cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.59zw3r29m
title: Time-series covering up to four decades reveals major changes and drivers of marine growth and proportion of repeat spawners in an Atlantic salmon population

description: 1. Wild Atlantic salmon populations have declined in many regions and are
 affected by diverse natural and anthropogenic factors. To facilitate
 management guidelines, precise knowledge of mechanisms driving population
 changes in demographics and life history traits is needed. 2. Our analyses
 were conducted on a) age and growth data from scales of salmon caught by
 angling in the river Etneelva, Norway, covering smolt year classes from
 1980 to 2018, b) extensive sampling of the whole spawning run in the fish
 trap from 2013 onwards, and c) time series of sea surface temperature,
 zooplankton biomass and salmon lice infestation intensity. 3. Marine
 growth during the first year at sea displayed a distinct stepwise decline
 across the four decades. Simultaneously, the population shifted from
 predominantly 1SW to 2SW salmon, and the proportion of repeat spawners
 increased from 3-7%. The latter observation most evident in females, and
 likely due to decreased marine exploitation. Female repeat spawners tended
 to be less catchable than males by anglers. 4. Depending on the
 time-period analysed, marine growth rate during the first year at sea was
 both positively and negatively associated with sea surface temperature.
 Zooplankton biomass was positively associated with growth while salmon
 lice infestation intensity was negatively associated with growth.
 Collectively these results are likely to be linked with both changes in
 oceanic conditions and harvest regimes. Our conflicting results regarding
 the influence of sea surface temperature on marine growth is likely to be
 caused by long-term increases in temperature which may have triggered (or
 coincided with) ecosystem shifts creating generally poorer growth
 conditions over time, but within shorter data sets warmer years gave
 generally higher growth. We encourage management authorities to expand the
 use of permanently monitored reference rivers with complete trapping
 facilities, like the river Etneelva, generating valuable long-term data
 for future analyses.
DOI: 10.5061/dryad.zs7h44jc2
title: The extrafollicular response is sufficient to drive initiation of autoimmunity and early disease hallmarks of lupus

description: Many autoimmune diseases are characterized by germinal center
 (GC)-derived, affinity-matured, class-switched autoantibodies, and
 strategies to block GC formation and progression are currently being
 explored clinically. However, extrafollicular responses can also play a
 role. The aim of this study was to investigate the contribution of the
 extrafollicular pathway to autoimmune disease development. We blocked the
 GC pathway by knocking out the transcription factor Bcl-6 in GC B cells,
 leaving the extrafollicular pathway intact. We tested the impact of this
 intervention in two murine models of systemic lupus erythematosus (SLE): a
 pharmacological model based on the chronic epicutaneous application of the
 Toll-like receptor (TLR)-7 agonist Resiquimod (R848), and 564Igi
 autoreactive B cell receptor knock-in mice. The B cell-intrinsic effects
 were further investigated in vitro and in autoreactive mixed bone marrow
 chimeras. GC block failed to curb autoimmune progression in the R848 model
 based on anti-dsDNA and plasma cell output, superoligomeric DNA complexes,
 and immune complex deposition in glomeruli. The 564Igi model confirmed
 this based on anti-dsDNA and plasma cell output. In vitro, loss of Bcl-6
 prevented GC B cell expansion and accelerated plasma cell differentiation.
 In a competitive scenario in vivo, B cells harboring the genetic GC block
 contributed disproportionately to the plasma cell output. We identified
 the extrafollicular pathway as a key contributor to autoimmune
 progression. We propose that therapeutic targeting of low-quality and
 poorly controlled extrafollicular responses could be a desirable strategy
 to curb autoreactivity, as it would leave intact the more stringently
 controlled and high-quality GC responses providing durable protection
 against infection.
description: Please see the README document ("README_file extrafollicular
 response is sufficient paper Voss LF et al 2022") and the
 accompanying published article: Voss LF et al. 2022. The extrafollicular
 response is sufficient to drive initiation of autoimmunity and early
 disease hallmarks of lupus. Frontiers in Immunology. Accepted. DOI:
 10.3389/fimmu.2022.1021370
DOI: 10.5061/dryad.s1rn8pk9p
title: Anther cones increase pollen release in buzz-pollinated Solanum flowers

