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Improving distribution models of sparsely-documented disease vectors by incorporating information on related species via joint modeling
<p>A necessary component of understanding vector-borne disease risk is the accurate characterization of the distributions of their vectors. Species distribution models have been successfully applied to data-rich species but may produce inaccurate results for sparsely-documented vectors. In light of global change, vectors that are currently not well-documented could become increasingly important, requiring tools to predict their distributions. One way to achieve this could be to leverage data on related species to inform the distribution of a<strong> </strong>sparsely-documented vector based on the assumption that the environmental niches of related species are not independent. Relatedly, there is a natural dependence of the spatial distribution of a disease on the spatial dependence of its vector. Here, we propose to exploit these correlations by fitting a hierarchical model jointly to data on multiple vector species and their associated human diseases to improve distribution models of sparsely-documented species. To demonstrate this approach, we evaluated the ability of twelve models—which differed in their pooling of data from multiple vector species and inclusion of disease data—to improve distribution estimates of sparsely-documented vectors. We assessed our models on two simulated data sets, which allowed us to generalize our results and examine their mechanisms. We found that when the focal species is sparsely documented, incorporating data on related vector species reduces uncertainty and improves accuracy by reducing overfitting. When data on vector species are already incorporated, disease data only marginally improve model performance. However, when data on other vectors are not available, disease data can improve model accuracy and reduce overfitting and uncertainty. We then assessed the approach on empirical data on ticks and tick-borne diseases in Florida and found that incorporating data on other vector species improved model performance. This study illustrates the value of exploiting correlated data via joint modeling to improve distribution models of data-limited species.</p>
Fig. 2 in Phlebotomine Sandflies - Potential Vectors of Avian Trypanosomes
Fig. 2. Light microscopy of live T. avium SIM3 trypanosomes in L. longipalpis (A) and P. arabicus (B) gut; Giemsa stained metacyclic trypomastigotes of T. avium (s. s.) strain SIM3 from L. longipalpis hindgut (C). Scanning electron microscopy of T. avium (s. s.) SIM3 in the gut of sandfly P. arabicus (D, E) and L. longipalpis (F). A detailed view of trypomastigotes at the epithelium (D); note the massive infection of trypomastigots covering the gut (E); rounded objects are developmental stages of gregarines Psychodiella chagasi (F).
Fig 1 in Phlebotomine Sandflies - Potential Vectors of Avian Trypanosomes
Fig 1. Infection rates and intensities in sandflies L. longipalpis and P. arabicus membrane-fed on Trypanosoma avium strains BUT15 and SIM3, and on canaries. Infection intensities: low – 1–100 parasites; medium – 100–1000 parasites; heavy –> 1000 parasites per gut. Numbers of dissected females shown above the columns. Data from repeated experimental feeding of L. longipalpis on SIM3 are pooled. Sandflies fed on membrane were dissected after 8 days, L. longipalpis fed on canaries were dissected 7–10 days after feeding.
Unveiling Energy Conversions of the Venus Atmosphere by the Bred Vectors
<p>This is the data for the paper: Unveiling Energy Conversions of the Venus Atmosphere by the Bred Vectors</p> <p><a href="../api/records/13790212/draft/files/BV-energy-equation.ipynb/content" target="_blank" rel="noopener noreferrer">BV-energy-equation.ipynb</a>: script for plotting</p> <p><span><a href="../api/records/13790212/draft/files/solar-position.csv/content" target="_blank" rel="noopener noreferrer">solar-position.csv</a></span>: solar positions</p> <p>control-run.tar.gz: control run data</p> <p>perturbed-run.tar.gz: perturbed run data</p>
Fig. 4 in Growing, losing or introducing? Cage aquaculture as a vector for the introduction of non-native fish in Furnas Reservoir, Minas Gerais, Brazil
Fig. 4. Main events along the production system (i.e. juvenile stocking, length classification and fish capture) and the moments in which escapes occur (solid arrows: AC = accidental; IN = intentional). S = small-sized fish; M = mediumsized; L = large-sized.
Fig. 2 in Growing, losing or introducing? Cage aquaculture as a vector for the introduction of non-native fish in Furnas Reservoir, Minas Gerais, Brazil
Fig. 2. Frequency of fish farmers (%) operating different number of cages in Furnas Reservoir (n = 19).
Fig. 3 in Growing, losing or introducing? Cage aquaculture as a vector for the introduction of non-native fish in Furnas Reservoir, Minas Gerais, Brazil
Fig. 3. Frequency of fish farmers (%) reporting the occurrence of fish escapes during different events of the production chain (n = 19). Accidental: length classification (LC); fish removal (FR); juvenile stocking (JS); cage damage (CD). Deliberate: intentional releases (IR).
