prompt_front: Now, answer the following question based on the text below, only give me the answer and do not output any other words.

Question: What are some reasons for the lack of data sharing in archaeobotany?

Read the following text and answer briefly.

Context 1: Sowing the Seeds of Future Research: Data Sharing, Citation and Reuse in Archaeobotany
Reading: Sowing the Seeds of Future Research: Data Sharing, Citation and Reuse in Archaeobotany
University of Oxford, GB
Lisa is a post-doctoral research fellow at All Souls College, University of Oxford  Her publications include the co-authored volume The Rural Economy of Roman Britain (Britannia Monographs, 2017)  Her research interests are focussed on agricultural practices in the later prehistoric and Roman period and the utilisation of archaeobotanical data to investigate human-plant relationships 
The practices of data sharing, data citation and data reuse are all crucial aspects of the reproducibility of archaeological research  This article builds on the small number of studies reviewing data sharing and citation practices in archaeology, focussing on the data-rich sub-discipline of archaeobotany  Archaeobotany is a sub-discipline built on the time-intensive collection of data on archaeological plant remains, in order to investigate crop choice, crop husbandry, diet, vegetation and a wide range of other past human-plant relationships  Within archaeobotany, the level and form of data sharing is currently unknown  This article first reviews the form of data shared and the method of data sharing in 239 articles across 16 journals which present primary plant macrofossil studies  Second, it assesses data-citation in meta-analysis studies in 107 articles across 20 journals  Third, it assesses data reuse practices in archaeobotany, before exploring how these research practices can be improved to benefit the rigour and reuse of archaeobotanical research 
Keywords: Archaeobotany, Data reuse, Data sharing, Open science
How to Cite: Lodwick, L , 2019  Sowing the Seeds of Future Research: Data Sharing, Citation and Reuse in Archaeobotany  Open Quaternary, 5(1), p 7  DOI: http://doi org/10 5334/oq 62
Accepted on 29 May 2019 Submitted on 25 Mar 2019
Archaeology is a discipline built on the production and analysis of quantitative data pertaining to past human behaviour  As each archaeological deposit is a unique occurrence, ensuring that the data resulting from excavation and analysis are preserved and accessible is crucially important  Currently, there is a general perception of a low level of data sharing and reuse  Such a low level of data availability would prevent the assessment of research findings and the reuse of data in meta-analysis (Kansa & Kansa 2013; Moore & Richards 2015)  As observed across scientific disciplines, there is a major problem in the reproduction of scientific findings, commonly known as the ‘replication crisis’ (Costello et al  2013)  A range of intersecting debates contribute to this, including access to academic findings (open access), open data, access to software and access to methodologies, which can be broadly grouped as open science practices  Without these, the way that scientific findings can be verified and built upon is impaired  Questions of reproducibility have been raised in recent years in archaeology, with considerations of a range of practices which can improve the reproducibility of findings, and a recent call for the application of open science principles to archaeology (Marwick et al  2017)  Discussion has so far focussed on access to grey literature (Evans 2015), data sharing (Atici et al  2013), data citation practices (Marwick & Pilaar Birch 2018) and computational reproducibility (Marwick 2017), with a focus on lithics, zooarchaeological evidence, and archaeological site reports 
Quantitative assessments of current levels of data sharing, data citation and reuse remain limited in archaeology  The focus of evaluation has been on the uptake of large-scale digital archives for the preservation and dissemination of digital data, such as the Archaeology Data Service (ADS), utilised by developer-led and research projects, and recommended for use by many research funders in the UK (Richards 2002; Wright and Richards 2018)  Much less focus has been paid to the data-sharing practices of individuals or small-groups of university-based researchers who may be disseminating their research largely through journal articles  Recent work on the availability of data on lithics assemblages found a low level of data sharing (Marwick & Pilaar Birch 2018) and there are perceptions of low levels of data reuse (Huggett 2018; Kintigh et al  2018)  Within zooarchaeology numerous studies have explored issues of data sharing and reuse (Kansa & Kansa 2013, 2014), and the sub-discipline is seen as one of the most advanced areas of archaeology in regards to open science (Cooper & Green 2016: 273)  Beyond zooarchaeology, however, explicit discussion has remained limited 
This paper assesses data sharing and reuse practices in archaeology through the case study of archaeobotany – a long established sub-discipline within archaeology which has well-established principles of data recording  Archaeobotany is an interesting case study for data sharing in archaeology as it straddles the division of archaeology between scientific and more traditional techniques  Quantitative data on archaeological plant remains are also of interest to a range of other fields, including ecology, environmental studies, biology and earth sciences  The key issues of data sharing and data reuse (Atici et al  2013) have been touched upon in archaeobotany over the past decade within broader discussions on data quality (Van der Veen, Livarda & Hill 2007; Van der Veen, Hill & Livarda 2013)  These earlier studies focussed on the quality and availability of archaeobotanical data from developer-funded excavations in Britain and Cultural Resource Management in North America (Vanderwarker et al  2016: 156)  However, no discussion of data-sharing and reuse in academic archaeobotany occurred  A recent review of digital methods in archaeobotany is the notable exception, with discussions of the challenges and methods of data sharing (Warinner & d’Alpoim Guedes 2014) 
Currently, we have no evidence for the levels of data sharing and reuse within archaeobotany  This article provides the first quantitative assessment of 1) data publication in recent archaeobotanical journal articles 2) data citation in recent archaeobotanical meta-analysis 3) the reuse of archaeobotanical datasets, in order to assess whether practices need to change and how such changes can take place 
2  Data Publication and Re-use Practices in Archaeobotany
2 1  History of data production and publication
