cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5491519.v1
title: Proa et al PeerJ Raw Data.zip

description: The form of the cranium can vary extensively among closely related species of papionins (Cercopithecidae, Primates), a fact that is often related to their adaptive differences to distinct diets. Yet, the form of the cranium can also vary greatly between males and females of the same species, even though both sexes tend to have the same diet. Here we use finite elements models and geometric morphometrics to test for differences in cranial biomechanical performance that could be attributed to differences in diet and feeding habits in male and female specimens of <i>Papio anubis</i> and <i>Theropithecus gelada</i>, two extant papionin species with known diets. It is expected that adaptation to that same diet must have occurred in both sexes, despite differences in form. Strain contour plots show that differences can be seen between male and female of each species, but differences between male and female <i>T. gelada </i>are much larger than those between male and female <i>P. anubis</i> for all bites. Nevertheless, larger differences in strain are seen between species, rather than between male and female of the same species. An analysis of deformations shows male and female of each species falling with each other, and away from the other species. <i>P. anubis</i> male and female deform almost identically, with the female deforming only slightly less than the male for all bites. Differences between male and female <i>T. gelada</i> are more marked, with the female deforming far less than the male particularly during incisor bites; the trajectory followed, though, is the same, with differences being mainly in magnitude of deformation. These results are an indicator that diet might have had a major adaptive effect on papionin cranial form, but they also indicate that papionin cranial form may be highly constrained by other non-masticatory functions. Also, these results highlight the difficulties in trying to interpret dietary ecology from modes and magnitudes of cranial deformation, which, being difficult in extant species with known diets and sexes, becomes extremely challenging when applied to extinct species.
DOI: 10.6084/m9.figshare.5491492.v2
title: Farmer and fisher entry decisions

description: Data to support statistical modeling of farmer and fisher entry and exit decisions in study communities of Nicaraguan Caribbean coast. The data file, fishprice.csv, was used to generate Fig. 5. The data file, roadexports.csv, was used to generate Fig. 6. The data file, foodoutlet.csv, was used to generate Fig. 7. All other data files were used to model farmer entry, farmer exit, fisher entry, and fisher exit decisions.
DOI: 10.6084/m9.figshare.5491324
title: A geometric approach to the alignment of sensor arrays in optical instruments

description: Demonstration of an algorithm to align a sensor array in an optical instrument by imaging a grid pattern of dots. Included in this dataset is all the computer code required to run the algorithm, as well as an example set of images that are used to run the algorithm. All code is in python and available open source.<br>The demonstration is provided in an ipython notebook, as well as .pdf and .html format. The image data is included as .jpg files.
DOI: 10.6084/m9.figshare.5491492.v1
title: Farm Enter

description: Data to support farm entry model in stated publication
DOI: 10.6084/m9.figshare.5491324.v1
title: A geometric approach to the alignment of sensor arrays in optical instruments

description: Demonstration of an algorithm to align a sensor array in an optical instrument by imaging a grid pattern of dots. Included in this dataset is all the computer code required to run the algorithm, as well as an example set of images that are used to run the algorithm. All code is in python and available open source.<br>The demonstration is provided in an ipython notebook, as well as .pdf and .html format. The image data is included as .jpg files.
DOI: 10.6084/m9.figshare.5491522.v1
title: Classified Forest Shapefile - 2009

description: This shapefile represents the maximum extent of forest cover (all species) for the year 2009. Details on how this was created can be found in the associated manuscript.<br>
DOI: 10.6084/m9.figshare.5488918.v2
title: alphavirus and flavivirus data

description: Jittered (5km) gps points of cases (alpha and flavi viruses) and raw data for lasso model and table 1.
DOI: 10.6084/m9.figshare.5488918
title: alphavirus and flavivirus data

description: Jittered (5km) gps points of cases (alpha and flavi viruses) and raw data for lasso model and table 1.
DOI: 10.6084/m9.figshare.5488756
title: Figures for "The topography of the environment alters the optimal search strategy for active particles"

description: Figures for "The topography of the environment alters the optimal search strategy for active particles"<br>
DOI: 10.6084/m9.figshare.5488690
title: Intrinsic vulnerability of the Isonzo/Soča high plain aquifer (NE Italy – W Slovenia)

