Visualization Of Tree Research Articles

Kssdtree: an interactive Python package for phylogenetic analysis based on sketching technique.

Sketching technologies have recently emerged as a promising solution for real-time, large-scale phylogenetic analysis. However, existing sketching-based phylogenetic tools exhibit drawbacks, including platform restrictions, deficiencies in tree visualization, and inherent distance estimation bias. These limitations collectively impede the overall convenience and efficiency of the analysis. In this study, we introduce Kssdtree, an interactive Python package designed to address these challenges. Kssdtree surpasses other sketching-based tools by demonstrating superior performance in terms of both accuracy and time efficiency on comprehensive benchmarking datasets. Notably, Kssdtree offers key advantages such as intra-species phylogenomic analysis and GTDB-based phylogenetic placement analysis, significantly enhancing the scope and depth of phylogenetic investigations. Through extensive evaluations and comparisons, Kssdtree stands out as an efficient and versatile method for real-time, large-scale phylogenetic analysis. The Kssdtree Python package is freely accessible at https://pypi.org/project/kssdtree and source code is available at https://github.com/yhlink/kssdtree. The documentation and instantiation for the software is available at https://kssdtree.readthedocs.io/en/latest. The video tutorial is available athttps://youtu.be/_6hg59Yn-Ws.

Genome microsatellite signature analysis in Adenoviridae family of viruses

Simple sequence repeats (SSRs) are present across both coding & non-coding regions of the genomes of all organisms with diversity in incidence, complexity, and repetition. The present study is focused on Adenoviridae which are non-enveloped viruses consisting of linear double-stranded DNA genome. The members of Adenoviridae are known to cause respiratory illnesses like the common cold (cough, runny nose, mild fever), pneumonia (occasionally), keratoconjunctivitis (infection in the eye known as pink eye), croup and cystitis (inflammation of the bladder). Our investigation aims to extract and analyse SSRs from 68 Adenoviridae genomes. Virus genome sequences were retrieved from NCBI and SSRs extracted from MISA. ETE3 and iTOL were used for the phylogenetic tree construction, annotation and visualization. The genome length of Adenoviridae genomes ranged from 26163 bp to 45667 bp while GC content varied from 33.6 % to 66.9 %. Genome wide analysis revealed a total incidence of 9861 SSRs and 793 cSSRs. The minimum and maximum range of SSR incidence is 112 (A67) to 203 (A61) respectively. The most prevalent mono, di and tri-SSR motif is “A”, “GC/CG” and “GAG/CTC” comprised of 1177, 1859 and 201 occurrences respectively. About 78 % SSRs are present in the coding region in the studied genomes. In terms of protein specific distribution, DNA polymerase enzyme had the highest incidence of 485 SSRs. The presence of mono-SSRs in the A/T region is a marker for host determination and divergence. The average mono-SSRs present in A/T region is 67.14 % and it ranged from 16.22 % to 99.11 %. The high prevalence of mono-SSRs in the A/T region was associated with human and related species as hosts. Further, the clustering of viruses as per their hosts was observed in the phylogenetic tree suggesting the role of host in viral evolution. The presence of unique and conserved cSSRs as genome markers has also been highlighted.

Genomic characterization of methicillin-resistant Staphylococcus aureus isolated from patients attending regional referral hospitals in Tanzania

