bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptomic profiling and microsatellite identification in cobia (Rachycentron canadum), using high throughput RNA-sequencing
Authors: Barbosa David Aciole , Araújo Bruno C. , Souza Branco Giovana , Simeone Alexandre S. , Hilsdorf Alexandre W. S. , Jabes Daniela L. , Nunes Luiz R. , Moreira Renata G. , Menegidio Fabiano B. 
Published: December 2020

ABSTRACTCobia (Rachycentron canadum) is a marine teleost species with great productive potential worldwide. However, the genomic information currently available for this species in public databases is limited. Such lack of information hinders gene expression assessments that might bring forward novel insights into the physiology, ecology, evolution, and genetics of this potential aquaculture species. In this study, we report the firstde novotranscriptome assembly ofR. canadumliver, improving the availability of novel gene sequences for this species. Illumina sequencing of liver transcripts generated 1,761,965,794 raw reads, which were filtered into 1,652,319,304 high-quality reads.De novoassembly resulted in 101,789 unigenes and 163,096 isoforms, with an average length of 950.61 and 1,617.34 nt, respectively. Moreover, we found that 126,013 of these transcripts bear potentially coding sequences, and 125,993 of these elements (77.3%) correspond to functionally annotated genes found in six different databases. We also identified 701 putative ncRNA and 35,414 putative lncRNA. Interestingly, homologues for 410 of these putative lncRNAs have already been observed in previous analyzes withDanio rerio,Lates calcarifer,Seriola lalandi dorsalis,Seriola dumeriliorEcheneis naucrates. Finally, we identified 7,894 microsatellites related to cobia’s putative lncRNAs. Thus, the information derived from the transcriptome assembly described herein will likely assist future nutrigenomics and breeding programs involving this important fish farming species.
Genomic basis of drought resistance inFagus sylvatica
Authors: Pfenninger Markus , Reuss Friederike , Kiebler Angelika , Schönnenbeck Philipp , Caliendo Cosima , Gerber Susanne , Cocchiararo Berardino , Reuter Sabrina , Blüthgen Nico , Mody Karsten , Mishra Bagdevi , Bálint Miklós , Thines Marco , Feldmeyer Barbara 
Published: December 2020

AbstractIn the course of global climate change, central Europe is experiencing more frequent and prolonged periods of drought. The drought years 2018 and 2019 affected European beeches (Fagus sylvaticaL.) differently: even in the same stand, drought damaged trees neighboured healthy trees, suggesting that the genotype rather than the environment was responsible for this conspicuous pattern. We used this natural experiment to study the genomic basis of drought resistance with Pool-GWAS. Contrasting the extreme phenotypes identified 106 significantly associated SNPs throughout the genome. Most annotated genes with associated SNPs (>70%) were previously implicated in the drought reaction of plants. Non-synonymous substitutions led either to a functional amino acid exchange or premature termination. A SNP-assay with 70 loci allowed predicting drought phenotype in 98.6% of a validation sample of 92 trees. Drought resistance in European beech is a moderately polygenic trait that should respond well to natural selection, selective management, and breeding.Impact StatementEuropean beech harbours substantial genetic variation at genomic loci associated with drought resistance and the loci identified in this study can help to accelerate and monitor adaptation to climate change.
Network reconstruction and modelling made reproducible with moped
Authors: Saadat Nima P , van Aalst Marvin , Ebenhöh Oliver 
Published: December 2020

