bluuebunny/crossref_metadata_2025 huggingface dataset:
Effectiveness of 2 and 3 mRNA COVID-19 Vaccines Doses against Omicron and Delta-Related Outpatient Illness among Adults, October 2021 – February 2022
Authors: Kim Sara S. , Chung Jessie R. , Talbot H. Keipp , Grijalva Carlos G. , Wernli Karen J. , Kiniry Erika , Martin Emily T. , Monto Arnold S. , Belongia Edward A. , McLean Huong Q. , Gaglani Manjusha , Mamawala Mufaddal , Nowalk Mary Patricia , Geffel Krissy Moehling , Tartof Sara Y. , Florea Ana , Lee Justin S. , Tenforde Mark W. , Patel Manish M. , Flannery Brendan ,   Strain Surveillance and Emerging Variants Team
Published: April 2022

Background

We estimated SARS-CoV-2 Delta and Omicron-specific effectiveness of 2 and 3 mRNA COVID-19 vaccine doses in adults against symptomatic illness in US outpatient settings.

Methods

Between October 1, 2021, and February 12, 2022, research staff consented and enrolled eligible participants who had fever, cough, or loss of taste or smell and sought outpatient medical care or clinical SARS-CoV-2 testing within 10 days of illness onset. Using the test-negative design, we compared the odds of receiving 2 or 3 mRNA COVID-19 vaccine doses among SARS-CoV-2 cases versus controls using logistic regression. Regression models were adjusted for study site, age, onset week, and prior SARS-CoV-2 infection. Vaccine effectiveness (VE) was calculated as (1 – adjusted odds ratio) x 100%.

Results

Among 3847 participants included for analysis, 574 (32%) of 1775 tested positive for SARS-CoV-2 during the Delta predominant period and 1006 (56%) of 1794 participants tested positive during the Omicron predominant period. When Delta predominated, VE against symptomatic illness in outpatient settings was 63% (95% CI: 51% to 72%) among mRNA 2-dose recipients and 96% (95% CI: 93% to 98%) for 3-dose recipients. When Omicron predominated, VE was 21% (95% CI: -6% to 41%) among 2-dose recipients and 62% (95% CI: 48% to 72%) among 3-dose recipients.

Conclusions

In this adult population, 3 mRNA COVID-19 vaccine doses provided substantial protection against symptomatic illness in outpatient settings when the Omicron variant became the predominant cause of COVID-19 in the U.S. These findings support the recommendation for a 3rdmRNA COVID-19 vaccine dose.
Age-based variability in the association between restraint use and injury type and severity
Authors: Benedetti Marco H. , Humphries Kayleigh D. , Codden Rachel , Sagar Shraddha , Kufera Joseph A. , Cook Lawrence J. , Norris Jesse , Stamatiadis Nikiforos , Vesselinov Roumen , Zhu Motao
Published: April 2022

Purpose

Previous studies have shown elderly individuals receive less relatively less protection from seat belts against fatal injuries, however it is less clear how seat belt protection against severe and torso injury changes with age. We estimated age-based variability in seat belt protection against fatal injuries, injuries with maximum abbreviated injury scale greater than 2 (MAIS3+), and torso injuries.

Methods

We leveraged the Crash Outcome Data Evaluation System (CODES) to analyze binary indicators of fatal, MAIS3+, and torso injuries. Using a matched cohort design and conditional Poisson regression, we estimated age-based relative risks (RR) of the outcomes associated with seat belt use.

Results

Seat belts were highly protective against fatal injuries for all ages. For ages 16-30, seat belt use was associated with 66% lower risk of MAIS3+ injury (RR 0.34, 95% CI 0.30, 0.38), whereas for ages 75 and older, seat belt use was associated with 38% lower risk of MAIS3+ injury (RR 0.62; 95% CI 0.45, 0.86). The association between restraint use and torso injury also appeared to attenuate with age.

Conclusions

Seat belt protection against MAIS3+ and torso injury attenuated with age. We encourage that injury prevention continues to be tailored to vulnerable populations like the elderly.
Learning-related contraction of grey matter in rodent sensorimotor cortex is associated with adaptive myelination
Authors: Mediavilla Tomás , Özalay Özgün , Estévez-Silva Héctor M. , Frias Bárbara , Orädd Greger , Sultan Fahad R. , Brozzoli Claudio , Garzón Benjamín , Lövdén Martin , Marcellino Daniel J.
Published: April 2022