Archaeobotanical data falls within the category of observational data in archaeology (Marwick & Pilaar Birch 2018)  Archaeobotanical data is considered as the quantitative assessment of plant macrofossils present within a sample from a discrete archaeological context, which can include species identification, plant part, levels of identification (cf  – confer or “compares to”), and a range of quantification methods including count, minimum number of individuals, levels of abundance and weight (Popper 1988)  Archaeobotanical data is usually entered into a two-way data table organised by sample number  Alongside the counts of individual taxa, other information is also necessary to interpret archaeobotanical data, including sample volume, flot volume, charcoal volume, flot weight, level of preservation, sample number, context number, feature number, feature type and period  Beyond taxonomic identifications, a range of other types of data are increasingly gathered on individual plant macrofossils (morphometric measurements, isotopic values, aDNA) 
Archaeobotanical training places a strong emphasis on recording data on a sample-by-sample basis (Jacomet & Kreuz 1999: 138–139; Jones & Charles 2009; Pearsall 2016: 97–107)  Time-consuming methodologies utilised in the pursuit of accurate sample-level data recording include sub-sampling and splitting samples into size fractions and counting a statistically useful number of items per sample (Van der Veen & Fieller 1982)  The creation of sample-level data means analysis is often undertaken on the basis of individual samples, for instance the assessment of crop-processing stages and weed ecological evidence for crop husbandry practices  The analysis of sample level data also enables archaeobotanical finds to be integrated alongside contextual evidence from archaeological sites  Requirements for the publication of this data are in place in some archaeological guidelines, for instance current Historic England guidelines for archaeological practice in England (Campbell, Moffett & Straker 2011: 8) 
From the earliest archaeobotanical reports, such as Reid’s work at Roman Silchester, the sample from which plant remains were recovered was noted (Lodwick 2017a), but often results were reported as a list of taxa, or long catalogues of detailed botanical descriptions with seed counts, such as Knörzer’s work at Neuss (Knörzer 1970)  Early systematic archaeobotanical reports displayed data within in-text tables, for example Jones’s work at Ashville (Jones 1978) and the two-way data table has been the standard form of reporting archaeobotanical data ever since  Often data tables are presented within book chapters or appendices, but the financial, space and time constraints of book publishing are limiting  Furthermore, there is the perception that specialist data was not necessary for publication (Barker 2001)  Hence, alternative methods of the dissemination of specialist archaeological data were pursued in the later twentieth century 
From the 1980s, archaeobotanical data tables were often consigned to microfiche following a Council for British Archaeology and Department of Environment report (Moore & Richards 2015: 31), with the example of the excavation of Roman Colchester where the contents of all archaeobotanical samples were available on microfiche (Murphy 1992)  An alternative in the 2000s was providing data tables on CD Rom as seen, for instance, in the CD accompanying the study of a Roman farmstead in the Upper Thames Valley (Robinson 2007) or the One Poultry excavations in London (Hill and Rowsome 2011)  Meanwhile, the inception of the Archaeology Data Service, a digital repository for heritage data, in 1996 meant archaeological datasets were increasingly digitally archived, for instance the data from the Channel Tunnel Rail Link Project (Foreman 2018) or a recent large-scale research excavation at Silchester (University of Reading 2018)  In these cases, archaeobotanical data is available to download as a  csv file 
Whilst the data publication strategy of large excavations was shifting, the availability of data from post-excavation assessment reports has remained challenging  So-called ‘grey literature’ results from the initial evaluation stage of developer-funded investigations and accompanying post-excavation assessment often contain a semi-quantitative evaluation of archaeobotanical samples on a scale of abundance  Whilst paper reports were initially deposited with county Historic Environment Records, a process of digitisation focussing on the Roman period has meant many pdfs are now available through the ADS (Allen et al  2018), whilst born-digital reports are now deposited through OASIS (Online AccesS to the Index of archaeological investigationS), as part of the reporting process (Evans 2015), althought the extent to which specialist appendices are included is variable 
These varying ‘publication’ strategies means archaeobotanical data is often available somewhere for recent developer-funded excavations and large-scale developer-funded excavations, even if much of this data is as a printed table or  pdf file (Evans 2015; Evans and Moore 2014)  However, academic journals are typically perceived as the most high-status publication venue for archaeobotanical data, and a crucial publication venue for academics in order to comply with institutional requirements and the norms of career progression  Aside from the problem of access to pay-walled journals by those without institutional subscriptions to all journals, the publication of primary data alongside research articles faces various problems, from the outright lack of inclusion of data, to problematic curation of supplementary data and a lack of peer review of data (Costello et al  2013; Warinner and d’Alpoim Guedes 2014: 155; Whitlock, 2011)  The extent of these problems for archaeobotany is currently unknown  Given the growth in archaeobotanical data production as methodologies are introduced into many new regions and periods over the last decade, it is vital that we know whether the mass of new data being produced is made available and is being reused 
Recent important advances within archaeobotanical data sharing have focussed on the construction of the ARBODAT database, developed by Angela Kreuz at the Kommission für Archäologische Landesforschung in Hessen  The database is used by a range of researchers in Germany, the Czech Republic, France and England (Kreuz & Schäfer 2002)  Data sharing enabled by the use of this database has facilitated research on Neolithic agriculture in Austria, Bulgaria and Germany (Kreuz et al  2005), and Bronze Age agriculture in Europe (Stika and Heiss 2012)  The use of this database makes data integration between specialists easier due to the shared data structure and metadata description, but often the primary archaeobotanical data is not made publicly available 
