bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kinetic sequencing (k-Seq) as a massively parallel assay for ribozyme kinetics: utility and critical parameters
Authors: Shen Yuning , Pressman Abe , Janzen Evan , Chen Irene 
Published: December 2020

ABSTRACTCharacterization of genotype-phenotype relationships of genetically encoded molecules (e.g., ribozymes) requires accurate quantification of activity for a large set of molecules. Kinetic measurement using high-throughput sequencing (e.g.,k-Seq) is an emerging assay applicable in various domains that potentially scales up measurement throughput to 105~ 106unique sequences. However, technical challenges introduced by sequence heterogeneity and DNA sequencing must be understood to realize the utility and limitations of such assays. We characterized thek-Seq method in terms of model identifiability, effects of sequencing error, accuracy and precision using simulated datasets and experimental data from a variant pool constructed from previously identified ribozymes. Relative abundance, kinetic coefficients, and measurement noise were found to affect the measurement of each sequence. We introduced bootstrapping to robustly quantify the uncertainty in estimating model parameters and proposed interpretable metrics to quantify model identifiability. These efforts enabled the rigorous reporting of data quality for individual sequences ink-Seq experiments. Critical experimental factors were examined, and general guidelines are proposed to maximize the number of sequences having precisely estimated and identifiable kinetic coefficients fromk-Seq data. Practices analogous to those laid out here could be applied to improve the rigor of similar sequencing-based assays.
Cingulate prediction of response to antidepressant and cognitive behavioral therapies for depression: Theory, meta-analysis, and empirical application
Authors: Strege Marlene V. , Siegle Greg J. , Young Kymberly 
Published: December 2020

AbstractObjectiveIn the interest of precision medicine, we sought to derive preclinical markers of neural mechanisms associated with treatment response in unipolar depression, separated by treatment type.MethodsWe conducted separate neuroimaging meta-analyses of neural predictors for response to Cognitive Behavioral Therapy (CBT) and Selective Serotonin Reuptake Inhibitors (SSRIs). We assessed whether reactivity of derived regions predicted clinical change in a preference trial of patients with major depressive disorder (MDD) who received CBT (n = 61) or SSRIs (n = 19).ResultsThe meta-analyses yielded regions within the perigenual (pgACC) and subgenual anterior cingulate cortex (sgACC) associated with SSRI and CBT response, respectively. In our sample, reactivity of the sgACC region was prognostic for response to CBT, but neither cingulate region was prognostic for response to SSRIs using a linguistic task; most prognostic SSRI studies used images. An exploratory analysis revealed a pgACC region for which reactivity to images was prognostic for response to SSRIs.ConclusionsResults suggest that neural reactivity of the sgACC and pgACC are associated with CBT and SSRI response for unipolar depression. Further research incorporating methodological considerations is necessary for translation.
SARS-CoV-2 in Brazil: analysis of molecular variance and genetic diversity in viral haplotypes found in the states of Rio de Janeiro, São Paulo, Paraná and Tocantins
Authors: de Albuquerque Rosane Maria , Da Silva Eduarda Doralice Alves Braz , Venâncio Dallynne Bárbara Ramos , da Silva Ramos Robson , Felix Pierre Teodósio 
Published: December 2020

AbstractIn this work, 18 sequences of the SARS-CoV-2 virus were used, from four Brazilian states (Rio de Janeiro, São Paulo, Paraná and Tocantins) with 09, 04, 04, 8 and 01 haplotypes, respectively, with lengths ranging from 234 to 29,903 bp. All sequences were publicly available on the National Biotechnology Information Center (NCBI) platform and were previously aligned with the MEGA X software, where all gaps and ambiguous sites were extracted for the construction of the phylogenetic tree. Of the 301 sites analyzed, 68% varied, 131 of which were parsimonium-informative sites. Phylogenetic analyses revealed the presence of two distinct subgroups, corroborated by the high FST(80%). The high degree of polymorphism found among these samples helped to establish a clear pattern of non-genetic structuring, based on the time of divergence between the groups. All molecular variance estimators confirmed that there was no consensus in the conservation of the studied sequences, also indicating a high variation for the protein products of the virus. In a highly miscegenational and diverse population such as the Brazilian population, this observation draws our attention to the need for an urgent increase in public health actions, awareness strategies, hygiene and distancing practices and not the other way around.
Sca1+cells as direct isolate (ex vivo) versusin vitrocultured exhibit differential proteomic signatures in murine skeletal muscle
Authors: Kapoor Saketh , Subba Pratigya , Shenoy P Sudheer , Bose Bipasha 
Published: December 2020

