bluuebunny/crossref_metadata_2025 huggingface dataset:
Identifying type 1 and 2 diabetes in population level data: assessing the accuracy of published approaches
Authors: Thomas Nicholas J , McGovern Andrew , Young Katherine G , Sharp Seth A , Weedon Michael N , Hattersley Andrew T , Dennis John , Jones Angus G
Published: April 2022

Aims

Population datasets are increasingly used to study type 1 or 2 diabetes, and inform clinical practice. However, correctly classifying diabetes type, when insulin treated, in population datasets is challenging. Many different approaches have been proposed, ranging from simple age or BMI cut offs, to complex algorithms, and the optimal approach is unclear. We aimed to compare the performance of approaches for classifying insulin treated diabetes for research studies, evaluated against two independent biological definitions of diabetes type.

Method

We compared accuracy of thirteen reported approaches for classifying insulin treated diabetes into type 1 and type 2 diabetes in two population cohorts with diabetes: UK Biobank (UKBB) n=26,399 and DARE n=1,296. Overall accuracy and predictive values for classifying type 1 and 2 diabetes were assessed using: 1) a type 1 diabetes genetic risk score and genetic stratification method (UKBB); 2) C-peptide measured at >3 years diabetes duration (DARE).

Results

Accuracy of approaches ranged from 71%-88% in UKBB and 68%-88% in DARE. All approaches were improved by combining with requirement for early insulin treatment (<1 year from diagnosis). When classifying all participants, combining early insulin requirement with a type 1 diabetes probability model incorporating continuous clinical features (diagnosis age and BMI only) consistently achieved high accuracy, (UKBB 87%, DARE 85%). Self-reported diabetes type alone had high accuracy (UKBB 87%, DARE 88%) but was available in just 15% of UKBB participants. For identifying type 1 diabetes with minimal misclassification, using models with high thresholds or young age at diagnosis (<20 years) had the highest performance. An online tool developed from all UKBB findings allows the optimum approach of those tested to be selected based on variable availability and the research aim.

Conclusion

Self-reported diagnosis and models combining continuous features with early insulin requirement are the most accurate methods of classifying insulin treated diabetes in research datasets without measured classification biomarkers.
Declining National Codeine Distribution in United States Hospitals and Pharmacies from 2011 to 2019
Authors: Kennalley Amy L. , Boureghda Youcef A. , Ganesh Jay G. , Watkins Adam M. , McCall Kenneth L. , Piper Brian J.
Published: April 2022

Background

Past research has identified pronounced regional disparities in use of different opioids but less is known for codeine. The primary objective of this study was to analyze the trends of distribution of prescriptions containing codeine in the United States (US) from 2010 to 2019. In addition, this study aimed to identify regional disparities in prescribed milligrams of codeine per person in 2019 and identify any unusual states.

Methods

The distribution of codeine via pharmacies, hospitals, and practitioners in kilograms was obtained from the Drug Enforcement Administration’s Automated Reports and Consolidated Ordering System (ARCOS) from 2010 to 2019. In addition, the number of prescriptions of codeine per 1,000 Medicaid enrollees was obtained from the State Drug Utilization Database.

Results

The total grams of codeine decreased (−25.0%) through all distributors from 2010 to 2019. The largest increase in total grams of codeine distributed between two consecutive years (2014 to 2015) was +28.9%. For a given distributor type, the largest decrease from 2010 to 2019 was hospitals (−89.6%). In 2019, the total mg of codeine per person distributed in Texas (11.46) was significantly higher relative to the national average (3.06, 1.88 SD). Codeine prescriptions to Medicaid patients peeked in the third quarter of 2016.

Conclusion

The peak of prescription codeine in 2011 was consistent with the overall peak in prescription opioids, with a subsequent decrease over the decade. This could be explained by relatively recent recommendations regarding the therapeutic use of codeine and how other antitussive agents may be of better use. The precipitous rise of codeine in Texas that we observed has been recognized in prior studies. These state-level disparities warrant further attention by opioid stewardship committees.
Representational integration and differentiation in the human hippocampus following goal-directed navigation
Authors: Fernandez Corey , Jiang Jiefeng , Wang Shao-Fang , Choi Hannah L. , Wagner Anthony D.
Published: April 2022

As we learn, dynamic memory processes build structured knowledge across our experiences. Such knowledge enables the formation of internal models of the world that we use to plan, make decisions, and act. Recent theorizing posits that mnemonic mechanisms of differentiation and integration – which at one level may seem to be at odds – both contribute to the emergence of structured knowledge. We tested this possibility using fMRI as human participants learned to navigate within local and global virtual environments over the course of three days. Pattern similarity analyses on entorhinal cortex, hippocampus, and ventromedial prefrontal cortex patterns revealed evidence that differentiation and integration work concurrently to build local and global environmental representations, and that variability in integration relates to differences in navigation efficiency. These results offer new insights into the neural machinery and the underlying mechanisms that translate experiences into structured knowledge that allows us to navigate to achieve goals.
General Features of Transmembrane Beta Barrels From a Large Database
Authors: Montezano Daniel , Bernstein Rebecca , Copeland Matthew M. , Slusky Joanna S. G.
Published: April 2022

