bluuebunny/crossref_metadata_2025 huggingface dataset:
Some people just want to watch the world burn: the prevalence, psychology and politics of the ‘Need for Chaos’
Authors: Arceneaux Kevin , Gravelle Timothy B. , Osmundsen Mathias , Petersen Michael Bang , Reifler Jason , Scotto Thomas J.
Published: February 2021

People form political attitudes to serve psychological needs. Recent research shows that some individuals have a strong desire to incite chaos when they perceive themselves to be marginalized by society. These individuals tend to see chaos as a way to invert the power structure and gain social status in the process. Analysing data drawn from large-scale representative surveys conducted in Australia, Canada, the United Kingdom and the United States, we identify the prevalence of
Need for Chaos
across Anglo-Saxon societies. Using Latent Profile Analysis, we explore whether different subtypes underlie the uni-dimensional construct and find evidence that some people may be motivated to seek out chaos because they want to rebuild society, while others enjoy destruction for its own sake. We demonstrate that chaos-seekers are not a unified political group but a divergent set of malcontents. Multiple pathways can lead individuals to ‘want to watch the world burn’.

This article is part of the theme issue ‘The political brain: neurocognitive and computational mechanisms’.
Bringing political psychology into the study of populism
Authors: Rovira Kaltwasser Cristóbal
Published: February 2021

Although it is true that populism is a contested concept in the social sciences, there is increasing consensus around the use of an ideational definition of populism within the political science literature. This definition has the advantage of providing a clear concept that can be employed to empirically study not only the supply side but also the demand side of the populist phenomenon. Not by chance, an increasing number of scholars are working with a set of survey items to measure the presence and relevance of populist ideas at the mass level, something that is usually conceived of as populist attitudes. Despite the incremental study of populist attitudes in political science, only very limited links with the political psychology literature have been established so far. In this short piece, I address this shortcoming by discussing two avenues for further research on populism that seek to promote much-needed dialogue between comparative politics and political psychology: political identities and conspiracy theories.

This article is part of the theme issue ‘The political brain: neurocognitive and computational mechanisms’.
The cognitive and perceptual correlates of ideological attitudes: a data-driven approach
Authors: Zmigrod Leor , Eisenberg Ian W. , Bissett Patrick G. , Robbins Trevor W. , Poldrack Russell A.
Published: February 2021

Although human existence is enveloped by ideologies, remarkably little is understood about the relationships between ideological attitudes and psychological traits. Even less is known about how cognitive dispositions—individual differences in how information is perceived and processed— sculpt individuals' ideological worldviews, proclivities for extremist beliefs and resistance (or receptivity) to evidence. Using an unprecedented number of cognitive tasks (
n
= 37) and personality surveys (
n
= 22), along with data-driven analyses including drift-diffusion and Bayesian modelling, we uncovered the specific psychological signatures of political, nationalistic, religious and dogmatic beliefs. Cognitive and personality assessments consistently outperformed demographic predictors in accounting for individual differences in ideological preferences by 4 to 15-fold. Furthermore, data-driven analyses revealed that individuals’ ideological attitudes mirrored their cognitive decision-making strategies. Conservatism and nationalism were related to greater caution in perceptual decision-making tasks and to reduced strategic information processing, while dogmatism was associated with slower evidence accumulation and impulsive tendencies. Religiosity was implicated in heightened agreeableness and risk perception. Extreme pro-group attitudes, including violence endorsement against outgroups, were linked to poorer working memory, slower perceptual strategies, and tendencies towards impulsivity and sensation-seeking—reflecting overlaps with the psychological profiles of conservatism and dogmatism. Cognitive and personality signatures were also generated for ideologies such as authoritarianism, system justification, social dominance orientation, patriotism and receptivity to evidence or alternative viewpoints; elucidating their underpinnings and highlighting avenues for future research. Together these findings suggest that ideological worldviews may be reflective of low-level perceptual and cognitive functions.

This article is part of the theme issue ‘The political brain: neurocognitive and computational mechanisms’.
Frischella japonica sp. nov., an anaerobic member of the Orbales in the Gammaproteobacteria, isolated from the gut of the eastern honey bee, Apis cerana japonica Fabricius
Authors: Wolter Laura A. , Suenami Shota , Miyazaki Ryo
Published: February 2021

The gut of honey bees is characterized by a stable and relatively simple community of bacteria, consisting of seven to ten phylotypes. Two closely related honey bees, Apis mellifera (western honey bee) and Apis cerana (eastern honey bee), show a largely comparable occurrence of those phylotypes, but a distinct set of bacterial species and strains within each bee species. Here, we describe the isolation and characterization of Ac13T, a new species within the rare proteobacterial genus

Frischella

from A. cerana japonica Fabricius. Description of Ac13T as a new species is supported by low identity of the 16S rRNA gene sequence (97.2 %), of the average nucleotide identity based on orthologous genes (77.5 %) and digital DNA–DNA hybridization relatedness (24.7 %) to the next but far related type strain

Frischella perrara

PEB0191T, isolated from A. mellifera. Cells of Ac13T are mesophilic and have a mean length of 2–4 µm and a width of 0.5 µm. Optimal growth was achieved in anoxic conditions, whereas growth was not observed in oxic conditions and strongly reduced in microaerophilic environment. Strain Ac13T shares several features with other members of the

