bluuebunny/crossref_metadata_2025 huggingface dataset:
Did national holidays accelerate COVID-19 diffusion in Bangladesh? A case study
Authors: Khan Mohammad Radid , Mottakin Sayem , Kabir Md. Ahsan , Hoque Md. Enamul , Amin Mohammad Ruhul , Islam Md. Shariful
Published: March 2022

Bangladesh registered 1573828 confirmed cases of COVID-19 and the death toll crossed the grim milestone of 27946 across the country as of 9th December, 2021. Despite the enforcement of stringent COVID-19 measures, including nationwide lockdowns, travel bans, tighter curbs on nonessential activities, and social distancing, the country witnessed an accelerated diffusion of coronavirus cases during the national events and festivals in 2020. The present study aims to examine the association between the national events / festivals and the transmission dynamics of COVID-19 by looking at the instantaneous reproduction number, Rt, of the 64 districts in Bangladesh. We further illustrate the COVID-19 diffusion explicitly in Dhaka Division at the first phase of the pandemic. The comprehensive analysis shows an escalation of Rt value in Dhaka and in all industrialized cities during the major events such as, Garments reopening and religious holidays in Bangladesh. Based on the analysis, a set of array measurements has been also suggested to evade the future pandemic risks while running the national festival activities.

Highlights

Bangladesh confirmed 1573828 coronavirus cases and 27946 deaths due to the current COVID-19 outbreak.

Country observed significant COVID-19 diffusion in its business hubs during national holidays.

Dhaka, the capital of Bangladesh, is the epicenter of the ongoing pandemic.

Calculated Rt value illustrates its escalation in Dhaka and its neighboring cities at the time of national events.

Bangladesh Government needs to consider interdisciplinary approaches and contextual policies to contain the future pandemic during any national events.
Comparison of Accelerometry-based Measures of Physical Activity
Authors: Karas Marta , Muschelli John , Leroux Andrew , Urbanek Jacek K , Wanigatunga Amal A , Bai Jiawei , Crainiceanu Ciprian M , Schrack Jennifer A
Published: March 2022

Background

Given the evolution of processing and analyzing accelerometry data over the past decade, it is of utmost importance that we as a field understand how newer (e.g., MIMS) summary measures compare to long-established ones (e.g., ActiGraph activity counts).

Objective

Our study aims to compare and harmonize accelerometry-based measures of physical activity (PA) to increase the comparability, generalizability, and translation of findings across studies using objective measures of PA.

Methods

High resolution accelerometry data were collected from 655 participants in the Baltimore Longitudinal Study on Aging who wore an ActiGraph GT9X device at wrist continuously for a week. Data were summarized at the minute-level as activity counts (AC; measure obtained from ActiGraph’s ActiLife software) and MIMS, ENMO, MAD, and AI (open-source measures implemented in R). The correlation between AC and other measures was quantified both marginally and conditionally on age, sex and BMI. Next, each pair of measures were harmonized using nonparametric regression of minute-level measurements.

Results

The study sample had the following characteristics: mean (sd) age of 69.8 (14.2), BMI of 27.3 (5.0) kg/m2, 54.5% females, and 67.9% white. The marginal participant-specific correlation between AC and MIMS, ENMO, MAD, and AI were 0.988, 0.867, 0.913 and 0.970, respectively. After harmonization, the mean absolute percentage error for predicting total AC from MIMS, ENMO, MAD, and AI was 2.5, 14.3, 11.3 and 6.3, respectively. The accuracy for predicting sedentary minutes based on AC (AC > 1853) using MIMS, ENMO, MAD and AI was 0.981, 0.928, 0.904, and 0.960, respectively. An R software with a unified interface for computation of the open-source measures from raw accelerometry data was developed and published as SummarizedActigraphy R package.

Conclusions

Our comparison of accelerometry-based measures of PA enables researchers to extend the knowledge from the thousands of manuscripts that have been published using ActiGraph AC to MIMS and other measures by demonstrating their high correlation and providing a harmonization mapping.
Sex and size matter: foraging ecology of offshore harbour porpoises in waters around Greenland
Authors: Louis Marie , Routledge Jennifer , Heide-Jørgensen Mads Peter , Szpak Paul , Lorenzen Eline
Published: March 2022

Individuals of different sex or age can vary in their resource use due to differences in behaviour, life history, energetic need, or size. Harbour porpoises are small cetaceans that rely on a constant prey supply to survive. Here, we use bone collagen carbon (δ13C) and nitrogen (δ15N) isotope compositions to elucidate sex and size differences in the foraging ecology of harbour porpoises from West Greenland. In this region, populations have a unique offshore, deep-water ecology. Female harbour porpoises are larger than males and we find that females have a higher trophic level than males, and δ15N positively correlates with size for females only. This indicates that size may matter in the ability of females to handle larger prey and/or dive deeper to catch higher trophic level prey. These results suggest that females, which also feed their calves, may be under different ecological constraints than males. We also analysed the harbour porpoise data with comparable stable isotope data from Greenland populations of belugas and narwhals. Consistent with their small body size, and a diet consisting primarily of capelin, we find that harbour porpoises have a lower trophic level than belugas and narwhals. Furthermore, harbour porpoises have the largest ecological niche of the three species, which is in accordance with tagging studies indicating they have a wide range in shelf and deep offshore waters of the sub-arctic and North Atlantic.
Visualizing the Transiently Populated Closed-State of Human HSP90 ATP Binding Domain
Authors: Henot Faustine , Rioual Elisa , Favier Adrien , Macek Pavel , Crublet Elodie , Josso Pierre , Brutscher Bernhard , Frech Matthias , Gans Pierre , Loison Claire , Boisbouvier Jerome
Published: March 2022

