bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antibody Response Following COVID-19 Boosters During the Omicron Wave in the United States: A Decentralized, Digital Health, Real-World Study
Authors: Doornek Tosha , Shao Nan , Burton Paul , Ceddia Francesca , Fraile Belen 
Published: August 2022

AbstractAs the coronavirus disease 2019 (COVID-19) pandemic evolves, new methods that enable real-world studies can provide public health information regarding long-term immunity following vaccination and booster campaigns. We conducted an observational trial to assess antibody levels against SARs-CoV-2 following COVID-19 vaccine boosters in adults in the United States during the omicron wave. This study utilized mobile health technology to recruit and enroll participants in combination with at-home blood collection self-conducted by participants and self-administration of surveys. The results show that when compared with the Pfizer-only primary/booster COVID-19 vaccine, the Moderna-only primary/booster vaccine substantially boosts and maintains high antibody titers over time against the ancestral strain and variants, including BA.1; the geometric mean ratios were generally statistically significantly greater when comparing the Moderna-only to the Pfizer-only vaccine/booster series over much of the study period. These observations suggest that priming/boosting with the Moderna vaccine may be highly protective against COVID-19; such data are vital to inform future recommendations for COVID-19 boosters and to assess the emergence of variants.
Testing, Tracing, and Vaccination Targets for Containment of the US Monkeypox Outbreak: A Modeling Study
Authors: Chitwood Melanie H. , Kwon Jiye , Savinkina Alexandra , Walker Jo , Bilinski Alyssa , Gonsalves Gregg 
Published: August 2022

AbstractWe estimate the levels of community testing, contact tracing, and vaccination required to reduce the effective reproduction number (Rt) of Monkeypox Virus (MPXV) below 1 for high risk men who have sex with men. We found that the critical threshold to vaccinate depends on the basic reproduction number of MPXV and on other public health measures. This analysis provides a framework for quantitative targets toward MPXV containment.
LC-MS/MS-PRM Quantification of IgG glycoforms using stable isotope labeled IgG1 Fc glycopeptide standard
Authors: Sanda Miloslav , Yang Qiang , Zong Guanghui , Chen He , Zheng Zhihao , Dhani Harmeet , Khan Khalid , Kroemer Alexander , Wang Lai-Xi , Goldman Radoslav 
Published: August 2022

ABSTRACTTargeted quantification of proteins is a standard methodology with broad utility, but targeted quantification of glycoproteins has not reached its full potential. The lack of optimized workflows and isotopically labeled standards limits the acceptance of glycoproteomics quantification. In this paper, we introduce an efficient and streamlined chemoenzymatic synthesis of a library of isotopically labeled glycopeptides of IgG1 which we use for quantification in an energy optimized LC-MS/MS-PRM workflow. Incorporation of the stable isotope labeled N-acetylglucosamine enables an efficient monitoring of all major fragment ions of the glycopeptides generated under the soft collision induced dissociation (CID) conditions which reduces the CVs of the quantification to 0.7-2.8%. Our results document, for the first time, that the workflow using a combination of stable isotope labeled standards with intra-scan normalization enables quantification of the glycopeptides by an electron transfer dissociation (ETD) workflow as well as the CID workflow with the highest sensitivity compared to traditional workflows., This was exemplified by a rapid quantification (13-minute) of IgG1 Fc glycoforms from COVID-19 patients.Graphic Abstract
Sleep/wake changes in perturbational complexity in rats and mice
Authors: Cavelli Matias Lorenzo , Mao Rong , Findlay Graham , Driessen Kort , Bugnon Tom , Tononi Giulio , Cirelli Chiara 
Published: August 2022

