bluuebunny/crossref_metadata_2025 huggingface dataset:
Easy353: A Tool to Get Angiosperms353 Genes for Phylogenomic Research
Authors: Zhang Zhen , Xie Pulin , Guo Yongling , Zhou Wenbin , Liu Enyan , Yu Yan
Published: December 2022

The Angiosperms353 gene set (AGS) consists of a set of 353 universal low-copy nuclear genes that were selected by examining more than 600 angiosperm species. These genes can be used for phylogenetic studies and population genetics at multiple taxonomic scales. However, current pipelines are not able to recover Angiosperms353 genes efficiently and accurately from high-throughput sequences. Here, we developed Easy353, a reference-guided assembly tool to recover the AGS from high-throughput sequencing (HTS) data (including genome skimming, RNA-seq, and target enrichment). Easy353 is an open-source user-friendly assembler for diverse types of high-throughput data. It has a graphical user interface and a command-line interface that is compatible with all widely-used computer systems. Evaluations, based on both simulated and empirical data, suggest that Easy353 yields low rates of assembly errors.
Genetic Drift Shapes the Evolution of a Highly Dynamic Metapopulation
Authors: Angst Pascal , Ameline Camille , Haag Christoph R , Ben-Ami Frida , Ebert Dieter , Fields Peter D
Published: December 2022

The dynamics of extinction and (re)colonization in habitat patches are characterizing features of dynamic metapopulations, causing them to evolve differently than large, stable populations. The propagule model, which assumes genetic bottlenecks during colonization, posits that newly founded subpopulations have low genetic diversity and are genetically highly differentiated from each other. Immigration may then increase diversity and decrease differentiation between subpopulations. Thus, older and/or less isolated subpopulations are expected to have higher genetic diversity and less genetic differentiation. We tested this theory using whole-genome pool-sequencing to characterize nucleotide diversity and differentiation in 60 subpopulations of a natural metapopulation of the cyclical parthenogen Daphnia magna. For comparison, we characterized diversity in a single, large, and stable D. magna population. We found reduced (synonymous) genomic diversity, a proxy for effective population size, weak purifying selection, and low rates of adaptive evolution in the metapopulation compared with the large, stable population. These differences suggest that genetic bottlenecks during colonization reduce effective population sizes, which leads to strong genetic drift and reduced selection efficacy in the metapopulation. Consistent with the propagule model, we found lower diversity and increased differentiation in younger and also in more isolated subpopulations. Our study sheds light on the genomic consequences of extinction–(re)colonization dynamics to an unprecedented degree, giving strong support for the propagule model. We demonstrate that the metapopulation evolves differently from a large, stable population and that evolution is largely driven by genetic drift.
Effect of flexion-resist and extension-assist knee orthosis on electromyographic activities of quadriceps during lateral stepping
Authors: Kobayashi Toshiki , Tee See Moon , Morikawa Masanori , Tashiro Tsubasa , Arima Satoshi , Maeda Noriaki , Leung Aaron K. L.
Published: December 2022

Knee orthoses can potentially reduce muscular activities of the quadriceps. The aim of this study was to investigate the effect of a custom flexion-resist and extension-assist knee orthosis on electromyographic activities of quadriceps during lateral stepping (step-up and step-down). Flexion resistance and extension assistance mechanisms were set by a pair of linear springs built into the orthotic knee joints. Electromyography (EMG) signals were collected from rectus femoris (RF), vastus medialis obliquus (VMO), and vastus lateralis (VL) during lateral step-up and lateral step-down activities in 7 healthy young adults. Peak normalized root mean square (RMS) EMG signals of each muscle, as well as VMO:VL ratio, were compared between orthotic and nonorthotic conditions using the Wilcoxon signed-rank test. The knee orthosis significantly reduced the normalized RMS EMG signals of the RF and VL during lateral stepping (p < 0.05). No significant difference was found in the VMO. The VMO:VL ratio significantly (p < 0.05) increased under orthotic condition. The experiments demonstrated that the knee orthosis reduces the peak normalized RMS EMG signals of RF and VL, and alter the VMO:VL ratio of quadriceps in healthy young adults. Therefore, this study suggests that the flexion-resist and extension-assist knee orthosis may be effective in reducing muscular activities of RF and VL, which may alleviate patellofemoral loading. Future studies should delve into the effects of the knee orthosis in individuals with patellofemoral pain.
Streptomyces acidipaludis sp. nov., an actinobacterium isolated from peat swamp forest soil
Authors: Nammali Achararak , Duangupama Thitikorn , Pittayakhajonwut Pattama , Intaraudom Chakapong , Suriyachadkun Chanwit , He Ya-Wen , Tanasupawat Somboon , Thawai Chitti
Published: December 2022

An actinobacterium strain PLK6-54T was isolated from Lankwai peat swamp forest soil collected from Yala province, Thailand. Strain PLK6-54T exhibited morphological and chemotaxonomic properties described for the genus

Streptomyces

. It formed a spiral spore chain directly on aerial mycelium. Growth was observed between 20 and 40 °C and at pH 5–8. The maximum NaCl for growth was 2 % (w/v). ll-Diaminopimelic acid, arabinose and ribose were detected in the whole-cell hydrolysate. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositolmannoside were detected as the phospholipids. The major menaquinones were MK-10(H2) and MK-9(H6). The major cellular fatty acids were iso-C16 : 0, anteiso-C15 : 0 and iso-C14 : 0. 16S rRNA gene sequence data supported the assignment of strain PLK6-54T to the genus

