bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tomato leaves under stress: A comparison of stress response to mild abiotic stress between a cultivated and a wild tomato species
Authors: Reimer Julia J. , Thiele Björn , Biermann Robin T. , Junker-Frohn Laura V. , Wiese-Klinkenberg Anika , Usadel Björn , Wormit Alexandra 
Published: September 2021

AbstractTomato is one of the most produced crop plants on earth and growing in the fields and greenhouses all over the world. Breeding with known traits of wild species can enhance stress tolerance of cultivated crops. In this study, we investigated responses of the transcriptome as well as primary and secondary metabolites in leaves of a cultivated and a wild tomato to several abiotic stresses such as nitrogen deficiency, chilling or warmer temperatures, elevated light intensities and combinations thereof.The wild species responded different to varied temperature conditions compared to the cultivated tomato. Nitrogen deficiency caused the strongest responses and induced in particular the secondary metabolism in both species but to much higher extent in the cultivated tomato. Our study supports the potential of a targeted induction of valuable secondary metabolites in green residues of horticultural production, that will otherwise only be composted after fruit harvest. In particular, the cultivated tomato showed a strong induction in the group of mono caffeoylquinic acids in response to nitrogen deficiency. In addition, the observed differences in stress responses between cultivated and wild tomato can lead to new breeding targets for better stress tolerance.
Free energy and stacking of eumelanin nanoaggregates
Authors: Soltani Sepideh , Sowlati-Hashjin Shahin , Tetsassi Feugmo Conrard Giresse , Karttunen Mikko 
Published: September 2021

AbstractEumelanin, a member of the melanin family, is a black-brown insoluble pigment. It possesses a broad range of properties such as antioxidation, free radical scavenging, photo-protection, and charge carrier transportation. Surprisingly, the exact molecular structure of eumelanin remains undefined. It is, however, generally considered to consist of two main building blocks, 5,6-dihydroxyindole (DHI) and 5,6-dihydroxyindole carboxylic acid (DHICA). We focus on DHI and report, for the first time, a computational investigation of structural properties of DHI eumelanin aggregates in aqueous solutions. First, multi-microsecond molecular dynamics (MD) simulations at different concentrations were performed to investigate aggregation and ordering of tetrameric DHI-eumelanin protomolecules. This was followed by umbrella sampling (US) and density functional theory (DFT) calculations to study the physical mechanisms of stacking. Aggregation occurs through formation of nanoscale stacks and was observed in all systems. Further analyses showed that aggregation and coarsening of the domains is due to decrease in hydrogen bonds between the eumelanins and water; while domains exist, there is no long-range order. The results show non-covalent stacks with and interlayer distance between eumelanin protomolecules being less than 3.5 Å. This is in good agreement with transmission electron microscopy data. Both free energy calculations and DFT revealed strong stacking interactions. The electrostatic potential map provides an explanation and a rationale for the slightly sheared relative orientations and, consequently, for the curved shapes of the nanoscale domains.
DeepConsensus: Gap-Aware Sequence Transformers for Sequence Correction
Authors: Baid Gunjan , Cook Daniel E. , Shafin Kishwar , Yun Taedong , Llinares-López Felipe , Berthet Quentin , Wenger Aaron M. , Rowell William J. , Nattestad Maria , Yang Howard , Kolesnikov Alexey , Töpfer Armin , Ammar Waleed , Vert Jean-Philippe , Vaswani Ashish , McLean Cory Y. , Chang Pi-Chuan , Carroll Andrew 
Published: September 2021

AbstractPacific BioScience (PacBio) circular consensus sequencing (CCS) generates long (10-25 kb), accurate “HiFi” reads by combining serial observations of a DNA molecule into a consensus sequence. The standard approach to consensus generation uses a hidden Markov model (pbccs). Here, we introduce DeepConsensus, which uses a unique alignment-based loss to train a gap-aware transformer-encoder (GATE) for sequence correction. Compared to pbccs, DeepConsensus reduces read errors in the same dataset by 42%. This increases the yield of PacBio HiFi reads at Q20 by 9%, at Q30 by 27%, and at Q40 by 90%. With two SMRT Cells of HG003, reads from DeepConsensus improve hifiasm assembly contiguity (NG50 4.9Mb to 17.2Mb), increase gene completeness (94% to 97%), reduce false gene duplication rate (1.1% to 0.5%), improve assembly base accuracy (Q43 to Q45), and also reduce variant calling errors by 24%.
Colloidal aggregators in biochemical SARS-CoV-2 repurposing screens
Authors: O’Donnell Henry R. , Tummino Tia A. , Bardine Conner , Craik Charles S. , Shoichet Brian K. 
Published: September 2021

