bluuebunny/crossref_metadata_2025 huggingface dataset:
Development and implementation of an automated electronic health record–linked registry for emergency general surgery
Authors: Mou Zongyang , Sitapati Amy M. , Ramachandran Mokhshan , Doucet Jay J. , Liepert Amy E.
Published: February 2022

INTRODUCTION

Despite adoption of the emergency general surgery (EGS) service by hospitals nationally, quality improvement (QI) and research for this patient population are challenging because of the lack of population-specific registries. Past efforts have been limited by difficulties in identifying EGS patients within institutions and labor-intensive approaches to data capture. Thus, we created an automated electronic health record (EHR)–linked registry for EGS.

METHODS

We built a registry within the Epic EHR at University of California San Diego for the EGS service. Existing EHR labels that identified patients seen by the EGS team were used to create our automated inclusion rules. Registry validation was performed using a retrospective cohort of EGS patients in a 30-month period and a 1-month prospective cohort. We created quality metrics that are updated and reported back to clinical teams in real time and obtained aggregate data to identify QI and research opportunities. A key metric tracked is clinic schedule rate, as we care that discontinuity postdischarge for the EGS population remains a challenge.

RESULTS

Our registry captured 1,992 patient encounters with 1,717 unique patients in the 30-month period. It had a false-positive EGS detection rate of 1.8%. In our 1-month prospective cohort, it had a false-positive EGS detection rate of 0% and sensitivity of 85%. For quality metrics analysis, we found that EGS patients who were seen as consults had significantly lower clinic schedule rates on discharge compared with those who were admitted to the EGS service (85% vs. 60.7%, p < 0.001).

CONCLUSION

An EHR-linked EGS registry can reliably conduct capture data automatically and support QI and research.

LEVEL OF EVIDENCE

Prognostic and epidemiological, level III.
Guppies (
Poecilia reticulata
) are deceived by visual illusions during obstacle negotiation
Authors: Santacà Maria , Bisazza Angelo , Agrillo Christian
Published: February 2022

Animals travelling in their natural environment repeatedly encounter obstacles that they can either detour or go through. Gap negotiation requires an accurate estimation of the opening's size to avoid getting stuck or being injured. Research on visual illusions has revealed that in some circumstances, transformation rules used to generate a three-dimensional representation from bidimensional retinal images fail, leading to systematic errors in perception. In Ebbinghaus and Delboeuf illusions, the presence of task-irrelevant elements causes us to misjudge an object's size. Susceptibility to these illusions was observed in other animals, although with large intraspecific differences. In this study, we investigated whether fish can accurately estimate gap size and whether during this process they may be deceived by illusory patterns. Guppies were extremely accurate in gap negotiation, discriminating holes with a 10% diameter difference. When presented with two identical holes surrounded by inducers to produce Ebbinghaus and Delboeuf patterns, guppies misperceived gap size in the predicted direction. So far, researchers have principally considered illusions as useful tools for exploring the cognitive processing underlying vision. Our findings highlight the possibility that they have important ecological implications, affecting the everyday interactions of an animal with its physical world besides its intra- and interspecific relationships.
Long-term abundance trends of insect taxa are only weakly correlated
Authors: van Klink Roel , Bowler Diana E. , Gongalsky Konstantin B. , Chase Jonathan M.
Published: February 2022

Changes in the abundances of animals, such as with the ongoing concern about insect declines, are often assumed to be general across taxa. However, this assumption is largely untested. Here, we used a database of assemblage-wide long-term insect and arachnid monitoring to compare abundance trends among co-occurring pairs of taxa. We show that 60% of co-occurring taxa qualitatively showed long-term trends in the same direction—either both increasing or both decreasing. However, in terms of magnitude, temporal trends were only weakly correlated (mean freshwater
r
= 0.05 (±0.03), mean terrestrial
r
= 0.12 (±0.09)). The strongest correlation was between trends of beetles and those of moths/butterflies (
r
= 0.26). Overall, even though there is some support for directional similarity in temporal trends, we find that changes in the abundance of one taxon provide little information on the changes of other taxa. No clear candidate for umbrella or indicator taxa emerged from our analysis. We conclude that obtaining a better picture of changes in insect abundances will require monitoring of multiple taxa, which remains uncommon, especially in the terrestrial realm.
Dental cementum virtual histology of Neanderthal teeth from Krapina (Croatia, 130–120 kyr): an informed estimate of age, sex and adult stressors
Authors: Cerrito Paola , Nava Alessia , Radovčić Davorka , Borić Dušan , Cerrito Leonardo , Basdeo Tricia , Ruggiero Guido , Frayer David W. , Kao Alexander P. , Bondioli Luca , Mancini Lucia , Bromage Timothy G.
Published: February 2022