AbstractIn humans, the level of consciousness can be assessed by quantifying the spatiotemporal complexity of cortical responses using the Perturbational Complexity Index (PCI) and related PCIst (st, state transitions). These measures are consistently high in wake and rapid eye movement (REM) sleep and low in dreamless non-REM (NREM) sleep, deep slow wave anesthesia, and coma. The neuronal mechanisms underlying the reduction of PCI/PCIst in unconscious states remain largely unexplored. The extent to which different cortical areas or layers contribute to these measures is also unknown. To address these questions, here we first validate the use of PCIst in freely moving rats (8 males) and mice (12, 4 females) by showing that its values are lower in NREM sleep and slow wave anesthesia than in wake or REM sleep, as in humans. We then show that low PCIst is associated with the occurrence of an OFF period of neuronal silence. Moreover, the stimulation of deep, but not superficial, cortical layers leads to reliable changes in PCIst across sleep/wake and anesthesia. Finally, consistent changes in PCIst can be measured independent of which single area is being stimulated or recorded, except for recordings in mouse prefrontal cortex. These experiments directly support the hypothesis that PCIst is low when an OFF period disrupts causal interactions in cortical networks. Moreover, they demonstrate that, as in humans, PCIst can be used for the reliable assessment of vigilance states in unresponsive animals, without the need to rely on behavioral outputs such as the righting reflex.Significance StatementThe level of consciousness can be assessed in humans by measuring the spatiotemporal complexity of cortical responses using the Perturbational Complexity Index (PCI) and related PCIst. These measures discriminate between conscious and unconscious conditions with high sensitivity and specificity and work in unresponsive patients. However, the neuronal mechanisms underlying PCI/ PCIst are largely unexplored. Moreover, since they reflect evoked responses from many cortical regions, it is unclear whether some areas or layers are more informative than others. Here we validate PCIst in rodents, provide direct evidence for the underlying neuronal mechanisms, and show that reliable changes in PCIst can almost always be obtained independent of which single area is stimulated or recorded, but only after stimulation of deep layers.
An efficient opal-suppressor tryptophanyl pair creates new routes for simultaneously incorporating up to three distinct noncanonical amino acids into proteins in mammalian cells
Authors: Osgood Arianna O. , Zheng Yunan , Roy Soumya Jyoti Singha , Loynd Conor , Jewel Delilah , Chatterjee Abhishek 
Published: August 2022

AbstractThe site-specific incorporation of multiple distinct noncanonical amino acids (ncAAs) into proteins in mammalian cells is an emergent technology with much potential. For each different ncAA to be incorporated, this technology requires a distinct orthogonal aminoacyl-tRNA synthetase (aaRS)/tRNA pair that recognizes a distinct nonsense codon. The aaRS/tRNA pairs currently available for ncAA mutagenesis in eukaryotes are all traditionally used to decode the TAG nonsense codon. Unfortunately, these pairs suppress the other two nonsense codons, TGA or TAA, at a significantly lower level, compromising the scope of multi-ncAA mutagenesis. Here we report that the bacteria-derived tryptophanyl (EcTrp) pair is an excellent TGA-suppressor in mammalian cells. Additionally, we show that this pair does not cross-react with any of the three previously established aaRS/tRNA pairs. Consequently, the TGA-suppressing EcTrp pair can be combined with TAG-suppressing pyrrolysyl (archaeal), tyrosyl (bacterial), or leucyl (bacterial) pairs to develop three new routes for dual-ncAA incorporation in mammalian cells. We show that all three platforms enable site-specific incorporation of two distinct ncAAs into proteins – including a full-length humanized antibody – with excellent fidelity and good efficiency. Finally, we combined the EcTrp pair with the bacterial Tyr pair and the archaeal pyrrolysyl pair to site-specifically incorporate different combinations of three distinct ncAAs into a reporter protein in mammalian cells.
DNA methylation clocks for clawed frogs reveal evolutionary conservation of epigenetic ageing
Authors: Zoller Joseph A. , Parasyraki Eleftheria , Lu Ake T. , Haghani Amin , Niehrs Christof , Horvath Steve 
Published: August 2022

