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Fig. 7 in Evolution of Poecilimon jonicus group (Orthoptera: Tettigoniidae): a history linked to the Aegean Neogene paleogeography

Fig. 7 Land-sea configuration in the Aegean area in different periods of the Neogene based on reconstructions by Popov et al. (2004) (with details taken from Creutzburg 1963 and Dermitzakis 1990) with historical biogeography hypothesis for the Messinian. a Late Serravallian (12–11 Ma), a possible time for the origin and early divergence of Barbitistini; b late Tortonian (8.5–7 Ma), transgression of the Mid-Aegean area in Tortonian

Fig. 6 Timetrees for the P in Evolution of Poecilimon jonicus group (Orthoptera: Tettigoniidae): a history linked to the Aegean Neogene paleogeography

Fig. 6 Timetrees for the P. jonicus group based on different phylogenies and time calibrations with node labels referring to the time estimation in millions of years. a BEAST maximum clade credibility tree inferred from COI and ND2 partitions calibrated for the substitution rate of COI; b BEAST chronogram and RelTime timetree inferred from the COI+ND2 phylogeny calibrated for the last separation of Crete (values above nodes, BEAST chronogram estimations; values below nodes, RelTime timetree estimations); c BEAST chronogram inferred from the 16S rRNA+12S rRNA phylogeny calibrated for the TMRCA (interval) of P. jonicus group (node 12) as suggested from the COI+ND2 chronogram. Different topologies of the trees are marked with "*" for the COI partitions and "**"for the ND2 partition on (a) and different topology of the BEAST and RelTime trees on (b). Numbers in white circles corre- spond to data in Supplementary material C. Light blue vertical band marks the onset of the northern hemisphere glaciation and dark blue lines mark major climatic switches in the Pleistocene. Uniform gray areas below the trees show united Aegean landmass (left) and re- unification of large areas in Messinian (right), while striped areas show disintegrated state of the Aegean

Fig. 4 in Evolution of Poecilimon jonicus group (Orthoptera: Tettigoniidae): a history linked to the Aegean Neogene paleogeography

Fig. 4 Phylogenetic relationships of the members of the Poecilimon jonicus group sensu lato with four outgroups from the genus Poecilimon and two outgroups from additional genera (P, Poecilimon; L., Leptophyes; I., Isophya). a Combined maximum likelihood and Bayesian inference phylogenetic trees based on a 1659 bp alignment of the COI+ ND2 mitochondrial dataset and b Bayesian inference phylogenetic tree based on a 1835 bp alignment of the 16S rRNA+12S rRNA mitochondrial dataset (Ullrich et al. 2010). Node values at branches show node support: above, ML bootstrap proportions; below, BI posterior probabilities; asterisk (*) indicates branches resolved by one of the analyses

Fig. 5 in Evolution of Poecilimon jonicus group (Orthoptera: Tettigoniidae): a history linked to the Aegean Neogene paleogeography

Fig. 5 Phylo-spatial dimension of the P. jonicus group based on the mtDNA phylogeny (data combined from COI+ND2 and 16S rRNA+12S rRNA datasets). Blue, "Anatolian" lineage; green, "Cretan" lineage; orange, "Balkan" lineage including Poecilimon inflatus

Fig. 3 in Evolution of Poecilimon jonicus group (Orthoptera: Tettigoniidae): a history linked to the Aegean Neogene paleogeography

Fig. 3 Phylogenetic relationships of the members of the Poecilimon jonicus group sensu lato with four outgroups from the genus Poecilimon and two outgroups from additional genera of Barbitistini (P, Poecilimon; L., Leptophyes; I., Isophya) based on Bayesian inference analysis of ITS1+ITS2 sequences. a 665 bp alignment-tree of sequences obtained in this study and from GenBank (Ullrich et al. 2010) and b 717 bp alignment-tree of sequences available from Ullrich et al. (2010). Node support is shown at (below) resolved branches

Fig. 2 in Evolution of Poecilimon jonicus group (Orthoptera: Tettigoniidae): a history linked to the Aegean Neogene paleogeography