2 2  Meta-analysis in archaeobotany
Beyond the need to preserve information, a key reason for the formal sharing of archaeobotanical data is in its reuse to facilitate subsequent research  There has been a long-standing concern within archaeobotany with the need to aggregate datasets and identify temporal and spatial patterns  The palaeobotanist Clement Reid maintained his own database of Quaternary plant records in the late nineteenth century (Reid 1899), which formed the foundation of Godwin’s Quaternary database (Godwin 1975)  Mid-twentieth century studies of prehistoric plant use compiled lists of archaeobotanical materials incorporating full references and the location of the archive (Jessen & Helbaek 1944)  The International Work Group for Palaeoethnobotany was itself founded in 1968 in part with the aim to compile archaeobotanical data, first realised through the publication of Progress in Old World Palaeoethnobotany (Van Zeist, Wasylikowa & Behre 1991), and subsequently through the publication of annual lists of new records of cultivated plants (Kroll 1997) 
To take England as an example, regional reviews produced by state heritage authorities have provided catalogues of archaeobotanical datasets in particular time periods and regions (e g  Murphy 1998)  When one archaeobotanist has undertaken the majority of study within a region, pieces of synthesis within books have provided a relatively comprehensive review, for instance in the Thames Valley, UK (Lambrick & Robinson 2009)  Over the last decade regional synthesis has occurred within several funded reviews which produced catalogues of sites with archaeobotanical data (Lodwick 2014; McKerracher 2018; Parks 2012) and a series of funded projects in France have enabled regional synthesis (Lepetz & Zech-Matterne 2017)  However, many of these reviews are not accompanied by an available underlying database, and draw upon reports which are themselves hard to access 
Through the 1990s and 2000s, a series of databases were constructed in order to collate data from sites in a particular region and facilitate synthetic research  However, these databases have all placed the role of data archiving onto later projects specifically funded to collate data, rather than sourcing datasets at the time of publication  Such a model is unsustainable, and is unlikely to result in all available datasets being compiled  The Archaeobotanical Computer Database (ABCD), published in 1996 in the first issue of Internet Archaeology, contained much of the archaeobotanical data from Britain available at the time of publication, largely at the level of individual samples  The database was compiled between 1989 and 1994 and is still accessible through the accompanying online journal publication (Tomlinson & Hall 1996)  The ABCD made major contributions to recent reviews of the Roman and Medieval periods (Van der Veen, Livarda & Hill 2008; Van der Veen, Hill & Livarda 2013)  However, the database could only be centrally updated, with the online resource remaining a static version, lacking much of the new data produced subsequent to the implementation of PPG16 in 1990  The ADEMNES database, created through a research project undertaken at the Universities of Freiburg and Tübingen, contains data from 533 eastern Mediterranean and Near Eastern sites (Riehl & Kümmel 2005)  Kroll has maintained the Archaeobotanical Literature Database to accompany the Vegetation History and Archaeobotany articles (Kroll 2005) now accessible as a database (Kirleis & Schmültz 2018)  Numerous other databases have collated archaeobotanical studies, including the COMPAG project (Fuller et al  2015), the Cultural Evolution of Neolithic Europe project (Colledge 2016), RADAR in the Netherlands (van Haaster and Brinkkemper 1995), BRAIN Botanical Records of Archaeobotany Italian Network (Mercuri et al  2015) and CZAD – Archaeobotanical database of Czech Republic (CZAD 2019) 
The majority of databases have a restricted regional coverage, whilst research-project driven period-specific databases provide overlapping content  Whilst there are a wide range of archaeobotanical databases available, few contain primary datasets (other than the ABCD) which can be downloaded as  csv files  Data which is most commonly available are bibliographic references per site, with some indications of mode of preservation, quantity of archaeobotanical data, and sometimes taxa present  The databases do not inter-relate to each other, and function primarily as bibliographic sources enabling researchers to find comparative sites or to identify published datasets which need to be re-tabulated prior to meta-analysis  The IWGP website curates a list of resources, but otherwise the resources are often disseminated through the archaeobotany jiscmail list 
Beyond the aim of cataloguing archaeobotanical data within a region and period, meta-analysis is often used in archaeobotany to identify spatial and chronological trends in a range of past human activities, for instance crop choice, crop husbandry practices, plant food consumption, the trade in luxury foods or the use of plants in ritual  Meta-analysis can be undertaken on the basis of simple presence/absence data per site, but in order for such analysis to be rigorous and comparable, sample-level data must be utilised  For instance, sample-level data is required for meta-studies, in order to identify high-quality samples of unmixed crops for weed ecology analysis (Bogaard 2004), to assess the importance of context in the evaluation of wild plant foods (Wallace et al  2019), or to use volumetric measurements as a proxy for scale (Lodwick 2017b)  The reuse of archaeobotanical data also extends to include datasets used as “controls” in commonly used forms of statistical analysis, for instance Jones’s weed data from Amorgos, Greece, which is utilised as a control group in discriminant analysis of crop-processing stage (Jones 1984), and ethnographic observations of crop items in different crop-processing stages (Jones 1990) 
2 3  Open data principles and solutions
