A general algorithm for consensus 3D cell segmentation from 2D segmented stacks.

Cell segmentation is the fundamental task. Only by segmenting, can we define the quantitative spatial unit for collecting measurements to draw biological conclusions. Deep learning has revolutionized 2D cell segmentation, enabling generalized solutions across cell types and imaging modalities. This has been driven by the ease of scaling up image acquisition, annotation and computation. However 3D cell segmentation, which requires dense annotation of 2D slices still poses significant challenges. Labelling every cell in every 2D slice is prohibitive. Moreover it is ambiguous, necessitating cross-referencing with other orthoviews. Lastly, there is limited ability to unambiguously record and visualize 1000's of annotated cells. Here we develop a theory and toolbox, u-Segment3D for 2D-to-3D segmentation, compatible with any 2D segmentation method. Given optimal 2D segmentations, u-Segment3D generates the optimal 3D segmentation without data training, as demonstrated on 11 real life datasets, >70,000 cells, spanning single cells, cell aggregates and tissue.

Rotamer-Controlled Dual Emissive α-Amino Acids.

The synthesis and photoluminescent properties of novel α-amino acids are described in which the biaryl benzotriazinone-containing chromophores were found to display dual emission fluorescence via locally excited (LE) and twisted intramolecular charge transfer (TICT) states. The intensity of each emission band could be controlled by the electronics and position of the substituents, and this led to the design of a 2-methoxyphenyl analogue that, due to twisting, displayed bright TICT fluorescence, solvatochromism, and pH sensitivity.

A rapid and bidirectional reporter of neural activity reveals neural correlates of social behaviors in Drosophila.

Neural activity is modulated over different timescales encompassing subseconds to hours, reflecting changes in external environment, internal state and behavior. Using Drosophila as a model, we developed a rapid and bidirectional reporter that provides a cellular readout of recent neural activity. This reporter uses nuclear versus cytoplasmic distribution of CREB-regulated transcriptional co-activator (CRTC). Subcellular distribution of GFP-tagged CRTC (CRTC::GFP) bidirectionally changes on the order of minutes and reflects both increases and decreases in neural activity. We established an automated machine-learning-based routine for efficient quantification of reporter signal. Using this reporter, we demonstrate mating-evoked activation and inactivation of modulatory neurons. We further investigated the functional role of the master courtship regulator gene fruitless (fru) and show that fru is necessary to ensure activation of male arousal neurons by female cues. Together, our results establish CRTC::GFP as a bidirectional reporter of recent neural activity suitable for examining neural correlates in behavioral contexts.

Development of Bifunctional, Raman Active Diyne-Girder Stapled α-Helical Peptides.

Stapled peptides are a unique class of cyclic α-helical peptides that are conformationally constrained via their amino acid side-chains. They have been transformative to the field of chemical biology and peptide drug discovery through addressing many of the physicochemical limitations of linear peptides. However, there are several issues with current chemical strategies to produce stapled peptides. For example, two distinct unnatural amino acids are required to synthesize i, i+7 alkene stapled peptides, leading to high production costs. Furthermore, low purified yields are obtained due to cis/trans isomers produced during ring-closing metathesis macrocyclisation. Here we report the development of a new i, i+7 diyne-girder stapling strategy that addresses these issues. The asymmetric synthesis of nine unnatural Fmoc-protected alkyne-amino acids facilitated a systematic study to determine the optimal (S,S)-stereochemistry and 14-carbon diyne-girder bridge length. Diyne-girder stapled T-STAR peptide 29 was demonstrated to have excellent helicity, cell permeability and stability to protease degradation. Finally, we demonstrate that the diyne-girder constraint is a Raman chromophore with potential use in Raman cell microscopy. Development of this highly effective, bifunctional diyne-girder stapling strategy leads us to believe that it can be used to produce other stapled peptide probes and therapeutics.

Facial Nerve High-Resolution Microanatomy Analysis of the Distal Intratemporal to Extracranial Pes Segment: Reconstructive Implications.

