cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v41ns1rx2
title: Effects of L-valine in layer diets containing 0.72% isoleucine

description: In a previous study with LSL-LITE layers (-23 to 30-week-old), isoleucine
 at 0.72% and 0.84% produced values for FCR at 1.45 and 1.44, respectively
 and shared significance with 0.78% isoleucine (1.49). Considering
 that FCR is an important standard in the poultry industry due to the cost
 for adding feed ingredients such as synthetic amino acids and the low FCR
 of 1.45, 0.72% isoleucine was chosen for further study with LSL-LITE
 layers (n = 490 at 33- to 40-week-old) to determine effects on production
 and egg quality. The study included 7 diets (2730 Kcal kg metabolizable
 energy and constant isoleucine at 0.72%) containing varying quantities of
 valine [0.72 (Control), 0.75, 0.78, 0.81, 0.84, 0.87 or 0.90%] x 7
 replicates x 10 hens/replicate. Significance at P &lt; 0.05 and P
 &lt; 0.10 was determined. Level and week were significant for
 feed intake, egg production, and FCR; the interaction of level x week
 (L*W) was significant for feed intake and FCR. An isoleucine:valine of
 1.233 corresponding to 0.72% isoleucine and 0.87% valine produced the
 lowest FCR of 1.30 (a 2.26% decrease compared to the Control at
 1.33 + 0.04) . All measurements for external egg quality, except
 shape index and eggshell thickness, were significant for level. Week was
 significant for all parameters except shell thickness; L*W was significant
 for external quality measurements except shape index and shell thickness.
 Level, week, and L*W were significant for internal egg quality
 measurements. Serum protein and H1 titer were significant for level.
 Various production, egg quality, and biochemical measurements were
 significantly different from the control (0.72% isoleucine and 0.72%
 valine) at 0.81 to 0.87% valine. Findings of this study will aid
 researchers and commercial producers in narrowing the range of isoleucine,
 valine, and leucine needed for effects on particular parameters. Knowledge
 gained from this and others studies will eventually lead to an
 understanding of synergistic and antagonistic effects of branched chain
 amino acids in feed for various genetic types of layers throughout their
 productive lifetime.
DOI: 10.5061/dryad.18931zcz5
title: Genetic control of arbuscular mycorrhizal colonization by Rhizophagus intraradices in Helianthus annuus (L.)

description: Plant symbiosis with arbuscular mycorrhizal (AM) fungi provides many
 benefits, including increased nutrient uptake, drought tolerance, and
 belowground pathogen resistance. To develop a better understanding of the
 genetic architecture of mycorrhizal symbiosis, we conducted a genome-wide
 association study (GWAS) of this plant-fungal interaction in cultivated
 sunflower. A diversity panel of cultivated sunflower (Helianthus annuus
 L.) was phenotyped for root colonization under inoculation with the AM
 fungus Rhizophagus intraradices. Using a mixed linear model approach with
 a high-density genetic map, we identified genomic regions that are likely
 associated with R. intraradices colonization in sunflower. Additionally,
 we used a set of twelve diverse lines to assess the effect that
 inoculation with R. intraradices has on dried shoot biomass and
 macronutrient uptake. Colonization amongst lines in the mapping panel
 ranged from 0-70% and was not correlated with mycorrhizal growth response,
 shoot phosphorus response, or shoot potassium response among the Core 12
 lines. Association mapping yielded three single nucleotide polymorphisms
 (SNPs) that were significantly associated with R. intraradices
 colonization. This is the first study to use GWAS to identify genomic
 regions associated with AM colonization in an Asterid eudicot species.
 Three genes of interest identified from the regions containing these SNPs
 are likely related to plant defense.
description: See full text of the article and associated metadata. The
 presented data are metrics of root colonization by the arbuscular
 mycorrhizal fungus <em>Rhizophagus intraradices</em> assessed
 in 288 inbred lines of sunflower in a greenhouse experiment. Data on shoot
 biomass and nutrient content in a subset of lines is also
 presented.
description: DataS1:<br> Root colonization data used for genome-wide
 association mapping.<br> <br> DataS2:<br> Above-ground
 dry biomass and nutrient concentrations in dried plant tissues,
 measured<br> using Inductively-Coupled Plasma Mass Spectrometry
 (ICP-MS) for the Core 12 lines.<br> <br> DataS3:<br>
 List of all genes within significant and suggestive regions.<br>
 <br> Supplemental Information:<br> Dataset legends,
 supplemental figures, and supplemental methods.
DOI: 10.5061/dryad.s1rn8pk8d
title: Data for: A novel function of banded stripes to prevent cannibalism in snake-eating snakes

