bluuebunny/crossref_metadata_2025 huggingface dataset:
Neutrophil and NETosis Modulation in Traumatic Heterotopic Ossification
Authors: Nunez Johanna H. , Juan Conan , Sun Yuxiao , Hong Jonathan , Bancroft Alec C. , Hwang Charles , Medrano Jessica , Huber Amanda K. , Tower Robert J , Levi Benjamin
Published: June 2023

Objective:

To characterize the role of neutrophil extracellular traps (NETs) in heterotopic ossification formation and progression and to use mechanical and pharmacological methods to decrease NETosis and mitigate heterotopic ossification (HO) formation.

Summary Background Data:

Traumatic heterotopic ossification (HO) is the aberrant osteochondral differentiation of mesenchymal progenitor cells following traumatic injury, burns, or surgery. While the innate immune response has been shown to be necessary for HO formation, the specific immune cell phenotype and function remains unknown. Neutrophils, one of the earliest immune cells to respond following HO inducing injuries, can extrude DNA, forming highly inflammatory neutrophil extracellular traps. We hypothesized that neutrophils and NETs would be diagnostic biomarkers and therapeutic targets for the detection and mitigation of HO.

Methods:

C57BL6J mice underwent burn/tenotomy (BT) (a well-established mouse model of HO) or a non-HO-forming sham injury. These mice were either 1) ambulated ad libitum, 2) ambulated ad libitum with daily intraperitoneal hydroxychloroquine (HCQ), ODN-2088 (both known to affect NETosis pathways), or control injections, or 3) had the injured hind limb immobilized. Single-cell analysis was performed to analyze neutrophils, NETosis, and downstream signaling following the HO-forming injury. Immunofluorescence (IF) microscopy was used to visualize NETosis at the HO site and neutrophils were identified using flow cytometry. Serum and cell lysates from HO sites were analyzed using ELISA for MPO-DNA and ELA2-DNA complexes to identify NETosis. Micro-CT (uCT) was performed on all groups to analyze the HO volume.

Results:

Molecular and transcriptional analyses revealed the presence of NETs within the HO injury site, which peaked in the early phases after injury. These NETs were highly restricted to the HO site, with gene signatures derived from both in vitro NET induction and clinical neutrophil characterizations showing a high degree of NET “priming” at the site of injury, but not in neutrophils in the blood or bone marrow. Cell-cell communication analyses revealed that this localized NET formation coincided with high levels of Toll-like receptor (TLR) signaling specific to neutrophils at the injury site. Reducing the overall neutrophil abundance within the injury site, either pharmacologically through treatment with hydroxychloroquine (HCQ), the TLR9 inhibitor OPN-2088, or mechanical treatment with limb offloading, results in mitigation of HO formation.

Conclusions:

These data provide a further understanding of the ability of neutrophils to form NETs at the injury site, clarify the role of neutrophils in HO, and identify potential diagnostic and therapeutic targets for HO mitigation.
Association of Pelvic Floor Disorders, Perceived Psychological Stress, and Military Service in U.S. Navy Servicewomen: A Cross-Sectional Survey
Authors: Greer Joy A. , Heye Kristen R. , McGlynn Andrea , Johansson Shorty , Vaccaro Christine M.
Published: June 2023

Importance

Pelvic floor disorders (PFDs) are linked to psychological stress and decreased work performance in civilian populations. Higher psychological stress is reported in female active-duty servicewomen (ADSW), which affects military readiness.

Objective

This study sought to associate PFDs, work-related challenges, and psychological stress in ADSW.

Study Design

We conducted a single-site, cross-sectional survey of ADSW seeking care in the urogynecology, family medicine, and women's health clinics between December 2018 and February 2020 using validated questionnaires to determine the prevalence of PFDs and the association with psychological stress, performance of military duties, and continued military service.

Results

One hundred seventy-eight U.S. Navy ADSW responded; most were seeking care for PFDs. The reported prevalence rates of PFDs were as follows: urinary incontinence, 53.7%; pelvic organ prolapse, 16.3%; fecal incontinence, 73.2%; and interstitial cystitis/bladder pain syndrome, 20.3%. Active-duty servicewomen with PFDs were more likely to have higher psychological stress scores (22.5 ± 3.7 vs 20.5 ± 4.2, P = 0.002) and body composition failures (22.0% vs 7.3%, P = 0.012), yet more strongly consider remaining on active service if they reported urinary incontinence (22.8% vs 1.8%) or interstitial cystitis/bladder pain syndrome (19.5% vs 1.8%; all P ≤ 0.001). No significant differences were noted in physical fitness failures or other military duties.

Conclusions

For these U.S. Navy ADSW with PFDs, there was no significant difference in duty performance but reported psychological stress levels were higher. The presence of PFD was associated with women more strongly considering ongoing military service compared with other factors such as family, job, or career path.
Comparison of Readmission Rates for Same-Day Versus Next-Day Discharge After Benign Vaginal Hysterectomy
Authors: Robison Elizabeth H. , Burger Kristina A. , Nekkanti Silpa , Hundley Andrew F. , Hudson Catherine O.
Published: June 2023

Importance

Same-day discharge (SDD) for laparoscopic hysterectomy is shown to be safe and acceptable, but data for vaginal hysterectomy (VH) are lacking.

