cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jwstqjq82
title: Effects of high and low-efficacy therapy in secondary progressive multiple sclerosis

description: Objective: To compare
 the clinical effectiveness of high- and low-efficacy
 treatments in patients with recently active and inactive secondary
 progressive multiple sclerosis (SPMS) after accounting for therapeutic
 lag. Methods: Patients treated with high- (natalizumab,
 alemtuzumab, mitoxantrone, ocrelizumab, rituximab, cladribine, fingolimod)
 or low-efficacy (interferon β, glatiramer acetate, teriflunomide)
 therapies after SPMS onset were selected from MSBase and OFSEP, two large
 observational cohorts. Therapeutic lag was estimated for each patient
 based on their demographic and clinical
 characteristics.  Propensity score was used to match
 patients treated with high and low-efficacy
 therapies.  Outcomes after disregarding the period of
 therapeutic lag were compared in paired, pairwise-censored analyses.
 Results: 1000 patients, 510 with active and 490 with inactive
 SPMS, were included in the primary analysis.  Patients
 with active SPMS treated with high-efficacy therapy experienced less
 frequent relapses than those on low-efficacy therapy (hazard ratio [HR]
 0.7, p=0.006).  In patients with inactive SPMS, there
 was no evidence for a difference in relapse number between groups
 (HR=0.8,p=0.39).  No difference in the risk of
 disability progression was observed. Conclusion: In treated
 patients with SPMS, high-efficacy therapy is superior to low-efficacy
 therapy in reducing relapses in patients with active, but not those with
 inactive, SPMS. However, more potent therapies do not offer an advantage
 in reducing disability progression in this patient group. Classification
 of Evidence: This study provides class III evidence that
 high-efficacy therapy is superior to low-efficacy therapy in reducing
 relapses in patients with active SPMS whilst disability progression is
 comparable between patients treated with high- and low-efficacy therapy.
DOI: 10.5061/dryad.vdncjsxt5
title: The effect of gold quantum dots/grating-coupled surface plasmons in inverted organic solar cells

description: We studied the effect of gold quantum dots (AuQDs)/grating-coupled surface
 plasmon resonance (GC-SPR) in inverted organic solar cells (OSCs). AuQDs
 are located within a GC-SPR evanescent field in inverted OSCs, indicating
 an interaction between GC-SPR and AuQDs’ quantum effects, subsequently
 giving rise to improvement in the performance of inverted OSCs. The
 fabricated solar cell device comprises an
 ITO/TiO2/P3HT:PCBM/PEDOT:PSS:AuQD/silver grating structure. The AuQDs were
 loaded into a hole transport layer (PEDOT:PSS) of the inverted OSCs to
 increase absorption in the near-ultraviolet (UV) light region and to emit
 visible light into the neighboring photoactive layer, thereby achieving
 light-harvesting improvement of the device. The grating structures were
 fabricated on P3HT:PCBM layers using a nanoimprinting technique to induce
 GC-SPR within the inverted OSCs. The AuQDs incorporated within the
 strongly enhanced GC-SPR evanescent electric field on metallic
 nanostructures in the inverted OSCs improved the short-circuit current and
 the efficiency of photovoltaic devices. In comparison with the reference
 OSC and OSCs with only green AuQDs or only metallic grating, the developed
 device indicates enhancement of up to 16% power conversion efficiency.
 This indicates that our light management approach allows for greater light
 utilization of the OSCs because of the synergistic effect of G-AuQDs and
 GC-SPR.
DOI: 10.5061/dryad.9s4mw6mfp
title: Incubation temperature as a constraint on clutch size evolution

