bluuebunny/crossref_metadata_2025 huggingface dataset:
GIS-based approach and multivariate statistical analysis for identifying sources of heavy metals in marine sediments from the coast of Hong Kong
Authors: Huang Fengwen , Chen Chen
Published: July 2022

Multiple methods consisting of geographic information system (GIS) technique, enrichment factor (EF), potential ecological risk index (PEI) and multivariate statistical methods was developed to identify anthropogenic heavy metal sources in marine sediments of Hong Kong. The distributions of heavy metals in sediments have been analyzed, and their pollution degrees, corresponding potential ecological risks and source identifications have been studied using geo-accumulation index, potential ecological risk index and integrated multivariate statistical methods, respectively. Three different types of anthropogenic inputs could be identified via multivariate analysis. Acoording to the findings, the first principal component might originate from the industrial discharges and shipping activities. The second principal component were identified from the natural sources. The third component mainly from the municipal discharges and industrial wastewater. These results provide baseline information for both the coastal environment management and the worldwide heavy metal distribution and assessment.
Phylogenetic Biodiversity Metrics Should Account for Both Accumulation and Attrition of Evolutionary Heritage
Authors: Rosindell James , Manson Kerry , Gumbs Rikki , Pearse William D. , Steel Mike
Published: July 2022

Abstract

Phylogenetic metrics are essential tools used in the study of ecology, evolution and conservation. Phylogenetic diversity (PD) in particular is one of the most prominent measures of biodiversity, and is based on the idea that biological features accumulate along the edges of phylogenetic trees that are summed. We argue that PD and many other phylogenetic biodiversity metrics fail to capture an essential process that we term attrition. Attrition is the gradual loss of features through causes other than extinction. Here we introduce ‘EvoHeritage’, a generalisation of PD that is founded on the joint processes of accumulation and attrition of features. We argue that whilst PD measures evolutionary history, EvoHeritage is required to capture a more pertinent subset of evolutionary history including only components that have survived attrition. We show that EvoHeritage is not the same as PD on a tree with scaled edges; instead, accumulation and attrition interact in a more complex non-monophyletic way that cannot be captured by edge lengths alone. This leads us to speculate that the one dimensional edge lengths of classic trees may be insufficiently flexible to capture the nuances of evolutionary processes. We derive a measure of EvoHeritage and show that it elegantly reproduces species richness and PD at opposite ends of a continuum based on the intensity of attrition. We demonstrate the utility of EvoHeritage in ecology as a predictor of community productivity compared with species richness and PD. We also show how EvoHeritage can quantify living fossils and resolve their associated controversy. We suggest how the existing calculus of PD-based metrics and other phylogenetic biodiversity metrics can and should be recast in terms of EvoHeritage accumulation and attrition.

Candidate cover image

Artistic cover image prepared for this manuscript. The central tree depicts the gain and loss of Evolutionary Heritage (EvoHeritage) along each edge with its many coloured sections. EvoHeritage is proposed as an expansion of the concept of phylogenetic diversity. Around the outside of the tree are species that feature in our two practical applications of the EvoHeritage calculus: mammals identified as ‘living fossils’ and plants included in our study of community productivity. The cover image was generated by James Rosin-dell following discussions with co-authors. The Caenolestes outline (representing shrew opossums) and Dromiciops outline (monito del monte) used as components of this image are credited to Sarah Werning and provided under a CC BY 3.0 license; both images were recoloured in brown and placed over a shaded circle. All other images used as components are from the public domain. We thank Mina Mincheva for useful feedback on earlier drafts of the cover image.
Adipocyte differentiation of 3T3-L1 cells under TAF, TDF and INSTIs selective challenge: an in vitro model
Authors: Perna A. , Carleo M.A. , Mascolo S. , Guida A. , Contieri M. , Sellitto C , Hay E. , De Blasiis P. , Lucariello A. , Guerra G. , Baldi A. , De Luca A. , Maggi P. , Esposito V.
Published: July 2022

Integrase strand transfer inhibitors (INSTI) are a recently available class of antiretroviral therapy (ART) medications with a good tolerability profile and a high genetic barrier to HIV drug resistance. However, several studies report more significant weight gain among persons receiving INSTI-based ART regimens for initial therapy compared to protease inhibitors (PIs) and nucleoside reverse transcriptase inhibitors (NNRTI)-based regimens. In our experimental setting, we used the in vitro model of adipogenesis of 3T3-L1 cells to investigate the effects of the NRTIs tenofovir disoproxil fumarate (TDF) and tenofovir alafenamide (TAF), alone or in combination with four integrase strand transfer inhibitors: raltegravir (RAL), elvitegravir (ELV), dolutegravir (DTG) and bictegravir (BIC) on adipose differentiation. In addition, protein expression levels of PPARɣ and C/EBPα, and the intracellular lipid accumulation by Red Oil staining, were used to monitor adipocyte differentiation. Compared to control, RAL, ELV, DTG, and BIC were all able to increase adipogenesis, being in this, RAL and ELV more efficient. On the other hand, TAF and TDF inhibited adipogenesis. Moreover, when used in combination with the other INSTI molecules, TAF and TDF were able to reduce the adipogenic effects of all four drugs. This ability was more evident when TAF was used in combination with DTG and BIC. All these data suggest that TAF and TDF have an inhibitory effect on adipogenesis in vitro and that they could also effectively counteract the increased adipogenesis caused by the treatment with INSTIs. Finally, to evaluate if the 3T3-L1 cell could express fibroblast-like features following INSTIs treatment, we evaluated the immunohistochemical expression of ER-TR7, a well-known fibroblastic marker. This last assay showed that treatment with INSTIs increased the expression of ER-TR7 compared to control and to cells treated with TAF o TDF.

