ScopeViewer: A Browser-Based Solution for Visualizing Spatial Transcriptomics Data.

Motivation: Spatial transcriptomics (ST) enables a high-resolution interrogation of molecular characteristics within specific spatial contexts and tissue morphology. Despite its potential, visualization of ST data is a challenging task due to the complexities in handling, sharing and visualizing large image datasets together with molecular information. Results: We introduce ScopeViewer, a browser-based software designed to overcome these challenges. ScopeViewer offers the following functionalities: (1) It visualizes large image data and associated annotations at various zoom levels, allowing for intricate exploration of the data; (2) It enables dual interactive viewing of the original images along with their annotations, providing a comprehensive understanding of the context; (3) It displays spatial molecular features with optimized bandwidth, ensuring a smooth user experience; and (4) It bolsters data security by circumventing data transfers. Availability: ScopeViewer is available at: https://datacommons.swmed.edu/scopeviewer.

Clinical and prostate multiparametric magnetic resonance imaging findings as predictors of general and clinically significant prostate cancer risk: A retrospective single-center study.

Background: To evaluate the predictive values of Prostate Imaging Reporting and Data System version 2 (PI-RADS v2), prostate-specific antigen (PSA) level, PSA density (PSAD), digital rectal examination findings, and prostate volume, individually and in combination, for the detection of prostate cancer (PCa) in biopsy-naive patients. Methods: We retrospectively analyzed 630 patients who underwent transrectal systematic prostate biopsy following prostate multiparametric magnetic resonance imaging. A standard 12-core biopsy procedure was performed. Univariate and multivariate analyses were performed to determine the significant predictors of clinically significant cancer but not PCa. Results: The median age, PSA level, and PSAD were 70 years, 8.6 ng/mL, and 0.18 ng/mL/mL, respectively. A total of 374 (59.4%) of 630 patients were biopsy-positive for PCa, and 241 (64.4%) of 374 were diagnosed with clinically significant PCa (csPCa). The PI-RADS v2 score and PSAD were independent predictors of PCa and csPCa. The PI-RADS v2 score of 5 regardless of the PSAD value, or PI-RADS v2 score of 4 plus a PSAD of <0.3 ng/mL/mL, was associated with the highest csPCa detection rate (36.1%-82.1%). Instead, the PI-RADS v2 score of <3 and PSAD of <0.3 ng/mL/mL yielded the lowest risk of csPCa. Conclusion: The combination of the PI-RADS v2 score and PSAD could prove to be a helpful and reliable diagnostic tool before performing prostate biopsies. Patients with a PI-RADS v2 score of <3 and PSAD of <0.3 ng/mL/mL could potentially avoid a prostate biopsy.

Corrigendum: CD317-Positive Immune Stromal Cells in Human "Mesenchymal Stem Cell" Populations.

[This corrects the article DOI: 10.3389/fimmu.2022.903796.].

CD317-Positive Immune Stromal Cells in Human "Mesenchymal Stem Cell" Populations.

Heterogeneity of bone marrow mesenchymal stromal cells (MSCs, frequently referred to as "mesenchymal stem cells") clouds biological understanding and hampers their clinical development. In MSC cultures most commonly used in research and therapy, we have identified an MSC subtype characterized by CD317 expression (CD317pos (29.77 ± 3.00% of the total MSC population), comprising CD317dim (28.10 ± 4.60%) and CD317bright (1.67 ± 0.58%) MSCs) and a constitutive interferon signature linked to human disease. We demonstrate that CD317pos MSCs induced cutaneous tissue damage when applied a skin explant model of inflammation, whereas CD317neg MSCs had no effect. Only CD317neg MSCs were able to suppress proliferative cycles of activated human T cells in vitro, whilst CD317pos MSCs increased polarization towards pro-inflammatory Th1 cells and CD317neg cell lines did not. Using an in vivo peritonitis model, we found that CD317neg and CD317pos MSCs suppressed leukocyte recruitment but only CD317neg MSCs suppressed macrophage numbers. Using MSC-loaded scaffolds implanted subcutaneously in immunocompromised mice we were able to observe tissue generation and blood vessel formation with CD317neg MSC lines, but not CD317pos MSC lines. Our evidence is consistent with the identification of an immune stromal cell, which is likely to contribute to specific physiological and pathological functions and influence clinical outcome of therapeutic MSCs.

The Comparison of Imaging and Clinical Methods to Estimate Prostate Volume: A Single-Centre Retrospective Study.

