bluuebunny/crossref_metadata_2025_split huggingface dataset:
ALiCE®: A versatile, high yielding and scalable eukaryotic cell-free protein synthesis (CFPS) system
Authors: Das Gupta Mainak , Flaskamp Yannick , Roentgen Robin , Juergens Hannes , Gimenez Jorge Armero , Albrecht Frank , Hemmerich Johannes , Ahmad Arfi Zulfaquar , Neuser Jakob , Spiegel Holger , Yeliseev Alexei , Song Lusheng , Qiu Ji , Williams Charles , Finnern Ricarda 
Published: November 2022

AbstractEukaryotic cell-free protein synthesis (CFPS) systems have the potential to simplify and speed up the expression and high-throughput analysis of complex proteins with functionally relevant post-translational modifications (PTMs). However, low yields and the inability to scale such systems have so far prevented their widespread adoption in protein research and manufacturing.Here, we present a detailed demonstration for the capabilities of a CFPS system derived fromNicotiana tabacumBY-2 cell culture (BY-2 lysate; BYL). BYL is able to express diverse, functional proteins at high yields in under 48 hours, complete with native disulfide bonds and N-glycosylation. An optimised version of the technology is commercialised as ‘ALiCE®’, engineered for high yields of up to 3 mg/mL. Recent advances in the scaling of BYL production methodologies have allowed scaling of the CFPS reaction. We show simple, linear scale-up of batch mode reporter proten expression from a 100 μL microtiter plate format to 10 mL and 100 mL volumes in standard Erlenmeyer flasks, culminating in preliminary data from 1 L reactions in a CELL-tainer® CT20 rocking motion bioreactor. As such, these works represent the first published example of a eukaryotic CFPS reaction scaled past the 10 mL level by several orders of magnitude.We show the ability of BYL to produce the simple reporter protein eYFP and large, multimeric virus-like particles directly in the cytosolic fraction. Complex proteins are processed using the native microsomes of BYL and functional expression of multiple classes of complex, difficult-to-express proteins is demonstrated, specifically: a dimeric, glycoprotein enzyme, glucose oxidase; the monoclonal antibody adalimumab; the SARS-Cov-2 receptor-binding domain; human epidermal growth factor; and a G protein-coupled receptor membrane protein, cannabinoid receptor type 2. Functional binding and activity are shown using a combination of surface plasmon resonance techniques, a serology-based ELISA method and a G protein activation assay. Finally, in-depth post-translational modification (PTM) characterisation of purified proteins through disulfide bond and N-glycan analysis is also revealed - previously difficult in the eukaryotic CFPS space due to limitations in reaction volumes and yields.Taken together, BYL provides a real opportunity for screening of complex proteins at the microscale with subsequent amplification to manufacturing-ready levels using off-the-shelf protocols. This end-to-end platform suggests the potential to significantly reduce cost and the time-to-market for high value proteins and biologics.
An update on eukaryotic viruses revived from ancient permafrost
Authors: Alempic Jean-Marie , Lartigue Audrey , Goncharov Artemiy E , Grosse Guido , Strauss Jens , Tikhonov Alexey N. , Fedorov Alexander N. , Poirot Olivier , Legendre Matthieu , Santini Sébastien , Abergel Chantal , Claverie Jean-Michel 
Published: November 2022