From observations in rodents, it has been suggested that the cellular basis of learning-dependent changes, detected using structural magnetic resonance imaging (MRI), may be increased dendritic spine density, alterations in astrocyte volume, and adaptations within intracortical myelin. Myelin plasticity is crucial for neurological function and active myelination is required for learning and memory. However, the dynamics of myelin plasticity and how it relates to morphometric-based measurements of structural plasticity remains unknown. We used a motor skill learning paradigm to evaluate experience-dependent brain plasticity by voxel-based morphometry (VBM) in longitudinal MRI, combined with a cross-sectional immunohistochemical investigation. Whole brain VBM revealed non-linear decreases in grey matter (GM) juxtaposed to non-linear increases in white matter (WM) that were best modelled by an asymptotic time course. Using an atlas-based cortical mask, we found non-linear changes with learning in primary and secondary motor areas and in somatosensory cortex. Analysis of cross-sectional myelin immunoreactivity in forelimb somatosensory cortex confirmed an increase in myelin immunoreactivity followed by a return towards baseline levels. The absence of significant histological changes in cortical thickness further suggests that non-linear morphometric changes are likely due to changes in intracortical myelin for which morphometric WM volume (WMV) data significantly correlated with myelin immunoreactivity. Together, these observations indicate a non-linear increase of intracortical myelin during learning and support the hypothesis that myelin is a component of structural changes observed by VBM during learning.
Inequities in COVID-19 vaccine and booster coverage across Massachusetts ZIP codes: large gaps persist after the 2021/22 Omicron wave
Authors: Bor Jacob , Assoumou Sabrina A , Lane Kevin , Diaz Yareliz , Ojikutu Bisola , Raifman Julia , Levy Jonathan I
Published: April 2022

Background. Inequities in COVID-19 vaccine coverage may contribute to future disparities in morbidity and mortality between Massachusetts (MA) communities.

Methods. We obtained public-use data on residents vaccinated and boosted by ZIP code (and by age group: 5-19, 20-39, 40-64, 65+) from MA Department of Public Health. We constructed population denominators for postal ZIP codes by aggregating Census-tract population estimates from the 2015-2019 American Community Survey. We excluded non-residential ZIP codes and the smallest ZIP codes containing 1% of the state's population. We mapped variation in ZIP-code level primary series vaccine and booster coverage and used regression models to evaluate the association of these measures with ZIP-code-level socioeconomic and demographic characteristics. Because age is strongly associated with COVID-19 severity and vaccine access/uptake, we assessed whether observed socioeconomic and racial inequities persisted after adjusting for age composition and plotted age-specific vaccine and booster coverage by deciles of ZIP-code characteristics.

Results. We analyzed data on 418 ZIP codes. We observed wide geographic variation in primary series vaccination and booster rates, with marked inequities by ZIP-code-level education, median household income, essential worker share, and racial-ethnic composition. In age-stratified analyses, primary series vaccine coverage was very high among the elderly. However, we found large inequities in vaccination rates among younger adults and children, and very large inequities in booster rates for all age groups. In multivariable regression models, each 10 percentage point increase in "percent college educated" was associated with a 5.0 percentage point increase in primary series vaccine coverage and a 4.9 percentage point increase in booster coverage. Although ZIP codes with higher "percent Black/Latino/Indigenous" and higher "percent essential workers" had lower vaccine coverage, these associations became strongly positive after adjusting for age and education, consistent with high demand for vaccines among Black/Latino/Indigenous and essential worker populations.

Conclusion. One year into MA's vaccine rollout, large disparities in COVID-19 primary series vaccine and booster coverage persist across MA ZIP codes.
Spatial heterogeneity alters the trade-off between growth and dispersal during a range expansion
Authors: Zamberletti Patrizia , Roques Lionel , Lavigne Florian , Papaïx Julien
Published: April 2022

Individuals who invest more in the development of their dispersal-related traits often reduce their investment in reproduction. Thus, there are two possible eco-evolutionary strategies: grow faster or disperse faster (R—Darbitrage). Here we explore, through a reaction-diffusion model, how spatial heterogeneity can shape theR—Dtrade-off by studying the spreading dynamics of a consumer species exploiting a resource in a spatially fragmented environment. Based on numerical simulations and analytical solutions derived from simpler models, we show that the classical mathematical symmetry between the effects of growth and dispersal on the spatial spreading speed is broken in the presence of competition between phenotypes. At the back of the forefront, the dynamics is almost always driven by theRspecialists. On the forefront, R-strategies are favored in spatially homogeneous environments, but the introduction of heterogeneity leads to a shift towards D-strategies. This effect is even stronger when spatial heterogeneity affects the diffusion term and when spatial fragmentation is lower. Introducing mutations between phenotypes produces an advantage towards the R-strategy and homogenizes the distribution of phenotypes, also leading to more polymorphism on the forefront.
Assessing TMS-evoked cognitive network responses depending on neurocognitive and oscillatory brain state: A simultaneous TMS-EEG-fMRI project
Authors: Janssens Shanice E. W. , de Graaf Tom A. , Duecker Felix , Schuhmann Teresa , Sack Alexander T.
Published: April 2022

