bluuebunny/crossref_metadata_2025 huggingface dataset:
Mutations in the Bone Morphogenetic Protein signaling pathway sensitize zebrafish and humans to ethanol-induced jaw malformations
Authors: Klem John R. , Schwantes-An Tae-Hwi , Abreu Marco , Suttie Michael , Gray Raeden , Vo Hieu , Conley Grace , Foroud Tatiana M. , Wetherill Leah ,   CIFASD, Lovely C. Ben
Published: June 2023

Fetal Alcohol Spectrum Disorders (FASD) describe ethanol-induced developmental defects including craniofacial malformations. While ethanol-sensitive genetic mutations contribute to facial malformations, the impacted cellular mechanisms remain unknown. Bmp signaling is a key regulator of epithelial morphogenesis driving facial development, providing a possible ethanol-sensitive mechanism. We found that zebrafish mutants for Bmp signaling components are ethanol-sensitive and affect anterior pharyngeal endoderm shape and gene expression, indicating ethanol-induced malformations of the anterior pharyngeal endoderm cause facial malformations. Integrating FASD patient data, we provide the first evidence that variants in the human Bmp receptor geneBMPR1Bassociate with ethanol-related differences in jaw volume. Our results show that ethanol exposure disrupts proper morphogenesis of, and tissue interactions between, facial epithelia that mirror overall viscerocranial shape changes and are predictive for Bmp-ethanol associations in human jaw development. Our data provide a mechanistic paradigm linking ethanol to disrupted epithelial cell behaviors that underlie facial defects in FASD.

Summary Statement

In this study, we apply a unique combination of zebrafish-based approaches and human genetic and facial dysmorphology analyses to resolve the cellular mechanisms driven by the ethanol-sensitive Bmp pathway.
Identification of spatial homogeneous regions in tissues with concordex
Authors: Jackson Kayla C. , Booeshaghi A. Sina , Gálvez-Merchán Ángel , Moses Lambda , Chari Tara , Kim Alexandra , Pachter Lior
Published: June 2023

Spatial homogeneous regions (SHRs) in tissues are domains that are homogeneous with respect to cell type composition. We present a method for identifying SHRs using spatial transcriptomics data, and demonstrate that it is efficient and effective at finding SHRs for a wide variety of tissue types. The method is implemented in a tool called concordex, which relies on analysis of k-nearest-neighbor (kNN) graphs. The concordex tool is also useful for analysis of non-spatial transcriptomics data, and can elucidate the extent of concordance between partitions of cells derived from clustering algorithms, and transcriptomic similarity as represented in kNN graphs.
Multimodal layer modelling revealsin-vivopathology in ALS
Authors: Northall Alicia , Doehler Juliane , Weber Miriam , Tellez Igor , Petri Susanne , Prudlo Johannes , Vielhaber Stefan , Schreiber Stefanie , Kuehn Esther
Published: June 2023

Amyotrophic lateral sclerosis (ALS) is a rapidly progressing neurodegenerative disease characterised by the loss of motor control. Current understanding of ALS pathology is largely based onpost-morteminvestigations at advanced disease stages. A systematicin-vivodescription of the microstructural changes that characterise early-stage ALS, and their subsequent development, is so far lacking.

Recent advances in ultra-high field (7T) MRI data modelling allow us to investigate cortical layersin-vivo. Given the layer-specific and topographic signature of pathology in ALS, we combined submillimeter structural 7T-MRI data (qT1, QSM), functional localisers of body parts (upper limb, lower limb, face) and automated layer modelling to systematically describe pathology in the primary motor cortex (M1), in 12 living ALS-patients with reference to 12 age-, gender-, handedness- and education-matched controls. Longitudinal sampling was performed for a subset of patients. We calculated multimodal pathology maps for each layer (superficial layer, layer 5a, layer 5b, layer 6) of M1 to identify hotspots of demyelination, iron and calcium accumulation in different cortical fields.

We show preserved mean cortical thickness and layer architectures of M1, despite significantly increased iron in layer 6 and significantly increased calcium in layer 5a and superficial layer, in patients compared to controls. The behaviorally first-affected cortical field shows significantly increased iron in L6 compared to other fields, while calcium accumulation is atopographic and significantly increased in the low-myelin borders between cortical fields compared to the fields themselves. A subset of patients with longitudinal data shows that the low-myelin borders are particularly disrupted, and that calcium hotspots but to a lesser extent iron hotspots precede demyelination. Finally, we highlight that a very-slow progressing patient (P4) shows a distinct pathology profile compared to the other patients.

