bluuebunny/crossref_metadata_2025_split huggingface dataset:
Amino acid availability is not essential for lifespan extension by dietary restriction in the fly
Authors: Gautrey Sarah L , Simons Mirre J P 
Published: July 2021

AbstractDietary restriction (DR) is one of the most potent ways to extend health- and lifespan. Key progress in understanding the mechanisms of DR, and ageing more generally, was made when dietary protein, and more specifically essential amino acids (EAA), were identified as the key dietary component to restrict to obtain DR’s health and lifespan benefits. This role of dietary amino acids has strongly influenced work on ageing mechanisms, especially in nutrient sensing, e.g. Tor and insulin(-like) signalling networks. Experimental biology in Drosophila melanogaster has been instrumental in generating and confirming the now dominant hypothesis that EAA availability is central to ageing. Here, we expand on previous work testing the involvement of EAA in DR through large scale (N=6,238) supplementation experiments across four diets and two genotypes in female flies. Surprisingly, we find that EAA are not essential to DR’s lifespan benefits. Importantly, we do identify the fecundity benefits of EAA supplementation suggesting the supplemented EAA were bioavailable. Furthermore, we find that the effects of amino acids on lifespan vary by diet and genetic line studied and that at our most restricted diet fecundity is constrained by other nutrients than EAA. We suggest that DR for optimal health is a concert of nutritional effects, orchestrated by genetic, diet and environmental interactions. Our results question the universal importance of amino acid availability in the biology of ageing and DR.
Ecology and transmission of a dengue virus serotype 4 identified in wild Aedes aegypti in Florida
Authors: Ayers Jasmine B. , Xie Xuping , Coatsworth Heather , Stephenson Caroline J. , Waits Christy M. , Shi Pei-Yong , Dinglasan Rhoel R. 
Published: July 2021

1AbstractDengue virus is the most prevalent mosquito-borne virus, causing approximately 390 million infections and 25,000 deaths per year. Aedes aegypti, the primary mosquito vector of dengue virus, is well established throughout the state of Florida, USA. Autochthonous transmission of dengue virus to humans in Florida has been increasing since 2009, alongside consistent importation of dengue cases. However, most cases of first infection with dengue are asymptomatic and the virus can be maintained in mosquito populations, complicating surveillance and leading to an underestimation of disease risk. Metagenomic sequencing of Aedes aegypti mosquitoes in Manatee County, Florida revealed the presence of dengue virus serotype 4 (DENV-4) genomes in mosquitoes from multiple trapping sites over 2 years, in the absence of a human DENV-4 index case and even though a locally acquired case of DENV-4 has never been reported in Florida. This finding suggested that: i) DENV-4 may circulate amongst humans undetected, ii) the virus was being maintained in the mosquito population, or iii) the detected complete genome sequence may not represent a viable virus. This study demonstrates that an infectious clone generated from the Manatee County DENV-4 (DENV-4M) sequence is capable of infecting mammalian and insect tissue culture systems, as well as adult female Aedes aegypti mosquitoes when fed in a blood meal. However, the virus is subject to a dose dependent infection barrier in mosquitoes, and has a kinetic delay compared to a phylogenetically related wild-type (WT) control virus from a symptomatic child, DENV-4H (strain Homo sapiens/Haiti-0075/2015, GenBank accession MK514144.1). DENV-4M disseminates from the midgut to the ovary and saliva at 14 days post-infection. Viral RNA was also detectable in the adult female offspring of DENV-4M infected mosquitoes. These results demonstrate that the virus is capable of infecting vector mosquitoes, is transmissible by bite, and is vertically transmitted, indicating a mechanism for maintenance in the environment without human-mosquito transmission. These findings suggest undetected human-mosquito transmission and/or long-term maintenance of the virus in the mosquito population is occurring in Florida, and underscore the importance of proactive surveillance for viruses in mosquitoes.Graphical AbstractIn order to better assess the public health risk posed by a detection of DENV-4 RNA in Manatee County, FL Aedes aegypti, we produced an infectious clone using the sequence from the wild-caught mosquitoes and characterized it via laboratory infections of mosquitoes and mosquito tissues.
Membrane activity of a DNA-based ion channel depends on the stability of its double-stranded structure
Authors: Morzy Diana , Joshi Himanshu , Sandler Sarah E. , Aksimentiev Aleksei , Keyser Ulrich F. 
Published: July 2021

