bluuebunny/crossref_metadata_2025 huggingface dataset:
The long and short of it: Benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies
Authors: Cook Ryan , Brown Nathan , Rihtman Branko , Michniewski Slawomir , Redgwell Tamsin , Clokie Martha , Stekel Dov J , Chen Yin , Scanlan David J , Hobman Jon L , Nelson Andrew , Jones Michael A , Smith Darren , Millard Andrew
Published: February 2023

Viral metagenomics has fuelled a rapid change in our understanding of global viral diversity and ecology. Long-read sequencing and hybrid approaches that combine long and short read technologies are now being widely implemented in bacterial genomics and metagenomics. However, the use of long-read sequencing to investigate viral communities is still in its infancy. While Nanopore and PacBio technologies have been applied to viral metagenomics, it is not known to what extent different technologies will impact the reconstruction of the viral community.

Thus, we constructed a mock phage community of previously sequenced phage genomes and sequenced using Illumina, Nanopore, and PacBio sequencing technologies and tested a number of different assembly approaches. When using a single sequencing technology, Illumina assemblies were the best at recovering phage genomes. Nanopore- and PacBio-only assemblies performed poorly in comparison to Illumina in both genome recovery and error rates, which both varied with the assembler used. The best Nanopore assembly had errors that manifested as SNPs and INDELs at frequencies ~4x and 120x higher than found in Illumina only assemblies respectively. While the best PacBio assemblies had SNPs at frequencies ~3.5 x and 12x higher than found in Illumina only assemblies respectively. Despite high read coverage, long-read only assemblies failed to recover a complete genome for any of the 15 phage, down sampling of reads did increase the proportion of a genome that could be assembled into a single contig.

Overall the best approach was assembly by a combination of Illumina and Nanopore reads, which reduced error rates to levels comparable with short read only assemblies. When using a single technology, Illumina only was the best approach. The differences in genome recovery and error rates between technology and assembler had downstream impacts on gene prediction, viral prediction, and subsequent estimates of diversity within a sample. These findings will provide a starting point for others in the choice of reads and assembly algorithms for the analysis of viromes.

Data Summary

All reads from virome sequencing were submitted to the ENA under study PRJEB56639. The assemblies are provided via FigShare (https://figshare.com/s/2d9b5121eb421d370455).

Author Notes

Eight Supplementary Tables and nine Supplementary Figures are available with the online version of this article.
New algorithm for pearl millet modelling in APSIM allowing a mechanistic simulation of tillers
Authors: Garin Vincent , Van Oosterom Erik , McLean Greg , Hammer Graeme , Murugesan Tharanya , Kaliamoorthy Sivasakthi , Diancumba Madina , Hajjarpoor Amir , Kholova Jana
Published: February 2023

We present a new algorithm for pearl millet simulation in APSIM. Compared to the actual released model, this new model increases the ability to simulate dynamic tillers by integrating recent progresses about biological understanding of the tillering mechanism. The new algorithm also offers the possibility to have an increased genetic control over key functions like canopy development and tillering through additional genotype related parameters. Next to model description, we also present the parametrization of 9444 and HHB 67-2, two genotypes broadly used in India. Overall, we could show that the new algorithm is able to reconstruct the main plant function like biomass accumulation and tillering. Some margin of improvement remains concerning the simulation of tiller cessation.
Overcoming resolution loss due to thermal magnetic field fluctuations from phase plates in transmission electron microscopy
Authors: Axelrod Jeremy J. , Petrov Petar N. , Zhang Jessie T. , Remis Jonathan , Buijsse Bart , Glaeser Robert M. , Mȕller Holger
Published: February 2023

We identify thermal magnetic field fluctuations, caused by thermal electron motion (“Johnson noise”) in electrically conductive materials, as a potential resolution limit in transmission electron microscopy with a phase plate. Specifically, resolution loss can occur if the electron diffraction pattern is magnified to extend phase contrast to lower spatial frequencies, and if conductive materials are placed too close to the electron beam. While our initial implementation of a laser phase plate (LPP) was significantly affected by these factors, a redesign eliminated the problem and brought the performance close to the expected level. The resolution now appears to be limited by residual Johnson noise arising from the electron beam liner tube in the region of the LPP, together with the chromatic aberration of the relay optics. These two factors can be addressed during future development of the LPP.
Tunable biomimetic bacterial membranes from binary and ternary lipid mixtures and their application in antimicrobial testing
Authors: Krok Emilia , Stephan Mareike , Dimova Rumiana , Piatkowski Lukasz
Published: February 2023

