bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inactivation of the entire Arabidopsis group II GH3s confers tolerance to salinity and drought
Authors: Casanova-Sáez Rubén , Mateo-Bonmatí Eduardo , Šimura Jan , Pěnčík Aleš , Novák Ondřej , Staswick Paul , Ljung Karin 
Published: September 2021

ABSTRACTIndole-3-acetic acid (IAA) controls a plethora of developmental processes. Thus, regulation of their levels is of great relevance for plant performance. Cellular IAA concentration depends on the combined result of its transport, biosynthesis and various redundant pathways to inactivate IAA, including oxidation and conjugation. Group II members of the GRETCHEN HAGEN 3 (GH3) gene family code for acyl acid amido synthetases catalysing the conjugation of IAA to amino acids. However, the high level of functional redundancy among them has hampered thorough analysis of their roles in plant development. In this work, we generated an Arabidopsis gh3.1,2,3,4,5,6,9,17 (gh3oct) mutant to knock-out the group II GH3 pathway. The gh3oct plants had an improved root architecture, were more tolerant to osmotic stresses due to locally increased IAA levels and were more drought tolerant. IAA metabolite quantification in gh3oct plants suggested the existence of additional GH3-like enzymes in IAA metabolism. Moreover, our data suggested that oxIAA production depends, at least partly, on the GH3 pathway. Targeted stress-hormone analysis further suggested an involvement of ABA in the differential response to salinity of gh3oct plants. Taken together, our data provide new insights into the roles of group II GH3s in IAA metabolism and hormone-regulated plant development.
Gene structure-based homology search identifies highly divergent putative effector gene family
Authors: Stern David L. , Han Clair 
Published: September 2021

AbstractHomology of highly divergent genes often cannot be determined from sequence similarity alone. For example, we recently identified in Hormaphis cornu a family of rapidly evolving bicycle genes, which encode novel proteins implicated as plant gall effectors. Sequence similarity search methods yielded few putative bicycle homologs in other species. Coding sequence-independent features of genes, such as intron-exon boundaries, often evolve more slowly than coding sequences, however, and can provide complementary evidence for homology. We found that a linear logistic regression classifier using only structural features of bicycle genes identified many putative bicycle homologs in other species. Independent evidence from sequence features and intron locations supported homology assignments. To test the potential roles of bicycle genes in other aphids, we sequenced the genome of a second gall- forming aphid, Tetraneura ulmi, and found that many bicycle genes are strongly expressed in the salivary glands of the gall forming foundress. In addition, bicycle genes are strongly overexpressed in the salivary glands of a non-gall forming aphid, Acyrthosiphon pisum, and in the non-gall forming generations of Hormaphis cornu. These observations suggest that Bicycle proteins may be used by multiple aphid species to manipulate plants in diverse ways. Incorporation of gene structural features into sequence search algorithms may aid identification of deeply divergent homologs, especially of rapidly evolving genes involved in host-parasite interactions.
Eco1-dependent cohesin acetylation anchors chromatin loops and cohesion to define functional meiotic chromosome domains
Authors: Barton Rachael E. , Massari Lucia F. , Robertson Daniel , Marston Adele L. 
Published: September 2021

AbstractCohesin organizes the genome by forming intra-chromosomal loops and inter-sister chromatid linkages. During gamete formation by meiosis, chromosomes are reshaped to support crossover recombination and two consecutive rounds of chromosome segregation. Here we show that Eco1 acetyltransferase positions both chromatin loops and sister chromatid cohesion to organize meiotic chromosomes into functional domains in budding yeast. Eco1 acetylates the Smc3 cohesin subunit in meiotic S phase to establish chromatin boundaries, independently of DNA replication. Boundary formation by Eco1 is critical for prophase exit and for the maintenance of cohesion until meiosis II, but is independent of the ability of Eco1 to antagonize the cohesin-release factor, Wpl1. Conversely, prevention of cohesin release by Wpl1 is essential for centromeric cohesion, kinetochore monoorientation and co-segregation of sister chromatids in meiosis I. Our findings establish Eco1 as a key determinant of chromatin boundaries and cohesion positioning, revealing how local chromosome structuring directs genome transmission into gametes.
Insight into mammary gland development and tumor prevention in a newly developed metastatic mouse model of breast cancer
Authors: To Briana , Broeker Carson , Jhan Jing-Ru , Rempel Rachel , Rennhack Jonathan P. , Hollern Daniel , Jackson Lauren , Judah David , Swiatnicki Matt , Bylett Evan , Kubiak Rachel , Honeysett Jordan , Reaz Shams , Nevins Joseph , Andrechek Eran 
Published: September 2021