AbstractMathematical modeling of metabolic networks is a powerful approach to investigate the underlying principles of metabolism and growth. Such approaches include, amongst others, differential equation based modeling of metabolic systems, constraint based modeling and topological analysis of metabolic networks. Most of these methods are well established and are implemented in numerous software packages, but these are scattered between different programming languages, packages and syntaxes. This complicates establishing straight forward pipelines integrating model construction and simulation. We present the Python package moped which serves as an integrative hub for reproducible construction, modification, curation and analysis of metabolic models. moped supports draft reconstruction of models directly from genome/proteome sequences and path-way/genome databases utilizing GPR annotations, providing a completely reproducible model construction and curation process within executable Python scripts. Alternatively, existing models published in SBML format can be easily imported. Models are represented as Python objects, for which a wide spectrum of easy-to-use modification and analysis methods exist. The model structure can be manually altered by adding, removing or modifying reactions, and gap filling reactions can be found and inspected. This greatly supports the development of draft models, as well as the curation and testing of models. Moreover, moped provides several analysis methods, in particular including the calculation of biosynthetic capacities using metabolic network expansion. The integration with other Python based tools is facilitated through various model export options. For example, a model can be directly converted into a CobraPy object for constraint-based analyses. moped is a fully documented and expandable Python package. We demonstrate the capability to serve as a hub for integrating reproducible model construction and curation, database import, topological analysis and export for constraint-based analyses.
Genetic variability in COVID-19-related genes in the Brazilian population
Authors: Secolin Rodrigo , de Araujo Tânia K. , Gonsales Marina C. , Rocha Cristiane S. , Naslavsky Michel , De Marco Luiz , Bicalho Maria A.C. , Vazquez Vinicius L. , Zatz Mayana , Silva Wilson A. , Lopes-Cendes Iscia 
Published: December 2020

ABSTRACTSARS-CoV-2 employs the angiotensin-converting enzyme 2 (ACE2) receptor and the transmembrane serine protease (TMPRSS2) to infect human lung cells. Previous studies have suggested that different host genetic backgrounds inACE2andTMPRSS2could contribute to differences in the rate of infection or severity of COVID-19. Recent studies also showed that variants in 15 genes related to type I interferon immunity to influenza virus could predispose to life-threatening COVID-19 pneumonia. Additional genes (SLC6A20, LZTFL1, CCR9, FYCO1, CXCR6, XCR1, IL6, CTSL, ABO, andFURIN) and HLA alleles have also been implicated in response to infection with SARS-CoV-2. Currently, Brazil has recorded the third-highest number of COVID-19 patients worldwide. We aim to investigate the genetic variation present in COVID-19-related genes in the Brazilian population. We analysed 27 candidate genes and HLA alleles in 954 admixed Brazilian exomes. We used the information available in two public databases (http://www.bipmed.organdhttp://abraom.ib.usp.br/), and additional exomes from individuals born in southeast Brazil, the region with the highest number of COVID-19 patients in the country. Variant allele frequencies were compared with the 1000 Genomes Project phase 3 (1KGP) and the gnomAD databases. We found 395 non-synonymous variants; of these, 325 were also found in the 1000 Genome Project phase 3 (1KGP) and/or gnomAD. Six of these variants were previously reported as putatively influencing the rate of infection or clinical prognosis for COVID-19. The remaining 70 variants were identified exclusively in the Brazilian sample, with a mean allele frequency of 0.0025.In silicoprediction of the impact in protein function revealed that three of these rare variants were pathogenic. Furthermore, we identified HLA alleles that were previously associated with COVID-19 response at loci DQB1 and DRB1. Our results showed genetic variability common to other populations, but also rare and ultra-rare variants exclusively found in the Brazilian population. These findings could potentially lead to differences in the rate of infection or response to infection by SARS-CoV-2 and should be further investigated in patients with the disease.
The impact of 1/factivity and baseline correction on the results and interpretation of time-frequency analyses of EEG/MEG data: A cautionary tale
Authors: Gyurkovics Máté , Clements Grace M. , Low Kathy A. , Fabiani Monica , Gratton Gabriele 
Published: December 2020