BACKGROUND: Current knowledge of facial nerve topography between the stylomastoid foramen to the pes anserinus is very limited. Elucidating this segment's intraneural microanatomy may be advantageous in certain clinical settings: the planning of nerve grafts for gaps extending from the proximal facial nerve trunk to distal branches or in determining coaptation sites for hypoglossal jump grafts to provide selective upper and lower facial tone. This study is the first to provide high-definition intraneural topography of the aforementioned segment to optimize reconstructive outcomes. METHODS: Sixteen facial nerves extending from the second genu to the pes anserinus were harvested from eight cadavers en bloc to preserve orientation. Specimens were imaged by micro-computed tomography using a serial 6-µm protocol and digitally reconstructed three-dimensionally to be analyzed using bioinformatic tools. RESULTS: No clinically significant fascicular separation was noted between 14.4 mm proximal to the stylomastoid foramen until 4.4 mm distal to the foramen. Fascicles remained separate throughout the remainder of the specimen and were found to undergo a mean rotation of 45.5 degrees ( P = 0.0002) between 8.9 and 13.7 mm distal to the stylomastoid foramen. This reliable clockwise rotation in left nerves and counterclockwise rotation in right nerves resulted in superficially oriented fascicles entering the upper division of the pes anserinus, whereas deep-oriented fascicles entered the lower division. CONCLUSION: Intraneural facial nerve topography and rotation are consistent from 4 to 14 mm distal to the stylomastoid foramen, enabling surgeons to accurately place grafts targeted to either the upper or lower face, thus optimizing functional accuracy and minimizing synkinesis.

A Crowdsourced Evaluation of Facial Averageness and Attractiveness.

BACKGROUND: Evolutionary psychologists have demonstrated that humans are attracted to individuals who possess average anatomy for the population. OBJECTIVES: The aim of this study was to prove that a composite of average facial features would be more attractive to raters than the cohort utilized to create the composite. METHODS: The male and female cohorts each consisted of 41 standardized frontal-view monochrome photographs, with 1 composite image derived from the other 40 real images. Amazon Mechanical Turk, a widely used crowdsourcing platform, was utilized to obtain ratings of images ranging from 1 to 7, with 1 and 7 being least and most attractive, respectively. The strength of the preference for the composite over the real images was assessed by the difference between the mean rating of the composite and real images. RESULTS: In total, 870 and 876 respondents were recruited to rate the male and female cohorts, respectively. For the male and female cohorts, the composite image was rated significantly higher than the rest of the cohort overall and across all ages, genders, and countries of residence (all P < 0.0001). For both cohorts, the strength of the preference was significantly higher for European respondents and lower for South American and nonbinary respondents (all P < 0.05). CONCLUSIONS: This study reveals that average facial anatomy is perceived as most attractive across all demographics, a finding that is hoped to serve as a stepping stone for further studies leading to objective cosmetic quantifications and integrating evidence-based medicine into aesthetic surgery.

Hydroxamic Acid-Modified Peptide Library Provides Insights into the Molecular Basis for the Substrate Selectivity of HDAC Corepressor Complexes.

Targeting the lysine deacetylase activity of class I histone deacetylases (HDACs) is potentially beneficial for the treatment of several diseases including human immunodeficiency virus (HIV) infection, Alzheimer's disease, and various cancers. It is therefore important to understand the function and mechanism of action of these enzymes. Class I HDACs act as catalytic components of seven large, multiprotein corepressor complexes. Different HDAC corepressor complexes have specific, nonredundant roles in the cell. It is likely that their specific functions are at least partly influenced by the substrate specificity of the complexes. To address this, we developed chemical tools to probe the specificity of HDAC complexes. We assessed a library of acetyl-lysine-containing substrate peptides and hydroxamic acid-containing inhibitor peptides against the full range of class I HDAC corepressor complexes. The results suggest that site-specific HDAC corepressor complex activity is driven in part by the recognition of the primary amino acid sequence surrounding a particular lysine position in the histone tail.