Human cognition arises from information exchange within and between functionally connected brain networks. Alterations in such signal propagation across networks are linked to numerous disorders. Brain-wide signal propagation can be experimentally studied with simultaneous transcranial magnetic stimulation (TMS) and functional magnetic resonance imaging (fMRI), where TMS pulses introduce a signal at a certain network node and fMRI charts its propagation through the network. Yet, this approach ignores the fact that the (network) impact of a TMS pulse depends on brain state, where brain state fluctuates spontaneously from moment to moment (e.g. oscillatory state) as well as depending on what a participant does (neurocognitive state). Here, we assessed TMS-evoked fMRI activations as a function of neurocognitive state (eyes open versus eyes closed in complete darkness) and oscillatory state (low versus high pre-TMS alpha power, as measured with simultaneous electroencephalography (EEG)). We applied supra-versus sub-threshold triple-pulse TMS to the right posterior parietal cortex in eight participants, while simultaneously recording EEG and fMRI during two different ocular states. In this first application of the multimodal TMS-EEG-fMRI paradigm to a cognitive network hub, we did not find evidence for a brain state modulation of TMS-induced signal propagation. Instead, we found state-independent TMS-evoked fMRI responses mostly in sensory areas such as the insula, superior temporal gyrus, anterior cingulate cortex, and thalamus, but also in the frontal eye fields. Interestingly, neurocognitive state did seem to modulate the fMRI response to indirect TMS effects such as sensory stimulation. These results lead to several important insights for future cognitive multimodal TMS experiments.
Evaluate the reliability of the apprenticeship in the first year of medical school: towards a reliable first level ultrasound examination
Authors: Turci Michela Cristina , Tassoni Massimo , Gajtani Florida , Previtera Antonino Michele , Magenta-Biasina Alberto , Biganzoli Elia Mario , Serrao Graziano
Published: April 2022

Objectives

Our aim was to motivate apprentices’ sonographer needs, to appraise their own measurements, to reduce inconsistencies within and between operators. Deep knowledge of ultrasound sectional anatomy is mandatory for an appropriate performance.

Methods

In three different weekdays, 3 sonographer apprentices (rater), randomly selected from a cohort of San Paolo Medical School first year students participated in vertically integrated study of living anatomy through ultrasound examination, repeated lumbar multifidus cross-sections scans on 6 subjects at lumbar level. The Agreement R package 0.8-1 was used to monitored the performances of each apprentice.

Results

The agreement (CCCintra 0.6749; CCCinter 0.556; CCCtotal is 0.5438) was further from least acceptable CCC of 0.92-0.95. The precision indices (precisionintra 0.6749; inter 0.801; total0.6274) were unsatisfactory, while the accuracy was high (0.9889 to 0.9913). The same occurred for the agreement on rater performances comparisons, where readings were high accurate (0.9537 to 0.9733) but moderately precise (0.7927 to 0.8895), not interchangeable TIR (1.173) but without rater supremacy. IIR (r1 vs r2 1.104, r1 vs r3 1.015, r2 vs r3 0.92) 95% confidence limits.

Conclusions

Apprentices were not reliable, repeatable, interchangeable. The weak link in the method seemed to be cultural weakness on vivo imaging morphologies, qualitative and quantitative measurement procedure on elementary statistical processing.
A systematic review of Hepatitis B virus (HBV) prevalence and genotypes in Kenya: Data to inform clinical care and health policy
Authors: Downs Louise O , Campbell Cori , Yonga Paul , Ansari M. Azim , Matthews Philippa C , Etyang Anthony O.
Published: April 2022

More than 20% of the global disease burden from chronic hepatitis B infection (CHB) is in Africa, however there is minimal high quality seroprevalence data from individual countries and little viral sequencing data available to represent the continent. We undertook a systematic review of the prevalence and genetic data available for hepatitis B virus (HBV) in Kenya using the Preferred Reporting Items for Systematic Review and Meta-analysis (PRISMA) 2020 checklist. We identified 23 studies reporting HBV prevalence and 25 studies that included HBV genetic data published in English between January 2000 and December 2021. We assessed study quality using the Joanna Briggs Institute critical appraisal checklist. Due to study heterogeneity, we divided the studies to represent low, moderate, high and very high-risk for HBV infection. We calculated pooled HBV prevalence within each group and evaluated available sequencing data. We also assessed whether reported HBV biomarkers could be applied to determine treatment eligibility. Eight studies were identified in the low-risk group, seven in the moderate risk group, five in the high-risk group and three in the very high-risk group for HBV infection. Pooled HBV prevalence was 3.31% (95% CI 2.62-4.01%), 5.58% (95% CI 3.46-7.7%), 6.17% (95% CI 4.4-9.94) and 31.39% (95% CI 9.5-53.09) respectively. Study quality was overall low, representing a small geographical location or a limited population subset. Only three studies detailed sample size calculation and 17/23 studies were cross sectional. Eight studies included genetic information on HBV, representing 247 individuals. Six studies sequenced one or two genes; two undertook whole genome sequencing, representing 22 participants. 92% people were infected with genotype A. Other genotypes included genotype D (6%), D/E recombinants (1%) or mixed populations (1%). Drug resistance mutations were reported by two studies. Seven studies presented additional biomarkers alongside HBsAg, however none provided sufficient information to deduce treatment eligibility.
A prospective observational study on BBV152 coronavirus vaccine use in adolescents and comparison with adults- first real-world safety analysis
Authors: Kaur Upinder , Anju KL , Chauhan Mayank , Joshi Aditi , Kansal Sangeeta , Jaisawal Vaibhav , Patwardhan Kishor , Chakrabarti Sankha Shubhra
Published: April 2022

Background

The BBV152 COVID-19 vaccine (COVAXIN) has recently been approved for adolescents. We provide the first real world safety data of COVAXIN use in adolescents and compare this with adults.

Methods

A prospective observational study is being conducted since January 2022. Enrolled adolescents and adults were contacted telephonically after 14 days of receiving the BBV152 vaccine. Primary outcome was vaccine safety assessed as rates of adverse events following immunization (AEFI). Severity grading of AEFIs was done using the FDA scale.

