bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of a paediatric cohort of dyslipidaemic patients using unsupervised learning methods provides insights into the biochemical phenotypes of familial hypercholesterolemia
Authors: Correia Marta , Bourbon Mafalda , Gama-Carvalho Margarida
Published: July 2022

Familial hypercholesterolaemia (FH) is a highly prevalent silent disease with known genetic causes and poor prognosis if undiagnosed into adulthood. Characterised by high levels of total cholesterol and low-density lipoprotein cholesterol from birth, the majority of cases that fit the clinical criteria for FH do not present mutations in the disease associated genes and seem to result from polygenic and/or environmental causes. In this study we have addressed the heterogeneity of extended blood biochemical and genetic parameters across a cohort of children using an unsupervised hierarchical clustering approach. In addition to correctly classifying individuals into the two classes recognized in clinical studies for familial hypercholesterolaemia (with and without genetic diagnosis), a subset of patients with mixed characteristics was systematically identified as representing a third category. The careful analysis of biochemical, genetic, and anthropomorphic characteristics that constitute hallmarks of each group provides detailed insights into the characteristics of each group, contributing to unravel the complexity of FH and dyslipidaemic phenotypes. The results presented here may assist in the future identification of novel biomarkers to efficiently identify FH+ individuals.
Geometry-driven migration efficiency of autonomous epithelial cell clusters
Authors: Vercurysse Eléonore , Brückner David B. , Gómez-González Manuel , Remson Alexandre , Luciano Marine , Kalukula Yohalie , Rossetti Leone , Trepat Xavier , Hannezo Edouard , Gabriele Sylvain
Published: July 2022

The directed migration of epithelial cell collectives through coordinated movements plays a crucial role in various physiological and pathological processes and is increasingly understood at the level of large confluent monolayers. However, numerous processes rely on the migration of small groups of polarized epithelial clusters in complex environments, and their responses to external geometries remain poorly understood. To address this, we cultivated primary epithelial keratocyte tissues on adhesive microstripes, creating autonomous epithelial clusters with well-defined geometries. We showed that their migration efficiency is strongly influenced by the contact geometry, and the orientation of cell-cell contacts with respect to the direction of migration. To elucidate the underlying mechanisms, we systematically explored possible cell-cell interactions using a minimal active matter model. Our investigations revealed that a combination of velocity and polarity alignment with contact regulation of locomotion captures the experimental data, which we then validated via force and intracellular stress measurements. Furthermore, we predict that this combination of rules enables efficient navigation in complex geometries, which we confirm experimentally. Altogether, our findings provide a conceptual framework for extracting interaction rules governing the behavior of active systems interacting with physical boundaries, as well as designing principles for collective navigation in complex microenvironments.
Adaptive sentinel testing in workplace for COVID-19 pandemic
Authors: Li Yi , Chen Mandy , George Joshy , Liu Edison T. , Murthy Karuturi R. Krishna
Published: July 2022

Testing and isolation of infectious employees is one of the critical strategies to make the workplace safe during the pandemic for many organizations. Adaptive testing frequency reduces cost while keeping the pandemic under control at the workplace. However, most models aimed at estimating test frequencies were structured for municipalities or large organizations such as university campuses of highly mobile individuals. By contrast, the workplace exhibits distinct characteristics: employee positivity rate may be different from the local community because of rigorous protective measures at workplace, or self-selection of co-workers with common behavioral tendencies for adherence to pandemic mitigation guidelines. Moreover, dual exposure to COVID19 occurs at work and home that complicates transmission modelling, as does transmission tracing at the workplace. Hence, we developed bi-modal SEIR model and R-shiny tool that accounts for these differentiating factors to adaptively estimate the testing frequency for workplace. Our tool uses easily measurable parameters: community incidence rate, risks of acquiring infection from community and work-place, workforce size, and sensitivity of testing. Our model is best suited for moderate-sized organizations with low internal transmission rates, no-outward facing employees whose position demands frequent in-person interactions with the public, and low to medium population positivity rates. Simulations revealed that employee behavior in adherence to protective measures at work and in their community, and the onsite workforce size have large effects on testing frequency. Reducing workplace transmission rate through workplace mitigation protocols and higher sensitivity of the test deployed, though to a lesser extent. Furthermore, our simulations showed that sentinel testing leads to only marginal increase in the number of infections even for high community incidence rates, suggesting that this may be a cost-effective approach in future pandemics. We used our model to accurately guide testing regimen for three campuses of The Jackson Laboratory.
Accounting for endogenous effects in decision-making with a non-linear diffusion decision model
Authors: Hoxha Isabelle , Chevallier Sylvain , Ciarchi Matteo , Glasauer Stefan , Delorme Arnaud , Amorim Michel-Ange
Published: July 2022