BackgroundMethicillin-resistant Staphylococcus aureus (MRSA) colonization increases the risk of subsequent infection by MRSA strain complex interlinking between hospital and community-acquired MRSA which increases the chance of drug resistance and severity of the disease.ObjectiveGenomic characterization of Staphylococcus aures strains isolated from patients attending regional referral hospitals in Tanzania.MethodologyA laboratory-based cross-sectional study using short read-based sequencing technology, (Nextseq550,Illumina, Inc. San diego, California, USA). The samples used were collected from patients attending selected regional referral hospitals in Tanzania under the SeqAfrica project. Sequences were analyzed using tools available in the center for genomic and epidemiology server, and visualization of the phylogenetic tree was performed in ITOL 6.0. SPSS 28.0 was used for statistical analysis.ResultsAmong 103 sequences of S. aureus, 48.5% (50/103) carry the mecA gene for MRSA. High proportions of MRSA were observed among participants aged between 18 and 34 years (52.4%), in females (54.3%), and among outpatients (60.5%). The majority of observed MRSA carried plasmids rep5a (92.0%), rep16 (90.0%), rep7c (90.0%), rep15 (82.0%), rep19 (80.0%) and rep10 (72.0%). Among all plasmids observed rep5a, rep16, rep20, and repUS70 carried the blaZ gene, rep10 carried the erm(C) gene and rep7a carried the tet(K) gene. MLST and phylogeny analysis reveal high diversity among MRSA. Six different clones were observed circulating at selected regional hospitals and MRSA with ST8 was dominant.ConclusionThe study reveals a significant presence of MRSA in Staphylococcus aureus strains from Tanzanian regional hospitals, with nearly half carrying the mecA gene. MRSA is notably prevalent among young adults, females, and outpatients, showing high genetic diversity and dominance of ST8. Various plasmids carrying resistance genes indicate a complex resistance profile, highlighting the need for targeted interventions to manage MRSA infections in Tanzania.

A Novel Taxonomy of Intraoperative Cholangiograms in Suspected Choledocholithiasis: A Tool for Advancing Laparoscopic Common Bile Duct Exploration Outcomes Research.

Cholangiography for visualization of the biliary tree during laparoscopic cholecystectomy is an important diagnostic roadmap in the context of suspected choledocholithiasis (CDL). The renewed interest in transcystic laparoscopic common bile duct exploration (LCBDE) necessitates a general description of the range of CDL presentations. Our aim was to establish a novel classification system of intraoperative cholangiograms (IOCs) to advance research efforts in this field. A novel cholangiogram classification system, featuring 8 distinct presentations of choledocholithiasis, was applied to a data set of 80 preintervention IOCs for suspected choledocholithiasis. The classification system is as follows: A (no common bile duct stones, duodenal filling present, and concern for air bubbles), B (no common bile duct stones, no duodenal filling, and concern for sludge), C1 (stone(s) < 2x size of cystic duct with duodenal filling), C2 (stone(s) < 2x size of cystic duct without duodenal filling), D1 (stone(s) ≥ 2x size of cystic duct with duodenal filling), D2 (stone(s) ≥ 2x size of cystic duct without duodenal filling), E1 (congenital anatomical variant and/or common duct stricture), and E2 (surgically altered biliary anatomy). Cholangiogram review yielded preintervention classifications for 6 of 8 variants (A-E): A (7.5%), B (3.75%), C1 (23.75%), C2 (42.5%), D1 (15%), and D2 (7.5%). Analysis of cystic duct diameter yielded no significant differences among classification groups, indicating no predominant pattern of cystic duct anatomy within a given classification. An IOC classification system for suspected choledocholithiasis is foundational to answering key clinical questions for transcystic laparoscopic common bile duct exploration.

Determining the patency of biliary tracts in dogs with gallbladder mucocele using near-infrared cholangiography with indocyanine green.

