cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4gt8g
title: Data from: Markovian language model of the DNA and its information content

description: This work proposes a Markovian memoryless model for the DNA that
 simplifies enormously the complexity of it. We encode nucleotide sequences
 into symbolic sequences, called words, from which we establish meaningful
 length of words and groups of words that share symbolic similarities.
 Interpreting a node to represent a group of similar words and edges to
 represent their functional connectivity allows us to construct a network
 of the grammatical rules governing the appearance of groups of words in
 the DNA. Our model allows us to predict the transition between groups of
 words in the DNA with unprecedented accuracy, and to easily calculate many
 informational quantities to better characterize the DNA. In addition, we
 reduce the DNA of known bacteria to a network of only tens of nodes, show
 how our model can be used to detect similar (or dissimilar) genes in
 different organisms, and which sequences of symbols are responsible for
 most of the information content of the DNA. Therefore, the DNA can indeed
 be treated as a language, a Markovian language, where a ‘word’ is an
 element of a group, and its grammar represents the rules behind the
 probability of transitions between any two groups.
description: codesDetails about what each
 code does for paper "Markovian language model of the DNA and its
 information content", Author: Srivastava, S. and Baptista, M. Upload
 the genomic sequence to be used by using fastaread command from matlab.
 genomenomode.m - Use this file for creating Fig. 1. and Fig. 2(a) and
 2(c). The code calculates Correlation. MIR.m - Use this file for Fig.
 2(b). calculates MIR. Needs additional file powerthres.m.
 thresholdgreater.m - Use this file for creating Fig. 3 and Fig. 4. The
 code applies threshold and the network can be created for selected
 thresholds. one_dim_gene.m - This code is needed for calculating the
 specificity and sensitivity in separated genes. It converts all the values
 into one dimension. This codes reads data generated by file
 gene_separated_genomenomod.m ROC_gene.m - Use this file for creating Fig.
 5. and calculating the sensitivity and specificity values for genes at
 different thresholds.
DOI: 10.5061/dryad.35tg5
title: Data from: Host provisioning behavior favors mimetic begging calls in a brood-parasitic cowbird

description: The vocalizations of some young brood-parasitic birds closely resemble
 those of their host’s young. Such similarities might arise because hosts
 bestow the greatest parental care in response to their own species’ call
 type. We used a playback experiment to assess the effectiveness of the
 nestling call structures of two brood parasites, the specialist screaming
 cowbird (Molothrus rufoaxillaris) and the generalist shiny cowbird (M.
 bonariensis), in stimulating parental provisioning in a shared host, the
 baywing (Agelaioides badius). Screaming cowbird begging calls closely
 resemble those of baywing young and thus should best exploit any bias for
 species-specific cues. Shiny cowbird calls, in contrast, are unlike
 baywings but can instead exploit non-specific sensory biases for long call
 duration and syllable repetition. We found playback of screaming cowbird’s
 mimetic calls elicited increases in feeding rates equivalent to those of
 playback of the host’s own young, while shiny cowbird calls failed to
 increase provisioning rates above those of no-broadcast control sessions.
 These results indicate that baywings discriminate between nestling call
 structures in favour of their own species calls when adjusting parental
 investment, and support the view that selection for optimal host
 provisioning can favour vocal mimicry by parasitic offspring.
description: dataset-Host
 provisioning behaviour favours mimetic begging calls in a brood parasitic
 cowbirdPlayback experiment to
 assess the effectiveness of the nestling call structures of two brood
 parasites, the specialist screaming cowbird (Molothrus rufoaxillaris) and
 the generalist shiny cowbird (M. bonariensis), in stimulating parental
 provisioning in 25 nests of a shared host, the baywing (Agelaioides
 badius). The effect of playback treatments on the number of feeding visits
 by baywing adults was analysed using generalised linear mixed models
 (GLMM) with log link function and Poisson error structure. Models were
 fitted using the glmer function included in lme4 package in R 3.1.2 (R
 Core Team 2014; Bates et al. 2015). Explanatory variables were playback
 treatment, treatment order and clutch composition (presence/absence of
 parasites), with nest identity included as a random
 effect.
DOI: 10.5061/dryad.hk64f
title: Data from: A mathematical model of marine bacteriophage evolution

