bluuebunny/crossref_metadata_2025 huggingface dataset:
Chernobyl-level radiation exposure damages bumblebee reproduction: a laboratory experiment
Authors: Raines Katherine E. , Whitehorn Penelope R. , Copplestone David , Tinsley Matthew C.
Published: October 2020

The consequences for wildlife of living in radiologically contaminated environments are uncertain. Previous laboratory studies suggest insects are relatively radiation-resistant; however, some field studies from the Chernobyl Exclusion Zone report severe adverse effects at substantially lower radiation dose rates than expected. Here, we present the first laboratory investigation to study how environmentally relevant radiation exposure affects bumblebee life history, assessing the shape of the relationship between radiation exposure and fitness loss. Dose rates comparable to the Chernobyl Exclusion Zone (50–400 µGy h
−1
) impaired bumblebee reproduction and delayed colony growth but did not affect colony weight or longevity. Our best-fitting model for the effect of radiation dose rate on colony queen production had a strongly nonlinear concave relationship: exposure to only 100 µGy h
−1
impaired reproduction by 30–45%, while further dose rate increases caused more modest additional reproductive impairment. Our data indicate that the practice of estimating effects of environmentally relevant low-dose rate exposure by extrapolating from high-dose rates may have considerably underestimated the effects of radiation. If our data can be generalized, they suggest insects suffer significant negative consequences at dose rates previously thought safe; we therefore advocate relevant revisions to the international framework for radiological protection of the environment.
High-resolution characterization of male ornamentation and re-evaluation of sex linkage in guppies
Authors: Morris Jake , Darolti Iulia , van der Bijl Wouter , Mank Judith E.
Published: October 2020

Coloration plays a key role in the ecology of many species, influencing how an organism interacts with its environment, other species and conspecifics. Guppies are sexually dimorphic, with males displaying sexually selected coloration resulting from female preference. Previous work has suggested that much of guppy colour pattern variation is Y-linked. However, it remains unclear how many individual colour patterns are Y-linked in natural populations as much of the previous work has focused on phenotypes either not found in the wild, or aggregate measures such as total colour area. Moreover, ornaments have traditionally been identified and delineated by hand, and computational methods now make it possible to extract pixels and identify ornaments with automated methods, reducing the potential for human bias. Here we developed a pipeline for semi-automated ornament identification and high-resolution image analysis of male guppy colour patterns and applied it to a multigenerational pedigree. Our results show that loci controlling the presence or the absence of individual male ornaments in our population are not predominantly Y-linked. However, we find that ornaments of similar colour are not independent of each other, and modifier loci that affect whole animal coloration appear to be at least partially Y-linked. Considering these results, Y-linkage of individual ornaments may not be important in driving colour changes in natural populations of guppies, or in expansions of the non-recombining Y region, while Y-linked modifier loci that affect aggregate traits may well play an important role.
Environmental DNA from multiple pathogens is elevated near active Atlantic salmon farms
Authors: Shea Dylan , Bateman Andrew , Li Shaorong , Tabata Amy , Schulze Angela , Mordecai Gideon , Ogston Lindsey , Volpe John P. , Neil Frazer L. , Connors Brendan , Miller Kristina M. , Short Steven , Krkošek Martin
Published: October 2020

The spread of infection from reservoir host populations is a key mechanism for disease emergence and extinction risk and is a management concern for salmon aquaculture and fisheries. Using a quantitative environmental DNA methodology, we assessed pathogen environmental DNA in relation to salmon farms in coastal British Columbia, Canada, by testing for 39 species of salmon pathogens (viral, bacterial, and eukaryotic) in 134 marine environmental samples at 58 salmon farm sites (both active and inactive) over 3 years. Environmental DNA from 22 pathogen species was detected 496 times and species varied in their occurrence among years and sites, likely reflecting variation in environmental factors, other native host species, and strength of association with domesticated Atlantic salmon. Overall, we found that the probability of detecting pathogen environmental DNA (eDNA) was 2.72 (95% CI: 1.48, 5.02) times higher at active versus inactive salmon farm sites and 1.76 (95% CI: 1.28, 2.42) times higher per standard deviation increase in domesticated Atlantic salmon eDNA concentration at a site. If the distribution of pathogen eDNA accurately reflects the distribution of viable pathogens, our findings suggest that salmon farms serve as a potential reservoir for a number of infectious agents; thereby elevating the risk of exposure for wild salmon and other fish species that share the marine environment.
Effects of genomic and functional diversity on stand-level productivity and performance of non-native Arabidopsis
Authors: Turner Kathryn G. , Lorts Claire M. , Haile Asnake T. , Lasky Jesse R.
Published: October 2020