description: 1. Elucidating factors that limit the number of offspring produced is
 fundamental to understanding life-history evolution. Here, we examine the
 hypothesis that parental ability to maintain an optimal physical
 developmental environment for all offspring constrains clutch size via
 effects on offspring quality. 2. Experimental laboratory studies of birds
 have shown that a &lt;1°C difference in average incubation temperature
 has diverse effects on fitness-related post-hatching offspring phenotypes.
 Thus, the inability of parents to maintain optimal incubation temperatures
 could constrain clutch sizes. 3. A fundamental question that has not been
 sufficiently addressed is whether larger clutch sizes lead to within nest
 variation in egg temperature that is large enough to produce offspring
 with different phenotypes within a brood. This could lead to differential
 survival among offspring, and could create a tradeoff between offspring
 number and quality. 4. We manipulated clutch size in nests of free-living
 wood ducks and measured incubation temperature among and within clutches
 using multiple temperature loggers. 5. As clutch size increased, average
 incubation temperatures were lower and more variable, and eggs took longer
 to hatch. Notably, the range in average incubation temperature among eggs
 within nests increased with clutch size and exceeded 1°C in large
 clutches. 6. Clutch size did not affect hatch success. In conjunction with
 our companion laboratory studies that used artificial incubation to
 document the effects of temperature variation on fitness-related traits in
 this species, our work suggests that suboptimal incubation temperatures
 could be a factor that limits clutch size through diminishing returns on
 post-hatch offspring quality.
description: The methods used to collect this dataset and data processing
 information can be found in the manuscript. 
description: 1. Clutch size includes the artificial egg temperature loggers 2. The average incubation temperature was calculated as the average of the average temperatures of the six mobile loggers  3. The temperature fluctuation was the average of the standard deviations in temperature of the six mobile loggers  4. The range in temperature among eggs was the range of the average temperatures (highest – lowest) of the six mobile loggers 5. The standard deviation in temperature among eggs within nests was calculated at the standard deviation among the average temperatures of the six mobile loggers 6. The number of eggs dumped after incubation started were new eggs there were found in the nest after incubation had started. This indicated that they were laid by a brod parasite. Thus, they were not included in the calculation of hatch success
DOI: 10.5061/dryad.z612jm6bd
title: Data from: Homoploid F1 hybrids and segmental allotetraploids of japonica and indica rice subspecies show similar and enhanced tolerance to N deficiency than parental lines

description: The datasets were generated to compare the phenotypic performance of two
 diploid rice subspecies indica and japonica (Oryza sativa L.) with the
 derived homoploid F1 hybrids (9N and N9) and segmental allopolyploids
 (99NN and NN99) under normal and low nitrogen conditions. Total gene
 expressions of 18 genes in critical growth-related pathways along with
 genotyping data by Sequenom MassARRAY of the plant groups were also
 involved to reveal the molecular rationale behind the morphological and
 physiological observations. The data were collected at the population
 level and falls into mainly 3 parts including i) phenotype (morphology and
 physiology) measurements for above and underground parts of the plants
 under normal and low-nitrogen conditions; ii) qRT-PCR quantification of
 the 18 involved genes by ΔΔCT method, and iii) genotyping dataset
 generated from Sequenom MassARRAY platform. The study shows that both
 hybridization and whole-genome duplication can confer rice better
 tolerance to low nitrogen conditions.
description: Regular phenotype measurement and qRT-PCR were carried out and
 genotyping data were obtained by the Sequenom MassARRAY platform. Detail
 can be seen in the M&M section of the study.
description: The total expression of the gene "Chl-7" by qRT-PCR in
 9N and N9 under N-limiting conditions were failed to be quantified; some
 other data points in total gene expression and genotyping datasets are
 missing. The instruction of the datasets can be found in
 Readme.txt.
DOI: 10.5061/dryad.pg4f4qrnn
title: Data from: Re-evaluation of the law of constant extinction for ruminants at different taxonomical scale

description: The “law of constant extinction,” proposed by Van Valen, states
 that long and short-lived taxa have equal chances of going extinct. This
 pattern of age-independent extinction was originally inferred using the
 fossil record of several different taxa and relied on survivorship curves
 built from the literal reading of the fossil record. Van Valen’s seminal
 work was mostly done at higher taxonomic levels, hence its prevalence at
 the species level could not be directly inferred. The surprisingly few
 subsequent studies done at the species level have challenged the
 prevalence of age-independent extinction, but those have, for the most
 part, failed to explicitly incorporate inherent biases of the fossil
 record. Using a recent Bayesian framework that accounts for several of
 those biases, including the fact that very short-living lineages might
 never make to the record itself, we showed that Ruminantia species present
 age-dependent extinction, where extinction probability decreases with
 species age. An analysis at the genus level suggested age-independent
 extinction but further examination suggested that the pattern might be
 more complex than previously reported by Van Valen. Our results indicate
 that different taxonomic levels may present different extinction regimes,
 which could justify the development of new macroevolutionary theory and
 methods.
DOI: 10.5061/dryad.931zcrjjg
title: Synthesis, characterization and CO2 adsorption studies of DABCO based pillared Zn-BDC and Co-BDC metal organic frameworks

