Revision and annotation of DNA barcode records for marine invertebrates: Report of the 8th iBOL conference hackathon

The accuracy of specimen identification through DNA barcoding and metabarcoding relies on reference libraries containing records with reliable taxonomy and sequence quality. The considerable growth in barcode data requires stringent data curation, especially in taxonomically difficult groups such as marine invertebrates. A major effort in curating marine barcode data in the Barcode of Life Data Systems (BOLD) was undertaken during the 8th International Barcode of Life Conference (Trondheim, Norway, 2019). Major taxonomic groups (crustaceans, echinoderms, molluscs, and polychaetes) were reviewed to identify those which had disagreement between Linnaean names and Barcode Index Numbers (BINs). The records with disagreement were annotated with four tags: A) MIS-ID (misidentified, mislabeled, or contaminated records), b) AMBIG (ambiguous records unresolved with the existing data), c) COMPLEX (species names occurring in multiple BINs), and d) SHARE (barcodes shared between species). A total of 83,712 specimen records corresponding to 7,576 species were reviewed and 39% of the species were tagged (7% MIS-ID, 17% AMBIG, 14% COMPLEX, and 1% SHARE). High percentages (>50%) of AMBIG tags were recorded in gastropods, whereas COMPLEX tags dominated in crustaceans and polychaetes. The high proportion of tagged species reflects either flaws in the barcoding workflow (e.g., misidentification, cross-contamination) or taxonomic difficulties (e.g., synonyms, undescribed species). Although data curation is essential for barcode applications, such manual attempts to examine large datasets are unsustainable and automated solutions are extremely desirable.The hackathon was organized with financial support from the European Union COST Action DNAqua-Net (CA 15219 https://dnaqua.net/) in the scope of the 8th International Barcode of Life Conference in Trondheim, Norway on 16 June 2019. DNAqua-Net is acknowledged for the funding provided and the local conference organizers for all the logistical support that ensured a successful event. Tyler Elliot and the rest of the BOLD team are acknowledged for their help with data queries and analytics. The authors also thank the hackathon participants for vibrant discussions during and after the event: Berry van der Hoorn, Katrine Konsghavn, Guy Paz, Mouna Rifi, Malin Strand, Anne Helene Tandberg, Adam Wall, and Endre Willassen. Marcos A. L. Teixeira was supported by a PhD grant from the Portuguese Foundation for Science and Technology (FCT I.P.) co-financed by ESF (SFRH/BD/131527/2017). Financial support granted by FCT to Sofia Duarte (CEECIND/00667/2017) and to Pedro E. Vieira (project NIS-DNA, PTDC/BIA-BMA/29754/2017) is also acknowledged. Sanna Majaneva was financially supported by the Norwegian Taxonomy Initiative (project no. 70184235). The authors thank the five reviewers who provided valuable input into the earlier version of the manuscript

Toxoplasma gondii infection, congenital toxoplasmosis, toxoplasmic retinochoroiditis and neurotoxoplasmosis: an overview

Introduction: The toxoplasmosis disease resulting from Toxoplasma gondii infection can manifest itself in many ways, however, congenital, ocular and cerebral forms require greater care. The infection by this protozoan is directly related to environmental and economic factors of the region. Objective: The present study, through a review in the literature, aimed to reinforce the knowledge about the infection caused by Toxoplasma gondii and its main clinical manifestations. Methods: This is a literature overview from academic books and scientific articles available in the Scientific Electronic Library Online, US National Library of Medicine National Institutes of Health and Google Scholar databases. To search the publications, the following descriptors were used: Toxoplasma gondii, toxoplasmosis, congenital toxoplasmosis, ocular toxoplasmosis and cerebral toxoplasmosis. The most relevant articles corresponding to the period from 2000 to 2017 were selected. Development: Toxoplasmosis may be of congenital or acquired origin after birth. The congenital form occurs during the embryonic/fetal life and through the passage of Toxoplasma gondii through the transplacental route. Ocular disease is common in both congenital and acquired infections and is closely associated with the presence of neurotoxoplasmosis in AIDS patients. Conclusion: Thus, immunocompromised patients and immunosuppressed patients are considered to be risk groups for Toxoplasma gondii infection