Biodiversity can affect the properties of groups of organisms, such as ecosystem function and the persistence of colonizing populations. Genomic data offer a newly available window to diversity, complementary to other measures like taxonomic or phenotypic diversity. We tested whether native genetic diversity in field experimental stands of
Arabidopsis thaliana
affected their aboveground biomass and fecundity in their colonized range. We constructed some stands of genotypes that we
a priori
predicted would differ in performance or show overyielding. We found no relationship between genetic diversity and stand total biomass. However, increasing stand genetic diversity increased fecundity in high-resource conditions. Polyculture (multiple genotype) stands consistently yielded less biomass than expected based on the yields of component genotypes in monoculture. This under-yielding was strongest in stands with late-flowering and high biomass genotypes, potentially due to interference competition by these genotypes. Using a new implementation of association mapping, we identified genetic loci whose diversity was associated with stand-level yield, revealing a major flowering time locus associated with under-yielding of polycultures. Our field experiment supports community ecology studies that find a range of diversity-function relationships. Nevertheless, our results suggest diversity in colonizing propagule pools can enhance population fitness. Furthermore, interference competition among genotypes differing in flowering time might limit the advantages of polyculture.
Krüppel-like factor/specificity protein evolution in the Spiralia and the implications for cephalopod visual system novelties
Authors: McCulloch Kyle J. , Koenig Kristen M.
Published: October 2020

The cephalopod visual system is an exquisite example of convergence in biological complexity. However, we have little understanding of the genetic and molecular mechanisms underpinning its elaboration. The generation of new genetic material is considered a significant contributor to the evolution of biological novelty. We sought to understand if this mechanism may be contributing to cephalopod-specific visual system novelties. Specifically, we identified duplications in the Krüppel-like factor/specificity protein (KLF/SP) sub-family of C2H2 zinc-finger transcription factors in the squid
Doryteuthis pealeii
. We cloned and analysed gene expression of the KLF/SP family, including two paralogs of the
DpSP6-9
gene. These duplicates showed overlapping expression domains but one paralog showed unique expression in the developing squid lens, suggesting a neofunctionalization of
DpSP6-9a
. To better understand this neofunctionalization, we performed a thorough phylogenetic analysis of SP6-9 orthologues in the Spiralia. We find multiple duplications and losses of the
SP6-9
gene throughout spiralian lineages and at least one cephalopod-specific duplication. This work supports the hypothesis that gene duplication and neofunctionalization contribute to novel traits like the cephalopod image-forming eye and to the diversity found within Spiralia.
The evolution of virulence inPseudomonas aeruginosaduring chronic wound infection
Authors: Vanderwoude Jelly , Fleming Derek , Azimi Sheyda , Trivedi Urvish , Rumbaugh Kendra P. , Diggle Stephen P.
Published: October 2020

Opportunistic pathogens are associated with a number of chronic human infections, yet the evolution of virulence in these organisms during chronic infection remains poorly understood. Here, we tested the evolution of virulence in the human opportunistic pathogenPseudomonas aeruginosain a murine chronic wound model using a two-part serial passage and sepsis experiment, and found that virulence evolved in different directions in each line of evolution. We also assessedP. aeruginosaadaptation to a chronic wound after 42 days of evolution and found that morphological diversity in our evolved populations was limited compared with that previously described in cystic fibrosis (CF) infections. Using whole-genome sequencing, we found that genes previously implicated inP. aeruginosapathogenesis (lasR,pilR,fleQ,rpoNandpvcA) contained mutations during the course of evolution in wounds, with selection occurring in parallel across all lines of evolution. Our findings highlight that: (i)P. aeruginosaheterogeneity may be less extensive in chronic wounds than in CF lungs; (ii) genes involved inP. aeruginosapathogenesis acquire mutations during chronic wound infection; (iii) similar genetic adaptations are employed byP. aeruginosaacross multiple infection environments; and (iv) current models of virulence may not adequately explain the diverging evolutionary trajectories observed in an opportunistic pathogen during chronic wound infection.
Molecular evaluation of quorum quenching potential of vanillic acid against Yersinia enterocolitica through transcriptomic and in silico analysis
Authors: Sivasankar Chandran , Jha Nisha Kumari , Singh Satya Rajan , Murali Ayaluru , Shetty Prathapkumar Halady
Published: October 2020

Introduction.

Yersinia enterocolitica

is one of the leading food-borne entero-pathogens causing various illnesses ranging from gastroenteritis to systemic infections. Quorum sensing (QS) is one of the prime mechanisms that control the virulence in

Y. enterocolitica

.

Hypothesis/Gap Statement. Vanillic acid inhibits the quorum sensing and other virulence factors related to

Y. enterocolitica

. It has been evaluated by transcriptomic and Insilico analysis. Therefore, it can be a prospective agent to develop a therapeutic combination against

Y. enterocolitica

.

Aim. The present study is focused on screening natural anti-quorum-sensing agents against

Y. enterocolitica

. The effect of selected active principle on various virulence factors was evaluated.

Methodology. In total, 12 phytochemicals were screened by swarming assay. MATH assay, EPS and surfactant production assay, SEM analysis, antibiotic and blood sensitivity assay were performed to demonstrate the anti-virulence activity. Further, RNA sequencing and molecular docking studies were carried out to substantiate the anti-QS activity.