Cholecystectomy is indicated for gallbladder mucoceles (GBM). Evaluating the patency of the biliary duct and precise biliary tree visualization is crucial for reducing the risk of compromised bile flow after surgery. Therefore, intraoperative cholangiography (IOC) is recommended during cholecystectomy to prevent biliary tract injury. Although indocyanine green (ICG) cholangiography has been extensively reported in human medicine, only one study has been conducted in veterinary medicine. Therefore, this study aimed to demonstrate the use of ICG for IOC to identify fluorescent biliary tract images and determine the patency of the common bile duct during cholecystectomy in dogs. This study comprised 27 dogs, consisting of 17 with gallbladder mucoceles (GBM) and 10 controls, specifically including dogs that had undergone elective cholecystectomy for GBM. ICG injection (0.25 mg/kg) was administered intravenously at least 45 minutes before surgery. During the operation, fluorescent images from cholangiography were displayed on the monitor and obtained in black-and-white mode for the comparison of fluorescence intensity (FI). The FI values of the gallbladders (GBs) and common bile duct (CBD) were measured using FI analyzing software (MGViewer V1.1.1, MetapleBio Inc.). The results demonstrated successful CBD patency identification in all cases. Mobile GBM showed partial gallbladder visibility, whereas immobile GBM showed limited visibility. Additionally, insights into the adequate visualization of the remaining extrahepatic biliary tree anatomy were provided, extending beyond the assessment of CBD patency and gallbladder intensity. Our study demonstrates the potential of fluorescent IOC using intravenous injection of ICG for assessing the patency of the cystic duct and common bile duct during cholecystectomy in patients with GBM, eliminating the need for surgical catheterization and flushing of the biliary ducts. Further research is warranted to investigate and validate the broader applicability of ICG cholangiography in veterinary medicine.

Matreex: Compact and Interactive Visualization for Scalable Studies of Large Gene Families.

Studying gene family evolution strongly benefits from insightful visualizations. However, the ever-growing number of sequenced genomes is leading to increasingly larger gene families, which challenges existing gene tree visualizations. Indeed, most of them present users with a dilemma: display complete but intractable gene trees, or collapse subtrees, thereby hiding their children's information. Here, we introduce Matreex, a new dynamic tool to scale up the visualization of gene families. Matreex's key idea is to use "phylogenetic" profiles, which are dense representations of gene repertoires, to minimize the information loss when collapsing subtrees. We illustrate Matreex's usefulness with three biological applications. First, we demonstrate on the MutS family the power of combining gene trees and phylogenetic profiles to delve into precise evolutionary analyses of large multicopy gene families. Second, by displaying 22 intraflagellar transport gene families across 622 species cumulating 5,500 representatives, we show how Matreex can be used to automate large-scale analyses of gene presence-absence. Notably, we report for the first time the complete loss of intraflagellar transport in the myxozoan Thelohanellus kitauei. Finally, using the textbook example of visual opsins, we show Matreex's potential to create easily interpretable figures for teaching and outreach. Matreex is available from the Python Package Index (pip install Matreex) with the source code and documentation available at https://github.com/DessimozLab/matreex.

A Pilot Study for Biliary Atresia Diagnosis: Fluorescent Imaging of Indocyanine Green in Stool

BackgroundBiliary atresia is the most common cause of obstructive jaundice in infants and conventional cholangiography is the current diagnostic gold standard. Fluorescent cholangiography with indocyanine green can enhance biliary tree visualization during surgery because it is exclusively excreted into the bile ducts and eventually into the intestine. Therefore, we hypothesized that indocyanine green presence in stool could confirm bile duct patency in infants. MethodsA prospective single center cohort study was performed on infants (age ≤ 12 months) with and without jaundice after obtaining IRB approval. Indocyanine green was administered intravenously (0.1 mg/kg). Soiled diapers collected post-injection were imaged for fluorescence. ResultsAfter indocyanine green administration, fluorescence was detected in soiled diapers for control patients (n = 4, x = 14 h22 m post-injection) and jaundiced patients without biliary atresia (n = 11, x = 13 h28 m post-injection). For biliary atresia patients (n = 7), post-injection soiled diapers before and after Kasai portoenterostomy were collected. Fluorescence was not detected in stool from 6 of 7 biliary atresia patients. As a test, indocyanine green detection in stool was 97% accurate for assessing biliary patency. ConclusionFluorescent Imaging for Indocyanine Green (FIInd Green) in stool is a fast and accurate approach to assess biliary patency non-invasively in infants. Level of EvidenceLevel III.