Debates over issues of data publication and meta-analysis have been on-going across scientific disciplines over the last decade (Editors 2009), and have been summarised within principles of open science, as recently set out in relation to archaeology (Marwick et al  2017)  Open Data is one of the three core principles for promoting transparency in social science (Miguel et al  2014)  The FAIR principles, developed by representatives from academia, industry, funding agencies, industry and publishers, provide four principles which data sharing should meet for use by both humans and machines – Findability, Accessibility, Interoperability, and Reusability (Wilkinson et al  2016)  A recent report assessing the adoption and impact of FAIR principles across academia in the UK included archaeology as a case study (Allen and Hartland 2018: 46)  It reported how the ADS was often used to archive data, but that “The journal itself provides the “story” about the data, the layer that describes what the data is, how it was collected and what the author thinks it means ” The report also raises the problem that smaller projects may not have the funding to utilise the ADS, meaning that other repositories are utilised  Increasingly, archaeological data is made available through a wide range of data repositories (OSF, Mendeley Data, Zenodo, Open Context), university data repositories (e g  ORA-Data), or social networking sites for academics (Academia edu, ResearchGate)  More widely in archaeology, some have observed that archaeological data is rarely published (Kintigh et al  2014), and recent reviews have reported low levels of data sharing (Huggett 2018; Marwick & Pilaar Birch 2018)  A closely related issue is that of data reuse  Responsible reuse of primary data encourages the sharing of primary data (Atici et al  2013), but levels of data reuse in archaeology are thought to remain low (Huggett 2018)  Principles for responsible data citation in archaeology have recently been developed summarising how datasets should be cited (Marwick & Pilaar Birch 2018) 
In order to assess the current status of data sharing, citation and data re-use in archaeobotany, a review was undertaken of the publication of primary data and the publication of meta-analysis in major archaeological journals over the last ten years, building on recent pilot studies within archaeology (Marwick & Pilaar Birch 2018)  The review of academic journals provided a contrast to recent assessments of archaeobotanical data deriving from developer-funded archaeology (Lodwick 2017c; Van der Veen, Hill & Livarda 2013)  Journal articles have been selected as the focus of this study as the provision of online supplementary materials in the majority of journals and the ability to insert hyperlinks to persistent identifiers (eg a DOI) to link to datasets available elsewhere should not limit the publication of data and references  Much archaeobotanical data is also published elsewhere, especially from projects not based in the university sector, that is commercial or community archaeology in the UK  Archaeobotanical datasets emanating from this research are more commonly published through monographs, county journal articles, and unpublished (or grey literature) reports, but these are beyond the scope of the current review 
All journal articles were included which represent the principle reporting of a new archaeobotanical assemblage  The selected journals fall within three groups  First, what is considered the specialist archaeobotanical journal (Vegetation History and Archaeobotany (VHA))  Second, archaeological science journals (Archaeological and Anthropological Sciences, Environmental Archaeology, The Holocene, Journal of Archaeological Science (JAS), Journal of Archaeological Science: Reports (JASR), Journal of Ethnobiology, Quaternary International, Journal of Wetland Archaeology), which can be considered as specialist sub-disciplinary journals which should be maintaining data-quality  Third, general archaeology journals (Antiquity, Journal of Field Archaeology, Oxford Journal of Archaeology, Journal of Anthropological Archaeology, Journal of World Prehistory)  Finally, the broader cross-disciplinary journals PLoS One and Proceedings of the National Academy of Sciences (PNAS) were included  Published articles from the past ten years (2009–2018) have been analysed in order to assess the availability of plant macrofossil data  This ten-year period brackets the period where most archaeological journals have moved online and adopted supplementary materials 
Data citation in synthetic studies has been assessed in the same range of publications  The extent of data reuse ranges from the analysis of whole sample data to the presence/absence of individual crops  The location of a data citation has been assessed in the same range of publications, with the addition of journals where occasional research incorporating archaeobotanical data is featured (Britannia, Journal of Archaeological Research, Ethnobiology Letters, Medieval Archaeology, Proceedings of the Prehistoric Society, World Archaeology)  The underlying dataset for the analysis is available in Lodwick 2019 
4 1  Primary data sharing
Here, the location of primary archaeobotanical data, that is sample level counts of macroscopic plant remains, was assessed for 239 journal articles across 16 journals (Lodwick 2019 Table 1)  Figure 1 shows the results grouped by journal  Overall, only 56% of articles shared their primary data  In, Antiquity, JAS, JASR, PLOS One, Quaternary International and VHA, the highest proportion of publications did not include their primary data, that is to say that the sample-by-sample counts of plant macrofossils was not available  This level of data is comparable to the findings of other pilot studies in archaeology  Marwick and Pilaar Birch found a data sharing rate of 53% from 48 articles published in Journal of Archaeological Science in Feb – May 2017 (Marwick & Pilaar Birch 2018: 7), and confirm previous assertions that data is often withheld in archaeology (Kansa 2012: 499)  This is better than some disciplines, with a 9% data sharing rate on publication found across high impact journal science publications (n = 500) (Alsheikh-Ali et al  2011) and 13% in biology, chemistry, mathematics and physics (n = 4370) (Womack 2015), yet still indicates that nearly half of articles did not include primary data  Primary archaeobotanical data is more likely to be shared in archaeobotanical and archaeological science journals than general archaeology journals  However, within the primary archaeobotanical journal, VHA, 51% of articles do not include their primary data (Figure 1) 
Chart showing the location of primary archaeobotanical data by journal in primary archaeobotanical data publications 
Where primary data was not shared, the data which was available ranged from summary statistics, typically counts or frequencies, reported either by site, site phase, or feature group  Figure 2 summarises these results by year, showing that there is a gradient within articles not sharing their full ‘raw’ data, from those only provided sample counts on one aspect of the archaeobotanical assemblage, to those only presenting data graphically or within discussion  Beyond full data, the most common form of data shared is either summary counts per site or summary counts per feature or phase  Whilst this data does enable some level of reuse, the results of any sample-level data analysis presented within an article cannot be verified, and the data cannot be reused for crop-processing or weed ecology analysis which requires sample level data  Furthermore, such data would have been collected on a sample-by-sample basis, but this information is lost from the resulting publication 
