cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.417ft
title: Data from: Long-lasting insecticidal net use and asymptomatic malaria parasitaemia among household members of laboratory-confirmed malaria patients attending selected health facilities in Abuja, Nigeria, 2016: a cross-sectional survey

description: Introduction: In Nigeria, malaria remains a major burden. There is the
 presupposition that household members could have common exposure to
 malaria parasite and use of long-lasting insecticidal net (LLIN) could
 reduce transmission. This study was conducted to identify factors
 associated with asymptomatic malaria parasitaemia and LLIN use among
 households of confirmed malaria patients in Abuja, Nigeria. Methods: A
 cross-sectional survey was conducted from March to August 2016 in twelve
 health facilities selected from three area councils in Abuja, Nigeria.
 Participants were selected using multi-stage sampling technique. Overall,
 we recruited 602 participants from 107 households linked to 107 malaria
 patients attending the health facilities. Data on LLIN ownership,
 utilization, and house characteristics were collected using a
 semi-structured questionnaire. Blood samples of household members were
 examined for malaria parasitaemia using microscopy. Data were analyzed
 using descriptive statistics, Chi-square, and logistic regression
 (α=0.05). Results: Median age of respondents was 16.5 years (Interquartile
 range: 23 years); 55.0% were females. Proportions of households that owned
 and used at least one LLIN were 44.8% and 33.6%, respectively.
 Parasitaemia was detected in at least one family member of 102 (95.3%)
 index malaria patients. Prevalence of asymptomatic malaria parasitaemia
 among study participants was 421/602 (69.9%). No association was found
 between individual LLIN use and malaria parasitaemia (odds ratio: 0.9, 95%
 confidence interval (95%CI): 0.6-1.3) among study participants. Having
 bushes around the homes was associated with having malaria parasitaemia
 (adjusted OR (aOR): 2.7, 95%CI: 1.7-4.2) and less use of LLIN (aOR: 0.4,
 95%CI: 0.2-0.9). Living in Kwali (aOR: 0.1, 95% CI: 0.0-0.2) was
 associated with less use of LLIN. Conclusion: High prevalence of
 asymptomatic malaria and low use of LLIN among household members of
 malaria patients portend the risk of intra-household common source of
 malaria transmission. We recommend household health education on LLIN use
 and environmental management. Study to explore the role of preventive
 treatment of household members of confirmed malaria patient in curbing
 transmission is suggested. Strategies promoting LLIN use need to be
 intensified in Kwali.
description: LLIN use and malaria
 parasitemia in Abuja analysisThe data was collected
 in the field from household members of laboratory-confirmed malaria
 patients
DOI: 10.5061/dryad.3583v22
title: Data from: Natural history and survival in stage 1 Val30Met transthyretin familial amyloid polyneuropathy

description: Objectives: To assess natural history and treatment effect on survival
 among transthyretin-associated familial amyloid polyneuropathy (TTR-FAP)
 Val30Met patients. Methods: Multi-institutional, hospital-based study of
 TTR-FAP Val30Met patients prospectively followed-up until December 2016,
 grouped into untreated (n = 1,771), liver transplant (LTx) (n = 957) or
 tafamidis-treated (n = 432) cohorts. Standardized mortality ratios (SMR),
 Kaplan-Meier and Cox methods were used to estimate excess mortality,
 survival probabilities and adjusted hazard ratios (HR) for all-cause
 mortality, respectively. Results: Disease-modifying treatments decreased
 TTR-FAP excess mortality from ten to four (SMR 3.92, 95% CI 2.64–5.59).
 Median overall survival of untreated and LTx-treated cohorts was 11.61
 (95% CI 11.14–11.87) and 24.73 years (95% CI 22.90-27.09), respectively,
 and was not reached in the tafamidis-treated cohort (maximum follow-up, 10
 years). Both disease-modifying treatments improved survival. Among
 early-onset patients (&lt;50 years of age) tafamidis reduced the
 mortality risk compared with untreated patients by 91% (HR 0.09, 95% CI
 0.03–0.25, p &lt; 0.001) and with LTx-treated patients by 63% (HR
 0.37, 95% CI 0.14–1.00, p = 0.050). Previous tafamidis treatment did not
 affect mortality risk after LTx (HR 0.83, 95% CI 0.25-2.78, p = 0.763).
 Among late-onset patients (≥50 years), tafamidis reduced mortality risk by
 82% compared with untreated patients (HR 0.18, 95% CI 0.06-0.49, p =
 0.001). Conclusions: LTx and tafamidis convey substantial survival
 benefits, but TTR-FAP mortality remains higher than in the general
 population. These results strongly reinforce the importance of timely
 diagnosis and earlier treatment, boosting the pursuit for an increased
 life expectancy.
description: Table 1. Characteristics
 of patientsCharacteristics of
 patients with TTR-FAP in all cohorts.Dryad Table
 1.pdf
DOI: 10.5061/dryad.pd612qp
title: Data from: Using partial aggregation in Spatial Capture Recapture