Orbaceae

, such as the major fatty acid profile, the respiratory quinone type and relatively low DNA G+C content, in accordance with its evolutionary relationship. Unlike

F. perrara

, strain Ac13T is susceptible to a broad range of antibiotics, which could be indicative for an antibiotic-free A. cerana bee keeping. In conclusion, we propose strain Ac13T as a novel species for which we propose the name Frischella japonica sp. nov. with the type strain Ac13T (=NCIMB 15259=JCM 34075).
Sequencing individual genomes with recurrent genomic disorder deletions: an approach to characterize genes for autosomal recessive rare disease traits
Authors: Yuan Bo , Schulze Katharina , Batzir Nurit Assia , Sinson Jefferson , Dai Hongzheng , Zhu Wenmiao , Bocanegra Francia , Fong Chin-To , Holder Jimmy , Nguyen Joanne , Schaaf Christian P. , Yang Yaping , Bi Weimin , Eng Christine , Shaw Chad , Lupski James R. , Liu Pengfei
Published: February 2021

In medical genetics, discovery and characterization of disease trait contributory genes and alleles depends on genetic reasoning, study design, and patient ascertainment; we now suggest a segmental haploid genetics approach to enhance gene discovery and molecular diagnostics. We present novel genomic insights to enhance discovery in the challenging context of autosomal recessive (AR) traits and bi-allelic variation. We demonstrate computationally that new mutation mediated by nonallelic homologous recombination (NAHR), involving recurrent deletions at 30 genomic regions, likely drives recessive disease burden for over 70% of loci within these segmental deletions or at least 2% of loci genome wide. Meta-analyses of literature-reported patients implicate that NAHR-deletions are depleted from the ascertained pool of AR trait alleles. Exome reanalysis of personal genomes from subjects harboring recurrent deletions uncovered new disease-contributing variants in genes includingCOX10,ERCC6, PRRT2andOTUD7A. Our data demonstrate that genomic sequencing of personal genomes with NAHR-deletions could dramatically foment allele and gene discovery, enhance clinical molecular diagnosis, and could potentially enable human haploid genetics screens as an approach to disease biology.
Patient prioritisation methods to shorten waiting times for elective surgery: a systematic review of how to improve access to surgery
Authors: Rathnayake Dimuthu , Clarke Mike , Jayasinghe Viraj
Published: February 2021

Background

Concern about long waiting times for elective surgeries is not a recent phenomenon, but it has been heightened by the impact of the COVID-19 pandemic and its associated measures. One way to alleviate the problem might be to use prioritisation methods for patients on the waiting list and a wide range of research is available on such methods. However, significant variations and inconsistencies have been reported in prioritisation protocols from various specialties, institutions, and health systems. To bridge the evidence gap in existing literature, this comprehensive systematic review will synthesise global evidence on policy strategies with a unique insight to patient prioritisation methods to reduce waiting times for elective surgeries. This will provide evidence that might help with the tremendous burden of surgical disease that is now apparent in many countries because of operations that were delayed or cancelled due to the COVID-19 pandemic and inform policy for sustainable healthcare management systems.

Methods

We searched PubMed, EMBASE, SCOPUS, Web of Science, and the Cochrane Library, with our most recent searches in January 2020. Articles published after 2013 on major elective surgery lists of adult patients were eligible, but cancer and cancer-related surgeries were excluded. Both randomised and non-randomised studies were eligible and the quality of studies was assessed with ROBINS-I and CASP tools. We registered the review in PROSPERO (CRD42019158455) and reported it in accordance with the PRISMA statement.

Results

The electronic search in five bibliographic databases yielded 7543 records (PubMed, EMBASE, SCOPUS, Web of Science, and Cochrane) and 17 eligible articles were identified in the screening. There were four quasi-experimental studies, 11 observational studies and two systematic reviews. These demonstrated moderate to low risk of bias in their research methods. Three studies tested generic approaches using common prioritisation systems for all elective surgeries in common. The other studies assessed specific prioritisation approaches for re-ordering the waiting list for a particular surgical specialty.

Conclusions

Explicit prioritisation tools with a standardised scoring system based on clear evidence-based criteria are likely to reduce waiting times and improve equitable access to health care. Multiple attributes need to be considered in defining a fair prioritisation system to overcome limitations with local variations and discriminations. Collating evidence from a diverse body of research provides a single framework to improve the quality and efficiency of elective surgical care provision in a variety of health settings. Universal prioritisation tools with vertical and horizontal equity would help with re-ordering patients on waiting lists for elective surgery and reduce waiting times.
Nanoscale Dynamics of Cellulase TrCel7A Digesting Cellulose
Authors: Haviland Zachary K. , Nong Daguan , Vasquez Kuntz Kate L. , Starr Thomas J. , Ma Dengbo , Tien Ming , Anderson Charles T. , Hancock William O.
Published: February 2021