Chart showing the form of archaeobotanical data shared by year in primary archaeobotanical data publications 
The forms in which data are made available vary across journals  The sharing of primary data within an article remains the most common data sharing form in archaeobotany (Figure 1)  Data tables in text require manual handling to extract data, in journals such as VHA, whilst in other journals in-text tables can be downloaded as  csv files  These however would not be citable as a separate dataset  Supplementary datasets are the third most common form of data sharing  Indeed, the use of electronic supplementary material has been advocated recently for by some journals, such as the Journal of Archaeological Science (Torrence, Martinón-Torres & Rehren 2015)  Microsoft Excel spreadsheets are the most common form of supplementary data, followed by  pdfs and then word documents (Figure 1)  Both  xlsx and  docx are proprietary file formats, and not recommended for long term archiving or open science principles  There is no indication of improvement over the last decade in the form of data sharing  In 2018, 50% of articles did not share their primary data, and where the data was shared, it was in proprietary forms ( docx,  xlsx) or those that do not easily facilitate data reuse ( pdf) (Figure 3) 
Chart showing the location of archaeobotanical data from 2009–2018 in primary archaeobotanical data publications 
Just one of the articles included in this review incorporated a dataset archived in a repository (Farahani 2018), in contrast to the substantial growth in data repositories across academic disciplines (Marcial & Hemminger 2010)  Other examples provide the underlying data for monograph publications, such as that of the archaeobotanical data from Gordion, Turkey (Marston 2017a, 2017b), Silchester, UK (Lodwick 2018; University of Reading 2018) and Vaihingen, Germany (Bogaard 2011a; Bogaard, 2011b) 
Several of the journals that have been assessed have research data policies  In the case of Vegetation History and Archaeobotany, sufficient papers have been surveyed to assess the impact of the research data policy on the availability of data  Figure 4 show the proportion of data sharing formats through time just for VHA (note the small sample size)  The introduction of a research data policy in 2016 encouraging data sharing in repositories has not resulted in any datasets being shared in that format  Of the 10 articles published in PLOS One after the introduction of a clear research data policy in 2014, 4 did not contain primary data  However, elsewhere, journals with no research data policy, such as Antiquity, has one of the lower levels of data sharing (Figure 1) 
Chart showing the location of primary archaeobotanical data in Vegetation History and Archaeobotany 
There are various reasons for why a primary dataset may be lacking  The option of providing supplementary datasets has been available in many of the journals here since before the start of the surveyed period (e g  Vegetation History and Archaeobotany in 2004), and so cannot be a reason for the absence of data publication in this journal while it may be a reason in other journals  Reasons suggested for a lack of data sharing within archaeology include technological limitations, and resistance amongst some archaeologists to making their data available due to cautions of exposing data to scrutiny, lost opportunities of analysis before others use it and loss of ‘capital’ of data (Moore & Richards 2015: 34–35)  Furthermore, control over how data tables is presented (taxa ordering, summary data presented) may also contribute to the preferential publishing of data within journal articles  Another factor to consider is the emphasis on the creation of new data through archaeological research (Huvila 2016)  The creation of a new archaeobotanical dataset through primary analysis is a key form of training in archaeobotany, and the perception of the value of the reuse of other previously published archaeobotanical journals may be low, hence not encouraging the sharing of well-documented datasets  Excellent exams of data reuse have resulted in influential studies (Bogaard 2004; Riehl 2008; Wallace et al  2019), and would hopefully encourage further data sharing in the future 
Given that there are numerous examples of meta-analysis which do take place in archaeobotany, it seems likely that the prevalent form of data sharing is through informal data sharing between individual specialists  However, this does not improve access to data in the long term, and is inefficient and time consuming, with large potential for data errors (Kansa & Kansa 2013), and relies on personal networks, which are likely to exclude some researchers  The absence of primary data in many archaeobotanical publications thus inhibits the verification of patterns observed within a dataset, and strongly limits the re-use potential of a dataset 
4 2  Data citation
One of the common arguments for increasing data sharing is an associated increase in the citation of the articles which have data available  Here, the data citation practices of meta-analyses of plant macrofossil data undertaken over the last decade have been reviewed  20 journals were consulted, including a wider range of period-specific journals, and 107 articles were assessed (Lodwick 2019 Table 2)  Data citation was assessed as ‘in text’ or ‘in table’ to refer to when the citation and the bibliographic reference were within the article, as ‘in supplementary data’ when the citation and reference were within the supplementary materials, and as ‘no citation’ when no citation and reference was provided 
21% of articles (n = 22) did not contain any citations to the underlying studies  16% (n = 17) contained citations within supplementary data files  50% of articles (n = 53) contained a citation within a table within the main article, and 14% (n = 15) contained citations within the main text  For the 21% of articles without data citations, the results of these studies could not be reproduced without consulting individual authors  The papers supplying the underlying data also received no credit for producing these datasets  Where articles contain citations within the main article (in text or table), full credit is provided to the underlying studies, a citation link is created through systems such as google scholar, and the study can be easily built upon in the future  Where the citation is provided within supplementary data, the original studies do receive attribution, but are not linked to so easily 