HSP90 are abundant molecular chaperones, assisting the folding of several hundred client proteins, including substrates involved in tumor growth or neurodegenerative diseases. A complex set of large ATP-driven structural changes occurs during HSP90 functional cycle. However, the existence of such structural rearrangements in apo HSP90 has remained unclear. Here, we identified a metastable excited state in the isolated HSP90 ATP binding domain. We used solution NMR and mutagenesis to characterize structures of both ground and excited states. We demonstrated that in solution the HSP90 ATP binding domain transiently samples a functionally relevant ATP-lid closed state, distant by more than 30 Å from the ground state. NMR relaxation and molecular dynamics were combined to characterize the energy landscape corresponding to the transition between these interconverting states. The precise description of the dynamics and structures sampled by human HSP90 ATP binding domain is a paramount piece of information for the future design of new therapeutic ligands.
Optimization of the precursor supply for an enhanced FK-506 production in Streptomyces tsukubaensis
Authors: Schulz Susann , Schall Christoph , Stehle Thilo , Breitmeyer Christian , Krysenko Sergii , Bera Agnieszka , Wohlleben Wolfgang
Published: March 2022

Tacrolimus (FK-506) is a macrolide widely used as immunosuppressant to prevent transplant rejection. Synthetic production of FK-506 is not efficient and costly, whereas the biosynthesis of FK-506 is complex and the level produced by the wild type strain, Streptomyces tsukubaensis, is very low. We therefore engineered FK-506 biosynthesis and the supply of the precursor L-lysine to generate strains with improved FK-506 yield. To increase FK-506 production, first the intracellular supply of the essential precursor lysine was improved in the native host S. tsukubaensis by engineering the lysine biosynthetic pathway. Therefore, a feedback deregulated aspartate kinase AskSt* of S. tsukubaensis was generated by site directed mutagenesis. Whereas overexpression of AskSt* resulted only in a 17% increase in FK-506 yield, heterologous overexpression of a feedback deregulated AskCg* from Corynebacterium glutamicum was proven to be more efficient. Combined overexpression of AskCg* and DapASt, showed a strong enhancement of the intracellular lysine pool following increase in the yield by approximately 73% compared to the wild type. Lysine is coverted into the FK-506 building block pipecolate by the lysine cyclodeaminase FkbL. Construction of a ΔfkbL mutant led to a complete abolishment of the FK-506 production, confirming the indispensability of this enzyme for FK-506 production. Chemical complementation of the ΔfkbL mutant by feeding pipecolic acid and genetic complementation with fkbL as well as with other lysine cyclodeaminase genes (pipAf, pipASt, originating from Actinoplanes friuliensis and Streptomyces pristinaespiralis, respectively) completely restored FK-506 production. Subsequently, FK-506 production was enchanced by heterologous overexpression of PipAf and PipASp in S. tsukubaensis. This resulted in a yield increase by 65% compared to the WT in the presence of PipAf from A. friuliensis. For further rational yield improvement, the crystal structure of PipAf from A. friuliensis was determined at 1.3 Å resolution with the cofactor NADH bound and at 1.4 Å with its substrate lysine. Based on the structure the Ile91 residue was replaced by Val91 in PipAf, which resulted in an overall increase of FK-506 production by approx. 100% compared to the WT.
Stress-tolerant, recyclable, and autonomously renewable biocatalyst platform enabled by engineered bacterial spores
Authors: Hui Yue , Cui Ziyu , Sim Seunghyun
Published: March 2022

Here, we describe a stress-tolerant, recyclable, and autonomously renewable biocatalyst platform based on T7 RNA polymerase-enabled high-density protein display on bacterial spores (TIED). TIED uses high-level T7 RNA polymerase-driven expression of recombinant proteins specifically in sporulating cells to allow spontaneous assembly of recombinant fusion proteins on B. subtilis spore surface. TIED enables a high loading density in the range of 106–107 recombinant enzymes per spore, robust catalytic activities of displayed enzymes comparable to the respective free enzymes, and enhanced kinetic stability of displayed enzymes in methanol and elevated temperatures. Further, we demonstrate TIED-enzymes to be not only recyclable, but fully renewable after loss of activity through induction of germination and sporulation, enabling perpetual reuse of these immobilized biocatalysts.

Graphical abstract

Schematic illustration of the T7 RNA polymerase-enabled high-density protein display (TIED) on bacterial spores and its unique features as a biocatalyst platform.
Effects of Transcranial Direct Current Stimulation in Children and Young People with Psychiatric Disorders: A Systematic Review
Authors: Gallop Lucy , Westwood Samuel J. , Lewis Yael D. , Campbell Iain C. , Schmidt Ulrike
Published: March 2022

Background

Transcranial Direct Current Stimulation (tDCS) has demonstrated benefits in adults with various psychiatric disorders, but its clinical utility in children and young people (CYP) remains unclear.

