Comprehensive benchmarking and guidelines of mosaic variant calling strategies.

Rapid advances in sequencing and analysis technologies have enabled the accurate detection of diverse forms of genomic variants represented as heterozygous, homozygous and mosaic mutations. However, the best practices for mosaic variant calling remain disorganized owing to the technical and conceptual difficulties faced in evaluation. Here we present our benchmark of 11 feasible mosaic variant detection approaches based on a systematically designed whole-exome-level reference standard that mimics mosaic samples, supported by 354,258 control positive mosaic single-nucleotide variants and insertion-deletion mutations and 33,111,725 control negatives. We identified not only the best practice for mosaic variant detection but also the condition-dependent strengths and weaknesses of the current methods. Furthermore, feature-level evaluation and their combinatorial usage across multiple algorithms direct the way for immediate to prolonged improvements in mosaic variant detection. Our results will guide researchers in selecting suitable calling algorithms and suggest future strategies for developers.

Mapping the immune cell landscape of severe atopic dermatitis by single-cell RNA-seq.

BACKGROUND: Efforts to profile atopic dermatitis (AD) tissues have intensified, yet comprehensive analysis of systemic immune landscapes in severe AD remains crucial. METHODS: Employing single-cell RNA sequencing, we analyzed over 300,000 peripheral blood mononuclear cells from 12 severe AD patients (Eczema area and severity index (EASI) > 21) and six healthy controls. RESULTS: Results revealed significant immune cell shifts in AD patients, including increased Th2 cell abundance, reduced NK cell clusters with compromised cytotoxicity, and correlated Type 2 innate lymphoid cell proportions with disease severity. Moreover, unique monocyte clusters reflecting activated innate immunity emerged in very severe AD (EASI > 30). While overall dendritic cells (DCs) counts decreased, a distinct Th2-priming subset termed "Th2_DC" correlated strongly with disease severity, validated across skin tissue data, and flow cytometry with additional independent severe AD samples. Beyond the recognized role of Th2 adaptive immunity, our findings highlight significant innate immune cell alterations in severe AD, implicating their roles in disease pathogenesis and therapeutic potentials. CONCLUSION: Apart from the widely recognized role of Th2 adaptive immunity in AD pathogenesis, alterations in innate immune cells and impaired cytotoxic cells have also been observed in severe AD. The impact of these alterations on disease pathogenesis and the effectiveness of potential therapeutic targets requires further investigation.

Design and Evaluation Challenges of Conversational Agents in Health Care and Well-being: Selective Review Study.

BACKGROUND: Health care and well-being are 2 main interconnected application areas of conversational agents (CAs). There is a significant increase in research, development, and commercial implementations in this area. In parallel to the increasing interest, new challenges in designing and evaluating CAs have emerged. OBJECTIVE: This study aims to identify key design, development, and evaluation challenges of CAs in health care and well-being research. The focus is on the very recent projects with their emerging challenges. METHODS: A review study was conducted with 17 invited studies, most of which were presented at the ACM (Association for Computing Machinery) CHI 2020 conference workshop on CAs for health and well-being. Eligibility criteria required the studies to involve a CA applied to a health or well-being project (ongoing or recently finished). The participating studies were asked to report on their projects' design and evaluation challenges. We used thematic analysis to review the studies. RESULTS: The findings include a range of topics from primary care to caring for older adults to health coaching. We identified 4 major themes: (1) Domain Information and Integration, (2) User-System Interaction and Partnership, (3) Evaluation, and (4) Conversational Competence. CONCLUSIONS: CAs proved their worth during the pandemic as health screening tools, and are expected to stay to further support various health care domains, especially personal health care. Growth in investment in CAs also shows the value as a personal assistant. Our study shows that while some challenges are shared with other CA application areas, safety and privacy remain the major challenges in the health care and well-being domains. An increased level of collaboration across different institutions and entities may be a promising direction to address some of the major challenges that otherwise would be too complex to be addressed by the projects with their limited scope and budget.

