bluuebunny/crossref_metadata_2025 huggingface dataset:
Multi-Parameter Quantitative Imaging of Tumor Microenvironments Reveals Perivascular Immune Niches Associated with Anti-Tumor Immunity
Authors: Stoltzfus Caleb R , Sivakumar Ramya , Kunz Leo , Pope BE Olin , Menietti Elena , Speziale Dario , Adelfio Roberto , Bacac Marina , Colombetti Sara , Perro Mario , Gerner Michael Y
Published: June 2021

Tumors are populated by a multitude of immune cell types with varied phenotypic and functional properties, which can either promote or inhibit anti-tumor responses. Appropriate localization and function of these cells within tumors is critical for protective immunity, with CD8 T cell infiltration being a biomarker of disease outcome and therapeutic efficacy. Recent multiplexed imaging approaches have revealed highly complex patterns of localization for these immune cell subsets and the generation of distinct tumor microenvironments (TMEs), which can vary among cancer types, individuals, and within individual tumors. While it is recognized that TMEs play a pivotal role in disease progression, a better understanding of their composition, organization, and heterogeneity, as well as how distinct TMEs are reshaped with immunotherapy, is necessary. Here, we performed spatial analysis using multi-parameter confocal imaging, histocytometry, and CytoMAP to study the microanatomical organization of immune cells in two widely used preclinical cancer models, the MC38 colorectal and KPC pancreatic murine tumors engineered to express human carcinoembryonic antigen (CEA). Immune responses were examined in either unperturbed tumors or after immunotherapy with a CEA T cell bispecific (CEA-TCB) surrogate antibody and anti-PD-L1 treatment. CEA-TCB mono and combination immunotherapy markedly enhanced intra-tumoral cellularity of CD8 T cells, dominantly driven by the expansion of TCF1− PD1+ effector T cells and with more minor increases in TCF1+PD1+ resource CD8 T cells. The majority of infiltrating T cells, particularly resource CD8 T cells, were colocalized with dendritic cells (DCs) or activated MHCII+ macrophages, but largely avoided the deeper tumor nest regions composed of cancer cells and non-activated macrophages. These myeloid cell – T cell aggregates were found in close proximity to tumor blood vessels, generating perivascular immune niches. This perivascular TME was present in untreated samples and markedly increased after CEA-TCB therapy, with its relative abundance positively associated with response to therapy. Together, these studies demonstrate the utility of advanced spatial analysis in cancer research by revealing that blood vessels are key organizational hubs of innate and adaptive immune cells within tumors, and suggesting the likely relevance of the perivascular immune TME in disease outcome.
Simple models highlight differences in the walking biomechanics of young children and adults
Authors: Rose Vivian L. , Arellano Christopher J.
Published: June 2021

Adults conserve metabolic energy during walking by minimizing the step-to-step transition work performed by the legs during double support and by utilizing spring-like mechanisms in their legs, but little is known as to whether children utilize these same mechanisms. To gain a better understanding, we studied how children (5-6 years) and adults modulate the mechanical and metabolic demands of walking at their preferred speed, across slow (75%), preferred (100%), and fast (125%) step frequencies. We quantified the 1) positive mass-specific work done by the trailing leg during step-to-step transitions and 2) the leg’s spring-likebehavior during single support. On average, children walked with a 36% greater net cost of transport (COT; J/kg/m) than adults (p=0.03), yet both groups increased their net COT at varying step frequencies. After scaling for speed, children generated ∼2-fold less trailing limb positive scaled mechanical work during the step-to-step transition (p=0.02). Unlike adults, children did not modulate their trailing limb positive work to meet the demands of walking at 75% and 125% of their preferred step frequency. In single support, young children operated their stance limb with much greater compliance than adultsvs. 11.35;p=.023). Our observations suggest that the mechanics of walking in children 5-6 years are fundamentally distinct from the mechanics of walking in adults and may help to explain a child’s higher net COT. These insights have implications for the design of assistive devices for children and suggest that children cannot be simply treated as scaled down versions of adults.
Fast and powerful statistical method for context-specific QTL mapping in multi-context genomic studies
Authors: Lu Andrew , Thompson Mike , Grace Gordon M , Dahl Andy , Ye Chun Jimmie , Zaitlen Noah , Balliu Brunilda
Published: June 2021

Recent studies suggest that context-specific eQTLs underlie genetic risk factors for complex diseases. However, methods for identifying them are still nascent, limiting their comprehensive characterization and downstream interpretation of disease-associated variants. Here, we introduce FastGxC, a method to efficiently and powerfully map context-specific eQTLs by leveraging the correlation structure of multi-context studies. We first show via simulations that FastGxC is orders of magnitude more powerful and computationally efficient than previous approaches, making previously year-long computations possible in minutes. We next apply FastGxC to bulk multi-tissue and single-cell RNA-seq data sets to produce the most comprehensive tissue- and cell-type-specific eQTL maps to date. We then validate these maps by establishing that context-specific eQTLs are enriched in corresponding functional genomic annotations. Finally, we examine the relationship between context-specific eQTLs and human disease and show that FastGxC context-specific eQTLs provide a three-fold increase in precision to identify relevant tissues and cell types for GWAS variants than standard eQTLs. In summary, FastGxC enables the construction of context-specific eQTL maps that can be used to understand the context-specific gene regulatory mechanisms underlying complex human diseases.
Profiling a single-stranded DNA region within an rDNA segment that is a loading site for bacterial condensin
Authors: Yano Koichi , Noguchi Hideki , Niki Hironori
Published: June 2021