description: This study focuses on pre-synthetic functionalized MOF material normally
 known as pillared layer MOFs. An additional component DABCO
 (1,4-diazabicyclo[2.2.2] octane) is added to the MOFs which works as a
 pillar to produce 3d structured MOFs. Zn-BDC-DABCO and Co-BDC-DABCO were
 studied for their performance in CO2 capture application. The addition of
 DABCO turns the 2d-layered metal-BDC lattice to a 3d structure with
 enhance performance for CO2 capture. The MOFs were characterized using
 XRD, SEM, TGA, FTIR and BET and the CO2 capture capacity was tested at
 25°C and 0-25 bar. Zn-BDC-DABCO and Co-BDC-DABCO showed a maximum
 adsorption capacity of 6.3 and 4.4 mol/kg CO2.
description: BET dataset.
DOI: 10.5061/dryad.x3ffbg7hr
title: Data from: Primary progressive aphasias and GRN mutations

description: Objective: To determine relative frequencies and linguistic profiles of
 primary progressive aphasia (PPA) variants associated with progranulin
 (GRN) mutations, and study their neuroanatomical correlates.
 Methods: PPA patients carrying GRN mutations (PPA-GRN) were
 selected amongst a national prospective research cohort of 1,696
 frontotemporal dementia (FTD) patients, including 235 patients with PPA.
 All PPA patients with amyloid-positive CSF biomarkers were excluded. In
 this cross-sectional study, speech/language and cognitive profiles were
 characterized with standardized evaluations, and grey matter (GM) atrophy
 patterns using voxel-based morphometry. Comparisons were performed with
 controls, and sporadic PPA patients. Results: Among the overall
 population of 235 patients, 45 (19%) carried GRN mutations. We studied 32
 of these and showed that logopenic PPA (lvPPA) was the most frequent
 linguistic variant (13, 41%), followed by non-fluent/agrammatic (nfvPPA:
 9, 28%) and mixed forms (8, 25%). Semantic variant was rather rare (2,
 6%). LvPPA patients, qualified as non-amyloid-lvPPA, presented canonical
 logopenic deficit. Seven out of 13 had a pure form, six showed subtle
 additional linguistic deficits not fitting criteria for mixed PPA, hence
 labelled as “logopenic-spectrum variant”. GM atrophy primarily involved
 left posterior temporal gyrus, mirroring neuroanatomical changes of
 amyloid-positive-lvPPA. NfvPPA patients presented agrammatism (89%) rather
 than apraxia of speech (11%). Conclusions: This study shows that
 most frequent PPA variant associated with GRN mutations is non-amyloid
 lvPPA, preceding nfvPPA and mixed forms, and illustrates that language
 network may be affected at different levels. GRN testing is indicated for
 PPA patients, whether familial or sporadic. This finding is important for
 upcoming GRN gene-specific therapies.
DOI: 10.5061/dryad.pnvx0k6m1
title: Data from: Model-based ordination for species with unequal niche widths

description: It is common practice for ecologists to examine species niches in the
 study of community composition. The response curve of a species in the
 fundamental niche is usually assumed to be quadratic. The center of a
 quadratic curve represents a species' optimal environmental
 conditions, and the width its ability to tolerate deviations from the
 optimum. Most multivariate methods assume species respond linearly to the
 environment of the niche, or with a quadratic curve that is of equal width
 for all species. However, it is widely understood that some species are
 generalists that can tolerate deviations from their optimal environment
 better than others. Rare species often tolerate a smaller range of
 environments than more common species, corresponding to a narrow
 niche.  We propose a new method, for ordination and fitting Joint
 Species Distribution Models, based on Generalized Linear Mixed-Effects
 Models, which relaxes the assumptions of equal tolerances. By explicitly
 estimating species maxima, and species optima, and tolerances per
 ecological gradient, we can better understand how species relate to each
 other.
description: This elevation data was provided by the Spatial Ecology Group at
 the University of Lausanne, specifically by Manuela D'Amen, and
 originally comes from the Swiss Federal Office of Topography.
DOI: 10.5061/dryad.kwh70rz31
title: Tourism and urban development as drivers for invertebrate diversity loss on tropical islands