A genome-wide study of gastric intramucosal neoplasia based on somatic copy number alterations, gene mutations, and mRNA expression patterns.

We performed comprehensive analyses of somatic copy number alterations (SCNAs) and gene expression profiles of gastric intramucosal neoplasia (IMN) using array-based methods in 97 intestinal-type IMNs, including 39 low-grade dysplasias (LGDs), 37 high-grade dysplasias (HGDs), and 26 intramucosal carcinomas (IMCs) with stromal invasion of the lamina propria to identify the molecular mechanism of IMN. In addition, we examined gene mutations using gene panel analyses. We used cluster analyses for exclusion of arbitrariness to identify SCNA patterns and expression profiles. IMNs were classified into two distinct subgroups (subgroups 1 and 2) based on SCNA patterns. Subgroup 1 showed a genomic stable pattern due to the low frequency of SCNAs, whereas subgroup 2 exhibited a chromosomal instability pattern due to the high frequencies of SCNAs and TP53 mutations. Interestingly, although the frequencies of LGD and HGD were significantly higher in subgroup 1 than in subgroup 2, IMC was commonly found in both types. Although the expression profiles of specific mRNAs could be used to categorise subgroups 1 and 2, no clinicopathological findings correlated with either subgroup. We examined signalling pathways specific to subgroups 1 and 2 to identify the association of each subgroup with signalling pathways based on gene ontology tree visualisation: subgroups 1 and 2 were associated with haem metabolism and chromosomal instability, respectively. These findings reveal a comprehensive genomic landscape that highlights the molecular complexity of IMNs and provide a road map to facilitate our understanding of gastric IMNs.

Tantalum oxide nanoparticles as versatile and high-resolution X-ray contrast agent for intraductal image-guided ablative procedure in rodent models of breast cancer

AbstractThere are limited options for primary prevention of breast cancer (BC). Experimental procedures to locally prevent BC have shown therapeutic efficacy in animal models. To determine the suitability of FDA-approved iodine-containing and various metal-containing (bismuth, gold, iodine, or tantalum) preclinical nanoparticle-based contrast agents for image-guided intraductal (ID) ablative treatment of BC in rodent models, we performed a prospective longitudinal study to determine the imaging performance, local retention and systemic clearance, safety profile, and compatibility with ablative solution of each contrast agent. At least six abdominal mammary glands (&gt;3 female FVB/JN mice and/or Sprague-Dawley rats, 10–11 weeks of age) were intraductally injected with commercially available contrast agents (Omnipaque® 300, Fenestra® VC, MVivoTM Au, MVivoTM BIS) or in-house synthesized tantalum oxide (TaOx) nanoparticles. Contrast agents were administered at stock concentration or diluted in 70% ethanol (EtOH) and up to 1% ethyl cellulose (EC) as gelling agent to assess their compatibility with our image-guided ablative procedure. Mammary glands were serially imaged by microCT for up to 60 days after ID delivery. Imaging data were analyzed by radiologists and deep learning to measure in vivo signal disappearance of contrast agents. Mammary glands and major organs were ultimately collected for histopathological examination. TaOx-containing solutions provided best imaging performance for nitid visualization of ductal tree immediately after infusion, low outward diffusion (&lt;1 day) and high homogeneity. Of all nanoparticles, TaOx had the highest local clearance rate (46% signal decay as stock and 36% as ablative solution 3 days after ID injection) and exhibited low toxicity. TaOx-containing ablative solution with 1% EC caused same percentage of epithelial cell death (88.62% ± 7.70% vs. 76.38% ± 9.99%, p value = 0.089) with similar minimal collateral damage (21.56 ± 5.28% vs. 21.50% ± 7.14%, p value = 0.98) in mouse and rat mammary glands, respectively. In conclusion, TaOx-nanoparticles are a suitable and versatile contrast agent for intraductal imaging and image-guided ablative procedures in rodent models of BC with translational potential to humans.

