bluuebunny/crossref_metadata_2025 huggingface dataset:
Past, present, and future of the Living Planet Index
Authors: Ledger Sophie E H , McRae Louise , Böhm Monika , Almond Rosamunde , Grooten Monique , Clements Chris , Currie Jessica , Galewski Thomas , Jenkins Martin , Painter Brett , Young Lucy , Loh Jonathan , Deinet Stefanie , Marconi Valentina , Scott-Gatty Kate , Hoffmann Michael , Freeman Robin
Published: June 2022

As we enter the next phase of international policy commitments to halt biodiversity loss (e.g. Post-2020 Biodiversity Framework), biodiversity indicators will play an important role forming the robust basis upon which targeted, and time sensitive conservation actions are developed. Population trend indicators are perhaps the most powerful tool in biodiversity monitoring due to their responsiveness to changes over short timescales and their ability to aggregate species trends from global down to at a sub-national or even local scale. We consider how the project behind the foremost population level indicator - the Living Planet Index - has evolved over the last 25 years, its value to the field of biodiversity monitoring, and how its components have portrayed a compelling account of the changing status of global biodiversity through its application at policy, research and practice levels. We explore ways the project can develop to enhance our understanding of the state of biodiversity and share lessons learned to inform indicator development and mobilise action.
scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes
Authors: Cha Junha , Yu Jiwon , Cho Jae-Won , Hemberg Martin , Lee Insuk
Published: June 2022

A major challenge in single-cell biology is identifying cell-type-specific gene functions, which may substantially improve precision medicine. Differential expression analysis of genes is a popular, yet insufficient approach, and complementary methods that associate function with cell type are required. Here, we describe scHumanNet (https://github.com/netbiolab/scHumanNet), a single-cell network analysis platform for resolving cellular heterogeneity across gene functions in humans. Based on cell-type-specific networks (CSNs) constructed under the guidance of the HumanNet reference interactome, scHumanNet displayed higher functional relevance to the cellular context than CSNs built by other methods on single-cell transcriptome data. Cellular deconvolution of gene signatures based on network compactness across cell types revealed breast cancer prognostic markers associated with T cells. scHumanNet could also prioritize genes associated with particular cell types using CSN centrality and identified the differential hubness of CSNs between disease and healthy conditions. We demonstrated the usefulness of scHumanNet by uncovering T-cell-specific functional effects ofGITR, a prognostic gene for breast cancer, and functional defects in autism spectrum disorder genes specific for inhibitory neurons. These results suggest that scHumanNet will advance our understanding of cell-type specificity across human disease genes.
Dopaminergic axons track somatic signaling in behaving mice
Authors: Azcorra Maite , Gaertner Zachary , Davidson Connor , Ramakrishnan Charu , Fenno Lief , Kim Yoon Seok , Deisseroth Karl , Awatramani Rajeshwar , Dombeck Daniel A.
Published: June 2022

Striatal dopamine released from the axons of midbrain dopamine neurons has been linked to a wide range of functions, including movement control and reward-based learning. Recent studies have reported functional signaling differences between axons and somas of dopamine neurons, suggesting that local modulation controls dopamine release and calling into question the classical view of somatic control. However, these experiments are technically challenging, making it difficult to ensure that axonal and somatic recordings come from the same neurons, particularly given the heterogeneity of dopaminergic cell types. Here we used genetic strategies to isolate key dopaminergic neuron subtypes and monitor their axonal and somatic signaling patterns in behaving mice. Contrary to the inferences drawn from previous studies, these experiments revealed a robust correlation between somatic and axonal signaling. Thus, by exploiting a previously unknown connection between genetic and functional diversity in dopamine neurons, we establish that subtypes must be considered to understand the mechanisms of dopamine release in striatum during behavior.
Bioactivation and detoxification of organophosphorus pesticides in freshwater planarians shares similarities with humans
Authors: Ireland Danielle , Rabeler Christina , Gong TaiXi , Collins Eva-Maria S.
Published: June 2022

Organophosphorus pesticides (OPs) are a chemically diverse class of insecticides that inhibit acetylcholinesterase (AChE). Many OPs require bioactivation to their active oxon form via cytochrome P450 to effectively inhibit AChE. OP toxicity can be mitigated by detoxification reactions performed by carboxylesterase and paraoxonase. The relative extent of bioactivation to detoxification varies among individuals and between species, leading to differential susceptibility to OP toxicity. Because of these species differences, it is imperative to characterize OP metabolism in model systems used to assess OP toxicity to adequately evaluate potential human hazard. We have shown that the asexual freshwater planarian Dugesia japonica is a suitable model to assess OP neurotoxicity and developmental neurotoxicity via rapid, automated testing of adult and developing organisms in parallel using morphological and behavioral endpoints. D. japonica has two cholinesterase enzymes with intermediate properties between AChE and butyrylcholinesterase that are sensitive to OP inhibition. Here, we demonstrate that this planarian contains the major OP metabolic machinery to be a relevant model for OP neurotoxicity studies. Adult and regenerating D. japonica can bioactivate chlorpyrifos and diazinon into their respective oxons. Significant AChE inhibition was only observed after in vivo metabolic activation but not when the parent OPs were directly added to planarian homogenate. Additionally, we found that D. japonica has both carboxylesterase and paraoxonase activity. Using specific chemical inhibitors, we show that carboxylesterase activity is distinct from cholinesterase activity. Taken together, these results further support the use of D. japonica for OP toxicity studies.
POSTRE: a tool to predict the pathological effects of human structural variants
Authors: Sánchez-Gaya Víctor , Rada-Iglesias Álvaro
Published: June 2022