AbstractTypically, time-frequency analysis (TFA) of electrophysiological data is aimed at isolating narrowband signals (oscillatory activity) from broadband non-oscillatory (1/f) activity, so that changes in oscillatory activity resulting from experimental manipulations can be assessed. A widely used method to do this is to convert the data to the decibel (dB) scale through baseline division and log transformation. This procedure assumes that, for each frequency, sources of power (i.e., oscillations and 1/factivity) scale by the same factor relative to the baseline (multiplicative model). This assumption may be incorrect when signal and noise are independent contributors to the power spectrum (additive model). Using resting-state EEG data from 80 participants, we found that the level of 1/factivity and alpha power are not positively correlated within participants, in line with the additive but not the multiplicative model. Then, to assess the effects of dB conversion on data that violate the multiplicativity assumption, we simulated a mixed design study with one between-subject (noise level, i.e., level of 1/factivity) and one within-subject (signal amplitude, i.e., amplitude of oscillatory activity added onto the background 1/factivity) factor. The effect size of the noise level × signal amplitude interaction was examined as a function of noise difference between groups, following dB conversion. Findings revealed that dB conversion led to the over- or under-estimation of the true interaction effect when groups differing in 1/flevels were compared, and it also led to the emergence of illusory interactions when none were present. This is because signal amplitude was systematically underestimated in the noisier compared to the less noisy group. Hence, we recommend testing whether the level of 1/factivity differs across groups or conditions and using multiple baseline correction strategies to validate results if it does. Such a situation may be particularly common in aging, developmental, or clinical studies.
Tubular lysosomes harbor active ion gradients and poise macrophages for phagocytosis
Authors: Suresh Bhavyashree , Saminathan Anand , Chakraborty Kasturi , Cui Chang , Becker Lev , Krishnan Yamuna 
Published: December 2020

AbstractLysosomes adopt dynamic, tubular states that regulate antigen presentation, phagosome resolution and autophagy. To date, tubular lysosomes have been studied either by inducing autophagy or by activating immune cells, both of which lead to cell states where lysosomal gene expression differs from the resting state. Therefore, it has been challenging to pinpoint the specific biochemical properties lysosomes acquire upon tubulation that could drive their functionality. We describe a DNA-based assembly that tubulates lysosomes in macrophages without activating them. Lumenal proteolytic activity maps at single lysosome resolution revealed that tubular lysosomes were less degradative. Further, they showed striking proximal to distal lumenal pH and Ca2+gradients. Such gradients had been predicted, but never previously observed. We now identify a role for tubular lysosomes whereby they poise resting macrophages for phagocytosis. The ability to tubulate lysosomes without having to starve or activate immune cells may help reveal new roles for tubular lysosomes.
Aggregation-related quenching of LHCII in liposomes revealed by single-molecule spectroscopy
Authors: Tutkus Marijonas , Chmeliov Jevgenij , Trinkunas Gediminas , Akhtar Parveen , Lambrev Petar H. , Valkunas Leonas 
Published: December 2020

AbstractIncorporation of membrane proteins into reconstituted lipid membranes is a common approach for studying their structure and function relationship in a native-like environment. In this work, we investigated fluorescence properties of liposome-reconstituted LHCII. By utilizing liposome labelling with the fluorescent dye molecules and single-molecule microscopy techniques, we were able to study truly liposome-reconstituted LHCII and compare them with bulk measurements and liposome-free LHCII aggregates on bound surface. Our results showed that fluorescence lifetime in bulk and of that for single liposome measurements were correlated. The fluorescence lifetimes of LHCII were shorter for liposome-free LHCII than for reconstituted LHCII. In the case of liposome-reconstituted LHCII, fluorescence lifetime showed dependence on the protein density reminiscent to concentration quenching. The dependence of fluorescence lifetime of LHCII on the liposome size was not significant. Our results demonstrated that fluorescence quenching can be induced by LHCII-LHCII interactions in reconstituted membranes, most likely occurring via the same mechanism as photoprotective non-photochemical quenching in vivo.
Inverse regulation of Vibrio cholerae biofilm dispersal by polyamine signals
Authors: Bridges Andrew A. , Bassler Bonnie L. 
Published: December 2020

