Gossamer: Scaling Image Processing and Reconstruction to Whole Brains.

Neuronal reconstruction-a process that transforms image volumes into 3D geometries and skeletons of cells-bottlenecks the study of brain function, connectomics and pathology. Unlike artistic domains with similar challenges (e.g., hair modeling), scientists need exact and complete segmentations to study subtle topological differences. Existing methods are disk-bound, dense-access, coupled, single-threaded, algorithmically unscalable and require manual cropping of small windows and proofreading of skeletons due to low topological accuracy. Designing a data-intensive parallel solution suited to a neurons' shape, topology and far-ranging connectivity is particularly challenging due to I/O and load-balance, yet by abstracting vision tasks such as segmentation and skeletonization into strategically ordered specializations of search, we progressively lower memory by 4 orders of magnitude. This enables 1 mouse brain to be fully processed in-memory on a single server, at 67× the scale with 870× less memory while having 78% higher automated yield than the highest performing alternative methods.

Liquid-liquid phase reaction between crystal violet and sodium hydroxide: kinetic study and precipitate analysis.

To investigate reaction order and kinetic parameters of the reaction between crystal violet (CV) and sodium hydroxide (NaOH), various concentrations of the reactants were applied. The present work also verifies the unknown solid product produced under highly concentrated conditions. The reaction orders of CV and NaOH were determined to be 1 and 1.08 by pseudo rate method, respectively, with a rate constant, k, of 0.054 [(M-1.08) s-1]. In addition to pseudo rate method, the half-life approach was used to calculate the overall reaction order to verify the accuracy of pseudo rate method. The overall reaction order was determined to be 1.9 by the half-life method. The overall reaction order based on the two methods studied was approximately 2. The precipitate formation was observed when high concentrations of CV (0.01-0.1 M) and NaOH (1.0 M) were applied. Fourier transform infrared (FTIR) spectroscopy was used to compare the spectra of the precipitate generated and a commercial solvent violet 9 (SV9). Based on the FTIR spectra, it was confirmed that the molecular structure of the precipitate matched that of solvent violet 9.

Barriers to Collection and Use of Patient-Reported Outcomes A Multi-Institutional Survey of Surgeons and Care Teams.

BACKGROUND: Currently there is a lack of insight into what total joint replacement (TJR) surgeons and care teams perceive to be the greatest barriers to collection and use of patient reported outcomes (PROs). The goal of this study was to provide insight on this topic using a multi-institutional survey. METHODS: A thorough literature review on PROs adoption and utilization was conducted to generate a 26-question survey. This survey was disseminated to joint replacement surgeons, associate providers (e.g., nurse practitioners and physician assistants), and other non-clinical health care staff involved in PRO collection at three institutions. Data from all respondents were analyzed qualitatively and using chi-square tests. RESULTS: Of 37 responses, 24 (65%) were from orthopedic surgeons and 13 (35%) from other clinical and administrative staff. Seventy-one percent of surgeons thought that integration into clinical workflow was the greatest barrier to initial implementation of PROs, while the greatest long-term limitations were accessibility (50%), patient engagement and compliance (50%), ability to represent their health in PROs (54%), and consistency across providers (50%). For PROs to be clinically useful, surgeons required that they should be linked to the EMR interface (65%), immediately available (59%), and are trended over time (59%). Fifty-four percent of surgeons across institutions believed administrative leadership was ultimately responsible for successful PROs implementation, while 46% of other staff believed that responsibility fell to surgeons and clinical staff. CONCLUSION: Surgeons perceive that the greatest barriers to PRO collection are workflow integration initially, and patient engagement, compliance, and ability to represent their health in PROs over the long term. Stakeholders inconsistently report which group is responsible for successful implementation.

Orthopedic Surgeon and Care Team Perceptions and Use of Patient-Reported Outcomes in Total Joint Replacement Patients.