The evolution of modern human reproductive scheduling is an aspect of our life history that remains vastly uncomprehended. The present work aims to address this gap by validating a non-destructive cutting-edge methodology to infer adult life-history events on modern teeth with known life history and then applying it to fossil specimens. We use phase-contrast synchrotron X-ray microtomography to visualize the dental cementum of 21 specimens: nine contemporary humans; 10 Neanderthals from Krapina (Croatia, 130–120 kyr); one Neolithic
Homo sapiens
from Ajmana (Serbia); and one Mesolithic
H. sapiens
from Vlasac (Serbia). We were able to correctly detect and time (root mean square error = 2.1 years;
R
2
= 0.98) all reproductive (menarche, parturition, menopause) and other physiologically impactful events in the modern sample. Nonetheless, we could not distinguish between the causes of the events detected. For the fossil specimens, we estimated age at death and age at occurrence of biologically significant events. Finally, we performed an exploratory analysis regarding possible sexual dimorphism in dental cementum microstructure, which allowed us to correctly infer the sex of the Neolithic specimen, for which the true value was known via DNA analysis.
Thomas Sackville's Hall of Fame: displaced, reinvented and preserved at Knole
Authors: Stoddart Olivia , Alabone Gerry
Published: February 2022

Between 1605 and 1608 Knole was transformed into a dazzling Renaissance palace by Thomas Sackville, 1st Earl of Dorset. All around its largest Gallery ran a frieze of nearly fifty oval portraits, of which thirty-eight survive on their original rectangular framed oak panels. In 1702 the paintings were prised from their walls and moved elsewhere in the house. The surviving panels had deteriorated, mostly owing to movement in their wood being restrained by their original engaged batten frames. Sources state that in 1793 the paintings restorer Francis Parsons was responsible for significant interventions that effectively changed the set from fragments of a fitted Jacobean decorative interior into a hang of individual paintings in a more contemporary neoclassical livery. Aesthetic changes made by Parsons reflect a change in taste during this era whilst simultaneously addressing the paintings' physical deterioration—principally interventions to the back of the panels in an attempt to keep the portraits flat. Additionally, the set was augmented with six portraits, possibly older than Sackville's original set. These treatments carried out during the eighteenth century to stabilize, restore, augment and update this important Jacobean portrait set demonstrate careful manipulation of their condition and significance.
Sparsifying priors for Bayesian uncertainty quantification in model discovery
Authors: Hirsh Seth M. , Barajas-Solano David A. , Kutz J. Nathan
Published: February 2022

We propose a probabilistic model discovery method for identifying ordinary differential equations governing the dynamics of observed multivariate data. Our method is based on the
sparse identification of nonlinear dynamics
(SINDy) framework, where models are expressed as sparse linear combinations of pre-specified candidate functions. Promoting parsimony through sparsity leads to interpretable models that generalize to unknown data. Instead of targeting point estimates of the SINDy coefficients, we estimate these coefficients via sparse Bayesian inference. The resulting method,
uncertainty quantification SINDy
(UQ-SINDy), quantifies not only the uncertainty in the values of the SINDy coefficients due to observation errors and limited data, but also the probability of inclusion of each candidate function in the linear combination. UQ-SINDy promotes robustness against observation noise and limited data, interpretability (in terms of model selection and inclusion probabilities) and generalization capacity for out-of-sample forecast. Sparse inference for UQ-SINDy employs Markov chain Monte Carlo, and we explore two sparsifying priors: the
spike and slab prior
, and the
regularized horseshoe prior
. UQ-SINDy is shown to discover accurate models in the presence of noise and with orders-of-magnitude less data than current model discovery methods, thus providing a transformative method for real-world applications which have limited data.
On blockage coefficients: flow past a body in a pipe
Authors: Martin P. A. , Skvortsov A. T.
Published: February 2022

Blockage coefficients characterize the presence of an object on uniform flow along a rigid pipe. The main purpose of the paper is to develop analytical methods for the calculation of these coefficients. For potential flow, blockage coefficients are related to the added mass of an object moving along a pipe. They also arise when matched asymptotic expansions are used to solve acoustic problems, in which Laplace’s equation is appropriate for related inner problems. Steady diffusion problems can also lead to similar harmonic problems. The paper includes some general results (such as a version of Webster’s horn equation for slender rigid objects) and some specific results for objects of various simple axisymmetric shapes (spheroids, spindles, finite circular cylinders, double cones and thin discs). Applications to various physical situations are expected in future work.
The biogeography of community assembly: latitude and predation drive variation in community trait distribution in a guild of epifaunal crustaceans
Authors: Gross Collin P. , Duffy J. Emmett , Hovel Kevin A. , Kardish Melissa R. , Reynolds Pamela L. , Boström Christoffer , Boyer Katharyn E. , Cusson Mathieu , Eklöf Johan , Engelen Aschwin H. , Eriksson Britas Klemens , Fodrie F. Joel , Griffin John N. , Hereu Clara M. , Hori Masakazu , Hughes A. Randall , Ivanov Mikhail V. , Jorgensen Pablo , Kruschel Claudia , Lee Kun-Seop , Lefcheck Jonathan , McGlathery Karen , Moksnes Per-Olav , Nakaoka Masahiro , O'Connor Mary I. , O'Connor Nessa E. , Olsen Jeanine L. , Orth Robert J. , Peterson Bradley J. , Reiss Henning , Rossi Francesca , Ruesink Jennifer , Sotka Erik E. , Thormar Jonas , Tomas Fiona , Unsworth Richard , Voigt Erin P. , Whalen Matthew A. , Ziegler Shelby L. , Stachowicz John J.
Published: February 2022