BACKGROUND: Prostate volume (PV) is a useful tool in risk stratification, diagnosis, and follow-up of numerous prostatic diseases including prostate cancer and benign prostatic hypertrophy. There is currently no accepted ideal PV measurement method. OBJECTIVE: This study compares multiple means of PV estimation, including digital rectal examination (DRE), transrectal ultrasound (TRUS), and magnetic resonance imaging (MRI), and radical prostatectomy specimens to determine the best volume measurement style. METHODS: A retrospective, observational, single-site study with patients identified using an institutional database was performed. A total of 197 patients who underwent robot-assisted radical prostatectomy were considered. Data collected included age, serum PSA at the time of the prostate biopsy, clinical T stage, Gleason score, and PVs for each of the following methods: DRE, TRUS, MRI, and surgical specimen weight (SPW) and volume. RESULTS: A paired t test was performed, which reported a statistically significant difference between PV measures (DRE, TRUS, MRI ellipsoid, MRI bullet, SP ellipsoid, and SP bullet) and the actual prostate weight. Lowest differences were reported for SP ellipsoid volume (M = -2.37; standard deviation [SD] = 10.227; t[167] = -3.011; and p = 0.003), MRI ellipsoid volume (M = -4.318; SD = 9.53; t[167] = -5.87; and p = 0.000), and MRI bullet volume (M = 5.31; SD = 10.77; t[167] = 6.387; and p = 0.000). CONCLUSION: The PV obtained by MRI has proven to correlate with the PV obtained via auto-segmentation software as well as actual SPW, while also being more cost-effective and time-efficient. Therefore, demonstrating that MRI estimated the PV is an adequate method for use in clinical practice for therapeutic planning and patient follow-up.

Complications of ventilation tube insertion in children with and without cleft palate: a nested case-control comparison.

IMPORTANCE: Optimizing hearing in patients with cleft lip and/or palate (CLP) by early recognition and management of otitis media with effusion is essential for speech development. Some evidence has suggested higher complication rates from ventilation tube (VT) insertion in patients with CLP and has led to a trend not to treat these patients surgically. However, studies have failed to match comparison groups for age and sex. OBJECTIVE: To compare complication rates from VT insertion in pediatric patients with and without CLP. DESIGN, SETTING, AND PARTICIPANTS: The study used a nested case-control design to evaluate 60 pediatric patients with CLP who underwent VT insertion at a children's hospital. The control group of age- and sex-matched patients was selected from a database of 2943 VT insertions. INTERVENTIONS: All patients were administered general anesthesia and underwent VT insertion by a pediatric otorhinolaryngology (ENT) team. MAIN OUTCOMES AND MEASURES: The primary outcomes were numbers of otorrhea complications. Secondarily, rates of attendance at an ENT clinic specifically for complications were evaluated. Finally, numbers of complications other than otorrhea were assessed but not statistically analyzed owing to the varied types and low numbers in each group. RESULTS: The control cohort had 151 documented cases of otorrhea compared with 121 in the CLP group (ratio 1.25:1); the difference between groups was not statistically significant (P = .52). There was no significant difference in mean ENT clinic visits per patient for complications between groups (0.80 in the CLP group, 0.78 for controls) (P = .66). Regarding complications other than otorrhea, the control group reported more than the CLP group (43 vs 25; ratio, 1.7:1). CONCLUSIONS AND RELEVANCE: Complication rates of VT placement among patients with CLP were not higher than those among patients without CLP. Therefore, treatment with VT insertion should be administered to patients with CLP under the same guidelines as for those without CLP. Indeed, there could be an argument for a shift in practice toward more aggressive treatment of patients with CLP, who are already vulnerable to speech and social developmental delay.

Patient involvement in quality improvement: is it time we let children, young people and families take the lead?

It is vital to involve children, young people and families in the design, delivery and improvement of their care. Their involvement can range from individuals giving feedback, such as patient stories, to collaborative work including patient groups and communities helping to develop and commission services. The methods for involving individuals and families include questionnaires and innovative ideas such as feedback Apps. Other methods include the 15 Steps Challenge which helps an organisation to view the care it delivers through a patients eyes and includes a 'walk around' involving a patient, carer, staff member and board member. The Experience Based Design approach is another method of reviewing a service and involves assessing how staff and patients feel when delivering and receiving care. Involving patient groups can be facilitated by working with schools and children's centres. The type of involvement will vary, but if carefully designed can allow meaningful participation and improvement of services.