AbstractThe global pathogen Vibrio cholerae undergoes cycles of biofilm formation and dispersal in the environment and the human host. Little is understood about biofilm dispersal. Here, we show that MbaA, a periplasmic polyamine sensor, and PotD1, a polyamine importer, regulate V. cholerae biofilm dispersal. Spermidine, a commonly produced polyamine, drives V. cholerae dispersal, whereas norspermidine, an uncommon polyamine produced by vibrios, inhibits dispersal. Spermidine and norspermidine differ by one methylene group. Both polyamines function to control dispersal via periplasmic detection by MbaA and subsequent signal relay. Biofilm dispersal fails in the absence of PotD1 because reuptake of endogenously produced norspermidine does not occur, so it accumulates in the periplasm where it stimulates MbaA. These results suggest that V. cholerae uses MbaA to monitor environmental polyamines, blends of which potentially provide information about numbers of ‘self’ and ‘other’. This information is used to dictate whether or not to disperse from biofilms.
PH domain and leucine rich repeat phosphatase 1 (Phlpp1) suppresses parathyroid hormone receptor 1 (Pth1r) expression and signaling during bone growth
Authors: Weaver Samantha R. , Taylor Earnest L. , Zars Elizabeth L. , Arnold Katherine M. , Bradley Elizabeth W. , Westendorf Jennifer J. 
Published: December 2020

ABSTRACTEndochondral ossification is tightly controlled by a coordinated network of signaling cascades including parathyroid hormone (PTH). PH domain and leucine rich repeat phosphatase (Phlpp1) affects endochondral ossification by suppressing chondrocyte proliferation in the growth plate, longitudinal bone growth, and bone mineralization. As such, Phlpp1−/−mice have shorter long bones, thicker growth plates, and proportionally larger growth plate proliferative zones. The goal of this study was to determine how Phlpp1 deficiency affects PTH signaling during bone growth. Transcriptomic analysis revealed greater Pth1r expression and H3K27ac enrichment at the Pth1r promoter in Phlpp1-deficient chondrocytes. PTH(1-34) enhanced and PTH(7-34) attenuated cell proliferation, cAMP signaling, CREB phosphorylation, and cell metabolic activity in Phlpp1-inhibited chondrocytes. To understand the role of Pth1r action in the endochondral phenotypes of Phlpp1-deficient mice, Phlpp1−/−mice were injected with Pth1r ligand PTH(7-34) daily for the first four weeks of life. PTH(7-34) reversed the abnormal growth plate and long bone growth phenotypes of Phlpp1−/−mice but did not rescue deficits in bone mineral density or trabecular number. These results demonstrate that elevated Pth1r expression and signaling contributes to increased proliferation in Phlpp1−/−chondrocytes and shorter bones in Phlpp1-deficient mice. Our data reveal a novel molecular relationship between Phlpp1 and Pth1r in chondrocytes during growth plate development and longitudinal bone growth.
Englishization and the politics of translation
Authors: Wilmot Natalie Victoria , Tietze Susanne 
Published: December 2020

Purpose
This study aims to investigate the treatment of translation within the international business and management (IBM) literature to highlight colonialist assumptions inscribed in this treatment as a result of the hegemonic status of English.

Design/methodology/approach
This investigation takes the form of a systemic literature review to examine the treatment of translation in the IBM literature through a postcolonial lens.

Findings
The findings demonstrate that despite growing interest in language in international business, matters of translation have received comparatively little attention. However, those articles that do address translation matters tend to do so in five key ways, including epistemological/methodological considerations, exploring translator agency, the investigations of the discursive void/conceptual fuzziness between languages, and approaches that discuss translation as social practice.

Research limitations/implications
Despite the authors’ critique of English-language hegemony, this literature review is restricted to English-language journals, which the authors acknowledge as problematic and discuss within the article.