Bacterial condensin preferentially loads to single-stranded DNA (ssDNA) in vitro and loads onto rDNA in vivo to support proper chromosome compaction. Thus, the actively transcribing rDNA would provide the ssDNA region for the topological loading of bacterial condensin. We attempted to detect the ssDNA region in the rrnI gene in situ. Non-denaturing sodium bisulfite treatment catalyzed the conversion of cytosines to thymines via uracils (CT-conversion) at locally melted DNA of a bacterial genome. Using next-generation sequencing, we generated an average of 11,000 reads covering each cytosine on the PCR-amplified rDNA segment to obtain the actual CT-conversion rate. In principle, the CT-conversion rate is an accurate guide to detect the formation of the ssDNA segment. We expected that an increment of the CT-conversion rate would reflect a trend toward ssDNA accumulation at a given site within the rDNA. We detected multiple ssDNA segments throughout the rDNA. The deletion mutations of the rDNA that affect the bacterial-condensin loading hindered the ssDNA formation only at the 100–500 bp segment downstream of the promoter. These data support the idea that the ssDNA segment plays a crucial role as the bacterial condensin-loading site and suggest the mechanism of condensin loading onto rDNA.
Probabilistic modeling methods for cell-free DNA methylation based cancer classification
Authors: Halla-aho Viivi , Lähdesmäki Harri
Published: June 2021

Background

cfMeDIP-seq is a low-cost method for determining the DNA methylation status of cell-free DNA and it has been successfully combined with statistical methods for accurate cancer diagnostics. We investigate the diagnostic classification aspect by applying statistical tests and dimension reduction techniques for feature selection and probabilistic modeling for the cancer type classification, and we also study the effect of sequencing depth.

Methods

We experiment with a variety of statistical methods that use different feature selection and feature extraction methods as well as probabilistic classifiers for diagnostic decision making. We test the (moderated) t-tests and the Fisher’s exact test for feature selection, principal component analysis (PCA) as well as iterative supervised PCA (ISPCA) for feature generation, and GLMnet and logistic regression methods with sparsity promoting priors for classification. Probabilistic programming language Stan is used to implement Bayesian inference for the probabilistic models.

Results and conclusions

We compare overlaps of differentially methylated genomic regions as chosen by different feature selection methods, and evaluate probabilistic classifiers by evaluating the area under the receiver operating characteristic (AUROC) scores on discovery and validation cohorts. While we observe that many methods perform equally well as, and occasionally considerably better than, GLMnet that was originally proposed for cfMeDIP-seq based cancer classification, we also observed that performance of different methods vary across sequencing depths, cancer types and study cohorts. Overall, methods that seem robust and promising include Fisher’s exact test and ISPCA for feature selection as well as a simple logistic regression model with the number of hyper and hypomethylated regions as features.
Tfap2b specifies an embryonic melanocyte stem cell that retains adult multi-fate potential
Authors: Brombin Alessandro , Simpson Daniel J. , Travnickova Jana , Brunsdon Hannah , Zeng Zhiqiang , Lu Yuting , Young Adelaide I.J. , Chandra Tamir , Patton E. Elizabeth
Published: June 2021

Melanocytes, our pigment producing cells, are replenished from multiple stem cell niches in adult tissues. Although pigmentation traits are known risk-factors for melanoma, we know little about melanocyte stem cell (McSC) populations other than hair follicle McSCs, and lack key lineage markers with which to identify McSCs and study their function. Here, we discover that Tfap2b, and a select set of its target genes, specifies an McSC population at the dorsal root ganglia in zebrafish. Functionally, Tfap2b is required for only a few late-stage embryonic melanocytes, and instead is essential for McSC-dependent melanocyte regeneration. Fate- mapping data reveal that tfap2b-expressing McSCs have multi-fate potential, and are the cell-of- origin for large patches of adult melanocytes, and two other pigment cell types, iridophores and xanthophores. Hence, Tfap2b confers McSC identity in early development, thereby distinguishing McSCs from other neural crest and pigment cell lineages, and retains multi-fate potential in the adult zebrafish.