Understanding the pathological impact of non-coding genetic variation is a major challenge in medical genetics. Accumulating evidences indicate that a significant fraction of genetic alterations, including structural variants (SVs), can cause human disease by altering the function of non-coding regulatory elements, such as enhancers. In the case of SVs, described pathomechanisms include changes in enhancer dosage and long-range enhancer-gene communication. However, there is still a clear gap between the need to predict and interpret the medical impact of non-coding variants, and the existence of tools to properly perform these tasks. To reduce this gap, we have developed POSTRE (Prediction Of STRuctural variant Effects), a computational tool to predict the pathogenicity of SVs implicated in a broad range of human congenital disorders. By considering disease-relevant cellular contexts, POSTRE identifies SVs with either coding or long-range pathological consequences with high specificity and sensitivity. Furthermore, POSTRE not only identifies pathogenic SVs, but also predicts the disease-causative genes and the underlying pathological mechanism (e.g, gene deletion, enhancer disconnection, enhancer adoption, etc.). POSTRE is available at https://github.com/vicsanga/Postre.
THE MAJOR ROLE OF JUNCTIONAL DIVERSITY IN THE HORSE ANTIBODY REPERTOIRE
Authors: Navas Carlena , Manso Taciana , Martins Fabio , Minto Lucas , Moreira Rennan , Minozzo João , Antunes Bruno , Vale André , McDaniel Jonathan R. , Ippolito Gregory C. , Felicori Liza F.
Published: June 2022

The sequencing of the antibody repertoire (Rep-seq) revolutionized the diversity of antigen B cell receptor studies, allowing deep and quantitative analysis to decipher the role of adaptive immunity in health and disease. Particularly, horse (Equus caballus) polyclonal antibodies have been produced and used since the century XIX to treat and prophylaxis of diphtheria, tuberculosis, tetanus, pneumonia, and, more recently, COVID-19. However, our knowledge about the horse B cell receptors repertories is minimal. We present a deep horse antibody heavy chain repertoire (IGH) characterization of non-immunized horses using HTS technology. In this study, we obtained a mean of 248,169 unique IgM clones and 66,141 unique IgG clones from four domestic adult horses. Rarefaction analysis showed sequence coverage was between 52 and 82% in IgM and IgG isotypes. We observed that besides horses antibody can use all of the functional IGHV genes, around 80% of their antibodies use only three IGHV gene segments, and around 55% use only one IGHJ gene segment. This limited VJ diversity seems to be compensated by the junctional diversity of these antibodies. We observed that the junctional diversity in horses antibodies is highly frequent, present in more than 90% of horse antibodies. Besides this, the length of this region seems to be higher in horse antibodies than in other species. N1 and N2 nucleotides addition range from 0 to 111 nucleotides. In addition, around 45% of the antibody clones have more than ten nucleotides in both N1 and N2 junction regions. This diversity mechanism may be one of the most important in providing variability to the equine antibody repertoire. This study provides new insights regarding horse antibody composition, diversity generation, and particularities compared to other species, such as the frequency and length of N nucleotide addition. This study also points out the urgent need to better characterize TdT in horses and in other species to better understand antibody repertoire characteristics.
Spatial Atlas of the Mouse Central Nervous System at Molecular Resolution
Authors: Shi Hailing , He Yichun , Zhou Yiming , Huang Jiahao , Wang Brandon , Tang Zefang , Tan Peng , Wu Morgan , Lin Zuwan , Ren Jingyi , Thapa Yaman , Tang Xin , Liu Albert , Liu Jia , Wang Xiao
Published: June 2022

Spatially charting molecular cell types at single-cell resolution across the three-dimensional (3D) volume of the brain is critical for illustrating the molecular basis of the brain anatomy and functions. Single-cell RNA sequencing (scRNA-seq) has profiled molecular cell types in the mouse brain1, 2, but cannot capture their spatial organization. Here, we employed an in situ sequencing technique, STARmap PLUS3, 4, to map more than one million high-quality cells across the whole adult mouse brain and the spinal cord, profiling 1,022 genes at subcellular resolution with a voxel size of 194 X 194 X 345 nm in 3D. We developed computational pipelines to segment, cluster, and annotate 231 molecularly defined cell types and 64 tissue regions with single-cell resolution. To create a transcriptome-wide spatial atlas, we further integrated the STARmap PLUS measurements with a published scRNA-seq atlas1, imputing 11,844 genes at the single-cell level. Finally, we engineered a highly expressed RNA barcoding system to delineate the tropism of a brain-wide transgene delivery tool, AAV-PHP.eB5, 6, revealing its single-cell resolved transduction efficiency across the molecular cell types and tissue regions of the whole mouse brain. Together, our datasets and annotations provide a comprehensive, high-resolution single-cell resource that integrates a spatial molecular atlas, cell taxonomy, brain anatomy, and genetic manipulation accessibility of the mammalian central nervous system (CNS).
Pre-Omicron vaccine breakthrough infection induces superior cross-neutralization against SARS-CoV-2 Omicron BA.1 than primo infection
Authors: Santos da Silva Eveline , Kohnen Michel , Gilson Georges , Staub Therese , Arendt Victor , Hilger Christiane , Servais Jean-Yves , Charpentier Emilie , Domingues Olivia , Snoeck Chantal J. , Ollert Markus , Seguin-Devaux Carole , Perez-Bercoff Danielle
Published: June 2022