Our data shows that layer-specific markers ofin-vivopathology can be identified in ALS-patients with a single 7T-MRI measurement after first diagnosis, and that such data provide critical insights into the individual disease state. Our data highlight the non-topographic architecture of ALS disease spread, and the role of calcium rather than iron accumulation in predicting future demyelination. We also highlight a potentially important role of low-myelin borders, that are known to connect to multiple areas within the M1 architecture, in disease spread. Importantly, the distinct pathology profile of a very-slow progressing patient (P4) highlights a distinction between disease duration and pathology progression. Our findings demonstrate the importance ofin-vivohistology for the diagnosis and prognosis of neurodegenerative diseases such as ALS.
A Molecular Communication model for cellular metabolism
Authors: Sakkaff Zahmeeth , Freiburger Andrew P. , Catlett Jennie L. , Cashman Mikaela , Immaneni Aditya , Buan Nicole R. , Cohen Myra B. , Henry Christopher , Pierobon Massimiliano
Published: June 2023

Understanding cellular engagement with its environment is essential to control and monitor metabolism. Molecular Communication theory (MC) offers a computational means to identify environmental perturbations that direct or signify cellular behaviors by quantifying the information about a molecular environment that is transmitted through a metabolic system. We developed an model that integrates conventional flux balance analysis metabolic modeling (FBA) and MC to mechanistically expand the scope of MC, and thereby uniquely blends mechanistic biology and information theory to understand how substrate consumption is captured reaction activity, metabolite excretion, and biomass growth. This is enabled by defining several channels through which environmental information transmits in a metabolic network. The information flow in bits that is calculated through this workflow further determines the maximal metabolic effect of environmental perturbations on cellular metabolism and behaviors, since FBA simulates maximal efficiency of the metabolic system. We exemplify this method on two intestinal symbionts –Bacteroides thetaiotaomicronandMethanobrevibacter smithii– and visually consolidated the results into constellation diagrams that facilitate interpretation of information flow from given environments and thereby cultivate the design of controllable biological systems. The unique confluence of metabolic modeling and information theory in this model advances basic understanding of cellular metabolism and has applied value for the Internet of Bio-Nano Things, synthetic biology, microbial ecology, and autonomous laboratories.
Comparative analysis of Respiratory Syncytial Virus frequency rates and viral load in different patient cohorts in a university hospital in Sao Paulo, Brazil, over an eight-year period (2005-2013)
Authors: de Souza Luna Luciano Kleber , Cruz Jessica Santiago , Souza Chaves Tânia do Socorro , Bellei Nancy
Published: June 2023

Respiratory Syncytial Virus (RSV) poses a global health concern, particularly in young children, the elderly, and those immunosuppressed. RSV viral load is essential for understanding transmission, disease severity, prevention, and treatment. This retrospective study aimed to analyze the frequency rates and viral loads of RSV infections in different patient cohorts and age groups over an eight-year period in a university hospital in São Paulo, Brazil. This study analyzed 1380 immunocompetent (IC) and immunosuppressed (IS) patients with acute respiratory tract infections. IC included patients suspected of having severe acute respiratory syndrome caused by influenza A (H1N1)pdm09 virus (SARS H1N1), chronic heart disease (HD), and those receiving primary care service (PC). The IS comprised transplant patients and individuals with human immunodeficiency virus (HIV) infection. Respiratory samples were collected between 2005 and 2013. RSV detection and quantification were performed by RT-qPCR. Viral load was expressed as Log10 copies of RNA/mL. The overall RSV infection rate was 17.3%, with higher rates in children (23.9%) than in adults (12.9%), particularly in children under two years of age (28.2%). Children in the SARS H1N1 and PC subgroups had higher infection rates (16.4% and 34.9%, respectively), with the highest rate in PC children aged 1 to <2 years (45.45%). Adults with HD had a significantly higher frequency rate (27.83%) than those in the SARS H1N1 (2.65%) and IS (15.16%) subgroups. The RSV viral load ranged from 2.43 to 10.15 Log10 RNA copies/mL (mean ±SD = 5.82 ± 2.19). Hospitalized patients had significantly higher viral loads (7.34 ± 1.9) than outpatients (4.38 ± 1.89). Elderly bone marrow transplant patients also had significantly higher viral loads (7.57 ± 2.41) than younger adults (5.12 ± 1.87). This study provides insights into the patterns and impacts of RSV infection in different patient cohorts in Brazil, contributing to developing effective prevention, treatment, and control strategies. Further investigations are needed to understand the susceptibility and risk factors associated with RSV infection.
Identification of three distinct cell populations for urate excretion in human kidney
Authors: Sakaguchi Yoshihiko M. , Wiriyasermkul Pattama , Matsubayashi Masaya , Miyasaka Masaki , Sakaguchi Nau , Sahara Yoshiki , Takasato Minoru , Kinugawa Kaoru , Sugie Kazuma , Eriguchi Masahiro , Tsuruya Kazuhiko , Kuniyasu Hiroki , Nagamori Shushi , Mori Eiichiro
Published: June 2023

In humans, uric acid is an end-product of purine metabolism. Urate excretion from human kidney is tightly regulated by reabsorption and secretion. At least eleven genes have been identified as human renal urate transporters. However, it remains unclear whether all renal tubular cells express the same set of urate transporters. Here we show that renal tubular cells are divided into three distinct cell populations for urate handling. Analysis of healthy human kidneys at single-cell resolution revealed that not all renal tubular cells expressed the same set of urate transporters. Only 32% of renal tubular cells were related to both reabsorption and secretion, while the remaining renal tubular cells were related to either reabsorption or secretion, at 5% and 63% respectively. These results provide physiological insight into the molecular function of the transporters and renal urate handling on cell-units. Our findings also suggest that three different tubular cell populations cooperate to regulate urate excretion from human kidney.

