OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows

Biomedical ontologies are key elements for building up the Life Sciences Semantic Web. Reusing and building biomedical ontologies requires flexible and versatile tools to manipulate them efficiently, in particular for enriching their axiomatic content. The Ontology Pre Processor Language (OPPL) is an OWL-based language for automating the changes to be performed in an ontology. OPPL augments the ontologists’ toolbox by providing a more efficient, and less error-prone, mechanism for enriching a biomedical ontology than that obtained by a manual treatment. Results We present OPPL-Galaxy, a wrapper for using OPPL within Galaxy. The functionality delivered by OPPL (i.e. automated ontology manipulation) can be combined with the tools and workflows devised within the Galaxy framework, resulting in an enhancement of OPPL. Use cases are provided in order to demonstrate OPPL-Galaxy’s capability for enriching, modifying and querying biomedical ontologies. Conclusions Coupling OPPL-Galaxy with other bioinformatics tools of the Galaxy framework results in a system that is more than the sum of its parts. OPPL-Galaxy opens a new dimension of analyses and exploitation of biomedical ontologies, including automated reasoning, paving the way towards advanced biological data analyses

Susceptibility of Wild-Caught Lutzomyia longipalpis (Diptera: Psychodidae) Sand Flies to Insecticide After an Extended Period of Exposure in Western São Paulo, Brazil

Background In Brazil, members of the sand fly species complex Lutzomyia longipalpis transmit Leishmania infantum, a protist parasite that causes visceral leishmaniasis. Male Lu. longipalpis produce a sex pheromone that is attractive to both females and males. During a cluster randomised trial, to determine the combined effect of synthetic sex-aggregation pheromone and insecticide on Le. infantum transmission Lu. longipalpis had been continuously exposed to insecticide for 30 months. The objective of this study was to determine the effect of continuous exposure to the insecticides used in the trial on the susceptibility of Lu. longipalpis population. Methods During the trial the sand flies had been exposed to either lambda-cyhalothrin [pheromone + residual insecticide spray (PI)], deltamethrin [dog collars (DC)] or no insecticide [control (C)], for 30 months (November 2012 to April 2015). The insecticide treatment regime was kept in place for an additional 12 months (May 2015-April 2016) during this susceptibility study. Sand flies collected from the field were exposed to WHO insecticide-impregnated papers cyhalothrin (0.05%), deltamethrin (0.5%) and control (silicone oil) in a modified WHO insecticide exposure trial to determine their susceptibility. Results We collected 788 Lu. longipalpis using CDC-light traps in 31 municipalities across the three trial arms. Probit analysis showed that the knockdown times (KDTs) of Lu. longipalpis collected from the lambda-cyhalothrin exposed PI-arm [KDT50: 31.1 min, confidence interval (CI): 29.6–32.6 and KDT90: 44.2 min, CI: 42.1–46.7] were longer than the KDTs from the non-insecticide-treated C-arm (KDT50: 26.3 min, CI: 25.1–27.6 and KDT90: 38.2, CI: 36.5–40.2) (no-overlapping 95% CIs). KDTs of Lu. longipalpis collected from the deltamethrin exposed DC-arm had similar values (KDT50: 13.7 min, CI: 10.1–16.2 and KDT90: 26.7 min, CI: 21.8–30.6) to those for the C-arm (KDT50: 13.5 min; CI: 12.2–14.8 and KDT90: 23.2 min, CI: 21.4–25.4) (overlapping CIs). The wild-caught unexposed Lu. longipalpis (C-arm), took approximately twice as long to knock down as laboratory-colonised specimens for both insecticides. Conclusions Our study reveals slight changes in KDT, in sand flies after prolonged exposure to lambda-cyhalothrin in the presence of pheromone. These changes are not considered to have reached the reference levels indicative of resistance in sand flies suggesting that pheromone and insecticide treatment at the level indicated in this study do not constitute a significant risk of increased insecticide resistance. Prolonged exposure to deltamethrin in dog collars did not result in changes to KDT

Validation of surrogate anthropometric indices in older adults: what is the best indicator of high cardiometabolic risk factor clustering?