Highlights

Tfap2b and its target genes specify McSCs with mixed pigment cell identities

Functional dependence on Tfap2b for melanocyte regeneration from the McSC

tfap2b specifies ErbB-dependent McSCs at the stem cell niche

Fate mapping reveals Tfap2b-McSCs have multi-fate potential for adult pigment cells
Multiplexed bioluminescence microscopy via phasor analysis
Authors: Yao Zi , Brennan Caroline K. , Scipioni Lorenzo , Chen Hongtao , Ng Kevin , Digman Michelle A. , Prescher Jennifer A.
Published: June 2021

Microscopic bioluminescence imaging has been historically challenging due to a lack of detection methods and easily resolved probes. Here we combine bioluminescence with phasor analysis, an optical method commonly used to distinguish spectrally similar fluorophores. Bioluminescent phasor enabled rapid differentiation of multiple luciferase reporters and resonance energy transfer processes. The merger of bioluminescence and phasor analysis provides a platform for routine, time-lapse imaging of collections of cellular features.
Single-cell RNA sequencing-based characterization of resident lung mesenchymal stromal cells in bronchopulmonary dysplasia
Authors: Mižíková I. , Lesage F. , Cyr-Depauw C. , Cook D. P. , Hurskainen M. , Hänninen S.M. , Vadivel A. , Bardin P. , Zhong S. , Carpen O. , Vanderhyden B. C. , Thébaud B.
Published: June 2021

Late lung development is a period of alveolar and microvascular formation, which is pivotal in ensuring sufficient and effective gas exchange. Defects in late lung development manifest in premature infants as a chronic lung disease named bronchopulmonary dysplasia (BPD). Numerous studies demonstrated the therapeutic properties of exogenous bone marrow and umbilical cord-derived mesenchymal stromal cells (MSCs) in experimental BPD. However, very little is known regarding the regenerative capacity of resident lung MSCs (L-MSCs) during normal development and in BPD. In this study we aimed to characterize the L-MSC population in homeostasis and upon injury. We used single-cell RNA sequencing (scRNA-seq) to profile in situ Ly6a+ L-MSCs in the lungs of normal and O2-exposed neonatal mice (a well-established model to mimic BPD) at three developmental timepoints (postnatal days 3, 7 and 14). Hyperoxia exposure increased the number, and altered the expression profile of L-MSCs, particularly by increasing the expression of multiple pro-inflammatory, pro-fibrotic, and anti-angiogenic genes. In order to identify potential changes induced in the L-MSCs transcriptome by storage and culture, we profiled 15,000 Ly6a+ L-MSCs after in vitro culture. We observed great differences in expression profiles of in situ and cultured L-MSCs, particularly those derived from healthy lungs. Additionally, we have identified the location of L-MSCs in the developing lung and propose Serpinf1 as a novel, culture-stable marker of L-MSCs. Finally, cell communication analysis suggests inflammatory signals from immune and endothelial cells as main drivers of hyperoxia-induced changes in L-MSCs transcriptome.
A new approach to measure forces at junction vertices in an epithelium
Authors: Villeneuve Clémentine , Mathieu Samuel , Lagoutte Emilie , Goud Bruno , Chavrier Philippe , Manneville Jean-Baptiste , Rossé Carine
Published: June 2021

The mechanical properties of cell-cell junctions are critical for the stability of an epithelium. Cell-cell junction ablation experiments are classically used as a readout for junctional mechanics. However, without the knowledge of the viscoelastic properties of the microenvironment of the ablated junction, tensile junctional forces cannot be measured. Here we combine laser ablation with intracellular microrheology and develop a model to measure tensile forces exerted on cell-cell junctions. We show that the overexpression of the proto-oncogene atypical Protein Kinase C iota (aPKCi) in a single cell within a normal epithelium induces a gradient of junctional tension with neighbouring cells. Our method allows us to demonstrate that junctions contacting the aPKCi-overexpressing cell display a mechanical asymmetry which correlates with the levels of E-cadherin and P-MLC2. Measuring intracellular viscoelasticity is crucial for accurate measurements of cell-cell junction mechanics in the context of development or cancer research.

Teaser

We combine cytoplasmic and junctional mechanics to detect asymmetry in forces exerted on cell-cell junctions.
Alpha peak frequency is linked to episodic memory impairment in pathological aging
Authors: Puttaert Delphine , Wens Vincent , Fery Patrick , Rovai Antonin , Trotta Nicola , Coquelet Nicolas , De Breucker Sandra , Sadeghi Niloufar , Coolen Tim , Goldman Serge , Peigneux Philippe , Bier Jean-Christophe , De Tiège Xavier
Published: June 2021

The Free and Cued Selective Reminding Test (FCSRT) is a largely validated neuropsychological test for the identification of amnestic syndrome from the early stage of Alzheimer’s disease (AD). Previous electrophysiological data suggested a slowing down of the alpha rhythm in the AD-continuum as well as a key role of this rhythmic brain activity for episodic memory processes. This study therefore investigates the link between alpha brain activity and alterations in episodic memory as assessed by the FCSRT. For that purpose, 37 patients with altered FCSRT performance underwent a comprehensive neuropsychological assessment, supplemented by 18F-fluorodeoxyglucose positron emission tomography/structural magnetic resonance imaging (18FDG-PET/MR), and 10 minutes of resting-state magnetoencephalography (MEG). The individual alpha peak frequency (APF) in MEG resting-state data was positively correlated with patients’ encoding efficiency as well as with the efficacy of semantic cues in facilitating patients’ retrieval of previous stored word. The APF also correlated positively with patients’ hippocampal volume and their regional glucose consumption in the posterior cingulate cortex. Overall, this study demonstrates that alterations in the ability to learn and store new information for a relatively short-term period are related to a slowing down of alpha rhythmic activity, possibly due to altered interactions in the extended mnemonic system. As such, a decreased APF may be considered as an electrophysiological correlate of short-term episodic memory dysfunction accompanying pathological aging.
Binding of phosphatidylserine-positive microparticles by PBMCs classifies disease severity in COVID-19 patients
Authors: Rausch Lisa , Lutz Konstantin , Schifferer Martina , Winheim Elena , Gruber Rudi , Rinke Linus , Hellmuth Johannes C. , Scherer Clemens , Muenchhoff Maximilian , Mandel Christopher , Bergwelt-Baildon Michael , Simons Mikael , Straub Tobias , Krug Anne B. , Kranich Jan , Brocker Thomas
Published: June 2021