Reconstruction of accurate yet simplified mimetic models of cell membranes is a very challenging goal of synthetic biology. To date, most of the research focuses on the development of eukaryotic cell membranes, while reconstitution of their prokaryotic counterparts has not been fully addressed, and the proposed models do not reflect well the complexity of bacterial cell envelopes. Here, we describe the reconstitution of biomimetic bacterial membranes with an increasing level of complexity, developed from binary and ternary lipid mixtures. Giant unilamellar vesicles composed of phosphatidylcholine (PC) and phosphatidylethanolamine (PE); PC and phosphatidylglycerol (PG); PE and PG; PE, PG and cardiolipin (CA) at varying molar ratios were successfully prepared by the electroformation method. Each of the proposed mimetic models focuses on reproducing specific membrane features such as membrane charge, curvature, leaflets asymmetry, or the presence of phase separation. GUVs were characterized in terms of size distribution, surface charge, and lateral organization. Finally, the developed models were tested against the lipopeptide antibiotic daptomycin. The obtained results showed a clear dependency of daptomycin binding efficiency on the amount of negatively charged lipid species present in the membrane. We anticipate that the models proposed here can be applied not only in antimicrobial testing but also serve as platforms for studying fundamental biological processes in bacteria as well as their interaction with physiologically relevant biomolecules.
Energy dependence of signalling dynamics and robustness in bacterial two component systems
Authors: Forrest Joshua , Pan Michael , Crampin Edmund J. , Rajagopal Vijay , Stumpf Michael PH
Published: February 2023

One of the best known ways bacteria cells understand and respond to the environment are through Two-Component Systems (TCS). These signalling systems are highly diverse in function and can detect a range of physical stimuli including molecular concentrations and temperature, with a range of responses including chemotaxis and anaerobic energy production.

TCS exhibit a range of different molecular structures and energy costs, and multiple types co-exist in the same cell. TCSs that incur relatively high energy cost are abundant in biology, despite strong evolutionary pressure to efficiently spend energy.

We are motivated to discern what benefits, if any, the more energetically expensive variants had for a cell.

We seek to answer this question by modelling energy flow through two variants of TCS. This was accomplished using bond graphs, a physics-based modelling framework that accurately models energy transfer through different physical domains. Our analysis demonstrates that energy availability can affect a cell’s signal sensitivity, noise filtering effectiveness, and the stimulus level where cell response is maximal. We also found that these properties are determined not by the molecular parameters themselves, but the reaction rate parameters that govern the reaction systems as a whole.

This suggests possible connections between the molecular structure and evolutionary purpose of any two-component system. This opens the door to new synthetic circuit design in systems biology, and we propose new hypotheses about this link between structure and purpose that could be experimentally verified.

Author summary

Two-component systems are the main way many bacteria sense and respond to their environment. They exist in such well-studied bacteria asE. coliwhere they have been shown to detect a range of stimuli including nutrients, temperature, acidity, and pressure.

Two-component systems are ubiquitous in bacteria yet have a deceptively simple structure. Knowing how they operate and the purpose of variations in signalling structure is helpful to our understanding of cellular biology and the design of synthetic biological circuits. Critical unanswered questions remain about the energy usage and functional benefits of these systems.

We sought to improve our understanding of two-component systems by applying a physics-based modelling framework. We found that tracking energy flow through the cell reveals new energy-dependent behaviour in signalling sensitivity, noise filtering, and maximal cell response. We also found that these properties are not strictly dependent on the molecular properties themselves, but from the configuration of the reaction system as a whole.
Model-based deconvolution for DSC-MRI: A comparison of accuracy, precision, and computational complexity of parametric transit time distributions
Authors: Sobhan Rashed , Gkogkou Pinelopi , Johnson Glyn , Cameron Donnie
Published: February 2023

Object

Dynamic susceptibility contrast MRI (DSC-MRI) is the current standard for cerebral perfusion estimation. Model-dependent approaches for DSC-MRI analysis involve assuming a parametric transit time distribution (TTD) to characterize the passage of contrast agent through tissue microvasculature. Here we compare the utility of four TTD models: namely, skewed-Gaussian, gamma, gamma-variate, and Weibull, to identify the optimal TTD for quantifying brain perfusion.

Materials and Methods

DSC-MRI data were acquired in nine subjects at 1.5T, and normal-appearing white- and gray-matter signals were assessed. TTDs were compared in terms of: goodness-of-fit, evaluated using RMSE; noise sensitivity, assessed via Monte-Carlo-simulated noisy conditions; and fit stability, quantified as the proportion of total fits converging to the global minimum. Computation times for model-fitting were also calculated.

Results

The gamma TTD showed higher fit stability, shorter computation times (p<0.008), and higher robustness against experimental noise as compared to other models. All functions showed similar RMSEs and the parameter estimates (p>0.008) were congruent with literature values.

Discussion

The gamma distribution represents the most suitable TTD for perfusion analysis. Moreover, due to its robustness against noise, the gamma TTD is expected to yield more reproducible estimates than the other models for establishing a standard, multi-center analysis pipeline.
The metaverse as a breakthrough for operations and supply chain management: implications and call for action
Authors: Queiroz Maciel M. , Fosso Wamba Samuel , Pereira Susana Carla Farias , Chiappetta Jabbour Charbel Jose
Published: February 2023

Purpose

The metaverse development is in the early stages in most organizations and supply chains. There has been exponential growth in metaverse investments by leading tech and other types of companies and governments worldwide. This article aims to shed light on the topic by providing detailed insights for the operations and supply chain management (O&SCM) community concerning the potential, opportunities and challenges associated with the metaverse.

