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Book ; Online: From Time Series to Networks in R with the ts2net Package

Ferreira, Leonardo N.

2022

Abstract: Network science established itself as a prominent tool for modeling time series and complex systems. This modeling process consists of transforming a set or a single time series into a network. Nodes may represent complete time series, segments, or ... ...

Abstract	Network science established itself as a prominent tool for modeling time series and complex systems. This modeling process consists of transforming a set or a single time series into a network. Nodes may represent complete time series, segments, or single values, while links define associations or similarities between the represented parts. R is one of the main programming languages used in data science, statistics, and machine learning, with many packages available. However, no single package provides the necessary methods to transform time series into networks. This paper presents ts2net, an R package for modeling one or multiple time series into networks. The package provides the time series distance functions that can be easily computed in parallel and in supercomputers to process larger data sets and methods to transform distance matrices into networks. Ts2net also provides methods to transform a single time series into a network, such as recurrence networks, visibility graphs, and transition networks. Together with other packages, ts2net permits using network science and graph mining tools to extract information from time series.
Keywords	Computer Science - Social and Information Networks ; Computer Science - Machine Learning
Subject code	006
Publishing date	2022-08-20
Publishing country	us
Document type	Book ; Online
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Article: Oxidative Damage and Antioxidants as Markers for the Selection of Emersion Hardening Treatments in Greenshell

Delorme, Natalí J / Burritt, David J / Zamora, Leonardo N / Welford, Mena R V / South, Paul M

Antioxidants (Basel, Switzerland)

2024 Volume 13, Issue 2

Abstract: Transport out of the water is one of the most challenging events for ... ...

Abstract	Transport out of the water is one of the most challenging events for juvenile
Language	English
Publishing date	2024-02-04
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704216-9
ISSN	2076-3921
ISSN	2076-3921
DOI	10.3390/antiox13020198
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Article ; Online: An Extended Admixture Pulse Model Reveals the Limitations to Human-Neandertal Introgression Dating.

Iasi, Leonardo N M / Ringbauer, Harald / Peter, Benjamin M

Molecular biology and evolution

2021 Volume 38, Issue 11, Page(s) 5156–5174

Abstract: Neandertal DNA makes up 2-3% of the genomes of all non-African individuals. The patterns of Neandertal ancestry in modern humans have been used to estimate that this is the result of gene flow that occurred during the expansion of modern humans into ... ...

Abstract	Neandertal DNA makes up 2-3% of the genomes of all non-African individuals. The patterns of Neandertal ancestry in modern humans have been used to estimate that this is the result of gene flow that occurred during the expansion of modern humans into Eurasia, but the precise dates of this event remain largely unknown. Here, we introduce an extended admixture pulse model that allows joint estimation of the timing and duration of gene flow. This model leads to simple expressions for both the admixture segment distribution and the decay curve of ancestry linkage disequilibrium, and we show that these two statistics are closely related. In simulations, we find that estimates of the mean time of admixture are largely robust to details in gene flow models, but that the duration of the gene flow can only be recovered if gene flow is very recent and the exact recombination map is known. These results imply that gene flow from Neandertals into modern humans could have happened over hundreds of generations. Ancient genomes from the time around the admixture event are thus likely required to resolve the question when, where, and for how long humans and Neandertals interacted.
MeSH term(s)	Animals ; DNA/genetics ; Gene Flow ; Genome ; Humans ; Neanderthals/genetics
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2021-07-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	998579-7
ISSN	1537-1719 ; 0737-4038
ISSN (online)	1537-1719
ISSN	0737-4038
DOI	10.1093/molbev/msab210
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Article ; Online: The small-world network of global protests

Leonardo N. Ferreira / Inho Hong / Alex Rutherford / Manuel Cebrian

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 8

Abstract: Abstract Protest diffusion is a cascade process that can spread over different regions of the planet. The way and the extension that this phenomenon can occur is still not properly understood. Here, we empirically investigate this question using protest ... ...

Abstract	Abstract Protest diffusion is a cascade process that can spread over different regions of the planet. The way and the extension that this phenomenon can occur is still not properly understood. Here, we empirically investigate this question using protest data from GDELT and ICEWS, two of the most extensive and longest-running data sets freely available. We divide the globe into grid cells and construct a temporal network for each data set where nodes represent cells and links are established between nodes if their protest events co-occur. We show that the temporal networks are small-world, indicating that the cells are directly linked or separated by a few steps on average. Furthermore, the average path lengths are decreasing through the years, which suggests that the world is becoming “smaller”. The persistent temporal hubs present in both data sets indicate that protests can spread faster through the hubs. This topological feature is consistent with the hypothesis that protests can quickly diffuse from one region to any other part of the globe.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
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Article ; Online: Review of gout clinic in a tertiary hospital setting.