Incluye correccionesThe present study evaluated the ability of five obesity-related parameters, including a body shape index (ABSI), conicity index (CI), body roundness index (BRI), body mass index (BMI), and waist-to-height ratio (WtHR) for predicting increased cardiometabolic risk in a population of elderly Colombians. A cross-sectional study was conducted on 1502 participants (60.3% women, mean age 70 ± 7.6 years) and subjects’ weight, height, waist circumference, serum lipid indices, blood pressure, and fasting plasma glucose were measured. A cardiometabolic risk index (CMRI) was calculated using the participants’ systolic and diastolic blood pressure, triglycerides, high-density lipoprotein and fasting glucose levels, and waist circumference. Following the International Diabetes Federation definition, metabolic syndrome was defined as having three or more metabolic abnormalities. All surrogate anthropometric indices correlated significantly with CMRI (p < 0.01). Receiver operating characteristic curve analysis of how well the anthropometric indices identified high cardiometabolic risk showed that WtHR and BRI were the most accurate indices. The best WtHR and BRI cut-off points in men were 0.56 (area under curve, AUC 0.77) and 4.71 (AUC 0.77), respectively. For women, the WtHR and BRI cut-off points were 0.63 (AUC 0.77) and 6.20 (AUC 0.77), respectively. In conclusion, BRI and WtHR have a moderate discriminating power for detecting high cardiometabolic risk in older Colombian adults, supporting the idea that both anthropometric indices are useful screening tools for use in the elderly

Waveform Capnography for Monitoring Ventilation during Cardiopulmonary Resuscitation: The Problem of Chest Compression Artifact

Sudden cardiac arrest (SCA) is the sudden cessation of the heart’s effective pumping function, confirmed by the absence of pulse and breathing. Without appropriate treatment, it leads to sudden cardiac death, considered responsible for half of the global cardiac disease deaths. Cardiopulmonary resuscitation (CPR) is a key intervention during SCA. Current resuscitation guidelines emphasize the use of waveform capnography during CPR in order to enhance CPR quality and improve patient outcomes. Capnography represents the concentration of the partial pressure of carbon dioxide (CO2) in respiratory gases and reflects ventilation and perfusion of the patient. Waveform capnography should be used for confirming the correct placement of the tracheal tube and monitoring ventilation. Other potential uses of capnography in resuscitation involve monitoring CPR quality, early identification of restoration of spontaneous circulation (ROSC), and determination of patient prognosis. An important role of waveform capnography is ventilation rate monitoring to prevent overventilation. However, some studies have reported the appearance of high-frequency oscillations synchronized with chest compressions superimposed on the capnogram. This chapter explores the incidence of chest compression artifact in out-of-hospital capnograms, assesses its negative influence in the automated detection of ventilations, and proposes several methods to enhance ventilation detection and capnography waveform

Task Failure during Exercise to Exhaustion in Normoxia and Hypoxia Is Due to Reduced Muscle Activation Caused by Central Mechanisms While Muscle Metaboreflex Does Not Limit Performance

