Genomic Diversity of the Retinta Breed Derived from Two Ancestral Bovine Lineages.

The Retinta breed, an autochthonous type of Spanish beef cattle, is highly adapted to breeding in its natural environment, which is characterized by a Mediterranean climate. The origins of this breed can be traced to two ancestral bovine stocks, which gave rise to distinct morphotypes differentiated primarily by coat color, alongside other significant traits such as growth, morphological conformation and temperament. Specifically, one morphotype comprises blond animals (Rubia Andaluza), genetically resembling the ancestral Bos taurus Aquitanicus, while the other encompasses brown- and red-colored animals (Retinta Extremeña) originating from Bos taurus Turdenatus stock. Over decades, these populations have undergone hybridization, leading to a unified population, albeit with the original subpopulations largely maintaining their genetic integrity. The objective of this study was to undertake genealogical and genomic characterization of these genetic lines, including a particular subpopulation within the blond animals (Tamarona cow). To achieve this, the genealogical records of 22,004 active animals were analyzed, and over 63,000 SNPs from a total of 1030 animals were examined for genomic characterization. Genealogical analysis revealed pedigree completeness and a high level of effective population size (Ne) across the entire population, yet relatively low Ne values within each pure line (ranging from 28.38 to 34.47). These findings underscore the ongoing efforts of the National Association of Retinta Breeders (ACRE) over the past decades to mitigate the loss of variability in this breed. The genomic characterization highlights the persistent differences within the original population and the predominant influence of the Retinto line within the current breed, as evidenced by principal component analysis (PCA) and admixture analysis. Furthermore, the identification of the Tamarona subpopulation within the blond lineage underlines its unique genetic composition, warranting its recognition as an official genetic line within the current Retinta breed. Given the small population size of these lines, particularly the Tamarona subpopulation, protective measures are imperative to preserve this distinct gene pool. Such measures would enhance the genetic diversity of the Retinta breed, which is essential for sustainable breeding practices in its natural habitats.

Genomic Characterization of Quality Wool Traits in Spanish Merino Sheep.

The native Spanish Merino breed was the founder of all the other Merino and Merino-derived breeds worldwide. Despite the fact that this breed was created and improved to produce the highest quality fine wool, the global wool market crisis led to the wholescale crossing of most of the herds with breeds for meat purposes. Nevertheless, there are still some purebred animals with a high potential for producing quality wool. The objective of this study was to characterize the current wool quality of the breed and identify genes associated with these parameters. To achieve this, over 12,800 records from the most representative animals of the breed (registered in the herd book) were analyzed using the Australian OFDA 2000 system, for parameters such as fiber diameter (FD), standard deviation (SD), coefficient of variation (CV), fibers over 15 microns (>15%), staple length (SL), and comfort factor (CRV). Additionally, animals with the most extreme FD values were whole-genome sequenced using NGS. Genome-wide association studies (GWAS) determined the association of 74 variants with the different traits studied, which were located in 70 different genes. Of these genes, EDN2, COL18A1, and LRP1B, associated with fibers over 15%, and FGF12 and ADAM17, associated with SL, play a key role in hair follicle growth and development. Our study reveals the great potential for recovering this breed for fine wool production, and identifies five candidate genes whose understanding may aid in that selection process.

Comparative Analysis of Microsatellite and SNP Markers for Genetic Management of Red Deer.

The analysis of population genetic structure and individual multilocus heterozygosity are crucial for wildlife management and conservation. Microsatellite markers have traditionally been used to assess these genetic parameters. However, single-nucleotide polymorphisms (SNPs) are becoming increasingly popular. Our goal here was to determine to what extent SNPs can provide better insights than microsatellites into the overall genetic status and population genetic processes in the species. To this end, we genotyped 210 red deer (Cervus elaphus) in the Spanish wild population with both 11 microsatellites and 31,712 SNPs. We compared parameters related to population genetic structure and individual multilocus heterozygosity obtained with both types of markers. Our results showed correlations between parameters measured using both microsatellites and SNPs, particularly those related to the level of genetic diversity and genetic differentiation. However, we found notably lower precision of microsatellites in measuring the distribution of genetic diversity among individuals. We conclude that microsatellites can be used to monitor the overall genetic status and detect broad patterns in red deer populations. Nevertheless, the greater precision of SNPs in inferring genetic structure and multilocus heterozygosity leads us to encourage scientists and wildlife managers to prioritize their use whenever possible.

