bluuebunny/crossref_metadata_2025 huggingface dataset:
Dry Eye Symptom Severity and Visual Field Reliability Metrics
Authors: Camp Andrew S. , Long Christopher P. , Galor Anat , Yamane Maya , Proudfoot James A. , Weinreb Robert N.
Published: March 2022

Précis:

Tracking failure frequency (TFF) increases with dry eye symptom severity and in the left eye.

Purpose:

Symptoms of dry eye disease are commonly encountered in glaucoma patients and can be exacerbated by topical glaucoma medications. Dry eye disease may influence the reliability of visual field (VF) tests and impact the accurate interpretation of the results.

Patients and Methods:

Patients at the Veterans Administration Medical Center San Diego completed the 5-item Dry Eye Questionnaire before VF testing between December 2018 and February 2019. VF reliability metrics were recorded for each patient. Standard reliability metrics included fixation losses, false positive, and false negative rates. Gaze tracking (GT) metrics included percent of stimuli with gaze deviations between 1 and 2 degrees, 3 and 5 degrees, 6 degrees or greater, and percent of stimuli with tracking failure (TFF). The use of glaucoma medications and artificial tears was also recorded.

Results:

A total of 494 patients completed the 5-item Dry Eye Questionnaire and VF testing. There was no association between dry eye symptom severity and standard reliability metrics or most GT metrics. However, TFF increased as dry eye symptom severity increased (P=0.015). TFF was also greater in the left eye, which was tested second (P=0.012); no other reliability metrics were related to laterality. Patients were more likely to use artificial tears with increased dry eye symptom severity (P<0.001), but there was no relationship between symptom severity and glaucoma medication use.

Discussion:

Dry eye symptom severity may influence the acceptable range or threshold of TFF when using GT metrics to determine VF reliability. Likewise, the acceptable range or threshold for TFF may be different between eyes.
Designing a Health Care Delivery Innovation Lab: Reflections From The First Year
Authors: Bardach Shoshana H. , Perry Amanda , Barnato Amber , Powell Lily , Kapadia Nirav S.
Published: March 2022

This article shares initial experiences designing and operating a new health care delivery innovation program at a rural academic medical center. The program was designed with the belief that dedicated team member time, senior leadership engagement, deliberate project/team selection, and robust, tailored project support would enable rapid and transformative health care redesign. Three teams were supported in the initial 1-year funding cycle; all 3 teams successfully designed, implemented, and tested new care models for different serious illness populations. Results demonstrated improved satisfaction, decreased length of stay, and a positive return on investment. Critical evaluation of current structures and processes will help identify refined strategies to support diverse teams that will challenge the norms of health care delivery and explore novel partnerships, approaches, and settings for care delivery. This article helps advance the conversation on how to think strategically and critically about current and future health care innovation efforts.
Clinical and Prognostic Role of Noninvasive Hemodynamic Assessment in Left Ventricular Assist Device Carriers
Authors: Pidello Stefano , Frea Simone , Attisani Matteo , Lodo Vittoria , Baronetto Andrea , Savi Lucia , Cingolani Marco , Rinaudo Andrea , Boffini Massimo , Rinaldi Mauro , De Ferrari Gaetano Maria
Published: March 2022

Persistence of heart failure symptoms or suboptimal hemodynamic is a frequent condition in LVAD carriers, associated with adverse outcome. Invasive hemodynamic optimization was associated with a better outcome. Our group recently validated an echocardiographic protocol to noninvasively assess hemodynamics of LVAD patients. Aim of this prospective study was to investigate its utility in clinical practice and its prognostic role.

From February 2016 to February 2019 fifty-five LVAD carriers (HVAD/HM3 34/21; age 61 ± 10 years, 89% males; INTERMACS profile at LVAD implantation ≤3 68%). A two-phased protocol was performed. First, the patient underwent clinical evaluation. Second, an echo-Doppler blinded to clinical data was performed. Clinical and echo-Doppler evaluation both identified patients with “optimal hemodynamic profile” (normal left and right estimated atrial pressures) versus other profiles. clinical evaluation overestimated the presence of an optimal profile compared with echo-Doppler (83% vs. 59%). The presence of overt heart failure identified patients with the highest risk of adverse outcomes (death or hospitalization for HF at 6 months: HR 15, 95% CI, 5.5–39, P < 0.001). An optimal profile by echo-Doppler was associated with a better outcome among patients without overt heart failure (death or hospitalization for HF at 6 months: HR 0.08, 95% CI, 0.01.5–0.64, P < 0.02). After echo-Doppler, the clinician modified treatment in 46 cases (37%). Noninvasive evaluation of hemodynamics by echo-Doppler adds significant prognostic information in LVAD patients without overt HF and is a valuable tool to tailor treatment in the outpatient follow-up of LVAD carriers.

Visual abstract: http://links.lww.com/ASAIO/A783
Small Intestinal Bacterial Overgrowth in Children: Clinical Features and Treatment Response
Authors: Peinado Fabregat Maria Isabel , Gardner Rebecca M. , Hassan Maheen A. , Kapphahn Kristopher , Yeh Ann Ming
Published: March 2022

Objectives:

To characterize the population of children diagnosed with small intestinal bacterial overgrowth (SIBO) based on breath test (BT), correlate symptomatology, and describe SIBO treatments and treatment efficacy.