The inter-and intra-observer reliability of volar angulation measurements in a fifth metacarpal neck fracture.

INTRODUCTION: The fifth metacarpal neck fracture is the most common metacarpal fracture. The palmar angulation from the fracture displacement is critical for determining treatment, yet there is no consensus regarding the angulation measurement method or the surgical cut-off value. This study aimed to identify a reliable measurement method for assessing palmar angulation. We evaluated inter-observer and intra-observer validation of measuring palmar angulation in oblique plain X-ray and computed tomography (CT) sagittal cuts. MATERIALS AND METHODS: We identified surgically treated patients for acute isolated fifth metacarpal neck fracture between January 1, 2008, and December 31, 2020, and obtained preoperative, opposite hand, and final follow-up oblique X-rays and sagittal computed tomography (CT) radiograms. The oblique radiograph was taken with a 45° posteroanterior pronation. The metacarpal neck palmar angulation was measured in the radiograms using the metacarpal neck-shaft center (MNSC) angle and the shaft articular surface (SAS) angle methods by three orthopedic surgeons in two sessions. For the CT radiograms, each measurer selected the sagittal slot at their discretion to measure the angle. The final palmar angulation was the average of six measurements (two sessions, three measurers per session). RESULTS: The study included 51 patients; the average age was 32.5 (range 18-73) years, with 46 men and 5 women. The MNSC angle inter-observer reliability was better than the SAS angle. The MNSC angle inter-observer reliability was better than that of SAS angle. Intraclass coefficients (ICCs) for the MNSC angle demonstrated an excellent inter-observer agreement among the three measurers in the first (0.93) and second (0.88) session compared to ICCs for the SAS angle in the first (0.81) and second (0.87) session. The MNSC angle intra-observer reliability was also better than the SAS angle, with higher ICCs. Preoperative CT radiograms were available for 42 patients. Using CT scans for measurements, in the two sessions, the MNSC angle inter-observer reliability was higher than that of the SAS angle [MNSC: 0.83; SAS: 0.35], second [MSNC: 0.85; SAS: 0.81]. The intra-observer reliability was also better in the MNSC angle. When comparing average value among obtained radiograms, the physiologic angulation of the opposite hand oblique X-ray had the smallest average value, followed by preoperative CT and preoperative oblique radiography. Overall, the SAS angle measurement had a slightly larger angle than the MNSC method in the fractured and non-fractured hand measurements. Finally, a serial comparison of the oblique X-rays (pre-and postoperative, final follow-up, and the opposite hand with closed reduction and internal fixation) indicated that the angulation significantly decreased, and the post-operative values did not differ from the final follow-up X-ray for either method. CONCLUSIONS: The palmar angulation measurement in 45° pronated oblique X-ray using the MNSC angle method had good-to-excellent reliability, with superior results to sagittal CT radiograms. Although the angle is likely overestimated, the MNSC method is reliable for judging the fracture degree and reduction adequacy after surgery compared to the non-fractured hand physiologic angulation.

Hierarchical Phased-Array Antennas Coupled to Al KIDs: A Scalable Architecture for Multi-band Millimeter/Submillimeter Focal Planes.

We present the optical characterization of two-scale hierarchical phased-array antenna kinetic inductance detectors (KIDs) for millimeter/submillimeter wavelengths. Our KIDs have a lumped-element architecture with parallel plate capacitors and aluminum inductors. The incoming light is received with a hierarchical phased array of slot dipole antennas, split into 4 frequency bands (between 125 GHz and 365 GHz) with on-chip lumped-element band-pass filters, and routed to different KIDs using microstriplines. Individual pixels detect light for the 3 higher-frequency bands (190-365 GHz), and the signals from four individual pixels are coherently summed to create a larger pixel detecting light for the lowest frequency band (125-175 GHz). The spectral response of the band-pass filters was measured using Fourier transform spectroscopy (FTS), the far-field beam pattern of the phased-array antennas was obtained using an infrared source mounted on a 2-axis translating stage, and the optical efficiency of the KIDs was characterized by observing loads at 294 K and 77 K. We report on the results of these three measurements.