description: The widespread evolution of tube-like anthers releasing pollen from apical
 pores is associated with buzz pollination, in which bees vibrate flowers
 to remove pollen. The mechanical connection among anthers in
 buzz-pollinated species varies from loosely held conformations, to anthers
 tightly held together with trichomes or bio-adhesives forming a
 functionally joined conical structure (anther cone). Joined anther cones
 in buzz-pollinated species have evolved independently across plant
 families and via different genetic mechanisms, yet their functional
 significance remains mostly untested. We used experimental manipulations
 to compare vibrational and functional (pollen release) consequences of
 joined anther cones in three buzz-pollinated species of Solanum
 (Solanaceae). We applied bee-like vibrations to focal anthers in flowers
 with (“joined”) and without (“free”) experimentally created joined anther
 cones, and characterised vibrations transmitted to other anthers and the
 amount of pollen released. We found that joined anther architectures cause
 non-focal anthers to vibrate at higher amplitudes than free architectures.
 Moreover, in the two species with naturally loosely held anthers, anther
 fusion increases pollen release, while in the species with a free but
 naturally compact architecture it does not. We discuss hypotheses for the
 adaptive significance of the convergent evolution of joined anther cones.
description: To measure the velocity of the vibrations applied and measured,
 we used a Doppler laser vibrometer (PDV-100, Polytec Ltd, Coventry, UK)
 set to 500mm/s maximum velocity and a Low Pass Filter at 22kHz. . The
 force applied by the shaker was simultaneously measured using the
 miniature force sensor. The signals of both the laser vibrometer and the
 force sensor were simultaneously acquired using a two-channel NI9250 Sound
 and Vibration module (NI Corporation (UK) Ltd, Newbury, UK) and a
 USB-powered data acquisition module (cDAQ-9171, NI). For each recorded
 vibration, we estimated the dominant frequency (Hz) and the RMS amplitude
 for both the velocity (mm/s) measured in the distal anther, and the force
 (mN) measured in the proximate anther. To estimate the number of pollen
 grains released after experimental buzzes, we used a particle counter
 (Multisizer 4e Coulter Counter, Indianapolis, USA).
DOI: 10.5061/dryad.4f4qrfjf1
title: Every day mitral valve reconstruction: what has changed over the last 15 years?

description: Mitral valve reconstruction (MVR) is one of the cardiosurgical procedures
 which cannot be substituted by any intervention owing to the quality of
 the quasi-anatomical, physiological repair. However, techniques and
 strategies have changed over the years. We looked at procedural
 characteristics and outcome in an all-comer, non-selected cohort of
 patients at our center. 738 out of 1977 patients were retrospectively
 analyzed receiving MVR with and without concomitant procedures at one
 center. The cohort was divided into three periods: P1: 2004-2009 (134
 patienst); P2: 2010-204 (294 patients); and P3 : 2015-1019 (310 patients).
 Clinical data from our own database were compiled. Demographic data,
 procedural characteristics, outcome data were compiled and case-wise
 organized (first row: Item-descriptions for respective columns).Statistics
 were performed: numerical data: Student's-t, Mann-Withney-U,
 Categorical data: Fisher, X², Cochrane Armitage, Risk-factor analyis,
 Kendall's Tau, Kaplan-Meier-Survival. The data set is strictly
 anonymized according to current European data protection law.
description: 15 years retrospective study, single center, clinical data,
 assessment of late survival, descriptive statistics, numerical data:
 Student's-t, Mann-Withney-U, Categorical data: Fisher,
 X<sup>2</sup>,  Cochrane-Armitage, Risk-factor analysis,
 Kendall's Tau, Kaplan-Meier-Survival Data are
 casewise (rows) organized. Demographic data and procedural items are
 organized in columns (see item-descrition in the first row).
 Note: no patient-sensitive information other than age and sex is
 provided due to restriction because of European data protection
 law.
description: Data are anonymized because they contain patient-sensitive data
 according to European data protection law
DOI: 10.5061/dryad.jsxksn0bt
title: Plastid phylogenomics shed light on intergeneric relationships and spatiotemporal evolutionary history of Melocanninae (Poaceae: Bambusoideae)