Highlight/Key points

We identified three distinct cell populations within the human renal anatomy that predict putative cellular transport mode, and our findings indicate cellular inhomogeneity with distinct roles such as urate secretion and reabsorption.

Our model of physiological urate handling demonstrates the excretion dynamics in human kidney in terms of single cell-units.

Our cellular urate transport analyses suggest the reversibility of some urate transporters even in certain physiological conditions.

The physiological function of SLC2A9 is not limited to urate reabsorption; it is also involved in urate secretion restriction.

This methodology can be applied to investigations of transport mechanisms in general, regardless of epithelial cell types, species, and substrates.
Comprehensive Assessment of Elevende novoHiFi Assemblers on Complex Eukaryotic Genomes and Metagenomes
Authors: Yu Wenjuan , Luo Haohui , Yang Jinbao , Zhang Shengchen , Jiang Heling , Zhao Xianjia , Hui Xingqi , Sun Da , Li Liang , Wei Xiu-qing , Lonardi Stefano , Pan Weihua
Published: June 2023

Background

Pacific Bioscience HiFi sequencing technology generates long reads (>10 kbp) with very high accuracy (less than 0.01% sequencing error). While severalde novoassembly tools are available for HiFi reads, there are no comprehensive studies on the evaluation of these assemblers.

Results

We evaluated the performance of elevende novoHiFi assemblers on (i) real data for three eukaryotic genomes, (ii) 34 synthetic datasets with different ploidy, sequencing coverage levels, heterozygosity rates and sequencing error rates, (iii) one real metagenomic dataset, and (iv) five synthetic metagenomic datasets with different composition abundance and heterozygosity rates. The nine assemblers were evaluated using QUAST (Quality Assessment Tool) and BUSCO (Benchmarking Universal Single-Copy Ortholog). We also used several additional criteria, namely, completion rate, single-copy completion rate, duplicated completion rate, average proportion of largest category, average distance difference, quality value, run-time and memory utilization. On complex eukaryotic genomes, Hifiasm had a clear advantage over the other assemblers in all tested experiments. On synthetic datasets, Hifiasm, HiCanu, and HiFlye performed equally well. Shasta and Peregrine had good performance across varying ploidy, but required high computational resources. On metagenomic datasets, Hifiasm-meta demonstrated a clear advantage over other assemblers.

Conclusion

We carried out a comprehensive benchmarking study of commonly used assemblers on complex eukaryotic genomes and metagenomes. Our study will help the research community to choose the most appropriate assembler for their data and identify possible improvements in assembly algorithms.
Epistasis Arises from Shifting the Rate-Limiting Step during Enzyme Evolution
Authors: Fröhlich Christopher , Bunzel H. Adrian , Buda Karol , Mulholland Adrian J. , van der Kamp Marc W. , Johnsen Pål J. , Leiros Hanna-Kirsti S. , Tokuriki Nobuhiko
Published: June 2023

The molecular mechanisms by which epistasis boosts enzyme activity remain elusive, undermining our ability to predict the evolution of pathogens and engineer novel biocatalysts. Here, we reveal how directed evolution of a β-lactamase yielded highly epistatic activity enhancements. Evolution selected four mutations that increase antibiotic resistance 40-fold, despite their marginal individual effects (≤ 2-fold). Synergistic improvements coincided with the introduction of super-stochiometric burst kinetics, indicating that epistasis is rooted in the enzyme’s conformational dynamics. Kinetic, structural, and dynamical analyses reveal that epistasis was driven by distinct effects of each mutation on the catalytic cycle. The first mutation acquired during evolution increases protein flexibility and accelerates substrate binding, which is rate-limiting in the wild-type enzyme. The ensuing mutations predominantly boosted the chemical steps by fine-tuning substrate interactions. Our work identifies an overlooked cause for epistasis: changing the rate-limiting step can result in substantial positive synergy boosting enzyme activity.
The super-healing MRL strain promotes muscle growth in muscular dystrophy through a regenerative extracellular matrix
Authors: O’Brien Joseph G. , Willis Alexander B. , Long Ashlee M. , Kwon Jason , Lee GaHyun , Li Frank , Page Patrick G.T. , Vo Andy H. , Hadhazy Michele , Crosbie Rachelle H. , Demonbreun Alexis R. , McNally Elizabeth M.
Published: June 2023