AbstractTo fight the SARS-CoV-2 pandemic, much effort has been directed toward drug repurposing, testing investigational and approved drugs against several viral or human proteins in vitro. Here we investigate the impact of colloidal aggregation, a common artifact in early drug discovery, in these repurposing screens. We selected 56 drugs reported to be active in biochemical assays and tested them for aggregation by both dynamic light scattering and by enzyme counter screening with and without detergent; seventeen of these drugs formed colloids at concentrations similar to their literature reported IC50s. To investigate the occurrence of colloidal aggregators more generally in repurposing libraries, we further selected 15 drugs that had physical properties resembling known aggregators from a common repurposing library, and found that 6 of these aggregated at micromolar concentrations. An attraction of repurposing is that drugs active on one target are considered de-risked on another. This study suggests not only that many of the drugs repurposed for SARS-CoV-2 in biochemical assays are artifacts, but that, more generally, when screened at relevant concentrations, drugs can act artifactually via colloidal aggregation. Understanding the role of aggregation, and detecting its effects rapidly, will allow the community to focus on those drugs and leads that genuinely have potential for treating COVID-19.Abstract FigureTable of Contents Graphic
Robust designation of meiotic crossover sites by CDK-2 through phosphorylation of the MutSγ complex
Authors: Haversat Jocelyn , Woglar Alexander , Klatt Kayla , Akerib Chantal C. , Roberts Victoria , Salazar Catcher C. , Chen Shin-Yu , Arur Swathi , Villeneuve Anne M. , Kim Yumi 
Published: September 2021

SUMMARYCrossover formation is essential for proper segregation of homologous chromosomes during meiosis. Here we show thatC. elegansCyclin-dependent kinase 2 (CDK-2) forms a complex with cyclin-like protein COSA-1 and supports crossover formation by promoting conversion of meiotic double-strand breaks (DSBs) into crossover-specific recombination intermediates. Further, we identify MutSγ component MSH-5 as a CDK-2 phosphorylation target. MSH-5 has a disordered C-terminal tail that contains 13 potential CDK phosphosites and is required to concentrate crossover-promoting proteins at recombination sites. Phosphorylation of the MSH-5 tail appears dispensable in a wild- type background, but when MutSγ activity is partially compromised, crossover formation and retention of CDK-2/COSA-1 at recombination sites are exquisitely sensitive to phosphosite loss. Our data support a model in which robustness of crossover designation reflects a positive feedback mechanism involving CDK-2-mediated phosphorylation and scaffold-like properties of the MSH-5 C-terminal tail, features that combine to promote full recruitment and activity of crossover-promoting complexes.
HIV-1 Induction of Tolerogenic DCs is Mediated by Cellular Interaction with Suppressive T Cells
Authors: Svanberg Cecilia , Nyström Sofia , Govender Melissa , Bhattacharya Pradyot , Che Karlhans F , Ellegård Rada , Shankar Esaki M , Larsson Marie 
Published: September 2021

AbstractHIV-1 infection gives rise to a multilayered immune impairment in most infected individuals. The crosstalk between Dendritic cells and T cells plays an important part in the induction of immune responses. The chronic presence of human immunodeficiency virus (HIV)-1 during the dendritic cells (DCs) priming and activation of T cells promotes the expansion of suppressor cells in a contact dependent manner. The mechanism behind the T cell side of this HIV induced impairment is well studied, whereas little is known about the reverse effects exerted on the DCs in this setting.Here we assessed the phenotype and transcriptome profile of mature DCs that have been in contact with suppressive T cells. The DCs in the HIV exposed DC-T cell coculture obtained a more tolerogenic/suppressive phenotype with increased expression of e.g., PDL1, Gal-9, HVEM, and B7H3, mediated by their cellular interaction with T cells. The transcriptomic analysis showed a clear type I IFN response profile as well as an activation of pathways involved in T cell exhaustion.Taken together, our data indicate that the prolonged and strong IFN type I signaling induced by the presence of HIV during DC-T cell cross talk could play an important role in the induction of the tolerogenic DCs and suppressed immune response.
Illusion of control in farmers’ investment and financing decisions
Authors: Labajova Katarina , Höhler Julia , Lagerkvist Carl-Johan , Müller Jörg , Rommel Jens 
Published: September 2021

PurposePeople’s tendency to overestimate their ability to control random events, known as illusion of control, can affect financial decisions under uncertainty. This study developed an artifactual field experiment on illusion of control for a farm machinery investment.Design/methodology/approachIn an experiment with two treatments, the individual farmer was either given or not given a sense of control over a random outcome. After each decision, the authors elicited perceived control, and a questionnaire collected additional indirect measures of illusion of control from 78 German farmers and 10 farm advisors.FindingsThe results did not support preregistered hypotheses of the presence of illusion of control. This null result was robust over multiple outcomes and model specifications. The findings demonstrate that cognitive biases may be small and difficult to replicate.Research limitations/implicationsThe sample is not representative for the German farming population. The authors discuss why the estimated treatment effect may represent a lower bound of the true effect.Originality/valueIllusion of control is well-studied in laboratory settings, but little is known about the extent to which farmers’ behavior is influenced by illusion of control.
Does firm's philanthropy lead to more missions: theory and evidence
Authors: He Ling-Yun , Zhang Hongzhen 
Published: September 2021