Large datasets contribute new insights to subjects formerly investigated by exemplars. We used co-evolution data to create a large, high-quality database of transmembrane β-barrels (TMBB). By applying simple feature detection on generated evolutionary contact maps, our method (IsItABarrel) achieves 95.88% balanced accuracy when discriminating among protein classes. Moreover, comparison with IsItABarrel revealed a high rate of false positives in previous TMBB algorithms. In addition to being more accurate than previous datasets, our database (available online) contains 1,894,206 bacterial TMBB proteins from 20 evolutionary classes, respectively 17 and 2.2 times larger than the previous sets TMBB-DB and OMPdb. We anticipate that due to its quality and size the database will serve as a useful resource where high quality TMBB sequence data is required. We found that TMBBs can be divided into 10 types, three of which have not been previously reported. We find tremendous variance in proteome percentage among TMBB-containing organisms with some using 6.79% of their proteome for TMBBs and others using as little as 0.27% of their proteome. The distribution of the lengths of the TMBBs is suggestive of previously hypothesized duplication events. In addition, we find that the C-terminal β-signal varies among different classes of bacteria though it is most commonly HyGHyGY+F. However, this β-signal is only characteristic of prototypical TMBBs. The nine non-prototypical barrel types have other C-terminal motifs and it remains to be determined if these alternative motifs facilitate TMBB insertion or perform any other signaling function.

Significance Statement

Outer membrane proteins (OMPs) control all interactions between Gram negative bacteria and their environments including uptake and efflux of antibiotics. We created an algorithm that identifies bacterial OMPs from sequence. The quality of our algorithm allows us to identify most OMPs (∼1.8 million) from prokaryotic genomes including >240,000 unrelated to previously structurally-resolved OMPs. We identify ten types of OMPs in our database. The largest type’s signal sequence—used for targeting the membrane-insertion machinery—varies by phylogenetic class. All other types of OMPs do not have a related signal sequence, raising new questions of how these proteins fold. Our web-accessible database will allow for further exploration of the varieties of outer membrane proteins to uncover new targets for controlling antibiotic resistance.
Building a Tissue-unbiased Brain Template of Fibre Orientation Distribution and Tractography with Multimodal Registration
Authors: Lv Jinglei , Zeng Rui , Ho Mai Phuong , D’Souza Arkiev , Calamante Fernando
Published: April 2022

A brain template provides a standard space for statistical analysis of brain structure and function. For decades, the T1- and T2-weighted brain templates have been widely used for brain grey matter anatomical and functional analysis. However, T1- and T2-weighted templates provide very limited information about the axonal organization within the white matter. Recent advances in Diffusion MRI have enabled the detailed modelling of the axonal fibre orientation distribution (FOD) in white matter. Therefore, building a FOD template is essential for more robust white matter anatomy related analysis; however, it is important that this template aligns well with the cortical and subcortical structures. From such a FOD template, a tractography template can be also generated by fibre tracking algorithms, which can be used for subsequent applications, such as to perform the joint structural and functional analysis while ensuring rigorous fibre-to-fibre correspondence. In this paper, we explore the potential of generating the FOD template based on multimodal registration, in order to constrain the tempalte unbiased to both white and grey matter. We combine the information from T1-weighted, T2-weighted and Diffusion MRI to generate a coherent transformation for FOD registration and template generation. Our FOD template preserves the structural details at the white-grey matter boundary. To illustrate the benefit of this new approach, the resulting tractography template was used for joint structural-functional connectivity analysis.
Assignment of structural transitions during mechanical unwrapping of nucleosomes and their disassembly products
Authors: Díaz-Celis César , Cañari-Chumpitaz Cristhian , Sosa Robert P. , Castillo Juan P. , Zhang Meng , Cheng Enze , Chen Andy , Vien Michael , Kim JeongHoon , Onoa Bibiana , Bustamante Carlos
Published: April 2022

Nucleosome DNA unwrapping and its disassembly into hexasomes and tetrasomes is necessary for genomic access and plays an important role in transcription regulation. Previous single-molecule mechanical nucleosome unwrapping revealed a low- and a high-force transitions, and force-FRET pulling experiments showed that DNA unwrapping is asymmetrical occurring always first from one side before the other. However, the assignment of DNA segments involved in these transitions remains controversial. Here, using high-resolution optical tweezers with simultaneous single-molecule FRET detection we show that the low-force transition corresponds to the undoing of the outer-wrap of one side of the nucleosome (~27 bp), a process that can occur either cooperatively or non-cooperatively, whereas the high-force transition corresponds to the simultaneous unwrapping of ~76 bp from both sides. This process may give rise stochastically to the disassembly of nucleosomes into hexasomes and tetrasomes whose unwrapping/rewrapping trajectories we establish. In contrast, nucleosome rewrapping does not exhibit asymmetry. To rationalize all previous nucleosome unwrapping experiments, it is necessary to invoke that mechanical unwrapping involves two nucleosome reorientations: one that contributes to the change in extension at the low-force transition, and another that coincides but does not contribute to the high-force transition.

