cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.66t1g1k1j
title: Insights into Mus musculus population structure across Eurasia revealed by whole-genome analysis

description: For more than 100 years, house mice (Mus musculus) have been used as a key
 animal model in biomedical research. House mice are genetically diverse,
 yet their genetic background at the global level has not been fully
 understood. Previous studies suggested that they originated in South Asia
 and diverged into three major subspecies almost simultaneously,
 approximately 350,000–500,000 years ago; however, they have spread across
 the world with the migration of modern humans in prehistoric and historic
 times (∼10,000 years ago to present), and undergone secondary contact,
 which have complicated the genetic landscape of wild house mice. In this
 study, we sequenced the whole genomes of 98 wild house mice collected from
 Eurasia, particularly East Asia, Southeast Asia, and South Asia. We found
 that although wild house mice consist of three major genetic groups
 corresponding to the three major subspecies, individuals representing
 admixture between subspecies are much more ubiquitous than previously
 recognized. Furthermore, several samples showed an incongruent pattern of
 genealogies between mitochondrial and autosomal genomes. Using samples
 likely retaining the original genetic components of subspecies with least
 admixture, we estimated the pattern and timing of divergence among the
 subspecies. The results are important for understanding the genetic
 diversity of wild mice on a global level and the information will be
 particularly useful in future biomedical and evolutionary studies using
 laboratory mice established from these wild mice.
DOI: 10.5061/dryad.rr4xgxd7f
title: Rise in temperature causes decreased fitness and higher extinction risks in endemic frogs at high altitude forested wetlands in northern Pakistan

description: The larvae of some amphibian species grow and develop more slowly at lower
 temperature and attain larger body size at the end of metamorphosis, but
 this is not true for all amphibians. We have for the first time provided
 empirical data by using a combination of field and lab-based studies with
 a robust sample size (360 adults, 1000 tadpoles) for Hazara Torrent Frog
 (Allopaa hazarensis) and Murree Hills Frog (Nanorana vicina). In this
 study, we examined how tadpoles responded to different temperatures
 through metamorphosis, body size, developmental complications or
 deformities, fitness, and survival. We found that the tadpoles of A.
 hazarensis and N. vicina showed the same response to elevated
 temperatures under laboratory conditions including faster metamorphosis,
 reduction in the body size, more frequent developmental complications or
 deformities such as edema and tail kinks, lower fitness and higher
 mortality at elevated temperatures (&gt;26 ◦C). The comparison of
 thermal sensitivity between the two species showed that N. vicina was more
 sensitive to higher temperatures. Pakistan has been experiencing changes
 in climatic patterns, and the ecosystems in northern Pakistan are losing
 biodiversity due to increasing temperature, frequency of drought and
 intensity of floods. It is feared that these frogs may experience local
 extinction in future. Our findings contribute to filling the information
 gap regarding impacts of temperature increase on biodiversity of high
 altitude forested montane ecosystems and is an important contribution to
 future studies associating biodiversity and climate change.
DOI: 10.5061/dryad.6q573n5z5
title: Detecting flying insects using car nets and DNA metabarcoding

description: Monitoring insects across space and time is challenging, due to their vast
 taxonomic and functional diversity. This study demonstrates how nets
 mounted on rooftops of cars (car nets) and DNA metabarcoding can be
 applied to sample flying insect richness and diversity across large
 spatial scales within a limited time period. During June 2018, 365 car net
 samples were collected by 151 volunteers during two daily time intervals
 on 218 routes in Denmark. Insect bulk samples were processed with a DNA
 metabarcoding protocol to estimate taxonomic composition, and the results
 were compared to known flying insect richness and occurrence data. Insect
 and hoverfly richness and diversity were assessed across biogeographic
 regions and dominant land cover types. We detected 15 out of 19 flying
 insect orders present in Denmark, with high proportions of especially
 Diptera compared to Danish estimates, and lower insect richness and
 diversity in urbanised areas. We found 319 species not known for Denmark
 and 174 species assessed in the Danish Red List. Our results indicate that
 the methodology can assess the flying insect fauna at large spatial scales
 to a wide extent, but may be, like other methods, biased towards certain
 insect orders.
description: Flying insects were collected with car nets during June 2018 in
 Denmark. Citizen scientists drove back and forth on 5 km routes and the
 insects were shipped to the Natural History Museum of Denmark in 96% EtOH.
 The insects were size sorted in two size fractions prior to DNA extraction
 with a non-destructive DNA lysis buffer and further processing with a DNA
 metabarcoding protocol. The full laboratory protocol for the research
 project 'InsectMobile' can be accessed here: https://dx.doi.org/10.17504/protocols.io.bmunk6ve. Only the output of fwh primer pair is used in this study.
description: Statistical analyses were carried out in RStudio on the original
 samples (size sorted samples were merged prior to analysis). Scripts can
 be found here: https://github.com/CecSve/InsectMobile_CarNet. The data in this Dryad repository are the data used in script 02.
DOI: 10.5061/dryad.tht76hdz6
title: Comprehensive comparative morphology and developmental staging of final instar larvae toward metamorphosis in the insect order Odonata