description: The paper presents the map of intrinsic groundwater vulnerability of the Isonzo/Soča High Plain, which is located between the Collio Hills and the Classical Karst Region and holds an aquifer shared between Italy and Slovenia. The map, produced at a scale of 1:25,000 and printed in A0 format, was obtained by means of the SINTACS method and shows the intrinsic vulnerability of the aquifer in terms of seven vulnerability classes, from extremely high to low. It is accompanied by four supplementary sketches that illustrate the geological framework, the bedrock top surface, the groundwater flow paths, the Hazard Index map and three diagrams that summarize the percentages of vulnerability classes and of Hazard Index classes of the study area.
DOI: 10.6084/m9.figshare.5488744
title: Benchmark dataset for evaluation of range-based people tracker classifiers in mobile robots

description: Benchmark dataset which can be used to evaluate the performance of different approaches for detecting and tracking people by using lidar sensors. Information contained at the dataset is specially suitable to be used as training data for neural network-based classifiers
DOI: 10.6084/m9.figshare.5488690.v1
title: Intrinsic vulnerability of the Isonzo/Soča high plain aquifer (NE Italy – W Slovenia)

description: The paper presents the map of intrinsic groundwater vulnerability of the Isonzo/Soča High Plain, which is located between the Collio Hills and the Classical Karst Region and holds an aquifer shared between Italy and Slovenia. The map, produced at a scale of 1:25,000 and printed in A0 format, was obtained by means of the SINTACS method and shows the intrinsic vulnerability of the aquifer in terms of seven vulnerability classes, from extremely high to low. It is accompanied by four supplementary sketches that illustrate the geological framework, the bedrock top surface, the groundwater flow paths, the Hazard Index map and three diagrams that summarize the percentages of vulnerability classes and of Hazard Index classes of the study area.
DOI: 10.6084/m9.figshare.5488687.v1
title: eye analysis hdf5

description: this file is required for the run_plots.py script
DOI: 10.6084/m9.figshare.5488660
title: Gold(I)-assisted catalysis – a comprehensive view on the [3,3]-sigmatropic rearrangement of allyl acetate

description: The unified reaction valley approach (URVA) combined with the local mode, ring puckering and electron density analysis is applied to elucidate the mechanistic differences of the non-catalysed and the Au[I]-N-heterocyclic carbene (NHC)-catalysed [3,3]-sigmatropic rearrangement of allyl acetate. Using a dual-level approach (DFT and DLPNO-CCSD(T)), the influence of solvation, counter-ions, bulky and electron withdrawing/donating substituents as well as the exchange of the Au[I]-NHC with a Au[I]-phosphine catalyst is investigated. The catalyst breaks up the rearrangement into two steps by switching between Au[I]–π and Au[I]–σ complexation, thus avoiding the energy-consuming CO cleavage in the first step. Based on local stretching force constants <i>k</i><sup><i>a</i></sup>(C=C), we derive for the first time a quantitative measure of the π-acidity of the Au[I] catalyst; in all catalysed reactions, the bond order <i>n</i>(C=C) drops from 2 to 1.65. The ring puckering analysis clarifies that all reactions start and end via a six-membered ring with a boat form. All Au[I]–σ-complex intermediates show a considerable admixture of the chair form. The non-catalysed [3,3]-sigmatropic rearrangement goes through a maximum of charge separation between the allyl and acetate units at the transition state, while all catalysed reactions proceed via a minimum of charge separation reached in the region of the Au[I]–σ-complex.
DOI: 10.6084/m9.figshare.5488756.v1
title: Dataset for "The topography of the environment alters the optimal search strategy for active particles"

description: Dataset for "The topography of the environment alters the optimal search strategy for active particles"<br>
DOI: 10.6084/m9.figshare.5488660.v1
title: Gold(I)-assisted catalysis – a comprehensive view on the [3,3]-sigmatropic rearrangement of allyl acetate

