuous rotary tillage cotton field
Authors: Dong Ming , Wang Yan , Wang Shulin , Feng Guoyi , Zhang Qian , Lin Yongzeng , Liang Qinglong , Wang Yongqiang , Qi Hong 
Published: January 2023

Abstract
Background
Restructuring tilth layers (RTL) is a tillage method that exchanges the 0–20 cm and 20–40 cm soil layers that can be applied during cotton cultivation to inhibit Verticillium wilt. This inhibitory effect may be related to changes in the soil microbial community after RTL. Therefore, we investigated the distribution of microbial communities after rotary tillage (CK) and RTL treatments to identify the reasons for reduction of Verticillium wilt in cotton fields subjected to RTL.
Results
Illumina high-throughput sequencing was used to sequence the bacterial 16S rRNA (V3–V4) and fungal internal transcribed spacer (ITS2) genes at soil depths of 0–20 and 20–40 cm. The incidence rate and incidence index of Verticillium wilt decreased by 28.57% and 42.64%, respectively, after RTL practice relative to CK. Moreover, RTL significantly enhanced the richness and evenness of bacteria at 20–40 cm and narrowed the difference in fungal evenness and richness between soil depths of 0–20 and 20–40 cm. The number of Verticillium dahlia decreased, while the relative abundance of biocontrol bacteria such as Bacillus and Pseudoxanthomonas increased significantly.
Conclusion
RTL improved bacterial diversity, decreased the number of Verticillium dahliae and increased the relative abundance of biocontrol bacteria, which may have suppressed the occurrence of Verticillium wilt in cotton fields.
Nomogram for predicting survival in patients with advanced hepatocellular carcinoma treated with PD-1 inhibitors: incorporating pre-treatment and post- treatment clinical parameters
Authors: Jia Guhe , Qiu Lupeng , Zheng Hongye , Qin Boyu , Sun Zhuoya , Shao Yangyang , Yang Zizhong , Shao Jiakang , Zhou Yuxin , Jiao Shunchang 
Published: January 2023

Abstract
Background: Immunotherapy has transformed cancer treatment patterns for advanced hepatocellular carcinoma (aHCC) in recent years. Therefore, the identification of predictive biomarkers has important clinical implications.
Methods: We collected medical records from 117 aHCC patients treated with anti-PD-1 antibody. Kaplan-Meier analysis and Cox proportional hazard regression were used to evaluate the association between peripheral blood biomarkers and overall survival (OS) and progression-free survival (PFS). Finally, the prognostic nomogram was constructed.
Results: The mPFS and mOS were 7.0 months and 18.7 months, respectively. According to Kaplan-Meier analysis and Cox regression analysis, we regarded the treatment regimen (p = 0.020), Hb at 6-week (p= 0.042), NLR at 6-week (p < 0.001), SII at 6-week (p = 0.125) as predictors of PFS, and AFP (p = 0.035), PLR (p = 0.012), Hb at 6-week (p = 0.010) and NLR at 6-week (p = 0.020) as predictors of OS. Furthermore, the results suggest that the OS and PFS nomogram model were in agreement with actual observations.
Conclusion: Biomarkers in peripheral blood can predict the prognosis of patients with aHCC treated with anti-PD-1 antibody. The development of nomogram models can help us to screen potential patients who can benefit from immunotherapy.
Measuring and simulating the biophysical basis of the acoustic contrast factor of biological cells
Authors: Harshbarger Cooper Lars , Pavlic Alen , Bernardoni Davide , Viol Amelie , Snedeker Jess Gerrit , Dual Jürg , Silvan Unai 
Published: January 2023