AbstractStructural DNA nanotechnology has emerged as a promising method for designing spontaneously-inserting and fully-controllable synthetic ion channels. However, both insertion efficiency and stability of existing DNA-based ion channels leave much room for improvement. Here, we demonstrate an approach to overcoming the unfavorable DNA-lipid interactions that hinder the formation of a stable transmembrane pore. Our all-atom MD simulations and experiments show that the insertion-driving cholesterol modifications, when introduced at an end of a DNA strand, are likely to cause fraying of the terminal base pairs as the DNA nanostructure adopts its energy-minimum configuration in the membrane. We also find that fraying of base pairs distorts nicked DNA constructs when embedded in a lipid bilayer. Here, we show that DNA nanostructures that do not have discontinuities (nicks) in their DNA backbones form considerably more stable DNA-induced conductive pores and insert into lipid membranes with a higher efficiency than the equivalent nicked constructs. Moreover, lack of nicks allows to design and maintain membrane-spanning helices in a tilted orientation within lipid bilayer. Thus, reducing the conformational degrees of freedom of the DNA nanostructures enables better control over their function as synthetic ion channels.
Gluconobacter oxydans Knockout Collection Finds Improved Rare Earth Element Extraction
Authors: Schmitz Alexa M. , Pian Brooke , Medin Sean , Reid Matthew C. , Wu Mingming , Gazel Esteban , Barstow Buz 
Published: July 2021

AbstractRare earth elements (REE) are critical components of our technological society and essential for renewable energy technologies. Traditional thermochemical processes to extract REE from mineral ores or recycled materials are costly and environmentally harmful1, and thus more sustainable extraction methods require exploration. Bioleaching offers a promising alternative to conventional REE extraction2–4, and is already used to extract 5% of the world’s gold, and ≈ 15% of the world’s copper supply5,6. However, the performance of REE bioleaching lags far behind thermochemical processes2,7–9. Despite this, to the best of our knowledge no genetic engineering strategies have yet been used to enhance REE bioleaching, and little is known of the genetics that confer this capability. Here we build a whole genome knockout collection for Gluconobacter oxydans B58, one of the most promising organisms for REE bioleaching10, and use it to comprehensively characterize the genomics of REE bioleaching. In total, we find 304 genes that notably alter production of G. oxydans’ acidic biolixiviant, including 165 that hold up under statistical comparison with wild-type. The two most impactful groups of genes involved in REE bioleaching have opposing influences on acid production and REE bioleaching. Disruption of genes underlying synthesis of the cofactor pyrroloquinoline quinone (PQQ) and the PQQ-dependent membrane-bound glucose dehydrogenase all but eliminates bioleaching. In contrast, disruption of the phosphate-specific transport system accelerates acid production and enhances bioleaching. We identified 6 disruption mutants, that increase bioleaching by at least 11%. Most significantly, disruption of pstC, encoding part of the phosphate-specific transporter, pstSCAB, enhances bioleaching by 18%. Taken together, these results give a comprehensive roadmap for engineering multiple sites in the genome of G. oxydans to further increase its bioleaching efficiency.
Z-DNA as a Touchstone for Additive Empirical Force Fields and a Refinement of the Alpha/Gamma DNA torsions for AMBER
Authors: Zgarbová Marie , Šponer Jiří , Jurečka Petr 
Published: July 2021

AbstractAlthough current AMBER force fields are relatively accurate for canonical B-DNA, many non-canonical structures are still described incorrectly. As non-canonical motifs are attracting increasing attention due to the role they play in living organisms, further improvement is desirable. Here, we have chosen Z-DNA molecule, can be considered a touchstone of the universality of empirical force fields, since the non-canonical α and γ backbone conformations native to Z-DNA are also found in protein-DNA complexes, i-motif DNA and other non-canonical DNAs. We show that spurious α/γ conformations occurring in simulations with current AMBER force fields, OL15 and bsc1, are largely due to inaccurate α/γ parameterization. Moreover, stabilization of native Z-DNA substates involving γ = trans conformations appears to be in conflict with the correct description of the canonical B-DNA structure. Because the balance of the native and spurious conformations is influenced by non-additive effects, this is a difficult case for an additive dihedral energy scheme such as AMBER. We propose new α/γ parameters, denoted OL21, and show that they improve the stability of native α/γ Z-DNA substates while keeping the canonical DNA description virtually unchanged, and thus represent a reasonable compromise within the additive force field framework. Although further extensive testing is needed, the new modification appears to be a promising step towards a more reliable description of non-canonical DNA motifs and provides the best performance for Z-DNA molecules among current AMBER force fields.
SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: a Computational Model of Epitope Loss in Variants of Concern
Authors: Triveri Alice , Serapian Stefano A. , Marchetti Filippo , Doria Filippo , Pavoni Silvia , Cinquini Fabrizio , Moroni Elisabetta , Rasola Andrea , Frigerio Francesco , Colombo Giorgio 
Published: July 2021