Understanding how cellulases catalyze the digestion of lignocellulose is a major goal of bioenergy research. Cel7A fromTrichoderma reeseiis a model exoglucanase that degrades cellulose strands from their reducing ends by processively cleaving individual cellobiose units. Despite being one of the most studied cellulases, the binding and hydrolysis mechanisms of Cel7A are still debated. We used single-molecule tracking to analyze the dynamics of 11,116 quantum dot-labeledTrCel7A binding to and moving processively along immobilizedGluconoacetobactercellulose. Enzyme molecules were localized with a spatial precision of a few nanometers and followed for hundreds of seconds. Most enzymes bound into a static state and dissociated without detectable movement. Processive enzymes moved an average distance of 39 nm at an average speed of 3.2 nm/s. Static binding episodes preceding and following processive runs were of similar duration to static binding events that lacked any processive movement. Transient jumps of >20 nm were observed, but no diffusive behavior indicative of a diffusive search of the enzyme for a free cellulose strand end was observed. These data were integrated into a three-state model in whichTrCel7A molecules can bind from solution into either a static or a processive state, and can reversibly switch between static and processive states before dissociating. From these results, we conclude that the rate-limiting step for cellulose degradation by Cel7A is the transition out of the static state either by dissociation from the cellulose surface or initiation of a processive run.
Investigating the chemolithoautotrophic and formate metabolism ofNitrospira moscoviensisby constraint-based metabolic modeling and13C-tracer analysis
Authors: Lawson Christopher E. , Mundinger Aniela B. , Koch Hanna , Jacobson Tyler B. , Weathersby Coty A. , Jetten Mike S. M. , Pabst Martin , Amador-Noguez Daniel , Noguera Daniel R. , McMahon Katherine , Lücker Sebastian
Published: February 2021

Nitrite-oxidizing bacteria belonging to the genusNitrospiramediate a key step in nitrification and play important roles in the biogeochemical nitrogen cycle and wastewater treatment. While these organisms have recently been shown to exhibit metabolic flexibility beyond their chemolithoautotrophic lifestyle, including the use of simple organic compounds to fuel their energy metabolism, the metabolic networks controlling their autotrophic and mixotrophic growth remain poorly understood. Here, we reconstructed a genome-scale metabolic model forNitrospira moscoviensis(iNmo686) and used constraint-based analysis to evaluate the metabolic networks controlling autotrophic and formatotrophic growth on nitrite and formate, respectively. Subsequently, proteomic analysis and13C-tracer experiments with bicarbonate and formate coupled to metabolomic analysis were performed to experimentally validate model predictions. Our findings support thatN. moscoviensisuses the reductive tricarboxylic acid cycle for CO2fixation. We also show thatN. moscoviensiscan indirectly use formate as a carbon source by oxidizing it first to CO2followed by reassimilation, rather than direct incorporation via the reductive glycine pathway. Our study offers the first measurements ofNitrospira’s in vivocentral carbon metabolism and provides a quantitative tool that can be used for understanding and predicting their metabolic processes.

Importance

Nitrospiraare globally abundant nitrifying bacteria in soil and aquatic ecosystems and wastewater treatment plants, where they control the oxidation of nitrite to nitrate. Despite their critical contribution to nitrogen cycling across diverse environments, detailed understanding of their metabolic network and prediction of their function under different environmental conditions remains a major challenge. Here, we provide the first constraint-based metabolic model ofN. moscoviensisrepresenting the ubiquitousNitrospiralineage II and subsequently validate this model using proteomics and13C-tracers combined with intracellular metabolomic analysis. The resulting genome-scale model will serve as a knowledge base ofNitrospirametabolism and lays the foundation for quantitative systems biology studies of these globally important nitrite- oxidizing bacteria.
SARS-CoV-2 serostatus of healthcare worker in the Austrian state Vorarlberg between June 2020 and January 2021
Authors: Atzl Michele , Muendlein Axel , Winder Thomas , Fraunberger Peter , Brandtner Eva-Maria , Geiger Kathrin , Klausberger Miriam , Duerkop Mark , Sprenger Lukas , Mutschlechner Beatrix , Volgger Andreas , Benda Magdalena , Severgnini Luciano , Jaeger Johannes B. , Drexel Heinz , Lang Alois , Leiherer Andreas
Published: February 2021

Background

Austria, and particularly its westernmost federal state Vorarlberg, developed an extremely high COVID-19 incidence rate in November 2020. Health care workers (HCW) may be at higher risk of contracting the disease within the working environment and therefore the seroprevalence in this population is of particular interest. Here, we analyzed SARS-CoV-2-specific antibody response in Vorarlberg HCW in a prospective cohort study.

Methods

A total of 395 HCW have been tested at three different time points for the prevalence of anti-SARS-CoV-2 IgG antibodies specific for NP and RBD. Enrollment started in June 2020 (t1), two months after the end of the first wave. Re-testing took place between October to November at the beginning of the second wave (t2), and again at the end of the second wave in January 2021 (t3).

Results

At t1, 3% of HCW showed a strong IgG-specific responses to either NP or RBD. At t2, the rate increased to 4%, and after the second wave in January 2021, 14% had a strong response, which was assessed to be stable for up to ten months. The amount of HCW with anti-SARS-CoV-2 IgG antibodies was 38% higher than the number of infections found by RT-PCR.