Genetic background shifts the severity of muscular dystrophy. In mice, the DBA/2J strain confers a more severe muscular dystrophy phenotype, whereas the Murphy’s Roth Large (MRL) strain has “super-healing” properties that reduce fibrosis. A comparative analysis of theSgcgnull model of Limb Girdle Muscular Dystrophy in the DBA/2J versus MRL strain showed the MRL background was associated with greater myofiber regeneration and reduced structural degradation of muscle. Transcriptomic profiling of dystrophic muscle in the DBA/2J and MRL strains indicated strain-dependent expression of the extracellular matrix (ECM) and TGF-β signaling genes. To investigate the MRL ECM, cellular components were removed from dystrophic muscle sections to generate decellularized “myoscaffolds”. Decellularized myoscaffolds from dystrophic mice in the protective MRL strain had significantly less deposition of collagen and matrix-bound TGF-β1 and TGF-β3 throughout the matrix, and dystrophic myoscaffolds from the MRL background were enriched in myokines. C2C12 myoblasts were seeded onto decellularized matrices fromSgcg−/−MRL andSgcg−/−DBA/2J matrices. Acellular myoscaffolds from the dystrophic MRL background induced myoblast differentiation and growth compared to dystrophic myoscaffolds from the DBA/2J matrices. These studies establish that the MRL background also generates its effect through a highly regenerative ECM, which is active even in muscular dystrophy.

Brief Summary

The extracellular matrix of the super-healing MRL mouse strain harbors regenerative myokines that improve skeletal muscle growth and function in muscular dystrophy.

Graphical Abstract
A Platform for Controlled Template-Independent Enzymatic Synthesis of RNA Oligonucleotides and Therapeutics
Authors: Wiegand Daniel J. , Rittichier Jonathan , Meyer Ella , Lee Howon , Conway Nicholas J. , Ahlstedt Daniel , Yurtsever Zeynep , Rainone Dominic , Kuru Erkin , Church George M.
Published: June 2023

Therapeutic RNA oligonucleotides have shown tremendous potential to manage and treat disease, yet current manufacturing methods cannot deliver on this promise. Here, we report the development and optimization of a novel, aqueous-based, template-independent enzymatic RNA oligonucleotide synthesis platform as an alternative to traditional chemical methodologies. Our platform is made possible by reversible terminator nucleoside triphosphates and an enzyme capable of their incorporation. We show that many common therapeutic RNA modifications are compatible with our process and demonstrate the enzymatic synthesis of natural and modified oligonucleotides in both liquid and solid phases. Our platform offers many unique advantages over chemical synthesis, including the realization of a more sustainable process to produce therapeutic RNA oligonucleotides.

One-Sentence Summary

An enzyme and novel nucleotide building blocks are used to synthesize RNA oligonucleotides template independently under aqueous conditions.
Matrix stiffening promotes perinuclear clustering of mitochondria
Authors: Daga Piyush , Thurakkal Basil , Rawal Simran , Das Tamal
Published: June 2023

Mechanical cues from the tissue microenvironment, such as the stiffness of the extracellular matrix, modulate cellular forms and functions. As numerous studies have shown, this modulation depends on the stiffness-dependent remodeling of cytoskeletal elements. In contrast, very little is known about how the intracellular organelles such as mitochondria respond to matrix stiffness and whether their form, function, and localization change accordingly. Here, we performed an extensive quantitative characterization of mitochondrial morphology, subcellular localization, dynamics and membrane tension on soft and stiff matrices. This characterization revealed that while matrix stiffness affected all these aspects, matrix stiffening most distinctively led to an increased perinuclear clustering of mitochondria. Subsequently, we could identify the matrix stiffness-sensitive perinuclear localization of filamin as the key factor dictating this perinuclear clustering. Photo-conversion labeling and fluorescent recovery after photobleaching experiments revealed that perinuclear and peripheral mitochondrial populations differed in their motility on the soft matrix but surprisingly they did not show any difference on the stiff matrix. Finally, perinuclear mitochondrial clustering appeared to be crucial for priming human mesenchymal stem cells towards osteogenesis on the stiff matrix. Taken together, we elucidate a dependence of mitochondrial localization on matrix stiffness, which possibly enables a cell to adapt to its microenvironment.
Synthesis and new evidence from the PROTECT UK National Core Study: Determining occupational risks of SARS-CoV-2 infection and COVID-19 mortality
Authors: Rhodes S , Beale S , Cherrie M , Mueller W , Holland F , Matz M , Basinas I , Wilkinson J , Gittins M , Farrell B , Hayward A , Pearce N , van Tongeren M
Published: June 2023

Introduction

The PROTECT National Core Study was funded by the UK Health and Safety Executive (HSE) to investigate routes of transmission for SARS-CoV-2 and variation between settings.

Methods

A workshop was organised in Oct 2022.We brought together evidence from five published epidemiological studies that compared risks of SARS-CoV-2 infection or COVID-19 mortality by occupation or sector funded by PROTECT relating to three non-overlapping data sets, plus additional unpublished analyses relating to the Omicron period. We extracted descriptive study level data and model results. We investigated risk across four pandemic waves using forest plots for key occupational groups by time-period.

Results

Results were largely consistent across different studies with different expected biases. Healthcare and social care sectors saw elevated risks of SARS-CoV-2 infection and COVID-19 mortality early in the pandemic, but thereafter this declined and varied by specific occupational subgroup. The education sector saw sustained elevated risks of infection after the initial lockdown period with little evidence of elevated mortality.