description: Oceanic islands harbour a disproportionately high number of endemic and
 threatened species. Rapidly growing human populations and tourism are
 posing an increasing threat to island biota, yet the ecological
 consequences of these human land uses on small oceanic island systems have
 not been quantified. Here, we investigated and compared the impact of
 tourism and urban island development on ground-associated invertebrate
 biodiversity and habitat composition on oceanic islands. To disentangle
 tourism and urban land uses, we investigated Indo-Pacific atoll islands,
 which either exhibit only tourism or urban development, or remain
 uninhabited. Within the investigated system, we show that species
 richness, abundance, and Shannon diversity of the ground-associated
 invertebrate community are significantly decreased on islands used for
 tourism and on islands with urban development, relative to uninhabited
 islands. Remote-sensing-based spatial data suggests that habitat
 fragmentation and a reduction in vegetation density are having significant
 effects on biodiversity on urban islands, whereas land use/ cover changes
 could not be linked to the documented biodiversity loss on tourist
 islands. This offers first direct evidence for a major terrestrial
 invertebrate loss on remote oceanic islands due to different human land
 uses with yet unforeseeable long-term consequences for the stability and
 resilience of oceanic island ecosystems.
DOI: 10.5061/dryad.51c59zw7d
title: Automated, high-throughput image calibration for parallel-laser photogrammetry

description: This contains the data required to recreate the analyses in this paper.
 The code for performing the machine learning and image processing methods
 presented in the paper are available as supplemental files to the
 manuscript, and are also available
 at https://github.com/ejlevy/Photogrammetry_Coding_InterLaser_Distance. Paper abstract: Parallel-laser photogrammetry is growing in popularity as a way to collect non-invasive body size data from wild mammals. Despite its many appeals, this method requires researchers to hand-measure (i) the pixel distance between the parallel laser spots (inter-laser distance) to produce a scale within the image, and (ii) the pixel distance between the study subject’s body landmarks (inter-landmark distance). This manual effort is time-consuming and introduces human error: a researcher measuring the same image twice will rarely return the same values both times (resulting in within-observer error), as is the case when two researchers measure the same image (resulting in between-observer error). Here, we present two independent methods that automate the inter-laser distance measurement of parallel-laser photogrammetry images. One method uses machine learning and image processing techniques in Python, and the other uses image processing techniques in ImageJ. Both of these methods reduce labor and increase precision without sacrificing accuracy. We first introduce the workflow of the two methods. Then, using two parallel-laser datasets of wild mountain gorilla and wild savannah baboon images, we validate the precision of these two automated methods relative to manual measurements and to each other. We also estimate the reduction of variation in final body size estimates in centimeters when adopting these automated methods, as these methods have no human error. Finally, we highlight the strengths of each method, suggest best practices for adopting either of them, and propose future directions for the automation of parallel-laser photogrammetry data. 
description: Data represent measurements taken of images of baboons and
 gorillas collected in Amboseli National Park and Bwindi Impenetrable
 National Park, respectively. Images were collected by photographing study
 animals while parallel lasers were projecting onto the animal. These
 images were then processed to measure the distance, in pixels, between the
 laser spots in the image. These measurements were taken in one of three
 ways: manually, with the ImageJ method, and with the skimage
 method.
description: Missing values are expected.
DOI: 10.5061/dryad.x0k6djhhn
title: Extirpated prairie species demonstrate more variable phenological responses to warming than extant congeners