PurposeInspired by the comparison of charity donations among candidates in rural elections, the authors linked the non-profit motives of charity to corporate pollution emissions. And on this basis, the authors aim to provide theoretical and empirical explanations for the relationship between corporate philanthropy and pollution. The authors find that the desire to pursue more pollution emissions stimulates the firm's philanthropy, which is similar to the public welfare donations in rural elections.Design/methodology/approachFirstly, the authors construct a game-theoretical framework consisting of an entrepreneur and a bureaucrat to study the environmental cost of corporate philanthropy through the impact on pollution emission by the firm. Secondly, the authors used various empirical methods, including hybrid OLS, IV-2SLS, PSM, etc., to empirically test the impact of a firm's philanthropy on corporate pollution emissions. Finally, the authors use the output and abatement input as intermediary variables and apply the intermediary effect model to test the impact mechanism between corporate philanthropy and corporate pollution emissions.FindingsTheoretical model finds that the firm invests more in philanthropy discharges more emissions when the theoretical model is in political equilibrium. Besides, empirical results show that corporate philanthropy will lead to more pollution emissions by reducing abatement input and increasing production. Finally, the heterogeneity test finds that compared with state-owned enterprises, the intention of non-state-owned enterprises' philanthropy for more pollution emission is more obvious. Moreover, the improvement of regional environmental regulation can significantly inhibit the realization of corporate philanthropy's poor motive.Practical implicationsThe results have obvious policy implications for China's future policy-making. Firstly, regulatory agencies should pay close attention to the charitable behaviors of firms with serious negative environmental externalities, and prevent them from replacing more pollution emissions with philanthropy. Besides, due to weak environmental supervision in rural areas, rural polluting enterprises will be more inclined to make charitable donations to the village collective to obtain more emission rights. Therefore, the government should strengthen environmental supervision in rural areas to prevent enterprises from wanton pollution.Originality/valueBy constructing a game-theoretical framework consisting of an entrepreneur and a bureaucrat, the authors expound on corporate philanthropy's pollution motivation and decision-making mechanism for the first time in theory. Besides, this paper finds that the desire to pursue more pollution emissions also stimulates the firm's philanthropy. This paper expands the literature on corporate charitable donation motivations.
Enhanced model of the innovation-decision process, for modular-technological-process innovations in construction
Authors: Gledson Barry 
Published: September 2021

Purpose
The purpose of this study is to establish an enhanced model of the innovation-decision process (IDP), specifically for construction. As context, innovation diffusion theory (IDT) is concerned with explaining how some innovations successfully stick whilst others fail to propagate. Because theoretical models provide abstracted representations of systems/phenomena, established IDT models can help decision-making units with innovation-related sense-marking and problem-solving. However, these occasionally fail or require enhancement to represent phenomena more successfully. This is apparent whenever middle-range theory seems ill-fitted to the complexity of construction.

Design/methodology/approach
Qualitative research via 13 semi-structured interviews occurred, with participants recruited via convenience and purposive sampling strategies. The study forms part of a broader mixed-method study (n = 246) informed by a research philosophy of pragmatism, investigating the applicability of classic IDT to the adoption of four-dimensional (4D) building information modelling (4D BIM) by the UK construction sector.

Findings
This diffusion study resulted in the adaptation of an existing IDP model, ensuring a better contextual fit. Classified more specifically as a modular-technological-process innovation, 4D BIM with its potential to provide construction planning improvements is used as a vehicle to show why, for construction, an existing model required theoretical extensions involving additional stages, decision-action points and outcomes.

Research limitations/implications
This model can assist construction industry actors with future adoption/rejection decisions around modular-technological-process innovations. It also aids the understanding of scholars and researchers, through its various enhancements and by reinforcing the importance of existing diffusion concepts of compatibility and trialability, for these innovation types.

