cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.34tmpg4jn
title: Qualitative responses from students during spring 2019

description: During the Spring Semester of 2020, an outbreak of a novel coronavirus
 (SARS-CoV-2) and the illnesses it caused (COVID-19) led to widespread
 cancelling of on-campus instruction at colleges and universities in the
 United States and other countries around the world. Response to the
 pandemic in university settings included a rapid and unexpected shift to
 online learning for faculty and students. The transition to teaching and
 learning online posed many challenges, and the experiences of students
 during this crisis may inform future planning for distance learning
 experiences during the ongoing pandemic and beyond. Herein, we discuss the
 experiences of first- and second- year university students enrolled in a
 biology seminar course as their classes migrated to online environments.
 Drawing on reported student experiences and prior research and resources,
 we discuss the ways we will adjust our own teaching for future iterations
 of the course while offering recommendations for instructors tasked with
 teaching in online environments.
description: We
 collected student responses under an IRB- approved protocol
 (#17-249).  Responses were completed as a particpation
 assignment. These assignments were modified to allow the author to capture the experiences of students newly engaged with distance learning, the perceptions of students own learning, and their interactions with faculty during the pandemic. Students responded to reflection questions two different times during the remote class: the first week of their quarantine at home and then three weeks into their remote learning experience. Questions and student responses were completed through Blackboard, and 14 of the 15 students responded to the questions within the allotted times.
DOI: 10.5061/dryad.9zw3r22d4
title: Defensive hypervariable regions confer superinfection exclusion in microviruses

description: Single-stranded DNA phages of the family Microviridae have fundamentally
 different evolutionary origins and dynamics than the more frequently
 studied double-stranded DNA phages. Despite their small size (generally
 &lt;5kb), which imposes extreme constraints on genomic innovation,
 they have adapted to become prominent members of viromes in numerous
 ecosystems and hold a dominant position among viruses in the human gut. We
 show that multiple, divergent lineages in the family Microviridae have
 independently become capable of lysogenizing hosts and have convergently
 developed hypervariable regions in their DNA pilot protein, which is
 responsible for injecting the phage genome into the host. By creating
 microviruses with combinations of genomic segments from different phages
 and infecting Escherichia coli as a model system, we demonstrate that this
 hypervariable region confers the ability of temperate Microviridae to
 prevent DNA injection and infection by other microviruses. The DNA pilot
 protein is present all microviruses but has been recruited repeatedly into
 this additional role as microviruses altered their lifestyle by evolving
 the ability to integrate in bacterial genomes, which linked their survival
 to that of their hosts. Our results emphasize that competition between
 viruses is a considerable and often overlooked source of selective
 pressure, and by producing similar evolutionary outcomes in distinct
 lineages, it underlies the prevalence of hypervariable regions in the
 genomes of microviruses and perhaps beyond.
description: This dataset ccontains protein and DNA alignments of microviral
 DNA pilot proteins and whole genomes used to generate figures in this
 work.
DOI: 10.6078/d1td7h
title: Supplementary table from: Spectrometry of Greta oto untreated and hexane treated clear wing regions and simulated reflectance spectra

