bluuebunny/crossref_metadata_2025_split huggingface dataset:
Precise transcriptional control of cellular quiescence by BRAVO/WOX5 complex in Arabidopsis roots
Authors: Betegón-Putze Isabel , Mercadal Josep , Bosch Nadja , Planas-Riverola Ainoa , Marquès-Bueno Mar , Vilarrasa-Blasi Josep , Frigola David , Burkart Rebecca Corinna , Martínez Cristina , Stahl Yvonne , Prat Salomé , Ibañes Marta , Caño-Delgado Ana I. 
Published: July 2020

SUMMARYRoot growth and development are essential features for plant survival and the preservation of terrestrial ecosystems. In the Arabidopsis primary root apex, stem-cell specific transcription factors BRAVO and WOX5 co-localize at the Quiescent Center (QC) cells, where they repress cell division so that these cells can act as a reservoir to replenish surrounding stem cells, yet their molecular connection remains unknown. Here, by using empirical evidence and mathematical modeling, we establish the precise regulatory and molecular interactions between BRAVO and WOX5. We found that BRAVO and WOX5 regulate each other besides forming a transcription factor complex in the QC necessary to preserve overall root growth and architecture. Our results unveil the importance of transcriptional regulatory circuits at the quiescent and stem cells to the control of organ initiation and growth of plant tissues.
Decreased utilization of allocentric coordinates during reaching movement in individuals with autism spectrum disorder
Authors: Umesawa Yumi , Atsumi Takeshi , Fukatsu Reiko , Ide Masakazu 
Published: July 2020

AbstractDespite numerous reports of abnormalities in limb motor controls in spatial orientation in individuals with autism spectrum disorder (ASD), the underlying mechanisms have not been elucidated. We studied the influence of allocentric coordinates on ongoing reaching movements, which has been reported to strongly affect the reaching movements of typically developing (TD) individuals. ASD and TD participants observed a target presented randomly on one of the four corners of a frame on a screen. After it disappeared, another frame was presented slightly shifted leftward/rightward. The participants touched the memorized position of the target relatively congruent with a reference frame (allocentric condition) or ignoring it (egocentric condition). Results suggested that touch positions were less affected by shift directions of reference frame in the allocentric condition in ASD participants, so that they tended to reach in egocentric manner. Our findings demonstrate that decreased utilization of visual landmarks in ongoing movement may underlie motor disabilities in autism.
An amended potassium persulfate ABTS antioxidant assay used for medicinal plant extracts revealed variable antioxidant capacity based upon plant extraction process
Authors: Mingle Cody E. , Newsome Anthony L. 
Published: July 2020

AbstractUse of potassium persulfate (K2S208) for oxidation of 7.0 mM ABTS to a stable ABTS radical for antioxidant studies was first reported in 1999. A feature of this popular antioxidant assay has been the requirement of an overnight reaction (6 to 12 h) for the formation of a stable ABTS colored radical. It is now reported that when the concentration of ABTS is lowered to 0.7 mM, complete oxidation to the stable cation radical occurs in 30 min, thus circumventing the necessary overnight step. Using this format, it is now possible to accurately assess antioxidant activity based on the potassium persulfate/ABTS format in less than one hour which includes formation time of a stable ABTS radical. This methodology documented the presence of antioxidant properties of plant extracts used in Traditional Chinese Medicine. The degree of antioxidant activity was directly related to the extraction method. Greater antioxidant activity was associated with butanol extraction. When incorporated into a microtiter plate format, it supported rapid assessment of multiple determinations of dilutions of plant extracts in less than one hour which included time required for formation of a stable ABTS radical. The ease, improved time prerequisites, and minimal reagent needs with the microtiter plate format, makes this design attractive. It would prove of particular interest to individuals engaged in both smaller and high-volume throughput antioxidant assays of food and health products, and other biological fluids and tissues.
Antigenic variation of SARS-CoV-2 in response to immune pressure
Authors: Forni Diego , Cagliani Rachele , Pontremoli Chiara , Mozzi Alessandra , Pozzoli Uberto , Clerici Mario , Sironi Manuela 
Published: July 2020

