Genetic structure and diversity of the rfb locus of pathogenic species of the genus Leptospira.

Leptospirosis is caused by pathogenic strains of the genus Leptospira and is considered the most widespread zoonotic bacterial disease. The genus is characterized by the large number of serology variants, which challenges developing effective serotyping methods and vaccines with a broad spectrum. Because knowledge on the genetic basis of the serological diversity among leptospires is still limited, we aimed to explore the genetic structure and patterns of the rfb locus, which is involved in the biosynthesis of lipopolysaccharides, the major surface antigen that defines the serovar in leptospires. Here, we used genomic data of 722 pathogenic samples and compared the gene composition of their rfb locus by hierarchical clustering. Clustering analysis showed that the rfb locus gene composition is species-independent and strongly associated with the serological classification. The samples were grouped into four well-defined classes, which cluster together samples either belonging to the same serogroup or from different serogroups but sharing serological affinity. Our findings can assist in the development of new strategies based on molecular methods, which can lead to better tools for serological identification in this zoonosis.

Clinical decision support system using a machine learning model to assist simultaneous cardiopulmonary auscultation: Open-label randomized controlled trial.

Background: The utility of a clinical decision support system using a machine learning (ML) model for simultaneous cardiac and pulmonary auscultation is unknown. Objective: This study aimed to develop and evaluate an ML system's utility for cardiopulmonary auscultation. Methods: First, we developed an ML system for cardiopulmonary auscultation, using cardiopulmonary sound files from our previous study. The technique involved pre-processing, feature extraction, and classification through several neural network layers. After integration, the output class was categorized as "normal," "abnormal," or "undetermined." Second, we evaluated the ML system with 24 junior residents in an open-label randomized controlled trial at a university hospital. Participants were randomly assigned to the ML system group (intervention) or conventional auscultation group (control). During training, participants listened to four cardiac and four pulmonary sounds, all of which were correctly classified. Then, participants classified a series of 16 simultaneous cardiopulmonary sounds. The control group auscultated the sounds using noise-cancelling headphones, while the intervention group did so by watching recommendations from the ML system. Results: The total scores for correctly identified normal or abnormal cardiopulmonary sounds in the intervention group were significantly higher than those in the control group (366/384 [95.3%] vs. 343/384 [89.3%], P = 0.003). The cardiac test score in the intervention group was better (111/192 [57.8%] vs. 90/192 [46.9%], P = 0.04); there was no significant difference in pulmonary auscultation. Conclusions: The ML-based system improved the accuracy of cardiopulmonary auscultation for junior residents. This result suggests that the system can assist early-career physicians in accurate screening.

Effects of Combinational Use of Additional Differential Diagnostic Generators on the Diagnostic Accuracy of the Differential Diagnosis List Developed by an Artificial Intelligence-Driven Automated History-Taking System: Pilot Cross-Sectional Study.

BACKGROUND: Low diagnostic accuracy is a major concern in automated medical history-taking systems with differential diagnosis (DDx) generators. Extending the concept of collective intelligence to the field of DDx generators such that the accuracy of judgment becomes higher when accepting an integrated diagnosis list from multiple people than when accepting a diagnosis list from a single person may be a possible solution. OBJECTIVE: The purpose of this study is to assess whether the combined use of several DDx generators improves the diagnostic accuracy of DDx lists. METHODS: We used medical history data and the top 10 DDx lists (index DDx lists) generated by an artificial intelligence (AI)-driven automated medical history-taking system from 103 patients with confirmed diagnoses. Two research physicians independently created the other top 10 DDx lists (second and third DDx lists) per case by imputing key information into the other 2 DDx generators based on the medical history generated by the automated medical history-taking system without reading the index lists generated by the automated medical history-taking system. We used the McNemar test to assess the improvement in diagnostic accuracy from the index DDx lists to the three types of combined DDx lists: (1) simply combining DDx lists from the index, second, and third lists; (2) creating a new top 10 DDx list using a 1/n weighting rule; and (3) creating new lists with only shared diagnoses among DDx lists from the index, second, and third lists. We treated the data generated by 2 research physicians from the same patient as independent cases. Therefore, the number of cases included in analyses in the case using 2 additional lists was 206 (103 cases × 2 physicians' input). RESULTS: The diagnostic accuracy of the index lists was 46% (47/103). Diagnostic accuracy was improved by simply combining the other 2 DDx lists (133/206, 65%, P<.001), whereas the other 2 combined DDx lists did not improve the diagnostic accuracy of the DDx lists (106/206, 52%, P=.05 in the collective list with the 1/n weighting rule and 29/206, 14%, P<.001 in the only shared diagnoses among the 3 DDx lists). CONCLUSIONS: Simply adding each of the top 10 DDx lists from additional DDx generators increased the diagnostic accuracy of the DDx list by approximately 20%, suggesting that the combinational use of DDx generators early in the diagnostic process is beneficial.