SARS-CoV-2 variants raise concern because of their high transmissibility and their ability to evade neutralizing antibodies elicited by prior infection or by vaccination. Here we compared the ability of sera from 70 unvaccinated COVID-19 patients infected before the emergence of variants of concern (VOCs) and from 16 vaccine breakthrough infection (BTI) cases infected with Gamma or Delta to neutralize the ancestral B.1 strain, and the Gamma, Delta and Omicron BA.1 variants using live virus. We further determined antibody levels against the Spike protein, the Receptor Binding Domain (RBD) and the N-terminal domain (NTD) of Spike. Convalescent sera featured considerable variability in neutralization of B.1 and in cross-neutralization of different strains, and neutralizing capacity moderately correlated with antibody levels against Spike and the RBD. All but one convalescent serum failed to neutralize Omicron BA.1. Overall, convalescent sera from patients with moderate disease had higher antibody levels and displayed higher neutralizing ability against all strains than patients with mild or severe forms of disease. Sera from BTI cases fell into one of two categories: half the sera had high neutralizing activity against the ancestral B.1 strain as well as against the infecting strain, while the other half had no or very low neutralizing activity against all strains. Although antibody levels against Spike and the RBD were lower in BTI cases than in unvaccinated convalescent sera, most neutralizing sera also retained partial neutralizing activity against Omicron BA.1, indicative of cross-neutralization between B.1, Delta and Omicron and suggestive of higher affinity, as confirmed by the IC50:Ab level ratios. Neutralizing activity of BTI sera was strongly correlated with antibodies against Spike and the RBD. Together, these findings highlight qualitative differences in antibody responses elicited by infection in vaccinated and unvaccinated individuals. They further suggest that breakthrough infection with a pre-Omicron variant boosts immunity and induces cross neutralizing antibodies against different strains, including Omicron BA.1.
Financial Incentives for Quitting Smoking in Pregnancy: Are they cost-effective?
Authors: McMeekin Nicola , Sinclair Lesley , Robinson-Smith Lyn , Mitchell Alex , Bauld Linda , Tappin David M , Boyd Kathleen A
Published: June 2022

Aims

To evaluate whether adding financial incentives to usual care is cost-effective in encouraging pregnant women to quit tobacco smoking, compared to usual care alone.

Design

Cost-effectiveness analysis (CEA) and cost-utility analysis (CUA) from a healthcare provider’s perspective, embedded in the Smoking Cessation in Pregnancy Incentives Trial (CPIT III). Long-term analyses were conducted from the same perspective, using an existing Markov model over a lifetime horizon.

Setting

Seven maternity smoking cessation sites in Scotland, England and Northern Ireland in the United Kingdom.

Participants

In the short-term analysis CPIT III participants were assessed: women 16 years or older, self-reporting as smokers, less than 24 weeks pregnant and English speaking (n=944). The same population was used for the lifetime analysis, plus their infants.

Measurements

Costs include financial incentive vouchers and postage, cessation support and nicotine replacement therapy and neonatal stays. The outcome measure was biochemically verified quit rate for the CEA and quality adjusted life-years (QALY) for CUA. Costs are presented in 2020 GBP sterling (£).

Data for the lifetime analysis came from the trial and was combined with data from published literature embedded in the model, reporting incremental cost per quitter and QALY. A 3.5% discount rate was applied.

Findings

The short-term incremental cost per quitter was £4,400, uncertainty in QALY gains resulted in a cost per QALY of £150,000. Results of sensitivity analyses confirm these results. The long-term analysis combined costs and outcomes for mother and infants, results show a cost saving of £37 (-£35 to £106) and increase in QALYs of 0.171 (0.124 to 0.229). These findings indicate that, over a lifetime, financial incentives are cost saving and improve health outcomes.

Conclusions

Offering up to £400 financial incentives, in addition to usual care, to support pregnant women to stop smoking is cost-effective over a lifetime for mother and infants.

Ethics

Ethics approval received from NHS West of Scotland Research Ethics Committee-2, August 2017.