AbstractThe development of breast cancer has been observed due to altered regulation of mammary gland developmental processes. Thus, a better understand of the normal mammary gland development can reveal possible mechanism in how normal cells are re-programmed to become malignant cells. E2F1-4 are part of the E2F transcription factor family with varied roles in mammary development. However, little is known about the role of E2F5 in mammary gland development. A combination of scRNAseq and predictive signature tools demonstrate the presence of E2F5 in the mammary gland and showed altered activity during the various phases of mammary gland development and function. Testing the hypothesis that E2F5 regulates mammary function, we generated a mammary-specific E2F5 knockout mouse model, resulting in modest mammary gland development changes. However, after a prolonged latency the E2F5 conditional knockout mice developed highly metastatic mammary tumors with metastases in both the lung and liver. Transplantation of the tumors revealed metastases to lymph nodes that was enriched through serial transplantation. Through whole genome sequencing and RNAseq analysis we identified, and then confirmedin vivo, that Cyclin D1 was dysregulated in E2F5 conditional knockout mammary glands and tumors. Based on these findings, we propose that loss of E2F5 leads altered regulation of Cyclin D1, which facilitates the development of mammary tumors.
Endotaxis: A neuromorphic algorithm for mapping, goal-learning, navigation, and patrolling
Authors: Zhang Tony , Rosenberg Matthew , Jing Zeyu , Perona Pietro , Meister Markus 
Published: September 2021

AbstractAn animal entering a new environment typically faces three challenges: explore the space for resources, memorize their locations, and navigate towards those targets as needed. Experimental work on exploration, mapping, and navigation has mostly focused on simple environments – such as an open arena [68], a pond [42], or a desert [44] – and much has been learned about neural signals in diverse brain areas under these conditions [12, 54]. However, many natural environments are highly structured, such as a system of burrows, or of intersecting paths through the underbrush. Similarly, for many cognitive tasks, a sequence of simple actions can give rise to complex solutions. Here we propose an algorithm that learns the structure of a complex environment, discovers useful targets during exploration, and navigates back to those targets by the shortest path. It makes use of a behavioral module common to all motile animals, namely the ability to follow an odor to its source [4]. We show how the brain can learn to generate internal “virtual odors” that guide the animal to any location of interest. Thisendotaxisalgorithm can be implemented with a simple 3-layer neural circuit using only biologically realistic structures and learning rules. Several neural components of this scheme are found in brains from insects to humans. Nature may have evolved a general mechanism for search and navigation on the ancient backbone of chemotaxis.
LRRC15 mediates an accessory interaction with the SARS-CoV-2 spike protein
Authors: Shilts Jarrod , Crozier Thomas W. M. , Teixeira-Silva Ana , Gabaev Ildar , Greenwood Edward J. D. , Watson Samuel James , Ortmann Brian M. , Gawden-Bone Christian M. , Pauzaite Tekle , Hoffmann Markus , Nathan James A. , Pöhlmann Stefan , Lehner Paul J. , Wright Gavin J. 
Published: September 2021