To determine whether task failure during incremental exercise to exhaustion (IE) is principally due to reduced neural drive and increased metaboreflex activation eleven men (22±2 years) performed a 10s control isokinetic sprint (IS; 80 rpm) after a short warm-up. This was immediately followed by an IE in normoxia (Nx, PIO2:143 mmHg) and hypoxia (Hyp, PIO2:73 mmHg) in random order, separated by a 120 min resting period. At exhaustion, the circulation of both legs was occluded instantaneously (300 mmHg) during 10 or 60s to impede recovery and increase metaboreflex activation. This was immediately followed by an IS with open circulation. Electromyographic recordings were obtained from the vastus medialis and lateralis. Muscle biopsies and blood gases were obtained in separate experiments. During the last 10s of the IE, pulmonary ventilation, VO2, power output and muscle activation were lower in hypoxia than in normoxia, while pedaling rate was similar. Compared to the control sprint, performance (IS-Wpeak) was reduced to a greater extent after the IE-Nx (11% lower P<0.05) than IE-Hyp. The root mean square (EMGRMS) was reduced by 38 and 27% during IS performed after IE-Nx and IE-Hyp, respectively (Nx vs. Hyp: P<0.05). Post-ischemia IS-EMGRMS values were higher than during the last 10s of IE. Sprint exercise mean (IS-MPF) and median (IS-MdPF) power frequencies, and burst duration, were more reduced after IE-Nx than IE-Hyp (P<0.05). Despite increased muscle lactate accumulation, acidification, and metaboreflex activation from 10 to 60s of ischemia, IS-Wmean (+23%) and burst duration (+10%) increased, while IS-EMGRMS decreased (-24%, P<0.05), with IS-MPF and IS-MdPF remaining unchanged. In conclusion, close to task failure, muscle activation is lower in hypoxia than in normoxia. Task failure is predominantly caused by central mechanisms, which recover to great extent within one minute even when the legs remain ischemic. There is dissociation between the recovery of EMGRMS and performance. The reduction of surface electromyogram MPF, MdPF and burst duration due to fatigue is associated but not caused by muscle acidification and lactate accumulation. Despite metaboreflex stimulation, muscle activation and power output recovers partly in ischemia indicating metaboreflex activation has a minor impact on sprint performance

First record of the mermithid nematode worm Isomermis lairdi parasitizing black flies in Spain

Funding Information: The authors declare that they have no conflicts of interest. We acknowledge the bioinformatics infrastructure of the Global Health and Tropical Medicine Center, which is funded through Fundação para a Ciência e a Tecnologia contract UID/04413/2020. Publisher Copyright: © 2022 Elsevier B.V.Mermithid nematodes are considered a promising biological control agent to reduce the population density of different blood-feeding vectors, i.e. black flies (Diptera: Simuliidae), which are important pests of medical and veterinary interest worldwide. Immature larvae of black flies were collected in a rill from La Rioja (Northern Spain) in the summer of 2016. Isomermis lairdi Mondet, Poinar & Bernadou, 1977 (Nematoda: Mermithidae) was found parasitizing eleven specimens of Simulium cryophilum s.l. (Rubtsov, 1959) (prevalence of 52%), which represent the first record of this nematode for Spain and the second for Europe. The confirmation of the nematode and the black fly species was carried out by both morphological and molecular approaches using the 18S ribosomal RNA and the cytochrome c oxidase subunit I genes. Phylogenetic analyses indicated that the collected specimens were Isomermis lairdi (99.4–99.9% identity with homologues from Africa) with a sequence divergence of 0.2%. The role of Isomermis lairdi as an alternative tool in the biological control of black flies in Spain should be further explored.publishersversionpublishe

Limited risk of Zika virus transmission by five Aedes albopictus populations from Spain

Background: Aedes albopictus, the Asian tiger mosquito, is an exotic invasive species in Europe. It has substantial public health relevance due to its potential role in transmitting several human pathogens. Out of the European coun‑ tries, Spain has one of the highest risk levels of autochthonous arbovirus transmission due to both the high density of Ae. albopictus and the extensive tourist infux from vector-endemic areas. This study aims to investigate the suscep‑ tibility of fve Ae. albopictus populations from mainland Spain and the Balearic Islands to a Brazilian Zika virus (ZIKV) strain. Methods: The F1 generation of each Ae. albopictus population was orally challenged with a ZIKV-infected blood meal (1.8×106 PFU/ml). At 7 and 14 days post-infection (dpi), mosquito bodies (thorax and abdomen) and heads were individually analysed through RT-qPCR to determine the infection rate (IR) and dissemination rate (DR), respectively. The saliva of infected mosquitoes was inoculated in Vero cells and the transmission rate was assessed by plaque assay or RT-qPCR on ~33 individuals per population. Results: The IR and DR ranged between 12–88%, and 0–60%, respectively, suggesting that ZIKV is capable of cross‑ ing the midgut barrier. Remarkably, no infectious viral particle was found in saliva samples, indicating a low ability of ZIKV to overcome the salivary gland barrier. A subsequent assay revealed that a second non-infective blood meal 48 h after ZIKV exposure did not infuence Ae. albopictus vector competence. Conclusions: The oral experimental ZIKV infections performed here indicate that Ae. albopictus from Spain become infected and disseminate the virus through the body but has a limited ability to transmit the Brazilian ZIKV strain through biting. Therefore, the results suggest a limited risk of autochthonous ZIKV transmission in Spain by Ae. albopictusinfo:eu-repo/semantics/publishedVersio