In conclusion, our experimental data support the evidence that in vitro challenge of 3T3-L1 cells with INSTIs is able to increase adipocytic differentiation and to drive a number of these cells toward the expression of fibroblastic features, with a different degree according to the various drugs used, while TAF and TDF have an antagonistic role on this phenomenon.
Plap-1/Aspn lineage tracing and single-cell transcriptomics reveals cellular dynamics in the periodontal ligament
Authors: Iwayama Tomoaki , Iwashita Mizuho , Miyashita Kazuya , Sakashita Hiromi , Matsumoto Shuji , Tomita Kiwako , Bhongsatiern Phan , Kitayama Tomomi , Ikegami Kentaro , Shimbo Takashi , Tamai Katsuto , Murayama Masanori A , Ogawa Shuhei , Iwakura Yoichiro , Yamada Satoru , Olson Lorin E , Takedachi Masahide , Murakami Shinya
Published: July 2022

Periodontal tissue supports teeth in the alveolar bone socket via fibrous attachment of the periodontal ligament (PDL). The PDL contains periodontal fibroblasts and stem/progenitor cells, collectively known as PDL cells (PDLCs), on top of osteoblasts and cementoblasts on the surface of alveolar bone and cementum, respectively. However, the characteristics and lineage hierarchy of each cell type remain poorly defined. This study identified periodontal ligament associated Protein-1 (Plap-1/Aspn) as a PDL-specific extracellular matrix. We generated knock-in mice expressing CreERT2 and GFP specifically in Plap-1-positive PDLCs. Genetic lineage tracing confirmed the long-standing hypothesis that PDLCs differentiated into osteoblasts and cementoblasts. A PDL single-cell atlas defined cementoblasts and osteoblasts as Plap-1-Ibsp+Sparcl1+ and Plap-1-Ibsp+Col11a2+, respectively. Other populations such as Nes+ mural cells, S100B+ Schwann cells, and other non-stromal cells were also identified. RNA velocity analysis suggested that Plap-1highLy6a+ cell population was the source of PDLCs. Lineage tracing of Plap-1+ PDLCs during the periodontal injury model showed periodontal tissue regeneration by PDLCs. Our study defines diverse cell populations in PDL and clarifies the role of PDLCs in periodontal tissue homeostasis and repair.
Automation of yeast spot assays using an affordable liquid handling robot
Authors: Taguchi Shodai , Suda Yasuyuki , Irie Kenji , Ozaki Haruka
Published: July 2022

The spot assay of the budding yeastSaccharomyces cerevisiaeis an experimental method that is used to evaluate the effect of genotypes, medium conditions, and environmental stresses on cell growth and survival. Automation of the spot assay experiments from preparing a dilution series to spotting to observing spots continuously has been implemented based on large laboratory automation devices and robots, especially for high-throughput functional screening assays. However, there has yet to be an affordable solution for the automated spot assays suited to researchers in average laboratories and with high customizability for end-users. To make reproducible spot assay experiments widely available, we have automated the plate-based yeast spot assay of budding yeast using Opentrons OT-2 (OT-2), an affordable liquid-handling robot, and a flatbed scanner. We prepared a 3D-printed mount for the Petri dish to allow for precise placement of the Petri dish inside the OT-2. To account for the uneven height of the agar plates, which were made by human hands, we devised a method to adjust the z-position of the pipette tips which is based on the weight of each agar plate. During the incubation of the agar plates, a flatbed scanner was used to automatically take images of the agar plates over time, allowing researchers to quantify and compare the cell density within the spots at optimal time pointsa posteriori. Furthermore, the accuracy of the newly developed automated spot assay was verified by performing spot assays with human experimenters and the OT-2 and quantifying the yeast-grown area of the spots. This study will contribute to the introduction of automated spot assays and the automated acquisition of growth processes in conventional laboratories that are not adapted for high-throughput laboratory automation.
Epidemiology and Determinants of Survival for Primary Intestinal Non-Hodgkin’s Lymphoma – A Population Based Study
Authors: Singh Vinit , Gor Dhairya , Gupta Varsha , Jacob Aasems , Du Doantrang , Eltoukhy Hussam , Meghal Trishal
Published: July 2022

Introduction

Gastrointestinal tract is the most common site of extra nodal non-Hodgkin’s lymphoma (EN-NHL). Most of the published data have been on gastric NHL with limited studies on primary intestinal - Non-Hodgkin’s Lymphoma (PI-NHL) considering rare incidence. We performed epidemiological and survival analysis for PI-NHL from the Surveillance, Epidemiology, and End Results (SEER) 18 database.