Design/methodology/approach

The authors mapped 15 benefits and 15 challenges regarding metaverse in O&SCM-related fields from the literature, which in turn were empirically tested by a panel with 150 experts from more than 12 countries, from operations and supply chains and with experience in metaverse technologies.

Findings

The authors found notable similarities and differences between metaverse adopters and non-adopters in the O&SCM. Accordingly, some benefits and challenges are expected before and after the implementation, but it's still relevant. In contrast, there are ones that change their importance after the implementation.

Research limitations/implications

First, this paper points out the need for an urgent call for action to develop high-quality research on the interplay between metaverse and O&SCM. Second, the metaverse will reshape several established business models by offering new products and services, consequently resulting in the remodeling of O&SCM. Third, our paper provides a call for action to engage the community of scholars and practitioners to consider the metaverse as one of the last frontiers of O&SCM in the digital age.

Originality/value

This paper is one of the first that investigates the metaverse benefits, challenges and expectations in the O&SCM. Also, it provides robust directions by an empirical approach to the metaverse as a new and important research stream for O&SCM and related fields. The authors provide a prospective research agenda that scholars and practitioners could use as a roadmap to capture metaverse opportunities in O&SCM.
Reflections on Sixth form education: a weight worth bearing?
Authors: Coates Lewis
Published: February 2023

Purpose

The purpose of this paper is to share experiences of attending Sixth Form (SF) and to provide reflections on coping, stress management and support for an underresearched cohort of students in Britain. This will be the first in several papers dedicated to the experiences of Sixth Form (SF) students and the need for more research into this area as well as the exploration of the sources of stress that SF students may face.

Design/methodology/approach

Reflective, narrative first-person approach with supporting literature and own research over the master’s thesis of the author and current PhD research.

Findings

Key reflections are SF education lacks support for students who may feel undersupported. Many things other than academics are occurring in this time of life and can become problematic to the students if not supported. Students experience a myriad of changes across this time period but are left behind the author’s support and revision systems that cater to General Certificate of Secondary Education students but are unable to provide support for SF students.

Social implications

Social implications are focussed on building awareness and research into the support needs and sources of stress for SF students.

Originality/value

This paper is one person’s experience with the institution of SF and the expectations, challenges and sources of stress that the author experienced. This paper contributes to the exploration of this underresearched cohort of students.
Facies‐constrained transdimensional amplitude versus angle inversion using machine learning assisted priors
Authors: Dhara Arnab , Sen Mrinal K. , Biswas Reetam
Published: February 2023

We present a methodology for seismic inversion that generates high‐resolution models of facies and elastic properties from pre‐stack data. Our inversion algorithm uses a transdimensional approach where, in addition to the layer properties, the number of layers is treated as unknown. In other words, the data itself determine the correct model parameterization, that is, the number of layers. The reversible jump Markov Chain Monte Carlo method is an effective tool to solve such transdimensional problems as it generates models of reservoir properties along with uncertainty estimates. However, current implementations of the reversible jump Markov Chain Monte Carlo algorithms do not account for the non‐Gaussian and multimodal nature of model parameters. The target elastic reservoir properties generally have multimodal and non‐parametric distribution at each location of the model. The number of modes is equal to the number of facies. Taking these factors into account, we extend the reversible jump Markov Chain Monte Carlo algorithm to simultaneously invert for discrete facies and continuous elastic reservoir properties. The proposed extension to the algorithm iteratively samples the facies, by moving from one mode to another, and elastic properties by sampling within the same mode. The integration of facies classification within the inversion reduces non‐uniqueness, improves convergence speed and produces geologically consistent results. The workflow uses machine learning to generate probabilistic priors for the model parameters. We validate our approach by applying it to a synthetic dataset generated from a well log with two facies and then to a complex synthetic two‐dimensional model involving three facies having overlapping elastic property distribution. Finally, we apply our algorithm to a field dataset acquired over an unconventional reservoir. Our algorithm demonstrates the usefulness of incorporating facies information in seismic inversion and also the feasibility of inverting for facies from seismic data.
Fixing big government or feeding private contractors? Empirical evidence from the case of municipal solid waste management
Authors: Park Seejeen , Moon M. Jae
Published: February 2023

The assumption of new public management (NPM) that governments can lower costs and improve service quality through a market mechanism, such as competition, has been under debate over several decades. To test the NPM assumption, this study investigates the effects of contracting out on cost savings by analysing municipal solid waste management data collected in 25 local governments in the Republic of Korea over a period of 14 years. Contrary to the NPM assumption, this study suggests that contracting out does not necessarily result in cost savings but rather causes additional financial burden on citizens.

Points for practitioners

Government officials are strongly encouraged to critically review market‐based managerial reforms.

Government officials need to assess both benefits and costs of contracting‐out practices prior to any outsourcing or privatisation decisions.