Investigating the Structure-Activity Relationship of 1,2,4-Triazine G-Protein-Coupled Receptor 84 (GPR84) Antagonists.

G-protein-coupled receptor 84 (GPR84) is a proinflammatory orphan G-protein-coupled receptor implicated in several inflammatory and fibrotic diseases. Several agonist and antagonist ligands have been developed that target GPR84; however, a noncompetitive receptor blocker that was progressed to phase II clinical trials failed to demonstrate efficacy. New high-quality antagonists are required to investigate the pathophysiological role of GPR84 and to validate GPR84 as a therapeutic target. We previously reported the discovery of a novel triazine GPR84 competitive antagonist 1. Here, we describe an extensive structure-activity relationship (SAR) of antagonist 1 and also present in silico docking with supporting mutagenesis studies that reveals a potential binding pose for this type of orthosteric antagonist. Lead compound 42 is a potent GPR84 antagonist with a favorable pharmacokinetic (PK) profile suitable for further drug development.

Stabilization of the RAS:PDE6D Complex Is a Novel Strategy to Inhibit RAS Signaling.

RAS is a major anticancer drug target which requires membrane localization to activate downstream signal transduction. The direct inhibition of RAS has proven to be challenging. Here, we present a novel strategy for targeting RAS by stabilizing its interaction with the prenyl-binding protein PDE6D and disrupting its localization. Using rationally designed RAS point mutations, we were able to stabilize the RAS:PDE6D complex by increasing the affinity of RAS for PDE6D, which resulted in the redirection of RAS to the cytoplasm and the primary cilium and inhibition of oncogenic RAS/ERK signaling. We developed an SPR fragment screening and identified fragments that bind at the KRAS:PDE6D interface, as shown through cocrystal structures. Finally, we show that the stoichiometric ratios of KRAS:PDE6D vary in different cell lines, suggesting that the impact of this strategy might be cell-type-dependent. This study forms the foundation from which a potential anticancer small-molecule RAS:PDE6D complex stabilizer could be developed.

Effectiveness of Telehealth in Rural and Remote Emergency Departments: Systematic Review.

BACKGROUND: Emergency telehealth has been used to improve access of patients residing in rural and remote areas to specialist care in the hope of mitigating the significant health disparities that they experience. Patient disposition decisions in rural and remote emergency departments (EDs) can be complex and largely dependent on the expertise and experience available at local (receiving-end) hospitals. Although there has been some synthesis of evidence of the effectiveness of emergency telehealth in clinical practice in rural and remote EDs for nonacute presentations, there has been limited evaluation of the influence of contextual factors such as clinical area and acuity of presentation on these findings. OBJECTIVE: The aims of this systematic review are to examine the outcome measures used in studying the effectiveness of telehealth in rural and remote EDs and to analyze the clinical context in which these outcome measures were used and interpreted. METHODS: The search strategy used Medical Subject Headings and equivalent lists of subject descriptors to find articles covering 4 key domains: telehealth or telemedicine, EDs, effectiveness, and rural and remote. Studies were selected using the Population, Intervention, Comparator, Outcomes of Interest, and Study Design framework. This search strategy was applied to MEDLINE (Ovid), Cochrane Library, Scopus, CINAHL, ProQuest, and EconLit, as well as the Centre for Reviews and Dissemination databases (eg, National Health Service Economic Evaluation Database) for the search period from January 1, 1990, to May 23, 2020. Qualitative synthesis was performed on the outcome measures used in the included studies, in particular the clinical contexts within which they were interpreted. RESULTS: A total of 21 full-text articles were included for qualitative analysis. Telehealth use in rural and remote EDs demonstrated effectiveness in achieving improved or equivalent clinical effectiveness, appropriate care processes, and-depending on the context-improvement in speed of care, as well as favorable service use patterns. The definition of effectiveness varied across the clinical areas and contexts of the studies, and different measures have been used to affirm the safety and clinical effectiveness of telehealth in rural and remote EDs. The acuity of patient presentation emerged as a dominant consideration in the interpretation of interlinking time-sensitive clinical effectiveness and patient disposition measures such as transfer and discharge rates, local hospital admission, length of stay, and ED length of stay. These, together with clinical area and acuity of presentation, are the outcome determination criteria that emerged from this review. CONCLUSIONS: Emergency telehealth studies typically use multiple outcome measures to determine the effectiveness of the services. The outcome determination criteria that emerged from this analysis are useful when defining the favorable direction for each outcome measure of interest. The findings of this review have implications for emergency telehealth service design and policies. TRIAL REGISTRATION: PROSPERO CRD42019145903; https://tinyurl.com/ndmkr8ry.

