bluuebunny/crossref_metadata_2025 huggingface dataset:
PelX is a UDP-N-acetylglucosamine C4-epimerase involved in Pel polysaccharide-dependent biofilm formation
Authors: Marmont Lindsey S. , Whitfield Gregory B. , Pfoh Roland , Williams Rohan J. , Randall Trevor E. , Ostaszewski Alexandra , Razvi Erum , Groves Ryan A. , Robinson Howard , Nitz Mark , Parsek Matthew R. , Lewis Ian A. , Whitney John C. , Harrison Joe J. , Howell P. Lynne
Published: May 2020

Pel is anN-acetylgalactosamine rich polysaccharide that contributes to the structure and function ofPseudomonas aeruginosabiofilms. ThepelABCDEFGoperon is highly conserved among diverse bacterial species, and thus Pel may be a widespread biofilm determinant. Previous annotation ofpelgene clusters led us to identify an additional gene,pelX, that is found adjacent topelABCDEFGin over 100 different bacterial species. ThepelXgene is predicted to encode a member of the short-chain dehydrogenase/reductase (SDR) superfamily of enzymes, but its potential role in Pel-dependent biofilm formation is unknown. Herein, we have usedPseudomonas protegensPf-5 as a model to understand PelX function asP. aeruginosalacks apelXhomologue in itspelgene cluster. We find thatP. protegensforms Pel-dependent biofilms, however, despite expression ofpelXunder these conditions, biofilm formation was unaffected in a ΔpelXstrain. This observation led to our identification of thepelXparalogue, PFL_5533, which we designatepgnE, that appears to be functionally redundant topelX. In line with this, a ΔpelXΔpgnEdouble mutant was substantially impaired in its ability to form Pel-dependent biofilms. To understand the molecular basis for this observation, we determined the structure of PelX to 2.1Å resolution. The structure revealed that PelX resembles UDP-N-acetylglucosamine (UDP-GlcNAc) C4-epimerases and, using1H NMR analysis, we show that PelX catalyzes the epimerization between UDP-GlcNAc and UDP-GalNAc. Taken together, our results demonstrate that Pel-dependent biofilm formation requires a UDP-GlcNAc C4-epimerase that generates the UDP-GalNAc precursors required by the Pel synthase machinery for polymer production.
An updated staging system for cephalochordate development: one table suits them all
Authors: Carvalho João E. , Lahaye François , Yong Luok Wen , Croce Jenifer C. , Escrivá Hector , Yu Jr-Kai , Schubert Michael
Published: May 2020

Chordates are divided into three subphyla: Vertebrata, Tunicata and Cephalochordata. Phylogenetically, the Cephalochordata, more commonly known as lancelets or amphioxus, constitute the sister group of Vertebrata and Tunicata. Lancelets are small, benthic, marine filter feeders, and their roughly three dozen described species are divided into three genera:Branchiostoma,EpigonichthysandAsymmetron. Due to their phylogenetic position and their stereotypical chordate morphology and genome architecture, lancelets are key models for understanding the evolutionary history of chordates. Lancelets have thus been studied by generations of scientists, with the first descriptions of adult anatomy and developmental morphology dating back to the 19thcentury. Today, several different lancelet species are used as laboratory models, predominantly for developmental, molecular and genomic studies. Surprisingly, however, a universal staging system and an unambiguous nomenclature for developing lancelets have not yet been adopted by the scientific community.

In this work, we characterized the development of the European amphioxus (Branchiostoma lanceolatum) using confocal microscopy and compiled a streamlined developmental staging system, from fertilization through larval life, including an unambiguous stage nomenclature. By tracing growth curves of the European amphioxus reared at different temperatures, we were able to show that our staging system permitted an easy conversion of any developmental time into a specific stage name. Furthermore, comparisons of embryos and larvae from the European lancelet (B. lanceolatum), the Florida lancelet (B. floridae), the Chinese lancelet (B. belcheri), the Japanese lancelet (B. japonicum) and the Bahamas lancelet (Asymmetron lucayanum) demonstrated that our staging system could readily be applied to other lancelet species.

Although the detailed staging description was carried out on developingB. lanceolatum, the comparisons with other lancelet species thus strongly suggested that both staging and nomenclature are applicable to all extant lancelets. We conclude that this description of embryonic and larval development will be of great use for the scientific community and that it should be adopted as the new standard for defining and naming developing lancelets. More generally, we anticipate that this work will facilitate future studies comparing representatives from different chordate lineages.
An Immunoinformatics Study to Predict Epitopes in the Envelope Protein of SARS-COV-2
Authors: Jakhar Renu , Gakhar S.K
Published: May 2020