Streptomyces

and showed that

Streptomyces rubidus

NBRC 102073T (99.0 %) was the closest relative. Moreover, the average nucleotide identity-blast (85.5 %) and digital DNA–DNA hybridization (30.7 %) values reported between strain PLK6-54T and its closest neighbour were below the threshold values for delineation of a novel species. Strain PLK6-54T could be distinguished from related validly described

Streptomyces

species by several phenotypic properties. The combination of genotypic and phenotypic data indicated that strain PLK6-54T is representative of a novel species of the genus

Streptomyces

. The name Streptomyces acidipaludis sp. nov. is proposed for strain PLK6-54T. The type strain is PLK6-54T (=TBRC 11250T=NBRC 114297T).
Guidance for creating individual and batch latinized binomial virus species names
Authors: Postler Thomas S. , Rubino Luisa , Adriaenssens Evelien M. , Dutilh Bas E. , Harrach Balázs , Junglen Sandra , Kropinski Andrew M. , Krupovic Mart , Wada Jiro , Crane Anya , Kuhn Jens H. , Mushegian Arcady , Rūmnieks Jānis , Sabanadzovic Sead , Simmonds Peter , Varsani Arvind , Zerbini F. Murilo , Callanan Julie , Draper Lorraine A. , Hill Colin , Stockdale Stephen R.
Published: December 2022

The International Committee on Taxonomy of Viruses recently adopted, and is gradually implementing, a binomial naming format for virus species. Although full Latinization of these names remains optional, a standardized nomenclature based on Latinized binomials has the advantage of comparability with all other biological taxonomies. As a language without living native speakers, Latin is more culturally neutral than many contemporary languages, and words built from Latin roots are already widely used in the language of science across the world. Conversion of established species names to Latinized binomials or creation of Latinized binomials de novo may seem daunting, but the rules for name creation are straightforward and can be implemented in a formulaic manner. Here, we describe approaches, strategies and steps for creating Latinized binomials for virus species without prior knowledge of Latin. We also discuss a novel approach to the automated generation of large batches of novel genus and species names. Importantly, conversion to a binomial format does not affect virus names, many of which are created from local languages.
A Proximity Sensor-Based Multipurpose Object Recognition Test System for Rodent Behavior Research
Authors: Vazquez Octavio G.G. , Demirhan Mehmet A. , Bannister Mackenzie , Sun Qian-Quan
Published: December 2022

We report an automated, low-cost, and open-source methodology for rodent object recognition tasks (ORT), which are widely used behavior paradigms. The system was designed with an effort of behavior standardization and improvement. When it combined with easily accessible 3-D manufacturing technology, this proximity capacitive sensor based method provides an opportunity to explore new, and high throughput hardware for NORT. The system’s software allows behavior data to be instantaneously monitored and its output can be plotted promptly immediately upon the completion of the behavior test, thus saving labor and time. The performance of this package is cross-verified with a widely used video-based automated software scoring method and examined its sensitivity to chemogenetic behavior manipulations. This integrated package is an affordable and accurate tool for translational recognition memory research and other type of research with frequent use of NORT paradigms.

Visual Abstract
The CD73 immune checkpoint promotes tumor cell metabolic fitness
Authors: Allard David , Cousineau Isabelle , Ma Eric , Allard Bertrand , Barèche Yacine , Fleury Hubert , Stagg John
Published: December 2022

CD73 is an ectonucleotidase overexpressed on tumor cells that suppresses anti-tumor immunity. Accordingly, several CD73 inhibitors are currently being evaluated in the clinic, including in large randomized clinical trials. Yet, the tumor cell-intrinsic impact of CD73 remain largely uncharacterized. Using metabolomics, we discovered that CD73 significantly enhances tumor cell mitochondrial respiration and aspartate biosynthesis. Importantly, rescuing aspartate biosynthesis was sufficient to restore proliferation of CD73-deficient tumors in immune deficient mice. Seahorse analysis of a large panel of mouse and human tumor cells demonstrated that CD73 enhanced oxidative phosphorylation (OXPHOS) and glycolytic reserve. Targeting CD73 decreased tumor cell metabolic fitness, increased genomic instability and suppressed poly ADP ribose polymerase (PARP) activity. Our study thus uncovered an important immune-independent function for CD73 in promoting tumor cell metabolism, and provides the rationale for previously unforeseen combination therapies incorporating CD73 inhibition.
Multiple paths towards repeated phenotypic evolution in the spiny-leg adaptive radiation (Tetragnatha; Hawaii)
Authors: Cerca José , Cotoras Darko D. , Santander Cindy G. , Bieker Vanessa C. , Hutchins Leke , Morin-Lagos Jaime , Prada Carlos F. , Kennedy Susan , Krehenwinkel Henrik , Rominger Andrew J. , Meier Joana , Dimitrov Dimitar , Struck Torsten H. , Gillespie Rosemary G.
Published: December 2022

