Infrastructure tools to support an effective Radiation Oncology Learning Health System.

PURPOSE: Radiation Oncology Learning Health System (RO-LHS) is a promising approach to improve the quality of care by integrating clinical, dosimetry, treatment delivery, research data in real-time. This paper describes a novel set of tools to support the development of a RO-LHS and the current challenges they can address. METHODS: We present a knowledge graph-based approach to map radiotherapy data from clinical databases to an ontology-based data repository using FAIR concepts. This strategy ensures that the data are easily discoverable, accessible, and can be used by other clinical decision support systems. It allows for visualization, presentation, and data analyses of valuable information to identify trends and patterns in patient outcomes. We designed a search engine that utilizes ontology-based keyword searching, synonym-based term matching that leverages the hierarchical nature of ontologies to retrieve patient records based on parent and children classes, connects to the Bioportal database for relevant clinical attributes retrieval. To identify similar patients, a method involving text corpus creation and vector embedding models (Word2Vec, Doc2Vec, GloVe, and FastText) are employed, using cosine similarity and distance metrics. RESULTS: The data pipeline and tool were tested with 1660 patient clinical and dosimetry records resulting in 504 180 RDF (Resource Description Framework) tuples and visualized data relationships using graph-based representations. Patient similarity analysis using embedding models showed that the Word2Vec model had the highest mean cosine similarity, while the GloVe model exhibited more compact embeddings with lower Euclidean and Manhattan distances. CONCLUSIONS: The framework and tools described support the development of a RO-LHS. By integrating diverse data sources and facilitating data discovery and analysis, they contribute to continuous learning and improvement in patient care. The tools enhance the quality of care by enabling the identification of cohorts, clinical decision support, and the development of clinical studies and machine learning programs in radiation oncology.

Interrogating the 5'UTR tandem repeats of retrotransposon roo of Drosophila about horizontal transfer.

Horizontal transfer in Drosophila has been inferred for several families of transposable elements. Specifically, the retroelement roo has been suggested to have been horizontally transferred between the species D. melanogaster, D. simulans, D. sechellia and D. yakuba. The inferences were based on the observation that divergence between transposable elements in different species was lower than the divergence found in typical nuclear genes and in the incongruence of phylogenies of the species and their TEs. Here, we address the question of the possible horizontal transfer of roo between species of the Drosophila genus by studying the presence absence of a duplication of 99 bp in the 5'UTR of the transposon, as well as comparing the sequences of the paralogous and orthologous duplicated repeats within and between species. First, the repeats were only found in five species of the melanogaster subgroup. Second, the date of occurrence of the duplication event originating the repeats was posterior to the split of the subgroup. The duplication date suggests an origin previous to the split of D. simulans and D. sechellia and close to the divergence of D. melanogaster from the D. simulans complex. These data point to horizontal transfer to the afrotropical species D. yakuba and D. erecta from one of the cosmopolitan species D. melanogaster or D. simulans. We propose that the parasitoid wasp Leptopilina could have been the vector of horizontal transfer after the observation that a sequence of 845 bp with high homology to a fragment of roo was isolated from this wasp.

First Record of Psorophora albipes in Quintana Roo, Mexico.

In Mexico the Psorophora genus includes 24 species divided into 3 subgenera: Grabhamia, Janthinosoma, and Psorophora. Some species occur in the Nearctic region of the country (northern Mexico), whereas other species occur in the Neotropical region (southern Mexico), and a few species occur in both regions. In Quintana Roo, Mexico, 7 species have been previously recorded: Ps. confinnis s.s., Ps. champerico, Ps. cyanescens, Ps. ferox, Ps. lutzii, Ps. ciliata, and Ps. lineata. In October 2013, 24 females of Ps. albipes were collected using CDC light traps. This is the first record of this species in Quintana Roo.

The mosquitoes (Diptera: Culicidae) of the Mexican Yucatan Peninsula: a comprehensive review on the use of taxonomic names.