COVID-19 is a new viral emergent human disease caused by a novel strain of Coronavirus. This virus has caused a huge problem in the world as millions of the people are affected with this disease in the entire world. We aimed to design a peptide vaccine for COVID-19 particularly for the envelope protein using computational methods to predict epitopes inducing the immune system and can be used later to create a new peptide vaccine that could replace conventional vaccines. A total of available 370 sequences of SARS-CoV-2 were retrieved from NCBI for bioinformatics analysis using Immune Epitope Data Base (IEDB) to predict B and T cells epitopes. Then we docked the best predicted CTL epitopes with HLA alleles. CTL cell epitopes namely interacted with MHC class I alleles and we suggested them to become universal peptides based vaccine against COVID-19. Potentially continuous B cell epitopes were predicted using tools from IEDB. The Allergenicity of predicted epitopes was analyzed by AllerTOP tool and the coverage was determined throughout the worlds. We found these CTL epitopes to be T helper epitopes also. The B cell epitope, SRVKNL and T cell epitope, FLAFVVFLL were suggested to become a universal candidate for peptide-based vaccine against COVID-19. We hope to confirm our findings by adding complementary steps of bothin vitroandin vivostudies to support this new universal predicted candidate.
Robustification of RosettaAntibody and Rosetta SnugDock
Authors: Jeliazkov Jeliazko R. , Frick Rahel , Zhou Jing , Gray Jeffrey J.
Published: May 2020

In recent years, the observed antibody sequence space has grown exponentially due to advances in high-throughput sequencing of immune receptors. The rise in sequences has not been mirrored by a rise in structures, as experimental structure determination techniques have remained low-throughput. Computational modeling, however, has the potential to close the sequence–structure gap. To achieve this goal, computational methods must be robust, fast, easy to use, and accurate. Here we report on the latest advances made in RosettaAntibody and Rosetta SnugDock—methods for antibody structure prediction and antibody–antigen docking. We simplified the user interface, expanded and automated the template database, generalized the kinematics of antibody–antigen docking (which enabled modeling of single-domain antibodies) and incorporated new loop modeling techniques. To evaluate the effects of our updates on modeling accuracy, we developed rigorous tests under a new scientific benchmarking framework within Rosetta. Benchmarking revealed that more structurally similar templates could be identified in the updated database and that SnugDock broadened its applicability without losing accuracy. However, there are further advances to be made, including increasing the accuracy and speed of CDR-H3 loop modeling, before computational approaches can accurately model any antibody.
Net reductions in greenhouse gas emissions from feed additive use in California dairy cattle
Authors: Feng Xiaoyu , Kebreab Ermias
Published: May 2020

The livestock industry is one of the main contributors to greenhouse gas emissions and there is an increasing demand for the industry to reduce its carbon footprint. Several studies have shown that feed additives 3-nitroxypropanol and nitrate to be effective in reducing enteric methane emissions. The objective of this study was to estimate the net mitigating effect of using 3-nitroxypropanol and nitrate on total greenhouse gas emissions in California dairy industry. A life cycle assessment approach was used to conduct a cradle-to-farm gate environmental impact analysis based on dairy production system in California. Emissions associated with crop production, feed additive production, enteric methane, farm management, and manure storage were calculated and expressed as kg CO2equivalents (CO2e) per kg of energy corrected milk. The total greenhouse gas emissions from baseline, two 3-nitroxypropanol and three nitrate scenarios were 1.12, 0.993, 0.991, 1.08, 1.07, and 1.09 kg CO2e/kg energy corrected milk. The average net reduction rates for 3-nitroxypropanol and nitrate were 11.7% and 3.95%, respectively. In both cases, using the feed additives on the whole herd slightly improved overall carbon footprint reduction compared to limiting its use during lactation phase. Although both 3-nitroxypropanol and nitrate had effects on decreasing the total greenhouse gas emission, the former was much more effective with no known safety issues in reducing the carbon footprint of dairy production in California.
Genetical control of 2D pattern and depth of the primordial furrow that codes 3D shape of the rhinoceros beetle horn
Authors: Adachi Haruhiko , Matsuda Keisuke , Niimi Teruyuki , Kondo Shigeru , Gotoh Hiroki
Published: May 2020

The head horn of the Asian rhinoceros beetle develops as extensively folded primordia before unfurling into its final 3D shape at the pupal molt. The information of the final 3D structure of the beetle horn is encoded in the folding pattern of the developing primordia. However, the developmental mechanism underlying epithelial folding of the primordia is unknown. In this study, we addressed this gap in our understanding of the developmental patterning of the 3D horn shape of beetles by focusing on the formation of surficial furrows that become the bifurcated 3D shape of the horn. By gene knockdown screening via RNAi, we found that knockdown of the geneNotchdisturbed overall horn primordia furrow depth without affecting 2D furrow pattern. In contrast, knockdown ofCyclinEaltered 2D horn primordia furrow pattern without affecting furrow depth. From these results, depth and 2D pattern of primordial surficial furrow are likely to be regulated independently during the development and both of change can alter the final 3D shape.