description: 1. Spatial capture-recapture (SCR) models are commonly used for analyzing
 data collected using non-invasive genetic sampling (NGS). Opportunistic
 NGS often leads to detections that do not occur at discrete detector
 locations. Therefore, spatial aggregation of individual detections into
 fixed detectors (e.g. center of grid cells) is an option to increase
 computing speed of SCR analyses. However, it may reduce precision and
 accuracy of parameter estimations. 2. Using simulations, we explored the
 impact that spatial aggregation of detections has on a trade-off between
 computing time and parameter precision and bias, under a range of
 biological conditions. We used three different observation models: the
 commonly used Poisson and Bernoulli models, as well as a novel way to
 partially aggregate detections (Partially Aggregated Binary model (PAB))
 to reduce the loss of information after aggregating binary detections. The
 PAB model divides detectors into K subdetectors and models the frequency
 of subdetectors with more than one detection as a binomial response with a
 sample size of K. Finally, we demonstrate the consequences of aggregation
 and the use of the PAB model using NGS data from the monitoring of
 wolverine (Gulo gulo) in Norway. 3. Spatial aggregation of detections,
 while reducing computation time, does indeed incur costs in terms of
 reduced precision and accuracy, especially for the parameters of the
 detection function. SCR models estimated abundance with a low bias
 (&lt; 10%) even at high degree of aggregation, but only for the
 Poisson and PAB models. Overall, the cost of aggregation is mitigated when
 using the Poisson and PAB models. At the same level of aggregation, the
 PAB observation models out-performs the Bernoulli model in terms of
 accuracy of estimates, while offering the benefits of a binary observation
 model (less assumptions about the underlying ecological process) over the
 count-based model. 4. We recommend that detector spacing after aggregation
 does not exceed 1.5 times the scale-parameter of the detection function in
 order to limit bias. We recommend the use of the PAB observation model
 when performing spatial aggregation of binary data as it can mitigate the
 cost of aggregation, compared to the Bernoulli model.
description: WOLVERINE
 DATAThe
 "WOLVERINE.Rdata" file contains the Rdata necessary to run the
 wolverines males and females empirical example at the original grid cell
 size (2*2kms) with a Bernoulli model. The README.R file contains the R
 script and data description necessary to run the JAGS
 models.WOLVERINE.RdataSCR.BERNOULLI.PAB.WOLVERINEJAGS model file to run the wolverine analysis associated with the WOLVERINE.Rdata file.
DOI: 10.5061/dryad.54s81
title: Data from: Social status, immune response, and parasitism in males: a meta-analysis

description: In male vertebrates, two conflicting paradigms—the energetic costs of high
 dominance rank and the chronic stress of low rank—have been proposed to
 explain patterns of immune function and parasitism. To date, neither
 paradigm has provided a complete explanation for status-related
 differences in male health. Here, we applied meta-analyses to test for
 correlations between male social status, immune responses, and parasitism.
 We used an ecomimmunological framework, which proposes that males should
 re-allocate investment in different immune components depending on the
 costs of dominance or subordination. Spanning 297 analyses, from 77
 studies on several vertebrate taxa, we found that most immune responses
 were similar between subordinate and dominant males, and neither dominant
 nor subordinate males consistently invested in predictable immune
 components. However, subordinate males displayed significantly lower
 delayed-type hypersensitivity and higher levels of some inflammatory
 cytokines than dominant males, while dominant males exhibited relatively
 lower immunoglobulin responses than subordinate males. Despite few
 differences in immunity, dominant males exhibited consistently higher
 parasitism than subordinate males, including protozoan blood parasites,
 ectoparasites, and gastrointestinal helminths. We discuss our results in
 the context of the costs of dominance and subordination, and advocate
 future work that measures both parasitism and immune responses in wild
 systems.
description: Social status, immune
 response, and parasitismDataset used for a
 meta-analysis of the association between male social status and measures
 of immune response and parasitism across the vertebrate
 sub-phylum.Tests of Immunity
 Revised.xls
DOI: 10.5061/dryad.f3rk4
title: Data from: Ecology and life history affect different aspects of the population structure of 27 high-alpine plants

