Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags.

Microbiomes feature recurrent compositional structures under given environmental conditions. However, these patterns may conceal diverse underlying population dynamics that require intrastrain resolution. Here we developed a genomic tagging system, termed wild-type isogenic standardized hybrid (WISH)-tags, that can be combined with quantitative polymerase chain reaction and next-generation sequencing for microbial strain enumeration. We experimentally validated the performance of 62 tags and showed that they can be differentiated with high precision. WISH-tags were introduced into model and non-model bacterial members of the mouse and plant microbiota. Intrastrain priority effects were tested using one species of isogenic barcoded bacteria in the murine gut and the Arabidopsis phyllosphere, both with and without microbiota context. We observed colonization resistance against late-arriving strains of Salmonella Typhimurium in the mouse gut, whereas the phyllosphere accommodated Sphingomonas latecomers in a manner proportional to their presence at the late inoculation timepoint. This demonstrates that WISH-tags are a resource for deciphering population dynamics underlying microbiome assembly across biological systems.

mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants, and isogenic strain populations.

MOTIVATION: DNA barcoding has become a powerful tool for assessing the fitness of strains in a variety of studies, including random transposon mutagenesis screens, attenuation of site-directed mutants, and population dynamics of isogenic strain pools. However, the statistical analysis, visualization, and contextualization of the data resulting from such experiments can be complex and require bioinformatic skills. RESULTS: Here, we developed mBARq, a user-friendly tool designed to simplify these steps for diverse experimental setups. The tool is seamlessly integrated with an intuitive web app for interactive data exploration via the STRING and KEGG databases to accelerate scientific discovery. AVAILABILITY AND IMPLEMENTATION: The tool is implemented in Python. The source code is freely available (https://github.com/MicrobiologyETHZ/mbarq) and the web app can be accessed at: https://microbiomics.io/tools/mbarq-app.

Dynamic assessment of scapholunate ligament status by real-time magnetic resonance imaging: an exploratory clinical study.

OBJECTIVE: Clinical-standard MRI is the imaging modality of choice for the wrist, yet limited to static evaluation, thereby potentially missing dynamic instability patterns. We aimed to investigate the clinical benefit of (dynamic) real-time MRI, complemented by automatic analysis, in patients with complete or partial scapholunate ligament (SLL) tears. MATERIAL AND METHODS: Both wrists of ten patients with unilateral SLL tears (six partial, four complete tears) as diagnosed by clinical-standard MRI were imaged during continuous active radioulnar motion using a 1.5-T MRI scanner in combination with a custom-made motion device. Following automatic segmentation of the wrist, the scapholunate and lunotriquetral joint widths were analyzed across the entire range of motion (ROM). Mixed-effects model analysis of variance (ANOVA) followed by Tukey's posthoc test and two-way ANOVA were used for statistical analysis. RESULTS: With the increasing extent of SLL tear, the scapholunate joint widths in injured wrists were significantly larger over the entire ROM compared to those of the contralateral healthy wrists (p<0.001). Differences between partial and complete tears were most pronounced at 5°-15° ulnar abduction (p<0.001). Motion patterns and trajectories were altered. Complete SLL deficiency resulted in complex alterations of the lunotriquetral joint widths. CONCLUSION: Real-time MRI may improve the functional diagnosis of SLL insufficiency and aid therapeutic decision-making by revealing dynamic forms of dissociative instability within the proximal carpus. Static MRI best differentiates SLL-injured wrists at 5°-15° of ulnar abduction.

A therapeutic strategy to target distinct sources of IgE and durably reverse allergy.

Immunoglobulin E (IgE) is a key driver of type 1 hypersensitivity reactions and allergic disorders, which are globally increasing in number and severity. Although eliminating pathogenic IgE may be a powerful way to treat allergy, no therapeutic strategy reported to date can fully ablate IgE production. Interleukin-4 receptor α (IL-4Rα) signaling is required for IgE class switching, and IL-4Rα blockade gradually reduces, but does not eliminate, IgE. The persistence of IgE after IL-4Rα blockade may be due to long-lived IgE+ plasma cells that maintain serological memory to allergens and thus may be susceptible to plasma cell-targeted therapeutics. We demonstrate that transient administration of a B cell maturation antigen x CD3 (BCMAxCD3) bispecific antibody markedly depletes IgE, as well as other immunoglobulins, by ablating long-lived plasma cells, although IgE and other immunoglobulins rapidly rebound after treatment. Concomitant IL-4Rα blockade specifically and durably prevents the reemergence of IgE by blocking IgE class switching while allowing the restoration of other immunoglobulins. Moreover, this combination treatment prevented anaphylaxis in mice. Together with additional cynomolgus monkey and human data, our studies demonstrate that allergic memory is primarily maintained by both non-IgE+ memory B cells that require class switching and long-lived IgE+ plasma cells. Our combination approach to durably eliminate pathogenic IgE has potential to benefit allergy in humans while preserving antibody-mediated immunity.