Abstract
The acoustic contrast factor (ACF) is calculated from the relative density and compressibility differences between a fluid and an object in the fluid. To name but one application, knowing the ACF of a biological cell represents a crucial step in the design of acoustophoretic systems, for instance to isolate cancer cells from a liquid biopsy such as blood without labels or physical contact. For biological cells the static compressibility is different from the high frequency counterpart relevant for the ACF. In this study, we started by characterizing the ACF of low vs. high metastatic cell lines with known associated differences in phenotypic static E-modulus. The change in the static E-modulus, however, was not reflected in a change of the ACF, prompting a more in depth analysis of the influences on the ACF. We demonstrate that static E-modulus increased biological cells through formaldehyde fixation have an increased ACF. Furthermore, the static E-modulus decreased biological cells treated with actin polymerization inhibitor cytochalasin D have a decreased ACF. Complementing these mechanical tests, a numerical COMSOL model was implemented and used to parametrically explore the effects of cell density, cell density ratios, dynamic compressibility and therefore the dynamic bulk modulus. Collectively the combined laboratory and numerical experiments reveal that a change in the static E-modulus alone might, but does not automatically lead to a change of the dynamic ACF for biological cells. This highlights the need for a multiparametic view of the biophysical basis of the cellular ACF, as well as the challenges in harnessing acoustophoretic systems to isolate circulating cells based on their mechanical properties alone.
Trend of clinical trials of new drugs for rare diseases in China in recent 10 years
Authors: Peng Ai , Fan Xue , Zou Linling , Chen Huan , Xiang Jin 
Published: January 2023

Abstract
Background: Rare disease is a general term for a disease that affects a small number of people but be recognized as a global public health priority. Governments worldwide are paying more and more attention to the academical research and drug investment of rare diseases. The conduct of rare disease clinical trials is still difficult, despite the promotion of government policies and the awakening of social consciousness. In this article, we outlined the characteristics and obstacles of clinical trials of rare diseases in China and expected to provide reference for subsequent clinical trials in this field.
Results: In the recent years, China has made some progress in clinical trials of rare diseases in the past 10 years. There are a total of 481 clinical trials on rare diseases, covering more than 10 rare diseases with high incidence. Clinical trial applications on rare diseases for a total of 481 were submitted and with an average annual growth rate of 28.2% from 2013 to 2022. The number of clinical trial application for rare diseases in 2016 dramatically increased by 80% compared to 2015 due to the policy document issued by China for clinical research in rare diseases in 2015. Besides, about 70% of applications registering for clinical trials could recruit subjects as expected. Despite this, the number of clinical trials of rare diseases in China is smaller than that of the United States, Europe and Japan, and the types of infant drugs are limited to biological products and chemical drugs lacking other new treatments.
Conclusions: Efforts have been made in recent years to develop clinical research on rare diseases in China. The number of clinical trials for rare diseases in China is growing steadily every year, which is inseparable from the support of the country, society and rare disease patients. Still, there is a large gap between China and other developed countries in this field and this merit further investigation.
Site Suitability Assessment for the Development of Wind Power Plant in Wolaita area, Southern Ethiopia: An AHP-GIS Model
Authors: Benti Natei Ermias , Alemu Yewubdar Berhanu , Chaka Mesfin Diro , Semie Addisu Gezahegn , Mekonnen Yedilfana 
Published: January 2023

