cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.46h5nc0
title: Data from: In silico study of the role of cell growth factors in photosynthesis using a virtual leaf tissue generator coupled to a microscale photosynthesis gas exchange model

description: Computational tools that allow in silico analysis of the role of cell
 growth and division on photosynthesis are scarce. We present a freely
 available tool that combines a virtual leaf tissue generator and a
 two-dimensional microscale model of gas transport during C3
 photosynthesis. A total of 270 mesophyll geometries were generated with
 varying degree of growth anisotropy, growth extent and extent of
 schizogenous airspace formation in the palisade mesophyll. The anatomical
 properties of the virtual leaf tissue and microscopic cross sections of
 actual leaf tissue of tomato (Solanum lycopersicum L.) were statistically
 compared. Model equations for transport of CO2 in the liquid phase of the
 leaf tissue were discretized over the geometries. The virtual leaf tissue
 generator produced a leaf anatomy of tomato that was statistically similar
 to real tomato leaf tissue. The response of photosynthesis to
 intercellular CO2 predicted by a model that used the virtual leaf tissue
 geometry compared well with measured values. The results indicate that the
 light-saturated rate of photosynthesis was influenced by interactive
 effects of extent and directionality of cell growth and degree of airspace
 formation through the exposed surface of mesophyll per leaf area. The tool
 could be used further in investigations of improving photosynthesis and
 gas exchange in relation to cell growth and leaf anatomy.
description: CODE_MOGES_RETTAThe file CODE_MOGES_RETTA contains two folders containing matlab files for the virtual leaf tissue generator (code_geometry) and the gas exchange model (code_photo). An example of the virtual leaf tissue generator outputs are stored in folders cords_1,cords_2 and cords_3, for three replicate geometries.
DOI: 10.5061/dryad.m31b1h7
title: Data from: Temperature compensation in a small rhythmic circuit

description: Temperature affects the conductances and kinetics of the ionic channels
 that underlie neuronal activity. Each membrane conductance has a different
 characteristic temperature sensitivity, which raises the question of how
 neurons and neuronal circuits can operate robustly over wide temperature
 ranges. To address this, we employed computational models of the pyloric
 network of crabs and lobsters. We employed a landscape optimization scheme
 introduced previously (Alonso and Marder, 2019) to produce multiple
 different models that exhibit a triphasic pyloric rhythm over a range of
 temperatures. We use the currentscapes introduced in (Alonso and Marder,
 2019) to explore the dynamics of model currents and how they change with
 temperature. We found that temperature changes the relative contributions
 of the currents to neuronal activity so that rhythmic activity smoothly
 slides through changes in mechanisms. Moreover, the responses of the
 models to extreme perturbations—such as gradually decreasing a current
 type—are often qualitatively different at different temperatures.
description: <strong>alonso_marder_tempcomp_2019_root</strong> This package contains code to reproduce the main results in the manuscript referenced above. The model is implemented in java and there are python scripts that call the model and plot their solutions. The package includes initial conditions and parameters for 36 different networks.
DOI: 10.5061/dryad.64r8fc0
title: Data from: The circular nature of recurrent life-cycle events: a test comparing tropical and temperate phenology

description: 1. The high diversity of plant species in the tropics has revealed complex
 phenological patterns and reproductive strategies occurring throughout the
 year. Describing and analysing tropical plant phenology, and detecting
 triggers, demands to consider the circular nature of recurrent life-cycle
 events and the use of appropriated statistical metrics. 2. Here we explore
 analytical pitfalls potentially affecting results of studies that do not
 consider the circular nature of phenology data when comparing resting and
 non-resting systems, especially when accounting for phylogeny. We discuss
 definitions of the widely-used first flowering date and revisit the
 literature on phylogenetic signal in plant phenology. We compare
 statistical analyses for tropical and temperate phenology by simulating
 communities with known phenological and phylogenetic structures. 3. We
 demonstrate that ignoring the circular nature of phenological data
 underestimates the phylogenetic signal in plant phenology. Using the
 proposed circular transformation for non-resting tropical ecosystems and
 resting temperate systems prevented errors, yielding precise comparisons.
 4. Synthesis. The analysis of both non-resting and resting systems must
 consider the circularity of phenological events. Circular statistics is
 the appropriate approach to calculate phenological parameters, identify
 phylogenetic signal and assess drivers, allowing accurate
 cross-comparisons of phenology across environments at large spatial
 scales.
description: R code for applying
 phylogenetic comparative methods to phenological
 datasetsThese files containing
 the analyses executed for the article "The circular nature of
 recurrent life-cycle events: a test comparing tropical and temperate
 phenology", accepted in Journal of Ecology. The function proposed
 here tests phylogenetic signal in plant phenology considering the
 circularity of temporal data. Any query or suggestion please write to
 v.staggemeier@gmail.comDRYAD_JE.zip
DOI: 10.5061/dryad.2220d7m
title: Data from: Age and sex prevalence estimate of Joubert Syndrome in Italy