The Yucatan Peninsula is a biogeographic province of the Neotropical region which is mostly encompassed by the 3 Mexican states of Campeche, Quintana Roo, and Yucatán. During the development of the International Joint Laboratory ELDORADO (Ecosystem, bioLogical Diversity, habitat mOdifications and Risk of emerging PAthogens and Diseases in MexicO), a French-Mexican collaboration between the IRD (Institut de Recherche pour le Développement) and UNAM (Universidad Nacional Autónoma de México) in Mérida, it became evident that many putative mosquito species names recorded in the Mexican Yucatan Peninsula were misidentifications/misinterpretations or from the uncritical repetition of incorrect literature records. To provide a stronger foundation for future studies, the mosquito fauna of the Mexican Yucatan Peninsula is here comprehensively reviewed using current knowledge of taxonomy, ecology, and distribution of species through extensive bibliographic research, and examination of newly collected specimens. As a result, 90 mosquito species classified among 16 genera and 24 subgenera are recognized to occur in the Mexican Yucatan Peninsula, including 1 new peninsula record and 3 new state records.

A review of the melliferous flora of Yucatan peninsula, Mexico, on the basis for the honey production cycle.

BACKGROUND: The Yucatan Peninsula (YP) is one of the most important regions in global apiculture. Hence, this work reviews and integrates the knowledge of the species diversity, growth habits, ecosystems, floral calendars during the apiculture production cycles and the types of vegetation represented in the melliferous flora (MF) of the YP; as a basis for proposing selection strategies locating suitable apiculture production areas for local beekeepers and help in the economic development of the region. METHODS: A comprehensive review of the MF literature was carried out using the snowball method to determine and update the number of species useful for apiculture. The growth habits and flower calendars were determined through a review of the literature and databases of specimens from the herbaria CICY, UCAM and MEXU. RESULTS: The YP reports a total of 935 taxa of MF (98 families and 498 genera); of these, Campeche has 812 taxa, followed by Quintana Roo (786) and Yucatán (767). The MF is made up of herbs (282), followed by shrubs (260), trees (229), climbers (82), woody climbers (67) palms (14) and parasitic plant (1). CONCLUSION: Of the 935 species of MF registered at the regional level, a high number of species have flowering throughout the year, however, not all of these species are considered useful for local commercial apiculture. Only a select group of 23 species are considered of major importance for local apiculture industry.

Expression of retrotransposons contributes to aging in Drosophila.

Retrotransposons are a class of transposable elements capable of self-replication and insertion into new genomic locations. Across species, the mobilization of retrotransposons in somatic cells has been suggested to contribute to the cell and tissue functional decline that occurs during aging. Retrotransposons are broadly expressed across cell types, and de novo insertions have been observed to correlate with tumorigenesis. However, the extent to which new retrotransposon insertions occur during normal aging and their effect on cellular and animal function remains understudied. Here, we use a single nucleus whole genome sequencing approach in Drosophila to directly test whether transposon insertions increase with age in somatic cells. Analyses of nuclei from thoraces and indirect flight muscles using a newly developed pipeline, Retrofind, revealed no significant increase in the number of transposon insertions with age. Despite this, reducing the expression of two different retrotransposons, 412 and Roo, extended lifespan, but did not alter indicators of health such as stress resistance. This suggests a key role for transposon expression and not insertion in regulating longevity. Transcriptomic analyses revealed similar changes to gene expression in 412 and Roo knockdown flies and highlighted changes to genes involved in proteolysis and immune function as potential contributors to the observed changes in longevity. Combined, our data show a clear link between retrotransposon expression and aging.

Discovering the fish fauna of a lagoon from the southeast of the Yucatan Peninsula, Mexico, using DNA barcodes.