Fig. 2 Distribution of the members of the Poecilimon jonicus group sensu lato—ranges of all species currently considered within the groups P. jonicus and P. inflatus including subspecies of P. jonicus shown with different colors as marked in the plates

Fig. 1 in Evolution of Poecilimon jonicus group (Orthoptera: Tettigoniidae): a history linked to the Aegean Neogene paleogeography

Fig. 1 General appearance of representatives of the Poecilimon jonicus group. a, b P. jonicus lobulatus (a male, b female); c P. werneri (female); d, e P. erimanthos (d male, e female); f P. inflatus lyciae (male); g, h

BRAIN Journal-Two new software behavioral design patterns: Obligation Link and History Reminder-Figure 5. The Sequence Diagram of the "History Reminder" design pattern

Analyzing the two main classes HistoryReminder and HistoryReminderOriginator of the “History Reminder” design pattern, we find that these two classes act as actors of the whole sequence of operations. The sequence diagram of the “History Reminder” design pattern is given below in Figure 5.

BRAIN Journal-Two new software behavioral design patterns: Obligation Link and History Reminder-Figure 4. The Flow chart of the "History Reminder" design pattern

The “History Reminder” design pattern has two main classes: HistoryReminder and HistoryReminderOriginator. The flow chart of the “History Reminder” design pattern is given in Figure 4.

BRAIN Journal-Two new software behavioral design patterns: Obligation Link and History Reminder-Figure 3. The class diagram of the "History Reminder" design pattern

The “History Reminder” design pattern consists of two basic classes. The first one is the HistoryReminder class and the second one is HistoryReminderOriginator class. Here, we have removed the Caretaker class which has been used to restore and save the memento state in the case of the traditional well-known Memento design pattern. The Caretaker object’s responsibility has been passed to the HistoryReminder object itself. It saves and restores the object within itself and returns it to the HistoryReminderOriginator object. The class diagram of the HistoryReminder design pattern is given below in Figure 3.

BRAIN Journal-Two new software behavioral design patterns: Obligation Link and History Reminder-Figure 2. The class diagram of the "Obligation Link" design pattern

Here is the structure of the “Obligation Link” design pattern described through another UML concept, called class diagrams. Contrary to the sequence diagrams which describe the behaviour, class diagrams specify static structural information about a program. The important information for a class, such as its attribute, operation, etc, along with relationship between classes can be specified using a class diagram

BRAIN Journal-Two new software behavioral design patterns: Obligation Link and History Reminder-Figure 1. The sequence diagram of the "Obligation Link" design pattern

A sequence diagram is used to model the flow of the logic of the system. A sequence diagram represents perhaps the most popular Unified Modelling Language (UML) diagram that describes the behavior of a scheme. Figure 1 shows the sequence diagram of “Obligation Link” design pattern.

opencc-by-4.0Feb 2018View details →

The effects of environmental history and thermal stress on coral physiology and immunity

This dataset has all data for the manuscript (Wall CB,  CA Ricci, GE Foulds, LD Mydlarz, RD Gates, HM Putnam (2018) The effects of environmental history and thermal stress on coral physiology and immunity. Marine Biology). Data included a zipped archive shape file for creating Kāne'ohe Bay map, physical data (light and temperature) from Kāne'ohe Bay and laboratory experiments, pCO2 data for Kāne'ohe Bay reef sites dowloaded from NOAA PMEL, and biological responses (PAM fluorometry, physiology, immune activity and oxidative profile).

opencc-by-4.0Mar 2018View details →

Data set for the paper "What are the Effects of History Length and Age on Mining Software Change Impact?"