Author Summary

In insects, some large structure is made under the old exoskeleton before the molting. Long horn of rhino-beetle is one of extreme cases. The beetle horn is compactly packed as furrowed primordia under the larval exoskeleton. At molting, the primordia is extended to form its final 3D horn shape as blowing up furrows like a balloon. This transformation from primordia to final horn does not required any living cell activities. Thus, characteristics of furrows of primordia actually determine the final 3D shape. However, molecular mechanisms and genetic basis of furrow formation is not well understood not only in beetle horn but also in any other insects. In this study, by using beetle horn as a model, we addressed what kind of genetic factors are contributed to primordial furrow formation. By gene knockdown screening, we found that knockdown of the geneNotchdisturbed primordial furrow depth without affecting 2D furrow pattern. In contrast, knockdown ofCyclinEaltered 2D furrow pattern without affecting furrow depth. In both case, final horn shapes were disturbed. From these results, we concluded that both of the depth and 2D pattern of primordial furrow can contribute final shape, but their development is controlled independently.
Chloroflexi persisting for millions of years in oxic and anoxic deep-sea clay
Authors: Vuillemin Aurèle , Kerrigan Zak , D’Hondt Steven , Orsi William D.
Published: May 2020

Chloroflexi are widespread in energy-limited subseafloor sediments, but how Chloroflexi respond to subseafloor energy limitation under oxic and anoxic conditions is poorly understood. Here, we characterize the diversity, abundance, activity, and metabolic potential of Chloroflexi in oxic and anoxic abyssal clay from three deep-sea cores covering up to 15 million years of sediment deposition, where Chloroflexi are a major component of the community throughout the entire cored sequence at all sites. In oxic red clay at two different sites, Chloroflexi communities exhibit net death over both 10-15 million year cored sequences, and gene expression was below detection despite the availability of oxygen as a high energy electron acceptor, indicating a reduced level of activity. In contrast at the anoxic site, Chloroflexi abundance and gene expression increase below the seafloor and peak in 2 to 3 million year old sediment. The anaerobic subseafloor Chloroflexi exhibited a homoacetogenic metabolism and potential for energetically efficient intracellular H2recycling that have been proposed to confer a fitness advantage in energy-limited subseafloor habitats. Our findings indicate that the expression of this energy efficient metabolism in Chloroflexi coincides with net growth over million year timescales in deep-sea anoxic clay.

Significance statement

Chloroflexi are widespread in energy-limited subseafloor sediments, both in oxic subseafloor sediments that are energetically limited by the availability of electron donors (organic matter) and in anoxic sediments that are energetically limited by the availability of high energy terminal electron acceptors. How Chloroflexi respond to these different forms of energy limitation over long time scales is poorly understood. We present new data that demonstrates how key differences in metabolism are manifested in different communities of aerobic and anaerobic Chloroflexi subsisting over millions of years in oxic and anoxic deep-sea clay. These data provide new insights into how certain Chloroflexi respond to different types of long-term energy limitation.
Predicting the evolution of sexual dimorphism in gene expression
Authors: Houle David , Cheng Changde
Published: May 2020

Sexual dimorphism in gene expression is likely to be the underlying source of dimorphism in a variety of traits. Many analyses implicitly make the assumption that dimorphism only evolves when selection favors different phenotypes in the two sexes, although theory makes clear that it can also evolve as an indirect response to other kinds of selection. Furthermore, previous analyses consider the evolution of a single transcript or trait at a time, ignoring the genetic covariance with other transcripts and traits. We first show which aspects of the genetic-variance covariance matrix,G, affect dimorphism when these assumptions about selection are relaxed. We then reanalyze gene expression data fromDrosophila melanogasterwith these predictions in mind. Dimorphism of gene expression for individual transcripts shows the signature of both direct selection for dimorphism and indirect responses to selection. To account for the effect of measurement error on evolutionary predictions, we estimated aGmatrix for eight linear combinations of expression traits. Sex-specific genetic variances in female- and male-biased transcription, as well as one relatively unbiased combination were quite unequal, ensuring that most forms of selection on these traits will have large effects on dimorphism. Predictions of response to selection based on the wholeGmatrix showed that sexually concordant and antagonistic selection are equally capable of changing sexual dimorphism. In addition, the indirect responses of dimorphism due to cross-trait covariances were quite substantial. The assumption that sexual dimorphism in transcription is an adaptation is likely to be incorrect in many specific cases.
Exploring amino acid functions in a deep mutational landscape
Authors: Dunham Alistair , Beltrao Pedro
Published: May 2020

Amino acids fulfil a diverse range of roles in proteins, each utilising its chemical properties in different ways in different contexts to create required functions. For example, cysteines form disulphide or hydrogen bonds in different circumstances and charged amino acids do not always make use of their charge. The repertoire of amino acid functions and the frequency at which they occur in proteins remains understudied. Measuring large numbers of mutational consequences, which can elucidate the role an amino acid plays, was prohibitively time consuming until recent developments in deep mutational scanning. In this study we gathered data from 28 deep mutational scanning studies, covering 6291 positions in 30 proteins, and used the consequences of mutation at each position to define a mutational landscape. We demonstrated rich relationships between this landscape and biophysical or evolutionary properties. Finally, we identified 100 functional amino acid subtypes with a data-driven clustering analysis and studied their features, including their frequencies and chemical properties such as tolerating polarity, hydrophobicity or being intolerant of charge or specific amino acids. The mutational landscape and amino acid subtypes provide a foundational catalogue of amino acid functional diversity, which will be refined as the number of studied protein positions increases.
The effect of autophagy and mitochondrial fission on Harderian gland is greater than apoptosis in male hamsters during different photoperiods
Authors: Wang Zhe , Xu Jin-Hui , Mou Jun-Jie , Zhao Xiang-Yu , Geng Xiao-Cui , Wu Ming , Xue Hui-Liang , Lei-Chen  , Xu Lai-Xiang
Published: May 2020