Conclusion

We found low numbers of SARS-CoV-2-seropositive HCW in a hotspot setting after the first wave but a very high increase during the second massive wave. Though the seroprevalence in HCW was comparable to the general population. Our findings offer support for the routine application of serological testing in management of the ongoing COVID-19 pandemic.

Main summary

A relatively low percentage of 3% SARS-CoV-2 seropositive HCW with strong IgG-specific antibody responses was found in the Austrian federal state Vorarlberg after the first wave increasing to 14% after the second massive wave lasting until January 2021.
Evaluation of VIDAS® diagnostic assay prototypes detecting dengue virus NS1 antigen and anti-dengue virus IgM and IgG antibodies
Authors: Somlor Somphavanh , Brossault Ludovic , Grandadam Marc
Published: February 2021

Dengue is a serious tropical disease caused by the mosquito-borne dengue virus (DENV). Performant, rapid and easy-to-use assays are needed for the accurate diagnosis of acute DENV infection. We evaluated the performance of three prototype assays developed for the VIDAS® automated platform to detect dengue NS1 antigen and anti-dengue IgM and IgG antibodies. Positive and negative agreement with competitor enzyme-linked immunosorbent assays (ELISA) and rapid diagnostic tests (RDT) was evaluated in 91 Lao patients (57 adults, 34 children) with acute DENV infection. The VIDAS® NS1 assay showed the best overall agreement (95.6%) with the competitor NS1 ELISA. Both VIDAS® NS1 and NS1 ELISA assays also demonstrated high sensitivity relative to DENV RNA RT-PCR set as gold standard (85.7% and 83.9%, respectively). In contrast, NS1 RDT was less sensitive relative to DENV RNA RT-PCR (72.7%). The overall agreement of VIDAS® IgM and IgG assays with the competitor assays was moderate (72.5% for IgM ELISA, 76.9% for IgG ELISA, and 68.7% for IgM and IgG RDT). In most analyses, test agreements of the VIDAS® assays were comparable in adults and children. Altogether, the VIDAS® dengue prototypes performed very well and appear to be suitable for routine detection of dengue NS1 antigen and anti-dengue IgM/IgG antibodies.
The aversive value of pain in human decision-making
Authors: Slimani Hocine , Rainville Pierre , Roy Mathieu
Published: February 2021

According to basic utilitarian principles, people should try to maximize rewards and minimize pain. Here, participants were put in a situation where monetary rewards were paired to electric shocks spanning between pain detection and tolerance thresholds. Monetary offers ranged linearly from $0 to $5 or $10 in Group1 and 2, respectively, and exponentially from $0 to $5 in Group3. The value of pain increased quadratically as a function of the anticipated pain intensity. While increasing the range of monetary offers increased the price requested to accept pain, skewing the distribution of rewards encouraged profit maximization. Participants scoring higher on harm avoidance and lower on persistence scales requested more money to accept pain. Accepting highly painful offers slowed decisions regardless of the value of the concurrent reward. Altogether, pain-related decisions are highly relative to the local range of available rewards and may be under the control of more automatic avoidance mechanisms.
Training-induced bioenergetic improvement in human skeletal muscle is associated with non-stoichiometric changes in the mitochondrial proteome without reorganization of respiratory chain content
Authors: Granata Cesare , Caruana Nikeisha J. , Botella Javier , Jamnick Nicholas A. , Huynh Kevin , Kuang Jujiao , Janssen Hans A. , Reljic Boris , Mellett Natalie A. , Laskowski Adrienne , Stait Tegan L. , Frazier Ann E. , Coughlan Melinda T. , Meikle Peter J. , Thorburn David R. , Stroud David A. , Bishop David J.
Published: February 2021

Mitochondrial defects are implicated in multiple diseases and aging. Exercise training is an accessible and inexpensive therapeutic intervention improving mitochondrial bioenergetics and quality of life. By combining a multi-omics approach with biochemical andin siliconormalization, we removed the bias arising from the training-induced increase in human skeletal muscle mitochondrial content to unearth an intricate and previously undemonstrated network of differentially prioritized mitochondrial adaptations. We show that changes in hundreds of transcripts, proteins, and lipids are not stoichiometrically linked to the increase in mitochondrial content. We demonstrate that enhancing electron flow to oxidative phosphorylation (OXPHOS) is more important to improve ATP generation than increasing the abundance of the OXPHOS machinery, and that training-induced supercomplex formation does not confer enhancements in mitochondrial bioenergetics. Our study provides a new analytical approach allowing unbiased and in-depth investigations of training-induced mitochondrial adaptations, challenging our current understanding and calling for careful reinterpretation of previous findings.
QTLs for potato tuber resistance toDickeya solaniare located on chromosomes II and IV
Authors: Lebecka Renata , Śliwka Jadwiga , Grupa-Urbańska Anna , Szajko Katarzyna , Marczewski Waldemar
Published: February 2021