Through time, there is a steady decrease in the proportion of studies without citations to the underlying data, whereby of the 17 meta-analysis articles published in 2018, only one had no data citations  In comparison, in 2009, 3 out of 8 meta-analysis articles contained no data citation (Figure 6)  Overall this is a more positive outlook on the reuse of published data, but the consistent presence of articles lacking data citation indicates that improvements are needed  Reasons for a lack of data citation may include restrictions on word counts imposed by journals, a lack of technical knowledge in making large databases available, or the wish to hold on to a dataset to optimise usage  Considering the type of journal (Figure 5), levels of data citation are worse in general archaeology journals, with sub-disciplinary journals showing slightly better levels of data citation  In particular VHA has a lack of consistency in where data citations are located 
Chart showing the location of data citations in meta-analysis journal articles by journal type 
Chart showing the location of data citations in meta-analysis journal articles from 2009–2018 
4 3  Reuse of archived archaeobotanical datasets
The majority of data citations assessed in the previous section are to articles or book chapters rather than data-sets  The ADS currently hosts 66 data archives which have been tagged as containing plant macro data, deriving mainly from developer-funded excavations but also some research excavations  However, in some of these the plant macro data is contained within a pdf  As, the archiving of archaeobotanical datasets in data repositories is still at an early stage, the reuse of these datasets is assessed here on a case-by-case basis  The archaeobotanical dataset from the Neolithic site of Vaihingen, Germany (Bogaard 2011b) has not been cited on google scholar  Metrics are provided through the ADS, showing this dataset has been downloaded 56 times with 477 individual visits (as of 25/2/19)  The archaeobotanical dataset from Gordion by Marston has no citations on Google Scholar (Marston 2017b), neither does the Giza botanical database (Malleson & Miracle 2018), but these are both very recently archived datasets  In contrast, the Roman Rural Settlement Project dataset, which includes site-level archaeobotanical data, has received greater levels of use, with 12 citations in Google Scholar, over 40,000 file downloads, and over 35,000 visits (Allen et al  2018) and the archaeobotanical computer database (Tomlinson & Hall 1996) has been cited 44 times, and is the major dataset underpinning other highly-cited studies (Van der Veen, Livarda & Hill 2008; Van der Veen, Hill & Livarda 2013)  Whilst there is clearly precedence for the reuse of archaeobotanical databases, current data citation practices within archaeobotany do not yet appear to be formally citing individual datasets, meaning an assessment of the reuse of archived archaeobotanical datasets is challenging 
5  Steps Forward
This review of data sharing, citation, and reuse practices in archaeobotany has found medium levels of data sharing, good levels of data citation, but so far limited levels of reuse of archived data sets  This picture is similar across archaeology, in part attributed to the status of archaeology as a small-science, where data-sharing takes place ad-hoc (Marwick & Pilaar Birch 2018)  Here, recommendations are discussed for improving these data practices within archaeobotany, of applicability more widely in archaeology 
Clearly an important step is improving the sharing of plant macrofossil data  Given the reasonable small size of most archaeobotanical datasets (a  csv file < 1mb), and a lack of ethical conflicts, there seems to be few reasons why the majority of archaeobotanical data couldn’t be shared  In the case of developer-funded derived data, issues of commercial confidentiality could limit the sharing of data  A key stage is establishing why levels of data sharing are not higher  Issues within archaeobotany may include the conflict between having to publish results within excavation monographs, which may take some time to be published, and have limited visibility due to high purchase costs and no digital access, and the need to publish journal articles for career progression within academia  The production of an archaeobotanical dataset is very time-consuming, and interim publication on notable aspects of an assemblage may be considered as a necessary publication strategy  More broadly, one important aspect is issues of equity in access to digital archiving resources (Wright & Richards 2018), such as differential access to funds, training and knowledge  A recent study in Sweden found that we need to know concerns, needs, and wishes of archaeologists in order to improve preservation of archaeological data (Huvila 2016), especially when control of ones data may be linked to perceptions of job security  In order to make improvements in data sharing and reuse across archaeology, we need improved training in data sharing and the reuse of data in higher education (Touchon & McCoy 2016; Cook et al  2018), improved training in data management (Faniel et al  2018), and crucially, the necessary software skills to make the reuse of archived datasets attainable (Kansa & Kansa 2014: 91)  Examples of good practice in archaeobotany are the Vaihingen and Gordion datasets which demonstrate how datasets can be archived in data repositories to accompany a monograph (Bogaard 2011b; Marston 2017b), whilst Farahani (2018) provides an excellent example of a journal article, where the primary data is supplied as a  csv in a cited data repository along with the R script for the analysis 
In tandem with the need to encourage authors to share their data, is the need for journals to create and implement research data policies  Given the existence of research data policies in many of the journals included here, this reflects other findings of the poor enforcement of data policies by journals (Marwick & Pilaar Birch 2018), supporting arguments that journals should not be relied upon to make data accessible, and data should instead by deposited in digital repositries  In order to implement change in data sharing, there is a role to play for learned societies and academic organisation in lobbying funding bodies, prioritising data sharing in research projects  A key step is through journal editorial boards, and the enforcement of any pre-existing research data policies (Nosek et al  2015)  Revi
Context 2: Outdoors	February 19, 2017
You are here: Home / Archives for Departments / OutdoorsActor Sam Waterson Hosts PBS Documentary on Lyme Land Trust January 14, 2017 by admin Leave a Comment Jack Tiffany, owner of Tiffany Farms on Rte  156 and an earlier pioneer in Lyme land preservation, is interviewed by PBS “Visionaries” documentary producers 