description: A plant species' genetic population structure is the result of a
 complex combination of its life history, ecological preferences, position
 in the ecosystem, and historical factors. As a result, many different
 statistical methods exist that measure different aspects of species’
 genetic structure. However, little is known about how these methods are
 interrelated and how they are related to a species’ ecology and life
 history. In this study, we used the IntraBioDiv AFLP-dataset from 27
 high-alpine species to calculate eight genetic summary statistics that we
 jointly correlate to a set of six ecological and life-history traits. We
 found that there is a large amount of redundancy among the calculated
 summary statistics and that there is a significant association with the
 matrix of species traits. In a multivariate analysis, two main aspects of
 population structure were visible among the 27 species. The first aspect
 is related to the species’ dispersal capacities and the second is most
 likely related to the species’ postglacial recolonisation of the Alps.
 Furthermore, we found that some summary statistics, most importantly
 Mantel’s r and Jost’s D, show different behaviour than expected based on
 theory. We therefore advise caution in drawing too strong conclusions from
 these statistics.
description: Data Meirmans et al
 IntrabioDivThis data package
 contains the genetic marker data (Amplified Fragment Length Polymorphisms)
 for 27 high-alpine species from the European Alps, as well as the
 geographic coordinates of every sampling location. The data have been
 collected as a part of the European research project IntraBioDiv, lead by
 Pierre Taberlet. For a complete list of members of the consortium see the
 included file "Consortium.pdf". The IntraBioDiv project was
 supported by the Commission of the European Union Sustainable Development,
 Global Change and Ecosystems Programme - GOCE-CT-2003-505376. We are
 grateful that the members of the IntraBioDiv consortium allowed us to use
 their data and make it available to the scientific
 community.
DOI: 10.5061/dryad.332dj
title: Data from: Determination of factors associated with natural soil suppressivity to potato common scab

description: Common scab of potatoes is a disease, which is difficult to manage due to
 complex interactions of the pathogenic bacteria (Streptomyces spp.) with
 soil, microbial community and potato plants. In Bohemian-Moravian
 Highlands in the Czech Republic two sites (Vyklantice and Zdirec) were
 selected for a study of common scab disease suppressivity. At both sites,
 a field with low disease severity occurs next to one with high severity
 and the situation was regularly observed over four decades although all
 four fields undergo a crop rotation. In the four fields, quantities of
 bacteria, actinobacteria and the gene txtB from the biosynthetic gene
 cluster of thaxtomin, the main pathogenicity factor of common scab, were
 analyzed by real-time PCR. Microbial community structure was compared by
 terminal fragment length polymorphism analysis. Soil and potato periderm
 were characterized by contents of carbon, nitrogen, phosporus, sulphur,
 calcium, magnesium, and iron. Quality of organic matter was assessed by
 high performance liquid chromatography of soil extracts. The study
 demonstrated that the suppressive character of the fields is locally
 specific. At Zdirec, the suppressivity was associated with low txtB gene
 copies in bulk soil, while at Vyklantice site it was associated with low
 txtB gene copies in the tuberosphere. The differences were discussed with
 respect to the effect of abiotic conditions at Zdirec and interaction
 between potato plant and soil microbial community at Vyklantice. Soil pH,
 Ca soil content or cation concentrations, although different were not in
 the range to predict the disease severity. Low severity of common scab was
 associated with low content of soil C, N, C/N, Ca and Fe suggesting that
 oligotrophic conditions may be favorable to common scab suppression.
description: Table S1. Chemical and
 biological properties of the bulk soil, potato tuberosphere and periderm
 at Vyklantice site.TableS1_Vyklantice.xlsxTable S2. Chemical and biological properties of the bulk soil, potato tuberosphere and periderm at Zdirec site.TableS2_Zdirec.xlsxTable S3. Common scab severity.TableS3_Common_scab_severity.xlsxTable S4. T-RFLP profiles of actinobacterial communities in the bulk soil and potato tuberosphere at Vyklantice site.TableS4_TRFLP_Vyklantice_soil.xlsxTable S5. T-RFLP profiles of actinobacterial communities in potato periderm at Vyklantice site.TableS5_TRFLP_Vyklantice_periderm.xlsxTable S6. T-RFLP profiles of actinobacterial communities in the bulk soil and potato tuberosphere at Zdirec site.TableS6_TRFLP_Zdirec_soil.xlsxTable S7. T-RFLP profiles of actinobacterial communities in potato periderm at Zdirec site.TableS7_TRFLP_Zdirec_periderm.xlsxTable S8. HPLC profiles of extractable low-molecular-weight substances in the bulk soil and potato tuberosphere.TableS8_HPLC_VyklanticeZdirec_soil.xlsx
DOI: 10.5061/dryad.g983j23
title: Data from: Shared environmental effects bias phenotypic estimates of assortative mating in a wild bird