Methods:

A retrospective cohort study of pediatric patients seen at Stanford Children’s Health Gastroenterology Clinics from 2012 to 2018 who had a positive BT, defined by a rise in hydrogen by ≥20 ppm, a baseline hydrogen level ≥20 ppm, or a methane value ≥10 ppm. The main outcome was symptom resolution, defined as complete or partial improvement after a course of treatment. Absolute standardized differences and Chi-square tests were used to assess associations.

Results:

From 98 children, 54 met inclusion and did not meet exclusion criteria (53.7% female). Lactulose substrate was used for 41 (75.9%) patients, whereas glucose was used for 13 (24.1%). Complete or partial resolution of symptoms was achieved in 13 of 16 (81.2%) patients who received probiotics with or without antibiotics versus 21 of 31 (67.7%) patients treated with antibiotics alone (P = 0.524). Metronidazole versus rifaximin versus other antibiotics showed no significant difference in symptom resolution (12 (63.2%), 13 (76.5%), 7 (77.8%), respectively, P = 0.601).

Conclusion:

Seventy-two percent of patients experienced at least partial symptom relief after treatment. We did not find a strong correlation between specific symptoms and analyte elevation. There was no difference in effectiveness between metronidazole and rifaximin to treat SIBO symptoms. Further research needs to be done to determine effective treatments for SIBO in pediatrics.
Sex and Racial/Ethnic Differences in Within-Stay Readmissions During Inpatient Rehabilitation Among Patients With Traumatic Brain Injury
Authors: Oyesanya Tolu O. , Cary Michael P. , Harris Walker Gabrielle , Yang Qing , Byom Lindsey , Prvu Bettger Janet
Published: March 2022

Objective

The aim of the study was to determine the association of sex and race/ethnicity with acute hospital readmissions (“within-stay readmissions”) during inpatient rehabilitation facility care versus patients discharged home without a within-stay readmission among traumatic brain injury patients.

Design

The study used a secondary analysis (N = 210,440) of Uniform Data System for Medical Rehabilitation data using multiple logistic regression.

Results

Within-stay readmissions occurred for 11.79% of female and 11.77% of male traumatic brain injury patients. Sex-specific models identified insurance, comorbidities, and complications factored differently in likelihood of within-stay readmissions among female than male patients but association of all other factors were similar per group. Within-stay readmissions differences were more pronounced by race/ethnicity: White, 11.63%; Black, 11.32%; Hispanic/Latino, 9.78%; and other, 10.61%. Descriptive bivariate analysis identified racial/ethnic patients with within-stay readmissions had greater days from traumatic brain injury to inpatient rehabilitation facility admission (White, 17.66; Black, 21.70; Hispanic/Latino, 23.81; other, 20.66) and lower admission cognitive and motor function. Factors differed across models predicting within-stay readmissions for race/ethnic groups; age, admission motor and cognitive function, complications, and length of stay were consistent across groups.

Conclusions

This study demonstrates disparities by race/ethnicity for inpatient rehabilitation facility within-stay readmissions among traumatic brain injury patients and factors predictive of this potentially preventable outcome by sex and race/ethnicity. Findings could inform care planning and quality improvement efforts for TBI patients.
Rehabilitation for Total Knee Arthroplasty: A Systematic Review
Authors: Konnyu Kristin J. , Thoma Louise M. , Cao Wangnan , Aaron Roy K. , Panagiotou Orestis A. , Bhuma Monika Reddy , Adam Gaelen P. , Balk Ethan M. , Pinto Dan
Published: March 2022

We sought to determine the comparative benefit and harm of rehabilitation interventions for patients who have undergone elective, unilateral TKA for the treatment of primary osteoarthritis. We searched PubMed, Embase, The Cochrane Register of Clinical Trials, CINAHL, PsycINFO, Scopus, and ClinicalTrials.gov from January 1, 2005 through May 3, 2021. We included randomized controlled trials and adequately-adjusted nonrandomized comparative studies of rehabilitation programs reporting performance-based, patient-reported, or healthcare utilization outcomes. Three researchers extracted study data and assessed risk of bias, verified by an independent researcher. The team assessed strength of evidence (SoE). Evidence from 53 studies RCTs suggests, various rehabilitation programs after TKA may lead to comparable improvements in pain, ranged of motion and activities of daily living. Rehabilitation in the acute phase may lead to increased strength but result in similar strength when delivered in the post-acute phase. No studies reported evidence of risk of harms due to rehabilitation delivered in the acute period following TKA; risk of harms among various post-acute rehabilitation programs appears comparable. All findings were of low SOE. Evaluation of rehabilitation after TKA needs a systematic overhaul to sufficiently guide future practice or research including the use of standardized intervention components and core outcomes.
Tongue Coating in COVID-19 Patients: A Case-Control Study
Authors: Wang Zhi Chun , Cai Xi Hong , Chan Jeremy , Chan Yi Yi , Chen Xiaotong , Cheng Ching Wan , Huang Donghui , Lao Bei-ni , Liu Xu-sheng , Lu Aiping , Wang Huixian , Zhang Helen , Zhang Xuebin , Zhang Shi Ping
Published: March 2022