SummaryThe interactions between severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) and human host factors enable the virus to propagate infections that lead to COVID-19. The spike protein is the largest structural component of the virus and mediates interactions essential for infection, including with the primary ACE2 receptor. We performed two independent cell-based systematic screens to determine whether there are additional proteins by which the spike protein of SARS-CoV-2 can interact with human cells. We discovered that in addition to ACE2, expression of LRRC15 also causes spike protein binding. This interaction is distinct from other known spike attachment mechanisms such as heparan sulfates or lectin receptors. Measurements of orthologous coronavirus spike proteins implied the interaction was restricted to SARS-CoV-2, suggesting LRRC15 represents a novel class of spike binding interaction. We localized the interaction to the C-terminus of the S1 domain, and showed that LRRC15 shares recognition of the ACE2 receptor binding domain. From analyzing proteomics and single-cell transcriptomics, we identify LRRC15 expression as being common in human lung vasculature cells and fibroblasts. Although infection assays demonstrated that LRRC15 alone is not sufficient to permit viral entry, we present evidence it can modulate infection of human cells. This unexpected interaction merits further investigation to determine how SARS-CoV-2 exploits host LRRC15 and whether it could account for any of the distinctive features of COVID-19.In briefWe present evidence from genome-wide screening that the spike protein of SARS-CoV-2 interacts with human cells expressing LRRC15. The interaction is distinct from previously known classes of spike attachment factors, and appears to have emerged recently within the coronavirus family. Although not sufficient for cell invasion, this interaction can modulate viral infection. Our data point to an unappreciated host factor for SARS-CoV-2, with potential relevance to COVID-19.Highlights- Two systematic cell-based screens for SARS-CoV-2 spike protein binding identify LRRC15 as a human host factor- Interaction with LRRC15 is reproducible in different human cell lines and independent of known glycan or ACE2 binding pathways- The C-terminal S1 domain of SARS-CoV-2 spike binds LRRC15 with sub-micromolar affinity, while related coronavirus spikes do not- LRRC15 is expressed in tissues with high ACE2 levels and may modulate infection
The role of information systems for digital transformation in the private sector: a review of Egyptian SMEs
Authors: Metawa Noura , Elhoseny Mohamed , Mutawea Maha 
Published: September 2021

PurposeThis paper aims to provide insights regarding the state of the art of digital transformation for small- and medium-sized enterprises (SMEs) in Egypt and propose avenues for future research.Design/methodology/approachA proposed framework for the digitization process in SMEs is developed by providing three layers of working steps toward full automation. The paper also provides an extensive analysis of the main requirements for improving the existing traditional information systems' performance in these enterprises. The challenges of digital transformation and the future research direction are discussed as well.FindingsThis paper provided an overview of the importance of digital transformation in real-life applications. The role of the information systems in building a digitalized information processing environment is covered as well. Also, a framework for the shifting process from the traditional approaches to the digitalized systems is proposed. Besides, the paper overviewed the future research directions related to digital transformation in SMEs, especially in Egypt. These research directions are related to technical challenges during the digital transformation process, such as cybersecurity, big data analytics and multimodality data.Originality/valueDespite the significant governmental and institutions' steps toward full automation and digital transformation, the traditional information systems, infrastructures, and unequipped employees make the digitizing process on-the-fly an open challenge. A technology shift that is not supported by a similar cultural change threatens digital business initiatives and increases the risk of their failure. This paper aims to provide insights regarding the state of the art of digital transformation for SMEs in Egypt and propose avenues for future research.
Has the low level of economic growth spurred informal sector activities in Uganda? An empirical analysis
Authors: Esaku Stephen 
Published: September 2021