Significance statement

Nucleosomes, the fundamental structural unit of chromatin, consists of ~147 DNA base pairs wrapped around a histone protein octamer. Determining the forces required to unwrap the DNA from the core particle and the stepwise transitions involved in the process are essential to characterize the strength of the nucleosomal barrier and its contribution as a mechanism of control of gene expression. Here, we performed combined optical tweezers and single-molecule fluorescence measurements to annotate the specific DNA segments unwrapping during the force transitions observed in mechanical unwrapping of nucleosomes. Furthermore, we characterize the mechanical signatures of subnucleosomal particles: hexasomes and tetrasomes. The characterization performed in this work is essential for the interpretation of ongoing studies of chromatin remodelers, polymerases, and histone chaperones.
Outer Membrane Vesicle Mediated Multidrug Resistance Gene Transfer in Avibacterium Paragallinarum
Authors: Xu Jie , Mei Chen , Zhi Yan , Liang Zhi-xuan , Zhang Xue , Wang Hong-jun
Published: April 2022

Infectious coryza is an acute upper respiratory tract infectious disease caused by Avibacterium paragallinarum, which can cause growth retardation and egg production decline of bred chickens, and bring great economic losses to poultry industry. A. Paragallinarum is a Gram-negative bacterium and can release outer membrane vesicles (OMVs). In this study, a comparative genomic analysis of A. Paragallinarum isolate P4chr1 and its OMVs were carried out, and the ability to transfer antibiotic resistance genes via the OMVs was studied. The sequencing and data analysis showed that genome size of A. paragallinarum P4chr1 is about 2.77 Mb and it has a 25 kb tolerance island covering 6 types of antibiotics and 11 resistance genes. The genome size of its OMVs is about 2.69 Mb, covering 97% genome length and almost all gene sequences of P4chr1. When purified and DNase treated A. paragallinarum P4chr1 OMVs were co-cultured with antibiotic sensitive A. paragallinarum Modesto strain on an antibiotic containing plate, the colonies grown on the plate were detected corresponding antibiotic resistance gene (ARG). However, antimicrobial susceptibility test exposed that drug resistance genes delivered by OMVs were not persistent, they only existed temporarily on the antibiotic plates. The antibiotic resistance and ARGs disappeared at second bacterial passage. Overall, this study is the first report to compare genomic characteristics of OMVs with its parent A. paragallinarum strain, and to study A. paragallinarum ARG transfer via OMVs. This work has provided useful data for further study on the issue of non-plasmid ARG transfer mediated by A. paragallinarum OMVs.
Cell division drives DNA methylation loss in late-replicating domains in primary human cells
Authors: Endicott Jamie L. , Nolte Paula A. , Shen Hui , Laird Peter W.
Published: April 2022

DNA methylation undergoes dramatic age-related changes, first described more than four decades ago1–4. Loss of DNA methylation at late-replicating regions of the genome attached to the nuclear lamina advances with age in normal tissues, and is further exacerbated in cancer5–7. We present here the first experimental evidence that this DNA hypomethylation is directly driven by proliferation-associated DNA replication. Loss of DNA methylation at low-density CpGs in A:T-rich, partially methylated domains (PMD solo-WCGWs), tracks cumulative population doublings in primary cell culture. Cell cycle deceleration resulted in a proportional decrease in the rate of DNA hypomethylation. Blocking DNA replication via Mitomycin C treatment halted methylation loss. Loss of methylation continued unabated after TERT immortalization until finally reaching a severely hypomethylated equilibrium. Ambient oxygen culture conditions increased the rate of methylation loss compared to low-oxygen conditions, suggesting that some methylation loss may occur during unscheduled, oxidative damage repair-associated DNA synthesis. Finally, we present and validate a model to estimate the relative cumulative replicative histories of human cells, which we call “RepliTali” (Replication Times Accumulated in Lifetime).
p66Shc is an apoptotic rheostat whose targeted ROS inhibition improves MI outcomes
Authors: Haslem Landon , Hays Jennifer M. , Schmitz Hannah , Matsuzaki Satoshi , Sjoelund Virginie , Byrum Stephanie D. , Humphries Kenneth M. , Frazer J. Kimble , Demeler Borries , Benbrook Doris M. , Tierney Ryan M. , Duggan Kelli D. , Hays Franklin A.
Published: April 2022

p66Shc is an oxidoreductase that responds to cell stress by translocating to mitochondria, where p66Shc produces pro-apoptotic reactive oxygen species (ROS). This study identifies ROS-active p66Shc as a monomer that produces superoxide anion independent of metal ions, inhibits cytochrome c peroxidase, and is regulated by environmental condition-induced structural changes. p66Shc anti-apoptotic functions, including: cytochrome c reduction, increased electron transport chain activity, and caspase cascade inhibition were also discovered. This study also demonstrates that p66Shc is a stress-dependent rheostat of apoptosis, regulated by p66Shc-mortalin complexes. These complexes decrease pro-apoptotic ROS production, without blocking p66Shc-mediated cytochrome c reduction. However, stress disrupts p66Shc-mortalin interactions, promoting apoptosis. Tipping p66Shc’s apoptotic balance toward anti-apoptotic functions by genetic knockdown or p66Shc-selective ROS inhibition decreased pro-apoptotic effects and improved outcomes in zebrafish myocardial infarction models, representing a potential new myocardial infarction treatment with promising results.
Single Nucleus Sequencing of Human Colon Visceral Smooth Muscle Cells, PDGFRα Cells, and Interstitial Cells of Cajal
Authors: Schneider Sabine , Hashmi Sohaib K. , Thrasher A. Josephine , Kothakapa Deepika R. , Wright Christina M. , Heuckeroth Robert O.
Published: April 2022

