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opencc-zeroDec 2019View details →

Data from: Habitat selection in transformed landscapes and the role of forest remnants and shade coffee in the conservation of resident birds

1. Biodiversity conservation in transformed landscapes is becoming increasingly important. However, most assessments of the value of modified habitats rely heavily on species presence and/or abundance, masking ecological processes such as habitat selection and phenomena like ecological traps, which may render species persistence uncertain. High species richness has been documented in tropical agroforestry systems but comparisons with native habitat remnants generally lack detailed information on species demography and habitat use. 2. We generated a multi-species, multi-measure framework to evaluate the role of habitat selection in the adaptation of species to transformed landscapes, and demonstrate that its use could affect how we value the contribution different land uses make to biodiversity conservation. 3. We analyzed seven years of capture-mark-recapture and observation data for twelve species of resident birds present in native forest remnants and shade coffee plantations in a mega-diverse region. We assessed whether species behaved adaptively by evaluating the correlation between measures of habitat preference (occurrence, abundance, fidelity, inter-seasonal variance and age) and performance (body condition, muscle, primary molt, breeding and juveniles) in forest and coffee, and generated hypotheses about their role in species persistence. 4. We documented adaptive habitat selection for seven species, non-ideal selection for four, and maladaptive selection for one. While many species showed equal-preference and/or equal performance in many traits, in general we found more evidence for birds preferring and/or performing better in forest than coffee, although relationships between our indicators and population adaptation need to be studied further before our proposed framework can be applied to more species and landscapes. 5. While shade coffee can act as a biodiversity-friendly matrix providing complementary or supplementary habitat to a wide range of resident bird species, protecting remnants of native vegetation is still of paramount importance for biodiversity conservation in agricultural landscapes. 28-Aug-2019

opencc-zeroDec 2016View details →

Data from: Different genetic structures revealed resident populations of a specialist parasitoid wasp in contrast to its migratory host

Genetic comparisons of parasitoids and their hosts are expected to reflect ecological and evolutionary processes that influence the interactions between species. The parasitoid wasp, Cotesia vestalis, and its host diamondback moth (DBM), Plutella xylostella, provide opportunities to test whether the specialist natural enemy migrates seasonally with its host or occurs as resident population. We genotyped 17 microsatellite loci and two mitochondrial genes for 158 female adults of C. vestalis collected from 12 geographical populations, as well as nine microsatellite loci for 127 DBM larvae from six separate sites. The samplings covered both the likely source (southern) and immigrant (northern) areas of DBM from China. Populations of C. vestalis fell into three groups, pointing to isolation in northwestern and southwestern China and strong genetic differentiation of these populations from others in central and eastern China. In contrast, DBM showed much weaker genetic differentiation and high rates of gene flow. TESS analysis identified the immigrant populations of DBM as showing admixture in northern China. Genetic disconnect between C. vestalis and its host suggests that the parasitoid did not migrate yearly with its host but likely consisted of resident populations in places where its host could not survive in winter.

opencc-zeroDec 2014View details →

Supporting dataset for manuscript: "Higher rate of tuberculosis in second generation migrants compared to native residents in a metropolitan setting in Western Europe" (PLoS ONE)

This is the supporting datafile for the manuscript entitled "Higher rate of tuberculosis in second generation migrants compared to native residents in a metropolitan setting in Western Europe" (Marx et al., PLoS ONE). The dataset includes anonymized, routinely collected notification data (variables labeled as "nd") for 314 individuals and anonymized survey data (i.e. data obtained through interviews; variables labeled as "sd") for a subset of 154 individuals. The data are published open-access, in accordance with the PLoS ONE data policy (2014).

opencc-zeroOct 2023View details →

Divergent molecular networks program functionally distinct CD8+ skin-resident memory T cells

Skin-resident CD8+ T cells comprise distinct IFN-γ- (TRM1) and IL-17-producing (TRM17) subsets that differentially contribute to immune responses. However, whether these populations employ common mechanisms to establish tissue residence is unknown. Here, we show that TRM1 and TRM17 cells navigate divergent trajectories to acquire tissue residency in skin. While TRM1 cells depend on a T-bet-Hobit-IL-15 axis, TRM17 cells develop independently of these factors. Instead, c-Maf commands a tissue-resident program in TRM17 cells parallel to that induced by Hobit in TRM1 cells, with an ICOS-c-Maf-IL-7 axis pivotal to TRM17 cell commitment. Accordingly, targeting this pathway enables ablation of skin TRM17 cells without compromising their TRM1 counterparts. Thus, skin-resident T cells rely on distinct molecular circuitries, which can be exploited to strategically modulate local immunity.

opencc-by-4.0Nov 2023View details →

Empirical data on growth and residency of juvenile Pacific salmon in North America estuaries

