Phytoplankton detection and recognition in freshwater digital microscopy images using deep learning object detectors.

Water quality can be negatively affected by the presence of some toxic phytoplankton species, whose toxins are difficult to remove by conventional purification systems. This creates the need for periodic analyses, which are nowadays manually performed by experts. These labor-intensive processes are affected by subjectivity and expertise, causing unreliability. Some automatic systems have been proposed to address these limitations. However, most of them are based on classical image processing pipelines with not easily scalable designs. In this context, deep learning techniques are more adequate for the detection and recognition of phytoplankton specimens in multi-specimen microscopy images, as they integrate both tasks in a single end-to-end trainable module that is able to automatize the adaption to such a complex domain. In this work, we explore the use of two different object detectors: Faster R-CNN and RetinaNet, from the one-stage and two-stage paradigms respectively. We use a dataset composed of multi-specimen microscopy images captured using a systematic protocol. This allows the use of widely available optical microscopes, also avoiding manual adjustments on a per-specimen basis, which would require expert knowledge. We have made our dataset publicly available to improve the reproducibility and to foment the development of new alternatives in the field. The selected Faster R-CNN methodology reaches maximum recall levels of 95.35%, 84.69%, and 79.81%, and precisions of 94.68%, 89.30% and 82.61%, for W. naegeliana, A. spiroides, and D. sociale, respectively. The system is able to adapt to the dataset problems and improves the results overall with respect to the reference state-of-the-art work. In addition, the proposed system improves the automation and abstraction from the domain and simplifies the workflow and adjustment.

Joint keypoint detection and description network for color fundus image registration.

Background: Retinal imaging is widely used to diagnose many diseases, both systemic and eye-specific. In these cases, image registration, which is the process of aligning images taken from different viewpoints or moments in time, is fundamental to compare different images and to assess changes in their appearance, commonly caused by disease progression. Currently, the field of color fundus registration is dominated by classical methods, as deep learning alternatives have not shown sufficient improvement over classic methods to justify the added computational cost. However, deep learning registration methods are still considered beneficial as they can be easily adapted to different modalities and devices following a data-driven learning approach. Methods: In this work, we propose a novel methodology to register color fundus images using deep learning for the joint detection and description of keypoints. In particular, we use an unsupervised neural network trained to obtain repeatable keypoints and reliable descriptors. These keypoints and descriptors allow to produce an accurate registration using RANdom SAmple Consensus (RANSAC). We train the method using the Messidor dataset and test it with the Fundus Image Registration Dataset (FIRE) dataset, both of which are publicly accessible. Results: Our work demonstrates a color fundus registration method that is robust to changes in imaging devices and capture conditions. Moreover, we conduct multiple experiments exploring several of the method's parameters to assess their impact on the registration performance. The method obtained an overall Registration Score of 0.695 for the whole FIRE dataset (0.925 for category S, 0.352 for P, and 0.726 for A). Conclusions: Our proposal improves the results of previous deep learning methods in every category and surpasses the performance of classical approaches in category A which has disease progression and thus represents the most relevant scenario for clinical practice as registration is commonly used in patients with diseases for disease monitoring purposes.

Automated inter-device 3D OCT image registration using deep learning and retinal layer segmentation.

Optical coherence tomography (OCT) is the most widely used imaging modality in ophthalmology. There are multiple variations of OCT imaging capable of producing complementary information. Thus, registering these complementary volumes is desirable in order to combine their information. In this work, we propose a novel automated pipeline to register OCT images produced by different devices. This pipeline is based on two steps: a multi-modal 2D en-face registration based on deep learning, and a Z-axis (axial axis) registration based on the retinal layer segmentation. We evaluate our method using data from a Heidelberg Spectralis and an experimental PS-OCT device. The empirical results demonstrated high-quality registrations, with mean errors of approximately 46 µm for the 2D registration and 9.59 µm for the Z-axis registration. These registrations may help in multiple clinical applications such as the validation of layer segmentations among others.

Diagnosis of Anaplasma marginale in cattle at the Iowa State University veterinary diagnostic laboratory 2003-2021.

Anaplasma marginale is a blood-borne rickettsia-like organism that infects cattle erythrocytes and causes anaplasmosis. This study reviews diagnostic data of all A. marginale diagnostics performed from 2003 to August 2021 in the Iowa State Veterinary Diagnostic Laboratory. Typically, the referring veterinarian's initial tentative diagnosis was based on presenting clinical signs or necropsy findings. Confirmatory testing at the ISU-VDL consisted of light microscopy evaluation of stained blood smears or molecular diagnostic procedures. A total of 94 cases were submitted with tissue samples from deceased animals, of which 79 were from Iowa and 15 were from other states. The most typical gross lesions were widespread yellow adipose tissue and splenomegaly. Typical histopathological lesions included marked bile stasis and hemosiderin-laden macrophages in the liver and spleen, respectively. Starting in 2013, when PCR was implemented to confirm cases of anaplasmosis, 315/1125 (28%) were positive to A. marginale, and 810 were negative, using a cut-off of 35.0 Ct. The average (±SD) of the positive PCR Ct was 19.5 (±6.0), and the first and third quartiles were 14.9 and 23.4. Most cases occurred between August and November, peaking in September, whether from necropsies or positive blood samples by PCR. The most common tick observed in Iowa, Dermacentor variabilis, is likely the main vector for transmission. Further surveys should be conducted to estimate seroprevalence by geographical location, the density of cattle populations, distribution of known vectors according to season, and strains of A. marginale.