AbstractOne quarter of the Northern hemisphere is underlain by permanently frozen ground, referred to as permafrost. Due to climate warming, irreversibly thawing permafrost is releasing organic matter frozen for up to a million years, most of which decomposes into carbon dioxide and methane, further enhancing the greenhouse effect. Part of this organic matter also consists of revived cellular microbes (prokaryotes, unicellular eukaryotes) as well as viruses that remained dormant since prehistorical times. While the literature abounds on descriptions of the rich and diverse prokaryotic microbiomes found in permafrost, no additional report about “live” viruses have been published since the two original studies describing pithovirus (in 2014) and mollivirus (in 2015). This wrongly suggests that such occurrences are rare and that “zombie viruses” are not a public health threat. To restore an appreciation closer to reality, we report the preliminary characterizations of 13 new viruses isolated from 7 different ancient Siberian permafrost samples, 1 from the Lena river and 1 from Kamchatka cryosol. As expected from the host specificity imposed by our protocol, these viruses belong to 5 different clades infectingAcanthamoeba spp. but not previously revived from permafrost: Pandoravirus, Cedratvirus, Megavirus, and Pacmanvirus, in addition to a new Pithovirus strain.
HIV–1 infection reduces NAD capping of host cell snRNA and snoRNA
Authors: Benoni Barbora , Potužník Jiří František , Škríba Anton , Benoni Roberto , Trylcova Jana , Tulpa Matouš , Spustová Kristína , Grab Katarzyna , Mititelu Maria-Bianca , Pačes Jan , Weber Jan , Stanek David , Kowalska Joanna , Bednarova Lucie , Keckesova Zuzana , Vopalensky Pavel , Gahurova Lenka , Cahova Hana 
Published: November 2022

AbstractNicotinamide adenine dinucleotide (NAD) is a critical component of the cellular metabolism and also serves as an alternative 5′ cap on various RNAs. However, the function of the NAD RNA cap is still under investigation. We studied NAD capping of RNAs in HIV–1–infected cells because HIV–1 is responsible for the depletion of the NAD/NADH cellular pool and causing intracellular pellagra. By applying the NAD captureSeq protocol to HIV–1–infected and uninfected cells, we revealed that four snRNAs (e.g. U1) and four snoRNAs lost their NAD cap when infected with HIV–1. Here, we provide evidence that the presence of the NAD cap decreases the stability of the U1/HIV–1 pre–mRNA duplex. Additionally, we demonstrate that reducing the quantity of NAD–capped RNA by overexpressing the NAD RNA decapping enzyme DXO results in an increase in HIV–1 infectivity. This suggests that NAD capping is unfavorable for HIV–1 and plays a role in its infectivity.Abstract Figure
CryoEM reveals unprecedented binding site for NaV1.7 inhibitors enabling rational design of potent hybrid inhibitors
Authors: Kschonsak Marc , Jao Christine C. , Arthur Christopher P. , Rohou Alexis L. , Bergeron Philippe , Ortwine Daniel , McKerrall Steven J. , Hackos David H. , Deng Lunbin , Chen Jun , Dragovich Peter S. , Volgraf Matthew , Wright Matthew R. , Payandeh Jian , Ciferri Claudio , Tellis John C. 
Published: November 2022

AbstractThe voltage-gated sodium (NaV) channel NaV1.7 has been identified as a potential novel pain target due to its striking human genetics. However, clinically available drugs (e.g. lidocaine, carbamazepine, etc.) are not selective among the nine NaV channel subtypes, NaV1.1-NaV1.9, and the two currently known classes of NaV1.7 subtype-selective inhibitors (aryl- and acylsulfonamides) have undesirable characteristics that may limit their development. Moreover, understanding of the structure-activity relationships of the acylsulfonamide class of NaV1.7 inhibitors, exemplified by the clinical development candidateGDC-0310, has been based solely on a single co-crystal structure of an arylsulfonamide inhibitor series. To advance inhibitor design targeting the NaV1.7 channel, we established an iterative system to routinely obtain high-resolution ligand-bound NaV1.7 structures using cryogenic electron microscopy (cryo-EM). We report thatGDC-0310engages the NaV1.7 voltage-sensing domain 4 (VSD4) through an unexpected binding mode orthogonal to the arylsulfonamide class binding pose, which identifies a previously unknown ligand binding site in NaV channels. This finding enabled the design of a novel hybrid inhibitor series that bridges the aryl and acylsulfonamide binding pockets and allows for the generation of molecules with substantially differentiated structures and properties. Overall, this study highlights the power of cryo-EM methods to pursue challenging drug targets using iterative and high-resolution structure-guided inhibitor design. It also underscores an important role of the membrane bilayer in the discovery of selective NaV channel modulators.
Differential effects of carbon nanotube and graphene on the tomato rhizosphere microbiome
Authors: You Yaqi , Kerner Patricia , Shanmugam Sudha , Khodakovskaya Mariya V. 
Published: November 2022