Practical implications
In exposing the limited treatment of translation within the literature, the authors provide a call to action for IBM scholars to be more explicit in their treatment of translation to ensure representation of cultural and linguistic Others, rather than providing domesticated accounts of multilingual research.

Originality/value
Although there have been other articles that have examined translation in the past, this paper is the first to do so through a postcolonial lens, demonstrating from a linguistic perspective the colonialist assumptions that are still prevalent in IBM knowledge production, as evidenced by the treatment of translation in the field.
Contesting extractivism: international business and people’s struggles against extractive industries
Authors: Flores Rafael Kruter , Bōhm Steffen , Misoczky Maria Ceci 
Published: December 2020

Purpose
This paper aims to introduce the special issue “Extractivism and the Links between International Business and People’s Struggles,” which is part of our joint research efforts oriented to advance critical knowledge on the impacts and strategies of extractive transnational corporations and social struggles against them.

Design/methodology/approach
This paper presents and discusses contemporary aspects of extractivism and their impacts on nature and livelihood. In a second moment, it introduces and reflects on the four articles that compose the special issue “Extractivism and the Links between International Business and People’s Struggles”.

Findings
Extractivism is destructive of nature and livelihoods. As reaction to its destructive logic, millions of people have organized to struggle against extractivist projects around the world. The publication of this special issue is part of authors’ joint research efforts oriented to advance critical knowledge on the impacts and strategies of extractive corporations and social struggles against them. The lessons that the authors learned in their research and their experiences in these struggles were the key motivating factors that led them to organize this special issue, exploring radical alternatives to extractivism, alternatives that have as fundamental criterion the production and reproduction of life.

Originality/value
The value of this introduction is to present and discuss the four articles of the special issue “Extractivism and the Links between International Business and People’s Struggles,” which compose a rich mosaic of themes that emerge in the struggles against extractive projects worldwide, creating a relevant picture of the main defies imposed by extractivism and its negative impacts, from political corporate social responsibility to discourses, from relational ontology to the relations among state, corporations and social movements.
The triple crisis of debt, demand and decarbonisation: a preliminary analysis of the impact of COVID-19 on commodity-dependent developing economies
Authors: Perry Keston K. 
Published: December 2020

Purpose
This paper aims to offer a preliminary overview and analysis of the impact of the COVID-19 crisis on commodity-dependent developing economies (CDDEs). Using debt, decarbonisation and demand as empirical and analytical prisms to understand impacts and dynamics, the paper offers “rent space” as a theoretical tool to appreciate the changing possibilities for using resource rents for capital accumulation and expand development frontiers. It maps out the certain common features among this group of developing countries facing an increasingly adverse and uncertain situation. It offers a political economic perspective on the global dynamics and internal political situation that constrain these countries’ ability to manage the effects of this external shock that date to the 2008 crisis, and to therefore shore up an effective recovery in the coming years.

Design/methodology/approach
The paper draws together secondary literature and evidence from a number of sources including the World Bank, United Nations and International Monetary Fund on the empirical situation in these countries in view of COVID-19. The paper uses a thematic approach to understand how the current crisis has exposed these embedded and worsening vulnerabilities in this group of countries.

Findings
Results demonstrate the wide-ranging effects of COVID-19 as an existential crisis of demand in short and medium term, the explosion of debt due to actually occurring financialisation and the looming medium and long-term consequences of decarbonisation that may oblige countries to abandon exploitation of fossil fuel resources.

Originality/value
In the final analysis, COVID-19 has revealed a number of lingering effects of the commodity boom and global financial crisis. The increased indebtedness that resulted not only underscores the long-term unviability of commodity-based development as a strategy but also reveals new unprecedented weaknesses and challenges. Given the current configuration of global and domestic political economy dynamics, the paper shows that the “rent space” in fossil fuel exporters is particularly constrained and shrinking, compared to mineral exporters, but all showing a trend towards concentration in commodity production overall and worsening prospects for green recovery or industrial pathway.