description: The order Odonata (dragonflies and damselflies) is among the most
 ancestral groups of winged insects with drastic morphological changes upon
 metamorphosis, and thus important for understanding evo-devo aspects of
 insects. However, basic developmental descriptions of Odonata have been
 scarce. In an attempt to establish the foundation of developmental and
 experimental biology of Odonata, we present an unprecedentedly
 comprehensive survey of dragonflies and damselflies, in total 158 larvae
 representing 49 species and 14 families, wherein morphological changes of
 all the final and/or penultimate instar larvae were photographed and
 monitored everyday. Although their morphology and development were
 diverse, we consistently identified two visually recognizable
 morphogenetic events in the final larval instar, namely start of wing
 expansion and onset of melanization on the wing sheaths, thereby
 categorizing the final instar into three stages. While the duration of the
 first stage ranged 4–66 days across diverse Odonata species, the
 second or third stages exhibited relatively small variation ranging
 3–22 days or 1–8 days, respectively, probably reflecting
 the steady and irreversible metamorphosis process after stage 2. We also
 described other characteristic morphological changes during the larval
 development, although they were observed only in some Odonata species and
 lineages.
description: <strong>Figure_S1_higher_quality_photos.pdf</strong><br> All the adjusted photos of F-0 instar larvae taken in this study. Individual data are shown in Table S1. <strong>Figure_S2_higher_quality_photos.pdf</strong><br> All the adjusted photos of F-1 instar larvae taken in this study. Individual data are shown in Table S1. <strong>Figure_S3_higher_quality_photos.pdf</strong><br> All the adjusted photos of the ventral heads focusing on the shrinking larval labium.
DOI: 10.5061/dryad.51c59zw7j
title: Codes for equivalent inhomogeneous inclusion method