description: Premise of the study. Shifting phenology in response to climate is one
 mechanism that can promote population persistence and geographic spread;
 therefore, species with limited ability to phenologically track changing
 environmental conditions may be more susceptible to population declines.
 Alternatively, apparently, nonresponding species may demonstrate divergent
 responses to multiple environmental conditions experienced across seasons.
 Methods. Capitalizing on herbarium records from across the Midwestern
 United States and detailed botanical surveys documenting local extinctions
 over the past century, we investigate whether extirpated and extant taxa
 differ in their phenological responses to temperature and precipitation
 experienced during winter and spring (during flowering and the growing
 season prior to flowering) or in their magnitude of flowering time shift
 over the past century. Key results. Although warmer temperatures across
 seasons advanced flowering, extirpated and extant species differed in the
 magnitude of their phenological responses to winter and spring warming.
 Extirpated species demonstrated inconsistent phenological responses to
 warmer spring temperatures. Meanwhile, extant species consistently
 advanced flowering in response to warmer spring temperatures. In contrast,
 extirpated species advanced flowering more than extant species in response
 to warmer winter temperatures. Greater spring precipitation tended to
 delay flowering for both extirpated and extant taxa. Finally, both
 extirpated and extant taxa delayed flowering over time. Conclusions. This
 study highlights the importance of understanding phenological responses to
 seasonal warming and indicates that extirpated species may demonstrate
 more variable phenological responses to temperature than extant congeners,
 a finding consistent with the hypothesis that appropriate phenological
 responses may reduce species’ likelihood of extinction.
description: See Phenology and local extinction_README.docx
DOI: 10.5061/dryad.ncjsxkstf
title: Drought-driven wildfire impacts on structure and dynamics in a wet Central Amazonian forest

description: While climate and human-induced forest degradation is increasing in the
 Amazon, fire impacts on forest dynamics remain understudied in the wetter
 regions of the basin, which are susceptible to large wildfires only during
 extreme droughts. To address this gap, we installed burned and unburned
 plots immediately after a wildfire in the northern Purus-Madeira (central
 Amazon) during the 2015 El-Niño. We measured all individuals ≥10cm in
 diameter at breast height, and conducted recensuses to track the
 demographic drivers of biomass change over three years. We also assessed
 how stem-level growth and mortality were influenced by fire intensity
 (proxied by char height) and tree morphological traits (size and wood
 density). Overall, the burned forest lost 27.3% stem density and 12.8%
 biomass, concentrated in small and medium trees. Mortality drove these
 losses in the first two years and recruitment decreased in the third year.
 Fire increased growth in lower wood-density and larger-sized trees, while
 char height had transitory strong effects increasing tree mortality. Our
 findings suggest that fire impacts are weaker in the wetter Amazon. Here
 trees of greater sizes and higher wood densities may confer a margin of
 fire resistance; however, this may not extend to higher-intensity fires
 arising from climate change.
DOI: 10.5061/dryad.4b8gthtbn
title: Mountain Bluebird Colour and Temperature Data

description: Birds exhibit a vast array of colours and ornaments and while much work
 has focused on understanding the function and evolution of carotenoid-
 based colours (red, orange, yellow), structural colouration (blue, green,
 purple, iridescent) can also play a key role in sexual signaling. Several
 studies have examined how factors such age may influence structural
 colour, however few studies have looked at how structural colour may be
 influenced by environmental conditions such as variation in weather
 conditions experienced during moult. In this study, we examined variation
 in structural colour expression in relation to age as well as rainfall and
 temperature during post-breeding moult for a population of Mountain
 Bluebirds (Sialia currucoides) in Western Canada over nine breeding
 seasons. Overall, we found structural colouration was explained by sex,
 age, and weather patterns during moult. At a population level, tail and
 rump feathers from males were more colourful (higher brightness and
 chroma, hue values shifted more towards UV) than females, and adults were
 more colourful than juvenals. Male and female rump feathers generally
 became less colourful with age. Noise-receptor colour models revealed
 colour differences were discernible among sexes, suggesting bluebird
 colouration is an important sexual signal. Tail and rump plumage variation
 was associated with weather during moulting periods, though the effects
 were sex- and age-dependent. Female plumage was generally more colourful
 following wetter and warmer early summers, while males were more colourful
 following warmer late summers, and plumage of older birds was more
 resilient to colour variation due to weather patterns. We suggest that
 more rainfall may increase insect abundance and thus improve food intake
 and overall condition of Mountain Bluebirds. This is one of the first
 studies to examine how both age and weather conditions concurrently
 influence the expression of structural colours in birds.