Methods

A total of 9143 PI-NHL cases of age ≥18 years were identified from the SEER 18 database for the period 2000-2015. 8568 Patients were included for survival analysis. Cause specific Survival (CSS) and overall survival analysis (OS) were done for PINHL and PI-diffuse large B-cell lymphoma (PI-DLBCL) using gender, age of onset, treatment, histology, stage, and Year of diagnosis. Survival analysis was done by using cox-proportional hazard model and Kaplan Meier plot with log-rank test.

Results

The percentage of PI-NHL of all the intestinal cancers and extra nodal non-Hodgkin’s lymphoma were 1.35 %, and 10.52%, respectively. The age-adjusted incidence was 0.9145/100,000 population for the study population. PI-NHL was more common among patients aged≥60 Years, male and non-Hispanics whites. Majority of patients were diagnosed at stage 1 and 2 (74%), and DLBCL (44.8%) was the most common histology. In OS analysis, Significant increased risk of mortality was seen with T-cell NHLs vs. DLBCL (HR – 2.56), patients aged ≥60 vs <60 Years (HR – 2.87), stage 4 vs Stage 1 (HR – 1.93), male vs. female (HR- 1.17), with best outcome seen in patient treated with combination of chemotherapy and surgery vs. none (HR – 0.45). Similar results were seen in CSS and for primary intestinal DLBCL as well. Significant improvement in outcomes was observed for PI-DLBCL patients receiving chemotherapy with/without surgery.

Conclusion

Findings from our large, population-based study reveal PI-NHL is a rare type of intestinal malignancy with significant difference in survival based on histological and epidemiological characteristics.
A simple SEIR-V model to estimate COVID-19 prevalence and predict SARS-CoV-2 transmission using wastewater-based surveillance data
Authors: Phan Tin , Brozak Samantha , Pell Bruce , Gitter Anna , Mena Kristina D. , Kuang Yang , Wu Fuqing
Published: July 2022

Wastewater-based surveillance (WBS) has been widely used as a public health tool to monitor SARS-CoV-2 transmission. However, epidemiological inference from WBS data remains understudied and limits its application. In this study, we have established a quantitative framework to estimate COVID-19 prevalence and predict SARS-CoV-2 transmission through integrating WBS data into an SEIR-V model. We conceptually divide the individual-level viral shedding course into exposed, infectious, and recovery phases as an analogy to the compartments in population-level SEIR model. We demonstrated that the temperature effect on viral losses in the sewer can be straightforwardly incorporated in our framework. Using WBS data from the second wave of the pandemic (Oct 02, 2020 – Jan 25, 2021) in the Great Boston area, we showed that the SEIR-V model successfully recapitulates the temporal dynamics of viral load in wastewater and predicts the true number of cases peaked earlier and higher than the number of reported cases by 16 days and 8.6 folds (R = 0.93), respectively. This work showcases a simple, yet effective method to bridge WBS and quantitative epidemiological modeling to estimate the prevalence and transmission of SARS-CoV-2 in the sewershed, which could facilitate the application of wastewater surveillance of infectious diseases for epidemiological inference and inform public health actions.
Fluorescence spectroscopy of low-level endogenous β-adrenergic receptor expression at the plasma membrane of differentiating human iPSC-derived cardiomyocytes
Authors: Gmach Philipp , Bathe-Peters Marc , Telugu Narasimha , Lohse Martin J , Annibale Paolo
Published: July 2022

The potential of human induced pluripotent stem cells (hiPSCs) to be differentiated into cardiomyocytes (CMs) mimicking the adult CMs functional morphology, marker genes and signaling characteristics has been investigated since over a decade. The evolution of the membrane localization of CM-specific G protein-coupled receptors throughout differentiation has received, however, only limited attention to date. We employ here advanced fluorescent spectroscopy, namely linescan Fluorescence Correlation Spectroscopy (FCS), to observe how the plasma membrane abundance of the β1- and β2-adrenergic receptors (β1/2-ARs), labelled using a bright and photostable fluorescent antagonist, evolves during long-term monolayer culture of hiPSC-derived CMs. We compare it to the kinetic of observed mRNA levels in wildtype (WT) hiPSCs and in two CRISPR/Cas9 knock-in clones. We conduct these observations against the backdrop of our recent report that β2-ARs, as opposed to β1-ARs, specifically segregate to the T-Tubular system of adult CMs.
Predatory fish preferentially target virtual prey with Lévy motion rather than Brownian motion
Authors: Ioannou Christos C. , Braga Carvalho Luis Arrochela , Budleigh Chessy , Ruxton Graeme D.
Published: July 2022

Of widespread interest in animal behaviour and ecology is how animals search their environment for resources, and whether these search strategies are optimal. However, movement also affects predation risk through effects on encounter rates, the conspicuousness of prey, and the success of attacks. Here we use predatory fish attacking a simulation of virtual prey to test whether predation risk is associated with movement behaviour. Despite often being demonstrated to be a more efficient strategy for finding resources, we find that prey displaying Lévy motion are twice as likely to be targeted by predators than prey utilising Brownian motion. This result emphasises that costs of predation risk need to be considered alongside the foraging benefits when comparing different movement strategies.
Direct calculation of cryo EM and crystallographic model maps for real-space refinement
Authors: Urzhumtsev Alexandre , Urzhumtseva Ludmila , Lunin Vladimir Y.
Published: July 2022