Fig. 1 in Growing, losing or introducing? Cage aquaculture as a vector for the introduction of non-native fish in Furnas Reservoir, Minas Gerais, Brazil
Fig. 1. Furnas Reservoir, Minas Gerais, Brazil. The circle indicates the study area (Carmo do Rio Claro town).
Protocol for transfection by microinjection into the eggs of the parasite vector snail Biomphalaria glabrata
<p><strong>1. Egg production</strong></p> <p>Place about 30 adult snails (10 mm diameter) into a 5.5-liter water tank. Place a piece of polystyrene of (3 x 3 cm) in each tank. There is the preferred support of <em>Biomphalaria glabrata</em> for laying its eggs. The snails are fed <em>ad libitum</em> with green lettuce leaves, they can also be fed with dry spirulina to boost reproduction. Maintain water at a temperature of 25 degrees Celsius.</p> <p><strong>2. Egg collection</strong></p> <p>Gently pick up several egg layers from the polystyrene with soft holding forceps and place the eggs into a petri dish with natural mineral water (e.g. Volvic) to prevent them from drying out.</p> <p>Start sorting the eggs under the stereoscopic microscope to choose only the gastrula stage and place them into another petri dish with natural mineral water.</p> <p> </p> <p><strong>3. Preparation of the transfection solution</strong></p> <p><strong>Material:</strong></p> <p>a. <em>in vivo</em> JetPEI transfection reagent</p> <p>b. 10% glucose solution</p> <p>c. 5% glucose solution</p> <p>d. Plasmids (dCas9-SunTag-BFP and scFv-DNMT3A-GFP)</p> <p>e. 0.2 ml microtubes</p> <p>f. P10 and P200 pipettes</p> <p>g. P10 and P200 pipette tips</p> <p>h. Permanent marker</p> <p>The glucose solution and the <em>in vivo</em> jetPEI transfection reagent are equilibrated at room temperature. </p> <p>Prepare 21 µl of each plasmid at a concentration of 78 and 88 ng / µl respectively (for a total volume of 42 µl =equals 3.5 µg of DNA) add the plasmid DNA to a 0.2 ml tube (labeled as Tube A) and mix with 21 µl of 10% glucose solution. </p> <p>In another microtube (labeled as Tube B), add 21 μl of 5% glucose solution and 1 μl of <em>in vivo</em> jetPEI. </p> <p> Prepare a third tube (labeled as Tube C) with 21 µl of 5% glucose solution and 0.5 µl of <em>in vivo</em> jetPEI to inject into embryos that will serve as controls. </p> <p>Leave the solutions at room temperature while you prepare the microinjection station. </p> <p> </p> <p> </p> <p><strong>4. Preparation of the micro-injection station</strong></p> <p><strong>Material:</strong></p> <p>a. Pre-pulled glass micropipettes (1mm diameter)</p> <p>b. Watch glass</p> <p>c. Modeling clay</p> <p>d. 35 mm and 90 mm petri dishes</p> <p>e. Mineral oil (M5904, SIGMA)</p> <p>f. Wash bottle with natural mineral water (Volvic)</p> <p>g. 0.2 ml microtubes</p> <p>h. 12-well cell culture plate</p> <p>i. Fine brush</p> <p>j. Phenol red solution</p> <p>k. Pasteur pipette or dropper</p> <p>l. Dissection forceps</p> <p>m. Soft holding forceps</p> <p>n. Snail eggs in the gastrula stage</p> <p>o. Drummond Scientific Nanoject III Programmable Nanoliter Injector</p> <p> </p> <p>Take a pre-pulled glass micropipette and cut it with a scalpel to have a ~ 0.2 mm tip slightly beveled if possible.</p> <p>Before attaching the micropipette to the programmable nanoliter injector, fill it with mineral oil. If this step is not done, the injector will not work properly. This can be done with a filling needle </p> <p>attached to a hamilton syringe of 10 microliters.</p> <p>When the micropipette is filled with oil, it must be fixed on the injector. For this it is necessary to: </p> <p>Slide the chuck and collet onto the glass micropipette, then slide the black O-ring with the seal onto the wire plunger </p> <p>With the micropipette attached to the injector, press the [EMPTY] icon until the plunger is fully extended. This step can be done with the footswitch by pressing once [EMPTY] then [STOP] and then proceeding [EMPTY] with the foot switch. A single beep is emitted when the plunger is fully extended.</p> <p>Fill the micropipette with 3 µl of the control solution or the transfection solution by placing the glass micropipette tip in a 0.2 ml tube with the solution to be injected and pressing the [FILL] icon. It is desirable to fill it at a slow rate, by pressing the [FILL] icon for a few seconds, then the [STOP] icon to allow the sample to equilibrate before pressing again the '[FILL] icon.