Photoperiod is an important factor of mammalian seasonal rhythm. We studied the morphological differences in HG which is a vital photosensitive organ of male striped dwarf hamsters (Cricetulus barabensis), under different photoperiods (short photoperiod, SP; moderate photoperiod, MP; long photoperiod, LP), and further investigated the molecular mechanisms related to these morphological differences. Results showed that body weight, carcass weight, and HG weight were lower in SP and LP. Protein expression of bax/bcl2 and Cytochrome C showed no significant differences, indicating that the level of apoptosis remained stable. Protein aggregation of LC3 and protein expression of LC3II/LC3I were higher in SP than. Furthermore, comparison of changes in the HG ultrastructure demonstrated autolysosome formation in the LP, which suggesting the lowest autophagy level in MP. Protein expression levels of ATP synthase and mitochondrial fission factor were highest in the MP, whereas citrate synthase, dynamin-related protein1, and fission1 remained unchanged in three groups. In summary, the significant up-regulation of autophagy under short and long photoperiod may be the main factor leading to the loss of HG weight and reduced mitochondrial energy supply.
Gene regulation gravitates towards either addition or multiplication when combining the effects of two signals
Authors: Sanford Eric M. , Emert Benjamin L. , Coté Allison , Raj Arjun
Published: May 2020

Signals often ultimately affect the transcription of genes, and often, two different signals can affect the transcription of the same gene. In such cases, it is natural to ask how the combined transcriptional response compares to the individual responses. Mechanistic models can predict a range of combined responses, with the most commonly applied models predicting additive or multiplicative responses, but systematic genome-wide evaluation of these predictions are not available. Here, we performed a comprehensive analysis of the transcriptional response of human MCF-7 cells to two different signals (retinoic acid and TGF-β), applied individually and in combination. We found that the combined responses exhibited a range of behaviors, but clearly favored both additive and multiplicative combined transcriptional responses. We also performed paired chromatin accessibility measurements to measure putative transcription factor occupancy at regulatory elements near these genes. We found that increases in chromatin accessibility were largely additive, meaning that the combined accessibility response was the sum of the accessibility responses to each signal individually. We found some association between super-additivity of accessibility and multiplicative or super-multiplicative combined transcriptional responses, while sub-additivity of accessibility associated with additive transcriptional responses. Our findings suggest that mechanistic models of combined transcriptional regulation must be able to reproduce a range of behaviors.
Plasmodium falciparumReplication factor C subunit 1 is involved in genotoxic stress response
Authors: Sheriff O , Aniweh Y , Lai Soak-Kuan , Loo HL , Sze S. K , Preiser PR
Published: May 2020

About half the world’s population is at risk of malaria, withPlasmodium falciparummalaria being responsible for the most malaria related deaths globally. Antimalarial drugs such as chloroquine and artemisinin are directed towards the proliferating intra-erythrocytic stages of the parasite, which is responsible for all the clinical symptoms of the disease. These antimalarial drugs have been reported to function via multiple pathways, one of which induces DNA damage via the generation of free radicals and reactive oxygen species. An urgent need to understand the mechanistic details of drug response and resistance is highlighted by the decreasing clinical efficacy of the front line drug, Artemisinin.

The replication factor C subunit 1 protein is an important component of the DNA replication machinery and DNA damage response mechanism. Here we show the translocation of PfRFC1 from an intranuclear localization to the nuclear periphery indicating an orchestrated progression of distinct patterns of replication in the developing parasites. PfRFC1 responds to genotoxic stress via elevated protein levels in soluble and chromatin bound fractions.

Reduction of PfRFC1 protein levels upon treatment with antimalarials suggests an interplay of replication and DNA repair pathways leading to cell death. Additionally, mislocalization of the endogenously tagged protein confirmed its essential role in parasites’ replication and DNA repair. This study provides key insights into DNA replication, DNA damage response and cell death inplasmodium falciparum.