Infection with SARS-CoV-2 is associated with thromboinflammation, involving thrombotic and inflammatory responses, in many COVID-19 patients. In addition, immune dysfunction occurs in patients characterized by T cell exhaustion and severe lymphopenia. We investigated the distribution of phosphatidylserine (PS), a marker of dying cells, activated platelets, and platelet-derived microparticles (PMP), during the clinical course of COVID-19. We found an unexpectedly high amount of blood cells loaded with PS+ PMPs for weeks after the initial COVID-19 diagnosis. Elevated frequencies of PS+PMP+ PBMCs correlated strongly with increasing disease severity. As a marker, PS outperformed established laboratory markers for inflammation, leucocyte composition, and coagulation, currently used for COVID-19 clinical outcome prognosis. PS+ PMPs preferentially bound to CD8+ T cells with gene expression signatures of proliferating effector rather than memory T cells. As PS+ PMPs carried programmed death-ligand 1 (PD-L1), they may affect T cell expansion or function. Our data provide a novel marker for disease severity and show that PS, which can trigger the blood coagulation cascade, the complement system, and inflammation, resides on activated immune cells. Therefore, PS may serve as a beacon to attract thromboinflammatory processes toward lymphocytes and cause immune dysfunction in COVID-19.
Structure and dynamics of the chromatin remodeler ALC1 bound to a PARylated nucleosome
Authors: Bacic Luka , Gaullier Guillaume , Sabantsev Anton , Lehmann Laura C. , Brackmann Klaus , Dimakou Despoina , Halic Mario , Hewitt Graeme , Boulton Simon J. , Deindl Sebastian
Published: June 2021

The chromatin remodeler ALC1 is recruited to and activated by DNA damage-induced poly(ADP-ribose) (PAR) chains deposited by PARP1/PARP2/HPF1 upon detection of DNA lesions. ALC1 has emerged as a candidate drug target for cancer therapy as its loss confers synthetic lethality in homologous recombination-deficient cells. However, structure-based drug design and molecular analysis of ALC1 have been hindered by the requirement for PARylation and the highly heterogeneous nature of this post-translational modification. Here, we reconstituted an ALC1 and PARylated nucleosome complex modified in vitro using PARP2 and HPF1. This complex was amenable to cryo-EM structure determination without cross-linking, which enabled visualization of several intermediate states of ALC1 from the recognition of the PARylated nucleosome to the tight binding and activation of the remodeler. Functional biochemical assays with PARylated nucleosomes highlight the importance of nucleosomal epitopes for productive remodeling and reveal that ALC1 preferentially slides nucleosomes away from DNA breaks.
A highly efficient reporter system for identifying and characterizing in vitro expanded hematopoietic stem cells
Authors: Che James L.C. , Bode Daniel , Kucinski Iwo , Cull Alyssa H. , Bain Fiona , Barile Melania , Boyd Grace , Belmonte Miriam , Jassinskaja Maria , Rubio-Lara Juan , Shepherd Mairi S. , Clay Anna , Wilkinson Adam C. , Nakauchi Hiromitsu , Yamazaki Satoshi , Göttgens Berthold , Kent David G.
Published: June 2021

Hematopoietic stem cells (HSCs) cultured outside the body are the fundamental component of a wide range of cellular and gene therapies. Recent efforts have achieved more than 200-fold expansion of functional HSCs, but their molecular characterization has not been possible due to the substantial majority of cells being non-HSCs and single cell-initiated cultures displaying substantial clone-to-clone variability. Using the Fgd5 reporter mouse in combination with the EPCR surface marker, we report exclusive identification of HSCs from non-HSCs in expansion cultures. Linking single clone functional transplantation data with single clone gene expression profiling, we show that the molecular profile of expanded HSCs is similar to actively cycling fetal liver HSCs and shares a gene expression signature with functional HSCs from all sources, including Prdm16, Fstl1 and Palld. This new tool can now be applied to a wide-range of functional screening and molecular experiments previously not possible due to limited HSC numbers.
Functional Redundancy in Ocean Microbiomes Controls Trait Stability
Authors: Royalty Taylor M. , Steen Andrew D.
Published: June 2021