Abstract
The engine behind any economy's growth is energy. The majority of energy sources are derived from fossil fuels, and the demand for energy produced using fossil fuels has increased since the Industrial Revolution. It is now obvious that the energy generated by these fossil fuels led to significant levels of toxic gases, which harmed the environment. Moreover, Ethiopia still lacks electricity despite having a vast amount of renewable energy resources. As a result, resources must be assigned to using renewable energy sources, like wind energy, as an alternative to the country's current power grid. This study aimed to conduct a site suitability assessment for the potential location of a wind power plant in the Wolaita area using geospatial methods. Many factors and criteria are considered in the process of selecting a suitable site. Geographic Information System (GIS) was employed to develop a multi-criteria approach for determining the most suitable locations for wind power plants. In this study, seven criteria were used. The Analytical Hierarchy Process (AHP) was used to evaluate these criteria, and all of these criteria were assigned a weighted score. These criteria were also given weights using pairwise comparison. The result or suitability map is scored in four categories, ranging from most suitable to unsuitable. According to the findings, 0.628% of the total area (28.00 km2) is deemed highly suitable for establishing wind farms. From a total area of 2433.96 km2, 54.61% of the land is considered to be moderately suitable. The remaining 0.85% (37.85 km2) of the total area is deemed least suitable for wind turbines, leaving 43.91% (1956.94 km2) not suitable. It has been identified that the study area's central, northwestern, and southern regions are superb locations for the establishment of wind farms. The results of this investigation will assist the Ethiopian government or any other organization working on the development of sustainable and renewable energy to speed up the investment process in renewable energy and increase the certainty of resource development. The results of this study could be used as a benchmark for the sector of wind energy.
Noval in nano-edible films applications in the production of high- quality dates Al Hulwah and Soukari for export
Authors: anean hosam el din aboul , Khafar Eman.A. Abdel , Al-Jahani Ghena M. Al-Jahani , alhajji Hajji Ali 
Published: January 2023

Abstract
The aim of this study was to improve the quality of Al Hulwah" and Soukari dates by using edible coatings and films that have a high potential to carry active ingredients such as nano materials. The substances used in this experiment were: control: without treatment, T1: AgNO3 and ZnONPs at 0.5% (0.015%) and 0.03 wt% of chitosan and gelatin, T2: 0.5% (0.015%)/(0.03) wt% chitosan/gelatin chitosan/gelatin combined with phenolic compound active Luria leaves extract LLE (0.15%). T3: AgNO3/ZnONPs 0.5% (0.015%)/0.03 wt% chitosan/gelatin combined with active phenolic compound Thyme Leaves Extract TLE (0.15%). T4: AgNO3/ZnONPs 0.5% (0.015%) or (0.03) chitosan/gelatin weight percent combined with phenolic compound active Green Coffee Extract GCE, 5% (0.15%). The effect of edible coating on fruit quality attributes, including alhulwuh and soukari dates, was investigated during storage at 2–4°C and 70–75% relative humidity. The rheological properties of edible solutions and suspensions were studied. Mechanical properties, particle size distribution, zeta potential emulsions, and scanning electron microscopy films were also measured. The results observed that the best samples were edible coatings with nanosuspensions (T2), followed by samples (T3 and T4 as nano materials on quality of Al Hulwah" and Soukari dates. The substances used in this experiment were: control: without treatment, T1: AgNO3 and ZnONPs at 0.5% (0.015%) and 0.03 wt% of chitosan and gelatin, T2: AgNO3/ZnONPs at 0.5% (0.015%)/(0.03) wt% of chitosan/gelatin combined with phenolic compound active Luria leaves extract LLE (0.15%). T3: AgNO3/ZnONPs 0.5% (0.015%)/0.03 wt% of chitosan/gelatin combined with phenolic compound active Thyme Leaves Extract TLE (0.15%) T4: AgNO3/ZnONPs 0.5% (0.015%) or (0.03) weight percent of chitosan/gelatin combined with phenolic compound active Green Coffee Extract GCE, 5% (0.15%). The effect of edible coating on quality attributes of fruits, including alhulwuh and soukari dates, was studied during storage at 2–4°C and relative humidity 70–75%. The rheological properties of edible solutions and suspensions were studied. Also measured were mechanical properties, particle size distribution, zeta potential emulsions, and scanning electron microscopy films. The results observed that the best samples were edible coatings with nanosuspensions (T2), followed by samples (T3 and T4), as compared with nanocoatings (control and T1) samples. Different analyses were determined on coated dates, such as weight loss, total soluble solids, total acidity, microbiological testing, and sensory evaluation tests. In contrast, the nanocoated Al Hulwah and Soukari dates were found to be of high quality when compared to the control and T1. Al Hulwah" and Soukari dates dipped in (T2, T3, and T4) solutions reduced weight loss percentage and fruit quality for 6 weeks of storage.
A dynamically coherent pattern of rhythms that matches between distant species across the evolutionary scale
Authors: Kembro J. M. , Flesia A. G. , Nieto P.S. , Caliva J.M. , Lloyd D. , Cortassa S. , Aon M.A. 
Published: January 2023