Importance

Frontline drugs have been found to induce DNA damage in the human malaria parasitePlasmodium falciparum.The genotoxic stress response inPlasmodiumand the interplay between DNA damage repair, replication and activation of programmed cell death pathways remains largely undescribed. This study shows a distinct pattern of localization of PfRFC1 during replication and DNA repair. PfRFC1 responds to genotoxic stress with an increase in protein expression. Interfering with the RFC complex formation or mislocalization of PfRFC1 is associated with disrupted genotoxic stress response. Additionally, a reduction of PfRFC1 protein levels is observed upon treatment with antimalarial drugs or under apoptosis like conditions, highlighting the role of DEVD/G like motif in mediating programmed cell death in these parasites. This study sheds light on the role of PfRFC1 in differentially responding to replication, genotoxic stress and programmed cell death inPlasmodiumparasites.
Rapid assessment of the impact of lockdown on the COVID-19 epidemic in Portugal
Authors: Ricoca Peixoto Vasco , Vieira Andre , Aguiar Pedro , Carvalho Carlos , Thomas Daniel , Abrantes Alexandre
Published: May 2020

Background: Portugal took early action to control the COVID19 epidemic, imposing a lockdown on March 16 when it recorded only 62 cases of COVID-19 per million inhabitants and no reported deaths. The Portuguese people complied quickly, reducing their overall mobility by 80% . We estimate the impact of the lockdown in Portugal in terms of reducing burden on the health service.
Methods: Using publicly available official data from the Portuguese Directorate-General of Health we forecasted epidemic curves for: Cases, hospital inpatients (overall and in ICU), and deaths without lockdown, assuming that the impact of containment measures would start 14 days after lockdown was implemented. We used exponential smoothing models for deaths, intensive care (ICU) and hospitalizations and an ARIMA model for number of cases. Models were selected considering fitness to the observed data to the 31st of March 2020. We then compared observed(with intervention) and forecasted curves( without intervention).
Results: Between April 1 and April 15, there were 146 fewer deaths(-25%), 5568 fewer cases (-23%) and, as of April 15, there were 519 fewer ICU inpatients(-69%) and 508 fewer overall hospital inpatients(-28%) than forecasted without lockdown. On April 15 the number of ICU inpatients could have reached 748, three times higher than the observed value (229) if the intervention had been delayed.
Conclusion: If the lockdown had not been implemented in mid-March, Portugal ICU capacity (528 ICU beds) would likely have been breached in the first half of April. The lockdown seems to have been effective in reducing transmission of SARS-Cov-2, serious Covid-19 illness and associated mortality, thereby decreasing demand on health services. Early action allowed time for the National Health Service to acquire protective equipment, to increase capacity to test and cope with the surge in hospital and ICU demand caused by the pandemic.
Phenol-chloroform-based RNA purification for detection of SARS-CoV-2 by RT-qPCR: comparison with automated systems
Authors: Dimke Henrik , Larsen Sanne L , Skov Marianne N , Larsen Hanne , Hartmeyer Gitte N , Moeller Jesper B
Published: May 2020

The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly reached pandemic levels. Sufficient testing for SARS-CoV-2 remains essential for tracking and containing the rapid spread of the virus. However, due to increased global demand, kits and proprietary reagents for RNA extraction are limited, which markedly reduce SARS-CoV-2 testing capabilities in many countries. Here, we explore the use of conventional acid guanidinium thiocyanate-phenol-chloroform (AGPC)-based RNA purification as an alternative to commercial automated systems for detection of SARS-CoV-2 by RT-qPCR. 87 clinical oropharyngeal or nasopharyngeal swab specimens were extracted by AGPC and compared to the commercial platforms, the Maxwell® RSC 48 instrument for automated RNA extraction and the fully integrated diagnostic system, the Cobas®6800 apparatus. Our results show that RNA extracted using the AGPC method is fully comparable to modern automated systems regarding analytical sensitivity, specificity and accuracy with respect to detection of SARS-CoV-2 as evaluated by RT-qPCR. Moreover, we find that the AGPC method is easily scalable and implemented in conventional laboratories. Taken together, these data identify conventional AGPC-based RNA extraction as a low cost and suitable alternative to automated systems for the detection of SARS-CoV-2, when automated systems, kits and reagents are not readily available.
COVID-19: The unreasonable effectiveness of simple models
Authors: Carletti Timoteo , Fanelli Duccio , Piazza Francesco
Published: May 2020

When the novel coronavirus disease SARS-CoV2 (COVID-19) was officially declared a pandemic by the WHO in March 2020, the scientific community had already braced up in the effort of making sense of the fast-growing wealth of data gathered by national authorities all over the world. However, despite the diversity of novel theoretical approaches and the comprehensiveness of many widely established models, the official figures that recount the course of the outbreak still sketch a largely elusive and intimidating picture. Here we show unambiguously that the dynamics of the COVID-19 outbreak belongs to the simple universality class of the SIR model and extensions thereof. Our analysis naturally leads us to establish that there exists a fundamental limitation to any theoretical approach, namely the unpredictable non-stationarity of the testing frames behind the reported figures. However, we show how such bias can be quantified self-consistently and employed to mine useful and accurate information from the data. In particular, we describe how the time evolution of the reporting rates controls the occurrence of the apparent epidemic peak, which typically follows the true one in countries that were not vigorous enough in their testing at the onset of the outbreak. The importance of testing early and resolutely appears as a natural corollary of our analysis, as countries that tested massively at the start clearly had their true peak earlier and less deaths overall.
Differentiating COVID-19 from other types of pneumonia with convolutional neural networks
Authors: Ozsahin Ilker , Onyebuchi Confidence , Sekeroglu Boran
Published: May 2020

INTRODUCTION

A widely-used method for diagnosing COVID-19 is the nucleic acid test based on real-time reverse transcriptase-polymerase chain reaction (RT-PCR). However, the sensitivity of real time RT-PCR tests is low and it can take up to 8 hours to receive the test results. Radiologic methods can provide higher sensitivity. The aim of this study is to investigate the use of X-ray and convolutional neural networks for the diagnosis of COVID-19 and to differentiate it from viral and/or bacterial pneumonia, as 2-class (bacterial pneumonia vs COVID-19 and viral pneumonia vs COVID-19) and 3- class (bacterial pneumonia, COVID-19, and healthy group (BCH), and among viral pneumonia, COVID- 19, and healthy group (VCH)) experiments.

