Find research datasets worth reusing

opencc-by-4.0Jul 2020View details →

The development dataset of the AI composition recognition competition, CSMT2020

The development dataset contains 6000 MIDI files with monophonic melodies generated by artificial intelligence algorithms. The tempo is between the 68bpm and 118bpm (beat per minute). The length of each melody is 8 bars, and the melody does not necessarily include complete phrase structures. There are two datasets with different music styles used as the training dataset of a certain number of algorithms, where the melodies in the development dataset are generated. The website of the challenge: <a href="http://www.csmcw-csmt.cn/data/2020/ai-composition-recognition2020/">http://www.csmcw-csmt.cn/data/2020/ai-composition-recognition2020</a> (Chinese instruction) <a href="https://ai-composition-recognition2020.github.io/english.html">https://ai-composition-recognition2020.github.io/english.html</a> (English instruction)

opencc-by-4.0Oct 2018View details →

Online Resource 1 – Maximal hoop stress developed in the lining of a tunnel excavated with a single shield TBM at the state of equilibrium (comparison between different calculation methods)

The maximal hoop stress developed in the lining of a tunnel at the state of equilibrium calculated with the various ConVergence-ConFinement (CV-CF) methods is compared with the results obtained with a 3D numerical model of a tunnel excavation. A sensibility analysis is performed in order to compare the performance of the CV-CF approaches. The choice of the values of the mechanical parameters of the ground and of the lining is carried out in an attempt to cover the large range of situations encountered within single shield TBM. The total set of results from the sensibility analysis is shown in this work. Results obtained from some empirical formula proposed by the authors are also included. A version 2 of the document with some minor corrections has been published.

opencc-zeroDec 2018View details →

Data from: Young but not defenseless: antifungal activity during embryonic development of a social insect

Termites live in environments heavily colonized by diverse microbial communities, including pathogens. Eggs laid within the nest likely experience similar pathogenic pressures as their older nestmates. Consequently, they may have also been under selective pressures to be immune-competent. Through in vitro experiments, we tested the ontogeny, location and strength of embryos' antifungal activity against the fungus Metarhizium brunneum. Extraembryonic washes and intraembryonic components were incubated with fungal conidia, which was then scored for viability. Fungistatic activity was location- and stage-dependent. Extraembryonic washes had relatively weak antifungal activity. Conversely, intraembryonic contents were highly antifungal, exhibiting increased potency through development. Boiling both embryonic washes and intraembryonic contents rescued conidia viability, indicating the antifungal agent(s) is (are) likely proteinaceous. Embryonic protein profiles shifted from putative vitellogenins in young embryos to multiple proteins in subsequent stages, suggesting that the increase in fungistatic activity may be due to the expression of endogenous proteins during embryogenesis. This study is the first to address embryonic antifungal activity in a hemimetabolous eusocial taxon. Our results support the hypothesis that microbes have been significant agents of selection, fostering the evolution of antifungal properties even in the most immature and supposed, most vulnerable stage of development.

opencc-zeroJul 2020View details →

Post-embryonic development of Fritzolenellus suggests the ancestral morphology of the early developmental stages in Trilobita

Trilobite development has been intensively explored during past decades, but information about ancestral character combinations in the early developmental stages of trilobites remains virtually unknown. Trilobites of the superfamily Olenelloidea are one of the earliest diverging groups. Study of their development coupled with the development of other early diverging trilobite groups can provide crucial information about the ancestral morphology of trilobite early stages. Herein we describe numerous well-preserved specimens of the olenelloid trilobite Fritzolenellus lapworthi. The earliest stages have circular cephala bearing intergenal spines and lacking genal spines. During subsequent development, morphological changes comprise the modification of the cephalic shape from circular to semi-circular, expansion of LA, gradual shortening of intergenal spines and origin and prolongation of genal spines. Trunk development of Fritzolenellus suggest that the development of macropleurae and macrospines are two independent processes and that origin of the opistotrunk is linked with the onset of phase 5 of cephalic development. The morphology of the early developmental stages of Fritzolenellus and some related taxa differs in many aspects from the morphology of equivalent stages of some other members of Olenelloidea. Consequently, two basic morphotypes are recognized during the early development of Olenelloidea – the Fritzolenellus and the Olenellus morphotypes. Comparison with Fallotaspidoidea and Redlichiina reveals that early developmental stages of these taxa share character combinations that are typical for Fritzolenellus morphotype. Such a comparison suggests that characters defining Fritzolenellus morphotype are ancestral for Trilobita. The Olenellus morphotype is likely a derived condition within Olenelloidea and might be related to predator deterrence.