Results. Vanillic acid (VA) has exhibited significant motility inhibition, thus indicating the anti-QS activity with MQIC of 400 µg ml−1 without altering the cell viability. It has also inhibited the violacein production in

Chromobacterium violaceum

ATCC 12472, which further confirms the anti-QS activity. VA has inhibited 16 % of cell-surface hydrophobicity (CSH), 52 % of EPS production and 60 % of surfactant production. Moreover, it has increased the sensitivity of

Y. enterocolitica

towards antibiotics. It has also made the cells upto 91 % more vulnerable towards human immune cells. The transcriptomic analysis by RNA sequencing revealed the down regulation of genes related to motility, virulence, chemotaxis, siderophores and drug resistance. VA treatment has also positively regulated the expression of several stress response genes. In furtherance, the anti-QS potential of VA has been validated with QS regulatory protein YenR by in silico molecular simulation and docking study.

Conclusion. The present study is possibly the first attempt to demonstrate the anti-QS and anti-pathogenic potential of VA against

Y. enterocolitica

by transcriptomic and in silico analysis. It also deciphers that VA can be a promising lead to develop biopreservative and therapeutic regimens to treat

Y. enterocolitica

infections.
Facultative methanotrophs – diversity, genetics, molecular ecology and biotechnological potential: a mini-review
Authors: Farhan Ul Haque Muhammad , Xu Hui-Juan , Murrell J. Colin , Crombie Andrew
Published: October 2020

Methane-oxidizing bacteria (methanotrophs) play a vital role in reducing atmospheric methane emissions, and hence mitigating their potent global warming effects. A significant proportion of the methane released is thermogenic natural gas, containing associated short-chain alkanes as well as methane. It was one hundred years following the description of methanotrophs that facultative strains were discovered and validly described. These can use some multi-carbon compounds in addition to methane, often small organic acids, such as acetate, or ethanol, although

Methylocella

strains can also use short-chain alkanes, presumably deriving a competitive advantage from this metabolic versatility. Here, we review the diversity and molecular ecology of facultative methanotrophs. We discuss the genetic potential of the known strains and outline the consequent benefits they may obtain. Finally, we review the biotechnological promise of these fascinating microbes.
Effectiveness and Safety of Combining Tofacitinib with a Biologic in Patients with Refractory Inflammatory Bowel Diseases
Authors: Alayo Quazim A. , Khatiwada Aava , Patel Anish , Zulfiqar Maria , Gremida Anas , Gutierrez Alexandra , Rood Richard P. , Ciorba Matthew A. , Christophi George , Deepak Parakkal
Published: October 2020

ABSTRACT AND KEY WORDS

Background

One therapeutic option with limited data among patients with active moderate-to-severe ulcerative colitis (UC) and Crohn’s disease (CD) despite biologic monotherapy is using a combination of a biologic with Tofacitinib (TBT). Our aim was to examine the effectiveness and safety of TBT in this subset of patients.

Methods

Data of IBD patients at 2 referral centers on TBT were extracted. The primary outcome was clinical response (>50% reduction in symptoms) at week 8 and/or 16 determined by Physician Global Assessment. Secondary outcome was clinical remission (resolution of symptoms), corticosteroid-free clinical response and remission, normalization of CRP and endoscopic/radiographic response and remission. Adverse events (AEs) including any abnormal lipid profile or surgical complications were also assessed.

Results

Thirty-five patients (25UC, 10CD) were included. Biologics combined with tofacitinib were vedolizumab (68.6%), ustekinumab (17.1%), and infliximab (14.3%) and the median follow-up duration was 4 months. A majority (57.2%) had failed at least two biologics prior to starting TBT. At weeks 8 and/or 16, 37.1% achieved clinical response with 5.7% in clinical remission. Among the 23 patients with endoscopically/radiographically active disease at baseline, 56.5% had endoscopic/radiographic response and 34.8% achieved remission. Three AEs occurred in 2 (5.7%) patients, with an IR of 20.5 (15.0–47.2)/100PYF. No VTE and herpes zoster was reported.

Conclusions

TBT is effective at inducing endoscopic/radiographic response and a modest clinical response in UC and CD patients with active clinical symptoms despite prior biologic monotherapy. No new safety signals were detected beyond those reported with tofacitinib monotherapy.
Differentially expressed genes reflect disease-induced rather than disease-causing changes in the transcriptome
Authors: Porcu Eleonora , Sadler Marie C. , Lepik Kaido , Auwerx Chiara , Wood Andrew R. , Weihs Antoine , Ribeiro Diogo M. , Bandinelli Stefania , Tanaka Toshiko , Nauck Matthias , Völker Uwe , Delaneau Olivier , Metspalu Andres , Teumer Alexander , Frayling Timothy , Santoni Federico A. , Reymond Alexandre , Kutalik Zoltán
Published: October 2020

Comparing transcript levels between healthy and diseased individuals allows the identification of differentially expressed genes, which may be causes, consequences or mere correlates of the disease under scrutiny. Here, we propose a bi-directional Transcriptome-Wide Mendelian Randomization (TWMR) approach that integrates summary-level data from GWAS and whole-blood eQTLs in a MR framework to investigate the causal effects between gene expression and complex traits.