Government officials need to make evidence‐based policy decisions and long‐term financial implications from the perspective of citizens.
Pillar 2: tax competition in low‐income countries and substance‐based income exclusion
Authors: Perry Victoria J.
Published: February 2023

Pillar 2 of the OECD's global tax reform proposal will have significant direct and indirect impacts for low‐income developing countries (LICs). Most interesting and problematic is the question as to how the global anti‐base erosion (GloBE) rules for a proposed global minimum effective tax will affect tax competition behaviour in LICs, and how LICs should respond when a critical mass of higher‐income economies adopt the new structure. Most LICs are source‐only countries, and they are very much in competition to attract foreign direct investment. Do LICs want to continue to compete using the tax system to the extent possible, to step back from that competition, or to take some intermediate course? Pillar 2 does not itself change a country's desired position on the competition spectrum – it merely affects how, and to what extent, that position can still be obtained. This paper posits that LICs should adopt qualified domestic minimum top‐up taxes, and that this will not itself have a negative impact on their competitiveness. The primary focus of the paper, however, is on the design of the substance‐based income exclusion (carve‐out), examining the following three questions. Should the GloBE have been designed without a carve‐out? Would there have been a better way of designing it? How will LICs be affected? The paper concludes that, as little real advantage is likely to accrue to LICs from intangible assets, minimising tax competition for those assets will have relatively little impact on them; and that, from an economic efficiency standpoint, shifting the tax burden away from a normal return and toward economic rents – albeit imperfectly – is a reasonable solution.
Nectar compounds impact bacterial and fungal growth and shift community dynamics in a nectar analog
Authors: Mueller Tobias G. , Francis Jacob S. , Vannette Rachel L.
Published: February 2023

Floral nectar is frequently colonised by microbes. However, nectar microbial communities are typically species‐poor and dominated by few cosmopolitan genera. One hypothesis is that nectar constituents may act as environmental filters. We tested how five non‐sugar nectar compounds as well as elevated sugar impacted the growth of 12 fungal and bacterial species isolated from nectar, pollinators, and the environment. We hypothesised that nectar isolated microbes would have the least growth suppression. Additionally, to test if nectar compounds could affect the outcome of competition between microbes, we grew a subset of microbes in co‐culture across a subset of treatments. We found that some compounds such as H2O2 suppressed microbial growth across many but not all microbes tested. Other compounds were more specialised in the microbes they impacted. As hypothesised, the nectar specialist yeast Metschnikowia reukaufii was unaffected by most nectar compounds assayed. However, many non‐nectar specialist microbes remained unaffected by nectar compounds thought to reduce microbial growth. Our results show that nectar chemistry can influence microbial communities but that microbe‐specific responses to nectar compounds are common. Nectar chemistry also affected the outcome of species interactions among microbial taxa, suggesting that non‐sugar compounds can affect microbial community assembly in flowers.
Incremental expenditures attributable to daily dispensation and witnessed ingestion for opioid agonist treatment in British Columbia: 2014–20
Authors: Nosyk Bohdan , Kurz Megan , Guerra‐Alejos Brenda Carolina , Piske Micah , Dale Laura , Min Jeong Eun
Published: February 2023

Background and aim

While daily witnessed opioid agonist treatment (OAT) ingestion is common in British Columbia (BC), Canada, and elsewhere, sparse evidence supports this resource‐intensive practice. Many settings across North America relaxed restrictions for take‐home dosing during the COVID‐19 pandemic and have reported consistent or improved patient outcomes. This study measured excess expenditures attributed to daily witnessed pharmacy dispensing compared with weekly or biweekly dispensation schedules.

Design, setting and participants

This study was a population‐level retrospective analysis. We included all methadone, buprenorphine/naloxone and slow‐release oral morphine dispensations in BC from 1 January 2014 to 30 December 2020. A total of 24 357 107 OAT dispensations among 51 195 unique individuals with 122 793 person‐years of follow‐up were included during the study period.

Measurements

Total expenditures for each person‐week of OAT with an estimated expenditure under two scenarios are as follows: (1) a weekly dispensation scenario and (2) a biweekly dispensation scenario.

Findings

We estimated excess expenditures attributable to current dispensing practices of between $38 million (2014) and $47.4 million (2018) compared with a hypothetical weekly dispensing schedule, and $43.9 million (2014) to $54.9 million (2018) compared with biweekly dispensing. The majority of these expenditures (58–64%) were attributed to pharmacy dispensing fees ($23 million in 2014 to $30 million in 2018 compared with weekly dispensing; $26.6 million in 2014 to $34.7 million in 2018 compared with biweekly dispensing).

Conclusion

Daily witnessed opioid agonist treatment ingestion results in more than $30 million in excess expenditures annually in the province of British Columbia, Canada compared with the costs of weekly or biweekly dispensation schedules.
Systematic review of isolated disseminated carcinomatosis of bone marrow from colorectal cancer
Authors: Chan Wai Kiu , Lin Norman Sihan , Tay Kon Voi , Teo Li‐Tserng
Published: February 2023

Background

Colorectal cancer (CRC) metastasis commonly occurs in the liver and lungs with bone metastasis rarely occurring in isolation. Disseminated carcinomatosis of bone marrow (DCBM) is extremely rare in CRC. We conducted a systematic review to provide more information on the diagnosis, treatment options, and prognosis of the condition.