Peptides derived from the SARS-CoV-2 receptor binding motif bind to ACE2 but do not block ACE2-mediated host cell entry or pro-inflammatory cytokine induction.

SARS-CoV-2 viral attachment and entry into host cells is mediated by a direct interaction between viral spike glycoproteins and membrane bound angiotensin-converting enzyme 2 (ACE2). The receptor binding motif (RBM), located within the S1 subunit of the spike protein, incorporates the majority of known ACE2 contact residues responsible for high affinity binding and associated virulence. Observation of existing crystal structures of the SARS-CoV-2 receptor binding domain (SRBD)-ACE2 interface, combined with peptide array screening, allowed us to define a series of linear native RBM-derived peptides that were selected as potential antiviral decoy sequences with the aim of directly binding ACE2 and attenuating viral cell entry. RBM1 (16mer): S443KVGGNYNYLYRLFRK458, RBM2A (25mer): E484GFNCYFPLQSYGFQPTNGVGYQPY508, RBM2B (20mer): F456NCYFPLQSYGFQPTNGVGY505 and RBM2A-Sc (25mer): NYGLQGSPFGYQETPYPFCNFVQYG. Data from fluorescence polarisation experiments suggested direct binding between RBM peptides and ACE2, with binding affinities ranging from the high nM to low µM range (Kd = 0.207-1.206 µM). However, the RBM peptides demonstrated only modest effects in preventing SRBD internalisation and showed no antiviral activity in a spike protein trimer neutralisation assay. The RBM peptides also failed to suppress S1-protein mediated inflammation in an endogenously expressing ACE2 human cell line. We conclude that linear native RBM-derived peptides are unable to outcompete viral spike protein for binding to ACE2 and therefore represent a suboptimal approach to inhibiting SARS-CoV-2 viral cell entry. These findings reinforce the notion that larger biologics (such as soluble ACE2, 'miniproteins', nanobodies and antibodies) are likely better suited as SARS-CoV-2 cell-entry inhibitors than short-sequence linear peptides.

A scalable open-source MATLAB toolbox for reconstruction and analysis of multispectral optoacoustic tomography data.

Multispectral photoacoustic tomography enables the resolution of spectral components of a tissue or sample at high spatiotemporal resolution. With the availability of commercial instruments, the acquisition of data using this modality has become consistent and standardized. However, the analysis of such data is often hampered by opaque processing algorithms, which are challenging to verify and validate from a user perspective. Furthermore, such tools are inflexible, often locking users into a restricted set of processing motifs, which may not be able to accommodate the demands of diverse experiments. To address these needs, we have developed a Reconstruction, Analysis, and Filtering Toolbox to support the analysis of photoacoustic imaging data. The toolbox includes several algorithms to improve the overall quantification of photoacoustic imaging, including non-negative constraints and multispectral filters. We demonstrate various use cases, including dynamic imaging challenges and quantification of drug effect, and describe the ability of the toolbox to be parallelized on a high performance computing cluster.

Heterozygous Mutation of Vegfr3 Reduces Renal Lymphatics without Renal Dysfunction.