The Drift-Diffusion Model (DDM) is widely accepted for two-alternative forced-choice decision paradigms thanks to its simple formalism and close fit to behavioral and neurophysiological data. However, this formalism presents strong limitations in capturing inter-trial dynamics at the single-trial level and endogenous influences. We propose a novel model, the non-linear Drift-Diffusion Model (nl-DDM), that addresses these issues by allowing the existence of several trajectories to the decision boundary. We show that the non-linear model performs better than the drift-diffusion model for an equivalent complexity. To give better intuition on the meaning of nl-DDM parameters, we compare the DDM and the nl-DDM through correlation analysis. This paper provides evidence of the functioning of our model as an extension of the DDM. Moreover, we show that the nl-DDM captures time effects better than the DDM. Our model paves the way toward more accurately analyzing across-trial variability for perceptual decisions and accounts for peri-stimulus influences.
Evidence for intercellular bridges and radial patterning of meiotic initiation in the human fetal ovary
Authors: Soygur Bikem , Derpinghaus Amber , Cunha Gerald R. , Baskin Laurence S. , Laird Diana J
Published: July 2022

Meiosis is the hallmark of reproduction. Our understanding of early oocyte development was improved by studying the spatiotemporal dynamics and mechanisms governing meiosis in mice, however, our knowledge of the meiotic initiation process in humans remains limited. Here, we utilized three-dimensional (3D) analysis to determine spatiotemporal dynamics of meiotic initiation in fetal human ovaries. Similar to mice, we found that the first meiotic cells appear in clusters in the center of human fetal ovaries as early at 9 weeks and that the initiation of meiosis propagates as a radial wave. Between developing germ cells in fetal human ovaries, we detected a component of the intercellular bridge, TEX14 protein. 3D quantification of germ cells in ovaries collected at the end of first trimester revealed, for the first time, considerable variation in the number of meiotic cells between individuals and asynchronous mitotic-meiotic transition. In addition to illustrating the geography of meiotic initiation in ovaries from the first trimester, we extended our 3D analysis approach to second trimester and showed heterogeneous spatial distribution of meiotic and non-meiotic germ cells in human fetal ovaries. This study is an important step towards better understanding of 3D structure of developing ovary and early stages of meiosis in humans.

Highlights

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Organic solvent-based clearing methods and confocal microscopy can be implemented to visualize and quantify germ cells in the intact human fetal ovary.

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Identification of a new, radial, pattern of meiotic initiation in the ovaries from the first trimester.

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Immunolocalization of the intercellular bridge component TEX14 between developing germ cells in the fetal ovary

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Maintenance of pre-meiotic germ cells in second trimester ovaries suggests less synchronous mitotic-meiotic stage transition.
Wnt5A Signaling Regulates Gut Bacterial Survival and T cell Homeostasis
Authors: Sengupta Soham , Jati Suborno , Maity Shreyasi , Sen Malini
Published: July 2022

In light of the demonstrated antagonism of Wnt5A signaling toward the growth of several bacterial pathogens, it was important to study the influence of Wnt5A on gut resident bacteria, and its outcome. Here we demonstrate that in contrast to inhibiting the survival of the established gut pathogen Salmonella enterica, Wnt5A clearly promotes the survival of the common gut commensals Enterococcus faecalis and Lactobacillus rhamnosus within macrophages through a self-perpetuating Wnt5A-Actin axis. A Wnt5A – Actin axis furthermore regulates the subsistence of the natural bacterial population of the Peyer’s patches, as is evident from the diminution in the countable bacterial colony forming units therein through the application of Wnt5A signaling and actin assembly inhibitors. Wnt5A dependency of the gut resident bacterial population is also manifested in the notable difference between the bacterial diversities associated with the feces and Peyer’s patches of Wnt5A heterozygous mice, which lack a functional copy of the Wnt5A gene, and the wild type counterparts. Alterations in gut commensal bacterial population resulting from either the lack of a copy of the Wnt5A gene or inhibitor mediated attenuation of Wnt5A signaling correlate with significantly different ratios of regulatory vs. activated CD4 T cells associated with the Peyer’s patches. Taken together, our study reveals the importance of Wnt5A signaling in shaping the gut commensal bacterial population and the T cell repertoire linked to it, thus unveiling a crucial control device for the maintenance of gut bacterial diversity and T cell homeostasis.

Significance Statement

Gut commensal bacterial diversity and T cell homeostasis are crucial entities of the host innate immune network. Yet molecular details of host directed signaling pathways that sustain the steady state of gut bacterial colonization and T cell activation remain unclear. Here we describe the protective role of a Wnt5A-Actin axis in the survival of several gut bacterial commensals, and its importance in shaping gut bacterial colonization and the associated T cell repertoire. This study opens up new avenues of investigation into the role of the Wnt5A-Actin axis in protection of the gut from dysbiosis related inflammatory disorders.
Critical roles for ‘housekeeping’ nucleases in Type III CRISPR-Cas immunity
Authors: Chou-Zheng Lucy , Hatoum-Aslan Asma
Published: July 2022