Ictiose Arlequim: Caso Clínico

Harlequin ichthyosis is a rare autosomal recessive congenital disease in which neonates present generalized hyperkeratotic plaques and deep fissures, ectropion, eclabium, malformation of the auricular pavilion and typical facies. Although several complications related to the skin restriction may occur, support in intensive care and early introduction of systemic retinoids, such as acitretin, have significantly contributed to patients' survival and improved prognosis. The purpose of this report is to present a rare case of harlequin ichthyosis and to discuss strategies for early diagnosis and first supportive care.Ictiose arlequim é uma doença congênita autossómica recessiva rara, na qual os recém-nascidos apresentam placas de hiperqueratose generalizadas e fissuras profundas, ectrópio, eclábio, malformação do pavilhão auricular e fácies típicas. Embora várias complicações relacionadas à restrição cutânea possam ocorrer, o suporte em terapia intensiva e a introdução precoce de retinóides sistémicos, como a acitretina, têm contribuído significativamente para a melhoria da sobrevida e do prognóstico dos doentes. O objetivo deste relato é apresentar um raro caso de ictiose arlequim e discutir estratégias para o diagnóstico precoce e o primeiro tratamento de suporte

Environmental Implications of pH in a Pervious Concrete Pavement on Highway BR-319, Amazonas, Brazil

http://sherpa.ac.uk/romeo/issn/0973-4929/This research studies the carbonation phenomenon of cement due to the reaction of its components with water. In this chemical reaction occurs the formation of calcium carbonate and the absorption of CO2 in the atmosphere, which contributes to the reduction of the Greenhouse Effect. However, carbonation also causes pathologies such as efflorescence, staining and corrosion of steel in concrete. This research shows the results of experiments with specimens of concrete permeable, made with cement and big aggregates (calcareous stone) in the ratio of 1: 4.4 (cement:stone) and a factor of 0.3 for water / cement. The specimens were kept in contact with water containing different amounts of CO2 - distilled, ionized alkaline, carbonated, and tap water. After the experiments were carried out, an increase in pH, a mean compressive strength of 12.3 MPa and a permeability rate of 1.28 l / h was observed. The results show that the permeable concrete did not present any pathologies resulting from the carbonation during the period of the research, which recommended the same for use in road pavements.info:eu-repo/semantics/publishedVersio

Uloga prirodnih spojeva kod raka mliječnih žlijezda u štakora; blagotvorni učinci vodenog ekstrakta Santolina chamaecyparissus L.

