bluuebunny/crossref_metadata_2025_split huggingface dataset:
SARS-CoV-2 spike S375F mutation characterizes the Omicron BA.1 variant
Authors: Kimura Izumi , Yamasoba Daichi , Nasser Hesham , Zahradnik Jiri , Kosugi Yusuke , Wu Jiaqi , Nagata Kayoko , Uriu Keiya , Tanaka Yuri L , Ito Jumpei , Shimizu Ryo , Tan Toong Seng , Butlertanaka Erika P , Asakura Hiroyuki , Sadamasu Kenji , Yoshimura Kazuhisa , Ueno Takamasa , Takaori-Kondo Akifumi , Schreiber Gideon ,   The Genotype to Phenotype Japan (G2P-Japan) Consortium, Toyoda Mako , Shirakawa Kotaro , Irie Takashi , Saito Akatsuki , Nakagawa So , Ikeda Terumasa , Sato Kei 
Published: April 2022

AbstractRecent studies have revealed the unique virological characteristics of Omicron, the newest SARS-CoV-2 variant of concern, such as pronounced resistance to vaccine-induced neutralizing antibodies, less efficient cleavage of the spike protein, and poor fusogenicity. However, it remains unclear which mutation(s) in the spike protein determine the virological characteristics of Omicron. Here, we show that the representative characteristics of the Omicron spike are determined by its receptor-binding domain. Interestingly, the molecular phylogenetic analysis revealed that the acquisition of the spike S375F mutation was closely associated with the explosive spread of Omicron in the human population. We further elucidate that the F375 residue forms an interprotomer pi-pi interaction with the H505 residue in another protomer in the spike trimer, which confers the attenuated spike cleavage efficiency and fusogenicity of Omicron. Our data shed light on the evolutionary events underlying Omicron emergence at the molecular level.HighlightsOmicron spike receptor binding domain determines virological characteristicsSpike S375F mutation results in the poor spike cleavage and fusogenicity in OmicronAcquisition of the spike S375F mutation triggered the explosive spread of OmicronF375-H505-mediated π-π interaction in the spike determines the phenotype of Omicron
Gain-of-function genetic screens in human cells identify SLC transporters overcoming environmental nutrient restrictions
Authors: Rebsamen Manuele , Girardi Enrico , Sedlyarov Vitaly , Scorzoni Stefania , Papakostas Konstantinos , Vollert Manuela , Konecka Justyna , Guertl Bettina , Klavins Kristaps , Wiedmer Tabea , Superti-Furga Giulio 
Published: April 2022

AbstractSolute carrier (SLC) transporters control fluxes of nutrients and metabolites across membranes and thereby represent a critical interface between the microenvironment and cellular and subcellular metabolism. Because of substantial functional overlap, the interplay and relative contributions of members of this family in response to environmental stresses remain poorly elucidated. In order to infer functional relationships between SLCs and metabolites, we developed a strategy to identify human SLCs able to sustain cell viability and proliferation under growth-limiting concentrations of essential nutrients. One-by-one depletion of 13 amino acids required for cell proliferation enabled gain-of-function genetic screens using a SLC-focused CRISPR/Cas9-based transcriptional activation approach to uncover transporters relieving cells from the growth-limiting metabolic bottleneck. We identified the cationic amino acid transporter SLC7A3 as a gene that, when upregulated, overcame low availability of arginine and lysine by increasing their uptake. SLC7A5 (LAT1), on the other hand, was able to sustain cellular fitness upon deprivation of several neutral amino acids. A genome-wide screen identified SLC7A3 as the single main gene product able to rescue cell survival in the limiting arginine conditions tested, demonstrating the potentially decisive role of transporters in overcoming nutrient limitations. Moreover, we identified metabolic compensation mediated by the glutamate/aspartate transporters SLC1A2 and SLC1A3 under glutamine-limiting conditions. Overall, this gain-of-function approach using human cells led to the definition of functional transporter-nutrient relationships and revealed that upregulation of transport activity may be sufficient to overcome environmental metabolic restrictions.
Saving the Devils is in the details: Tasmanian Devil facial tumor disease can be eliminated with interventions
Authors: Drawert Brian , Matthew Sean , Powell Megan , Rumsey Bryan 
Published: April 2022

