cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j9kd51ccn
title: Transcript expression data. Environmental responsiveness of flowering time in cassava genotypes and associated transcriptome changes

description: To advance understanding of the mechanistic factors regulating cassava
 flowering, the leaf transcriptomes at 1) two stages of plant development
 were compared in two genotypes at Ubiaja and Ibadan, Nigeria; and 2) three
 controlled-environment growth chambers.
description: For the first data set, three biological replicates were analyzed
 for two locations, two genotypes, and two stages of plant development. 
 Field experiments were conducted from June 2017 to January 2018 at two
 field stations in Nigeria: Ibadan (7.4° N and 3.9°E, 230 m asl) in Oyo
 State and Ubiaja (6.6° N and 6.4° E, 221 m asl) in Edo State.  At each
 location the land was tilled and ridged with no extra nutrients or soil
 amendments added. Fields were kept free of weeds with hand weeding. 
 Cassava stem cuttings of similar lengths (about 20 cm each), were planted
 simultaneously in June 17, 2017 at both locations. For the second data set
 in controlled-environment growth chambers, three biological replicates
 were analyzed for three temperatures, three genotypes, and two stages of
 plant development.  Plants were grown in three growth chambers set at
 22°C/18°C, 28°C/24°C, and 34°C/30°C, day/ night temperatures,
 respectively. Photoperiod was held constant at 12 h light and 12 h dark.  
 Growth chambers were Conviron Controlled Environments, Ltd (Winnipeg,
 Manitoba, Canada) model PGW 36 walk-in growth rooms (135 X 245 X 180 cm
 [ht.]) with ten 400 W high pressure sodium and ten 400 W metal halide
 lamps providing about 600 μmol photons (400-700 nm) m-2 s-1 at 1 m above
 the soil surface. RNA extraction:  In brief (see
 published paper for details): total RNA was extracted from each sample by
 a modified CTAB protocol. Samples were ground to a fine powder in a mortar
 and pestle chilled with liquid N2;  chloroform was added, mixed, 
 centrifuged and the top layer was used.  Samples were purified on silica
 RNA columns and eluted with RNAase-free water.  3 ́RNA-seq libraries were
 prepared  at the Cornell Genomics facility using the Lexogen QuantSeq
 3’ mRNA-Seq Library Prep Kit FWD.  See published paper for details.  The
 libraries were quantified with the intercalating dye QuantiFluor, evenly
 pooled sequenced on one lane of an Illumina NextSeq500 sequencer,
 single-end 1x86bp de-multiplexed based upon six base i7 indices using
 Illumina bcl2fastq2 software (version 2.18; Illumina, Inc., San Diego,
 CA).   Illumina adapters were removed from the de-multiplexed fastq files
 using Trimmomatic (version 0.36; Bolger et al. 2014). Poly-A tails and
 poly-G stretches of at least 10 bases in length were then removed keeping
 reads at least 18 bases in length after trimming The trimmed reads were
 aligned to the Manihot esculenta genome assembly 520_v6
 (https://genome.jgi.doe.gov) using the STAR aligner (version 2.7.0f;
 (Dobin et al., 2012)).   Matrix table with raw gene counts for every gene
 and every sample.
description: Metadata are provided in the uploaded file.
DOI: 10.5061/dryad.b5mkkwhdf
title: Vibration-Based Fault Detection in Drone using Artificial Intelligence

