Otters are semiaquatic, carnivorous mammals known for their playful behavior, webbed feet, and dense fur coats.
These charismatic creatures belong to the Mustelidae family and are found in various habitats, including freshwater rivers, lakes, and coastal regions around the world.
Otters are skilled swimmers, adept at hunting fish, crustaceans, and other aquatic prey.
They are recognized for their unique adaptations, such as the ability to close their ears and nose while diving, and their tendency to hold hands while resting on their backs.
Otters play a crucial role in maintaining the balance of aquatic ecosystems and are often considered indictators of environmental health.
Conservationists work to protect otter populations, which face threats from habitat loss, pollution, and hunting.
Otter enthusiasts can enjoy observing these fascinating animals in their natural habitats and learning more about their fascinating lifestyle and behaviors.
The spatial scan statistic [20 ] has among other things been used to study human granulocytic ehrlichiosis near Lyme in Connecticut [21 (link)], soft-tissue sarcoma and non-Hodgkin's lymphoma clusters with high dioxin emission levels [22 (link)], childhood mortality in rural Burkina Faso [23 (link)], bovine tuberculoisis in Argentina [24 (link)] and Toxoplasma gondii infection of southeast sea, otters [25 (link)]. The spatial scan statistic imposes a circular window on the map and lets the circle centroid move across the study region. For any given position of the centroid, the radius of the window is changed continuously to take any value between zero and some upper limit. Let Lj(i) be the likelihood under the alternate hypothesis that there is a cluster in county i and its j closest neighbors, and let L0 be the likelihood under the null hypothesis. It can then be shown that As this likelihood ratio is maximized over all circles, it identifies the one that constitutes the most likely cluster. The test statistic is where I is the indicator function with value 1 when and 0 otherwise. The null hypothesis of no clustering is rejected when T is large.
Song C, & Kulldorff M. (2003). Power evaluation of disease clustering tests. International Journal of Health Geographics, 2, 9.
The claw samples used for the validation study were measured with callipers (Scienceware, Pequannock, NJ, USA) and ranged in length from 1.0 to 4.5 mm, with a mean of 2.6 ± 0.1 mm (n = 168). Samples were washed and crushed using modifications of methods described previously by Tegethoff et al. (2011) (link) and Levitt (1966) (link), respectively. In brief, claws were washed once with 1 ml distilled water and then twice with 1 ml 100% methanol by vortexing for 10 s. Samples were air dried, transferred to 2.0 ml cryovials (Corning Inc., Corning, NY, USA) and placed at −196°C for a minimum of 10 min in a liquid nitrogen dry shipper (Taylor-Wharton, Theodore, AL, USA). Frozen samples were placed in a steel cylinder and given several hard blows with a steel pestle to homogenize the claw sections. The crushed claw pieces were weighed using a Mettler Toledo balance (model AB54-S; ±0.0001 g; Mettler Toledo International, Inc., Columbus, OH, USA) and transferred to 7 ml glass scintillation vials (VWR, Mississauga, ON, Canada). Corticosterone was extracted from the samples in 100% methanol using a ratio of 0.005 g/ml by agitating for 24 h on an orbital shaker (Montreal Biotech Inc., Kirkland, PQ, Canada) at 200 rpm. Samples were then centrifuged at 2300 g for 10 min, and the extract was pipetted off into a new vial. The extract was dried in a fume hood and reconstituted in 150 µl enzyme immunoassay buffer solution (0.1 mm sodium phosphate buffer, pH 7.0, containing 9 g of NaCl and 1 g of bovine serum albumin per litre), resulting in a 1.13- to 16.53-fold concentration. Reconstituted samples were sonicated for 20 s in an Elmasonic waterbath (Elma GmbH & Co. KG, Singen, BW, Germany) and then loaded and incubated on microtitre plates as described by Terwissen et al. (2013) (link), before analysis. Claw CORT values were quantified using modifications of an enzyme immunoassay described previously (Metrione and Harder, 2011 (link); Watson et al., 2013 (link)). Antisera were diluted as follows: goat anti-rabbit IgG (GARG) polyclonal antibody (Sigma-Aldrich, Mississauga, ON, Canada), 0.25 µg/well; and CORT polyclonal antibody (CJM006; C. Munro, University of California, Davis, CA, USA), 1:200 000. The cross-reactivities of the antisera have been described previously (GARG and CORT; Metrione and Harder, 2011 (link); Watson et al., 2013 (link)). Corticosterone–horseradish peroxidase conjugate (C. Munro, University of California, Davis, CA, USA) was diluted 1:1 000 000. Standard solutions used were created with synthetic CORT (Steraloids Q1550; 39–10 000 pg/ml). The control consisted of a laboratory stock of pooled fecal extracts obtained from spotted-necked otters (Hydrictis maculicollis) that was run at 65% binding.