Objective

This PRISMA systematic review used published and ongoing studies to examine the effects of tDCS on disorder-specific symptoms, mood and neurocognition in CYP with psychiatric disorders.

Methods

We searched Medline via PubMed, Embase, PsychINFO via OVID, and Clinicaltrials.gov up to January 2022. Eligible studies involved multiple session (i.e. treatment) tDCS in CYP (≤ 25 years-old) with psychiatric disorders. Two independent raters assessed the eligibility of studies and extracted data using a custom-built form.

Results

Of 28 eligible studies (participant N= 379), the majority (n = 23) reported an improvement in at least one outcome measure of disorder-specific symptoms. Few studies (n = 9) examined tDCS effects on mood and/or neurocognition, but findings were mainly positive. Overall, tDCS was well-tolerated with minimal side-effects. Of 11 eligible ongoing studies, many are sham-controlled RCTs (n = 9) with better blinding techniques and a larger estimated participant enrolment (M = 74.7; range: 11-172) than published studies.

Conclusions

Findings provide encouraging evidence of tDCS-related improvement in disorder-specific symptoms, but evidence remains limited, especially in terms of mood and neurocognitive outcomes. Ongoing studies appear to be of improved methodological quality; however, future studies should broaden outcome measures to more comprehensively assess the effects of tDCS and develop dosage guidance (i.e. treatment regimens).
Relative effectiveness of booster vs. 2-dose mRNA Covid-19 vaccination in the Veterans Health Administration: Self-controlled risk interval analysis
Authors: Korves Caroline , Izurieta Hector S. , Smith Jeremy , Zwain Gabrielle M. , Powell Ethan I. , Balajee Abirami , Ryder Kathryn , Young-Xu Yinong
Published: March 2022

Importance

Previous studies have analyzed effectiveness of booster mRNA Covid-19 vaccination and compared it with 2-dose primary series for both Delta and Omicron variants. Observational studies that estimate effectiveness by comparing outcomes among vaccinated and unvaccinated individuals may suffer from residual confounding and exposure misclassification.

Objective

To estimate relative effectiveness of booster vaccination versus the 2-dose primary series with self-controlled study design

Design, Setting and Participants

We used the Veterans Health Administration (VHA) Corporate Data Warehouse to identify U.S. Veterans enrolled in care ≥2 years who received the 2-dose primary mRNA Covid-19 vaccine series and a mRNA Covid-19 booster following expanded recommendation for booster vaccination, and who had a positive SARS-CoV-2 test during the Delta (9/23/2021-11/30/2021) or Omicron (1/1/22-3/1/22) predominant period. Among them, we conducted a self-controlled risk interval (SCRI) analysis to compare odds of SARS-CoV-2 infection during a booster exposure interval versus a control interval.

Exposures

control interval (days 4-6 post-booster vaccination, presumably prior to gain of booster immunity), and booster exposure interval (days 14-16 post-booster vaccination, presumably following gain of booster immunity)

Outcomes and Measures

Positive PCR or antigen SARS-CoV-2 test. Separately for Delta and Omicron periods, we used conditional logistic regression to calculate odds ratios (OR) of a positive test for the booster versus control interval and calculated relative effectiveness of booster versus 2-dose primary series as (1-OR)*100. The SCRI approach implicitly controlled for time-fixed confounders.

Results

We found 42 individuals with a positive SARS-CoV-2 test in the control interval and 14 in the booster exposure interval during Delta period, and 137 and 66, respectively, in Omicron period. For the booster versus 2-dose primary series, the odds of infection were 70% (95%CI: 42%, 84%) lower during the Delta period and 56% (95%CI: 38%, 67%) lower during Omicron. Results were similar for ages <65 and ≥65 years in the Omicron period. In sensitivity analyses among those with prior Covid-19 history, and age stratification, ORs were similar to the main analysis.

Conclusions

Booster vaccination was more effective relative to a 2-dose primary series, the relative effectiveness was consistent across age groups and was higher during the Delta predominant period than during the Omicron period.
Toxoplasma gondii infection and insomnia: a case control seroprevalence study
Authors: Alvarado-Esquivel Cosme , Estrada-Martínez Sergio , Pérez-Álamos Alma Rosa , Ramos-Nevarez Agar , Botello-Calderon Karina , Alvarado-Félix Ángel Osvaldo , Vaquera-Enríquez Raquel , Alvarado-Félix Gustavo Alexis , Sifuentes-Alvarez Antonio , Guido-Arreola Carlos Alberto , Rábago-Sánchez Elizabeth , Saenz-Soto Leandro
Published: March 2022

Aim

To determine the association between Toxoplasma gondii (T. gondii) infection and insomnia.

Materials and methods

Through an age-and gender-matched case-control study, 577 people with insomnia (cases) and 577 people without insomnia (controls) were tested for anti-T. gondii IgG and IgM antibodies using commercially available enzyme-immunoassays.

