Easy recognition and high autoimmune hepatitis specificity of smooth muscle antibodies giving an actin microfilament immunofluorescent pattern on embryonal vascular smooth muscle cells.

Smooth muscle antibodies (SMA) with anti-microfilament actin (MF-SMA) specificity are regarded as highly specific markers of type 1 autoimmune hepatitis (AIH-1) but their recognition relying on immunofluorescence of vessel, glomeruli, and tubules (SMA-VGT pattern) in rodent kidney-tissue, is restricted by operator-dependent interpretation.A gold standard method for their identification is not available. We assessed and compared the diagnostic accuracy for AIH-1 of an embryonal-aorta vascular-smooth-muscle(VSM) cell line-based assay with those of the rodent-tissue based assay for the detection of MF-SMA pattern in AIH-1 patients and controls. Sera from 138 AIH-1 patients and 295 controls (105 primary biliary cholangitis,40 primary sclerosing cholangitis,50 chronic viral hepatitis,20 alcohol-related liver disease,40 steatotic liver disease,and 40 healthy controls) were assayed for MF-SMA and for SMA-VGT using VSM-based and rodent tissue-based assays, respectively. MF-SMA and SMA-VGT were found in 96(70%) and 87(63%) AIH-1 patients, and 2 controls (p<0.0001).Compared with SMA-VGT, MF-SMA showed similar specificity (99%), higher sensitivity (70% vs 63%,p=ns) and likelihood ratio for a positive test (70 vs 65). Nine (7%) AIH-1 patients were MF-SMA positive despite being SMA-VGT negative. Overall agreement between SMA-VGT and MF-SMA was 87% (kappa coefficient 0.870,[0.789-0.952]). MF-SMA were associated with higher serum γ-globulin [26(12-55) vs 20 g/l(13-34),p<0.005] and immunoglobulin G (IgG) levels [3155(1296-7344) vs 2050 mg/dl(1377-3357), p<0.002]. The easily recognizable IFL MF-SMA pattern on VSM cells strongly correlated with SMA-VGT and has an equally high specificity for AIH-1. Confirmation of these results in other laboratories would support the clinical application of the VSM cell-based assay for reliable detection of AIH-specific SMA.

A Structural In Silico Analysis of the Immunogenicity of L-Asparaginase from Penicillium cerradense.

L-asparaginase is an essential drug used to treat acute lymphoid leukemia (ALL), a cancer of high prevalence in children. Several adverse reactions associated with L-asparaginase have been observed, mainly caused by immunogenicity and allergenicity. Some strategies have been adopted, such as searching for new microorganisms that produce the enzyme and applying protein engineering. Therefore, this work aimed to elucidate the molecular structure and predict the immunogenic profile of L-asparaginase from Penicillium cerradense, recently revealed as a new fungus of the genus Penicillium and producer of the enzyme, as a motivation to search for alternatives to bacterial L-asparaginase. In the evolutionary relationship, L-asparaginase from P. cerradense closely matches Aspergillus species. Using in silico tools, we characterized the enzyme as a protein fragment of 378 amino acids (39 kDa), including a signal peptide containing 17 amino acids, and the isoelectric point at 5.13. The oligomeric state was predicted to be a homotetramer. Also, this L-asparaginase presented a similar immunogenicity response (T- and B-cell epitopes) compared to Escherichia coli and Dickeya chrysanthemi enzymes. These results suggest a potentially useful L-asparaginase, with insights that can drive strategies to improve enzyme production.

A parametric study on pulse duplicator design and valve hemodynamics.

BACKGROUND: In vitro assessment is mandatory for artificial heart valve development. This study aims to investigate the effects of pulse duplicator features on valve responsiveness, conduct a sensitivity analysis across valve prosthesis types, and contribute on the development of versatile pulse duplicator systems able to perform reliable prosthetic aortic valve assessment under physiologic hemodynamic conditions. METHODS: A reference pulse duplicator was established based on literature. Further optimization process led to new designs that underwent a parametric study, also involving different aortic valve prostheses. These designs were evaluated on criteria such as mean pressure differential and pulse pressure (assessed from high-fidelity pressure measurements), valve opening and closing behavior, flow, and regurgitation. Finally, the resulting optimized setup was tested under five different hemodynamic settings simulating a range of physiologic and pathologic conditions. RESULTS: The results show that both, pulse duplicator design and valve type significantly influence aortic and ventricular pressure, flow, and valve kinematic response. The optimal design comprised key features such as a compliance chamber and restrictor for diastolic pressure maintenance and narrow pulse pressure. Additionally, an atrial reservoir was included to prevent atrial-aortic interference, and a bioprosthetic valve was used in mitral position to avoid delayed valve closing effects. CONCLUSION: This study showed that individual pulse duplicator features can have a significant effect on valve's responsiveness. The optimized versatile pulse duplicator replicated physiologic and pathologic aortic valve hemodynamic conditions, serving as a reliable characterization tool for assessing and optimizing aortic valve performance.