Data set for the paper What are the Effects of History Length and Age on Mining Software Change Impact? by Leon Moonen, Thomas Rolfsnes, David Binkley and Stefano di Alesio. In Journal of Empirical Software Engineering (EMSE), 2018, Springer. https://doi.org/10.1007/s10664-017-9588-z Available from https://evolveit.bitbucket.io/publications/emse2018/ Please cite this work by referring to the corresponding journal publication (a preprint is included in this package). The goal of Software Change Impact Analysis is to identify artifacts (typically source-code files or individual methods therein) potentially affected by a change. Recently, there has been increased interest in mining software change impact based on evolutionary coupling. A particularly promising approach uses association rule mining to uncover potentially affected artifacts from patterns in the system’s change history. Two main considerations when using this approach are the history length, the number of transactions from the change history used to identify the impact of a change, and history age, the number of transactions that have occurred since patterns were last mined from the history. Although history length and age can significantly affect the quality of mining results, few guidelines exist on how to best select appropriate values for these two parameters. In this paper, we empirically investigate the effects of history length and age on the quality of change impact analysis using mined evolutionary coupling. Specifically, we report on a series of systematic experiments using three state-of-the-art mining algorithms that involve the change histories of two large industrial systems and 17 large open source systems. In these experiments, we vary the length and age of the history used to mine software change impact, and assess how this affects precision and applicability. Results from the study are used to derive practical guidelines for choosing history length and age when applying association rule mining to conduct software change impact analysis.

opencc-by-4.0May 2018View details →

Individual life histories Sanderlings Calidris alba at six non-breeding locations along East-Atlantic flyway

The data file contains individual encounter histories of 1,358 adult Sanderlings (Calidris alba) that winter in six different areas, England, France, Portugal, Mauritania, Ghana or Namibia and were observed between 2007-2013 in the main study site, their winter area (between 1 November – 1 March) and/or outside the main study site, during the interval between encounter occasions at the main study sites (during migration in Europe between 15 March and 15 October and at least 2 latitudinal degrees north of the median winter latitude). Encounter histories are coded as ‘LDLD’ (“Live, dead, live, dead”), where L codes for life encounters in the main study site (0: not observed, 1: observed) and D for (life or dead) encounters outside the main study sites (0: not observed, 1: observed dead, 2: observed alive). The encounter history of an individual starts with the first observation in its wintering region in the year after marking. Winter regions are indicated by the last six columns of the data file which are separated by spaces, where a 1 in the first column indicates England, the second column indicates France, the third Portugal, the fourth Mauritania, the fifth Ghana and the sixth Namibia. Further details can be found in the methods section in the manuscript.

opencc-by-4.0Sep 2018View details →

Data archive for 'Cognitive bias in relation to developmental history and stress response in European starlings (Sturnus vulgaris)'

Data files and R code for Gott et al. 'Cognitive bias in relation to developmental history and stress response in European starlings (Sturnus vulgaris)'. One .csv file gives the trial-by-trial data from the cognitive bias experiment. The other gives individual-level summary variables. Both are used by the R script. Uploaded 9th September 2018

opencc-by-nc-4.0Oct 2018View details →

The SHAMSA database 1.0 – Sources for the History and Analysis of Music/Dance in South Asia, c. 1700–1900.