Originality/value
An enhanced model of the IDP, specifically for construction, is established. This construction-centric contribution to IDT will be of interest to construction scholars and to practitioners.
Media multiplicity and collaborative innovation with suppliers: evidence from China
Authors: Liu Ruihong , He Yuanqiong , Ding Xiu-Hao , Li Jianhong 
Published: September 2021

PurposeBased on media choice theories and real option theory, this study aims to explore the role of communication media portfolio in achieving collaborative innovation with suppliers.Design/methodology/approachUsing data of the Study of Competitiveness, Technology and Firm Linkages 2002 collected by the World Bank and the Enterprise Survey Organization of the Chinese National Bureau of Statistics, this study employed logit model to test the hypotheses. Moreover, some robustness analyses were conducted.FindingsThis study suggests that media multiplicity increases the probability for a firm to achieve collaborative innovation with suppliers on the basis of real option theory. Furthermore, distance from the suppliers and relationship formality make media multiplicity further important in collaborative innovation with suppliers.Originality/valueThrough investing how communication media portfolio affecting collaborative innovation with suppliers and the contingency factors, this study complements existing studies just concentrating on supplier capabilities, relationships with suppliers and characteristics of supplier network. Moreover, this study contributes in the information system field by exploring the role of media portfolio rather than individual media.
Queering critical literacies: disidentifications and queer futurity in an afterschool storytelling and roleplaying game
Authors: Storm Scott , Jones Karis 
Published: September 2021

PurposeThis paper aims to describe the critical literacies of high school students engaged in a youth participatory action research (YPAR) project focused on a roleplaying game,Dungeons and Dragons, in a queer-led afterschool space. The paper illustrates how youth critique and resist unjust societal norms while simultaneously envisioning queer utopian futures. Using a queer theory framework, the authors consider how youth performed disidentifications and queer futurity.Design/methodology/approachThis study is a discourse analysis of approximately 85 hours of audio collected over one year.FindingsYouth engaged in deconstructive critique, disidentifications and queer futurity in powerful enactments of critical literacies that involved simultaneous resistance, subversion, imagination and hope as youth envisioned queer utopian world-building through their fantasy storytelling. Youth acknowledged the injustice of the present while radically envisioning a utopian future.Originality/valueThis study offers an empirical grounding for critical literacies centered in queer theory and explores how youth engage with critical literacies in collaboratively co-authored texts. The authors argue that queering critical literacies potentially moves beyond deconstructive critique while simultaneously opening spaces for resistance, imagination and utopian world-making through linguistic and narrative-based tools.
Project managing in post-conflict environments: an exploration of the resource profiles of Sri Lankan non-governmental organizations involved in development projects
Authors: Nanthagopan Yogarajah , Williams Nigel L. 
Published: September 2021

PurposeThe aim of this study is to examine the configuration of project resources in organizations operating in a post-conflict country environment using a Resource-Based View (RBV) perspective.Design/methodology/approachData collection was undertaken using a quantitative survey study of Non-Governmental Organizations (NGOs) involved in development projects in Sri Lanka, which obtained 445 responses. An Exploratory Factor Analysis and subsequent Confirmatory Factor Analysis were performed to identify and confirm the Project Management (PM) resource profile composition of these organizations.FindingsThe study identified resource profiles incorporated items at the team, organizational and collaborative social resource levels and did not differ significantly by organization type. This suggests that the current focus of PM RBV research that implicitly uses a competitive advantage derived framework may need to be adapted for contexts such as post-conflict environments.Research limitations/implicationsFor organizations seeking to deliver projects in developing countries, the findings indicate that relational capacity in the form of a collaborative social resource may be required to adapt team and organizational resources to post-conflict environments.Practical implicationsThe lessons learnt from NGOs can be of value to other organisations seeking to operate in post-conflict environments. The findings from this research reveal that organizations in Sri Lanka establish resource profiles that meet domestic and external requirements. For the management of these organizations, recognition of the inherent contradictions of this strategy can enable the optimization of resource profiles, improving organizational efficiencies.Originality/valueThe study has used insights from NGOs involved in international and local development projects to extend current knowledge of PM resources. While NGOs are distinctive, the critical PM resources identified here may be of value to private and public organizations seeking to develop project resource profiles adapted to emerging markets.
Environmental performance, environmental management and company valuation
Authors: Abrams Roy , Han Seungmin , Hossain Mehdi Tanzeeb 
Published: September 2021

PurposeThis paper aims to investigate the relationship between environmental performance and management and company valuation. With a specific focus on company valuation, this study shows how a firm’s environmental activities, including its environmental management practices, are perceived and valued by its stockholders.Design/methodology/approachNewsweek’s green ranking data between 2014 and 2016 were used to support this analysis. Environmental performances and environmental management practices of 345 Fortune 500 companies from various industries were included in the data set.FindingsThe analysis finds higher valuations for US companies that are more efficient in managing greenhouse gas emissions. In addition, it empirically shows that investors place a higher value on companies with the following environment-related management policies: initiatives that reward top management for achieving environmental goals and third-party auditing of environmental performance.Originality/valueBy incorporating corporate environmental management practices as an additional environmental performance criterion, this research fills a gap in the literature on the potential relationship between corporate environmental performance and company valuation.