A comprehensive analysis of the genetic diversity and environmental adaptability in worldwide Merino and Merino-derived sheep breeds.

BACKGROUND: To enhance and extend the knowledge about the global historical and phylogenetic relationships between Merino and Merino-derived breeds, 19 populations were genotyped with the OvineSNP50 BeadChip specifically for this study, while an additional 23 populations from the publicly available genotypes were retrieved. Three complementary statistical tests, Rsb (extended haplotype homozygosity between-populations), XP-EHH (cross-population extended haplotype homozygosity), and runs of homozygosity (ROH) islands were applied to identify genomic variants with potential impact on the adaptability of Merino genetic type in two contrasting climate zones. RESULTS: The results indicate that a large part of the Merino's genetic relatedness and admixture patterns are explained by their genetic background and/or geographic origin, followed by local admixture. Multi-dimensional scaling, Neighbor-Net, Admixture, and TREEMIX analyses consistently provided evidence of the role of Australian, Rambouillet and German strains in the extensive gene introgression into the other Merino and Merino-derived breeds. The close relationship between Iberian Merinos and other South-western European breeds is consistent with the Iberian origin of the Merino genetic type, with traces from previous contributions of other Mediterranean stocks. Using Rsb and XP-EHH approaches, signatures of selection were detected spanning four genomic regions located on Ovis aries chromosomes (OAR) 1, 6 and 16, whereas two genomic regions on OAR6, that partially overlapped with the previous ones, were highlighted by ROH islands. Overall, the three approaches identified 106 candidate genes putatively under selection. Among them, genes related to immune response were identified via the gene interaction network. In addition, several candidate genes were found, such as LEKR1, LCORL, GHR, RBPJ, BMPR1B, PPARGC1A, and PRKAA1, related to morphological, growth and reproductive traits, adaptive thermogenesis, and hypoxia responses. CONCLUSIONS: To the best of our knowledge, this is the first comprehensive dataset that includes most of the Merino and Merino-derived sheep breeds raised in different regions of the world. The results provide an in-depth picture of the genetic makeup of the current Merino and Merino-derived breeds, highlighting the possible selection pressures associated with the combined effect of anthropic and environmental factors. The study underlines the importance of Merino genetic types as invaluable resources of possible adaptive diversity in the context of the occurring climate changes.

Prevalence of Sex-Related Chromosomal Abnormalities in a Large Cohort of Spanish Purebred Horses.

Chromosomal abnormalities are largely associated with fertility impairments in the domestic horse. To date, over 600 cases of individuals carrying abnormal chromosome complements have been reported, making the domestic horse the species with the highest prevalence. However, studies analyzing the prevalence of chromosomal diseases in whole populations are scarce. We, therefore, employed a two-step molecular tool to screen and diagnose chromosomal abnormalities in a large population of 25,237 Pura Raza Español horses. Individuals were first screened using short tandem repeats parentage testing results and phenotypic evaluations. Those animals showing results suggesting chromosomal abnormalities were re-tested using a single nucleotide polymorphism (SNP)-based diagnostic methodology to accurately determine the chromosomal complements. Thirteen individuals showed a positive screening, all of which were diagnosed as chromosomally abnormal, including five 64,XY mares with sex development disorders (DSD) and four cases of blood chimerism (two male/female and two female/female cases). In addition, we detected one Turner and one Klinefelter syndrome and two individuals carrying complex karyotypes. The overall prevalence in the entire population was ~0.05%, with the prevalence of 64,XY DSD and blood chimerism ~0.02% and ~0.016%, respectively. However, the overall results should be taken with caution since the individuals carrying Turner syndrome (in full (63,X) or mosaic (mos 63,X/64,XX) forms) cannot be detected due to limitations in the methodology employed. Finally, the lack of agreement between populational studies performed using karyotyping or molecular methods is discussed. To our knowledge, this is the largest populational study performed evaluating the prevalence of the most common chromosomal abnormalities in the domestic horse.

Morphostructural Differences between the Historical Genetic Lines of the Spanish Merino Sheep.