BACKGROUND: The recent shift toward value-based health care and bundled payments in orthopedic surgery has increased the use patient-reported outcomes (PROs) in standard clinical care. Such assessments of patient function and satisfaction are particularly important among total joint arthroplasty (TJA) patients to monitor postoperative health. PURPOSE: The purpose of this study was to assess orthopedic care team perceptions of current and future PRO usage and compare current rates and modes of PRO collection between three urban, academic health care systems. METHODS: A literature search was conducted on current PRO uses and barriers to their adoption to generate a 26-question survey. The survey was disseminated to orthopedic surgeons and care team members at three academic health care institutions (institutions A, B, and C). Responses were analyzed for qualitative and quantitative insights. RESULTS: Among institutions A, B, and C, PRO collection generally declined from baseline (60%, 90%, 89%) to 6 weeks (67%, 82%, 71%) and 3 months postoperatively (44%, 36%, 47%). However, there were large variations in reported PRO collection intervals among institutions. Respondents reported assessing patient baseline functional status as the most useful current application of PROs and cited the prediction of patient benefit from TJA as the most useful future application for PROs. Though respondents were largely optimistic about PRO utility in clinical care, a small minority remained skeptical. CONCLUSIONS: Perceptions of PRO utilization and collection intervals varied considerably among respondents. For PROs to be an accurate and useful clinical tool, standardization and thorough understanding of PRO collection among orthopedic care team members is essential.

Cellular anatomy of the mouse primary motor cortex.

An essential step toward understanding brain function is to establish a structural framework with cellular resolution on which multi-scale datasets spanning molecules, cells, circuits and systems can be integrated and interpreted1. Here, as part of the collaborative Brain Initiative Cell Census Network (BICCN), we derive a comprehensive cell type-based anatomical description of one exemplar brain structure, the mouse primary motor cortex, upper limb area (MOp-ul). Using genetic and viral labelling, barcoded anatomy resolved by sequencing, single-neuron reconstruction, whole-brain imaging and cloud-based neuroinformatics tools, we delineated the MOp-ul in 3D and refined its sublaminar organization. We defined around two dozen projection neuron types in the MOp-ul and derived an input-output wiring diagram, which will facilitate future analyses of motor control circuitry across molecular, cellular and system levels. This work provides a roadmap towards a comprehensive cellular-resolution description of mammalian brain architecture.

Trans Woman Voice Questionnaire Scores Highlight Specific Benefits of Adjunctive Glottoplasty With Voice Therapy in Treating Voice Feminization.

BACKGROUND: Treatment options to assist patients to produce a more perceptually feminine voice include voice therapy (VT) and surgeries to elevate pitch such as the Wendler glottoplasty (WG). The Trans Woman Voice Questionnaire (TWVQ) is a validated quality of life measure for trans women's self-reported perceptions of their voice and is frequently administered before and after such interventions. The 30 statements broadly pertain to how feminine a patient feels their voice is, how effortful it is to produce their voice, and how their voice impacts them psychosocially, making it a useful and specific outcome measure when treating trans females for voice concerns. OBJECTIVE: To compare quality of life outcomes between VT and VT with adjunct WG (VT+WG) based on changes in ratings of individual statements on the TWVQ. MATERIALS AND METHODS: A retrospective case series of 31 trans female patients treated was completed. A total of 17 patients underwent VT and 14 underwent VT with adjunctive WG. Ratings for each of the 30 TWVQ statements were compared before and after treatment for each group. Wilcoxon rank-sum tests were used to compare rating changes before and after treatment. Spearman rank-order correlation tests were used to assess the association between total TWVQ score and "current voice" rating. RESULTS: WG was associated with statistically significantly improved ratings for every statement on the TWVQ except one. In contrast, VT was associated with statistically significant improvements in 16 of the 30 statements, which largely pertained to patient emotions surrounding their voice rather than physical aspects such as pitch and dysphonia. Furthermore, while both WG+VT and VT improved the "current voice" rating significantly, WG improved the score by nearly 1 unit more. Lastly, we found a positive association between the total TWVQ score and current voice rating, indicating that lower scores were associated with more self-perceived feminine-sounding voices (P < 0.01). CONCLUSIONS: Both VT and VT+WG result in improvements in the TWVQ. The specific statements on the TWVQ offer insight into specific quality of life treatment outcomes, with VT associated with improvements in mostly psychosocial aspects of voice production and VT+WG with both psychosocial and physical aspects.