CRISPR-Cas systems are a family of adaptive immune systems that use small CRISPR RNAs (crRNAs) and CRISPR-associated (Cas) nucleases to protect prokaryotes from invading plasmids and viruses (i.e. phages). Type III systems launch a multi-layered immune response that relies upon both Cas and non-Cas cellular nucleases, and although the functions of Cas components have been well described, the identities and roles of non-Cas participants remain poorly understood. Previously, we showed that the Type III-A CRISPR-Cas system in Staphylococcus epidermidis employs two degradosome-associated nucleases, PNPase and RNase J2, to promote crRNA maturation and eliminate invading nucleic acids (Chou-Zheng and Hatoum-Aslan, 2019). Here, we identify RNase R as a third ‘housekeeping’ nuclease critical for immunity. We show that RNase R works in concert with PNPase to complete crRNA maturation, and identify specific interactions with Csm5, a member of the Type III effector complex, which facilitate nuclease recruitment/stimulation. Further, we demonstrate that RNase R and PNPase are required to maintain robust anti-plasmid immunity, particularly when targeted transcripts are sparse. Altogether, our findings expand the known repertoire of accessory nucleases required for Type III immunity and highlight the remarkable capacity of these systems to interface with diverse cellular pathways to ensure successful defense.
Topological screen identifies hundreds of Cp190 and CTCF dependent Drosophila chromatin insulator elements
Authors: Kahn Tatyana G. , Savitsky Mikhail , Kuong Chikuan , Jacquer Caroline , Cavalli Giacomo , Chang Jia-Ming , Schwartz Yuri B.
Published: July 2022

Drosophila insulators were the first DNA elements discovered to regulate gene expression by delimiting chromatin contacts. Remarkably, it is still unclear how many of them exist in the Drosophila genome and whether they have a pervasive impact on the genome folding. Contrary to vertebrates, there is no evidence that fly insulators block cohesin-mediated chromatin loop extrusion. Therefore, their mechanism of action remains an open question. To bridge these gaps, we mapped genomic contacts, transcriptomes and binding landscapes of insulator associated proteins in Drosophila cells deficient for CTCF and Cp190. With this approach, we discovered hundreds of chromatin insulator elements. Their study indicates that Drosophila insulators play a minor role in shaping the overall chromosome folding patterns but impact chromatin contacts locally at many individual loci. Our observations argue that Cp190 promotes co-binding of other insulator proteins and that the model, where Drosophila insulators block chromatin contacts by forming loops, needs revision. The extended catalogue of insulator elements presented here provides a significant new resource to study mechanisms that shape the folding of eukaryotic genomes.
Thalamus sends information about arousal but not valence to the amygdala
Authors: Leppla Chris A , Keyes Laurel R , Glober Gordon , Matthews Gillian A , Batra Kanha , Jay Maya , Feng Yu , Chen Hannah S , Mills Fergil , Delahanty Jeremy , Olson Jacob M , Nieh Edward H , Namburi Praneeth , Wildes Craig , Wichmann Romy , Beyeler Anna , Kimchi Eyal Y , Tye Kay M
Published: July 2022

Rationale

The basolateral amygdala (BLA) and medial geniculate nucleus of the thalamus (MGN) have both been shown to be necessary for the formation of associative learning. While the role that the BLA plays in this process has long been emphasized, the MGN has been less well-studied and surrounded by debate regarding whether the relay of sensory information is active or passive.

Objectives

We seek to understand the role the MGN has within the thalamoamgydala circuit in the formation of associative learning.

Methods

Here, we use optogenetics to dissect the MGN-BLA circuit and explore the specific subpopulations for evidence of learning and synthesis of information that could impact downstream BLA encoding. We employ various machine learning techniques to investigate function within neural subpopulations. We introduce a novel method to investigate tonic changes across trial-by-trial structure, which offers an alternative approach to traditional trial-averaging techniques.

Results

We find that the MGN appears to encode arousal but not valence, unlike the BLA which encodes for both. We find that the MGN and the BLA appear to react differently to expected and unexpected outcomes; the BLA biased responses toward reward prediction error and the MGN focused on anticipated punishment. We uncover evidence of tonic changes by visualizing changes across trials during inter-trial intervals (baseline epochs) for a subset of cells.

Conclusion

We conclude that the MGN-BLA projector population acts as both filter and transferer of information by relaying information about the salience of cues to the amygdala, but these signals are not valence-specified.

Preface

In tribute to Nadia Chaudhri, and her discoveries regarding how contexts can modulate the representation of cues in the amygdala (Sciascia et al., 2015), and other mesolimbic circuit components (Chaudhri et al., 2009, 2008; Valyear et al., 2020), here we explore what information processing precedes entry into the basolateral amygdala (BLA) from the thalamus and develop visualization approaches for exploring across-trial temporal dynamics in addition to within-trial population activity.
The 16S rRNA Gene Is Not a Precise Classifier for Luteibacter Species
Authors: Baltrus David A. , Carter Morgan E.
Published: July 2022

Luteibacter species are found throughout agricultural and plant associated microbial communities, and have largely been identified and classified through comparisons of the 16S rRNA genes. Through comparisons of 16S classifications with whole genome phylogenies and ANI, we highlight a somewhat unique situation whereby Luteibacter pinisoli and Luteibacter sp. 9143 would be classified as the same species using 16S rRNA sequences but are clearly differentiated by these other metrics. We present this case as an outlier, but also as an example for the challenges of classification solely using 16S rRNA gene sequences.
Regulatory networks driving expression of genes critical for glioblastoma are controlled by the transcription factor c-Jun and the pre-existing epigenetic modifications
Authors: Roura Adria-Jaume , Szadkowska Paulina , Poleszak Katarzyna , Dabrowski Michal J. , Ellert-Miklaszewska Aleksandra , Wojnicki Kamil , Ciechomska Iwona A. , Stepniak Karolina , Kaminska Bozena , Wojtas Bartosz
Published: July 2022

Background

Glioblastoma (GBM, WHO grade IV) is an aggressive, primary brain tumor. Despite gross surgery and forceful radio- and chemotherapy, survival of GBM patients did not improve over decades. Several studies reported transcription deregulation in GBMs but regulatory mechanisms driving overexpression of GBM-specific genes remain largely unknown. Transcription in open chromatin regions is directed by transcription factors (TFs) that bind to specific motifs, recruit co-activators/repressors and the transcriptional machinery. Identification of GBM-related TFs-gene regulatory networks may reveal new and targetable mechanisms of gliomagenesis.