Real-space refinement of atomic models improves them by their fit to experimental scattering electrostatic potential maps in cryo electron microscopy and to electron density maps in crystallography. This procedure has a number of advantages in comparison with reciprocal-space refinement, is complementary to it in crystallographic studies and is the principal technique in cryo EM. An accurate real-space refinement of atomic models can be done by comparison of the model maps, calculated according to the respective theory, with the experimental ones, when the former mimic imperfections of the latter, mainly a limited resolution and an atomic disorder. Calculation of model maps as a sum of contributions of individual atoms means that these contributions - atomic images in the given map – should also be affected by the resolution and positional disorder. This blurs atomic images and surrounds their central peak by Fourier ripples. These ripples can be described by a specially designed function which allows combining both principal effects of map imperfection in an analytic way. The atomic images, at any resolution and with any value of the atomic displacement parameter, can be decomposed into a linear combination of such functions with the precalculated parameter values. As a consequence, each map value becomes an analytic function of atomic parameters including displacement parameter and a local resolution if required. Using the chain rule for the score function which compares the maps, such model results in analytic expressions for its partial derivatives with respect to all atomic parameters allowing an efficient real-space refinement. At the same time, for practical calculations atomic images are cut at some truncation distance, i.e., include a limited number of ripples. This introduced in the model maps errors which are not present in the experimental maps. Due to oscillating behavior of the atomic images, the choice of the value of this truncation distance is not straightforward and discussed in this work.

Synopsis

A new method is suggested to calculate maps of a limited and eventually inhomogeneous resolution as an analytic function of all atomic parameters, including local resolution.
Identification of novel antiviral drug candidates using an optimized SARS-CoV-2 phenotypic screening platform
Authors: Bojkova Denisa , Reus Philipp , Panosch Leona , Bechtel Marco , Rothenburger Tamara , Kandler Joshua , Pfeiffer Annika , Wagner Julian U.G. , Shumliakivska Mariana , Dimmeler Stefanie , Olmer Ruth , Martin Ulrich , Vondran Florian , Toptan Tuna , Rothweiler Florian , Zehner Richard , Rabenau Holger , Osman Karen L. , Pullan Steven T. , Carroll Miles , Stack Richard , Ciesek Sandra , Wass Mark N , Michaelis Martin , Cinatl Jindrich
Published: July 2022

Reliable, easy-to-handle phenotypic screening platforms are needed for the identification of anti-SARS-CoV-2 compounds. Here, we present caspase 3/7 activity as a read-out for monitoring the replication of SARS-CoV-2 isolates from different variants, including a remdesivir-resistant strain, and of other coronaviruses in a broad range of cell culture models, independently of cytopathogenic effect formation. Compared to other cell culture models, the Caco-2 subline Caco-2-F03 displayed superior performance, as it possesses a stable SARS-CoV-2 susceptible phenotype and does not produce false-positive hits due to drug-induced phospholipidosis. A proof-of-concept screen of 1796 kinase inhibitors identified known and novel antiviral drug candidates including inhibitors of PHGDH, CLK-1, and CSF1R. The activity of the PHGDH inhibitor NCT-503 was further increased in combination with the HK2 inhibitor 2-deoxy-D-glucose, which is in clinical development for COVID-19. In conclusion, caspase 3/7 activity detection in SARS-CoV-2-infected Caco-2F03 cells provides a simple phenotypic high-throughput screening platform for SARS-CoV-2 drug candidates that reduces false positive hits.
Identification of long non-coding RNAs as substrates for cytoplasmic capping enzyme
Authors: Mukherjee Avik , Islam Safirul , Kieser Rachel E. , Kiss Daniel L. , Mukherjee Chandrama
Published: July 2022

Cytoplasmic capping returns a cap to specific mRNAs thus protecting uncapped RNAs from decay. Prior to the identification of cytoplasmic capping, uncapped mRNAs were thought to be degraded. Here, we test whether long non-coding RNAs (lncRNAs) are cytoplasmic capping enzyme (cCE) substrates. The subcellular localization of fourteen lncRNAs associated with sarcomas were examined in U2OS osteosarcoma cells. We used 5’ rapid amplification of cDNA ends (RACE) to assay uncapped forms of these lncRNAs. Inhibiting cytoplasmic capping elevated uncapped forms of selected lncRNAs indicating a plausible role of cCE in targeting them. Analysis of published cap analysis of gene expression (CAGE) data shows increased prevalence of certain 5’-RACE cloned sequences suggesting that these uncapped lncRNAs are cytoplasmic capping targets.
Structure of Geobacter OmcZ filaments suggests extracellular cytochrome polymers evolved independently multiple times
Authors: Wang Fengbin , Chan Chi H. , Suciu Victor , Mustafa Khawla , Si Dong , Hochbaum Allon I. , Egelman Edward H. , Bond Daniel R.
Published: July 2022

