Find research datasets worth reusing

opencc-zeroDec 2016View details →

Data from: Combining niche-shift and population genetic analyses predicts rapid phenotypic evolution during invasion

Rapid evolution of non-native species can facilitate invasion success, but recent reviews indicate that such microevolution rarely yields expansion of the climatic niche in the introduced habitats. However, because some invasions originate from a geographically restricted portion of the native species range and its climatic niche, it is possible that the frequency, direction and magnitude of phenotypic evolution during invasion has been underestimated. We explored the utility of niche-shift analyses in the red seaweed Gracilaria vermiculophylla, which expanded from the northeastern coastline of Japan to North America, Europe and northwestern Africa within the last 100 years. A genetically-informed climatic niche shift analysis indicates that native source populations occur in colder and highly seasonal habitats, while most non-native populations typically occur in warmer, less seasonal habitats. This climatic niche expansion predicts that non-native populations evolved greater tolerance for elevated heat conditions relative to native source populations. We assayed 935 field-collected and 325 common-garden thalli from 40 locations and as predicted, non-native populations had greater tolerance for ecologically-relevant extreme heat (40ºC) than did Japanese source populations. Non-native populations also had greater tolerance for cold and low-salinity stresses relative to source populations. The importance of local adaptation to warm temperatures during invasion was reinforced by evolution of parallel clines: populations from warmer, lower-latitude estuaries had greater heat tolerance than did populations from colder, higher-latitude estuaries in both Japan and eastern North America. We conclude that rapid evolution plays an important role in facilitating the invasion success of this and perhaps other non-native marine species. Genetically-informed ecological niche analyses readily generate clear predictions of phenotypic shifts during invasions, and may help to resolve debate over the frequency of niche conservatism versus rapid adaptation during invasion.

opencc-zeroDec 2017View details →

Data from: Plant diversity and density predict belowground diversity and function in an early successional alpine ecosystem

Despite decades of interest, few studies have provided evidence supporting theoretical expectations for coupled relationships between aboveground and belowground diversity and ecosystem functioning in non-manipulated naturalecosystems. We characterized plant species richness and density, soil bacterial, fungal and eukaryotic species richness and phylogenetic diversity (using 16S, ITS, and 18S gene sequencing), and ecosystem function (levels of soil C and N, and rates of microbial enzyme activities) along a natural gradient in plant richness and density in high-elevation, C-deficient soils to examine the coupling between above- and belowground systems. Overall, we observed a strong positive relationship between aboveground (plant richness and density) and belowground (bacteria, fungi, and non-fungal eukaryotes) richness. In addition to the correlations between plants and soil communities, C and N pools, and rates of enzyme activities increased as plant and soil communities became richer and more diverse. Our results suggest that the theoretically expected positive correlation between above- and belowground communities does exist in natural systems, but may be undetectable in late successional ecosystems due to the buildup of legacy organic matter that results in extremely complex belowground communities. In contrast, microbial communities in early successional systems, such as the system described here, are more directly dependent on contemporary inputs from plants and therefore are strongly correlated with plant diversity and density.

opencc-zeroFeb 2020View details →

Variable prediction accuracy of polygenic scores within an ancestry group

Fields as diverse as human genetics and sociology are increasingly using polygenic scores based on genome-wide association studies (GWAS) for phenotypic prediction. However, recent work has shown that polygenic scores have limited portability across groups of different genetic ancestries, restricting the contexts in which they can be used reliably and potentially creating serious inequities in future clinical applications. Using the UK Biobank data, we demonstrate that even within a single ancestry group (i.e., when there are negligible differences in linkage disequilibrium or in causal alleles frequencies), the prediction accuracy of polygenic scores can depend on characteristics such as the socio-economic status, age or sex of the individuals in which the GWAS and the prediction were conducted, as well as on the GWAS design. Our findings highlight both the complexities of interpreting polygenic scores and underappreciated obstacles to their broad use.

opencc-by-4.0Sep 2021View details →

Improving Build Outcome Prediction usingTextual Analysis of Source Code

The uploaded data sets contain code deltas and their corresponding feature vectors. Those were derived from 13 open-source Java-based projects.

opencc-by-4.0Jul 2021View details →

BEIRUT: Repository Mining for Defect Prediction

This artifact includes two CSV files. The sample_metrics.csv contains a sample of 153 metrics extracted from project <a href="https://ratis.apache.org/">ratis</a>. The sample_prediction.csv contains a sample of the prediction results from the application of defect prediction to the extracted metrics.