MicroRNA­606 inhibits the growth and metastasis of triple­negative breast cancer by targeting Stanniocalcin 1.

Triple­negative breast cancer (TNBC) is associated with a poor prognosis; however, treatments for TNBC are limited, with poor outcomes. MicroRNAs (miRNAs/miRs) are small non­coding RNA molecules that are able to regulate gene expression. The present study aimed to identify differentially expressed miRNAs in patients with breast cancer, and to investigate the functional role of the identified miRNA targets and their effects in vitro and in vivo. Transfection with miR­606 suppressed TNBC cell proliferation, migration, invasion and tumor sphere­forming ability, as determined using trypan blue, Transwell and sphere formation assays. Moreover, miR­606 induced the apoptosis of TNBC cells, as determined by flow cytometric analysis. Furthermore, intratumoral injections of miR­606 mimics suppressed tumor growth in MDA­MB­231 xenografts. In addition, MDA­MB­231 cells transfected with miR­606 mimics exhibited decreased lung metastatic nodules in a mouse tail vein injection model. Notably, miR­606 and STC1 expression had opposing effects on the overall survival of patients with TNBC. The results of the present study suggested a novel tumor suppressor function for miR­606 in TNBC, thus indicating its potential application in the development of anticancer miRNA therapeutics.

The Effect of an mHealth Self-Monitoring Intervention (MI-BP) on Blood Pressure Among Black Individuals With Uncontrolled Hypertension: Randomized Controlled Trial.

BACKGROUND: Hypertension is one of the most important cardiovascular disease risk factors and affects >100 million American adults. Hypertension-related health inequities are abundant in Black communities as Black individuals are more likely to use the emergency department (ED) for chronic disease-related ambulatory care, which is strongly linked to lower blood pressure (BP) control, diminished awareness of hypertension, and adverse cardiovascular events. To reduce hypertension-related health disparities, we developed MI-BP, a culturally tailored multibehavior mobile health intervention that targeted behaviors of BP self-monitoring, physical activity, sodium intake, and medication adherence in Black individuals with uncontrolled hypertension recruited from ED and community-based settings. OBJECTIVE: We sought to determine the effect of MI-BP on BP as well as secondary outcomes of physical activity, sodium intake, medication adherence, and BP control compared to enhanced usual care control at 1-year follow-up. METHODS: We conducted a 1-year, 2-group randomized controlled trial of the MI-BP intervention compared to an enhanced usual care control group where participants aged 25 to 70 years received a BP cuff and hypertension-related educational materials. Participants were recruited from EDs and other community-based settings in Detroit, Michigan, where they were screened for initial eligibility and enrolled. Baseline data collection and randomization occurred approximately 2 and 4 weeks after enrollment to ensure that participants had uncontrolled hypertension and were willing to take part. Data collection visits occurred at 13, 26, 39, and 52 weeks. Outcomes of interest included BP (primary outcome) and physical activity, sodium intake, medication adherence, and BP control (secondary outcomes). RESULTS: We obtained consent from and enrolled 869 participants in this study yet ultimately randomized 162 (18.6%) participants. At 1 year, compared to the baseline, both groups showed significant decreases in systolic BP (MI-BP group: 22.5 mm Hg decrease in average systolic BP and P<.001; control group: 24.1 mm Hg decrease and P<.001) adjusted for age and sex, with no significant differences between the groups (time-by-arm interaction: P=.99). Similar patterns where improvements were noted in both groups yet no differences were found between the groups were observed for diastolic BP, physical activity, sodium intake, medication adherence, and BP control. Large dropout rates were observed in both groups (approximately 60%). CONCLUSIONS: Overall, participants randomized to both the enhanced usual care control and MI-BP conditions experienced significant improvements in BP and other outcomes; however, differences between groups were not detected, speaking to the general benefit of proactive outreach and engagement focused on cardiometabolic risk reduction in urban-dwelling, low-socioeconomic-status Black populations. High dropout rates were found and are likely to be expected when working with similar populations. Future work is needed to better understand engagement with mobile health interventions, particularly in this population. TRIAL REGISTRATION: ClinicalTrials.gov NCT02955537; https://clinicaltrials.gov/study/NCT02955537. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): RR2-10.2196/12601.