A multimodal and integrated approach to interrogate human kidney biopsies with rigor and reproducibility: guidelines from the Kidney Precision Medicine Project.

Comprehensive and spatially mapped molecular atlases of organs at a cellular level are a critical resource to gain insights into pathogenic mechanisms and personalized therapies for diseases. The Kidney Precision Medicine Project (KPMP) is an endeavor to generate three-dimensional (3-D) molecular atlases of healthy and diseased kidney biopsies by using multiple state-of-the-art omics and imaging technologies across several institutions. Obtaining rigorous and reproducible results from disparate methods and at different sites to interrogate biomolecules at a single-cell level or in 3-D space is a significant challenge that can be a futile exercise if not well controlled. We describe a "follow the tissue" pipeline for generating a reliable and authentic single-cell/region 3-D molecular atlas of human adult kidney. Our approach emphasizes quality assurance, quality control, validation, and harmonization across different omics and imaging technologies from sample procurement, processing, storage, shipping to data generation, analysis, and sharing. We established benchmarks for quality control, rigor, reproducibility, and feasibility across multiple technologies through a pilot experiment using common source tissue that was processed and analyzed at different institutions and different technologies. A peer review system was established to critically review quality control measures and the reproducibility of data generated by each technology before their being approved to interrogate clinical biopsy specimens. The process established economizes the use of valuable biopsy tissue for multiomics and imaging analysis with stringent quality control to ensure rigor and reproducibility of results and serves as a model for precision medicine projects across laboratories, institutions and consortia.

Specific viral RNA drives the SARS CoV-2 nucleocapsid to phase separate.

A mechanistic understanding of the SARS-CoV-2 viral replication cycle is essential to develop new therapies for the COVID-19 global health crisis. In this study, we show that the SARS-CoV-2 nucleocapsid protein (N-protein) undergoes liquid-liquid phase separation (LLPS) with the viral genome, and propose a model of viral packaging through LLPS. N-protein condenses with specific RNA sequences in the first 1000 nts (5'-End) under physiological conditions and is enhanced at human upper airway temperatures. N-protein condensates exclude non-packaged RNA sequences. We comprehensively map sites bound by N-protein in the 5'-End and find preferences for single-stranded RNA flanked by stable structured elements. Liquid-like N-protein condensates form in mammalian cells in a concentration-dependent manner and can be altered by small molecules. Condensation of N-protein is sequence and structure specific, sensitive to human body temperature, and manipulatable with small molecules thus presenting screenable processes for identifying antiviral compounds effective against SARS-CoV-2.

Voice Outcomes After Radiation for Early-Stage Laryngeal Cancer.

OBJECTIVES: Radiation treatment for laryngeal cancer has been shown to cause tissue changes to the vocal folds, which can result in degradation of voice. Our objective in this study was to investigate changes in perceptual, acoustic, and patient-reported outcomes over an extended period of follow-up after radiation. DESIGN: Retrospective review. METHODS: All patients treated with radiation for early-stage laryngeal carcinoma (in situ, T1, or T2) by a single surgeon from 2011-2018 were reviewed. Demographics and treatment information were recorded. Only patients with at least two dates of follow-up with acoustic data (cepstral spectral index of dysphonia [CSID]) and patient-reported surveys (voice handicap index-10 [VHI-10]) were included. Voice samples were rated by two senior speech-language pathologists on the grade, roughness, breathiness, asthenia, and strain scale. RESULTS: Of 115 patients with early-stage laryngeal cancer, 31 patients met inclusion criteria. The average follow-up from time of treatment was 9.6 years (range 3.0-20.3 years), and the average time in between the first and last voice recordings was 2.6 years (range 0.3-5.5 years). The lesions represented were carcinoma in situ (n = 4), T1 (n = 22), and T2 (n = 5). The VHI-10 scores worsened slightly (mean increase +0.27, median +1) from first to last measurements as did the CSID score (median increase +7.0, median +7.4), though neither reached statistical significance when correlated with time since radiation (P = 0.269 and P = 0.0850). Perceptual analysis as rated by two speech-language pathologists raters showed excellent inter-rater reliability (Cronbach's alpha = 0.84), with no significant change over time (mean +0.39, median, with P = 0.347). Grade, roughness, breathiness, asthenia, and strain, VHI-10, and CSID were all correlated (all pairwise comparisons P < 0.001). CONCLUSION: Perceptual, acoustic, and patient-reported outcomes years after radiation for early-stage laryngeal cancer do not show voice degradation over time in this preliminary analysis. Further research with a larger cohort may elucidate voice changes in this population.