Predicted distribution of a rare and understudied forest carnivore: Humboldt martens (Martes caurina humboldtensis)

Many mammalian species have experienced range contractions. Following a reduction in distribution that has resulted in apparently small and disjunct populations, the Humboldt marten (Martes caurina humboldtensis) was recently designated as federally Threatened and state Endangered. This subspecies of Pacific marten occurring in coastal Oregon and northern California, also known as coastal martens, appear unlike martens that occur in snow-associated regions in that vegetation associations appear to differ widely between Humboldt marten populations. We expected current distributions represent realized niches, but estimating factors associated with long-term occurrence was challenging for this rare and little-known species. Here, we assessed the predicted contemporary distribution of Humboldt martens and interpret our findings as hypotheses correlated with the subspecies' niche to inform strategic conservation actions. We modeled Humboldt marten distribution using a maximum entropy (Maxent) approach. We spatially-thinned 10,229 marten locations collected from 1996–2020 by applying a minimum distance of 500-m between locations, resulting in 384 locations used to assess correlations of marten occurrence with biotic and abiotic variables. We independently optimized the spatial scale of each variable and focused development of model variables on biotic associations (e.g., hypothesized relationships with forest conditions), given that abiotic factors such as precipitation are largely static and not alterable within a management context. Humboldt marten locations were positively associated with increased shrub cover (salal (Gautheria shallon)), mast producing trees (e.g., tanoak, Notholithocarpus densiflorus), increased pine (Pinus sp.) proportion of total basal area, annual precipitation at home-range spatial scales, low and high amounts of canopy cover and slope, and cooler August temperatures. Unlike other recent literature, we found little evidence that Humboldt martens were associated with old-growth structural indices. This case study provides an example of how limited information on rare or lesser-known species can lead to differing interpretations, emphasizing the need for study-level replication in ecology. Humboldt marten conservation would benefit from continued survey effort to clarify range extent, population sizes, and fine-scale habitat use.

openother-ncJul 2021View details →

PSYCHE-D: predicting change in depression severity using person-generated health data (DATASET)

This dataset is made available under <a href="https://creativecommons.org/licenses/by-nc/4.0/">Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)</a>. See LICENSE.pdf for details. Dataset description Parquet file, with: <ul> <li>35694 rows</li> <li>154 columns</li> </ul> The file is indexed on [participant]_[month], such that 34_12 means month 12 from participant 34. All participant IDs have been replaced with randomly generated integers and the conversion table deleted. Column names and explanations are included as a separate tab-delimited file. Detailed descriptions of feature engineering are available from the linked publications. File contains aggregated, derived feature matrix describing person-generated health data (PGHD) captured as part of the DiSCover Project (<a href="https://clinicaltrials.gov/ct2/show/NCT03421223">https://clinicaltrials.gov/ct2/show/NCT03421223</a>). This matrix focuses on individual changes in depression status over time, as measured by PHQ-9. The DiSCover Project is a 1-year long longitudinal study consisting of 10,036 individuals in the United States, who wore consumer-grade wearable devices throughout the study and completed monthly surveys about their mental health and/or lifestyle changes, between January 2018 and January 2020. The data subset used in this work comprises the following: <ul> <li>Wearable PGHD: step and sleep data from the participants’ consumer-grade wearable devices (Fitbit) worn throughout the study</li> <li>Screener survey: prior to the study, participants self-reported socio-demographic information, as well as comorbidities</li> <li>Lifestyle and medication changes (LMC) survey: every month, participants were requested to complete a brief survey reporting changes in their lifestyle and medication over the past month</li> <li>Patient Health Questionnaire (PHQ-9) score: every 3 months, participants were requested to complete the PHQ-9, a 9-item questionnaire that has proven to be reliable and valid to measure depression severity</li> </ul> From these input sources we define a range of input features, both static (defined once, remain constant for all samples from a given participant throughout the study, e.g. demographic features) and dynamic (varying with time for a given participant, e.g. behavioral features derived from consumer-grade wearables). The dataset contains a total of 35,694 rows for each month of data collection from the participants. We can generate 3-month long, non-overlapping, independent samples to capture changes in depression status over time with PGHD. We use the notation ‘SM0’ (sample month 0), ‘SM1’, ‘SM2’ and ‘SM3’ to refer to relative time points within each sample. Each 3-month sample consists of: PHQ-9 survey responses at SM0 and SM3, one set of screener survey responses, LMC survey responses at SM3 (as well as SM1, SM2, if available), and wearable PGHD for SM3 (and SM1, SM2, if available). The wearable PGHD includes data collected from 8 to 14 days prior to the PHQ-9 label generation date at SM3. Doing this generates a total of 10,866 samples from 4,036 unique participants.