AbstractTasmanian Devils facial tumor disease is severely impacting the population of this wild animal. We developed a computational model of the population of Tasmanian Devils, and the change induced by DFTD. We use this model to test possible intervention strategies Tasmanian conservationists could do. We investigate bait drop vaccination programs, diseased animal removals programs, and evolution of natural immunity. We conclude that a combination of intervention strategies gives the most favorable outcome.An additional goal of this paper is for reproducibility of our results. Our StochSS software platform features the ability to share and reproduce the computational notebooks that created all of the results in the paper. We endeavor that all readers should be able to reproduce our results with minimum effort.
Evolutionary adaptation of the folding pathway for secretability
Authors: Smets Dries , Tsirigotaki Alexandra , Smit Jochem H. , Krishnamurthy Srinath , Portaliou Athina G. , Vorobieva Anastassia , Vranken Wim , Karamanou Spyridoula , Economou Anastassios 
Published: April 2022

AbstractSecretory preproteins of the Sec pathway bear signal peptides and are targeted post-translationally to cross the plasma membrane or ER through translocases. After translocation and signal peptide cleavage, mature domains fold to native states in the bacterial periplasm or after further trafficking. During cytoplasmic transit, mature domains must remain non-folded for translocase recognition and translocation. Here, we sought the structural basis for the delayed folding mechanism of mature domains and how this is regulated by signal peptides. To address this, we compared how evolution diversified a periplasmic peptidyl-prolyl isomerase PpiA mature domain from its structural twin cytoplasmic PpiB. Using global and local hydrogen deuterium exchange mass spectrometry we showed that PpiA is a slower folder. We defined at near-residue resolution hierarchical folding initiated by similar foldons in the twins, that displayed different order and rates. Folding is delayed in PpiA by less hydrophobic/bulky native contacts, frustrated residues and a critical β -turn in the early folding region and by signal peptide-driven disorder, which disrupts foldon hierarchy. When selected PpiA residues and its signal peptide were grafted onto PpiB they converted it into a slow folder with enhancedin vivosecretion. These data reveal the structural basis of non-folding in a secretory protein, that allows its trafficking.
Genomic insights into present local adaptation and future climate change vulnerability of a keystone forest tree species in East Asian
Authors: Sang Yupeng , Long Zhiqin , Dan Xuming , Feng Jiajun , Shi Tingting , Jia Changfu , Zhang Xinxin , Lai Qiang , Yang Guanglei , Zhang Hongying , Xu Xiaoting , Liu Huanhuan , Jiang Yuanzhong , Ingvarsson Pär K. , Liu Jianquan , Mao Kangshan , Wang Jing 
Published: April 2022

ABSTRACTRapid global climate change is posing a huge threat to biodiversity. Assessments of the adaptive capacity for most taxa is usually performed on the species as a whole, but fails to incorporate intraspecific adaptive variation that may play a fundamental role in buffering future shifting climates. Here we generate a chromosome-scale genome assembly forPopulus koreana, a pioneer and keystone tree species in East Asia temperate forests. We also obtain whole-genome sequences of 230 individuals collected from 24 natural populations. An integration of population genomics and environmental variables was performed to reveal the genomic basis of local adaptation to diverse climate variable. We identify a set of climate-associated single nucleotide polymorphisms (SNPs), insertions-deletions (Indels) and structural variations (SVs), in particular numerous adaptive non-coding variants distributed across the genome ofP. koreana. We incorporate these variants into an environmental modelling scheme to predict spatiotemporal responses ofP. koreanato future climate change. Our results highlight the insights that the integration of genomic and climate data can shed on the future evolutionary adaptive capacities of a species to changing environmental conditions.
Emergence and clonal expansion of Vibrio aestuarianus lineages pathogenic for oysters in Europe
Authors: Mesnil Aurélie , Jacquot Maude , Garcia Céline , Tourbiez Delphine , Canier Lydie , Bidois Audrey , Dégremont Lionel , Cheslett Deborah , Geary Michelle , Vetri Alessia , Roque Ana , Furones Dolors , Garden Alison , Orozova Petya , Arzul Isabelle , Sicard Mathieu , Charrière Guillaume , Destoumieux-Garzón Delphine , Travers Marie-Agnès 
Published: April 2022