AbstractThe SARS-CoV-2 spike (S) protein is exposed on the viral surface and is the first point of contact between the virus and the host. For these reasons it represents the prime target for Covid-19 vaccines. In recent months, variants of this protein have started to emerge. Their ability to reduce or evade recognition by S-targeting antibodies poses a threat to immunological treatments and raises concerns for their consequences on vaccine efficacy.To develop a model able to predict the potential impact of S-protein mutations on antibody binding sites, we performed unbiased multi-microsecond molecular dynamics of several glycosylated S-protein variants and applied a straightforward structure-dynamics-energy based strategy to predict potential changes in immunogenic regions on each variant. We recover known epitopes on the reference D614G sequence. By comparing our results, obtained on isolated S-proteins in solution, to recently published data on antibody binding and reactivity in new S variants, we directly show that modifications in the S-protein consistently translate into the loss of potentially immunoreactive regions. Our findings can thus be qualitatively reconnected to the experimentally characterized decreased ability of some of the Abs elicited against the dominant S-sequence to recognize variants. While based on the study of SARS-CoV-2 Spike variants, our computational epitope-prediction strategy is portable and could be applied to study immunoreactivity in mutants of proteins of interest whose structures have been characterized, helping the development/selection of vaccines and antibodies able to control emerging variants.
Gamification effects on users' motivation to contribute knowledge in a Portuguese Q&A community
Authors: Oliveira Jordao do Amaral Isabel , Kang Minhyung 
Published: July 2021

PurposeThis research investigates the detailed mechanisms of how gamification affordances influence intrinsic and internalized extrinsic motivation and ultimately improve the quality and quantity of knowledge contribution.Design/methodology/approachSurvey responses from 154 users of Stack Overflow in Portuguese were analyzed by the partial least squares–structural equation modeling approach to validate the research model.FindingsChallenge and goal setting influence individuals to reach the flow state, which increases the quantity of knowledge contribution. Rewards enhance the quality of knowledge contribution through perceived self-worth. Social comparison increases perceived reputation, but its impact does not ultimately lead to knowledge contribution.Originality/valueThe current study differentiated types of motivation and dimensions of knowledge contribution when exploring the effects of gamification affordances. This perspective was proven helpful to understand the various gamification affordances' influence on knowledge contribution.
What matters for the future? Comparing Globe's future orientation with Hofstede's long-term orientation
Authors: Alipour Ali 
Published: July 2021

PurposeThis paper aims to compare the future orientation (FO) society practices dimension of the Globe model with Hofstede's long-term orientation (LTO) by testing their causal effects on three firm-level variables: cash holdings, long-term investments and acquisitions. In doing so, this research challenges the already taken-for-granted assumption in the empirical research that the two dimensions are equivalent.Design/methodology/approachHierarchical linear modeling (HLM) was used to test the hypotheses on 7,065 firms across 49 countries between 2000 and 2017.FindingsThe findings show that the causal impacts of FO society practices and LTO on a given construct are not consistent. Although LTO increases cash holdings, the impact of FO society practices on this variable is insignificant. Additionally, unlike FO society practices, which significantly increases long-term investments and acquisitions, LTO does not influence long-term investments and decreases acquisitions.Originality/valueThis study is valuable since it addresses the confusion surrounding the similarities and differences between FO society practices and LTO. Despite the dissimilarity also emphasized by Globe, Hofstede claims that they are equivalent, and the great majority of the empirical literature has assumed them to be equivalent in their analyses. Addressing this confusion, this research provides further empirical evidence that these two dimensions are dissimilar. The additional important contribution of the study is theorizing and examining the impact of FO society practices and LTO on the firm-level outcomes that reflect their temporal orientation (i.e. long-term investments and acquisitions), which is surprisingly neglected in the literature.
Downside systematic risk in Pakistani stock market: role of corporate governance, financial liberalization and investor sentiment
Authors: Hussain Shahzad , Akbar Muhammad , Malik Qaisar Ali , Ahmad Tanveer , Abbas Nasir 
Published: July 2021

Purpose
The purpose of this paper is to examine the impact of corporate governance, investor sentiment and financial liberalization on downside systematic risk and the interplay of socio-political turbulence on this relationship through static and dynamic panel estimation models.

Design/methodology/approach
The evidence is based on a sample of 230 publicly listed non-financial firms from Pakistan Stock Exchange (PSX) over the period 2008–2018. Furthermore, this study analyzes the data through Blundell and Bond (1998) technique in the full sample as well sub-samples (big and small firms).