opencc-zeroJul 2020View details →

Data from: Thyroid hormone receptor beta mutations alter photoreceptor development and function in Danio rerio (zebrafish)

We investigate mutations in trβ2, a splice variant of thrb, identifying changes in function, structure, and behavior in larval and adult zebrafish retinas. Two N-terminus CRISPR mutants were identified. The first is a 6BP+1 insertion deletion frameshift resulting in a truncated protein. The second is a 3BP in frame deletion with intact binding domains. ERG recordings of isolated cone signals showed that the 6BP+1 mutants did not respond to red wavelengths of light while the 3BP mutants did respond. 6BP+1 mutants lacked optomotor and optokinetic responses to red/black and green/black contrasts. Both larval and adult 6BP+1 mutants exhibit a loss of red-cone contribution to the ERG and an increase in UV-cone contribution. Transgenic reporters show loss of cone trβ2 activation in the 6BP+1 mutant but increase in the density of cones with active blue, green, and UV opsin genes. Antibody reactivity for red-cone LWS1 and LWS2 opsin was absent in the 6BP+1 mutant, as was reactivity for arrestin3a. Our results confirm a critical role for trβ2 in long-wavelength cone development.

opencc-zeroJul 2020View details →

Relative size underlies alternative morph development in a salamander

Size thresholds commonly underlie the induction of alternative morphological states. However, the respective importance of absolute and relative size to such thresholds remains uncertain. If absolute size governs expression, morph frequency should differ among environments that influence absolute sizes (e.g. resources, competition), and individuals of the same morph should have similar average sizes across environments. If relative size determines expression, the frequency of each morph may not differ among environments, but morphs within each environment should differ in size relative to one another. We tested these predictions in a salamander (Ambystoma talpoideum) that develops into either a terrestrial metamorph or an aquatic paedomorph. To generate size variation within and among environments, we reared individuals in mesocosm ponds across three conspecific densities. We found that morph frequency did not differ among density treatments, and the morphs were not similarly sized within each density treatment. Instead, within each environment, relatively larger individuals became metamorphs and relatively smaller individuals became paedomorphs. Relative size therefore determined morph development, highlighting the importance of an individual's social context to size-dependent morph induction.

Data from: Prevalence of afebrile malaria and development of risk-scores for gradation of villages: a study from a hot-spot in Odisha

Introduction: Malaria is a public health emergency in India and Odisha. The national malaria elimination programme aims to expedite early identification, treatment and follow-up of malaria cases in hot-spots through a robust health system, besides focusing on efficient vector control. This study, a result of mass screening conducted in a hot-spot in Odisha, aimed to assess prevalence, identify and estimate the risks and develop a management tool for malaria elimination. Methods: Through a cross-sectional study and using WHO recommended Rapid Diagnostic Test (RDT), 13221 individuals were screened. Information about age, gender, education and health practices were collected along with blood sample (5 µl) for malaria testing. Altitude, forestation, availability of a village health worker and distance from secondary health center were captured using panel technique. A multi-level poisson regression model was used to analyze association between risk factors and prevalence of malaria, and to estimate risk scores. Results: The prevalence of malaria was 5.8% and afebrile malaria accounted for 79 percent of all confirmed cases. Higher proportion of Pv infections were afebrile (81%). We found the prevalence to be 1.38 (1.1664 - 1.6457) times higher in villages where the Accredited Social Health Activist (ASHA) didn't stay; the risk increased by 1.38 (1.0428 - 1.8272) and 1.92 (1.4428 - 2.5764) times in mid- and high-altitude tertiles. With regard to forest coverage, villages falling under mid- and highest-tertiles were 2.01 times (1.6194 - 2.5129) and 2.03 times (1.5477 - 2.6809), respectively, more likely affected by malaria. Similarly, villages of mid tertile and lowest tertile of education had 1.73 times (1.3392 - 2.2586) and 2.50 times (2.009 - 3.1244) higher prevalence of malaria. Conclusion: Presence of ASHA worker in villages, altitude, forestation, and education emerged as principal predictors of malaria infection in the study area. An easy-to-use risk-scoring system for ranking villages based on these risk factors could facilitate resource prioritization for malaria elimination.