Chlorpyrifos should be banned in agriculture and livestock production in Colombia

Chlorpyrifos (CPF) is a pesticide widely used in Colombia´s agriculture, including crops, farm animals and pets, despite it has been banned for use in the European Union and the United States. Studies demonstrate that even low blood levels of CPF -which do not inhibit blood acetylcholinesterase- can lead to child developmental and neurological disorders such as smaller head circumference and brain alterations, and psychomotor and cognitive deficits related to learning ability, attention and memory. In adults, CPF is an endocrine disruptor and breast carcinogen. High direct and indirect economic costs have been associated with CPF exposure. Not only farmers and their families -who have the highest exposures- but the general population consuming crops sprayed with CPF are also at risk. For these reasons CPF was recently banned by the European Union (2020) and the USA (2021). Pesticide regulation policies vary greatly depending on which and how scientific studies are used to assess health risks. Pesticide evaluations funded by the chemical industry should be rectified to avoid conflicts of interest. Furthermore, political alignment with the interests of the industry should not take precedence over independent scientific evidence. It is discouraging, to say the least, that until stricter health laws are passed in Colombia, CPFs and related pesticides will continue to be imported from those countries that have already banned them. Colombian scientists should raise their voice to challenge blind acceptance of profits over unintended consequences, and efforts to prevent pesticide´s abuse should be encouraged.

El clorpirifos (CPF) es un pesticida ampliamente utilizado en la agricultura de Colombia, incluidos cultivos, animales de granja y mascotas, a pesar de haber sido prohibido en la Unión Europea y Estados Unidos. Los estudios han demostrado que incluso niveles bajos de CPF en sangre -que no inhiben la acetilcolinesterasa sanguínea- pueden provocar trastornos neurológicos y del desarrollo infantil, como menor circunferencia de la cabeza y alteraciones cerebrales, y déficits psicomotores y cognitivos relacionados con la capacidad de aprendizaje, la atención y la memoria. En adultos, el CPF es un disruptor endocrino y causante de cáncer de mama. Altos costos económicos directos e indirectos se han asociado con la exposición al CPF. No solo los trabajadores agrícolas y sus familias, que están más expuestos, sino también la población en general que consume cultivos rociados con CPF también están en riesgo. Por estas razones el CPF fue prohibido recientemente por la Unión Europea (2020) y los EE. UU. (2021). Las políticas de regulación de plaguicidas varían mucho según los estudios científicos escogidos para evaluar los riesgos para la salud. Las evaluaciones de plaguicidas financiadas por la industria química deben rectificarse para evitar conflictos de interés. Además, ante la evidencia científica independiente no debería prevalecer la alineación política con los intereses de dicha industria. Es desalentador, por decir lo menos, que hasta que se aprueben leyes de salud más estrictas en Colombia se seguirán importando CPF y pesticidas relacionados desde aquellos países que ya los han prohibido. Los científicos colombianos deben alzar la voz para desafiar la aceptación ciega de ganancias por encima de las consecuencias no deseadas en salud pública, y se deben alentar los esfuerzos para prevenir el abuso de pesticidas.

Clorpirifós (CPF) é um pesticida registrado amplamente utilizado na agricultura colombiana, incluindo lavouras, animais de fazenda e animais de estimação, apesar de ter sido proibido na União Europeia e nos Estados Unidos. Estudos têm demonstrado que mesmo níveis baixos de CPF no sangue -que não inibem a acetilcolinesterase sanguínea-podem levar a distúrbios neurológicos e de desenvolvimento em crianças, como menor perímetro cefálico e alterações cerebrais, além de déficits psicomotores e cognitivos relacionados à capacidade de aprendizagem, atenção e memoria. Em adultos, o CPF é um desregulador endócrino e cancerígeno da mama. Altos custos econômicos diretos (devido ao tratamento) e indiretos (devido à perda de produtividade) têm sido associados à exposição ao CPF. Não apenas os trabalhadores agrícolas e suas famílias, que têm as maiores exposições, mas a população em geral que consome culturas pulverizadas com CPF também estão em risco. Por essas razões, o CPF foi recentemente proibido pela União Europeia (2020) e pelos EUA (2021). As políticas de regulamentação de pesticidas variam muito, dependendo de quais (e como) os estudos científicos são usados para avaliar os riscos à saúde. As avaliações de pesticidas financiadas pela indústria química devem ser retificadas para evitar conflitos de interesse. Além disso, o alinhamento político com os interesses da indústria não deve ter precedência sobre as evidências científicas independentes. É desanimador - para dizer o mínimo - que até que leis de saúde mais rígidas sejam aprovadas na Colômbia, o CPF e tóxicos relacionados continuarão a ser importados dos países que já os proibiram.

Efectos colaterales del uso de la ivermectina en ganadería: comunidad de las boñigas en Colombia / Side effects of ivermectin use in livestock: dung community in Colombia / Efeitos colaterais do uso de ivermectina na pecuária: comunidade boñigas na Colômbia

Resumen La ivermectina es el antiparasitario más usado en veterinaria a nivel mundial desde que entró al mercado en 1981. La U.S. Food and Drug Administration (FDA) americana en su valoración de riesgos determinó que, si bien es muy tóxica para organismos acuáticos, es improbable que, con las aplicaciones registradas para uso animal y por sus propiedades fisicoquímicas, se lleguen a contaminar cursos de agua. Sin embargo, los efectos de la ivermectina (IVM) sobre la fauna de invertebrados no blanco si pueden tener gran repercusión en la ecología de los pastizales por los costes asociados a la presencia de las boñigas no degradadas. De hecho, las pérdidas económicas por disminuir la calidad de los pastizales y reducir la superficie de los pastos disponible y apetecibles al ganado se han calculado en hasta 380 millones de dólares para la economía americana. La ivermectina afecta a un grupo muy beneficioso y diverso taxonómicamente que habita las boñigas, incluyendo a moscas coprófagas, avispas parasíticas, y escarabajos coprófagos y depredadores. Algunos estudios muestran que las boñigas de animales tratados con IVM pueden permanecer en los pastizales sin muestras apreciables de degradación hasta 340 días, mientras que las de animales no tratados son degradadas casi totalmente después de 80 días. Además, estudios de campo y laboratorio han mostrado que la sensibilidad de muchos insectos ocurre a concentraciones muy por debajo de las que se excretan con las heces de bovinos tratados con IVM. Los efectos sobre la reproducción y desarrollo de larvas de coleópteros ocurren incluso a concentraciones que son de hasta 10 veces por debajo de las que producen mortalidad. En Colombia se han identificado al menos 68 especies de la subfamilia Scarabaeinae que integran la comunidad de las boñigas del bovino. La mayor diversidad de escarabajos estercoleros se ha asociado a bosques y sistemas silvopastoriles que incorporan arboles nativos y proveen hábitats favorables para su supervivencia.