Methods

Studies were identified by performing searches on MEDLINE and EMBASE electronic databases according to the PRISMA statement standards. We included a single patient whom we treated for metastatic CRC presenting with DCBM in our study. Statistical analysis was performed using SPSS software version 23.0.

Results

A search through 5502 unique studies yielded 14 studies that were eventually included. There was a total of 17 cases of DCBM in CRC with back pain and constitutional symptoms as the most common presenting complaints. DCBM in CRC was associated with markedly elevated CEA of 275.57 (95% CI 17.13–534.00). There was no predilection for site of primary tumour. Overall median survival was 120 days (95% CI 64.43–175.58). The median survival for patients who received chemotherapy was 240 days (95% CI 71.11–408.89), as compared to 9 days (95% CI 1.80–16.20) for patients who received best supportive treatment.

Conclusion

DCBM from CRC is extremely rare. Bone marrow examination remains the gold standard for diagnosis. Colonic stenting or surgical diversion may be more appropriate than primary resection in obstructed CRC in view of the poor prognosis. Systemic chemotherapy shows promise in increasing median survival.
Evaluation of two rapid commercial assays for detection of Streptococcus agalactiae from vaginal samples
Authors: Koliwer‐Brandl Hendrik , Nil Ahmed , Birri Jana , Sachs Maike , Zimmermann Roland , Zbinden Reinhard , Balsyte Dalia
Published: February 2023

Introduction

Streptococcus agalactiae, also known as group B streptococci (GBS), is associated with invasive infections in neonates. Identification of GBS vaginal colonization in pregnant women before delivery is essential for treatment with antibiotics to prevent intrapartum vertical transmission to the newborn. This study was designed to evaluate applicability of two rapid real‐time PCRs in comparison to standard culture identification.

Material and methods

We compared the Xpert GBS assay, hereafter referred to as Xpert, and GenomEra GBS PCR, hereafter referred to as GenomEra. The standard culture identification consisted of two different agar plates as well as an enrichment broth.

Results

We analyzed vaginal samples of 260 pregnant women; 42 samples were tested GBS‐positive by using standard culture as a gold standard, 30 by Xpert, and 37 by GenomEra. Xpert and GenomEra assays performed with sensitivities of 71.4% and 88.1% as well as specificities of 98.6% and 99.1%, respectively. Twelve vaginal samples were false‐negative by Xpert and five samples by GenomEra. Interestingly, three negative Xpert results of standard culture‐positive samples exhibited high Ct‐values indicating the presence of GBS. If higher Ct‐values are taken into consideration, the sensitivity of Xpert increases up to 78.6%. Moreover, only three Xpert PCRs had to be repeated, whereas two Genomera were invalid even after repetition and further 15 GenomEra PCRs were repeated because of borderline results or inhibition of the PCR test.

Conclusions

In this study, GenomEra assay performed with a higher sensitivity than the Xpert PCR. On the other hand, the Xpert assay needs less hands‐on‐time for a sample preparation and requires approximately four‐fold less repetitions as compared to the GenomEra assay. This robust performance of the Xpert assay make it applicable as a rapid intrapartum point‐of‐care test, although a higher sensitivity would be desirable. Therefore, culture in the 35–37 week of gestation remains the gold standard to detect vaginal colonization.
IgG antispike persistence and immunophenotype in children infected by SARS‐CoV‐2
Authors: García‐Salido Alberto , Flores‐Pérez Patricia , González‐Murillo África , Sánchez‐Marcos Elena , Leoz‐Gordillo Inés , Cano‐Fernández Julia , Castillo‐Robleda Ana , Nieto‐Moro Montserrat , Jiménez‐García Raquel
Published: February 2023

Aim

The immune status of children recovering from SARS‐CoV‐2 infection is not completely understood. We describe IgG antispike persistence in children infected during the first two pandemic waves. In addition, we compared with healthy controls their leukocyte populations and CD64 expression.

Methods

Cross‐sectional study. Carried out from October 2021 to February 2022 in nonreinfected and nonvaccinated children with SARS‐CoV‐2 in 2020. The presence of antispike IgG was studied using chemiluminescent immunoassay. Leukocyte populations were analysed using flow cytometry and marked for CD45, CD4, CD8 and CD64. Statistical minor than 0.05 was considered significant.

Results

One hundred and eighty‐three control and 77 patients were included. IgG antispike determinations were performed after a median of 501 days (262–464); 52 of 77 children were positive. Cases showed significantly higher percentages of monocytes, lymphocytes, CD8+ and CD4+. In addition, CD64 expression was higher in monocytes and neutrophils. The presence of IgG antispike was accompanied by a higher percentage of CD64+ neutrophils.