Conclusions

Increased in risk of infection and mortality were consistently observed for occupations in high risk sectors particularly during the early stage of the pandemic. The education sector showed a different pattern compared to the other high risk sectors, as relative risk of infections remained high in the later phased of the pandemic, although no increased in COVID-19 mortality (compared to low-risk occupations) was observed in this sector in any point during the pandemic.
Identifying multi-resolution clusters of diseases in ten million patients with multimorbidity in primary care in England
Authors: Beaney Thomas , Clarke Jonathan , Salman David , Woodcock Thomas , Majeed Azeem , Aylin Paul , Barahona Mauricio
Published: June 2023

Identifying clusters of co-occurring diseases can aid understanding of shared aetiology, management of co-morbidities, and the discovery of new disease associations. Here, we use data from a population of over ten million people with multimorbidity registered to primary care in England to identify disease clusters through a two-stage process. First, we extract data-driven representations of 212 diseases from patient records employing i) co-occurrence-based methods and ii) sequence-based natural language processing methods. Second, we apply multiscale graph-based clustering to identify clusters based on disease similarity at multiple resolutions, which outperforms k-means and hierarchical clustering in explaining known disease associations. We find that diseases display an almost-hierarchical structure across resolutions from closely to more loosely similar co-occurrence patterns and identify interpretable clusters corresponding to both established and novel patterns. Our method provides a tool for clustering diseases at different levels of resolution from co-occurrence patterns in high-dimensional electronic healthcare record data.
Structure and replication cycle of a virus infecting climate-modulating algaEmiliania huxleyi
Authors: Homola Miroslav , Büttner Carina R. , Füzik Tibor , Křepelka Pavel , Holbová Radka , Nováček Jiří , Chaillet Marten , Förster Friedrich , Wilson William H. , Schroeder Declan C. , Plevka Pavel
Published: June 2023

The globally distributed marine algaEmiliania huxleyiproduces reflective calcite disks (coccoliths) that increase the albedo of ocean water and thus reduce the heat absorption in the ocean, which cools the Earth’s climate. The population density ofE. huxleyiis restricted by nucleocytoplasmic large DNA viruses, includingE. huxleyivirus 201 (EhV-201). Despite the impact ofE. huxleyiviruses on the climate, there is limited information about their structure and replication. Here we show that the dsDNA genome inside the EhV-201 virion is protected by an inner membrane, capsid, and outer membrane decorated with numerous transmembrane proteins. The virions are prone to deformation, and parts of their capsids deviate from the icosahedral arrangement. EhV-201 virions infectE. huxleyiby using their fivefold vertex to bind to a host cell and fuse the virus’s inner membrane with the plasma membrane. Whereas the replication of EhV-201 probably occurs in the nucleus, virions assemble in the cytoplasm at the surface of endoplasmic reticulum-derived membrane segments. Genome packaging initiates synchronously with the capsid assembly and completes through an aperture in the forming capsid. Upon the completion of genome packaging, the capsids change conformation, which enables them to acquire an outer membrane by budding into intracellular vesicles. EhV-201 infection induces a loss of surface protective layers fromE. huxleyicells, which allows the continuous release of virions by exocytosis. Our results provide insight into how EhVs bypass the surface protective layers ofE. huxleyiand exploit the organelles of an infected cell for progeny assembly.
Texture-based residual stress analysis of laser powder bed fused Inconel 718 parts
Authors: Schröder Jakob , Evans Alexander , Luzin Vladimir , Abreu Faria Guilherme , Degener Sebastian , Polatidis Efthymios , Čapek Jan , Kromm Arne , Dovzhenko Gleb , Bruno Giovanni
Published: June 2023

Although layer-based additive manufacturing methods such as laser powder bed fusion (PBF-LB) offer an immense geometrical freedom in design, they are typically subject to a build-up of internal stress (i.e.thermal stress) during manufacturing. As a consequence, significant residual stress (RS) is retained in the final part as a footprint of these internal stresses. Furthermore, localized melting and solidification inherently induce columnar-type grain growth accompanied by crystallographic texture. Although diffraction-based methods are commonly used to determine the RS distribution in PBF-LB parts, such features pose metrological challenges in their application. In theory, preferred grain orientation invalidates the hypothesis of isotropic material behavior underlying the common methods to determine RS. In this work, more refined methods are employed to determine RS in PBF-LB/M/IN718 prisms, based on crystallographic texture data. In fact, the employment of direction-dependent elastic constants (i.e.stress factors) for the calculation of RS results in insignificant differences from conventional approaches based on the hypothesis of isotropic mechanical properties. It can be concluded that this result is directly linked to the fact that the {311} lattice planes typically used for RS analysis in nickel-based alloys have high multiplicity and less strong texture intensities compared with other lattice planes. It is also found that the length of the laser scan vectors determines the surface RS distribution in prisms prior to their removal from the baseplate. On removal from the baseplate the surface RS considerably relaxes and/or redistributes; a combination of the geometry and the scanning strategy dictates the sub-surface RS distribution.
Optimal estimated standard uncertainties of reflection intensities for kinematical refinement from 3D electron diffraction data
Authors: Khouchen Malak , Klar Paul Benjamin , Chintakindi Hrushikesh , Suresh Ashwin , Palatinus Lukas
Published: June 2023