AbstractStem cell antigen-1 (Sca-1) is a glycosyl-phosphatidylinositol-anchored membrane protein that is expressed in a sub-population of muscle stem and progenitor cell types. Reportedly, Sca-1 regulates the myogenic property of myoblasts andSca-1-/-mice exhibited defective muscle regeneration. Although the role of Sca-1 in muscle development and maintenance is well-acknowledged, molecular composition of muscle derived Sca-1+cells is not characterized. Here, we applied a high-resolution mass spectrometry-based workflow to characterize the proteomic landscape of mouse hindlimb skeletal muscle derived Sca-1+cells. Furthermore, we characterized the impact of the cellular microenvironments on the proteomes of Sca-1+cells. The proteome component of freshly isolated (ex vivo) Sca-1+cells was compared with that of Sca-1+cells expanded in cell culture (in vitro). The analysis revealed significant differences in the protein abundances in the two conditions reflective of their functional variations. The identified proteins were enriched in various biological pathways. Notably, we identified proteins related to myotube differentiation, myotube cell development and myoblast fusion. We also identified a panel of cell surface marker proteins that can be leveraged in future to enrich Sca-1+cells using combinatorial strategies. Comparative analysis implicated the activation of various pathways leading to increased protein synthesis underin vitrocondition. We report here the most comprehensive proteome map of Sca-1+cells that provides insights into the molecular networks operative in Sca-1+cells. Importantly, through our work we generated the proteomic blueprint of protein abundances significantly altered in Sca-1+cells underex vivoandin vitroconditions.
Absence-like epileptic spike-wave discharges in adult Lister Hooded rats and their pharmacological modulation
Authors: Nyitrai Gabriella , Diószegi Pálma , Somogyi Gergely , Czurkó András 
Published: December 2020

AbstractEfforts to advance translation through pre-clinical behavioural and pharmacological tests prompted attention to rat strain differences. Particularly the use of touchscreen technology for cognitive testing initiated the widespread use of Lister Hooded and Long Evans rats and they differed in pharmacological sensitivity to certain drugs. One possible reason for this rat strain difference could be that Long Evans rats produce high-amplitude spike-wave discharges (SWDs) in their cortical EEG recordings, while no information available about Lister Hooded rats in this regard. As a serendipitous observation, we noticed the presence of SWDs during the EEG recordings of Lister Hooded rats. In this study, therefore, we examined these spontaneous SWDs in two groups of Lister Hooded rats. The number and sum duration of the SWDs were similar to that was observed in other rat strains. We found SWDs during wakefulness, slow-wave sleep (SWS) and rapid eye movement (REM) sleep, their duration was the longest during wakefulness, but their number and sum duration were also high during REM. The GABA-B receptor agonist baclofen exacerbated, while the GABA-B antagonist SCH50911 reduced the occurrence of the recorded SWDs. Typical anti-seizure medications, valproate and diazepam, decreased the number and sum duration of SWDs. Although the two rat strains typically used in touchscreen experiments are similar in term of SWDs, the occurrence and possible pharmacological modulation of SWDs are considerable during their use in behavioural experiments.
Cicada timetree by BEAST v1.X verified the recently and exponentially increasing base substitution rates
Authors: Osozawa Soichi , Wakabayashi John 
Published: December 2020