Conclusion

In our series, the SARS‐CoV‐2 IgG antispike protein was usually positive beyond 1 year after infection. Furthermore, leukocyte populations from cases differ from controls, with higher CD64 expression on neutrophils and monocytes. Prospective clinical observations are required to confirm the implications of these findings.
What explains inconsistencies in field‐based ecosystem mapping?
Authors: Naas Adam Eindride , Halvorsen Rune , Horvath Peter , Wollan Anders Kvalvåg , Bratli Harald , Brynildsrud Katrine , Finne Eirik Aasmo , Keetz Lasse Torben , Lieungh Eva , Olson Christine , Simensen Trond , Skarpaas Olav , Tandstad Hilde Riksheim , Torma Michal , Værland Espen Sommer , Bryn Anders
Published: February 2023

Questions

Field‐based ecosystem mapping is prone to observer bias, typically resulting in a mismatch between maps made by different mappers, that is, inconsistency. Experimental studies testing the influence of site, mapping scale, and differences in experience level on inconsistency in field‐based ecosystem mapping are lacking. Here, we study how inconsistencies in field‐based ecosystem maps depend on these factors.

Location

Iškoras and Guollemuorsuolu, northeastern Norway, and Landsvik and Lygra, western Norway.

Methods

In a balanced experiment, four sites were field‐mapped wall‐to‐wall to scales 1:5000 and 1:20,000 by 12 mappers, representing three experience levels. Thematic inconsistency was calculated by overlay analysis of map pairs from the same site, mapped to the same scale. We tested for significant differences between sites, scales, and experience‐level groups. Principal components analysis was used in an analysis of additional map inconsistencies and their relationships with site, scale and differences in experience level and time consumption were analysed with redundancy analysis.

Results

On average, thematic inconsistency was 51%. The most important predictor for thematic inconsistency, and for all map inconsistencies, was site. Scale and its interaction with site predicted map inconsistencies, but only the latter were important for thematic inconsistency. The only experience‐level group that differed significantly from the mean thematic inconsistency was that of the most experienced mappers, with nine percentage points. Experience had no significant effect on map inconsistency as a whole.

Conclusion

Thematic inconsistency was high for all but the dominant thematic units, with potentially adverse consequences for mapping ecosystems that are fragmented or have low coverage. Interactions between site and mapping system properties are considered the main reasons why no relationships between scale and thematic inconsistency were observed. More controlled experiments are needed to quantify the effect of other factors on inconsistency in field‐based mapping.
Recognition of facial emotions across the lifespan: 8‐year‐olds resemble older adults
Authors: Ruffman Ted , Kong Qiuyi , Lim Hui Mei , Du Kangning , Tiainen Emilia
Published: February 2023

On standard emotion recognition tasks with relatively long or unlimited stimuli durations, recognition improves as children grow older, whereas older adults are worse than young adults. Crucially, it was unknown (a) how older adults compare to age groups below young adulthood and (b) whether children can recognize emotions at shorter durations, with short durations likely common in real life. We compared emotion recognition in 5‐year‐olds, 8‐year‐olds, young adults and older adults at very brief durations (50 ms, 250 ms) as well as standard unlimited durations. Eight‐year‐olds were better than 5‐year‐olds, young adults than all groups, and there was a striking similarity between 8‐year‐olds and older adults, providing the first clear indication that older adults' recognition abilities are equivalent to that of an 8‐year‐old at all durations. Emotion recognition was above chance on all emotions and durations among the three older age groups and on most stimuli for 5‐year‐olds.
A shift towards collaboration: Examining practitioner's economic development practices in Ontario during the COVID‐19 pandemic
Authors: Sutton Jesse , Arku Godwin , Oosterbaan Catherine
Published: February 2023

Regional collaboration has been suggested as a more effective way to promote economic development than competitive approaches. In Ontario, despite attempts by the provincial government to encourage regional collaboration, research finds that municipalities are still engaging in inter‐territorial competition. In this article, we conducted interviews with thirty‐seven practitioners to determine if economic development practices in Ontario have shifted towards more collaborative approaches during the COVID‐19 pandemic. The article finds that regional collaboration, as an economic development practice, has intensified in the province during the recent pandemic. Practitioners noted three reasons for engaging in regional collaboration: pool resources, reduce duplication, and complete regionally task‐oriented goals.
Estrone analogs as potential inhibitors targeting EGFR‐MAPK pathway in non‐small‐cell lung cancer
Authors: Acheampong Felix , Ostlund Trevor , Mahnashi Mater , Halaweish Fathi
Published: February 2023