description: Melocanninae is sister to other subtribes of Paleotropical woody bamboos
 with some 90 species mainly concentrated in Asia. However, phylogenetic
 relationships within the subtribe are poorly known. Here, we filled the
 gaps in complete plastome data of Melocanninae, reconstructed the
 phylogeny of Melocanninae, and further estimated divergence time and
 ancestral distribution range. Our results showed that the two major
 genera, Cephalostachyum and Schizostachyum, were paraphyletic. Species of
 Cephalostachyum were resolved in two successive basal clades, while
 Annamocalamus was embedded in the Schizostachyum clade. Different plastid
 regions provided inconsistent signals for the relationship of Melocanna
 and Pseudostachyum. Conservative loci supported a successive divergence
 rather than sister relationship between them and the difference may be
 caused by long-branch attraction. We infer that Melocanninae originated in
 the East Himalaya to northern Myanmar in the early Miocene. Three routes
 were revealed in forming its present biogeographic pattern: in situ
 diversification on the Asian mainland; dispersing southwest to Sri Lanka
 and to the Western Ghats in South India; and spreading southeast to
 Malesia and Oceania via the Indo-China Peninsula. The rapid uplift of the
 Tibetan Plateau and the intensification of Asian monsoons since the
 Miocene and the sea-level-fall events since the late Miocene might be
 potential driving forces for diversification of Melocanninae and,
 particularly the latter event, for the species radiation of
 Schizostachyum.
DOI: 10.5061/dryad.3j9kd51m4
title: Alternative combinations of tillage practices and crop rotations can foster earthworm density and bioturbation

description: Earthworms, which contribute to important soil functions, suffer from
 intensive agriculture. Their response depends among other things on the
 earthworm ecological group (anecic, endogeic, epigeic) and the combination
 of the applied farming practices. To advice on methodological adaptations
 that enhance earthworm-mediated soil functions, effects of different
 practices on earthworms need to be studied in concert. We investigated the
 effects of tillage intensity (conventional, reduced, no tillage) and crop
 rotation diversity (simple = wheat, barley; diverse = wheat, peas, oil
 seed rape) on earthworm density and community composition in a Swedish
 long-term experiment. Furthermore, we calculated annual earthworm
 bioturbation to quantify the effects of farming practices on earthworm
 functions. Total earthworm densities did not vary between the different
 tillage intensities, but were on average 58% higher in the diverse than in
 the simple crop rotation. The pattern was mainly due to the response of
 the most abundant endogeic earthworms, which were not affected by tillage
 intensity, but were nearly two times more abundant in the diverse than in
 the simple crop rotation. Densities of anecic earthworms were 17 times
 higher under no tillage than conventional tillage. Anecic earthworms also
 benefitted from a diversified crop rotation, but the response depended on
 tillage intensity. The level of bioturbation reflected the response of
 anecic earthworms, and was more than four times higher under no tillage,
 549 g dw m -2 year -1, than under conventional tillage. We conclude that
 highest earthworm bioturbation is best achieved with no tillage. However,
 earthworm densities and potentially bioturbation can be increased also by
 a diversified crop rotation, when reducing tillage intensity is not
 feasible.
DOI: 10.5061/dryad.tqjq2bw1t
title: Re-surveys reveal biotic homogenization of Orthoptera assemblages as a consequence of environmental change

description: Aim: Biodiversity loss is a major global challenge. While population
 trends of vertebrates are well documented, insect declines have not been
 sufficiently studied and their drivers are still not fully understood.
 This inhibits the implementation of sensible conservation action.
 Repeating historical surveys can help to reveal the patterns and drivers
 of insect declines. Location: Central Europe Time period: 2018 to 2020
 Methods: We resurveyed 199 study sites in which Orthoptera assemblages had
 been recorded between 1986 and 1999. Results: Our results show a
 significant increase in species per site (α-diversity), but simultaneously
 a homogenization of Orthoptera assemblages (decreasing Sorensen’s
 β-diversity). Highly mobile species significantly increased in site
 occupancy compared to species with low mobility. Some Orthoptera species
 showed significant altitudinal range shifts, including species with
 positive trends (i.e. expansion to higher altitudes) and negative trends
 (i.e. extinction at lower altitudes). Abandonment of extensively used
 grassland sites and the associated afforestation had negative effects on
 Orthoptera, underlining the importance of extensive grassland management.
 Protected areas had a high efficacy for conservation as trends in site
 occupancy were generally more positive in protected areas than in
 unprotected sites. Main conclusions: Our results provide insights into the
 patterns and drivers of orthopteran assemblage turnover, including major
 effects of agricultural land use change and climate change. These results
 are essential for implementing or adapting conservation action, as they
 show that traditional land use practices and reduction of nitrogen input
 are important to preserve Orthoptera. Insect monitoring is crucial for
 understanding global and regional insect population trends and for
 preventing species extinctions. It is therefore critical to repeat
 historical surveys in order to understand global biodiversity change and
 implement the necessary actions.
DOI: 10.5061/dryad.612jm645d
title: Risk stratification and prognostic value of basic coagulation parameters among COVID-19 patients