AbstractApplication of carbonaceous nanomaterials (CNMs) to the soil-plant system can affect plant physiology, with positive results ranging from enhanced seed germination and root system development to improved stress tolerance. The underlying mechanisms are not fully understood. Plant rhizosphere microbiomes at the soil-root interface are strongly influenced by the host plant and play a key role in the plant host’s development and health. Yet few studies have characterized changes in plant rhizosphere microbiomes following applications of CNMs to the soil-plant system. Here we investigated the effects of multi-walled carbon nanotube (CNT) and graphene on microbial communities in the ectorhizosphere of tomato plants versus surrounding bulk soil. Pot experiments were conducted where tomato plants were exposed to CNT or graphene at 200 mg/kg soil for four weeks. Ectorhizosphere and bulk soils were then collected and analyzed for physicochemical properties and microbiome structure and function. While graphene had a limited impact on the tomato rhizosphere microbiome, CNT significantly increased microbial alpha diversity, induced greater divergence of beta diversity, enhanced microbial interactions, and potentially impacted community functions such as aromatic compound degradation, antioxidant synthesis, and redox cofactor biosynthesis. Furthermore, CNT induced stronger and/or unique microbiome alterations in the tomato rhizosphere compared to bulk soil. Our findings reveal the differential modulating effects of two widely-used CNMs on plant rhizosphere microbiomes and highlight an imminent need to understand complex plant root-microbe interplays in the CNM-impacted rhizosphere. These results have implication for realizing the full potential of phytoapplication of CNMs toward improved and sustainable plant production.
Health, socioeconomic and genetic predictors of COVID-19 vaccination uptake: a nationwide machine-learning study
Authors: Hartonen Tuomo , Jermy Bradley , Sõnajalg Hanna , Vartiainen Pekka , Krebs Kristi , Vabalas Andrius ,   FinnGen,   Estonian Biobank Research Team, Leino Tuija , Nohynek Hanna , Sivelä Jonas , Mägi Reedik , Daly Mark , Ollila Hanna M. , Milani Lili , Perola Markus , Ripatti Samuli , Ganna Andrea 
Published: November 2022

AbstractReduced participation in COVID-19 vaccination programs is a key societal concern. Understanding factors associated with vaccination uptake can help in planning effective immunization programs. We considered 2,890 health, socioeconomic, familial, and demographic factors measured on the entire Finnish population aged 30 to 80 (N=3,192,505) and genome-wide information for a subset of 273,765 individuals. Risk factors were further classified into 12 thematic categories and a machine learning model was trained for each category. The main outcome was uptaking the first COVID-19 vaccination dose by 31.10.2021, which has occurred for 90.3% of the individuals.The strongest predictor category was labor income in 2019 (AUC evaluated in a separate test set = 0.710, 95% CI: 0.708-0.712), while drug purchase history, including 376 drug classes, achieved a similar prediction performance (AUC = 0.706, 95% CI: 0.704-0.708). Higher relative risks of being unvaccinated were observed for some mental health diagnoses (e.g. dissocial personality disorder, OR=1.26, 95% CI : 1.24-1.27) and when considering vaccination status of first-degree relatives (OR=1.31, 95% CI:1.31-1.32 for unvaccinated mothers)We derived a prediction model for vaccination uptake by combining all the predictors and achieved good discrimination (AUC = 0.801, 95% CI: 0.799-0.803). The 1% of individuals with the highest risk of not vaccinating according to the model predictions had an average observed vaccination rate of only 18.8%.We identified 8 genetic loci associated with vaccination uptake and derived a polygenic score, which was a weak predictor of vaccination status in an independent subset (AUC=0.612, 95% CI: 0.601-0.623). Genetic effects were replicated in an additional 145,615 individuals from Estonia (genetic correlation=0.80, 95% CI: 0.66-0.95) and, similarly to data from Finland, correlated with mental health and propensity to participate in scientific studies. Individuals at higher genetic risk for severe COVID-19 were less likely to get vaccinated (OR=1.03, 95% CI: 1.02-1.05).Our results, while highlighting the importance of harmonized nationwide information, not limited to health, suggest that individuals at higher risk of suffering the worst consequences of COVID-19 are also those less likely to uptake COVID-19 vaccination. The results can support evidence-informed actions for COVID-19 and other areas of national immunization programs.
Intention and preference for long-acting injectable PrEP among MSM in the Netherlands: a diffusion of innovation approach
Authors: Wang Haoyi , Zimmermann Hanne M. L. , van de Vijver David , Jonas Kai J. 
Published: November 2022