While early genetic and low resolution structural observations suggested that extracellular conductive filaments on metal reducing organisms such as Geobacter were composed of Type IV pili, it has now been established that bacterial c-type cytochromes can polymerize to form extracellular filaments capable of long-range electron transport. Atomic structures exist for two such cytochrome filaments, formed from the hexaheme cytochrome OmcS and the tetraheme cytochrome OmcE. Due to the highly conserved heme packing within the central OmcS and OmcE cores, and shared pattern of heme coordination between subunits, it has been suggested that these polymers have a common origin. We have now used cryo-EM to determine the structure of a third extracellular filament, formed from the Geobacter sulfurreducens octaheme cytochrome, OmcZ. In contrast to the linear heme chains in OmcS and OmcE, the packing of hemes, heme:heme angles, and between-subunit heme coordination is quite different in OmcZ. A branched heme arrangement within OmcZ leads to a highly surface exposed heme in every subunit, which may account for the formation of conductive biofilm networks, and explain the higher measured conductivity of OmcZ filaments. This new structural evidence suggests that conductive cytochrome polymers arose independently on more than one occasion from different ancestral multiheme proteins.
Pandemic modelling for regions implementing an elimination strategy
Authors: Hurford Amy , Martignoni Maria M. , Loredo-Osti J.C. , Anokye Francis , Arino Julien , Husain Bilal Saleh , Gaas Brian , Watmough James
Published: July 2022

During the COVID-19 pandemic, some countries, such as Australia, China, Iceland, New Zealand, Thailand, and Vietnam successfully implemented an elimination strategy, enacting strict border control and periods of lockdowns to end community transmission. Atlantic Canada and Canada’s territories implemented similar policies, and reported long periods with no community cases. In Newfoundland and Labrador (NL), Nova Scotia, and Prince Edward Island a median of 80% or more of daily reported cases were travel-related from July 1, 2020 to May 31, 2021. With increasing vaccination coverage, it may be appropriate to exit an elimination strategy, but most existing epidemiological frameworks are applicable only to situations where most cases occur in the community, and are not appropriate for regions that have implemented an elimination strategy. To inform the pandemic response in regions that are implementing an elimination strategy, we extend importation modelling to consider post-arrival travel restrictions, and pharmaceutical and non-pharmaceutical interventions in the local community. We find that shortly after the Omicron variant had begun spreading in Canada, the expected daily number of spillovers, infections spread to NL community members from travelers and their close contacts, was higher than any time previously in the pandemic. By December 24, 2021, the expected number of spillovers was 44% higher than the previous high, which occurred in late July 2021 shortly after travel restrictions were first relaxed. We develop a method to assess the characteristics of potential future community outbreaks in regions that are implementing an elimination strategy. We apply this method to predict the effect of variant and vaccination coverage on the size of hypothetical community outbreaks in Mount Pearl, a suburb of the St. John’s metropolitan area in NL. Our methodology can be used to evaluate alternative plans to relax public health restrictions when vaccine coverage is high in regions that have implemented an elimination strategy. This manuscript was submitted as part of a theme issue on“Modelling COVID-19 and Preparedness for Future Pandemics”.
Slow waning of antibodies following a third dose of BNT162b2 in adults who had previously received two doses of inactivated vaccine
Authors: Cowling Benjamin J. , Cheng Samuel M. S. , Martín-Sánchez Mario , Au Niki Y. M. , Chan Karl C. K. , Li John K. C. , Luk Leo L. H. , Tsang Leo C. H. , Ip Dennis K. M. , Poon Leo L. M. , Leung Gabriel M. , Peiris J. S. Malik , Leung Nancy H. L.
Published: July 2022

Introduction

Third doses of COVID-19 vaccination provide an important boost to immunity, reducing the risk of symptomatic infection and the risk of severe disease. Third doses have been particularly important for improving protection against variants. However, waning of clinical protection particularly against Omicron has been noted after receipt of third doses.

Methods

We administered BNT162b2 as a third dose to adults aged ≥30 years who had previously received two doses of inactivated vaccination. We collected blood before the third dose and again after one month and six months, and tested sera using a spike receptor binding domain IgG enzyme-linked immunosorbent assay, a surrogate virus neutralization test, and live virus plaque reduction neutralization assay against ancestral virus and Omicron BA.2.

Results

We administered BNT162b2 as a third dose to 314 adults. We found robust antibody responses to the ancestral strain at six months after receipt of BNT162b2. Antibody responses to Omicron BA.2 were weaker after the third dose and had declined to a low level by six months. From a small number of participants we observed that natural infection or a fourth dose of vaccination generated similar antibody levels against ancestral virus, but infection generated higher antibody level against Omicron BA.2 than vaccination, suggesting a potential advantage in the breadth of antibody response from hybrid immunity.

Conclusions

While antibody levels against the ancestral strain remained robust at six months after the third dose, antibody levels against Omicron BA.2 had fallen to low levels suggesting the potential benefits of a fourth dose.
Comparing methods to predict baseline mortality for excess mortality calculations
Authors: Ferenci Tamás
Published: July 2022

Background

The World Health Organization (WHO)’s excess mortality estimates presented in May 2022 stirred controversy, due in part to the high estimate provided for Germany, which was later attributed to the spline model used. This paper aims to reproduce the problem using synthetic datasets, thus allowing the investigation of its sensitivity to parameters, both of the mortality curve and of the used method, thereby shedding light on the conditions that gave rise to this error and identifying possible remedies.