The repeated evolution of phenotypes is ubiquitous in nature and offers some of the clearest evidence of the role of natural selection in evolution. The genomic basis of repeated phenotypic evolution is often complex and can arise from a combination of gene flow, shared ancestral polymorphism andde novomutation. Here, we investigate the genomic basis of repeated ecomorph evolution in the adaptive radiation of the Hawaiian spiny-legTetragnatha. This radiation comprises four ecomorphs that are microhabitat-specialists, and differ in body pigmentation and size (Green, Large Brown, Maroon, and Small Brown). Using 76 newly generated low-coverage, whole-genome resequencing samples, coupled with population genomic and phylogenomic tools, we studied the evolutionary history of the radiation to understand the evolution of the spiny-leg lineage and the genetic underpinnings of ecomorph evolution. Congruent with previous works, we find that each ecomorph has evolved twice, with the exception of the Small Brown ecomorph, which has evolved three times. The evolution of the Maroon and the Small Brown ecomorphs likely involved ancestral hybridization events, whereas the Green and the Large Brown ecomorphs likely evolved because of either standing genetic variation orde novomutation. Pairwise comparisons of ecomorphs based on the fixation index (FST) show that divergent genomic regions include genes with functions associated with pigmentation (melanization), learning, neuronal and synapse activity, and circadian rhythms. These results show that the repeated evolution of ecomorphs in the Hawaiian spiny-legTetragnathais linked to multiple genomic regions and suggests a previously unknown role of learning and circadian rhythms in ecomorph.
Tree segmentation in airborne laser scanning data is only accurate for canopy trees
Authors: Cao Yujie , Ball James G. C. , Coomes David A. , Steinmeier Leon , Knapp Nikolai , Wilkes Phil , Disney Mathias , Calders Kim , Burt Andrew , Lin Yi , Jackson Tobias D.
Published: December 2022

Individual tree segmentation from airborne laser scanning data is a longstanding and important challenge in forest remote sensing. There are a number of segmentation algorithms but robust intercomparison studies are rare due to the difficulty of obtaining reliable reference data. Here we provide a benchmark data set for temperate and tropical broadleaf forests generated from labelled terrestrial laser scanning data. We compare the performance of four widely used tree segmentation algorithms against this benchmark data set. All algorithms achieved reasonable accuracy for the canopy trees, but very low accuracy for the understory trees. The point cloud based algorithm AMS3D (Adaptive Mean Shift 3D) had the highest overall accuracy, closely followed by the 2D raster based region growing algorithm Dalponte2016+. This result was consistent across both forest types. This study emphasises the need to assess tree segmentation algorithms directly using benchmark data. We provide the first openly available benchmark data set for tropical forests and we hope future studies will extend this work to other regions.
Cloud gazing: demonstrating paths for unlocking the value of cloud genomics through cross-cohort analysis
Authors: Deflaux Nicole , Selvaraj Margaret Sunitha , Condon Henry Robert , Mayo Kelsey , Haidermota Sara , Basford Melissa A. , Lunt Chris , Philippakis Anthony A. , Roden Dan M. , Denny Josh C. , Musick Anjene , Collins Rory , Allen Naomi , Effingham Mark , Glazer David , Natarajan Pradeep , Bick Alexander G.
Published: December 2022

The rapid growth of genomic data has led to a new research paradigm where data are stored centrally in Trusted Research Environments (TREs) such as theAll of UsResearcher Workbench (AoU RW) and the UK Biobank Research Analysis Platform (RAP). To characterize the advantages and drawbacks of different TRE attributes in facilitating cross-cohort analysis, we conducted a Genome-Wide Association Study (GWAS) of standard lipid measures on the UKB RAP and AoU RW using two approaches: meta-analysis and pooled analysis. We curated lipid measurements for 37,754All of Usparticipants with whole genome sequence (WGS) data and 190,982 UK Biobank participants with whole exome sequence (WES) data. For the meta-analysis, we performed a GWAS of each cohort in their respective platform and meta-analyzed the results. We separately performed a pooled GWAS on both datasets combined. We identified 490 and 464 significant variants in meta-analysis and pooled analysis, respectively. Comparison of full summary data from both meta-analysis and pooled analysis with an external study showed strong correlation of known loci with lipid levels (R2∼83-97%). Importantly, 90 variants met the significance threshold only in the meta-analysis and 64 variants were significant only in pooled analysis. These method-specific differences may be explained by differences in cohort size, ancestry, and phenotype distributions inAll of Usand UK Biobank. We noted approximately 20% of variants significant in only the pooled analysis or significant in only the meta-analysis were most prevalent in non-European, non-Asian ancestry individuals. Pooled analyses included more variants than meta-analyses. Pooled analysis required about half as many computational steps as meta-analysis. These findings have important implications for both platform implementations and researchers undertaking large-scale cross-cohort analyses, as technical and policy choices lead to cross-cohort analyses generating similar, but not identical results, particularly for non-European ancestral populations.
AAV-mediated Expression of a Novel Conformational Anti-Aggregated α-Synuclein Antibody Prolongs Survival in a Genetic Model of α-Synucleinopathies
Authors: Düchs Matthias , Blazevic Dragica , Rechtsteiner Philipp , Kenny Cynthia , Lamla Thorsten , Low Sarah , Savistchenko Jimmy , Neumann Manuela , Melki Ronald , Schönberger Tanja , Stierstorfer Birgit , Wyatt David , Igney Frederik , Ciossek Thomas
Published: December 2022