BACKGROUND: Lymphatic abnormalities are observed in several types of kidney disease, but the relationship between the renal lymphatic system and renal function is unclear. The discovery of lymphatic-specific proteins, advances in microscopy, and available genetic mouse models provide the tools to help elucidate the role of renal lymphatics in physiology and disease. METHODS: We utilized a mouse model containing a missense mutation in Vegfr3 (dubbed Chy ) that abrogates its kinase ability. Vegfr3 Chy/+ mice were examined for developmental abnormalities and kidney-specific outcomes. Control and Vegfr3 Chy/+ mice were subjected to cisplatin-mediated injury. We characterized renal lymphatics using tissue-clearing, light-sheet microscopy, and computational analyses. RESULTS: In the kidney, VEGFR3 is expressed not only in lymphatic vessels but also, in various blood capillaries. Vegfr3 Chy/+ mice had severely reduced renal lymphatics with 100% penetrance, but we found no abnormalities in BP, serum creatinine, BUN, albuminuria, and histology. There was no difference in the degree of renal injury after low-dose cisplatin (5 mg/kg), although Vegfr3 Chy/+ mice developed perivascular inflammation. Cisplatin-treated controls had no difference in total cortical lymphatic volume and length but showed increased lymphatic density due to decreased cortical volume. CONCLUSIONS: We demonstrate that VEGFR3 is required for development of renal lymphatics. Our studies reveal that reduced lymphatic density does not impair renal function at baseline and induces only modest histologic changes after mild injury. We introduce a novel quantification method to evaluate renal lymphatics in 3D and demonstrate that accurate measurement of lymphatic density in CKD requires assessment of changes to cortical volume.

Rethinking Autonomous Surgery: Focusing on Enhancement over Autonomy.

CONTEXT: As robot-assisted surgery is increasingly used in surgical care, the engineering research effort towards surgical automation has also increased significantly. Automation promises to enhance surgical outcomes, offload mundane or repetitive tasks, and improve workflow. However, we must ask an important question: should autonomous surgery be our long-term goal? OBJECTIVE: To provide an overview of the engineering requirements for automating control systems, summarize technical challenges in automated robotic surgery, and review sensing and modeling techniques to capture real-time human behaviors for integration into the robotic control loop for enhanced shared or collaborative control. EVIDENCE ACQUISITION: We performed a nonsystematic search of the English language literature up to March 25, 2021. We included original studies related to automation in robot-assisted laparoscopic surgery and human-centered sensing and modeling. EVIDENCE SYNTHESIS: We identified four comprehensive review papers that present techniques for automating portions of surgical tasks. Sixteen studies relate to human-centered sensing technologies and 23 to computer vision and/or advanced artificial intelligence or machine learning methods for skill assessment. Twenty-two studies evaluate or review the role of haptic or adaptive guidance during some learning task, with only a few applied to robotic surgery. Finally, only three studies discuss the role of some form of training in patient outcomes and none evaluated the effects of full or semi-autonomy on patient outcomes. CONCLUSIONS: Rather than focusing on autonomy, which eliminates the surgeon from the loop, research centered on more fully understanding the surgeon's behaviors, goals, and limitations could facilitate a superior class of collaborative surgical robots that could be more effective and intelligent than automation alone. PATIENT SUMMARY: We reviewed the literature for studies on automation in surgical robotics and on modeling of human behavior in human-machine interaction. The main application is to enhance the ability of surgical robotic systems to collaborate more effectively and intelligently with human surgeon operators.

Interpretable deep learning uncovers cellular properties in label-free live cell images that are predictive of highly metastatic melanoma.

