Critical Assessment of Metagenome Interpretation: the second round of challenges.

Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilers markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses.

Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2.

BACKGROUND: Fungi play a key role in several important ecological functions, ranging from organic matter decomposition to symbiotic associations with plants. Moreover, fungi naturally inhabit the human body and can be beneficial when administered as probiotics. In mycology, the internal transcribed spacer (ITS) region was adopted as the universal marker for classifying fungi. Hence, an accurate and robust method for ITS classification is not only desired for the purpose of better diversity estimation, but it can also help us gain a deeper insight into the dynamics of environmental communities and ultimately comprehend whether the abundance of certain species correlate with health and disease. Although many methods have been proposed for taxonomic classification, to the best of our knowledge, none of them fully explore the taxonomic tree hierarchy when building their models. This in turn, leads to lower generalization power and higher risk of committing classification errors. RESULTS: Here we introduce HiTaC, a robust hierarchical machine learning model for accurate ITS classification, which requires a small amount of data for training and can handle imbalanced datasets. HiTaC was thoroughly evaluated with the established TAXXI benchmark and could correctly classify fungal ITS sequences of varying lengths and a range of identity differences between the training and test data. HiTaC outperforms state-of-the-art methods when trained over noisy data, consistently achieving higher F1-score and sensitivity across different taxonomic ranks, improving sensitivity by 6.9 percentage points over top methods in the most noisy dataset available on TAXXI. CONCLUSIONS: HiTaC is publicly available at the Python package index, BIOCONDA and Docker Hub. It is released under the new BSD license, allowing free use in academia and industry. Source code and documentation, which includes installation and usage instructions, are available at https://gitlab.com/dacs-hpi/hitac .

CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance.

SUMMARY: The ongoing pandemic caused by SARS-CoV-2 emphasizes the importance of genomic surveillance to understand the evolution of the virus, to monitor the viral population, and plan epidemiological responses. Detailed analysis, easy visualization and intuitive filtering of the latest viral sequences are powerful for this purpose. We present CovRadar, a tool for genomic surveillance of the SARS-CoV-2 Spike protein. CovRadar consists of an analytical pipeline and a web application that enable the analysis and visualization of hundreds of thousand sequences. First, CovRadar extracts the regions of interest using local alignment, then builds a multiple sequence alignment, infers variants and consensus and finally presents the results in an interactive app, making accessing and reporting simple, flexible and fast. AVAILABILITY AND IMPLEMENTATION: CovRadar is freely accessible at https://covradar.net, its open-source code is available at https://gitlab.com/dacs-hpi/covradar. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Clinical Characteristics and Outcomes of Patients with Aneurysmal Subarachnoid Hemorrhage: A Prospective Multicenter Study in a Middle-Income Country.