Background and Aims

Smooth muscle cells (SMCs), Interstitial cells of Cajal (ICCs), and PDGFRα+ cells (PαCs) form a functional syncytium in the bowel known as the ‘SIP syncytium’. The SIP syncytium works in concert with the enteric nervous system (ENS) to coordinate bowel motility. However, our understanding of individual cell types that form this syncytium and how they interact with each other remains limited, with no prior single cell RNAseq analyses focused on human SIP syncytium cells.

Methods

We analyzed single-nucleus RNA sequencing data from 10,749 human colon SIP syncytium cells (5572 SMC, 372 ICC, and 4805 PαC nuclei) derived from 15 individuals.

Results

Consistent with critical contractile and pacemaker functions and with known ENS interactions, SIP syncytium cell types express many ion channels including mechanosensitive channels in ICCs and PαCs. PαCs also prominently express ECM-associated genes and the inhibitory neurotransmitter receptor for vasoactive intestinal peptide (VIPR2), a novel finding. We identified two PαC clusters that differ in expression of many ion channels and transcriptional regulators. Interestingly, SIP syncytium cells co-express 6 transcription factors (FOS, MEIS1, MEIS2, PBX1, SCMH1, and ZBTB16) that may be part of a combinatorial signature that specifies these cells. Bowel region-specific differences in SIP syncytium gene expression may correlate with regional differences in function, with right (ascending) colon SMCs and PαCs expressing more transcriptional regulators and ion channels than SMCs and PαCs in left (sigmoid) colon.

Conclusion

These studies provide new insights into SIP syncytium biology that may be valuable for understanding bowel motility disorders and lead to future investigation of highlighted genes and pathways.

Synopsis

In this first single nucleus RNASeq analysis of human SIP syncytium, we identify novel features of SIP syncytium cells, including two types of PDGFRα+ cells, a SIP-specific combinatorial transcription factor signature, and colon region differences in gene expression.
Combined nanometric and phylogenetic analysis of unique endocytic compartments in Giardia lamblia sheds light on the evolution of endocytosis in Fornicata
Authors: Santos Rui , Ástvaldsson Ásgeir , Pipaliya Shweta V. , Zumthor Jon Paulin , Dacks Joel B. , Svärd Staffan , Hehl Adrian B. , Faso Carmen
Published: April 2022

Giardia lamblia, a parasitic protist of the metamonada supergroup, has evolved one of the most diverged endocytic compartment systems investigated so far. Peripheral endocytic compartments, currently known as peripheral vesicles or vacuoles (PVs), perform bulk uptake of fluid phase material which is then digested and sorted either to the cell cytosol or back to the extracellular space. Here, we present a quantitative morphological characterization of these organelles using volumetric electron microscopy and super-resolution microscopy (SRM). We defined a morphological classification for the heterogenous population of PVs and performed a comparative analysis of PVs and endosome-like organelles in representatives of phylogenetically-related taxa,Spironucleus spp.andTritrichomonas foetus. To investigate the as-yet insufficiently understood connection between PVs and clathrin assemblies inG. lamblia, we further performed an in-depth search for two key elements of the endocytic machinery, clathrin heavy chain (CHC) and clathrin light chain (CLC) across different lineages in Metamonada. Our data point to the loss of abona fideCLC in the last Fornicata common ancestor (LFCA) with the emergence of a protein analogous to CLC (GlACLC) in theGiardiagenus. Taken together, this provides the first comprehensive nanometric view ofGiardia’s endocytic system architecture and sheds light on the evolution of GLACLC analogues in the Fornicata supergroup and, specific to Giardia, as a possible adaptation to the formation and maintenance of stable clathrin assemblies at PVs.
Targeted Sequencing of Alzheimer’s Disease Genes in Gujarat Cohort
Authors: Budhbhatti Urvi , Joshi Chaitanya , Chauhan Ajay , Bhatt Deeptiben , Parmar Chirag , Damani Vishalbhai , Patel Amrutlal
Published: April 2022