description: Objective: To estimate the prevalence of Joubert syndrome (JS) in Italy
 applying standards of descriptive epidemiology, and to provide a molecular
 characterization of the described patients cohort. Methods: We enrolled
 all patients with a neuroradiologically confirmed diagnosis of JS and
 resident in Italy in 2018, and calculated age and sex prevalence, assuming
 a Poisson distribution. We also investigated the correlation between
 proband chronological age and age at diagnosis, and performed
 Next-Generation Sequencing (NGS) analysis on probands’ DNA when available.
 Results: We identified 284 JS patients: the overall, female- and
 male-specific population-based prevalence rates were 0.47 (95% CI
 0.41-0.53), 0.41 (95% CI 0.32-0.49) and 0.53 (95% CI 0.45-0.61) per
 100,000 population, respectively. When considering only patients in the
 age range from 0 to 19 years, the corresponding population-based
 prevalence rates rose to 1.7 (95% CI 1.49-1.97), 1.62 (95% CI 1.31-1.99)
 and 1.80 (95% CI 1.49-2.18) per 100,000 population. NGS analysis allowed
 identifying the genetic cause in 131 out of 219 screened probands. Age at
 diagnosis was available for 223 probands, with a mean of 6.67 ± 8.10
 years, and showed a statistically significant linear relationship with
 chronological age (r2=0.79; p&lt;0.001). Conclusions: We estimated for
 the first time the age and sex prevalence of JS in Italy, and investigated
 their genetic profile. The obtained population-based prevalence rate was
 approximately 10 times higher than that available in literature for
 children population.
description: Table e-1
 List of
 JS-associated genes included in targeted NGS panel table e-1.docx
 
 Table
 e-2 Categories of JS
 probands, based on their genetic status table e-2.docx
 
 Table
 e-3 Population-based
 prevalence rate of molecularly confirmed JS in Italy (per 100,000
 population, year 2018) table e-3.docx
DOI: 10.5061/dryad.50n9762
title: Data from: Starving the enemy? Feeding behavior shapes host-parasite interactions

description: The loss of appetite that typically accompanies infection or the mere
 exposure to parasites is traditionally considered a negative by-product of
 infection, benefitting neither the host nor the parasite. In fact,
 numerous medical and veterinary practices directly or indirectly subvert
 this ‘illness-mediated anorexia’. However, the ecological factors that
 influence it, its effects on disease outcomes, or why it evolved remains
 poorly resolved. We explore how hosts use anorexia to defend against
 infection and how parasites can manipulate anorexia to enhance
 transmission. Then, we use a coevolutionary model to illustrate how
 changes to anorexia could alter disease dynamics and virulence evolution.
 Anorexia could be exploited to improve host health and disease management;
 we propose an interdisciplinary approach to minimize unintended
 consequences.
description: READMESynopsis of
 supplementary materialsAdditional literature
 cited in the review Table S1This excel file provides
 the Metadata for the studies that we reviewed for this
 manuscript.HitePfenningCresslerStarvingTheEnemyReviewPapersOnAnorexiaTable_S1July2019.csvStudies illustrating common medical interventions that alter the magnitude and/or duration of parasite-mediated anorexiaTable S2: This excel file provides a list of studies illustrating common medical interventions that alter the magnitude and/or duration of parasite-mediated anorexia (which we mention multiple times in the Main Text).HitePfenningCresslerStarvingTheEnemyTableS2July2019.csvHitePfenningCresslerStarvingTheEnemyTable_S3July2019Table S3: The excel file provides the data used for Figure 1 in Box 2 in the Main Text.Table S4: overview of the search terms, methods, and search engines usedTable S4: This excel file provides an overview of the search terms, methods, and search engines used for our literature review of &gt; 140 studies on parasite-mediated anorexia.HitePfenningCresslerStarvingTheEnemyTable_S4Jul2019.csv
DOI: 10.5061/dryad.p88hj77
title: Data from: Safety and efficacy of dual antiplatelet pretreatment in ischemic stroke patients treated with intravenous thrombolysis: a systematic review and meta-analysis