Breast cancer is the most diagnosed cancer among women, and a leading cause of death worldwide. Santolina chamaecyparissus L. is a plant with multiple health benefits, including anticancer and anti-diabetic properties. This study aimed to assess the chemopreventive effects of S. chamaecyparissus aqueous extract (SCE) in an animal model of mammary cancer. A total of 28 four-week-old female Wistar rats were divided into four groups: control, MNU-induced (IND), SCE-supplemented (SCE), and SCE+IND. SCE was added to drinking water (12.72 mg/kg body weight) ad libitum. MNU was administered via the intraperitoneal route at 50 days of age. Weekly monitoring of body weight, food/drink intake, humane endpoints, and number of mammary tumours were recorded. Twenty weeks after MNU administration, animals were sacrificed by anaesthetic overdose and a necropsy was performed. Blood samples were used to determine blood count and serum biochemistry analysis, while kidney and liver samples were analysed for oxidative stress. Tumour samples were collected for gene expression and histology studies. SCE chemical composition was analysed by LC-MS and contained 19 phenolic compounds, with the most abundant being myricetin-O-glucuronide and 1,3-O-dicaffeoylquinic acid. Two animals in the IND group were sacrificed due to exceeding the humane endpoint limits. SCE supplementation delayed mammary tumour development, reducing its volume and weight. SCE had a positive impact on haematological parameters, particularly the neutrophil-lymphocyte ratio (P=0.026). No significant differences were observed in serum biochemistry, except for creatinine kinase MB, or in oxidative stress markers. Gene expression analysis showed significantly reduced VEGF expression levels (P=0.0158) in tumours from SCE+IND. These findings suggest that SCE is deserving of further study to identify the individual compounds and to understand its influence on animal models during cancer development.Rak dojke najčešće je dijagnosticiran rak u žena i vodeći uzrok smrti na svijetu. Santolina chamaecyparissus L. je biljka s višestrukim blagotvornim učincima za zdravlje, uključujući antitumorska i antidijabetička svojstva. Cilj je ove studije bio procijeniti kemopreventivne učinke vodenog ekstrakta S. chamaecyparissus (SCE) na životinjama obeljelim od raka mliječnih žlijezda. Dvadeset i osam četiri ženki starih tjedna wistar štakora podijeljeno je u četiri skupine: kontrolnu, MNU-inducirano (IND), s dodatkom SCE (SCE) i SCE+IND. Skupini SCE je dodan vodi za piće (12,72 mg/kg tjelesne mase) ad libitum; MNU je primijenjen intraperitonealnim putem u 50. danu života. Tjedno je bilježeno praćenje tjelesne mase, unosa hrane/tekućine, humano usmrćivanje i broj tumora mliječnih žlijezda. Dvadeset tjedana nakon primjene MNU, životinje su žrtvovane predoziranjem anestetikom i obavljena je razudba. Uzorci krvi su rabljeni za određivanje krvne slike i analizu biokemije seruma, dok su uzeti uzorci bubrega i pluća rabljeni za analize oksidativnog stresa. Uzorci tumora su prikupljeni za studije ekspresije gena i histološke studije. Analiziran je kemijski sastav skupine SCE pomoću LC-MS i otkriveno je da sadrži 19 fenolnih spojeva od kojih su najobilniji bili miricetin-O-glukuronid i 1,3-O-dikafeoilkina kiselina. Dvije životinje iz IND skupini žrtvovane su zbog prekoračenja ograničenja za humano usmrćivanje. Skupini SCE dodatak je odgodio razvoj tumora mliječnih žlijezda, smanjujući njegov volumen i masu. Skupina SCE je imala pozitivni učinak na hematološke parametre, posebice na omjer neutrofila i limfocita (P=0,026). Nikakve značajne razlike nisu otkrivene u biokemiji seruma, osim kreatinin kinaze MB, niti u markerima oksidativnog stresa. Analiza ekspresije gena pokazala je značajno smanjene razina ekspresije VEGF (P=0,0158) u tumora iz skupine SCE+IND. Ovi nalazi ukazuju da bi skupinu SCE trebalo dodatno ispitati da bi se identificirali pojedinačni spojevi i razumio njegov utjecaj na životinjama oboljelih od raka mliječnih žlijezda

Curcumin—A Natural Medicament for Root Canal Disinfection: Effects of Irrigation, Drug Release, and Photoactivation

Introduction Curcumin incorporation into polymeric fibers was tested for its antimicrobial properties and potential use in root canal disinfection. Methods Curcumin-modified fibers were processed via electrospinning and tested against a 7-day old established Actinomyces naeslundii (An) biofilm. The medicaments tested were as follows: curcumin-modified fibers at 2.5 and 5.0 mg/mL, curcumin-based irrigant at 2.5 and 5.0 mg/mL, saline solution (negative control), and the following positive controls: 2% chlorhexidine, 1% NaOCl, and triple antibiotic paste (TAP, 1 mg/mL). All medicaments, except for the positive controls, were allocated according to the light exposure protocol: photoactivation with an LED every 30 s for 4 min or without photoactivation. After treatment, the medicaments were removed and 1 mL of saline solution was added; the biofilm was scraped from the well and used to prepare a 1:2000 dilution. Spiral plating was done using anaerobic blood agar plates. After 24 h, colony-forming units (CFU/mL, n=11/group) were counted to determine the antimicrobial effects. Results Data exhibited significant antimicrobial effects on positive control groups, followed by the curcumin irrigants, and lastly, the photoactivated curcumin-modified fibers. There was a significant reduction of viable bacteria in curcumin-based irrigants, which was greater than the TAP-treated group. Curcumin-free fibers, saline, and the non-photoactivated curcumin-modified fibers did not display antimicrobial activity. Conclusions Curcumin seems to be a potential alternative to TAP when controlling infection, but it requires a minimal concentration (2.5 mg/mL) to be effective. Photoactivation of curcumin-based medicaments seems to be essential to obtain greater antibiofilm activity