description: This code determines the stress and strain fields of multiple spherical
 /circular inhomogeneities by Equivalent Inhomogeneous Inclusion Method
 (EIIM). EIIM is an inverse of Equivalent Inclusion Method and simulates
 the subdomains of matrix with known strains with equivalent inhomogeneous
 inclusions. The stress and strain fields of multiple inhomogeneities are
 decomposed into the superposition of matrix under applied load and each
 solitary inhomogeneous inclusion with polynomial eigenstrains by the
 iteration of EIIM. 
description: There are two programs in the attachment. Codes for
 2D EIIM deals with multiple circular inhomogeneity problems, and codes for
 3D EIIM deals with multiple spherical inhomogeneity problems. We recommend
 the readers the papers Multiple ellipsoidal/elliptical inhomogeneities
 embedded in infinite matrix by equivalent inhomogeneous inclusion method
 for a better understanding of the programs. 
 main_2D（3D）<br> The two programs start with
 main_2D and main_3D, respectively.
 Residual_Elastic_Field_2D (3D)<br> This
 subprogram calculates the residual stress and strain fields of multiple
 inhomogeneities by EIIM.
 Polynomial_EigenF_ItoM_2D (3D)<br> This
 subprogram transforms the inhomogeneous inclusion with polynomial
 eigenstress to homogeneous inclusion with polynomial eigenstress, as a
 homogeneous inclusion with polynomial eigenstrain has analytical
 solutions.
 Equivalent_Eigenstress_2D (3D)<br> This
 subprogram evaluates the equivalent eigenstress of the jth inhomogeneity
 resulted from the ith inhomogeneity. The non-uniform eigenstrain are
 approximate by polynomials.
 Trsform_X_Q_2D(3D)<br> This subprogram returns
 the polynomial form of points.
 T0_Strainoutside_2D(3D)<br> This subprogram
 evaluates the strain outside the incluions with uniform
 eigenstrain.
 T1_Strainoutside_2D(3D)<br> This subprogram
 evaluates the strain outside the incluions with linear
 eigenstrain.
 T1_Cell_3D<br> This subprogram returns
 Eshelby's tensors of spherical incluison with linear
 eigensrain.
 Dense_area<br> Much time is occupied by the
 calculations of stress and strain of nodes. To save time, Dense_area makes
 the nodes close to the boundary of the fiber become dense while the nodes
 away from the fibers are spare.
 Createfigure<br> Plot the stress and strain
 fields of multiple inhomogeneities. The field contours are close to those
 of Abaqus.
 84fiber_positions.xls<br> An example of 84
 fibers embeded in infinite matrix is presented in the paper Multiple
 ellipsoidal/elliptical inhomogeneities embedded in infinite matrix by
 equivalent inhomogeneous inclusion method. The position of the 84fibers
 are stored in this xls file, the first and second columns are,
 respectively, the x- and y-coordinates of the center of fibers. The EIIM
 code for circular inhomogeneities can evaluate the stress and strain
 fields of the 84 fibers.
DOI: 10.5061/dryad.4qrfj6q91
title: Recent changes in mountain birch forest structure and understory vegetation depend on the seasonal timing of reindeer grazing

description: 1. Subarctic forest-tundra ecotones dominated by mountain birch (Betula
 pubescens ssp. czerepanovii) is an important habitat for semi-domestic
 reindeer (Rangifer tarandus). The seasonal timing of reindeer grazing may
 direct vegetation trajectories in these systems, because in the summer
 ranges, mountain birches are subjected to browsing, while in the winter
 ranges, reindeer feed on understorey vegetation and arboreal lichens but
 leave the mountain birches intact. 2. Based on earlier research, we
 predicted that (1) summer browsing dampens ongoing vegetation
 ‘shrubification’ in semi-dry and dry mountain birch forests and (2)
 ‘shrubification’ is accompanied by a decline in lichens. We tested these
 predictions through re-analysing forest structure and understorey
 vegetation after 12 years in areas where winter and summer ranges had been
 separated since the 1980’s. We also tested how changes in lichen
 abundances align with changes in shrub abundances through correlation
 analyses. 3. The number of tall mountain birch seedlings had increased
 twice as fast in winter than summer ranges, while big mountain birches had
 increased in summer ranges. The dominant evergreen dwarf shrub mountain
 crowberry (Empetrum nigrum ssp. hermaphroditum) had increased to a greater
 extent in winter ranges in a semidry habitat, and to a greater extent in
 summer ranges in a dry habitat. Deciduous dwarf shrub and graminoid
 biomass had increased similarly in summer and winter ranges. 4. We found
 no evidence to support that increasing shrub abundances had contributed to
 a decline in lichens; instead, the lichen cover increased with increasing
 number of mountain birch seedlings. 5. Synthesis and application. The
 vegetation trajectories of dry and semi-dry subarctic mountain birch
 forests depend greatly on whether the area is used as a winter or a summer
 range. The recent changes in vegetation are likely to lead to improved
 summer forage availability for the reindeer, while the opposite may be
 true for the winter forage availability. 01-Feb-2021
DOI: 10.5281/zenodo.18396593
title: FAST FOOD AND POOR NUTRITION: HEALTH RISKS