METHODS

225 COVID-19, 1,583 healthy control, 2,780 bacterial pneumonia, and 1,493 viral pneumonia chest X-ray images were used. 2-class- and 3-class-experiments were performed with different convolutional neural network (ConvNet) architectures, with different variations of convolutional layers and fully-connected layers.

RESULTS

The results showed that bacterial pneumonia vs COVID-19 and viral pneumonia vs COVID- 19 reached a mean ROC AUC of 97.32% and 96.80%, respectively. In the 3-class-experiments, macro-average F1 scores of 95.79% and 94.59% were obtained in terms of detecting COVID-19 among BCH and VCH, respectively.

CONCLUSIONS

The ConvNet was able to distinguish the COVID-19 images among non-COVID-19 images, namely bacterial and viral pneumonia as well as normal X-ray images.
Takagi–Taupin dynamical X-ray diffraction simulations of asymmetric X-ray diffraction from crystals: the effects of surface undulations
Authors: Macrander Albert
Published: May 2020

Dynamical X-ray diffraction simulations from crystals with surface undulations are reported. The Takagi–Taupin equations are applied and used to derive results in good agreement with experimental data reported in a separate paper [Macrander, Pereira, Huang, Kasman, Qian, Wojcik & Assoufid (2020). J. Appl. Cryst.
53, 789–792]. The development of Uragami [J. Phys. Soc. Jpn, (1969), 27, 147–154] is followed. Although previous work by Olekhnovich & Olekhnovich [Acta. Cryst. (1980), A36, 22–27] treated a crystal in the shape of a round cylinder, there do not seem to be any reports of previous dynamical X-ray diffraction treatments specifically for surface undulations. The significance of the present work is that it bridges the diffraction treatment of more classical dynamical diffraction theory, which assumes a flat surface, and the simple kinematic diffraction theory. The kinematic theory has, to date, been the primary means of simulating X-ray diffraction from surfaces.
Doctoral Apprenticeships and the “ladder of opportunity”
Authors: Senior Rowena , Cleaver Elizabeth , Queiros Gilmar , King Helen , Barnett Kirstin
Published: May 2020

Purpose

This discussion paper supports the new development of Apprenticeships at Level 8 of the UK’s Framework for Higher Education Qualifications (QAA, 2014). This exciting development, one that employers and universities had been waiting for paves the way for, apprenticeships, sold as the ladder of opportunity, to go all the way to the top.

Design/methodology/approach

Here, we explore in brief the emergence of the new apprenticeship landscape and the importance of the addition of this new highest of levels.

Findings

Importantly, however, we make the case that such progress needs to be met with an equally progressive approach to the design of the new doctoral pathway.

Research limitations/implications

We sketch out a possible shell for the assessment of a Doctoral Apprenticeship, one that allows for flexible occupationally relevant inputs to create an applicable role-based and academically rigourous whole.

Originality/value

The importance of such a design is discussed within the context of the potential for impact in three priority areas: social justice, broadening the talent pool and ensuring the relevance and sustainability of the doctoral award.
Increasing sustainable consumption: message framing and in-store technology
Authors: Jäger Anna-Katharina , Weber Anja
Published: May 2020

Purpose

This study investigates the potential of two different digital in-store technologies and advertisement message framings according to the construal-level theory for increasing sustainable consumption. This paper aims to provide managerial implications for the promotion of sustainable products at the point of sale as well as to theoretically contribute by integrating the literature streams of perceptual research, point-of-sale marketing and construal-level theory.

Design/methodology/approach

The authors tested their hypotheses in a two-week field experiment with a 2 (product label: organic vs local) × 2 (message framing: high vs low construal level) × 2 (presentation technology: digital signage vs augmented reality) between-subjects factorial design. The study was conducted in two grocery stores of different sizes using milk as a test product. Purchase data, as well as attention data gathered by facial recognition software, were analyzed.

Findings

Even though the magic mirror augmented reality application attracted significantly more attention, it did not significantly boost sales compared to the digital signage technology. In the larger store, the sales of the advertised sustainable products were significantly higher in both technology conditions than in the control condition without advertisement. If consumers pay enough attention to the promotion, results indicate that using messages with a concrete low-level construal is more useful for organic goods.