Estimating the error in the merged reflection intensities requires a full understanding of all the possible sources of error arising from the measurements. Most diffraction-spot integration methods focus mainly on errors arising from counting statistics for the estimation of uncertainties associated with the reflection intensities. This treatment may be incomplete and partly inadequate. In an attempt to fully understand and identify all the contributions to these errors, three methods are examined for the correction of estimated errors of reflection intensities in electron diffraction data. For a direct comparison, the three methods are applied to a set of organic and inorganic test cases. It is demonstrated that applying the corrections of a specific model that include terms dependent on the original uncertainty and the largest intensity of the symmetry-related reflections improves the overall structure quality of the given data set and improves the final R
all factor. This error model is implemented in the data reduction software PETS2.
Synthesis, crystal structure and Hirshfeld surface analysis of naphthalene-2,3-diyl bis(3-benzyloxy)benzoate
Authors: Anil Kumar H. , Selvanandan S. , Srinivasa H. T. , Venkateshappa G. , Palakshamurthy B. S.
Published: June 2023

In the title compound, C38H28O6, the dihedral angles between the naphthalene ring system and its pendant benzyloxy rings A and B are 88.05 (7) and 80.84 (7)°, respectively. The dihedral angles between the A and B rings and their attached phenyl rings are 49.15 (8) and 80.78 (8)°, respectively. In the extended structure, the molecules are linked by weak C—H...O and C—H...π hydrogen bonds, and π–π stacking interactions, which variously generate C(11) chains and R
2
2(12) loops as part of a three-dimensional network. The Hirshfeld surface [fingerprint contributions = H...H (42.3%), C...H/H...C (40.3%) and O...H/H...O (15.7%)] and intermolecular interaction energies are reported, with dispersion (E
dis = −428.6 kJ mol−1) being the major contributor.
Co-crystallization of N′-benzylidenepyridine-4-carbohydrazide and benzoic acid via autoxidation of benzaldehyde
Authors: Setshedi Itumeleng B. , Lemmerer Andreas , Smith Mark G.
Published: June 2023

The 1:1 co-crystal N′-[(2-methylphenyl)methylidene]pyridine-4-carbohydrazide–benzoic acid (1/1), C13H11N3O·C7H6O2, formed unexpectedly after autoxidation of benzaldehyde during the slow evaporation process of a solution of isoniazid in benzaldehyde. The original intent of the synthesis was to modify isoniazid with benzaldehyde and crystallize the product in order to improve efficacy against Mycobacteria species, but benzoic acid formed spontaneously and co-crystallized with the intended product, N′-benzylidenepyridine-4-carbohydrazide.
Overall protein structure quality assessment using hydrogen-bonding parameters
Authors: Afonine Pavel V. , Sobolev Oleg V. , Moriarty Nigel W. , Terwilliger Thomas C. , Adams Paul D.
Published: June 2023

Atomic model refinement at low resolution is often a challenging task. This is mostly because the experimental data are not sufficiently detailed to be described by atomic models. To make refinement practical and ensure that a refined atomic model is geometrically meaningful, additional information needs to be used such as restraints on Ramachandran plot distributions or residue side-chain rotameric states. However, using Ramachandran plots or rotameric states as refinement targets diminishes the validating power of these tools. Therefore, finding additional model-validation criteria that are not used or are difficult to use as refinement goals is desirable. Hydrogen bonds are one of the important noncovalent interactions that shape and maintain protein structure. These interactions can be characterized by a specific geometry of hydrogen donor and acceptor atoms. Systematic analysis of these geometries performed for quality-filtered high-resolution models of proteins from the Protein Data Bank shows that they have a distinct and a conserved distribution. Here, it is demonstrated how this information can be used for atomic model validation.
Implementation of circular economy in construction projects: a procurement strategy approach
Authors: Ahmed Siraj , Majava Jukka , Aaltonen Kirsi
Published: June 2023

Purpose

The purpose of this study is to investigate the benefits and challenges of implementing circular economy (CE), as well as shed light on the influence of procurement strategy in CE implementation in construction projects.

Design/methodology/approach

A qualitative research approach with abductive reasoning was adopted. The empirical data were collected from the construction industry in the United Arab Emirates (UAE).

Findings

The results reveal that clients, consultants and contractors have limited awareness, knowledge and motivation to implement CE in construction projects. The absence of incentives to design projects following CE principles, lack of involvement of contractors and suppliers, non-use of materials that use CE principles and current procurement strategies are the main challenges for the implementation of CE in the UAE.

Originality/value

Previous research offers limited knowledge on CE and its implementation in construction projects particularly from a procurement strategy perspective. The findings of the study provide new knowledge of the benefits, challenges and role of procurement strategy for implementing CE. It is suggested that collaborative and partnering-based procurement methods are needed to facilitate the effective implementation of CE.
The influence of the pillars of digital academic entrepreneurship on university students’ entrepreneurial intention
Authors: Garcez Ana , Franco Mário , Silva Ricardo
Published: June 2023

Purpose

This study aims to analyse the influence of the pillars (hard and soft skills) of digital academic entrepreneurship on students' entrepreneurial intention.