Findings

A total of 698 adolescents and 326 adults were enrolled. AEFIs occurred in 36.3% adolescents after first and in 37.9% after second dose. Systemic involvement was seen in 15-17% adolescents. Injection site pain and fever were the common AEFIs. Majority of AEFIs were mild-moderate. Severe and atypical AEFIs were observed in 0.9% and 0.6% adolescents respectively. Majority of AEFIs recovered in 1-2 days. In >2% adolescents, AEFIs were persisting at 14-day follow-up since the second dose. No difference in AEFI incidence and patterns was observed between adolescents and adults. Regression analysis showed females and those with history of allergy to be respectively at 1.5-times and 3-times increased risk of AEFIs among adolescents.

Interpretation

COVAXIN carries an overall favorable short term safety profile in adolescents. The observed AEFI rates in adolescents are much lower than that reported with mRNA vaccines. Female adolescents and those with history of allergy need watchfulness. With some AEFIs persisting at 14 days, a longer follow-up is recommended to strengthen the safety data of these vaccines.

Funding

No funding support
Dynamic rewiring of electrophysiological brain networks during learning
Authors: Ruggeri Paolo , Miehlbradt Jenifer , Kabbara Aya , Hassan Mahmoud
Published: April 2022

Human learning is an active and complex process. However, the brain mechanisms underlying human skill learning and the effect of learning on the communication between brain regions, at different frequency bands, are still largely unknown. Here, we tracked changes in large-scale electrophysiological networks over a 6-week training period during which participants practiced a series of motor sequences during 30 home training sessions. Our findings showed that brain networks become more flexible with learning in all the frequency bands from theta to gamma ranges. We found consistent increase of flexibility in the prefrontal and limbic areas in the theta and alpha band, and over somatomotor and visual areas in the alpha band. Specific to the beta rhythm, we revealed that higher flexibility of prefrontal regions during the early stage of learning strongly correlated with better performance measured during home training sessions. Our findings provide novel evidence that prolonged motor skill practice results in higher, frequency-specific, temporal variability in brain network structure.

AUTHOR SUMMARY

We investigated the large-scale organization of electrophysiological brain networks of a cohort of 30 participants practicing a series of motor sequences during 6 weeks of training. With learning, we observed a progressive modulation of the dynamics of prefrontal and limbic regions from theta to alpha frequencies, and of centro-parietal and occipital regions within visuomotor networks in the alpha band. In addition, higher prefrontal regional flexibility during early practice correlated with learning occurring during the 6 weeks of training. This provides novel evidence of a frequency-specific reorganization of brain networks with prolonged motor skill learning and an important neural basis for non-invasive research into the role of cortical functional interactions in (visuo)motor learning.
An oligogenic inheritance test detects risk genes and their interactions in congenital heart defects and developmental comorbidities
Authors: Pittman Maureen , Lee Kihyun , Srivastava Deepak , Pollard Katherine S.
Published: April 2022

Exome sequencing of thousands of families has revealed many individual risk genes for congenital heart defects (CHD), yet most cases cannot be explained by a single causal mutation. Further, those who carryde novoand inherited mutations in known risk genes often demonstrate variable phenotypes even within the same family, indicating the presence of genetic modifiers. To explore oligogenic causes of CHD without assessing billions of variant combinations, we developed an efficient, simulation-based method to detect gene sets that carry damaging variants in probands at a higher rate than expected given parental genotypes. We implemented this approach in software called Gene Combinations in Oligogenic Disease (GCOD) and applied it to a cohort of 3382 trios with exome sequencing. This analysis detected 353 high-confidence risk genes in 202 pairs that appear together in multiple probands but rarely or never appear in combination in their unaffected parents. Stratifying analyses by specific CHD diagnosis and considering gene combinations of higher orders yielded an additional 244 gene sets. The oligogenic genes we discovered cluster in pathways specific to heart development and suggest new molecular disease mechanisms, such as arylsulfatase activity andde novonucleotide biosynthesis. Finally, by combining CHD families with an autism spectrum disorder cohort, we were able to detect 925 oligogenic sets transmitted in renal disease, a known co-morbidity of both conditions. As genome sequencing is applied to more families and other disorders, GCOD will enable detection of increasingly large, novel gene combinations, shedding light on combinatorial causes of genetic diseases.
Characteristics and outcomes of COVID-19 patients during B.1.1.529 (Omicron) dominance compared to B.1.617.2 (Delta) in 89 German hospitals
Authors: Leiner Johannes , Pellissier Vincent , Hohenstein Sven , König Sebastian , Schuler Ekkehard , Möller Robert , Nachtigall Irit , Bonsignore Marzia , Hindricks Gerhard , Kuhlen Ralf , Bollmann Andreas
Published: April 2022

Background

The SARS-CoV-2 variant of concern B.1.1.529 (Omicron) was first described in November 2021 and soon became the dominant variant worldwide. Existing data suggests a reduced disease severity in comparison to B.1.617.2 (Delta). Differences in characteristics and in-hospital outcomes of patients with COVID-19 in Germany during the Omicron period compared to Delta are not thoroughly studied. Surveillance for severe acute respiratory infections (SARI) represents an integral part of infectious disease control in Germany.