Diagnostic errors in uncommon conditions: a systematic review of case reports of diagnostic errors.

OBJECTIVES: To assess the usefulness of case reports as sources for research on diagnostic errors in uncommon diseases and atypical presentations. CONTENT: We reviewed 563 case reports of diagnostic error. The commonality of the final diagnoses was classified based on the description in the articles, Orphanet, or epidemiological data on available references; the typicality of presentation was classified based on the description in the articles and the judgment of the physician researchers. Diagnosis Error Evaluation and Research (DEER), Reliable Diagnosis Challenges (RDC), and Generic Diagnostic Pitfalls (GDP) taxonomies were used to assess the factors contributing to diagnostic errors. SUMMARY AND OUTLOOK: Excluding three cases in that commonality could not be classified, 560 cases were classified into four categories: typical presentations of common diseases (60, 10.7 %), atypical presentations of common diseases (35, 6.2 %), typical presentations of uncommon diseases (276, 49.3 %), and atypical presentations of uncommon diseases (189, 33.8 %). The most important DEER taxonomy was "Failure/delay in considering the diagnosis" among the four categories, whereas the most important RDC and GDP taxonomies varied with the categories. Case reports can be a useful data source for research on the diagnostic errors of uncommon diseases with or without atypical presentations.

Effect of Prior Antibiotic Treatment on Blood Culture in an Outpatient Department of General Internal Medicine: A Retrospective Case-Control Analysis.

Purpose: The effect of antibiotics administered before blood cultures performed in general internal medicine outpatient settings is not well known. Patients and Methods: We conducted a retrospective case-control study including adult patients who underwent blood cultures in the general internal medicine outpatient department of a Japanese university hospital between 2016 and 2022. Patients with positive blood cultures were included as cases and matched patients with negative blood cultures were included as controls. Univariable and multivariable logistic regression analyses were performed. Results: A total of 200 patients and 200 controls were included. Antibiotics were administered prior to blood culture in 20% of patients (79/400). Oral antibiotics were prescribed to 69.6% of the prior antibiotics (55/79). Prior antibiotic use was significantly lower among patients with positive than negative blood cultures (13.5% vs 26.0%, p = 0.002) and was an independent predictive factor in univariable (odds ratio, 0.44; 95% confidence interval, 0.26-0.73; p = 0.002) and multivariable (adjusted odds ratio, 0.31; 95% confidence interval, 0.15-0.63; p = 0.002) logistic regression models for positive blood culture. The area under the receiver operating characteristic (AUROC) curve of the multivariable model for predicting positive blood cultures was 0.86. Conclusion: There was a negative correlation between prior antibiotic use and positive blood cultures in the general internal medicine outpatient department. Therefore, physicians should interpret the negative results of blood cultures performed after the administration of antibiotics with care.

Diagnostic Accuracy of Differential-Diagnosis Lists Generated by Generative Pretrained Transformer 3 Chatbot for Clinical Vignettes with Common Chief Complaints: A Pilot Study.

The diagnostic accuracy of differential diagnoses generated by artificial intelligence (AI) chatbots, including the generative pretrained transformer 3 (GPT-3) chatbot (ChatGPT-3) is unknown. This study evaluated the accuracy of differential-diagnosis lists generated by ChatGPT-3 for clinical vignettes with common chief complaints. General internal medicine physicians created clinical cases, correct diagnoses, and five differential diagnoses for ten common chief complaints. The rate of correct diagnosis by ChatGPT-3 within the ten differential-diagnosis lists was 28/30 (93.3%). The rate of correct diagnosis by physicians was still superior to that by ChatGPT-3 within the five differential-diagnosis lists (98.3% vs. 83.3%, p = 0.03). The rate of correct diagnosis by physicians was also superior to that by ChatGPT-3 in the top diagnosis (53.3% vs. 93.3%, p < 0.001). The rate of consistent differential diagnoses among physicians within the ten differential-diagnosis lists generated by ChatGPT-3 was 62/88 (70.5%). In summary, this study demonstrates the high diagnostic accuracy of differential-diagnosis lists generated by ChatGPT-3 for clinical cases with common chief complaints. This suggests that AI chatbots such as ChatGPT-3 can generate a well-differentiated diagnosis list for common chief complaints. However, the order of these lists can be improved in the future.