</p> <p>Note: The piston continues to extend or retract until the [STOP] icon is pressed, or until the fully extended or fully retracted position is reached.</p> <p> </p> <p>5. Microinjection</p> <p>Place a watch glass into a 35mm petri dish and secure it on one side with modeling clay to form a slope. Use soft handling forceps to transfer an egg mass and lay it on the slope side of the watch glass so that the egg mass is in a sloping position.</p> <p>Remove excess water from the eggs with absorbent paper. Rehydrate if necessary with a fine brush to improve the visibility of the embryos. To inject the sample, return to the operating mode screen by pressing the [EXIT] icon, then select the injection mode by pressing the [INJECT] icon. Set the injection volume to 30nL and the flow rate to 20nL per second using the icons [+] and [-] respectively. Press the [INJECT] icon to inject the sample. </p> <p>Inject 30nL of the microinjection solution into each egg. Place the microinjected egg masses in a 12-well cell culture plate and note with a marker whether they were microinjected with the control solution or with the solution containing the plasmids.</p> <p>We colored the injection solution with red phenol to facilitate the visibility in this video.</p> <p><strong>Monitor the expression of the plasmids</strong></p> <p>Monitor the plasmids expression 72 h after microinjection in a contrast / fluorescent microscope or in a fluorescent stereo microscope. Then sort the fluorescent snails and perform a second micro-injection with a solution containing 10 µl of single guide RNA (at a concentration of 2ng / µl), add 0.5 µl of <em>in vivo</em> jetPEI reagent and 10 µl of 5% glucose solution. 3 days after the second microinjection, collect the hatched snails in a 1.5 ml tube containing 25 µl of lysis buffer for DNA and RNA purification.</p> <p>In this photo produced under a confocal microscope we washed a veliger larva in PBS solution, then we fixed it with 4% paraformaldehyde solution and then we placed it in a slide with two drops of the Dako fluorescence mounting medium. </p> <p>96 after the transfection we can observe the expression of the green fluorescent protein, the blue fluorescent protein and the co-localization of both proteins. </p> <p>This protocol is used to perform DNA methylation changes in a target gene. This transfection protocol can be used with other plasmids, with small interfering RNAs, or with messenger RNAs.</p> <p>Produced at IHPE (http://ihpe.univ-perp.fr)</p>
Data from: Virus infection and host plant suitability affect feeding behaviors of cannabis aphid (Hemiptera: Aphididae), a newly described vector of potato virus Y
<p>Aphids are the most prolific vectors of plant viruses resulting in significant yield losses to crops worldwide. P<span>otato virus Y (PVY) </span>is transmitted in a non-persistent manner by 65 species of aphids. <span>With the increasing acreage of hemp </span>(<i>Cannabis sativa</i> L.) (Rosales: Cannabaceae) <span>in the U.S, we were interested to know if the cannabis aphid (<i>Phorodon cannabis</i> Passerini) </span><span>(Hemiptera: Aphididae) </span><span>is a potential vector of PVY.</span> Here, we conduct transmission assays and utilize the electrical penetration graph (EPG) technique to determine whether cannabis aphids can transmit PVY to hemp (host) and potato (non-host) (<i>Solanum tuberosum</i> L.) (Solanales: Solanaceace). We show for the first time that the cannabis aphid is an efficient vector of PVY to hemp (96%) and potato (91%) using cohorts of aphids. In contrast, individual aphids transmitted the virus more efficiently to hemp (63%) compared to potato (19%). During the initial 15 minutes of EPG recordings, aphids demonstrated lower number and time spent performing intracellular punctures on potato compared to hemp, which may in part explain low virus transmission to potato using individual aphids. During the entire 8-hour recording, viruliferous aphids spent less time ingesting phloem compared to non-viruliferous aphids on hemp. This reduced host suitability could potentially cause aphids to disperse to more suitable hosts thereby increasing virus transmission. Overall, our study shows that cannabis aphid is an efficient vector of PVY, and that virus infection and host plant suitability affect feeding behaviors of the cannabis aphid in ways which may increase virus transmission.</p>