description: The wings of butterflies and moths (Lepidoptera) are typically covered
 with thousands of flat, overlapping scales that endow the wings with
 colorful patterns. Yet, numerous species of Lepidoptera have evolved
 highly transparent wings, which often possess scales of altered morphology
 and reduced size, and the presence of membrane surface nanostructures that
 dramatically reduce reflection. Optical properties and anti-reflective
 nanostructures have been characterized for several ‘clearwing’
 Lepidoptera, but the developmental processes underlying wing transparency
 are unknown. Here, we apply confocal and electron microscopy to create a
 developmental time-series in the glasswing butterfly, Greta oto, comparing
 transparent and non-transparent wing regions. We find that during early
 wing development, scale precursor cell density is reduced in transparent
 regions, and cytoskeletal organization during scale growth differs between
 thin, bristle-like scale morphologies within transparent regions and flat,
 round scale morphologies within opaque regions. Next, we show that
 nanostructures on the wing membrane surface are composed of two layers: a
 lower layer of regularly arranged nipple-like nanostructures, and an upper
 layer of irregularly arranged wax-based nanopillars composed predominantly
 of long-chain n-alkanes. By chemically removing wax-based nanopillars,
 along with optical spectroscopy and analytical simulations, we demonstrate
 their role in generating anti-reflective properties. These findings
 provide insight into morphogenesis and composition of naturally organized
 micro- and nanostructures and may provide bioinspiration for new
 anti-reflective materials.
description: The wing reflection measurements were performed on a Cary 5000 UV-Vis-NIR
 spectrophotometer, equipped with a light source of tungsten halogen and an
 integrating sphere diffuse reflectance accessory (Internal DRA 1800). Wing
 measurements from the dorsal wing surface were recorded using three
 different individuals for untreated and three different individuals for
 hexane treatments with unpolarized light with a spot size of 100 µm for an
 incident angle of 8o to avoid the loss of direct specular reflectance
 component through the aperture. All measurements were taken in the dark to
 avoid possible stray illumination from the surrounding environment and we
 performed two technical replicates for each individual wing. A reference
 measurement was done with a calibrated commercial white spectralon
 standard to calculate the relative diffuse reflectance. The reflectance
 measurements and mean data are presented in S2 Table.
DOI: 10.6078/d1pm6z
title: Data for: Nitrous oxide formation by corona discharge: Isotopic composition measurements and atmospheric applications

description: Agricultural practices have led to a greater use of nitrogen-containing
 fertilizers and an increase in N2O, an important greenhouse gas and
 ozone-depleting substance. Isotopic measurements can be used to
 differentiate sources of N2O in the atmosphere, and the data presented
 here explore the isotopic composition of N2O formed in a low-temperature
 plasma, similar to some forms of lightning in the atmosphere. A corona
 discharge was used to generate N2O under flowing and static conditions, at
 pressures from approximately 0.1 to 10 Torr, a discharge voltage of 5 kV,
 and a discharge current of 1500 mA. Additional experiments were conducted
 by varying the discharge current between 75 to 1500 μA at ~0.5 Torr.
 Samples were analyzed using an isotope ratio mass spectrometer, and we
 find that the isotopic composition of N2O produced differs in unique ways
 from that of other sources to the atmosphere. These differences suggest
 that isotopic measurements of atmospheric N2O samples can be used to
 determine/investigate whether observations of local and regional
 enhancements in N2O are due to lightning, as well as to constrain the
 source of N2O in the upper stratosphere, mesosphere and thermosphere.
description: ​​​​​​The experimental
 methods and data processing are described in detail in Smith et al.
 (2021).
description: Experiments in Table 2
 are the averages of similar groups of experiments that are shown in Table
 S2. Specifically, Table 2-Averaged experimental results are the following
 from Table S2-unaveraged experimental results.
 1500 μA at 0.500,
 0.550, and 0.520 Torr (rows 2-4)
 300 μA at 0.550 and
 0.540 Torr (rows 7-8) 150 μA at 0.560, 0.57,
 and 0.56 Torr (rows 9-11) 1500 μA at 9.76 and
 9.73 Torr (rows 18-19) 1500 μA at 9.85 and
 9.69 Torr static runs (rows 20-21)
 For additional usage
 notes please see comments in the excel file.
DOI: 10.5061/dryad.zgmsbcc9m
title: Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history

description: Quinoa germplasm preserves useful and substantial genetic variation, yet
 it remains untapped due to a lack of implementation of modern breeding
 tools. We have integrated field and sequence data to characterize a large
 diversity panel of quinoa. Whole-genome sequencing of 310 accessions
 revealed 2.9 million polymorphic high confidence SNP loci. Highland and
 Lowland quinoa were clustered into two main groups, with FST divergence of
 0.36 and fast LD decay of 6.5 and 49.8 Kb, respectively. A genome-wide
 association study uncovered 600 SNPs stably associated with 17 agronomic
 traits. Two candidate genes are associated with thousand seed weight, and
 a resistance gene analog is associated with downy mildew resistance. We
 also identified pleiotropically acting loci for four agronomic traits that
 are highly responding to photoperiod hence important for the adaptation to
 different environments. This work demonstrates the use of
 re-sequencing data of an orphan crop, which is partially domesticated to
 rapidly identify marker-trait association and provides the underpinning
 elements for genomics-enabled quinoa breeding.
description: This data set contains
 genotype and phenotype data reported in this publication. CSV file
 includes the phenotype data, and genotype data is provided in .vcf format.
 For additional information please see the ReadMe file. 
description: Phenotype data were collected from a field experiment in
 Kiel.  Accession ID and names are given in the Table
 S1  Abbreviations:  DTB- Days to
 bolting DTF - Days to Flowering
 DTBtoDTF- Duration between bolting and flowering
 DTM - Days to Maturity PH- Plant
 height PD -Panicle density NoB-
 Nuber of branches STL- Stem lying 
 Saponin- Foam height (Saponin content) Yield-
 Seed yield (g) per plant  FC- Flower color (conditional
 mean) SC- Stem color  (conditional mean)
 GT- Growth type (conditional mean) PSH-
 Panicle shape  (conditional mean)
DOI: 10.5061/dryad.qfttdz0g5
title: A rare 300 kilometer dispersal by an adult male white-tailed deer