QTL mapping and marker development for tolerance to sulfur phytotoxicity in melon (Cucumis Melo)

Elemental sulfur is an effective, inexpensive fungicide for many foliar pathogens, but severe phytotoxicity prohibits its use on many melon varieties. Sulfur phytotoxicity causes chlorosis and necrosis of leaf tissue, leading to plant death in the most sensitive lines, while other varieties have little to no damage. A high-density, genotyping-by-sequencing (GBS)-based genetic map of a recombinant inbred line (RIL) population segregating for sulfur tolerance was used for a quantitative trait loci (QTL) mapping study of sulfur phytotoxicity in melon. One major (qSulf-1) and two minor (qSulf-8 and qSulf-12) QTL were associated with sulfur tolerance in the population. <a name="_Hlk40443716">The development of Kompetitive Allele-Specific PCR (KASP) markers developed across qSulf-1 decreased the QTL interval from 239 kb (cotyledons) and 157 kb (leaves) to 97 kb (both tissues). </a>The markers were validated for linkage to sulfur tolerance in a set of melon cultivars. These KASP markers can be incorporated into melon breeding programs for introgression of sulfur tolerance into elite melon germplasm.

opennotspecifiedMar 2020View details →

FIGURE 1 in Larval development and osteology of Callanthias platei (Teleostei: Callanthiidae) from Desventuradas Islands, South Pacific

FIGURE 1. Larval development of Callanthias platei, lateral view. A. Preflexion larva, 3 mm SL (MNHNCL ICT 7605). B. Flexion larva, 4.48 mm SL (MNHNCL ICT 7606). C. Postflexion larva, 6.09 mm SL (MNHNCL ICT 7603).

opennotspecifiedMar 2020View details →

FIGURE 3 in Larval development and osteology of Callanthias platei (Teleostei: Callanthiidae) from Desventuradas Islands, South Pacific

FIGURE 3. Osteological development of vertebral column, dorsal, anal and pelvic fins of Callanthias platei, lateral view. Red/pink structures, bone; blue structures, cartilage. A. 3 mm SL. B. 4.48 mm SL. C. 5.31 mm SL. D. 6.09 mm SL. adr: anal distal radial; apr: anal proximal radial; ap: anal pterygiophore; as: anal spine; asr: anal soft ray; ddr: dorsal distal radial; dmr: dorsal middle radial; dp: dorsal pterygiophore; dpr: dorsal proximal radial; ds: dorsal spine; dsr: dorsal soft ray; ha: haemal arch; hs: haemal spine; na: neural arch ns: neural spine; p: pelvis; pr: pelvic ray; ps: pelvic spine; snc: supraneural cartilages; v: vertebra.

Data from: Variation in thermal traits describing sex determination and development in Western Australian sea turtle populations

Both the development rate and sex of sea turtle embryos depend on incubation temperature, as all species are ectotherms and show temperature-dependent sex determination (TSD). Theory predicts that selection should act on populations to optimise developmental times and primary sex ratios. In this study, we use a consistent methodology to measure development rates and model the reaction norm that defines TSD in three populations of flatback turtles (Natator depressus) and two populations of green turtles (Chelonia mydas) that nest in Western Australia. We show that development rates vary between and within species, likely reflecting adaptation to local beach microclimates. Similarly, the parameters that define the TSD reaction norm vary between the two species, and among N. depressus populations, with pivotal temperatures (TPIV) varying by 1.5 °C (29.6 – 31.1 °C), and the transitional ranges of temperatures (TRT) varying by 1.4 – 3.3 °C. In contrast, we found a similar TPIV for the two C. mydas populations, but a wider TRT at the northernmost tropical rookery. Our findings support the view that thermal parameters in geographically-separated populations of sea turtles are broadly similar, but the variation we describe will be highly relevant for predicting how populations will respond to climate change.