description: Background: COVID-19 is a viral disease caused by a new strain of
 coronavirus. Currently, prognosis and risk stratification of COVID-19
 patients is done by the disease's clinical presentation. Therefore,
 identifying laboratory biomarkers for disease prognosis and risk
 stratification of COVID-19 patients is critical for prompt treatment.
 Therefore, the main objective of this study was to assess the risk
 stratification and prognostic value of basic coagulation parameters and
 factors associated with disease severity among COVID-19 patients,
 Northwest Ethiopia. Methods: A follow-up study was conducted among
 conveniently recruited COVID-19 patients attended from March to June 2021.
 Socio-demographic and clinical data were collected using a structured
 questionnaire and checklist, respectively. Prothrombin time (PT) and
 activated partial thromboplastin time (APTT) were analyzed by the HUMACLOT
 DUE PLUS® machine. Descriptive statistics were used to summarize the
 socio-demographic and clinical characteristics of study participants.
 Kruskal Wallis tests were used to compare the difference between
 parametric and non-parametric continuous variables, respectively. The area
 under the receiver operating characteristic curve (AUC) was used to
 evaluate the value of PT and APTT in the risk stratification and disease
 prognosis of COVID-19 patients. Ordinal logistic regression was used to
 identify the factors associated with disease severity and prognosis. A
 P-value &lt; 0.05 was defined as statistically significant for all
 results. Result: Baseline PT at a cut-off value ≥ 16.25 seconds
 differentiated severe COVID-19 patients from mild and moderate patients
 (AUC: 0.89, 95% CI: 0.83–0.95). PT also differentiated
 mild COVID-19 patients from moderate and severe patients at
 a cut-off value ≤ 15.35 seconds (AUC: 0.90, 95% CI:
 0.84–0.96). Moreover, alcohol drinkers were 3.52 times more likely chance
 of having severe disease than non-drinkers (95% CI: 1.41–8.81). A one-year
 increment in age also increased the odds of disease severity by 6% (95%
 CI: 3–9%). An increment of ≥ 0.65 seconds from the baseline PT predicted
 poor prognosis (AUC: 0.93, 0.87–0.99).   Conclusions and
 recommendations: Prolonged baseline PT was observed in severe COVID-19
 patients. Prolonged baseline PT was also predicted to worsen prognosis. An
 increase from the baseline PT was associated with worsen prognosis.
 Therefore, PT can be used as a risk stratification and prognostic marker
 in COVID-19 patients.
DOI: 10.5061/dryad.dv41ns211
title: Data from: Factors influencing dispersal initiation and timing in a facultative cooperative breeder

description: Natal dispersal is a high-risk endeavor where decisions on whether and
 when to disperse have long-term consequences. Among facultative
 cooperative breeders, juveniles often forego dispersal and remain
 philopatric for one or more breeding seasons. This decision is key to the
 formation of cooperative breeding groups and could have significant
 effects on reproductive success. We investigated the probability and
 initiation of dispersal in the cooperatively breeding Brown-headed
 Nuthatch (Sitta pusilla) to determine the influence that social
 environments had on dispersal. This study was concurrent with another
 study where manipulation of population sex ratios increased the prevalence
 and size of cooperative groups. The concurrent manipulations enabled us to
 evaluate social effects on dispersal as a plausible mechanism driving the
 relationship between adult sex ratios and cooperation. We evaluated which
 factors best predicted whether males dispersed, and the timing of
 dispersal for both sexes. We considered variables related to the immediate
 nesting environment as well as characteristics of the local population.
 Social environments were related to dispersal for both males and females.
 Juvenile males dispersed earlier when a helper was present in the natal
 group. Females dispersed earlier in settings with more adult neighbors and
 when a lower proportion of those neighbors were males. Females with
 shorter tarsi relative to their siblings dispersed earlier, suggesting
 that size-based competitive interactions may also affect dispersal
 decisions. Our results suggest juveniles disperse more readily when they
 fledge in constrained social environments, and that competition with
 conspecifics is a major driver of dispersal in the Brown-headed Nuthatch.
DOI: 10.5061/dryad.zpc866t9v
title: Data from: Looking for compensation at multiple scales in a wetland bird community