Baxter-Gilbert J.H., Riley J.L., Mastromonaco G.F., Litzgus J.D, & Lesbarrères D. (2014). A novel technique to measure chronic levels of corticosterone in turtles living around a major roadway. Conservation Physiology, 2(1), cou036.
Hair samples were delivered to the Endocrinology Laboratory at the Toronto Zoo for analysis. The hair was cut into 5 mm pieces and placed into a 7 ml glass scintillation vial to be weighed. To avoid contamination with other biological fluids that may have artificially elevated cortisol levels, all hair samples were washed with 100% methanol by vortexing in a tube for 10 s and immediately removing all of the 100% methanol using a pipettor. Immediately thereafter, 80% methanol in water (v:v) was added to the samples, at a ratio of 0.001–0.005 g/ml, and samples were vortexed for 5–10 s. Samples were then mixed for 24 h on a plate shaker (MBI Orbital Shaker; Montreal Biotechnologies Inc., Montreal, QC, Canada). After 24 h, the vials were centrifuged for 10 min at 2400g. The supernatants were pipetted off into clean glass vials and dried down under air in a fume hood. The dried extracts were stored at −20°C until analysis. Samples were removed from the freezer and brought to room temperature on the laboratory bench prior to analysis. Reconstitution of the dried-down extracts was done by adding assay buffer (from Cortisol EIA Kit, no. K003-H1; Arbor Assays, Ann Arbor, MI, USA) and sonicating for 20 s followed by vortexing for 10 s. Final volumes of assay buffer added to each sample resulted in chipmunk extracts being neat. All samples were centrifuged for 1 min at 1200g immediately prior to dispensing onto the microtitre plate. Cortisol concentrations in the reconstituted extracts were assayed following the manufacturer's instructions for the Cortisol EIA Kit. The detection limit of the assay was 45.4 pg/ml as per manufacturer's specifications. Results are presented as nanograms of cortisol per gram of hair. The efficiency of the hair extraction procedure was analysed through recovery of exogenous cortisol added to chipmunk hair samples prior to extraction. Briefly, 10 samples of at least 0.001 g each from a pool of chipmunk hair were used; five samples were spiked with 5 µl of 52 pg/µl cortisol in 100% methanol, and five samples were left unspiked. The samples were mixed and then extracted and assayed as described above. The percentage efficiency was calculated using the following formula: amount observed/amount expected × 100%, where the amount observed is the value obtained from the spiked sample minus background and the amount expected is the calculated amount added. The percentage efficiency is presented as the mean ± SEM. Assay validation was carried out as follows. First, parallel displacement between the standard curve and a serial dilution of a pooled chipmunk hair extract was used to detect immunological similarities between the standard and sample hormones. The resulting curves were plotted as relative dose vs. percentage antibody bound, and linear regression analysis was performed. Sample dilution was selected based on 50% binding of the pooled sample curve. Second, possible interference of components within the extract with antibody binding was analysed through recovery of exogenous cortisol added to pooled chipmunk hair extracts. Briefly, 75 µl aliquots of extract from a pooled chipmunk hair sample were spiked with 75 µl of each hormone standard. The samples were assayed as described above. The percentage recovery was calculated using the following formula: amount observed/amount expected × 100%, where the amount observed is the value obtained from the spiked sample and the amount expected is the calculated amount of standard hormone added plus the amount of endogenous hormone in the unspiked sample. The percentage recovery is presented as the mean ± SEM. The graph was plotted as hormone added vs. hormone recovered, and regression analysis was used to determine whether there was a significant relationship between them. Third, for both species, all hair samples were processed, extracted and analysed at the same time in an attempt to minimize the effects of possible variation associated with day-to-day differences in extraction and assay efficiency. All samples were assayed in duplicate, with the mean of the two results being presented. Only duplicates with <10% coefficients of variation (CVs) were accepted as data; an average of 5.2% intra-assay CV was observed across all duplicates. The inter-assay CV, based on controls of laboratory stocks of pooled faecal extracts obtained from female spotted-necked otters (Hydrictis maculicollis) run at 65% binding, was 4.5%.