AbstractLong-acting injectable PrEP (LAI-PrEP) is efficacious in preventing HIV among MSM and will be soon available in Europe. This study investigates the intention to use LAI-PrEP among MSM in the Netherlands by employing a diffusion of innovation approach, comparing PrEP naïve, discontinued MSM, oral PrEP early adopters and majority users. 309 MSM were surveyed on their intention and preference of LAI-PrEP. 83% showed high/very-high interest of, and 63% showed high/very-high intention to use LAI-PrEP. Early-adopters of oral PrEP use did not show increased intention to use LAI-PrEP and neither did PrEP naïve nor PrEP discontinued MSM, indicating a missing innovator effect for LAI-PrEP. Among the 218 current oral PrEP users, suboptimal oral PrEP adherence determined LAI-PrEP preference but did not determine LAI-PrEP intention. To reach the full potential of LAI-PrEP, a targeted strategy towards current oral PrEP users with suboptimal adherence seems indicated.
The influence of institutional conditions on firms’ process innovation – evidence from firms based on a multi-country analysis
Authors: Durst Susanne , Leyer Michael 
Published: November 2022

Purpose
Our understanding of the influence of institutional conditions on process innovation is still limited, despite managers’ need to know which factors should be considered in decision-making and governments should be aware of how to foster process innovation through the provision of attractive institutions. Therefore, this paper aims to examine how institutional dimensions such as workforce, political instability, labor regulation, corruption, tax administration and transportation influence process innovation in smaller firms located in emerging countries other than the BRICS (Brazil, Russia, India, China and South Africa).

Design/methodology/approach
A data set from the World Bank Enterprise Surveys questioning over 20,000 companies from 41 emerging countries supplemented by the gross domestic product (GDP) per capita for each country was used and analyzed by the means of general linear mixed models. The analysis emphasized small- and medium-sized enterprises (SMEs) and excluded BRICS countries.

Findings
The findings demonstrate which institutional factors matter for process innovation depending on company size and GDP.

Research limitations/implications
This paper advances research on the influence of institutions on firm innovation – the institution–process innovation relationship in emerging countries other than the BRICS in particular. By considering the role of company size and GDP per capita on the institution–process innovation relationship, the paper offers more nuanced insights compared with prior studies and thus makes a strong contribution to the innovation theory. The data used are not suitable for a longitudinal study the same refers to capturing the variety found in the countries even those coming from the same geographic area.

Practical implications
The results provide practitioners, e.g. managers of SMEs, with concrete ideas on how to improve process innovation in their companies. Other actors such as policymakers too can benefit from the results as they will allow the design of more target group-oriented measures, aspects that can ultimately lead to more sustainable businesses.

Originality/value
By focusing on process innovation and emerging countries, the paper contributes to growing research efforts in emerging countries beyond the BRICS. Thus, the results add more diversity to the study of process innovation and its influencing external (institutional) factors. The emphasis on SMEs also allows us to highlight differences between different categories of SMEs.
Active learning: a consideration in collection development in health sciences libraries?
Authors: Cisney Lori 
Published: November 2022

Purpose
Active learning is an important component of medical education and information literacy instruction. The purpose of this study is to provide a preliminary investigation to determine whether health sciences librarians consider active learning when making decisions about the library collection.

Design/methodology/approach
An online survey was conducted among health sciences librarians.

Findings
Nineteen librarians completed the survey and most are not considering active learning when making collection decisions.