description: Colour pattern are widespread in the animal kingdom and have various
 functions that play key roles in many ecological interactions. We present
 a novel function for the evolution of banded stripes in preventing
 cannibalism in snakes that feed on other snakes—ophiophagy. We first
 examined the phylogenetic relationship between ophiophagy and banded
 stripes by categorising pattern types and known diet of 3,568 snake
 species. We then conducted a series of behavioural predation experiments
 with California kingsnake (Lampropeltis californiae) morphs, with and
 without band stripes, and a non- ophiophagous prey species, the corn snake
 (Elaphe guttata). We found 75% of ophiophagous snakes had banded stripe
 patterns. Body pattern type and ophiophagy was highly conserved across
 snake phylogeny, and the evolution of ophiophagy was co-dependent with
 banded stripe patterns. Our behavioural experiments revealed banded
 stripes on both inter- and intraspecific prey subjects reduced the
 probability of predation attempts, and that kingsnakes took longer to
 strike prey with banded stripes. Overall, the evolution of ophiophagy in
 snakes appears to be facilitated by the evolution of banded stripe
 patterns and may help reduce cannibalism in ophiophagous species.
DOI: 10.6086/d1d11h
title: Traffic and accident data for AEB environmental impact research

description: As one of the key advances in vehicle safety, Automatic Emergency Braking
 (AEB) has been introduced in the U.S. and the number of vehicles equipped
 with this technology has increased significantly in recent years. Most of
 existing studies have evaluated this technology at the individual vehicle
 level or focused on its safety performance. In this study, we tried to
 quantify its effectiveness on the energy consumption and tailpipe
 emissions. Towards this end, we: 1) performed literature review on AEB
 technology; 2) built a database including real-world traffic state
 measurements, traffic accident records, roadway geometry, and weather
 information; 3) developed a data-driven method to estimate the
 environmental impacts caused by the accidents that could be mitigated by
 AEB; and 4) conducted case study to show the efficacy of the proposed
 method. The results showed that the AEB technology may improve energy
 economy by up to 34.6% and reduce pollutant emissions (e.g., CO, HC, NOx
 and PM) by as much as 22.5% if the selected accidents could be avoided.
description: The main data sources include California Freeway Performance
 System (PeMS) and Highway Safety Information System (HSIS). The former is
 related to real-world traffic information collected from inductive loop
 detectors across California highways, while the latter involves accident
 related records, roadway geometry, and limited meteorological data. These
 two datasets need to be synchronized in both space and time for estimating
 environmental impacts of target accidents.
DOI: 10.5061/dryad.3tx95x6gz
title: Tree and sequence alignment used for diet reconstruction of Laurasiatheria

description: Background: Laurasiatheria contains taxa with diverse diets, while the
 molecular basis and evolutionary history underlying their dietary
 diversification are less clear. Results: In this study, we used the
 recently developed molecular phyloecological approach to examine the
 adaptive evolution of digestive system-related genes across both
 carnivorous and herbivorous mammals within Laurasiatheria. Our results
 show an intensified selection of fat and/or protein utilization across all
 examined carnivorous lineages, which is consistent with their high-protein
 and high-fat diets. Intriguingly, for herbivorous lineages (ungulates),
 which have a high-carbohydrate diet, they show a similar selection pattern
 as that of carnivorous lineages. Our results suggest that for the
 ungulates, which have a specialized digestive system, the selection
 intensity of their digestive system-related genes does not necessarily
 reflect loads of the nutrient components in their diets but appears to be
 positively related to the loads of the nutrient components that are
 capable of being directly utilized by the herbivores themselves. Based on
 these findings, we reconstructed the dietary evolution within
 Laurasiatheria, and our results reveal the dominant carnivory during the
 early diversification of Laurasiatheria. In particular, our results
 suggest that the ancestral bats and the common ancestor of ruminants and
 cetaceans may be carnivorous as well. We also found evidence of the
 convergent evolution of one fat utilization-related gene, APOB, across
 carnivorous taxa. Conclusions: Our molecular phyloecological results
 suggest that digestive system-related genes can be used to determine the
 molecular basis of diet differentiations and to reconstruct ancestral
 diets.
DOI: 10.5061/dryad.0cfxpnw31
title: Both diversity and functional composition affect productivity and water use efficiency in experimental temperate grasslands