Results

We predicted TFs-regulated networks in GBMs in silico and intersected them with putative TF binding sites identified in the accessible chromatin in human glioma cells and GBM patient samples. The Cancer Genome Atlas and Glioma Atlas datasets (DNA methylation, H3K27 acetylation, transcriptomic profiles) were explored to elucidate TFs-gene regulatory networks and effects of the epigenetic background. In contrast to the majority of tumors, c-Jun expression was higher in GBMs than in normal brain and c-Jun binding sites were found in multiple genes overexpressed in GBMs such as VIM, FOSL2 or UPP1. Binding of c-Jun to the VIM gene promoter is stronger in GBM cells than in cells derived from benign glioma as evidenced by gel shift and supershift assays. Regulatory regions of a majority of the c-Jun targets have distinct DNA methylation in GBMs suggesting the contribution of DNA methylation to the c-Jun-dependent regulation.

Conclusions

We identified distinct TFs-gene networks in GBMs compared to benign gliomas, a predominant role of c-Jun in controlling genes driving gliomagenesis and a modulatory role of DNA methylation.
Corruption of DNA End-Joining in Mammalian Chromosomes by Progerin Expression as Revealed by a Model Cell Culture System
Authors: Joudeh Liza A. , DiCintio Alannah J. , Ries Madeline R. , Gasperson Andrew S. , Griffin Kennedy E. , Robbins Victoria P. , Bonner Makenzie , Nolan Sarah , Black Emma , Waldman Alan S.
Published: July 2022

Hutchinson-Gilford Progeria Syndrome (HGPS) is a rare genetic condition characterized by features of accelerated aging and a life expectancy of about 14 years. HGPS is commonly caused by a point mutation in the LMNA gene which codes for lamin A, an essential component of the nuclear lamina. The HGPS mutation alters splicing of the LMNA transcript, leading to a truncated, farnesylated form of lamin A termed “progerin.” HGPS is associated with accumulation of genomic DNA double-strand breaks (DSBs), suggesting altered DNA repair. DSB repair normally occurs by either homologous recombination (HR), an accurate, templated form of repair, or by non-homologous end joining (NHEJ), an error-prone non-templated rejoining of DNA ends. Some NHEJ events occur via high-fidelity joining of DNA ends and we refer to such events as precise ligation (PL). Previously, we reported that expression of progerin correlated with increased NHEJ relative to HR. We now report on progerin’s impact on the nature of DNA end-joining. We used a model system involving a DNA end-joining reporter substrate integrated into the genome of cultured thymidine kinase-deficient mouse fibroblasts. Some cells were engineered to express progerin. DSBs were induced in the substrate through expression of endonuclease I-SceI, and DSB repair events were recovered through selection for thymidine kinase function. Progerin expression correlated with a significant shift away from PL and toward error-prone NHEJ. Our work suggests that progerin suppresses interactions between complementary sequences at DNA termini, shifting DSB repair toward low-fidelity DNA end-joining and perhaps contributing to aging through compromised genome stability.
Differential effects of ankle constraints on foot placement control between normal and split belt treadmills
Authors: Hos Mayra , van Iersel Lieke , van Leeuwen Moira , Bruijn Sjoerd M.
Published: July 2022

Mediolateral ankle moment control contributes to gait stability. Ankle moments can be constrained by walking with a shoe with a ridge underneath the sole, narrowing the mediolateral support surface. In our previous study, such ankle moment constraints resulted in an increased step width and a decrease in the degree of foot placement control, as defined by the percentage of variance in foot placement that can be explained by CoM state. However, since our previous study was performed on a split-belt treadmill and the narrow ridge could fit inside the gap between the belts, it is not evident whether these effects can be attributed to the constrained ankle moment control or to avoidance of this gap. Therefore, we investigated if the effects of ankle moment constraints are dependent on whether participants walk on a normal treadmill or a split-belt treadmill. We included fourteen healthy young adults. Walking with constrained ankle moment control resulted in a wider step width on both treadmills. Yet, the increase in step width was larger on the split-belt treadmill compared to on the normal treadmill. We only found a decreased degree of foot placement control on the split-belt treadmill, whilst the degree of foot placement control increased on the normal treadmill. We conclude that the effects of ankle moment constraints reported in our previous study were confounded by the use of a split-belt treadmill. For future research, we recommend using a normal treadmill whenever possible, because the gap in a split-belt treadmill might affect gait parameters.
Variable impact of geochemical gradients on the functional potential of bacteria, archaea, and phages from the permanently stratified Lac Pavin
Authors: Jaffe Alexander L. , Bardot Corinne , Le Jeune Anne-Hélène , Liu Jett , Colombet Jonathan , Perrière Fanny , Billard Hermine , Castelle Cindy J. , Lehours Anne-Catherine , Banfield Jillian F.
Published: July 2022