Pollinator community predicts trait-matching between oil-producing flowers and a guild of oil-collecting bees

The impact of pollinator community diversity on trait-matching in plant-pollinator interactions is poorly studied, even though many mutualisms involve multiple interaction partners. We studied ten communities in which one to three species of oil-collecting Rediviva bee pollinate the long-spurred, oil-producing flowers of Diascia 'floribunda' to examine how pollinator diversity affects covariation of functional traits across sites and trait-matching within sites. Floral spur-length was significantly correlated with weighted grand mean foreleg length of the local bee community but not with foreleg length of individual bee species. The closeness of trait-matching varied among populations and was inversely related to pollinator community diversity. For all bee species, trait-matching was closest at sites characterized by exclusive, pairwise interactions. Reduced trait-matching associated with increased community diversity for individual pollinator species, but close matching at the community level support the importance of community context for shaping interacting traits of flowers and pollinators.

opencc-zeroDec 2020View details →

Hydraulic prediction of drought-induced plant dieback and top-kill depends on leaf habit and growth form

Hydraulic failure caused by severe drought contributes to aboveground dieback and whole-plant death. The extent to which dieback or whole-plant death can be predicted by plant hydraulic traits has rarely been tested among species with different leaf habits and/or growth forms. We investigated 19 hydraulic traits in 40 woody species in a tropical savanna and their potential correlations with drought response during an extreme drought event during the El Niño–Southern Oscillation in 2015. Plant hydraulic trait variation was partitioned substantially by leaf habit but not growth form along a trade-off axis between traits that support drought tolerance versus avoidance. Semi-deciduous species and shrubs had the highest branch dieback and top-kill (complete aboveground death) among the leaf habits or growth forms. Dieback and top-kill were well explained by combining hydraulic traits with leaf habit and growth form, suggesting integrating life history traits with hydraulic traits will yield better predictions.

Predicting the competitive interactions and trophic niche consequences of a globally invasive fish with threatened native species

1. Novel trophic interactions between invasive and native species potentially increase levels of inter-specific competition in the receiving environment. However, theory on the trophic impacts of invasive fauna on native competitors is ambiguous, as while increased inter-specific competition can result in the species having constricted and diverged trophic niches, the species might instead increase their niche sizes, especially in omnivorous species. 2. The competitive interactions between an omnivorous invasive fish, common carp Cyprinus carpio, and a tropically analogous native and threatened fish, crucian carp Carassius carassius, were tested using comparative functional responses (CFRs). A natural pond experiment then presented the species in allopatry and sympatry, determining the changes in their trophic (isotopic) niche sizes and positions over four years. These predictive approaches were complemented by assessing their trophic relationships in wild populations. 3. CFRs revealed that compared to crucian carp, carp had a significantly higher maximum consumption rate. Coupled with a previous cohabitation growth study, these results predicted that competition between the species is asymmetric, with carp the superior competitor. 4. The pond experiment used stable isotope metrics to quantify shifts in the trophic (isotopic) niche sizes of the fishes. In allopatry, the isotopic niches of the two species were similar sized and diverged. Conversely, in sympatry, carp isotopic niches were always considerably larger than those of crucian carp and were strongly partitioned. Sympatric crucian carp had larger isotopic niches than allopatric conspecifics, a likely response to asymmetric competition from carp. However, carp isotopic niches were also larger in sympatry than allopatry. In the wild populations, the carp isotopic niches were always larger than crucian carp niches, and were highly divergent. 5. The superior competitive abilities of carp predicted in aquaria experiments were considered to be a process involved in sympatric crucian carp having larger isotopic niches than in allopatry. However, as sympatric carp also had larger niches than in allopatry, this suggests other ecological processes were also likely to be involved, such as those relating to fish prey resources. These results highlight the inherent complexity in determining how omnivorous invasive species integrate into food-webs and alter their structure.