description: Despite the key roles that dispersal plays in individual animal fitness
 and meta-population gene flow, it remains one of the least understood
 behaviors in many species. In large mammalian herbivores, dispersals might
 span long distances and thereby influence landscape-level ecological
 processes, such as infectious disease spread. Here we describe and analyze
 an exceptional long-distance dispersal by an adult white-tailed deer
 (Odocoileus virginianus) in the central United States. We also conducted a
 literature survey to compare the dispersal to previous studies. This
 dispersal was remarkable for its length, duration, and the life history
 stage of the dispersing individual. Dispersal is typical of juvenile deer
 seeking to establish post-natal home ranges, but this dispersal was
 undertaken by an adult male (age = 3.5). This individual dispersed ~300 km
 over a 22-day period by moving, on average, 13.6 km/day and achieving a
 straight-line distance of ~215 km, which was ~174 km longer than any other
 distance recorded for an adult male deer in our literature survey. During
 the dispersal, which occurred during the hunting season, the individual
 crossed a major river seven times, an interstate highway, a railroad, and
 eight state highways. Movements during the dispersal were faster (mean =
 568.1 m/h) and more directional than those during stationary home range
 periods before and after the dispersal (mean = 56.9 m/h). Likewise,
 movements during the dispersal were faster (mean = 847.8 m/h) and more
 directional at night than during the day (mean =166.4 m/h), when the
 individual frequently sheltered in forest cover. This natural history
 event highlights the unpredictable nature of dispersal and has important
 implications for landscape-level processes such as chronic wasting disease
 transmission in cervids. More broadly, our study underscores how
 integrating natural history observations with modern technology holds
 promise for understanding potentially high impact but rarely recorded
 ecological events.
description: Methods are described in the journal aricle.
description: The data contain four columns: id = the
 individual animal id y = latitude in decimal
 degrees x = longitude in decimal degrees
 t = time in day/month/year HH:MM format
DOI: 10.5061/dryad.rfj6q5792
title: Predicting the effects of reservoir water level management on the reproductive output of a riparian songbird

description: Yellow warblers were monitored in Revelstoke, British Columbia, Canada for
 12 breeding seasons spanning 2005 to 2017. Data on the breeding biology of
 individually marked warblers was used to construct an individual-based
 model describing the effects of reservoir operations on the reproductive
 output of yellow warblers. This model was parameterised using data on the
 breeding biology of approximately 30 breeding pairs per year that
 a provided data on nest sites (ground elevation and nest height),
 breeding phenology (date of first egg for each clutch initiated), clutch
 size, brood parasitism by brown-headed cowbirds, nest fate and whether
 females re-nested following nest failure or success. The raw data was
 filtered, excluding nests that failed due to abandonment following brood
 parasitism and flooding, and formatted to allow estimation of nest
 survival rates using Program MARK. 
description: Data was collected by monitoring a marked population of breeding
 birds from early May to the middle of July in 2005 to 2017 (with the
 exception of 2007). The data has been formatted to
 allow description of nest elevation, the timing of breeding, clutch size,
 daily survival rates and the probability of re-nesting following nest
 failure or the fledging of young.
description: The data is provided in a series of sheets within an Excel
 file. The variables in each sheet are described in the
 Readme file. Cells with missing values are
 empty.
DOI: 10.5061/dryad.w0vt4b8qk
title: Figure e-1.- Effect of APOE alleles on cognitive domain-specific composite measures.