Findings
The authors document that corporate governance mechanism reduces the downside risk, whereas investor sentiment and financial liberalization increase the investors’ exposure toward downside risk. Particularly, the results provide some new insights that the socio-political turbulence as a moderator weakens the impact of corporate governance and strengthens the effect of investor sentiment and financial liberalization on downside risk. Consistent with prior studies, the analysis of sub-samples reveals some statistical variations in large and small-size sampled firms. Theoretically, the findings mainly support agency theory, noise trader theory and the Keynesians hypothesis.

Originality/value
Stock market volatility has become a prime area of concern for investors, policymakers and regulators in emerging economies. Primarily, the existence of market volatility is attributed to weak governance, irrational behavior of market participants, the liberation of financial policies and sociopolitical turbulence. Therefore, the present study provides simultaneous empirical evidence to determine whether corporate governance, investor sentiment and financial liberalization hinder or spur downside risk in an emerging economy. Furthermore, the work relates to a small number of studies that examine the role of socio-political turbulence as a moderator on the relationship of corporate governance, investor sentiment and financial liberalization with downside systematic risk.
Perspectives, progress and prospects; researching women’s entrepreneurship in emerging economies
Authors: Anderson Alistair , Ojediran Funmi 
Published: July 2021

Purpose
The purpose of this paper is to review the literature on women’s entrepreneurship in emerging economies. This is a thematic review to identify patterns and trends to better understand this literature. From the analysis, this study offers ideas for useful and theoretically informed research. In addition, this paper proposes the concept of restricted agency that helps to explain the practice.

Design/methodology/approach
This study identifies the nature, what is interesting, what it sees as important and considers what is neglected in this literature. The analysis sought important issues, interesting directions and the potential for useful future work. Thematic analysis is ideal for messy and unstructured material such as the literature used in this study as the data set. The process is qualitative, iterative and inductive but ontologically appropriate for the socially produced knowledge of the literature.

Findings
This paper finds the literature tends towards descriptive papers. Few papers make substantial contributions to theory. Many papers reported the barriers women to encounter, reporting general and typical processes of responding to obstacles and the implications for practice. Interestingly this study perceives overcoming and sometimes using, the cultural and physical restraints of gendered entrepreneurship. This paper proposes the concept of restricted agency explaining the gendering of entrepreneurs and explains what they can do. Moreover, the concept helps explain why and what. Most promising theoretically, is how the application of this agency is slowly and contextually differently changing the rules of the game.

Research limitations/implications
This study covers a large and extensive literature, so might have missed themes.

Originality/value
This paper starts with the notion of the “otherness” of women’s entrepreneurship. The literature is good at explaining both how and why women’s entrepreneurship is different and in effect, marginalised. This study conceptualises this gendering process as a restricted agency. Moreover, the concept helps explain why and what. Most promising theoretically, is how the application of this agency is slowly and contextually differently changing the rules of the game. It may be the mechanism for emancipation.
Introduction of a new AAC symbol classification system: the multidimensional quaternary symbol continuum (MQSC)
Authors: Pampoulou Eliada , Fuller Donald R. 
Published: July 2021

PurposeWhen the augmentative and alternative communication (ACC) model (Lloyd et al., 1990) was proposed, these components of symbols were not considered, nor were they contemplated when superordinate (Lloyd and Fuller, 1986) and subordinate levels (Fuller et al., 1992) of AAC symbol taxonomy were developed. The purpose of this paper is to revisit the ACC model and propose a new symbol classification system called multidimensional quaternary symbol continuum (MQSC)Design/methodology/approachThe field of AAC is evolving at a rapid rate in terms of its clinical, social, research and theoretical underpinnings. Advances in assessment and intervention methods, technology and social issues are all responsible to some degree for the significant changes that have occurred in the field of AAC over the last 30 years. For example, the number of aided symbol collections has increased almost exponentially over the past couple of decades. The proliferation of such a large variety of symbol collections represents a wide range of design attributes, physical attributes and linguistic characteristics for aided symbols and design attributes and linguistic characteristics for unaided symbols.FindingsTherefore, it may be time to revisit the AAC model and more specifically, one of its transmission processes referred to as the means to represent.Originality/valueThe focus of this theoretical paper then, is on the current classification of symbols, issues with respect to the current classification of symbols in terms of ambiguity of terminology and the evolution of symbols, and a proposal for a new means of classifying the means to represent.Peer reviewThe peer review history for this article is available at: https://publons.com/publon10.1108/JET-04-2021-0024