Targeted left ventricular lead positioning to the site of latest activation in cardiac resynchronization therapy: a systematic review and meta-analysis.

AIMS: Several studies have evaluated the use of electrically- or imaging-guided left ventricular (LV) lead placement in cardiac resynchronization therapy (CRT) recipients. We aimed to assess evidence for a guided strategy that targets LV lead position to the site of latest LV activation. METHODS AND RESULTS: A systematic review and meta-analysis was performed for randomized controlled trials (RCTs) until March 2023 that evaluated electrically- or imaging-guided LV lead positioning on clinical and echocardiographic outcomes. The primary endpoint was a composite of all-cause mortality and heart failure hospitalization, and secondary endpoints were quality of life, 6-min walk test (6MWT), QRS duration, LV end-systolic volume, and LV ejection fraction. We included eight RCTs that comprised 1323 patients. Six RCTs compared guided strategy (n = 638) to routine (n = 468), and two RCTs compared different guiding strategies head-to-head: electrically- (n = 111) vs. imaging-guided (n = 106). Compared to routine, a guided strategy did not significantly reduce the risk of the primary endpoint after 12-24 (RR 0.83, 95% CI 0.52-1.33) months. A guided strategy was associated with slight improvement in 6MWT distance after 6 months of follow-up of absolute 18 (95% CI 6-30) m between groups, but not in remaining secondary endpoints. None of the secondary endpoints differed between the guided strategies. CONCLUSION: In this study, a CRT implantation strategy that targets the latest LV activation did not improve survival or reduce heart failure hospitalizations.

VSIG4 interaction with heparan sulfates inhibits VSIG4-complement binding.

V-set and immunoglobulin domain-containing 4 (VSIG4) is a complement receptor of the immunoglobulin superfamily that is specifically expressed on tissue resident macrophages, and its many reported functions and binding partners suggest a complex role in immune function. VSIG4 is reported to have a role in immune surveillance as well as in modulating diverse disease phenotypes such as infections, autoimmune conditions, and cancer. However, the mechanism(s) governing VSIG4's complex, context-dependent role in immune regulation remains elusive. Here, we identify cell surface and soluble glycosaminoglycans, specifically heparan sulfates, as novel binding partners of VSIG4. We demonstrate that genetic deletion of heparan sulfate synthesis enzymes or cleavage of cell-surface heparan sulfates reduced VSIG4 binding to the cell surface. Furthermore, binding studies demonstrate that VSIG4 interacts directly with heparan sulfates, with a preference for highly sulfated moieties and longer glycosaminoglycan chains. To assess the impact on VSIG4 biology, we show that heparan sulfates compete with known VSIG4 binding partners C3b and iC3b. Furthermore, mutagenesis studies indicate that this competition occurs through overlapping binding epitopes for heparan sulfates and complement on VSIG4. Together these data suggest a novel role for heparan sulfates in VSIG4-dependent immune modulation.

Insights into the Age Dependency of Compositional MR Biomarkers Quantifying the Health Status of Cartilage in Metacarpophalangeal Joints.

(1) Background: We aim to investigate age-related changes in cartilage structure and composition in the metacarpophalangeal (MCP) joints using magnetic resonance (MR) biomarkers. (2) Methods: The cartilage tissue of 90 MCP joints from 30 volunteers without any signs of destruction or inflammation was examined using T1, T2, and T1ρ compositional MR imaging techniques on a 3 Tesla clinical scanner and correlated with age. (3) Results: The T1ρ and T2 relaxation times showed a significant correlation with age (T1ρ: Kendall-τ-b = 0.3, p < 0.001; T2: Kendall-τ-b = 0.2, p = 0.01). No significant correlation was observed for T1 as a function of age (T1: Kendall-τ-b = 0.12, p = 0.13). (4) Conclusions: Our data show an increase in T1ρ and T2 relaxation times with age. We hypothesize that this increase is due to age-related changes in cartilage structure and composition. In future examinations of cartilage using compositional MRI, especially T1ρ and T2 techniques, e.g., in patients with osteoarthritis or rheumatoid arthritis, the age of the patients should be taken into account.

A review of JAK and IL-23 inhibitors to treat vitiligo.

Vitiligo is an autoimmune skin disorder resulting in the depigmentation of skin characterised by patches of varying sizes and shapes. A common disorder of pigmentation that affects 0.5%-2% of the global population. Despite its well-understood autoimmune pathogenesis, the targets for effective cytokine intervention remain unclear. Current first-line treatments include oral or topical corticosteroids, calcineurin inhibitors and phototherapy. These treatments are limited, have varying efficacies, and are associated with significant adverse events or can be time-consuming. Therefore, biologics should be explored as a potential treatment for vitiligo. There are currently limited data for the use of JAK and IL-23 inhibitors for vitiligo. A total of 25 studies were identified in the review. There is promising evidence regarding the use of JAK and IL-23 inhibitors for the treatment of vitiligo.