AbstractFollowing the recent publication of global cicada phylogenetic trees by Marshall et al. (2018), Łukasik et al. (2018), and Simon et al. (2019), we developed a new dated tree incorporating mostly endemic east Asian cicada data for totally 113 specimens, using the mostly advanced BEAST v1.X software applied the relaxed clock model. Fossil calibrations as old as Triassic were adopted after Moulds (2018), and a Quaternary geological event calibration was adopted following Osozawa et al. (2012), applying the calibration function of BEAST. Our timetree suggests that Tettigarctidae had cicada basal lineage as old as 200 Ma, and Derotettiginae was next as old as 100 Ma. Tibicininae was a sister of the resting Cicadidae, and Tettigomyiinae, Cicadettinae, and Cicadina started simultaneous branching and radiation around 40 Ma. We made a base substitution rate vs age diagram based on the timetree using the BEAST function, and it strongly suggested an exponential increase of base substitution rate approaching the present. The consequent increased cicada biodiversity including generation of cryptic species might have been driven by the generation and spreading of C4 grasses and the following Quaternary glaciations and severe environmental change.
Adaptation ofBacillus thuringiensisto plant colonization affects differentiation and toxicity
Authors: Lin Yicen , Alstrup Monica , Pang Janet Ka Yan , Maróti Gergely , Er-Rafik Mériem , Tourasse Nicolas , Økstad Ole Andreas , Kovács Ákos T. 
Published: December 2020

AbstractBacillus cereusgroup (Bacillus cereus sensu lato) has a diverse ecology, including various species that are vertebrate or invertebrate pathogens. Few isolates from theB. cereusgroup have however been demonstrated to benefit plant growth. Therefore, it is crucial to explore how bacterial development and toxicity evolves during plant colonization. Herein, we investigatedBacillus thuringiensis(Cry-) adaptation to the colonization ofArabidopsis thalianaroots, and monitored changes in cellular differentiation in experimentally evolved isolates. Isolates from two populations displayed improved iterative ecesis on roots and increased toxicity against insect larvae. Molecular dissection and recreation of a causative mutation revealed the importance of a non-sense mutation in therhotranscription terminator gene. Transcriptome analysis revealed how Rho impacts variousB. thuringiensisgenes involved in carbohydrate metabolism and virulence. Our work suggests that evolved multicellular aggregates have a fitness advantage over single cells when colonizing plants, creating a trade-off between swimming and multicellularity in evolved lineages, in addition to unrelated alterations in pathogenicity.ImportanceBiologicals-based plant protection relies on the use of safe microbial strains. During application of biologicals to the rhizosphere, microbes adapt to the niche, including genetic mutations shaping the physiology of the cells. Here, the experimental evolution ofBacillus thuringiensislacking the insecticide crystal toxins was examined on the plant root to reveal how adaptation shapes the differentiation of this bacterium. Interestingly, evolution of certain linages led to increased emetic toxin production, hemolysis and insect larvae pathogenesis inB. thuringiensisdriven by transcriptional rewiring. Further, our detailed study reveals how inactivation of the transcription termination protein Rho promotes aggregation on the plant root in addition to altered differentiation and pathogenesis inB. thuringiensis.
Horizontal gene transfer and recombination analysis of SARS-CoV-2 genes helps discover its close relatives and shed light on its origin
Authors: Makarenkov Vladimir , Mazoure Bogdan , Rabusseau Guillaume , Legendre Pierre 
Published: December 2020

