bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lineage Recording Reveals the Phylodynamics, Plasticity and Paths of Tumor Evolution
Authors: Yang Dian , Jones Matthew G. , Naranjo Santiago , Rideout William M. , Min Kyung Hoi (Joseph) , Ho Raymond , Wu Wei , Replogle Joseph M. , Page Jennifer L. , Quinn Jeffrey J. , Horns Felix , Qiu Xiaojie , Chen Michael Z. , Freed-Pastor William A. , McGinnis Christopher S. , Patterson David M. , Gartner Zev J. , Chow Eric D. , Bivona Trever G. , Chan Michelle M. , Yosef Nir , Jacks Tyler , Weissman Jonathan S. 
Published: October 2021

SUMMARYTumor evolution is driven by the progressive acquisition of genetic and epigenetic alterations that enable uncontrolled growth, expansion to neighboring and distal tissues, and therapeutic resistance. The study of phylogenetic relationships between cancer cells provides key insights into these processes. Here, we introduced an evolving lineage-tracing system with a single-cell RNA-seq readout into a mouse model of Kras;Trp53(KP)-driven lung adenocarcinoma which enabled us to track tumor evolution from single transformed cells to metastatic tumors at unprecedented resolution. We found that loss of the initial, stable alveolar-type2-like state was accompanied by transient increase in plasticity. This was followed by adoption of distinct fitness-associated transcriptional programs which enable rapid expansion and ultimately clonal sweep of rare, stable subclones capable of metastasizing to distant sites. Finally, we showed that tumors develop through stereotypical evolutionary trajectories, and perturbing additional tumor suppressors accelerates tumor progression by creating novel evolutionary paths. Overall, our study elucidates the hierarchical nature of tumor evolution, and more broadly enables the in-depth study of tumor progression.
Single-particle cryo-EM structures from iDPC-STEM at near-atomic resolution
Authors: Lazić Ivan , Wirix Maarten , Leidl Max Leo , de Haas Felix , Beckers Maximilian , Pechnikova Evgeniya V. , Müller-Caspary Knut , Egoavil Ricardo , Bosch Eric G.T. , Sachse Carsten 
Published: October 2021

AbstractElectron cryo-microscopy (cryo-EM) is becoming one of the routine tools for structure determination of biological macromolecules. Commonly, molecular images are obtained by conventional transmission electron microcopy (CTEM) using underfocus and subsequently computationally combined into a high-resolution 3D structure. Here, we apply scanning transmission electron microscopy (STEM) using the integrated differential phase contrast mode also known as iDPC-STEM to the cryo-EM test specimen of tobacco mosaic virus (TMV). The micrographs show complete contrast transfer to high resolution and enable the cryo-EM structure determination at 3.5 Å resolution using single-particle based helical reconstruction. A series of cryo-EM TMV maps was resolved at near-atomic resolution taken at different convergence semi-angle (CSA) beams and share identical features with maps obtained by CTEM of a previously acquired same-sized TMV data set. The associated map B-factors from iDPC-STEM match those obtained by CTEM recordings using 2ndgeneration direct electron detection devices. These data show that STEM imaging in general, and in particular the iDPC-STEM approach, can be applied to vitrified single-particle specimens to determine near-atomic resolution cryo-EM structures of biological macromolecules.
Getting out of a mammalian egg: the egg tooth and caruncle of the echidna
Authors: Fenelon Jane C , Abbie Bennetts , Neal Anthwal , Pyne Michael , Johnston Stephen D , Evans Alistair R , Tucker Abigail S , Renfree Marilyn B 
Published: October 2021

AbstractIn the short-beaked echidna, Tachyglossus aculeatus, after an initial period of in utero development, the egg is laid in the pouch and incubated for 10 days. During this time, the fetuses develop an egg tooth and caruncle to help them hatch. However, there are only a few historical references that describe the development of the monotreme egg tooth. Using unprecedented access to echidna pre- and post-hatching tissues, the egg tooth and caruncle were assessed by micro-CT, histology and immunofluorescence, to map the changes at the morphological and molecular level. Unlike mammalian tooth germs that develop by invagination of a placode, the echidna egg tooth developed by evagination, similar to that of the first teeth in some reptiles. The egg tooth ankylosed to the premaxilla, rather than forming a mammalian thecodont attachment, with loss of the egg tooth post-hatching associated with high levels of odontoclasts, and apoptosis. The caruncle formed as a separate mineralisation from the adjacent nasal capsule, and as observed in birds and turtles, the nasal region epithelium expressed markers of cornification. Together, this highlights that the monotreme egg tooth shares many similarities with reptilian teeth, suggesting that this tooth is conserved from a common ancestor of mammals and reptiles.
Applying And Promoting Open Science In Ecology - Surveyed Drivers And Challenges
Authors: Strømme Christian B. , Lane A. Kelly , Halbritter Aud H. , Law Elizabeth , Nater Chloe R. , Nilsen Erlend B. , Boutouli Grace D. , Egelkraut Dagmar D. , Telford Richard J. , Vandvik Vigdis , Cotner Sehoya H. 
Published: October 2021