Mastromonaco G.F., Gunn K., McCurdy-Adams H., Edwards D.B, & Schulte-Hostedde A.I. (2014). Validation and use of hair cortisol as a measure of chronic stress in eastern chipmunks (Tamias striatus). Conservation Physiology, 2(1), cou055.
A 1-kb Pst1 fragment of the Chlamydomonas DHC1b cDNA was inserted in the Pst1 site of pMAL-cR1 (New England Biolabs, Inc.). Expression of this construct in Escherichia coli produced a protein in which 315 amino acids (starting at the sequence QQFDAH and ending at NKLSFL) of DHC1b were fused to the maltose-binding protein. The fusion protein was purified by amylose affinity chromatography and antibodies were produced in rabbits (Research Genetics Inc.). Anti-DHC1b antibodies were purified by adsorption to and release from another DHC1b fusion protein made from the pThioHisB vector (Invitrogen Corp.) and bound to polyvinylidene difluoride membrane (Immobilon-P; Millipore Corp., Waters Chromatography) (Olmsted, 1981 (link); King et al., 1996 (link)). For Western blots, flagella were isolated and fractionated as described in Pazour et al. (1998) (link), except that the demembranated axonemes were washed three times with buffer containing 10 mM MgATP2−, and extracted with 0.6 M KCl to solubilize dynein arms. Whole cell extracts were made by resuspending log-phase cells in SDS-sample buffer, heating at 50°C for 10 min, and repeatedly drawing the sample through a 26-gauge needle to shear the DNA. Proteins were separated by SDS-PAGE (Pfister et al., 1982 (link)) and blotted onto polyvinylidene difluoride membrane by the two-step procedure of Otter et al. (1987) (link). Western blotting was as described in Pazour et al. (1998) (link).
Pazour G.J., Dickert B.L, & Witman G.B. (1999). The DHC1b (DHC2) Isoform of Cytoplasmic Dynein Is Required for Flagellar Assembly. The Journal of Cell Biology, 144(3), 473-481.
The data used here are based on the 2044 georeferenced tick locations in Germany described by Rubel et al. (2014 (link)). These are composed of 1051 compiled tick locations, which have been extended by 776 Ixodes ricinus locations from Estrada-Peña et al. (2013 (link)) and 217 I. ricinus locations from GBIF (2014 ). Here, this dataset is extended by 1448 new tick locations, 900 locations of which were digitized from literature and 548 new tick locations provided by the authors. Thus, the entire data set used here consists of 3492 georeferenced tick locations. The geographical coordinates of the new tick locations are provided in the supplement together with an indication of their accuracy and the sources. The coordinates are given in decimal degrees with a measure of accuracy divided into high (± 30 m), medium (± 1 km) and low (± 10 km) precision, identical to those previously used by Rubel et al. (2014 (link), 2018 (link), 2020 (link)). The tick locations are mapped using R, a language and environment for statistical computing (R Development Core Team 2019 ). However, they are not evenly distributed across Germany. For example, the areas around the large cities Berlin, Hanover, Leipzig and Stuttgart are particularly well covered with data, since research groups have been dealing with ticks and tick-borne diseases here for a long time. Large-scale studies on the tick infestation of wildlife, such as those on red foxes (Vulpes vulpes) in Thuringia (Meyer-Kayser et al. 2012 (link)) and on the Eurasian otter (Lutra lutra) in Upper Lusatia (Christian 2012 ), also lead to an unusual clustering of tick locations. In order to achieve a more realistic representation of the distribution of the individual tick species, these clusters were reduced in a two-stage process. First, the tick locations of the two studies mentioned were reduced with the help of a random selection. For example, from the study by Meyer-Kayser et al. (2012 (link)), only 25 of the 106 available I. canisuga locations were shown in the corresponding map. The following numbers of tick locations that have been selected to avoid