Correction: The Effect of an mHealth Self-Monitoring Intervention (MI-BP) on Blood Pressure Among Black Individuals With Uncontrolled Hypertension: Randomized Controlled Trial.

[This corrects the article DOI: 10.2196/57863.].

Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis.

Single-cell transcriptome data provide a unique opportunity to explore the gene networks of a particular cell type. However, insufficient capture rate and high dimensionality of single-cell RNA sequencing (scRNA-seq) data challenge cell-type-specific gene network (CGN) reconstruction. Here, we demonstrated that the imputation of scRNA-seq data enables reconstruction of CGNs by effective retrieval of gene functional associations. We reconstructed CGNs for seven primary and nine metastatic breast cancer cell lines using scRNA-seq data with imputation. Key genes for primary or metastatic cell lines were prioritized based on network centrality measures and CGN hub genes that were presumed to be the major determinant of cell type characteristics. To identify novel genes in breast cancer metastasis, we used the average rank difference of centrality between the primary and metastatic cell lines. Genes predicted using CGN centrality analysis were more enriched for known breast cancer metastatic genes than those predicted using differential expression. The molecular chaperone CCT2 was identified as a novel gene for breast metastasis during knockdown assays of several candidate genes. Overall, our study demonstrated an effective CGN reconstruction technique with imputation of scRNA-seq data and the feasibility of identifying key genes for particular cell subsets using single-cell network analysis.

Establishment of reference standards for multifaceted mosaic variant analysis.

Detection of somatic mosaicism in non-proliferative cells is a new challenge in genome research, however, the accuracy of current detection strategies remains uncertain due to the lack of a ground truth. Herein, we sought to present a set of ultra-deep sequenced WES data based on reference standards generated by cell line mixtures, providing a total of 386,613 mosaic single-nucleotide variants (SNVs) and insertion-deletion mutations (INDELs) with variant allele frequencies (VAFs) ranging from 0.5% to 56%, as well as 35,113,417 non-variant and 19,936 germline variant sites as a negative control. The whole reference standard set mimics the cumulative aspect of mosaic variant acquisition such as in the early developmental stage owing to the progressive mixing of cell lines with established genotypes, ultimately unveiling 741 possible inter-sample relationships with respect to variant sharing and asymmetry in VAFs. We expect that our reference data will be essential for optimizing the current use of mosaic variant detection strategies and for developing algorithms to enable future improvements.

The Association of Low Skeletal Muscle Mass with Complex Distal Radius Fracture.

Objectives: Sarcopenia is a skeletal muscle loss disease with adverse outcomes, including falls, mortality, and cardiovascular disease (CVD) in older patients. Distal radius fractures (DRF), common in older people, are strongly related to falls. We aimed to investigate the correlation between DRF and low skeletal muscle mass, which strongly correlated to sarcopenia. Methods: We performed a retrospective review of data from patients diagnosed with or without DRF in our institute between 2015 and 2020. Finally, after propensity score matching, data from 115 patients with and 115 patients without DRF were used for analyses. Multivariate logistic regression analysis was performed for sex, body mass index (BMI), the presence of low skeletal muscle mass, bone quality measured by dual-energy X-ray absorptiometry (DXA), and comorbidities (diabetes mellitus, CVD). Results: We found that female sex (odds ratio = 3.435, p = 0.015), CVD (odds ratio = 5.431, p < 0.001) and low skeletal muscle mass (odds ratio = 8.062, p = 0.001) were significant predictors for DRF. BMI and osteoporosis were not statistically significantly related to DRF. Conclusions: Women with low skeletal muscle mass and CVD may be more responsible for DRF than osteoporosis.