Registration details

Trial registration number: ISRCTN15236311, date registered 09/10/2017 https://doi.org/10.1186/ISRCTN15236311
Brain aerobic glycolysis and resilience in Alzheimer disease
Authors: Goyal Manu S. , Blazey Tyler , Metcalf Nicholas V. , McAvoy Mark P. , Strain Jeremy , Rahmani Maryam , Durbin Tony J. , Xiong Chengjie , Benzinger Tammie L.-S. , Morris John C. , Raichle Marcus E. , Vlassenko Andrei G.
Published: June 2022

The distribution of brain aerobic glycolysis (AG) in normal young adults correlates spatially with amyloid-beta (Aβ) deposition in individuals with dementia of the Alzheimer type (DAT) and asymptomatic individuals with brain amyloid deposition. Brain AG decreases with age but the functional significance of this decrease with regard to the development of DAT symptomatology is poorly understood. Using PET measurements of regional blood flow, oxygen consumption and glucose utilization—from which we derive AG—we find that cognitive impairment is strongly associated with loss of the typical youthful pattern of AG. In contrast, amyloid positivity without cognitive impairment was associated with preservation of youthful brain AG, which was even higher than that seen in typical, cognitively unimpaired, amyloid negative adults. Similar findings were not seen for blood flow nor oxygen consumption. Finally, in cognitively unimpaired adults, white matter hyperintensity burden was found to be specifically associated with decreased youthful brain AG. Our results implicate preserved AG as a factor in brain resilience to amyloid pathology and suggest that white matter disease may be a cause and/or consequence of this impaired resilience.
Enhancement of mitochondrial function fosters B cell immune memory
Authors: Shukla Ashima , Tiwari Ashutosh , Saulnier Olivier , Hendrikse Liam , Hall Bryan , Rickert Robert , Taylor Michael D , Shukla Vipul , Bagchi Anindya
Published: June 2022

Differentiation of T and B cells to effector and memory cell fates are associated with extensive metabolic changes which are accompanied by altered mitochondrial dynamics. However, whether alterations in mitochondrial structure and function plays an active role in regulating effector versus memory cell fate decisions during immune responses remains unclear. Our studies here characterize changes in mitochondrial dynamics in activated B cells and show that increased mitochondrial mass and activity is a distinct feature of memory B cell lineage commitment in vivo. Using a directed screen of mitochondrial modulators, we identify mitochondrial fission inhibitor, Mdivi-1 as an agent that could enhance mitochondrial mass and function leading to augmented memory B cell differentiation. The enhanced memory B cell responses mediated by Mdivi-1, translated to more robust recall responses upon secondary antigen exposures. Moreover, Mdivi-1 when used in combination with subunit (SARS-CoV2) and inactivated (H1N1 influenza) vaccines led to remarkably improved vaccine efficacies and protection from lethal viral (H1N1) challenge. Single-cell transcriptomics revealed enhanced commitment to memory lineage differentiation in B cells following Mdivi-1 treatment. We propose that mitochondrial modulators such as Mdivi-1 are a novel class of “immune enhancers” that specifically reinforces immunological memory and could be broadly applied to improve the fidelity of immune responses and vaccine efficacies.
Rare genetic variants impact muscle strength
Authors: Huang Yunfeng , Bodnar Dora , Chen Chia-Yen , Gurria Gabi , Sanderson Mark ,   Biogen Biobank Team, Shi Jun , Meilleur Katherine G , Hurles Matthew E. , Gerety Sebastian S. , Tsai Ellen A. , Runz Heiko
Published: June 2022

Muscle strength is highly heritable and predictive for multiple adverse health outcomes including mortality. Here, we present a rare protein-coding variant association study in 340,319 individuals for hand grip strength, a proxy measure of muscle strength. We identify six significant genes (KDM5B, OBSCN, GIGYF1, TTN, RB1CC1, EIF3J), propose shared mechanisms between brain and muscle function and demonstrate additive effects between rare and common genetic variation on muscle strength.
Neural Correlates of Remotely versus In-person Administered Symbol Digit Modalities Test in Multiple Sclerosis
Authors: Buyukturkoglu Korhan , Dworkin Jordan D. , Leiva Victor , Provenzano Frank A. , Guevara Pamela , De Jager Philip L. , Leavitt Victoria M. , Riley Claire S.
Published: June 2022

Background

Prior studies in multiple sclerosis (MS) support reliability of telehealth-delivered cognitive batteries, although, to date, none have reported predictive external validity, i.e., relationships of cognitive test performance to neural correlates across administration modalities. In this study we aimed to compare brain-behavior relationships, using the Symbol Digit Modalities Test (SDMT), the most reliable and sensitive cognitive measure in MS, measured from patients seen via telehealth versus in-person.

Methods

SDMT was administered to individuals with MS either in-person (N=60, mean age=39.7) or remotely via video conference (N=51, mean age=47.4). Magnetic resonance imaging (MRI) data was collected in 3-Tesla scanners. Using 3D-T1 images cerebral, cortical, deep gray, cerebral white matter and thalamic nuclei volumes were calculated. Using a meta-analysis approach with an interaction term for participant group, individual regression models were run for each MRI measure having SDMT as the outcome variable in each model. In addition, the correlation and average difference between In-person and Remote group effect sizes across the MRI measures were calculated. Finally, for each MRI variable I2score was quantified to test the heterogeneity between the groups.