Abstract Ivermectin (IVM) has been the world most widely used antiparasitic agent in veterinary medicine since it came to the market in 1981. The U.S. Food and Drug Administration (FDA) in its risk assessment determined that, although it is very toxic to aquatic organisms, it is unlikely to contaminate water courses from current applications registered for animal use. However, the effects of IVM on non-target invertebrate fauna can have great impact on grassland ecology due to the costs associated with the presence of undegraded dung. In fact, the economic losses from lowering the quality of pastures and reducing the area of pasture available and palatable to livestock have been estimated in $380 million for the American economy. Ivermectin affects a highly beneficial and taxonomically diverse group that inhabits dung, including dung flies, parasitic wasps, and coprophilus and predatory dung beetles. Some studies show that dung from IVM-treated animals can remain in pasture without appreciable signs of degradation for up to 340 days, while those from untreated animals are almost completely degraded after 80 days. In addition, field and laboratory studies have shown the susceptibility of many insects to occur at concentrations well below those excreted in the feces of cattle treated with IVM. Effects on reproduction and development of coleopteran larvae occur at concentrations that can be 10 times lower of those causing mortality. In Colombia, at least 68 species of the subfamily Scarabaeinae have been identified in dung communities. The greater diversity of dung beetles has been associated with forests and silvopastoral systems that incorporate native trees and provide favorable habitats for their survival.

Resumo A ivermectina (IVM) tem sido o agente antiparasitário mais utilizado no mundo na medicina veterinária desde que chegou ao mercado em 1981. A US. Food and Drug Administration (FDA) em sua avaliação de risco determinou que, embora seja muito tóxico para organismos aquáticos, é improvável que contamine cursos d'água a partir de aplicações atuais registradas para uso animal. No entanto, os efeitos do IVM na fauna de invertebrados não-alvo podem ter grande impacto na ecologia das pastagens devido aos custos associados à presença de esterco não degradado. De fato, as perdas econômicas decorrentes da redução da qualidade das pastagens e da redução da área de pastagem disponível e palatável para o gado foram estimadas em US$ 380 milhões para a economia americana. A ivermectina afeta um grupo altamente benéfico e taxonomicamente diverso que habita o esterco, incluindo moscas do esterco, vespas parasitas e coprófilos e escaravelhos predadores. Alguns estudos mostram que o esterco de animais tratados com MIV pode permanecer no pasto sem sinais apreciáveis de degradação por até 340 dias, enquanto os de animais não tratados são quase completamente degradados após 80 dias. Além disso, estudos de campo e de laboratório mostraram que a suscetibilidade de muitos insetos ocorre em concentrações bem abaixo daquelas excretadas nas fezes de bovinos tratados com MIV. Os efeitos sobre a reprodução e desenvolvimento de larvas de coleópteros ocorrem em concentrações que podem ser 10 vezes menores daquelas que causam mortalidade. Na Colômbia, pelo menos 68 espécies da subfamília Scarabaeinae foram identificadas em comunidades de esterco. A maior diversidade de escaravelhos tem sido associada a florestas e sistemas silvipastoris que incorporam árvores nativas e proporcionam habitats favoráveis à sua sobrevivência.

High antimicrobial resistance in Salmonella spp. and Escherichia coli isolates from swine fecal samples submitted to a veterinary diagnostic laboratory in Colombia

Background: Commensal microflora such as Escherichia coli and Enterococcus spp. are representative indicators of antimicrobial resistance (AMR) as they are part of the normal intestinal microflora and can acquire and disseminate AMR to pathogenic or zoonotic bacteria like Salmonella spp. Objective: To investigate the state of AMR among E. coli and Salmonella spp., potential pathogens in humans, isolated from cecal contents of pigs submitted to a veterinary diagnostic laboratory in Colombia from 2016 to 2019. Methods: Susceptibility testing was conducted using the Kirby-Bauer disk diffusion method according to the Clinical and Laboratory Standards Institute guidelines for antimicrobial zone diameter breakpoints. An E. coli strain (ATCC 25922) was used as the quality control organism. Isolates showing resistance to three or more antimicrobial classes were classified as multidrug-resistant (MDR) as defined by a joint group of the European Centre for Disease prevention and Control and the Center for Disease Control and Prevention of the USA. Results: A total of 112 E. coli and 192 Salmonella spp. colonies were isolated from 557 samples received between 2016 and 2019. In order of decreasing frequency, E. coli was resistant to tetracycline (100%), sulfamethoxazol-trimethoprim (97.5%), amoxicillin (86.4%), enrofloxacin (82.6%), tylosin (82.1%), doxycycline (59%), neomycin (50%), ciprofloxacin (45.5%), ceftiofur (35%), gentamicin (30%), tilmicosin (29%), and fosfomycin (12.5%). When compared with E. coli, Salmonella spp. was generally resistant to the same agents with slightly less resistance (between 10-30%) to eight of the antimicrobials tested. Salmonella spp. showed <20% resistance to three antimicrobials, as follows: neomycin (17%), gentamicin (16%), and fosfomycin (14%). Multi-resistance occurred in 68.7% (77/112) of E. coli and 70.3% (135/192) of Salmonella spp. isolates. Resistance of Salmonella spp. was alarming to all the critically important antimicrobials tested: fluoroquinolones (enrofloxacin, ciprofloxacin), ceftiofur (third- generation cephalosporin), and macrolides (tylosin). Conclusions: According to our results, there is a high level of multi- drug resistance (MDR) in E. coli and Salmonella spp. It is necessary to implement a nationwide antimicrobial resistance monitoring program in Colombia, together with proper antimicrobial prescribing guidelines for pigs. The indiscriminate use of antimicrobial growth promoters by the swine industry is generating widespread bacterial resistance and should be discontinued.