Opportunities and challenges to non-communicable disease (NCD) research and training in Pakistan: a qualitative study from Pakistan.

INTRODUCTION: Most of the global non-communicable disease (NCD)-related death burden is borne by low and middle-income countries (LMICs). In LMICs like Pakistan, however, a major gap in responding to NCDs is a lack of high-quality research leading to policy development and implementation of NCDs. To assess institutional opportunities and constraints to NCD research and training we conducted a situational analysis for NCD research and training at Aga Khan University Pakistan. METHODS: We conducted a descriptive exploratory study using grounded theory as a qualitative approach: semistructured interviews of 16 NCD stakeholders (three excluded) and two focus group discussions with postgraduate and undergraduate trainees were conducted. A simple thematic analysis was done where themes were identified, and then recurring ideas were critically placed in their specific themes and refined based on the consensus of the investigators. RESULTS: The major themes derived were priority research areas in NCDs; methods to improve NCD research integration; barriers to NCD research in LMICs like Pakistan; design of NCD research programme and career paths; and NCD prevention at mass level, policy and link to the government. In general, participants opined that while there was an appetite for NCD research and training, but few high-quality research training programmes in NCDs existed, such programmes needed to be established. The ideal NCD research and training programmes would have in-built protected time, career guidance and dedicated mentorship. Most participants identified cardiovascular diseases as a priority thematic area and health information technology and data science as key methodological approaches to be introduced into research training. CONCLUSION: We conclude from this qualitative study on NCD research and training that high-quality research training programmes for NCDs are rare. Such programmes need to be established with in-built protected time, career guidance and mentorship for the trainees to improve their research capacity in Pakistan.

Magnetic resonance imaging in patients with temporary external pacemakers.

AIMS: To describe safety and feasibility of magnetic resonance imaging (MRI) in patients with transvenous temporary external pacemakers and whether artefacts affect the diagnostic image quality during cardiac MRI. METHODS AND RESULTS: We reviewed records of all patients treated with temporary external pacing between 2016 and 2020 at a tertiary centre. Temporary pacing was established using a transvenous standard active fixation pacing lead inserted percutaneously and connected to a MRI-conditional pacemaker taped to the skin. All patients undergoing cardiac or non-cardiac MRI during temporary transvenous pacing were identified. Before MRI, devices were programmed according to guidelines for permanent pacemakers, and patients were monitored with continuous electrocardiogram during MRI. Of 827 consecutive patients receiving a temporary external pacemaker, a total of 44 (5%) patients underwent MRI (mean age 71 years, 13 [30%] females). Cardiac MRI was performed in 22 (50%) patients, while MRI of cerebrum, spine, and other regions was performed in the remaining patients. Median time from implantation of the temporary device to MRI was 6 (3-11) days. During MRI, we observed no device-related malfunction or arrhythmia. Nor did we detect any change in lead sensing, impedance, or pacing threshold. We observed no artefacts from the lead or pacemaker compromising the diagnostic image quality of cardiac MRI. MRI provided information to guide the clinical management in all cases. CONCLUSION: MRI is feasible and safe in patients with temporary external pacing established with a regular MRI-conditional pacemaker and a standard active fixation lead. No artefacts compromised the diagnostic image quality.

UTE-T2* versus conventional T2* mapping to assess posterior cruciate ligament ultrastructure and integrity-an in-situ study.

Background: Clinical-standard morphologic magnetic resonance imaging (MRI) is limited in the refined diagnosis of posterior cruciate ligament (PCL) injuries. Quantitative MRI sequences such as ultrashort echo-time (UTE)-T2* mapping or conventional T2* mapping have been theorized to quantify ligament (ultra-) structure and integrity beyond morphology. This study evaluates their diagnostic potential in identifying and differentiating partial and complete PCL injuries in a standardized graded injury model. Methods: Ten human cadaveric knee joint specimens were imaged on a clinical 3.0 T MRI scanner using morphologic, conventional T2* mapping, and UTE-T2* mapping sequences before and after standardized arthroscopic partial and complete PCL transection. Following manual segmentation, quantitative T2* and underlying texture features (i.e., energy, homogeneity, and variance) were analyzed for each specimen and PCL condition, both for the entire PCL and its subregions. For statistical analysis, Friedman's test followed by Dunn's multiple comparison test was used against the level of significance of P≤0.01. Results: For the entire PCL, T2* was significantly increased as a function of injury when acquired with the UTE-T2* sequence [entire PCL: 11.1±3.1 ms (intact); 10.9±4.6 ms (partial); 14.3±4.9 ms (complete); P<0.001], but not when acquired with the conventional T2* sequence [entire PCL: 10.0±3.2 ms (intact); 11.4±6.2 ms (partial); 15.5±7.8 ms (complete); P=0.046]. The PCL subregions and texture variables showed variable changes indicative of injury-associated disorganization. Conclusions: In contrast to the conventional T2* mapping, UTE-T2* mapping is more receptive in the detection of structural damage of the PCL and allows quantitative assessment of ligament (ultra-)structure and integrity that may help to improve diagnostic differentiation of distinct injury states. Once further substantiated beyond the in-situ setting, UTE-T2* mapping may refine diagnostic evaluation of PCL injuries and -possibly- monitor ligament healing, ageing, degeneration, and inflammation.