Results

Administration modality did not affect the association of SDMT with MRI measures. Brain tissue volumes showing high associations with the SDMT in one group also showed high associations in the other (r= 0.83; 95% CI = [0.07, 0.86]). The average difference between the In-person and the Remote group effect sizes was not significant (βRemote- βIn-person= 0.14, 95% CI = [-0.04, 0.34]). Across MRI measures, the average I2value was 14%, reflecting very little heterogeneity in the relationship of SDMT to brain volume.

Conclusion

We found consistent relationships to neural correlates across in-person and remote SDMT administration modalities. Hence, our study can be considered a step towards providing predictive external validity to remote administration of the SDMT in MS.

Highlights

Symbol Digit Modalities Test (SDMT) was administered to individuals with MS either in-person or remotely via video conference.

Administration modality did not affect the association of SDMT with MRI measures.

Brain tissue volumes showing high associations with the SDMT in one group also showed high associations in the other.

The average difference between the In-person and the Remote group effect sizes was not significant.

This study can be considered a step towards providing predictive external validity to remote administration of the SDMT in MS.
A novel workflow for the safe and effective integration of AI as supporting reader in double reading breast cancer screening: A large-scale retrospective evaluation
Authors: Ng Annie Y. , Glocker Ben , Oberije Cary , Fox Georgia , Nash Jonathan , Karpati Edith , Kerruish Sarah , Kecskemethy Peter D.
Published: June 2022

Objectives

To evaluate the effectiveness of a novel strategy for using AI as a supporting reader for the detection of breast cancer in mammography-based double reading screening practice. Instead of replacing a human reader, here AI serves as the second reader only if it agrees with the recall/no-recall decision of the first human reader. Otherwise, a second human reader makes an assessment, enacting standard human double reading.

Design

Retrospective large-scale, multi-site, multi-device, evaluation study.

Participants

280,594 cases from 180,542 female participants who were screened for breast cancer with digital mammography between 2009 and 2019 at seven screening sites in two countries (UK and Hungary).

Main outcome measures

Primary outcome measures were cancer detection rate, recall rate, sensitivity, specificity, and positive predictive value. Secondary outcome was reduction in workload measured as arbitration rate and number of cases requiring second human reading.

Results

The novel workflow was found to be superior or non-inferior on all screening metrics, almost halving arbitration and reducing the number of cases requiring second human reading by up to 87.50% compared to human double reading.

Conclusions

AI as a supporting reader adds a safety net in case of AI discordance compared to alternative workflows where AI replaces the second human reader. In the simulation using large-scale historical data, the proposed workflow retains screening performance of the standard of care of human double reading while drastically reducing the workload. Further research should study the impact of the change in case mix for the second human reader as they would only assess cases where the AI and first human reader disagree.
Availability and readiness of healthcare facilities and their effects on under-five mortality in Bangladesh: Analysis of linked data
Authors: Khan Md. Nuruzzaman , Trisha Nahidha Islam , Rashid Md. Mamunur
Published: June 2022

Background

Under-five mortality is unacceptably high in Bangladesh instead of governmental level efforts to reduce its prevalence over the years. Increased availability and access to the healthcare services can play a significant role to reduce under-five mortality. We explored the associations of several forms of child mortality with health facility level factors adjusted for individual-, household-, and community level factors.

Methods

The 2017-18 Bangladesh Demographic and Health Survey data and 2017 Bangladesh Health Facility Survey data were linked and analysed. Our outcome variables were neonatal mortality, infant mortality, and under-five mortality. Health facility level factors were considered as major explanatory variables. They were the basic management and administrative system of the healthcare facility, availability of the child healthcare services at the nearest healthcare facility, readiness of the nearest healthcare facility to provide child healthcare services and the average distance of the nearest healthcare facility providing child healthcare services. The associations between the outcome variables and explanatory variables were determined using the multilevel mixed-effect logistic regression model.

Results

Reported under-five, infant and neonatal mortality were 40, 27, and 22 per 10000 live births, respectively. The likelihood of neonatal mortality was found to be declined by 15% for every unit increase in the score of the basic management and administrative system of the mothers’ homes nearest healthcare facility where child healthcare services are available. Similarly, the availability and readiness of the mothers’ homes nearest healthcare facilities to provide child healthcare services were found to be linked with the 18-24% reduction in neonatal and infant mortality. On contrary, for every kilometre increased distance between mothers’ homes and their nearest healthcare facility was found to be associated with a 15-20% increase in the likelihoods of neonatal, infant and under-five mortality.