large-scale clusters caused by data from this study were used: 25(106) for I. canisuga, 30(149) for I. hexagonus, and 50(195) for I. ricinus. Similarly, only 20(34) tick locations from the study by Christian (2012 ) were used for I. hexagonus. To further avoid local clustering and associated sampling biases in the dataset a spatial thinning algorithm was applied (Aiello-Lammens et al. 2015 (link)). The ‘thin’ function in the spThin R package provided by Aiello-Lammens et al. (2019 ) uses a randomization approach and returns a dataset with the maximum number of locations for a given thinning distance, here 8 km. The maps for the individual tick species (Figs. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11) therefore not only show the number of tick locations mapped, but also the total number of available tick locations in brackets. Tick species, for which only a few locations are known, are grouped according to their host preferences as proposed by Hornok et al. (2020 (link)). For example, the bat ticks Carios vespertilionis, Ixodes ariadnae, Ixodes simplex, and Ixodes vespertilionis are depicted in the same map.
Recorded locations of Haemaphysalis concinna and Haemaphysalis punctata in Germany
Recorded locations of Hyalomma marginatum, Hyalomma rufipes and Rhipicephalus sanguineus in Germany. These species are not endemic in Germany, but are continuously introduced
Recorded locations of Ixodes acuminatus, Ixodes apronophorus and Ixodes trianguliceps in Germany
Recorded locations of Ixodes arboricola, Ixodes frontalis and Ixodes rugicollis in Germany
Rubel F., Brugger K., Chitimia-Dobler L., Dautel H., Meyer-Kayser E, & Kahl O. (2021). Atlas of ticks (Acari: Argasidae, Ixodidae) in Germany. Experimental & Applied Acarology, 84(1), 183-214.
All analyses were performed using netZooPy v0.8.1, the Python distribution of the netZoo (netzoo.github.io). NetZoo methods are implemented in R, Python, MATLAB, and C. netZooR v1.3 is currently implemented in R v4.2 and available through GitHub (https://github.com/netZoo/netZooR) and Bioconductor (https://bioconductor.org/packages/netZooR) and includes PANDA, LIONESS, CONDOR, MONSTER, ALPACA, PUMA, SAMBAR, OTTER, CRANE, SPIDER, EGRET, DRAGON, and YARN. netZooPy v0.8.1 is implemented in Python v3.9 and includes PANDA, LIONESS, CONDOR, PUMA, SAMBAR, OTTER, and DRAGON. netZooM v0.5.2 is implemented in MATLAB 2020b (The Mathworks, Natick, MA, USA) and includes PANDA, LIONESS, PUMA, OTTER, and SPIDER. netZooC v0.2 implements PANDA and PUMA.
Ben Guebila M., Wang T., Lopes-Ramos C.M., Fanfani V., Weighill D., Burkholz R., Schlauch D., Paulson J.N., Altenbuchinger M., Shutta K.H., Sonawane A.R., Lim J., Calderer G., van IJzendoorn D.G., Morgan D., Marin A., Chen C.Y., Song Q., Saha E., DeMeo D.L., Padi M., Platig J., Kuijjer M.L., Glass K, & Quackenbush J. (2023). The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks. Genome Biology, 24, 45.
Semi-structured in-depth interviews were conducted to glean additional qualitative insights on clinician experiences, perceived benefits and limitations, and reasons for their willingness or unwillingness to adopt POC HPV testing, patient self-sampling and self-testing with a rapid HPV test, among other topics as part of a larger study about cervical cancer screening. Recruitment for the interviews initially occurred through email invitations sent to our team’s network of clinicians in Indiana, and survey respondents who consented to being contacted for a follow-up interview were also invited to interview by the study team. We conducted virtual interviews via Zoom with 20 clinicians from August 2020 to October 2021. Interviews lasted 30 to 60 minutes and were audio recorded and transcribed verbatim using a digital transcribing platform, Otter.ai. Interview participants volunteered and were compensated upon completion of the interview with a $25 electronic gift card. Transcripts were reviewed and edited for accuracy by research assistants.