While considerable evidence exists of biogeographic patterns in the intensity of species interactions, the influence of these patterns on variation in community structure is less clear. Studying how the distributions of traits in communities vary along global gradients can inform how variation in interactions and other factors contribute to the process of community assembly. Using a model selection approach on measures of trait dispersion in crustaceans associated with eelgrass (Zostera marina) spanning 30° of latitude in two oceans, we found that dispersion strongly increased with increasing predation and decreasing latitude. Ocean and epiphyte load appeared as secondary predictors; Pacific communities were more overdispersed while Atlantic communities were more clustered, and increasing epiphytes were associated with increased clustering. By examining how species interactions and environmental filters influence community structure across biogeographic regions, we demonstrate how both latitudinal variation in species interactions and historical contingency shape these responses. Community trait distributions have implications for ecosystem stability and functioning, and integrating large-scale observations of environmental filters, species interactions and traits can help us predict how communities may respond to environmental change.
Clade-wide variation in bite-force performance is determined primarily by size, not ecology
Authors: Isip Justin E. , Jones Marc E. H. , Cooper Natalie
Published: February 2022

Performance traits are tightly linked to the fitness of organisms. However, because studies of variation in performance traits generally focus on just one or several closely related species, we are unable to draw broader conclusions about how and why these traits vary across clades. One important performance trait related to many aspects of an animal’s life history is bite-force. Here, we use a clade-wide phylogenetic comparative approach to investigate relationships between size, head dimensions and bite-force among lizards and tuatara (lepidosaurs), using the largest bite-force dataset collated to date for any taxonomic group. We test four predictions: that bite-force will be greater in larger species, and for a given body size, bite-force will be greatest in species with acrodont tooth attachment, herbivorous diets, and non-burrowing habits. We show that bite-force is strongly related to body and head size across lepidosaurs and, as predicted, larger species have the greatest bite-forces. Contrary to our other predictions, tooth attachment, diet and habit have little predictive power when accounting for size. Herbivores bite more forcefully simply because they are larger. Our results also highlight priorities for future sampling to further enhance our understanding of broader evolutionary patterns.
Unveiling the genomic potential of Pseudomonas type strains for discovering new natural products
Authors: Saati-Santamaría Zaki , Selem-Mojica Nelly , Peral-Aranega Ezequiel , Rivas Raúl , García-Fraile Paula
Published: February 2022

Microbes host a huge variety of biosynthetic gene clusters that produce an immeasurable array of secondary metabolites with many different biological activities such as antimicrobial, anticarcinogenic and antiviral. Despite the complex task of isolating and characterizing novel natural products, microbial genomic strategies can be useful for carrying out these types of studies. However, although genomic-based research on secondary metabolism is on the increase, there is still a lack of reports focusing specifically on the genus

Pseudomonas

. In this work, we aimed (i) to unveil the main biosynthetic systems related to secondary metabolism in

Pseudomonas

type strains, (ii) to study the evolutionary processes that drive the diversification of their coding regions and (iii) to select

Pseudomonas

strains showing promising results in the search for useful natural products. We performed a comparative genomic study on 194

Pseudomonas

species, paying special attention to the evolution and distribution of different classes of biosynthetic gene clusters and the coding features of antimicrobial peptides. Using EvoMining, a bioinformatic approach for studying evolutionary processes related to secondary metabolism, we sought to decipher the protein expansion of enzymes related to the lipid metabolism, which may have evolved toward the biosynthesis of novel secondary metabolites in

Pseudomonas

. The types of metabolites encoded in

Pseudomonas

type strains were predominantly non-ribosomal peptide synthetases, bacteriocins, N-acetylglutaminylglutamine amides and ß-lactones. Also, the evolution of genes related to secondary metabolites was found to coincide with

Pseudomonas

species diversification. Interestingly, only a few

Pseudomonas

species encode polyketide synthases, which are related to the lipid metabolism broadly distributed among bacteria. Thus, our EvoMining-based search may help to discover new types of secondary metabolite gene clusters in which lipid-related enzymes are involved. This work provides information about uncharacterized metabolites produced by

Pseudomonas

type strains, whose gene clusters have evolved in a species-specific way. Our results provide novel insight into the secondary metabolism of

Pseudomonas

and will serve as a basis for the prioritization of the isolated strains. This article contains data hosted by Microreact.
Comparative genomics and evolutionary analysis of Lactococcus garvieae isolated from human endocarditis
Authors: Francés-Cuesta Carlos , Ansari Iván , Fernández-Garayzábal José Francisco , Gibello Alicia , González-Candelas Fernando
Published: February 2022

Lactococcus garvieae

is a well-known pathogen of fish, but is rarely involved in infections in humans and other mammals. In humans, the main clinical manifestation of

L. garvieae

infections is endocarditis usually related to the ingestion of contaminated food, such as undercooked fish and shellfish. This study presents the first complete genomic sequence of a clinical