Whereas we have previously developed a TWMR approach to elucidate gene expression to trait causal effects, here we are adapting the method to shed light on the causal imprint of complex traits on transcript levels. We termed this new approach reverse TWMR (revTWMR). Integrating bi-directional causal effects between gene expression and complex traits enables to evaluate their respective contributions to the correlation between gene expression and traits. We uncovered that whole blood gene expression-trait correlation is mainly driven by causal effect from the phenotype on the expression rather than the reverse. For example, BMI- and triglycerides-gene expression correlation coefficients robustly correlate with trait-to-expression causal effects (r=0.09, P=1.54×10−39 and r=0.09, P=1.19×10−34, respectively), but not detectably with expression-to-trait effects.

Genes implicated by revTWMR confirmed known associations, such as rheumathoid arthritis and Crohn’s disease induced changes in expression of TRBV and GBP2, respectively. They also shed light on how clinical biomarkers can influence their own levels. For instance, we observed that high levels of high-density lipoprotein (HDL) cholesterol lowers the expression of genes involved in cholesterol biosynthesis (SQLE, FDFT1) and increases the expression of genes responsible for cholesterol efflux (ABCA1, ABCG1), two key molecular pathways in determining HDL levels. Importantly, revTWMR is more robust to pleiotropy than polygenic risk score (PRS) approaches which can be misled by pleiotropic outliers. As one example, revTWMR revealed that the previously reported association between educational attainment PRS and STX1B is exclusively driven by a highly pleiotropic SNP (rs2456973), which is strongly associated with several hematological and anthropometric traits.

In conclusion, our method disentangles the relationship between gene expression and phenotypes and reveals that complex traits have more pronounced impact on gene expression than the reverse. We demonstrated that studies comparing the transcriptome of diseased and healthy subjects are more prone to reveal disease-induced gene expression changes rather than disease causing ones.
From multiplex serology to serolomics – a novel approach to the antibody response against the SARS-CoV-2 proteome
Authors: Butt Julia , Murugan Rajagopal , Hippchen Theresa , Olberg Sylvia , van Straaten Monique , Wardemann Hedda , Stebbins Erec , Kräusslich Hans-Georg , Bartenschlager Ralf , Brenner Hermann , Laketa Vibor , Schöttker Ben , Müller Barbara , Merle Uta , Waterboer Tim
Published: October 2020

Background

The emerging SARS-CoV-2 pandemic entails an urgent need for specific and sensitive high-throughput serological assays to assess SARS-CoV-2 epidemiology. We therefore aimed at developing a fluorescent-bead based SARS-CoV-2 multiplex serology assay for detection of antibody responses to the SARS-CoV-2 proteome.

Methods

Proteins of the SARS-CoV-2 proteome and protein N of SARS-CoV-1 and common cold Coronaviruses (ccCoVs) were recombinantly expressed inE. colior HEK293 cells. Assay performance was assessed in a Covid-19 case cohort (n=48 hospitalized patients from Heidelberg) as well as n=85 age- and sex-matched pre-pandemic controls from the ESTHER study. Assay validation included comparison with home-made immunofluorescence and commercial Enzyme-linked immunosorbent (ELISA) assays.

Results

A sensitivity of 100% (95% CI: 86%-100%) was achieved in Covid-19 patients 14 days post symptom onset with dual sero-positivity to SARS-CoV-2 N and the receptor-binding domain of the spike protein. The specificity obtained with this algorithm was 100% (95% CI: 96%-100%). Antibody responses to ccCoVs N were abundantly high and did not correlate with those to SARS-CoV-2 N. Inclusion of additional SARS-CoV-2 proteins as well as separate assessment of immunoglobulin (Ig) classes M, A, and G allowed for explorative analyses regarding disease progression and course of antibody response.

Conclusion

This newly developed SARS-CoV-2 multiplex serology assay achieved high sensitivity and specificity to determine SARS-CoV-2 sero-positivity. Its high throughput ability allows epidemiologic SARS-CoV-2 research in large population-based studies. Inclusion of additional pathogens into the panel as well as separate assessment of Ig isotypes will furthermore allow addressing research questions beyond SARS-CoV-2 sero-prevalence.
PERFORMANCE EVALUATION OF A SARS-COV-2 RAPID ANTIGENTEST: TEST PERFORMANCE IN THE COMMUNITY IN THE NETHERLANDS
Authors: Van der Moeren N. , Zwart V.F. , Lodder E.B. , Van den Bijllaardt W. , Van Esch H.R.J.M. , Stohr J.J.J.M. , Pot J. , Welschen I. , Van Mechelen P.M.F. , Pas S.D. , Kluytmans J.A.J.W.
Published: October 2020

Objectives

This study was primarily conducted to evaluate clinical sensitivity and specificity of the SARS-CoV-2 rapid antigen test ‘BD Veritor System for Rapid Detection of SARS-CoV-2’ (VRD) compared to real time reverse transcriptase polymerase chain reaction (qRT-PCR). Furthermore, the VRD sensitivity for different Ct-value groups (Ct <20; Ct 20-25, Ct 25-30 and Ct ≥30) and different intervals since symptom onset (< 7 days; ≥ 7 days) were examined.

Design

Prospective performance evaluation study.

Setting

Municipal Health Service (GGD) COVID-19 test centres in West-Brabant, the Netherlands

Participants

In order to evaluate clinical specificity, 352 symptomatic adults (≥18 years) who presented at a participating GGD test centre for a COVID-19 test between September 28 and October 7 2020 were included. In order to evaluate clinical sensitivity, 123 symptomatic adults (≥18 years) who were tested positive with qRT-PCR in a participating GGD test centre between September 26 and October 6 were included.