Objective

The aim of this study was to compare 30-day readmission rates, timing, and reasons for readmission for SDD versus next-day discharge (NDD) after VH.

Study Design

This was a retrospective cohort study using the American College of Surgeons National Surgical Quality Improvement Program database from 2012 to 2019. Cases of VH with or without prolapse repair were identified by Current Procedural Terminology codes. The primary outcome was 30-day readmissions after SDD versus NDD. Secondary outcomes included reasons for and time to readmission and a subanalysis evaluating 30-day readmissions for those with prolapse repair. Unadjusted and adjusted odds ratios were determined using univariate and multivariate analyses.

Results

There were 24,277 women included; 4,073 (16.8%) were SDD. The 30-day readmission rate was low (2.0%; 95% confidence interval [CI], 1.8–2.2%), with no difference in odds of readmission for SDD versus NDD after VH in multivariate analysis (SDD adjusted odds ratio [aOR], 0.9; 95% CI, 0.7–1.2). Results were similar in our subanalysis of VH with prolapse surgery (SDD aOR, 0.94; 95% CI, 0.55–1.62). Median time to readmission was 11 days and did not differ (SDD interquartile range, 5, 16 [range, 0–29] vs NDD, 7, 16 [range, 1–30]; Z = −1.30; P = 0.193). The most common reasons for readmission were bleeding (15.9%), infection (11.6%), bowel obstruction (8.7%), pain (6.8%), and nausea/emesis (6.8%).

Conclusions

Same-day discharge after VH did not have an increased odds of 30-day readmission compared with NDD. This study, with preexisting data, supports the practice of SDD after benign VH in low-risk patients.
Five-Year Collis-Nissen Gastroplasty Outcomes for Type III-IV Hiatal Hernia with Short Esophagus: A Prospective Observational Study
Authors: Montcusí Blanca , Jaume-Bottcher Sofia , Álvarez Idoia , Ramón José M , Sánchez-Parrilla Juan , Grande Luis , Pera Manuel
Published: June 2023

Background:

To assess the 5-year outcomes of patients undergoing Collis-Nissen gastroplasty for type III-IV hiatal hernia with short esophagus.

Study Design:

From a prospective observational cohort of patients who underwent antireflux surgery for type III-IV hiatal hernia between 2009 and 2020, those with short esophagus (abdominal length <2.5 cm) in whom a Collis-Nissen procedure was performed and reached at least 5 years of follow-up were identified. Hernia recurrence, patient´s symptoms, and quality of life were assessed annually by barium meal X-ray, upper endoscopy, and validated symptoms and Quality of Life (QOLRAD) questionnaires.

Results:

Of the 114 patients with Collis-Nissen gastroplasty, 80 patients who completed a 5-year follow-up were included (mean age 71 years). There were no postoperative leaks or deaths. Recurrent hiatal hernia (any size) was identified in 7 patients (8.8%). Heartburn, regurgitation, chest pain, and cough were significantly improved at each follow-up interval (P < 0.05). Preoperative dysphagia disappeared or improved in 26 of 30 patients, while new-onset dysphagia occurred in 6. Mean postoperative quality of life scores significantly improved at all dimensions (P < 0.05).

Conclusions:

Collis gastroplasty combined with Nissen fundoplication provides low hernia recurrence, good control of symptoms, and improved quality of life in patients with large hiatal hernia and short esophagus.
Omicron vs. the Rest: Assessing the Competitive Dynamics and Coinfection Scenarios of COVID-19 Strains on a Social Network
Authors: Jabraeilian Hamed , Jamali Yousef
Published: June 2023

The rapid spread and evolving nature of COVID-19 variants have raised concerns regarding their competitive dynamics and coinfection scenarios. In this study, we assess the competitive interactions between the Omicron variant and other prominent variants (Alpha, Beta, and Delta) on a social network, considering both single infection and coinfection states. Using the SIRS model, we simulate the progression of these variants and analyze their impact on infection rates, mortality, and overall disease burden. Our findings demonstrate that the Alpha and Beta strains exhibit comparable contagion levels, with the Alpha strain displaying higher infection and mortality rates. Moreover, the Delta strain emerges as the most prevalent and virulent strain, surpassing the other variants. When introduced alongside the less virulent Omicron strain, the Delta strain results in higher infection and mortality rates. However, the Omicron strain’s dominance leads to an overall increase in disease statistics. Remarkably, our study highlights the efficacy of the Omicron variant in supplanting more virulent strains and its potential role in mitigating the spread of infectious diseases. The Omicron strain demonstrates a competitive advantage over the other variants, suggesting its potential to reduce the severity of the disease and alleviate the burden on healthcare systems. These findings underscore the importance of monitoring and understanding the dynamics of COVID-19 variants, as they can inform effective prevention and mitigation strategies, particularly with the emergence of variants that possess a relative advantage in controlling disease transmission.
Spontaneous activity in peripheral sensory nerves – a systematic review
Authors: Choi Dongchan , Goodwin George , Stevens Edward B. , Soliman Nadia , Namer Barbara , Denk Franziska
Published: June 2023

In the peripheral nervous system, spontaneous activity in sensory neurons is considered to be one of the two main drivers of chronic pain states, alongside neuronal sensitization. Despite this, the precise nature and timing of this spontaneous activity in neuropathic pain is not well-established.