Methods

Administrative data from 89 German Helios hospitals was retrospectively analysed. Laboratory-confirmed SARS-CoV-2 infections were identified by ICD-10-code U07.1 and SARI cases by ICD-10-codes J09-J22. COVID-19 cases were stratified by concomitant SARI. A nine-week observational period between December 6, 2021 and February 6, 2022 was defined and divided into three phases with respect to the dominating virus variant (Delta, Delta to Omicron transition, Omicron). Regression analyses adjusted for age, gender and Elixhauser comorbidities were applied to assess in-hospital patient outcomes.

Results

A total cohort of 4,494 inpatients was analysed. Patients in the Omicron dominance period were younger (mean age 61.6 vs. 47.8; p<0.01), more likely to be female (54.7% vs. 47.5%; p<0.01) and characterized by a lower comorbidity burden (mean Elixhauser comorbidity index 8.2 vs. 5.4; p<0.01). Comparing Delta and Omicron periods, patients were at significantly lower risk for intensive care treatment (adjusted odds ratio 0.64 [0.51-0.8]; p<0.001), mechanical ventilation (adjusted odds ratio 0.38 [0.28-0.51]; p<0.001), and in-hospital mortality (adjusted odds ratio 0.42 [0.32-0.56]; p<0.001). This also applied to the separate COVID-SARI group. During the Delta to Omicron transition, case numbers of COVID-19 without SARI exceeded COVID-SARI.

Conclusion

Patient characteristics and outcomes differ during the Omicron dominance period as compared to Delta suggesting a reduced disease severity with Omicron infections. SARI surveillance might play a crucial role in assessing disease severity of future SARS-CoV-2 variants.
Environmental filtering and habitat (mis)matching of riverine invertebrate metacommunities
Authors: Murray-Stoker David , Murray-Stoker Kelly M. , Kong Fan Peng , Amanat Fathima
Published: April 2022

Aim

Metacommunities are assembled through a combination of local and regional processes, with the relative importance of the drivers of assembly depending on ecological context. Global change can alter community assembly at both local and regional levels, potentially shifting communities into disequilibrium with their local environmental conditions. In this study, we evaluated the spatial variation in environmental filtering and habitat matching of 1078 riverine macroinvertebrate communities distributed across nine ecoregions within the conterminous United States.

Location

Conterminous United States.

Taxon

Freshwater macroinvertebrates.

Methods

We first quantified spatial patterns in environmental filtering, habitat matching, and functional trait diversity. We then used boosted regression trees to identify (1) functional trait predictors of environmental filtering and habitat matching and (2) environmental, landscape, and network variables that predict functional trait abundances.

Results

Our results demonstrated that environmental filtering but not habitat matching varied strongly by ecoregion. We also found that functional trait diversity varied by ecoregion, but not as strongly as the signatures of environmental filtering. We did not identify consistent functional trait predictors for both environmental filtering and habitat matching, with trait predictors instead varying by individual traits, trait categories, and ecoregions. Notwithstanding inconsistent trait predictors, environmental filtering was primarily influenced by habitat preference traits while habitat matching was primarily influenced by both habitat preference and dispersal traits. Predictors of functional traits also varied by trait category and ecoregion, with habitat preference and dispersal traits primarily influenced by network variables.

Main conclusions

Our study demonstrates the contingent patterns and drivers of environmental filtering and habitat matching on a macroecological scale. We aim for this work to provide the foundation on which trait-environment relationships can be further quantified and causal explanations established in the context of community disequilibrium and applied to conservation and management of freshwater systems.
CCDC66 regulates primary cilium length and signaling competence via multi-site interactions with transition zone and axonemal proteins
Authors: Conkar Deniz , Odabasi Ezgi , Deretic Jovana , Batman Umut , Frikstad Kari-Anne M. , Patzke Sebastian , Firat-Karalar Elif Nur
Published: April 2022

The primary cilium is a conserved microtubule-based organelle that serves as a hub for many signaling pathways. It functions as part of the centrosome/cilium complex, which also contains the basal body and the centriolar satellites. Little is known about the mechanisms by which the microtubule-based axoneme of the cilium is assembled with proper length and structure, particularly in terms of the activity of microtubule-associated proteins (MAPs) and the crosstalk between the different compartments of the centrosome/cilium complex. Here, we analyzed CCDC66, a MAP implicated in cilium biogenesis and ciliopathies affecting eye and brain. Live-cell imaging revealed that CCDC66 compartmentalizes between centrosomes, centriolar satellites, and the ciliary axoneme and tip during cilium assembly and disassembly. CCDC66 loss-of-function in human cells causes defects in cilium assembly, length and morphology. Notably, CCDC66 interacts with the MAPs and ciliopathy proteins CEP104 and CSPP1 and cooperates with them during axonemal length regulation. Moreover, CCDC66 interacts with the transition zone protein CEP290 selectively at the centriolar satellites. Its loss disrupts basal body recruitment of transition zone proteins and IFT-B machinery and causes defective Hedgehog signaling. Overall, our results establish CCDC66 as a multifaceted regulator of the primary cilium, and propose a mechanistic insight into how the cooperation of ciliary MAPs as well as subcompartments ensures assembly of a functional cilium.
Puf3p facilitates fermentative mitochondrial functions via monosome-enriched nuclear-encoded mitochondrial mRNAs in budding yeast
Authors: Hayashi Sachiko , Iwamoto Kazumi , Yoshihisa Tohru
Published: April 2022