Results

An overall clinical specificity of 100% (95%CI: 98.9%-100%) and sensitivity of 80.7% (95% CI: 73,2%-86,9%) was found for the VRD compared to qRT-PCR. Sensitivity was the highest for low Ct-value categories and for specimen obtained within the first days after disease onset. For specimen obtained within 7 days after onset of symptoms, the overall sensitivity was 91.0% (95% CI: 82,4%-96,3%) and 98,6% (95% CI: 92,3%-100%) for samples with qRT-PCR Ct-value beneath 30.

Conclusion

The VRD is a promising diagnostic test for COVID-19 community screening for symptomatic individuals within 7 days after symptom onset in function of disease control. The clinical sensitivity was highest when viral load was high, which correlated with the duration of symptoms. Further research on practical applicability and the optimal position of the test within the current testing landscape is needed.
An agent-based model of spread of a pandemic with validation using COVID-19 data from New York State
Authors: Datta Amitava , Winkelstein Peter , Sen Surajit
Published: October 2020

We introduce a simple agent based model where each agent carries an effective viral load that captures the instantaneous state of infection of the agent and simulate the spread of a pandemic and subsequently validate it by using publicly available COVID-19 data. Our simulation tracks the temporal evolution of a virtual city or community of agents in terms of contracting infection, recovering asymptomatically, or getting hospitalized. The virtual community is divided into family groups with 2-6 individuals in each group. Agents interact with other agents in virtual public places like at grocery stores, on public transportation and in offices. We initially seed the virtual community with a very small number of infected individuals and then monitor the disease spread and hospitalization over a period of fifty days, which is a typical time-frame for the initial spread of a pandemic. An uninfected or asymptomatic agent is randomly selected from a random family group in each simulation step for visiting a random public space. An uninfected agent contracts infection if the public place is occupied by other infected agents. We have calibrated our simulation rounds according to the size of the population of the virtual community for simulating realistic exposure of agents to a contagion. Our simulation results are consistent with the publicly available hospitalization and ICU patient data from different communities of varying sizes in New York state. Our model can predict the trend in epidemic spread and hospitalization from a set of simple parameters and could be potentially useful in exploring strategies to keep a community safe.
Brain organization, not size alone, as key to high-level vision: Evidence from marmoset monkeys
Authors: Kell Alexander J.E. , Bokor Sophie L. , Jeon You-Nah , Toosi Tahereh , Issa Elias B.
Published: October 2020

Bigger brains are thought to support richer abilities, including perceptual abilities. But bigger brains are typically organized differently (e.g., with more cortical areas). Thus, the extent to which a neural system’s size versus organization underlies complex abilities remains unclear. The marmoset monkey is evolutionarily peculiar: it has a small brain, yet many cortical areas. We used this natural experiment to test organization as source of high-level visual abilities independent of size, via large-scale psychophysics comparing marmosets to different species on identical tasks. Marmosets far out—performed rats—a marmoset-sized rodent—on a simple visual recognition task. On another visual task, which is difficult for both humans and machines, marmosets achieved high performance. Strikingly, their image-by-image behavior revealed that they did so in a manner highly similar to humans—marmosets were nearly as human-like as were macaques. These results suggest a key role for brain organization—not simply size—in the evolution of sophisticated abilities.
Extending the range of COVID-19 risk factors in a Bayesian network model for personalised risk assessment
Authors: Prodhan Georgina , Fenton Norman
Published: October 2020

A need is emerging for individuals to gauge their own risks of coronavirus infection as it becomes apparent that contact tracing to contain the spread of the virus is not working in many societies. This paper presents an extension of an existing Bayesian network model for an application in which people can add their own personal risk factors to calculate their probability of exposure to the virus and likely severity if they do catch the illness. The data need not be shared with any central authority. In this way, people can become more aware of their individual risks and adjust their behaviour accordingly, as many countries prepare for a second wave of infections or a prolonged pandemic. This has the advantage not only of preserving privacy but also of containing the virus more effectively by allowing users to act without the time lag of waiting to be informed that a contact has been tested and confirmed COVID-19 positive. Through a nuanced assessment of individual risk, it could also release many people from isolation who are judged highly vulnerable using cruder measures, helping to boost economic activity and decrease social isolation without unduly increasing transmission risk. Although much has been written and reported about single risk factors, little has been done to bring these factors together in a user-friendly way to give an overall risk rating. The causal probabilistic model presented here shows the power of Bayesian networks to represent the interplay of multiple, dependent variables and to predict outcomes. The network, designed for use in the UK, is built using detailed data from government and health authorities and the latest research, and is capable of dynamic updates as new information becomes available. The focus of the paper is on the extended set of risk factors.
Saliva as a testing sample for SARS-CoV-2 detection by RT-PCR in low prevalence community settings
Authors: Gavars Didzis , Gavars Mikus , Perminov Dmitry , Stasulans Janis , Stana Justine , Metla Zane , Pavare Jana , Tauckels Eriks , Gulbis Egils , Dumpis Uga
Published: October 2020

Objectives

The number of COVID-19 cases is increasing globally and there is an urgency for a simple non-invasive method for the detection of SARS-CoV-2. Our study aimed to demonstrate that saliva can be used as a specimen for SARS-CoV-2 detection notably for the screening of extensive population groups via pooling.