Theory predicts that functional redundancy in microbial communities increases trait stability, meaning that traits or functions are less likely to be lost from the community when species go extinct. However, few experiments have empirically tested this prediction, especially in the context of microbial communities and at the landscape scale. In part, the lack of metrics for functional redundancy in microbial ecosystems has prevented addressing this question. In a companion manuscript we proposed a quantitative metric for functional redundancy called Contribution Evenness (CE) that is optimized to reflect trait stability. Here, we use CE to predict the stability of marine microbial functions to species and transcription loss. Using transcriptomes deposited in the Ocean Microbial Reference Gene Catalog (OM-RGC.v2), a catalog of genes and transcripts sequenced by the TARA Ocean expedition, we quantified the functional redundancy for 4,314 KEGG Orthologs (KOs) across 124 marine sites. Functional redundancy was highly correlated with a latent variable consisting of four ocean physiochemical parameters: oxygen and chlorophyll a concentrations, depth, and salinity. Functional redundancy was higher at the poles than in non-polar regions. Simultaneously, regional β-diversity for individual functions was higher for functions with higher functional redundancy. These observations provide evidence that higher functional redundancy indicates increased stability of microbial ecosystem functions on spatiotemporal scales consistent with surface ocean mixing. We suggest that future changes in ocean physiochemistry could likely influence this stability for functions with lower functional redundancy.

Importance

Functional redundancy describes the state of multiple species performing the same function. Theory suggests functional redundancy stabilizes microbial community functions from disturbances leading to species loss or other changes to the microbiome. Previous work suggests that functional redundancy is common in ocean microbiomes which implies traits should be more stable among metacommunities. Some laboratory experiments demonstrate this idea, but it is difficult to test in the natural world. In a companion manuscript, we proposed a functional redundancy metric sensitive to trait stability. Here, we used this metric to show that functional redundancy varied substantially among ocean microbiomes and that regions with higher functional redundancy had higher regional trait stability. Last, we noted that variations in functional redundancy strongly correlated to ocean physiochemistry. Thus, changes in ocean physiochemistry via climate change may alter community traits to become more or less resistant to disturbance relative to contemporary conditions.
Disturbed retinoid metabolism upon loss of rlbp1a impairs cone function and leads to subretinal lipid deposits and photoreceptor degeneration in the zebrafish retina
Authors: Schlegel Domino K. , Ramkumar Srinivasagan , Lintig Johannes von , Neuhauss Stephan C. F.
Published: June 2021

The RLBP1 gene encodes the 36 kDa cellular retinaldehyde binding protein, CRALBP, a soluble retinoid carrier, in the visual cycle of the eyes. Mutations in RLBP1 are associated with recessively inherited clinical phenotypes, including Bothnia dystrophy, retinitis pigmentosa, retinitis punctata albescens, fundus albipunctatus, and Newfoundland rod-cone dystrophy. However, the etiology of these retinal disorders is not well understood. Here, we generated homologous zebrafish models to bridge this knowledge gap. Duplication of the rlbp1 gene in zebrafish and cell-specific expression of the paralogs rlbp1a in the retinal pigment epithelium and rlbp1b in Müller glial cells allowed us to create intrinsically cell type-specific knockout fish lines. Using rlbp1a and rlbp1b single and double mutants, we investigated the pathological effects on visual function. Our analyses revealed that rlbp1a was essential for cone photoreceptor function and chromophore metabolism in the fish eyes. rlbp1a mutant fish displayed reduced chromophore levels and attenuated cone photoreceptor responses to light stimuli. They accumulated 11-cis and all-trans-retinyl esters which displayed as enlarged lipid droplets in the RPE reminiscent of the subretinal yellow-white lesions in patients with RLBP1 mutations. During aging, these fish developed retinal thinning and cone and rod photoreceptor dystrophy. In contrast, rlbp1b mutants did not display impaired vision. The double mutant essentially replicated the phenotype of the rlbp1a single mutant. Together, our study showed that the rlbp1a zebrafish mutant recapitulated many features of human blinding diseases caused by RLBP1 mutations and provided novel insights into the pathways for chromophore regeneration of cone photoreceptors.

Graphical Abstract
Introduction to molecular replacement: a time perspective
Authors: Dodson Eleanor
Published: June 2021

This article provides an introduction to the crystal phasing technique known as molecular replacement. The available software is reviewed, and the prospects for future developments are considered. Several examples are described in detail to illustrate potential problems. A brief account of past progress is included. The basic crystallographic equations underlying the procedures are given in an appendix.
Entropic pressure controls the oligomerization of the Vibrio cholerae ParD2 antitoxin
Authors: Garcia-Rodriguez Gabriela , Girardin Yana , Volkov Alexander N. , Singh Ranjan Kumar , Muruganandam Gopinath , Van Dyck Jeroen , Sobott Frank , Versées Wim , Charlier Daniel , Loris Remy
Published: June 2021

ParD2 is the antitoxin component of the parDE2 toxin–antitoxin module from Vibrio cholerae and consists of an ordered DNA-binding domain followed by an intrinsically disordered ParE-neutralizing domain. In the absence of the C-terminal intrinsically disordered protein (IDP) domain, V. cholerae ParD2 (VcParD2) crystallizes as a doughnut-shaped hexadecamer formed by the association of eight dimers. This assembly is stabilized via hydrogen bonds and salt bridges rather than by hydrophobic contacts. In solution, oligomerization of the full-length protein is restricted to a stable, open decamer or dodecamer, which is likely to be a consequence of entropic pressure from the IDP tails. The relative positioning of successive VcParD2 dimers mimics the arrangement of Streptococcus agalactiae CopG dimers on their operator and allows an extended operator to wrap around the VcParD2 oligomer.
Crystal structures of Scone: pseudosymmetric folding of a symmetric designer protein
Authors: Mylemans B. , Killian T. , Vandebroek L. , Van Meervelt L. , Tame J. R. H. , Parac-Vogt T. N. , Voet A. R. D.
Published: June 2021