ABSTRACTDNA methylation-based biomarkers of ageing (epigenetic clocks) have been developed for many mammals, but not yet for amphibian species. We generated DNA methylation data from African clawed frogs (Xenopus laevis) and Western clawed frogs (Xenopus tropicalis), from adult tissues, whole embryos, and tadpoles. We used an array platform designed for CpGs that are highly conserved in mammals to build multiple DNA methylation-based estimators of age for Xenopus. We found that dual species clock could be developed that apply to both humans and frogs (human-clawed frog clocks), and whose high accuracy supports that epigenetic ageing processes are evolutionary conserved outside mammals. Crossing vast evolutionary distances, we characterize age-related CpGs in Xenopus and mammalian species. Highly conserved positively age-related CpGs are located in neural-developmental genes such as uncx, tfap2d as well as nr4a2 implicated in age-associated disease. As in human clocks, positively age-related CpGs are associated with Polycomb repressive complex 2 (PRC2) target sites. Negative age-related CpGs are associated with genes involved in synaptic transmission. We conclude that signatures of epigenetic ageing are evolutionary conserved between frogs and mammals and that the associated genes relate to neural-developmental processes, altogether opening opportunities to employ Xenopus as a model organism to study development and ageing.
Longitudinal analyses after COVID-19 recovery or prolonged infection reveal unique immunological signatures after repeated vaccinations
Authors: Hisamatsu Daisuke , Ikeda Akari , Ito Lisa , Matsushita Yasushi , Hiki Makoto , Mori Hirotake , Tabe Yoko , Naito Toshio , Akazawa Chihiro 
Published: August 2022

AbstractBackgroundTo strategically develop preventive and therapeutic measures against coronavirus disease 2019 and its causative virus, SARS-CoV-2, it is critical to fully characterize immune response and sustained immune activation following viral infection and vaccination. However, the mechanisms controlling intrapersonal variation in antibody titers against SARS-CoV-2 antigens remain unclear. To gain further insights into how we can optimize therapeutic and preventive care, we performed a robust molecular and cellular investigation of immune responses in infected, recovered, and vaccinated individuals.MethodsWe evaluated the expression of 29 cytokines and assessed their correlation with neutralizing potency. We further investigated memory B-cell response in patients infected with the original SARS-CoV-2 strain or other variants of concern, and in vaccinated individuals.ResultsCorrelation analyses showed that the relationship between neutralizing activity and cytokine expression differed according to disease severity and viral strain. Furthermore, long-term longitudinal analyses revealed that post-vaccination neutralizing potential was more strongly associated with various cytokine expression levels in recovered patients than in naïve individuals. Notably, we found a similar distribution of virus-specific antibody gene families in triple-vaccinated individuals and a patient with COVID-19 pneumonia for one year.ConclusionOur results showed that distinct immune responses occur depending on the viral strain suggesting that therapeutic options should be selected on a case-by-case basis. Furthermore, longitudinal analyses revealed biomarker candidates that correlated with repeated vaccination that may be applicable to therapies regulating specific immune responses and novel monoclonal antibodies.FundingThis work was supported by the Institutional Funds, YOKOYAMA Foundation for Clinical Pharmacology (#YRY-2121), and the Japan Society for the Promotion of Science (JSPS)/ Ministry of Education, Culture, Sports, Science, and Technology (MEXT) KAKENHI; Grant-in-Aid for Early-Career Scientists (#21K15888).
RapidAIM 2.0: a high-throughput assay to study functional response of human gut microbiome to xenobiotics
Authors: Li Leyuan , Mayne Janice , Beltran Adrian , Zhang Xu , Ning Zhibin , Figeys Daniel 
Published: August 2022