AbstractBackgroundThe SARS-CoV-2 pandemic is among the most dangerous infectious diseases that have emerged in recent history. Human CoV strains discovered during previous SARS outbreaks have been hypothesized to pass from bats to humans using intermediate hosts, e.g. civets for SARS-CoV and camels for MERS-CoV. The discovery of an intermediate host of SARS-CoV-2 and the identification of specific mechanism of its emergence in humans are topics of primary evolutionary importance. In this study we investigate the evolutionary patterns of 11 main genes of SARS-CoV-2. Previous studies suggested that the genome of SARS-CoV-2 is highly similar to the horseshoe bat coronavirus RaTG13 for most of the genes and to some Malayan pangolin coronavirus (CoV) strains for the receptor binding (RB) domain of the spike protein.ResultsWe provide a detailed list of statistically significant horizontal gene transfer and recombination events (both intergenic and intragenic) inferred for each of 11 main genes of the SARS-Cov-2 genome. Our analysis reveals that two continuous regions of genes S and N of SARS-CoV-2 may result from intragenic recombination between RaTG13 and Guangdong (GD) Pangolin CoVs. Statistically significant gene transfer-recombination events between RaTG13 and GD Pangolin CoV have been identified in region [1215-1425] of gene S and region [534-727] of gene N. Moreover, some significant recombination events between the ancestors of SARS-CoV-2, RaTG13, GD Pangolin CoV and bat CoV ZC45-ZXC21 coronaviruses have been identified in genes ORF1ab, S, ORF3a, ORF7a, ORF8 and N. Furthermore, topology-based clustering of gene trees inferred for 25 CoV organisms revealed a three-way evolution of coronavirus genes, with gene phylogenies of ORF1ab, S and N forming the first cluster, gene phylogenies of ORF3a, E, M, ORF6, ORF7a, ORF7b and ORF8 forming the second cluster, and phylogeny of gene ORF10 forming the third cluster.ConclusionsThe results of our horizontal gene transfer and recombination analysis suggest that SARS-Cov-2 could not only be a chimera resulting from recombination of the bat RaTG13 and Guangdong pangolin coronaviruses but also a close relative of the bat CoV ZC45 and ZXC21 strains. They also indicate that a GD pangolin may be an intermediate host of SARS-CoV-2.
Integrating technology subjects with design studio teaching: comparing curriculum of architecture education in Australia and Iran
Authors: Saghafi Mahmoud Reza , Crowther Philip 
Published: December 2020

PurposeDesign studio and technology subjects are two dominant parts of the architecture curriculum. How to integrate these different parts of the curriculum is one of the important challenges in architecture education around the world. With increasing internationalisation of both the profession and higher education, an understanding of similarities and differences across the globe is important. This paper illustrates two different approaches to such integration in two very different contexts: case studies at the Queensland University of Technology (QUT) in Australia and the University of Tehran (UT) in Iran.Design/methodology/approachThe study implemented a case study approach based on document analysis methods. This paper explores the integrated role of technology subjects in architecture education, followed by a critique of the teaching of technology within the design studio. The analysis is conducted across four significant features of the curriculum.FindingsOverall, in both programmes, the aim is for students to develop architectural knowledge and skills; although the Iranian programme has a stronger focus on knowledge, the Australian programme has a stronger focus on the application of knowledge and skills, particularly within the design studio projects.Originality/valueThe comparative analysis of architectural education in these two different contexts offers an insight into alternative approaches to teaching technology. Such an insight may offer guidance in curriculum development to support the exploration of new hybrid approaches as well as supporting international student mobility.
Flexible flow shop scheduling with interval grey processing time
Authors: Wang Yuquan , Xie Naiming 
Published: December 2020

Purposepurpose of this paper is providing a solution for flexible flow shop scheduling problem with uncertain processing time in aeronautical composite lay-up workshop.Design/methodology/approachA flexible flow scheduling model and algorithm with interval grey processing time is established. First, according to actual needs of composite laminate shop scheduling process, interval grey number is used to represent uncertain processing time, and interval grey processing time measurement method, grey number calculation and comparison rules, grey Gantt chart, and other methods are further applied. Then a flexible flow shop scheduling model with interval grey processing time (G-FFSP) is established, and an artificial bee colony algorithm based on an adaptive neighbourhood search strategy is designed to solve the model. Finally, six examples are generated for simulation scheduling, and the efficiency and performance of the model and algorithm are evaluated by comparing the results.FindingsResults show that flexible flow shop scheduling model and algorithm with interval grey processing time can provide an optimal solution for composite lay-up shop scheduling problems and other similar flow shop scheduling problems.Social implicationsUncertain processing time is common in flexible workshop manufacturing, and manual scheduling greatly restricts the production efficiency of workshop. In this paper, combined with grey system theory, an intelligent algorithm is used to solve flexible flow shop scheduling problem to promote intelligent and efficient production of enterprises.Originality/valueThis paper applies and perfects interval grey processing time measurement method, grey number calculation and comparison rules, grey Gantt chart and other methods. A flexible flow shop scheduling model with interval grey processing time is established, and an artificial bee colony algorithm with an adaptive domain search strategy is designed. It provides a comprehensive solution for flexible flow shop scheduling with uncertain processing time.
The increased importance of competitor benchmarking as a strategic management tool during COVID-19 recovery
Authors: Magnini Vincent P. , Crotts John C. , Calvert Esra 
Published: December 2020