The Merino breed, which originates from Spain, is the most emblematic livestock breed in the world, since it is the first with a worldwide extension and has had an important impact on the genetic origin of several of the main current sheep populations. For this reason, it is of vital importance to typify the historical genetic lines of the original Spanish Merino breed and thereby ensure the conservation of its variability. In the present study, we used 337 purebred animals (males and females) registered in the Genealogical Book of the Native Merino Breed. All the animals were descendants of herds from six ancestral genetic lines (Maesso, Egea, Granda, López-Montenegro, Hidalgo, and Donoso). Significant differences were found in all the morphometric traits and indexes between the different genetic lines. Using discriminant analysis, 84% of the animals were classified correctly into their historical genetic lines. Furthermore, the distances between the lines, calculated by a cluster test, showed that Hidalgo, Maesso, and Donoso had the most clearly defined lines, while the Granda, López-Montenegro, and Egea lines were more similar to each other. All this demonstrates the rich genetic variability existing in the genuine gene pool of the Merino sheep breed.

Genomic Population Structure of the Main Historical Genetic Lines of Spanish Merino Sheep.

According to historiographical documentation, the Romans first began to select Merino sheep in the Iberian Peninsula during the first century, with the aim of obtaining a breed appreciated for the quality of its wool. This process continued locally during the Middle Ages, when Spanish sheep were protected, and their export to foreign countries was banned. It was during the 16th century when individual Merino sheep were allowed to spread around the world to be used to improve the wool quality of local breeds. However, the wool crisis of the 1960s shifted the selection criteria of the Merino breed towards meat production at the expenses of wool. Consequently, individuals that display the genetic and phenotypic characteristics of those sheep originally bred in the kingdom of Spain in the Middle Ages are extremely difficult to find in commercial herds. In this study, we characterized the genetic basis of 403 individuals from the main historical Spanish Merino genetic lines (Granda, Hidalgo, Lopez-Montenegro, Maeso, Donoso and Egea), which were bred in isolation over the last 200 years, using a genomic approach based on genotyping data from the Axiom™ Ovine 50K SNP Genotyping Array. Our analysis included measuring population structure, genomic differentiation indexes, runs of homozygosity (ROH) patterns, and an analysis of molecular variance (AMOVA). The results showed large genetic differences between the historical lines, even though they belong to the same breed. In addition, ROH analysis showed differences due to increased inbreeding among the ancient generations compared with the modern Merino lines, confirming the breed's ancestral and closed origin. However, our results also showed a high variability and richness within the Spanish historical Merino lines from a genetic viewpoint. This fact, together with their great ability to produce high-quality wool, suggests that ancestral Merino lines from Spain should be considered a valuable genetic population to be maintained as a resource for the improvement of wool-producing sheep breeds all around the world.

Longitudinal K-means approaches to clustering and analyzing EHR opioid use trajectories for clinical subtypes.

Identification of patient subtypes from retrospective Electronic Health Record (EHR) data is fraught with inherent modeling issues, such as missing data and variable length time intervals, and the results obtained are highly dependent on data pre-processing strategies. As we move towards personalized medicine, assessing accurate patient subtypes will be a key factor in creating patient specific treatment plans. Partitioning longitudinal trajectories from irregularly spaced and variable length time intervals is a well-established, but open problem. In this work, we present and compare k-means approaches for subtyping opioid use trajectories from EHR data. We then interpret the resulting subtypes using decision trees, examining how each subtype is influenced by opioid medication features and patient diagnoses, procedures, and demographics. Finally, we discuss how the subtypes can be incorporated in static machine learning models as features in predicting opioid overdose and adverse events. The proposed methods are general, and can be extended to other EHR prescription dosage trajectories.

Defining Data Migration Across Multidisciplinary Ambulatory Clinics Using Participatory Design.

OBJECTIVE: This study aimed to develop an institutional approach for defining data migration based on participatory design principles. METHODS: We outline a collaborative approach to define data migration as part of an electronic health record (EHR) transition at an urban hospital with 20 ambulatory clinics, based on participatory design. We developed an institution-specific list of data for migration based on physician end-user feedback. In this paper, we review the project planning phases, multidisciplinary governance, and methods used. RESULTS: Detailed data migration feedback was obtained from 90% of participants. Depending on the specialty, requests for historical laboratory values ranged from 2 to as many as 145 unique laboratory types. Lookback periods requested by physicians varied and were ultimately assigned to provide the most clinical data. This clinical information was then combined to synthesize an overall proposed data migration request on behalf of the institution. CONCLUSION: Institutions undergoing an EHR transition should actively involve physician end-users and key stakeholders. Physician feedback is vital for developing a clinically relevant EHR environment but is often difficult to obtain. Challenges include physician time constraints and overall knowledge about health information technology. This study demonstrates how a participatory design can serve to improve the clinical end-user's understanding of the technical aspects of an EHR implementation, as well as enhance the outcomes of such projects.