AbstractOpen Science (OS) comprises a variety of practices and principles that are broadly intended to improve the quality and transparency of research, and the concept is gaining traction. Since OS has multiple facets and still lacks a unifying definition, it may be interpreted quite differently among practitioners. Moreover, successfully implementing OS broadly throughout science requires a better understanding of the conditions that facilitate or hinder OS engagement, and in particular, how practitioners learn OS in the first place. We addressed these issues by surveying OS practitioners that attended a workshop hosted by the Living Norway Ecological Data Network in 2020. The survey contained scaled-response and open-ended questions, allowing for a mixed-methods approach. Out of 128 registered participants we obtained survey responses from 60 individuals. Responses indicated usage and sharing of data and code, as well as open access publications, as the OS aspects most frequently engaged with. Men and those affiliated with academic institutions reported more frequent engagement with OS than women and those with other affiliations. When it came to learning OS practices, only a minority of respondents reported having encountered OS in their own formal education. Consistent with this, a majority of respondents viewed OS as less important in their teaching than in their research and supervision. Even so, many of the respondents’ suggestions for what would help or hinder individual OS engagement included more knowledge, guidelines, resource availability and social and structural support; indicating that formal instruction can facilitate individual OS engagement. We suggest that the time is ripe to incorporate OS in teaching and learning, as this can yield substantial benefits to OS practitioners, student learning, and ultimately, the objectives advanced by the OS movement.
Wheat grain width: A clue for re-exploring visual indicators of grain weight
Authors: Haghshenas Abbas , Emam Yahya , Jafarizadeh Saeid 
Published: October 2021

AbstractMean grain weight (MGW) is among the most frequently measured parameters in wheat breeding and physiology. Although in the recent decades, various wheat grain analyses (e.g. counting, and determining the size, color, or shape features) have been facilitated thanks to the automated image processing systems, MGW estimations has been limited to using few number of image-derived indices; i.e. mainly the linear or power models developed based on the projected area (Area). Following a preliminary observation which indicated the potential of grain width in improving the predictions, the present study was conducted to explore potentially more efficient indices for increasing the precision of image-based MGW estimations. For this purpose, an image archive of the grains was processed, which was harvested from a two-year field experiment carried out with 3 replicates under two irrigation conditions and included 15 cultivar mixture treatments (so the archive was consisted of 180 images taken from an overall number of more than 72000 grains). It was observed that among the more than 30 evaluated indices of grain size and shape, indicators of grain width (i.e. Minor & MinFeret) along with 8 other empirical indices had a higher correlation with MGW, compared with Area. The most precise MGW predictions were obtained using the Area×Circularity, Perimeter×Circularity, and Area/Perimeter indices. In general, two main common factors were detected in the structure of the major indices, i.e. either grain width or the Area/Perimeter ratio. Moreover, comparative efficiency of the superior indices almost remained stable across the 4 environmental conditions. Eventually, using the selected indices, ten simple linear models were developed and validated for MGW prediction, which indicated a relatively higher precision than the current Area-based models. The considerable effect of enhancing image resolution on the precision of the models has been also evidenced. It is expected that the findings of the present study improve the precision of the image-based MGW estimations, and consequently facilitate wheat breeding and physiological assessments.
Objective vs subjective design newness
Authors: Sung Billy , Hartley Nicole , Vanman Eric , Hooshmand Reyhane 
Published: October 2021