Results

Anti-T. gondii IgG antibodies were found in 71 (12.3%) of 577 individuals with insomnia and in 46 (8.0%) of 577 controls (OR=1.62; 95% CI: 1.09-2.39; P=0.01). Men with insomnia had a higher (16/73: 21.9%) seroprevalence of T. gondii infection than men without insomnia (5/73: 6.8%) (OR: 3.81; 95% CI: 1.31-11.06; P=0.009). The rate of high (>150 IU/ml) anti-T. gondii IgG antibody levels in cases was higher than the one in controls (OR=2.21; 95% CI: 1.13-4.31; P=0.01). Men with insomnia had a higher (8/73: 11.0%) rate of high anti-T. gondii IgG antibody levels than men without insomnia (0/73: 0.0%) (P=0.006). The rate of high anti-T. gondii IgG antibody levels in cases >50 years old (11/180: 6.1%) was higher than that (3/180: 1.7%) in controls of the same age group (OR: 3.84; 95% CI: 1.05-14.00; P=0.05). No difference in the rate of IgM seropositivity between cases and controls was found (OR=1.33; 95% CI: 0.57-3.11; P=0.50).

Conclusions

Results of this seroepidemiology study suggest that infection with T. gondii is associated with insomnia. Men older than 50 years with T. gondii exposure might be prone to insomnia. Further research to confirm the association between seropositivity and serointensity to T. gondii and insomnia are needed.
Molecular and spatial epidemiology of HCV among people who inject drugs in Boston, Massachusetts
Authors: Stopka Thomas J. , Yaghi Omar , Li Min , Paintsil Elijah , Chui Kenneth , Landy David , Heimer Robert
Published: March 2022

Integration of genetic, social network, and spatial data has the potential to improve understanding of transmission dynamics in established HCV epidemics. Sequence data were analyzed from 63 viremic people who inject drugs recruited in the Boston area through chain referral or time-location sampling. HCV subtype 1a was most prevalent (57.1%), followed by subtype 3a (33.9%). The phylogenetic distances between sequences were no shorter comparing individuals within versus across networks, nor by location or time of first injection. Social and spatial networks, while interesting, may be too ephemeral to inform transmission dynamics when the date and location of infection are indeterminate.
Distinct genome-wide DNA methylation and gene expression signatures in classical monocytes from African American patients with systemic sclerosis
Authors: Allen Peter C. , Smith Sarah , Wilson Robert C. , Wirth Jena R. , Wilson Nathan H. , Frost DeAnna Baker , Flume Jonathan , Gilkeson Gary S. , Cunningham Melissa A. , Langefeld Carl D. , Absher Devin M. , Ramos Paula S.
Published: March 2022

Background

Systemic sclerosis (SSc) is a multisystem autoimmune disorder that has an unclear etiology and disproportionately affects women and African Americans. Despite this, African Americans are dramatically underrepresented in SSc research. Additionally, monocytes show heightened activation in SSc and in African Americans relative to European Americans. In this study, we sought to investigate DNA methylation and gene expression patterns in classical monocytes in a health disparity population.

Methods

Classical monocytes (CD14++CD16-) were FACS-isolated from 34 self-reported African American women. Samples from 12 SSc patients and 12 healthy controls were hybridized on MethylationEPIC BeadChip array, while RNA-seq was performed on 16 SSc patients and 18 healthy controls. Analyses were computed to identify differentially methylated CpGs (DMCs), differentially expressed genes (DEGs), and CpGs associated with changes in gene expression (eQTM analysis).

Results

We observed modest DNA methylation and gene expression differences between cases and controls. The genes harboring the top DMCs, the top DEGs, as well as the top eQTM loci were enriched for metabolic processes. Genes involved in immune processes and pathways showed a weak upregulation in the transcriptomic analysis. While many genes were newly identified, several other have been previously reported as differentially methylated or expressed in different blood cells from patients with SSc, supporting for their potential dysregulation in SSc.

Conclusions

While contrasting with results found in other blood cell types in largely European-descent groups, the results of this study support that variation in DNA methylation and gene expression exists among different cell types and individuals of different genetic, clinical, social, and environmental backgrounds. This finding supports the importance of including diverse, well-characterized patients to understand the different roles of DNA methylation and gene expression variability in the dysregulation of classical monocytes in diverse populations, which might help explaining the health disparities.
Structure of a Rad52 homolog from bacteriophage in complex with a novel duplex intermediate of DNA annealing
Authors: Caldwell Brian J. , Norris Andrew , Wysocki Vicki H. , Bell Charles E.
Published: March 2022

Human Rad52 protein binds to ssDNA and promotes the annealing of complementary strands. This activity is central to multiple DNA repair pathways and Rad52 is a target for cancer therapeutics. Previous crystal structures of the DNA binding domain of Rad52 revealed an 11-mer ring that binds to ssDNA in an extended conformation with the bases exposed for homology recognition. While this complex is likely involved in the early stages of annealing, there is no structure of Rad52 with two strands of DNA bound simultaneously, and its mechanism of annealing is poorly understood. To approach this problem, we have turned to the RecT/Redβ family of annealing proteins from bacteriophage, which are distant homologs of Rad52 that form stable complexes with a duplex intermediate of annealing. We have used single particle cryo-electron microscopy (cryo-EM) to determine a 3.4 Å structure of a RecT homolog from a prophage of Listeria innocua (LiRecT) in complex with two complementary 83-mer oligonucleotides that were added to the protein sequentially. The structure reveals a left-handed helical filament of the protein bound to a novel conformation of DNA duplex that is highly extended and under-wound. The duplex is bound at a stoichiometry of 5 bp/monomer to a deep, narrow, positively-charged groove that runs along the outer surface of the filament. Data from native mass spectrometry confirm that the filament complex seen by cryo-EM also exists in solution. Collectively, these data provide new insights into the mechanism of annealing by LiRecT and by homologous proteins including human Rad52.
Groundwater metabolome responds to recharge in fractured sedimentary strata
Authors: Zerfaß Christian , Lehmann Robert , Ueberschaar Nico , Sanchez-Arcos Carlos , Totsche Kai-Uwe , Pohnert Georg
Published: March 2022