Impaired Reproductive Function in Equines: From Genetics to Genomics.

Fertility is one of the key factors in the economic and productive success of the equine industry. Despite this, studies on the genetic causes affecting reproductive performance are scarce, especially in mares, where the genetic architecture of the reproductive traits is extremely complex. Today, with the increasing availability of new genomic methodologies for this species, we are presented with an interesting opportunity to understand the genetic basis of equine reproductive disorders. These include, among others, novel techniques for detecting chromosomal abnormalities, whose association with infertility in horses was established over 50 years ago; new sequencing technologies permitting an accurate detection of point mutations influencing fertility, as well as the study of inbreeding and molecular homozygosity, which has been widely suggested as one of the main causes of low reproductive performance in horses. Finally, over the last few years, reproductive performance has also been associated with copy number variants and candidate genes detected by genome-wide association studies on fertility traits. However, such studies are still scarce, probably because they depend on the existence of large and accurate phenotypic datasets of reproductive and/or fertility traits, which are still difficult to obtain in equines.

Effect of the US-Mexico border region in cardiovascular mortality: ecological time trend analysis of Mexican border and non-border municipalities from 1998 to 2012.

BACKGROUND: An array of risk factors has been associated with cardiovascular diseases, and developing nations are becoming disproportionately affected by such diseases. Cardiovascular diseases have been reported to be highly prevalent in the Mexican population, but local mortality data is poor. The Mexican side of the US-Mexico border has a culture that is closely related to a developed nation and therefore may share the same risk factors of cardiovascular diseases. We wanted to explore if there was higher cardiovascular mortality in the border region of Mexico compared to the rest of the nation. METHODS: We conducted a population based cross-sectional time series analysis to estimate the effects of education, insurance and municipal size in Mexican border (n = 38) and non-border municipalities (n = 2360) and its association with cardiovascular age-adjusted mortality rates between the years 1998-2012. We used a mixed effect linear model with random effect estimation and repeated measurements to compare the main outcome variable (mortality rate), the covariates (education, insurance and population size) and the geographic delimiter (border/non-border). RESULTS: Mortality due to cardiovascular disease was consistently higher in the municipalities along the US-Mexico border, showing a difference of 78 · 5 (95% CI 58 · 7-98 · 3, p < 0 · 001) more cardiovascular deaths after adjusting for covariates. Larger municipal size and higher education levels showed a reduction in cardiovascular mortality of 12 · 6 (95% CI 11 · 4-13 · 8, p < 0 · 001) deaths and 8 · 6 (95% CI 5 · 5-11 · 8, p < 0 · 001) deaths respectively. Insurance coverage showed an increase in cardiovascular mortality of 3 · 6 (95% CI 3 · 1-4 · 0, p < 0 · 001) deaths per decile point increase. There was an increase in cardiovascular mortality of 0 · 3 (95% CI -0 · 001-0 · 6, p = 0 · 050) deaths per year increase in the non-border but a yearly reduction of 2 · 9 (95% CI 0 · 75-5.0, p = 0 · 008) deaths in the border over the time period of 1998-2012. CONCLUSION: We observed that the Mexican side of the US-Mexico border region is disproportionately affected by cardiovascular disease mortality as compared to the non-border region of Mexico. This was not explained by education, population density, or insurance coverage. Proximity to the US culture and related diet and habits can be explanations of the increasing mortality trend.