BACKGROUND: Aneurysmal subarachnoid hemorrhage (SAH) is associated with high mortality and long-term functional impairment. Data on clinical management and functional outcomes from developing countries are scarce. We aimed to define patient profiles and clinical practices and evaluate long-term outcomes after SAH in a middle-income country. METHODS: This was a prospective study including consecutive adult patients admitted with SAH to two reference centers in Brazil from January 2016 to February 2020. The primary outcome was functional status at 6 months using the modified Rankin Scale. Mixed multivariable analysis was performed to determine the relationship between clinical variables and functional outcomes. RESULTS: From 471patients analyzed, the median time from symptom onset to arrival at a study center was 4 days (interquartile range 0-9). Median age was 55 years (interquartile range 46-62) and 353 (75%) patients were women. A total of 426 patients (90%) were transferred from nonspecialized general hospitals, initial computed tomography revealed thick hemorrhage in 73% of patients (modified Fisher score of 3 or 4), and 136 (29%) had poor clinical grade (World Federation of Neurological Surgeons score of 4 or 5). A total of 312 (66%) patients underwent surgical clipping, and 119 (25%) underwent endovascular coiling. Only 34 patients (7%) underwent withdrawal or withholding of life-sustaining therapy during their hospital stay, and in-hospital mortality was 24%. A total of 187 (40%) patients had an unfavorable long-term functional outcome (modified Rankin Scale score of 4 to 6). Factors associated with unfavorable outcome were age (adjusted odds ratio [OR] 1.05, 95% confidence interval [CI] 1.03-1.08), hypertension (adjusted OR 1.81, 95% CI 1.04-3.16), poor clinical grade (adjusted OR 4.92, 95% CI 2.85-8.48), external ventricular drain (adjusted OR 3.8, 95% CI 2.31-6.24), postoperative deterioration (adjusted OR 2.33, 95% CI 1.32-4.13), cerebral infarction (adjusted OR 3.16, 95% CI 1.81-5.52), rebleeding (adjusted OR 2.95, 95% CI 1.13-7.69), and sepsis (adjusted OR 2.68, 95% CI 1.42-5.05). CONCLUSIONS: Our study demonstrated that SAH management in a middle-income country diverges significantly from published cohorts and current guidelines, despite comparable clinical profiles on presentation and admission to high-volume referral centers. Earlier aneurysm occlusion and increased use of endovascular therapy could potentially reduce modifiable in-hospital complications and improve functional outcomes in Brazil.

Near-Fall Detection in Unexpected Slips during Over-Ground Locomotion with Body-Worn Sensors among Older Adults.

Slip-induced falls are a growing health concern for older adults, and near-fall events are associated with an increased risk of falling. To detect older adults at a high risk of slip-related falls, this study aimed to develop models for near-fall event detection based on accelerometry data collected by body-fixed sensors. Thirty-four healthy older adults who experienced 24 laboratory-induced slips were included. The slip outcomes were first identified as loss of balance (LOB) and no LOB (NLOB), and then the kinematic measures were compared between these two outcomes. Next, all the slip trials were split into a training set (90%) and a test set (10%) at sample level. The training set was used to train both machine learning models (n = 2) and deep learning models (n = 2), and the test set was used to evaluate the performance of each model. Our results indicated that the deep learning models showed higher accuracy for both LOB (>64%) and NLOB (>90%) classifications than the machine learning models. Among all the models, the Inception model showed the highest classification accuracy (87.5%) and the largest area under the receiver operating characteristic curve (AUC), indicating that the model is an effective method for near-fall (LOB) detection. Our approach can be helpful in identifying individuals at the risk of slip-related falls before they experience an actual fall.

Genetic diversity and karyotype of Pitcairnia azouryi: an endangered species of Bromeliaceae endemic to Atlantic Forest inselbergs.

Plant species of various families, such as those of Bromeliaceae, occur on inselbergs where they are subject to geographic isolation and environmental conditions that can lead to genetic erosion. This, in turn, can result in the loss of natural populations due to homozygosis, or changes in ploidy that may lead to reproductive isolation. The genetic diversity of five natural populations of Pitcairnia azouryi was measured using nine microsatellite markers transferred from P. albiflos and P. geyskesii. Chromosome numbers and nuclear DNA content were also evaluated. The results indicated moderate genetic differentiation among populations (FST = 0.188), and significant gene flow (Nm = 1.073) in four of the five populations. P. azouryi has, predominantly, 2n = 50 chromosomes and DNA content of 2C = 1.16 pg, but the tetraploid condition was found (2n = 100 and 2C = 2.32 pg) in seedlings of an individual of the most geographically isolated population. The moderate level of genetic structuring observed for P. azouryi seems to be related to its disjoint geographical distribution and the locally aggregated spatial structure of the populations, which are isolated from each other, hindering the inter and intrapopulational gene flow. This interpretation was also evidenced by the mantel test (r = 0.777, P < 0.05). The occurrence of diploid individuals with tetraploid seedlings is indicative of events of eupolyploidization, possibly due to the environmental conditions of this geographically isolated population.

Treatment of bilateral popliteal artery aneurysms.