Evolution and Biogeographic History of Rubyspot Damselflies (Hetaerininae: Calopterygidae: Odonata)

The damselflies Hetaerininae, a subfamily of Calopterygidae, comprise four genera distributed from North to South America: Hetaerina, Mnesarete, Ormenophlebia and Bryoplathanon. While several studies have focused on the intriguing behavioral and morphological modifications within Hetaerina, little of the evolutionary history of the group is well understood. Understanding the biogeographical history of Hetaerininae is further complicated by uncertainty in important geological events, such as the closure of the Central American Seaway (CAS). We generated a phylogenetic hypothesis to test the relationships and divergence times within Hetaerininae using IQtree and BEAST2 and found that Mnesarete and Ormenophlebia render Hetaerina paraphyletic. Reclassification of the genera within Hetaerininae is necessary based on our results. We also tested the fit to our dataset of two different hypotheses for the closure of CAS. Our results supported a gradual closure, starting in the Oligocene and ending in the Pliocene. Using Ancestral Character State Reconstruction, we found that the rubyspot, which is associated with higher fecundity in several species, was ancestral for Hetaerininae and subsequently lost four times. Estimates of diversification in association with the rubyspot are needed to understand the plasticity of this important character. Forest habitat was the ancestral state for Hetaerininae, with transitions to generalist species of Hetaerina found primarily in the Mesoamerican region. These results add to our understanding of the relationship between morphology, biogeography and habitat in a charismatic group of damselflie

The cellular and synaptic architecture of the mechanosensory dorsal horn

The deep dorsal horn is a poorly characterized spinal cord region implicated in processing low-threshold mechanoreceptor (LTMR) information. We report an array of mouse genetic tools for defining neuronal components and functions of the dorsal horn LTMR-recipient zone (LTMR-RZ), a role for LTMR-RZ processing in tactile perception, and the basic logic of LTMR-RZ organization. We found an unexpectedly high degree of neuronal diversity in the LTMR-RZ: seven excitatory and four inhibitory subtypes of interneurons exhibiting unique morphological, physiological, and synaptic properties. Remarkably, LTMRs form synapses on between four and 11 LTMR-RZ interneuron subtypes, while each LTMR-RZ interneuron subtype samples inputs from at least one to three LTMR classes, as well as spinal cord interneurons and corticospinal neurons. Thus, the LTMR-RZ is a somatosensory processing region endowed with a neuronal complexity that rivals the retina and functions to pattern the activity of ascending touch pathways that underlie tactile perception

Optical mapping compendium of structural variants across global cattle breeds

Structural variants (SV) have been linked to important bovine disease phenotypes, but due to the difficulty of their accurate detection with standard sequencing approaches, their role in shaping important traits across cattle breeds is largely unexplored. Optical mapping is an alternative approach for mapping SVs that has been shown to have higher sensitivity than DNA sequencing approaches. The aim of this project was to use optical mapping to develop a high-quality database of structural variation across cattle breeds from different geographical regions, to enable further study of SVs in cattle. To do this we generated 100X Bionano optical mapping data for 18 cattle of nine different ancestries, three continents and both cattle sub-species. In total we identified 13,457 SVs, of which 1,200 putatively overlap coding regions. This resource provides a high-quality set of optical mapping-based SV calls that can be used across studies, from validating DNA sequencing-based SV calls to prioritising candidate functional variants in genetic association studies and expanding our understanding of the role of SVs in cattle evolution

Antimicrobial stewardship programs in seven Latin American countries: facing the challenges