description: Many experiments have shown that biodiversity promotes ecosystem
 functioning and stability and that this relationship varies with resource
 availability. However, we still have a poor understanding of the
 underlying physiological and ecological mechanisms driving diversity
 effects and how they may interact with soil nutrient availability. We
 collected data in a grassland experiment factorially manipulating
 fertilization, species richness, functional composition
 (slow-growing vs. fast-growing species), and functional diversity
 in resource economic traits. We measured aboveground productivity,
 nitrogen (N) uptake, photosynthesis, and water use efficiency by combining
 a 15N labelling approach with productivity, gas exchange, and
 stable isotope measurements in three years differing in rainfall. We found
 that sown species richness increased aboveground productivity, N uptake
 and photosynthesis, suggesting that species richness is the most important
 driver of ecosystem productivity and nutrient cycling. Similarly,
 photosynthesis was affected by functional composition but not by
 functional diversity. Water use efficiency was reduced by sown species
 richness for communities dominated by slow growing species but not for
 communities dominated by fast growing species. Fertilization increased
 productivity, N uptake and water use efficiency. The positive effects of
 high species richness on ecosystem functions were independent of fertility
 levels. Synthesis. Our results provide evidence that high species richness
 in temperate grasslands could enhance productivity and reduce the negative
 impacts of drought events. Multiple factors and community characteristics
 are important in driving enhanced ecosystem functioning in biodiverse
 grasslands and seem to affect functioning and stability through different
 mechanisms.
description: The data collection and processing is described in full in the
 manuscript.
DOI: 10.5061/dryad.66t1g1k2t
title: Data from: Age estimation using methylation-sensitive high-resolution melting (MS-HRM) in both healthy felines and those with chronic kidney disease

description: Age is an important ecological tool in wildlife conservation. However, it
 is difficult to estimate in most animals, including felines — most of whom
 are endangered. Here, we developed the first DNA methylation-based
 age-estimation technique — as an alternative to current age-estimation
 methods — for two feline species that share a relatively long genetic
 distance with each other: domestic cat (Felis catus; 79 blood samples) and
 an endangered Panthera, the snow leopard (Panthera uncia; 11 blood
 samples). We measured the methylation rates of two gene regions using
 methylation-sensitive high-resolution melting (MS-HRM). Domestic cat age
 was estimated with a mean absolute deviation (MAD) of 3.83 years. Health
 conditions influenced accuracy of the model. Specifically, the models
 built on cats with chronic kidney disease (CKD) had lower accuracy than
 those built on healthy cats. The snow leopard-specific model (i.e. the
 model that resets the model settings for snow leopards) had a better
 accuracy (MAD = 2.10 years) than that obtained on using the domestic cat
 model directly. This implies that our markers could be utilised across
 species, although changing the model settings when targeting different
 species could lead to better estimation accuracy. The snow
 leopard-specific model also successfully distinguished between sexually
 immature and mature individuals.
description: The cat data and the snow leopard data csv files are the raw
 data used in the analysis. The R script could be
 referred to in both the R markdown file and the pdf file.
 Please refer to Readme file to see the detailed explanation for
 the datasets.
DOI: 10.5061/dryad.m905qfv1t
title: Varying digestible isoleucine level to determine effects on performance, egg quality, serum biochemistry, and ileal protein digestibility in diets of young laying hens