Recent years have seen an increase in the development of computational proteins, including symmetric ones. A ninefold-symmetric β-propeller protein named Cake has recently been developed. Here, attempts were made to further engineer this protein into a threefold-symmetric nine-bladed propeller using computational design. Two nine-bladed propeller proteins were designed, named Scone-E and Scone-R. Crystallography, however, revealed the structure of both designs to adopt an eightfold conformation with distorted termini, leading to a pseudo-symmetric protein. One of the proteins could only be crystallized upon the addition of a polyoxometalate, highlighting the usefulness of these molecules as crystallization additives.
Ambidextrous sustainability, organisational structure and performance in hybrid organisations
Authors: Maine Joshua , Florin Samuelsson Emilia , Uman Timur
Published: June 2021

Purpose

Drawing on paradox theory, this study explores how ambidextrous sustainability relates to organisational performance in hybrid organisations represented by Swedish municipal housing corporations, and how this relationship is contingent on the organisational structure of these organisations.

Design/methodology/approach

The study relies on the data collected from Swedish municipal housing corporations. These data sources consist of a survey sent to the management team members in Swedish municipal housing corporations, financial and non-financial archival data on these corporations, interviews with the management team and board members, and observations of meetings involving the management team and board of directors at a Swedish municipal housing corporation. Quantitative data of the study were analysed using descriptive statistics, correlation analysis and linear multiple regression analysis. Qualitative data were analysed employing deductive thematic analysis and were used to illustrate and discuss the results of the quantitative analysis.

Findings

The quantitative findings show that ambidextrous sustainability, i.e. the alignment between an explorative orientation and an exploitative orientation towards sustainability, has a weakly positive relationship with financial performance and a positive relationship with social performance in hybrid organisations represented by Swedish municipal housing corporations. The study further shows that a high level of the structural element “connectedness” weakened the relationship between the ambidextrous sustainability and financial performance of the organisation in the study. In contrast, a lower level of connectedness reinforced and strengthened this relationship. Our qualitative material illustrates how the quantitative findings could be explained by the interaction between the board of directors and the management team of these hybrid organisations.

Originality/value

The study shows how ambidextrous sustainability, employed for conceptualisation of the sustainability strategy in hybrid organisations, represented by Swedish municipal housing corporations, can impact on facets of performance (i.e. financial, social and environmental) differently. The study further highlights the importance of organisational structures in these relationships in a hybrid context.
A multivariate regression approach toward prioritizing BIM adoption barriers in the Ethiopian construction industry
Authors: Alemayehu Shihunegn , Nejat Ali , Ghebrab Tewodros , Ghosh Souparno
Published: June 2021

Purpose

Building information modeling (BIM) is a process of creating an intelligent virtual model integrating project data from design to construction and operation. BIM models enhance the process of communicating the progress of construction to stakeholders and facilitate integrated project delivery, coordination and clash detection. However, barriers within the construction industry in Ethiopia has led to slow BIM adoption in the country. The aim of this paper is to identify perceived BIM barriers, provide a platform to quantify their importance and develop a regression model to link individual's personal/professional attributes to their perception of BIM barrier.

Design/methodology/approach

To address the objectives of this research, an online survey was developed to collect feedback from construction professionals in Ethiopia on 20 major adoption barriers extracted from a thorough review of literature. Relative importance index and strength of consensus metric were employed to identify the significance of barriers. This was then succeeded by performing exploratory factor analysis to determine the major constructs of BIM barriers which was then used to develop a multivariate regression model linking respondents' personal attributes to their perception of BIM barrier.

Findings

Results revealed the importance of project complexity and BIM maturity level in prioritizing barriers that are more relevant under various contexts. More specifically, results indicated the following study highlights: Project complexity led to higher perceived weights for lack of appropriate physical/cloud infrastructures, and a BIM standard. Higher levels of BIM maturity signified the importance of BIM internal issues such as liability, licensing and maintenance issues among other adoption barriers. Female participants tended not to consider intangibility of BIM benefits as a major barrier towards BIM adoption compared to male participants. Age of the participants turned out to be the least important factor in their prioritization of BIM perceived adoption barriers.

Originality/value

While many research studies have explored BIM adoption barriers in various countries around the world, none to the best of the authors' knowledge have attempted to develop a model to highlight the impact of individuals' personal/professional attributes on their perception of adoption barriers within their community which can help with prioritizing the barriers that are deemed to be more important given the characteristics of the community under study. Our result indicated the importance of BIM maturity level and project complexity in prioritizing barriers associated with BIM adoption within Ethiopia's construction industry.
Exploring the current issues, challenges and opportunities in tea tourism: a morphological analysis
Authors: Mondal Sanjana , Samaddar Kaushik
Published: June 2021

Purpose

In quest of exploring the issues, challenges and opportunities prevailing in the tea tourism industry, this study aims to present a comprehensive morphological analysis (MA). More specifically, it identifies critical dimensions that bear significance for the sustainable growth of tea tourism.