AbstractCrassostrea gigas oysters represent a significant global food source, with 4.7 million tons harvested per year. In 2001, the bacterium V. aesturianus francensis emerged as a pathogen that causes adult oyster mortality in France and Ireland. Its impact on oyster aquaculture has increased in Europe since its reemergence in 2012. To better understand the evolutionary mechanisms leading to the emergence and persistence over time of this pathogen, we conducted a survey of mollusk diseases through national reference laboratories (NRLs) across Europe. We analyzed 54 new genomes of V. aestuarianus (Va) isolated from multiple environmental compartments since 2001, in areas with and without bivalve mortalities. We used a combination of comparative genomics and population genetics approaches to show that Va francensis lineages have undergone clonal expansion in Europe, likely after a recent selective bottleneck. Low mutation and recombination rates may have selected particular virulent genotypes. Furthermore, we identified a specific cus-cop-containing island conferring copper resistance to Va francensis whose acquisition may have favored the emergence of pathogenic lineages adapted to oysters.
Financial strength of banking sector in Bangladesh: a CAMEL framework analysis
Authors: Afroj Farhana 
Published: April 2022

PurposeThis paper investigates the financial strength of banks in Bangladesh and factors affecting the financial strength over the years 2010–2015 on 35 banks.Design/methodology/approachAdditive value function with CAMEL rating (capital stength, asset quality, managerial efficiency, earning ability, liquidity) has been employed to calculate banks’ financial strength index (FSI). In the second stage, panel regression has been exercised to find out the determinants of banks’ financial strength.FindingsEmpirical finding exhibits that the Islamic banks of Bangladesh are financially stronger and outperform conventional and Islamic window banks with higher liquidity. In the ownership category, private banks have more financial strength with higher capital strength, asset quality, managerial efficiency and earning ability than public banks. Bank size, loan recovery, salary and banking sector development positively affect whereas the loan-asset negatively affect the bank’s financial strength in Bangladesh.Research limitations/implicationsThis study has its limitations despite its importance. CAMELS is a more improved form than using CAMEL. But because of the data deficiency on “S” which represents sensitivity, it would not be possible to use CAMELS framework. Further researchers could incorporate this.Practical implicationsGovernment and banks should allow Islamic banks to enter the market on easy terms because of their outstanding performance in the existing market. In addition, banks should provide loans with consideration so that they cannot create credit risk. In addition, they should calculate composite financial strength annually to understand which components they need to work on.Originality/valueThis study extends the extant result on the composite FSI. It is hard to examine the financial strength of banks using only ratio value, which misleads most of the time. The study offers evidence on how the FSI provides more rigorous results and what are the factors contribute most to the financial strength of banks.
A qualitative study on how Danish landscape architectural firms understand and work with accessibility
Authors: Gramkow Marie Christoffersen , Merit Marcus Tang , Stigsdotter Ulrika Karlsson 
Published: April 2022

PurposeDuring the past decade, Danish policies and legislation have increasingly focused on accessibility, which, by virtue of adopting the UN Sustainable Development Goals, has spurred new demands for the expertise of Danish landscape architects. Surveys indicate as much as 27% of the Danish population have a physical disability. Therefore, landscape architectural firms play an important role in designing accessible, public and green spaces, which could reduce the number of people who experience disability in their everyday life arising from inaccessible designs. Despite this, peer-reviewed research has not attempted to qualitatively understand how landscape architects approach accessibility in their daily practice.Design/methodology/approachBased on a grounded theory analysis of 15 semi-structured qualitative interviews with randomly selected landscape architectural firms, this study aims to describe how landscape architectural firms approach and perceive accessibility.FindingsThe results of the study show a complex understanding of accessibility among practising landscape architects, with firms focusing on the role of Danish building regulations, the programming of accessibility and professional aesthetic dilemmas. Moreover, accessibility is perceived with some frustration as an element that takes valuable space from green areas due to clients' lack of willingness to provide resources for integrated solutions, landscape architects' own limited expertise and knowledge of integrated accessibility solutions and insufficient regulatory leeway.Originality/valueAs accessibility is a major element of the tasks within contemporary landscape architecture, graduates need additional training in accessibility, which, in turn, necessitates additional research into accessible design solutions.
Leader, context and CSR: evidence from Taiwan
Authors: Ling Ya-Hui 
Published: April 2022