description: Assortative mating is pervasive in wild populations and commonly described
 as a positive correlation between the phenotypes of males and females
 across mated pairs. This correlation is often assumed to reflect
 non-random mate choice based on phenotypic similarity. However, phenotypic
 resemblance between mates can also arise when their traits respond
 plastically to a shared environmental effect creating a (within-pair)
 residual correlation in traits. Using long-term data collected in pairs of
 wild blue tits and a covariance partitioning approach, we empirically
 demonstrate that such residual covariance indeed exists and can generate
 phenotypic correlations (or mask assortative mating) in behavioural and
 morphometric traits. These findings i) imply that residual covariance is
 likely to be common and bias phenotypic estimates of assortative mating,
 which can have consequences for evolutionary predictions, ii) call for the
 use of rigorous statistical approaches in the study of assortative mating,
 and iii) show the applicability of one of these approaches in a common
 study system.
description: Morphometric and
 behavioural data collected in blue tit pairs (7 traits)Data collected in a wild
 population blue tits breeding in South-western Finland between 2003 and
 2017. The names of males' and females' traits end, respectively
 with "_m" and "_f". Wing, tarsus, head-bill (Head) and
 tail lengths are in mm and weight is in g. Handling aggression
 (Aggression) is on a 1-5 scale and breath rate (BR) is expressed as a
 number of breaths per second. The birds' age at the time of
 measurement is in years.Data_BT_7traits_19618.csvDefence data collected in wild blue titsBehavioural data collected from 2007 to 2017 in a wild population of blue tits breeding in South-western Finland. The number of times males and females attacked an observer during a 2 minutes test is reported, respectively in the columns"Nr_attacks_m" and "Nr_attacks_f". The square root of this number ("Attacks_m" and "Attacks_f".) was used for our analyses.The birds' age at the time of measurement is in years.Data_BT_Defence.csv
DOI: 10.5061/dryad.808p0
title: Data from: Towards a general perspective on life-history evolution and diversification in parasitoid wasps