Background: Aquatic ecosystems in the tropics are typically environments with a high species richness of fishes. These systems are also among the most vulnerable in the world, threatening the overall biodiversity of tropical regions. As a first step, it is important to enumerate the species in any ecosystem to promote its conservation. This study aims to inventory the ichthyofauna in the Chile Verde Lagoon, Quintana Roo, on the Yucatan Peninsula, a system fortunately well protected in Mexico, based on faunal surveys backed up with mtDNA barcodes. Methods: We collected larvae, juveniles, and adults of fishes in the lagoon with a variety of sampling gear targeting various life stages. Species were identified using both morphology and DNA barcodes. The abundance of species and ichthyoplankton biomass (wet weight, suction technique) were calculated from 43 samples. Results: We collected 197 adult and juvenile fishes and 3,722 larvae, of which 306 specimens were DNA-sequenced with a success rate of 96.7%. We identified 13 families, 24 genera, and 27 species in our inventory. The species number was estimated to comprise 75% of the potential total richness using the Chao 1 richness estimator. Clupeids and gobiids accounted for 87.9% of the total abundance of fishes, and, together with cyprinodontids, also accounted for the highest ichthyoplankton biomass. Conclusion: Adult and juvenile fishes were identified by morphology and meristic values, however larvae required DNA barcoding to identify species. The high biomass and abundance of larvae of clupeids, gobiids and cyprinodontids suggests that the Chile Verde Lagoon may be important for reproduction of these species in the region. Microgobius microlepis, a marine goby species, is reported for the first time in an inland oligohaline system. This study provides a basis for future environmental assessment and biomonitoring of the Chile Verde Lagoon in the Yucatan Peninsula of Mexico.

Two new species of Trichoglossum (Geoglossaceae, Ascomycota) from south Mexico.

Two new species of Trichoglossum are described from south Mexico based on morphological and molecular evidence. Trichoglossumcaespitosum is characterized by the caespitose ascomata, rough and coiled paraphyses and the ascospores with 9-11 septa. Trichoglossumtropicale is characterized by the capitate ascomata, clavate and straight paraphyses and the ascospores with 10-12 septa. Both species grow in the tropical forests of the Yucatán peninsula. Here we provide descriptions and photographs for these species, together with a phylogenetic analyses based on the DNA sequences of nuc rDNA (ITS region and 28S gene) and a comparative table for the species known for America.

New Records and Updated Checklist of Mosquito Species in Quintana Roo, Mexico, Using DNA-Barcoding.

Collections of mosquitoes were conducted as part of the entomological vector surveillance in Quintana Roo State, Mexico, during September 2015. Species collected included Anopheles gabaldoni, An. darlingi, Psorophora columbiae, Culex inflictus, Cx. trifidus, Cx. lactator, and Wyeomyia guatemala s.l. All the specimens were identified by morphological and molecular characters (DNA-barcoding). This is the 1st time these species are reported in the Mexican state of Quintana Roo. This research updates and increases the list of species of mosquitoes in Quintana Roo from 79 to 86.

Genetic diversity of HLA system in two populations from Quintana Roo, Mexico: Cancún and rural Quintana Roo.

We studied HLA class I (HLA-A, -B) and class II (HLA-DRB1, -DQB1) alleles by PCR-SSP based typing in 98 Mexicans from the state of Quintana Roo living in the city of Cancún (N = 48) and rural communities (N = 50), to obtain information regarding allelic and haplotypic frequencies and their linkage disequilibrium. We found that the most frequent haplotypes in Quintana Roo include ten Native American and two European haplotypes. Admixture estimates revealed that the main genetic components in Quintana Roo are Native American (80.85 ±â€¯3.70% by ML; 60.20% of Native American haplotypes) and European (15.19 ±â€¯14.25% by ML; 26.02% of European haplotypes), and a less prominent African genetic component (3.96 ±â€¯10.75% by ML; 6.63% of African haplotypes).

Anchialine cave-dwelling sponge fauna (Porifera) from La Quebrada, Mexico, with the description of the first Mexican stygobiont sponges.

Porifera has been relatively well studied from underwater caves worldwide. However, sponges in Mexico are only known from two anchialine caves: La Quebrada and El Aerolito, both in Cozumel Island. An ecological study found that sponges have the second highest species richness and density in La Quebrada. The aim of the present work is to describe the sponge biodiversity inhabiting the dark zone of La Quebrada anchialine cave. A total of ten species were found and are described herein, six are new species to science vis. Calyx maya n. sp. a thinly branched sponge; Haliclona (Reniera) stygobia n. sp. globe-shaped with the thinnest diameter of oxeas in its group; Haliclona (Halichoclona) chankanaabiis n. sp. tubular habit with the smallest oxeas in its group; Neosiphonia microtriaeneae n. sp. characterized by very small dichotriaenes; Svenzea germanyanezi n. sp. a lone conical shape; and Diplastrella cozumella n. sp. for its tri to multilobed tylostyles. The other four species are previously known from open reefs or deep-sea: Discodermia adhaerens, Siphonidium ramosum, Cinachyrella kuekenthali, and Plakinastrella onkodes. This is the only inventory of Porifera in Mexican caves up to now, thus the species here described are the first stygobiont sponges from Mexico with an endemism rate of Porifera in this anchialine cave of 60%. Conservation programs are needed to preserve this unique and special ecosystem.