Dataset compiling empirical data on estuarine growth and residency of Pacific salmon in North America. We conducted a systematic literature review to create this database, starting with a literature search in Web of Science Core Collection through Simon Fraser University's library proxy on April 24th, 2018, using the search parameters (salmon, Oncorhynchus) AND (estuary*) AND (residen* OR growth OR survival OR mortality), which returned 681 results (these results were presented in Arbeider 2018). We updated the search on March 29th, 2020, which produced 24 additional papers published after April 2018, and again on July 7th, 2022 which yielded another 31 papers published since March 2020. From these results, we extracted papers that research Pacific salmonids and whose study estuary was in North America. From this reduced list of papers, we extracted growth and residency parameters, as well as other relevant data. For complete methods please refer to:Arbeider, M. et al. (In press). The estuarine growth and residency of juvenile Pacific salmon in North America: a compilation of empirical data. Canadian Journal of Fisheries and Aquatic Sciences.

openJan 2024View details →

Dataset of "A multi-method approach to drafting candidate entrustable professional activities for a general internal medicine residency programme"

The present Dataset is related to a study on "A multi-method approach to drafting candidate entrustable professional activities for a general internal medicine residency programme" and include : <ul> <li>The  "Voting sheet model" used for the 1st round of voting according to the RAND appropriateness method</li> <li>The tables of aggregate results after round 1 and after round 2 of the RAND appropriateness method, with subgroup analysis</li> <li>A document describing which items where chosen to be included in round 2 of voting and why (file name "Summary_Decisions_.....")</li> <li>The list of candidate EPA (Entrustable Professional Activities) selected after 2 round of rating by the expert panel. This list of 225 EPA had not yet undergone the quality check using the EQual-Criteria (DOI: 10.1097/ACM.0000000000001908)</li> </ul> Methods: We set up a multi-step approach including a systematic review of the international literature; four national focus groups; a national consensus process using a RAND appropriateness method and a quality check of the selected candidate EPAs using Equal criteria. Results: These steps generated a final list of 247 candidate EPAs in GIM that were submitted for the national consensus process. After two rounds of rating, experts agreed on the appropriateness for the GIM postgraduate training of 225 of the candidate EPAs. Twenty-two of the proposed EPAs were deemed inappropriate and disagreement persisted only for two EPAs.   General description of the data set  : o   Nature: aggregated, analysed data o   Mode of collection: experimental o   Format: unstructured text, database

opencc-zeroJan 2024View details →

Relative breeding timing and reproductive success of a resident montane bird species

The phenological match-mismatch hypothesis predicts that animals that better synchronize critical life history events with the peak availability of their primary food source should have higher fitness. If phenological match-mismatch determines breeding success, most individuals in a population may be expected to breed simultaneously within a given year because selection has favored mechanisms that allow for the tracking of optimal food abundance. Therefore, individuals that breed too early or too late relative to the bulk of the population ("peak" of breeding) should experience decreased fitness. Using 11 years of data, we investigated the effect of relative breeding timing on breeding success in resident mountain chickadees (Poecile gambeli) across two elevations in the Sierra Nevada mountains, USA. Chickadees that bred during the peak of nesting did not have the highest breeding success; instead, birds that bred earliest performed best at high elevation, while at low elevation early and peak nests performed similarly. Breeding success decreased linearly with relative timing at both high and low elevations, and the relationship between breeding success and timing differed among years. Our results suggest that phenological match-mismatch may not be the main driver of within-year variation in breeding success in animals residing in montane environments.

opencc-by-sa-4.0Mar 2024View details →

Campina de Faro pilot - data from residents interviews - INCULTUM

Survey of local communities to gather ideas and identify their needs, with the aim of improving cultural tourism experiences.

Figure 5 in Revised taxonomy of eastern North Pacific killer whales ( Orcinus orca ): Bigg's and resident ecotypes deserve species status

Figure 5. Global phylogenetic trees of killer whales based on (a) haplotypes from 452 mitogenomes and (b) 49 nuclear genome sequences. Reprinted with permission from Morin et al. [15] (figure 2; by permission from John Wiley & Sons, licence 5458310335802) and [9] (electronic supplementary material, figure S3b, by permission from Andrew D. Foote). Black branches in (a) lead to haplotypes that are from animals that have not been identified to ecotype (see electronic supplementary material, table S1 from [15]).