description: The unified reaction valley approach (URVA) combined with the local mode, ring puckering and electron density analysis is applied to elucidate the mechanistic differences of the non-catalysed and the Au[I]-N-heterocyclic carbene (NHC)-catalysed [3,3]-sigmatropic rearrangement of allyl acetate. Using a dual-level approach (DFT and DLPNO-CCSD(T)), the influence of solvation, counter-ions, bulky and electron withdrawing/donating substituents as well as the exchange of the Au[I]-NHC with a Au[I]-phosphine catalyst is investigated. The catalyst breaks up the rearrangement into two steps by switching between Au[I]–π and Au[I]–σ complexation, thus avoiding the energy-consuming CO cleavage in the first step. Based on local stretching force constants <i>k</i><sup><i>a</i></sup>(C=C), we derive for the first time a quantitative measure of the π-acidity of the Au[I] catalyst; in all catalysed reactions, the bond order <i>n</i>(C=C) drops from 2 to 1.65. The ring puckering analysis clarifies that all reactions start and end via a six-membered ring with a boat form. All Au[I]–σ-complex intermediates show a considerable admixture of the chair form. The non-catalysed [3,3]-sigmatropic rearrangement goes through a maximum of charge separation between the allyl and acetate units at the transition state, while all catalysed reactions proceed via a minimum of charge separation reached in the region of the Au[I]–σ-complex.
DOI: 10.6084/m9.figshare.5488588.v2
title: EgoNet identifies differential ego-modules and pathways related to prednisolone resistance in childhood acute lymphoblastic leukemia

description: <b>Purpose:</b> To extract feature ego-modules and pathways in childhood acute lymphoblastic leukemia (ALL) resistant to prednisolone treatment, and further to explore the mechanisms behind prednisolone resistance. <b>Materials and methods:</b> EgoNet algorithm was used to identify candidate ego-network modules, mainly via constructing differential co-expression network (DCN); selecting ego genes; collecting ego-network modules; refining candidate modules. Afterwards, statistical significance was calculated for these candidate modules. Biological functions of differential ego-network modules were identified using Reactome database. To verify this proposed method can lead to truly positive findings in clinical settings, support vector machine (SVM) was utilized to compute the AUC values for each significant pathway using 3-fold cross-validation method. To predict the reliability of our findings, another established method (attract) was used to identify the differential attractor modules using the same microarray profile. <b>Results:</b> After eliminating the modules with classification accuracy &lt; 0.9 and node number &lt; 15, only ego-network module 30 was eligible. After significance calculation, module 30 was significant. Module 30 was enriched in APC/C-mediated degradation of cell cycle proteins. The AUC for the significant pathway of APC/C-mediated degradation of cell cycle proteins was 0.915. Although the attract method obtained more modules, the module identified by our proposed method owned more gene nodes, and had more classification ability (AUC = 0.915). <b>Conclusion:</b> One differential ego-network module identified in childhood ALL resistance to prednisolone based on DCN and EgoNet, might be helpful to reveal the mechanisms underlying prednisolone resistance in childhood ALL.
DOI: 10.6084/m9.figshare.5488342
title: Fishery and Hatchery Effects on an Endangered Salmon Population with Low Productivity

description: We estimated the natural spawner–fry stock–recruitment relationship and juvenile survival rates for Sacramento River winter Chinook Salmon <i>Oncorhynchus tshawytscha</i> in California and used these estimates to examine the expected numbers of spawners and fishing mortality under different fishing mortality rates and levels of hatchery supplementation. A stochastic, age-structured population dynamics model was fit to fry and female spawner abundance data for the years 1996–2010. Estimated survival rates of fry through the end of the first year in the ocean were generally &lt;0.5%. Estimated survival rates of hatchery-origin fish from egg to the end of the first year in the ocean were on average about four times greater than the estimated maximum rate for natural-origin fish. The hatchery program was estimated to increase the number of spawners returning to natural spawning areas and thereby increase the fishing mortality rate that could be sustained. Assessing the past or future net effect of the hatchery on the size of the natural population would require quantifying any potential reduction in the productivity of the natural population as a result of reduced fitness of hatchery-origin fish spawning in natural spawning areas. Received February 21, 2013; accepted December 14, 2013.
DOI: 10.6084/m9.figshare.5488276
title: prf fit and mapper glm results

description: this file is necessary to reproduce the analyses performed in run_plots.py
DOI: 10.6084/m9.figshare.5488276.v1
title: prf fit and mapper glm results

description: this file is necessary to reproduce the analyses performed in run_plots.py
DOI: 10.6084/m9.figshare.5488342.v1
title: Fishery and Hatchery Effects on an Endangered Salmon Population with Low Productivity