Conclusion

The availability of health facilities providing child healthcare services close to residence and their improved management, infrastructure, and readiness to provide child healthcare services play a significant role in reducing under-five mortality in Bangladesh. Policies and programs should prioritize to increase the availability and accessibility of health facilities that provide child healthcare services.
COVID-19 vaccine booster strategies in light of emerging viral variants: Frequency, timing, and target groups
Authors: Kelly Sherrie L , Le Rutte Epke A , Richter Maximilian , Penny Melissa A , Shattock Andrew J
Published: June 2022

Background

Vaccinations have reduced severe burden of COVID-19 and allowed for lifting of non-pharmaceutical interventions. However, with immunity waning alongside emergence of more transmissible variants of concern, vaccination strategies must be examined.

Methods

Here we apply a SARS-CoV-2 transmission model to identify preferred frequency, timing, and target groups for vaccine boosters to minimise public health burden and health systems risk. We estimated new infections and hospital admissions averted over two-years through annual or biannual boosting of those eligible (those who received doses one and two) who are 1) most vulnerable (60+ or persons with comorbidities) or 2) those 5+, at universal (98% of eligible) or lower coverage (85% of those 50+ or with comorbidities and 50% of 5−49-year-olds who are eligible) representing moderate vaccine fatigue and/or hesitancy. We simulated three emerging variant scenarios: 1) no new variants; 2) 25% more infectious and immune-evading, Omicron-level severity, variants emerge annually and become dominant; and 3) emerge biannually. We further explored the impact of varying seasonality, variant severity, timing, immune evasion, and infectivity, and vaccine infection blocking assumptions.

Results

To minimise COVID-19-related hospitalisations over the next two years, boosters should be provided for all those eligible annually three-four months ahead of peak winter whether or not new variants of concern emerge. Only boosting those most vulnerable is unlikely to ensure reduced stress on health systems. Moreover, boosting all eligible protects those most vulnerable more than only boosting the vulnerable group. Conversely, more hospitalisations could be averted per booster dose through annual boosting of those most vulnerable versus all eligible, an indication of cost-effectiveness. Whereas increasing to biannual boosting showed diminishing returns. Results were robust when key model parameters were varied. However, we found that the more frequently variants emerge, the less the effect boosters will have, regardless of whether administered annually or biannually.

Conclusions

Well-timed and targeted vaccine boosters preferencing vulnerable, and if possible, all those eligible to receive boosters, can minimise infections and hospital admissions. Findings provide model-based evidence for decision-makers to plan for administering COVID-19 boosters ahead of winter 2022−2023 to help mitigate the health burden and health system stress.
Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea
Authors: Somee Maryam Rezaei , Amoozegar Mohammad Ali , Mehdi Dastgheib Seyed Mohammad , Shavandi Mahmoud , Maman Leila Ghanbari , Bertilsson Stefan , Mehrshad Maliheh
Published: June 2022

Hydrocarbons (HCs) are organic compounds composed solely of carbon and hydrogen. They mainly accumulate in oil reservoirs, but aromatic HCs can also have other sources and are widely distributed in the biosphere. Our perception of pathways for biotic degradation of major HCs and genetic information of key enzymes in these bioconversion processes have mainly been based on cultured microbes and are biased by uneven taxonomic representation. Here we use Annotree to provide a gene-centric view of aerobic degradation of aliphatic and aromatic HCs in a total of 23446 genomes from 123 bacterial and 14 archaeal phyla. Apart from the widespread genetic potential for HC degradation in Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes, genomes from an additional 18 bacterial and 3 archaeal phyla also hosted key HC degrading enzymes. Among these, such degradation potential has not been previously reported for representatives in the phyla UBA8248, Tectomicrobia, SAR324, and Eremiobacterota. While genomes containing full pathways for complete degradation of HCs were only detected in Proteobacteria and Actinobacteriota, other lineages capable of mediating such key steps could partner with representatives with truncated HC degradation pathways and collaboratively drive the process. Phylogeny reconstruction shows that the reservoir of key aerobic hydrocarbon-degrading enzymes in Bacteria and Archaea undergoes extensive diversification via gene duplication and horizontal gene transfer. This diversification could potentially enable microbes to rapidly adapt to novel and manufactured HCs that reach the environment.
Effects of microplastic ingestion on hydrogen production and microbiomes in the gut of the terrestrial isopod Porcellio scaber
Authors: Hink Linda , Holzinger Anja , Sandfeld Tobias , Weig Alfons R. , Schramm Andreas , Feldhaar Heike , Horn Marcus A.
Published: June 2022

Microplastic (MP) pollution is an environmental burden. MP enters food webs via ingestion by macrofauna, including isopods (Porcellio scaber) in terrestrial ecosystems. However, MP-effects on the host and its gut microbiome are largely unknown. We tested the hypothesis that biodegradable (polylactic acid, PLA) and non-biodegradable (polyethylene terephthalate, PET; polystyrene, PS) MP have contrasting effects on P. scaber mediated by changes of the associated gut microbiome. Although the isopods avoided food containing PS, isopod fitness after eight-week MP-exposure was unaffected. Qualitative and quantitative 16S rRNA gene and 16S rRNA analyses of gut microbiomes indicated general MP effects, MP-type specific indicator taxa, and stimulation by PLA compared to MP-free controls. Isopods emitted hydrogen, and its production increased and decreased after PLA-food and PET- or PS-food ingestion, respectively, relative to controls as indicated by microsensor measurements. Gut pH was unaffected by MP. We identified the gut of P. scaber as significant mobile source of reductant for soil microbiomes likely due to Enterobacteriaceae related fermentation activities that were stimulated by lactate generated during PLA-degradation. The findings suggest negative effects of PET and PS on gut fermentation, modulation of isopod hydrogen emissions by MP pollution, and the potential of MP to affect terrestrial food webs.
Rapid and sensitive on-site genetic diagnostics of pest fruit flies using CRISPR-Cas12a
Authors: Alon Dan Mark , Partosh Tamir , Burstein David , Pines Gur
Published: June 2022