Figure 3 in Revised taxonomy of eastern North Pacific killer whales ( Orcinus orca ): Bigg's and resident ecotypes deserve species status

Figure 3. PCA plot of first two principal components based on (a) 88 SNPs: offshore (n = 3), resident (n = 11), Bigg's (n = 30) from data in Morin et al. [15]; (b) 26 microsatellites: offshore (n = 5), resident (n = 250), Bigg's (n = 116) (samples genotyped at ≥20 loci) [56]; unpublished); (c) 3678 RADseq SNPs: offshore (n = 7), resident (n = 52) and Bigg's (n = 37) populations [57,62]; (d) 1 00 000 (subset from 6 371 282) SNPs from 147 high-coverage genomes of offshore (n = 7), Bigg's (n = 14) and resident (n = 126) samples from multiple geographically and behaviourally defined subpopulations (Alaska, northern and southern resident populations) (based on subset of SNP genotype data from [113]. See Supplementary Materials for methods and data set information.

Figure 7 in Revised taxonomy of eastern North Pacific killer whales ( Orcinus orca ): Bigg's and resident ecotypes deserve species status

Figure 7. Photographs of neotype skulls for (a) Orcinus rectipinnus (USNM 594671) and (b) Orcinus ater (USNM 594672).

Figure 1 in Revised taxonomy of eastern North Pacific killer whales ( Orcinus orca ): Bigg's and resident ecotypes deserve species status

Figure 1. Expected range maps for (a) resident and (b) Bigg's killer whales, including locations of samples used for mitogenome analysis (figure 5a, resident n = 106, Bigg's n = 93) [15]. Distribution ranges have been inferred based on published identifications of individuals that are identified by ecotype [48–53]. Sample distributions cover the known ranges of both ecotypes, with the exception of residents of Oregon and northern California, and both ecotypes off northern Japan (Hokkaido) in the western Pacific [48,54]. Sample maps for microsatellite data are in electronic supplementary material, figure S2.

Figure 8 in Revised taxonomy of eastern North Pacific killer whales ( Orcinus orca ): Bigg's and resident ecotypes deserve species status

Figure 8. Vertical images of (a) an adult male Bigg's killer whale (BKW) from the West Coast Transient population of Bigg's killer whales and (b) an adult male resident killer whale (RKW) from the sympatric Southern Resident population of resident killer whales. Images are scaled to the estimated asymptotic lengths of 7.3 m [20] and 6.9 m [145], respectively. Vertical images were collected using an octocopter drone using methods described by Durban et al. [146], provided by John Durban and Holly Fearnbach.

Figure 6 in Revised taxonomy of eastern North Pacific killer whales ( Orcinus orca ): Bigg's and resident ecotypes deserve species status

Figure 6. Illustrations of (a) O. ater and (b) O. rectipinnus from Scammon [138,140]. These illustrations were likely made by Scammon, or made under his guidance from his field notes and sketches. Whether they represent renderings of specific specimens, or composite sketches, is unknown.

Figure 2. Canonical variate 1 and 2 in Revised taxonomy of eastern North Pacific killer whales ( Orcinus orca ): Bigg's and resident ecotypes deserve species status

Figure 2. Canonical variate 1 and 2 plots for cranial shape features that distinguish among ecotypes for (a) skull morphology (resident (n = 17), Bigg's (n = 13) and offshore (n = 6)) and (b) dentary bone morphology (resident (n = 21), Bigg's (n = 12) and offshore (n = 8) specimens) (reprinted from [103]).

Figure 4. Structure assignment probability plots for K in Revised taxonomy of eastern North Pacific killer whales ( Orcinus orca ): Bigg's and resident ecotypes deserve species status

Figure 4. Structure assignment probability plots for K = 3 groups from (a) 26 microsatellites: offshore (n = 5), resident (n = 250), Bigg's (n = 116) samples genotyped at ≥ 20 loci) (56; unpublished); (b) 3340 RADseq SNPs (polymorphic in sample set): offshore (n = 7), resident (n = 52) and Bigg's (n = 37) populations [57,62]. Vertical bars represent the individual assignment probability for each group inferred by Structure (groups identified by shading), with samples sorted by a priori ecotype assignment. See electronic supplementary material for methods and data set information.

opencc-by-4.0Nov 2021View details →

An epidemiological Study to Assess Household Transmission & Associated Risk Factors for COVID-19 Disease amongst Residents of Delhi, India.