Here, we have carried out a systematic search and data extraction of existing electrophysiological literature to shed light on which fibre types have been shown to maintain spontaneous activity and over what time frame. We examined bothin vivorecordings of pre-clinical models of neuropathic pain, as well as microneurography recordings in humans.

Our analyses reveal that there is broad agreement on the presence of spontaneous activity in neuropathic pain conditions, even months after injury or years after onset of neuropathic symptoms in humans. However, due to the highly specialised nature of the electrophysiological methods used to measure spontaneous activity, there is also a high degree of variability and uncertainty around these results. Specifically, there are very few directly controlled experiments, with little directly comparable data between human and animals.

Given that spontaneous peripheral neuron activity is considered to be a key mechanistic feature of chronic pain conditions, it may be beneficial to conduct further experiments in this space.
Natural monobacterial environments modulate viral infection inCaenorhabditis elegans
Authors: González Rubén , Félix Marie-Anne
Published: June 2023

The microbes associated with an organism play a pivotal role in modulating their host susceptibility to viral infections. However, the influence of individual microbes on viral infections is not well understood. Here, we examined the impact of 67 naturally bacterial associates onCaenorhabditis eleganssusceptibility to Orsay virus. Our findings reveal that viral infection ofC. elegansis significantly influenced by monobacterial environments. The majority of tested natural bacterial environments reducedC. elegans viral infection while some increased susceptibility compared to anEscherichia colienvironmental reference. The reduction in viral infection is not caused by degradation of the virions or poor nutrition ofC. elegansby the bacteria. The reduction in viral infection does not require known antiviral responses, including RNA interference and transcriptional regulation downstream of the RIG-I homolog DRH-1. However, one bacterium,LelliottiaJUb276, reduced susceptibility but does not induce resistance to viral infection indrh-1mutants. Our research underscores the importance of considering the natural biotic environment in studies of viral infections and provides insights for future research on host-microbes-virus interactions and viral immunity.

AUTHOR CONTRIBUTIONS

Conceptualization: RG, MAF; Formal analysis: RG; Investigation: RG; Resources: MAF; Data Curation: RG; Writing - Original Draft: RG, MAF; Writing - Review & Editing: RG, MAF; Visualization: RG; Supervision: MAF; Project administration: RG, MAF; Funding acquisition: RG, MAF.
Digital-robotic markers for hallucinations in Parkinson’s disease
Authors: Albert Louis , Potheegadoo Jevita , Herbelin Bruno , Bernasconi Fosco , Blanke Olaf
Published: June 2023

Hallucinations are frequent non-motor symptoms in Parkinson’s disease (PD) associated with dementia and higher mortality. Despite their high clinical relevance, current assessments of hallucinations are based on verbal self-reports and interviews that are limited by important biases. Here, we used virtual reality (VR), robotics, and digital online technology to quantify presence hallucination (PH) in laboratory and home-based settings. We establish that elevated numerosity estimation of digital humans in VR is a digital marker for experimentally induced PH in healthy participants, as confirmed across several control conditions and analyses. We translated the digital marker (numerosity estimation) to an online procedure that 170 PD patients carried out remotely at their homes, revealing that PD patients with disease-related PH (but not control PD patients) showed higher numerosity estimation. Numerosity estimation enables quantitative monitoring of hallucinations, is an easy-to-use unobtrusive online method, reaching people far away from medical centers, translating neuroscientific findings using robotics and VR, to patients’ homes without specific equipment or trained staff.
Demystifying the Visual Word Form Area: Visual and Nonvisual Response Properties of Ventral Temporal Cortex with precision fMRI
Authors: Li Jin , Hiersche Kelly J. , Saygin Zeynep M.
Published: June 2023

The functional nature of the visual word form area (VWFA), a region in left ventrotemporal cortex (VTC), remains debated after over two decades of investigation. Here we use precision fMRI to comprehensively examine the VWFA’s responses to numerous visual and nonvisual stimuli. We find that the VWFA is a distinct region that while showing moderate activation to non-word visual stimuli, its response to words towers above other conditions. Interestingly, the VWFA is also the only VTC region uniquely engaged in auditory language processing, in contrast with the ubiquitous attentional effect within the VTC. However, this language selectivity is dwarfed by its visual responses. This suggests the VWFA primarily functions as a visual look-up orthographic dictionary. Searching within the entire VTC further reveals an additional language cluster in anterior fusiform preferring general visual semantics. Our detailed examination of the VWFA in direct comparison to other VTC regions clarifies the long-standing controversies about its functionality.
The transcriptional regulator EarA and intergenic terminator sequences modulate archaellation inPyrococcus furiosus
Authors: Stöckl Richard , Nißl Laura , Reichelt Robert , Rachel Reinhard , Grohmann Dina , Grünberger Felix
Published: June 2023