SummaryThe ongoing evolution of SARS-CoV-2 is expected to be at least partially driven by the selective pressure imposed by the human immune system. We exploited the availability of a large number of high-quality SARS-CoV-2 genomes, as well as of validated epitope predictions, to show that B cell epitopes in the spike glycoprotein (S) and in the nucleocapsid protein (N) have higher diversity than non-epitope positions. Similar results were obtained for other human coronaviruses. Conversely, in the SARS-CoV-2 population, epitopes for CD4+and CD8+T cells were not more variable than non-epitope positions. A significant reduction in epitope variability was instead observed for some of the most immunogenic proteins (S, N, ORF8, and ORF3a). Analysis over longer evolutionary time-frames indicated that this effect is not due to differential constraints. These data indicate that SARS-CoV-2 is evolving to elude the host humoral immune response, whereas recognition by T cells might benefit the virus.
HistoFlow: Label-Efficient and Interactive Deep Learning Cell Analysis
Authors: Henning Tim , Bergner Benjamin , Lippert Christoph 
Published: July 2020

Instance segmentation is a common task in quantitative cell analysis. While there are many approaches doing this using machine learning, typically, the training process requires a large amount of manually annotated data. We present HistoFlow, a software for annotation-efficient training of deep learning models for cell segmentation and analysis with an interactive user interface.It provides an assisted annotation tool to quickly draw and correct cell boundaries and use biomarkers as weak annotations. It also enables the user to create artificial training data to lower the labeling effort. We employ a universal U-Net neural network architecture that allows accurate instance segmentation and the classification of phenotypes in only a single pass of the network. Transfer learning is available through the user interface to adapt trained models to new tissue types.We demonstrate HistoFlow for fluorescence breast cancer images. The models trained using only artificial data perform comparably to those trained with time-consuming manual annotations. They outperform traditional cell segmentation algorithms and match state-of-the-art machine learning approaches. A user test shows that cells can be annotated six times faster than without the assistance of our annotation tool. Extending a segmentation model for classification of epithelial cells can be done using only 50 to 1500 annotations.Our results show that, unlike previous assumptions, it is possible to interactively train a deep learning model in a matter of minutes without many manual annotations.
Ratatosk – Hybrid error correction of long reads enables accurate variant calling and assembly
Authors: Holley Guillaume , Beyter Doruk , Ingimundardottir Helga , Kristmundsdottir Snædis , Eggertsson Hannes P. , Halldorsson Bjarni V. 
Published: July 2020

AbstractMotivationLong Read Sequencing (LRS) technologies are becoming essential to complement Short Read Sequencing (SRS) technologies for routine whole genome sequencing. LRS platforms produce DNA fragment reads, from 103to 106bases, allowing the resolution of numerous uncertainties left by SRS reads for genome reconstruction and analysis. In particular, LRS characterizes long and complex structural variants undetected by SRS due to short read length. Furthermore, assemblies produced with LRS reads are considerably more contiguous than with SRS while spanning previously inaccessible telomeric and centromeric regions. However, a major challenge to LRS reads adoption is their much higher error rate than SRS of up to 15%, introducing obstacles in downstream analysis pipelines.ResultsWe present Ratatosk, a new error correction method for erroneous long reads based on a compacted and colored de Bruijn graph built from accurate short reads. Short and long reads color paths in the graph while vertices are annotated with candidate Single Nucleotide Polymorphisms. Long reads are subsequently anchored to the graph using exact and inexact fc-mer matches to find paths corresponding to corrected sequences. We demonstrate that Ratatosk can reduce the raw error rate of Oxford Nanopore reads 6-fold on average with a median error rate as low as 0.28%. Ratatosk corrected data maintain nearly 99% accurate SNP calls and increase indel call accuracy by up to about 40% compared to the raw data. An assembly of the Ashkenazi individual HG002 created from Ratatosk corrected Oxford Nanopore reads yields a contig N50 of 43.22 Mbp and less misassemblies than an assembly created from PacBio HiFi reads.Availabilityhttps://github.com/DecodeGenetics/RatatoskContactguillaume.holley@decode.is
Mode of Targeting to the Proteasome Determines GFP Fate
Authors: Bragança Christopher E. , Kraut Daniel A. 
Published: July 2020