Permanently stratified lakes contain diverse microbial communities that vary with depth, and so serve as useful models for studying the relationships between microbial community structure and geochemistry. Recent work has shown that these lakes can also harbor numerous bacteria and archaea from novel lineages, including those from the Candidate Phyla Radiation (CPR). However, the extent to which geochemical stratification differentially impacts carbon metabolism and overall genetic potential in CPR bacteria compared to other organisms is not well defined. Here, we determine the distribution of microbial lineages along an oxygen gradient in Lac Pavin, a deep, stratified lake in central France, and examine the influence of this gradient on their metabolism. Genome-based analyses revealed an enrichment of distinct C1 and CO2 fixation pathways in the oxic lake interface and anoxic zone/sediments, suggesting that oxygen likely plays a role in structuring metabolic strategies in non-CPR bacteria and archaea. Notably, we find that oxidation of methane and its byproducts is largely spatially separated from methane production, which is mediated by diverse communities of sediment methanogens that vary on the centimeter scale. In contrast, we detected evidence for RuBisCO throughout the water column and sediments, including form II/III and form III-related enzymes encoded by CPR bacteria in the water column and DPANN archaea in the sediments. Overall, CPR bacteria and phages did not show strong signals of gene content differentiation by depth, despite the fact that distinct species groups populate different lake and sediment compartments. Thus, environmental gradients in Lac Pavin probably select for the capacities of CPR bacteria and phages to a lesser extent than other bacteria and archaea, possibly because selection on the former groups is indirect and depends on host characteristics.
ALIBY: ALFA Nanobody-Based Toolkit for Imaging and Biochemistry in Yeast
Authors: Akhuli Dipayan , Dhar Anubhav , Viji Aileen Sara , Bhojappa Bindu , Palani Saravanan
Published: July 2022

Specialized epitope tags continue to be an integral component in various biochemical and cell biological applications such as fluorescence microscopy, immunoblotting, immunoprecipitation, and protein purification. However, until recently, no single tag could offer this complete set of functionalities on its own. Here, we present a plasmid-based toolkit named ALIBY (ALFA Toolkit for Imaging and Biochemistry in Yeast) that provides a universal workflow to adopt the versatile ALFA tag/NbALFA system within the well-established model organism Saccharomyces cerevisiae. The kit comprises of tagging plasmids for labelling a protein-of-interest with the ALFA tag, and detection plasmids encoding a fluorescent protein-tagged NbALFA for live-cell imaging purposes. We demonstrate the suitability of ALIBY for visualizing the spatiotemporal localization of yeast proteins (i.e., cytoskeleton, nucleus, centrosome, divisome and exocyst) in live cells. Our approach has yielded an excellent signal-to-noise ratio without off-targeting or effect on cell growth. In summary, our yeast-specific toolkit aims to simplify and further advance the live-cell imaging of differentially abundant yeast proteins while also being suitable for biochemical applications.

Importance

In yeast research, conventional fluorescent protein tags and small epitope tags are widely used to study the spatiotemporal dynamics and activity of proteins. Though proven to be efficient, these tags lack the versatility for usage across different cell biological and biochemical studies of a given protein-of-interest. Therefore, there is an urgent need for a unified platform for visualization, biochemical, and functional analyses of proteins-of-interest in yeast. Herein, we have engineered ALIBY, a plasmid-based toolkit which expands the benefits of the recently developed ALFA tag/NbALFA system to studies in the well-established model organism Saccharomyces cerevisiae. We demonstrate that ALIBY provides a simple and versatile strain construction workflow for long duration live-cell imaging and biochemical applications in yeast.
Staphylococcus aureusBreast Implant Infection Isolates Display Recalcitrance to Antibiotic Pocket Irrigants
Authors: Duran Ramirez Jesus M. , Gomez Jana , Hanson Blake , Isa Taha , Myckatyn Terence , Walker Jennifer N
Published: July 2022

Breast implant-associated infections (BIAIs) are a common complication following breast prostheses placement and account for ∼100,000 infections annually. The frequency, high cost of treatment, and morbidity make BIAIs a significant health burden for women. Thus, effective BIAI prevention strategies are urgently needed. This study tests the efficacy of one infection prevention strategy: the use of a triple antibiotic pocket irrigant (TAPI) againstStaphylococcus aureus, the most common cause of BIAIs. TAPI, which consists of 50,000 U bacitracin, 1 g cefazolin, and 80 mg gentamicin diluted in 500 mL of saline, is used to irrigate the breast implant pocket during surgery. We usedin vitroandin vivoassays to test the efficacy of each antibiotic in TAPI, as well as TAPI at the concentration used during surgery. We found that planktonically grownS. aureusBIAI isolates displayed susceptibility to gentamicin, cefazolin, and TAPI. However, TAPI treatment enhanced biofilm formation of BIAI strains. Furthermore, we compared TAPI treatment of aS. aureusreference strain (JE2) to a BIAI isolate (117) in a mouse BIAI model. TAPI significantly reduced infection of JE2 at 1- and 7-days post infection (dpi). In contrast, BIAI strain 117 displayed high bacterial burdens in tissues and implants, which persisted out to 14-dpi despite TAPI treatment. Lastly, we demonstrated that TAPI was effective againstP. aeruginosareference (PAO1) and BIAI strainsin vitroandin vivo. Together, these data suggestS. aureusBIAI strains employ unique mechanisms to resist antibiotic prophylaxis treatment and promote chronic infection.
Surface integrity analysis of machined surface of Ni-Ti shape memory alloy during wire spark erosion machining
Authors: Singh Thakur , Kumar Jatinder , Misra Joy Prakash
Published: July 2022

Purpose

The purpose of this paper is to analyze the surface integrity, including recast layer thickness, surface crack density, X-ray diffractions study and microhardness for Ni53.49Ti46.51 shape memory alloy (SMA) during wire-spark erosion machining.