PurposeIn this paper, the authors examine how economic growth shapes the shadow economy in the long and short run.Design/methodology/approachUsing annual time series data from Uganda, drawn from various data sources, covering the period from 1991 to 2017, the authors apply the ARDL modeling approach to cointegration.FindingsThis paper finds that an increase in economic growth significantly reduces the size of the shadow economy, in both the long and short run, all else equal. However, the long-run relationship between the shadow economy and growth is non-linear. The results suggest that the rise of the shadow economy could partially be attributed to the slow and sluggish rate of economic growth.Practical implicationsThese findings imply that addressing informality requires addressing underlying factors of underdevelopment since improvements in economic growth also translate into a reduction in the size of the shadow economy in the short and long run.Originality/valueThese findings reveal that the low level of economic growth is an issue because it spurs informal sector activities in the short run. However, as the economy improves, it becomes an incentive for individuals to operate in the informal sector. Additionally, tackling shadow activities in the short run could help improve tax revenue collection.
Food education in Finnish primary education – defining themes and learning objectives using the Delphi technique
Authors: Laitinen Aija Liisa , Tilles-Tirkkonen Tanja , Karhunen Leila , Talvia Sanna 
Published: September 2021

PurposeThe importance of food education in primary schools has been globally recognised. However, more detailed definitions of its learning objectives are rarely found. The study aimed to define multisectoral themes and learning objectives for food education in primary education in Finland.Design/methodology/approachA descriptive three-round Delphi study was conducted with experts in food education in various organisations. In the first questionnaire, the participants were asked to define possible objectives for food education related to general objectives for basic education. Respondents of the first questionnaire formed a research panel (n = 22). These panellists were then invited to complete the second (n = 16) and third questionnaires (n = 12), where the objectives were further modified. Qualitative content analysis and Bloom's taxonomy were applied in the process of creating the learning objectives.FindingsIn the iterative process, 42 learning objectives for food education in primary schools were defined. Further, “Sustainability and ethics of food systems” was defined as the cross-cutting theme of food education. In addition, 13 subthemes were defined, which fell into three thematic categories: personal (e.g. feelings), practical (e.g. eating) and intangible (e.g. culture) issues.Originality/valueThe defined learning objectives for a holistic food education may be used in advancing primary school curriculum in Finland and perhaps other countries.
Hidden flows assessment in the agri-food sector: evidence from the Italian beef system
Authors: Amicarelli Vera , Fiore Mariantonietta , Bux Christian 
Published: September 2021

PurposeThe study proposes Material Flow Analysis (MFA) methodology as a tool to measure and qualify food waste in the Italian beef supply chain in each stage of the food supply chain, from farm to fork. In particular, the authors attempt to: (1) measure resources consumption and waste generation toward companies' and policymakers' sustainable evaluations; (2) enhance consumers' education in the field of agri-food resilience and sustainability.Design/methodology/approachMFA is applied to the entire Italian sector of beef consumed as packaged fresh product in 2020, during the Covid-19 pandemic. The analysis regards bovine, which represent roughly one-third of the national meat flow. To collect data, bottom-up and top-down mixed approach is applied. Subsequently, MFA results are used to calculate the wastage-related losses in terms of embedded natural resources (e.g. water, energy).FindingsIn 2020, it results that the Italian meat industry slaughtered more than 1.15 Mt of bovine to produce approximately 0.29 Mt of fresh meat, 0.69 Mt of by-products and over 0.015 Mt of food waste at households, while 0.15 Mt of beef meat is destined to catering services and food industry (out-of-boundaries). In terms of hidden natural resources, it emerged that, on average, more than 94bn m3 of water, approximately 101,000 TJ of energy and over 11,500 t of PET and PE trays are required to sustain the entire beef system.Originality/valueThis research is one of the few studies proposing MFA methodology as a tool to measure food waste and hidden associated flows in the agri-food sector. This analysis shows its utility in terms of natural resources (water, energy, materials) and waste quality/quantity evaluation, hidden flows accounting and development of new educational strategies toward food waste minimization and sustainability at household consumption.
Information-centric influence strategies for quality assurance in reverse logistics supply chains: external stakeholders' perspective
Authors: Wijewickrama M.K.C.S. , Chileshe Nicholas , Rameezdeen Raufdeen , Ochoa J. Jorge 
Published: September 2021