description: We estimated the natural spawner–fry stock–recruitment relationship and juvenile survival rates for Sacramento River winter Chinook Salmon <i>Oncorhynchus tshawytscha</i> in California and used these estimates to examine the expected numbers of spawners and fishing mortality under different fishing mortality rates and levels of hatchery supplementation. A stochastic, age-structured population dynamics model was fit to fry and female spawner abundance data for the years 1996–2010. Estimated survival rates of fry through the end of the first year in the ocean were generally &lt;0.5%. Estimated survival rates of hatchery-origin fish from egg to the end of the first year in the ocean were on average about four times greater than the estimated maximum rate for natural-origin fish. The hatchery program was estimated to increase the number of spawners returning to natural spawning areas and thereby increase the fishing mortality rate that could be sustained. Assessing the past or future net effect of the hatchery on the size of the natural population would require quantifying any potential reduction in the productivity of the natural population as a result of reduced fitness of hatchery-origin fish spawning in natural spawning areas. Received February 21, 2013; accepted December 14, 2013.
DOI: 10.6084/m9.figshare.5488234
title: Design matrix for AF model

description: This file is required when wanting to run AF modeling
DOI: 10.6084/m9.figshare.5488246
title: frames for plotting pRF results

description: This file indicates which index in from the results conforms to which fitted pRF parameter
DOI: 10.6084/m9.figshare.5488246.v1
title: frames for plotting pRF results

description: This file indicates which index in from the results conforms to which fitted pRF parameter
DOI: 10.6084/m9.figshare.5488234.v1
title: Design matrix for AF model

description: This file is required when wanting to run AF modeling
DOI: 10.6084/m9.figshare.5488234.v2
title: Design matrix for AF model

description: This file is required when wanting to run AF modeling
DOI: 10.6084/m9.figshare.5488234.v4
title: Design matrix for AF model

description: This file is required when wanting to run AF modeling
DOI: 10.6084/m9.figshare.5488093
title: Supplementary Material for: Increased Platelet-Monocyte Interaction in Stable COPD in the Absence of Platelet Hyper-Reactivity

description: <b><i>Background:</i></b> Chronic obstructive pulmonary disease (COPD) is well known for its cardiovascular co-morbidities. Increased platelet-monocyte interaction is found in COPD and may reflect altered platelet function and a potential role for anti-platelet therapy. <b><i>Objectives:</i></b> The objectives were to investigate platelet-monocyte interaction, platelet activation and reactivity and plasmatic coagulation in stable COPD. <b><i>Methods:</i></b> Platelet-monocyte interaction and platelet activation were determined by flow cytometry in 30 stable COPD patients and 25 controls. Platelet activation was measured by binding of fibrinogen to the activated fibrinogen receptor and platelet P-selectin expression at baseline and after platelet stimulation with platelet agonists. Plasmatic coagulation was measured by D-dimer and thrombin generation. <b><i>Results:</i></b> Platelet-monocyte interaction was increased in stable COPD (median fluorescence intensity of platelet CD61 was 19.8 [IQR 14.0-33.2] vs. 10.0 [IQR 8.7-16.7], <i>p</i> = 0.002). In contrast, platelet activation and reactivity, reflected by fibrinogen binding and P-selectin expression, were the same in both groups. Plasma P-selectin and interleukin-6 were increased in COPD (<i>p</i> = 0.01 and <i>p</i> = 0.02, respectively), whereas soluble fibrinogen, D-dimer and thrombin generation were similar. <b><i>Conclusions:</i></b> Increased platelet-monocyte interaction was found in the absence of platelet hyper-reactivity and activation of plasmatic coagulation in stable COPD. Future clinical evaluation of the effects of different anti-platelet drugs in COPD is warranted, as anti-platelet therapy may interfere with platelet-monocyte interaction.
DOI: 10.6084/m9.figshare.5488069
title: Supplementary Material for: Early Environmental Enrichment Enhances Abnormal Brain Connectivity in a Rabbit Model of Intrauterine Growth Restriction