description: In attempting to explain the marked interspecific variation evident in
 many components of life-history in parasitoid wasps, biologists have
 sought to identify general predictors of suites of ‘important’
 life-history traits. Two predictors currently in general use are: (1) the
 parasitoid mode of larval development in relation to future host growth
 and development [no further host growth and development (= idiobiosis)
 versus continued host growth and development (= koinobiosis)]; and (2) the
 ovigeny index (the degree to which the lifetime potential complement of
 eggs is mature at the start of adult life in females). These have been
 postulated to share several life-history correlates, and an earlier
 comparative analysis showed the predictors to be associated. Two questions
 are thus posed: which life-history variables are actually common to both
 idio/koinobiosis and the ovigeny index, and which are responsible for the
 link between these two axes of life-history diversity? Through comparative
 analyses of a database of life-history traits for 133 parasitoid wasp
 species, four life-history correlates out of the 11 we investigated are
 shown to account for the association between the two predictors: the
 relative level of resource investment per egg (degree of yolk richness,
 which is lower in koinobionts), pre-adult lifespan (longer in
 koinobionts), female lifespan (shorter in koinobionts), and maximum egg
 load (larger in koinobionts). Our findings pave the way for full
 integration of the dichotomous hypothesis with the ovigeny index
 hypothesis, to provide a holistic perspective on parasitoid wasp
 life-history diversity and evolution.
description: Life history parameters
 in parasitoid HymenopteraThe dataset comprises an
 Excel file including the taxonomy, phylogeny, and life history parameters
 (along with the independent contrasts of their untransformed values) of
 133 species of hymenopteran parasitoids.OI.xls
DOI: 10.5061/dryad.ps4m1
title: Data from: On the evolutionary consequences of increasing litter size with multiple paternity in wild boar (Sus scrofa scrofa)

description: Understanding how some species may be able to evolve quickly enough to
 deal with anthropogenic pressure is of prime interest in evolutionary
 biology, conservation and management. Wild boar (Sus scrofa scrofa)
 populations keep growing all over Europe despite increasing hunting
 pressure. In wild boar populations subject to male-selective harvesting,
 the initially described polygynous mating system may switch to a
 promiscuous/polyandrous one. Such a change in the mating system, where
 potentially more males sire a litter at one reproductive event, may be
 associated with the retention of high genetic diversity and an increase of
 litter size. We tested these hypotheses by estimating the number of sires
 per litter based on a 6-year long monitoring of a wild boar population
 subject to particularly high harvesting pressure. Our results show a high
 and stable genetic diversity and high rates of multiple paternity compared
 to other populations, thus depicting a promiscuous/polyandrous mating
 system in this population. We also show that litter size is positively
 linked to the number of sires, suggesting that multiple paternity
 increases fecundity. We finally discuss that multiple paternity may be one
 of the factors allowing rapid evolution of this population by maintaining
 both genetic and phenotypic diversity.
description: Wild boar population,
 sex, age, weigh, litter size, maximal number of paternal allele, number of
 father estimated with Gerud, number of father estimated with Cervus, ID of
 father identified by CervusONCFS_Gayet_et_al1.xlsxWild boar genotypesONCFS_Gayet_et_al2.xlsx
DOI: 10.5061/dryad.2g5f9
title: Data from: Benthic communities under anthropogenic pressure show resilience across the Quaternary

description: The Southeast Pacific is characterized by rich upwelling systems that have
 sustained and been impacted by human groups for at least 12 ka. Recent
 fishing and aquaculture practices have put a strain on productive coastal
 ecosystems from Tongoy Bay, in north-central Chile. We use a temporal
 baseline to determine whether potential changes to community structure and
 composition over time are due to anthropogenic factors, natural climatic
 variations or both. We compiled a database (n = 33 194) with mollusc
 species abundances from the Mid-Pleistocene, Late Pleistocene, Holocene,
 dead shell assemblages and live-sampled communities. Species richness was
 not significantly different, neither were diversity and evenness indices
 nor rank abundance distributions. There is, however, an increase in
 relative abundance for the cultured scallop Argopecten, while the
 previously dominant clam Mulinia is locally very rare. Results suggest
 that impacts from both natural and anthropogenic stressors need to be
 better understood if benthic resources are to be preserved. These findings
 provide the first Pleistocene temporal baseline for the south Pacific that
 shows that this highly productive system has had the ability to recover
 from past alterations, suggesting that if monitoring and management
 practices continue to be implemented, moderately exploited communities
 from today have hopes for recovery.
description: Supp material_Martinelli
 et al.Supplementary Figures
 and TablesMartinelli et
 al._OpSciR Code for plots and
 analysessize_tongoySize data for Argopecten and MuliniaTB_DADead shell assemblage community dataTB_HOLHolocene assemblage community dataTB_Live122012 live community dataTB_Live911991 live community dataTB_LPLate Pleistocene assemblage community dataTB_MPMid Pleistocene assemblage community data