AbstractOur gut microbiome functions like an organ, having its own set of functions and roles which can be modulated by various types of xenobiotic and biotic components. High-throughput screening approaches that are established based onin vitroorex vivocell, tissue or organ models greatly accelerate drug discovery and our understanding of biological and pathological processes within these systems. There was a lack of a high-throughput compatible functional screening approach of the gut microbiome until we recently developed the RapidAIM (Rapid Assay of Individual Microbiome). RapidAIM combines an optimized culturing model, which maintains the taxonomic and functional profiles of the human gut microbiomein vitro, and a high-throughput metaproteomics workflow to gain deep functional insights into microbiome responses. This protocol describes the most recently optimized 2.0 version of RapidAIM, consisting of extensive details on stool sample collection, biobanking,in vitroculturing and stimulation, microbiome sample processing, and metaproteomics measurement and data analysis. To demonstrate the typical outcome of the protocol, we show an example of using RapidAIM 2.0 to evaluate the effect of prebiotic kestose onex vivoindividual human gut microbiomes biobanked with five different workflows; we also show that kestose had consistent functional effects across individuals and can be used as positive control in the assay.
Rapid generation of precision preclinical cancer models using regulatable in vivo base editing
Authors: Katti Alyna , Foronda Miguel , Zimmerman Jill , Zafra Maria Paz , Goswami Sukanya , Gardner Eric E. , Diaz Bianca J. , Simon Janelle M , Wuest Alexandra , Luan Wei , Fernandez Maria Teresa Calvo , Kadina Anastasia P. , Walker John A , Holden Kevin , Sánchez Rivera Francisco J. , Lowe Scott W. , Dow Lukas E. 
Published: August 2022

ABSTRACTSingle nucleotide variants (SNVs) comprise the majority of cancer-associated genetic changes and can have diverse effects on protein function. Despite a comprehensive catalogue of SNVs across human cancers, little is known about their impact on tumor initiation and progression. To enable the functional interrogation of cancer-associated SNVs, we developed a murine system for temporal and regulatable in vivo cytosine base editing (iBE). The iBE mice show robust, doxycycline-dependent expression across a broad range of tissues with no evidence of DNA or RNA off-target effects. Transient iBE induction drives efficient creation of individual or multiple SNVs in intestinal, lung, and pancreatic organoids, while temporal iBE regulation allows controlled sequential genome editing. Moreover, in situ delivery of plasmid-based or synthetic sgRNAs to target tissues facilitates the simple and rapid generation of pre-clinical cancer models. Overall, iBE is a powerful in vivo platform to define and interrogate the genetic drivers of cancer.
Simulation of the mechanical behavior of self-healing composite materials
Authors: Madia Evgenia , Tserpes Konstantinos , Polydoropoulou Panagiota , Pantelakis Spyros 
Published: August 2022

Purpose
The purpose of this study is the investigation of self-healing materials containing encapsulated healing agents embedded in a polymer matrix with dispersed catalysts. In recent years, the high performance and design flexibility of composite materials have led to their widespread use in the aeronautics, space, automotive and marine fields. Simultaneously, as the need for advanced material properties has increased, many studies have been conducted on multifunctional materials, focusing on different fields of their desired capabilities.

Design/methodology/approach
A multiscale model was developed to simulate the effect of microcapsules on the mechanical behavior of the polymer matrix. Furthermore, the effects of microcapsule diameter and microcapsule concentration on the mechanical behavior of the composite were studied. Digimat and Ansys software were used to simulate the self-healing composites.

Findings
There is a trade-off between the efficiency of the microcapsules and the degradation of the properties of the composite material.

Originality/value
The generated model simulated an encapsulated healing agent in a polymeric matrix.
The undigital behavior of innovative startups: empirical evidence and taxonomy of digital innovation strategies
Authors: Centobelli Piera , Cerchione Roberto , Esposito Emilio , Passaro Renato , Quinto Ivana 
Published: August 2022

PurposeThis paper aims to conceptualize the digital behavior of startups and investigate the emerging behaviors about digital strategies of the Italian startup firms enrolled in the Startup Act policy initiative. Digital technologies were divided into intra- and inter-organizational digital infrastructures, and this categorization offers startups the opportunity to identify a set of enabling technologies that could be used to improve their digital strategies.Design/methodology/approachAn empirical analysis has been conducted to investigate the degree of adoption of digital intra- and inter-organizational digital infrastructures in the entire population of 6,178 Italian firms listed in the Register of Innovative Startups.FindingsThe paper proposes a taxonomy bringing together four startup behaviors for adopting digital technologies: digital follower, technical influencer, social influencer and digital leader. From the perspective of policy makers, considering the financial efforts that public authorities are supporting in the last decade, implications are mainly concerned with policy measures aimed both to reinforce the overall adoption of digital technologies and to develop a balanced adoption of intra- and inter-organizational digital infrastructures.Originality/valueMeasures addressed to support female and foreign entrepreneurship could be useful to support a more dynamic and well-balanced cultural and racial contamination, thus improving the adoption of digital tools.
How do Islamic banks manage earnings? Application of various measurement models in the Iranian Islamic banking system
Authors: Ghaemi Asl Mahdi , Ghasemi Doudkanlou Mohammad 
Published: August 2022