Alzheimer’s Disease (AD) is the most common type of dementia affecting cognitive and behavioural functions. It’s a complex disease that results from the modest effect of gene interaction and environmental factors, as a result of which its exact pathogenesis is still unknown. In the present study, we have performed an association study of exonic regions of 94 genes with AD using the Haloplex target enrichment method and genotyping of 4 genes NOTCH4(rs367398), NEP(rs61760379), APOE (rs121918398), and ATP7B(rs1801243) using PCR RFLP technique. In this study, we screened 32 AD cases and 11 control samples. We have identified 19 variants assigned to 16 genes that were significantly associated with AD with a p-value < 0.05. However, no variants have passed multiple test corrections except NOTCH4/rs367398 genotyped using the PCR-RFLP approach. The functional enrichment analysis of the significant genes for the disease indicates that the genes are significantly involved in AD. Also, functional enrichment analysis for biological processes using ClueGo and network analysis using the STRING database indicated that the genes are directly and indirectly playing a role in AD pathogenesis. The eQTL analysis of the variants with GTEx dataset indicate that out of 19 variants ACHE/rs1799806 and NOTCH4/rs367398 variants is showing significant eQTL for the neighbouring genes for different brain regions and whole blood. Regardless, additional studies with a large cohort are required to establish the role and prevalence of these variants in the local population of Gujarat.
Asymmetric survival in single-cell lineages of cyanobacteria in response to photodamage
Authors: Tay Jian Wei , Cameron Jeffrey C.
Published: April 2022

Summary paragraph

Oxygenic photosynthesis is driven by the coupled action of the light-dependent pigment protein complexes, photosystem I and II, located within the internal thylakoid membrane system. However, photosystem II is known to be prone to photooxidative damage. Thus, photosynthetic organisms have evolved a repair cycle to continuously replace the damaged proteins in photosystem II. However, it has remained difficult to deconvolute the damage and repair processes using traditional ensemble approaches. Here we demonstrate an automated approach using time-lapse fluorescence microscopy and computational image analysis to study the dynamics and effects of photodamage in single cells at sub-cellular resolution in cyanobacteria. By growing cells in a two-dimensional layer, we avoid shading effects, thereby generating uniform and reproducible growth conditions. Using this platform, we analyzed the growth and physiology of multiple strains simultaneously under defined photoinhibitory conditions stimulated by UV-A light. Our results reveal an asymmetric cellular response to photodamage between sibling cells and the generation of an elusive subcellular structure, here named a ‘photoendosome’, derived from the thylakoid which could indicate the presence of a previously unknown photoprotective mechanism. We anticipate these results to be a starting point for further studies to better understand photodamage and repair at the single-cell level.
Specific targeting of plasmids with Argonaute enables genome editing
Authors: Esyunina Daria , Okhtienko Anastasiia , Olina Anna , Prostova Maria , Aravin Alexei A. , Kulbachinskiy Andrey
Published: April 2022

Prokaryotic Argonautes (pAgos) are programmable nucleases involved in cell defense against invading DNA. Recent studies showed that pAgos can bind small single-stranded guide DNAs (gDNAs) to recognize and cleave complementary DNA in vitro. In vivo pAgos preferentially target plasmids, phages and multicopy genetic elements. Here, we reveal that CbAgo nuclease from Clostridium butyricum can be used for genomic DNA cleavage and engineering in bacteria. CbAgo-dependent targeting of genomic loci with plasmid-derived gDNAs promotes recombination between plasmid and chromosomal DNA. Efficient genome cleavage and recombineering depends on the catalytic activity of CbAgo, its interactions with gDNAs, and the extent of homology between plasmid and chromosomal sequences. Specific targeting of plasmids with Argonautes can be used to integrate plasmid-encoded sequences into the chromosome thus enabling genome editing.

One-Sentence Summary

Prokaryotic Argonaute nuclease induces DNA interference between plasmid and chromosomal DNA to promote genome recombineering.
RNA localization mechanisms transcend cell morphology
Authors: Goering Raeann , Arora Ankita , Taliaferro J. Matthew
Published: April 2022

RNA molecules are localized to specific subcellular regions through interactions between RNA regulatory elements and RNA binding proteins (RBPs). Generally, our knowledge of the mechanistic details behind the localization of a given RNA is restricted to a particular cell type. Here, we show that RNA/RBP interactions that regulate RNA localization in one cell type predictably regulate localization in other cell types with vastly different morphologies. To determine transcriptome-wide RNA spatial distributions across the apicobasal axis of human intestinal epithelial cells, we used our recently developed RNA proximity labeling technique, Halo-seq. We found that mRNAs encoding ribosomal proteins (RP mRNAs) were strongly localized to the basal pole of these cells. Using reporter transcripts and single molecule RNA FISH, we found that pyrimidine-rich TOP motifs in the 5′ UTRs of RP mRNAs were suﬃcient to drive basal RNA localization. Interestingly, the same TOP motifs were also suﬃcient to drive RNA localization to the neurites of mouse neuronal cells. In both cell types, the regulatory activity of the TOP motif was dependent on it being at the extreme 5′ end of the transcript, was abolished upon perturbation of the TOP-binding protein LARP1, and was reduced upon inhibition of kinesins. To extend these findings, we compared subcellular RNAseq data from neuronal and epithelial cells. We found that the basal compartment of epithelial cells and the projections of neuronal cells were enriched for highly similar sets of RNAs, indicating that broadly similar mechanisms may be transporting RNAs in both cell types. These findings identify the first RNA element known to regulate RNA localization across the apicobasal axis of epithelial cells, establish LARP1 as an RNA localization regulator, and demonstrate that RNA localization mechanisms cut across cell morphologies.
Beta infection combined with Pfizer BNT162b2 vaccination leads to broadened neutralizing immunity against Omicron
Authors: Cele Sandile , Bernstein Mallory , Karim Farina , Khan Khadija , Ganga Yashica , Jule Zesuliwe , Reedoy Kajal , Lustig Gila , Samsunder Natasha , Mazibuko Matilda , Hwa Shi-Hsia , Manickchund Nithendra , Gottberg Anne von , Magula Nombulelo , Lessells Richard J. , de Oliveira Tulio , Abdool Karim Salim S. , Hanekom Willem ,   COMMIT-KZN Team, Gosnell Bernadett I. , Moosa Mahomed-Yunus S. , Sigal Alex
Published: April 2022