description: To ascertain an appropriate level of isoleucine for LSL-LITE layers (23-
 to 30-week-old), diets containing total isoleucine concentrations (levels)
 of 0.66 (Control), 0.69, 0.72, 0.75, 0.78, 0.81, and 0.84% were fed as 7
 treatments (2730 kcal/kg metabolizable energy) x 7 replicates x 10 birds
 per replicate.  Significance for performance, egg quality, serum
 bioc Level, week, and level*week (L*W) were significant for production,
 egg mass, and feed intake.  Level and week were significant for
 FCR. Week was significant for weight gain. Level was significant for egg
 weight, specific gravity, and shell thickness; week was also significant
 for these external egg parameters as well as shape index and proportional
 shell thickness.  L*W was significant for all except shape
 index.  For internal egg measurements, level was significant for
 proportional yolk, proportional albumen, yolk index, and yolk:albumen.
 Week was significant for internal egg parameters while L*W significantly
 affected Haugh unit, proportional albumen weight, yolk index, albumen
 index, and yolk color.  Level was significant for globulin and
 glucose in serum. Isoluecine at 0.72%, 0.81% and 0.84% produced the lowest
 FCR, an important standard in the poultry industry.  Considering
 the low FCR of 1.45 and cost for inclusion as a dietary ingredients, 0.72%
 isoleucine was chosen for further study.
DOI: 10.5061/dryad.2z34tmpnc
title: Visual pursuit behavior in mice maintains the pursued prey on the retinal region with least optic flow

description: Mice have a large visual field that is constantly stabilized by vestibular
 ocular reflex (VOR) driven eye rotations that counter head-rotations.
 While maintaining their extensive visual coverage is advantageous for
 predator detection, mice also track and capture prey using vision.
 However, in the freely moving animal quantifying object location in the
 field of view is challenging. Here, we developed a method to digitally
 reconstruct and quantify the visual scene of freely moving mice performing
 a visually based prey capture task. By isolating the visual sense and
 combining a mouse eye optic model with the head and eye rotations, the
 detailed reconstruction of the digital environment and retinal features
 were projected onto the corneal surface for comparison, and updated
 throughout the behavior. By quantifying the spatial location of objects in
 the visual scene and their motion throughout the behavior, we show that
 the prey image consistently falls within a small area of the
 VOR-stabilized visual field. This functional focus coincides with the
 region of minimal optic flow in the visual field and consequently minimal
 motion-induced image blur during pursuit. The functional focus lies in the
 upper-temporal part of the retina and coincides with the reported high
 density-region of Alpha-ON sustained retinal ganglion cells.
description: Data was collected as described in the methods section of the
 corresponding paper and preprint.
description: Data structure CSV files contain tracking data
 of position and pointing angle of eyes of the mouse, and position of the
 cricket. MV files contain control code for our custom written Multiview
 software OBJ files are in Wavefront format, which can be opened e.g. in
 Blender Usage of data To generate the eye views used in our publication,
 CSV files need to be processed with our custom written software Multiview,
 using the provided control script. This will generate folders containing
 PNG/OpenEXRfiles for rendered view, optic flowetc., with one file per
 frame, eye and output type. The data can be visualised
 by: Multiview load_scene_scan.mv Path of Wavefront
 obj-file path of trajectory csv-file The data can be
 rendered and exported by: Multiview load_scene_scan.mv
 Path of Wavefront obj-file path of trajectory csv-file starting frame end
 frame output-folder
DOI: 10.5061/dryad.mcvdnck23
title: Introduced populations of the garden lupine are adapted to local generalist snails but have lost alkaloid diversity