Design/methodology/approach

Four persuasive process parameters, that is, spark on time (SON), spark off time (SOFF), wire feed (WF) and spark gap voltage (SV), have been chosen for the current investigation. Efforts have been done to explore the effects of above said parameters on the machined surface of Ni-Ti SMA by embracing box Behnken design of response surface methodology (RSM). Cutting speed and ten-point mean roughness (Rz) has been taken into account as response variables. Analysis of variance test was also performed for both response parameters with the coefficient of determination (R2) 0.9610 for cutting speed and 0.9252 for ten-point mean Rz.

Findings

The recast layer thickness from 7.83 to 12.13 µm was developed near the machined surface at different parametric settings. The least surface crack density was found at the lowest value of ten-point mean Rz, while most surface crack density was identified at the highest value of cutting speed. The microhardness near the machined surface was increased by approximately 1.8 times bulk-hardness of Ni53.49Ti46.51 SMA.

Originality/value

Some researchers have done a study on average surface roughness, but very few investigators concentrated on ten-point mean Rz. Surface crack density is an essential aspect of machined parts; other researchers have seldom reported it. The novelty of this research work is that the influence of SON, SV, WF and SOFF on cutting speed, Rz, recast layer thickness, micro-hardness and surface crack density proximate the machined surface while machining workpiece material.
Metaverse: welcome to the new fraud marketplace
Authors: Smaili Nadia , de Rancourt-Raymond Audrey
Published: July 2022

Purpose

The purpose of this study is to examine the risks of the metaverse ecosystem. This study provides an overview of the metaverse and its evolution and discusses the various fraud risks it poses for organizations (including boards of directors, forensic accountants, auditors and accountants). Given the advantages of the metaverse and the growing interest it is attracting from organizations, this paper sheds light on the importance of mitigating its risks.

Design/methodology/approach

Based on a systematic review of the literature on the metaverse and analysis of the fraud triangle, this study examines the different fraud risks it poses. More specifically, this study analyzes 21 articles on the metaverse published between 2021 and 2022 and attempts to answer the following research questions: What are the risks inherent in the metaverse? What are the fraud risks associated with it? What are the opportunities and pressures it brings? What is the rationalization underlying its use? This study conducts the analysis on two levels, that of the individual (user) and that of the organization. This paper summarizes the findings of publications on the metaverse in 2021 and 2022 to discover its various definitions and the opportunities and risks it represents.

Findings

This paper offers an insightful discussion of the advantages and risks the metaverse can bring. Because this analysis shows that any organization could be vulnerable to metaverse risks, this study provides organizations with strategies to deter, detect and prevent fraud and reputational risks. Regulatory bodies, financial authorities, board of directors and fraud investigators should all consider these risks before investing in the metaverse.

Originality/value

This paper adds new insights to the scarce research on the metaverse and cybersecurity by exploring the opportunities and risks it presents. It has several implications for organizations, boards of directors, management and regulatory authorities.
Remote OPAC users’ search query reformulation (SQR) patterns: a transaction log analysis
Authors: Ndumbaro Faraja
Published: July 2022

Purpose

Users' search logs are implicit feedbacks on how searchers interact with online information retrieval (IR) systems. The purpose of this paper is to analyze search query reformulation (SQR) patterns of University of Dar es Salaam remote OPAC users.

Design/methodology/approach

Qualitative and quantitative analysis of transaction logs were employed to ascertain the characteristics of search queries and the patterns in which remote OPAC users reformulate their search queries. The study covered a period of six months, commencing from January to June 2019.

Findings

A total of 30,474 search hits were submitted by remote OPAC users during the period under study. Individuals from academic and research institutions, computing consortia, and telecommunication companies are the main users of the system. Most of the searches originated from North America and Europe, with few searches coming from China and India. Besides improving search results, SQRs are linked with the existence of multiple information demands as manifested by the use of heterogeneous headwords within individual search episodes.

Research limitations/implications

Data collected covered only six months. Similarly, it was however not possible to analyze users' search query formulation within specific contexts such as task-based information searching.

Practical implications

A query recommendation system should be integrated into the OPAC functionalities to improve users' search experiences. Alternatively, there should be a migration to a new system that offers more advanced search features and functionalities.

Originality/value

The study has contributed new insights in SQR studies particularly on how non-institutional affiliated users translate their information needs into search queries during information searching processes.