It has been suggested that COVID-19 patients have distinct tongue features, which may help to monitor the development of their condition. To determine if there was any specific tongue coating feature in COVID-19, this study investigated the difference in tongue coating between COVID-19 subjects and subjects with other acute inflammatory diseases characterized by fever. Tongue images taken with smartphones from three age-matched groups, namely, COVID group (n=92), non-COVID febrile group (n=92), and normal control group (n=92), were analyzed by two blinded raters according to a tongue coating scoring scheme, which assessed the levels of thick fur, slimy or greasy fur, discolored fur and composite index of tongue coating. Compared with control, significant increases in all coating indexes were found in the COVID group (P<0.001), as well as in the non-COVID febrile group (P<0.001). However, no difference was observed between COVID and non-COVID febrile groups for all coating indexes measured. In COVID-19 subjects, their scores of coating indexes had weak but significant correlations with certain inflammatory biomarkers, including WBC and neutrophil - lymphocyte ratio. It is concluded that COVID-19 subjects have pathological tongue coating patterns that are associated with inflammatory responses, and these coating patterns can help to indicate the direction of disease development.
3D Bioprinted perfusable and vascularized breast tumor model for dynamic screening of chemotherapeutics and CAR-T cells
Authors: Dey Madhuri , Kim Myong Hwan , Nagamine Momoka , Dogan Mikail , Kozhaya Lina , Unutmaz Derya , Ozbolat Ibrahim T.
Published: March 2022

Despite substantial advancements in development of cancer treatments, lack of standardized and physiologically-relevant in vitro testing platforms limit the rapid and early screening of anti-cancer agents. A major barrier in this endeavor, is the complex interplay between the tumor microenvironment and host immune response and lack of predictive biomarkers for clinical benefit. To tackle this challenge, we have developed a dynamic-flow based three-dimensionally (3D) bioprinted vascularized breast tumor model, responding to chemo and immunotherapeutic treatments. Heterotypic tumor spheroids, comprising metastatic breast cancer cells (MDA-MB-231), human umbilical vein endothelial cells (HUVECs) and human dermal fibroblasts (HDFs), precisely bioprinted at pre-defined distances from a perfused vasculature, exhibited tumor angiogenesis and cancer invasion. Proximally bioprinted tumors (∼100 μm) exhibited enhanced capillary sprouting, anastomosis to perfused vasculature and increased cancer cell migration as compared to distally bioprinted spheroids (∼500 μm). Proximally bioprinted tumors treated with varying dosages of doxorubicin for 72 h enabled functional analysis of drug response, wherein, tumors portrayed a dose-dependent drug response behavior with ∼70% decrease in tumor volume for 1 μM dose. Additionally, a cell based immune therapy approach was explored by perfusing HER2-targeting chimeric antigen receptor (CAR) modified CD8+ T cells for 24 or 72 h through the central vasculature. Extensive CAR-T cell recruitment to the endothelium and substantial T cell activation and infiltration in the tumor site, resulted in ∼70% reduction in tumor growth for high CAR treatment densities, after 72 h of treatment. The presented 3D model paves the way for a robust, precisely fabricated and physiologically-relevant 3D tumor microenvironment platform for future translation of anti-cancer therapies to personalized medicine for cancer patients.

One Sentence Summary

A physiologically-relevant 3D bioprinted perfusable vascularized tumor model capable of dynamic screening of chemo and immunotherapeutics.
Adversarial attacks and adversarial robustness in computational pathology
Authors: Laleh Narmin Ghaffari , Truhn Daniel , Veldhuizen Gregory Patrick , Han Tianyu , van Treeck Marko , Buelow Roman D. , Langer Rupert , Dislich Bastian , Boor Peter , Schulz Volkmar , Kather Jakob Nikolas
Published: March 2022

Artificial Intelligence (AI) can support diagnostic workflows in oncology by aiding diagnosis and providing biomarkers. AI applications are therefore expected to evolve from academic prototypes to commercial products in the coming years. However, AI applications are vulnerable to adversarial attacks, such as malicious interference with test data aiming to cause misclassifications. Therefore, it is essential for the use of AI-based diagnostic devices to secure them against such attacks before widespread use. Unfortunately, no resistant systems exist in computational pathology so far.

To address this problem, we investigate the susceptibility of convolutional neural networks (CNNs) to multiple types of white- and black-box attacks. We demonstrate that both attacks can easily confuse CNNs in clinically relevant pathology tasks and impair classification performance. Classical adversarially robust training and dual batch normalization (DBN) are possible mitigation strategies but require precise knowledge of the type of attack used in the inference.

We demonstrate that vision transformers (ViTs) perform equally well compared to CNNs at baseline and are orders of magnitude more robust to different types of white-box and black-box attacks. At a mechanistic level, we show that this is associated with a more robust latent representation of clinically relevant categories in ViTs compared to CNNs.