Path-finding algorithm as a dispersal assessment method for invasive species with human-vectored long-distance dispersal event
<p><strong>Aim</strong>: An assessment method that can precisely represent human-vectored long-distance dispersals (HVLDD) is currently in need for effective management of invasive species. Here, we focused on HVLDD happening along roads and proposed a path-finding algorithm as a more precise dispersal assessment tool than the most widely used Euclidean distance method by using pine wilt disease (PWD) as a case study.</p> <p><strong>Location</strong>: Busan Metropolitan City, Republic of Korea</p> <p><strong>Methods</strong>: A path-finding algorithm, which calculates distances by considering spatial distribution of road networks, was tested for its effectiveness in estimating dispersal distances of HVLDD events. To this end, annual HVLDD cases were classified from entire PWD occurrence data from 2016 to 2019 and their dispersal distances were calculated using the path-finding algorithm and the Euclidean distance method. We constructed potential dispersal ranges based on the occurrence points in 2016, 2017, and 2018 using the respective year's mean dispersal distance for both methods, and their performances in accounting for each subsequent year's HVLDD cases were compared to determine which method calculated more precise distances. The information on which road class contributed more to dispersal occurrences and distances was analysed as well using the proposed algorithm.</p> <p><strong>Results</strong>: The potential dispersal ranges of the path-finding algorithm accounted for more future anthropogenic infection cases than the ones that used the Euclidean distance method, validating its higher functionality. It also revealed that most HVLDDs started and ended on small roads, and large roads constituted the majority of the total dispersal length.</p> <p><strong>Main Conclusions</strong>: The path-finding algorithm has proven to be a more effective dispersal assessment method for HVLDD events. It can help design effective control strategies. Thus, we encourage using the path-finding algorithm for dispersal assessment of invasive species that move along road networks, as well as for the development of more powerful HVLDD prediction models.a</p>
A Double-Edged Sword: Parental care increases risk of offspring infection by a maternally-vectored parasite
<p>Parental care can protect offspring from predators but can also create opportunities for parents to vector parasites to their offspring. We hypothesized that the risk of infection by maternally-vectored parasites would increase with the frequency of mother-offspring contact. Ammophila spp. wasps (Hymenoptera: Sphecidae) build nests in which they rear single offspring. Ammophila species exhibit varied offspring provisioning behaviors: some species enter the nest once to provision a single, large caterpillar, whereas others enter the nest repeatedly to provision with many smaller caterpillars. We hypothesized that each nest visit increases the risk of offspring parasitism by Paraxenos lugubris (Strepsiptera: Xenidae), whose infectious stages ride on the mother wasp (phoresy) to reach the vulnerable Ammophila offspring. We quantified parasitism risk by external examination of museum-curated Ammophila specimens—the anterior portion of P. lugubris protrudes between the adult host's abdominal sclerites and reflects infection during the larval stage. As predicted, Ammophila species that receive larger numbers of provisions incur greater risks of parasitism, with nest provisioning behavior explaining ca. 90% of the interspecific variation in mean parasitism. These findings demonstrate that parental care can augment, rather than reduce, risk of parasite transmission to offspring.</p>
Transmission vectors of essential Tsimane knowledge and skills: dataset and code.