Different structural variants of roo retrotransposon are active in Drosophila melanogaster.

Retrotransposon roo is one of the most active elements in Drosophila melanogaster. The level of nucleotide diversity between copies of roo is very low but structural variation in the 5'-UTR is considerable. Transposition of roo at high frequency (around 5 × 10-2 per generation) has been shown previously in the set of mutation accumulation lines named Oviedo. Here we isolated thirteen individual insertions by inverse PCR and sequenced the 5' end of the elements (between 1663 and 2039 nt) including the LTR, the 5'-UTR and a fragment of 661 nucleotides from the ORF, to study whether the new transposed copies come from a unique variant (the master copy model) or different elements are able to move (the transposon model). The elements in the Oviedo lines presented the same structural variants as the reference genome. Different structural variants were active, a behaviour compatible with the "transposon model" in which the copies localized in multiple sites in the genome are able to transpose. At the level of sequence, the copies of roo in our lines are highly similar to the elements in the reference genome. The phylogenetic tree shows a shallow diversification with unsupported nodes denoting that all the elements currently active are very young. This observation together with the great polymorphism in insertion sites implies a rapid turnover of the elements.

Crinoidea y Asteroidea (Echinodermata) del talud de la península de Yucatán, de la Colección Nacional de Equinodermos de México / Crinoidea and Asteroidea (Echinodermata) from the slope of the Yucatan Peninsula, Colección Nacional de Equinodermos, Mexico

Resumen Introducción: Las especies de las clases Crinoidea y Asteroidea se distribuyen en gran variedad de hábitats en todos los océanos desde la zona intermareal hasta grandes profundidades, existen pocos registros en aguas mexicanas, a profundidades superiores a los 200 m, los escasos registros existentes datan de documentos históricos de la literatura especializada y los ejemplares se resguardan en colecciones científicas extranjeras. Objetivo: Contribuir a la recopilación de información de los ejemplares resguardados en la Colección Nacional de Equinodermos (CNE) del Instituto de Ciencias del Mar y Limnología (ICML), UNAM y proveer un inventario de las especies de crinoideos y asteroideos que habitan en zonas profundas del talud de la Península de Yucatán, México. Métodos: Del año 2005 al 2014 se recolectaron ejemplares de crinoideos y asteriodeos en cuatro cruceros en el B/O "Justo Sierra" BIOREPES 1 y 2 y COBERPES 2 y 6. Se realizaron arrastres con red camaronera en 80 estaciones de muestreo. Resultados: El listado taxonómico comprende 1146 ejemplares, de los cuales 204 son crinoideos del orden Comatulida, distribuidos en tres familias tres géneros y tres especies y 942 asteroideos distribuidos en seis órdenes, 11 familias, 21 géneros y 28 especies. Se obtuvieron los registros nuevos para la CNE: Democrinus rawsonii y Atelecrinus balanoides en crinoideos. Astropecten alligator, Hymenaster modestus, Calyptraster personatus, Pteraster militarioides militarioides, Sclerasterias contorta en asteroideos. Con esta información se incrementan los registros de crinoideos y asteroideos (de profundidad mayor a 200 m) para los estados de Yucatán (16) y Quintana Roo (16).