Our results are in line with previous theoretical studies. We show that ViTs are robust learners in computational pathology. This implies that large-scale rollout of AI models in computational pathology should rely on ViTs rather than CNN-based classifiers to provide inherent protection against adversaries.
A systematic comparison of current bioinformatic tools for glycoproteomics data
Authors: Rangel-Angarita Valentina , Mahoney Keira E. , Ince Deniz , Malaker Stacy A.
Published: March 2022

Glycosylation is one of the most common post-translational modifications and generates an enormous amount of proteomic diversity; changes in glycosylation are associated with nearly all disease states. Intact glycoproteomics seeks to determine the site-localization and composition of glycans along a protein backbone via mass spectrometry. Following data acquisition, raw files are analyzed using search algorithms to define peptide sequence, glycan composition, and site localization. Glycoproteomics is rapidly expanding, creating the pressing need to establish bioinformatic community standards. Recently, several new search algorithms were released, many of which vary in terms of search strategy, localization system, score cutoffs, and glycan databases, thus warranting a comprehensive comparison of these new programs along with existing programs. Here, we analyzed three common samples: an enriched cell lysate, a mixture of 6 glycoproteins, and a mucin-domain glycoprotein. All raw files were searched with comparable parameters among software and the results were extensively manually validated to compare accuracy and completion of the output. Our results highlight the continued need for manual validation of glycopeptide spectral matches, especially for O-glycopeptides. Despite this, O-Pair outperformed all other programs in correct identification of O-glycopeptides and its localization system proved to be useful. On the other hand, Byonic and pGlyco performed best for N-glycoproteomics; the former was best for proteome-wide searches, but the latter identified more N-glycosites in less complex samples. Overall, we summarize the strengths, weaknesses, and potential improvements for these search algorithms.

TOC Figure
Feasibility and Sensitivity of Saliva GeneXpert MTB/RIF Ultra for Tuberculosis Diagnosis in Adults in Uganda
Authors: Byanyima Patrick , Kaswabuli Sylvia , Musisi Emmanuel , Nabakiibi Catherine , Zawedde Josephine , Sanyu Ingvar , Sessolo Abdul , Andama Alfred , Worodria William , Huang Laurence , Davis J. Lucian
Published: March 2022

The objective of this prospective, observational study carried out at China-Uganda Friendship Hospital-Naguru in Kampala, Uganda, was to determine the performance of GeneXpert MTB/RIF Ultra (Xpert) testing on saliva for active tuberculosis (TB) disease among consecutive adults undergoing diagnostic evaluation. We calculated sensitivity to determine the diagnostic performance in comparison to that of the composite reference standard of Mycobacterium tuberculosis liquid and solid cultures on two spot sputum specimens. GeneXpert Ultra on saliva had a sensitivity of 90% (95% confidence interval [CI], 81-96%); this was similar to that of sputum fluorescence smear microscopy (FM) of 87% (95% CI, 77-94%). Sensitivity was 24% lower (95% CI for difference 2-48%, p=0.003) among persons living with HIV (71%, 95%CI 44-90%) than among persons living without HIV (95%, 95%CI 86-99%) and 46% lower (95% CI for difference 14-77%, p<0.0001) among sputum microscopy positive (96%, 95% CI 87-99%) than among sputum microscopy negative patients (50%, 95% CI 19-81%). Semi-quantitative Xpert grade was higher in sputum than in paired saliva samples from the same patient. In conclusion, saliva specimens appear to be feasible and similarly sensitive to sputum for active TB diagnosis using molecular testing, suggesting promise as a non-sputum diagnostic test for active TB in high-burden settings.
Enabling Health Outcomes of Nature-based Interventions: A Systematic Scoping Review
Authors: Nejade Rachel , Grace Daniel , Bowman Leigh R.
Published: March 2022

Background

The burden of poor mental health and non-communicable disease is increasing, and some practitioners are turning to nature to provide the solution. Nature-based interventions could offer cost-effective solutions that benefit both human health and the environment by reconnecting individuals with nature. Importantly, the relative success of these interventions depends upon the accessibility of green and blue spaces, and the way in which people engage with them.

Aims and Objectives

A scoping review was conducted to establish the evidence base for nature-based interventions as a treatment for poor mental and physical health, and to assess whether and how enablers influence engagement with natural outdoor environments.

Methods

This scoping review followed the PRISMA-ScR and the associated Cochrane guidelines for scoping reviews. A literature search was performed across five databases and the grey literature, and articles were selected based on key inclusion and exclusion criteria. Exposure was the active engagement with natural environments. The primary outcome was mental health and the secondary outcome was physical health, both defined using established metrics. All data was extracted to a charting table and reported as a narrative synthesis.

Results

The final analysis included thirty-nine studies. Most of these focused on green spaces, with only five dedicated to blue spaces. Six nature-based health intervention types were identified: (i) educational interventions, (ii) physical activity in nature, (iii) wilderness therapy, (iv) leisure activities, (v) gardening and (vi) changes to the built environment. Of the 39 studies, 92.2% demonstrated consistent improvements across health outcomes when individuals engaged with natural outdoor environments (NOEs). Furthermore, of 153 enablers that were found to influence engagement, 78% facilitated engagement while 22% reduced engagement. Aspects such as the sense of wilderness, accessibility, opportunities for physical activity and the absence of noise/ air pollution all increased engagement.