Executive summary: Studying the spread and epidemiological characteristics of COVID-19 virus specially in household settings are needed to prepare our self-better in preventing and controlling this epidemic. In this study we proposed a conceptual framework of four level of determinates and tried to understand the transmission dynamics of COVID-19 among household contacts along with clinical, epidemiological and virologic characteristics of the infection.  Aims & Objectives: <ol> <li>the proportion of asymptomatic cases and symptomatic cases;</li> <li>the incubation period of COVID-19 and the duration of infectiousness and of detectable shedding;</li> <li>the serial interval of COVID-19 infection; </li> <li>clinical risk factors for COVID-19, and the clinical course and severity of disease; </li> <li>high-risk population subgroups;</li> <li>the secondary infection rate and secondary clinical attack rate of COVID-19 infection among household contacts; and</li> <li>the associations of various factors across four dimensions interaction associated with risk of transmission</li> </ol> Methodology: This was a case-ascertained study where all susceptible contacts of a laboratory confirmed COVID-19 case were studied prospective for four weeks after their enrolment. It was done in New Delhi, during the end of first wave as well as whole second wave from December 2020 to July 2021. The study team collected the key information by questionnaire along with blood and oro-nasal swab during the household visits. Follow-up was done on day 7, 14 and 28 for observing the disease characteristic and symptomatology along with confirmation by serum and oro-nasal swab testing. Daily characteristics of the infection were noted by the participants on symptoms diary. Results: We enrolled 99 households, each having one laboratory-confirmed COVID-19 index case along with their 318 susceptible contacts. By the end of the follow-up, secondary infection rate was seen at 55.5%, while seroconversion in 46.6%.  Hospitalization and case fatality rate was 3.83% and 1.7% respectively. Among epidemiological characteristics we observed serial interval of 8.0 ± 6.7 days, generation time 3.8  ± 6.4, while secondary attack rate was 54.9%. The predictors of secondary infection among individual contact level were being female (OR:2.13, 95% CI:1.27 - 3.57), age of the household contact (1.01;1.00 - 1.03), symptoms at baseline (3.39; 1.61- 7.12) and during follow-up (3.18; 1.64 - 6.19), while only symptoms during follow-up (3.81: 1.43 - 10.14) and being RT-PCR positive (8.32; 3.22 -21.54) was significantly and independently associated with seroconversion among household contacts. Among index case-level age of the primary case (1.03; 1.01 -1.04) and any symptoms during follow-up (6.29; 1.83-21.63) significantly and independently associated with secondary infection while any symptoms during follow-up was associated with seroconversion among household contacts. Among household-level characteristics having more rooms (4.44; 2.16 - 9.13) independently associated with secondary infection, while more rooms (3.98; 1.23 -12.90) along with overcrowding (0.37; 0.16 - 0.82) associated with seroconversion. Among contact pattern only taking care of the index case (2.02;1.21- 3.38) was significantly and independently associated with secondary infection, while none was associated with seroconversion. Conclusion: A high secondary cases and secondary attack rate was seen in our study. This highlights the need to adopts strict measure and advocate COVID appropriate behaviours in order to break the transmission chain at household level. The targeted approach at household contacts with higher risk would be efficient in limiting the development of infection among susceptible contacts.

opencc-zeroMay 2022View details →

Conflict over the eukaryote root resides in strong outliers, mosaics and missing data sensitivity of site-specific (CAT) mixture models

Abstract Phylogenetic reconstruction using concatenated loci ("phylogenomics" or "supermatrix phylogeny") is a powerful tool for solving evolutionary splits that are poorly resolved in single gene/protein trees (SGTs). However, recent phylogenomic attempts to resolve the eukaryote root have yielded conflicting results, along with claims of various artefacts hidden in the data. We have investigated these conflicts using two new methods for assessing phylogenetic conflict. ConJak uses whole marker (gene or protein) jackknifing to assess deviation from a central mean for each individual sequence, while ConWin uses a sliding window to screen for incongruent protein fragments (mosaics). Both methods allow selective masking of individual sequences or sequence fragments in order to minimize missing data, an important consideration for resolving deep splits with limited data. Analyses focused on a set of 76 eukaryotic proteins of bacterial-ancestry previously used in various combinations to assess the branching order among the three major divisions of eukaryotes: Amorphea (mainly animals, fungi and Amoebozoa), Diaphoretickes (most other well-known eukaryotes and nearly all algae) and Excavata, represented here by Discoba (Jakobida, Heterolobosea, and Euglenozoa). ConJak analyses found strong outliers to be concentrated in under-sampled lineages, while ConWin analyses of Discoba, the most under-sampled of the major lineages, detected potentially incongruent fragments scattered throughout. Phylogenetic analyses of the full data using an LG-gamma model support a Discoba sister scenario (neozoan-excavate root), which rises to 99-100% bootstrap support with data masked according to either protocol. However, analyses with two site-specific (CAT) mixture models yielded widely inconsistent results and a striking sensitivity to missing data. The neozoan-excavate root places Amorphea and Diaphoretickes as more closely related to each other than either is to Discoba, a fundamental relationship that should remain unaffected by additional taxa.

opencc-by-4.0Sep 2022View details →

Results of SPOT surveys for tourists, residents and entrepreneurs in the case studies - dataset

This is a dataset of three surveys conducted within the scope of the SPOT project. The purpose of this dataset is to provide the results of the surveys for tourists, residents and entrepreneurs of the fifteen participating case studies.