Prion-like transmission of pathology in α-synucleinopathies like Parkinson’s disease or multiple system atrophy is increasingly recognized as one potential mechanism to address disease progression. Active and passive immunotherapies targeting insoluble, aggregated α-synuclein are already being actively explored in the clinic with mixed outcomes so far. Here, we report the identification of 306C7B3, a highly selective, aggregate-specific α-synuclein antibody with picomolar affinity devoid of binding to the monomeric, physiologic protein. 306C7B3 binding is Ser129-phosphorylation independent and shows high affinity to several different aggregated α-synuclein polymorphs, increasing the likelihood that it can also bind to the pathological seeds assumed to drive disease progression in patients. In support of this, highly selective binding to pathological aggregates in postmortem brains of MSA patients was demonstrated, with no staining in samples from other human neurodegenerative diseases.

To achieve CNS exposure of 306C7B3, an Adeno-Associated Virus (AAV) based approach driving expression of the secreted antibody within the brain of (Thy-1)-[A30P]-hα-Synuclein mice was used. Widespread central transduction after intrastriatal inoculation was ensured by using the AAV2HBKO serotype, with transduction being spread to areas far away from the inoculation site. Treatment of (Thy-1)-[A30P]-hα-Synuclein mice at the age of 12 months demonstrated significantly increased survival, with 306C7B3 concentration reaching 3.9 nM in the cerebrospinal fluid.

These results suggest that AAV-mediated expression of 306C7B3 has great potential as a disease-modifying therapy for α-synucleinopathies as it ensures CNS exposure of the antibody, thereby mitigating the selective permeability of the blood-brain barrier.
Tsetse flies choose birthing sites guided by environmental but not pheromonal cues
Authors: Adden Andrea K. , Haines Lee R. , Acosta-Serrano Álvaro , Prieto-Godino Lucia L.
Published: December 2022

Tsetse flies significantly impact public health and economic development in sub-Saharan African countries by transmitting the fatal disease African trypanosomiasis. Unusually, instead of laying eggs, tsetse birth a single larva that immediately burrows into the soil to pupate. Where the female chooses to larviposit is therefore crucial for offspring survival. Previous studies showed that a putative larval pheromone,n-pentadecane, attracts gravid femaleGlossina morsitans morsitansto appropriate larviposition sites. However, this attraction could not be reproduced in field experiments. Here, we resolve this disparity by designing naturalistic laboratory experiments that closely mimic the characteristics found in the wild. We show that gravid tsetse were neither attracted to the putative pheromone nor, interestingly, to pupae placed in the soil. In contrast, females appear to choose larviposition sites based on environmental cues. We conclude that it is the substrate, rather than larval pheromones, which drives larviposition site selection under naturalistic conditions.
Changes in gut microbiome composition drive fentanyl intake and striatal proteomic changes
Authors: Hofford Rebecca S. , Meckel Katherine R. , Wang Weiwei , Kim Michelle , Godino Arthur , Lam TuKiet T. , Kiraly Drew D.
Published: December 2022

Opioid use disorder (OUD) is a public health crisis currently being exacerbated by increased rates of use and overdose of synthetic opioids, primarily fentanyl. Therefore, the identification of novel biomarkers and treatment strategies to reduce problematic fentanyl use and relapse to fentanyl taking is critical. In recent years, there has been a growing body of work demonstrating that the gut microbiome can serve as a potent modulator of the behavioral and transcriptional responses to both stimulants and opioids. Here, we advance this work to define how manipulations of the microbiome drive fentanyl intake and fentanyl seeking in a translationally relevant drug self-administration model. Additionally, we utilize global proteomic analysis of the nucleus accumbens following microbiome manipulation and fentanyl administration to define how microbiome status alters the functional proteomic landscape in this key limbic substructure. These findings establish clear relevance for gut-brain signaling in OUD, and lay foundations for further translational work in this space.
The telomere-to-telomere, gapless, phased diploid genome and methylome of the green algaScenedesmus obliquusUTEX 3031 reveals significant heterozygosity and functional separation of the haplotypes
Authors: Biondi Thomas C. , Kruse Colin P.S. , Koehler Samuel I. , Kwon Taehyung , Eng Wyatt , Kunde Yuliya , Gleasner Cheryl D. , Mak Kayley T. You , Polle Juergen , Hovde Blake T. , Hanschen Erik R. , Starkenburg Shawn R.
Published: December 2022

Recent advances in sequencing technologies have improved contiguity of de novo genome assemblies. Nevertheless, the genomes of all eukaryotic organisms which are polyploid remain unfinished, limiting understanding of genetic and structural variation in diploid or polyploid organisms. Herein, we report the methodology and analysis of a 100% complete, gapless, phased, telomere-to-telomere diploid genome assembly of the eukaryote,Scenedesmus obliquusUTEX 3031 (DOE0152Z). Analysis of the fully assembled and resolved haplotypes revealed significant genomic rearrangements. Inter-haplotype heterogeneity was significant on most chromosomes yet one chromosome pair (Chromosome 15) was found to contain nearly no heterozygosity. Analysis of the 5mC methylation patterns revealed divergence in active gene content across haplotypes. Assembly of fully resolved chromosome pairs enabled complete resolution of genomic rearrangements and heterogeneity of haplotypes, the genomic basis of trait gain/loss, and evolutionary divergence across chromosome pairs. Further, when combined with 5mC methylation patterns, the assembly provides critical annotation information for genetic engineering approaches to achieve full knock-outs in allelic pairs.
Differential dysregulation of β-TrCP1 and -2 by HIV-1 Vpu leads to inhibition of canonical and non-canonical NF-κB pathways in infected cells
Authors: Pickering Suzanne , Sumner Jonathan , Kerridge Claire , Neil Stuart
Published: December 2022