Defining and Optimizing Value in Total Joint Arthroplasty From the Patient, Payer, and Provider Perspectives.

BACKGROUND: The purpose of this study is to define value in bundled total joint arthroplasty (TJA) from the differing perspectives of the patient, payer/employer, and hospital/provider. METHODS: Demographic, psychosocial, clinical, financial, and patient-reported outcomes (PROs) data from 2017 to 2018 elective TJA cases at a multihospital academic health system were queried. Value was defined as improvement in PROs (preoperatively to 1 year postoperatively) for patients, improvement in PROs per $1000 of bundle cost for payers, and the normalized sum of improvement in PROs and hospital bundle margin for providers. Bivariate analysis was used to compare high value vs low value (>50th percentile vs <50th percentile). Multivariate analysis was performed to identify predictors. RESULTS: A total of 280 patients had PRO data, of which 71 had Medicare claims data. Diabetes (odds ratio [OR], 0.45; P = .02) predicted low value for patients; female gender (OR, 0.25), hypertension (OR, 0.17), pulmonary disease (OR, 0.12), and skilled nursing facility discharge (OR, 0.17) for payers (P ≤ .03 for all); and pulmonary disease (OR, 0.16) and skilled nursing facility discharge (OR, 0.19) for providers (P ≤ .04 for all). CONCLUSION: This is the first article to define value in TJA under a bundle payment model from multiple perspectives, providing a foundation for future studies analyzing value-based TJA.

Publisher Correction: Somatic APP gene recombination in Alzheimer's disease and normal neurons.

In this Article, the top label in Fig. 5d should read 'DISH 3/16' instead of 'DISH 3/17'. This error has been corrected online.

Somatic APP gene recombination in Alzheimer's disease and normal neurons.

The diversity and complexity of the human brain are widely assumed to be encoded within a constant genome. Somatic gene recombination, which changes germline DNA sequences to increase molecular diversity, could theoretically alter this code but has not been documented in the brain, to our knowledge. Here we describe recombination of the Alzheimer's disease-related gene APP, which encodes amyloid precursor protein, in human neurons, occurring mosaically as thousands of variant 'genomic cDNAs' (gencDNAs). gencDNAs lacked introns and ranged from full-length cDNA copies of expressed, brain-specific RNA splice variants to myriad smaller forms that contained intra-exonic junctions, insertions, deletions, and/or single nucleotide variations. DNA in situ hybridization identified gencDNAs within single neurons that were distinct from wild-type loci and absent from non-neuronal cells. Mechanistic studies supported neuronal 'retro-insertion' of RNA to produce gencDNAs; this process involved transcription, DNA breaks, reverse transcriptase activity, and age. Neurons from individuals with sporadic Alzheimer's disease showed increased gencDNA diversity, including eleven mutations known to be associated with familial Alzheimer's disease that were absent from healthy neurons. Neuronal gene recombination may allow 'recording' of neural activity for selective 'playback' of preferred gene variants whose expression bypasses splicing; this has implications for cellular diversity, learning and memory, plasticity, and diseases of the human brain.

Clinical and Economic Impact of an Integrated Care Team Model on Targeted, High-Risk Medicare Patients With Type 2 Diabetes.

IN BRIEF "Quality Improvement Success Stories" are published by the American Diabetes Association in collaboration with the American College of Physicians, Inc., and the National Diabetes Education Program. This series is intended to highlight best practices and strategies from programs and clinics that have successfully improved the quality of care for people with diabetes or related conditions. Each article in the series is reviewed and follows a standard format developed by the editors of Clinical Diabetes. The following article describes a referral-based program for managing high-risk patients with type 2 diabetes in California.

Nanoscale helium ion microscopic analysis of collagen fibrillar changes following femtosecond laser dissection of human cornea.