Popliteal artery aneurysms are the most frequent type of peripheral aneurysm, accounting for 85% of the all of these aneurysms. Usually asymptomatic, they are generally diagnosed during clinical examination. Incidence is higher among males and seniors. They are bilateral in 50% of the cases and 60% are associated with abdominal aortic aneurysms. This paper describes a 72-year-old male patient who presented with two bilateral pulsatile masses, one in each popliteal region, was otherwise asymptomatic, and had a history of hypertension and dyslipidemia. Clinical examination and ultrasound imaging confirmed a diagnosis of bilateral aneurysms of the popliteal arteries. Popliteal artery aneurysms can be treated with open bypass surgery, with or without aneurysm resection, or with endovascular surgery. This Therapeutic Challenge discusses these possibilities.

Carbonyl-heterobimetallic Ru(II)/Fe(II)-complexes containing polypyridyl ligands: Synthesis, characterization, cellular viability assays and interactions with biomolecules.

This paper describes on the interaction studies of carbonyl heterobimetallic compounds of Ru(II)/Fe(II) containing polypyridyl ligands, with general formula ct-[RuCl(CO)(N-N)(dppf)]PF6, N-N = 1,10-phenanthroline (phen) 5; dipyrido[3,2-f:2',3'-h]quinoxaline (dpq) 6; dipyrido[3,2-a:2',3'-c]phenazine (dppz) 7; dipyrido[3,2-f:2',3'-h]quinoxalino[2,3-b]quinoxaline (dpqQX) 8 and dppf = 1,1'-bis(diphenylphosphino) ferrocene], with calf thymus DNA (ct-DNA) and bovine serum albumin (BSA). Also, it describes the cellular viability assays of these complexes in tumorigenic and non-tumorigenic cell lines. The carbonyl complexes 5-8 and their respective precursors with formula cis-[RuCl2(N-N)(dppf)], N-N = phen (1), dpq (2), dppz (3) and dpqQX (4), were characterized by elemental analysis and spectroscopic techniques (FTIR, UV-vis, 1H and 31P{1H} NMR). Also, a cyclic voltammetry study was performed for all complexes. The crystal structure of the complex 3 is presented and discussed. Spectrofluorimetric titrations shows spontaneous and strong interaction of 5-8 with BSA, through a static quenching mechanism, resulting in binding constants in the order of 104-106 L mol-1, at 310 K. Viscosity measurements and circular dichroism spectra prompts interactions of 5-8 with ct-DNA via non-classical intercalations or by an electrostatic pathway. MTT assays in breast tumor cells MDA-MB-231 and in non-tumorigenic cells MCF-10A and V79-4 cell lines revealed IC50 values ranging from 0.19 to 1.11 µmol L-1, 1.07-3.18 µmol L-1 and 1.29-3.85 µmol L-1 respectively, for complexes 5-8.

True Aneurysm of the Dorsal Artery of the Foot: Case Report and Review of the Literature.

True aneurysm of the dorsal artery of the foot is extremely rare, and its clinical manifestations are little known. A case of a true dorsalis pedis artery aneurysm in a 51-year-old man, with no history of local trauma or injury on his foot, is presented. Clinical examination and ultrasonic imaging confirmed the aneurysm. Dorsalis pedis artery aneurysm after this had been exposed, the proximal and distal stumps of the dorsal artery of the foot were isolated and ligated, and the aneurysm was resected.

The Urban Toolkit: A Grammar-Based Framework for Urban Visual Analytics.