Lung cancer is the deadliest human cancer globally, with non‐small‐cell lung cancer (NSCLC) being the most frequent type. Epidermal growth factor receptor (EGFR), a central regulator of tumor progression is frequently overexpressed in NSCLC and is a key drug target along with its downstream pathways. Here, we describe the biological evaluation of previously synthesized estrone analogs as potent inhibitors of NCI‐H226 cells. Two of the analogs, MMA307 and MM320, significantly inhibited the proliferation of NCI‐H226 cells with IC50 doses of 2.88 ± 0.21 and 9.68 ± 0.24 μM, respectively, compared with the positive control and chemotherapy, sorafenib, IC50 of 20.62 ± 1.32 μM. Exposing NCI‐H226 cells to IC50 concentration of MMA307 and MMA320 resulted in the downregulation of EGFR and phospho‐EGFR expression levels, and suppression of activated MAPK‐ERK1/2 signaling proteins; phospho‐B‐Raf, phospho‐MEK1/2, and phospho‐ERK1/2. Furthermore, the downregulation of cyclin D1 and concomitant upregulation of phospho‐cyclin D1 and p21waf1/cip1 were observed after the compounds' addition to NCI‐H226 cells resulting in G1 phase cell cycle arrest. MMA320 but not MMA307 downregulated the expression levels of Dyrk1B, a checkpoint kinase at the G1–S phase transition of the cell cycle. Additionally, molecular dynamic simulations were performed and found that MMA307 and MMA320 have higher binding affinities than sorafenib in MEK, BRAF, cyclin D1, and Dyrk1B (dual‐specificity tyrosine phosphorylation‐regulated kinase 1B). To conclude, the present study is the first to report on the antiproliferative potential of novel estrone analogs and provide evidence that MMA307 and MMA320 are promising novel lead candidates for the development of antilung cancer drugs.
Teacher depressive symptoms and children's school readiness in Ghana
Authors: Peele Morgan , Wolf Sharon , Behrman Jere R. , Aber J. Lawrence
Published: February 2023

This study investigated associations between kindergarten teachers' (N = 208) depressive symptoms and students' (Ghanaian nationals, N = 1490, Mage = 5.8) school‐readiness skills (early literacy, early numeracy, social–emotional skills, and executive function) across 208 schools in Ghana over one school year. Teachers' depressive symptoms in the fall negatively predicted students' overall school‐readiness skills in the spring, controlling for school‐readiness skills in the fall. These results were primarily driven by social–emotional skills (r = .1–.3). There was evidence of heterogeneity by students' fall skill levels; teacher depressive symptoms predicted more negative spring overall school readiness for children who had higher fall school‐readiness skills. Findings underscore the importance of teachers' mental health in early childhood education globally, with implications for policy and practice.
Hypersensitivity to permanent tattoos: Literature summary and comprehensive review of patch tested tattoo patients 1997–2022
Authors: Schubert Steffen , Kluger Nicolas , Schreiver Ines
Published: February 2023

We outline constituents of tattoo and permanent make‐up ink with regard to inflammatory tattoo reactions and population‐based confounders. The comprehensive review of patch‐tested tattoo patients between 1997 and 2022 shows that tattoo allergy cannot be reliably diagnosed via patch testing with today's knowledge. Weak penetration and slow haptenization of pigments, unavailability of pigments as test allergens and a lack of knowledge concerning relevant epitopes hamper the diagnosis of tattoo allergy. Patch testing p‐phenylenediamine and disperse (textile) dyes is not able to close this gap. Sensitization to metals was associated with all types of tattoo complications, although often not clinically relevant for the tattoo reaction. Binders and industrial biocides are frequently missing on ink declarations and should be patch tested. The pigment carbon black (C.I. 77266) is no skin sensitizer. Patch tests with culprit inks were usually positive with cheap ink products for non‐professional use or with professionally used inks in patients with eczematous reactions characterized by papules and infiltration. Tape stripping before patch testing and patch test readings on Day 8 or 10 may improve the diagnostic quality. The meaningfulness of the categorical EU‐wide ban of Pigment Green 7 and Pigment Blue 15:3 is not substantiated by the presented data.
fundiversity: a modular R package to compute functional diversity indices
Authors: Grenié Matthias , Gruson Hugo
Published: February 2023

Functional diversity is widely used and widespread. However, the main packages used to compute functional diversity indices are not flexible and not adapted to the volume of data used in modern ecological analyses. We here present fundiversity, an R package that eases the computation of classical functional diversity indices. It leverages parallelization and memoization (caching results in memory) to maximize eﬀiciency with data with thousands of columns and rows. We also did a performance comparison with packages that provide analog functions. In addition to being more flexible, fundiversity was always an order of magnitude quicker than alternatives. fundiversity aims to be a lightweight, eﬀicient tool to compute functional diversity indices, which can be used in a variety of contexts. Because it has been designed following clear principles, it is easy to extend. We hope the wider community will adopt it and we welcome all contributions.
Time for optimism in amyotrophic lateral sclerosis
Authors: Corcia Philippe , Lunetta Christian , Vourc'h Patrick , Pradat Pierre‐François , Blasco Hélène
Published: February 2023

Background and purpose

Amyotrophic lateral sclerosis (ALS) is among the most common motor neuron diseases in adults. Nevertheless, ALS remains fatal, despite decades of research and clinical trials, which has led to negative conclusions until recently in regard to four specific treatments. It is well known that we can learn from failures, and we consider that the time has come to present positive insight on this disease.

Methods

We did a literature search using PubMed and Scopus for articles published in English from 1 January 2016, to 30 June 2022 dealing with “amyotrophic lateral sclerosis”, diagnosis, treatment, and biomarkers.

Results

A comprehensive review of the literature on diagnosis, monitoring, and treatment of this condition showed convincing evidence that we are now able to diagnose earlier as well as to better monitor and treat ALS.