PurposeThis study examines the influence of context on Taiwanese senior managers' corporate social responsibility (CSR) decisions. The study seeks to identify the current profiles of managerial CSR perspectives and organizational CSR investments in Taiwan. In particular, whether a non-Friedman perspective is more prevalent than a Friedman perspective and whether community-related CSR is more prevalent than other CSR practices in Taiwan remain unclear. The study also seeks to identify the relationship between managers' CSR perspective profiles and organizational CSR investment profiles in Taiwan.Design/methodology/approachThe sample was selected from the Taiwanese top companies list. Altogether, 150 valid responses from senior managers of 150 companies were returned.FindingsThe reported evidence shows that senior managers' Friedman/non-Friedman CSR perspective has a great influence in directing a firm's CSR decision in Taiwan. Managers holding the Friedman perspective are slightly more than those holding the non-Friedman CSR perspective, but both perspectives are popular. There is a tendency for firms to make either more or less investments in all CSR dimensions. A Friedman perspective tends to be associated with low CSR investments, and a non-Friedman perspective tends to be associated with high CSR investments.Originality/valueA major contribution of this study is to offer a different perspective from the Western view regarding CSR implementation in a Chinese-dominant culture society. The study extends the upper echelon theory that managerial CSR perspectives can be a driver of a firm's CSR decision-making. The study also offers further evidence for the institutional theory that CSR is contextually dependent.
Jute for Life: reconciling the social and business goals through sustainable entrepreneurship
Authors: Tiwari Mitali , Nakra Amit 
Published: April 2022

Learning outcomes
The case has practical value exhibiting forces creating sustainable livelihood at grassroots level and at the same time depicting how business and social goals can be reconciled through innovative mechanisms.

Case overview/synopsis
The case covers the journey of a social enterprise lead by a woman entrepreneur, run by women workers and providing livelihood to several rural women entrepreneurs through providing skill development training in making hand-made jute bags.

Complexity academic level
MBA and BBA

Supplementary materials
Teaching notes are available for educators only.

Subject code
CSS 3: Entrepreneurship
How to benefit from digital platform capabilities? Examining the role of knowledge bases and organisational routines updating
Authors: Liu Longjun , Fan Qing , Liu Ruhong , Zhang Guiqing , Wan Wenhai , Long Jing 
Published: April 2022

PurposeThis study aims to explore whether digital platform capabilities (integration and reconstruction) affect technological innovation through knowledge bases in the dimensions of breadth and depth and the moderating role of organisational routines updating.Design/methodology/approachHierarchical regression, mediation effect test macro and bootstrap were conducted to empirically analyse two waves of longitudinal survey data from 179 Chinese technology firms.FindingsResults confirmed that knowledge bases (breadth and depth) mediated the effect of digital platform capabilities (integration and reconstruction) on technological innovation and that updating of organisational routines moderated the relationship between knowledge bases and technological innovation.Practical implicationsThese findings offer guidance to firms that aim to achieve technological innovation and advantages, highlighting the importance of digital platform capabilities, knowledge bases and organisational routines updating.Originality/valueAdvancing from existing digital strategies and firm innovation literature, the authors provide a new perspective (knowledge bases) to respond to the information technology (IT) paradox and understand the role of digital platform capabilities in improving technological innovation.
The match-up hypotheses revisited: matching social judgments and advertising messaging in celebrity endorsements
Authors: Bauer Brittney C. , Carlson Brad D. , Johnson Clark D. 
Published: April 2022

Purpose
Although endorsers are thought to be highly effective when they match-up with a product, the current understanding of endorser match-up offers little insight for distinctions between equally attractive and trustworthy endorsers who have equivalent expertise in the product category, yet still diverge in their performance. Therefore, the main purpose of this research is to understand how a match between social judgments (i.e. warmth vs competence) of a celebrity endorser and specific advertising appeals (i.e. symbolic vs utilitarian) can improve consumer responses to an endorsement.