PurposeThis study aims to identify and compare the measurement models of earnings management (EM) appropriate to the Iranian Islamic banking system. The importance of reported profit figures has motivated business executives, who also perform financial reporting, to manipulate these figures. These measures are referred to as “earnings management,” which negatively influence the quality of reported earnings and financial statements' reliability.Design/methodology/approachIn this study, four methods, namely, Jones (1991), modified Jones (Dechow et al., 1995), Kasznik (1999) and Kothari et al. (2005), were used to measure the EM index in 25 Iranian Islamic banks (IBs) registered with the Tehran Stock Exchange and/or the Central Bank of Iran. The study covered the period 2005–2020. Following the aforementioned methods, this research implemented templates that were repeatedly tested in subsequent studies using accruals to discover EM.FindingsThe results show that the Kasznik (1999) model is the preferred and compatible model with the Iranian Islamic banking system's accrual behaviour due to the consistency of the measurement coefficients with theoretical and previous research findings. Therefore, total accruals, including discretionary accruals and non-discretionary accruals, have the most correspondence with (1) property, machinery and equipment; (2) the change in cash flow from operating activities; and (3) the difference of change in revenue (ΔREV) and change in net receivable accounts (ΔREC).Originality/valueThis is the first investigation in the Iranian Islamic banking system. The research contributes to the Iranian Islamic banking system literature on the implements of EM, which could be appealed to in the context of developing countries like Iran. Finally, this study highlights the different EM capabilities in Islamic banking systems similar to the Iranian banking arrangement.
The impact of supply chain social capital on supply chain performance: a longitudinal analysis
Authors: Ye Yuxiao , Yang Lu , Huo Baofeng , Zhao Xiande 
Published: August 2022

Purpose
Drawing on the resource-based view (RBV), this study aims to investigate the impact of social capital, namely, structural (information sharing), cognitive (shared value) and relational (relationship commitment) capital in the supplier and the customer side on supply chain performance in a longitudinal design. It further aims to examine the moderating effect of change in competition intensity.

Design/methodology/approach
Based on two-wave data collected from 203 manufacturers in China, this study uses the ordinary least square and first-difference regression methods to test the proposed relationships.

Findings
The results show the effect of social capital on supply chain performance and the dynamic nature of supply chain social capital. The causal analysis further reveals the significance of supplier-side structural and relational capital in improving supply chain performance. Moreover, competitive intensity plays an important moderating role.

Originality/value
This study, to the best of the authors’ knowledge, is one of the first to demonstrate the longitudinal effect of supply chain social capital on supply chain performance.
Integrated optimization of design and production for personalized products
Authors: Cheng Bayi , Shi Xinyan , Gao Junwei , Zhu Huijun 
Published: August 2022

Purpose
The purpose of this paper is to study the profit optimization of manufacturers who provide personalized products to customers, thus avoiding additional operational costs and response times in the production process of personalized product design.

Design/methodology/approach
First, the authors present an integrated model for optimizing profit where the design and production of personalized products are both considered. The authors propose the concept of personalization level and four cases of personalization level are considered including top, high, medium and low levels. Polynomial-time optimal rules are provided for each level by analyzing 17 subcases where all possible personalized products are considered. Then, the authors compare the obtained profit of personalized products with the optimal profit of standardized products.

Findings
At low and high levels of personalization, personalized manufacturing is more profitable for specific products with specific characteristics. At the top and middle level of individuation, assuming that the product has certain characteristics, whether the best choice to produce personalized products depends on the level of individuation chosen by customers.

Originality/value
An important decision issue for manufacturers is whether to produce personalized or standardized products. In this study, the authors consider this decision problem and analyze the operational functions of personalized products. The authors hope to provide theoretical support in the operational management of manufacturers offering personalized products.