Soft rot is a bacterial disease that causes heavy losses in potato production worldwide. The goal of this study was to identify quantitative trait loci (QTLs) for potato tuber resistance to bacteriumDickeya solaniand for tuber starch content to study the relationship between these traits. A highly resistant diploid hybrid of potato was crossed with a susceptible hybrid to generate the F1 mapping population. Tubers that were wound-inoculated with bacteria were evaluated for disease severity expressed as the mean weight of rotted tubers, and disease incidence measured as the proportion of rotten tubers. Diversity array technology (DArTseq™) was used for genetic map construction and QTLs analysis. The most prominent QTLs for disease severity and incidence were identified in overlapping regions on potato chromosome IV and explained 22.4% and 22.9% of the phenotypic variance, respectively. The second QTL for disease severity was mapped to chromosome II and explained 16.5% of the variance. QTLs for starch content were detected on chromosomes III, V, VI, VII, VIII, IX, XI, and XII in regions different than the QTLs for soft rot resistance. Two strong and reproducible QTLs for resistance toDickeya solanion potato chromosomes IV and II might be useful for further study of candidate genes and marker development in potato breeding programs. The relationship between tuber resistance to bacteria and the starch content in potato tubers was not confirmed by QTL mapping, which makes the selection of genotypes highly resistant to soft rot with a desirable starch content feasible.
Inhibition of SARS-CoV-2 infection in human cardiomyocytes by targeting the Sigma-1 receptor disrupts cytoskeleton architecture and contractility
Authors: Salerno José Alexandre , Torquato Thayana , Temerozo Jairo R. , Goto-Silva Livia , Mendes Mayara , Sacramento Carolina Q. , Fintelman-Rodrigues Natalia , Vitoria Gabriela , Souza Leticia , Ornelas Isis , Veríssimo Carla , Karmirian Karina , Pedrosa Carolina , Dias Suelen da Silva Gomes , Soares Vinicius Cardoso , Aragão Luiz Guilherme HS , Puig-Pijuan Teresa , Salazar Vinícius W. , Dariolli Rafael , Biagi Diogo , Furtado Daniel Rodrigues , Borges Helena L. , Bozza Patrícia , Guimarães Marília Zaluar , Souza Thiago Moreno L. , Rehen Stevens K.
Published: February 2021

Heart dysfunction, represented by conditions such as myocarditis and arrhythmia, has been reported in COVID-19 patients. Therapeutic strategies focused on the cardiovascular system, however, remain scarce. The Sigma-1 receptor (S1R) has been recently proposed as a therapeutic target because its inhibition reduces SARS-CoV-2 replication. To investigate the role of S1R in SARS-CoV-2 infection in the heart, we used human cardiomyocytes derived from induced pluripotent stem cells (hiPSC-CM) as an experimental model. Here we show that the S1R antagonist NE-100 decreases SARS-CoV-2 infection and viral replication in hiPSC-CMs. Also, NE-100 reduces cytokine release and cell death associated with infection. Because S1R is involved in cardiac physiology, we investigated the effects of NE-100 in cardiomyocyte morphology and function. We show that NE-100 compromises cytoskeleton integrity and reduces beating frequency, causing contractile impairment. These results show that targeting S1R to challenge SARS-CoV-2 infection may be a useful therapeutic strategy but its detrimental effects in vivo on cardiac function should not be ignored.
Recovery of small plasmid sequences via Oxford Nanopore sequencing
Authors: Wick Ryan R. , Judd Louise M. , Wyres Kelly L. , Holt Kathryn E.
Published: February 2021

Oxford Nanopore Technologies (ONT) sequencing platforms currently offer two approaches to whole-genome native-DNA library preparation: ligation and rapid. In this study, we compared these two approaches for bacterial whole-genome sequencing, with a specific aim of assessing their ability to recover small plasmid sequences. To do so, we sequenced DNA from seven plasmid-rich bacterial isolates in three different ways: ONT ligation, ONT rapid and Illumina. Using the Illumina read depths to approximate true plasmid abundance, we found that small plasmids (<20 kbp) were underrepresented in ONT ligation read sets (by a mean factor of ∼4) but were not underrepresented in ONT rapid read sets. This effect correlated with plasmid size, with the smallest plasmids being the most underrepresented in ONT ligation read sets. We also found lower rates of chimeric reads in the rapid read sets relative to ligation read sets. These results show that when small plasmid recovery is important, ONT rapid library preparations are preferable to ligation-based protocols.

Impact statement

Researchers who use Oxford Nanopore Technologies (ONT) platforms to sequence bacterial genomes can currently choose from two library preparation methods. The first is a ligation-based approach, which uses ligase to attach sequencing adapters to the ends of DNA molecules. The second is a rapid approach, which uses a transposase enzyme to cleave DNA and attach adapters in a single step. There are advantages to each preparation, for example ligation can produce better yields but rapid is a simpler procedure. Our study reveals another advantage of rapid preparations: they are more effective at sequencing small plasmids. We show that sequencing of ligation-based libraries yields fewer reads derived from small plasmids, making such plasmids harder to detect in bacterial genomes. Since small plasmids can contain clinically relevant genes, including antimicrobial resistance (AMR) or virulence determinants, their exclusion could lead to unreliable conclusions that have serious consequences for AMR surveillance and prediction. We therefore recommend that researchers performing ONT-only sequencing of bacterial genomes should consider using rapid preparations whenever small plasmid recovery is important.