HiRegEx: Interactive Visual Query and Exploration of Multivariate Hierarchical Data.

When using exploratory visual analysis to examine multivariate hierarchical data, users often need to query data to narrow down the scope of analysis. However, formulating effective query expressions remains a challenge for multivariate hierarchical data, particularly when datasets become very large. To address this issue, we develop a declarative grammar, HiRegEx (Hierarchical data Regular Expression), for querying and exploring multivariate hierarchical data. Rooted in the extended multi-level task topology framework for tree visualizations (e-MLTT), HiRegEx delineates three query targets (node, path, and subtree) and two aspects for querying these targets (features and positions), and uses operators developed based on classical regular expressions for query construction. Based on the HiRegEx grammar, we develop an exploratory framework for querying and exploring multivariate hierarchical data and integrate it into the TreeQueryER prototype system. The exploratory framework includes three major components: top-down pattern specification, bottom-up data-driven inquiry, and context-creation data overview. We validate the expressiveness of HiRegEx with the tasks from the e-MLTT framework and showcase the utility and effectiveness of TreeQueryER system through a case study involving expert users in the analysis of a citation tree dataset.

Visual Explanation for Open-Domain Question Answering With BERT.

Open-domain question answering (OpenQA) is an essential but challenging task in natural language processing that aims to answer questions in natural language formats on the basis of large-scale unstructured passages. Recent research has taken the performance of benchmark datasets to new heights, especially when these datasets are combined with techniques for machine reading comprehension based on Transformer models. However, as identified through our ongoing collaboration with domain experts and our review of literature, three key challenges limit their further improvement: (i) complex data with multiple long texts, (ii) complex model architecture with multiple modules, and (iii) semantically complex decision process. In this paper, we present VEQA, a visual analytics system that helps experts understand the decision reasons of OpenQA and provides insights into model improvement. The system summarizes the data flow within and between modules in the OpenQA model as the decision process takes place at the summary, instance and candidate levels. Specifically, it guides users through a summary visualization of dataset and module response to explore individual instances with a ranking visualization that incorporates context. Furthermore, VEQA supports fine-grained exploration of the decision flow within a single module through a comparative tree visualization. We demonstrate the effectiveness of VEQA in promoting interpretability and providing insights into model enhancement through a case study and expert evaluation.

GoTreeScape: Navigate and Explore the Tree Visualization Design Space.

Declarative grammar is becoming an increasingly important technique for understanding visualization design spaces. The GoTreeScape system presented in the paper allows users to navigate and explore the vast design space implied by GoTree, a declarative grammar for visualizing tree structures. To provide an overview of the design space, GoTreeScape, which is based on an encoder-decoder architecture, projects the tree visualizations onto a 2D landscape. Significantly, this landscape takes the relationships between different design features into account. GoTreeScape also includes an exploratory framework that allows top-down, bottom-up, and hybrid modes of exploration to support the inherently undirected nature of exploratory searches. Two case studies demonstrate the diversity with which GoTreeScape expands the universe of designed tree visualizations for users. The source code associated with GoTreeScape is available at https://github.com/bitvis2021/gotreescape.

Indocyanine green fluorescent cholangiography: The new standard practice to perform laparoscopic cholecystectomy in pediatric patients. A comparative study with conventional laparoscopic technique