Understanding the sources, structure and fate of dissolved organic matter (DOM) in groundwater is paramount for protection and sustainable use of this vital resource. On its passage through the Critical Zone, DOM is subject to biogeochemical conversions. Therefore, it carries valuable cross-habitat information for monitoring and predicting the stability of groundwater ecosystem services and assessing these ecosystems’ response to fluctuations caused by external impacts such as climatic extremes. Challenges arise from insufficient knowledge on groundwater metabolite composition and dynamics due to a lack of consistent analytical approaches for long-term monitoring. Our study establishes groundwater metabolomics to decipher the complex biogeochemical transport and conversion of DOM. We explore fractured sedimentary bedrock along a hillslope recharge area by a 5-year untargeted metabolomics monitoring of oxic perched and anoxic phreatic groundwater. A summer with extremely high temperatures and low precipitation was included in the monitoring. Water was accessed by a sampling well-transect and regularly collected for liquid chromatography-mass spectrometry (LC-MS) investigation. Dimension reduction of the resulting complex data set by principal component analysis revealed that metabolome dissimilarities between distant wells coincide with transient cross-stratal flow indicated by groundwater levels. Time series of the groundwater metabolome data provides detailed insights into subsurface responses to recharge dynamics. We demonstrate that dissimilarity variability between groundwater bodies with contrasting aquifer properties coincides with recharge dynamics. This includes groundwater high- and lowstands as well as recharge and recession phases. Our monitoring approach allows to survey groundwater ecosystems even under extreme conditions. The metabolome was otherwise highly variable lacking seasonal patterns and did not segregate by geographic location of sampling wells, thus ruling out vegetation or (agricultural) land use as primary driving factor. Patterns that emerge from metabolomics monitoring give insight into subsurface ecosystem functioning and water quality evolution, essential for sustainable groundwater use and climate change-adapted management.
Development of a novel high-throughput screen for the identification of new inhibitors of protein S-acylation
Authors: Salaun Christine , Takizawa Hiroya , Galindo Alex , Munro Kevin R. , McLellan Jayde , Sugimoto Isamu , Okino Tomotaka , Tomkinson Nicholas C.O. , Chamberlain Luke H.
Published: March 2022

Protein S-acylation is a reversible post-translational modification that modulates the localisation and function of many cellular proteins. S-acylation is mediated by a family of zinc finger DHHC domain-containing proteins encoded by 23 distinct ZDHHC genes in the human genome. These enzymes catalyse S-acylation in a two-step process involving “auto-acylation” of the cysteine residue in the catalytic DHHC motif followed by transfer of the acyl chain to a substrate cysteine. S-acylation is essential for many fundamental physiological processes, and there is growing interest in zDHHC enzymes as novel drug targets for a range of disorders. However, there is currently a lack of chemical modulators of S-acylation either for use as tool compounds or for potential development for therapeutic purposes. In this study, we developed and implemented a novel FRET-based high throughput assay for the discovery of compounds that interfere with auto-acylation of zDHHC2, an enzyme that is implicated in neuronal S-acylation pathways. A screen of >350,000 compounds identified two related tetrazole containing compounds (TTZ-1 and -2) that inhibited both zDHHC2 auto-acylation and substrate S-acylation in cell-free systems. Furthermore, these compounds were also active in HEK293T cells, where they inhibited substrate S-acylation mediated by different zDHHC enzymes, with some apparent isoform selectivity. Resynthesis of the hit compounds confirmed their activity, providing sufficient quantities of material for further investigations. The assays developed herein provide novel strategies to screen for zDHHC inhibitors, and the identified compounds add to the chemical toolbox for interrogating the cellular activities of S-acylation and zDHHC enzymes.
Biomolecular condensation orchestrates clathrin-mediated endocytosis in plants
Authors: Dragwidge Jonathan Michael , Wang Yanning , Brocard Lysiane , Meyer Andreas De , Hudeček Roman , Eeckhout Dominique , Grones Peter , Buridan Matthieu , Chambaud Clément , Pejchar Přemysl , Potocký Martin , Winkler Joanna , Vandorpe Michael , Serre Nelson , Fendrych Matyáš , Bernard Amelie , Jaeger Geert De , Pleskot Roman , Fang Xiaofeng , Damme Daniël Van
Published: March 2022

Clathrin-mediated endocytosis (CME) is an essential cellular internalisation pathway involving the dynamic assembly of clathrin and accessory proteins to form membrane-bound vesicles. In plants, the evolutionarily ancient TSET/TPLATE complex (TPC) plays an essential, but not well-defined role in CME. Here, we show that two highly disordered TPC subunits, AtEH1 and AtEH2 function as scaffolds to drive biomolecular condensation of the complex. These condensates specifically nucleate on the plasma membrane through interactions with anionic phospholipids, and facilitate the dynamic recruitment and assembly of clathrin, early-, and late-stage endocytic accessory proteins. Importantly, clathrin forms ordered assemblies within the condensate environment. Biomolecular condensation therefore acts to promote dynamic protein assemblies throughout clathrin-mediated endocytosis. Furthermore, the disordered region sequence properties of AtEH1 regulate the material properties of the endocytic condensatesin vivoand alteration of these material properties influences endocytosis dynamics, and consequently plant adaptive growth.