description: Recent years have seen a huge increase in the study of drones. There is a
 lot of published articles regarding drone, focusing on control
 optimization, fault detection, safety mechanisms, etc. In fault detection,
 most of the studies focused on the effects of faulty propellers
 and rotors, and there is very limited academic research on drone arms. In
 this paper, a fault detection based on the vibration of the multirotor
 arms using artificial intelligence (AI) is proposed. There are some cases
 where due to an accident, the arm of the multirotor crack or loose. This
 is normally unnoticeable without disassembly and if not taken care of, it
 would have likely resulted in a sudden loss of flight stability, which
 will lead to a crash. Two types of AI methods are incorporated in this
 study, namely, fuzzy logic and neuro-fuzzy, using the fuzzy logic and
 ANFIS toolbox in the MATLAB software, respectively. For the neuro-fuzzy
 approach, we use 100 and 1000 datasets to determine the effects
 of the dataset size on the neuro-fuzzy performance. Both datasets
 are divided into training (80%), testing (10%), and checking data (10%).
 The guidelines for constructing the AI algorithms are based on the
 experimental data for five experimental conditions; (i) (a) Original
 multirotor condition without modifying the multirotor arms, (b) 100%
 screwed multirotor arms condition (full tighten), (c) 50% screwed
 multirotor arms condition (half tighten), (d) 10% screwed multirotor arms
 condition, and (e) Unscrewed multirotor arm conditions. Their results are
 compared to determine the best method in predicting the safety of the
 multirotor. Both methods provided acceptable decision making but the
 neuro-fuzzy approach depends on the dataset used as overfit model might
 give incorrect decision making. Because the vibration data are collected
 in an indoor environment, this framework is more suitable for early
 prediction before flying the multirotor outdoor. A video
 demonstrating the real-time deployment of our proposed method is included
 in the mp4 format.
description: For the neuro-fuzzy technique, the input data are randomly
 generated by the MATLAB software, whereas the output data are determined
 by the user, based on the experimental works and data. These experimental
 data are the vibration output data of the multirotor, obtained using the
 SW420 vibration sensors, placed at the multirotor arms.  
description: NeuroFuzzy_100_Dataset.xlsx
 Contains 100 datasets in the Excel format used to train and
 evaluate the neuro-fuzzy algorithm 
 NeuroFuzzy_1000_Dataset.xlsx Contains 1000
 datasets in the Excel format used to train and evaluate the neuro-fuzzy
 algorithm 
 Experimental_Data.xlsx Contains the raw
 experimental vibration data in the Excel format 
 AUTHOR_DATASET__ReadmeTemplate.txt
 Contains further information regarding the datasets of this
 study 
 MultirotorDetection.mp4 A video in the mp4
 format demonstrating the real-time deployments of our AI
 algorithms
DOI: 10.5061/dryad.cvdncjt4g
title: Sperm competition risk affects ejaculate strategy in terms of sperm number but not sperm size in squid

description: In polygamous species, the mode of sperm storage in females influences
 evolution of sperm quantitative and qualitative traits because it provides
 the arena for sperm competition, cryptic female choice and fertilization
 processes. In this study, we compared ejaculate traits of two squid
 species, Heterololigo bleekeri and Loligo
 reynaudii. Both species show dimorphic sperm traits associated with
 alternative reproductive tactics where consort and sneaker males transfer
 sperm to different storage sites within a female (on the oviduct and near
 the mouth, respectively). Due to differences in reproductive behaviours
 and sperm placement, sperm competition risk is expected to be higher in
 sneakers than in consorts of both species, and higher overall
 in L. reynaudii. Our results demonstrate that the instantaneous
 number of released sperm is adjusted to the expected sperm competition
 risk via an elaborate sperm package. Consort sperm are similar in size,
 however, sneaker sperm have a significantly longer flagellum
 in H. bleekeri than in L. reynaudii, most
 likely due to intra-tactic conflicts associated with sperm storage
 conditions. From consideration of the different mating tactics,
 we suggest that while levels of sperm competition determine quantitative
 traits, sperm quality traits are determined more by the mode of sperm
 storage and fertilization.
description: See Materials & Methods of the paper below; <br>
 Yoko Iwata, Noriyosi Sato, Noritaka Hirohashi, Yoshiro Watanabe, Warwick
 H. H. Sauer, Paul W. Shaw. (2021) Sperm competition risk affects ejaculate
 strategy in terms of sperm number but not sperm size in squid. Journal of
 Evolutionary Biology<br>
 https://onlinelibrary.wiley.com/doi/10.1111/jeb.13894
DOI: 10.5061/dryad.1zcrjdfsb
title: Variability, heritability and condition-dependence of the multidimensional male colour phenotype in a passerine bird