BackgroundThis study aimed to compare outcomes of standard laparoscopic cholecystectomy and indocyanine green fluorescent cholangiography laparoscopic cholecystectomy over a 10-year period. MethodsFrom 2013 to 2023, 173 laparoscopic cholecystectomies were performed in 2 pediatric surgery units: 83 using standard technique (G1) and 90 using indocyanine green fluorescent cholangiography (G2). Patients included 96 girls and 77 boys, with a median age of 12.3 years (range 4–17) and a median weight of 51 kg (range 19–114). The 2 groups were compared regarding the following: (1) perioperative complications rate; (2) overall length of surgery (T1); (3) length of cystic duct isolation, clipping, and sectioning (T2); (4) time of gallbladder removal (T3); (5) degree of visualization of biliary tree; (6) safety and feasibility of indocyanine green fluorescent cholangiography; (7) incidence of anatomical anomalies detected intraoperatively. ResultsAll laparoscopic cholecystectomies were accomplished without conversion to open. The perioperative complications rate was significantly higher in G1 compared with G2 (12% vs 0%; P = .0007). Median T1, T2, and T3 were significantly longer in G1 (90, 37, 35 minutes) compared with G2 (55, 17, 19 minutes) (P = .0001), respectively. The visualization rate of the complete biliary tree was significantly higher in G2 (98.8%) than in G1 (80.7%) (P = .0001). No adverse reactions to indocyanine green were recorded. The incidence of biliary anomalies detected intraoperatively was significantly higher in G2 (7.8%) than in G1 (1.2%) (P = .03). ConclusionIndocyanine green fluorescent cholangiography can be considered the new standard practice to perform laparoscopic cholecystectomy in pediatrics. Indocyanine green fluorescence provided superior visualization of biliary anatomy, increased detection of anatomic variants, faster procedure, and fewer complications compared with conventional technique. Indocyanine green fluorescent cholangiography was safe, feasible, simple, inexpensive, and a timesaving tool.

HantaNet: A New MicrobeTrace Application for Hantavirus Classification, Genomic Surveillance, Epidemiology and Outbreak Investigations.

Hantaviruses zoonotically infect humans worldwide with pathogenic consequences and are mainly spread by rodents that shed aerosolized virus particles in urine and feces. Bioinformatics methods for hantavirus diagnostics, genomic surveillance and epidemiology are currently lacking a comprehensive approach for data sharing, integration, visualization, analytics and reporting. With the possibility of hantavirus cases going undetected and spreading over international borders, a significant reporting delay can miss linked transmission events and impedes timely, targeted public health interventions. To overcome these challenges, we built HantaNet, a standalone visualization engine for hantavirus genomes that facilitates viral surveillance and classification for early outbreak detection and response. HantaNet is powered by MicrobeTrace, a browser-based multitool originally developed at the Centers for Disease Control and Prevention (CDC) to visualize HIV clusters and transmission networks. HantaNet integrates coding gene sequences and standardized metadata from hantavirus reference genomes into three separate gene modules for dashboard visualization of phylogenetic trees, viral strain clusters for classification, epidemiological networks and spatiotemporal analysis. We used 85 hantavirus reference datasets from GenBank to validate HantaNet as a classification and enhanced visualization tool, and as a public repository to download standardized sequence data and metadata for building analytic datasets. HantaNet is a model on how to deploy MicrobeTrace-specific tools to advance pathogen surveillance, epidemiology and public health globally.

Multidetector computed tomography evaluation of obstructive jaundice: a cross-sectional study from a tertiary hospital of Nepal