Methods

A negative binomial model was used accounting for long-term change, seasonality, flu seasons, and heat waves. Simulated mortality curves from this model were then analysed using simple methods (mean, linear trend), the WHO method, and the method of Acosta and Irizarry.

Results

The performance of the WHO’s method with its original parametrization was indeed very poor, however it can be profoundly improved by a better choice of parameters. The Acosta–Irizarry method outperformed the WHO method despite being also based on splines, but it was also dependent on its parameters. Linear extrapolation could produce very good results, but was highly dependent on the choice of the starting year, while the average was the worst in almost all cases.

Conclusions

Splines are not inherently unsuitable for predicting baseline mortality, but caution should be taken. In particular, the results suggest that the key issue is that the splines should not be too flexible to avoid overfitting. Even after having investigated a limited number of scenarios, the results suggest that there is not a single method that outperforms the others in all situations. As the WHO method on the German data illustrates, whatever method is chosen, it remains important to visualize the data, the fit, and the predictions before trusting any result. It will be interesting to see whether further research including other scenarios will come to similar conclusions.
COVID-19 vaccine effectiveness against progression to in-hospital mortality — Zambia, 2021-2022
Authors: Chanda Duncan , Hines Jonas Z , Itoh Megumi , Fwoloshi Sombo , Minchella Peter A , Zyambo Khozya D. , Sivile Suilanji , Kampamba Davies , Chirwa Bob , Chanda Raphael , Mutengo Katongo , Kayembe Mazinga F. , Chewe Webster , Chipimo Peter , Mweemba Aggrey , Agolory Simon , Mulenga Lloyd B.
Published: July 2022

Background

COVID-19 vaccines are highly effective for reducing severe disease and mortality. However, vaccine effectiveness data is limited from sub-Saharan Africa, where SARS-CoV-2 epidemiology has differed from other regions. We report COVID-19 vaccine effectiveness against progression to in-hospital mortality in Zambia.

Methods

We conducted a retrospective cohort study among admitted patients at eight COVID-19 treatment centers across Zambia during April 2021 through March 2022. Patient demographic and clinical information including vaccination status and hospitalization outcome (discharged or died) werecollected. Multivariable logistic regression was used to assess the odds of in-hospital mortality by vaccination status, adjusted for age, sex, number of comorbid conditions, disease severity, and COVID-19 treatment center. Vaccine effectiveness of ≥1 vaccine dose was calculated from the adjusted odds ratio.

Results

Among 1,653 patients with data on their vaccination status and hospitalization outcome, 365 (22.1%) died. Overall, 236 (14.3%) patients had received ≥1 vaccine dose before hospital admission. For patients who had received ≥1 vaccine dose, 22 (9.3%) died compared with 343 (24.2%) among unvaccinated patients (p <0.01). The median time since receipt of a first vaccine dose was 52.5 days (IQR: 28-107). Vaccine effectiveness for progression to in-hospital mortality among hospitalized patients was 64.8% (95% CI: 42.3-79.4%).

Conclusions

Among patients admitted to COVID-19 treatment centers in Zambia, COVID-19 vaccination was associated with lower progression to in-hospital mortality. These data are consistent with evidence from other countries demonstrating benefit of COVID-19 vaccination against severe complications. Vaccination is a critical tool for reducing the consequences of COVID-19 in Zambia.

Key points

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Receipt of ≥1 COVID-19 vaccine dose reduced progression to in-hospital mortality in Zambia by 64.8%

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Mortality benefit of COVID-19 vaccines was sustained during the period of omicron transmission in Zambia
Foxi3 Suppresses Signaling Center Fate and is Necessary for the Early Development of Mouse Teeth
Authors: Mogollón Isabel , Kangasniemi Niko , Moustakas-Verho Jacqueline Emmanuel , Ahtiainen Laura
Published: July 2022

Tooth morphogenesis is regulated by ectodermal-mesenchymal interactions which are controlled by reiteratively used, evolutionarily conserved pathways. How these signals translate into different cellular behaviors is beginning to be understood. Embryonic cell behaviors are regulated by signaling centers that define organ position, size, and shape. The recently identified initiation knots (IKs) and the well-known enamel knots (EK) are tooth epithelial signaling centers that drive proliferation of the neighboring cells and are involved at different stages of morphogenesis, from the early epithelial thickening to the final formation of shape. Signaling center cell fate and maintenance can be regulated by numerous factors. Here, we studied the early stages of murine incisor and molar epithelial morphogenesis and overcame the previous shortage of early-stage mutant models to functionally manipulate the initiation processes of tooth morphogenesis. We achieved the early conditional knock down of the forkhead-box transcription factor Foxi3 during tooth initiation and used imaging approaches to explore cellular and molecular disease mechanisms, specifically those related to signaling center dysfunction in tooth dysplasia. We show that early deficiency of Foxi3 in incisors and molars frequently arrests growth at bud stage, whereas later knockdown of Foxi3 affects tooth downgrowth and shape. Cell-level analyses revealed a decrease in epithelial proliferation and the ectopic appearance of cells with hallmarks of signaling centers: quiescent cell state and canonical Wnt activity. However, the distribution of these cells was wider all over the tooth buds with abnormal decrease of apoptosis. We postulate that, depending on Foxi3 expression levels, the bud cells shift commitment into signaling center fate, ultimately leading to growth arrest or growth/shape changes, implicating Foxi3 as a regulator of cell fates between the signaling centers and proliferating bud cells.
A highly multiplexed assay to monitor pathogenicity, fungicide resistance and gene flow in the fungal wheat pathogenZymoseptoria tritici
Authors: Bellah Hadjer , Gazeau Gwilherm , Gélisse Sandrine , Amezrou Reda , Marcel Thierry C. , Croll Daniel
Published: July 2022