description: Elaborate ornamental traits are commonly assumed to be honest signals of
 individual quality, owing to the presumed costs involved in their
 production and/or maintenance. Such traits are often highly variable,
 possibly because of condition-dependence and/or high underlying genetic
 variation, and it has been suggested that their expression should be more
 sensitive to condition and/or more heritable than non-ornamental traits.
 Many bird species display colourful plumage with multiple distinct patches
 of different developmental origins, forming complex colour phenotypes.
 Despite this complexity, colourful ornaments are often studied in
 isolation, without comparison to suitable non-ornamental controls. Based
 on plumage reflectance data collected over 8 years, we assessed the
 signalling potential of the multidimensional male colour phenotype in a
 tropical bird: the purple-crowned fairy-wren Malurus coronatus.
 Specifically, we tested the predictions that the express ion of putative
 ornamental colours (purple and black –the breeding colours– and blue) is
 (1) more variable, (2) more heritable and (3) more condition-dependent
 compared to year-round non-ornamental colours (buff-white and brown). Our
 results show that ornamental colours exhibit greater levels of
 variability, and some chromatic components of purple and blue colouration
 appear slightly heritable (h² = 0.19-0.30). However, contrary to
 predictions of heightened condition-dependence in ornaments, only
 brightness of the buff-white and brown colouration increased with male
 body condition, although brightness of the purple colouration was related
 to male age as expected. Despite partial support for predictions, the lack
 of consistent patterns illustrates the complexity of visual signals and
 highlights the need to study colour phenotypes in their entirety.
DOI: 10.5068/d1w988
title: Environmental map layers for Los Angeles environmental assessment project

description: In an increasingly urbanized world, there is a need to study urban areas
 as their own class of ecosystems as well as assess the impacts of
 anthropogenic impacts on biodiversity. However, collecting a sufficient
 number of species observations to estimate patterns of biodiversity in a
 city can be costly. Here we investigated the use of community
 science-based data on species occurrences, combined with species
 distribution models (SDMs), built using MaxEnt and remotely-sensed
 measures of the environment, to predict the distribution of a number of
 species across the urban environment of Los Angeles. By selecting species
 with the most accurate SDMs, and then summarizing these by class, we were
 able to produce two species richness models (SRMs) to predict biodiversity
 patterns for species in the class Aves and Magnoliopsida and how they
 respond to a variety of natural and anthropogenic environmental
 gradients.    We found that species considered
 native to Los Angeles tend to have significantly more accurate SDMs than
 their non-native counterparts. For all species considered in this study we
 found environmental variables describing anthropogenic activities, such as
 housing density and alterations to land cover, tend to be more influential
 than natural factors, such as terrain and proximity to freshwater, in
 shaping SDMs. Using a random forest model we found our SRMs could account
 for approximately 54% and 62% of the predicted variation in species
 richness for species in the classes Aves and Magnoliopsida respectively.
 Using community science-based species occurrences, SRMs can be used to
 model patterns of urban biodiversity and assess the roles of environmental
 factors in shaping them.
description: Source data for environmental layers are linked and described
 here.
description: These are all geotiffs covering the urban boundaries of Los
 Angeles.  The coordinate reference system for these maps are EPSG:
 3310.
DOI: 10.5061/dryad.vdncjsxv6
title: Disease seasonality estimation dataset for: Do psychiatric diseases follow annual cyclic seasonality?

description: Seasonal affective disorder famously follows annual cycles, with incidence
 elevation in the fall and spring. Should some version of cyclic annual
 pattern be expected from other psychiatric disorders? Would annual cycles
 be similar for distinct psychiatric conditions? This study probes these
 questions using two very large datasets describing the health histories of
 150 million unique Americans and the entire Swedish population. We
 performed two types of analysis, using “uncorrected” and “corrected”
 observation. The former analysis focused on counts of daily patient visits
 associated with each disease. The latter analysis instead looked at
 proportion of disease-specific visits within the total volume of visits
 for a time interval. In the uncorrected analysis, we found that
 psychiatric diseases’ annual patterns were remarkably similar across the
 studied diseases in both countries, with the magnitude of annual variation
 significantly higher in Sweden than in the US for psychiatric, but not
 infectious diseases. In the corrected analysis, only one group of patients
 – eleven to 20 years old – reproduced all regularities we observed for
 psychiatric disorders in the uncorrected analysis; the annual
 healthcare-seeking visit patterns associated with other age groups changed
 drastically. Analogous analyses over infectious diseases were less
 divergent over these two types of computation. Comparing two sets of
 results in context of published psychiatric disease seasonality studies,
 we tend to believe that our uncorrected results are likely to capture the
 real trends, while the corrected results reflect mostly
 artefacts determined by dominantly fluctuating health-seeking visits across year. In the spirit of full disclosure, we present both unredacted sets of results even-handedly and leave the verdict to the readers.
description: The data we used for analyses can be found in the data directory,
 organized by geographic regions (four high-latitude states, two
 low-latitude states, and the whole US). The data is packaged in a
 hierarchical python dictionary. Please refer to the project's web
 page for the usage: https://github.com/hanxinzhang/seasonality.
DOI: 10.5061/dryad.7h44j0ztr
title: Searching for deep-seated thrust faults on the moon