Originality/value

This study is the first investigating a combination of in-store technology and construal-level message framing for the promotion of sustainable products. It extends the retailing literature by proposing a two-step approach on how to use in-store technology effectively: (1) gaining attention and (2) matching messages to existing cognitions.
IMP: it’s time to get emotional! Understanding the role of negative emotions in dynamic decision-making processes
Authors: Koporcic Nikolina , Nietola Miika , Nicholson John D.
Published: May 2020

Purpose

The purpose of this paper is to investigate the current industrial marketing and purchasing (IMP) research that has a vague positioning of the bounded rationality of an actor. By borrowing insights from other disciplines, this study aims to develop the IMP approach further by acknowledging the importance of individuals who act and make decisions on behalf of their companies.

Design/methodology/approach

This study is conceptual. By examining the IMP studies in combination with decision-making literature from behavioral economics and psychology, this paper provides a new understanding of the phenomenon in question.

Findings

This study demonstrates that individual decision-making is not as rational as has previously been thought, thus indicating the bounded rationality of the actor. After examining the most common negative emotions that influence the decision-making process, the paper presents a research agenda. It provides a series of research topics and methodological choices for future IMP research endeavors.

Research limitations/implications

As this paper is conceptual, empirical research is needed to examine the role of negative emotions in dynamic decision-making processes.

Practical implications

Managerial implications of this paper are focused on providing instructions for managers on how to deal with negative emotions in dynamic decision-making processes.

Originality/value

To the best of the authors’ knowledge, this paper is one of the first papers that attempts to connect the IMP studies with the dynamics of decision-making by examining negative emotions in the business world.
Question your teaspoons: tea-drinking, coping and commercialisation across three planning organisations
Authors: Schoneboom Abigail , Slade Jason
Published: May 2020

Purpose

As part of a wider ethnographic project that examines the significance of the public interest across three public and private sector UK planning organisations, this paper uses tea-drinking as a lens to understand structural forces around outsourcing and commercialisation. Reflecting across the five case studies, the analysis supports Burawoy's (2017) recent critique of Desmond's Relational Ethnography (2014). Using Perec's (1997[1973]) notion of the “infra-ordinary” as an anchor, it highlights the insight that arises from an intimate focus on mundane rituals and artefacts.

Design/methodology/approach

The data were gathered through participant observation, chronicling the researchers' encounters with tea in each of the sites. A respondent-led photography exercise was successful at two sites. Up to 40 days of ethnographic fieldwork were carried out in each site.

Findings

The tea-drinking narratives, while providing an intact description of discrete case study sites, exist in conversation with each other, providing an opportunity for comparison that informs the analysis and helping us to understand the meaning-making process of the planners both in and across these contexts.

Originality/value

The paper contributes to critical planning literature (Murphy and Fox-Rogers, 2015; Raco et al., 2016), illuminating structural forces around outsourcing and commercialisation. It also generates methodological reflection on using an everyday activity to probe organisational culture and promote critical reflection on “weighty” issues across study sites.
Member and structural fragility of reinforced concrete structure under fire
Authors: Chaudhary Ranjit Kumar , Roy Tathagata , Matsagar Vasant
Published: May 2020

Purpose

Despite recognizing the significance of risk-based frameworks in fire safety engineering, the usual approach in structural fire design is largely member/component level, wherein effect of uncertainties influencing the fire resistance of structures are not explicitly considered. In this context, a probabilistic framework is presented to investigate the vulnerability of a reinforced concrete (RC) members and structure under fire loading scenario.

Design/methodology/approach

The RC structures exposed to fire are modeled in a finite element (FE) platform incorporating material and geometric nonlinearity, in which the transient thermo-mechanical analysis is carried out by suitably incorporating the temperature variation of thermal and mechanical properties of both concrete and steel rebar. The stochasticity in the system is considered in structural resistance, thermal and fire model parameters, and the subsequent fragility curves are developed considering threshold limit state of deflection.

Findings

The fire resistance of RC structure is reported to be significantly lower in comparison to the RC members, thereby illustrating the current prescriptive design approaches based on studies of structural member behavior to be crucial from a safety and reliability point of view.

Practical implications

The framework developed for the vulnerability assessment of RC structures under fire hazard through FE analysis can be effectively used to estimate the structural fire resistance for other similar structure to enhance safety and reliability of structures under such extreme threats.

Originality/value

The paper proposes a novel methodology for vulnerability assessment of three-dimensional RC structures under fire hazard through FE analysis and provides comparison of the structural fragility with fragility developed for structural members. Moreover, the research emphasizes to assume 3D behavior of the structure rather than the approximate 2D behavior.
Contemporary architecture of Cairo (1990–2020): mutational plurality of “ISMS”, decolonialism, and cosmopolitanism
Authors: El-Ashmouni Marwa M. , Salama Ashraf M.
Published: May 2020

Purpose

The purpose of this paper is to develop an analytical account on the contemporary architecture of Cairo with emphasis on the past three decades, from the early 1990s to the present. The paper critically analyses narratives of the plurality of “isms”, within architectural vocabulary and discourse, that resulted from the contextual particularities that shaped it.