description: This scientific article provides a comprehensive analysis of poor nutrition as a major public health problem and examines the harmful effects of regular fast food consumption on human health. Poor nutrition is characterized as an unbalanced dietary pattern that fails to meet the physiological and biological needs of the human body, particularly due to excessive intake of high-calorie foods rich in fats, refined carbohydrates, sugar, salt, and food additives. The study highlights that fast food products are energy-dense yet nutritionally poor, lacking essential vitamins, minerals, dietary fiber, and biologically active compounds necessary for normal metabolic processes. Based on an in-depth review of scientific literature and international health data, the article demonstrates that long-term consumption of fast food is strongly associated with obesity, insulin resistance, metabolic syndrome, cardiovascular diseases, gastrointestinal disorders, hypovitaminosis, weakened immune function, and reduced work capacity. Special attention is given to the impact of poor nutrition on children and adolescents, as it negatively affects growth, development, and cognitive performance. The findings emphasize that unhealthy eating habits have both medical and social consequences and contribute significantly to the global burden of chronic non-communicable diseases. The article concludes that adherence to the principles of rational and balanced nutrition, combined with increased physical activity and nutritional education, plays a crucial role in disease prevention, health promotion, and the improvement of overall
DOI: 10.5061/dryad.dncjsxkzh
title: Measuring quality of routine primary care data

description: Objective: Routine primary care data may be used for the
 derivation of clinical prediction rules and risk scores. We sought to
 measure the impact of a decision support system (DSS) on data completeness
 and freedom from bias. Materials and Methods: We used the
 clinical documentation of 34 UK General Practitioners who took part in a
 previous study evaluating the DSS. They consulted with 12 standardized
 patients. In addition to suggesting diagnoses, the DSS facilitates data
 coding. We compared the documentation from consultations with the
 electronic health record (EHR) (baseline consultations) vs. consultations
 with the EHR-integrated DSS (supported consultations). We measured the
 proportion of EHR data items related to the physician’s final diagnosis.
 We expected that in baseline consultations, physicians would document only
 or predominantly observations related to their diagnosis, while in
 supported consultations, they would also document other observations as a
 result of exploring more diagnoses and/or ease of coding.
 Results: Supported documentation contained significantly more
 codes (IRR=5.76 [4.31,
 7.70] P&lt;0.001) and less free text (IRR =
 0.32 [0.27, 0.40] P&lt;0.001) than baseline
 documentation. As expected, the proportion of diagnosis-related data was
 significantly lower (b=-0.08 [-0.11, -0.05] P&lt;0.001) in
 the supported consultations, and this was the case for both codes and free
 text. Conclusions: We provide evidence that data entry in the EHR
 is incomplete and reflects physicians’ cognitive biases. This has serious
 implications for epidemiological research that uses routine data. A DSS
 that facilitates and motivates data entry during the consultation can
 improve routine documentation.
DOI: 10.5281/zenodo.18396592
title: FAST FOOD AND POOR NUTRITION: HEALTH RISKS

description: This scientific article provides a comprehensive analysis of poor nutrition as a major public health problem and examines the harmful effects of regular fast food consumption on human health. Poor nutrition is characterized as an unbalanced dietary pattern that fails to meet the physiological and biological needs of the human body, particularly due to excessive intake of high-calorie foods rich in fats, refined carbohydrates, sugar, salt, and food additives. The study highlights that fast food products are energy-dense yet nutritionally poor, lacking essential vitamins, minerals, dietary fiber, and biologically active compounds necessary for normal metabolic processes. Based on an in-depth review of scientific literature and international health data, the article demonstrates that long-term consumption of fast food is strongly associated with obesity, insulin resistance, metabolic syndrome, cardiovascular diseases, gastrointestinal disorders, hypovitaminosis, weakened immune function, and reduced work capacity. Special attention is given to the impact of poor nutrition on children and adolescents, as it negatively affects growth, development, and cognitive performance. The findings emphasize that unhealthy eating habits have both medical and social consequences and contribute significantly to the global burden of chronic non-communicable diseases. The article concludes that adherence to the principles of rational and balanced nutrition, combined with increased physical activity and nutritional education, plays a crucial role in disease prevention, health promotion, and the improvement of overall
DOI: 10.5061/dryad.gmsbcc2md
title: Across borders: external factors and prior behavior influence North Pacific albatross associations with fishing vessels