Data summary

Supplementary figures, tables, data and code can be found at:github.com/rrwick/Small-plasmid-Nanopore
Automatic segmentation and cardiac mechanics analysis of evolving zebrafish using deep-learning
Authors: Zhang Bohan , Pas Kristofor , Ijaseun Toluwani , Cao Hung , Fei Peng , Lee Juhyun
Published: February 2021

Objective

In the study of early cardiac development, it is important to acquire accurate volume changes of the heart chambers. Although advanced imaging techniques, such as light-sheet fluorescent microscopy (LSFM), provide an accurate procedure for analyzing the structure of the heart, rapid and robust segmentation is required to reduce laborious time and accurately quantify developmental cardiac mechanics.

Methods

The traditional biomedical analysis involving segmentation of the intracardiac volume is usually carried out manually, presenting bottlenecks due to enormous data volume at high axial resolution. Our advanced deep-learning techniques provide a robust method to segment the volume within a few minutes. Our U-net based segmentation adopted manually segmented intracardiac volume changes as training data and produced the other LSFM zebrafish cardiac motion images automatically.

Results

Three cardiac cycles from 2 days post fertilization (dpf) to 5 dpf were successfully segmented by our U-net based network providing volume changes over time. In addition to understanding the cardiac function for each of the two chambers, the ventricle and atrium were separated by 3D erode morphology methods. Therefore, cardiac mechanical properties were measured rapidly and demonstrated incremental volume changes of both chambers separately. Interestingly, stroke volume (SV) remains similar in the atrium while that of the ventricle increases SV gradually.

Conclusion

Our U-net based segmentation provides a delicate method to segment the intricate inner volume of zebrafish heart during development; thus providing an accurate, robust and efficient algorithm to accelerate cardiac research by bypassing the labor-intensive task as well as improving the consistency in the results.
IL-32 is a metabolic regulator promoting survival and proliferation of malignant plasma cells
Authors: Aass Kristin Roseth , Mjelle Robin , Kastnes Martin H. , Tryggestad Synne S. , van den Brink Luca M. , Westhrin Marita , Zahoor Muhammad , Moen Siv H. , Buene Glenn , Misund Kristine , Sponaas Anne-Marit , Ma Qianli , Sundan Anders , Groen Richard WJ , Slørdahl Tobias S. , Waage Anders , Standal Therese
Published: February 2021

IL-32 is a non-classical cytokine expressed in cancers, inflammatory diseases and infections. IL-32 can have both extracellular and intracellular functions, and its receptor is not identified. We here demonstrate that endogenously expressed, intracellular IL-32 binds to components of the mitochondrial respiratory chain and promotes oxidative phosphorylation. Knocking out IL-32 in malignant plasma cells significantly reduced survival and proliferationin vitroandin vivo. High throughput transcriptomic and MS-metabolomic profiling of IL-32 KO cells revealed that loss of IL-32 leads to profound perturbations in metabolic pathways, with accumulation of lipids, pyruvate precursors and citrate, indicative of reduced mitochondrial function. IL-32 is expressed in a subgroup of multiple myeloma patients with an inferior prognosis. Primary myeloma cells expressing IL-32 were characterized by a plasma cell gene signature associated with immune activation, proliferation and oxidative phosphorylation. We propose a novel concept for regulation of metabolism by an intracellular cytokine and identify IL-32 as an endogenous growth and survival factor for malignant plasma cells. IL-32 is a potential prognostic biomarker and a treatment target in multiple myeloma.
Annealing of focused ion beam damage in gold microcrystals: an in situ Bragg coherent X-ray diffraction imaging study
Authors: Yang David , Phillips Nicholas W. , Song Kay , Harder Ross J. , Cha Wonsuk , Hofmann Felix
Published: February 2021

Focused ion beam (FIB) techniques are commonly used to machine, analyse and image materials at the micro- and nanoscale. However, FIB modifies the integrity of the sample by creating defects that cause lattice distortions. Methods have been developed to reduce FIB-induced strain; however, these protocols need to be evaluated for their effectiveness. Here, non-destructive Bragg coherent X-ray diffraction imaging is used to study the in situ annealing of FIB-milled gold microcrystals. Two non-collinear reflections are simultaneously measured for two different crystals during a single annealing cycle, demonstrating the ability to reliably track the location of multiple Bragg peaks during thermal annealing. The thermal lattice expansion of each crystal is used to calculate the local temperature. This is compared with thermocouple readings, which are shown to be substantially affected by thermal resistance. To evaluate the annealing process, each reflection is analysed by considering facet area evolution, cross-correlation maps of the displacement field and binarized morphology, and average strain plots. The crystal's strain and morphology evolve with increasing temperature, which is likely to be caused by the diffusion of gallium in gold below ∼280°C and the self-diffusion of gold above ∼280°C. The majority of FIB-induced strains are removed by 380–410°C, depending on which reflection is being considered. These observations highlight the importance of measuring multiple reflections to unambiguously interpret material behaviour.
The effect of green tea polyphenols addition on the physicochemical, microbiological and bioactive characteristics of yogurt
Authors: Mediza Romero María Laura , von Staszewski Mariana , Martínez María Julia
Published: February 2021

Purpose

The purpose of this paper is to evaluate the effect of green tea polyphenols addition on physicochemical, microbiological and bioactive characteristics of yogurt.