ABSTRACTThe Ubiquitin-proteasome system (UPS) is the canonical pathway for protein degradation in eukaryotic cells. Green fluorescent protein (GFP) is frequently used as a reporter in proteasomal degradation assays. However, there are multiple variants of GFP in use, and these variants have different stabilities. We previously found that the proteasome’s ability to unfold and degrade substrates is enhanced by polyubiquitin chains on the substrate, and that proteasomal ubiquitin receptors mediate this activation. Herein we investigate how the fate of GFP variants of differing stabilities is determined by the mode of targeting to the proteasome. We compared two targeting systems: linear Ub4degrons and the UBL domain from yeast Rad23, both of which are commonly used in degradation experiments. Surprisingly, the UBL degron allows for degradation of the most stable sGFP-containing substrates, while the Ub4degron does not. Destabilizing the GFP by circular permutation allows degradation with either targeting signal, indicating that domain stability and mode of targeting combine to determine substrate fate. Finally, we show that the ubiquitin receptor Rpn13 is primarily responsible for the enhanced ability of the proteasome to degrade stable UBL-tagged substrates.
Estimating the burden of COVID-19 on mortality, life expectancy and lifespan inequality in England and Wales: A population-level analysis
Authors: Aburto José Manuel , Kashyap Ridhi , Schöley Jonas , Angus Colin , Ermisch John , Mills Melinda C. , Dowd Jennifer Beam 
Published: July 2020

AbstractObjectiveTo determine the impact of the COVID-19 pandemic on mortality, life expectancy and lifespan inequality in the first half of 2020 (from week 1 to week 26 starting June 22) in England and Wales.DesignDemographic analysis of all-cause mortality from week 1 through week 26 of 2020 using publicly available death registration data from the Office for National Statistics.Setting and populationEngland and Wales population by age and sex in 2020.Main outcome measureAge and sex-specific excess mortality risk and deaths above a baseline adjusted for seasonality in the first half of 2020. We additionally provide estimates of life expectancy at birth and lifespan inequality defined as the standard deviation in age at death.ResultsWe estimate that there have been 53,937 (95% Prediction Interval: 53,092, 54,746) excess deaths in the first half of 2020, 54% of which occurred in men. Excess deaths increased sharply with age and men experienced elevated risks of death in all age groups. Life expectancy at birth dropped 1.7 and 1.9 years for females and males relative to the 2019 levels, respectively. Lifespan inequality also fell over the same period.ConclusionsQuantifying excess deaths and their impact on life expectancy at birth provides a more comprehensive picture of the full COVID-19 burden on mortality. Whether mortality will return to - or even fall below - the baseline level remains to be seen as the pandemic continues to unfold and diverse interventions are put in place.Summary boxesWhat is already known on this topicCOVID-19 related deaths may be misclassified as other causes of death thereby underestimating the full impact of the pandemic on mortality. Excess mortality, the difference between observed deaths and what would have been expected in the absence of the pandemic, is a useful metric to quantify the overall impact of the pandemic on mortality and population health. Life expectancy at birth and lifespan inequality assess the cumulative impact of the pandemic on population health.What this study addsWe examine death registration data from the Office for National Statistics from 2015 to week 26 (mid-year) in 2020 to quantify the impact of the COVID-19 pandemic on mortality in England and Wales thus far. We estimate excess mortality risk by age and sex, and quantify the impact of excess mortality risk on excess deaths, life expectancy and lifespan inequality. During weeks 10 through 26 of 2020, elevated mortality rates resulted in 53,937 additional deaths compared with baseline mortality. Life expectancy at birth for males and females in the first half of 2020 was 78 and 81.8 years, which represent a decline of 1.9 and 1.7 years of life lost relative to the year 2019. Lifespan inequality, a measure of the spread or variation in ages at death, declined due to the increase of mortality at older ages.
A three-dimensional musculoskeletal model of the dog
Authors: Stark Heiko , Fischer Martin S. , Hunt Alexander , Young Fletcher , Quinn Roger , Andrada Emanuel 
Published: July 2020