está disponible en el texto completo

Antecedentes: Flora comensal como espécies de Escherichia coli e Enterococcus são tipicamente escolhidas como indicadores representativos de la resistência antimicrobiana (AMR), pois fazem parte da flora intestinal normal e podem adquirir e disseminar AMR a bactérias patogênicas ou zoonóticas como Salmonella spp. Objetivo: Investigar o estado da AMR entre E. coli e Salmonella spp. isolados do conteúdo cecal de porcos colombianos submetidos ao Laboratório de Diagnóstico Veterinário de 2016 a 2019, ambos sendo patógenos potenciais em humanos. Métodos: O teste de suscetibilidade foi conduzido usando o método de difusão em disco Kirby-Bauer de acordo com as diretrizes do Instituto de Padrões Clínicos e Laboratoriais para pontos de quebra de diâmetro da zona antimicrobiana. A cepa de E. coli (ATCC 25922) foi usada como organismo de controle de qualidade. Os isolados que apresentam resistência a três ou mais classes de antimicrobianos foram classificados como multirresistentes (MDR), conforme definido por um grupo conjunto do Centro Europeu para Prevenção e Controle de Doenças e Centro para Controle e Prevenção de Doenças dos EUA. Resultados: Um total de 112 E. coli e 192 Salmonella spp. foram isolados de 557 amostras submetidas entre 2016 e 2019. Em ordem decrescente de frequência, a resistência a E. coli foi: tetraciclina (100%), sulfametoxazol-trimetoprim (97,5%), amoxicilina (86,4%), enrofloxacina (82,6%), tilosina (82,1%), doxiciclina (59%), neomicina (50%), ciprofloxacina (45,5%), ceftiofur (35%), gentamicina (30%), tilmicosina (29%) e fosfomicina (12,5%). Quando comparada com E. coli, Salmonella spp. foi geralmente resistente aos mesmos agentes com resistência ligeiramente menor (entre 10-30%) a oito dos antimicrobianos. Apenas três antimicrobianos apresentaram resistência a Salmonella spp. abaixo de 20% da seguinte forma: neomicina (17%), gentamicina (16%) e fosfomicina (14%). Multi-resistência ocorreu em 68,7% (77/112) de E. coli e 70,3% (135/192) de Salmonella spp. isolados. Resistência de Salmonella spp. foi alarmante para todos os antimicrobianos criticamente importantes testados: fluoroquinolonas (enrofloxacina, ciprofloxacina), ceftiofur (cefalosporina de terceira geração) e macrolídeos (tilosina). Conclusões: Esses resultados indicam um alto nível de resistência a múltiplos medicamentos (MDR) e que um Programa Nacional de Monitoramento da Resistência Antimicrobiana é necessário para a Colômbia, juntamente com a implementação de diretrizes de prescrição de antimicrobianos para suínos. O uso indiscriminado de antimicrobianos para promoção de crescimento na indústria suína está claramente promovendo resistência generalizada e deve ser interrompido.

Color fundus image registration using a learning-based domain-specific landmark detection methodology.

Medical imaging, and particularly retinal imaging, allows to accurately diagnose many eye pathologies as well as some systemic diseases such as hypertension or diabetes. Registering these images is crucial to correctly compare key structures, not only within patients, but also to contrast data with a model or among a population. Currently, this field is dominated by complex classical methods because the novel deep learning methods cannot compete yet in terms of results and commonly used methods are difficult to adapt to the retinal domain. In this work, we propose a novel method to register color fundus images based on previous works which employed classical approaches to detect domain-specific landmarks. Instead, we propose to use deep learning methods for the detection of these highly-specific domain-related landmarks. Our method uses a neural network to detect the bifurcations and crossovers of the retinal blood vessels, whose arrangement and location are unique to each eye and person. This proposal is the first deep learning feature-based registration method in fundus imaging. These keypoints are matched using a method based on RANSAC (Random Sample Consensus) without the requirement to calculate complex descriptors. Our method was tested using the public FIRE dataset, although the landmark detection network was trained using the DRIVE dataset. Our method provides accurate results, a registration score of 0.657 for the whole FIRE dataset (0.908 for category S, 0.293 for category P and 0.660 for category A). Therefore, our proposal can compete with complex classical methods and beat the deep learning methods in the state of the art.

ISODRIP, a model to transfer the δ18O signal of precipitation to drip water - Implementation of the model for Eagle Cave (central Spain).

The isotope signature of cave waters provides an excellent opportunity to better understand the recharge in karst regions and the complexity of drainage systems in the vadose zone. We have developed a cave isotope hydrological model (ISODRIP) that requires entering basic hydrometeorological information and a precipitation δ18O record to simulate the discharge and δ18O signals of different drip sites. The model includes four different modules to simulate various flow route regimes: continuous and discontinuous drips under diffuse or preferential flows. We use precipitation and cave water δ18O records that were obtained in Eagle Cave (central Spain) during a 5-year period to test our model and to better understand the dynamics of karst aquifers. Eagle Cave waters do not record evaporation. The δ18O signals do not have seasonality, although they record intra-annual and inter-annual variability. Additionally, cave water δ18O signal falls within the range of the annual average weighted isotope composition of precipitation. Well-mixed cave waters, that characterize diffuse flows, record 1‰ δ18O variability, whereas partially-mixed waters, that flow along preferential drainage routes, have up to 3‰ δ18O variability. The results suggest that precipitation takes on average 15 months to reach the cave through the diffuse flow network, whereas under preferential flow the transit time is highly variable depending on the previous condition of the system. ISODRIP includes a soil layer above the vadose zone that controls large recharge events, together with direct recharge components that bypass the soil layer enabling at least some recharge all year round. Thus, the simulations reproduce the observed lack of seasonal bias in the cave water δ18O composition in relation to the average weighted isotope composition of precipitation. This research highlights the importance of understanding recharge dynamics and the configuration of particular drips sites to properly interpret speleothem δ18O records.