Over the last decade, femtosecond lasers have emerged as an important tool to perform accurate and fine dissections with minimal collateral damage in biological tissue. The most common surgical procedure in medicine utilizing femtosecond laser is LASIK. During the femtosecond laser dissection process, the corneal collagen fibers inevitably undergo biomechanical and thermal changes on a sub-micro- or even a nanoscale level, which can potentially lead to post-surgical complications. In this study, we utilized helium ion microscopy, complemented with transmission electron microscopy to examine the femtosecond laser-induced collagen fibrillar damage in ex vivo human corneas. We found that the biomechanical damage induced by laser etching, generation of tissue bridges, and expansion of cavitation bubble and its subsequent collapse, created distortion to the surrounding collagen lamellae. Femtosecond laser-induced thermal damage was characterized by collapsed collagen lamellae, loss of collagen banding, collagen coiling, and presence of spherical debris. Our findings have shown the ability of helium ion microscopy to provide high resolution images with unprecedented detail of nanoscale fibrillar morphological changes in order to assess a tissue damage, which could not be resolved by conventional scanning electron microscopy previously. This imaging technology has also given us a better understanding of the tissue-laser interactions in a nano-structural manner and their possible effects on post-operative wound recovery.

Technological advances in minimally invasive radiofrequency ablation of cardiac tissues.

Ablative techniques have been sought in many circumstances as alternatives to surgical resection/incision. Besides being minimally invasive, potential benefits of ablation include greater speed and improved access to target tissue compared with other surgical techniques. There is a wide variety of ablation technologies currently in use for medical treatment. These include but are not limited to tissue heating by radiofrequency (RF) current, microwaves, laser, and high intensity ultrasound. RF is among the most heavily used because of its relatively low complexity and cost. Ablative techniques have proven to be viable alternatives to surgical resection/incision of tissue. Although there are other means of tissue heating besides RF, RF is the most commonly used technique in operating rooms because of the reliability of transmural lesions and the low complexity of the system. Optimal systems account for the heterogeneous nature of tissue and variations in tissue property through the ablation cycle. It is important to monitor and assure adequate energy delivery by selecting the appropriate configuration of devices. Energy delivery varies between the various generators and systems, some more responsive than others with relative to changes in tissue impedance that will affect the end results of the operation.

Design, synthesis, and structure-activity relationships of alkylcarbamic acid aryl esters, a new class of fatty acid amide hydrolase inhibitors.

Fatty acid amide hydrolase (FAAH), an intracellular serine hydrolase enzyme, participates in the deactivation of fatty acid ethanolamides such as the endogenous cannabinoid anandamide, the intestinal satiety factor oleoylethanolamide, and the peripheral analgesic and anti-inflammatory factor palmitoylethanolamide. In the present study, we report on the design, synthesis, and structure-activity relationships (SAR) of a novel class of potent, selective, and systemically active inhibitors of FAAH activity, which we have recently shown to exert potent anxiolytic-like effects in rats. These compounds are characterized by a carbamic template substituted with alkyl or aryl groups at their O- and N-termini. Most compounds inhibit FAAH, but not several other serine hydrolases, with potencies that depend on the size and shape of the substituents. Initial SAR investigations suggested that the requirements for optimal potency are a lipophilic N-alkyl substituent (such as n-butyl or cyclohexyl) and a bent O-aryl substituent. Furthermore, the carbamic group is essential for activity. A 3D-QSAR analysis on the alkylcarbamic acid aryl esters showed that the size and shape of the O-aryl moiety are correlated with FAAH inhibitory potency. A CoMSIA model was constructed, indicating that whereas the steric occupation of an area corresponding to the meta position of an O-phenyl ring improves potency, a region of low steric tolerance on the enzyme active site exists corresponding to the para position of the same ring. The bent shape of the O-aryl moieties that best fit the enzyme surface closely resembles the folded conformations observed in the complexes of unsaturated fatty acids with different proteins. URB524 (N-cyclohexylcarbamic acid biphenyl-3-yl ester, 9g) is the most potent compound of the series (IC(50) = 63 nM) and was therefore selected for further optimization.