Conclusion

Further research is still needed to establish the magnitude and relative effect of nature- based interventions, as well as to quantify the compounding effect of enablers on mental and physical health. This must be accompanied by a global improvement in study design. Nevertheless, this review has documented the increasing body of heterogeneous evidence in support of NBIs as effective tools to improve mental, physical, and cognitive health outcomes. Enablers that facilitate greater engagement with natural outdoor environments, such as improved biodiversity, sense of wilderness and accessibility, as well as opportunities for physical activity and an absence of pollution, will likely improve the impact of nature-based interventions and further reduce public health inequalities.
Human cell-camouflaged nanomagnetic scavengers restore immune homeostasis in a rodent model with bacteremia
Authors: Park Sung Jin , Kwon Seyong , Lee Min Seok , Jang Bong Hwan , Guzmán-Cedillo Axel E. , Kang Joo H.
Published: March 2022

Bloodstream infection caused by antimicrobial resistance pathogens is a global concern because it is difficult to treat with conventional therapy. Here we report scavenger magnetic nanoparticles enveloped by nanovesicles derived from blood cells (MNVs), which magnetically eradicate an extreme range of pathogens in an extracorporeal circuit. We quantitatively reveal that glycophorin A and complement receptor (CR) 1 on red blood cell (RBC)-MNVs predominantly capture human fecal bacteria, carbapenem-resistant (CR)E. coli, and extended-spectrum beta-lactamases-positive (ESBL-positive)E. coli, vancomycin-intermediateS. aureus(VISA), endotoxins, and proinflammatory cytokines in human blood. Additionally, CR3 and CR1 on white blood cell-MNVs mainly contribute to depleting the virus envelope proteins of Zika, SARS-CoV-2, and their variants in human blood. Supplementing opsonins into the blood significantly augments the pathogen removal efficiency due to its combinatorial interactions between pathogens and CR1 and CR3 on MNVs. The extracorporeal blood cleansing enables full recovery of lethally infected rodent animals within seven days by treating them twice in series. We also validate that parameters reflecting immune homeostasis, such as blood cell counts, cytokine levels, and transcriptomics changes, are restored in blood of the fatally infected rats after treatment.
Should individuals be paid to participate in mass drug administration to control malaria?
Authors: Fryer Helen , Peyton-Jones Meg
Published: March 2022

Mass drug administration (MDA) is a malaria control strategy in which antimalarial drugs are offered to a whole community. Although MDA can potentially clear malaria from a community, it is not routinely used in eradication efforts because of ethical concerns and past failures to achieve lasting elimination. One potential means to improving the outcome of MDA is to incentivize individuals to participate, for example, through monetary payments. In this study our aim is to inform the decision to use MDA to eradicate malaria and explore whether individuals should be incentivized to participate. Through the lens of a mathematical model, we clarify how the costs and benefits of MDA are context-dependent. We highlight that in a community experiencing a good improvement in clinical case management – relative to the prevalence of malaria in the community – the addition of MDA can catalyze stable elimination. However, participation rates are critical and individuals who avoid every round of treatment can prevent elimination. We explore how, in this scenario, individual incentives could change the cost-benefit breakdown, measured at three levels – personal, local community and wider community.
Severe Acute Respiratory Coronavirus-2 Antibody and T cell response after a third vaccine dose in hemodialysis patients compared with healthy controls
Authors: Simon Benedikt , Rubey Harald , Gromann Martin , Knopf-Völkerer Astrid , Hemedi Boris , Zehetmayer Sonja , Kirsch Bernhard
Published: March 2022

1.

Hemodialysis patients (HD patients) have a high health risk from Severe Acute Respiratory Coronavirus-2 (SARS-CoV-2) infection. In this study, we assess the impact of a third vaccine dose (3D) on antibody levels and T cell response in HD patients and compare the results to those of a healthy control group.

We conducted a prospective cohort study consisting of 60 HD patients and 65 healthy controls. All of them received two doses of the Comirnaty mRNA vaccine and a third mRNA vaccine dose (Spikevax or Comirnaty). The SARS-CoV-2 S antibody response in all participants was measured 6 months after the second vaccine dose and 6 to 8 weeks after administration of the 3D. We also assessed INF-γ secretion 6–8 weeks after the 3D in 24 healthy controls, 17 HD patients with a normal and 20 HD patients with a low or no antibody response after the second dose. The groups were compared using univariate quantile regressions and multiple analyses. The adverse effects of vaccines were assessed via a questionnaire.

After the 3D, the SARS-CoV-2-specific antibody and INF-γ titers of most HD patients were comparable to those of healthy controls. A subgroup of HD patients who had shown a diminished antibody response after the first two vaccine doses developed a significantly lower antibody and INF-γ response compared to responder HD patients and controls, even after the 3D. A new strategy is needed to protect this patient group from severe COVID-19 infection.
A microfluidic platform to investigate the role of mechanical constraints on tissue reorganization
Authors: Tlili Sham , Graner François , Delanoë-Ayari Hélène
Published: March 2022