Natural genetic variation in the HAIRS ABSENT (H) gene increases type-VI glandular trichomes in both wild and domesticated tomatoes.

Glandular trichomes produce and exude secondary metabolites, conferring insect resistance in many crop species. Whereas some of its wild relatives are insect-resistant, tomato (Solanum lycopersicum) is not. Identifying the genetic changes that altered trichome development and biochemistry during tomato domestication would contribute to breeding for insect resistance. A mutation in the HAIRS ABSENT (H) gene, which encodes a C2H2 zinc finger protein (ZFP8), leads to reduced trichome density. Several geographic accessions of S. pimpinellifolium, the wild ancestor of domesticated tomato, have glabrous organs that resemble the phenotype caused by h. Here, we investigated allelic diversity for H in tomato and S. pimpinellifolium accessions and their associated trichome phenotypes. We also evaluated how the developmental stage can affect trichome development in glabrous and non-glabrous plants. We found that glabrous accessions of S. pimpinellifolium have different ZFP8 nucleotide sequence changes, associated with altered trichome development and density. We also found that while the glabrous appearance of h mutants is caused by a lower density of long trichomes, the density of type-VI glandular trichomes is increased, particularly in the adult stages of plant development. These insights on the genetic control of trichome development may contribute to breeding for insect resistance in tomatoes and other crops.

The systemic immune response due to cholesterol crystal embolization syndrome: a case report.

BACKGROUND: Cholesterol crystal embolization syndrome (CES) occurs when an atherosclerotic plaque causes small-vessel embolization, resulting in multi-organ damage. Although CES is pathologically characterized by an infiltration of eosinophils, the implication of the systemic inflammatory response represented by hypereosinophilia is unclear in clinical practice. Herein we present the case of a patient diagnosed with CES who developed multiple allergic organ injuries, including daptomycin-related dermatitis and later vancomycin-induced acute tubulointerstitial nephritis, which was successfully treated by the withdrawal of each medicine with or without corticosteroid therapy, one by one. CASE PRESENTATION: A 76-year-old Japanese man diagnosed with thoracic aneurysm rupture underwent total arch replacement through the open stent graft technique. Postoperatively, he developed methicillin-resistant Staphylococcus epidermidis bacteremia, which was treated with daptomycin. Subsequently, he presented with palpable purpura on both dorsal feet, erythema around his body, and hypereosinophilia. Daptomycin was replaced with vancomycin due to suspicion of drug-induced erythema. The erythema gradually faded. On nine days after vancomycin therapy, the systemic erythema rapidly reappeared followed by acute renal failure. The renal function decline prompted hemodialysis. A skin biopsy revealed cholesterol embolization, whereas a kidney biopsy revealed acute tubulointerstitial nephritis. After vancomycin discontinuation and initiation of systemic corticosteroid treatment, his kidney function was restored to the baseline level. CONCLUSIONS: The present case highlights cholesterol embolization can cause allergic complications in addition to direct organ damage.

Genetic basis underlying the serological affinity of leptospiral serovars from serogroups Sejroe, Mini and Hebdomadis.

Leptospirosis is a widely distributed zoonosis caused by pathogenic strains of bacteria of the genus Leptospira (Phylum Spirochaetes). Its agents are commonly classified based on their antigenic characteristics into serogroups and serovars, which are relevant for epidemiologic studies and vaccine development. Serological tests are considered laborious and require a specialized infrastructure. Some molecular methods have been proposed to accelerate these procedures, but they still can not replace the immunological tests, thus requiring a further understanding of the genetic basis underlying the serological classification. In this work, we focused on elucidating the genetic factors determinant for the serogroup Sejroe, which is one of the most prevalent serogroups in livestock. For this, we conducted a comparative analysis using >700 leptospiral genomic samples available in the public database. The analysis showed that the genes comprising the rfb locus are the main genetic factors associated with the serological classification. Samples from the serogroup Sejroe have an rfb locus with a conserved gene composition that differs from most other serogroups. Hebdomadis and Mini were the only serogroups whose samples have an rfb locus with similar gene composition to those from serogroup Sejroe, corroborating with the serological affinity shared by them. Finally, we could determine a small region in the rfb locus in which each of those three serogroups can be distinguished by its gene composition. This is the first work that uses an extensive repertoire of genomic data of leptospiral samples to elucidate the molecular basis of the serological classification and open the road to more reliable strategies based on molecular methods for serodiagnosis.

Auxin-driven ecophysiological diversification of leaves in domesticated tomato.