Omicron (B.1.1.529) shows extensive escape from vaccine immunity, although vaccination reduces severe disease and death1. Boosting with vaccines incorporating variant spike sequences could possibly broaden immunity2. One approach to choose the variant may be to measure immunity elicited by vaccination combined with variant infection. Here we investigated Omicron neutralization in people infected with the Beta (B.1.351) variant and subsequently vaccinated with Pfizer BNT162b2. We observed that Beta infection alone elicited poor Omicron cross-neutralization, similar to what we previously found3 with BNT162b2 vaccination alone or in combination with ancestral or Delta virus infection. In contrast, Beta infection combined with BNT162b2 vaccination elicited neutralization with substantially lower Omicron escape.
Integrating sustainability practices into the Irish construction supply chain: main contractors' perspective
Authors: Ewuga Duga , Adesi Michael
Published: April 2022

Purpose

The low level of sustainable practices in the architectural, engineering and construction (AEC) sector continues to increase. In driving sustainability practice adoption and implementation, construction-contracting firms have introduced sustainability practices to their supply chain network. This study examines the strategies adopted by large construction-contracting firms in Ireland to integrate sustainability practices into their supply chain.

Design/methodology/approach

The study adopts the mixed-method approach using questionnaires and interviews to collect data. The relative importance index (RII) was used to analyse the data collected through the questionnaire survey. In terms of theoretical underpinning, the study was positioned in the resourced-based view (RBV) theory, which focusses on the link between a firm's internal characteristics and performance.

Findings

The results revealed that, in building a long-term relationship, trust, knowledge of the construction process, commitment, a common goal and mutual support were the key factors considered. While in developing their supply chain, suppliers' assessment and promoting competition in the supply chain were ranked high amongst the mechanisms utilised. Additional findings revealed that long-term relationships with a supply chain organisation have little impact on the project sustainability performance; instead, close collaboration and trust amongst the project team influenced the project sustainability performance.

Research limitations/implications

The study focusses only on the main contractor's organisation. Further study will require exploring the supply chain organisations to provide a deeper understanding.

Practical implications

The research demonstrates that for construction-contracting firms to contribute positively to sustainability objectives, they will have to collaborate closely with their supply chain.

Originality/value

The study provided practical and empirical evidence to guide construction-contracting firms to develop strategies to drive and implement sustainable construction practices.
Communication in service ecosystems through value propositions: dilemmas and future research avenues
Authors: Verleye Katrien , Reber Bryan
Published: April 2022

Purpose

This paper aims to provide insight into communication strategies that may enable service ecosystem actors to co-create economic, social and/or environmental value.

Design/methodology/approach

To achieve this end, the authors rely upon the literature on value propositions, which represent strategic tools for communicating about the value package (i.e. the benefits that actors can offer to one another along with its costs). This literature stream – in combination with the communication literature – allows the authors to unravel five dilemmas that service ecosystem actors face when communicating about the value package with one another.

Findings

To co-create value in service ecosystems with the help of value propositions, actors need to reflect upon (1) whether to involve third parties when sending messages about their value package (cf. sender), (2) what information to share about their value package (cf. message), (3) whether to invest resources in face-to-face communication when conveying messages about the value package (cf. channel), (4) whether to reach out to a broad audience with value package messages (cf. receiver) and (5) whether to engage in institutional work through communication in response to various interpretations of messages about the value package (cf. effect).

Originality/value

This research advances the literature on value co-creation in service ecosystems by relying upon communication theory to unravel the dilemmas that come along with using and/or creating value propositions as strategic tools for communication.
Applying the national mental health policy in conflict-affected regions: towards better social inclusion (Ukrainian case)
Authors: Quirke Eleanor , Klymchuk Vitalii , Gusak Nataliia , Gorbunova Viktoriia , Sukhovii Oleksii
Published: April 2022

Purpose

The ongoing armed conflict in Ukraine has had wide-ranging health, social and economic consequences for the civilian population. It has emphasised the need for comprehensive and sustainable reform of the Ukrainian mental health system. The Ukrainian Government has approved a vision for national mental health reform. This study aims to draw on the lessons of mental health reform in other conflict-affected settings to identify areas of priority for applying the national mental health policy in conflict-affected regions in the direction of better social inclusion of people with mental health conditions (Donetsk and Luhansk regions, directly affected by the conflict).

Design/methodology/approach

A literature review was conducted to identify lessons from implementing mental health reform in other conflict-affected settings. Findings were summarized, and best practices were applied to the national and regional policy context.