description: 1. Understanding encounters between marine predators and fisheries across
 national borders and outside national jurisdictions offers new
 perspectives on unwanted interactions to inform ocean management and
 predator conservation. Although seabird-fisheries overlap has been
 documented at many scales, remote identification of vessel encounters has
 lagged because vessel movement data often is lacking. 2. Here, we reveal
 albatross-fisheries associations throughout the North Pacific Ocean. We
 identified commercial fishing operations using Global Fishing Watch data
 and algorithms to detect fishing vessels. We compiled GPS tracks of adult
 black-footed (Phoebastria nigripes) and Laysan (P. immutabilis)
 albatrosses, and juvenile short-tailed albatrosses (P. albatrus). We
 quantified albatross-vessel encounters based on the assumed distance that
 birds perceive a vessel (≤30km), and associations when birds approached
 vessels (≤3km). For each event we quantified bird behavior, environmental
 conditions, and vessel characteristics and then applied Boosted Regression
 Tree models to identify drivers and the duration of these associations. 3.
 In regions of greater fishing effort short-tailed and Laysan albatross
 associated with fishing vessels more frequently. However, fishing method
 (e.g. longline, trawl) and flag nation did not influence association
 prevalence nor the duration short-tailed albatross attended fishing
 vessels. Laysan albatross were more likely to approach longer vessels.
 Black-footed albatross were the most likely to approach vessels (61.9%),
 but limited vessel encounters (n=21) prevented evaluation of meaningful
 explanatory models for this species of high bycatch concern. 4. Temporal
 variables (time of day and month) and bird behavioral state helped explain
 when short-tailed albatross were in close proximity to a vessel, but
 environmental conditions were more important for explaining interaction
 duration. Laysan albatross were more likely to associate with vessels
 while searching and during the last 60% (by time) of their trips. 5. Our
 results provide specific species-fisheries insight regarding contributing
 factors of high-risk associations that could lead to bycatch of albatross
 within national waters and on the high-seas. 6. Policy implications. Given
 the global availability of Global Fishing Watch data, our methods can be
 applied to other marine predators to identify spatio-temporal patterns,
 vessel specific attributes, and predator behaviors associated with fishing
 vessel associations thus enabling predictive modeling and targeted
 mitigation measures.
description: The dataset contains the processed detection (&lt;30km) and
 associations (&lt;3km) between AIS vessel data and GPS bird tracking
 data. The data collection and processing methods are outlined in the
 associated manuscript. 
description: Missing values are coded as NA.
DOI: 10.5061/dryad.0zpc866wz
title: Biogeographic diversification of Eranthis (Ranunculaceae) reflects the geological history of the three great Asian plateaus

description: The evolutionary history of organisms with poor dispersal abilities
 usually parallels geological events. Collisions of the Indian and Arabian
 plates with Eurasia greatly changed Asian topography and affected regional
 and global climate as well as biotic evolution. However, the geological
 evolution of Asia related to these two collisions remains debated. Here,
 we used Eranthis, an angiosperm genus with poor seed dispersal ability and
 a discontinuous distribution across Eurasia , to shed light on the
 orogenesis of the Qinghai-Tibetan, Iranian and Mongolian plateaus. Our
 phylogenetic analyses show that Eranthis comprises four major geographic
 clades: east Qinghai-Tibetan Plateau clade (I-1), North Asian clade (I-2),
 west Qinghai-Tibetan Plateau clade (II-1), and Mediterranean clade (II-2).
 Our molecular dating and biogeographic analyses indicate that within
 Eranthis, four vicariance events well correlate with the two early uplifts
 of the Qinghai-Tibetan Plateau during the late Eocene and the
 Oligocene–Miocene boundary and the two uplifts of the Iranian Plateau
 during the middle and late Miocene. The origin and divergence of the
 Mongolian Plateau taxa are related to the two uplifts of the Mongolian
 Plateau during the middle and late Miocene. Additionally, our results are
 in agreement with the hypothesis that the central part of Tibet only
 reached an altitude of &lt; 2.3 km at ~40 Ma. This study highlights
 that organismal evolution could be related to the formation of the three
 great Asian plateaus, hence contributing to the knowledge on the timing of
 the key tectonic events in Asia