Design/methodology/approach

Two incorporation methods of polyphenols were evaluated: direct addition or incorporated within protein particles of whey protein concentrate and gelatin. During yogurt’s shelf life, structure characteristics (water holding capacity, textural and rheological parameters), lactic acid bacteria (LAB) viability and polyphenols antioxidant activity were analyzed. Also, polyphenol bioaccesibility afterin vitrodigestion was evaluated.

Findings

Polyphenols addition (by the two methods used) did not affect the dynamics of the fermentation process, nor the LAB viability during storage. The color parametera* for the yogurts with the highest polyphenol concentrations showed positive values (tending to red), but not visible to the naked eye. Because of the ability of polyphenols to interact with milk proteins, yogurts with polyphenols presented higher values in firmness and cohesiveness with respect to the control. Additionally, the incorporation of polyphenols in protein particles increased even more these parameters because of the higher protein content of these formulations. After simulated digestion, a high polyphenol bioaccesibility was observed, and the antioxidant activity was retained, which could be explained by the “protector” effect of the milk matrix.

Practical implications

Yogurt supplementation with green tea polyphenols is feasible for the development of functional food. However, the use of protein particles would not provide an extra benefit because milk proteins already act as protective molecules of polyphenols.

Originality/value

This study shows not only the physico-chemical implications of including polyphenols in yogurt but also their bioaccesibility after anin vitrodigestion, revealing a suitable manner for delivery of antioxidants in a dairy product like yogurt.
Developing professional networks: the missing link to graduate employability
Authors: English Peter , de Villiers Scheepers Margarietha Johanna , Fleischman David , Burgess Jacqueline , Crimmins Gail
Published: February 2021

Purpose

Responding to increasing external pressure, universities are developing new strategies to illustrate the impact of their degrees on graduate employability. This paper investigates how alumni regard the development of their professional networks during their tertiary education in relation to employability and the associated pedagogical implications.

Design/methodology/approach

A qualitative approach using semi-structured interviews with 18 business and arts alumni from a regional university.

Findings

The findings reveal the importance of developing a professional network by cultivating social capital while at university. Alumni identify all forms of work-integrated learning (WIL), connectedness through social media, the role of university staff and volunteering as concrete ways to develop a professional network and enhance employability.

Research limitations/implications

This paper has pedagogical implications to develop graduate employability and WIL. Universities should draw from alumni networks to help develop students' bridging capital through industry-facing WIL projects. Educators should design assessment tasks in which students develop contacts and networking capabilities with alumni and other professionals using various platforms (e.g. social media). In addition, educators should promote the benefits of voluntary work and invite alumni and other industry stakeholders to co-design and co-teach areas of curriculum.

Originality/value

Drawing from the experiences of alumni re-routes the channel of communication from institutions expressing the importance of professional networks in relation to employability, to credible industry alumni confirming this importance. Few previous studies have taken this “outside-in approach” to emphasise and validate the importance of developing professional networks in relation to employability, particularly at regional universities.
The value of project management to competitiveness: key factors from a holistic and practical perspective
Authors: Silva Cláudia Sousa , Pereira Cláudia , Magano José
Published: February 2021

Purpose

The contribution of project success and the organisation's efficiency is consensual in the literature. However, the value of project management (PM) brings to the organisation's effectiveness through the alignment with strategy, contributing to its competitiveness and business success, is yet little explored. This study addresses the literature gap that concerns the relationship between PM and the organisation's competitiveness, proposing a holistic conceptual model to understand of how PM brings value to the organisation. This work also aims to demonstrate the practical implications of theoretical contributions to the value of PM. For this, a detailed action research (AR) was planned to show how researchers and practitioners could work and collaborate in a real problem and prove the AR approach's adequacy to the PM field.

Design/methodology/approach

The methodology starts with a systematic literature review (SLR), followed by content analysis to develop a conceptual model of PM's value. To validate the theoretical constructs and transfer the results to real context, an AR plan is then carried out to support a specific PM problem presented by an automotive industry company.

Findings

The results have theoretical and practical implications. An original conceptual model is developed–the value of PM: Key factors–defending a multidimensional and holistic perspective to understand the PM's value. A set of key factors was identified, structured, interrelated and exemplified their practical implementation in a single company. In addition to the technical key factors identified in the literature review, the AR plan unveils crucial social aspects to improve PM's value, such as leadership, strong communication and open processes. This work shows the central role of PM methodologies in integrating and interconnecting the key factors, emphasizing the projects' strategic level.

Research limitations/implications

The present work was developed in a specific and particular organisational context and industry.

Practical implications

The AR plan presents a company's original programme–Hyper Competitiveness (HC) Temple–implemented in an automotive company. Project management professionals could understand how this company implemented each key factor, defended in a conceptual model and lead the project's results to the business value.