Mechanical constraints have a high impact on development processes, and there is a need for new tools to investigate the role of mechanosensitive pathways in tissue reorganization during development. We present here experiments where embryonic cell aggregates are aspired through constrictions in microfluidic channels, generating highly heterogeneous flows and high cell deformations that can be imaged using two-photon microscopy. This approach provides a way to measure in situ local viscoelastic properties of 3D tissues and connect them to intracellular and intercellular events such as cell shape changes and cell rearrangements. Perspectives include applications on organoids to investigate and quantify rheological properties of tissues, and to understand how constraints affect development.
Surface motility favors co-dependent interaction between Pseudomonas aeruginosa and Burkholderia cenocepacia
Authors: Morin Charles , Landry May , Groleau Marie-Christine , Déziel Eric
Published: March 2022

Interactions between different bacterial species shape bacterial communities and their environments. The opportunistic pathogens Pseudomonas aeruginosa and Burkholderia cenocepacia both can colonize the lungs of individuals affected by cystic fibrosis. Using the social surface behavior called swarming motility as a study model of interactions, we noticed intricate interactions between B. cenocepacia K56-2 and P. aeruginosa PA14. While strain K56-2 does not swarm under P. aeruginosa favorable swarming conditions, co-inoculation with a non-motile PA14 flagellum-less ΔfliC mutant restored spreading for both strains. We show that P. aeruginosa provides the wetting agent rhamnolipids allowing K56-2 to perform swarming motility, while aflagellated PA14 seems able to «hitchhike» along with K56-2 cells in the swarming colony.

Importance

Pseudomonas aeruginosa and Burkholderia cenocepacia are important opportunistic pathogens often found together in the airways of persons with cystic fibrosis. Laboratory co-culture of both species often ends with one taking over the other. We used a surface motility assay to study the social interactions between population of these bacterial species. Under our conditions, B. cenocepacia cannot swarm without supplementation of the wetting agent produced by P. aeruginosa. In a mixed colony of both species, an aflagellated mutant of P. aeruginosa provides the necessary wetting agent to B. cenocepacia, allowing both bacteria to swarm and colonize a surface. We highlight this peculiar interaction where both bacteria set aside their antagonistic tendencies to cooperate.
The cGAS-STING pathway affects vertebral bone but does not promote intervertebral disc cell senescence or degeneration
Authors: Ottone Olivia K. , Kim Cheeho , Collins John. A. , Risbud Makarand V.
Published: March 2022

The DNA-sensing cGAS-STING pathway promotes the senescence-associated secretory phenotype (SASP) and mediates type-I interferon inflammatory responses to foreign viral and bacterial DNA as well as self-DNA. Studies of the intervertebral disc in humans and mice demonstrate associations between aging, increased cell senescence, and disc degeneration. Herein we assessed the role of STING in SASP promotion in STING gain- (N153S) and loss-of-function mouse models. N153S mice evidenced elevated circulating levels of proinflammatory markers including IL-1β, IL-6, and TNF-α and exhibited a mild trabecular and cortical bone phenotype in caudal vertebrae. Interestingly, despite systemic inflammation, the structural integrity of the disc and knee articular joint remained intact, and cells did not show a loss of their phenotype or elevated SASP. Transcriptomic analysis of N153S tissues demonstrated an upregulated immune response by disc cells, which did not closely resemble inflammatory changes in human tissues. Interestingly, STING-/-mice also showed a mild vertebral bone phenotype, but the absence of STING did not improve the age-associated disc phenotype or reduce the abundance of SASP markers. Overall, the analyses of N153S and STING-/-mice that the cGAS-STING pathway is not a major contributor to SASP induction and consequent disc aging and degeneration but may play a minor role in the maintenance of trabecular bone in the vertebrae. This work contributes to a growing body of work demonstrating that systemic inflammation is not a key driver of disc degeneration.
Local actuation of organoids by magnetic nanoparticles
Authors: Abdel Fattah Abdel Rahman , Kolaitis Niko , Van Daele Katrien , Rustandi Andika Gregorius , Ranga Adrian
Published: March 2022

Tissues take shape during development through a series of morphogenetic movements guided by local cell-scale forces. While current in vitro approaches subjecting tissues to homogenous stresses, it is currently no possible to recapitulate highly local spatially varying forces. Here we develop a method for local actuation of organoids using embedded magnetic nanoparticles. Sequential aggregation of magnetically labelled human pluripotent stem cells followed by actuation by a magnetic field produces localized magnetic clusters within the organoid. These clusters impose local mechanical forces on the surrounding tissue in response to applied global magnetic fields. We show that precise, spatially defined actuation provides short-term mechanical tissue perturbations as well as long-term cytoskeleton remodeling. We demonstrate that local magnetically-driven actuation guides asymmetric growth and proliferation, leading to enhanced patterning in human neural organoids. We show that this approach is applicable to other model systems by observing polarized patterning in paraxial mesoderm organoids upon local magnetic actuation. This versatile approach allows for local, controllable mechanical actuation in multicellular constructs, and is widely applicable to interrogate the role of local mechanotransduction in developmental and disease model systems.
Lineage tracing via associative chromosome/plasmid barcoding with siBar
Authors: Mei Han , Nekrutenko Anton
Published: March 2022