The HIV-1 Vpu protein is expressed late in the virus lifecycle to promote infectious virus production and avoid innate and adaptive immunity. This includes the inhibition of the NF-κB pathway which, when activated, leads to the induction of inflammatory responses and the promotion of antiviral immunity. Here we demonstrate that Vpu can inhibit both canonical and non-canonical NF-κB pathways, through the direct inhibition of the F-box protein β-TrCP, the substrate recognition portion of the Skp1-Cul1-F-box (SCF)β-TrCPubiquitin ligase complex. There are two paralogues of β-TrCP (β-TrCP1/BTRC and β-TrCP2/FBXW11), encoded on different chromosomes, which appear to be functionally redundant. Vpu, however, is one of the few β-TrCP substrates to differentiate between the two paralogues. We have found that patient-derived alleles of Vpu, unlike those from lab-adapted viruses, trigger the degradation of β-TrCP1 while co-opting its paralogue β-TrCP2 for the degradation of cellular targets of Vpu, such as CD4. The potency of this dual inhibition correlates with stabilisation of the classical IκBα and the phosphorylated precursors of the mature DNA-binding subunits of canonical and non-canonical NF-κB pathways, p105/NFκB1 and p100/NFκB2, in HIV-1 infected CD4+ T cells. Both precursors act as alternative IκBs in their own right, thus reinforcing NF-κB inhibition at steady state and upon activation with either selective canonical or non-canonical NF-κB stimuli. These data reveal the complex regulation of NF-κB late in the viral replication cycle, with consequences for both the pathogenesis of HIV/AIDS and the use of NF-κB-modulating drugs in HIV cure strategies.
Are remote mental healthcare interventions cost-effective? A systematic review of economic evaluations of remote mental healthcare
Authors: Clark Amy , Appleton Rebecca , Kalocsanyiova Erika , Gkaintatzi Evdoxia , McCrone Paul
Published: December 2022

Background

Remote interventions known as telemental health care increased in use due to the COVID-19 pandemic when social distancing requirements were in place. Whilst there is some evidence regarding the cost-effectiveness of telemental health prior to the pandemic, there is a need for further evaluation due to the increase in remote care.

Aims

To systematically review the literature to explore whether remote mental health care interventions are cost-effective in terms of incremental cost per quality adjusted life year and in relation to condition specific outcomes compared to usual care or an alternative intervention.

Method

A multilayer search strategy was conducted to build on the searches of a previous systematic review, as well as including grey literature and economic models. Six databases (PubMed, EMBASE, Cochrane Central, PsychINFO, CINAHL, and EconLit) were searched for literature relating to the cost effectiveness of telemental health. Quality appraisal was conducted for all included studies, and findings were synthesised using narrative synthesis.

Results

7386 studies were identified of which 59 met our inclusion criteria and were included in the synthesis of findings. 45 studies were rated as very good or excellent quality. Of the 59 included studies, 40 indicated that the telemental health intervention was cost-effective, whilst a further 16 suggested the intervention had potential to be cost-effective, but there was some uncertainty in the findings. Three studies reported that the intervention was not cost-effective.

Conclusions

This evidence will be used to inform practice in the UK as we respond to and recover from the COVID-19 pandemic.
Keratinocyte desmosomal cadherin Desmoglein 1 as a mediator and target of paracrine signaling in the melanoma niche
Authors: Burks Hope E. , Pokorny Jenny L. , Koetsier Jennifer L. , Roth-Carter Quinn R. , Arnette Christopher R. , Gerami Pedram , Seykora John T. , Johnson Jodi L. , Green Kathleen J.
Published: December 2022

Melanoma is an aggressive cancer typically arising from transformation of melanocytes residing in the basal layer of the epidermis, where they are in direct contact with surrounding keratinocytes. The role of keratinocytes in shaping the melanoma tumor microenvironment remains understudied. We previously showed that temporary loss of the keratinocyte-specific cadherin, Desmoglein 1 (Dsg1) controls paracrine signaling between normal melanocytes and keratinocytes to stimulate the protective tanning response. Here, we provide evidence that melanoma cells hijack this intercellular communication by secreting factors that keep Dsg1 expression low in surrounding keratinocytes, which in turn generate their own paracrine signals that enhance melanoma spread through CXCL1/CXCR2 signaling. Evidence suggests a model whereby paracrine signaling from melanoma cells increases levels of the transcriptional repressorSnai2(Slug), and consequently decreases the Dsg1 transcriptional activatorGrhl1(Grainyhead like 1), a known promoter of epidermal differentiation and barrier function. Together, these data support the idea that paracrine crosstalk between melanoma cells and keratinocytes resulting in chronic keratinocyte Dsg1 reduction contributes to melanoma cell movement associated with tumor progression.
JMJD3 Deficiency in Midbrain Dopamine Neurons Disturbs Dopamine Synthesis and Aggravates Chronic Inflammatory Pain
Authors: He Xi-Biao , Guo Fang , Zhang Wei , Le Weidong , Zheng Yong , Ma Yongjun , Lee Sang-Hun , Wang Hui-Jing , Wu Yi , Zhou Qinming
Published: December 2022