description: To explore how particularities of a cell-virus system affects viral
 evolution, we formulate a mathematical model of marine bacteriophage
 evolution. The intrinsic simplicity of real-life phage-bacteria systems
 allows to have a reasonably simple model. The model constructed in this
 paper is based upon Beretta-Kuang model of bacteria-phage interaction.
 Compared to the Beretta-Kuang model, the model assumes the existence of a
 multitude of viral variants which correspond to continuously distributed
 phenotypes. It is noteworthy that this model does not include any explicit
 law or mechanism of evolution; instead it is assumed, in agreement to the
 principles of Darwinian evolution, that evolution in this system can occur
 as a result of random mutations and natural selection. Simulations with a
 leaner fitness landscape (which is chosen for the convenience of
 demonstration only) show that a pulse-type traveling wave moving towards
 increasing Darwinian fitness appears in the phenotype space. This implies
 that the overall fitness of a viral quasispecies steadily increasing in
 time. That is, the simulations demonstrate that for an uneven fitness
 landscape random mutations combined with a mechanism of natural selection
 lead to the Darwinian evolution. It is noteworthy that in this system the
 speed of propagation of this wave (and hence the rate of evolution) is not
 constant but varies, depending on the current viral fitness and the
 abundance of susceptible bacteria.
description: Model of bacteriophage
 evolutionImplementation of the
 model in Matlab. The model is a 3-equations model, combined with
 appropriated boundary and initial conditions (based on biological
 background and on the bibliography). Then, the solution is derived using
 an explicit method.BPvect.mBPvect_RobinMatlab code. Evolution of marine bacteriophage modeled by a 3-equation system, solved explicitely applying Robin boundary conditions for infected cell population and Neumann boundary conditions on the virus.
DOI: 10.5061/dryad.p1j71
title: Data from: Lexicon-enhanced sentiment analysis framework using rule-based classification scheme

description: With the rapid increase in social networks and blogs, the social media
 services are increasingly being used by online communities to share their
 views and experiences about a particular product, policy and event. Due to
 economic importance of these reviews, there is growing trend of writing
 user reviews to promote a product. Nowadays, users prefer online blogs and
 review sites to purchase products. Therefore, user reviews are considered
 as an important source of information in Sentiment Analysis (SA)
 applications for decision making. In this work, we exploit the wealth of
 user reviews, available through the online forums, to analyze the semantic
 orientation of words by categorizing them into +ive and -ive classes to
 identify and classify emoticons, modifiers, general-purpose and
 domain-specific words expressed in the public’s feedback about the
 products. However, the un-supervised learning approach employed in
 previous studies is becoming less efficient due to data sparseness, low
 accuracy due to non-consideration of emoticons, modifiers, and presence of
 domain specific words, as they may result in inaccurate classification of
 users’ reviews. Lexicon-enhanced sentiment analysis based on Rule-based
 classification scheme is an alternative approach for improving sentiment
 classification of users’ reviews in online communities. In addition to the
 sentiment terms used in general purpose sentiment analysis, we integrate
 emoticons, modifiers and domain specific terms to analyze the reviews
 posted in online communities. To test the effectiveness of the proposed
 method, we considered users reviews in three domains. The results obtained
 from different experiments demonstrate that the proposed method overcomes
 limitations of previous methods and the performance of the sentiment
 analysis is improved after considering emoticons, modifiers, negations,
 and domain specific terms when compared to baseline methods.
description: Python and NLTK-based
 Source CodeThe python-based source
 code deals with development of sentiment analysis system with emphasis on
 modifiers, emoticons, SWN and others. The read me text file is self
 explanatory for installation.pyhton-based-source
 code.rar
DOI: 10.5061/dryad.b58j2
title: Data from: Individual resource limitation combined with population-wide pollen availability drives masting in the valley oak (Quercus lobata)