Crop pathogens pose severe risks to global food production due to the rapid rise of resistance to pesticides and host resistance breakdowns. Predicting future risks requires monitoring tools to identify changes in the genetic composition of pathogen populations. Here we report the design of a microfluidics-based amplicon sequencing assay to multiplex 798 loci targeting virulence and fungicide resistance genes, and randomly selected genome-wide markers for the fungal pathogenZymoseptoria tritici. The fungus causes one of the most devastating diseases on wheat showing rapid adaptation to fungicides and host resistance. We optimized the primer design by integrating polymorphism data from 632 genomes of the same species. To test the performance of the assay, we genotyped 192 samples in two replicates. Analysis of the short-read sequence data generated by the assay showed a fairly stable success rate across samples to amplify a large number of loci. The performance was consistent between samples originating from pure genomic DNA as well as material extracted directly from infected wheat leaves. In samples with mixed genotypes, we found that the assay recovers variations in allele frequencies. We also explored the potential of the amplicon assay to recover transposable element insertion polymorphism relevant for fungicide resistance. As a proof-of-concept, we show that the assay recovers the pathogen population structure across French wheat fields. Genomic monitoring of crop pathogens contributes to more sustainable crop protection and yields.
Auditor characteristics and the financial reporting quality: the moderating role of the client business strategy
Authors: Soroushyar Afsaneh
Published: July 2022

Purpose

This study examines whether and how a client's business strategy can affect the relationship between auditor characteristics and financial reporting quality.

Design/methodology/approach

In this study, auditor industry specialization and tenure were used as proxies for auditor characteristics. The client business strategy was measured using the resource allocation index method. Finally, discretionary accruals are used to assess financial reporting quality. This study includes 1,450 firm-year observations and 145 companies listed on the Tehran Stock Exchange (TSE) over a ten-year period from 2011 to 2020. The research hypotheses were analyzed using a multivariate regression model and panel data.

Findings

The results show that auditor industry specialization increases financial reporting quality. This relationship improves when the client's business strategy deviates from the industry–normal strategy. The research findings state that auditor tenure has a positive association with financial reporting quality, and this relationship is strengthened when the company's business strategy deviates from the normal industry strategy.

Practical implications

The findings of this study provide important evidence for investors, firm management, and auditing firms. Investors must consider the auditor characteristics when selecting companies listed on the TSE. Managers of Iranian companies are advised to consider the auditor's characteristics when choosing an audit firm to increase financial reporting quality. Audit firms should evaluate their business strategies in audit planning to increase the quality of financial reporting.

Originality/value

To the best of the authors’ knowledge, this is the first empirical study to examine the relationship between auditor characteristics and the financial reporting quality in the emerging capital market by considering the clients' business strategy.
Digitalization in corporate communications: understanding the emergence and consequences of CommTech and digital infrastructure
Authors: Brockhaus Jana , Buhmann Alexander , Zerfass Ansgar
Published: July 2022

Purpose

This article studies the digitalization of corporate communications and the emergence of communication technology (CommTech). The authors show communicators' expectations regarding digitalization, gauge the current level of digitalization across communication departments and agencies and examine the effectiveness of strategic approaches to manage digitalization.

Design/methodology/approach

The authors conceptualize the phenomenon of CommTech and propose a framework for studying CommTech's emergence and consequences by combining (1) recent theorizing on digitalization in corporate communications, (2) the concept of digital maturity from information systems research and (3) a socio-technical approach to analyze the development of work systems. The authors apply this framework in a quantitative study (n = 2,664) among communication practitioners from 46 countries.

Findings

While digitalization of both communication activities and the underlying support infrastructure is seen as critically important among communicators, a large fraction of communication departments and agencies are still assessed as digitally immature. Further, data reveal the relevance of different (technology, tasks, structure and people) dimensions of digitalization strategies and the influence of such strategies on the digital maturity of communications.

Practical implications

The framework and empirical instruments developed in this study help practitioners to uncover and evaluate the level of digital maturity of communication departments and agencies. This allows to identify current challenges and future opportunities for improvement.

Originality/value

The authors propose a concise definition for the much-debated concept of CommTech and develop a new theoretical framework for understanding CommTech's emergence and consequences in the profession. This empirical work constitutes the first large-scale study on the digital maturity of communication departments and agencies.
Parallel-in-space-and-time finite-element analysis of electric machines using time step overlapping in a massively parallel computing environment
Authors: Takahashi Yasuhito , Fujiwara Koji , Iwashita Takeshi
Published: July 2022

Purpose

This study aims to enhance the parallel performance of a parallel-in-space-and-time (PinST) finite-element method (FEM) using time step overlapping. The effectiveness of the developed method is clarified in a magnet eddy-current loss analysis of a practical interior permanent magnet synchronous motor (IPMSM) using a massively parallel computing environment.