While cities around the world are looking for smart ways to use new advances in data collection, management, and analysis to address their problems, the complex nature of urban issues and the overwhelming amount of available data have posed significant challenges in translating these efforts into actionable insights. In the past few years, urban visual analytics tools have significantly helped tackle these challenges. When analyzing a feature of interest, an urban expert must transform, integrate, and visualize different thematic (e.g., sunlight access, demographic) and physical (e.g., buildings, street networks) data layers, oftentimes across multiple spatial and temporal scales. However, integrating and analyzing these layers require expertise in different fields, increasing development time and effort. This makes the entire visual data exploration and system implementation difficult for programmers and also sets a high entry barrier for urban experts outside of computer science. With this in mind, in this paper, we present the Urban Toolkit (UTK), a flexible and extensible visualization framework that enables the easy authoring of web-based visualizations through a new high-level grammar specifically built with common urban use cases in mind. In order to facilitate the integration and visualization of different urban data, we also propose the concept of knots to merge thematic and physical urban layers. We evaluate our approach through use cases and a series of interviews with experts and practitioners from different domains, including urban accessibility, urban planning, architecture, and climate science. UTK is available at urbantk.org.

The effect of the molecular structures of dicyanomethylene compounds on their supramolecular assembly, photophysical and electrochemical properties.

Two series of flexible dicyanomethylene compounds, specifically, class 1 and class 2 compounds, have been designed and synthesised. In class 1 compounds, the dicyanomethylene groups are separated by glycol chain spacers of different lengths, whereas, in class 2 compounds, the spacers are alkyl linkers of different lengths. The notion underlying the design of these compounds is that in class 1 molecules, the spacers contain donor oxygen atoms that could not only form hydrogen bonds during the course of crystal packing but also promote withdrawing effects that modify the photophysical and electrochemical properties of these molecules in solution; in contrast, these effects would be absent for class 2 molecules. However, this study revealed that, with respect to crystal packing, the size of the spacers and their even and odd numbers of atoms are more important than their chemical nature. All of the synthesised compounds exhibited blue emission in the solid state and in CH2Cl2 solutions. The photophysical and electrochemical properties of these compounds in solution were not significantly affected by the type and length of the spacer that was used in each molecule. In the solid state, however, the compound with the shortest spacer showed the highest Stokes shift. The electronic transitions for the synthesized compounds in solution were explained by density functional theory and time-dependent density functional theory calculations, which indicated that the methylene moieties control the properties of both classes of compounds and that the spacers do not conjugate with the end groups. These two series of flexible dicyanomethylene compounds could be utilised as molecular building blocks for the development of new solids with novel properties.

A Comparison of Spatiotemporal Visualizations for 3D Urban Analytics.

Recent technological innovations have led to an increase in the availability of 3D urban data, such as shadow, noise, solar potential, and earthquake simulations. These spatiotemporal datasets create opportunities for new visualizations to engage experts from different domains to study the dynamic behavior of urban spaces in this under explored dimension. However, designing 3D spatiotemporal urban visualizations is challenging, as it requires visual strategies to support analysis of time-varying data referent to the city geometry. Although different visual strategies have been used in 3D urban visual analytics, the question of how effective these visual designs are at supporting spatiotemporal analysis on building surfaces remains open. To investigate this, in this paper we first contribute a series of analytical tasks elicited after interviews with practitioners from three urban domains. We also contribute a quantitative user study comparing the effectiveness of four representative visual designs used to visualize 3D spatiotemporal urban data: spatial juxtaposition, temporal juxtaposition, linked view, and embedded view. Participants performed a series of tasks that required them to identify extreme values on building surfaces over time. Tasks varied in granularity for both space and time dimensions. Our results demonstrate that participants were more accurate using plot-based visualizations (linked view, embedded view) but faster using color-coded visualizations (spatial juxtaposition, temporal juxtaposition). Our results also show that, with increasing task complexity, plot-based visualizations perform better in preserving efficiency (time, accuracy) compared to color-coded visualizations. Based on our findings, we present a set of takeaways with design recommendations for 3D spatiotemporal urban visualizations for researchers and practitioners. Lastly, we report on a series of interviews with four practitioners, and their feedback and suggestions for further work on the visualizations to support 3D spatiotemporal urban data analysis.

PROWIS: A Visual Approach for Building, Managing, and Analyzing Weather Simulation Ensembles at Runtime.