Design/methodology/approach

The present study adopted a triangulation method of research involving an ethnographic study (ES) followed by a series of focus group sessions carried out from the prominent tea-producing districts in India. This study accords equal importance to both the demand and supply perspectives of tea tourism and its stakeholders.

Findings

Critical dimensions such as improper planning and marketing efforts, limited collaboration among stakeholders, the involvement of local people, socio-economic inequality and consumer’s attitude towards tea tourism were identified as major issues and challenges.

Research limitations/implications

The present research limits its scope to the geographical boundary within India keeping cross-boundary research for future study. This study will aid future researchers and scholars in expanding the domain of tea tourism.

Practical implications

The present study bears significance to the policymakers, governing bodies, marketers, tour operators in embracing a socio-economic perspective while undertaking a suitable strategy towards marketing of tea tourism and ensuring its sustainable development.

Originality/value

This study makes a novel attempt in blending the ES, focus group sessions and MA, together in a single research initiative, making it a single point reference in tea tourism literature.
Exploring the impact of COVID-19 pandemic on women entrepreneurs in Pakistan
Authors: Mustafa Faisal , Khursheed Ambreen , Fatima Maham , Rao Marriam
Published: June 2021

Purpose

The purpose of this paper is to explore the impact of COVID-19 lockdown on micro-businesses owned by women borrowers of microfinance institutions and to provide policy suggestions to assist women entrepreneurs in managing such an unexpected crisis from a qualitative perspective within developing countries such as Pakistan.

Design/methodology/approach

The study adopts a qualitative research design to explore the impact of COVID-19 on women’s entrepreneurial activities. Seven women entrepreneurs were selected and semi-structured interviews with focused group discussion under case study research design are used. Thereby providing a contemporary view of the issues faced by women entrepreneurs in the period of huge social and economic upheaval.

Findings

The results provide valuable insights about how the COVID-19 crisis affected women entrepreneurs by particularly considering household income, business sales, lifestyle and mental health. The liquidation of women-led businesses indicated the necessity to reconsider creativity and digitalization for business survival. Moreover, the results also revealed that the impact of the COVID-19 pandemic on the physical, mental and economic well-being of women highlights the need for considering gender gap issues in forming response policies for COVID-19 in developing countries.

Originality/value

As the COVID-19 crisis is a recent and existing phenomenon, this study is among the first to explore particularly the impact of the COVID-19 outbreak on micro-enterprises mainly owned and managed by women. Thereby claiming that COVID-19 not only physically but also psychologically affected women entrepreneurs. Moreover, the study highlights a need of skill focused training programs for women entrepreneurs to make sure that they can protect their businesses during such difficult times.
Examining a migration-based phenomenon of heroin use in an urban drug scene in Sao Paulo, Brazil
Authors: Ribeiro Marcelo , Frajzinger Rosana , Ogata Perrenoud Luciane , Fischer Benedikt
Published: June 2021

Purpose

Brazil’s street-based drug use is mostly characterized by non-injection psychostimulant (e.g. crack-cocaine) drug use in Brazil, with limited interventions and service availability. Recently, an influx of multi-ethnic migrants within an urban drug scene in Sao Paulo was associated with heroin use, a drug normatively absent from Brazil. The purpose of this paper is to characterize and compare heroin use-related characteristics and outcomes for an attending sub-sample of clients from a large community-based treatment centre (“CRATOD”) serving Sao Paulo’s local urban drug scene.

Design/methodology/approach

All non-Brazilian patients (n= 109) receiving services at CRATOD for 2013–2016 were identified from patient files, divided into heroin users (n= 40) and non-heroin users (n= 69). Based on chart reviews, select socio-demographic, drug use and health status (including blood-borne-virus and other infections per rapid test methods) were examined and bi-variately compared. Multi-variate analyses examined factors independently associated with heroin use.

Findings

Most participants were male and middle-aged, poly-drug users and socio-economically marginalized. While heroin users primarily originated from Africa, they reported significantly more criminal histories, drug (e.g. injection) and sex-risk behaviors and elevated rates of BBV (e.g. Hepatitis C Virus and HIV). A minority of heroin users attending the clinic was provided methadone treatment, mostly for detoxification.

Originality/value

This study documented information on a distinct sample of mostly migration-based heroin users in Sao Paulo, Brazil. Based on the local experience, global migration dynamics can bring changes to established drug use cultures and services, including new challenges for drug use-related related behaviors and therapeutic interventions that require effective understanding and addressing.
Stakeholders of public-private partnerships in Poland: an analysis of an evolving phenomenon
Authors: Kusio Tomasz
Published: June 2021

Purpose

According to the growing role of stakeholders in the implementation of public-private partnership (PPP) initiatives, the purpose of this study is to diagnose the maturity of PPPs in Poland, taking into account the range of stakeholders’ participation in public-private initiatives.