Filed Under: Lyme, Outdoors Application Deadline for Environmental Leadership Scholarship is Feb  1 January 8, 2017 by admin Leave a Comment Applications are now being accepted for the Virginia R  Rollefson Environmental Leadership Scholarship, a $1,000 award to recognize a high school student who has demonstrated leadership and initiative in promoting conservation, preservation, restoration, or environmental education 
Filed Under: Lyme, News, Old Lyme, Outdoors, Top Story Preserves in Lyme Now Closed for Hunting During Weekdays November 17, 2016 by admin Leave a Comment Starting yesterday, Wednesday, Nov  16, the following Preserves in Lyme will be closed Monday through Friday until Tuesday, Dec  20, 2016, except to licensed hunters with valid consent forms from the Town of Lyme Open Space Coordinator:
Banningwood Preserve
Beebe Preserve
Chestnut Hill Preserve
Eno Preserve
Hand Smith
Honey Hill Preserve
Jewett Preserve
Mount Archer Woods
Pickwick’s Preserve
Plimpton Preserve
Slawson Preserve
These preserves, owned by the Town of Lyme or the Lyme Land Conservation Trust, will be open on Saturdays and Sundays during this hunting period as no hunting is allowed on weekends 
The hunting program is fully subscribed 
For more information on the hunting program in Lyme, visit http://www lymelandtrust org/stewardship/hunting-program/
Filed Under: Lyme, Outdoors, Top Story Town of Old Lyme Offers Part-time Land Steward Opportunity October 11, 2016 by admin Leave a Comment The Town of Old Lyme is seeking a part-time individual to maintain and manage the trail systems on its major preserves  Keeping trails cleared, maintaining markers, kiosks, entrances, parking areas, and managing for wildlife and other natural resources are the priorities 
For more information, visit the job posting on the home page of the Town’s web page at http://www oldlyme-ct gov/Pages/index 
To learn about the Open Space Commission and the properties it manages, visit http://www oldlyme-ct gov/Pages/OldLymeCT_Bcomm/open_space
Filed Under: Old Lyme, Outdoors, Top Story CT Fund for the Environment Annual Meeting to be Held Sunday in Hartford September 22, 2016 by admin Leave a Comment Engaging and educating communities for preservation of the Long Island Sound tidal estuary
Save the Sound is celebrating National Estuaries Week Sept  17 – 24 with a series of interactive and educational events throughout the Long Island Sound region  This annual celebration of estuaries—the vital coastal zones where freshwater rivers meet salty seas—is sponsored by Restore America’s Estuaries and its member organizations including Save the Sound  This year’s events call attention to the many benefits of thriving coastal ecosystems, including how estuary conservation efforts support our quality of life and economic well-being 
“The Long Island Sound estuary is not only where freshwater rivers meet the saltwater Atlantic, but where wildlife habitat meets beaches and boating, and where modern industry meets traditional oystering,” said Curt Johnson, executive director of Save the Sound, which is a bi-state program of Connecticut Fund for the Environment (CFE) 
Johnson continued, “All over the country, estuaries are the lifeblood of coastal economies  From serving as natural buffers to protect our coastlines from storms to providing unique habitat for countless birds, fish, and wildlife, estuaries deserve our protection and our thanks ”
Save the Sound is celebrating estuaries with a number of events this week, including the release of a new video, a presentation on Plum Island at the Old Lyme-Phoebe Griffin Noyes Library and the CFE/Save the Sound annual meeting:
Aerial view of Plum Island lighthouse  (From Preserve Plum Island website)
Chris Cryder, Special Projects Coordinator for Save the Sound and Outreach Coordinator for the Preserve Plum Island Coalition, will host Preserving Plum Island for Future Generations, a special presentation on the importance of conserving the wildlife habitats and historic buildings of Plum Island, New York 
Plum Island flanks Plum Gut in the Long Island Sound estuary’s eastern end, where fast-moving tides create highly productive fishing grounds  The talk is part of a multi-week series featuring photographs and paintings of Plum Island, and lectures on its ecology, geology, and history 
Old Lyme-Phoebe Griffin Noyes Library, 2 Library Lane, Old Lyme, Connecticut
Register by calling the library at 860-434-1684 
The Annual Meeting of Connecticut Fund for the Environment and its bi-state program Save the Sound will take place in the Planet Earth exhibit at the Connecticut Science Center  The event is open to the public with registration, and will feature a keynote address from Curt Spalding, administrator of EPA’s New England Region  Spalding is a leader in combatting nitrogen pollution and in climate change resilience planning efforts for New England 
Connecticut Science Center, 250 Columbus Blvd, Hartford, Connecticut
4 – 7 p m
RSVP to mlemere@ctenvironment org
To celebrate the contributions of volunteers to restoring the Long Island Sound estuary, Save the Sound has released a new video of a habitat restoration planting at Hyde Pond in Mystic  Following removal of the old Hyde Pond dam and opening 4 1 miles of stream habitat for migratory fish last winter (see time lapse video here), in May about 30 volunteers planted native vegetation along the Whitford Brook stream bank, under the direction of U S  Fish and Wildlife Service, CT DEEP’s Fisheries division, and Save the Sound staff 
Find more information on the project’s benefits and funders here 
Look for the planting video on Save the Sound’s website, YouTube, Facebook, and Twitter accounts 
Filed Under: Old Lyme, Outdoors 750+ Volunteers Clean Beaches from Norwalk to New London Including Griswold Point in Old Lyme September 17, 2016 by admin Leave a Comment Kendall Perkins displays a skull she found during Save The Sound‘s Coastal Clean-up Day held yesterday at White Sand Beach 
Save the Sound, a bi-state program of Connecticut Fund for the environment, organized 31 cleanups across Connecticut’s shoreline this weekend  The efforts are part of International Coastal Cleanup, which brings together hundreds of thousands of people each year to remove plastic bags, broken glass, cigarette butts, and other trash from the world’s shores and waterways  One of the areas included in the cleanup effort was from White Sand Beach to the tip of Griswold Point in Old Lyme 
The event was founded by Ocean Conservancy in 1985, and Save the Sound has served as the official Connecticut coordinator for the last 14 years 
“We didn’t plan it this way, but I can’t imagine a better way to celebrate the 31st anniversary of International Coastal Cleanup Day than with 31 cleanups!” said Chris Cryder, special projects coordinator for Save the Sound  “The cleanup just keeps growing, in Connecticut and worldwide  We have some terrific new and returning partners this year, including the SECONN Divers, folks from the U S  District Court, multiple National Charity League chapters, and many more ”