Methods

To demonstrate that saliva is an appropriate specimen for SARS-CoV-2 detection a field study including 3,660 participants was performed between September 29 and October 1, 2020. We collected paired nasopharyngeal/oropharyngeal swabs (NPS) and saliva specimens and processed them within 24 hours of collection. We performed 36 serial measurements of 8 SARS-CoV-2 positive saliva samples to confirm the stability of the specimen and completed 37 pools of saliva samples by adding one positive specimen per pool.

Results

Saliva specimens were stable for testing for up to 24 hours. Overall, 44 salival samples (1.2%) tested positive for SARS-CoV-2 during the field study. The results of saliva samples were consistent with those obtained from NPS from the same patient with 90% sensitivity (95% CI 68.3%-98.7%) and 100% specificity during the first two weeks after the onset of symptoms. Using pooling strategy 796 RT-PCR tests were performed. All pools showed 100% positivity in different pooling proportions.

Conclusions

Our findings demonstrate that saliva is an appropriate specimen for pooling and SARS-CoV-2 screening with accurate diagnostic performance. Patient-performed simple specimen collection allows testing an extensive number of people rapidly, obtaining results of the spread of SARS-CoV-2 and allowing authorities to take timely measures.
High-throughput detection of antibodies targeting the SARS-CoV-2 Spike in longitudinal convalescent plasma samples
Authors: Anand Sai Priya , Prévost Jérémie , Richard Jonathan , Perreault Josée , Tremblay Tony , Drouin Mathieu , Fournier Marie-Josée , Lewin Antoine , Bazin Renée , Finzi Andrés
Published: October 2020

Background

The SARS-CoV-2 virus is the cause of the ongoing coronavirus disease 2019 (COVID-19) pandemic, infecting millions of people and causing more than a million deaths. The SARS-CoV-2 Spike glycoproteins mediate viral entry and represent the main target for antibody responses. Humoral responses were shown to be important for preventing and controlling infection by coronaviruses. A promising approach to reduce the severity of COVID-19 is the transfusion of convalescent plasma. However, longitudinal studies revealed that the level of antibodies targeting the receptor-binding domain (RBD) of the SARS-CoV-2 Spike declines rapidly after the resolution of the infection.

Study Design and Methods

To extend this observation beyond the RBD domain, we performed a longitudinal analysis of the persistence of antibodies targeting the full-length SARS-CoV-2 Spike in the plasma from 15 convalescent donors. We generated a 293T cell line constitutively expressing the SARS-CoV-2 Spike and used it to develop a high-throughput flow cytometry-based assay to detect SARS-CoV-2 Spike specific antibodies in the plasma of convalescent donors.

Results and Conclusion

We found that the level of antibodies targeting the full-length SARS-CoV-2 Spike declines gradually after the resolution of the infection. This decline was not related to the number of donations, but strongly correlated with the decline of RBD-specific antibodies and the number of days post-symptom onset. These findings help to better understand the decline of humoral responses against the SARS-CoV-2 Spike and provide important information on when to collect plasma after recovery from active infection for convalescent plasma transfusion.
Restructuring of genomic provinces of surface ocean plankton under climate change
Authors: Frémont Paul , Gehlen Marion , Vrac Mathieu , Leconte Jade , Delmont Tom O. , Wincker Patrick , Iudicone Daniele , Jaillon Olivier
Published: October 2020

The impact of climate change on diversity, functioning and biogeography of marine plankton remains a major unresolved issue. Here, niche theory is applied to plankton metagenomes of 6 size fractions, from viruses to meso-zooplankton, sampled during theTaraOceans expedition. Niches are used to derive plankton size-dependent structuring of the oceans south of 60°N inclimato-genomicprovinces characterized by signature genomes. By 2090, assuming the RCP8.5 high warming scenario, provinces would be reorganized over half of the considered ocean area and quasi-systematically displaced poleward. Particularly, tropical provinces would expand at the expense of temperate ones. Sea surface temperature is identified as the main driver of changes (50%) followed by phosphate (11%) and salinity (10%). Compositional shifts among key planktonic groups suggest impacts on the nitrogen and carbon cycles. Provinces are linked to estimates of carbon export fluxes which are projected to decrease on average by 4% in response to biogeographical restructuring.
A thematic analysis of highly retweeted early COVID-19 tweets: consensus, information, dissent and lockdown life
Authors: Thelwall Mike , Thelwall Saheeda
Published: October 2020

Purpose

Public attitudes towards COVID-19 and social distancing are critical in reducing its spread. It is therefore important to understand public reactions and information dissemination in all major forms, including on social media. This article investigates important issues reflected on Twitter in the early stages of the public reaction to COVID-19.

Design/methodology/approach

A thematic analysis of the most retweeted English-language tweets mentioning COVID-19 during March 10–29, 2020.