Highlights

AtEH subunits are endocytic scaffolds which drive condensation of the TPC

AtEH1 condensates nucleate on the plasma membrane via lipid interactions

Condensation of AtEH1/TPC facilitates clathrin re-arrangement and assembly

AtEH1 IDR1 composition controls condensate properties to regulate endocytosis
A correlational study between microstructural, macrostructural and functional age-related changes in the human visual cortex
Authors: Malakshan Sahar Rahimi , Daneshvarfard Farveh , Moghaddam Hamid Abrishami
Published: March 2022

Age-related changes in the human brain can be investigated from either structural or functional perspectives. Analysis of structural and functional age-related changes throughout the lifespan may help to understand the normal brain development process and monitor the structural and functional pathology of the brain. This study, combining dedicated electroencephalography (EEG) and magnetic resonance imaging (MRI) approaches in adults (20-78 years), highlights the complex relationship between micro/macrostructural properties and the functional responses to visual stimuli. Here, we aimed to relate age-related changes of the latency of visual evoked potentials (VEPs) to micro/macrostructural indexes and find any correlation between micro/macrostructural features, as well. We studied age-related structural changes in the brain, by using the MRI and diffusion-weighted imaging (DWI) as preferred imaging methods for extracting brain macrostructural parameters such as the cortical thickness, surface area, folding and curvature index, gray matter volume, and microstructural parameters such as mean diffusivity (MD), radial diffusivity (RD) and axial diffusivity (AD). All the mentioned features were significantly correlated with age in V1 and V2 regions of the visual cortex. Furthermore, we highlighted, negative correlations between structural features extracted from T1-weighted images and DWI. The latency and amplitude of the three dominants peaks (C1, P1, N1) of the VEP were considered as the brain functional features to be examined for correlation with age and structural features of the corresponding age. We observed significant correlations between mean C1 latency and GM volume averaged in V1 and V2. In hierarchical models, the structural index did not contributed to significant additional variance in the C1 latency after accounting for the variance associated with age. However, the age explained significant additional variance in the model after accounting for the variance associated with the structural feature.
Cytokine and chemokine profile in patients hospitalized with COVID-19: A comparative study
Authors: Tufa Abdisa , Gebremariam Tewodros Haile , Manyazewal Tsegahun , Getinet Tewodros , Webb Dominic-Luc , Hellström Per M. , Genet Solomon
Published: March 2022

Abnormal cytokine and chemokine concentrations during SARS-CoV-2 infection may represent disease severity. We aimed to assess plasma cytokine and chemokine concentrations in patients with SARS-CoV-2 in Addis Ababa, Ethiopia. In this study, 260 adults: 126 hospitalized patients with confirmed COVID-19 sorted into severity groups: severe (n=68) and mild or moderate (n=58), and 134 healthy controls were enrolled. We quantified 39 plasma cytokines and chemokines using multiplex ELISA. Spearman rank correlation and Mann-Whitney U test were used to identify mechanistically coupled cytokines/chemokines and compare disease severity. Compared to healthy controls, patients with COVID-19 had significantly higher levels of interleukins 1α, 2, 6, 7, 8, 10 and 15, C-reactive protein (CRP), serum amyloid A (SAA), intercellular adhesion molecule 1 (ICAM-1), vascular cell adhesion protein 1 (VCAM-1), IFN-γ-inducible protein-10 (IP-10), macrophage inflammatory protein-1 alpha (MIP-1α), eotaxin-3, interferon-gamma (IFN-ϒ), tumor necrosis factor-α (TNF-α), basic fibroblast growth factor (bFGF), placental growth factor (PlGF), and fms-like tyrosine kinase 1 (Flt-1). Patients with severe COVID-19 had higher IL-10 and lower macrophage-derived chemokine (MDC) compared to the mild or moderate group (P<0.05). In the receiver operating characteristic curve, SAA, IL-6 and CRP showed strong sensitivity and specificity predicting the severity and prognosis of COVID-19. Greater age and higher CRP had a significant association with disease severity (P<0.05). Our findings reveal that CRP, SAA, VCAM-1, IP-10, MDC and IL-10 levels are promising biomarkers for COVID-19 disease severity, suggesting that plasma cytokines/chemokines could be used as warning indicators of COVID-19 severity, aid in COVID-19 prognosis and treatment.