L. garvieae

strain isolated from a patient with endocarditis and its comparative analysis with other genomes. This human isolate contains a circular chromosome of 2 099 060 bp and one plasmid of 50 557 bp. In comparison with other fully sequenced

L. garvieae

strains, the chromosomal DNA of

L. garvieae

Lg-Granada carries a low proportion of insertion sequence elements and a higher number of putative prophages. Our results show that, in general,

L. garvieae

is a highly recombinogenic species with an open pangenome in which almost 30 % of its genome has undergone horizontal transfers. Within the genus Lactococcus, L. lactis is the main donor of genetic components to

L. garvieae

but, taking Lg-Granada as a representative, this bacterium tends to import more genes from

Bacilli

taxa than from other

Lactococcus

species.
Evidence for common ancestry and microevolution of passerine-adapted Salmonella enterica serovar Typhimurium in the UK and USA
Authors: Fu Yezhi , Smith Jared C. , Shariat Nikki W. , M’ikanatha Nkuchia M. , Dudley Edward G.
Published: February 2022

The evolution of

Salmonella enterica

serovar Typhimurium (S. Typhimurium) within passerines has resulted in pathoadaptation of this serovar to the avian host in Europe. Recently, we identified an S. Typhimurium lineage from passerines in North America. The emergence of passerine-adapted S. Typhimurium in Europe and North America raises questions regarding its evolutionary origin. Here, we demonstrated that the UK and US passerine-adapted S. Typhimurium shared a common ancestor from ca. 1838, and larids played a key role in the clonal expansion by disseminating the common ancestor between North America and Europe. Further, we identified virulence gene signatures common in the passerine- and larid-adapted S. Typhimurium, including conserved pseudogenes in fimbrial gene lpfD and Type 3 Secretion System (T3SS) effector gene steC. However, the UK and US passerine-adapted S. Typhimurium also possessed unique virulence gene signatures (i.e. pseudogenes in fimbrial gene fimC and T3SS effector genes sspH2, gogB, sseJ and sseK2), and the majority of them (38/47) lost a virulence plasmid pSLT that was present in the larid-adapted S. Typhimurium. These results provide evidence that passerine-adapted S. Typhimurium share a common ancestor with those from larids, and the divergence of passerine- and larid-adapted S. Typhimurium might be due to pseudogenization or loss of specific virulence genes.
Best of intent, worst of both worlds: why sequentially combining epidemiological designs does not improve signal detection in vaccine safety surveillance
Authors: Arshad Faaizah , Schuemie Martijn J. , Minty Evan P. , Alshammari Thamir M. , Lai Lana Y.H. , Duarte-Salles Talita , Fortin Stephen , Nyberg Fredrik , Ryan Patrick B. , Hripcsak George , Prieto-Alhambra Daniel , Suchard Marc A.
Published: February 2022

Background

Vaccine safety surveillance commonly includes a serial testing approach with a sensitive method for “signal generation” and specific method for “signal validation.” Whether serially combining epidemiological designs improves both sensitivity and specificity is unknown.

Methods

We assessed the overall performance of serial testing using three administrative claims and one electronic health record database. We compared Type I and II errors before and after empirical calibration for historical comparator, SCCS, and the serial combination of those designs against six vaccine exposure groups with 93 negative control and 279 imputed positive control outcomes.

Results

Historical comparator mostly had lower Type II error than SCCS. SCCS had lower Type I error than the historical comparator. Before empirical calibration, serial combination increased specificity and decreased sensitivity. Type II errors mostly exceeded 50%. After empirical calibration, Type I errors returned to nominal; sensitivity was lowest when the methods were combined.

Conclusion

We recommend against the serial approach in vaccine safety surveillance. While serial combination produced fewer false positive signals compared to the most specific method, it generated more false negative signals compared to the most sensitive method. Using the noisy historical comparator in front of SCCS deteriorated overall performance in evaluating safety signals.

Key Messages

Using the serial approach in vaccine safety surveillance did not improve overall performance: specificity increased but sensitivity decreased.

Without empirical calibration, Type II errors exceeded 50%; after empirical calibration, Type I error rates returned to nominal with negligible change to Type II error rates.

While prior research has suggested high sensitivity of the historical comparator method in distinguishing true safety signals, there were cases when self-controlled case series was more sensitive.

Vaccine safety surveillance is becoming increasingly important, so monitoring systems should closely consider the utility and sequence of epidemiological designs.
Practical application of indicators for genetic diversity in CBD post-2020 Global Biodiversity Framework implementation
Authors: Thurfjell Henrik , Laikre Linda , Ekblom Robert , Hoban Sean , Sjögren-Gulve Per
Published: February 2022

Genetic diversity is a key aspect of biological variation for the adaptability and survival of populations of species, which must be monitored to assure maintenance. We used data from the Swedish Red-List 2020 and a recent government report to apply three indicators for genetic diversity proposed for the post-2020 Global Biodiversity Framework of the Convention on Biological Diversity (CBD). We made more detailed indicator assessments for mammals and herptiles.