Bactrocera zonata, a major fruit pest species, is gradually spreading west from its native habitat in East Asia. In recent years it has become a major threat to the Mediterranean area, with the potential of invading Europe, the Americas, and Australia. To prevent its spreading, monitoring efforts in plantation sites and border controls are carried out. Despite these efforts, and due to morphological similarities between B. zonata and other pests in relevant developmental stages, the monitoring process is challenging, time-consuming, and requires external assistance from professional labs. CRISPR-Cas12a genetic diagnostics has been rapidly developing in recent years and provides an efficient tool for the genetic identification of pathogens, viruses, and other genetic targets. Here we design a CRISPR-Cas12a detection assay that differentially detects two major pest species, B. zonata and Ceratitis capitata. Our easy-to-use and affordable assay employs a simple DNA extraction technique together with isothermal amplification, and Cas12a-based detection. We demonstrate the specificity and high sensitivity of this method, and its relevance for on-site applications. This method is highly modular, and the presented target design method can be applied to a wide array of pests.

Key Massage

Distinguishing different pest fruit flies on-site is crucial for prevention of global spreading but can be difficult

We present a genetic identification assay for rapid, on-site detection of pest using CRISPR-Cas12a

The method is affordable, quick and easy-to-use, and can be applied in border controls or on-site

The design process can be easily tailored for any pest, and can greatly benefit developing countries
Generating random unit cells
Authors: Andrews Lawrence C. , Bernstein Herbert J.
Published: June 2022

Methods of generating random unit-cell data for testing software are discussed. Working within the space S
6 appears to be the most expeditious.
Assessing the impact of peripheral vision on construction site safety
Authors: Kiral Isik Ates , Demirkesen Sevilay
Published: June 2022

Purpose

This study aims to observe the impact of peripheral vision on construction safety. The study further intends to create awareness of eye diseases in construction safety, an important root cause for most construction-related hazards and accidents.

Design/methodology/approach

This study focuses on the impact of peripheral vision in terms of construction site safety. Experiments were conducted with construction employees with different qualifications, ages, expertise and previous safety training experience. The experiments were conducted with an experiment set consisting of a tangent screen to measure the peripheral angle of the participants. The study measured peripheral vision, which helped determine the vision field accordingly. In this context, a total of 32 participants were investigated in terms of their peripheral visual angle and the field of vision. The data collected were analyzed in terms of several statistical tests such as One-Sample t-test, multivariate ANOVA and multiple linear regression.

Findings

The results of the study indicated that there are significant differences in peripheral vision in terms of age of participants, work qualification, work experience, area of expertise and previous safety training experience. The study further revealed that most of the participants failed to satisfy both OSHA requirements about peripheral vision, and normal limits defined in the previous literature. The study further implies that participants, who reported previous sight problems or eye diseases are more vulnerable to construction site accidents.

Originality/value

Construction site safety remains a major concern for most construction companies despite the latest developments in technology. Several companies are struggling with poor safety performance, occupational injuries and illnesses, and work-related accidents resulting in fatalities. However, the root causes behind several construction accidents are still vague due to different dynamics in the construction industry. Among these root causes, poor sight, vision and or eye diseases constitute an important part. Hence, the study provides empirical evidence with the workers checked for eye health to help policymakers and industry practitioners in terms of developing awareness for eye-related injuries and accidents and review their safety programs accordingly.
IIBES: a proposed framework to improve the identity-based encryption system for securing federated learning
Authors: Patel Maitri , Patel Rajan , Patel Nimisha , Shah Parita , Gulati Kamal
Published: June 2022

Purpose

In the field of cryptography, authentication, secrecy and identification can be accomplished by use of secret keys for any computer-based system. The need to acquire certificates endorsed through CA to substantiate users for the barter of encoded communications is one of the most significant constraints for the extensive recognition of PKC, as the technique takes too much time and susceptible to error. PKC’s certificate and key management operating costs are reduced with IBC. IBE is a crucial primeval in IBC. The thought behind presenting the IBE scheme was to diminish the complexity of certificate and key management, but it also gives rise to key escrow and key revocation problem, which provides access to unauthorised users for the encrypted information.

Design/methodology/approach

This paper aims to compare the result of IIBES with the existing system and to provide security analysis for the same and the proposed system can be used for the security in federated learning.

Findings

Furthermore, it can be implemented using other encryption/decryption algorithms like elliptic curve cryptography (ECC) to compare the execution efficiency. The proposed system can be used for the security in federated learning.