Rodriguez N.M., Brennan L.P., Claure L., Balian L.N., Champion V.L, & Forman M.R. (2023). Leveraging COVID-era innovation for cervical cancer screening: Clinician awareness and attitudes toward self-sampling and rapid testing for HPV detection. PLOS ONE, 18(3), e0282853.
We followed the best practice guidelines for qualitative research in public health to analyze our data [27 (link)]. An initial codebook was created by reviewing several interviews and identifying the repeating concepts and themes. The codebook defined 4 initial domains to be used in the analysis: COVID-19, technology, emotional regulation and compassion, and mental health. Double coding was conducted to ensure an intercoder reliability of at least 75% agreement on theme interpretation. After transcription, code queries were run for each of the 4 domains of the established codebook. Commonalities and representative themes across the quotes were analyzed, and 4 overarching themes were produced (outlined in the Results section). On the basis of the empirical evidence suggesting differential impact of the pandemic based on demographic factors and feedback from our SMEs in phase 1 that adolescents from marginalized groups may be more isolated or more exposed to pandemic-related death and grief [28 (link)], we explored whether the themes on technology use that emerged from our data differed based on key demographics, such as gender identity, sexual orientation, and race. Interviews were transcribed using Otter Transcription Software and coded using NVivo (version 12; QSR International) qualitative software [29 ].
Rimel S.E., Bam D., Farren L., Thaanum A., Smith A., Park S.Y., Boeldt D.L, & Nicksic Sigmon C.A. (2023). Technology Use During the COVID-19 Pandemic and the Ways in Which Technology Can Support Adolescent Well-being: Qualitative Exploratory Study. JMIR Formative Research, 7, e41694.
Semi-structured interviews were the study's core method of data collection. Acting as a conversation with purpose (49 ), this method provided a means by which to thoroughly explore health professionals' experiences and perspectives by allowing for elaboration of topics deemed personally significant, while also ensuring that the major and most relevant topics were covered (50 ). Qualitative interviewing can pose challenges related to recall and selective memories; however, these issues are tempered since qualitative research is not concerned with the positivistic search for objective facts. Rather, it is considered both valuable and valid “for the express purpose of understanding people's interpretations of their world” [(51 (link)), p. 9]. Following ethical approval from the Research Ethics Committee of the Centre for Health Policy and Management and Center for Global Health in Trinity College Dublin's School of Medicine, data collection took place over a three-month period between March and May 2022. The interviews took place via online video conferencing and due to the understandably busy schedules of participating health professionals, ranged between 36 and 75 minutes, with most lasting between 45 and 60 minutes. The interview schedule covered a range of topics, including the background and triggers for the response, the impact of COVID-19 on its development or direction, facilitators and barriers to implementation and key learnings or reflections on enabling better access to universal integrated care during a crisis (see Supplementary material for more detail). With participants' consent, all interviews were digitally recorded and transcribed verbatim (assisted by otter.ai).3 Adopting a team-based approach for applied researchers, we used word processing and spreadsheet software (Microsoft Word and Excel) via an online document management and collaboration platform to structure and organize the data for analysis (52 (link), 53 (link)). Two researchers (SP and LMC) analyzed (i.e., coded) the data, while a third member of the team (SB) coded ~10–20% of same. Following numerous in-depth team discussions, this culminated in the development of coding categories related to themes and conceptual constructs that were emergent and grounded in the data rather than developed a priori (54 ). The coding process meant that data related to a range of specific topics could be extracted from each participant's narrative and collated into corresponding codebooks or files (55 (link)). Salient patterns and observations were teased out through an in-depth analysis of the data in each topic-specific codebook, which facilitated the interrogation of key concepts and themes (56 (link)). Adopting a complexity-informed approach, dedicated analytic attention was also paid to the interactions between different components of the health system via agents to help explain the patterns observed (57 (link)). Although complexity had been identified as potentially relevant to the analytic approach prior to data collection, an inductive approach to theorizing was used throughout the analysis stages of the research. Theorizing, in the social sciences, refers to attempts to understand or explain phenomena and is distinct from theory, which is the final or fixed articulation. In this study, transcripts were analyzed for themes and concepts relevant to answering the empirical research questions outlined above. During this process, the research team regularly discussed the continued relevance of complexity in light of the emerging patterns of observation. This led to the identification of emergence, inter-dependedness and self-organization as key principles to be utilized and ensured that the conceptual framework employed was ultimately driven by the findings. In keeping with recommended practice and procedures for qualitative analysis, a number of measures were taken to ensure the trustworthiness and credibility of the interpretation of data (58 ). These included checking data for negative cases (i.e., outliers) (59 ) and regular discussions between the researchers that enabled multiple perspectives, insights, and interpretations to be considered (60 (link)). The analytic approach was also guided by the perspective that saturation was achieved when no new information on dimensions of experience or meaning were emerging from the data (61 (link)).