Antimicrobial Prescribing Practices in Dogs and Cats by Colombian Veterinarians in the City of Medellin.

This study surveyed the prescribing behavior of Colombian companion animal veterinarians and compared the responses to the current guidelines of the International Society for Companion Animals on Infectious Diseases (ISCAID). A convenience sample of 100 primary-care veterinary practitioners was selected from the city of Medellin. A questionnaire was designed to present hypothetical clinical scenarios regarding prescription choices for systemic antimicrobials. The numbers of veterinarians empirically prescribing a course of systemic antimicrobials for each scenario were-perioperative elective surgeries (86%), superficial pyoderma (90%), lower urinary tract disease (52%), acute hemorrhagic diarrhea (50%), and kennel cough (46%). For urinary tract disease, cultures and susceptibility testing were only performed by half of the respondents, suggesting lower diagnostic standards. In superficial pyoderma cases, cytology was performed in the following percent of cases-0% (24), 20% (30), 40% (17), 60% (11), 80% (8), and 100% (10). Antimicrobials were over-prescribed relative to emerging standard for elective surgeries (86%), kennel cough (46%), and acute hemorrhagic diarrhea (50%). Critically important antimicrobials, such as fluoroquinolones, were applied commonly for superficial pyoderma (18%), kennel cough (12%), and lower urinary tract disease in dogs (20%) and cats (26%). In conclusion, antimicrobial prescribing behavior was inconsistent with current guidelines, and antimicrobial use could be improved by appropriate diagnostic steps allowing choice of an optimal antimicrobial drug. Overall, we documented the widespread use of antimicrobials for the treatment of these four common disease conditions.

Fully automatic detection and classification of phytoplankton specimens in digital microscopy images.

BACKGROUND AND OBJECTIVE: The proliferation of toxin-producing phytoplankton species can compromise the quality of the water sources. This contamination is difficult to detect, and consequently to be neutralised, since normal water purification techniques are ineffective. Currently, the water analyses about phytoplankton are commonly performed by the specialists with manual routine analyses, which represents a major limitation. The adequate identification and classification of phytoplankton specimens requires intensive training and expertise. Additionally, the performed analysis involves a lengthy process that exhibits serious problems of reliability and repeatability as inter-expert agreement is not always reached. Considering all those factors, the automatization of these analyses is, therefore, highly desirable to reduce the workload of the specialists and facilitate the process. METHODS: This manuscript proposes a novel fully automatic methodology to perform phytoplankton analyses in digital microscopy images of water samples taken with a regular light microscope. In particular, we propose a method capable of analysing multi-specimen images acquired using a simplified systematic protocol. In contrast with prior approaches, this enables its use without the necessity of an expert taxonomist operating the microscope. The system is able to detect and segment the different existing phytoplankton specimens, with high variability in terms of visual appearances, and to merge them into colonies and sparse specimens when necessary. Moreover, the system is capable of differentiating them from other similar objects like zooplankton, detritus or mineral particles, among others, and then classify the specimens into defined target species of interest using a machine learning-based approach. RESULTS: The proposed system provided satisfactory and accurate results in every step. The detection step provided a FNR of 0.4%. Phytoplankton detection, that is, differentiating true phytoplankton from similar objects (zooplankton, minerals, etc.), provided a result of 84.07% of precision at 90% of recall. The target species classification, reported an overall accuracy of 87.50%. The recall levels for each species are, 81.82% for W. naegeliana, 57.15% for A. spiroides, 85.71% for D. sociale and 95% for the "Other" group, a set of relevant toxic and interesting species widely spread over the samples. CONCLUSIONS: The proposed methodology provided accurate results in all the designed steps given the complexity of the problem, particularly in terms of specimen identification, phytoplankton differentiation as well as the classification of the defined target species. Therefore, this fully automatic system represents a robust and consistent tool to aid the specialists in the analysis of the quality of the water sources and potability.

Automatic Detection of Freshwater Phytoplankton Specimens in Conventional Microscopy Images.

Water safety and quality can be compromised by the proliferation of toxin-producing phytoplankton species, requiring continuous monitoring of water sources. This analysis involves the identification and counting of these species which requires broad experience and knowledge. The automatization of these tasks is highly desirable as it would release the experts from tedious work, eliminate subjective factors, and improve repeatability. Thus, in this preliminary work, we propose to advance towards an automatic methodology for phytoplankton analysis in digital images of water samples acquired using regular microscopes. In particular, we propose a novel and fully automatic method to detect and segment the existent phytoplankton specimens in these images using classical computer vision algorithms. The proposed method is able to correctly detect sparse colonies as single phytoplankton candidates, thanks to a novel fusion algorithm, and is able to differentiate phytoplankton specimens from other image objects in the microscope samples (like minerals, bubbles or detritus) using a machine learning based approach that exploits texture and colour features. Our preliminary experiments demonstrate that the proposed method provides satisfactory and accurate results.

Prevalence of Antimicrobial Resistance in Bacterial Isolates from Dogs and Cats in a Veterinary Diagnostic Laboratory in Colombia from 2016-2019.