Scalable and versatile container-based pipelines for de novo genome assembly and bacterial annotation.

Background: Advancements in DNA sequencing technology have transformed the field of bacterial genomics, allowing for faster and more cost effective chromosome level assemblies compared to a decade ago. However, transforming raw reads into a complete genome model is a significant computational challenge due to the varying quality and quantity of data obtained from different sequencing instruments, as well as intrinsic characteristics of the genome and desired analyses. To address this issue, we have developed a set of container-based pipelines using Nextflow, offering both common workflows for inexperienced users and high levels of customization for experienced ones. Their processing strategies are adaptable based on the sequencing data type, and their modularity enables the incorporation of new components to address the community's evolving needs. Methods: These pipelines consist of three parts: quality control, de novo genome assembly, and bacterial genome annotation. In particular, the genome annotation pipeline provides a comprehensive overview of the genome, including standard gene prediction and functional inference, as well as predictions relevant to clinical applications such as virulence and resistance gene annotation, secondary metabolite detection, prophage and plasmid prediction, and more. Results: The annotation results are presented in reports, genome browsers, and a web-based application that enables users to explore and interact with the genome annotation results. Conclusions: Overall, our user-friendly pipelines offer a seamless integration of computational tools to facilitate routine bacterial genomics research. The effectiveness of these is illustrated by examining the sequencing data of a clinical sample of Klebsiella pneumoniae.

Complete Genome Sequence of Pantoea stewartii RON18713 from Brazil Nut Tree Phyllosphere Reveals Genes Involved in Plant Growth Promotion.

The Amazonian rainforest is a hyper-diverse ecosystem in the number of species and the myriad of intertaxon relationships that are mostly understudied. In order to characterize a dominant and economically important Amazonian species, the Brazil nut tree (Bertholletia excelsa Bonpl.), at the genome level, wegenerated high-coverage long-read sequencing data from the leaves of a single individual. The genome assembly revealed an unexpected discovery: two circular contigs that could be assigned to the chromosome and a plasmid of a Pantoea stewartii strain. Comparative genomics revealed that this strain belongs to the indologenes subspecies and displays high synteny with other strains isolated from diseased leaves of the neotropical palm Bactris gasipaes Kunth. Investigation of pathogenicity-related genes revealed the absence of the entire type III secretion system gene cluster in the plasmid, which was otherwise highly similar to a plasmid from an isolate known to cause disease in Dracaena sanderiana Mast. In contrast, several genes associated with plant-growth promoting traits were detected, including genes involved in indole-3-acetic acid (IAA) production, phosphate solubilization, and biosynthesis of siderophores. In summary, we report the genome of an uncultivated P. stewartii subsp. indologenes strain associated with the Brazil nut tree and potentially a plant growth-promoting bacteria.

Changing Epidemiology of Tinea Capitis in Athens, Greece: The Impact of Immigration and Review of Literature.

Mass population movements have altered the epidemiology of tinea capitis (TC) in countries receiving refugees. Periodic monitoring of the local pathogen profiles may serve as a basis for both the selection of appropriate empirical antifungal therapy and the implementation of preventive actions. Therefore, we investigated the impact of an unprecedented immigration wave occurring in Greece since 2015 on the epidemiological trends of TC. All microbiologically confirmed TC cases diagnosed during the period 2012-2019 in a referral academic hospital for dermatological disorders in Athens, Greece, were retrospectively reviewed. A total of 583 patients were recorded, where 348 (60%) were male, 547 (94%) were children and 160 (27%) were immigrants from Balkan, Middle Eastern, Asian as well as African countries. The overall annual incidence of TC was 0.49, with a significant increase over the years (p = 0.007). M. canis was the predominant causative agent (74%), followed by T. violaceum (12%), T. tonsurans (7%) and other rare dermatophyte species (7%). M. canis prevalence decreased from 2014 to 2019 (84% to 67%, p = 0.021) in parallel with a three-fold increase in T. violaceum plus T. tonsurans rates (10% to 32%, p = 0.002). An increasing incidence of TC with a shift towards anthropophilic Trichophyton spp. in Greece could be linked to the immigration flows from different socioeconomic backgrounds.

Tailoring crystallinity for hemocompatible and durable PEEK cardiovascular implants.