For indicator 1, the proportion of populations with effective population size Ne>500, 33% of 22557 investigated species had a population estimate. For herptiles and mammals, 70% and 49%, respectively likely had Ne>500.

For indicator 2, the proportion of populations or range remaining within species, 20% of all species evaluated for the Red-List have data. Meanwhile, 32% of the herptile and 84% of the mammal populations are maintaining their populations/range.

For indicator 3, the number of species/populations in which genetic diversity is monitored using DNA-based methods, there are studies on 3% of species, and 0.3% are monitored. In contrast 68% of mammals and 29% of herptiles are studied using DNA, and 8% of mammals and 24% of herptiles are genetically monitored.

We conclude that the Red List provide data suitable for evaluating the genetic indicators, but the data quality can be improved. There is a synergy in estimating the genetic indicators in parallel with the Red-Listing process. We propose that indicator values could be included in national Red-Listing as a new category - “genetically threatened”, based on the genetic indicators.
Edible formulations of chicken egg derived IgY antibodies neutralize SarsCoV2 Omicron RBD binding to human ACE2
Authors: Meher Kranti , Sivakumar S. , Kadiyala Gopi , Iyer Subramanian , Vangala Subhramanyam , Chandran Satish , Saxena Uday
Published: February 2022

SarsCoV2 virus driven pandemic continues to surge propelled by new mutations such as seen in Omicron strain. Omicron is now rapidly becoming the dominant strain globally with more than 30 mutations in the spike protein. The mutations have resulted in Omicron strain escaping most of the neutralizing antibodies generated by the current set of approved vaccines and diluting the protection offered by the vaccines and therapeutic monoclonal antibodies.

This has necessitated the need for newer strategies to prevent this strain from spreading. Towards this unmet need we have developed chicken egg derived anti-RBD IgY antibodies that neutralize the binding of Omicron RBD to human ACE2. Furthermore, we have formulated the edible IgY as flavored beverages to allow for use as oral rinse and prevent the entry of Omicron in the oropharyngeal passage, a major access and accumulation point for this strain in humans.
Age-related differences in GABA: Impact of analysis technique
Authors: Simmonite M. , Peltier S.J. , Polk T. A.
Published: February 2022

Previous research using magnetic resonance spectroscopy (MRS) has indicated that GABA levels decline in multiple brain regions over the course of healthy aging. However, brain atrophy also occurs during healthy aging, and as a result the tissue composition of MRS voxels (i.e., the percentage of grey matter, white matter, and cerebrospinal fluid in the voxel) may also differ between age groups. Many authors therefore argue for applying a correction to GABA estimates in order to control for differences in tissue composition. Here, we use data from a large healthy aging study to investigate the influence of three tissue correction strategies on age-group differences in GABA. We also evaluate the use of different analysis packages and reference metabolites on group differences. A 3T MEGA-PRESS sequence was used to obtain spectra from seven voxels placed in the visual, auditory, and sensorimotor cortex of 58 young adults (aged 18-29 years) and 85 older adults. We obtained several different estimates of GABA concentrations from the spectra using two analysis software packages (Gannet 3.1 and LCModel), three reference metabolites (water, creatine and N-acetylaspartate) and four tissue correction strategies. Young adults consistently demonstrated significantly higher GABA concentrations in the visual, auditory, and sensorimotor cortex when we used an uncorrected GABA estimate referenced either to water or creatine. When uncorrected GABA was referenced to N-acetylaspartate, age-related differences were observed only in the right ventral visual cortex. Similarly, when any of the four tissue corrections were applied to the data, only age-related differences in the left and right ventral visual cortex voxels remained. Correlations between GABA concentration estimates obtained from different software packages were moderate, as were correlations between uncorrected GABA estimates when different baseline metabolites were used. Correlations between all tissue corrections we explored were extremely high. These results confirm that reports of age-related differences in GABA concentrations are driven, at least in part, by changes in tissue composition.
3D bioprinting of an implantable xeno-free vascularized human skin graft
Authors: Baltazar Tania , Jiang Bo , Moncayo Alejandra , Merola Jonathan , Albanna Mohammad Z. , Saltzman W. Mark , Pober Jordan S.
Published: February 2022

Bioengineered tissues or organs produced using matrix proteins or components derived from xenogeneic sources pose risks of allergic responses, immune rejection, or even autoimmunity. Here, we report successful xeno-free isolation, expansion, and cryopreservation of human endothelial cells, fibroblasts, pericytes and keratinocytes from a single donor. We further demonstrate the bioprinting of a human skin substitute with a dermal layer containing xeno-free cultured human endothelial cells (EC), fibroblasts, and pericytes in a xeno-free bioink containing human collagen type I and fibronectin layered in a biocompatible polyglycolic acid (PGA) mesh and subsequently seeded with xeno-free human keratinocytes to form an epidermal layer. Following implantation of such bilayered skin grafts on the dorsum of immunodeficient mice, keratinocytes form a mature stratified epidermis with rete ridge-like structures. The ECs and pericytes form human EC-lined perfused microvessels within 2 weeks after implantation, preventing graft necrosis, and eliciting further perfusion of the graft by angiogenic host microvessels. In summary, we describe the fabrication of a bioprinted vascularized bilayered skin substitute under completely xeno-free culture conditions demonstrating feasibility of a xeno-free approach to complex tissue engineering.
Stress granules promote chemoresistance by triggering cellular quiescence
Authors: Khong Anthony , Ripin Nina , de Vasconcelos Luisa Macedo , Spencer Sabrina , Parker Roy
Published: February 2022