description: 1. Masting, the synchronized production of variable seed crops, is
 widespread among woody plants, but there is no consensus about the
 underlying proximate mechanisms. To understand this population-level
 behavior, it is necessary to dissect the behavior of individual trees as
 well as the interactions that synchronize them. 2. Here we test a model of
 masting in which variability in seed set is driven by resource limitation
 within trees and synchrony is driven by pollen limitation due to
 phenological asynchrony in some years. 3. We used a 35-year seed set data
 set and a 12-year phenological data set to analyze seed production of 84
 valley oaks (Quercus lobata) in central coastal California. Individual
 trees varied tremendously in their seed production patterns; trees with
 high levels of seed production were less variable over time, but showed
 stronger negative autocorrelation between years, suggesting that they are
 more resource-limited than unproductive trees. In years of more
 asynchronous flowering, Q. lobata produced fewer seeds, consistent with
 the importance of phenological synchrony. 4. We parametrized a model with
 these results to investigate how individual resource limitation and
 population-wide pollen limitation – a consequence of asynchronous
 flowering during cold spring temperatures – interact to shape annual
 variation in seed production. The model illustrates that this proximate
 abiotic driver can synchronize the behavior of individuals, resulting in
 population-wide seed production patterns that closely resemble the field
 data. 5. Synthesis: Our findings support the hypothesis that an
 interaction between two proximate mechanisms, individual resource
 limitation and environmental variation affecting population-wide pollen
 availability, drives masting in this population of Quercus lobata. This
 combination of internal and external proximate drivers may underlie
 masting behavior in many wind-pollinated plants.
description: population summary seed
 production & temperatureMean population relative
 crop size and dTmax (relative mean maximum temperature for April) for
 Quercus lobata at Hastings Natural History Reserve, Carmel Valley, CA,
 USAlongsum_jecol.csvrelative cost of fruiting for individual treesrcf values for individual Q. lobata trees, as estimated by log-log relationship between mean relative crop size and rcf in Isagi et al., 1997 model. See R-code associated with articleprep_trees.csvtemperature dataDelta mean maximum April Temperature 1939-2014 for Hastings RAWS weather station. Hastings Natural History Reserve, Carmel Valley, CA. Delta= annual value - minimum value. Values beyond the 99% percentile were substituted with 99th percentile value.long_model_weather_data.csv
DOI: 10.5061/dryad.7j258v6
title: Data from: Fluctuating thermal environments and time-dependent effects on fruit fly egg-hatching performance

description: Organismal performance in a changing environment is dependent on temporal
 patterns and duration of exposure to thermal variability. We
 experimentally assessed the time-dependent effects of thermal variability
 (i.e. patterns of thermal exposure) on the hatching performance of
 Drosophila melanogaster. Flies were collected in central Chile and
 maintained for four generations in laboratory conditions. Fourth
 generation eggs were acclimated to different thermal fluctuation cycles
 until hatching occurred. Our results show that the frequency of extreme
 thermal events has a significant effect on hatching success. Eggs exposed
 to 24h cycles of thermal fluctuation had a higher proportion of eggs that
 hatched than those acclimated to shorter (6 and 12h) and longer cycles
 (48h). Furthermore, eggs subjected to frequent thermal fluctuations
 hatched earlier than those acclimated to less frequent thermal
 fluctuations. Overall, we show that, egg-to-adult viability is dependent
 on the pattern of thermal fluctuations experienced during ontogeny; thus,
 the pattern of thermal fluctuation experienced by flies has a significant
 and until now unappreciated impact on fitness.
description: cavieres et
 alHatching performance of
 Drosophila melanogaster. Eggs were maintained in one of four treatments
 that differed in time-scales of thermal variability (6h, 12h, 24h, 48h,
 and control)
DOI: 10.5061/dryad.801v4
title: Data from: A Model of a Temporal Method to Determine the Refractive Index Change in a Dual Ring Resonator