Leonardo, Nieves / Lester, Susan / Whittle, Samuel / Rischmueller, Maureen

Internal medicine journal

2020 Volume 50, Issue 1, Page(s) 117–120

Abstract: Although updated consensus guidelines, and effective therapies, are available for management of gout, suboptimal management remains an issue. Barriers were identified and addressed as part of a dedicated, structured gout clinic. More frequent ... ...

Abstract	Although updated consensus guidelines, and effective therapies, are available for management of gout, suboptimal management remains an issue. Barriers were identified and addressed as part of a dedicated, structured gout clinic. More frequent appointments resulted in a faster rate of serum urate reduction, and the clinic provided the opportunity for the education of both patients and general practitioners in the management of gout.
MeSH term(s)	Aged ; Aged, 80 and over ; Ambulatory Care/statistics & numerical data ; Australia ; Disease Management ; Female ; Gout/blood ; Gout/drug therapy ; Gout Suppressants/therapeutic use ; Guideline Adherence ; Hospitalization ; Humans ; Linear Models ; Male ; Middle Aged ; Practice Guidelines as Topic ; Retrospective Studies ; Tertiary Care Centers ; Treatment Outcome ; Uric Acid/blood
Chemical Substances	Gout Suppressants ; Uric Acid (268B43MJ25)
Language	English
Publishing date	2020-01-13
Publishing country	Australia
Document type	Journal Article
ZDB-ID	2045436-3
ISSN	1445-5994 ; 1444-0903
ISSN (online)	1445-5994
ISSN	1444-0903
DOI	10.1111/imj.14689
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Article ; Online: The small-world network of global protests.

Ferreira, Leonardo N / Hong, Inho / Rutherford, Alex / Cebrian, Manuel

Scientific reports

2021 Volume 11, Issue 1, Page(s) 19215

Abstract: Protest diffusion is a cascade process that can spread over different regions of the planet. The way and the extension that this phenomenon can occur is still not properly understood. Here, we empirically investigate this question using protest data from ...

Abstract	Protest diffusion is a cascade process that can spread over different regions of the planet. The way and the extension that this phenomenon can occur is still not properly understood. Here, we empirically investigate this question using protest data from GDELT and ICEWS, two of the most extensive and longest-running data sets freely available. We divide the globe into grid cells and construct a temporal network for each data set where nodes represent cells and links are established between nodes if their protest events co-occur. We show that the temporal networks are small-world, indicating that the cells are directly linked or separated by a few steps on average. Furthermore, the average path lengths are decreasing through the years, which suggests that the world is becoming "smaller". The persistent temporal hubs present in both data sets indicate that protests can spread faster through the hubs. This topological feature is consistent with the hypothesis that protests can quickly diffuse from one region to any other part of the globe.
Language	English
Publishing date	2021-09-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-98628-y
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Article ; Online: Behavioural and physiological responses of juvenile geoduck (Panopea zelandica) following acute thermal stress.

Sharma, Shaneel S / Venter, Leonie / Frost, Emily J / Alfaro, Andrea C / Ragg, Norman L C / Zamora, Leonardo N

Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology

2023 Volume 269, Page(s) 110892

Abstract: Climate extremes, such as heatwaves, are expected to become more intense and of longer duration in the near future. These climatic conditions may have a significant impact on the prospects of establishing a new aquaculture industry for the endemic New ... ...