The regulation of archaellation, the formation of archaeal flagella-like appendages called archaella, is crucial for the motility, adhesion, and survival of archaeal organisms. Although the heavily archaellated and highly motilePyrococcus furiosusis a key model organism for understanding the production and function of archaella in Euryarchaea, the transcriptional regulation of archaellum assembly is so far unknown. Here we show that the transcription factor EarA is the master regulator of the archaellum (arl) operon transcription, which is further modulated by intergenic transcription termination signals.EarAdeletion or overexpression strains demonstrate that EarA is essential for archaellation inP. furiosusand governs the degree of archaellation. Providing a single-molecule update on the transcriptional landscape of thearloperon inP. furiosus, we identify sequence motifs for EarA binding upstream of thearloperon and intergenic terminator sequences as critical elements for fine-tuning the expression of the multicistronicarlcluster. Furthermore, transcriptome re-analysis across differentThermococcalesspecies demonstrated a heterogeneous production of major archaellins, suggesting a more diverse composition of archaella than previously recognized. Overall, our study provides novel insights into the transcriptional regulation of archaellation and highlights the essential role of EarA inPyrococcus furiosus. These findings advance our understanding of the mechanisms governing archaellation and have implications for the functional diversity of archaella.
Helical reconstruction of VP39 reveals principles for baculovirus nucleocapsid assembly
Authors: Benning Friederike M. C. , Jenni Simon , Garcia Coby Y. , Nguyen Tran H. , Zhang Xuewu , Chao Luke H.
Published: June 2023

Baculoviruses are insect-infecting pathogens with wide applications as biological pesticides,in vitroprotein production vehicles and gene therapy tools. Its cylindrical nucleocapsid, which encapsulates and protects the circular double-stranded viral DNA encoding proteins for viral replication and entry, is formed by the highly conserved major capsid protein VP39. The mechanism for VP39 assembly remains unknown. We determined a 3.2 Å electron cryomicroscopy helical reconstruction of an infectious nucleocapsid ofAutographa californicamultiple nucleopolyhedrovirus, revealing how dimers of VP39 assemble into a 14-stranded helical tube. We show that VP39 comprises a unique protein fold conserved across baculoviruses, which includes a Zinc finger domain and a stabilizing intra-dimer sling. Analysis of sample polymorphism revealed that VP39 assembles in several closely-related helical geometries. This VP39 reconstruction reveals general principles for baculoviral nucleocapsid assembly.
Sucrose overconsumption impairs feeding circuit dynamics and promotes palatable food intake
Authors: Lorch Carolyn M. , Hayes Nikolas W. , Xia Jessica L. , Fleps Stefan W. , McMorrow Hayley E. , Province Haley S. , Frydman Joshua A. , Parker Jones G. , Beutler Lisa R.
Published: June 2023

Rapid gut-brain communication is critical to maintain energy balance and is disrupted in diet-induced obesity through mechanisms that remain obscure. Specifically, the role of carbohydrate overconsumption in the regulation of interoceptive circuits has been minimally examinedin vivo. Here we report that an obesogenic high-sucrose diet (HSD) selectively blunts silencing of hunger-promoting AgRP neurons following intragastric delivery of glucose, whereas we previously showed that overconsumption of a high-fat diet (HFD) selectively attenuates lipid-induced neural silencing. By contrast, both HSD and HFD reversibly dampen rapid AgRP neuron sensory inhibition following chow presentation and promote intake of more palatable foods. Our findings reveal that excess sugar and fat pathologically modulate feeding circuit activity in both macronutrient-dependent and -independent ways, and thus may additively exacerbate obesity.
Notch signaling and Bsh homeodomain activity are integrated to diversifyDrosophilalamina neuron types
Authors: Xu Chundi , Ramos Tyler B. , Marshall Owen , Doe Chris Q.
Published: June 2023

Notch signaling is an evolutionarily conserved pathway for specifying binary neuronal fates, yet how it specifies different fates in different contexts remains elusive. In our accompanying paper, using theDrosophilalamina neuron types (L1-L5) as a model, we show that the primary homeodomain transcription factor (HDTF) Bsh activates secondary HDTFs Ap (L4) and Pdm3 (L5) and specifies L4/L5 neuronal fates. Here we test the hypothesis that Notch signaling enables Bsh to differentially specify L4 and L5 fates. We show asymmetric Notch signaling between newborn L4 and L5 neurons, but they are not siblings; rather, Notch signaling in L4 is due to Delta expression in adjacent L1 neurons. While Notch signaling and Bsh expression are mutually independent, Notch is necessary and sufficient for Bsh to specify L4 fate over L5. The NotchONL4, compared to NotchOFFL5, has a distinct open chromatin landscape which allows Bsh to bind distinct genomic loci, leading to L4-specific identity gene transcription. We propose a novel model in which Notch signaling is integrated with the primary HDTF activity to diversify neuron types by directly or indirectly generating a distinct open chromatin landscape that constrains the pool of genes that a primary HDTF can activate.
Machine-learning-based motion tracking revealed the inverse correlation between adhesivity and surface motility of the leptospirosis spirochete
Authors: Abe Keigo , Koizumi Nobuo , Nakamura Shuichi
Published: June 2023