Single species acute lethal toxicity tests are not predictive of relative population, community and ecosystem effects of two salinity types

Human mediated salinity increases are occurring in freshwaters globally, with consequent negative effects on freshwater biodiversity. Salinity comprises multiple anions and cations. While total concentrations are typically used to infer effects, individual ion concentrations and ion ratios are critical in determining effects. Moreover, estimates of toxicity from single species laboratory tests, may not accurately predict relative effects on populations, communities and ecosystems. Here we compare salinity increases from synthetic marine salts (SMS) and sodium bicarbonate (NaHCO3) in an outdoor mesocosm experiment in south-eastern Australia. We found different effects of salt types on stream macroinvertebrates at the population, community, and ecosystem function levels, where similar effects were predicted from single species laboratory tests. Our results caution against the use of single species laboratory derived toxicological data to predict both environmentally safe salinity levels and the relative effects of different salt sources on freshwater biodiversity.

opencc-by-4.0Mar 2021View details →

Implementation of an adaptive bias-aware extended Kalman filter for sea-ice data assimilation in the HARMONIE-AROME numerical weather prediction system: numerical experiments

This data set provides the post-processed output of the numerical experiments performed to assess the possible effects of applying sea ice data assimilation within the surface analysis procedure of the HARMONIE-AROME NWP system. Results of five numerical experiments are provided: <ul> <li>HA-REF – reference experiment without sea ice data assimilation applied, and with blending for upper-air initialization</li> <li>HA-EKF – sensitivity experiment with sea ice data assimilation applied, and with blending for upper-air initialization</li> <li>3DVAR-REF – reference experiment without sea ice data assimilation applied, and with 3DVAR for the upper-air analysis</li> <li>3DVAR-EKF – sensitivity experiment with sea ice data assimilation applied, and with 3DVAR for the upper-air analysis</li> <li>3DVAR-EKF-TS – sensitivity experiment with sea ice data assimilation, and with 3DVAR for the upper-air analysis using coupled surface and atmospheric data assimilation procedures</li> </ul> For the HA-REF and HA-EKF experiments a subset of the gridded model output is provided; for the 3DVAR-REF, 3DVAR-EKF and 3DVAR-EKF-TS experiments a subset of the gridded model output and model data extracted at the positions of the SYNOP and TEMP stations within the model domain are provided. Additionally, in-situ observations, covering the same time period as the 3DVAR-REF, 3DVAR-EKF, 3DVAR-EKF-TS experiments, are provided.

opencc-by-4.0Jul 2021View details →

Dataset for the publication of "WRF model parameter calibration to improve the prediction of tropicalcyclones over the Bay of Bengal using Machine Learning-basedMultiobjective Optimization"

The dataset consists of the modified WRF model software, that can be extracted and used in any Linux system with preinstalled required software. The namelists_file.zip consists of the namelist.input files that are used for the default and calibration simulations with different driving data namely, FNL files at 1deg with two nested domains, ERA files at 1deg with two nested domains, ERA files at 0.25deg with a single domain, and the ERA files at 0.25deg with two nested domains.

opencc-by-4.0Aug 2021View details →

Data deposition of the article 'Multi-Omics analysis identifies a lncRNA-related prognostic signature to predict bladder cancer recurrence'

Data deposition of the article 'Multi-Omics analysis identifies a lncRNA-related prognostic signature to predict bladder cancer recurrence'

opencc-zeroAug 2021View details →

Data for: Ecology and behavior predict an evolutionary trade-off between song complexity and elaborate plumages in antwrens (Aves, Thamnophilidae)

The environment can impose constraints on signal transmission properties such that signals should evolve in predictable directions (Sensory Drive Hypothesis). However, behavioral and ecological factors can limit investment in more than one sensory modality leading to a trade-off in use of different signals (Transfer Hypothesis). In birds, there is mixed evidence for both sensory drive and transfer hypothesis. Few studies have tested sensory drive while also evaluating the transfer hypothesis, limiting understanding of the relative roles of these processes in signal evolution. Here, we assessed both hypotheses using acoustic and visual signals in male and female antwrens (Thamnophilidae), a species-rich group that inhabits diverse environments and exhibits behaviors, such as mixed-species flocking, that could limit investment in different signal modalities. We uncovered significant effects of habitat (sensory drive) and mixed-species flocking behavior on both sensory modalities, and we revealed evolutionary trade-offs between song and plumage complexity, consistent with the transfer hypothesis. We also showed sex- and trait-specific responses in visual signals that suggest both natural and social selection play an important role in the evolution of sexual dimorphism. Altogether, these results support the idea that environmental (sensory drive) and behavioral pressures (social selection) shape signal evolution in antwrens.