Parker S., Mac Conghail L., Siersbaek R, & Burke S. (2023). How to not revert to type: Complexity-informed learnings from the pandemic response for health system reform and universal access to integrated care. Frontiers in Public Health, 11, 1088728.
Interviews were transcribed from Zoom audio files using Otter.ai. Transcripts were cleaned, deidentified, and verified by KF and EM. Final transcripts were independently coded by two researchers (KF and EM), who both identify as cisgender females. Coders met weekly to review coding discrepancies and new themes as they were identified. We used NVivo [18 ] for coding and employed inductive thematic analysis [19 ] to identify themes. Interrater reliability was calculated and found 94.3% agreement between coders.
Ferrucci K.A., McPhillips E., Lapane K.L., Jesdale B.M, & Dubé C.E. (2023). Provider perceptions of barriers and facilitators to care in eating disorder treatment for transgender and gender diverse patients: a qualitative study. Journal of Eating Disorders, 11, 36.
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NVivo version 12 is a software tool designed for qualitative and mixed-method research. It provides features for organizing, analyzing, and visualizing unstructured data, such as interview transcripts, documents, and multimedia files.
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The DNeasy Blood & Tissue Kit is a DNA extraction and purification kit designed for the efficient isolation of high-quality genomic DNA from a variety of sample types, including whole blood, tissue, and cultured cells. The kit utilizes a silica-based membrane technology to capture and purify DNA, providing a reliable and consistent method for DNA extraction.
NVivo is a qualitative data analysis software package developed by QSR International. It is designed to assist researchers in organizing, analyzing, and managing qualitative data, such as interview transcripts, focus group discussions, and open-ended survey responses. The software provides tools for coding, categorizing, and identifying themes within the data.
The ABI PRISM 310 Automated Sequencer is a capillary electrophoresis-based instrument designed for DNA sequencing analysis. It automates the DNA sequencing process, providing efficient and high-throughput capabilities for researchers.
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TaqMan PCR Master Mix is a ready-to-use solution for real-time PCR amplification. It contains all the necessary components, including DNA polymerase, dNTPs, and buffer, to perform the PCR reaction.
The RNeasy Mini QIAcube Kit is a ready-to-use kit designed for the automated purification of total RNA from a variety of sample types using the QIAcube instrument. The kit utilizes QIAGEN's silica-membrane technology to ensure high-quality RNA extraction.
MATLAB 2020b is a high-performance numerical computing environment and programming language. It provides a wide range of tools for data analysis, algorithm development, and visualization. MATLAB 2020b offers a flexible platform for scientific and engineering computations, with a focus on matrix manipulation, signal processing, and optimization.
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Exonuclease I is an enzyme that catalyzes the removal of single-stranded DNA from the 3' end. It has a high specificity for single-stranded DNA and is commonly used in molecular biology applications to remove unwanted single-stranded DNA.
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The QIAamp DNA Stool Mini Kit is a laboratory equipment product designed for the purification of genomic DNA from stool samples. It is a tool for extracting and isolating DNA from biological specimens.
NVivo 13 is a qualitative data analysis software developed by QSR International. It provides tools for organizing, analyzing, and gaining insights from unstructured data, such as interviews, open-ended survey responses, and documents.