Chronic pain is associated with midbrain dopamine levels. The molecules and mechanisms modulating this association remain to be elucidated. By using conditional knockout mice, we report that JMJD3 deficiency in midbrain dopamine neurons causes prolonged mechanical hyperalgesia regardless of sex and age. Both genetic defect and pharmaceutical inhibition of JMJD3 decrease dopamine level in midbrain and striatum, resulting from reduced tyrosine hydroxylase expression in midbrain dopamine neurons. Furthermore, epigenetic experiments reveal that JMJD3 is indispensable for the transcription of tyrosine hydroxylase through direct and indirect manners. These findings suggest JMJD3 and midbrain dopamine neurons as novel players and pharmaceutical targets for chronic pain regulation.
Porcine and human aortic valve endothelial and interstitial cell isolation and characterization
Authors: Nehl D. , Goody PR. , Maus K. , Pfeifer A. , Aikawa E. , Bakthiary F. , Zimmer S. , Nickenig G. , Jansen F. , Hosen MR.
Published: December 2022

Background

Calcific aortic valve stenosis is defined by pathological changes in the aortic valve and their predominant cell types: valvular interstitial (VICs) and endothelial cells (VECs). Understanding the cellular and molecular mechanisms of this disease is a prerequisite to identify potential pharmacological treatment strategies. In this study, we present a unique aortic valve cell isolation technique to acquire specific human and porcine cell populations and compared VICs and VECs of these species with each other for the first time.

Methods and Results

Aortic valve cells were isolated from human explants from patients undergoing surgical aortic valve replacement or porcine valvular tissue. Pure VEC and VIC populations could be verified by gene expression analysis and immunofluorescence staining showing a highly significant upregulation of endothelial markers in VECs and mesenchymal markers in VICs, respectively. Further analysis and comparison of cells inin vitroexperiments revealed that endothelial-to-mesenchymal transition could be induced in hVECs, leading to significant increase of mesenchymal markers.In vitrocalcification experiments of VICs induced by osteogenic medium or pro-calcifying medium demonstrated a pronounced calcification marker expression and visible calcific deposition in Alizarin red staining in both species.

Conclusion

This study aims to initiate a first step towards standardization of a reproducible isolation technique for pure human and porcine VEC and VIC populations. Comparison of human and porcine aortic valve cells demonstrated that porcine cells might serve as an alternative cellular model system, in settings, where human tissues are difficult to obtain.

Statements and Declarations

The authors declare no relevant financial or non-financial interests to disclose.
High-efficiency transfection ofAcanthamoeba castellaniiusing a cationic polymer
Authors: Moreno Anaísa B. , Ek Viktor , Eriksson Jens , Sellin Mikael E. , Guy Lionel
Published: December 2022

The free-living amoebaAcanthamoeba castellaniiis an ecologically, clinically, and evolutionarily important microorganism.A. castellaniiamoebae are directly pathogenic to humans and serve as reservoirs for bacterial pathogens (e.g.,Legionella pneumophila) but also regulate the proliferation of other microorganisms in the soil. Despite their importance, no reliable genetic system has been developed, hampering the use ofA. castellaniiand related species as model organisms. TransfectingA. castellaniiwith plasmids is possible with commercial kits, but it is expensive, inefficient, and vulnerable to product discontinuation. In this contribution, we present a method for efficient transfection ofA. castellaniiwith readily available and inexpensive polyethylenimines. We systematically explore the method’s parameters, obtaining up to 100-fold higher efficiency than currently used protocols. The method presented here provides a robust step towards a complete genetic toolbox forA. castellanii, hence expanding its use as a model organism.
Reconstruction of a potential coefficient in the Rayleigh–Love equation with non-classical boundary condition
Authors: Huntul M.J. , Tamsir Mohammad
Published: December 2022

Purpose

The purpose of this paper is to reconstruct the potential numerically in the fourth-order Rayleigh–Love equation with boundary and nonclassical boundary conditions, from additional measurement.

Design/methodology/approach

Although, the aforesaid inverse identification problem is ill-posed but has a unique solution. The authors use the cubic B-spline (CBS) collocation and Tikhonov regularization techniques to discretize the direct problem and to obtain stable as well as accurate solutions, respectively. The stability, for the discretized system of the direct problem, is also carried out by means of the von Neumann method.

Findings

The acquired results demonstrate that accurate as well as stable solutions for the a(t) are accessed for λ∈ {10–8, 10–7, 10–6, 10–5}, when p ∈ {0.01%, 0.1%} for both linear and nonlinear potential coefficient a(t). The stability analysis shows that the discretized system of the direct problem is unconditionally stable.

Research limitations/implications

Since the noisy data are introduced, the investigation and analysis model real circumstances where the practical quantities are naturally infested with noise.

Practical implications

The acquired results demonstrate that accurate as well as stable solutions for the a(t) are accessed for λ∈ {10–8, 10–7, 10–6, 10–5}, when p ∈ {0.01%, 0.1%} for both linear and nonlinear potential coefficient a(t). The stability analysis shows that the discretized system of the direct problem is unconditionally stable.