Bacterial motility is generally a critical virulence factor for pathogenic species, and thus studies on bacterial motility are significant given that they elucidate the mechanisms of infection and disease. Although fluorescent labeling has been the mainstream approach to detecting individual bacteria in a population or in host tissues, it contains problems related to protein expression stability and interference with bacterial physiology. Here, we applied machine learning to microscopic image analysis to achieve label-free motion tracking of the zoonotic bacteriumLeptospira interroganson cultured animal cells. The label-free method allowed us to measure various leptospiral strains isolated from human and animal patients, and natural reservoirs, showing that fast mobility on kidney cells tends to result in severe symptom. We also analyzed the surface locomotion of mutant strains lacking outer membrane proteins (OMPs) and revealed that the loss of OMPs reduced adherence and facilitated motility on cultured kidney cells. The behavior of clinical isolates and OMP-deficient mutants on cultured cells showed the inverse correlation between adhesion and mobility, which could affect infection outcomes. Thus, our computer vision technique eliminated the restriction on available bacterial strains and provided information that could help in understanding the mechanisms underlying motility-dependent bacterial pathogenicity.
dadi-cli: Automated and distributed population genetic model inference from allele frequency spectra
Authors: Huang Xin , Struck Travis J. , Davey Sean W. , Gutenkunst Ryan N.
Published: June 2023

dadi is a popular software package for inferring models of demographic history and natural selection from population genomic data. But using dadi requires Python scripting and manual parallelization of optimization jobs. We developed dadi-cli to simplify dadi usage and also enable straighforward distributed computing.

Availability and Implementation

dadi-cli is implemented in Python and released under the Apache License 2.0. The source code is available athttps://github.com/xin-huang/dadi-cli. dadi-cli can be installed via PyPI and conda, and is also available through Cacao on Jetstream2https://cacao.jetstream-cloud.org/.
Using mixture density networks to emulate a stochastic within-host model ofFrancisella tularensisinfection
Authors: Carruthers Jonathan , Finnie Thomas
Published: June 2023

For stochastic models with large numbers of states, analytical techniques are often impractical, and simulations time-consuming and computationally demanding. This limitation can hinder the practical implementation of such models. In this study, we demonstrate how neural networks can be used to develop emulators for two outputs of a stochastic within-host model ofFrancisella tularensisinfection: the dose-dependent probability of illness and the incubation period. Once the emulators are constructed, we employ Markov Chain Monte Carlo sampling methods to parameterize the within-host model using records of human infection. This inference is only possible through the use of a mixture density network to emulate the incubation period, providing accurate approximations of the corresponding probability distribution. Notably, these estimates improve upon previous approaches that relied on bacteria counts from the lungs of macaques. Our findings reveal a 50% infectious dose of approximately 10 colony-forming units and we estimate that the incubation period can last for up to 11 days following low dose exposure.

Author summary

Francisella tularensisis a highly infectious bacterium that remains in the top category of biothreat agents. Release of aerosolized bacteria could lead to many cases of acute and severe pneumonia over the days following. Mathematical modelling can contribute to the response to such an outbreak, combining dispersion models and disease models to identify the source of release and predict where cases are most likely to occur. However, these models can be computationally demanding and time consuming to run. In this article, we use neural networks to emulate the likelihood of disease and the duration of the incubation period from a stochastic within-host model. This enables rapid predictions to be made across a wide range of doses, thereby improving the practical applications of the model.
Translational regulation enhances distinction of cell types in the nervous system
Authors: Ichinose Toshiharu , Kondo Shu , Kanno Mai , Shichino Yuichi , Mito Mari , Iwasaki Shintaro , Tanimoto Hiromu
Published: June 2023

Multicellular organisms are composed of specialized cell types with distinct proteomes. While recent advances in single-cell transcriptome analyses have revealed differential expression of mRNAs, cellular diversity in translational profiles remains underinvestigated. By performing RNA-seq and Ribo-seq in genetically-defined cells in theDrosophilabrain, we here revealed substantial posttranscriptional regulations that augment the cell-type distinctions at the level of protein expression. Specifically, we found that translational efficiency of proteins fundamental to neuronal functions, such as ion channels and neurotransmitter receptors, was maintained low in glia, leading to their preferential translation in neurons. Notably, distribution of ribosome footprints on these mRNAs exhibited a remarkable bias towards the 5′ leaders in glia. Using transgenic reporter strains, we provide evidence that the small upstream open reading frames (uORFs) in the 5’ leader confer selective translational suppression in glia. Overall, these findings underscore the profound impact of translational regulation in shaping the proteomics for cell-type distinction and provide new insights into the molecular mechanisms driving cell-type diversity.
Scipion Flexibility Hub: an integrative framework for advanced analysis of conformational heterogeneity in cryoEM
Authors: Herreros D. , Krieger J. M. , Fonseca Y. , Conesa P. , Harastani M. , Vuillemot R. , Hamitouche I. , Serrano Gutiérrez R. , Gragera M. , Melero R. , Jonic S. , Carazo J. M. , Sorzano C. O. S.
Published: June 2023

Understanding how structure and function meet to drive biological processes is progressively shifting the cryoEM field towards a more advanced analysis of macromolecular flexibility. Thanks to techniques such as single-particle analysis and electron tomography, it is possible to image a macromolecule in different states, information that can subsequently be extracted through advanced image-processing methods to build a richer approximation of a conformational landscape. However, the interoperability of all of these algorithms remains a challenging task that is left to users, preventing them from defining a single flexible workflow in which conformational information can be addressed by different algorithms. Therefore, in this work, a new framework integrated into Scipion is proposed called the Flexibility Hub. This framework automatically handles intercommunication between different heterogeneity software, simplifying the task of combining the software into workflows in which the quality and the amount of information extracted from flexibility analysis is maximized.
A FEM in frequency domain for a transient electric field in non-sinusoidal steady state under the non-sinusoidal periodic voltage
Authors: Wen Teng , Wei Xiaoyun , Li Xuebao , Cao Boyuan , Zhao Zhibin
Published: June 2023

Purpose

This paper aims to focus on the finite element method in the frequency domain (FD-FEM) for the transient electric field in the non-sinusoidal steady state under the non-sinusoidal periodic voltage excitation.