Peer review

The peer review history for this article is available at: https://publons.com/publon/10.1108/OIR-09-2020-0389
It takes a community to maintain a tree hollow: Food web complexity enhances decomposition and wood mould production
Authors: Wetherbee Ross , Birkemoe Tone , Asplund Johan , Renčo Marek , Sverdrup‐Thygeson Anne
Published: July 2022

Veteran trees are keystone structures and play vital roles in ecosystems. Tree hollows, which are filled with a mix of leaves and wood that is transformed by the biotic community into wood mould, represent an important microhabitat. Tree hollow communities consist of three major groups of organisms: microbes, mesofauna (nematodes, mites and springtails) and macrofauna (beetles, millipedes and other insects). Little is known about the interplay between associated biota and their importance for decomposition and wood mould production. The aim of this study was to test how initial food web complexity in artificial tree hollows influences community structure, decomposition, and wood mould production. We used large wooden boxes to imitate natural hollows, and mounted them on 20 veteran oaks in Southern Norway. The food webs were manipulated into three levels: (i) a complex community with macrofauna and mesofauna, (ii) a simple community without macrofauna, and (iii) only the defaunated material. Three boxes (one of each treatment, N = 60 boxes) were mounted on each oak and left in the field from May 2017 to October 2019 (28 months). After the field experiment, macrofauna and mesofauna were collected and identified, mass loss in the boxes was determined, and nitrogen and phosphorus concentrations in the wood mould were measured. We found that the complex community treatment had the greatest diversity of beetles and the highest number of predatory macrofauna. The nematodes within the complex community treatment had greater trophic structuring with K‐selected species associated with stable conditions. The nematodes communities also indicated that the complex community had a balanced decomposition pathway, while the simple community was dominated by fungi and the defaunated community by bacteria. Lastly, we found that the boxes with the complex community treatment had the highest overall rate of mass loss, and greater amounts of wood mould with higher concentrations of nitrogen and phosphorus. Our results indicate that macrofauna in artificial hollows increase trophic structuring, enhance decomposition rates and wood mould production, and mediate the decomposition pathway. These findings highlight the importance of food web complexity for promoting biodiversity and ecosystem functioning in veteran tree hollows.

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One Religion, Two Paths: Making Sense of US and Belgian Catholic Hospitals' Approaches to IVF
Authors: Martucci Jessica , Stahl Ronit Y. , Vandendriessche Joris
Published: July 2022

This article comparatively analyses the development of Catholic hospitals' approaches to In‐Vitro Fertilisation (IVF) in Belgium and the U.S. Our comparison highlights the different cultures of Catholic healthcare in each of these countries, and their different relation to Vatican opinion on medical matters. We first discuss the roots of Catholic healthcare in both countries and the history of IVF as a viable medical therapy for infertility. Next, we turn to the Catholic University of Leuven (Belgium) where an infrastructure for bioethics brought patient needs and progressive thinking into conversation with Church pronouncements, creating room for IVF within the walls of a Catholic hospital. We then contrast this trajectory with the subsequent versions of the Ethical and Religious Directives for Catholic Health Care (ERDs) in the U.S. The ERDs came to serve as a binding policy document for American clinicians and centralized medical authority in the hands of the U.S. bishops, who adhered closely to the Vatican ban. Comparing the two contexts, we demonstrate how within the Catholic Church approaches to IVF unfolded along two different paths: one of restriction through a unified conservative voice, controlled by the bishops (U.S.), and one of bio‐ethical decision‐making in dialogue with progressive Catholicism (Belgium).
Psychological well‐being and salivary markers of inflammation: The moderating effect of age
Authors: Lee Sung‐Ha , Chey Jeanyung , Ahn Woo‐Young , Woo Choong‐Wan , Youm Yoosik , Kim Hairin , Oh Naeun , Park Hyeyoung , Gim Suhwan , Lee Eunjin , Choi Incheol
Published: July 2022

Increasing evidence suggests a significant impact of higher psychological well‐being (PWB) on health outcomes; however, such associations have been studied exclusively in middle‐aged to older adults. This study examined the aging effect on PWB measures as well as the moderating effect of age on the link between PWB and inflammation, using salivary markers by comparing the younger adults (n = 127; Mage = 22.98 years) versus older adults (n = 75; Mage = 75.60 years). Older adults showed significantly lower levels of PWB, particularly regarding purpose in life and personal growth. Moreover, higher purpose in life was associated with lower salivary IL‐1ß and IL‐6 (b = 0.83, p < .001; b = 0.81, p < .01) only in the older adult group but not in younger adults. These findings highlight the potential buffering effect of the sense of living well on physiological pathways in later life.
Vancomycin‐resistant Enterococcus faecium: should we screen on admission?
Authors: Hertz Frederik Boetius , Nielsen Karen Leth , Olsen Markus Harboe , Ebdrup Søren Røddik , Nielsen Christina , Kirkby Nikolai Soren , Frimodt‐Møller Niels , Møller Kirsten
Published: July 2022