Automated measurement of alpha angle on 3D-magnetic resonance imaging in femoroacetabular impingement hips: a pilot study.

BACKGROUND: Femoroacetabular impingement (FAI) syndrome is an established pre-osteoarthritic condition. Diagnosis is based on both clinical and radiographic parameters. An abnormal manually calculated alpha angle in magnetic resonance imaging (MRI) is traditionally utilized to diagnose abnormal femoral head-neck offset. This pilot study aimed to assess the feasibility of automated alpha angle measurements in patients with FAI syndrome, and to compare automated with manual measurements data with regard to the time and effort needed in each method. METHODS: Alpha angles were measured with manual and automated techniques, using postprocessing software in nineteen hip MRIs of FAI syndrome patients. Two observers conducted manual measurements. Intra- and inter-observer reproducibility and correlation of manual and automated alpha angle measurements were calculated using intra-class correlation (ICC) analysis. Both techniques were compared regarding the time taken (in minutes) and effort required, measured as the amount of mouse button presses performed. RESULTS: The first observer's intra-observer reproducibility was good (ICC 0.77; p < 0.001) while the second observer's was good-to-excellent (ICC 0.93; p < 0.001). Inter-observer reproducibility between both observers in the first (ICC 0.45; p < 0.001) and second (ICC 0.56; p < 0.001) manual alpha angle assessment was moderate. The intra-class correlation coefficients between manual and automated alpha angle measurements were ICC = 0.24 (p = 0.052; observer 1, 1st measurement), ICC = 0.32 (p = 0.015; observer 1, 2nd measurement), ICC = 0.50 (p < 0.001; observer 2, 1st measurement), and ICC = 0.45 (p < 0.001; observer 2, 2nd measurement). Average runtime for automatic processing of the image data for the automated assessment was 16.6 ± 1.9 min. Automatic alpha angle measurements took longer (time difference: 14.6 ± 3.9 min; p < 0.001) but required less effort (difference in button presses: 231 ± 23; p < 0.001). While the automatic processing is running, the user can perform other tasks. CONCLUSIONS: This pilot study demonstrates that objective and reliable automated alpha angle measurement of MRIs in FAI syndrome hips is feasible. Trial registration The Ethics Committee of the University of Düsseldorf approved our study (Registry-ID: 2017084398).

Lorentzian-Corrected Apparent Exchange-Dependent Relaxation (LAREX) Ω-Plot Analysis-An Adaptation for qCEST in a Multi-Pool System: Comprehensive In Silico, In Situ, and In Vivo Studies.

Based on in silico, in situ, and in vivo studies, this study aims to develop a new method for the quantitative chemical exchange saturation transfer (qCEST) technique considering multi-pool systems. To this end, we extended the state-of-the-art apparent exchange-dependent relaxation (AREX) method with a Lorentzian correction (LAREX). We then validated this new method with in situ and in vivo experiments on human intervertebral discs (IVDs) using the Kendall-Tau correlation coefficient. In the in silico experiments, we observed significant deviations of the AREX method as a function of the underlying exchange rate (kba) and fractional concentration (fb) compared to the ground truth due to the influence of other exchange pools. In comparison to AREX, the LAREX-based Ω-plot approach yielded a substantial improvement. In the subsequent in situ and in vivo experiments on human IVDs, no correlation to the histological reference standard or Pfirrmann classification could be found for the fb (in situ: τ = −0.17 p = 0.51; in vivo: τ = 0.13 p = 0.30) and kba (in situ: τ = 0.042 p = 0.87; in vivo: τ = −0.26 p = 0.04) of Glycosaminoglycan (GAG) with AREX. In contrast, the influence of interfering pools could be corrected by LAREX, and a moderate to strong correlation was observed for the fractional concentration of GAG for both in situ (τ = −0.71 p = 0.005) and in vivo (τ = −0.49 p < 0.001) experiments. The study presented here is the first to introduce a new qCEST method that enables qCEST imaging in systems with multiple proton pools.