description: Objective: Conflicting data exist regarding the safety and efficacy of IV
 thrombolysis (IVT) in acute ischemic stroke (AIS) patients receiving dual
 antiplatelet pretreatment (DAPP). The aim of the present systematic review
 and meta-analysis is to assess the safety and outcome of DAPP history
 among AIS patients treated with IVT. Methods: We performed a comprehensive
 literature review to identify studies that investigated the safety and
 efficacy of DAPP among AIS patients treated with IVT. Results: We
 identified 9 studies comprising 66,675 patients. In unadjusted analyses,
 DAPP was associated with higher likelihood of pooled symptomatic
 intracranial hemorrhage (sICH, OR = 2.26, 95% CI 1.39–3.67) and 3-month
 mortality (OR = 1.47, 95% CI 1.27–1.73). DAPP was also related to higher
 odds of sICH according to SITS-MOST (OR = 2.71, 95% CI 2.05–3.59), ECASS
 II (OR=2.23, 95% CI 1.46–3.40) and NINDS (OR=1.59, 95% CI 1.38–1.83)
 definitions. There was no association between DAPP and 3-month favorable
 functional outcome (FFO, mRS 0-1), and 3-month functional independence
 (FI, mRS 0-2). In adjusted analyses, history of DAPP was not associated
 with pooled sICH (OR=2.03, 95% CI 0.75–5.25), 3-month mortality (OR=1.11,
 95% CI 0.87–1.40), 3-month FFO (OR=0.92, 95% CI 0.77–1.09), and 3-month FI
 (OR=1.01, 95% CI 0.89–1.15). Conclusions: After adjustment for potential
 confounders DAPP appears not to be associated with higher risk of adverse
 outcomes in AIS patients treated with IVT.
description: AppendixR1.DAPP.IVT_Supplement (For Neurology).docxPRISMA checklistDAPP.IVT_PRISMA checklist (for Neurology).docxMOOSE checklistR1.DAPP.IVT_MOOSE checklist (for Neurology).doc
DOI: 10.5061/dryad.79ck1tm
title: Data from: Geographical variation in bill size provides evidence for Allen’s rule in a cosmopolitan raptor

description: Aim. Avian beak morphology is a good example of how anatomical structures
 evolved in response to different selective pressures, such as diet and
 vocalizations, but also thermoregulation. The latter function was
 neglected until recently, but convincing evidence has been provided about
 the birds’ capacity to regulate heat dissipation through their highly
 vascularized bill. According to this adaptive function and coherently with
 the ecogeographical “Allen’s rule”, which predicts smaller body appendages
 in colder climates, large beaks should be favoured in warm environments.
 Here, we tested this prediction in the cosmopolitan common barn owl group.
 Location. World Time period. 1809-2017 Major taxa studied. Tyto alba
 species complex Methods. We analysed the variation in bill length relative
 to body size according to temperature, latitude and elevation in 7619 barn
 owls. The specimens were collected by 140 museums, and represent three
 distinct evolutionary lineages, occurring in geographically separated
 regions and covering the entire distribution range of the species complex:
 the Afro-Palearctic Tyto alba, the Australasian T. javanica, and the
 American T. furcata. Results. In the three lineages, bill becomes larger
 with increasing temperature. This convergent pattern of evolution of
 smaller bills in colder climates is associated with a latitudinal
 variation in temperature, as small-billed individuals occurred at higher
 latitudes than conspecifics living closer to the Equator. Moreover, in T.
 furcata large-billed birds mostly occur at lower elevation closer to the
 Equator, bill length decreasing progressively with concomitant increase in
 latitude and elevation. Discussion. These findings provide evidence of
 repeated evolution of bill size on a global scale that is compatible with
 the Allen’s rule. These results suggest a role of the bill as a potential
 heat-exchange surface, also in nocturnal raptors, which are not directly
 exposed to solar radiation and whose bill shape primarily evolved to hunt
 and consume animal prey.
description: Geographical variation
 in bill size provides evidence for Allen’s rule in a cosmopolitan
 raptor_data
DOI: 10.5061/dryad.1281jm4
title: Data from: Chemical preservation of tail feathers from Anchiornis huxleyi, a theropod dinosaur from the Tiaojishan Formation (Upper Jurassic, China)