Design/methodology/approach

The developed PinST FEM is a combination of the domain decomposition method as a parallel-in-space (PinS) method and a parallel time-periodic explicit error correction (PTP-EEC) method, which is one of the parallel-in-time (PinT) approaches. The parallel performance of the PinST FEM is further improved by overlapping the time steps with different processes in the PTP-EEC method.

Findings

By applying the overlapping PTP-EEC method, the convergence of the transient solution to its steady state can be accelerated drastically. Consequently, the good parallel performance of the PinST FEM is achieved in magnetic field analyses of the practical IPMSM using a massively parallel computing environment, in which over 10,000 processes are used.

Originality/value

In this study, the PinST FEM based on time step overlapping is newly developed and its effectiveness is demonstrated in a massively parallel computing environment, in which using either the PinS or PinT method alone cannot achieve sufficient parallel performance. This finding implies a new direction of parallel computing approaches for electromagnetic field computation.
Drivers of digital supply chain transformation in SMEs and large enterprises – a case of COVID-19 disruption risk
Authors: Ngo Vu Minh , Pham Hiep Cong , Nguyen Huan Huu
Published: July 2022

Purpose

Digital transformation in supply chains (SCs) has emerged as one of the most effective ways to minimize SC disruption risks. Given the unprecedented impact of the COVID-19 pandemic on global SCs, this study aims to identify and provide empirical evidence about the drivers of digital SC transformation, considering the interactivity between environmental dynamism, technology, and organizational capabilities during the pandemic era.

Design/methodology/approach

Using partial least squares structural equation modeling (PLS-SEM), this study examines 923 firms in Vietnam to ascertain the drivers of digital SC transformation between small- and medium-sized enterprises (SMEs) and large enterprises, based on the technology–organization–environment (TOE) as an overarching framework.

Findings

This study finds that greater digital SC transformation adoption could be achieved under the interactivity between the TOE components of firms' technological competencies, learning capabilities, and disruptions in socioeconomic environments due to the COVID-19 pandemic. Moreover, a multigroup analysis shows that the drivers of digital SC transformation differ between SMEs and large enterprises. SMEs were found to be more motivated by the COVID-19 disruption risk when adopting digital SC models.

Originality/value

This study represents an original and novel contribution from Vietnam as an emerging market to the literature on the impact of COVID-19 on the global value chain. Apart from the unique dataset at the firm level, the analysis of interactions between external and internal drivers of digital SC transformation could provide crucial managerial implications for SMEs to survive major disruptions, such as those caused by the COVID-19 pandemic.
“Managing the “new normal”: the future of operations and supply chain management in unprecedented times”
Authors: Alexander Anthony , Blome Constantin , Schleper Martin C. , Roscoe Samuel
Published: July 2022

Purpose

The purpose of this article is to discuss the theme of managing operations and supply chains in the so-called “new normal”. It reflects the themes emerging from recent research and how these might be conceptualized.

Design/methodology/approach

The article reviews research presented at the EurOMA 2021 conference and eight papers subsequently developed into full journal papers. It considers conceptual themes contained in these papers and how they reflect recent turbulent events in the external business environment.

Findings

The article notes the themes of resilience in relation to the Covid-19 pandemic, environmental sustainability, especially climate change and the Sustainable Development Goals, and the significance of digital technologies. Additional themes relating to inter-organizational relationships, complexity and manager cognition are also considered. In order to provide useful insights for future disruptions, general concepts on epistemology and responsiveness are described.

Originality/value

The article discusses general principles across cutting-edge research in operations and supply chain management, to support improved performance to add economic and social value.
Relationship between ecosystem innovation and performance measurement models
Authors: da Silva Deoclécio Junior Cardoso , Lopes Luis Felipe Dias , Santos Costa Vieira da Silva Luciana , da Silva Wesley Vieira , Teixeira Clarissa Stefani , Veiga Claudimar
Published: July 2022

Purpose

This study examines the relationship between the innovation ecosystem and performance measurement models. Although the innovation ecosystem and measurement models are widely recognized, the existing literature lacks a comprehensive understanding of the relationship between the proposed themes. Furthermore, it does not reveal how studies can be grouped to propose a thematic typology of the relationship.

Design/methodology/approach

The authors present a systematic literature review conducted in the Web of Science and Scopus databases, from a textual corpus that aided the proposition of the typology that aims to provide answers regarding the addressed themes.

Findings

The results of this review are based on a total of sixty peer-reviewed articles from the innovation ecosystem literature and performance measurement models between 1995 and 2020. The results make several contributions to the literature. First, by integrating evidence from empirical studies, the authors identified a typology formed by three classes: (1) ecosystem agents (2) analytical focus and (3) structured measurement tools. Second, the authors verified the relationship between the themes and discovered the existence of gaps to be filled, with the proposition of three drivers. Third, the authors presented a comprehensive mapping of field studies with a descriptive analysis of the textual corpus.

Originality/value

The results of the research provide important implications for researchers, managers and policy makers. Furthermore, the authors suggest directions for future research, including the need to examine the performance of the entire innovation ecosystem, integrating the different agents that exist for performance measurement.