description: <b><i>Introduction:</i></b> The structural correspondence of neurodevelopmental impairments related to intrauterine growth restriction (IUGR) that persists later in life remains elusive. Moreover, early postnatal stimulation strategies have been proposed to mitigate these effects. Long-term brain connectivity abnormalities in an IUGR rabbit model and the effects of early postnatal environmental enrichment (EE) were explored. <b><i>Materials and Methods:</i></b> IUGR was surgically induced in one horn, whereas the contralateral one produced the controls. Postnatally, a subgroup of IUGR animals was housed in an enriched environment. Functional assessment was performed at the neonatal and long-term periods. At the long-term period, structural brain connectivity was evaluated by means of diffusion-weighted brain magnetic resonance imaging and by histological assessment focused on the hippocampus. <b><i>Results:</i></b> IUGR animals displayed poorer functional results and presented altered whole-brain networks and decreased median fractional anisotropy in the hippocampus. Reduced density of dendritic spines and perineuronal nets from hippocampal neurons were also observed. Of note, IUGR animals exposed to enriched environment presented an improvement in terms of both function and structure. <b><i>Conclusions:</i></b> IUGR is associated with altered brain connectivity at the global and cellular level. A strategy based on early EE has the potential to restore the neurodevelopmental consequences of IUGR.
DOI: 10.6084/m9.figshare.5488051
title: Cost-Utility Analysis of a Six-Weeks <i>Ganoderma Lucidum-</i>Based Treatment for Women with Fibromyalgia: A Randomized Double-Blind, Active Placebo-Controlled Trial

description: <b>Purpose:</b> To determine the effectiveness of adding <i>Ganoderma lucidum</i> (GL) to standard care for patients with fibromyalgia (FM), and to examine the costs per quality-adjusted life year (QALY) gained from this nutritional supplementation. <b>Materials and methods:</b> This was a randomised controlled trial with a random allocation of participants to two groups; experimental group and active-placebo controlled group. A total of 26 women with FM participated in the experimental group. These participants were instructed to take 3 g of micromilled GL twice a day for six weeks. EQ-5D-5L was used to obtain the utilities and a non-parametric bootstrap was used to plot the acceptability curve. <b>Results:</b> Of the women initially recruited, over 81% completed the experimental treatment. The incremental QALY in the GL group was 0.177, and the incremental QALY in the active placebo group was 0.101. Therefore, the difference in terms of QALYs was 0.076 and the incremental cost-utility ratio was €1348.55/QALYs. The cost-utility acceptability curve showed 90% probability that the addition of GL to the standard care as a nutritional supplement is cost-effective. <b>Conclusions:</b> The GL as nutritional supplementation in patients with FM is cost-effective in women with FM. To authors’ knowledge, the current study reports the first cost-utility analysis of GL as a nutritional supplement.
DOI: 10.6084/m9.figshare.5488045.v1
title: Mortality Salience Effect in the Perspective of Uncertainty

description: Study1 directly explored how self-uncertainty affects conformity. Study2 tested the hypothesis that self-uncertainty mediates the effect of <i>MS </i>on conformity. Study 3 investigated the relationship of death-anxiety, self-uncertainty and conformity traits.
DOI: 10.6084/m9.figshare.5488051.v1
title: Cost-Utility Analysis of a Six-Weeks <i>Ganoderma Lucidum-</i>Based Treatment for Women with Fibromyalgia: A Randomized Double-Blind, Active Placebo-Controlled Trial

description: <b>Purpose:</b> To determine the effectiveness of adding <i>Ganoderma lucidum</i> (GL) to standard care for patients with fibromyalgia (FM), and to examine the costs per quality-adjusted life year (QALY) gained from this nutritional supplementation. <b>Materials and methods:</b> This was a randomised controlled trial with a random allocation of participants to two groups; experimental group and active-placebo controlled group. A total of 26 women with FM participated in the experimental group. These participants were instructed to take 3 g of micromilled GL twice a day for six weeks. EQ-5D-5L was used to obtain the utilities and a non-parametric bootstrap was used to plot the acceptability curve. <b>Results:</b> Of the women initially recruited, over 81% completed the experimental treatment. The incremental QALY in the GL group was 0.177, and the incremental QALY in the active placebo group was 0.101. Therefore, the difference in terms of QALYs was 0.076 and the incremental cost-utility ratio was €1348.55/QALYs. The cost-utility acceptability curve showed 90% probability that the addition of GL to the standard care as a nutritional supplement is cost-effective. <b>Conclusions:</b> The GL as nutritional supplementation in patients with FM is cost-effective in women with FM. To authors’ knowledge, the current study reports the first cost-utility analysis of GL as a nutritional supplement.