description: A panel of geochemical techniques is used here to investigate the
 taphonomy of fossil feathers preserved in association with the skeleton of
 the Jurassic theropod Anchiornis huxleyi. Extant buzzard feathers were
 analysed in parallel to test whether the soft tissues morphologically
 preserved in the fossil also exhibit a high degree of chemical
 preservation. Scanning electron microscopy (SEM) and energy dispersive
 spectroscopy (EDS) indicate that clays and iron oxide pseudomorphs occur
 in the surrounding sediment and also reveal the preservation of
 melanosome-like microbodies in the fossil. Carbon gradient along a depth
 profile and co-occurrence of carbon and sulphur was shown in the fossil by
 elastic backscattering (EBS) and particle-induced X-ray emission (PIXE).
 The molecular composition of modern and fossil soft tissues was assessed
 from micro-Attenuated Total Reflectance Fourier Transform Infrared
 spectroscopy (micro-ATR FTIR), solid-state 13C nuclear magnetic resonance
 (13C CP-MAS NMR) and pyrolysis- gas chromatography-mass spectrometry in
 the presence of TMAH (TMAH-Py-GC-MS). Results show that the proteinaceous
 material that comprises the modern feathers is not present in the fossil
 feathers. The latter and the embedding sediment exhibit a highly aliphatic
 character. However, substantial differences could be evidenced between
 these samples, revealing that the organic matter of the fossil feathers
 is, at least partially, derived from original constituents of the
 feathers. The preservation of the fossil feathers, primarily expressed by
 the preservation of their morphology, seems to be associated with in situ
 polymerization of endogenous lipids. Sulphur probably played a role in the
 fossil preservation although no natural sulphurization took place.
description: Supplementary material
 for the main manuscriptCincottaetal.SI.docx
DOI: 10.5281/zenodo.18393500
title: TELEKOMMUNIKATSIYA TARMOQLARIDA KRIPTOGRAFIK PROTOKOLLAR VA ALGORITMLARNI TADQIQ QILISH

description:  Maqolada telekommunikatsiya tarmoqlarida kriptografik protokollar va algoritmlarni tadqiq qilish masalalari keng qamrovda o‘rganildi. Tadqiqot doirasida simmetrik va assimetrik shifrlash algoritmlari, TLS, IPsec va SSH protokollari, mobil (LTE, 5G), bulutli, IoT va M2M tarmoqlari uchun yengil kriptografik yechimlar, shuningdek kvantga chidamli algoritmlar, sun’iy intellekt va blokcheyn texnologiyalarining xavfsizlikka ta’siri tahlil qilindi. Tadqiqot natijalari telekommunikatsiya tarmoqlarida xavfsizlikni ta’minlash, protokollarni optimallashtirish va samarali kriptografik yechimlarni tanlashda ilmiy asos yaratadi.
DOI: 10.5281/zenodo.18393501
title: TELEKOMMUNIKATSIYA TARMOQLARIDA KRIPTOGRAFIK PROTOKOLLAR VA ALGORITMLARNI TADQIQ QILISH

description:  Maqolada telekommunikatsiya tarmoqlarida kriptografik protokollar va algoritmlarni tadqiq qilish masalalari keng qamrovda o‘rganildi. Tadqiqot doirasida simmetrik va assimetrik shifrlash algoritmlari, TLS, IPsec va SSH protokollari, mobil (LTE, 5G), bulutli, IoT va M2M tarmoqlari uchun yengil kriptografik yechimlar, shuningdek kvantga chidamli algoritmlar, sun’iy intellekt va blokcheyn texnologiyalarining xavfsizlikka ta’siri tahlil qilindi. Tadqiqot natijalari telekommunikatsiya tarmoqlarida xavfsizlikni ta’minlash, protokollarni optimallashtirish va samarali kriptografik yechimlarni tanlashda ilmiy asos yaratadi.
DOI: 10.5061/dryad.ft3qd24
title: Data from: Life history alterations upon oral and haemocoelic bacterial exposure in the butterfly Melitaea cinxia