Background: The utilization of advanced multidetector computed tomography (MDCT) technology along with postprocessing reconstruction techniques has significantly enhanced the clarity of visualization of the hepato-biliary tree. Therefore, this study was conducted to evaluate the diagnostic statistics of MDCT and its associated features in the evaluation of obstructive jaundice, with respect to surgical or histopathological diagnoses. Methods and methodology: The authors conducted a cross-sectional study among 30 participants with obstructive jaundice using purposive sampling. The authors calculated the diagnostic statistics of non-neoplastic and neoplastic types, along with specific etiologies of obstructive jaundice identified through MDCT using a statistical package for social sciences (SPSS) v21 and MedCalc v12.3.0. The ethical clearance was obtained from the institutional review committee of BPKIHS, Nepal (Ref no: Acd/291/075/076-IRC). Results: The sensitivity and the negative predictive value of MDCT for non-neoplastic cause to detect obstructive jaundice were 100% (95% CI: 79.41–100.00) and 100% (95% CI: 75.29–100.00), while the specificity and the positive predictive value for neoplastic cause to detect obstructive jaundice were 100% (95% CI: 79.41–100.00) and 100% (95% CI: 75.29–100.00), respectively. Similarly, the accuracy for either non-neoplastic or neoplastic cause was 96.67% (95% CI: 82.78–99.92). The most common cause of obstructive jaundice was choledocholithiasis (33.34%) followed by cholangiocarcinoma (20%), ampullary carcinoma (13.33%), and choledochal cyst (13.33%). The diagnostic accuracy of the individual etiology of common causes of obstructive jaundice ranged from 82.78 to 100%. Biliary obstruction was most frequently observed in the periampullary region (83.33%), followed by the proximal common bile duct (6.67%), hilar region (6.67%), and intrahepatic region (3.33%). Conclusion: The MDCT could serve as the initial and time-efficient excellent imaging modality for diagnosing various causes of obstructive jaundice with greater accuracy. It can differentiate non-neoplastic from neoplastic causes of obstructive jaundice.

MuTATE-an R package for comprehensive multi-objective molecular modeling.

Comprehensive multi-omics studies have driven advances in disease modeling for effective precision medicine but pose a challenge for existing machine-learning approaches, which have limited interpretability across clinical endpoints. Automated, comprehensive disease modeling requires a machine-learning approach that can simultaneously identify disease subgroups and their defining molecular biomarkers by explaining multiple clinical endpoints. Current tools are restricted to individual endpoints or limited variable types, necessitate advanced computation skills, and require resource-intensive manual expert interpretation. We developed Multi-Target Automated Tree Engine (MuTATE) for automated and comprehensive molecular modeling, which enables user-friendly multi-objective decision tree construction and visualization of relationships between molecular biomarkers and patient subgroups characterized by multiple clinical endpoints. MuTATE incorporates multiple targets throughout model construction and allows for target weights, enabling construction of interpretable decision trees that provide insights into disease heterogeneity and molecular signatures. MuTATE eliminates the need for manual synthesis of multiple non-explainable models, making it highly efficient and accessible for bioinformaticians and clinicians. The flexibility and versatility of MuTATE make it applicable to a wide range of complex diseases, including cancer, where it can improve therapeutic decisions by providing comprehensive molecular insights for precision medicine. MuTATE has the potential to transform biomarker discovery and subtype identification, leading to more effective and personalized treatment strategies in precision medicine, and advancing our understanding of disease mechanisms at the molecular level. MuTATE is freely available at GitHub (https://github.com/SarahAyton/MuTATE) under the GPLv3 license.

Retracted: COVID-19 Infection Structure Analysis Based on Minimum Spanning Tree Visualization in the Kingdom of Saudi Arabia Regions

Retracted: COVID-19 Infection Structure Analysis Based on Minimum Spanning Tree Visualization in the Kingdom of Saudi Arabia Regions

Near-infrared fluorescence cholangiography in dogs: A pilot study.

To determine the effect of indocyanine green (ICG) dose and timing of administration on near-infrared fluorescence (NIRF) imaging of the normal canine biliary tree. Preclinical prospective study. Eight purpose-bred beagles. The dogs were randomized to receive two of four intravenous ICG dose (low [L]:0.05 mg/kg or high [H]:0.25 mg/kg)/time (0 and 3 h prior to NIRF) combinations. NIRF images were collected every 10 min for 120 min. Target (cystic duct)-to-background (liver) ratios were calculated for all timepoints and compared. ICG cholangiography was successful in all dogs. The contrast ratio was above 1 in the L0 group by 20 min and reached its peak at 100 min. In the H0 group, the ratio was above 1 by 60 min and reached its peak at 90 min. Contrast ratios above 2 (fluorescence twice as bright in the cystic duct compared to the liver) were maintained from 180 to 300 min for L3 and H3 and was achieved after 80 min for L0. Low dose ICG provided better ratios early after injection compared to the high dose which remained highly concentrated in the liver tissue after injection. Both doses provided excellent visualization of the biliary tree at 3 h post injection, low dose ICG provided better ratios from 3 to 5 h post injection. Based on these results, 0.05 mg/kg of ICG administered at anesthetic premedication, or as early as 3 h prior to laparoscopic surgery should yield optimal fluorescence images. This study provides guidelines for NIRF cholangiography in clinically normal dogs.