PurposeWhile all recoveries are good, some are better than others with regard to their speed and/or magnitude. Many revenue-related key performance indicators (KPIs), such as comparisons to budgets and forecasts that were designed pre-pandemic to assess a hotel's or destination's performance are no longer valid. Therefore, the primary purpose of this conceptual paper is to highlight the need to peg financial-related KPIs relative to competitors' performance during and following a radical market disruption. The secondary purpose of this paper is to summarize advances reported in the literature and in the industry related to competitor benchmarking and accurately identifying competitor sets.Design/methodology/approachThis conceptual paper synthesizes research from disparate sources to offer a series of recommendations to the industry regarding best practices for developing and monitoring revenue-related KPIs during pandemic recovery. Such KPIs will be different based upon hospitality or tourism sector but must be largely founded upon benchmarking off comparable operations.FindingsIndustry disruptions triggered by COVID-19 underscore the need (1) to increasingly utilize competitor-based revenue KPI benchmarks; (2) to have reliable competitor benchmarking data more readily available for use by hotels and destination marketing organizations (DMOs) and (3) for both hotels and DMOs to more accurately identify their competitive sets.Originality/valueThe recommendations offered in this paper are anchored with appropriate theories and empirical research; and as a consequence, offer guidance for the industry for KPI formulation during and following the pandemic.
The role of entry exams on higher education: a case study on reforming qualifier exam policies to improve student success while maintaining program quality
Authors: Basavaraj Prateek , Sedghi Mahlagha , Garibay Ivan , Ozmen Garibay Ozlem , Guha Arup Ratan 
Published: December 2020

PurposeSome degree programs in colleges and universities utilize entrance exams to ensure that students pursuing a given degree have mastered foundational concepts needed for that program. However, often these exams become a barrier to student success. The purpose of this study is to discuss the impact of policies governing an undergraduate Computer Science (CS) entry/qualifying exam at a large public university in the United States on overall student success in the program. This case study focuses on whether reforming program policies impacts students' time-to-degree, graduation and mastery in CS core skills.Design/methodology/approachThis case study describes how the CS student success was improved by updating program policies based on institutional data and the input of course instructors. The policy changes include introducing a maximum limit to attempt the exam, changing the exam requirements as well as the structure of the exam itself.FindingsThe pass rates of students taking this qualifying exam were significantly and consistently low over the years. Students who were potentially a better fit for programs other than CS delayed their start in those other programs by taking and failing to pass the CS qualifying exam multiple times. As a result of implementing new CS program policies, many more students attempted the exam at an appropriate time. Also, they graduated on time in the years 2016–2018.Originality/valueThis paper presents a case study in which the graduation rates and time to degree of a CS program with a qualifying exam were improved after a policy intervention. The results demonstrate that simple policy changes can improve student success. Findings from this study may guide other programs with similar characteristics to improve their student success.
Financial fraud investigative interviewing – corporate investigators’ beliefs and practices: a qualitative inquiry
Authors: King Michael 
Published: December 2020

Purpose
The purpose of this paper is to examine the investigative interviewing processes in the context of financial frauds, as experienced by corporate investigators.

Design/methodology/approach
A diverse sample of 33 corporate investigators individually participated in in-depth interviews.

Findings
This study examined perceptions of investigative interviewing of those undertaking fraud investigations. The corporate investigator’s response indicated understanding of the necessary skills required to conduct interviews. The findings suggest that the investigator agreed on the interviewing skills that are required to conduct interviews; however, upon reflection, they may not use the skills during interviews.

Originality/value
This study is the first to reveal limitations in corporate investigators’ investigative interviewing and fills a gap in the academic literature by examining corporate investigators’ beliefs and practices in conducting their private investigations of corporate and white-collar crime.