Heterobaric leaves have bundle sheath extensions (BSEs) that compartmentalize the parenchyma, whereas homobaric leaves do not. The presence of BSEs affects leaf hydraulics and photosynthetic rate. The tomato (Solanum lycopersicum) obscuravenosa (obv) mutant lacks BSEs. Here, we identify the obv gene and the causative mutation, a nonsynonymous amino acid change that disrupts a C2H2 zinc finger motif in a putative transcription factor. This mutation exists as a polymorphism in the natural range of wild tomatoes but has increased in frequency in domesticated tomatoes, suggesting that the latter diversified into heterobaric and homobaric leaf types. The obv mutant displays reduced vein density, leaf hydraulic conductance and photosynthetic assimilation rate. We show that these and other pleiotropic effects on plant development, including changes in leaf insertion angle, leaf margin serration, minor vein density, and fruit shape, are controlled by OBV via changes in auxin signaling. Loss of function of the transcriptional regulator AUXIN RESPONSE FACTOR 4 (ARF4) also results in defective BSE development, revealing an additional component of a genetic module controlling aspects of leaf development important for ecological adaptation and subject to breeding selection.

Taxallnomy: an extension of NCBI Taxonomy that produces a hierarchically complete taxonomic tree.

BACKGROUND: NCBI Taxonomy is the main taxonomic source for several bioinformatics tools and databases since all organisms with sequence accessions deposited on INSDC are organized in its hierarchical structure. Despite the extensive use and application of this data source, an alternative representation of data as a table would facilitate the use of information for processing bioinformatics data. To do so, since some taxonomic-ranks are missing in some lineages, an algorithm might propose provisional names for all taxonomic-ranks. RESULTS: To address this issue, we developed an algorithm that takes the tree structure from NCBI Taxonomy and generates a hierarchically complete taxonomic table, maintaining its compatibility with the original tree. The procedures performed by the algorithm consist of attempting to assign a taxonomic-rank to an existing clade or "no rank" node when possible, using its name as part of the created taxonomic-rank name (e.g. Ord_Ornithischia) or interpolating parent nodes when needed (e.g. Cla_of_Ornithischia), both examples given for the dinosaur Brachylophosaurus lineage. The new hierarchical structure was named Taxallnomy because it contains names for all taxonomic-ranks, and it contains 41 hierarchical levels corresponding to the 41 taxonomic-ranks currently found in the NCBI Taxonomy database. From Taxallnomy, users can obtain the complete taxonomic lineage with 41 nodes of all taxa available in the NCBI Taxonomy database, without any hazard to the original tree information. In this work, we demonstrate its applicability by embedding taxonomic information of a specified rank into a phylogenetic tree and by producing metagenomics profiles. CONCLUSION: Taxallnomy applies to any bioinformatics analyses that depend on the information from NCBI Taxonomy. Taxallnomy is updated periodically but with a distributed PERL script users can generate it locally using NCBI Taxonomy as input. All Taxallnomy resources are available at http://bioinfo.icb.ufmg.br/taxallnomy .

Plant Aquaporins: Diversity, Evolution and Biotechnological Applications.

The plasma membrane forms a permeable barrier that separates the cytoplasm from the external environment, defining the physical and chemical limits in each cell in all organisms. The movement of molecules and ions into and out of cells is controlled by the plasma membrane as a critical process for cell stability and survival, maintaining essential differences between the composition of the extracellular fluid and the cytosol. In this process aquaporins (AQPs) figure as important actors, comprising highly conserved membrane proteins that carry water, glycerol and other hydrophilic molecules through biomembranes, including the cell wall and membranes of cytoplasmic organelles. While mammals have 15 types of AQPs described so far (displaying 18 paralogs), a single plant species can present more than 120 isoforms, providing transport of different types of solutes. Such aquaporins may be present in the whole plant or can be associated with different tissues or situations, including biotic and especially abiotic stresses, such as drought, salinity or tolerance to soils rich in heavy metals, for instance. The present review addresses several aspects of plant aquaporins, from their structure, classification, and function, to in silico methodologies for their analysis and identification in transcriptomes and genomes. Aspects of evolution and diversification of AQPs (with a focus on plants) are approached for the first time with the aid of the LCA (Last Common Ancestor) analysis. Finally, the main practical applications involving the use of AQPs are discussed, including patents and future perspectives involving this important protein family.

Sequence analysis of the cDNA encoding for SpCTx: a lethal factor from scorpionfish venom (Scorpaena plumieri).