The susceptibility to antimicrobials of bacterial isolates from dogs (n = 1256) and cats (n = 94) was retrospectively evaluated in a veterinary diagnostic laboratory over a 4-year period (2016-2019). Out of 1316 isolates in dogs, 771 were Staphylococcus spp. distributed as follows: Staph. pseudointermedius (n = 406), Staph. intermedius (n = 160), Staph. aureus (n = 104), and Staph. coagulase-negative (n = 101). In common, all Staphylococcus spp. showed a high prevalence (20-50%) of resistance to ampicillin, cephalosporin, enrofloxacin, gentamicin, tetracycline, and trimethoprim-sulfonamide, but a low prevalence (1-10%) of resistance to amoxicillin-clavulanate. With regards to the other families of bacteria, the number of antimicrobials for which resistance was high (>20%) in dogs was: Enterobacteriaceae (7/12), Enterococcus spp. (10/16), E. coli (11/15), Pseudomonas spp. (10/13), and Streptococcus spp. (4/9). For urinary tract infections caused by E. coli or Enterobacteriaceae (Klebsiella spp., Proteus spp.), amikacin and florfenicol were the only drugs that demonstrated 100% in vitro efficacy. Multi-drug resistance was observed in 18.7% (246/1316) and 22% (21/97) of the isolates from dogs and cats, respectively. Except for Pseudomonas spp., known for intrinsic resistance, resistance in other bacteria was likely attributed to high selection pressure. In conclusion, empirical antimicrobial use cannot be recommended to treat most common infections, and selection should be based on results from susceptibility testing.

Millennial climate oscillations controlled the structure and evolution of Termination II.

The controls that affect the structure and timing of terminations are still poorly understood. We studied a tufa deposit from the Iberian Peninsula that covers Termination II (T-II) and whose chronology was synchronized to speleothem records. We used the same chronology to synchronize ocean sediments from the North Atlantic to correlate major climate events in a common timescale. We identify two stages within T-II. The first stage started with the increase of boreal summer integrated solar insolation, and during this stage three millennial climate oscillations were recorded. These oscillations resulted from complex ocean-atmosphere interactions in the Nordic seas, caused by the progressive decay of Northern Hemisphere ice-sheets. The second stage commenced after a glacial outburst that caused the collapse of the Thermohaline Circulation, a massive Heinrich event, and the onset of the Bipolar Seesaw Mechanism (BSM) that eventually permitted the completion of T-II. The pace of the millennial oscillations during the first stage of T-II controlled the onset of the second stage, when the termination became a non-reversible and global phenomenon that accelerated the deglaciation. During the last the two terminations, the BSM was triggered by different detailed climate interactions, which suggests the occurrence of different modes of terminations.

Interpretation of the larval immersion test with ivermectin in populations of the cattle tick Rhipicephalus (Boophilus) microplus from Colombian farms.

Interpreting in vitro bioassays used to determine resistance against acaricides in Rhipicephalus microplus can be challenging without parallel in vivo studies that assess for lost efficacy. The larval immersion test (LIT) is currently the most widely used bioassay to detect ivermectin resistance. The objective of this study was to compare results of the LIT and a field trial using ivermectin in naturally infested cattle. Criteria to consider ticks as resistant with the LIT were based on discriminating doses (DD) and the ratio of lethal concentration (LC) in test populations over the LC of the susceptible Deutch strain, known as the resistance ratio (RR). Ticks were collected from 4 farms, two where ivermectin provided good control of tick infestations and two that claimed lack of efficacy. In two farms where administration of a long-acting ivermectin formulation reduced body tick counts to 45 and 25% of the initial counts at 10-days post-treatment, the RR50 and RR99 were approximately 6 and 20, respectively. The LC50 value approximated the DD for the two farms with claimed resistance, suggesting that about half of the population in each farm was resistant. These LIT values are equal to those reported for the most resistant ticks, which supports the use of the LIT to predict control failure in field situations. The two farms where ivermectin provided good control of tick infestations had LC50s similar to the susceptible strain, although for one farm the LC99 and RR99 suggested incipient resistance.

Giardia is the most prevalent parasitic infection in dogs and cats with diarrhea in the city of Medellín, Colombia.

Parasitic agents are a common cause of diarrhea in dogs and cats and, thus, determining their prevalence is essential to establish preventive and control measures. This retrospective study examined the fecal tests records from 1111 dogs and 203 cats with diarrhea submitted to a diagnostic laboratory in the city of Medellin between January and May 2018. The detection of parasites was carried out by direct smears and simple flotation methods. Parasitic organisms were detected in feces from 464 (41.7%) dogs and 96 (47.3%) cats. In order of decreasing prevalence, the parasites detected in dogs were: Giardia intestinalis (13%), ancylostomids (12.6%), Entamoeba spp. (6.1%), coccidian oocysts (5.8%), Toxocara spp. (5.6%) and Dipylidium caninum (1.3%). In cats, the prevalence was: Giardia intestinalis (20%), coccidian oocysts (8.9%), Entamoeba spp. (7.9%), ancylostomids (6.4%), Toxocara spp. (2.5%) and Dipylidium caninum (2%). Age, but not gender, was a predisposing factor, as puppies and kittens had significantly higher infection rates that older age categories. The majority of Giardia intestinalis positive cases occurred in puppies (109/145, 75.2%) and kittens (19/36, 52.8%), making this parasite the most prevalent in amongst animals with diarrhea. Out of 117 positive infections in the adult dog population, ancylostomids accounted for 56 cases (47.9%) and was the most common parasite in this age group. In conclusion, although these results do not imply a cause and effect relationship, they are an estimate of the type of parasites that may be most commonly associated with diarrhea in dogs and cats. The lower diagnostic sensitivity of the traditional methods used here as compared to more contemporary techniques like fecal flotation with centrifugation and PCR, may have underestimated the actual prevalence and diminished the detection of co-infections. Future studies should aim to have diagnostic panels that also screen for other enteric pathogens, including bacterial and viral agents.