Yeasts generally grow with a highly glycolytic metabolism and restrain mitochondrial biogenesis except for some Fe/S proteins. Respiratory mitochondrial functions and biosynthesis pathways are well studied, however how cells coordinate basal fermentative mitochondrial functions is not fully understood. We show that a part of nuclear-encoded mitochondrial mRNAs, which preferentially translated in monosomes, are regulated by Puf3p upon glucose-rich media. Especially, of those monosome-enriched nuclear-encoded mitochondrial mRNAs, CAT5/COQ7 mRNA has a variant of the canonical Puf3p binding site on its 3’-UTR. Western blot analysis showed that Puf3p represses the translation of Cat5p regardless of fermentable or respiratory media. In vitro binding assay revealed that Puf3p directly binds to CAT5 mRNA via the non-canonical Puf3p binding site.

Mutants harboring the substitution of the non-canonical Puf3p binding site in CAT5 mRNA grew normally but impaired Cat5p expressions apparently, indicating CAT5 mRNA is a bona fide Puf3p target. Overall, Puf3p, a general key modulator for nuclear-encoded mitochondrial mRNAs, fine-tunes translation of a subset of nuclear-encoded mitochondrial mRNAs including mRNAs with non-canonical Puf3p binding sites under the fermentation. This may be required to keeping the fundamental functions of yeast mitochondria at proper levels.
A chemomechanical model of sperm locomotion reveals two modes of swimming
Authors: Li Chenji , Chakrabarti Brato , Castilla Pedro , Mahajan Achal , Saintillan David
Published: April 2022

The propulsion of mammalian spermatozoa during reproduction relies on the spontaneous periodic oscillation of their flagella. These oscillations are driven internally by the coordinated action of ATP-powered dynein motors that exert active sliding forces between microtubule doublets, resulting in bending waves that propagate along the flagellum and enable locomotion of the cell through the viscous medium. In this work, we present a chemomechanical model of a freely swimming spermatozoon that uses a sliding-control model of the flagellar axoneme capturing the coupling of motor kinetics with elastic deformations and accounts for the effect of non-local hydrodynamic interactions between the sperm head and flagellum. Nonlinear simulations of the model equations are shown to produce realistic beating patterns and swimming trajectories, which we analyze as a function of sperm number and motor activity. Our results demonstrate that the swimming velocity does not vary monotonically with dynein activity, but instead displays two local maxima corresponding to distinct modes of swimming, each characterized by qualitatively different waveforms and trajectories.
Single-cell colocalization analysis using a deep generative model
Authors: Kojima Yasuhiro , Mii Shinji , Hayashi Shuto , Hirose Haruka , Ishikawa Masato , Akiyama Masashi , Enomoto Atsushi , Shimamura Teppei
Published: April 2022

1

Analyzing colocalization of single cells with heterogeneous molecular phenotypes is essential for understanding cell-cell interactions, cellular responses to external stimuli, and their biological functions in diseases and tissues. However, high-throughput methods for identifying spatial proximity at single-cell resolution are practically unavailable. Here, we introduce DeepCOLOR, a computational framework based on a deep generative model that recovers inter-cellular colocalization networks with single cell resolution by the integration of single cell and spatial transcriptomes. It segregates cell populations defined by the colocalization relationships and predicts cell-cell interactions between colocalized single cells. DeepCOLOR could identify plausible cell-cell interaction candidates in mouse brain tissues, human squamous cell carcinoma samples, and human lung tissues infected with SARS-CoV-2 by reconstructing spatial colocalization maps at single-cell resolution. DeepCOLOR is typically applicable to studying cell-cell interactions in any spatial niche. Our newly developed computational framework could help uncover molecular pathways across single cells connected with colocalization networks.
Enabling SAT single pilot operations: tactical separation system design advancements in the COAST project
Authors: Di Vito Vittorio , Torrano Giulia , Cerasuolo Giovanni , Ferrucci Michele
Published: April 2022

Purpose

This paper aims to describe the advancements of the activities that have been carried out, in the Cost-Optimized Avionics SysTem (COAST) project, to complete the design and in-flight demonstration of the Tactical Separation System (TSS), which is an automatic support system to the pilot’s decision-making, onboard on small air transport (SAT) vehicles under single pilot operations, in the separation management.

Design/methodology/approach

In the framework of the Clean Sky 2 funded project COAST, some enabling technologies for single pilot operations in the EASA CS-23 category vehicles are designed and demonstrated in flight. Among the relevant flight management technologies addressed in the project, the specific one devoted to the real-time support to pilot’s decision-making in maintaining the vehicle self-separation is the TSS, designed by the Italian Aerospace Research Centre.

Findings

The TSS design started in the year 2016 and has been completed in the year 2021 after successful in-flight demonstration in the dedicated flight test campaign. The system has been validated by means of several simulation campaigns and finally demonstrated its effectiveness in providing its intended functionalities (situational awareness, conflict detection, conflict resolution) to the pilot in real flight trials, involving the presence of real conflicting aircraft.