Cells respond to cellular stress by forming stress granules, molecular condensates containing non-translating messenger ribonucleoproteins. Stress granules form during chemotherapy and promote cell survival and chemoresistance, although the mechanism of this effect is not understood. We provide several lines of evidence that stress granules enhance cell survival by promoting cellular quiescence. First, we see a correlation between spontaneous stress granule formation and cell-cycle exit under non-stress conditions. Second, cells deficient in proteins required for stress granule formation (G3BP1/2) are less likely to exit the cell cycle under non-stress, stress, and chemotherapeutic conditions. Third, rescuing stress granule formation in G3BP1/2 knockout cells restores the fraction of cycling cells to wild-type levels. Finally, cells with enhanced stress granule formation (ddx6 knockout cells) show an increased propensity to exit the cell cycle. These results suggest that stress granules are important regulators of cellular quiescence, which could enable the identification of new anti-chemoresistance therapies that target stress granules.
Identification of phenotype-specific networks from paired gene expression–cell shape imaging data
Authors: Barker Charlie George , Petsalaki Eirini , Giudice Girolamo , Sero Julia , Ekpenyong Emmanuel Nsa , Bakal Chris , Petsalaki Evangelia
Published: February 2022

The morphology of breast cancer cells is often used as an indicator of tumor severity and prognosis. Additionally, morphology can be used to identify more fine-grained, molecular developments within a cancer cell, such as transcriptomic changes and signaling pathway activity. Delineating the interface between morphology and signaling is important to understand the mechanical cues that a cell processes in order to undergo epithelial-to-mesenchymal transition and consequently metastasize. However, the exact regulatory systems that define these changes remain poorly characterized. In this study, we used a network-systems approach to integrate imaging data and RNA-seq expression data. Our workflow allowed the discovery of unbiased and context-specific gene expression signatures and cell signaling subnetworks relevant to the regulation of cell shape, rather than focusing on the identification of previously known, but not always representative, pathways. By constructing a cell-shape signaling network from shape-correlated gene expression modules and their upstream regulators, we found central roles for developmental pathways such as WNT and Notch, as well as evidence for the fine control of NF-kB signaling by numerous kinase and transcriptional regulators. Further analysis of our network implicates a gene expression module enriched in the RAP1 signaling pathway as a mediator between the sensing of mechanical stimuli and regulation of NF-kB activity, with specific relevance to cell shape in breast cancer.
Structural and functional analysis of the SET3 histone deacetylase complex
Authors: Reyes Alexis A. , Fishbain Susan , He Yuan
Published: February 2022

The SET3 complex (SET3C) is a seven-subunit histone deacetylase complex that is capable of transcriptional regulation. Methylated histone 3 marks recruit SET3C to the nucleosome, and the SET3C catalytic subunits deacetylate the histone 3 and 4 tails. There is very limited structural knowledge of the SET3C subunits, with most subunits having unknown structures or functions. Here, a catalytically active SET3 complex was endogenously purified from Saccharomyces cerevisiae and utilized for negative-stain electron microscopy (EM) to determine an apo model for the holo complex. The negative-stain EM 3D model revealed a three-lobe architecture, with each lobe extending from a central point.
Pivotal role of a conserved histidine in Escherichia coli ribonuclease HI as proposed by X-ray crystallography
Authors: Liao Zengwei , Oyama Takuji , Kitagawa Yumi , Katayanagi Katsuo , Morikawa Kosuke , Oda Masayuki
Published: February 2022

The ribonuclease (RNase) H family of enzymes catalyze the specific cleavage of RNA strands of RNA/DNA hybrid duplexes and play an important role in DNA replication and repair. Since the first report of the crystal structure of RNase HI, its catalytic mechanisms, which require metal ions, have been discussed based on numerous structural and functional analyses, including X-ray crystallography. In contrast, the function of the conserved histidine residue (His124 in Escherichia coli) in the flexible loop around the active site remains poorly understood, although an important role was suggested by NMR analyses. Here, novel high-resolution X-ray crystal structures of E. coli RNase HI are described, with a particular focus on the interactions of divalent cations with His124 oriented towards the active site. The enzyme–Mg2+ complex contains two metal ions in the active site, one of which has previously been observed. The second ion lies alongside the first and binds to His124 in an octahedral coordination scheme. In the enzyme–Zn2+ complex a single metal ion was found to bind to the active site, showing a tetrahedral coordination geometry with the surrounding atoms, including His124. These results provide structural evidence that His124 plays a crucial role in the catalytic activity of RNase HI by interacting weakly and transiently with metal ions in the catalytic center.
Making or remaking people and places through festivals: an island tourism perspective
Authors: Li Yiping , Lau Chammy
Published: February 2022

Purpose

This study aims to investigate two festivals that are held annually in Hong Kong, to explore the essence of festival meanings – the extent to which the perceived sociocultural benefits of festivals articulate the production of a sense of place (SOP) and its respective locality.