Polymers have the potential to replace metallic or bioprosthetic heart valve components due to superior durability and inertness while allowing for native tissue-like flexibility. Despite these appealing properties, certain polymers such as polyetheretherketone (PEEK) have issues with hemocompatibility, which have previously been addressed through assorted complex processes. In this paper, we explore the enhancement of PEEK hemocompatibility with polymer crystallinity. Amorphous, semi-crystalline and crystalline PEEK are investigated in addition to a highly crystalline carbon fiber (CF)/PEEK composite material (CFPEEK). The functional group density of the PEEK samples is determined, showing that higher crystallinity results in increased amount of surface carbonyl functional groups. The increase of crystallinity (and negatively charged groups) appears to cause significant reductions in platelet adhesion (33 vs. 1.5 % surface coverage), hemolysis (1.55 vs. 0.75 %∙cm-2), and thrombin generation rate (4840 vs. 1585 mU/mL/min/cm2). In combination with the hemocompatibility study, mechanical characterization demonstrates that tailoring crystallinity is a simple and effective method to control both hemocompatibility and mechanical performance of PEEK. Furthermore, the results display that CFPEEK composite performed very well in all categories due to its enhanced crystallinity and complete carbon encapsulation, allowing the unique properties of CFPEEK to empower new concepts in cardiovascular device design.

Computational Protocol for DNA Methylation Profiling in Plants Using Restriction Enzyme-Based Genome Reduction.

Epigenetics can be described as heritable phenotype changes that do not involve alterations in the underlying DNA sequence. Having widespread implications in fundamental biological phenomena, there is an increased interest in characterizing epigenetic modifications and studying their functional implications. DNA methylation, particularly 5-methylcytosine (5mC), stands out as the most studied epigenetic mark and several methodologies have been created to investigate it. With the development of next-generation sequencing technologies, several approaches to DNA methylation profiling were conceived, with differences in resolution and genomic scope. Besides the gold standard whole-genome bisulfite sequencing, which is costly for population-scale studies, genomic reduced representation methods emerged as viable alternatives to investigate methylation loci. Whole-genome bisulfite sequencing provides single-base methylation resolution but is costly for population-scale studies. Genomic reduction methods emerged as viable alternatives to investigate a fraction of methylated loci. One of such approaches uses double digestion with the restriction enzymes PstI and one of the isoschizomers, MspI and HpaII, with differential sensitivity to 5mC at the restriction site. Statistical comparison of sequencing reads counts obtained from the two libraries for each sample (PstI-MspI and PstI-HpaII) is used to infer the methylation status of thousands of cytosines. Here, we describe a general overview of the technique and a computational protocol to process the generated data to provide a medium-scale inventory of methylated sites in plant genomes. The software is available at https://github.com/wendelljpereira/DArTseqMet .

Genomic and physiological characterization of Novosphingobium terrae sp. nov., an alphaproteobacterium isolated from Cerrado soil containing a mega-sized chromid.

A novel bacterial strain, designated GeG2T, was isolated from soils of the native Cerrado, a highly biodiverse savanna-like Brazilian biome. 16S rRNA gene analysis of GeG2T revealed high sequence identity (100%) to the alphaproteobacterium Novosphingobium rosa; however, comparisons with N. rosa DSM 7285T showed several distinctive features, prompting a full characterization of the new strain in terms of physiology, morphology, and, ultimately, its genome. GeG2T cells were Gram-stain-negative bacilli, facultatively anaerobic, motile, positive for catalase and oxidase activities, and starch hydrolysis. Strain GeG2T presented planktonic-sessile dimorphism and cell aggregates surrounded by extracellular matrix and nanometric spherical structures were observed, suggesting the production of exopolysaccharides (EPS) and outer membrane vesicles (OMVs). Despite high 16S rDNA identity, strain GeG2T showed 90.38% average nucleotide identity and 42.60% digital DNA-DNA hybridization identity with N. rosa, below species threshold. Whole-genome assembly revealed four circular replicons: a 4.1 Mb chromosome, a 2.7 Mb extrachromosomal megareplicon, and two plasmids (212.7 and 68.6 kb). The megareplicon contains a few core genes and plasmid-type replication/maintenance systems, consistent with its classification as a chromid. Genome annotation shows a vast repertoire of carbohydrate-active enzymes and genes involved in the degradation of aromatic compounds, highlighting the biotechnological potential of the new isolate. Chemotaxonomic features, including polar lipid and fatty acid profiles, as well as physiological, molecular, and whole-genome comparisons showed significant differences between strain GeG2T and N. rosa, indicating that it represents a novel species, for which the name Novosphingobium terrae is proposed. The type strain is GeG2T (= CBMAI 2313T = CBAS 753 T).