Antecedentes: Diversos estudios han demostrado que más del 50% de los antibióticos utilizados en los hospitales son innecesarios o inadecuados y que la resistencia a los antimicrobianos puede suponer cada año hasta 20.000 millones de dólares de sobrecostes médicos. Por otro lado, los programas de administración de antimicrobianos (PEA) reducen significativamente el uso inadecuado de antimicrobianos, la aparición de resistencias a los antimicrobianos, las infecciones asociadas a la atención sanitaria y los costes en el ámbito hospitalario. Objetivo: Evaluar el desarrollo de ASP y el ahorro de antibióticos en 7 hospitales latinoamericanos utilizando indicadores cuantitativos estandarizados en todas las instituciones de salud participantes. Métodos: Se realizó un estudio de intervención, donde se realizaron evaluaciones pre y post utilizando una herramienta de puntuación estandarizada adaptada de los estándares de acreditación de la Joint Commission International y, del Instituto Colombiano de Normas Técnicas y Certificación. Se evaluó ASP de 7 hospitales latinoamericanos entre 2019 y 2020. Se realizó una evaluación pre-intervención en cada hospital para cuantificar el grado de desarrollo de la ASP (ASP Development score). Con base en estos resultados, se implementó una capacitación in situ adaptada en cada hospital, seguida de una evaluación posterior a la intervención para cuantificar la mejora de los indicadores de desarrollo de ASP. Además, se estimó el ahorro monetario en antimicrobianos derivado de la intervención del PEA. Resultados: En la evaluación previa a la intervención, la puntuación media de desarrollo del PEA en las 7 instituciones fue del 65,8% (40-94,3%). Los puntos con la puntuación más baja fueron los relacionados con el seguimiento y la comunicación de los progresos y el éxito del PEA. Para la evaluación posterior a la intervención, 2 instituciones no pudieron participar debido a la presión impuesta por la pandemia COVID-19. Para los 5/7 hospitales restantes, la puntuación media del desarrollo del PEA fue del 82,3%, con un aumento del 12,0% en comparación con la medición previa a la intervención de las mismas instituciones (puntuación media previa a la intervención 70,3% (48,2%-94,3%) Los puntos con un aumento significativo fueron los indicadores clave de rendimiento, la educación de los AMS y la formación de los prescriptores. Tres de los siete (3/7) hospitales informaron de ahorros monetarios en antibióticos asociados a la intervención ASP. Conclusiones: El uso de la herramienta descrita demostró ser útil para evaluar áreas específicas del desarrollo del PEA que eran deficientes y adaptar las intervenciones para los hospitales participantes, en consecuencia, ayudó a mejorar el desarrollo del PEA en las instituciones que se sometieron al análisis previo y posterior a la intervención. Además, las estrategias mostraron ahorros monetarios en los costes antimicrobianos cuando se midieron. © 2023, Los autores.Background: Studies have shown that more than 50% of the antibiotics used in hospitals are unnecessary or inappropriate and, that antimicrobial resistance may cost up to 20 billion USD in excess medical costs each year. On the other hand, Antimicrobial Stewardship Programs (ASP) significantly reduce inappropriate antimicrobial use, emergence of antimicrobial resistance, healthcare associated infections, and costs in hospital settings. Objective: To evaluate the development of ASP and antibiotic savings in 7 Latin American hospitals using standardized quantitative indicators in all the participating health care institutions. Methods: An interventional study was conducted, where pre- and post- evaluations were performed using a standardized score tool adapted from the Joint Commission International accreditation standards and, the Colombian Institute of Technical Standards and Certification. We evaluated ASP from 7 Latin American hospitals between 2019 and 2020. A pre-intervention evaluation was done in each hospital to quantify the degree of development of the ASP (ASP Development score). Based on these results, tailored on-site training was implemented in each hospital, followed by a post-intervention evaluation to quantify improvement of ASP-development indicators. In addition, monetary savings in antimicrobials derived from the ASP intervention were estimated. Results: In the pre-intervention evaluation, the average ASP development score for the 7 institutions was 65.8% (40-94.3%). The items with the lowest development score were those related to monitoring and communicating the ASP progress and success. For the post-intervention evaluation, 2 institutions couldn’t participate due to the pressure imposed by the COVID-19 pandemic. For the remaining 5/7 hospitals, the average ASP development score was 82.3% with an increase of 12.0% when compared to the pre-intervention measurement of the same institutions (average pre-intervention score 70.3% (48.2%-94.3%) The items with a significant increase were key performance indicators, AMS education and training of the prescribers. Three of the seven (3/7) hospitals reported antibiotic monetary savings associated to the ASP intervention. Conclusions: The use of the tool described shown to be useful to evaluate specific areas of ASP-development that were lacking and tailor interventions for the participating hospitals, consequently, it helped improve ASP-development in the institutions that underwent pre- intervention and post-intervention analysis. In addition, the strategies showed monetary savings on antimicrobial costs when measured. © 2023, The Author(s)