Disarmament is the New War, Gold is the New Opium, and Ecohealth is the Historic Victim.

In Colombia, the convergence of drug trafficking, illegal armed groups, and gold production and trade threatens peace and stability in the post-FARC (Revolutionary Armed Forces of Colombia) era, as had the narcotics trade previously. Armed groups and criminal organizations have increased and consolidated their influence over illegal mining and may be diverting US$5 billion from Colombia's annual economy. As of 2014, 46% of the total area (78 939 ha) exploited for alluvial gold was in the Afro-Colombian Pacific States, in which unregulated mining was the main driver of deforestation. The informal job market represents 49% of the workforce and absent other economic alternatives, this workforce of ex-guerrillas, organized crime groups and corrupt officials will sustain the black markets that permeate gold mining. Human health consequences of unregulated gold mining are largely unrecognized, but include the spread of malaria and other insect-borne diseases, and we suggest diseases such as babesiosis.

Survey of Pain Knowledge and Analgesia in Dogs and Cats by Colombian Veterinarians.

A questionnaire study was conducted among 131 veterinarians practicing in the city of Medellin, Colombia, to assess views on pain evaluation and management in dogs and cats. When pain recognition and quantification abilities were used as a perceived competence of proper pain assessment, only 83/131 (63.4%, confidence interval (CI) 0.55⁻0.72) were deemed to have satisfactory skills, with the rest considered to be deficient. There were 49/131 (37.4) veterinarians who had participated in continuing education programs and were more confident assessing pain, with an odds ratio (±standard error) of 2.84 ± 1.15 (p = 0.01; CI 1.27⁻6.32). In addition, the odds of using pain scales was 4.28 ± 2.17 (p < 0.01, CI 1.58⁻11.55) greater if they had also participated in continuing education programs. The term multimodal analgesia was familiar to 77 (58.7%) veterinarians who also claimed to use more than one approach to pain control. Nevertheless, homeopathy was the preferred alternative approach in 71/77 (92%). There were major misconceptions on side effects and/or contraindications for use of opioids and non-steroidal anti-inflammatory drugs (NSAIDs) by most veterinarians. In addition, the lack of multimodal analgesia by at least 40% of the practitioners, combined with heavy reliance on weak analgesics (i.e., tramadol) or those with no proven record of efficacy (homeopathic remedies), denotes major deficits in education at the undergraduate level and a need for additional continuing education designed to fulfill the gaps in knowledge identified in this study, and overcome ideological convictions not supported by scientific evidence.

PREVALENCIA DE Babesia caballi, Theileria equi Y TRIPANOSOMIASIS Y ANÁLISIS DE FACTORES DE RIESGO EN EQUINOS DE ANTIOQUIA, COLOMBIA / PREVALENCE OF Babesia caballi, Theileria equi AND TRYPANOSOMIASIS AND ANALYSIS OF RISK FACTORS IN HORSES OF ANTIOQUIA, COLOMBIA

RESUMEN Esta investigación, se llevó a cabo, debido a la poca información nacional existente en hemoparásitos equinos y su objetivo fue determinar la prevalencia de babesiosis y tripanosomiasis, en el Valle de Aburrá y Rionegro, municipios de Antioquia (Colombia), así como algunos factores de riesgo asociados a la presentación de seropositividad, a estas enfermedades. En 223 predios, con una población de 1.008 equinos, se tomó muestra de sangre venosa, para realizar el diagnóstico serológico y molecular. La información epidemiológica fue obtenida, a través de la aplicación de una encuesta dirigida a las personas a cargo de los animales. Para el análisis estadístico, se aplicó Chi cuadrado de independencia y la Prueba Exacta de Fisher, cuando fue necesario. Para las asociaciones bivariadas, se calcularon estimaciones del riesgo (OR) por variable explicativa, con sus respectivos intervalos de confianza, del 95% (I.C. 95%). Se encontró una prevalencia del 11,9%, para babesiosis y de 1,9%, para tripanosomiasis; como factor de protección, se encontró el hecho de salir a una feria. Para la piroplasmosis, el lugar geográfico, el sexo, estar castrado, ser positivos a Anemia Infecciosa Equina (AIE), estrongílidos u oxiurus fueron factores de riesgo. Para tripanosomiasis, el factor de riesgo fue estar infestado con Dermacentor nitens o ser mular. Se deben reforzar métodos de vigilancia epidemiológica activa, sobre todo, en casos de movilización continua de equinos o desarrollo de eventos, que involucren presencia masiva de ejemplares.

ABSTRACT This research was carried out due to the little existing national information on equine hemoparasites; the objective was to determine babesiosis and trypanosomiasis prevalence in the Aburrá Valley and Rionegro Antioquia (Colombia) as well as some risk factors associated with the seropositivitie of these diseases. In 223 lots with a population of 1.008 equine venous blood sample was taken for serological diagnosis and molecular. Epidemiological information was obtained through the application of a survey addressed to persons in charge of the animals. For the statistical analysis, Chi square of independence or Fisher's Exact Test was applied when necessary. For the bivariate associations, risk estimates (OR) were calculated by explanatory variable, with their respective 95% confidence intervals (95% CI).It was found a prevalence of 11.9% for babesiosis and 1.9% for trypanosomiasis and as protection factor found the fact of going to trade fairs. Geographic location, sex and being neutered, be positive for Equine Infectious Anemia (AIE), strongyles or oxiurus was a risk factor for piroplasmosis. For Trypanosomiasis the risk factor was to be infested with ticks Dermacentor nitens or be mule. Methods of active epidemiological surveillance should be reinforced, especially in cases of continuous mobilization of equines or development of events that involve massive presence of horses.