We describe a new method, siBar, which enables simultaneous tracking of plasmids and chromosomal lineages within a bacterial host. siBar involves integration of a linearized plasmid construct carrying a unique combination of two molecular barcodes. Upon recircularization one barcode remains integrated into the host chromosome, while the other remains on the plasmid allowing direct observation of expansion and contraction of adaptive lineages. We also performed a pilot evolution experiment that allowed us to assess the barcode complexity and establish an analytical framework for the analysis of siBar data.
A non-invasive method for time-lapse imaging of microbial interactions and biofilm dynamics
Authors: Molina-Santiago Carlos , Pearson John R. , Berlanga-Clavero María Victoria , Pérez-Lorente Alicia Isabel , de Vicente Antonio , Romero Diego
Published: March 2022

Complex interactions between microbial populations can greatly affect the overall properties of a microbial community, sometimes leading to cooperation and mutually beneficial coexistence, or to competition and the death or displacement of particular organisms or sub-populations. Interactions between different biofilm populations are highly relevant in diverse scientific areas, from antimicrobial resistance to microbial ecology. The utilization of modern microscopic techniques has provided new and interesting insight into how bacteria interact at the cellular level to form and maintain microbial biofilms. However, our ability to follow complex intra- and inter-species interactions in vivo at the microscopic level has remained somewhat limited. Here, we detail BacLive, a novel non-invasive method for tracking bacterial growth and biofilm dynamics using high resolution fluorescence microscopy and an associated ImageJ processing macro (https://github.com/BacLive) for easier data handling and image analysis. Finally, we provide examples of how BacLive can be used in the analysis of complex bacterial communities.

Importance

Communication and interactions between single cells are continuously defining the structure and composition of microbial communities timely and spatially. Methods routinely used to the study of these communities at cellular level rely on sample manipulation what deprives from microscopic time lapse experiments on a given sample. BacLive is conceived as a method for the non-invasive study of the formation and development of bacterial communities, such as biofilms, and the dynamics of formation of specialized subpopulations in time-lapse experiments. In addition we prove that BacLive largely simplifies the analysis of the data generated.
Rational design of Cas9 ribonucleoprotein with a “gRNA-shRNA” for multidimensional genome manipulation and enhanced homology-directed repair
Authors: Qiao Jie , Sun Wenli , Yin Wenhao , Ma Lixin , Liu Yi
Published: March 2022

Gene perturbation approaches have evolved as powerful tools for understanding the function of genes and curing inherited diseases. Here, we develop a method that combines the merits of RNAi and CRISPR technology by rational design of Cas9 ribonucleoprotein (RNP) with a “gRNA-shRNA” component. The RNP, termed Cas9-RNAi, has a gRNA containing a 3’ extension that can be processed to a functional siRNA via dorsha/dicer enzyme mediated cleavage within cells. We prepared the Cas9-RNAi RNPs by streamline co-expression of Cas9 enzymes and the “gRNA-shRNA” ribonucleotides in Escherichia coli strain HT115(DE)3. Transferring the Cas9-RNAi RNPs into mammalian cells achieves multidimensional genome manipulation, e.g., simultaneously knock out and knock down the target genes. Moreover, by introduction of a shRNA against the gene of human DNA ligase 4 (LIG4), significantly improved homology-directed repair was attained. Together, we develop a simple-to-use CRISPR RNP tool that has great potentials in precise genome editing, gene function analysis and gene therapy.
A bipartite, low-affinity roadblock domain-containing GAP complex regulates bacterial front-rear polarity
Authors: Szadkowski Dobromir , Carreira Luís António Menezes , Søgaard-Andersen Lotte
Published: March 2022

The Ras-like GTPase MglA is a key regulator of front-rear polarity in rod-shaped Myxococcus xanthus cells. MglA-GTP localizes to the leading cell pole and stimulates assembly of the two motility machineries. MglA-GTP localization is spatially constrained by its cognate GEF, the RomR/RomX complex, and GAP, the MglB Roadblock-domain protein. RomR/RomX and MglB localize similarly with low and high concentrations at the leading and lagging poles, respectively. Yet, GEF activity dominates at the leading and GAP activity at the lagging pole by unknown mechanisms. Here, we identify RomY as a co-GAP that stimulates MglB GAP activity. The MglB/RomY interaction is low affinity, restricting complex formation to the lagging pole with the high MglB concentration. Our data support a model wherein RomY, by forming a low-affinity complex with MglB, ensures that MglB GAP activity is spatially precisely confined to the lagging pole, thereby constraining MglA-GTP to the leading pole establishing front-rear polarity.
Circulating miR-30b-5p is upregulated in Cavalier King Charles Spaniels affected by early myxomatous mitral valve disease
Authors: Bagardi Mara , Ghilardi Sara , Zamarian Valentina , Ceciliani Fabrizio , Brambilla Paola G. , Lecchi Cristina
Published: March 2022