SARS-CoV-2 as a Zooanthroponotic Infection: Spillbacks, Secondary Spillovers, and Their Importance.

In the midst of a persistent pandemic of a probable zoonotic origin, one needs to constantly evaluate the interplay of SARS-CoV-2 (severe acute respiratory syndrome-related coronavirus-2) with animal populations. Animals can get infected from humans, and certain species, including mink and white-tailed deer, exhibit considerable animal-to-animal transmission resulting in potential endemicity, mutation pressure, and possible secondary spillover to humans. We attempt a comprehensive review of the available data on animal species infected by SARS-CoV-2, as presented in the scientific literature and official reports of relevant organizations. We further evaluate the lessons humans should learn from mink outbreaks, white-tailed deer endemicity, zoo outbreaks, the threat for certain species conservation, the possible implication of rodents in the evolution of novel variants such as Omicron, and the potential role of pets as animal reservoirs of the virus. Finally, we outline the need for a broader approach to the pandemic and epidemics, in general, incorporating the principles of One Health and Planetary Health.

Building an interdisciplinary program of cardiovascular research at the Swiss Federal Institute of Technology- the ETHeart story.

In this backstory, researchers from Swiss Federal Institute of Technology (ETH Zurich) who initiated an interdisciplinary program to generate innovative solutions for different cardiovascular diseases, such as myocardial infarction, valvular replacement, and movement-based rehabilitation therapy, discuss the benefits and challenges of interdisciplinary research.

Digitizing Wildlife: The Case of a Reptile 3-D Virtual Museum.

In this article, we design and develop a 3-D virtual museum with holistic metadata documentation and a variety of reptile behaviors and movements. First, we reconstruct the reptile's mesh in high resolution, and then create its rigged/skinned digital counterpart. We acquire the movement of two subjects using an optical motion capture system, accelerometers, and RGB-vision cameras; these movements are then segmented and annotated to various behaviors. The 3-D environment, virtual reality (VR), and augmented reality (AR) functionalities of our online repository serve as tools for interactively educating the public on animals, which are difficult to observe and study in their natural environment. It also reveals important information regarding animals' intangible characteristics (e.g., behavior), that is critical for the preservation of wildlife. Our museum is publicly accessible, enabling motion data reusability, and facilitating learning applications through gamification. We conducted a user study that confirms the naturalness and realism of our reptiles, along with the ease of use and usefulness of our museum.

Conservative treatment vs thrombus removal for Iliofemoral vein thrombosis in patients with congenital abnormalities of the inferior vena cava: a case report and systematic review of the literature.

Congenital abnormalities of the Inferior Vena Cava (IVC) should be suspected in cases of Deep Venous Thrombosis (DVT), especially in young patients, with no other risk factors and apparent causes. Currently, there is no guidance regarding the management of such patients. We report a case of Iliofemoral vein thrombosis in a young patient with congenital absence of the IVC that was successfully treated with catheter-directed thrombolysis (CDT) and perform a systematic review of the literature to identify evidence about the epidemiology, clinical presentation, management, and prognosis of this rare cause of DVT. A total of 42 studies reporting on 56 cases were included in the review. The mean age of the patients at the presentation of their first DVT episode is 23.6 years, 83.9% of patients were males, conservative management with anticoagulation was used in 68% of the reported cases, and thrombolysis was used in 32% of the cases. Only 10.7% of patients presented with PE potentially justified by the abnormal anatomy of the deep veins which makes the propagation of thrombi into the pulmonary arteries less possible. Comparing the long-term outcomes of the two treatment groups; 42.3% of the patients treated conservatively vs 15.4% of the patients treated with thrombolysis developed chronic symptoms (residual heaviness, pain, swelling, and cramping). 11.5% of patients who received conservative treatment developed post-thrombotic syndrome. None of the patients treated with thrombolysis developed post-thrombotic syndrome. There were no procedure-related complications and thrombolysis was well tolerated by the entirety of the thrombolysis treatment group. Recurrence of DVT occurred in 13% of the patients treated conservatively and in 7.7% of patients treated with thrombolysis. Thrombus removal by means of thrombolysis is the recommended treatment and can offer excellent short and long-term results. Anticoagulation with NOACs may be prescribed for life to prevent recurrence or for at least 6 months and then reconsidered following further evaluation of patients' bleeding risk. It may be of value to organise an international registry for such patients. Guidelines issued by the relevant scientific societies will then be able to make a clear recommendation about the management of such patients.