Lagrangian Atmospheric Model output for the Control, Onset and Development experiments

This dataset consists of model outputs from the Control, Onset and Development experiments. Each experiment has six ensembles which were integrated for three years. 6-hourly instantaneous surface (1000hPa) zonal and meridional wind speed (m/s) between 31°S-31°N is recorded in uv1000hPa_{Control, Onset, Development}_ens{1, 2, 3, 4, 5, 6}.dat. 6-hourly accumulated precipitation (mm) between 32°S-32°N is stored in precip_{ Control, Onset, Development}_ens{1, 2, 3, 4, 5, 6}.dat. Note the precip.*dat records accumulated rainfall for the past 6 hours. The missing data is recorded as nan.

openother-openAug 2020View details →

poojaruhal/RP-commenting-practices-social-media: RP-commenting-practices-social-media: RP_TOSEM_2020 v.1.0.1 Second release of of the replication Package for the paper "What do Developers Discuss about Code Comment Conventions on Social Media"

RP-commenting-practices-social-media Replication Package for the paper "What do Developers Discuss about Code Comment Conventions on Social Media?" Structure <pre><code>Paper-presenation.pdf Makar_tool/ Data/ stackoverfow_questions_with_answers_by_tags.csv stackoverfow_tags_metrics.csv apache_mailing_list.csv mailing_lists_ASF_@dev_@users_1.csv mailing_lists_ASF_@dev_@users_2.csv quora.csv sample_stackoverfow_questions_with_answers_by_tags.csv Schemas/ apache_mailing_lists.json quora.json stackoverfow_questions_answers_by_tag.json stackoverfow_tag_count.json stackoverfow_tag_metrics.json RQ1/ LDA_input/ stackoverfow_raw_dataset.csv LDA_output/ Mallet/ output_csv/ docs-in-topics.csv topic-words.csv topics-in-docs.csv topics-metadata.csv output_html/ all_topics.html Docs/ Topics/ RQ2/ datasource_rawdata/ mailing_lists_selection_criteria.csv quora.csv stackoverflow.csv manual_analysis_output/ stackoverflow_quora_taxonomy.xlsx </code></pre> Contents of the Replication Package Paper-presenation.pdf presents the highlights of the work in a presenation. Makar_tool/ contains the data processed using the tool for the study <ul> <li> Data/ <ul> <li><code>stackoverfow_questions_with_answers_by_tags.csv</code> - all stackoverflow questions used in the study as stored in Makar <ul> <li><code>stackoverfow_tags_metrics.csv</code> - all data containing the calculations done for stackoverflow tag selection</li> <li><code>apache_mailing_list.csv</code> - statistically significant sample of <code>mailing_lists_ASF_@dev_@users_1.csv</code> and <code>mailing_lists_ASF_@dev_@users_2.csv</code> used in the study</li> <li><code>mailing_lists_ASF_@dev_@users_1.csv</code> - mailing list data used in the study as stored in Makar (part 1)</li> <li><code>mailing_lists_ASF_@dev_@users_2.csv</code> - mailing list data used in the study as stored in Makar (part 2)</li> <li><code>quora.csv</code> - all quora questions used in the study as stored in Makar</li> <li><code>sample_stackoverfow_questions_with_answers_by_tags</code> - statistically significant sample of <code>stackoverfow_questions_with_answers_by_tags.csv</code> used in the study</li> </ul> </li> </ul> </li> <li> Schemas/ <ul> <li><code>apache_mailing_lists.json</code> - data schema used in Makar to store mailing list data</li> <li><code>quora.json</code> - data schema used in Makar to store quora data</li> <li><code>stackoverfow_questions_answers_by_tag.json</code> - data schema used in Makar to store stackoverflow questions data</li> <li><code>stackoverfow_tag_count.json</code> - data schema used in Makar to lookup number of questions per tag available in stackoverflow</li> <li><code>stackoverfow_tag_metrics.json</code> - data schema used in Makar to stackoverflow tag metrics data</li> </ul> </li> <li> RQ1/ - contains the data used to answer RQ1 <ul> <li>LDA_input/ - input data used for LDA analysis <ul> <li><code>stackoverfow_raw_dataset.csv</code> - stackoverflow questions used to perform LDA analysis</li> </ul> </li> <li>LDA_output/ <ul> <li>Mallet/ - contains the LDA output generated by MALLET tool <ul> <li>output_csv/ <ul> <li><code>docs-in-topics.csv</code> - documents per topic</li> <li><code>topic-words.csv</code> - most relevant topic words</li> <li><code>topics-in-docs.csv</code> - topic probability per document</li> <li><code>topics-metadata.csv</code> - metadata per document and topic probability <ul> <li>output_html/ - Browsable results of mallet output</li> </ul> </li> <li><code>all_topics.html</code></li> <li><code>Docs/</code></li> <li><code>Topics/</code></li> </ul> </li> </ul> </li> </ul> </li> </ul> </li> <li> RQ2/ - contains the data used to answer RQ2 <ul> <li>datasource_rawdata/ - contains the raw data for each source <ul> <li><code>mailing_lists_selection_criteria.csv</code> - criteria used to select mailing_lists.</li> <li><code>quora.csv</code> - contains the processed dataset (like removing HTML tags). To know more about the preprocessing steps, please refer to the reproducibility section in the paper. The data is preprocessed using Makar tool.</li> <li><code>stackoverflow.csv</code> - contains the processed stackoverflow dataset. To know more about the preprocessing steps, please refer to the reproducibility section in the paper. The data is preprocessed using Makar tool.</li> </ul> </li> <li>manual_analysis_output/ <ul> <li><code>stackoverflow_quora_taxonomy.xlsx</code> - contains the classified dataset of stackoverflow and quora and description of taxonomy. <ul> <li><code>Taxonomy</code> - contains the description of the first dimension and second dimension categories. Second dimension categories are further divided into levels, separated by <code>|</code> symbol.</li> <li><code>stackoverflow-posts</code> - the questions are labelled relevant or irrelevant and categorized into the first dimension and second dimension categories. <ul> <li><code>quota-posts</code> - the questions are labelled relevant or irrelevant and categorized into the first dimension and second dimension categories.</li> </ul> </li> </ul> </li> </ul> </li> </ul> </li> </ul>