Design/methodology/approach

The introductory study on the stakeholders of PPPs has been based on the report analysis of Polish initiatives and the case studies’ comparative analysis. The cases represent touristic projects realized within PPPs.

Findings

The results of the study indicate that the PPPs’ personal context, though recognized internationally, is to a very low extent present in the Polish case. As the PPP market is still in the process of development, the stakeholders’ issue should be taken into consideration in the processes of the PPP development in Poland.

Practical implications

As regional development is continuously a key issue, especially in rural areas context, the PPP initiatives are of great importance, and therefore the discussion of pros and cons in this context may contribute to the legislation at the regional level.

Originality/value

The study sheds some light and gives some interesting perspectives on the issue of the personal context of PPPs and social capital. Also, the text describes the path of developing PPPs in Poland and especially the touristic projects. The research part presents the original case study comparative analysis based on table-oriented form and as such enables the new way of contextual analysis.
Drivers of workforce agility: a dynamic capability perspective
Authors: Ajgaonkar Suchitra , Neelam Netra Ganesh , Wiemann Judith
Published: June 2021

Purpose

This paper aims to represent an exploration of drivers of workforce agility under the lens of dynamic capabilities to advance the existing workforce literature on agility and strategic human resource management.

Design/methodology/approach

In-depth qualitative interviews with senior information technology professionals, managers, directors and leadership were conducted. Data coding and analysis followed the Gioia methodology to develop a theoretical framework.

Findings

The theoretical paradigm of workforce agility is seeing revisions. In the past it was solely connected to resource-based view theory, current literature superficially speaks of the link with dynamic capability but lacks comprehensive and strategic understanding. The research brings in the evolutionary change by viewing workforce agility directly under the lens of dynamic capability theory and recognizes workforce agility as a high-level strategy. Based on the analysis of the qualitative interviews this study has developed a conceptual heuristic of workforce agility drivers, interlinked with dynamic capabilities micro-foundations – “sensing”, “seizing”, and “continual renewal”. This paper conceptualizes workforce agility as a response to high pressures for the dynamic capability of the company, which requires reconfiguration and redeployment of external and internal human resources and an inherent need to bring some stability to the internal resources of the company.

Originality/value

There is a growing body of literature linking organizational agility with dynamic capabilities, which overlooks workforce agility. This study is theory-based research on workforce agility, which guides practitioners in making human resource processes more agile.
See it, hear it, feel it: embodying a patient experience through immersive virtual reality
Authors: Hannans Jaime A. , Nevins Colleen M. , Jordan Kristin
Published: June 2021

Purpose

The aim of the study was to explore aspects of learning in terms of gain in knowledge, confidence and empathy with immersive virtual reality (VR) from the patient perspective in undergraduate nursing students.

Design/methodology/approach

A pilot study integrating immersive VR experiences during clinical courses was facilitated based on the INACSL (2016) standards for simulation practices with a convenience sample of 165 nursing students in three levels of cohorts, using two different VR scenario simulations. Quantitative and qualitative data were collected through pre- and post-surveys.

Findings

Student participants embodied patients with chronic disease using immersive VR. Findings showed substantial gains in most measures of knowledge, confidence and empathy, with slightly less difference seen in lower level nursing students particularly with empathy and understanding.

Research limitations/implications

Embodiment through immersive VR scenarios was shown to increase learner development. The positive findings from the pilot study justified continuance of integration of immersive VR in nursing education, recommending further use and research.

Originality/value

Simulated learning for nursing has known benefits on knowledge and understanding. Immersive VR is gaining recognition within nursing education as a method to enhance cognitive and affective knowledge. This paper hopes to add insights on the impact of immersive VR for student learning and encourage discussion about the future for innovative immersive teaching and learning approaches for experiential learning.
Influence of active methodologies: projects and cases in the development of digital competences with mobile devices
Authors: Agila-Palacios Martha Vanessa , Muñoz-Repiso Ana García-Valcárcel , Ramírez-Montoya María Soledad
Published: June 2021

Purpose

The purpose of this paper is to analyze the influence of two active methodologies on digital competences development using mobile devices. The first methodology is project-oriented learning (POL); the second one is case-based learning (CBL). The analyzed digital competences belong to the communication and collaboration area of framework DIGCOMP.

Design/methodology/approach

This article shows the results of the quantitative stage with a design pre-experimental pre-test–post-test. A questionnaire was designed and applied to an intentional sample from two different courses. In total, 178 students completed the questionnaire in the pre-test, and after five months, 38 students completed the questionnaire in the post-test.

Findings

The results show that students to whom POL was applied increase by 7% competence of interaction with mobile technology. The results also show that the students to whom CBL was applied to increase all four competencies (interaction +8%, share +6%, collaboration +5%, netiquette +4%).

Research limitations/implications

Self-perception for the evaluation of digital competence and the short study time are limitations to generalize the results, so a longitudinal study is necessary and complemented with qualitative analysis, to present a better validation of the contribution of active methodologies to the development of digital competences.

Originality/value

The rapid advance of technology and the results of various investigations make evident the need of digital competences development. The most common process is digital literacy through techno-functional training. However, these research results confirm that it is possible to promote these digital competences from a practical view and implicitly in active methodologies educational practices.