description: This paper describes the simulation and modelling of a novel temporal
 method to determine the refractive index change in a dual ring micro-ring
 resonator. The refractive index change information of a covering analyte
 of the sense resonator is realized as a modulated output signal. Two
 dimensional Finite difference time domain (FDTD) is used to graphically
 demonstrate the temporal operation. The beam propagation method (BPM) and
 the finite element method (FEM) are used to determine coupling
 coefficients, ring loss and effective index. As a result of the dual ring
 resonator’s geometrical arrangement, the sensor output undergoes a
 modulated wavelength (or frequency) shift from the micrometre wavelength
 (or terahertz frequency) to a centimetre wavelength (or gigahertz
 frequency) range. BPM and FEM data obtained from partial micro-ring arcs
 and a derived temporal equation are used in a MATLAB program to model the
 temporal output. The minimum down converted frequency realized in this
 model is 1.8 gigahertz (from 192.9 terahertz), corresponding to an analyte
 refractive index change of 35.63x10-6 in the sense micro-ring. The maximum
 down converted frequency is 14.44 gigahertz (from 192.9 terahertz), which
 corresponds to an analyte refractive index change of 285.55x10-6 in the
 sense micro-ring. The limit of detection is 10.3x10-6RIU.
description: temporal_1MATLAB file to plot the modulated output of the data generated in the FEMSIM files.Neff_vs_Lambda_H2O_fs_mode_neffrDispersion data file for application in the temporal_1.m program file.Neff_vs_Lambda_H2O_fs_mode_neffrplot file of the Neff_vs_Lambda_H2O_fs_mode_neffr.pde data file.neff_vs_lambda_ana_1_new_fs_mode_neffrDispersion data file for analyte cover in sense ring
DOI: 10.6092/unibo/amsacta/8764
title: INTELLIMAN. WP5. Grasping, Manipulation and Arm-Hand Coordination. T5_3. Understanding and Reasoning Manipulation Task Structures. GNN Topology Learning. v0

description: This dataset provides the source code and trained model weights used to implement and evaluate a graph-based approach for the perception and topological representation of Deformable Multi-Linear Objects (DMLOs), also referred to as Branched Deformable Linear Objects (BDLOs). These objects, such as automotive wiring harnesses, exhibit complex branching structures that are challenging for robotic perception and manipulation. The released material enables the reproduction of a pipeline that estimates a coherent graph representation of DMLOs starting from binary scene masks. Graph nodes are sampled along estimated object centerlines, while a graph neural network is employed to predict graph connectivity and to classify node types based on local topology and orientation. A solver then combines these predictions to generate a consistent topological representation of the objects. The code and model weights were produced in the framework of the Horizon Europe IntelliMan project and were used in the experiments presented in the associated publication: A. Caporali, K. Galassi, R. Zanella and G. Palli, "GNN Topology Representation Learning for Deformable Multi-Linear Objects Dual-Arm Robotic Manipulation", in IEEE Transactions on Automation Science and Engineering, vol. 22, pp. 14738-14751, 2025, DOI: 10.1109/TASE.2025.3562231.
DOI: 10.5281/zenodo.17973496
title: SHM_415566_HST_3D

description: Photogrammetric 3D model of a Middle Neolithic pottery rim fragment in the Pitted Ware Culture/Fagervik III style collected from Fagervik in Östergötland and held in the collections of the National Historical Museums in Stockholm. The fragment shows a herringbone pattern of cord impressions as well as deeper impressions.

Link to the Dynamic Collection platform  

https://dyncolldev.ht.lu.se/plus/artifact_view.php?item=668

Link to Sök I Samlingarna  

https://samlingar.shm.se/object/AD48B67E-FBD2-497F-9B97-59251125D66A
DOI: 10.5281/zenodo.17973497
title: SHM_415566_HST_3D

description: Photogrammetric 3D model of a Middle Neolithic pottery rim fragment in the Pitted Ware Culture/Fagervik III style collected from Fagervik in Östergötland and held in the collections of the National Historical Museums in Stockholm. The fragment shows a herringbone pattern of cord impressions as well as deeper impressions.