opencc-by-4.0Aug 2020View details →

Artifact for the ICSME 2020 Paper - What Developers (Care to) Know About Their System

This archive contains the supplementary material for the paper "What Developers (Care to) Recall: An Interview Survey on Smaller Systems" by Jacob Krüger and Regina Hebig, accepted at ICSME 2020.

Data from: Mechanisms for the development of microform patterns in peatlands of the Hudson Bay Lowland

Spatial surface patterns of hummocks, hollows, ridges, and pools (microtopography) are common features of many northern peatlands and are particularly distinct within the vast peatlands of the Hudson Bay Lowland (HBL), Canada. Hypotheses and models describe how small-scale feedbacks among vegetation, hydrology, and nutrients cause spatial differences in peat accumulation that enable microforms and surface patterns to develop over time. Empirical tests of the predictions from theoretical models of these proposed feedback mechanisms are limited, particularly in large peatland complexes such as the HBL. We investigate feedbacks controlling peatland structure and function in an ombrogenous bog and a minerogenous fen in the HBL. Our sites represent surface patterns found in many northern peatlands, specifically spatially irregular hummocks and hollows, and parallel ridges and pools that are perpendicular to slope. We found the occurrence of different spatial patterns depends on position within a peat landform, with these differences attributed to the ecohydrological setting. In turn, the ecohydrological setting, with different water table depths, nutrient availability, and species composition, influences the strength and direction of feedback mechanisms at the microform scale. Our data support the prediction of a positive feedback between plant productivity and acrotelm thickness for peat accumulation and hummock growth, and that this may be enhanced by water ponding on slopes to form ridge-pool tracks. We did not find evidence to support the proposed feedback among evapotranspiration (ET)-driven transport of water and nutrients for the development of hummocks. Our results suggest a combination of mechanisms operating at various temporal and spatial scales are associated with the development of surface patterns in northern peatlands.