Originality/value

The TSS contributes enabling the implementation of single pilot operations in CS-23 category vehicles, thanks to the possibility to support the pilot with provision of consolidated traffic picture, detection of conflicting surrounding traffic and suggestion of suitable conflict resolution manoeuvre real-time during the flight, through dedicated human–machine interface designed on purpose. The TSS supports the new separation modes that are envisaged in the future SESAR ATM target concept, with particular reference to the possible delegation of the separation responsibility to the pilot.
Proposing a sequential iterative method based on a per-unit model for rotor shape optimization in permanent magnet assisted synchronous reluctance motors
Authors: Jamali Fard Ali , Mirsalim Mojtaba
Published: April 2022

Purpose

During the design process of synchronous reluctance motors (SynRMs), one crucial step, after its main dimensioning, is optimizing the rotor geometry for maximum average torque and minimum torque ripple. However, because of the complexity of rotor flux-barrier layers geometry, the number of rotor geometrical parameters is high and this step could be quite complex and time-consuming. To obtain a good performance, one needs a robust algorithm to optimize the rotor geometry. The purpose of this paper is to present a sequential iterative method for rotor shape optimization in SynRMs based on the per-unit rotor model to maximize the average torque and minimize the torque ripple.

Design/methodology/approach

In the presented method, at first, rotor geometrical parameters are classified into several groups based on their geometrical similarities, and then optimization is done on these individual groups iteratively. The method starts with an arbitrary feasible rotor geometry and proceeds to optimize it. Because the method’s performance depends on initial rotor geometry, different cases are studied to investigate the convergence and robustness of the method. The MATLAB software is used to implement the optimization algorithm, and the ANSYS Maxwell software is used for the finite element analysis.

Findings

The performance of the proposed method is studied on a three-phase 0.75 kW-1,500 rpm permanent magnet assisted SynRM. The results show that the method improves the average torque while reducing the torque ripple. Even if the method starts with an inappropriate initial rotor geometry, it is robust enough and converges within an acceptable number of iterations.

Originality/value

The value of this paper is in introducing a per-unit rotor model. When the authors optimize the rotor geometry for a specific motor rating, it can be scaled up or down for other ratings with little effort. In this work, the number of rotor poles is four and the number of rotor flux-barrier layers per pole is three. Other combinations could be analyzed in future studies.
Are older applicants less likely to be invited to a job interview? – an experimental study on ageism
Authors: Berde Éva , Mágó Mánuel László
Published: April 2022

Purpose

The main goal of this paper is to test whether older Hungarian women face age discrimination in the job market. The theoretical framework of this paper measures the level of discrimination and highlights that age discrimination leads to a waste of human resources.

Design/methodology/approach

Two pairs of fictitious CVs were created; each pair included a younger (34 years old) and an older woman (60 years old) with an age difference of 26 years. One pair was designed for office assistant positions, the other for economic analyst positions. The contents of the CVs with photos were entirely fabricated except for active email addresses and phone numbers to allow responses to be tracked. LinkedIn accounts were also created for the analysts. Applications were sent over a four-month period from November 2019. The rate of invitation to interviews was analysed with mathematical statistical methods and a small probability model.

Findings

The younger job seekers were invited to interviews about 2.2 times more often than the older ones. Based on the authors’ probability model, employers evaluate the skills of older applicants at only 45–67% of their actual skills.

Research limitations/implications

The experiment had to be stopped due to the Covid-19 lockdown as there were no new job postings.

Originality/value

The experiment demonstrates that age discrimination exists in Hungary. In addition to traditional audit job applications through HR portals, we used LinkedIn too. The small probability model applies an old framework in a new environment.
Investigating the causes of construction delay on the perspective of organization-sectors involved in the construction industry of Bangladesh
Authors: Nafe Assafi Mohammad , Hoque Md. Ikramul , Hossain Md. Mehrab
Published: April 2022

Purpose

Construction delay always causes massive damage to the advancing construction industries, which is no different in the case of Bangladeshi construction industries. This paper aims to investigate the major delay factors causing construction delays in public-funded, mixed and private-funded construction projects of Bangladesh. Also, it offers preventive suggestions from expert stakeholders to reduce the recurrence of delays.

Design/methodology/approach

At first, an extensive literature review was conducted to identify the thirty-seven major delay factors categorized under seven groups. A questionnaire was then developed for survey at ongoing construction projects at a different division of Bangladesh. Next, data from 110 respondents were collected, and the delay factors were ranked based on the Relative Importance Index (RII); lastly, probable solutions were suggested for top-ranked delay factors based on opinions from expert stakeholders in the construction sector of Bangladesh.

Findings

The overall RII ranking of the 37 delay factors showed “Construction mistakes and defective work,” “Contract modifications by the client” and “Adverse weather condition” as the top three factors causing the delay. For public-funded projects, “Construction mistakes and defective work” and “Slow decision making by a consultant” are the top delay factors. For mixed projects, “Slow decision making of the client” and “Construction mistakes and defective work ranked top, and for private-funded projects, “Financial problems and payment delay of the client” and “Adverse weather condition” ranked top. These nuances of ranking in individual project types ascertain that the causes of delay vary in terms of project features.