Findings

The main themes identified for the 87 qualifying tweets accounting for 14 million retweets were: lockdown life; attitude towards social restrictions; politics; safety messages; people with COVID-19; support for key workers; work; and COVID-19 facts/news.

Research limitations/implications

Twitter played many positive roles, mainly through unofficial tweets. Users shared social distancing information, helped build support for social distancing, criticised government responses, expressed support for key workers and helped each other cope with social isolation. A few popular tweets not supporting social distancing show that government messages sometimes failed.

Practical implications

Public health campaigns in future may consider encouraging grass roots social web activity to support campaign goals. At a methodological level, analysing retweet counts emphasised politics and ignored practical implementation issues.

Originality/value

This is the first qualitative analysis of general COVID-19-related retweeting.
Moderating effects of perceived risk on the determinants–outcome nexus of e-money behaviour
Authors: Susanto Perengki , Hoque Mohammad Enamul , Hashim Nik Mohd Hazrul Nik , Shah Najeeb Ullah , Alam Mohammad Nur A.
Published: October 2020

Purpose

In recent years, the usage rate of electronic money (e-money) has grown rapidly in many countries around the world and is becoming widely accepted in developing nations due to evolving market conditions and buying patterns. This study explores the determinants of customers' behavioural intention (BI) and actual usage behaviour (UB) of e-money service in a transition economic setting. Additionally, since there has been limited research on moderating influences, this study introduces perceived risk (PR) as a moderator, underpinned by relevant technology acceptance and behavioural theories.

Design/methodology/approach

The proposed model and hypothesised variable relationships are tested using partial least squares-structural equation modelling (PLS-SEM) with survey data from 337 e-money service users in Indonesia.

Findings

The empirical results revealed that facilitating conditions (FCs), hedonic motivation (HM), price value (PV), habit (HT) and PR are important determinants of customers’ BI towards e-money and most of these variables also affect actual UB of e-money services. Performance expectancy (PE), effort expectancy (EE) and social influence (SI) emerged to be insignificant determinants. The study also uncovered that PR negatively moderates the links between EE, SI, HM, PV and BI towards e-money services. Likewise, PR has an adverse effect on the BI–actual UB relationship.

Research limitations/implications

A large portion of the sample comprised young individuals with tertiary education. In essence, the sample represents the millennial generation and they are generally characterised as responsive, innovative and technology literate. Future studies could advance the present understanding by comparing different customer backgrounds and country.

Practical implications

The results shed light into the key factors that enhance e-money usage behaviours and have direct managerial implications with regard to brand strategy and market targeting. The findings imply that e-money service providers should take initiatives to retain users with effective and personalised marketing efforts, particularly via mobile media brand promotions.

Originality/value

While there has been considerable discussion on how PR may impact on initial preference and adoption of e-money, existing studies seem to fall short in conceptualising and empirically examining the moderating role of PR on the determinants and outcome of e-money BI.
The Government of Jamaica (GoJ) COVID-19 pandemic stimulus response: an opportunity to regulate and formalize?
Authors: Ricketts Heather
Published: October 2020

Purpose

The purpose of the paper is to determine whether the Government of Jamaica's COVID-19 Allocation of Resources for Employees (CARE) Stimulus Response program provides a sufficient opportunity for formalization of the informal economy.

Design/methodology/approach

A careful examination of the program has been conducted, specifically through reading the CARE brochure, reading the budget presentation by the Minister of Finance in which the program was introduced and details highlighted, following program updates at COVID-19 Press briefings and the Minister's Twitter account, and following related articles and programs via original and social media.

Findings

This paper suggests that any capitalizing on the opportunity to promote formalization is insufficient. Early data show increased applications for licenses and registration by informal operators, but the CARE program is only short-term, and the benefits of formalization will have to surpass those of informality to be sufficiently attractive. Other attractors must necessarily involve simplifying the process of contributing to the National Insurance Scheme; and offering unemployment insurance; along with access to finance, education and training and policymaking opportunities. COVID-19 provides the possibility of a “new deal” for the informal economy that could yield productivity gains and more inclusive development.

Originality/value

This is one of the earliest examinations of how the short-term financial support schemes implemented by the GoJ as its COVID-19 Stimulus Response has been used as an incentive to formalize the large informal economy.
Does remittance inflow stimulate electricity consumption in India? An empirical insight
Authors: Sahoo Malayaranjan , Sethi Narayan
Published: October 2020

Purpose

The purpose of this paper is to examine whether remittance inflow stimulate electricity consumption in India with other macroeconomic variables such as FDI, trade openness and urbanization in energy demand function from 1975–2017.

Design/methodology/approach

We have applied structural break and co-integration tests for stationarity and long-run relationship between the variables. The Toda–Yamamatoo causality is employed for investigation of causal relationship between the variables, and robustness of causality linkages is also tested by applying innovative accounting approach (IAA).

Findings

Our empirical analysis shows there is presence of long-run relationship among the variables. We find that remittance inflows stimulate electricity consumption in India. Industrialization is positively linked with electricity demand. However, trade openness declines the electricity consumption, but urbanization increases it. Furthermore, remittances inflows cause electricity consumption.