Design/methodology/approach

The study utilises a comparative analysis approach to examine visitors’ views of the festivals. It constructs a theoretical framework of the interaction mechanism between tourism and place evolution by relying largely on the notion of place as the centre of meanings. Data sources include interview, questionnaire, observation and a literature review.

Findings

The findings suggest festival meanings are crucial elements in fostering SOP and shaping the identification of place uniqueness. Being part of local tradition and tourism resource, festival representations are not only passive reflections of prevailing cultural values drawn from current stereotypes and images, but they also play a prominent role in shaping values, behaviours and identities by contributing to the socialisation process. Cultural regeneration through festivals may ultimately contribute to the ontological construction of a place.

Research limitations/implications

Given the unknown profile of the participants to both festivals, this study employed a convenience sampling method which might have limited the power of generalising the research outcome to other festivals. Besides, this study overlooked the potential differences (or lack of difference) in perceptions of the local residents who visited both festivals for the first time and other residents. Future studies may consider other aspects of festivals and place conceptions widely used in the tourism research field, to validate whether additional insights or hidden festival-to-place relationships can be found in the process of hosting and promoting festivals.

Originality/value

The existing studies of tourism–place relationship, especially those repelling scientific-positivist methodological paradigm, tend to overemphasise the role of tourism in unmaking places. In contrast, the interrogation of island festivals as the centre of meaning offers an alternative perspective to highlight the process that tourism dialectically contributes to place evolution. Tourism unmakes places while possessing a dialectic role of making places.
Experiences of workers with post-COVID-19 symptoms can signpost suitable workplace accommodations
Authors: Lunt Jenny , Hemming Sally , Elander James , Baraniak Amy , Burton Kim , Ellington Destiny
Published: February 2022

Purpose

The prevalence and multi-system nature of post-COVID-19 symptoms warrants clearer understanding of their work ability implications within the working age population. An exploratory survey was undertaken to provide empirical evidence of the work-relevant experiences of workers recovering from COVID-19.

Design/methodology/approach

A bespoke online survey based on a biopsychosocial framework ran between December 2020 and February 2021. It collected quantitative ratings of work ability and return-to-work status, qualitative responses about return-to-work experiences, obstacles and recommendations, along with views on employer benefits for making accommodations. A sample of 145 UK workers recovering from COVID-19 was recruited via social media, professional networks and industry contacts. Qualitative data was subject to thematic analysis. Participants were mainly from health/social care (50%) and educational settings (14%).

Findings

Just over 90% indicated that they had experienced at least some post-COVID-19 symptoms, notably fatigue and cognitive effects. For 55%, symptoms lasted longer than six months. Only 15% had managed a full return-to-work. Of the 88 who provided workability ratings, just 13 and 18% respectively rated their physical and mental workability as good or very good. Difficulties in resuming work were attributed to symptom unpredictability, their interaction with job demands, managing symptoms and demands in parallel, unhelpful attitudes and expectations. Manager and peer support was reported as variable.

Originality/value

Workplace health management characterised by flexible long-term collaborative return-to-work planning, supported by more COVID-centric absence policies and organisational cultures, appear pivotal for sustaining the return-to-work of the large segments of the global workforce affected by post-COVID-19 symptoms.
Femininity penalty: challenges and barriers faced by STEM woman entrepreneurs in an emerging economy
Authors: Adikaram Arosha S. , Razik Ruwaiha
Published: February 2022

Purpose

This study aims to explore the challenges and barriers encountered by Science, Technology, Engineering and Mathematics (STEM) women entrepreneurs in an emerging country context – Sri Lanka – within a context of strict gender role stereotyping beliefs and norms.

Design/methodology/approach

Using qualitative research methodology, 15 in-depth, in-person, semi-structured interviews were conducted with STEM women entrepreneurs using the theoretical lenses of intersectionality and social role theories in tandem.

Findings

Findings revealed that participants were confronted with an array of structural/administrative and gender-related challenges at the intersections of gender, entrepreneurship and characteristics mapped with STEM fields. Accordingly, lack of access and reach to networks and opportunities, procedural obstacles, difficulties in staffing, difficulties in obtaining finances, lack of understanding and support from family and society, difficulties in managing work-life, and legitimacy obstacles appear to restrain the participants in starting and running their businesses. These challenges have their roots embedded in a complex web of ideologies and expectations related to gender.

Originality/value

This research contributes to the scant body of literature on STEM women entrepreneurship in general and specifically to the literature on challenges facing STEM women entrepreneurs from the perspective of a non-Western – emerging economy, which is built on strong cultural strictures and gender ideologies.
Citizenship fatigue and psychological ownership among employees in family hotels: moderating effect of family management
Authors: Azila-Gbettor Edem Maxwell
Published: February 2022

Purpose

This paper examines the relationships between citizenship fatigue, organisational- and job-based psychological ownership and family management among family hotel employees in Ghana.