Weather forecasting is essential for decision-making and is usually performed using numerical modeling. Numerical weather models, in turn, are complex tools that require specialized training and laborious setup and are challenging even for weather experts. Moreover, weather simulations are data-intensive computations and may take hours to days to complete. When the simulation is finished, the experts face challenges analyzing its outputs, a large mass of spatiotemporal and multivariate data. From the simulation setup to the analysis of results, working with weather simulations involves several manual and error-prone steps. The complexity of the problem increases exponentially when the experts must deal with ensembles of simulations, a frequent task in their daily duties. To tackle these challenges, we propose ProWis: an interactive and provenance-oriented system to help weather experts build, manage, and analyze simulation ensembles at runtime. Our system follows a human-in-the-loop approach to enable the exploration of multiple atmospheric variables and weather scenarios. ProWis was built in close collaboration with weather experts, and we demonstrate its effectiveness by presenting two case studies of rainfall events in Brazil.

Oral desmoplastic melanoma mimicking inflammatory hyperplasia.

INTRODUCTION: Desmoplastic melanoma (DM) arising in the oral cavity is a rare neoplasm that may be confused with a variety of non-melanocytic benign or malignant lesions. OBJECTIVES: To present a case of DM in the oral mucosa mimicking fibrous inflammatory hyperplasia, discusses the difficulties involved in the diagnosis and offers a literature review on the clinicopathologic and immunohistochemincal aspects of this neoplasm. CASE REPORT: A 62-year-old white male, smoker, was referred with a chief complaint of pain and swelling in the palate. The oral examination revealed multiple brown-to-black patches and a non-pigmented sessile nodule located on the mucosa of the hard palate. The clinical diagnosis of the pigmented lesions was either oral melanosis or melanoma. The nodular lesion was clinically diagnosed as fibrous inflammatory hyperplasia. Incisional biopsy was performed on the pigmented lesion and the microscopic sections revealed a melanotic macule. The nodular lesions histologically revealed an amelanotic desmoplastic melanoma. CONCLUSIONS: Reactive lesions close to a pigmented area should be investigated with great care.

A Tale of Two Centers: Visual Exploration of Health Disparities in Cancer Care.

The annual incidence of head and neck cancers (HNC) worldwide is more than 550,000 cases, with around 300,000 deaths each year. However, the incidence rates and disease-characteristics of HNC differ between treatment centers and different populations, due to undetermined reasons, which may or not include socioeconomic factors. The multi-faceted and multi-variate nature of the data in the context of the emerging field of health disparities research makes automated analysis impractical. Hence, we present a visual analysis approach to explore the health disparities in the data of HNC patients from two different cohorts at two cancer care centers. Our approach integrates data from multiple sources, including census data and city data, with custom visual encodings and with a nearest neighbor approach. Our design, created in collaboration with oncology experts, makes it possible to analyze the patients' demographic, disease characteristics, treatments and outcomes, and to make significant comparisons of these two cohorts and of individual patients. We evaluate this approach through two case studies performed with domain experts. The results demonstrate that this visual analysis approach successfully accomplishes the goal of comparing two cohorts in terms of different significant factors, and can provide insights into the main source of health disparities between the two centers.

UrbanRama: Navigating Cities in Virtual Reality.

Exploring large virtual environments, such as cities, is a central task in several domains, such as gaming and urban planning. VR systems can greatly help this task by providing an immersive experience; however, a common issue with viewing and navigating a city in the traditional sense is that users can either obtain a local or a global view, but not both at the same time, requiring them to continuously switch between perspectives, losing context and distracting them from their analysis. In this article, our goal is to allow users to navigate to points of interest without changing perspectives. To accomplish this, we design an intuitive navigation interface that takes advantage of the strong sense of spatial presence provided by VR. We supplement this interface with a perspective that warps the environment, called UrbanRama, based on a cylindrical projection, providing a mix of local and global views. The design of this interface was performed as an iterative process in collaboration with architects and urban planners. We conducted a qualitative and a quantitative pilot user study to evaluate UrbanRama and the results indicate the effectiveness of our system in reducing perspective changes, while ensuring that the warping doesn't affect distance and orientation perception.