Originality/value

On the basis of findings, we conclude that due to positive impacts of remittances inflows, trade openness and urbanization, policymakers in the Indian economy need to be careful while designing sustainable environment policy. Otherwise, any sustainable environment policy in the name of protecting green environment will hamper the growth of remittance inflows, urbanization and FDI. If this exists, it may be argued that sustainable growth in India will not be possible in the face of sustainable environment policy.
Biased assessment of ongoing admixture using STRUCTURE in the absence of reference samples
Authors: Ravagni Sara , Sanchez‐Donoso Ines , Vilà Carles
Published: October 2020

Detection of hybridization and introgression is important in ecological research as in conservation and evolutionary biology. STRUCTURE is one of the most popular software to study introgression and allows estimating what proportion of the genome of each individual belongs to each ancestral population, even in cases where no reference sample from the ancestral nonadmixed populations is previously identified. In spite of its frequent use, some studies have indicated that ancestry estimates may not always be reliable. We simulated population data under different conditions with regard to the genetic differentiation between ancestral populations, number of loci considered, number of alleles per marker and hybridization rate, and analysed data with STRUCTURE. When reference samples were not included, the comparison of the known degree of admixture for each simulated individual and the value estimated with STRUCTURE revealed a strong underestimation of the level of introgression, classifying many admixed individuals as nonadmixed. This derives from an inaccurate estimation of the ancestral allele frequencies. When samples from the nonadmixed ancestral population were included as reference in the analyses, the bias in the estimations was reduced. The most accurate estimates were obtained when potentially admixed samples were few in relation to reference samples. Thus, whenever possible, a very large proportion of nonadmixed reference samples should be included in admixture assessments and different approaches should be combined. The misestimate of the amount of introgression can impair our understanding of the evolutionary history of species and misguide conservation efforts.
Drinking Motives as Moderators of In‐the‐Moment Drinking Risks in Response to Trauma‐Related Distress
Authors: Zaso Michelle J. , Read Jennifer P.
Published: October 2020

Background

Trauma exposure and posttraumatic stress disorder (PTSD) symptomatology are linked to increased risk for problematic drinking, yet the factors that increase such risk remain largely unknown. Theoretical models suggest that affectively oriented drinking motives may be central to trauma‐related drinking. Specifically, individual‐level motivations to drink to regulate affect may be important for moderating drinking urges that occur acutely in response to trauma cues. Further, elevated distress associated with PTSD symptomatology may increase any affectively motivated, momentary drinking risks. However, research has yet to examine these dynamic affective processes. In a large experimental sample, the current study tested whether affective (i.e., coping and enhancement) drinking motives and PTSD symptomatology moderated individuals’ drinking urge in response to a trauma cue in a laboratory cue reactivity paradigm.

Methods

College drinkers (n = 611, 53% female) were recruited and selected across levels of trauma exposure and PTSD symptomatology by a structured clinical interview. Participants were randomized to a personalized trauma or neutral cue, reporting on their urge to drink alcohol before and after cue exposure. Drinking motives were assessed at the end of the experimental session.

Results

Trauma cue associations with drinking urge were moderated by coping, but not enhancement, motives. Specifically, stronger coping motives were associated with increases in urge to drink alcohol following exposure to a trauma but not neutral cue. PTSD classification did not significantly moderate these associations.

Conclusions

Coping motives may increase drinking urge immediately following exposure to trauma cues and may differentiate individuals most at risk for problematic drinking during trauma‐associated distress. Findings support momentary negative affect processes driving dynamic, immediate trauma‐related drinking risks.
Comorbid rectus abdominis diastasis is a risk factor for recurrence of umbilical hernia in Japanese patients
Authors: Nishihara Yuichi , Asami Momoko , Shimada Takehiro , Kawaguchi Yoshiki , Omoto Kenichiro
Published: October 2020

Introduction

Rectus abdominis diastasis (RAD) is characterized by thinning and widening of the linea alba and laxity of the ventral abdominal muscle. RAD, when coexistent with umbilical hernia, is considered a risk factor for hernia recurrence. We investigated the impact of comorbid RAD in patients with umbilical hernia who had undergone hernia repair.

Methods

We enrolled 30 patients who had undergone umbilical hernia repair using either a laparoscopic or anterior approach between April 2006 and May 2018. We diagnosed RAD according to preoperative CT. The outcomes of patients with umbilical hernia, the RAD group, and the non‐RAD group were compared, especially in terms of recurrence.

Results

Twenty‐five patients (83%) presented with RAD, including three patients (12%) with postoperative recurrence who were allocated to the RAD group. The median BMI in the RAD group was 27.2 kg/m2. In the RAD group, a prosthesis mesh was used in 12 patients (48%), and nonabsorbable suture material was used in four patients (16%). There was no statistically significant difference between the two groups in terms of age, hernial orifice diameter, surgical technique, or operative time.

Conclusion

The rate of comorbid umbilical hernia in Japanese patients with RAD was high, as was the recurrence rate of umbilical hernia. We strongly recommend preoperative detection of RAD. We also recommend mesh‐based repair of the midline and nonabsorbable suture material to decrease the recurrence rate, irrespective of hernia size.