Design/methodology/approach

Firstly, the boundary value problem of the transient electric field in the frequency domain is described, and the finite element equation of the FD-FEM is derived by Galerkin’s method. Secondly, the constrained electric field equation on the boundary in the frequency domain (FD-CEFEB) is also derived, which can solve the electric field intensity on the boundary and the dielectric interface with high accuracy. Thirdly, the calculation procedures of the FD-FEM with FD-CEFEB are introduced in detail. Finally, a numerical example of the press-packed insulated gate bipolar transistor under the working condition of the repetitive turn-on and turn-off is given.

Findings

The FD-CEFEB improves numerical accuracy of electric field intensity on the boundary and interfacial charge density, which can be achieved by modifying the existing FD-FEMs’ code in appropriate steps. Moreover, the proposed FD-FEM and the FD-CEFEB will only increase calculation costs by a little compared with the traditional FD-FEMs.

Originality/value

The FD-CEFEB can directly solve the electric field intensity on the boundary and the dielectric interface with high accuracy. This paper provides a new FD-FEM for the transient electric field in the non-sinusoidal steady state with high accuracy, which is suitable for combined insulation structure with a long time constant.
White DEI professionals' perception of their contribution to advancing workplace diversity, equity and inclusion: leveraging and decentering whiteness
Authors: Evan Rebecca J. , Sisco Stephanie , Fashant Crystal Saric , Nandyal Neela , Robbins Stacey
Published: June 2023

Purpose

This research applies social identity theory (SIT) to examine how White diversity, equity, and inclusion (DEI) professionals perceive their role and contributions to advancing workplace DEI.

Design/methodology/approach

Interpretative phenomenological analysis (IPA) was used to structure and guide the study, and data were collected from interviews with 16 White DEI professionals.

Findings

The SIT concept of social categorization was selected as a framework to discuss the findings, which were divided into two sections: in-group identity and out-group identity. The participants' in-group identities demonstrated how the participants leveraged the participants' Whiteness to grant the participants the influence and agency to perform DEI work. The participant's out-group identities revealed how the participants attempted to decenter the participants' Whiteness and unpack insecurities related to the participants' White identity and DEI contributions. Each of these findings has been associated with a specific role: leader, beneficiary, ally and pathfinder.

Practical implications

The practical implications of this study are critically examining White DEI employees' lived experience to develop an understanding of Whiteness while holding White people accountable for DEI efforts within workplaces.

Originality/value

Deeper and more honest conversations are needed to explore the phenomenon of how White DEI professionals enact and perceive the DEI contributions of the White DEI professionals. Therefore, this paper will provide further discussion on literature concerning White individuals engaged in organizational-level DEI work.
Proposing a framework for analyzing the effect of lean and agile innovation on lean and agile supply chain
Authors: Nikneshan Payam , Shahin Arash , Davazdahemami Hamid
Published: June 2023

Purpose

This study aims to propose an integrated framework for analyzing the effect of lean and agile innovation on the lean and agile supply chains.

Design/methodology/approach

The literature was reviewed and the dimensions of lean and agile supply chain/innovation were extracted. The statistical population included the managers and experts of pharmaceutical companies in Isfahan province. Eight pharmaceutical companies were selected. A researcher-made questionnaire was used to investigate the research variables. The face and content validity of the questionnaire and the data reliability were confirmed. After data collection, the studied companies were positioned in a two-by-two matrix and the associated data of two cells of the matrix, i.e. high lean supply chain/innovation and high agile supply chain/innovation were used for further statistical effect analysis using Smart-PLS.

Findings

The research results indicated that with the improvement of lean innovation in pharmaceutical companies, the lean supply chain improved by 97.9%; and with the improvement of agile innovation, the agile supply chain improved by 97.1%.

Practical implications

Considering lean innovation, pharmaceutical companies should deal with the process of conceptualizing innovation, and regarding agility strategy, their focus should be more on generating ideas to improve their agile supply chain. This study was performed during the COVID-19 pandemic and offers appropriate innovation strategies to improve the supply chain of pharmaceutical companies.

Originality/value

The literature review implies that no research has been conducted on the selected and classified variables of this study. Also, using the positioning matrix before statistical analysis distinguishes this paper from similar studies.
Integrated applications of building information modeling in project cost management: a systematic review
Authors: Farouk Abdelrahman M. , Rahman Rahimi A.
Published: June 2023

Purpose

Implementing building information modeling (BIM) in construction projects offers many benefits. However, the use of BIM in project cost management is still limited. This study aims to review the current trends in the application of BIM in project cost management.