The impact of learning opportunities on the development of learning and decision making: an experiment with passerine birds

Learning abilities have been shown to be influenced by the developmental context, namely through experiments that imposed severe nutritional and/or environmental constraints (i.e. lack of enrichment). In contrast, we know little on the impact of opportunities for learning on the development of cognition in animals, despite that such opportunities are known to influence human cognitive development. We exposed young zebra finches (Taenopygia guttata) (n=26) to one of three experimental conditions, i.e. an environment where (i) the presence of food was predicted by one colour cue (associative learning), (ii) a combination of two-colour cues (conditional learning), or (iii) colour cues were non-informative (control). After conducting two different discrimination tasks, our results show that experience with predictive cues can cause increased choice accuracy and decision-making speed. Our first learning task showed that individuals in the associative treatment outperformed the control treatment, while task 2 showed that individuals in the conditional treatment shad shorter latencies when making choices compared to the control treatment. We found no support for a speed-accuracy trade-off. This dataset provides a rare longitudinal and experimental examination of the effect of predictive vs non-predictive cues during development on the cognition of adult animals.

Data from: Development of an adrenocortical cancer humanized mouse model to characterize anti-PD1 effects on tumor microenvironment

Context: While the development of immune checkpoint inhibitors has transformed treatment strategies of several human malignancies, research models to study immunotherapy in ACC are lacking. Objective: To explore the effect of anti-PD1 immunotherapy on the alteration of the immune milieu in ACC in a newly generated preclinical model and correlate with the response of the matched patient. Design, Setting and Intervention: To characterize the CU-ACC2-M2B patient-derived xenograft in a humanized mouse model, evaluate the effect of a PD-1 inhibitor therapy and compare to the CU-ACC2 patient with metastatic disease. Results: Characterization of the CU-ACC2-hu-CB-BRGS model confirmed ACC origin and match with the original human tumor. Treatment of the mice with pembrolizumab demonstrated significant tumor growth inhibition (TGI = 60%) compared to controls, which correlated with increased tumor infiltrating lymphocyte activity, with an increase of human CD8+ T cells (p<0.05), HLA-DR+ T cells (p<0.05) as well as Granzyme B+ CD8+ T cells (<0.001). In parallel, treatment of the CU-ACC2 patient, who had progressive disease, demonstrated a partial response with 79%-100% reduction in the size of target lesions, and no new sites of metastasis. Pre-treatment analysis of the patient's metastatic liver lesion demonstrated abundant intra-tumoral CD8+ T cells by immunohistochemistry. Conclusions: Our study reports the first humanized ACC PDX mouse model which may be useful to define mechanisms and biomarkers of response and resistance to immune-based therapies, to ultimately provide more personalized care for patients with ACC.

opencc-zeroJun 2019View details →

Data from: Gene expression in the phenotypically plastic Arctic charr (Salvelinus alpinus): a focus on growth and ossification at early stages of development

Gene expression during development shapes the phenotypes of individuals. Although embryonic gene expression can have lasting effects on developmental trajectories, few studies consider the role of maternal effects, such as egg size, on gene expression. Using qPCR, we characterize relative expression of 14 growth and/or skeletal promoting genes across embryonic development in Arctic charr (Salvelinus alpinus). We test to what extent their relative expression is correlated with egg size and size at early life‐stages within the study population. We predict smaller individuals to have higher expression of growth and skeletal promoting genes, due to less maternal resources (i.e., yolk) and prioritization of energy toward ossification. We found expression levels to vary across developmental stages and only three genes (Mmp9, Star, and Sgk1) correlated with individual size at a given developmental stage. Contrary to our hypothesis, expression of Mmp9 and Star showed a non‐linear relationship with size (at post fertilization and hatching, respectively), whilst Sgk1 was higher in larger embryos at hatching. Interestingly, these genes are also associated with craniofacial divergence of Arctic charr morphs. Our results indicate that early life‐stage variation in gene expression, concomitant to maternal effects, can influence developmental plasticity and potentially the evolution of resource polymorphism in fishes.

CESM1.2 simulation output for: The role of westerly wind bursts during different seasons versus ocean heat recharge in the development of extreme El Niño in a climate model

This is the subset of CESM1.2 model simulation output that was used for analysis and visualization of Yu and Fedorov [2020] (DOI:10.1029/2020GL088381). Please refer to README for details.