Are Outcomes Comparable for Repair of AO/OTA Type 13C1 and Type 13C2 Distal Humeral Fractures Using the Paratricipital Approach?

Background: Studies have reported favorable outcomes using the paratricipital approach for fixation of distal humeral intra-articular fractures. However, literature evaluating the clinical results of the approach remains limited. The objective of this study was to compare clinical outcomes between type 13C2 and type 13C1 distal humeral fractures after open reduction and internal fixation performed using the same approach and same type of plate. Methods: A total of 52 adults with type 13C1 or 13C2 distal humeral fractures were treated surgically at our institution during 2006 to 2018. We retrospectively analyzed data from 29 of these patients (19 with type 13C1 fractures and 10 with 13C2 fractures) who met the inclusion criteria. All subjects were followed for a minimum of 2 years postoperatively. Clinical and radiologic results were analyzed to determine differences in outcomes between the two types of fractures. Clinical results were evaluated using elbow range of motion (ROM), Mayo Elbow Performance Score (MEPS), and Quick Disabilities of the Arm, Shoulder and Hand (Q-DASH) score. Alignment, fracture union, and presence of posttraumatic arthritis were evaluated radiologically. Results: The patients' mean age was 51 years, and the mean duration of follow-up was 29 months. Mean ROM was 129.5° ± 21.5° in the type 13C1 group and 123.0° ± 20.6° in the 13C2 group (p = 0.20). Mean Q-DASH score was 12.6 ± 11.7 in the 13C1 group and 16.2 ± 19.8 in the 13C2 group (p = 0.60). Mean MEPS was 92.9 ± 8.5 in the 13C1 group and 85.0 ± 14.1 in the 13C2 group (p = 0.09). Carrying angle did not differ significantly between the 13C1 and 13C2 groups. No patient in either group exhibited nonunion or posttraumatic arthritis. Conclusions: Although the paratricipital approach has the disadvantage of limited visualization of articular surfaces, there were no differences in surgical outcomes between type 13C1 and type 13C2 distal humeral fractures after fixation using this approach. Thus, surgeons may need to consider using the paratricipital approach for open reduction and internal fixation of 13C2 distal humeral fractures.

Nucleophilicity and accessibility calculations of alkanolamines: applications to carbon dioxide absorption reactions.

Both nucleophilicities and accessibilities of three alkanolamines [monoethanolamine (MEA), (2-(methylamino)ethanol (MAE), and 2-amino-2-methyl-1-propanol (AMP)] were calculated to predict their reactivities with CO(2). After DFT geometry-optimization calculations, the global, group, and atomic nucleophilicities of each amine were obtained using MP2 quantum mechanical calculations. Only global nucleophilicity matched an experimental pK(a) order (MAE > AMP > MEA). However, it failed to predict the slow rate of the sterically hindered AMP and the order of rate constants, MAE > MEA > AMP. The accessibilities of amines to CO(2) have been calculated by MD simulations by monitoring collisions at the reaction centers: N atoms in amines and C in CO(2). The accessibility results indicate that global nucleophilicity needs quantitative correction for steric effects to predict better reactivities of amines with CO(2).

Crystal structure and electronic properties of 2-amino-2-methyl-1-propanol (AMP) carbamate.

A crystal structure of a carbamate of 2-amino-2-methyl-1-propanol (AMP-carbamate) has been elucidated and its structural and electronic properties investigated by density functional theory calculations and natural bond orbital analyses.