Design/methodology/approach

This study systematically reviews the literature on the application of BIM in project cost management. A total of 46 related articles were identified and analyzed using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses method.

Findings

Eighteen approaches to applying BIM in project cost management were identified. The approaches can be grouped into cost control and cost estimation. Also, BIM can be applied independently or integrated with other techniques. The integrated approaches for cost control include integration with genetic algorithms, Monte Carlo simulation, lean construction, integrated project delivery, neural network and value engineering. On the contrary, integrated approaches for cost estimation include integration with cost-plus pricing, discrepancy analysis, construction progress curves, estimation standards, algorithms, declarative mappings, life cycle sustainability assessment, ontology, Web-based frameworks and structured query language.

Originality/value

To the best of the authors’ knowledge, this study is the first to systematically review prior literature on the application of BIM in project cost management. As a result, the study provides a comprehensive understanding of the current state of the art and fills the literature gap. Researchers and industry professionals can use the study findings to increase the benefits of implementing BIM in construction projects.
Rippling effect of liquidity risk in the sovereign term structure
Authors: Anthony Rintu , Prasanna Krishna
Published: June 2023

Purpose

The study attempts to identify the linkages in the term structure of illiquidity and the impact of global and domestic factors on sovereign bonds in emerging Asia. The objective of the study ensues on defining the direction of illiquidity spillover across bonds of varying tenors.

Design/methodology/approach

This study explores the joint dynamics of contemporary liquidity risk premia and its time-varying effect on the term structure spectrum using the Diebold and Yilmaz (2012) spillover framework.

Findings

A substantial relationship was found to exist between the liquidity of bonds with closer terms to maturity. The macroeconomic environment primarily impacts the liquidity of 10-year bonds, and they spiral down to the subsequent bond liquidity, exhibiting a rippling effect. The authors further show that the direction of liquidity shock transmission is from long- to medium- and thence to short-term bonds. Among the global factors, foreign investments and S & P 500 VIX significantly affect the liquidity of 10-year bonds.

Research limitations/implications

The study has several implications for academicians, policymakers and domestic and global investment professionals. The drivers of liquidity risk and the transmission across the term structure help investors in designing efficient portfolio diversification strategies. The results are relevant for cross-border investors in the valuation of emerging Asian sovereign bonds while deciding on asset allocations and hedging strategies. The monetary regulators strive on a continuous basis to improve the liquidity in sovereign bond markets in order to ensure efficient funding of development activities. This study finds that short-term bonds are more liquid than long-term bonds. Their auction framework with higher series of short-term bond issues helps to provide the required liquidity in the markets.

Practical implications

The term structure of illiquidity is upward sloping, inferring a higher underlying liquidity risk of long-term bonds compared to short-term bonds. This finding suggests that a higher representation of short-term bonds in the auction framework helps to enhance the overall market liquidity.

Originality/value

This study offers insights into the debate on the shape of the term structure of illiquidity and the point of origination of liquidity shocks. Further, the direction of spillover across a wide spectrum of bonds is also demonstrated.
Improving the Quality of CAP Strategic Planning through Enhancing the Role of Agricultural Economics
Authors: Erjavec Emil , Rac Ilona
Published: June 2023

Extending strategic planning to the full range of Common Agricultural Policy (CAP) interventions could improve the impacts of this controversial public policy. Science, particularly agricultural economics, can play a role in improving the quality of planning and implementation of a reformed CAP. The preparation of Member States' Strategic Plans (SP) is rather formalistic, while the plans are not very rigorously designed. A major weakness is related to the CAP's political‐economic characteristics and lies in the selection and definition of interventions: financially strong but poorly targeted interventions tend to be pre‐fixed, which prevents a stronger focus on the results and quality of planning. The intervention logic functions as a black box, as the links between policy priorities and interventions are merely implied, with no clear, evidence‐based links. Therefore, European decision makers should re‐examine the concept of CAP SP and especially improve a support system and capacity building for SP designers. Greater involvement of academic research and scientific methods and tools in the preparation, monitoring and evaluation of plans, could significantly improve the quality of planning. This would require increased investment in research and dialogue among representatives of academia, government and the nongovernmental sector.
Mortality in older patients admitted to an ICU for COVID‐19: A systematic review
Authors: Bianco Céline , Guidet Bertrand , Flaatten Hans , Dechartres Agnès , Vallet Hélène
Published: June 2023

Purpose

The objective was to conduct a systematic review of mortality and factors independently associated with mortality of older patients admitted to an intensive care unit (ICU) for COVID‐19.

Materials and Methods

Data sources were MEDLINE, EMBASE, the Cochrane Library, and references of included studies. Two reviewers independently selected studies evaluating mortality of older patients (≥ 70 years) admitted to an ICU for COVID‐19. They extracted general characteristics, mortality rate, and factors independently associated with mortality. The methodological quality of each study was evaluated by using the Critical Appraisal Skills Programme checklist.

Results

We selected 36 studies (11,989 patients). Many of the studies were conducted in Europe (42%) and many were retrospective (61%) and multicenter (61%). ICU mortality ranged from 8% to 90%, 1‐month mortality from 33% to 90% and 3‐month mortality, reported in five studies, from 46% to 60%. Frailty, assessed by the Clinical Frailty Score (CFS), was significantly associated with 1‐month and 3‐month mortality respectively in two studies (hazard ratio [HR]: 3.2 [2.56–4.13] and HR: 2.83 [95% CI: 1.96–4.08]).