Denmark has experienced an increase in the proportion of invasive vancomycin‐resistant Enterococcus faecium (VRE) since 2002 (e.g. <4% in 2015, 7.1% in 2017 and 12% in 2018). At Rigshospitalet, we employ active screening at departments with high prevalence or in case of outbreaks. This includes the collection of rectal swabs specifically for VRE screening. Our purpose was to describe the carrier prevalence of vancomycin‐resistant enterococci among acute patients admitted to the Neurointensive Care Unit, Department of Neuroanaesthesiology, Rigshospitalet, Copenhagen, Denmark (NICU). Between April 2018 and January 2019, we investigated 99 consecutive rectal swabs from patients admitted to NICU. The primary outcome was prevalence of VRE carriage. The median age was 64 years (range 23–87) and gender was equally distributed (Female = 47, Male = 46). 26 (28%) had previously been admitted within 179 days and 67 patients (72%) had no hospital admissions within 180 days prior to the admission to NICU. Of the 93 rectal swabs, 2 (2%, 95% CI 0.26–7.55%) were positive for vanA and none were positive for vanB. Routine screening of all patients at admission may be effective in hospital settings with high VRE prevalence, whereas the benefit of screening for VRE in hospitals with a low prevalence may be restricted to specific patient populations.
Natural naphthoquinones and their derivatives as potential drug molecules against trypanosome parasites
Authors: Rani Ruma , Sethi Khushboo , Kumar Sanjay , Varma Rajender S. , Kumar Rajender
Published: July 2022

Over the past decades, a number of 1,4‐naphthoquinones have been isolated from natural resources and several of naphthoquinone derivatives with diverse structural motif have been synthesized; they possess a multitude of biochemical properties and modulate numerous pharmacological roles that offer new targets for addressing the challenges pertaining to novel drug developments. Among natural naphthoquinones, lapachol, α‐lapachone, β‐lapachone, lawsone, juglone, and plumbagin have been evaluated for its potential as antitrypanosomal activities. The chemotherapeutic drugs available for combating human trypanosomiasis, that is, American trypanosomiasis and African trypanosomiasis caused by Trypanosoma cruzi and Trypanosoma brucei, respectively, and animal tripanosomosis caused by Trypanosoma evansi have a problem of drug resistance and several toxic effect. Therefore, search of alternative effective drug molecules, without toxic effects, have enthused the researchers for searching new drug entity with potential clinical efficacy. In the search for new antitrypanosomal compound, this review focuses on different natural quinones and their synthetic derivatives associated with antitrypanosomal studies. In this context, this review will be useful for the development of new antitrypanosomal drugs mainly based on different structural modification of natural and synthetic naphthoquinones.
Financial disclosure transparency and employee wages
Authors: Bai John (Jianqiu) , Serfling Matthew , Shaikh Sarah
Published: July 2022

We test the hypothesis that less transparent financial disclosures are an undesirable firm attribute that increase the amount of information and unemployment risk that employees bear, resulting in a wage premium. Using establishment‐level wage data from the U.S. Census Bureau, we document that firms with less transparent disclosures pay their employees more, especially when employees bear greater information acquisition costs, have more influence in the wage‐setting process, and own more stock. Our results hold after utilizing instrumental variables and exploiting two quasi‐natural experiments. Overall, our results suggest that disclosure choices can generate externalities on an important group of stakeholders.
Hinotori Surgical Robot System, a novel robot‐assisted surgical platform: Preclinical and clinical evaluation
Authors: Hinata Nobuyuki , Yamaguchi Raizo , Kusuhara Yoshito , Kanayama Hiroomi , Kohjimoto Yasuo , Hara Isao , Fujisawa Masato
Published: July 2022

Objectives

To evaluate the safety and efficacy of the hinotori™ Surgical Robot System in preclinical and clinical studies.

Methods

Preclinical studies on 10 living female porcine and four fresh male cadavers were conducted. Different types of urologic surgical procedures were performed by experienced urological surgeons using the hinotori system: partial nephrectomy, vesicourethral anastomosis, and pelvic lymph node dissection in porcine, and partial nephrectomy, radical prostatectomy, and pelvic lymph node dissection in cadavers. In a multi‐institutional single‐arm clinical study, radical prostatectomy was performed in 30 patients with localized prostate cancer to evaluate safety outcomes. The primary endpoint was safety profiles, including device errors and perioperative complications, and the secondary endpoints were console time, blood loss, and positive surgical margin rate.

Results

The preclinical results were similar to those reported for the daVinci surgical system. The performance of the hinotori was equivalent to that of the daVinci surgical system, based on a global assessment by the surgeons. Safety was confirmed in a first‐in‐human clinical study of robot‐assisted radical prostatectomy using hinotori in 30 patients. The procedures were completed as planned in all cases, and three (10%) perioperative adverse events were observed.

Conclusions

The safety of the newly developed hinotori surgical system was shown in the present preclinical and clinical studies. Further studies are required to confirm its clinical efficacy.
Avoiding the Death Risk of Avoiding a Dread Risk
Authors: López-Rousseau Alejandro
Published: July 2022

After the airplane attacks of September 11, 2001, in the United States, many Americans drove instead of flying, to avoid the risk of terrorism. As a result, there were extra car accidents in which many people died. This study tested whether a similar effect occurred in Spain after the train bombings of March 11, 2004, in Madrid. Data on train travel, highway traffic, and fatal highway accidents were analyzed for the months immediately following March 11. Results show that, like Americans, Spaniards avoided the dread risk of terror attacks, but unlike Americans, they did not confront the death risk of fatal accidents instead. A sociopolitical interpretation for these findings is offered.