Design/methodology/approach

Three lines of inquiry are envisioned as overarching aspects of architecture: the chronological, the interventional and the representational. These discussions are underpinned by the discourse of decolonialisation and cosmopolitanism, posited sequentially by Frantz Fanon in The Wretched of the Earth (1961), and Ulrich Beck in The Cosmopolitan Vision (2004). The analysis expands to interrogate these two notions as prelude for reflecting on representations of selected projects: The Smart Village (2001); the Great Egyptian Museum (2002), Al-Azhar Park (2005), American University in Cairo New Campus (2008/2009), and the New Administrative Capital (2018).

Findings

The investigation on the interventional and the representational levels via aspects of discursivity and contradictions highlights that decolonisation and cosmopolitanism are two inseparable facets in the architectural practice in Egypt’s 21st century. These indivisible notions are based on idiosyncratic core to human experience, which emerged from concurrent overturning historical and secular everyday life striving to suppress ideological supremacy.

Research limitations/implications

Further detailed examples can be developed to offer discerning elucidations relevant to both notions of cosmopolitanism and decolonialisation.

Originality/value

The paper offers novel theoretical analysis of Cairo’s most recent architecture. The reflection on the notions of decolonialisation and cosmopolitanism is a timely example of the complex cultural encounters that have shaped the Egyptian architecture, given the recent interventions by the “Modern State” that legitimised such notions.
Characterization of PfiT/PfiA toxin–antitoxin system of Pseudomonas aeruginosa that affects cell elongation and prophage induction
Authors: Zander Itzhak , Shmidov Ester , Roth Shira , Ben‐David Yossi , Shoval Irit , Shoshani Sivan , Danielli Amos , Banin Ehud
Published: May 2020

Toxin–antitoxin (TA) systems are small genetic modules usually consisting of two elements—a toxin and an antitoxin. The abundance of TA systems among various bacterial strains may indicate an important evolutionary role. Pseudomonas aeruginosa, which can be found in a variety of niches in nature, is an opportunistic pathogen for various hosts. While P. aeruginosa strains are very versatile and diverse, only a few TA systems were characterized in this species. Here, we describe a newly characterized TA system in P. aeruginosa that is encoded within the filamentous Pf4 prophage. This system, named PfiT/PfiA, is a homologue of the ParE/YefM TA system. It is a type II TA system, in which the antitoxin is a protein that binds the toxic protein and eliminates the toxic effect. PfiT/PfiA carries several typical type II characteristics. Specifically, it constitutes two small genes expressed in a single operon, PfiT inhibits growth and PfiA eliminates this effect, PfiA binds PfiT, and PfiT expression results in elongated cells. Finally, we assigned a novel function to this TA system, where an imbalance between PfiT and PfiA, favouring the toxin, resulted in cell elongation and an increase in virion production.
Mind the channel! An affordance perspective on how digital voice channels encourage or discourage employee voice
Authors: Ellmer Markus , Reichel Astrid
Published: May 2020

We apply an affordance lens on qualitative data from three case organisations using a digital voice channel providing employees with the opportunity to speak up via answering periodic mini‐surveys and making comments in an anonymous mini‐forum. We find that imbrications of material and social agencies (i.e., the voice channel's features and managerial reactions to voice) in the respective organisational contexts culminate in employees perceiving the channel as either affording or constraining voice, leading to perceived voice outcomes that eventually encourage or discourage them to speak up. Whether voice is encouraged or discouraged partly results from the mere interaction between employees and the digital voice channel independent of managerial reactions. Our findings thus challenge the emphasis on managerial behaviour and reactions to voice in explaining voice behaviour and outcomes in extant literature.
An investigation of micronutrient supplementation in weaner lambs to improve growth rates in southeast Australia
Authors: Rast L , Hernández‐Jover M , Martin S , Abuelo A
Published: May 2020

Objective

A producer survey by questionnaire assessed supplements used in sheep and reasons for use. This was followed by field trials on eight sheep properties in SE NSW to determine the effect of commonly used commercially available supplements on growth rates of Merino and crossbred lambs.

Design

On each property, 450 lambs were selected at weaning and randomly allocated to nine groups of 50 sheep (eight treatment and a control group). Supplements were applied as per manufacturer's recommendation every 6–12 weeks. At each application, all sheep were weighed and data on general flock health and management were collected.

Results

All but one of the survey respondents (n = 77) had used supplements in their sheep at some stage. The reasons for use were most commonly for general health and production benefits (n = 21; 26.9%) and to prevent or treat specific diseases/deficiencies (n = 7; 9.0%).

The average daily weight gains (ADWG) of the lambs over the trial period varied from 0.074 kg to 0.213 kg/head/day. Statistical analysis showed that overall there was not a significant difference (P = 0.587) between ADWG among lambs that received supplements and lambs that did not.

Conclusion

Results of this study show that application of supplements were not linked to improved growth rates in clinically normal crossbred and Merino lambs under the trial farm conditions between weaning and 15 months of age. Effects of supplements on health and production in adult sheep and how supplement response can be best measured in sheep flocks (especially in relation to health and welfare) and linked to productivity requires further investigation.