BACKGROUND: Lethal factors are multifunctional oligomeric proteins found in the venomous apparatus of Scorpaeniformes fish. These toxins elicit not only an array of biological responses in vitro but also cardiovascular disorders and strong hemolytic, nociceptive and edematogenic activities in vivo. This work describes the cloning and molecular identification of two toxin subunits, denominated Sp-CTx-α and Sp-CTx-ß, from scorpionfish venom (Scorpaena plumieri). METHODS: The primary structures were deduced after cDNA amplification by PCR with primers from conserved sequences described in Scorpaeniformes toxins. Following DNA sequencing and bioinformatic analysis, the tridimensional structures of both subunits were modeled. RESULTS: The translated sequences (702 amino acids, each subunit) show homology with other lethal factors, while alignment between Sp-CTx-α and Sp-CTx-ß shows 54% identity. The subunits lack N-terminal signal sequences and display masses of approximately 80 kDa each. Both Sp-CTx subunits display a B30.2/SPRY domain at the C-terminal region with typically conserved motifs as described in these toxins. Secondary structure prediction identified six α-helices 18 residues long in both α and ß subunits, some of them amphiphilic with their N-terminal flanked by many basic residues, creating a cationic site associated with the cytolytic activity of these toxins. Antimicrobial potential sites were identified in Sp-CTx and share some features with other peptides presenting variable and broad-spectrum activity. A phylogenetic tree built to represent these toxins supports the proximity between scorpionfish, lionfish and stonefish. CONCLUSION: The study identified a putative toxin protein whose primary structure is similar to other fish toxins and with potential for production of antivenom against scorpionfish envenomation in Brazil. As a prelude to structure-function studies, we propose that the toxin is structurally related to pore-forming marine toxins.

Whole Genome Sequencing of the Pirarucu (Arapaima gigas) Supports Independent Emergence of Major Teleost Clades.

The Pirarucu (Arapaima gigas) is one of the world's largest freshwater fishes and member of the superorder Osteoglossomorpha (bonytongues), one of the oldest lineages of ray-finned fishes. This species is an obligate air-breather found in the basin of the Amazon River with an attractive potential for aquaculture. Its phylogenetic position among bony fishes makes the Pirarucu a relevant subject for evolutionary studies of early teleost diversification. Here, we present, for the first time, a draft genome version of the A. gigas genome, providing useful information for further functional and evolutionary studies. The A. gigas genome was assembled with 103-Gb raw reads sequenced in an Illumina platform. The final draft genome assembly was ∼661 Mb, with a contig N50 equal to 51.23 kb and scaffold N50 of 668 kb. Repeat sequences accounted for 21.69% of the whole genome, and a total of 24,655 protein-coding genes were predicted from the genome assembly, with an average of nine exons per gene. Phylogenomic analysis based on 24 fish species supported the postulation that Osteoglossomorpha and Elopomorpha (eels, tarpons, and bonefishes) are sister groups, both forming a sister lineage with respect to Clupeocephala (remaining teleosts). Divergence time estimations suggested that Osteoglossomorpha and Elopomorpha lineages emerged independently in a period of ∼30 Myr in the Jurassic. The draft genome of A. gigas provides a valuable genetic resource for further investigations of evolutionary studies and may also offer a valuable data for economic applications.

Sequence analysis of the cDNA encoding for SpCTx: a lethal factor from scorpionfish venom ( Scorpaena plumieri )

Background: Lethal factors are multifunctional oligomeric proteins found in the venomous apparatus of Scorpaeniformes fish. These toxins elicit not only an array of biological responses in vitro but also cardiovascular disorders and strong hemolytic, nociceptive and edematogenic activities in vivo. This work describes the cloning and molecular identification of two toxin subunits, denominated Sp-CTx- and Sp-CTx-, from scorpionfish venom ( Scorpaena plumieri ). Methods: The primary structures were deduced after cDNA amplification by PCR with primers from conserved sequences described in Scorpaeniformes toxins. Following DNA sequencing and bioinformatic analysis, the tridimensional structures of both subunits were modeled. Results: The translated sequences (702 amino acids, each subunit) show homology with other lethal factors, while alignment between Sp-CTx- and Sp-CTx- shows 54% identity. The subunits lack N-terminal signal sequences and display masses of approximately 80 kDa each. Both Sp-CTx subunits display a B30.2/SPRY domain at the C-terminal region with typically conserved motifs as described in these toxins. Secondary structure prediction identified six -helices 18 residues long in both and subunits, some of them amphiphilic with their N-terminal flanked by many basic residues, creating a cationic site associated with the cytolytic activity of these toxins. Antimicrobial potential sites were identified in Sp-CTx and share some features with other peptides presenting variable and broad-spectrum activity...