There is a growing interest in developing new molecular markers of heart disease in young Cavalier King Charles Spaniels affected by myxomatous mitral valve disease. The aim of the study was to measure the abundance of 3 circulating microRNAs and their application as potential biomarkers in the plasma of Cavalier King Charles Spaniels with early asymptomatic myxomatous mitral valve disease. 33 dogs affected by the disease in American College of Veterinary Internal Medicine (ACVIM) stage B1 were divided in three groups (11 younger than 3 years, 11 older than 3 years and younger than 7 years, and 11 older than 7 years), and 11 healthy (ACVIM stage A) Cavalier King Charles Spaniels were included as the control group. This is a prospective cross-sectional study. The abundance of three circulating microRNAs (miR-1-3p, miR30b-5p, and miR-128-3p) was measured by quantitative real-time PCR using TaqMan® probes. Diagnostic performance was evaluated by calculating the area under the receiver operating curve (AUC). miR-30b-5p was significantly higher in ACVIM B1 dogs compared to ACVIM A subjects, and the area under the receiver operating curve was 0.79. According to the age of dogs, the abundance of miR-30b-5p was statistically significantly higher in group B1<3y (2.3 folds,P= 0.034), B1 3-7y (2.2 folds,P= 0.028), and B1>7y (2.7 folds,P= 0.018) than in group A. The area under the receiver operating curves were fair in discriminating between group B1<3y and group A (AUC 0.780), between B1 3-7y and A (AUC 0.78), and good in discriminating between group B1>7y and A (AUC 0.822). miR-30b-5p changed in the plasma of dogs at the asymptomatic stage of disease, particularly at a young age.
Fgf8 dosage regulates jaw shape and symmetry through pharyngeal-cardiac tissue relationships
Authors: Zbasnik Nathaniel , Dolan Katie , Buczkowski Stephanie A. , Green Rebecca , Hallgrimsson Benedikt , Marcucio Ralph S. , Moon Anne M. , Fish Jennifer L.
Published: March 2022

Background

Asymmetries in craniofacial anomalies are commonly observed. With respect to the facial skeleton, the left side is more commonly and/or severely affected than the right. Such asymmetries complicate treatment options. Mechanisms underlying variation in disease severity between individuals as well as within individuals (asymmetries) are still relatively unknown.

Results

Developmental reductions in Fibroblast growth factor 8 (Fgf8) have a dosage dependent effect on jaw size, shape, and symmetry. Further, Fgf8 mutants have directionally asymmetric jaws with the left side being more affected than the right. Defects in lower jaw development begin with an early disruption to Meckel’s cartilage, which is discontinuous and appears as two separate condensations in Fgf8 mutants. All skeletal elements associated with the proximal condensation are dysmorphic in the mutants, which is exemplified by a malformed and mis-oriented malleus. At later stages, Fgf8 mutants exhibit syngnathia, which falls into 2 broad categories: bony fusion of the maxillary and mandibular alveolar ridges and zygomatico-mandibular fusion. All of these morphological defects exhibit both inter- and intra-individual variation.

Conclusions

We hypothesize that these asymmetries are linked to asymmetries in heart development resulting in higher levels of Fgf8 on the right side of the face during development, which may buffer the right side to mild developmental perturbations. This mutant mouse is a good model for future investigations of mechanisms underlying human syngnathia and facial asymmetry.
Linking self-congruity, perceived quality and satisfaction to brand loyalty in a tourism destination: the moderating role of visit frequency
Authors: Tran Phuong Kim Thi , Nguyen Phong Dong , Le Angelina Hanh Nhat , Tran Vinh Trung
Published: March 2022

Purpose

This study aims to examine the direct and indirect relationship between self-congruity and destination brand loyalty (DBL) based on the conceptual linkages of cognition, affect and conation. A multiple-step, multiple mediator model is investigated to explain the indirect effect of self-congruity on DBL through perceived destination quality (PDQ) and tourist satisfaction (TS). The moderating impact of visit frequency in these relationships is also proposed and empirically evaluated.

Design/methodology/approach

The conceptual model and research hypotheses were assessed by applying covariance-based structural equation modeling (SEM), mediating and multi-group analysis. An online survey was used to collect data from 347 domestic tourists visiting a destination in Vietnam.

Findings

The results support the link from self-congruity to PDQ, TS and then to DBL. Visit frequency was found to moderate the links between the research concepts.

Research limitations/implications

Future research would benefit from considering other self-congruity components (e.g. social self-congruity and ideal social self-congruity) and moderating variables (e.g. cultural distance). This would provide insights into the relationships between self-congruity and tourist behaviors and could be based on comparisons in different destinations to achieve more wide-ranging results.

Originality/value

The effect of self-congruity on DBL that evolves from linking self-congruity to PDQ and TS to increase DBL was examined within a tourism destination context. This study is valuable to destination managers as it provides suggestions to improve DBL.
Identifying hidden semantic structures in Instagram data: a topic modelling comparison
Authors: Egger Roman , Yu Joanne
Published: March 2022

Purpose

Intrigued by the methodological challenges emerging from text complexity, the purpose of this study is to evaluate the effectiveness of different topic modelling algorithms based on Instagram textual data.

Design/methodology/approach

By taking Instagram posts captioned with #darktourism as the study context, this research applies latent Dirichlet allocation (LDA), correlation explanation (CorEx), and non-negative matrix factorisation (NMF) to uncover tourist experiences.

Findings

CorEx outperforms LDA and NMF by classifying emerging dark sites and activities into 17 distinct topics. The results of LDA appear homogeneous and overlapping, whereas the extracted topics of NMF are not specific enough to gain deep insights.

Originality/value

This study assesses different topic modelling algorithms for knowledge extraction in the highly heterogeneous tourism industry. The findings unfold the complexity of analysing short-text social media data and strengthen the use of CorEx in analysing Instagram content.