Conclusion

In this systematic review of older patients admitted to an ICU with COVID‐19, we documented high heterogeneity of mortality rates.
Just visiting: A qualitative study of Australian allied health professionals' experiences working in residential aged care facilities during the COVID‐19 pandemic
Authors: Meulenbroeks Isabelle , Seaman Karla , Raban Magdalena Z. , Wabe Nasir , Westbrook Johanna
Published: June 2023

Objectives

Internationally, the COVID‐19 pandemic has negatively impacted health professionals' experiences of delivering effective care. The experiences of health professionals are important: poor experience has been associated with poorer patient outcomes and high staff turnover. This study aimed to narratively explore the impact of the COVID‐19 pandemic on the experience of delivering allied health (AH) care in Australian residential aged care (RAC).

Methods

Semistructured interviews were conducted in February–May 2022 with AH professionals who had experience working in RAC during the pandemic. Interviews were audio‐recorded, transcribed verbatim and thematically analysed in NVivo 20. Twenty‐five per cent of interview transcripts were independently analysed by three researchers to create a coding structure.

Results

Three themes were identified from interviews with 15 AH professionals to describe experiences delivering care pre‐COVID‐19, during COVID‐19, and perceptions of care delivery in future. Prepandemic AH in RAC was believed to be under‐resourced, delivering low‐quality and reactive care. During the pandemic, pauses in, and the slow resumption of, AH services exacerbated professionals' feelings of being undervalued in resident care and in the workforce. Participants were optimistic about the impact AH could have in RAC in future if practice was embedded, multidisciplinary and funded appropriately.

Conclusions

AH professionals' experiences of delivering care in RAC are often poor, regardless of the pandemic. Further research on multidisciplinary practice and health professional experience in RAC is needed.
The end of bamboo houses in northern Laos
Authors: Stolz Rosalie
Published: June 2023

While we know much about the beginnings of houses, we rarely know about their endings. Yet, to understand the temporality of houses and the entanglement of the biographies of houses and their residents, the analysis of their endings is particularly relevant. The case of Khmu houses is especially suggestive here, for it shows that the end of a house is not an exceptional phenomenon, nor a symptom of crisis, but an inevitable and intended part of its life cycle. Unintended ends, on the other hand, may continue to be animated. While bamboo houses can be assumed to have reached their end due to the widespread use of timber and, increasingly, of concrete. However, bamboo as a building material still appears convenient for fulfilling certain ends, which means that it may resurface even in novel ways.
Prospective evaluation of pregnancy outcomes after gestational exposure to prazosin
Authors: Zitoun Natalie , Campbell M. Karen , Matsui Doreen , Garcia‐Bournissen Facundo
Published: June 2023

Aims

Prazosin is an antihypertensive medication which can be used to help with post‐traumatic stress disorder (PTSD) symptoms. Little data is currently available on its safety in pregnancy. The aim of this study was to assess the fetal and pregnancy safety associated with prazosin exposures in early pregnancy.

Methods

Subjects were 11 patients who took prazosin during pregnancy and were counselled at the FRAME clinic in London Health Sciences Centre (Ontario, Canada) between 1 January 2000 and 31 December 2021. Data on their other exposures and pregnancy outcomes were collected from medical records and through telephone questionnaires.

Results

It was found that 6/11 (54.5%) subjects did not report any adverse outcomes and experienced uneventful pregnancies. There were two miscarriages. Birthweights were within the normal range for the remaining nine pregnancies. Adverse events reported were consistent with background population expectation, including: one postpartum haemorrhage, one case of preeclampsia, one preterm birth, two NICU admissions, and two caesarean sections.

Conclusions

For these 11 subjects, pregnancy outcomes after exposure to prazosin were consistent with typical outcomes from unexposed pregnancies. More data are needed to conclude that prazosin is safe for use in pregnant subjects. However, the lack of adverse effects above baseline is reassuring to future patients who may be unintentionally exposed to prazosin while pregnant. Therefore, this study contributes valuable data towards monitoring safety of prazosin in pregnancy.
T cell immune profiling of respiratory syncytial virus for the development of a targeted immunotherapy
Authors: Papayanni Penelope Georgia , Koukoulias Kiriakos , Kuvalekar Manik , Watanabe Ayumi , Velazquez Yovana , Ramos Carlos A. , Leen Ann M. , Vasileiou Spyridoula
Published: June 2023

Respiratory syncytial virus (RSV)‐associated viral infections are a major public health problem affecting the immunologically naïve/compromised populations. Given the RSV‐associated morbidity and the limited treatment options, we sought to characterize the cellular immune response to RSV to develop a targeted T cell therapy for off‐the‐shelf administration to immunocompromised individuals. Here we report on the immunological profiling, as well as manufacturing, characterization and antiviral properties of these RSV‐targeted T cells. A randomized, phase 1/2 clinical trial evaluating their safety and activity in haematopoietic stem cell transplant recipients as an off‐the‐shelf multi‐respiratory virus‐directed product is currently underway (NCT04933968, https://clinicaltrials.gov).