AbstractDogs are an interesting object of investigation because of the wide range of body size, body mass, and physique. In the last several years, the number of clinical and biomechanical studies on dog locomotion has increased. However, the relationship between body structure and joint load during locomotion, as well as between joint load and degenerative diseases of the locomotor system (e.g. dysplasia), are not sufficiently understood. In vivo measurements/records of joint forces and loads or deep/small muscles are complex, invasive, and sometimes ethically questionable. The use of detailed musculoskeletal models may help in filling that knowledge gap. We describe here the methods we used to create a detailed musculoskeletal model with 84 degrees of freedom and 134 muscles. Our model has three key-features: Three-dimensionality, scalability, and modularity. We tested the validity of the model by identifying forelimb muscle synergies of a beagle at walk. We used inverse dynamics and static optimization to estimate muscle activations based on experimental data. We identified three muscle synergy groups by using hierarchical clustering. Predicted activation patterns exhibited good agreement with experimental data for most of the forelimb muscles. We expect that our model will speed up the analysis of how body size, physique, agility, and disease influence joint neuronal control and loading in dog locomotion.
Influence of governance regime on controller roles – supervisory board members’ perspectives on business unit controller roles and role conflict
Authors: Steens Bert , de Bont Anouk , Roozen Frans 
Published: July 2020

Purpose
The plethora of changes in the corporate governance landscape over the past two decades has the potential to tighten governance regimes and influence the preference of supervisory board members vis-à-vis the involved decision-making role of business unit (BU) controllers and their independent fiduciary role. Stricter financial reporting and compliance requirements may lead organizations to prioritize the latter role. However, recent studies support the need to balance these roles, inducing the potential for role conflict. The purpose of this study is to shed light on the influence of a tight and loose governance regime on this balance as preferred by supervisory board members.

Design/methodology/approach
This study uses a unique data set from an experiment among 73 supervisory board members. The authors take their perspective because compliance with governance codes and corporate policies are relevant topics for their function.

Findings
The authors find evidence for the preference of supervisory board members for “all-round” BU controllers who, irrespective of the governance regime, demonstrate substantial levels of fiduciary and decision-making qualities and deal with the resulting role conflict.

Originality/value
The outcomes of the experiment among supervisory board members provide evidence for their preferences concerning the balance of the two primary controller roles and for the potential of role conflict. The authors have not found studies that provide such empirical evidence.
Can academic leadership competencies have effect on students' cognitive, skill and affective learning outcomes? Higher education perspective
Authors: Radwan Omaymah , Ghavifekr Simin , Abdul Razak Ahmad Zabidi 
Published: July 2020

PurposeThe main purpose is to analyse the effect of academic leadership competencies (LCs) on student learning outcomes (SLOs) in terms of cognitive, skill and affective aspects.Design/methodology/approachThe study utilised quantitative research that focussed on correlation design by randomly distributing questionnaires containing 53 items to a total of 496 faculty members in Saudi Arabia public higher education institutions (HEIs). The data was analysed using SPSS (V.24) and SEM-AMOS.FindingsResults show a direct and significant effect of academic LC on students' cognitive, skill and affective learning outcomes in public HEIs.Research limitations/implicationsThe main limitation was that the participants of public HEIs were from Saudi Arabia. However, the findings have provided valuable understandings and a comprehensive conclusion about the impact of academic LC on SLOs in terms of cognitive, skill and affective aspects. The study recommended that different LC should be further developed. Future studies proposed to investigate the factors that support academic leaders to affect SLOs directly in HEIs.Originality/valueThe findings contribute to the body of knowledge regarding the significant and direct effect of academic LC on SLOs in HEIs. The findings have the potential to reflect positively on the academic leaders in public HEIs. The findings act as a guide for HEIs in terms of the importance of academic LC for having desirable SLOs. This study is crucial for educational policymakers and practitioners of academic leadership as the academic leaders' effort will greatly contribute to the HEIs as well as the nation's development in general.
How to improve teachers’ instructional practices: the role of professional learning activities, classroom observation and leadership content knowledge in Turkey
Authors: Özdemir Nedim 
Published: July 2020