IMPORTANCE

SARS-CoV-2 triggers inflammatory reaction resulting in respiratory discomfort and in critical case may result in death. Cytokines and chemokines are inflammatory biomarkers that regulate and determine the nature of immune responses. Measuring cytokine and chemokine levels is useful in stratification, management and treatment of COVID-19 patients as well as guide resource allocations and therapeutic options. Here, we examined ctytokine and chemokine profiles in COVID-19 patients. Understanding how distinct cytokines and chemokines change over time as COVID-19 disease progresses might aid clinicians in detecting severe illness earlier and thereby improve patient prognosis.
Efficient solution of particle shape functions for the analysis of powder total scattering data
Authors: Leonardi Alberto , Neder Reinhard , Engel Michael
Published: March 2022

Structural characterization of powder samples via total scattering methods, in either real or reciprocal space, must take into account the effect of particle shape. Here, the shape contribution of a set of ideally isolated particles to the small-angle scattering (SAS) component of the intensity profile is modelled using the shape function [Svergun & Koch (2003). Rep. Prog. Phys.
66, 1735–1782]. The shape function is obtained by orientational averaging of common volume functions (CVFs) for a discrete set of directions. The effects of particle size and size dispersity are accounted for via scaling of the CVFs and their convolution with the underlying probability distribution. The method is applied to shapes with CVFs expressed analytically or by using discrete tables. The accurate calculation of SAS particle shape contributions up to large momentum transfer demonstrates the reliability and flexibility of modelling shape functions from sets of CVFs. The algorithm presented here is computationally efficient and can be directly incorporated into existing routines for analysis of powder total scattering data.
Two-dimensional recurrence relations and Takagi–Taupin equations. I. Dynamical X-ray diffraction by a perfect crystal
Authors: Punegov Vasily , Kolosov Sergey
Published: March 2022

The dynamical diffraction of spatially restricted X-ray beams in a thick perfect crystal is studied using two-dimensional recurrence relations and the Takagi–Taupin (T-T) equations. It is shown that the two-dimensional recurrence relations are transformed into T-T equations when passing from a crystal with an array of discrete lattice planes to a model of continuous periodic electron density. The results of calculations of the X-ray diffraction field inside the crystal and the angular distribution of the scattering intensity in reciprocal space based on these two approaches are presented. It is shown that, when using the two-dimensional recurrence relations and T-T equations, the calculated contours of reciprocal-space maps and their qx
sections are similar to each other, and the qz
sections completely coincide.
Situational variables that affect consumers' suboptimal food purchasing behavior in China
Authors: Cao Shiyang , Gong Shunlong , Bai Li
Published: March 2022

Purpose

Refusing to purchase suboptimal food plays an important role in food waste. However, it is still unclear what factors in the shopping situation will affect consumers' decision to purchase suboptimal food. The purpose of this paper is to identify the situational factors that affect consumers' suboptimal food purchase and provide a basis for designing effective intervention strategies for follow-up suboptimal food sales.

Design/methodology/approach

Based on in-depth interviews with 25 Chinese consumers, this study uses the grounded theory to find out the situational factors that influence consumers' purchase of suboptimal food.

Findings

These situational factors are divided into nine categories and 21 subcategories. Compared with general situational factors that affect consumers' food purchase decisions, some unique factors and remarkable roles are found. It is found that the channel of information release, store hygiene, salesmen and point-of-sale presentation are more important in influencing consumers' decisions to buy suboptimal food. Based on the findings, marketing suggestions for food retailers are put forward.

Originality/value

This paper fills in the research gaps on understanding the impacts of situational factors on suboptimal food purchase and particularly reveals the effects of face concept on the purchase. The research findings can provide a theoretical basis for subsequent large-quantitative research, and in view of the similarities between Chinese culture and East Asian culture, these findings are valuable not only for the Chinese food retailers but also for the international retailers wishing to enter the Chinese or East Asian markets.
The rise of online food delivery culture during the COVID-19 pandemic: an analysis of intention and its associated risk
Authors: Poon Wai Chuen , Tung Serene En Hui
Published: March 2022

Purpose

This study aims to understand consumer behaviour in the context of online food delivery (OFD), especially given the mandatory lockdown imposed in some countries that have modified the behaviour of consumers. Using model goal-directed behaviour (MGB), this study was conducted to investigate consumer perceived risk on the use of OFD services.

Design/methodology/approach

Responses of food delivery services users were collected online throughout April 2020 to understand their risk profile and behaviour. A total of 339 responses were collected and subsequently analysed using partial least square (PLS). Both measurement and structural model were evaluated to ensure that the structural equation modelling (SEM) is valid.

Findings

The results revealed that attitude (ATT), subjective norm (SN), positive anticipated emotion (PAE) and negative anticipated emotion (NAE) and perceived behavioural control (PBC) significantly influenced users' desire. It was also found that PBC significantly influenced users' intention. The empirical result suggests that performance, privacy, financial, physical and the risk of contracting COVID-19 negatively influenced users' desire. In contrast, only physical and the risk of contracting COVID-19 negatively influenced users' intention to use OFD services.

Practical implications

These findings provide OFD service providers and scholars with significant insights into what compels urbanites to adopt OFD services amid a health pandemic. It also allows OFD companies to realign their operation in addressing these concerns and changes in consumer behaviour.