Originality/value

The potential term in the fourth-order Rayleigh–Love equation from additional measurement is reconstructed numerically, for the first time. The technique establishes that accurate, as well as stable solutions are obtained.
Factors affecting the construction quality in Bangladesh
Authors: Hoque Md. Ikramul , Hasan Muzamir
Published: December 2022

Purpose

Quality is a sensitive and high-priority issue in the global construction including in Bangladesh. This research is intended to provide necessary information to stakeholders and authorities for better management of the construction quality in Bangladesh. Therefore, this study seeks to find and prioritize the factors affecting the construction quality in Bangladesh.

Design/methodology/approach

In total 65 factors were extracted and categorized from the literature and expert panel discussion. Subsequently, these factors were designed in a questionnaire under 13 major groups for a survey where 176 construction professionals participated and returned their completed survey form. Collected data were tested by the Cronbach Alpha to check the reliability before proceeding to the Relative Importance Index (RII) analysis for determining the relative ranks of identified factors.

Findings

Statistical analysis of survey data represents that the most significant factors are: lack of management commitment, lack of technical skill and experience of the consultant, delays in progress investigation, political interference and contractor's desire for unrealistic profit. The most crucial major groups of factors influencing the construction quality are management, material, consultant, cost and time and contract-related major groups.

Originality/value

It will contribute to the body of knowledge, as it points out the impact of factors affecting quality in Bangladeshi construction. Authorities and stakeholders can be helped by the overview of the high and low ranks factors, understanding the diverse characteristics of factors and making more aware the industry about the quality issues which need to be a top concern to solve. Other developing countries that share the same socio-economic context as Bangladesh can be benefit from the results of this study to control quality issues in construction.
Cognitive-affective-motivation factors influencing international visitors' destination satisfaction and loyalty
Authors: Omo-Obas Promise , Anning-Dorson Thomas
Published: December 2022

Purpose

This paper seeks to understand the interrelationships between destination attractiveness, satisfaction, attachment and visitors' loyalty and to determine the potential moderating effect of generational cohorts. Using expectancy disconfirmation and generational cohort theories, the paper explains how visitors' cognitive knowledge and motivation factors influence international visitors' attraction and maintenance and their behavioral/attitudinal loyalty.

Design/methodology/approach

Data were collected from 390 international visitors to South Africa during the Southern Hemisphere's summertime via a quantitative research method. A two-stage approach of structural equation modeling was used to analyze the hypothesized model.

Findings

There was no relationship between visitors' loyalty and destination image or destination image and destination trust. However, destination image has a significant effect on visitors' satisfaction. Additionally, visitors' experience had a positive effect on satisfaction and loyalty, while destination trust and destination attachment were positively related.

Practical implications

The findings show that the tourism sector could reap greater benefits from international tourists if a deeper understanding of different generational cohorts was obtained. There was a varying effect of destination marketing organizations' efforts on different generational cohorts' attraction, trust, satisfaction, feelings and expectations. This study proposes that direct marketing organizations should focus on building brand trust, as it is key to attracting different generational cohorts. Lastly, the study found that generational cohort segmentation accrues many benefits and creates and enhances superior advantages.

Originality/value

The paper provides evidence that more than a destination's attractiveness is required to achieve loyalty; segmenting and understanding different generational cohorts' cognitive, affective and motivation aids in generating better response actions to tourists' changing needs and meeting their demands.
“Too quality”! Professional boundary setting and the ISO 56000 standard on innovation management. In honor of Dorothy E. Smith (1926–2022)
Authors: Lindstrøm Maria Duclos
Published: December 2022

Purpose

The purpose of the paper is to pay homage to Dorothy E. Smith (1926–2022), and her lifelong significance for organizational ethnography. Building on Smith, the empirical purpose of the paper is to analyze professional boundary setting on behalf of innovation management as it occurred in the recent International Organization for Standardization (ISO) Technical Committees (TC) 279 committee on innovation management.

Design/methodology/approach

The paper is an ethnographic study of the drafting and publication of a novel international management standard on innovation management, the ISO 56000-series published in 2019. It is based on fieldwork from the ISO committee and integrates relevant standardization documents, observations and interviews.

Findings

The paper analyzes four occasions for textual professional boundary work ranging from negotiations of content and choice of ISO standard formats to the unprecedented high-level liaison agreements across international organizations. In each instance, the analysis depicts distinct textual features related to ISO standardization. The analysis shows how the standard becomes positioned as extending and complementing the ISO 9001, not as a radical, freestanding alternative to quality management.

Originality/value

The paper presents original data from the ISO standardization committee. It develops Smith's general textual ontology into a theoretical framework for analyzing how professional boundary setting occurs in the textually structured context of ISO standardization. It gives attention to the implications of questions of objectification and standardization as these apply to contemporary research into innovation and organization.
Leaders' role: now and then
Authors: Turi Jamshid Ali , Sorooshian Shahryar
Published: December 2022

Purpose

The purpose of the study is to assess the project leader's role in normal and new normal situations. This study aims to investigate the project leadership role in unforeseen situations and the new normal situations.