PurposeThis study focused on the impact of principals' leadership content knowledge, evaluation practices and teachers' professional learning activities on classroom instruction.Design/methodology/approachData were collected from 425 teachers who worked in 46 elementary and lower secondary public schools within two provinces in Turkey. Teachers were asked to fill out a questionnaire on principals’ leadership content knowledge, evaluation feedback, professional learning activities and changed instructional practices. This study employed multilevel structural equation modeling (MSEM) by using the Bayesian estimation method to analyze the research hypotheses.FindingsFindings indicate that if teachers perceive the evaluation progress as more useful, then they will participate in more professional learning activities, and they will be more effective in their classroom practices. This study also indicates that teachers' professional learning activities stimulate their instructional practices.Research limitations/implicationsAlthough the number of schools and teachers allows using multilevel analysis, it limits the findings generalized beyond the sample. To compensate for this limitation, the author confirmed that the sample was representative of the larger population by examining the size of students and teachers, SES and teachers' job experience. The author also conducted a Bayesian estimator to strengthen the test of significance of effects.Practical implicationsThis study underlines the critical role of leadership content knowledge in evaluating practices and providing useful feedback perceived by teachers in elementary and secondary schools. Principals should lead to instruction by knowing how to address a lack of teachers' pedagogical content knowledge and classroom practices. The Ministry of Education should support principals in becoming effective instructional leaders to observe teachers and provide them meaningful feedback on teaching.Originality/valueDespite increased interest in this construct, research on principals' and teachers' responses to adapt the recent form of teachers’ performance evaluation systems is scant, especially in developing countries’ context. Moreover, little is known about the paths through which principals can enhance classroom practices by providing useful feedback. Given these trends in policy and practice context, this study provides empirical evidence that principals can enact the teachers' performance evaluation that affects classroom instruction.
Examining the interrelatedness among human resources management practices, entrepreneurial traits and corporate entrepreneurship in emerging markets: an evidence from Egypt
Authors: Shehata Gamal Mohamed , Montash Mohammed Abdel-Hakim , Areda Mohamed Raafat 
Published: July 2020

PurposeThe main purpose of this paper is to investigate the relationships among a set of human resources management (HRM) practices, entrepreneurial traits (ET) and corporate entrepreneurship (CE) in an emerging market such as the Egyptian one.Design/methodology/approachThis research is explanatory in nature where it explains the causal relationships between the variables. Data was collected from 230 human resources (HR) managers and professional serving in top Egyptian financial institutions. Data was analyzed using structural equation modeling with relevant goodness-of-fit statistics.FindingsThe results of this study indicate that HRM practices have significant impact on the development of ET of personnel currently operating in the Egyptian financial institutions. Besides, the results confirm the effect of HRM practices on ET, which in turn have significant impact on CE.Practical implicationsThis research provides an appropriate direction for HR managers on how to best design HR programs directed toward the development of strong CE orientation. It also highlights the core ET needed to enhance CE in emerging economies. The validated hypothetical relationships of this model serve as the baseline for those managers to plan, execute and measure the consequences of those HRM programs.Originality/valueAlthough HRM is widely considered as a critical driving force for CE, there is a remarkable scarcity of empirical research examining the role of ET. The conceptual model tested in this research typically deepens both HRM scholars and managers’ understanding of how they can best connect HRM practices to ET and CE in emerging economies. The findings of this study open the door for a new venue of research in the HRM area of study, particularly in emerging markets that search for a fast-growing rate of economic prosperity. The findings of this study lend support for HRM as an antecedent to CE rather than vice versa.