Originality/value

As a result, a novel enhanced IBE scheme: IIBES is suggested and implemented in JAVA programming language using RSA algorithm, which eradicates the key escrow problem through eliminating the need for a KGC and key revocation problem by sing sub-KGC (SKGC) and a shared secret with nonce. IIBES also provides authentication through IBS as well as it can be used for securing the data in federated learning.
Unleashing the potential of digital technologies in emergency supply chain: the moderating effect of crisis leadership
Authors: Dubey Rameshwar
Published: June 2022

Purpose

The stakeholders are now demanding more visibility and role clarity in the emergency supply chain to improve collaborative efforts. Using a contingent resource-based view (C-RBV), the author studies crisis leadership as a complementary organizational resource for the successful adoption of digital technologies (DTs) in the emergency supply chain. The author further examined the relationships between DTs on information visibility and collaboration under the moderating effects of crisis leadership.

Design/methodology/approach

The author gathered data from 117 NGOs in India using a multi-informant questionnaire. The author further tested the research hypotheses using variance-based structural equation modeling (PLS-SEM).

Findings

DTs under the interaction effect of crisis leadership have a significant influence on the information visibility and the collaboration in the humanitarian context. The findings of the study extend the C-RBVs to create a better understanding of applications of DTs in alleviating human suffering due to crises.

Practical implications

The author provides some direction to the managers engaged in the humanitarian supply chain, contemplating using emerging technologies to enhance information visibility and collaboration.

Originality/value

The current study offers some useful implications for theory. The study findings suggest that the DTs under the moderating effect of the crisis leadership significantly improve the information visibility and the collaboration among the emergency supply chain relief workers. These findings contribute to the C-RBV literature by expanding the scope of the theory. To date, the C-RBV is yet to be explored in humanitarian or emergency settings. Further, the study empirically tests the moderating role of crisis leadership which is touted to be the game-changer, particularly in crises or emergencies.
An efficient approach for the elevator button manipulation using the visual-based self-driving mobile manipulator
Authors: Nguyen Toan Van , Jeong Jin-Hyeon , Jo Jaewon
Published: June 2022

Purpose

Because mobile manipulators are unable to climb stairs, the elevator operation is a crucial capacity to help those kinds of robot systems work in modern multifloor buildings. Here, the elevator button manipulation is considered as an efficient approach to fulfill that requirement. Previously, some studies presented elevator button recognition algorithms while some others designed schemes for the button manipulation work. However, the mobile robot, the manipulator and the camera in their robot systems are asynchronous. Besides, the time-consuming calibration for the camera is inevitable, especially in changeable environments. This paper aims to present an alternative method for the elevator button manipulation to overcome mentioned shortcomings.

Design/methodology/approach

In this paper, the elevator button manipulation is conducted by using the visual-based self-driving mobile manipulator in which the autonomous mobile robot, the manipulator and the camera cooperate more efficiently. Namely, the mobile robot does not need to be located exactly in front of the elevator panel as the manipulator has the ability to adjust the initial frame of the camera based on the system kinematic synchronization. In addition, the proposed method does not require the real world coordinates of elevator buttons, but uniquely using their pixel positions. By doing this, not only is the projection from two-dimensional pixel coordinates to three-dimensional (3D) real world coordinates unnecessary, but also the calibration of the camera is not required.

Findings

The proposed method is experimentally verified by using a visual-based self-driving mobile manipulator. This robotic system is the integration of an autonomous mobile robot, a manipulator and a camera mounted on the end-effector of the manipulator.

Research limitations/implications

Because the surface of the elevator button panel is usually mirror-like, the elevator button detection is easily affected by the glare and the brightness of the environmental light condition.

Practical implications

This robot system can be used for the goods delivery or the patrol in modern multifloor buildings.

Originality/value

This paper includes three new features: simultaneously detecting and manipulating elevator buttons without the projection from pixel coordinates to 3D real world coordinates, a kinematic synchronization to help the robot system eliminate accumulated errors and a safe human-like elevator button manipulation.
Determinants of annual reports complexity in the United States of America: an application of the Tobit model
Authors: Bendriouch Fatimazahra , Jabbouri Imad , M'hamdi Mohamed , Satt Harit , Katona Sara , Serir Rhita
Published: June 2022

Purpose

This paper explores the factors that shape the complexity of company annual reports in the USA. Using a general-to-specific modeling approach, this study examines the determinants of annual reports' tone complexity.

Design/methodology/approach

Negative relationships were found between agency problems and tone; agency costs and readability of annual reports; profitability and tone; and ownership structure and tone complexity.

Findings

These relationships helped to confirm several of this study’s hypotheses, whereas positive associations were found between investment growth opportunities and tone complexity, which contradicts one of our initial hypotheses. Findings reveal that the more complex the language in an annual report is, the more difficult it is to strategically make a judgment or decision about the reported financial situation.

Originality/value

Analyzing these variables allows security analysts and investors to obtain important information, not available in the financial statements, which would enhance their understanding of the firm and improve their recommendations and investment decision-making process.