Design/methodology/approach
A preliminary study empirically distinguishes perceptions of warmth and competence from prevailing celebrity endorser evaluative criteria. Then, the authors conduct multiple 2 (warmth vs competence) × 2 (symbolic vs utilitarian) between-subjects experiments to demonstrate the effect of matching social judgments and advertising messaging, across celebrity genders (i.e. male and female), forms of marketing communications (i.e. print ads and interactive online ads) and types of brands (i.e. well-established and new/unknown).

Findings
The findings demonstrate that matching celebrity endorser social judgments with the appropriate type of advertising messaging positively influences consumer response to the brand for both male and female endorsers. Additionally, despite a commonly held belief that celebrity endorsements are more effective at changing attitudes than actual behaviors, for interactive online ads, the authors find that the match strategy can motivate consumer response through two different pathways. For well-established brands, the match improves overall brand response predominately through cognitive and behavioral mechanisms. Alternatively, for new or unknown brands, the match initially impacts affective responses, which are subsequently related to consumers shopping a brand’s product category, rating a brand higher in customer recommendations, choosing a brand’s products over top competitors and paying more for the brand’s offerings.

Originality/value
The main contribution of this research is the demonstrated support for an alternative and effective application of the match-up hypothesis, based on a fit between the endorser and the advertising messaging itself.
Determination of the world stock indices' co-movements by association rule mining
Authors: Kartal Burcu , Sert Mehmet Fatih , Kutlu Melih 
Published: April 2022

PurposeThis study aims to provide preliminary information to the investor by determining which indices co-movement, with the data mining method.Design/methodology/approachIn this context, data sets containing daily opening and closing prices between 2001 and 2019 have been created for 11 stock market indexes in the world. The association rule algorithm, one of the data mining techniques, is used in the analysis of the data.FindingsIt is observed that the US stock market indices take part in the highest confidence levels between association rules. The XU100 stock index co-movement with both the European stock market indices and the US stock indices. In addition, the Hang Seng Index (HSI) (Hong Kong) takes part in the association rules of all stock market indices.Originality/valueThe important issue for data sets is that the opening/closing values of the same day or the previous day are taken into account according to the open or closed status of other stock market indices by taking the opening time of the stock exchange index to be created. Therefore, data sets are arranged for each stock market index, separately. As a result of this data set arranging process, it is possible to find out co-movements of the stock market indexes. It is proof that the world stock indices have co-movement, and this continues as a cycle.
Information needs and information-seeking behaviour of maritime students: a systematic literature review using the PRISMA method
Authors: Chlomoudis Constantinos , Konstantinou Anastasia , Kostagiolas Petros , Pallis Petros 
Published: April 2022

PurposeDigital information seeking behavior incorporates the effective information seeking, retrieving and using in maritime studies. Moreover, digital information literacy skills support the employment of digital tools and information databases for decision making and for performing specific tasks online. The main aim of this paper is to explore the relevant research for the information needs and information seeking behaviour of maritime students.Design/methodology/approachA systematic literature review over scholarly publications in English language over the last decade was performed through PRISMA method.FindingsThe systematic literature review resulted to 22 related publications that are consistent with the criteria of the systematic literature review. These publications are analysed and discussed. The need for further research in the area of information seeking behaviour of students of maritime studies as well as of digital information literacy is exposed.Originality/valueThis work explores the behavioural patterns surrounding the central role of information for maritime students as well as for decision-making in the maritime sector. Digital information literacy competencies are discussed in order to be included in the curricula of maritime studies.