Practical implications

The outcome of this project will help identify the significant delay factors based on their severity of effectiveness associated with public-funded, mixed and private-funded projects in Bangladesh. The suggestions regarding preventing these delay factors obtained through the opinions of expert stakeholders can help reduce the effect of these delays in the context of Bangladesh and in countries where the similarity in construction environment prevails.

Originality/value

Previously, studies on construction delays in Bangladesh focused mainly on identifying the delays using qualitative analysis techniques. This study is based on a unique methodology of integrating quantitative research on delay factor identification and qualitative research on preventive measures following the opinions gathered from expert stakeholders in the construction sector.
Stock return synchronicity in a weak information environment: evidence from African markets
Authors: Kyiu Anthony , Jones Edward , Li Hao
Published: April 2022

Purpose

This study investigates the level of stock return synchronicity in African markets with the aim of establishing whether, contrary to conventional wisdom, stock return synchronicity can be low in countries with relatively weak information environments.

Design/methodology/approach

The authors use a sample of five African countries (Botswana, Ghana, Kenya, Nigeria and South Africa) and a total of 616 firms over the period 2005–2015. This study's main measure of synchronicity is the R2 from a regression of stock returns on index returns. The authors also carry out regression analysis to investigate the main firm-level drivers of synchronicity.

Findings

On average, firms in African markets do not exhibit high levels of stock return synchronicity, providing support for the view that stock return synchronicity can be low in markets with relatively weak transparency. The authors, however, observe an increase in the level of synchronicity during the global financial crisis, notably for Ghana and Kenya. In the regression analysis, the main firm-level driver of synchronicity is firm size, while contrary to some previous studies, ownership structure has no impact. The authors also find evidence of the impact of changes in accounting regulation, notably the mandatory adoption of IFRS, on the level stock synchronicity.

Originality/value

This study contributes to the understanding of stock return synchronicity and how price discovery can vary between different information environments. The authors argue that stock returns in African countries may not always fit the stereotypical view that they are synchronous. The level of synchronicity among firms suggests that corporate events may carry some stock price implications.
Multiaxial fatigue under variable amplitude loadings: review and solutions
Authors: Deng Qing-Yun , Zhu Shun-Peng , He Jin-Chao , Li Xue-Kang , Carpinteri Andrea
Published: April 2022

Purpose

Engineering components/structures with geometric discontinuities normally bear complex and variable loads, which lead to a multiaxial and random/variable amplitude stress/strain state. Hence, this study aims how to effectively evaluate the multiaxial random/variable amplitude fatigue life.

Design/methodology/approach

Recent studies on critical plane method under multiaxial random/variable amplitude loading are reviewed, and the computational framework is clearly presented in this paper.

Findings

Some basic concepts and latest achievements in multiaxial random/variable amplitude fatigue analysis are introduced. This review summarizes the research status of four main aspects of multiaxial fatigue under random/variable amplitude loadings, namely multiaxial fatigue criterion, method for critical plane determination, cycle counting method and damage accumulation criterion. Particularly, the latest achievements of multiaxial random/variable amplitude fatigue using critical plane methods are classified and highlighted.

Originality/value

This review attempts to provide references for further research on multiaxial random/variable amplitude fatigue and to promote the development of multiaxial fatigue from experimental research to practical engineering application.
Resilience in food processing supply chain networks: empirical evidence from the Indian dairy operations
Authors: Prakash Gyan
Published: April 2022

Purpose

This paper identifies sources of disruptions that impede resilience in the dairy supply chain in an emerging economy context.

Design/methodology/approach

A case study approach is used. The unit of analysis is the Indian dairy supply chain (IDSC). Data were collected from nine major dairy cooperatives and five major private firms operating across the Indian states. A total of 28 face-to-face semi-structured interviews were conducted with two individuals from each case dairy organisation during January 2016 to December 2017.

Findings

Disruption sources in the IDSC are both external and internal and impact the quality of products and the distribution network. Compared to developed economies, in an emerging economy context such as India, the number of disruptions is very high. These disruptions negatively impact resilience and affect efficiency, flexibility, responsiveness and product quality.

Research limitations/implications

The findings stress the importance of integration across upstream and downstream processes in the IDSC. However, contextual factors should also be considered when designing the supply chain configuration. Small supply sources may be conceptualised as distributed sources that can be consolidated on the move using logistics and IT-enabled solutions. Moreover, the underlying processes of the dairy supply chain need to adapt to the external environment, and internal causes of disruptions should be eliminated through process redesign.

Practical implications

The findings highlight that the efficient operation of the IDSC is challenged by disruptions, the fragmentation of various stages and poor support infrastructure. The findings may be useful in managing supply networks which have linkages in emerging economies.

Social implications

The upstream stage of the IDSC involves many small- and medium-sized unorganised producers. The overall inefficiency and poor value generation across the entire IDSC constrain the livelihood and interests of these unorganised producers. Therefore, supply chain design needs to be aligned with social context.

Originality/value

The central contribution of this article is to present sources of disruptions that impact dairy supply chain performance in an emerging economy context. Areas requiring process improvement are also highlighted.