Originality/value

The research originality lies in rethinking PM's value to organisations from a holistic perspective: multi-dimensional, temporal, life cycle, multi-organisational, pointing out a set of technical and social key factors.
An evaluation of offsite construction skill profiles
Authors: Ginigaddara Buddhini , Perera Srinath , Feng Yingbin , Rahnamayiezekavat Payam
Published: February 2021

Purpose

This paper aims to evaluate the existing and emerging Offsite Construction (OSC) skills. Construction industry is inherently labour oriented, fashioning poor labour productivity, low sustainability, slow and costly processes. These shortcomings promote OSC alongside driving forces such as industrialisation, automation and digitalisation. However, the traditional construction skills are not on par with the complexity, where robots, co-bots and digital-driven automated systems create the need for novel OSC skills.

Design/methodology/approach

Data collection is executed through a Roundtable activity hosting Construction Management academics form Australian universities specialising in construction technology. They engaged in ranking of skills along with creating a word cloud for the question, “what are the future construction skills that will be more beneficial in an OSC platform?” Word cloud is reviewed in a discussion approach while skills ranking data is analysed using descriptive statistics.

Findings

The most prominent OSC skills are logistics manager, project manager and digital producer. Attributes of skills that come under construction trades workers, design, engineering and specialist professionals will vary based on onsite-offsite percentage combination in a construction project. Study reviews the required construction skills at two ends of a continuum featuring the trade-based skills; bricklayer, concreter and carpenter at one end (traditional build) and the heavily digitalised and automated skills at the other end (OSC). The noticeable transition towards OSC urges industry practitioners, policy-makers and education providers to focus on understanding and cultivating key OSC skills.

Originality/value

This study describes the transition of skills from onsite to OSC. It is presented as one of the earliest attempts to evaluate OSC skill profiles.
Challenges in the implementation of circular economy in manufacturing industry
Authors: Chhimwal Madhukar , Agrawal Saurabh , Kumar Girish
Published: February 2021

Purpose

The circular economy concepts are useful for resource conservation, eliminating waste and enhancing the efficiency of production to improve the sustainability of the system. The application of CE in Indian manufacturing industry is in nascent stage. India’s manufacturing sector significantly contributes to the economic development of the nation; therefore, this study aims to identify and analyze the sustainability related challenges faced during the implementation of the circularity concept.

Design/methodology/approach

Comprehensive survey of literature and the use of Pareto analysis yield ten significant challenges which are further analyzed using fuzzy-Decision-Making Trial and Evaluation Laboratory approach.

Findings

Findings revealed that noncompliance of environmental laws, revenue generation, design issues owing to technological limitations and less preference to refurbished and reused product are some of the major challenges to the CE practices in the manufacturing industry.

Research limitations/implications

The results will help the researchers and practitioners in strategic decision-making for the improved application of circularity in the production process.

Originality/value

This paper contributes to the identification and prioritization of sustainability-related challenges faced during the implementation of a novel concept by a developing economy.
Effect of weather on online food ordering
Authors: Liu Da , Wang Wenbo , Zhao Yinchuan
Published: February 2021

Purpose

Weather affects consumer decision-making. However, academic research on how weather factors affect specific takeaway foods is limited. This paper aims to fill in the gap and therefore to contribute to online marketing and operation.

Design/methodology/approach

Web crawler techniques were first exploited to collect takeaway food ordering data from Meituan, the world’s largest GMV platform. Then statistics models and a time series regression model were selected to study the weather impact on online orders.

Findings

The findings highlight that certain weather factors, such as temperature, air quality and rainfall have clear effects on most category takeaway orders.

Originality/value

Quantitative analysis of weather impacts on the takeaway ordering business will help to guide the online service platforms for marketing promotion and the settled businesses to make reasonable arrangements for inventory and marketing tactics.
Designing supply chain performance system: a strategic study on Indian manufacturing sector
Authors: Jha Ajay , Sharma R.R.K. , Kumar Vimal , Verma Pratima
Published: February 2021

Purpose

A well-designed supply chain performance measurement system, should account for not only the capabilities and performance attributes of the focal firm but also its supply chain partners. The purpose of this paper is to help design a system that strikes a balance between the strategic objectives of the focal firm and its supply partners vis-à-vis the requirements of supply chain performance (cost, quality, speed and customer taste).

Design/methodology/approach

A theoretical framework on the strategic supply chain performance measurement system is developed based on existing literature and subsequently tested using a survey on 136 successful manufacturing organizations in India. The organizations were clustered into three strategy types and compared using analysis of variance on ranks to look for differences in preference for performance parameters.

Findings

The study examined the five dimensions of the supply chain practices, namely, strategic supply/distribution network, customer relationship, internal operations, information sharing and social and environmental responsiveness. The empirical results demonstrate the inclusion of business strategy orientation in designing today’s supply chain and hence its performance measurement system. Not supported hypotheses were addressed in the light of contextual factors.

Research limitations/implications

The study is confined to finding preferences of non-financial aspects of supply chain performance and tier-1 suppliers. The research helps better design and benchmark supply chain performance metrics, based on the strategic choice of the firm.

Originality/value

This paper highlights the shortcomings in the existing performance measurement and gaps in the existing literature in the supply chain context. Further, it gives a holistic view of strategic supply chain performance measurement design.