Abstract
We address the temporal organization of circadian and ultradian rhythms (URs), crucial for understanding biological timekeeping in behavior, physiology, metabolism, and alignment with geophysical time. Using a newly developed five-step wavelet-based approach to analyze high-resolution time series of metabolism in yeast cultures and spontaneous movement, metabolism, and feeding behavior in mice, rats, and quails, we describe a dynamically coherent pattern of rhythms spanning over a broad range of temporal scales (hours to minutes). The dynamic pattern found shares key features among the four, evolutionary distant, species analyzed. Specifically, a branching appearance given by splitting periods from 24h into 12h, 8h and below in mammalian and avian species, or from 14 h down to 0.07h in yeast. Scale-free fluctuations with long-range correlations prevail below ~4 h. Synthetic time series modeling support a scenario of coexisting behavioral rhythms, with circadian and URs at the center of the emergent pattern observed.
Studies on intensity distribution of point spread function of Hanning, Gaussian and Co-sinusoidal amplitude filters with complex pupil function
Authors: Anitha P. , Rani S. Vidya , Sabitha N. , Sagar D. Karuna 
Published: January 2023

Abstract
A novel procedure for shaping the lateral and axial component of the point spread function of the optical imaging system. It is possible to develop an apodized point spread function of an optical system with Hanning, Gaussian and Co-sinusoidal amplitude filters and phase filters [2], Complex pupil filters are introduced to improve the resolving power of an optical imaging system of three zone aperture [3]. Three zone aperture shading with amplitude and phase with all possible combinations in each zone have been tested for better results The optical system achieves super-resolver state with Hanning amplitude complex pupil function in the last zone of defocusing with (-π/4) and (π/3) phase filter condition. The lateral resolution of the central maxima is enhanced and the suppression of side lobes by the highest level of amplitude and phase apodization.
Combining VAE with GTCN for Pan-cancer Prediction and Biomarker Identification using Multi-omics Data
Authors: Chen Xin , Tie Yun , Liu Fenghui , Zhang Dalong , Qi Lin 
Published: January 2023

Abstract
Objective: To overcome the phenomenon of “dimensionality curse” and class imbalance existing in biomolecule data and take full advantage of it to realize pan-cancer prediction and biomarker identification.
Methods: We collected a total of 6133 samples with 33 types of tumor from the cancer genome atlas (TCGA), which had been classified and labeled for training,validation and testing, composed of multi-omics data, including DNA methylation,RNA expression and reverse phase protein array (RPPA). Then, we integrate variational autoencoder (VAE) and graph convolution neural networks (GTCN) as an entity capable of projecting high-dimensional features to low latent space, generating samples similar to input data, fulfilling pan-cancer prediction and vital biomarkers associated with specific tumor types. The suggested model’s performance was tested following 10-fold cross validation and then compared to main-flow relevant models.
Results: The average accuracy of the proposed model reached 93.90±1.01% after 10-fold cross validation in pan-cancer prediction task. Additional relevant evaluation metrics F1 score, precision and recall were 92.03±0.3%, 90.05±1.02% and 91.08±1.0%, respectively. For the prediction performance of single type of cancer,such as LGG and BRCA datasets, the proposed model achieved 83.46±0.19% and 84.02±0.25% prediction accuracy, separately. Furthermore, the model also identified a few essential biomarkers which were proved by the survival curve analysis.
Conclusion: We developed a pan-cancer prediction and biomarker identificationsystem based on joining VAE and GTCN using multi-omics data. This approach indicates multi-omics data have close relationship with cancer and is conducive to understanding of the mechanism of cancer formation. The predictive results canbe consulted by doctors. Keywords: Multi-omics data; Variational auto-encoder; Graph tree convolutionnetwork; Pan-cancer prediction; Biomarker identification