Abstract Introduction: The species of the Crinoidea and Asteroidea classes are distributed in a wide variety of habitats in all oceans from the intertidal zone to great depths, there are few Mexican records in depths greater than 200 m, the few existing records date from historical documents in the specialized literature and the specimens are kept in foreign scientific collections. Objective: Contribute to the collection of information on the specimens kept in the Colección Nacional de Equinodermos (CNE) of Instituto de Ciencias del Mar y Limnología (ICML), UNAM and provide an inventory of the species of crinoids and asteroids that inhabit deep areas of the slope of the Yucatan Peninsula, Mexico. Methods: From 2005 to 2014, specimens of crinoids and asterioids were collected through four cruises in the B/O "Justo Sierra" BIOREPES 1 and 2 and COBERPES 2 and 6, shrimp net trawls were carried out at 80 sampling stations. Results: The taxonomic list includes 1146 specimens, of which 204 crinoids are of the order Comatulida, distributed in three families, three genera and three species and 942 asteroids distributed in six orders, 11 families, 21 genera and 28 species. New records were obtained for CNE: Democrinus rawsonii and Atelecrinus balanoides in crinoids. Astropecten alligator, Hymenaster modestus, Calyptraster personatus, Pteraster militarioides militarioides, Sclerasterias contorta in asteroids. With this information, the records of crinoids and asteroids (deeper than 200 m) increase for the states of Yucatan (16) and Quintana Roo (16).

Stephanosporamayana (Stephanosporaceae, Russulales), a new sequestrate fungus from Yucatán Peninsula, Mexico.

Stephanosporamayana is presented as a new species from the Yucatán Peninsula, Mexico. This species is distinguished by the yellowish pileus, basidiospores with a small corona (4-6 × 1-2.5 µm), and variable size (8.0-17.0 × 6.0-11.0), thin pileus (21-40 µm) and the ecological association to lowland forest with Haematoxylumcampechianum, Gymnopodiumfloribundum, Coccolobadiversifolia, Metopiumbrownei and Pinuscaribaea. It differs from the American species of Stephanospora, like S.michoacanensis and S.chilensis, by its larger basidiospores. Descriptions, photographs and discussions are presented.

Mixed Toxoplasma gondii infection and new genotypes in feral cats of Quintana Roo, México.

Toxoplasmosis is a zoonosis caused by Toxoplasma gondii that infects homeothermic animals, including humans. To date, as many as 287 genotypes have been described worldwide. Genetic characterization of the parasite is crucial because the parasite type can determine the presentation and severity of toxoplasmosis. Previously, we reported that the Yucatán Peninsula has a frequency of infection of over 70% in humans and other animals; moreover, there are seven species of felids, including domestic cats; thus, we hypothesized that this might be a region with a high diversity of the parasite. Nevertheless, no genotyping of this protozoan has been performed in this region. Thus, the aim of this study was to genotype T. gondii from naturally infected feral cats of Quintana Roo, within the Yucatán Peninsula, and to describe its genetic variability. Eleven feral cats were captured and bled to obtain the buffy coat; then, they were euthanized to collect target organs or tissues to extract DNA. Samples were processed by PCR for diagnosis, and ten polymorphic markers were genotyped by PCR-RFLP. Atypical GRA6 gene products were cloned and sequenced. Ten of the eleven cats were PCR positive for toxoplasmosis in blood; of these, seven had mixed infections. Also, two isolates were obtained from the heart and diaphragm of two animals. At least 23 different genotypes were detected, from which 18 are new worldwide. From the atypical GRA6 gene cloning and sequencing analysis, a mixed infection was discovered, due to one strain identical to GT1 and another to VAND. In conclusion, T. gondii genetic diversity in the region is high and different from that in other regions, with new genotypes exclusive to México and some others shared with USA and South America.

First Records of Psorophora cilipes and Culex theobaldi in Quintana Roo State, Mexico.

Collections of mosquitoes were conducted for the surveillance of species of medical importance in the state of Quintana Roo, Mexico, in June of 2017. Species collected included Psorophora (Psorophora) cilipes and Culex (Melanoconion) theobaldi, both new records for the state. Psorophora cilipes was previously recorded in Mexico State and Cx. theobaldi in Chiapas State. With the addition of these species, the mosquito fauna of Quintana Roo State now includes 81 species. Quintana Roo and Tamaulipas State with 82 species are the most mosquito-rich states in Mexico, based on currently available records. The specimens collected in this study were deposited in the Culicidae collection of the Universidad Autónoma Agraria Antonio Narro Unidad Laguna.

First Record of Invasive Mosquito Aedes albopictus in Tabasco and Yucatan, Mexico.