Anopheles Gambiae: do invasor silencioso ao "feroz mosquito africano" no Brasil (1930-1940) / Anopheles gambiae: the silent invader to "fierce African mosquito" in Brazil (1930-1940)

Esta tese tem como objetivo abordar a chegada, o alastramento e o extermínio do mosquito africano Anopheles gambiae no Brasil, do ponto de vista científico e político, observando os condicionantes históricos que o tornaram objeto de um importante projeto de cooperação em saúde pública com a Fundação Rockefeller (FR). A história do A. gambiae no Brasil pode ser dividida em três fases quecorrespondem diretamente à movimentação e medidas que resultaram no extermínio desse mosquito. Na primeira fase, que vai de 1930-1932, vai da sua identificação na cidade de Natal, capital do Rio Grande do Norte, até sua expulsão pelo Serviço Cooperativo de Febre Amarela (SCFA) da FR. A segunda fase, iniciada em 1932, é conhecida como “era silenciosa”, que durou aproximadamente cinco anos, em que o A. gambiae se alastrou para o estado do Ceará sem chamar a atenção dos poderes públicos. A última fase se inicia com a epidemia de 1938, que levou a criação emergencial do SMNE, um grande serviço cooperativo que erradicou o A. gambiae do Brasil em1940. O que proponho nesta tese, é mostrar a importância de se compreender o percurso do A. gambiae no Brasil a partir do processo histórico que o fez ser inicialmente entendido como um problema emergencial local, tratado de maneira paliativa, para finalmente, oito anos após a suachegada, ter sido enquadrado em um experimento de demonstração em saúde pública de relevânciainternacional. Nesse percurso, busco entender a agência histórica desse mosquito a partir da trajetória do mesmo durante sua estada no Brasil, bem como os revezes, reações e iniciativas científicas e políticas que levaram à erradicação do mesmo. Para sustentar a minha proposta, buscoanalisar artigos científicos, relatórios de campo, documentos institucionais e periódicos que colocam o mosquito invasor no centro de narrativas que o perseguem.(AU)

Sex reversal syndrome in the horse: four new cases of feminization in individuals carrying a 64,XY SRY negative chromosomal complement.

Horses are characterized as having a greater rate of chromosomal abnormalities than other species, which are mainly related to the sex chromosome pair and produce a series of different anomalies known as disorders in sexual development (DSD). In the present study, three Pura Raza Española (PRE) and one Menorquín (MEN) horses were studied and an incompatibility in their genetic and phenotypic sex were detected. Animals were karyotyped by conventional and molecular cytogenetic analyses and characterized using genomic techniques. Although all individuals, were totally unrelated, these animals had the same abnormality (64,XY SRY negative DSD) despite having an anatomically normal external mare phenotype. Therefore, this syndrome could remain undiagnosed in a large percentage of cases because the physiological and morphological symptoms are rare. In the present study, a slight gonadal dysgenesis was observed only in older individuals. Interestingly this chromosomal abnormality has been previously reported less than twenty times, and never in the PRE or MEN horses. With the present research, it is demonstrated that the use of genetic and cytogenetic diagnostic tools in veterinary practice could be an important complementary test to determine the origin of unexplained reproductive failures among horses.

Vaccination coverage in the US Commonwealth of the Northern Mariana Islands, 2005.

BACKGROUND: In July 2005, a house-to-house survey was conducted to determine vaccination coverage achieved through routine health services on the three inhabited islands (Saipan, Rota, and Tinian) of the US Commonwealth of the Northern Mariana Islands (CNMI). METHODS: A population-based cluster survey was conducted on Saipan; clusters and households were selected by systematic random sampling. On the smaller islands of Rota and Tinian, all households were visited. Vaccination histories and demographic information were obtained during household interview for all children aged 19-35 months, children aged 6 years, and adults aged 65 years and older. Vaccination histories for children were supplemented by hospital/clinic records and an electronic vaccination registry. RESULTS: Among 295 children aged 19-35 months, estimated coverage with the primary vaccination series was 80 percent; coverage with individual vaccines was generally higher. Among 193 children aged 6 years, coverage for vaccines required at school-aged was 83 percent. Among 226 adults aged 65 years and older, 52 percent received influenza vaccine during the previous season while 21 percent had ever received pneumococcal vaccine. CONCLUSIONS: The CNMI has achieved the US Healthy People 2010 objective of 80 percent coverage for the standard vaccination series among children aged 19-35 months. High coverage levels among 6-year-old children may reflect the benefit of school entry requirements. Influenza and pneumococcal vaccination among older adults remains low. Efforts to ensure that children and older adults throughout the CNMI are equally well-protected should continue. Strategies to address parental awareness of vaccinations that are due should be explored and may be facilitated by upgrading the electronic vaccination registry.