Originality/value

Against the backdrop of the pandemic, this study provides insights for OFD providers in developing new strategies and approaches for business development and consumer retention in a post-pandemic world.
Steering supply chains from a complex systems perspective
Authors: Abbasi Maisam , Varga Liz
Published: March 2022

Purpose

The purpose of this research is to systematically review the properties of supply chains demonstrating that they are complex systems, and that the management of supply chains is best achieved by steering rather than controlling these systems toward desired outcomes.

Design/methodology/approach

The research study was designed as both exploratory and explanatory. Data were collected from secondary sources using a comprehensive literature review process. In parallel with data collection, data were analyzed and synthesized.

Findings

The main finding is the introduction of an inductive framework for steering supply chains from a complex systems perspective by explaining why supply chains have properties of complex systems and how to deal with their complexity while steering them toward desired outcomes. Complexity properties are summarized in four inter-dependent categories: Structural, Dynamic, Behavioral and Decision making, which together enable the assessment of supply chains as complex systems. Furthermore, five mechanisms emerged for dealing with the complexity of supply chains: classification, modeling, measurement, relational analysis and handling.

Originality/value

Recognizing that supply chains are complex systems allows for a better grasp of the effect of positive feedback on change and transformation, and also interactions leading to dynamic equilibria, nonlinearity and the role of inter-organizational learning, as well as emerging capabilities, and existing trade-offs and paradoxical tensions in decision-making. It recognizes changing dynamics and the co-evolution of supply chain phenomena in different scales and contexts.
What's in it for me and you? Exploring managerial perceptions of employees' work-related social media use
Authors: Pekkala Kaisa , Auvinen Tommi , Sajasalo Pasi , Valentini Chiara
Published: March 2022

Purpose

This study focuses on managers' perceptions of employees' communicative role in social media, and explores the changes in the contractual nature of employment relations in mediatized workplaces in which the boundaries of professional and private life are becoming more fluid.

Design/methodology/approach

A qualitative approach was employed to explore this relatively new phenomenon. The data, comprising 24 interviews with managers responsible for corporate communication and human resources in knowledge-intensive organizations, was thematically analysed.

Findings

The analysis shows that employees' work-related social media use creates new types of exchanges and dependencies between an organization and individual employees, which relate to employees' representation, knowledge and networks.

Originality/value

The study is among the first to examine the exchanges and dependencies in an employment relationship that emerge from increased use of social media for professional purposes.
The impact of performance-based rewards and developmental performance appraisal on innovation: the mediating role of innovative work behaviour
Authors: Thneibat Motasem M. , Sweis Rateb J.
Published: March 2022

Purpose

The aim of this paper is to study and empirically test the relationship between employees' perceptions of the two motivation-enhancing human resource management (HRM) practices of reward and performance appraisal and both incremental and radical innovation. The paper examines whether innovative work behaviour (IWB) mediates the hypothesised relationship.

Design/methodology/approach

Data were collected from 313 unit managers in manufacturing, pharmaceutical and technology companies in Jordan. Structural equation modelling (SEM) using AMOS v27 was employed to analyse the data and test the hypotheses.

Findings

The study finds that employees perceive rewards to be significant and to directly influence incremental and radical innovation. Additionally, employees perceive that performance appraisal to be significant for incremental innovation. The study also finds that IWB mediates the relationship between rewards, performance appraisal and incremental and radical innovation. No support was found for the impact of performance appraisal on radical innovation.

Originality/value

Distinctively, this paper considers both incremental and radical innovation in studying the link between HRM practices and innovation. It also takes an intra-organisational perspective by considering employees' perceptions of rewards and performance in fostering innovation. Additionally, it assesses the impact of IWB in mediating the relationship between rewards, performance appraisal and innovation. IWB is rarely empirically studied in the HRM–innovation link specifically when linked with radical and incremental innovation.
Virtual shopping: segmenting consumer attitudes towards augmented reality as a shopping tool
Authors: Romano Beatrice , Sands Sean , Pallant Jason Ian
Published: March 2022

Purpose

Increasingly, retailers are adopting technologies such as augmented reality (AR) as tools to enhance the customer experience. However, little is known about consumers' differing attitudes towards AR. The aim of this study is to explore how consumers differ in terms of the value they receive from using AR, as well as the trade-offs they experience when using the technology for shopping. Moreover, the study explores the individual characteristics that lead to these differences by segmenting consumers according to their perceptions of and attitudes towards AR as a shopping tool.

Design/methodology/approach

To identify the segments, latent class analysis was conducted on the data collected from an online survey of 503 US consumers.

Findings

The analysis yielded four distinct segments of consumers who vary in their attitude towards AR as a shopping tool – AR Averse, AR Hesitant, AR Open and AR Enthusiastic. Covariate analysis indicated that the factors which drive membership of these segments include perceived ease of use, perceived usefulness and psychographic characteristics such as innovativeness, time pressure and shopping enjoyment.

Practical implications

The heterogeneity of consumer attitudes towards AR is driven by consumers' perceptions of decision confidence (how they see AR enhancing their ability to make choices), information overload (the potential for AR to over-stimulate shoppers) and experiential value (the derived value from engaging with AR). Hence, retailers should leverage these dimensions when communicating the value of AR in assisting consumers when shopping.

Originality/value

This study highlights that heterogeneity exists in consumer attitudes towards AR, and suggests that the attitude towards AR is not a fixed value, but can change through education.