Haemonchosis en una ternera raza Brahman en el trópico alto del Nordeste Antioqueño / Haemonchosis in a Brahman calf in the high tropics of the Antioquian Northeast / Hemoncose em uma bezerra raça Brahman no trópico alto do nordeste da Antioquia

Resumen La haemonchosis es una parasitosis que, en bovinos, a diferencia de los pequeños rumiantes, raramente causa mortalidad. No obstante, cargas parasitarias que normalmente son subclínicas en terneros bien alimentados, pueden convertirse en clínicas causando la muerte, cuando la condición corporal es pobre. Este reporte describe un caso de haemonchosis fatal en un ternero Brahman de 7 meses y el resultado del tratamiento con albendazol (10 mg/kg PO) en 17 terneros congéneres. La finca es de cría y levante de ganado de carne y está ubicada en el trópico alto, en el municipio de Yarumal, Antioquia, a una altura de 2.353 m.s.n.m y una temperatura promedio de 14 ºC. En la producción no reportan plan sanitario adicional a la vacunación contra aftosa. El diagnóstico se sospechó inicialmente con base en observaciones clínico-patológicas de una anemia severa con hipoproteinemia de etiología no inflamatoria, y se confirmó en el examen post-mortem por la presencia de cientos de nematodos adultos de Haemonchus spp. en el abomaso, y un recuento de 19.200 huevos por gramo (HPG) de heces de trichostrongylidos. El coprocultivo de heces mostró que el 70, 20, y 10% de dichos huevos pertenecían a especies de Haemonchus, Coperia, y otros géneros de nematodos, respectivamente. El tratamiento con albendazol fue eficaz reduciendo las cargas parasitarias en los 17 terneros tratados desde niveles moderados (200-700 HPG) y altos (>700 HPG), a niveles bajos (16-100 HPG). Se redujo por completo la infección en la mitad de los animales tratados y solo estuvo por debajo del 90% en 3 animales. Debido a que la media del porcentaje de reducción de huevos fue del 95% se deduce que no existe resistencia al albendazol. En conclusión, este caso revela que la haemonchosis en terneros debe incluirse dentro de los diagnósticos diferenciales de mortalidad en el trópico colombiano y la realización de necropsias y exámenes coprológicos periódicos son imprescindibles para poder instaurar medidas preventivas y de control de dichas parasitosis.

Abstract Haemonchosis is a parasitic disease that in cattle, unlike small ruminants, rarely causes mortality. However, parasitic burdens that are usually subclinical in well-fed calves may become clinical causing death when body condition is poor. This report describes a case of fatal haemonchosis in a 7-month-old Brahman calf and the results of treatment with albendazole (10 mg/kg PO) in 17 cohort calves. The farm, dedicated to breeding and rearing beef calves, was located in the high tropics of the Andes, municipality of Yarumal (Antioquia), at 2,353 meters of altitude with an annual mean temperature of 14 °C. Apart from vaccination for foot and mouth disease, the animals are not subjected to any other treatments. The diagnosis was initially suspected based on clinico-pathological observations of a severe anemia with hypoproteinemia of non-inflammatory etiology, and was confirmed in the postmortem examination by the presence of hundreds of adult nematodes of Haemonchus spp. in the abomasum and a count of 19,200 eggs per gram of feces (EPG) of trichostrongylids. Stool culture showed that 70, 20, and 10% of these eggs belonged to Haemonchus, Coperia and other nematode genera, respectively. Albendazole treatment was effective in reducing parasitic loads in 17 treated calves from moderate (200-700 OPG) and high levels (> 700 EPG) to low levels (16-100 EPG). The infection was completely eliminated in half of the treated animals and was reduced to below 90% in only 3 animals. Because the mean egg reduction percentage was 95%, it can be inferred that there is no resistance to albendazole. In conclusion, this case reveals that haemonchosis should be included in the differential diagnosis of mortality in calves in the Colombian tropics, and that necropsies and periodic coprological examinations are necessary to establish preventive and control measures of this parasitosis.

Resumo A hemoncose é uma doença parasitária que no gado, ao contrário dos pequenos ruminantes, raramente causa mortalidade. No entanto, cargas parasitas que geralmente são subclínicas em bezerros bem alimentados, podem tornar-se clinicamente causadores de morte quando a condição corporal é ruim. Este relato descreve um caso de hemoncose fatal em um bezerro Brahman de 7 meses de idade e os resultados do tratamento com albendazol (10 mg/kg PO) em 17 bezerros da coorte. A fazenda, dedicada à criação de bezerras, está localizada no trópico alto dos Andes, município de Yarumal (Antioquia), a 2.353 metros de altitude, com temperatura média anual de 14 ºC. Além da vacinação para a febre aftosa, os animais não são submetidos a outros tratamentos. O diagnóstico foi inicialmente suspeito com base em observações clínico-patológicas de uma anemia grave com hipoproteinemia de etiologia não inflamatória, e foi confirmado no exame post-mortem pela presença de centenas de nematóides adultos de Haemonchus spp. no abomaso e uma contagem de 19.200 ovos por grama de fezes (EPG) de tricostrongilídeos. A cultura de fezes mostrou que 70, 20 e 10% desses ovos pertenciam a Haemonchus, Coperia e outros gêneros de nematóides, respectivamente. O tratamento com albendazol foi eficaz na redução das cargas parasitas em 17 bezerros tratados de níveis moderados (200-700 OPG) e altos (> 700 EPG) para níveis baixos (16-100 EPG). A infecção foi completamente eliminada em metade dos animais tratados e foi reduzida para menos de 90% em apenas 3 animais. Como a porcentagem média de redução de ovos foi de 95%, pode-se inferir que não há resistência ao albendazol. Em conclusão, este caso revela que a hemoncose deve ser incluída no diagnóstico diferencial de mortalidade em bezerros nos trópicos colombianos, e que necropsias e exames coprológicos periódicos são necessários para estabelecer medidas preventivas e de controle desta parasitose.