Findings

The literature described emergencies as an opportunity to build sustainable mental health systems. A systematic and long-term view for reform is required to capitalise on this opportunity. For better social inclusion, implementation of the concept for mental health and mental health action plans in Donetsk and Luhansk regions should prioritise raising mental health awareness and reducing stigma; developing the capacity of local authorities in the development and coordination of services; tailoring mental health service provision according to the availability of services and population need; targeting the needs of particularly vulnerable groups and embedding the activities of humanitarian actors in local care pathways.

Research limitations/implications

This study summarises the literature on mental health reform in conflict-affected settings and applies key findings to Eastern Ukraine. This study has drawn on various sources, including peer-reviewed journals and grey literature and made several practical recommendations. Nevertheless, potentially relevant information could have been contained in sources that were excluded based on their publication in another language (i.e. not in English). Indeed, while the included studies provided rich examples of mental health reform implemented in conflict-affected settings, further research is required to better understand the mechanisms for effecting sustainable mental health reform in conflict-affected settings

Originality/value

The paper describes opportunities for developing a local community-based mental health-care system in Ukraine, despite the devastating effects of the ongoing war.
Leading with two eyes: leadership failures and possibilities in the management of a pulp mill’s wicked problem
Authors: McKinnon Mairi N. , Long Brad S.
Published: April 2022

Purpose

The motivation for this paper comes from Canada’s Truth and Reconciliation’s (TRC) Calls to Action, and in particular, the call for more meaningful consultation and respectful, consent-based relationships between businesses and Indigenous communities in Canada. To this end, this study empirically examines leadership in the context of a wicked problem faced by a pulp and paper mill and suggest an Indigenous epistemology as helpful to inform the leadership behaviours employed in this company.

Design/methodology/approach

Firstly, this study established that the problem faced by the company aligns with the characteristics of wicked problems, hence necessitating a collective leadership approach. This study then compiled a database from publicly available documents and inductively coded this data to identify themes that told us something about the leadership behaviours employed by the company as it attempted to resolve the problem at hand.

Findings

This study provides evidence that the company did not employ collective leadership when attempting to tame its wicked problem. It then shows that the context in which the firm operates lends itself well to the Mi’kmaw concept of Two-Eyed Seeing as a guiding principle that could have informed the company’s leadership and contributed to a long-overdue process of reconciliation. This study proposes several specific actions that plausibly could have helped produce such an outcome.

Originality/value

This paper helps fill a void in applications of the wicked problem construct to businesses. Further, this study suggests that the problem faced by this firm remained difficult to tame precisely because it failed to employ a collective leadership approach. The contribution to the leadership literature comes from introducing Two-Eyed Seeing and showing how it may help produce leadership that is inherently more collective in nature. Beyond its instrumental value, this approach may nurture more consent-based relationships between businesses and Indigenous communities in Canada, as called for by the TRC, hence contributing to reconciliation with a long-suffering neighbouring Indigenous community.
Quantifying predator functional responses under field conditions reveals interactive effects of temperature and interference with sex and stage
Authors: Coblentz Kyle E. , Squires Amber , Uiterwaal Stella , Delong John P.
Published: April 2022

Predator functional responses describe predator feeding rates and are central to predator–prey theory. Originally defined as the relationship between predator feeding rates and prey densities, it is now well known that functional responses are shaped by a multitude of factors. However, much of our knowledge about how these factors influence functional responses is based on laboratory studies that are generally logistically constrained to examining only a few factors simultaneously and that have unclear links to the conditions organisms experience in the field.

We apply an observational approach for measuring functional responses to understand how sex/stage differences, temperature and predator densities interact to influence the functional response of zebra jumping spiders on midges under natural conditions.

We used field surveys of jumping spiders to infer their feeding rates and examine the relationships between feeding rates, sex/stage, midge density, predator density and temperature using generalized additive models. We then used the relationships supported by the models to fit parametric functional responses to the data.

We find that feeding rates of zebra jumping spiders follow some expectations from previous laboratory studies such as increasing feeding rates with body size and decreasing feeding rates with predator densities. However, in contrast to previous results, our results also show a lack of temperature response in spider feeding rates and differential decreases in the feeding rates of females and juveniles with densities of different spider sexes/stages.

Our results illustrate the multidimensional nature of functional responses in natural settings and reveal how factors influencing functional responses can interact with one another through behaviour and morphology. Further studies investigating the influence of multiple mechanisms on predator functional responses under field conditions will increase our understanding of the drivers of predator–prey interaction strengths and their consequences for communities and ecosystems.
Individualized and Combined Effects of Future Urban Growth and Climate Change on Irrigation Water Use in Central Arizona
Authors: Wang Zhaocheng , Vivoni Enrique R.
Published: April 2022