Tree Skeletonization with DBSCAN Clustering Using Terrestrial Laser Scanning Data

A tree skeleton reflects the geometric and structural characteristics of a tree. Terrestrial laser scanning (TLS) provides an effective means to construct tree skeletons that can capture the surface and topological features of trees. However, it is difficult to construct a tree skeleton located at the geometric centre of the tree with a detailed hierarchy of branches because of the natural intricate topology of the tree and the defects of the tree point cloud scanned by TLS. In this study, we presented a tree-skeletonization method based on density-based spatial clustering of applications with noise (DBSCAN) using TLS data. First, outliers were removed using DBSCAN, and the point-traversal order of each point was recorded. Next, a tree point cloud was divided into several tree slices using contour planes, and several tree segments were obtained by applying DBSCAN to each tree slice. Tree skeleton points were retrieved from each tree segment after the point-inversion transformation. Then, the adjacent relationship between skeleton points and the flow weight of each skeleton point was calculated based on the point-traversal order. After that, the skeleton points were classified into stems and different levels of branch points using the flow weights of the skeleton points, and the branch hierarchies were identified. Finally, the tree skeleton was optimized using the angle consistency. The positional deviation dp and directivity deviation dd were presented in this study to verify the validity of the constructed tree skeleton. From the visualization results, the constructed tree skeleton effectively reflected the geometrical structure and branch hierarchies of the tree. The averages of dp and dd were 0.418 cm and 8.474 degrees, respectively. The results demonstrated the validity of the presented method. It will help improve the visualization and accurate measurement of trees.

Identification of the ideal weight-based indocyanine green dose for fluorescent cholangiography.

Ideal visualization of fluorescent cholangiography during laparoscopic cholecystectomy is when maximum fluorescence into biliary ducts and absent signal into liver parenchyma, defined as "signal to background ratio" (SBR), is obtained. Such condition is mainly dependent by indocyanine green (ICG) dose and timing. The aim of this study was to identify the ideal ICG dose to obtain the best possible intraoperative visualization of the extra-hepatic biliary tree. The first part of the study was used to define a range of small weight-based ICG dosages using the mathematical function bisection method. During the second part of the study, the midpoint dose of the identified range, was tested in 50 consecutive cholecystectomies using a laser-based fluorescence laparoscopic camera (SynergyID system by Arthrex, Naples, FL, USA). Timing administration was set at 1h before surgery, since this is the most common situation in clinical practice. Fluorescence intensity of bile ducts and liver parenchyma were assessed both subjectively, by blinded operative surgeon, as well as objectively, using an image analysis software (Fiji plugin), before and after Calot's triangle dissection. Fourteen patients were included in the first part of the study and ICG dose between 0.01191406 and 0.0119873mg/kg was identified. The second part confirmed previous results after testing the dosage equal to 0.0119mg/kg (midpoint of the defined range) in 50 consecutive cholecystectomies. Cystic duct was identified in 66 and 100% of cases before and after dissection of Calot's triangle respectively. On the other hand, common bile duct was identified in 82 and 92% before and after dissection respectively. Subjective and objective SBRs confirmed the benefit of the identified ICG dose. ICG dose calculated by 0.0119mg/kg administered one hour before surgery allows an ideal intraoperative visualization of the extra-hepatic biliary tree. ISRCTN10190039.