description: Compensatory dynamics, during which community composition shifts despite a
 near-constant total community size, are usually rare: synchronous dynamics
 prevail in natural communities. This is a puzzle for ecologists, because
 of the key role of compensation in explaining the relation between
 biodiversity and ecosystem functioning. However, most studies so far have
 considered compensation in either plants or planktonic organisms, so that
 evidence for the generality of such synchrony is limited. Here, we extend
 analyses of community-level synchrony to wetland birds. We analyse a
 35-year monthly survey of a community where we suspected that compensation
 might occur due to potential competition and changes in water levels,
 favouring birds with different habitat preferences. We perform both
 year-to-year analyses by season, using a compensation/synchrony index, as
 well as multiscale analyses using a wavelet-based measure, which allows
 for both scale- and time-dependence. We analyse synchrony both within and
 between guilds, with guilds defined either as tightknit phylogenetic
 groups or larger functional groups. We find that abundance and biomass
 compensation are rare, likely due to the synchronizing influence of
 climate (and other drivers) on birds, even after considering several
 temporal scales of covariation (during either cold or warm seasons, above
 or below the annual scale). Negative covariation in abundance at the guild
 or community level did only appear at the scale of a few months or several
 years. We also found that synchrony varies with taxonomic and functional
 scale: the rare cases where compensation appeared consistently in
 year-to-year analyses were between rather than within functional groups.
 Our results suggest that abundance compensation may have more potential to
 emerge between broad functional groups rather than between species, as
 well as at relatively long temporal scales (multiple years for
 vertebrates), above that of the dominant synchronizing driver.
description: Counts of birds were performed at the Teich Ornithological
 Reserve, Arcachon Bay, France (44.64°N / -1.02°E), by the staff of the
 Teich reserve, over the whole study period (1973-2016). The reserve
 comprises 120 ha of wetlands, and the counts have been aggregated at the
 reserve scale (summed over 18 sectors where the counts were performed) and
 the monthly scale using maximum observed abundance.
  
description: See description of data production and detailed methods at https://doi.org/10.5281/zenodo.6368332 (last deposited Zenodo version at https://doi.org/10.5281/zenodo.6367146 and up to date version at https://github.com/fbarraquand/BirdTimeSeries_Teich).<br><br>
DOI: 10.5061/dryad.vmcvdncvn
title: Trait-mediated competition drives an ant invasion and alters functional diversity

description: The assumption that differences in species’ traits reflect their different
 niches has long influenced how ecologists infer processes from assemblage
 patterns. For instance, many assess the importance of environmental
 filtering versus classical limiting-similarity competition in driving
 biological invasions by examining whether invaders’ traits are similar or
 dissimilar to those of residents, respectively. However, mounting evidence
 suggests that hierarchical differences between species’ trait values can
 distinguish their competitive abilities (e.g., for the same resource)
 instead of their niches. Whether such trait-mediated hierarchical
 competition explains invasions and structures assemblages is less
 explored. We integrate morphological, dietary, physiological and
 behavioural trait analyses to test whether environmental filtering,
 limiting-similarity competition, or hierarchical competition explain
 invasions by fire ants on ant assemblages. We detect both competition
 mechanisms; invasion success is not only explained by limiting similarity
 in body size and thermal tolerance (presumably allowing the invader to
 exploit different niches from residents), but also by the invader’s
 superior position in trait hierarchies reflecting competition for common
 trophic resources. We find that the two mechanisms generate complex
 assemblage-level functional diversity patterns (overdispersion in some
 traits, clustering in others) suggesting their effects are likely missed
 by analyses restricted to a few traits and composite trait diversity
 measures.