The invasive mosquito Aedes albopictus is currently distributed in most of the southern Mexican region. Since the species was first recorded in the state of Tamaulipas, in northeastern Mexico in 1988, it has expanded its distribution throughout the Sierra Madre Oriental and Gulf of Mexico to the Neotropical region of the country. Currently the species occurs in the states of Tamaulipas, Coahuila, Nuevo Leon, Veracruz, Chiapas, Morelos, Quintana Roo, Sinaloa, San Luis Potosi, and Hidalgo. This is the first report of the mosquito in the states of Tabasco and Yucatan and the confirmation of its presence in Quintana Roo state. Aedes albopictus has been incriminated as a secondary vector of diseases such as those caused by dengue, chikungunya, and Zika viruses, which have caused epidemic outbreaks in most tropical and subtropical regions of Mexico; therefore, surveillance for the detection of Ae. albopictus is paramount so that targeted control strategies can be implemented for its control throughout Mexico.

New species of Mutillid Mimicking Enoclerus Gahan (Coleoptera: Cleridae: Clerinae) from Mexico and Central America.

Six new species of Enoclerus are described: E. delusus n. sp. from Costa Rica and Panamá, E. incanus n. sp. from México, E. zip n. sp. from México and El Salvador, E. reductesignatus n. sp. from Panamá, and E. citrinifrons n. sp. and E. philogenes n. sp. from Costa Rica. The new species are hypothesized to participate in a Batesian mimicry complex with boldly marked diurnal mutillid wasps as their model. Enoclerus crabronarius var. deletus Wolcott is elevated to species rank as E. deletus Wolcott new status. The identity of E. crabronarius is discussed.

An HcpR paralog of Desulfovibrio gigas provides protection against nitrosative stress.

Desulfovibrio gigas belongs to the group of sulfate reducing bacteria (SRB). These ubiquitous and metabolically versatile microorganisms are often exposed to reactive nitrogen species (RNS). Nonetheless, the mechanisms and regulatory elements involved in nitrosative stress protection are still poorly understood. The transcription factor HcpR has emerged as a putative regulator of nitrosative stress response among anaerobic bacteria. HcpR is known to orchestrate the expression of the hybrid cluster protein gene, hcp, proposed to be involved in cellular defense against RNS. According to phylogenetic analyses, the occurrence of hcpR paralog genes is a common feature among several Desulfovibrio species. Within the D. gigas genome we have identified two HcpR-related sequences. One of these sequences, hcpR1, was found in the close vicinity of the hcp gene and this finding prompted us to proceed with its functional characterization. We observed that the growth of a D. gigas strain lacking hcpR1 is severely impaired under nitrosative stress. An in silico search revealed several putative targets of HcpR1 that were experimentally validated. The fact that HcpR1 regulates several genes encoding proteins involved in nitrite and nitrate metabolism, together with the sensitive growth phenotype to NO displayed by an hcpR1 mutant strain, strongly supports a relevant role of this factor under nitrosative stress. Moreover, the finding that several Desulfovibrio species possess HcpR paralogs, which have been transmitted vertically in the evolution and diversification of the genus, suggests that these sequences may confer adaptive or survival advantage to these organisms, possibly by increasing their tolerance to nitrosative stress.

Vacuum ultraviolet photolysis of diclofenac and the effects of its treated aqueous solutions on the proliferation and migratory responses of Tetrahymena pyriformis.

The effects of dissolved O2, phosphate buffer and the initial concentration of diclofenac on the vacuum ultraviolet photolysis of this contaminant molecule were studied. Besides kinetic measurements, the irradiated, multicomponent samples were characterized via the proliferation and migratory responses (in sublethal concentrations) of the bioindicator eukaryotic ciliate Tetrahymena pyriformis. The results suggest that hydroxyl radicals, hydrogen atoms and hydroperoxyl radicals may all contribute to the degradation of diclofenac. The aromatic by-products of diclofenac were presumed to include a hydroxylated derivative, 1-(8-chlorocarbazolyl)acetic acid and 1-(8-hydroxycarbazolyl)acetic acid. The biological activity of photoexposed samples reflected the chemical transformation of diclofenac and was also dependent on the level of dissolved O2. The increase in toxicity of samples taken after different irradiation times did not exceed a factor of two. Our results suggest that the combination of vacuum ultraviolet photolysis with toxicity and chemotactic measurements can be a valuable method for the investigation of the elimination of micropollutants.