A temporal comparison of sex-aggregation pheromone gland content and dynamics of release in three members of the Lutzomyia longipalpis (Diptera: Psychodidae) species complex

Background: Lutzomyia longipalpis is the South American vector of Leishmania infantum, the etiologic agent of visceral leishmaniasis (VL). Male L. longipalpis produce a sex-aggregation pheromone that is critical in mating, yet very little is known about its accumulation over time or factors involved in release. This laboratory study aimed to compare accumulation of pheromone over time and determine factors that might influence release in three members of the L. longipalpis species complex. Methodology/Principal findings: We investigated male sex-aggregation pheromone gland content at different ages and the release rate of pheromone in the presence or absence of females under different light conditions by gas chromatography-mass spectrometry (GC-MS). Pheromone gland content was determined by extraction of whole males and pheromone release rate was determined by collection of headspace volatiles. Pheromone gland content appeared age-related and pheromone began to accumulate between 6 to 12 h post eclosion and gradually increased until males were 7–9 days old. The greatest amount was detected in 9-day old Campo Grande males ((S)-9-methylgermacrene-B; X ± SE: 203.5 ± 57.4 ng/male) followed by Sobral 2S males (diterpene; 199.9 ± 34.3) and Jacobina males ((1S,3S,7R)-3-methyl-α-himachalene; 128.8 ± 30.3) at 7 days old. Pheromone release was not continuous over time. During a 4-hour period, the greatest quantities of pheromone were released during the first hour, when wing beating activity was most intense. It was then substantially diminished for the remainder of the time. During a 24 h period, 4–5 day old male sand flies released approximately 63 ± 11% of the pheromone content of their glands, depending on the chemotype. The presence of females significantly increased pheromone release rate. The light regime under which the sand flies were held had little influence on pheromone release except on Sobral 2S chemotype. Conclusions/Significance: Accumulation of pheromone appears to occur at different rates in the different chemotypes examined and results in differing amounts being present in glands over time. Release of accumulated pheromone is not passive, but depends on biotic (presence of females) and abiotic (light) circumstances. There are marked differences in content and release between the members of the complex suggesting important behavioural, biosynthetic and ecological differences between them. Author summary: The Dipteran subfamily Phlebotominae includes the genera Lutzomyia and Phlebotomus among which several species are important vectors of parasitic and bacterial pathogens. The sand fly Lutzomyia longipalpis is considered the main vector of visceral leishmaniasis (VL) in the New World. Based on the main component of the male sex-aggregation pheromone gland, different sex pheromone-producing populations (chemotypes) of L. longipalpis are recognized in Brazil. Given the importance of the sex-aggregation pheromones in the biology of this species complex, we present here the first attempt to study how pheromone accumulates in the glands over time and factors that might influence its release in the three most common chemotypes from Brazil. Our results demonstrated that pheromone first starts to accumulate a few hours post-eclosion (6–12 h) and this continues over 15 days. Pheromone release is a dynamic process which varies between the 3 chemotypes depending on biotic factors, such as light regime and presence/absence of conspecific females. This work provides valuable information, critical to our understanding of the behaviour and ecology of L. longipalpis sand flies and which will contribute to investigations to improve field-based pheromone control and monitoring of L. longipalpis sand flies