Originality/value
Very little literature has been published about active learning as a consideration in collection development decisions by health sciences librarians.
On the path of common prosperity with Chinese characteristics
Authors: Li Zhengtu 
Published: November 2022

PurposeIn human history, poverty for most and prosperity for few is the norm. Thus, no theory or practice of common prosperity has been developed. Marxism first formulated the theory of common prosperity, and the classical Marxist authors conducted theoretical exploration on the issue of common prosperity, forming a series of scientific conclusions.Design/methodology/approachThe century-long practical history of the Communist Party of China (CPC) is the great practice of leading the Chinese people in getting rid of poverty, letting some people and regions get rich first and ultimately achieving the goal of common prosperity.FindingsCommon prosperity is the great practice of the CPC that leads all Chinese people in building a modern socialist country in an all-round way in the new era.Originality/valueThe path of common prosperity with Chinese characteristics will certainly arise in the process of the great practice of common prosperity with Chinese characteristics. Based on the anti-poverty theory and the “spirit of poverty alleviation” from the battle against poverty with Chinese characteristics, the theory of common prosperity and its spirit with Chinese characteristics will certainly be formed. The above conclusions constitute the basic principles of the theory of common prosperity with Chinese characteristics.
Platform marketplaces: unifying our understanding of lateral exchange markets
Authors: Gleim Mark R. , Stevens Jennifer L. , Johnson Catherine M. 
Published: November 2022

Purpose
This research paper aims to provide conceptual clarity for marketplaces within the lateral exchange market framework. The advances in digital technologies have been critical to the growth of new marketplaces and forms of exchange. While there are many different names and manifestations of these marketplaces, the common thread is they all require digital platform intermediation. These marketplaces are referred to by a variety of names and characteristics, and a clear consensus has yet to be achieved.

Design/methodology/approach
This research uses a conceptual approach rooted in the marketing literature.

Findings
This study differentiates and defines the sharing economy, collaborative consumption and access-based consumption, as well as introduces the concept of liquid ownership – all under the LEM framework. Defining characteristics for each marketplace are noted to present a consistent classification of the focal concepts for the advancement of research and theory.

Research limitations/implications
As the number and types of lateral exchange marketplaces continue to grow, researchers need to have a clear delineation of the concepts. This research seeks to provide clarity on the disparate literature streams and introduces the concept of liquid ownership to allow for the advancement of research and theory surrounding these forms of consumption.

Practical implications
Understanding existing marketplaces is vital for online platforms as they develop new offerings and differentiate themselves in the marketplace. Additionally, opportunities for traditional businesses abound as they pursue new market opportunities and adapt to changing technologies. Thus, research questions concerning consumers and platform managers are presented.

Originality/value
This research contributes conceptual clarity on elements commonly associated with the sharing economy while expanding it to include elements found in LEMs. The concept of liquid ownership is also presented to reflect the evolving consumption landscape. Research opportunities and questions are provided to guide future scholarly work.
The ethics of talent development: frameworks and identities
Authors: Reinert Kenneth , Debebe Gelaye 
Published: November 2022

Purpose
This paper aims to examine the ethics of authentic talent development in socioeconomic context by considering a set of alternative ethical frameworks. It juxtaposes the ideals of civic virtue, which involve a concern for the common good, with the reality that socioeconomic deprivation and sociocultural practices severely constrain talent development opportunities and choice.

Design/methodology/approach
The paper draws on several frameworks complementary to the ideals of civic virtue – the basic goods approach, human capital theory, the capabilities approach and the ethic of care – to elucidate the barriers to talent development embodied in sociocultural context, as well as policy and institutional practices to overcoming these barriers.

Findings
While multiple ethical frameworks are necessary to fully capture the issues related to authentic talent development in socioeconomic context, a focus on the ethic of care and basic goods provision is an important starting point. There are also a few fundamental starting points for human resource development in responding to ethical concerns regarding authentic talent development.

Originality/value
While the prevailing approach to talent development is implicitly based on a logic of social identity ascription, this paper promotes an alternative approach based on the ethics of civic virtue. While the former is oriented to the support of social hierarchies based on identity, the latter is oriented to fostering both social and human well-being via choice and authentic talent development.