PurposeThe paper aims to examine whether (1) deviation of design (i.e. objective design newness) is distinct to consumers' perception of design newness (i.e. subjective design newness) and (2) subjective design newness rather than objective design newness evokes the emotion of interest and enhances product evaluation.Design/methodology/approachIn total five sets of quasi-experiments were conducted on the natural manipulations of design newness. Specifically, the first four studies examine consumers' perception of design newness, feeling-of-interest and product evaluation toward old and new Apple's iOS (i.e., iPhone OS) icons when a new Apple's iOS is released. The fifth study generalized the findings to the new design of XiaoMi MiPhone.FindingsAcross five quasi-experimental studies, the authors found that (1) consumers do not necessarily perceive an objectively new design to be subjectively new; (2) subjective design newness, but not objective design newness, evokes interest and (3) interest, in turn, enhances product evaluation and behavioral intention toward an innovation.Research limitations/implicationsThe current finding extended the current literature on design newness by demonstrating that subjective (vs objective) design newness provides a more holistic account of consumers' interest and positive product evaluation toward the innovations.Practical implicationsThe research showed that simply updating or altering the design of a product does not evoke consumers' perception of design newness and positive product evaluation. Instead, designer and managers must explore ways to evoke consumers' perception of novelty, complexity, unfamiliarity, atypicality and difference. Furthermore, the current finding demonstrated that subjective design newness can be used to evoke consumer interest and, therefore, result in positive purchase evaluation.Originality/valueThe current research is the first to examine (1) the difference between objective and subjective design newness, (2) the emotional response toward design newness and (3) the emotion of interest as a mediator that explain the strong relationship between design newness and positive product evaluation.
The business paradigm: explanation for patterns of business interactions
Authors: Leszczyński Grzegorz , Mandjak Tibor , Margitay Tihamér , Zieliński Marek 
Published: October 2021

Purpose
This paper aims to introduce the concept of business paradigm to conceptualize and explain differences in business interaction patterns in the IMP research.

Design/methodology/approach
The concept of the interaction and the concepts related to and driven from it describe the business at both a general level. At the same time, the IMP points out the uniqueness of business interactions. This paper addresses the specific lies between the general and the particular by referring to various patterns of interactions. To close that gap, this paper implies the Kuhnian philosophy of science to conceptualize the business paradigm.

Findings
The business paradigm is a socially constructed collective term. It simultaneously captures the cognitive (what business is and what rules it has) and social (business community) dimensions of the actor’s behavior and actions. It has two interdependent dimensions: cognitive and social. It determines how the actors view and do business, and it explains the variations of interactions.

Research limitations/implications
Not applicable as it is a conceptual paper.

Practical implications
Not applicable as it is a conceptual paper.

Social implications
Not applicable as it is a conceptual paper.

Originality/value
The concept of the business paradigm is a theoretical extension of the IMP actor’s theory. The dimensions of the business paradigm capture the psychological and sociological characteristics of the business actor. The business paradigm application provides an opportunity to find that business can be different because actors in various communities have various views on what business is and how it should be properly run. Adding the business paradigm concept to the IMP theory implies strengthening the theory explanation power because the interaction explains the business’s general characteristics. The business relationship explains the business’s unique features, and the business paradigm explains the various interaction patterns.
Privacy concerns with COVID-19 tracking apps: a privacy calculus approach
Authors: Fernandes Teresa , Costa Marta 
Published: October 2021

Purpose
The COVID-19 pandemic represents a unique challenge for public health worldwide. In this context, smartphone-based tracking apps play an important role in controlling transmission. However, privacy concerns may compromise the population’s willingness to adopt this mobile health (mHealth) technology. Based on the privacy calculus theory, this study aims to examine what factors drive or hinder adoption and disclosure, considering the moderating role of age and health status.

Design/methodology/approach
A cross-sectional survey was conducted in a European country hit by the pandemic that has recently launched a COVID-19 contact-tracing app. Data from 504 potential users was analyzed through partial least squares structural equation modeling.

Findings
Results indicate that perceived benefits and privacy concerns impact adoption and disclosure and confirm the existence of a privacy paradox. However, for young and healthy users, only benefits have a significant effect. Moreover, older people value more personal than societal benefits while for respondents with a chronical disease privacy concerns outweigh personal benefits.

Originality/value
The study contributes to consumer privacy research and to the mHealth literature, where privacy issues have been rarely explored, particularly regarding COVID-19 contact-tracing apps. The study re-examines the privacy calculus by incorporating societal benefits and moving from a traditional “self-focus” approach to an “other-focus” perspective. This study further adds to prior research by examining the moderating role of age and health condition, two COVID-19 risk factors. This study thus offers critical insights for governments and health organizations aiming to use these tools to reduce COVID-19 transmission rates.
Triggering sustainable professional agency: using change laboratory to tackle unequal access to educational success collectively
Authors: Spante Maria , Varga Anita , Carlsson Linnéa 
Published: October 2021

Purpose
This study aims to depict how a change laboratory (CL) promotes sustainable professional practice at the workplace to tackle unequal access to educational success.

Design/methodology/approach
The empirical findings are from a CL focusing on school professionals’ agency and a follow-up study one year after the CL.

Findings
The study shows how the staff gained insight that professional agency is a collective and relational practice. Furthermore, the staff explored how to make a difference with viable means to create new workplace models for students’ success despite experiencing a conundrum.