The Lanzhou Brucella Leak: The Largest Laboratory Accident in the History of Infectious Diseases?

An inadequacy in sanitizing processes in a biopharmaceutical plant in Lanzhou, China, during July and August 2019, led to the aerosolization of Brucella that was subsequently spread through wind to nearby settlements and academic institutes, resulting in >10 000 human brucellosis cases, as of November 2020. The leak, possibly the largest laboratory accident in the history of infectious diseases, underlines the particular characteristics of Brucella that have made the pathogen a historical entity in biodefense research and a major cause of laboratory-associated infections. It further underlines the need for enhanced vigilance and strict regulatory interventions in similar facilities.

Unified waste metrics: A gamified tool in next-generation strategic planning.

A gamification approach for tackling waste management planning and urban development provide a more engaging and interactive experience with high pedagogical potential. Existing serious games involving waste management are complex in their data ingestion, use, and presentation, limiting individuals' opportunities to gain knowledge and decision-making skills transferrable to the real world. Simulations, by comparison, provide either an oversimplified and unrealistic user interface or explore in depth individual rather than aggregate key performance indicators for waste management, limiting potential knowledge retention. There is a clear opportunity in creating an informative, easy-to-use simulation-based game to help stakeholders build understanding of waste management policies, performance, and causal relationships. This gamified tool provides clear feedback through quick-visibility performance indicators (i.e., waste accumulation index, waste compositional analysis, prevention activities etc.) and offers the opportunity, through multi-criteria decision making, of simulating real-life scenarios and previewing the possible outcomes of certain in-game actions. The research question is how the process of gamification might serve as powerful tool for educating decision makers. The results are considered as a reference point to any policy maker intending to assess environmental performance, proposed activities to reach Circular Economy targets, and European Green Deal and UN Sustainable Development Goals.

Endovascular treatment of a giant renal artery aneurysm associated with an arteriovenous fistula: Report of a case and review of the literature.

Renal artery aneurysm (RAA) concomitant with a renal arteriovenous fistula (RAVF) has been infrequently reported in the literature. We report a case of a 42-year-old man suffering from a giant RAA combined with a congenital high-flow RAVF. The contrast-enhanced CTA showed a 12.7-cm RAA synchronous with an RAVF between the right renal artery and a draining vein. After a comprehensive preoperative assessment, an endovascular approach was decided. Successful embolization was performed using an Amplatzer vascular Plug, and multiple coils. Completion angiogram demonstrated no flow into the RAA. The results of longterm follow-up demonstrate that endovascular techniques are safe and effective for the management of RAAs combined with high-flow RAVF.

A Novel Multidrug Resistant, Non-Tn4401 Genetic Element-Bearing, Strain of Klebsiella pneumoniae Isolated From an Urban Lake With Drinking and Recreational Water Reuse.

Antimicrobial resistance (AMR) is an increasing and urgent issue for human health worldwide, as it leads to the reduction of available antibiotics to treat bacterial infections, in turn increasing hospital stays and lethality. Therefore, the study and genomic surveillance of bacterial carriers of resistance in and outside of clinical settings is of utter importance. A colony of multidrug resistant (MDR) bacteria identified as Klebsiella spp., by 16S rDNA amplicon sequencing, has been isolated from an urban lake in Brazil, during a drug-degrading bacterial prospection. Genomic analyses revealed the bacteria as Klebsiella pneumoniae species. Furthermore, the in silico Multilocus Sequence Typing (MLST) identified the genome as a new sequence type, ST5236. The search for antimicrobial resistance genes (ARGs) detected the presence of genes against beta-lactams, fosfomycin, acriflavine and efflux pumps, as well as genes for heavy metal resistance. Of particular note, an extended-spectrum beta-lactamase gene (blaCTX-M-15) has been detected in close proximity to siphoviridae genes, while a carbapenemase gene (KPC-2) has been found in an extrachromosomal contig, within a novel non-Tn4401 genetic element (NTEKPC). An extrachromosomal contig found in the V3 isolate is identical to a contig of a K. pneumoniae isolate from a nearby hospital, which indicates a putative gene flow from the hospital network into Paranoá lake. The discovery of a MDR isolate in this lake is worrisome, as the region has recently undergone periods of water scarcity causing the lake, which receives treated wastewater effluent, and is already used for recreational purposes, to be used as an environmental buffer for drinking water reuse. Altogether, our results indicate an underrepresentation of environmental K. pneumoniae among available genomes, which may hamper the understanding of the population dynamics of the species in the environment and its consequences in the spread of ARGs and virulence genes.