PurposeThe purpose of this paper is twofold: firstly, to identify the information-centric strategies of external stakeholders that influence the quality assurance (QA) in the reverse logistics supply chains (RLSC) of demolition waste (DW) and, secondly, to recognize the determinants for using each strategy.Design/methodology/approachSemi-structured interviews were conducted with 21 professionals representing five external stakeholder groups: state and local government agencies, non-government organizations (NGOs), forward supply chain upstream and downstream actors. The data was analyzed based on Creswell's five-step process, and the conventional content analysis was used for coding and generating themes.FindingsThe study found seven information-centric influence strategies: regulating, monitoring, leading, incentivizing, demolition approval, forming contracts and specifications. The state government organizations were the most dominant in influencing the QA in RLSC. All external stakeholders use both aggressive and cooperative strategies. The urgent, legitimate and economic core of the issue decides the type of strategy to exert an information-centric influence over the QA in RLSC of DW.Originality/valueTo the author's best knowledge, this study is one of the first investigations performed based on a theoretical basis within the context of RLSC in the construction industry (CI). This study used empirical data to elaborate the stakeholder theory while providing new knowledge on stakeholder influence, particularly those relevant to information sharing. Thus, this study developed a theoretical base that future researchers in the study domain could use.
Crime rate, real earnings management and managerial ability
Authors: Simamora Alex Johanes 
Published: September 2021

PurposeThis paper aims to examine the effect of managerial ability (MA) on real earnings management and the effect of real earnings management by higher ability managers on future profitability, at a different level of the crime rate.Design/methodology/approachThe research sample includes 864 manufacturing firms-years listed on the Indonesian Stock Exchange. MA uses an efficiency score by data envelopment analysis. Real earnings management is measured by abnormal activities. The crime rate is measured by logarithm natural of the number of crimes per 100.000 citizens in the region where the firm is headquartered. Data analysis uses fixed-effect regression.FindingsMA increases real earnings management in the region where the firm is headquartered with a higher crime rate while MA will reduce real earnings management in the region where the firm is headquartered with a lower crime rate. Also, real earnings management by higher-ability managers gives a signal of better future profitability in the region where the firm is headquartered with a lower crime rate.Originality/valueThis research contributes to filling the previous gap of managerial characteristics ability-related on real earnings management by providing regional crime rate as a determinant factor of managers’ ethical behavior. This research is the first one to considers the regional crime rate treatment to the relationship between MA and real earnings management especially in Indonesia. This research also provides new evidence of efficient real earnings management for a lower crime rate group of samples to give a signal of better future profitability.
An introduction to the topological derivative
Authors: Amstutz Samuel 
Published: September 2021

PurposeThis paper provides a self-contained introduction to the mathematical aspects of the topological derivative.Design/methodology/approachFull justifications are given on simple model problems following a modern approach based on the averaged adjoint state technique. Extensions are discussed in relation with the literature on the field.FindingsClosed expressions of topological derivatives are obtained and commented.Originality/valueSeveral cases are covered in a unified and didactic presentation. Some elements of proof are novel.
Inverse homogenization using the topological derivative
Authors: Ferrer Àlex , Giusti Sebastián Miguel 
Published: September 2021

PurposeThe purpose of this study is to solve the inverse homogenization problem, or so-called material design problem, using the topological derivative concept.Design/methodology/approachThe optimal topology is obtained through a relaxed formulation of the problem by replacing the characteristic function with a continuous design variable, so-called density variable. The constitutive tensor is then parametrized with the density variable through an analytical interpolation scheme that is based on the topological derivative concept. The intermediate values that may appear in the optimal topologies are removed by penalizing the perimeter functional.FindingsThe optimization process benefits from the intermediate values that provide the proposed method reaching to solutions that the topological derivative had not been able to find before. In addition, the presented theory opens the path to propose a new framework of research where the topological derivative uses classical optimization algorithms.Originality/valueThe proposed methodology allows us to use the topological derivative concept for solving the inverse homogenization problem and to fulfil the optimality conditions of the problem with the use of classical optimization algorithms. The authors solved several material design examples through a projected gradient algorithm to show the advantages of the proposed method.