description: The lunar maria are large expanses of basalt that infill antecedent impact
 basins and show evidence for post-emplacement deformation. Landforms
 within many of these basins suggest a period of compressive tectonics,
 although the mechanism for their formation remains an open question.
 Previous work for Mare Crisium demonstrated that basin-circumferential
 wrinkle ridges, which typically demarcate the inner edge of an annulus of
 elevated terrain, are the result of deep-seated thrust faults that
 preferentially form along the boundary of an elevated, superisostatic
 portion of mantle and a thick, subisostatic collar of crustal material.
 Here, we show that a similar fault architecture exists for several other
 mascon-bearing basins, including Maria Serenititis, Nectaris, Moscoviense,
 and, to a lesser degree, Humorum and Imbrium. These deeply penetrating
 basin-circumferential thrust faults, as for Mare Crisium, form a (partial)
 outward-dipping ring-fault system that bounds the elevated mantle plug
 beneath each basin as a geometric consequence of mascon evolution. If this
 geometric arrangement is unique to the Moon, then some characteristic(s)
 of lunar mascon evolution enables the formation of such mascon-bounding
 faults. Despite the ubiquitous nature of mascon-bound thrust ring faults
 at several lunar basins, the prevalence of such structures at mascon
 basins on other terrestrial worlds remains an open question.
DOI: 10.5061/dryad.m37pvmd2g
title: Sinocarum muliense (Apiaceae), a new species from Sichuan, China

description: Sinocarum muliense (Apiaceae), is proposed as a new species from Sichuan,
 southwest China. Here is the nuclear ribosomal DNA internal transcribed
 spacer (ITS) sequences of Sinocarum used in the manuscript.
DOI: 10.5061/dryad.wdbrv15pb
title: Data - Leech removal is not the primary driver of basking behavior in a freshwater turtle

description: Leaving the water to bask (usually in the sun) is a common behavior for
 many freshwater turtles, with some species also engaging in “nocturnal
 basking.” Ectoparasite removal is an obvious hypothesis to explain
 nocturnal basking and has also been proposed as a key driver of diurnal
 basking. However, the efficacy of basking, day or night, to remove leeches
 has not been experimentally tested. Therefore, we examined the number of
 leeches that were removed from Krefft’s river turtles (Emydura macquarii
 krefftii) after experimentally making turtles bask at a range of times of
 day, durations, and temperatures. Turtles had high initial leech loads,
 with a mean of 32.1 leeches per turtle. Diurnal basking under a heat lamp
 for 3 h at ~28°C significantly reduced numbers of leeches relative to
 controls. In diurnal trials, 90.9% of turtles lost leeches (mean loss of
 7.1 leeches per turtle), whereas basking for 30 mins under the same
 conditions was not effective (no turtles lost leeches, and all turtles
 were still visibly wet). Similarly, “nocturnal basking” at ~23°C for 3 h
 was not effective at removing leeches. Only 18% of turtles lost leeches
 (one turtle lost one leech and another lost four leeches). Diurnal basking
 outdoors under direct sunlight for 20 min (mean temp = 34.5°C) resulted in
 a small reduction in leeches, with 50% of turtles losing leeches and an
 average loss of 0.7 leeches per turtle. These results indicate basking can
 remove leeches if temperatures are high or basking durations are long.
 However, it was only effective at unusually long basking durations in this
 system. Our data showed even the 20-min period was longer than 70.1% of
 natural diurnal basking events, many of which took place at cooler
 temperatures. Therefore, leech removal does not appear to be the purpose
 of the majority of basking events.
DOI: 10.5061/dryad.gb5mkkwq3
title: Vegetation resistance and resilience to a decade-long dry period in the temperate grasslands in China