description: Life history strategies often shape biological interactions by specifying
 the parameters for possible encounters, such as the timing, frequency or
 way of exposure to parasites. Consequentially alterations in life history
 strategies are closely intertwined with such interaction processes.
 Understanding the connection between life history alterations and
 host-parasite interactions can therefore be important to unveil potential
 links between adaptation to environmental change and changes in
 interaction processes. Here we studied how two different host-parasite
 interaction processes, oral and haemocoelic exposure to bacteria, affect
 various life histories of the Glanville fritillary butterfly Melitaea
 cinxia. We either fed or injected adult butterflies with the bacterium
 Micrococcus luteus and observed for differences in immune defenses,
 reproductive life histories and longevity, compared to control exposures.
 Our results indicate differences in how female butterflies adapt to the
 two exposure types. Orally infected females showed a reduction in clutch
 size and an earlier onset of reproduction, whereas, a reduction in egg
 weight was observed for haemocoelically exposed females. Both exposure
 types also led to shorter intervals between clutches and a reduced life
 span. These results indicate a relationship between host-parasite
 interactions and changes in life history strategies. This relationship
 could cast restrictions on the ability to adapt to new environments, and
 consequentially influence the population dynamics of a species in changing
 environmental conditions.
description: 1a_OralExposure_GeneExpressionRaw gene expression values for oral exposure for the selected genes of interest and three reference genes.The file additionally contains measurements for male butterflies, which were not used in the publication.1b_OralExposure_EncapsulationCalculated grey values of the inserted nylon filaments for encapsulation measurements after oral exposure.1c_OralExposure_ReproductionMeasurements of life history traits after oral exposure.1d_OralExposure_LifespanSurvival after oral exposure.2a_HaemExposure_GeneExpressionRaw gene expression values for haemocoelic exposure for the selected genes of interest and three reference genes.The file additionally contains measurements for male butterflies, which were not used in the publication.2b_HaemExposure_EncapsulationCalculated grey values of the inserted nylon filaments for encapsulation measurements after haemocoelic exposure.2c_HaemExposure_ReproductionMeasurements of life history traits after haemocoelic exposure.2d_HaemExposure_LifespanSurvival after haemocoelic exposure.Analysis Script (R markdown)R markdown script for the data analysis. To run the script, the data files 1a-1d & 2a-2d need to be located in the same folder as this script.AnalysisV3.RmdAnalysis Script (rendered)Rendered output for the data analysis.AnalysisV3.html
DOI: 10.5061/dryad.29pm4qs
title: Data from: Salty Sensors, Fresh Ideas: The use of molecular and imaging sensors in understanding plankton dynamics across marine and freshwater ecosystems

description: In situ molecular and imaging instrumentation development has advanced our
 knowledge of plankton processes in marine ecosystems. However, these
 technologies are not yet being applied widely in freshwater ecosystems.
 Here, we advocate for the use of marine molecular and imaging in situ
 sensors in freshwater ecosystems to answer a range of questions from
 fundamental plankton ecology to applied environmental issues. To
 accomplish this, we briefly review a selection of marine in situ
 instrumentation developed for the collection of molecular and imaging
 information on plankton communities. In addition, we interviewed a
 selection of instrumentation developers to determine if the transfer of
 sensor technology from marine to freshwater ecosystems is feasible and to
 illuminate the process of creating in situ sensors. Finally, we discuss
 the status of in situ sensors in freshwater ecosystems and how some of the
 reviewed technology could be transferred to lakes to address basic and
 applied research questions.
description: Deployment geographical
 location of in-situ of molecular and imaging systemsThis dataset is
 comprised of the approximate sampling deployment locations of in situ
 sensors. Molecular sensors include the Automatic Flow Injection Sampler
 (AFIS); Autonomous In Situ Fixation Multi-Sampler (AFIS-SYS); Autonomous
 Microbial Genosensor (AMG); Autonomous Microbial Sampler (AMS); Biological
 OsmoSampling System (BOSS); Deep-Sea ESP (D-ESP); Environmental Sample
 Processor (ESP); In Situ Filtration and Fixation Sampler (IFFS); In Situ
 Autonomous Biosampler (IS-ABS); Submersible Incubation Device (SID);
 Microbial Sampler-Submersible Incubation Device (MS-SID); Suspended
 Particulate Rosette Sampler (SUPR); and Suspended Particulate Rossette
 Sampler- Remote Environmental Monitoring UnitS (SUPR-REMUS). Imaging
 systems include: FlowCytobot (FCB); Imaging FlowCytobot (IFCB); In Situ
 Ichthyoplankton Imaging System (ISIIS); Lightframe On-sight Keyspecies
 Investigation (LOKI) system; Laser Optical Plankton Counter (LOPC
 –including the SOLOPC); Optical Plankton Counter (OPC); Shadowed Image
 Particle Profiling and Evaluation Recorder (SIPPER); Scripps Plankton
 Camera (SPC); Underwater Vision Profiler (UVP); Video Plankton Recorder
 (VPR); and ZOOplankton Visualization System (ZOOVIS).in_situ_sensors_dataset_final.xlsx