Comparative genomics of Bordetella pertussis and prediction of new vaccines and drug targets.

Pertussis is a highly contagious respiratory disease caused by Bordetella pertussis, a Gram-negative bacterium described over a century ago. Despite broad vaccine coverage and treatment options, the disease is remerging as a public health problem especially in infants and older children. Recent data indicate re-emergence of the disease is related to bacterial resistance to immune defences and decreased vaccine effectiveness, which obviously suggests the need of new effective vaccines and drugs. In an attempt to contribute with solutions to this great challenge, bioinformatics tools were used to genetically comprehend the species of these bacteria and predict new vaccines and drug targets. In fact, approaches were used to analysis genomic plasticity, gene synteny and species similarities between the 20 genomes of Bordetella pertussis already available. Furthermore, it was conducted reverse vaccinology and docking analysis to identify proteins with potential to become vaccine and drug targets, respectively. The analyses showed the 20 genomes belongs to a homogeneous group that has preserved most of the genes over time. Besides that, were found genomics islands and good proteins to be candidates for vaccine and drugs. Taken together, these results suggests new possibilities that may be useful to develop new vaccines and drugs that will help the prevention and treatment strategies of pertussis disease caused by these Bordetella strains. Communicated by Ramaswamy H. Sarma.

Pan-genomic analyses of 47 complete genomes of the Rickettsia genus and prediction of new vaccine targets and virulence factors of the species.

The genus Rickettsia belongs to the Proteobacteria phylum and these bacteria infect animals and humans causing a range of diseases worldwide. The genus is divided into 4 groups and despite the public health threat and the knowledge accumulated so far, the mandatory intracellular bacteria behaviour and limitation for in vitro culture makes it difficult to create new vaccines and drug targets to these bacteria. In an attempt to overcome these limitations, pan-genomic approaches has used 47 genomes of the genus Rickettsia, in order to describe species similarities and genomics islands. Moreover, we conducted reverse vaccinology and docking analysis aiming the identification of proteins that have great potential to become vaccine and drug targets. We found out that the bacteria of the four Rickettsia groups have a high similarity with each other, with about 90 to 100% of identity. A pathogenicity island and a resistance island were predicted. In addition, 8 proteins were also predicted as strong candidates for vaccine and 9 as candidates for drug targets. The prediction of the proteins leads us to believe in a possibility of prospecting potential drugs or creating a polyvalent vaccine, which could reach most strains of this large group of bacteria.Communicated by Ramaswamy H. Sarma.

Titanium Allergy Caused by Dental Implants: A Systematic Literature Review and Case Report.

(1) Background: Hypersensitivity reactions to metals may arise in predisposed patients chronically exposed to metallic materials, including dental implants made of titanium alloys. The purpose of this article was to systematically review titanium allergy manifestations in patients treated with dental implants and report a clinical case; (2) Methods: A systematic electronic search was performed for articles published in the English language until July 2021. The following eligibility criteria were adopted: (1) Population: individuals undergoing titanium and/or titanium alloy implant-supported rehabilitations; (2) Exposure: peri-implant soft tissue reactions attributable to implant insertion; (3) Outcome: evidence of titanium allergy, diagnostic methods, and forms of resolution; (3) Results: The included studies, in summary, presented evidence that titanium should not be considered an inert material, being able to trigger allergic reactions, and may be responsible for implant failure. A 55-year-old male patient received 3 implants in the posterior region of the left mandible and presented an epulis-like lesion developed from the peri-implant mucosa. The immunohistochemical analysis of the biopsy specimen confirmed the initial diagnosis of allergic reaction to titanium; (4) Conclusions: Although the evidence is weak, and titanium allergy has a low incidence, hypersensitivity reactions should not be underestimated. A rapid and conclusive diagnosis is mandatory to prevent further complications.