description: Supplemental Figure of our original article "Association of APOE
 Genotype with Heterogeneity of Cognitive Decline Rate in Alzheimer's
 Disease" published in Neurology showing model
 1-based trajectories of cognitive domain-specific composite
 measures by APOE genotype, as well as the difference
 of the APOEe2 and APOEe4 groups with respect to the
 APOEe3/e3 reference group.
description: Please, see Methods section of our <em>Neurology</em>
 article "Association of <em>APOE</em> Genotype with
 Heterogeneity of Cognitive Decline Rate in Alzheimer's
 Disease".
DOI: 10.5061/dryad.hqbzkh1fj
title: Spatial phylogenomics of acrobat ants in Madagascar—mountains function as cradles for recent diversity and endemism

description: Aim: A crucial step to protecting biodiversity is assessing
 species diversity and endemism. We delineate spatial
 patterns of diversity in Malagasy ants on a phylogenetic and taxonomic
 level to identify centers of diversity and endemism, and evaluate the
 ‘museum vs cradle’ hypothesis with regard to ant endemism.
 Location: Madagascar Taxon: Ants,
 genus Crematogaster. Methods: We estimated distribution
 models for 33 Crematogaster species and generated a
 phylogeny based on ultraconserved elements. We calculated species
 richness (SR), phylogenetic diversity (PD), weighted (WE), phylogenetic
 endemism(PE), randomized phylogenetic diversity (PD-sig), and relative
 phylogenetic diversity (RPD) and endemism (RPE). Categorical
 analyses of neo- and paleo-endemism (CANAPE) and the
 phylo-jaccard index were used to delineate centers of neo- and
 paleo-endemism. We correlated these measures with elevation metrics to
 investigate the role of mountains in generating ant endemism.
 Results: We found extensive phylogenetic clustering
 (significantly low PD-sig) and short branches (low RPD) at higher
 elevations in central and south-central to southern Madagascar. In
 contrast, phylogenetic overdispersion (significantly high PD-sig) and long
 branches (high RPD) predominate at lower elevations in eastern humid and
 northern western dry forests. CANAPE and phylo-jaccard estimated five
 centers of endemism, whereby neo- and mixed endemism were significantly
 correlated with higher elevations, and paleo-endemism with lower
 elevations.  Main Conclusions: Centers of ant endemism
 are located in western dry and humid forests of northern Madagascar,
 eastern humid forests, and in the southern Central Highland
 region. Mountainous areas appear to be cradles of recent
 diversification for acrobat ants, whereas lower elevations may be regarded
 as centers of paleo-endemism and thus museums for relict lineages. Species
 diversification among acrobat ants may have coincided with the arrival of
 a new biome in the central highlands of Madagascar.
DOI: 10.5281/zenodo.18396672
title: MECHANISMS FOR USING THE SCIENTIFIC HERITAGE OF JADID ENLIGHTENERS IN PREPARING FUTURE TEACHERS FOR PROFESSIONAL ACTIVITY

description: This scientific article analyzes the pedagogical views of Mahmudkhoja Behbudi, Abdulla Avloni, and Abdurauf Fitrat, who were prominent representatives of the Uzbek enlightenment movement at the beginning of the 20th century. The ideas of the Jadid enlighteners regarding education and upbringing, as well as their requirements for the teacher’s personality, the content of education, teaching methods, and organizational forms, are examined from a scientific and theoretical perspective. The article substantiates mechanisms for using the scientific heritage of the Jadids in the process of preparing future teachers for professional activity. The significance of Jadid pedagogical views in shaping modern pedagogical competencies is revealed, and effective ways of their application in the system of higher pedagogical education are presented.
DOI: 10.5281/zenodo.18396673
title: MECHANISMS FOR USING THE SCIENTIFIC HERITAGE OF JADID ENLIGHTENERS IN PREPARING FUTURE TEACHERS FOR PROFESSIONAL ACTIVITY