description: Intraspecific variation in growth and defence among plant populations can
 be driven by differences in (a)biotic conditions, such as herbivory and
 resources. Introduction of species to novel environments affects
 simultaneously herbivory encountered by a plant and resource availability
 both directly and via altered competitive environment. Here, we address
 the question of how growth (leaf mass per area (LMA), plant size) and
 resistance traits (leaf alkaloids, leaf trichomes, resistance to a
 generalist snail) vary and covary between native and introduced
 populations of the garden lupine, Lupinus polyphyllus. We focused
 specifically on evolved differences among populations by measuring traits
 from plants grown from seed in a common environment. Plants from the
 introduced populations were more resistant against the generalist snail,
 Arianta arbustorum, and they had more leaf trichomes and higher LMA than
 plants from the native populations. The composition of alkaloids differed
 between native and introduced populations, with the native populations
 having more diversity in alkaloids among them. Resistance was positively
 associated with plant size and LMA across all populations. Other trait
 associations differed between native and introduced areas, implying that
 certain trade-offs may be fundamentally different between native and
 introduced populations. Our results suggest that, for the introduced
 populations, the loss of native herbivores and the alterations in resource
 availability have led to a lower diversity in leaf alkaloids among
 populations and may facilitate the evolution of novel trait optima without
 compensatory trade-offs. Such phytochemical similarity among introduced
 populations provides novel insights into mechanisms promoting successful
 plant invasions.
description: Obervations of herbivory on Lupinus polyphyllus in the field in
 USA and Finland. Lupinus polyphyllus were grown from
 seed in a greenhouse to measure resistance (leaf palatability to Arianta
 arbustorum, leaf trichomes) and growth (leaf mass per area, plant size).
 Leaf samples for alkaloid content were analysed usingan ultra-high
 performance liquid chromatograph coupled with a photodiode array detector
 (UHPLC-DAD).
DOI: 10.5061/dryad.x0k6djhk9
title: New incidence or recurrence hepatocellular carcinoma (HCC) in genotype 4 hepatitis C virus treated with sofosbuvir/daclatasvir with or without ribavirin

description: Background: Several studies have resulted in controversial data about the
 recurrence or new incidence of hepatocellular carcinoma (HCC) in patients
 with hepatitis C who were treated with direct-acting antivirals (DAAs).
   Aim: This observational study aimed to assess the occurrence
 rate of HCC in patients who developed a sustained virological response
 (SVR).. Methods: A six-month prospective study was done at the
 National Hepatology and Tropical Medicine Research Institute [NHTMRI] in
 Cairo, Egypt on 150 chronic hepatitis C (CHC) patients treated with
 sofosbuvir and daclatasvir with or without ribavirin. Patients were
 assigned into two groups according to their laboratory values to either
 receive sofosbuvir/daclatasvir and ribavirin (S/D/R) or receive only
 sofosbuvir/daclatasvir (S/D). The main outcome measure was the occurrence
 of HCC. Results: SVR-12 was 100%. 8.5% of patients developed HCC in the
 S/D/R group, while 0% in the S/D group. Conclusion:  New
 incidence or recurrence of HCC may occur in CHC genotype 4 cirrhotic
 patients receiving sofosbuvir/daclatasvir and ribavirin (difficult to
 treat) although achieving SVR. The cause of HCC development in this study
 is cirrhosis, not the administered DAAs.
DOI: 10.5061/dryad.v6wwpzgwv
title: Characteristics of the naturalized flora of Southern Africa largely reflect the non-random introduction of alien species for cultivation

description: This dataset contains data on the cultivated alien and native flora of
 Southern Africa associated with data on geographic origins, growth form,
 functional traits, and naturalization status extracted from different data
 sources described in Omer, A. et al.
 2021. Characteristics of the naturalized flora of Southern Africa
 largely reflect the non-random introduction of alien species for
 cultivation– Ecography.  doi: 10.1111/ecog.05669.  It is
 frequently overlooked, however, that patterns in origin, phylogeny, and
 traits of naturalized alien species might largely reflect which species
 have been introduced in the first place.
 This study quantifies and assesses such introduction
 biases by analyzing 5317 plant species introduced for cultivation (i.e.
 primarily as ornamental garden plants) in the 10 countries composing
 Southern Africa. The main results show that this cultivated alien
 flora represents a non-random subset of the global flora and that this
 bias at the introduction stage largely contributes to patterns in
 geographic origin, phylogenetic composition, and traits of the naturalized
 flora of Sothern Africa.