Link to the Dynamic Collection platform  

https://dyncolldev.ht.lu.se/plus/artifact_view.php?item=668

Link to Sök I Samlingarna  

https://samlingar.shm.se/object/AD48B67E-FBD2-497F-9B97-59251125D66A
DOI: 10.5061/dryad.dh182
title: Data from: Population connectivity and phylogeography of the Mediterranean endemic skate Raja polystigma and evidence of its hybridization with the parapatric sibling R. montagui

description: The genetic structure and population connectivity of the Mediterranean
 endemic speckled skate Raja polystigma were investigated in 10 population
 samples (N = 232) at 7 exon-primed nuclear microsatellites and at 3
 mitochondrial DNA sequence markers. The phylogeographic and population
 genetic analyses revealed that R. polystigma in the western and central
 Mediterranean represents a near-panmictic population, with a subtle but
 significant mitochondrial divergence of the Adriatic deme. Nuclear
 genotypes revealed that 2.5% of the total individuals exhibited an admixed
 ancestry with the sibling species R. montagui (spotted ray). Individuals
 with admixed ancestry were detected along with purebred individuals in the
 Algerian, southern Tyrrhenian, Sicilian and Adriatic R. polystigma
 population samples, but they were absent or rare in Sardinian and northern
 Tyrrhenian ones. Since the 2 species co-occur in the southwestern
 Mediterranean, we suggested that this area may act as a secondary hybrid
 zone.
description: Frodella et al_Raja
 microsatellite dataThis file contains the 6
 microsatellite loci genotype data used for the associated publication.
 Genotypes are presented in a 2 digit genepop format. There are 128
 individuals divided into 9 populations. The population order is: 1) WI 2)
 Al_CladeM 3) AL_CladeP 4) NT 5) ST 6) SI 7) ES 8) WS 9)
 AD
DOI: 10.5061/dryad.6mj22
title: Data from: Optimal lineage principle for age-structured populations

description: We present a formulation of branching and aging processes that allows
 distributions along lineages to be studied within populations, and
 provides a new interpretation of classical results in the theory of aging.
 We establish a variational principle for the stable age distribution along
 lineages. Using this optimal lineage principle, we show that the response
 of a population’s growth rate to age-specific changes in mortality and
 fecundity – a key quantity which was first calculated by Hamilton – is
 given directly by the age distribution along lineages. We apply our method
 also to the Bellman-Harris process, in which both mother and progeny are
 rejuvenated at each reproduction event, and show that this process can be
 mapped to the classic aging process such that age statistics in the
 population and along lineages are identical. Our approach provides both a
 theoretical framework for understanding the statistics of aging in a
 population, and a new method of analytical calculations for populations
 with age structure. We discuss generalizations for populations with
 multiple phenotypes, and more complex aging processes. We also provide a
 first experimental test of our theory applied to bacterial populations
 growing in a microfluidics device.
description: DRYAD_DATA_UPLOADRaw lineage data for both glucose and lactose experiments used in Figure 3. README file is supplied within the .zip archive.
DOI: 10.5061/dryad.q5553
title: Data from: Dietary carotenoid availability affects avian color discrimination

description: Carotenoid pigments are found in the retinas of many vertebrate species,
 where they serve a range of functions. In birds, carotenoid-containing
 retinal oil droplets act as optical filters, modifying the light reaching
 the underlying visual pigment and thereby enhancing color vision. Dietary
 carotenoid manipulation is known to affect the allocation of carotenoids
 to the retina, although the effects this has on vision are less well
 understood. Using dietary manipulations, in which juvenile Japanese quail
 (Coturnix japonica) received either a high- or a low-carotenoid diet, we
 tested the effects of carotenoid availability on the ability to perform a
 color discrimination task. Birds on both diet treatments were able to make
 a relatively coarse discrimination between colors that appeared to humans
 as yellow-orange and orange; however, only high-carotenoid diet birds were
 able to make a finer-scale discrimination involving intermediate colors,
 showing that dietary carotenoid availability can directly affect the
 ability of birds to make chromatic discriminations. This finding has
 implications for our understanding of trade-offs in carotenoid allocation
 between vision and other key functions such as sexual ornamentation and
 health maintenance, and suggests that variation in dietary carotenoid
 availability may affect the ability of animals to make ecologically
 pertinent color discriminations, such as between sexual signals or cryptic
 food items.
description: Supplementary
 DataData on subject identity
 (ID), hatching cohort (Cohort), experimental diet group (Diet), rewarded
 colour (Reward), discrimination level (Level), latency to choose
 (Latency), and whether or not a correct choice was made
 (Error).