Design/methodology/approach

The review is based on the content and contextual analysis. Most of the information was covered in the daily newspapers and practices were recorded in the media and social media. Moreover, recent articles were consulted for the comprehension of the phenomenon.

Findings

The study finds that leaders are supposed to develop strategies to balance the organizational needs and workers' priorities. An agile approach, empathetic and collaborative approach may be more helpful to handle volatility, unstable situations, complexity and ambiguity (VUCA) situations.

Research limitations/implications

The study leaders are expected to develop new strategies, collaborative thinking and a healthy workplace environment for social, emotional, physical, and psychological safety to make projects more productive.

Originality/value

The review assessed the kind of leaders required in the new normal situation after coronavirus disease 2019 (COVID-19) around the globe. Such a contribution is anticipated to serve as a call for emerging leadership frameworks for the VUCA work environments of the future.
Coloniality as a Barrier to Climate Action: Hierarchies of Power in a Coal‐Based Economy
Authors: van Ryneveld Tara Nair , Islar Mine
Published: December 2022

South Africa has a coal‐based energy system and extractive economy, largely responsible for its high emission levels relative to countries with similar GDP. This extractive, coal‐based economy began during British colonisation and today shows few signs of transitioning rapidly to limit climate change. This paper interrogates the role of coloniality in climate delay, given that colonisation is responsible for establishing fossil fuel dependence in South Africa. Combining theory on decolonisation, specifically colonial hierarchies of power, with a critical discourse analysis, this research uses interview and policy data to show how colonial power hierarchies can lead to climate delay in South Africa, through normalising emissions intensive development and silencing alternatives. In doing so, it highlights the need to recognise the colonial foundations of climate change and the potential for a coalition between decolonisation and climate action to motivate for radical change both in South Africa and at a global level.
Higher independent mobility to school among adolescents: A secondary analysis using cross‐sectional data between 2010 and 2017 in Spanish youth
Authors: Gálvez‐Fernández Patricia , Chillón Palma , Saucedo‐Araujo Romina Gisele , Faulkner Guy , Huertas‐Delgado Francisco Javier , Herrador‐Colmenero Manuel
Published: December 2022

Aim

To describe and to analyse the associations between independent mobility to school (IM) with gender and age in Spanish youth aged 6–18 years old from 2010 to 2017. Moreover, to study the changes in the rates of IM from 2010 to 2017 by gender and age.

Methods

Cross‐sectional data were obtained from 11 Spanish studies. The study sample comprised 3460 children and 1523 adolescents. Logistic regressions models (IM with gender and age) and multilevel logistic regressions (IM with time period) were used.

Results

Boys had higher odds ratio (OR) of IM than girls in children (OR = 1.86; CI: 1.50–2.28, p < 0.01). Adolescents showed higher IM than children: 12–14 years old (OR: 6.30; CI: 1.65–23.97) and 14–16 years old (OR: 7.33; CI: 1.18–45.39) had higher IM than 6–8 years old for boys (all, p < 0.05). Moreover, 12–14 years old (OR: 4.23; CI: 1.01–17.81) had higher IM than 6–8 years old for girls (p < 0.001). IM was not associated with the time period.

Conclusion

The IM is higher in boys and in adolescents, highlighting the relevance to promote IM strategies targeting girls and children. In these strategies is essential the support of researchers, public health practitioners and families to achieve positive results.
Inflammatory mediators for predicting the risk of trauma‐induced root resorption: A systematic review
Authors: Johnson Riya Marie , Tewari Nitesh , Kumar Vijay , Rahul Morankar , Mathur Vijay Prakash , Bhawal Ujjal Kumar
Published: December 2022

Background/Aim

External inflammatory root resorption (EIRR) and external replacement root resorption (ERRR) are the most common adverse outcomes after luxation injuries or dental injuries. They are usually detected radiographically after considerable progression. It can be envisaged that evaluation of inflammatory mediators might serve as an objective and reliable method of predicting the risk of resorption. The aim of this systematic review was to assess the evidence regarding the risk of resorption and to provide future research directions.

Methods

An a priori protocol was prepared by a multidisciplinary expert group, as per the Cochrane handbook and PRISMA guidelines. The systematic search was conducted in six databases and grey‐literature sources. Scrutiny of titles and abstracts, and later full‐text articles was performed, and data were extracted. Risk of bias analysis was done by using the Joanna Briggs Institute's Critical Appraisal Checklist for analytical cross‐sectional and cohort studies.

Results

Eight studies were included in the systematic review and could be categorized as per the source of biomarkers, namely epithelial cells from mucosa, gingival crevicular fluid and extracted teeth. The studies utilizing epithelial cells had been conducted between 2015 and 2018 in Brazil and did not find any correlation with EIRR. Two of the studies with extracted teeth found differences in the immunologic profiles of teeth with resorption. Three studies evaluating gingival crevicular fluid found increased levels of dentine sialoprotein and Interleukin‐1‐α.

Conclusion

Among the three sources, the inflammatory gingival crevicular fluid appeared to be the most non‐invasive source of biomarkers for predicting trauma‐induced root resorption, although the evidence about this came from two studies with moderate and one study with high risk of bias. The primary studies in this systematic review showed variability in terms of the sample sizes, age of the patients, the grading/classification of trauma‐induced resorption and the evaluation methods which must be addressed by future researchers.