opencc-by-4.0Mar 2020View details →

Code and data sets for "DeepLC can predict retention times for peptides that carry as-yet unseen modifications"

Code used to prepare the data sets, calibrate retention times, generate DeepLC models, make predictions, and generate the figures. See README.md for more information on how to use these files and reproduce the results reported in the manuscript titled "DeepLC can predict retention times for peptides that carry as-yet unseen modifications".

opencc-zeroAug 2021View details →

A trait-based framework for predicting foodborne pathogen risk from wild birds

Recent foodborne illness outbreaks have heightened pressures on growers to deter wildlife from farms, jeopardizing conservation efforts. However, it remains unclear which species, particularly birds, pose the greatest risk to food safety. Using >11,000 pathogen tests and 1,565 bird surveys covering 139 bird species from across the western U.S.A., we examined the importance of 11 traits in mediating wild bird risk to food safety. We tested whether traits associated with pathogen exposure (e.g., habitat associations, movement, and foraging strategy) and pace-of-life (clutch size and generation length) mediated foodborne pathogen prevalence and proclivities to enter farm fields and defecate on crops. Campylobacter spp. were the most prevalent enteric pathogen (8.0%), while Salmonella and Shiga-toxin producing E. coli (STEC) were rare (0.46% and 0.22% prevalence, respectively). We found that several traits related to pathogen exposure predicted pathogen prevalence. Specifically, Campylobacter and STEC-associated virulence genes were more often detected in species associated with cattle feedlots and bird feeders, respectively. Campylobacter was also more prevalent in species that consumed plants and had longer generation lengths. We found that species associated with feedlots were more likely to enter fields and defecate on crops. Our results indicated that canopy-foraging insectivores were less likely to deposit foodborne pathogens on crops, suggesting growers may be able to promote pest-eating birds and birds of conservation concern (e.g., via nest boxes) without necessarily compromising food safety. As such, promoting insectivorous birds may represent a win-win-win for bird conservation, crop production, and food safety. Collectively, our results suggest that separating crop production from livestock farming may be the best way to lower food safety risks from birds. More broadly, our trait-based framework suggests a path forward for co-managing wildlife conservation and food safety risks in farmland by providing a strategy for holistically evaluating the food safety risks of wild animals, including under-studied species.

opencc-by-4.0Aug 2021View details →

Clinical outcome prediction in COVID-19 patients by lymphocyte subsets analysis and monocytes' iTNF-α expression