Irrigation in agricultural and urban settings is responsible for nearly 80% of the water use in the Phoenix Metropolitan Area. Over the last three decades, there has been a continuous decrease in cropland area and its water consumption. Meanwhile, urbanization has increased outdoor irrigation to maintain residential areas and parks. Given these trends, irrigation water use (IWU) is subject to large uncertainties which challenge land and water management. In this work, we used a land surface model with an irrigation module to quantify urban and agricultural IWU under the individualized and combined effects of future urban growth and anticipated climate change. A large set of scenario combinations (96 in total) allowed us to bracket plausible pathways of IWU change in the 21st Century. We found that land use change reduced IWU by −4.6% to −0.1% due to savings from crop‐urban conversion, while climate change effects led to increases in IWU by +3.8% to +8.6%. When combined, total IWU changed from +2.5% to +5.8% in the intermediate future (2041–2070) and from −0.5% to 6.8% in the far future (2071–2100). These outcomes suggest that water savings from land use change will likely not be able to compensate for the increasing demand from urban irrigation when considering climate change, under current irrigation practices. Our approach to model the interconnections between land and water under climate change can be used to support sustainable water planning in cities in other arid regions.
Limited time‐specific and longitudinal effects of depressive and manic symptoms on cognition in bipolar spectrum disorders
Authors: Easter Rebecca E. , Ryan Kelly A. , Estabrook Ryne , Marshall David F. , McInnis Melvin G. , Langenecker Scott A.
Published: April 2022

Objectives

Previous research suggests that cognitive performance worsens during manic and depressed states in bipolar disorder (BD). However, studies have often relied upon between‐subject, cross‐sectional analyses and smaller sample sizes. The current study examined the relationship between mood symptoms and cognition in a within‐subject, longitudinal study with a large sample.

Methods

Seven hundred and seventy‐three individuals with BD completed a neuropsychological battery and mood assessments at baseline and 1‐year follow‐up. The battery captured eight domains of cognition: fine motor dexterity, visual memory, auditory memory, emotion processing, and four aspects of executive functioning: verbal fluency and processing speed; conceptual reasoning and set shifting; processing speed with influence resolution; and inhibitory control. Structural equation modeling was conducted to examine the cross‐sectional and longitudinal relationships between depressive symptoms, manic symptoms, and cognitive performance. Age and education were included as covariates. Eight models were run with the respective cognitive domains.

Results

Baseline mood positively predicted 1‐year mood, and baseline cognition positively predicted 1‐year cognition. Mood and cognition were generally not related for the eight cognitive domains. Baseline mania was predictive in one of eight baseline domains (conceptual reasoning and set shifting); baseline cognition predicted 1‐year symptoms (inhibitory control—depression symptoms, visual memory—manic symptoms).

Conclusions

In a large community sample of patients with bipolar spectrum disorder, cognitive performance appears to be largely unrelated to depressive and manic symptoms, suggesting that cognitive dysfunction is stable in BD and is not dependent on mood state in BD. Future work could examine how treatment affects relationship between cognition and mood.

Significant Outcomes

Cognitive dysfunction appears to be largely independent of mood symptoms in bipolar disorder.

Limitations

The sample was generally highly educated (M = 15.22), the majority of the subsample with elevated manic symptoms generally presented with concurrent depressive elevated symptoms, and the study did not stratify recruitment based on mood state.
Early childhood factors in the development of oral health behaviours in adolescence: A structural equation modelling approach
Authors: Costa Natália C. , Knorst Jessica K. , Brondani Bruna , Menegazzo Gabriele R. , Mendes Fausto M. , Ardenghi Diego M. , Ardenghi Thiago M.
Published: April 2022

Objectives

Oral health behaviour is a learning process that begins in the early years of an individual’s life. The aim of this study was to evaluate the associations between demographic, socioeconomic, and psychosocial factors and oral health behaviours during the transition period from childhood to adolescence.

Methods

This was a cohort study with a follow‐up of 7 years. The baseline assessment occurred in 2010 with a random sample of 639 preschool children from southern Brazil. Demographic, socioeconomic and psychosocial oral health conditions were assessed at baseline. Oral health habit variables were collected at follow‐up and included questions regarding dental care and oral hygiene behaviours. Structural equation modelling was performed to assess the direct and indirect relationships between predictors at baseline in oral health behaviours at follow‐up.

Results

A total of 449 children were re‐examined at follow‐up (70.3% cohort retention rate). Factors directly related to poorer oral health behaviours (lower use of dental services, dental visits for emergency reasons and lower frequency of toothbrushing) were lower household income, lower maternal education, lower frequency of visits to neighbours or friends, and male sex. Considering indirect pathways, the household income and maternal education at baseline influenced oral health behaviours at follow‐up via visits to neighbours or friends.

Conclusions

Our findings suggest that household income, maternal education and social capital play an important role in the development of oral health behaviours during the transition from childhood to adolescence. Acquisition of healthy oral behaviours is an important factor to consider in childhood. With this knowledge, public health policies can be developed to intervene in specific causal factors and improve oral health during this transitional period.
Vegetative lesions associated with inhaled cocaine use
Authors: Fabregat-Pratdepadua Maria , del Alcázar-Viladomiu Elena , Verdaguer-Faja Júlia , Pi-Sunyer Ariadna Quer , Carrascosa José-Manuel
Published: April 2022

We present two cases of vegetating exudative lesions involving the oral mucosa, in patients that are cocaine users, with findings in biopsy and in direct immunofluorescence consistent with the diagnosis of pyostomatitis vegetans–pyodermatitis vegetans.