<p>In our research report <strong><em>Cultural transmission vectors of essential knowledge and skills among Tsimane forager-farmers</em></strong>, we examine reported patterns of culture transmission contributing to 92 essential skills among a sample of 421 Tsimane forager-horticulturalists. We collected data for the study using a <em>Skills Survey </em>to identify vectors and types of influence responsible for the transmission of 92 skills important among Tsimane (Schniter et al. 2015). Here we provide the anonymized data for Schniter et al.’s 2022 study (as both a .csv file and as a .sav file) as well as both code and outputs (as an .spv file) for statistical analyses performed using IBM SPSS Version 24.</p> <p>For additional details about the <em>Skills Survey </em>see</p> <p>Schniter, E., Gurven, M., Kaplan, H. S., Wilcox, N. T., & Hooper, P. L. (2015). Skill ontogeny among Tsimane forager‐horticulturalists. <em>American journal of physical anthropology</em>, <em>158</em>(1), 3-18.</p> <p>Attached:</p> <p>TransmissionData.csv</p> <p>TransmissionData.sav</p> <p>Regressions&Frenquencies.spv</p>
Climatic niche conservatism in a clade of disease vectors (Diptera: Phlebotominae)
<p>Sandflies of the family Psychodidae show notable diversity in both disease vector status and climatic niche. Psychodid species' ranges can be solely tropical, confined to the temperate zones, or span both. We obtained observation site data, and associated climate data, for 223 psychodid species to understand which aspects of climate most closely predict distribution. Temperature and seasonality are strong determinants of species occurrence within the clade. We built a mitochondrial DNA phylogeny of Psychodidae, and found a positive relationship between pairwise genetic distance and climate niche differentiation, which indicates strong niche conservatism. This result is also supported by strong phylogenetic signals of metrics of climate differentiation. Finally, we used ancestral trait reconstruction to infer the tropicality (i.e., proportion of latitudinal range in the tropics minus the proportion of the latitudinal range in temperate areas) of ancestral species, and counted transitions to and from tropicality states, finding that tropical and temperate species respectively produced almost entirely tropical and temperate descendant species, a result consistent for vector and non-vector species. Taken together, these results imply that while vectors of Leishmania can survive in a variety of climates, their climate niches are strongly predicted by phylogeny.</p>
Angle measurements with 3D Vector antenna for localization purposes – open-access datasets
<p>This dataset contains data on positioning measurements of the angle of arrival (AoA) as well as the azimuth angle estimation using the MUSIC Algorithm. The data was collected from four ports (p1,p2,p3,p4) of a 3D Vector Antenna (3D VA) provided by ENAC. Data were captured in a laboratory environment with conditions that affect the positioning performance. </p>
Sentiment Analysis of RUU PDP with Naive Bayes, Support Vector Machine, and Random Forest Classification Algorithm
<p>Dataset from the results of data crawling via Twitter which discusses the Rancangan Undang Undang Pelindungan Data Pribadi to be used in the sentiment analysis process. The dataset is divided into several parts according to the process executed on RapidMiner.</p>
Study of the non-vector spread of the pine nematode Bursaphelenchus xylophilus through sawdust
<p>The goal of the study was to assess the possibility of <em>Pinus sylvestris</em> trees to be infested with pinewood nematode <em>B. xylophilus</em> through PWN-infested sawdust. The trials were conducted in climatic room at a temperature of 26℃ and at humidity of 60-70% from June to October, 2020. Each trial included 4-year-old seedlings of 12 <em>Pinus sylvestris </em>pines.</p> <p>The experiment contained seven trials, including the control: 1) uninjured stem + PWN-infested sawdust, 2) injured stem + PWN-infested sawdust, 3) injured stem + PWN-infested sawdust is 2.5 cm from the stem, 4) uninjured roots + PWN-infested sawdust in soil, 5) injured roots + PWN-infested sawdust in soil, 6) injured roots without sawdust, and 7) control. At the end of the experiment, the number of pinewood nematodes in the stem and roots of infested seedlings was counted. The number of nematodes is based on 100 grams wet weight of woody substrate and 100 cm<sup>3</sup> for soil substrate. We counted the number of wilted pine seedlings taking into account wilt classes (from 0 to 5) in different trials at the 20th week of the experiment. </p>
C-PHRASE Vectors
<p>The C-PHRASE semantic vectors described in the following paper:</p> <p>N.T. Pham, G. Kruszewski, A. Lazaridou, M. Baroni <a href="https://www.aclweb.org/anthology/P15-1094">Jointly optimizing word representations for lexical and sentential tasks with the C-PHRASE model.</a> Proceedings of ACL 2015 (53rd Annual Meeting of the Association for Computational Linguistics).</p> <p>The vectors are the rows of a dense matrix stored in a text file using the tab-delimited format (the first element of each line corresponds to a word, followed by the values in the vector representing it). The text file is then compressed and split it into two files to make the download easier. Please download the following parts, and then concatenate them as shown below:</p> <ul> <li>cphrase.txt.zip_aa</li> <li>cphrase.txt.zip_ab</li> </ul> <p><code>cat cphrase.txt.zip_* > cphrase.txt.zip</code> <br> </p>
Figure 10. Conceptual diagram illustrating vector quantization codeword formation-Development an Automatic Speech to Facial Animation Conversion for Improve Deaf Lives
<p>After the conversion process converts the analogue speech signal into a series words,<br> then converting recognized word to facial animation based on VRML.</p>
Supplementary material from the study on survival of African swine fever virus in feed, bedding materials and mechanical vectors, and their potential role in virus transmission
<p><span>Supplementary material from the experimental studies developed to analyse the survival of African swine fever virus in feed, bedding materials and mechanical vectors, and their potential role in virus transmission. </span></p> <p> </p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.