The SHAMSA* bibliographical database and digital collection has been developed as part of the European Research Council project Musical Transitions to European Colonialism in the Eastern Indian Ocean (MUSTECIO, Grant no. 263643, PI Katherine Butler Schofield, 2011–2015/16). The attached xlsx document, licensed as a CC-BY-NC resource, provides the bibliographical metadata of Version 1.0 of the database. It describes well over 300 major written sources c. 1700-1900 for the history and analysis of North Indian (Hindustani) music and dance in Mughal and British-colonial South Asia. About one third – well over 100 – of these sources are also currently held in digital copies in the Department of Music at King’s College London. The SHAMSA digital collection already constitutes the largest single repository of primary written sources on Indian music and dance in the world, and is planned to be a major ongoing resource for future researchers on Indian music, dance, and cultural history. The sources of SHAMSA 1.0 were located and consulted Jan 2011– Dec 2015 by members of the Awadh Case Study of the ERC Musical Transitions project, including James Kippen, David Lunn, Allyn Miner, Katherine Butler Schofield, Margaret E Walker, and Richard David Williams. The initial collection has clearly defined limits: it 1) focusses on the Gangetic plains region between Delhi, Lucknow, and Calcutta; 2) during the timeframe c. 1700-1900 i.e. explicitly before the era of recorded sound (but with some key 17C and 20C outliers, and some materials from e.g. Hyderabad, Kashmir). 3) The linguistic focus of the collection is on works largely in Persian, Brajbhasha/Hindavi, Hindi, Urdu and Bengali, but with some works in Sanskrit, English, and other Northern Indian vernacular languages. Sources include music and dance treatises, biographical works (tazkiras), song collections, ethnographic works, department archives, encyclopedias, cosmographies, theatre scripts, moral and ethical tracts, histories, and a tiny handful of the large number of extant ragamala painting sets (for a comprehensive treatment of ragamala sets see e.g. Ebeling 1973 and the <a href="http://rmc.library.cornell.edu/EAD/htmldocs/RMM08400.html">Ebeling digital image collection</a> at Cornell). It is critically important to note that this is by no means a complete collection of everything written on music and dance in Northern India in the period of transition from the Mughal to the British empires. We have been completely overwhelmed by the volume and richness of the materials we have uncovered for the history of music and dance before the period of recorded sound. This bibilography should be considered a mere starting point; we are already aware of a large number of sources, especially visual, that we have not yet included. Version 1.0 consists only of (largely) textual sources that at least one of the team members personally consulted 2011–15, and considered to include substantial and noteworthy musical and/or dance-related contents (very occasionally key sources are also included that we know about, but have been unable to locate yet despite our best efforts.) We know that there are many more written and visual sources for North Indian forms of music and dance beyond the geographical, temporal, and/or linguistic scope of the current version of this database – for example for Panjab, Rajasthan, Gujarat, Maharashtra, etc. – but even considering our core region and timeframe we keep uncovering more sources all the time, and aim to update the open access versions of the database periodically. We would be delighted to hear from anyone who has information about sources that are not yet in our database that we might be able to consult and include, or about any verifiable errors in the metadata that need correcting. Well over one third of the works in the bibliographical file are already available to consult as digital copies in situ at King’s College London. The copyright statuses of these copies are exceedingly complex; but we aim to make as many of these available via Creative Commons licenses as and when we gain approval from the holders of the original documents to do so. Please do <a href="https://www.kcl.ac.uk/artshums/depts/music/people/acad/butlerschofield/index.aspx">get in touch</a> with Dr Katherine Schofield at King’s College London if you wish to consult the digital copies in the SHAMSA collection, or if you have suggestions of works whose metadata should be included in the bibliographical list. (Version 1.0 was completed 1 Jan 2016, and checked/exported 2 Oct 2018.)   *Deriving from the Persian word "shams", meaning "sun", a shamsa is both a ray of solar light often indicating the bestowal of special knowledge or enlightenment, and the technical term for an illuminated orb-like frontispiece in Islamicate manuscripts that often encloses the patron's name, titles, and/or portrait — see for example the beautiful shamsa for the Mughal emperor Shah Jahan that adorns the SHAMSA Community page (Metropolitan Museum of Art). In later lithographed works on music in Urdu, the title of the manuscript would often be enclosed in a shamsa. But the name SHAMSA also pays homage to the first Persian treatise on North Indian music written by an imperial hereditary musician, the Shams al-Aswat by Ras Baras Khan (1698), in which he named shams as the presiding star of the musical note Ma, the fourth scale degree (MUSTECIO 0131/British Library, I O Islamic 1746, f. 19r).

opencc-zeroNov 2018View details →

Herbarium specimen image of Tectaria incisa, part of the collection of Finnish Museum of Natural History LUOMUS, University of Helsinki

Part of a training dataset of scanned herbarium specimens. The data paper and a summary landing page will be published on Zenodo as it gets published. Content of this deposition: - A JSON-LD datafile listing the label data associated with this herbarium specimen. The Darwin and Dublin Core data standards are used for most values. - A JPEG image file of the scanned herbarium sheet. - A lossless TIFF image from which the JPEG image has been derived.

opencc-zeroNov 2018View details →

Herbarium specimen image of Pellaea rotundifolia, part of the collection of Finnish Museum of Natural History LUOMUS, University of Helsinki