Deep learning has emerged as the technique of choice for identifying hidden patterns in cell imaging data but is often criticized as "black box." Here, we employ a generative neural network in combination with supervised machine learning to classify patient-derived melanoma xenografts as "efficient" or "inefficient" metastatic, validate predictions regarding melanoma cell lines with unknown metastatic efficiency in mouse xenografts, and use the network to generate in silico cell images that amplify the critical predictive cell properties. These exaggerated images unveiled pseudopodial extensions and increased light scattering as hallmark properties of metastatic cells. We validated this interpretation using live cells spontaneously transitioning between states indicative of low and high metastatic efficiency. This study illustrates how the application of artificial intelligence can support the identification of cellular properties that are predictive of complex phenotypes and integrated cell functions but are too subtle to be identified in the raw imagery by a human expert. A record of this paper's transparent peer review process is included in the supplemental information. VIDEO ABSTRACT.

A Silver Lining? Fewer Non-Severe Acute Respiratory Syndrome Coronavirus 2 Respiratory Viruses During the Coronavirus Disease 2019 Pandemic.

Nonpharmaceutical interventions (NPIs) have "flattened the curve" of the coronavirus disease 2019 pandemic; however the effect of these interventions on other respiratory viruses is unknown. We used aggregate level case count data for 8 respiratory viruses and compared the institutional and statewide case counts before and during the period that NPIs were active. We observed a 61% decrease (incidence rate ratio, 0.39; 95% confidence interval, .37-.41; P < .001) in non-severe acute respiratory syndrome coronavirus 2 respiratory viral infections when NPIs were implemented. This finding, if further verified, should guide future public health initiatives to mitigate viral epidemics.

Stapled ACE2 peptidomimetics designed to target the SARS-CoV-2 spike protein do not prevent virus internalization.

COVID-19 is caused by a novel coronavirus called severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2). Virus cell entry is mediated through a protein-protein interaction (PPI) between the SARS-CoV-2 spike protein and angiotensin-converting enzyme 2 (ACE2). A series of stapled peptide ACE2 peptidomimetics based on the ACE2 interaction motif were designed to bind the coronavirus S-protein RBD and inhibit binding to the human ACE2 receptor. The peptidomimetics were assessed for antiviral activity in an array of assays including a neutralization pseudovirus assay, immunofluorescence (IF) assay and in-vitro fluorescence polarization (FP) assay. However, none of the peptidomimetics showed activity in these assays, suggesting that an enhanced binding interface is required to outcompete ACE2 for S-protein RBD binding and prevent virus internalization.

Effectiveness and cost-effectiveness of TeleStroke consultations to support the care of patients who had a stroke presenting to regional emergency departments in Western Australia: an economic evaluation case study protocol.

INTRODUCTION: The Western Australia (WA) Acute TeleStroke Programme commenced incrementally across regional WA during 2016-2017. Since the introduction of the TeleStroke Programme, there has been monitoring of service outputs, including regional patient access to tertiary stroke specialist advice and reperfusion treatment; however, the impact of consultation with a stroke specialist via telehealth (videoconferencing or telephone) on the effectiveness and cost-effectiveness of stroke care and the drivers of cost-effectiveness has not been systematically evaluated. METHODS AND ANALYSIS: The aim of the case study was to examine the impact of consultation with a stroke specialist via telehealth on the effectiveness and cost-effectiveness of stroke and transient ischaemic attack care using a mixed methods approach. A categorical decision tree model will be constructed in collaboration with clinicians and programme managers. A before and after comparison using state-wide administrative datasets will be used to run the base model. If sample size and statistical power permits, the cases and comparators will be matched by stroke type and presence of CT scan at the initial site of presentation, age category and presenting hospital. The drivers of cost-effectiveness will be explored through stakeholder interviews. Data from the qualitative analysis will be cross-referenced with trends emerging from the quantitative dataset and used to guide the factors to be involved in subgroup and sensitivity analysis. ETHICS AND DISSEMINATION: Ethics approval for this case study has been granted from the Western Australian Country Health Service Human Research and Ethics Committee (RGS3076). Reciprocal approval has been granted from Curtin University Human Research Ethics Office (HRE2019-0740). Findings will be disseminated publicly through conference presentation and peer-review publications. Interim findings will be released as internal reports to inform the service development.