Design/methodology/approach

This was done by adopting a quantitative methodology involving empirical research with a sample of 761 university students from two countries and adopting structural equation analysis to validate the theoretical model proposed.

Findings

The results indicate a direct influence between hard and soft skills and entrepreneurial intention, and a positive, indirect influence between these and entrepreneurial intention mediated by the dimensions of the theory of planned behaviour (TPB) – entrepreneurial attitude, subjective norms and perceived behavioural control. Therefore, the pillars of digital academic entrepreneurship have a direct and indirect influence on university students' entrepreneurial intention.

Practical implications

This study also contributes to better operationalization of entrepreneurial education in university environments, since the development of hard and soft skills can be planned better based on the model proposed here. Considering the relations between the dimensions of hard and soft skills and those of TPB, this study shows there can be an influence on students' entrepreneurial intention.

Originality/value

In this study, a new and innovative construct is inserted in the model of entrepreneurial intention: “structural pillars of digital academic entrepreneurship” through structural equation modelling, to determine the degree of influence of these pillars (hard and soft skills) constructs on HEI students' entrepreneurial intention.
Brazilian agtech scalability: proposal and assessment of a local multidimensional model
Authors: Bertucci Ramos Paulo Henrique , Pedroso Marcelo Caldeira
Published: June 2023

Purpose

This study aims to propose and assess a model with the main elements influencing Brazilian agtech scalability with the aim of supporting the scalability process of startups that find themselves in the stage of initial conception of the business model.

Design/methodology/approach

The research was conducted using the design science research (DSR) method. The data for assessing the proposed model were collected through in-depth interviews. The answers were analyzed quantitatively, using descending hierarchical classification (DHC), correspondence factor analysis (CFA), and level of agreement; and qualitatively, using content analysis.

Findings

Considering the Brazilian context, the objective, environmental, structural, and evaluative dimensions presented positive characteristics for the main criteria analyzed (operational viability, generality, clarity, adaptation to the reality studied, completeness, consistency, comprehensibility, and structural simplicity). Specific improvements were proposed in all the criteria analyzed.

Originality/value

The artifact can be considered a strategic guide for agtechs that have yet to overcome the barrier of initial conception of the business model. The model enables the identification of the main problems that agtechs can encounter in their life cycle, as well as seeking solutions in advance.
Industry talent branding: a collaborative and strategic approach to reducing hospitality’s talent challenge
Authors: Manoharan Ashokkumar , Scott-Young Christina , McDonnell Anthony
Published: June 2023

Purpose

The COVID-19 pandemic exacerbated the talent challenges faced by hospitality organisations. This paper aims to propose a new concept – industry talent branding – which, is argued, offers industry stakeholders the opportunity to reduce such issues through working more collaboratively and strategically to magnify the pool in which individual organisations compete for talent.

Design/methodology/approach

This paper proposes a conceptual framework of industry talent branding, based on brand equity theory, signalling theory and the employer branding literature.

Findings

Industry talent branding opens a potentially new stream of research on how talent attraction and retention issues may be addressed. The authors propose that there is merit in moving beyond the organisational-level phenomenon of employer branding to industry talent branding through articulating a broader collaborative and strategic agenda to increase and widen the talent pool available to organisations.

Research limitations/implications

The proposed framework offers the hospitality industry and its encompassing stakeholders a means to adopt a more proactive, collective and strategic approach to address long-standing talent challenges.

Originality/value

This paper combines brand equity and signalling theories to develop the concept of industry talent branding, defined as a strategically curated, yet realistic impression of the employee value proposition (i.e. the benefits and rewards received by employees in return for their work performance) available within the industry, that by design will sustainably attract new employees into the industry and retain existing talent.
Shaping individual paths for decision-making: a fuzzy set approach of religious and humanistic beliefs leading to the (non)acceptance of euthanasia
Authors: Soares Maria Eduarda , Teixeira Alfredo , Tavares Patrícia
Published: June 2023

Purpose

While the influence of individual beliefs on decision-making has been widely acknowledged, the interaction of different types of beliefs remains an under-researched topic. This study analyses how the simultaneous influence of religious beliefs and nonreligious beliefs shapes individual decision-making. This study aims to contribute to inform organizational decisions on topics potentially associated with these two types of beliefs, including corporate social responsibility matters. This study also aims to provide insights to ethical decision-making in situations of absence of social consensus, a subject that is relevant for individuals, organizations and policymakers.

Design/methodology/approach

This study uses fuzzy set qualitative comparative analysis to identify how different configurational groupings of Christian beliefs and humanistic beliefs lead to the acceptance or nonacceptance of euthanasia in a sample of individuals who identify as Catholic.

Findings

Among individuals sharing a Catholic religious affiliation, the authors identify three different configurations of beliefs – Cultural Catholics (religious beliefs are absent and humanistic beliefs are present), Observant Catholics (religious beliefs are present and humanistic beliefs are irrelevant) and Secular Catholics (both religious beliefs and humanistic beliefs are present).