Conclusions

Although ALS is often difficult to diagnose and remains incurable, there are many indications that an optimistic view of ALS management in the coming years is now realistic.
Role of selective attention in fatigue in neurological disorders
Authors: Kuppuswamy Annapoorna
Published: February 2023

Background

Chronic fatigue is a significant symptom in several diseases including traumatic and degenerative neurological disorders. While several studies have investigated the correlates of chronic fatigue, there is as yet no unifying framework to explain chronic fatigue.

Methods

In this narrative review, I investigate the role of selective attention in the development of chronic fatigue and discuss results within the framework of the sensory attenuation model of fatigue, which posits that fatigue is the phenomenological output of altered attention to sensory input. Following a short introduction of this framework, I present results from investigations that address attentional mechanisms in fatigue in multiple sclerosis, stroke, traumatic brain injury and Parkinson's disease.

Results

Attention was quantified in all four disease models using a variety of outcome measures, including behavioural, neurophysiological, structural and functional brain connectivity. The range of measures precluded direct comparison of results across disease conditions; however, in all four disease models there was evidence of poor selective attention that explained levels of chronic fatigue, supporting the sensory attenuation model of fatigue as a disease‐independent mechanism of fatigue. Evidence was lacking to draw any conclusions about the direction of causality.

Conclusion

The role of selective attention in development of fatigue is indicated. Future studies must focus on establishing causality and exploring attentional circuitry as a potential therapeutic target.
Seizure forecasting: Where do we stand?
Authors: Andrzejak Ralph G. , Zaveri Hitten P. , Schulze‐Bonhage Andreas , Leguia Marc G. , Stacey William C. , Richardson Mark P. , Kuhlmann Levin , Lehnertz Klaus
Published: February 2023

A lot of mileage has been made recently on the long and winding road toward seizure forecasting. Here we briefly review some selected milestones passed along the way, which were discussed at the International Conference for Technology and Analysis of Seizures—ICTALS 2022—convened at the University of Bern, Switzerland. Major impetus was gained recently from wearable and implantable devices that record not only electroencephalography, but also data on motor behavior, acoustic signals, and various signals of the autonomic nervous system. This multimodal monitoring can be performed for ultralong timescales covering months or years. Accordingly, features and metrics extracted from these data now assess seizure dynamics with a greater degree of completeness. Most prominently, this has allowed the confirmation of the long‐suspected cyclical nature of interictal epileptiform activity, seizure risk, and seizures. The timescales cover daily, multi‐day, and yearly cycles. Progress has also been fueled by approaches originating from the interdisciplinary field of network science. Considering epilepsy as a large‐scale network disorder yielded novel perspectives on the pre‐ictal dynamics of the evolving epileptic brain. In addition to discrete predictions that a seizure will take place in a specified prediction horizon, the community broadened the scope to probabilistic forecasts of a seizure risk evolving continuously in time. This shift of gears triggered the incorporation of additional metrics to quantify the performance of forecasting algorithms, which should be compared to the chance performance of constrained stochastic null models. An imminent task of utmost importance is to find optimal ways to communicate the output of seizure‐forecasting algorithms to patients, caretakers, and clinicians, so that they can have socioeconomic impact and improve patients' well‐being.
Current management of generalized pustular psoriasis
Authors: Kodali Nilesh , Blanchard Isabella , Kunamneni Sruthi , Lebwohl Mark G.
Published: February 2023

Generalized pustular psoriasis (GPP) is a rare subset of psoriasis involving episodes of sterile pustules accompanied by inflammation and, often, systemic involvement. The inflammatory nature of GPP has potential for severe multisystem complications including high‐output cardiac failure, infections, digestive system issues, and disfiguring or lethal acute flare episodes. The disease tends to have higher prevalence in females and Asians. The IL‐1/IL‐36 inflammatory pathway is a critical facet of GPP's pathology. Genetic mutations that are associated with GPP include modifications of Interleukin 36 Receptor Antagonist (IL36RN), Caspase Recruitment Domain Family Member 14 (CARD14), Adaptor Related Protein Complex 1 Subunit Sigma 3 (AP1S3), Myeloperoxidase (MPO) and Serpin Peptidase Inhibitor Clade A Member 3 (SERPINA3) genes. Treatment guidelines for GPP are not well‐entrenched. Currently, only one GPP‐specific treatment, the interleukin‐36 receptor antagonist (IL‐36Ra) spesolimab, has been approved for use in the United States. Additional anti‐IL‐36 pathway therapies are currently being developed. Other treatment options include other biologic therapies such as IL‐17 inhibitors, IL‐23 inhibitors and TNFα inhibitors. Non‐biologic therapeutic options include retinoids, cyclosporine and methotrexate. Treatment options differ throughout the world; most countries utilize retinoids, cyclosporine and methotrexate as first‐line non‐biologic options. China and United Kingdom have no GPP‐specific biologic therapies approved for use, while several biologic therapies are approved for use in Japan. This review aims to serve as an update on the current global management of GPP while also including relevant aspects of disease pathogenesis, diagnosis, clinical presentation, histopathology, aetiology and epidemiology.