Raw Box & Whiskers plot related to a manuscript submitted to "Biology" journal - MDPI - https://www.mdpi.com/journal/biology - https://doi.org/10.3390/biology10080735 Manuscript Title: Clinical outcome prediction in COVID-19 patients by lymphocyte subsets analysis and monocytes’ iTNF-α expression Authors: Gabriele Madonna 1&dagger;, Silvia Sale 2&dagger;, Mariaelena Capone 1, Chiara De Falco 2, Valentina Santocchio 2, Tiziana Di Matola 2, Giuseppe Fiorentino 3, Caterina Pirozzi 2, Anna D’Antonio 2, Rocco Sabatino 2, Lidia Atripaldi4, Umberto Atripaldi 4, Marcello Raffone 5, Marcello Curvietto 1, Antonio Maria Grimaldi 1, Vito Vanella 1, Lucia Festino 1, Luigi Scarpato 1, Marco Palla 1, Michela Spatarella 6, Francesco Perna 7, Pellegrino Cerino 8, Gerardo Botti 9, Roberto Parrella 10, Vincenzo Montesarchio 11, Paolo Antonio Ascierto 1&dagger;&dagger;* and Luigi Atripaldi 2&dagger;&dagger; Affiliations: 1 Melanoma, Cancer Immunotherapy and Development Therapeutics Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Napoli, Italy 2 UOC Biochimica Clinica, AORN Ospedali dei Colli - Monaldi – Cotugno - CTO, Napoli, Italy 3 UOC Fisiopatologia e Riabilitazione respiratoria, AORN Ospedali dei Colli - Monaldi – Cotugno - CTO, Napoli, Italy 4 University of Campania "Luigi Vanvitelli", Naples, Italy 5 UOC Microbiologia e Virologia, AORN Ospedali dei Colli - Monaldi – Cotugno - CTO, Napoli, Italy 6 UOSD di Farmacia, AORN Ospedali dei Colli - Monaldi – Cotugno - CTO, Napoli, Italy 7 Università degli Studi di Napoli "Federico II", Naples, Italy. 8 Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici (Na), Italy. 9 Scientific Direction, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Napoli, Italy 10 UOC Malattie Infettive ad Indirizzo Respiratorio, AORN Ospedali dei Colli - Monaldi – Cotugno -CTO, Napoli, Italy 11 UOC Oncologia, AORN Ospedali dei Colli - Monaldi – Cotugno - CTO, Napoli, Italy &dagger;These authors have contributed equally to this work and share first authorship &dagger;&dagger;These authors have contributed equally to this work and share senior authorship *Correspondence: Abstract of submitted Manuscript: T In December 2019 a novel coronavirus, “SARS-CoV-2”, was recognized as the cause of Coronavirus disease-2019 (COVID-19-disease). Several studies have explored the changes and the role of inflammatory cells and cytokines in the immunopathogenesis of disease, but until today the results have been controversial. Based on these premises, we carried out a retrospective assessment of monocytes’ intracellular TNF-α expression (iTNF-α) and on frequencies of lymphocyte sub-populations in twenty-five patients with moderate/severe COVID-19-disease. We found lymphopenia in all COVID-19 infected subjects compared with healthy subjects. On initial observation, in patients with favorable outcome we detected high absolute eosinophils count and high CD4+/CD8+ T lymphocytes ratio, while in the exitus group we observed high neutrophils and CD8+ T lymphocytes counts. During infection, in patients with favorable outcome we observed a rise in lymphocyte count, in monocytes and in Treg lymphocytes counts, in CD4+ and in CD8+ T lymphocytes count but a reduction in CD4+/CD8+ T lymphocytes ratio. Instead, in the exitus group we observed a reduction in Treg lymphocytes counts and a decrease in iTNF-α expression. Our preliminary findings point to a modulation of the different cellular mediators of immune system, which probably have a key role in the outcome of the COVID-19-disease. Funding: This work was supported by Grants from “Regione Campania” through “POR FESR CAMPANIA 2014-2020”, CUP H64I20000300002. Cite: Madonna, G.; Sale, S.; Capone, M.; De Falco, C.; Santocchio, V.; Di Matola, T.; Fiorentino, G.; Pirozzi, C.; D’Antonio, A.; Sabatino, R.; Atripaldi, L.; Atripaldi, U.; Raffone, M.; Curvietto, M.; Grimaldi, A.M.; Vanella, V.; Festino, L.; Scarpato, L.; Palla, M.; Spatarella, M.; Perna, F.; Cerino, P.; Botti, G.; Parrella, R.; Montesarchio, V.; Ascierto, P.A.; Atripaldi, L. Clinical Outcome Prediction in COVID-19 Patients by Lymphocyte Subsets Analysis and Monocytes’ iTNF-α Expression. Biology 2021, 10, 735. doi: <a href="https://doi.org/10.3390/biology10080735">10.3390/biology10080735</a>

opencc-by-4.0Aug 2021View details →

Supplementary Information for Consonance-emerging Hebbian Learning neural network model predicts discreteness of musical scales and the Natural Just Intonation scale

The following phenomena and features are apparent in music and auditory perception in general: the discreteness of the tones in musical scales [1], the prevalence of the tonal frequency span of one semitone (100 cents) in musical scales across cultures [1], the list of tonal intervals ordered by consonance [2], and the musical performers’ preference of the Natural Just-Intonation scale [3] (A). However, researchers still have no agreement about the causes and the emergence of said phenomena (A). Here we show that the consonance-pattern emerging neural network model introduced in our previous study [4], predicts and yields all the said phenomena (A) with a precision of 1/100th of a semitone (1 cent). This precision is beyond the resolution of human hearing [5], [6], [7]. Since the Hebbian learning paradigm and harmonicity are the main features of our model, we propose that they are sufficient conditions for any system to yield the said phenomena (A). Therefore, they have a crucial role in processing pitch, consonance, and music perception in general. As a consequence, we additionally propose that the mentioned phenomena (A) are a balanced result of the joint workings of the Hebbian paradigm (nurture and cultural exposure) and harmonicity (auditory physics and biology).