Originality/value

Previous research has put forward the role of religion-related variables, such as religious affiliation and level of religiosity, for views on euthanasia. This study provides a more detailed analysis of the role of belief systems, identifying how different configurational groupings of beliefs lead to a decision grounded in moral and ethical considerations but for which there is an absence of social consensus.
Risk-based reliability assessment and testing stop time based software system modeling
Authors: Gupta Priyanka , Anand Adarsh , Tamura Yoshinobu , Ram Mangey
Published: June 2023

Purpose

The ideology of this article is to study the performance concerns of SDN Controllers, with the help of developed SRGM and thereby obtain its optimal testing duration. The effect of undetected uncertainty in the parameter values have also been catered in the proposal.

Design/methodology/approach

These uncertainties in the parameter values are studied as the risk of not meeting desired set of requirements, whose removal causes additional cost. Considering these two constructs as attributes of MAUT, the controller's optimal testing duration is obtained.

Findings

The article focuses towards obtaining the optimal duration for which the SDN Controllers must be tested. It was observed that the inculcation of risk-attribute has provided the higher utility value as compared to any other existing scenarios.

Originality/value

Plenty of SRGM have been proposed in the literature which talks about the testing stop time determination problems. But, none of them have considered the impact of risk of not meeting the requirements (reliability) along with cost to obtain its testing stop time. Further, validation of the proposed model in presented with the help of two releases versions of SDN controller platform, ONOS, entitled as “Kingfisher” and “Loon” and has acquired promising results.
Does tourism flow in cities drive green practices in the current smart city trajectories? Empirical evidence from Italy
Authors: Marchesani Filippo , Masciarelli Francesca
Published: June 2023

Purpose

The concept of a smart city is becoming more closely linked to tourism destinations. The relationship between the environment, sustainability and tourism has become more interrelated. An eco-friendly city environment can influence tourists’ decisions, but tourist flows can also negatively impact the local ecosystem by increasing energy consumption, air pollution and environmental sustainability. In this research letter, the authors reverse this perspective, moving into smart city trajectories, highlighting that increasing tourism in cities drives the city to advance a green transition to respond to the imbalance generated by large flows of tourists that increase the users-density of the city. Thus, the purpose of this study is to investigate the symbiotic relationship between increasing tourism in cities and the imperative for a green transition.

Design/methodology/approach

This study builds on the generalized method of moment approach and an 11-year panel data set covering 30 Italian cities to investigate the relationship between tourism flow and the cities’ green practices embedded in the smart environment dimension.

Findings

This study provides empirical evidence that a large flow of tourists in cities positively affects the cities’ green transition, contributing to the advancement of smart tourism and smart city debate.

Research limitations/implications

The study focuses only on one country, and although its results may be generalizable to the European Union, it is not representative at a global level and requires further research.

Practical implications

This study offers practical implications underscoring the benefits of large tourism inflow in managing and implementing smart city projects.

Social implications

Tourism and overtourism may lead to a city reaction regarding green practices, which can have a multiplier benefit on the urban environment.

Originality/value

To the best of the authors’ knowledge, this is one of the first study attempt to investigate the tourism flow as a driver of smart city implementation, considering the city’s reaction to tourism and overtourism conditions in the city that would lead to the ecological and sustainable collapse of a city.
“Does anyone know? Can you get any help?” Experiences from an ambassador-facilitated health programme: insights from a qualitative study
Authors: Bond Charlotte Brøgger , Stochkendahl Mette Jensen , Søgaard Karen , Andersen Lotte Nygaard
Published: June 2023

Purpose

Health ambassadors are co-workers assigned to facilitate healthy choices amongst the ambassadors'' colleagues and are increasingly used in workplace health promotion. In a municipality in the southern region of Denmark, occupational health and safety (OHS) representatives were appointed as health ambassadors to facilitate the development of healthy lifestyle initiatives at the ambassadors' workplace and the uptake of various health offers from the municipality's workplace health programme amongst the ambassadors' colleagues. The aim of this study was to understand how employees and managers from the municipality experienced the health ambassador-facilitated implementation of the health programme.

Design/methodology/approach

The study was designed as an interview study with (n = 13) semi-structured interviews. Using purposeful sampling, the authors invited participants who held different positions (e.g. managers and regular employees) on two different work teams in the municipality. The work teams (a construction team and a healthcare team) differed in gender profile and work tasks but were both categorised as physically heavy work. Malterud's systematic text condensation was used to devise the strategy for the analysis.

Findings

The authors' findings show that the employees considered health a private matter that the workplace should not interfere with, and this challenged the implementation of the health programme. Secondly, the health ambassadors were not properly trained to facilitate health initiatives amongst the ambassadors' colleagues; instead, the managers were the driving force in the implementation of health initiatives.

Originality/value

The study provides useful insights into the processes of implementing health in the workplace and emphasises the importance of involving employees in design and planning of initiatives for workplace health promotion.