Design/methodology/approach

A total of 479 workers took part in the study by completing either a self-reported questionnaire or an interviewer-administered questionnaire. The hotels and respondents were selected using purposive and convenience sampling techniques, respectively. IBM SPSS version 21 and partial least squares structural equation model were used to process and analyse the data.

Findings

Citizenship fatigue was found to be a negative predictor of organisational- and job-based psychological ownership. Additionally, job- and organisational-based psychological ownership were positively predicted by family management. Furthermore, family management positively moderates the relation between citizenship fatigue and organisational- and job-based psychological ownership.

Originality/value

This study appears to be one of the first to have investigated a model linking family management, citizenship fatigue and psychological ownership in the family hotel context.
Changing tourists’ preferences in the hotel industry amid COVID-19 pandemic
Authors: Ongsakul Viput , Kajla Tanveer , Raj Sahil , Khoa Tran Tien , Ahmed Zafar U.
Published: February 2022

Purpose

The paper aims to find the preferences of different tourist type. Since, COVID-19 pandemic has brought the international hospitality industry to a standstill, there are some early signs of recovery. For this industry’s long-term recovery, the tourists’ changing preferences need to be analyzed. Moreover, with different types of tourists, a more nuanced and in-depth study is required to analyze the preferences of each tourist type.

Design/methodology/approach

The research focuses on the changing preferences of the tourist by comparatively analyzing the pre-COVID-19 and current COVID-19 phase. The study extracted online data from TripAdvisor and identified themes by applying Latent Dirichlet Allocation (LDA).

Findings

The study’s findings confirmed the change in preferences of the different types of tourists during the COVID-19 pandemic by performing thematic analysis. New themes emerged in the pandemic phase, providing more insights into tourists’ changing preferences in the current COVID-19 phase. The study also found that specific dominant themes in the pre-COVID-19 phase were replaced by new themes in the current COVID-19 phase.

Originality/value

To the best of the authors’ knowledge, this study is the first to compare the pre-COVID-19 and current COVID-19 phase themes to decipher the new themes that managers of the hotels should consider to win back tourists’ confidence during the pandemic. The unraveling of changing preferences of the different tourist types in the current COVID-19 pandemic is the novel contribution of the study.
Organizational capabilities and value creation for stakeholders: evidence from publicly traded companies
Authors: Barakat Simone R. , Boaventura João Maurício G. , Gabriel Marcelo L.D.S.
Published: February 2022

Purpose

This paper investigates specific organizational capabilities related to stakeholder relationship capability and the effect of the latter on value creation.

Design/methodology/approach

The authors propose and test whether organizational capabilities related to knowledge, engagement, moral and adaptation are positively related to stakeholder relationship capability. The authors then test the effect of stakeholder relationship capability on the creation of greater value for stakeholders. The study tests the hypotheses with paneled data composed of a sample of 116 publicly traded companies in Brazil for a total of 275 observations taken over three years.

Findings

The findings show that there is a positive and significant relationship between knowledge, engagement, moral and adaptation capabilities and stakeholder relationship capability. Stakeholder relationship capability has been shown to have a positive and significant effect on greater value creation for stakeholders.

Practical implications

Analysis of the processes and practices that serve as the basis for each capability is meaningful for managerial practices, as it offers a more detailed understanding of the routines pertaining to each capability. Practical discussions on operational procedure levels are a meaningful and attainable way for managers to apply stakeholder theory.

Originality/value

The investigation of the specific capabilities enabling value creation between the company and its stakeholders contributes to the discussion of the connections between stakeholder theory and the resource-based view (RBV).
Non-profit sport collaboration effectiveness: how do the partner selection factors and the collaboration process matter?
Authors: Lefebvre Arthur , Zeimers Géraldine , Zintz Thierry
Published: February 2022

Purpose

The purpose of this study is to investigate the relationship between partner selection factors and effectiveness of collaboration between sport clubs, as well as the mediating role of collaboration process dimensions on this relationship.

Design/methodology/approach

Data were collected via an online survey targeting representatives of sport clubs in Belgium (n = 631). Hierarchical multiple linear regression and mediation analyses were conducted using SPSS macro PROCESS.

Findings

The results indicate that two partner selection factors – shared vision and pre-existing relationships – are related to collaboration effectiveness. Moreover, this association is mediated by the collaboration process and, more particularly, by two informal (social) dimensions of this process: mutuality and trust.

Practical implications

Practically, this study suggests sport clubs representatives to chiefly pay attention to partner selection characteristics when deciding to collaborate with other sport clubs. They should assess their potential partners and eventually choose sport clubs that share a similar vision and/or with whom they already have pre-existing relationships.

Originality/value

This paper extends knowledge on non-profit sport collaboration effectiveness by empirically examining its relationship to the partner selection factors and collaboration process. It helps establish the distinctiveness of this collaboration form. The paper also brings new knowledge on the interconnections between antecedents, process and effectiveness of sport collaboration.