description: This scientific article analyzes the pedagogical views of Mahmudkhoja Behbudi, Abdulla Avloni, and Abdurauf Fitrat, who were prominent representatives of the Uzbek enlightenment movement at the beginning of the 20th century. The ideas of the Jadid enlighteners regarding education and upbringing, as well as their requirements for the teacher’s personality, the content of education, teaching methods, and organizational forms, are examined from a scientific and theoretical perspective. The article substantiates mechanisms for using the scientific heritage of the Jadids in the process of preparing future teachers for professional activity. The significance of Jadid pedagogical views in shaping modern pedagogical competencies is revealed, and effective ways of their application in the system of higher pedagogical education are presented.
DOI: 10.7280/d1wx12
title: Dataset for: Vibrometry as a noncontact alternative to dynamic and viscoelastic mechanical testing in cartilage

description: Physiological loading of knee cartilage is highly dynamic and may
 contribute to the progression of osteoarthritis. Thus, an understanding of
 cartilage’s dynamic mechanical properties is crucial in cartilage
 research. In this study, vibrometry was used as a fast (2 hours),
 noncontact, and novel alternative to the slower (30 hours), traditional
 mechanical and biochemical assays for characterization of cartilage from
 the condyle, patella, trochlear groove, and meniscus. Finite-element
 models predicted tissue resonant frequencies and bending modes, which
 strongly correlated with experiments (R2=0.93). Vibrometry-based
 viscoelastic properties significantly correlated with moduli from stress
 relaxation and creep tests, with correlation strengths reaching up to
 0.78. Loss modulus also strongly correlated with GAG content. Dynamic
 properties measured by vibrometry significantly differed among various
 knee cartilages, ranging between 6.1-56.4MPa. Interestingly, meniscus
 viscoelastic properties suggest that contrary to common belief, it may
 lack shock absorption abilities; instead, condylar hyaline cartilage may
 be a better shock absorber. These data demonstrate for the first time that
 vibrometry is a noncontact approach to dynamic mechanical characterization
 of hyaline and fibrocartilage cartilage with concrete relationships to
 standard quasistatic mechanical testing and biochemical composition. Thus,
 with a single tool, vibrometry greatly facilitates meeting multiple
 regulatory recommendations for mechanical characterization of cartilage
 replacements.
DOI: 10.5061/dryad.9ghx3ffgm
title: The results of RNA seq analysis: Curcumin promotes progression of AApoAII amyloidosis and peroxisome proliferation in mice by activating the PPARα signaling pathway

description: Curcumin is a polyphenol compound that exhibits multiple physiological
 activities. To elucidate the mechanisms by which curcumin affects systemic
 amyloidosis, we investigated amyloid deposition and molecular
 changes in a mouse model of amyloid apolipoprotein A-II
 (AApoAII) amyloidosis, in which mice were fed a
 curcumin-supplemented diet. Curcumin supplementation for 12 weeks
 significantly increased AApoAII amyloid deposition relative to
 controls, especially in the liver and spleen. Liver weights and
 plasma ApoA-II and high-density lipoprotein concentrations were
 significantly elevated in curcumin-supplemented
 groups. RNA-sequence analysis revealed that curcumin intake
 affected hepatic lipid metabolism via the peroxisome
 proliferator-activated receptor (PPAR) pathway, especially PPARα
 activation, resulting in increased Apoa2 mRNA expression. The
 increase in liver weights was due to activation of PPARα and
 peroxisome proliferation. Taken together, these results
 demonstrate that curcumin is a PPARα activator and may affect
 expression levels of proteins involved in amyloid deposition to
 influence amyloidosis and metabolism in a complex manner.
DOI: 10.5061/dryad.4j0zpc89x
title: Multisensory integration facilitates perceptual restoration of an interrupted call in frog

description: How to render an interrupted sound as a complete signal is a common
 challenge faced by human and non-human animals during vocal communication.
 Using video and audio playbacks, we showed that neither inserting white
 noise into the silent gap of an interrupted call nor displaying the
 dynamic inflating-deflating vocal sac in that same gap restored attraction
 of the call equivalent to that of a complete call. Simultaneously
 presenting a dynamic vocal sac along with white noise in the gap, however,
 rescued the interrupted call making it as attractive as a complete call.
 This suggests that the multisensory cue might have caused female frogs to
 “hear” the missing sound as happens when humans experience auditory
 induction. Regardless, such novel multisensory integration suggests that
 multimodal signals can provide insurance against imperfect sender coding
 in a noisy environment, and the communication benefits to the receiver
 from multisensory integration may be an important selective force favoring
 multimodal signal evolution.