Abstract	Climate extremes, such as heatwaves, are expected to become more intense and of longer duration in the near future. These climatic conditions may have a significant impact on the prospects of establishing a new aquaculture industry for the endemic New Zealand geoduck, Panopea zelandica. This study focused on characterising animal behaviour, haemocytes , and heat shock protein (HSP70 & HSP90) mRNA expression following exposure to elevated temperatures, such as those encountered during marine heatwaves around 20 °C and an extreme scenario of 25 °C, contrasted to an ambient temperature of 17 °C. After 24 h of heat challenge, P. zelandica were found to be significantly influenced by the thermal changes, as there were differences recorded in all the responses examined. With increasing temperatures, juvenile geoduck were observed to fully emerge from the sediment a behaviour that has not previously been quantified nor associated with stress in this species. The ability of P. zelandica juveniles to re-bury still warrants further investigation, as adults are unable to do so. Haemocyte analyses revealed an increase in the abundance of granulocytes, cellular aggregations, and size of these aggregations at the highest temperature exposure. Increased expression of the hsp70 gene in the haemolymph after exposure at 25 °C for 24 h was detected and attributed to attempts to mitigate protein denaturation caused by thermal stress. The inter-individual variability in the response of heat shock proteins recorded could aid in future selective breeding programs if it is reflected in net thermotolerance. P. zelandica shows great potential for growing in subtidal habitats around New Zealand, and this study highlights the importance of temperature considerations when selecting potential farm and reseeding locations.
MeSH term(s)	Animals ; Temperature ; Hot Temperature ; Thermotolerance ; Heat-Shock Proteins ; HSP70 Heat-Shock Proteins/genetics ; HSP70 Heat-Shock Proteins/metabolism ; Stress, Physiological
Chemical Substances	Heat-Shock Proteins ; HSP70 Heat-Shock Proteins
Language	English
Publishing date	2023-08-11
Publishing country	England
Document type	Journal Article
ZDB-ID	121247-3
ISSN	1879-1107 ; 0305-0491 ; 1096-4959
ISSN (online)	1879-1107
ISSN	0305-0491 ; 1096-4959
DOI	10.1016/j.cbpb.2023.110892
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Article: A comprehensive species sampling sheds light on the molecular phylogenetics of Calothecinae (Poaceae, Pooideae, Poeae): Evidence for a new subtribe and multiple genera within the Chascolytrum clade

da Silva, Leonardo N. / Saarela, Jeffery M. / Essi, Liliana / de Souza‐Chies, Tatiana T.

Journal of systematics and evolution. 2022 May, v. 60, no. 3

2022

Abstract: The circumscription of the grass subtribe Calothecinae has undergone several changes since its description. Currently, it comprises Chascolytrum and the recently described genera Laegaardia and Paramochloa. Here we evaluate the circumscription of ... ...

Abstract	The circumscription of the grass subtribe Calothecinae has undergone several changes since its description. Currently, it comprises Chascolytrum and the recently described genera Laegaardia and Paramochloa. Here we evaluate the circumscription of Calothecinae and the recently proposed infrageneric classification of Chascolytrum based on a phylogeny with more comprehensive taxon and molecular marker sampling than in previous studies. We sampled all Calothecinae genera, all but one Chascolytrum species, two South American Trisetum s.l., and representatives of the subtribes Agrostidinae, Brizinae, Echinopogoninae, Koeleriinae, Phalaridinae, and Torreyochloinae within Poaceae tribe Poeae. We performed Bayesian and Maximum Likelihood analyses of four plastid DNA regions (atpF‐atpH, matK, rps16 intron, and trnL‐trnF) and two nuclear ribosomal regions (ITS and ETS). Our results revealed that neither Calothecinae nor Chascolytrum is monophyletic, as currently recognized, because Trisetum brasiliense and Trisetum bulbosum are nested within Chascolytrum. We include these two Trisetum species in Calothecinae as incertae sedis. Laegaardia and Paramochloa form a clade that is sister to the Chascolytrum + Trisetum clade, and based on morphological characters, we transfer the former to the new subtribe Paramochloinae. Our Chascolytrum phylogeny is better resolved and supported than in previous studies, and based on these results, we divide Chascolytrum into nine genera, including two new ones: Boldrinia (gen. nov.), Calotheca, Chascolytrum, Erianthecium, Lombardochloa, Microbriza, Poidium, Rhombolytrum, and Rosengurttia (gen. nov.). We provide a key to Calothecinae genera, descriptions of the genera, nomenclatural information, and keys to species of each genus. In addition, six new combinations are proposed.
Keywords	Bayesian theory ; Trisetum ; genetic markers ; grasses ; introns ; monophyly ; plastid DNA ; statistical analysis
Language	English
Dates of publication	2022-05
Size	p. 691-712.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2516638-4
ISSN	1759-6831 ; 1674-4918
ISSN (online)	1759-6831
ISSN	1674-4918
DOI	10.1111/jse.12750
Database	NAL-Catalogue (AGRICOLA)

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Article: Physiological responses of juvenile New Zealand geoduck (Panopea zelandica) following emersion and recovery

Sharma, Shaneel / Venter, Leonie / Alfaro, Andrea C. / Ragg, Norman L.C. / Delorme, Natalí J. / Zamora, Leonardo N.