Research limitations/implications
This study examined participants’ perspectives in workplace change and provided support for further research examining how professionally and collectively designed models gain sustainability in schools.

Practical implications
This study provides empirical data of how professional agency for change driven by collective visions can be accelerated with the interventionist method CL among school professionals.

Social implications
This study emphasizes the value of professional collective learning at the workplace, driven by several professional groups in school, and the need to follow up to detect sustainable change.

Originality/value
This study emphasizes the value of professional collective learning at the workplace, driven by several professional groups in school, and the need to follow up to detect sustainable change.
Improvement on modal curvatures methods for multiple damage identification in beams
Authors: Cinque Daniele , Santos Jose Viriato Araujo dos , Gabriele Stefano , Marfia Sonia , Lopes Hernâni 
Published: October 2021

PurposeThe purpose of this paper is to present a study on the application of four damage factors to several single and multiple damage scenarios of aluminium beams. Each one of these damage factors is defined by the information given by modal curvatures of the beams.Design/methodology/approachThe methodology consisted of a first experimental stage in which the modal rotations were measured with shearography and a subsequent numerical analysis in order to obtain the modal curvatures. To this end, three finite difference formulae were applied. The modal curvatures were then used to calculate the damage factors.FindingsIt was found that the profile of the damage factors varies according to the finite difference formula used. In view of the findings, the differences among the damage factors analysed are highlighted and some final recommendations to improve damage identifications via modal curvature-based are presented.Originality/valueTo the best of the authors’ knowledge, the application and comparison of several finite difference formulae and corresponding optimal sampling has not been carried out before. With the proposed approach, it is possible to identify multiple damages, which is still a great challenge. The post-processing of shearography measurements with a numerical method, which is inherently a multidisciplinary approach, is also a substantial improvement upon other type of approaches found in the literature.
The determinants of the COVID-19 related stock price overreaction and volatility
Authors: Sun Yiyang Val , Liu Bin , Prodromou Tina 
Published: October 2021

Purpose
This study aims to investigate which stock characteristics and corporate governance variables affect stock price overreaction and volatility during the COVID-19 pandemic period.

Design/methodology/approach
A set of stock characteristics and corporate governance variables which may affect price overreaction and volatility were identified following a review of the literature. A dummy variable was created for the cross-sectional analysis to take into account the unique sector effect in the consumer staples sector. Out of sample analysis was conducted to confirm the robustness of the main results.

Findings
The empirical results consistently show that size, dividend and trading volume determine the stock price reactions when the market is in turmoil during the pandemic period. Board size and average board tenure exhibit moderate effects on reducing the stock price reactions, but the effects become insignificant while controlling for the firm characteristics in the regressions. The results remain robust when tested out of the sample. More interestingly, a consumer staples sector effect is identified and tested. The test results show that the consumer staples sector effect mitigates the stock price reactions.

Practical implications
The results have practical implications for investors who aim to manage desired levels of risk in their portfolios during the pandemic. The results also provide meaningful insights to stock market speculators regarding pandemic-related speculation opportunities.

Originality/value
This study makes a meaningful connection between the irrational stock market anomalies and the COVID-19 pandemic.
The role of farm-to-table activities in agritourism towards sustainable development
Authors: Pehin Dato Musa Siti Fatimahwati , Chin Wei Lee 
Published: October 2021

PurposeThe purpose of this paper is to evaluate the role of farm-to-table (FTT) activities in agritourism towards sustainable development based on three agritourism farms in Brunei.Design/methodology/approachThe study is based on qualitative data using semi-structured interviews with 23 participants involved in the management of the farms. In-depth interviews are considered the most appropriate approach to gain the unexplored perspectives of the agriculture community at the three agritourism farms.FindingsThe study found that FTT activities imparted in agritourism contribute towards sustainable development economically, socially and environmentally. FTT leads to the establishment of small medium and micro enterprises, which, in turn, creates employment for the local people. It also plays a part in preserving the ethno-culinary heritage of indigenous food, promoting food localism and sustainable agriculture. These findings suggest that FTT activities play an important role in revitalizing the local community. The outcome of this empirical research may enable planners to better formulate regional policy based on a balanced approach taking into account the three dimensions of sustainability towards agritourism development. From a theoretical standpoint, this study adds value to the literature by identifying the contributions of FTT activities towards sustainable development emphasising on the consumption of local ethnic food and food localism.Originality/valueThe contributions of agritourism for local farms has not been extensively discussed especially in Brunei’s local agriculture industry. This study will provide evidence that FTT activities contribute towards a moderate form of food activism; one that re-forges the disrupted linkages between people, nature and cultural heritage.