description: The duration of climate anomalies has been increasing across the globe,
 leading to ecosystem function loss. Thus, we need to understand the
 responses of the ecosystem to long-term climate anomalies. It remains
 unclear how ecosystem resistance and resilience respond to long-term
 climate anomalies, e.g., continuous dry years at a regional scale. Taking
 the opportunity of a 13-year dry period in the temperate grasslands in
 northern China, we quantified the resistance and resilience of the
 grassland in response to this periodic dry period. We found vegetation
 resistance to the dry period increased with mean annual precipitation
 (MAP), while resilience increased at first until at MAP of 250 mm and then
 decreased slightly. No trade-off between resistance and resilience was
 detected when MAP &lt; 250 mm. Our results highlight that xeric
 ecosystems are most vulnerable to the long-term dry period. Given expected
 increases in drought severity and duration in the coming decades, our
 findings may be helpful to identify vulnerable ecosystems in the world for
 the purpose of adaptation.
DOI: 10.5061/dryad.v6wwpzgwb
title: Coevolution’s conflicting role in the establishment of beneficial associations

description: Reciprocal adaptation between hosts and symbionts can drive the
 maintenance of symbioses, resulting in coevolution and beneficial
 genotypic interactions. Consequently, hosts may experience decreased
 fitness when paired with non-sympatric partners compared to sympatric
 symbionts. However, coevolution does not preclude conflict—host
 and symbiont can act to advance their own fitness interests, which do not
 necessarily align with those of their partner. Despite coevolution’s
 importance in extant symbioses, we know little about its role in shaping
 the origin of symbioses. Here, we tested the role of coevolution in
 establishing a novel association by experimentally (co)evolving a host
 with a protective bacterium under environmental stress. While evolution in
 the presence of non-evolving bacteria facilitated host adaptation,
 co-passaged hosts did not exhibit greater adaptation rates than hosts
 paired with non-evolving bacteria. Furthermore, co-passaged hosts
 exhibited greater fecundity when paired with sympatric, co-passaged
 bacteria compared to co-passaged bacteria with which they did not share an
 evolutionary history. Thus, shared evolutionary history between the hosts
 and microbes actually reduced host fitness and has the potential to impede
 evolution of new beneficial associations.
DOI: 10.5061/dryad.kh1893263
title: Parasitism and host dispersal plasticity in an aquatic model system

description: Dispersal is a central determinant of spatial dynamics in communities and
 ecosystems, and various ecological factors can shape the evolution of
 constitutive and plastic dispersal behaviours. One important driver of
 dispersal plasticity is the biotic environment. Parasites, for example,
 influence the internal condition of infected hosts and define external
 patch quality. Thus state-dependent dispersal may be determined by
 infection status and context-dependent dispersal by the abundance of
 infected hosts in the population. A prerequisite for such dispersal
 plasticity to evolve is a genetic basis on which natural selection can
 act. Using interconnected microcosms, we investigated dispersal in
 experimental populations of the freshwater protist Paramecium caudatum in
 response to the bacterial parasite Holospora undulata. For a collection of
 20 natural host strains, we found substantial variation in constitutive
 dispersal, and to a lesser degree in dispersal plasticity. First,
 infection tended to increase or decrease dispersal relative to uninfected
 controls, depending on strain identity, potentially indicative of
 state-dependent dispersal plasticity. Infection additionally decreased
 host swimming speed compared to the uninfected counterparts. Second, for
 certain strains, there was a weak negative association between dispersal
 and infection prevalence, such that uninfected hosts tended to disperse
 less when infection was more frequent in the population, indicating
 context-dependent dispersal plasticity. Future experiments may test
 whether the observed differences in dispersal plasticity are sufficiently
 strong to react to natural selection. The evolution of dispersal
 plasticity as a strategy to mitigate parasite effects spatially may have
 important implications for epidemiological dynamics.
description: The readme file contains an explanation of each of the variables
 in the 3 datasets. The information on variable measurements and the
 experimental details can be found in the associated manuscript referenced
 above.