Comparative biochemistry and physiology. 2022 Mar., v. 41

2022

Abstract: The New Zealand geoduck clam is a unique seafood delicacy, with animals selling for up to $US 220–330/kg. Stress accumulated during transport of juveniles to grow-out sites represent a bottleneck in the aquaculture process. In this study, the ... ...

Abstract	The New Zealand geoduck clam is a unique seafood delicacy, with animals selling for up to $US 220–330/kg. Stress accumulated during transport of juveniles to grow-out sites represent a bottleneck in the aquaculture process. In this study, the physiological responses of juvenile geoducks following emersion (3- and 8-h), and recovery (1- and 5-days) were investigated. An integrated approach of flow cytometry, osmolality and metabolomics, along with behavioural assessments was used. Both cellular and chemical haemolymph parameters and metabolite profiles were recorded for P. zelandica juveniles and are reported herein for the first time. An increase in haemolymph osmolality was experienced with an increase in emersion period, with significant differences seen between the 3- and 8-h emersion groups after 5 days of recovery. Viability measures of haemocytes varied insignificantly between experimental groups, creating baseline ranges. The proportion of haemocytes undergoing respiratory burst activity did not appear to be affected by emersion and re-immersion. Haemocyte mitochondrial membrane potential was highest following 1-day of recovery, likely linked to metabolic readjustment, and increased glycolysis, taking place following emersion. Metabolomics analyses suggest that protein, lipid and carbohydrate metabolite classes assist with energy production in geoducks. Activation of anaerobic metabolic pathways, with a high dependence on succinate, were prominent in the 8-h exposure group, with metabolic recovery still taking place following 5-days of immersion, mainly due to proteins restoring energy reserves. Elucidating the physiological responses of juvenile geoduck subjected to transport stress can aid cultivation methods already underway to develop a novel, high value aquaculture industry.
Keywords	Panopea ; aquaculture ; aquaculture industry ; carbohydrates ; clams ; energy ; flow cytometry ; glycolysis ; hemocytes ; juveniles ; lipids ; membrane potential ; metabolites ; metabolomics ; mitochondrial membrane ; osmolality ; respiratory burst ; seafoods ; succinic acid ; viability ; New Zealand
Language	English
Dates of publication	2022-03
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	2212119-5
ISSN	1878-0407 ; 1744-117X
ISSN (online)	1878-0407
ISSN	1744-117X
DOI	10.1016/j.cbd.2021.100929
Database	NAL-Catalogue (AGRICOLA)

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Book ; Online: Semantic Limits of Dense Combinatorial Objects

Coregliano, Leonardo N. / Razborov, Alexander A.

2019

Abstract: The theory of limits of discrete combinatorial objects has been thriving for the last decade or so. The syntactic, algebraic approach to the subject is popularly known as "flag algebras", while the semantic, geometric one is often associated with the ... ...

Abstract	The theory of limits of discrete combinatorial objects has been thriving for the last decade or so. The syntactic, algebraic approach to the subject is popularly known as "flag algebras", while the semantic, geometric one is often associated with the name ``graph limits''. The language of graph limits is generally more intuitive and expressible, but a price that one has to pay for it is that it is better suited for the case of ordinary graphs than for more general combinatorial objects. Accordingly, there have been several attempts in the literature, of varying degree of generality, to define limit objects for more complicated combinatorial structures. This paper is another attempt at a workable general theory of dense limit objects. Unlike previous efforts in this direction (with notable exception of [Ashwini Aroskar and James Cummings. Limits, regularity and removal for finite structures. Technical Report arXiv:1412.2014 [math.LO], arXiv e-print, 2014.]), we base our account on the same concepts from the first-order logic and the model theory as in the theory of flag algebras. We show how our definition naturally encompasses a host of previously considered cases (graphons, hypergraphons, digraphons, permutons, posetons, colored graphs, etc.), and we extend the fundamental properties of existence and uniqueness to this more general case. We also give an intuitive general proof of the continuous version of the Induced Removal Lemma based on the completeness theorem for propositional calculus. We capitalize on the notion of an open interpretation that often allows to transfer methods and results from one situation to another. Again, we show that some previous arguments can be quite naturally framed using this language. Comment: 127 pages, 4 figures
Keywords	Mathematics - Combinatorics ; Computer Science - Discrete Mathematics ; Primary: 03C13. Secondary: 28A99 ; 60C05 ; 05D40
Subject code	004
Publishing date	2019-10-19
Publishing country	us
Document type	Book ; Online
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