Cryder continued, “The diversity of the groups involved really reflects the truth that ocean health affects all of us  Clean beaches and oceans are safer for beachgoers and boaters, they’re healthier for wildlife that aren’t eating plastic or getting tangled up in trash, and they’re economic powerhouses for the fishing and tourism industries ”
The cleanups are co-hosted by a wide array of local partners including high schools, youth groups, and scout troops; churches; boaters and divers; watershed associations, park stewards, and land trusts  Twenty-eight cleanups will be held Saturday, with three more on Sunday and others through mid-October, for a total of 70 cleanups statewide 
Based on the estimates of cleanup captains, between 750 and 900 volunteers were expected to pitch in on Saturday alone  Last year, a total of 1,512 volunteers participated in Save the Sound cleanups throughout the fall  They collected more than three tons of litter and debris from 58 sites on Connecticut beaches, marshes, and riverbanks 
Over the event’s three-decade history, 11 5 million volunteers have collected 210 million pounds of trash worldwide  Every piece of trash volunteers find is tracked, reported to Save the Sound, and included in Ocean Conservancy’s annual index of global marine debris  The data is used to track trends in litter and devise policies to stop it at its source 
Filed Under: Old Lyme, Outdoors, Top Story Stonewell Farm Hosts Two-Day Workshop on Dry Stone Wall Building, Sept  24, 25 September 13, 2016 by admin Leave a Comment Andrew Pighill’s work includes outdoor kitchens, wine cellars, fire-pits, fireplaces and garden features that include follies and other whimsical structures in stone 
KILLINGWORTH — On Sept  24 and 25, from 9 a m  to 4 p m  daily, Andrew Pighills, master stone mason, will teach a two-day, weekend long workshop on the art of dry stone wall building at Stonewell Farm in Killingworth, CT 
Participants will learn the basic principles of wall building, from establishing foundations, to the methods of dry laid (sometimes called dry-stacked) construction and ‘hearting’ the wall  This hands-on workshop will address not only the structure and principles behind wall building but also the aesthetic considerations of balance and proportion 
This workshop expresses Pighill’s commitment to preserve New England’s heritage and promote and cultivate the dry stone wall building skills that will ensure the preservation of our vernacular landscape 
This workshop is open to participants, 18 years of age or older, of all levels of experience  Note the workshop is limited to 16 participants, and spaces fill up quickly 
You must pre-register to attend the workshop  The price for the workshop is $350 per person  Stonewell Farm is located at 39 Beckwith Rd , Killingworth CT 06419
If you have any questions or to register for the workshop, contact the Workshop Administrator Michelle Becker at 860-322-0060 or mb@mbeckerco com
At the end of the day on Saturday you’ll be hungry, tired and ready for some rest and relaxation, so the wood-fired Stone pizza oven will be fired up and beer, wine and Pizza Rustica will be served 
About the instructor: Born in Yorkshire, England, Andrew Pighills is an accomplished stone artisan, gardener and horticulturist  He received his formal horticulture training with The Royal Horticultural Society and has spent 40+ years creating gardens and building dry stone walls in his native England in and around the spectacular Yorkshire Dales and the English Lake District  Today, Pighills is one of a small, but dedicated group of US-based, certified, professional members of The Dry Stone Walling Association (DSWA) of Great Britain  Having moved to the United States more than 10 years ago, he now continues this venerable craft here in the US, building dry stone walls, stone structures and creating gardens throughout New England and beyond 
His particular technique of building walls adheres to the ancient methods of generations of dry stone wallers in his native Yorkshire Dales  Pighills’ commitment to preserving the integrity and endurance of this traditional building art has earned him a devoted list of private and public clients here and abroad including the English National Trust, the English National Parks, and the Duke of Devonshire estates  His stone work has been featured on British and American television, in Charles McCraven’s book The Stone Primer, and Jeffrey Matz’s Midcentury Houses Today, A study of residential modernism in New Canaan Connecticut  He has featured in the N Y Times, on Martha Stewart Living radio, and in the Graham Deneen film short “Dry Stone”, as well as various media outlets both here and in the UK, including an article in the Jan/Feb 2015 issue of Yankee Magazine 
Pighills is a DSWA fully qualified dry stone walling instructor  In addition to building in stone and creating gardens, Pighills teaches dry stone wall building workshops in and around New England  He is a frequent lecturer on the art of dry stone walling, and how traditional UK walling styles compare to those found in New England  His blog, Heave and Hoe; A Day in the Life of a Dry Stone Waller and Gardener, provides more information about Pighills 
For more information, visit www englishgardensandlandscaping com
Filed Under: Outdoors CT Port Authority Chair Tells Lower CT River Local Officials, “We’re All on One Team” August 27, 2016 by Olwen Logan 2 Comments Enjoying a boat ride on the Connecticut River, but still finding time for discussions, are (from left to right) Chester First Selectwoman Lauren Gister, Old Lyme First Selectwoman and Connecticut Port Authority (CPA) board member Bonnie Reemsnyder, Essex First Selectman Norm Needleman, CPA Chairman Scott Bates and Deep River First Selectman Angus McDonald, Jr 
Filed Under: Chester, Deep River, Essex, News, Old Lyme, Outdoors, Politics, Top Story House Approves Courtney-Sponsored Amendment Restricting Sale of Plum Island July 10, 2016 by admin 2 Comments Representative Joe Courtney
Local Congressional Representative Joe Courtney (CT-02) announced Thursday (July 7) that a bipartisan amendment he had led, along with Representatives Rosa DeLauro (CT-03), Lee Zeldin (R-NY) and Peter King (R-NY), to prohibit the sale of Plum Island was passed by the House of Representatives 
The amendment, which will prohibit the General Services Administration (GSA) from using any of its operational funding to process or complete a sale of Plum Island, was made to the Financial Services and General Government Appropriations Act of 2017  
In a joint statement, the Representatives said, “Our amendment passed today is a big step toward permanently protecting Plum Island as a natural area  Plum Island is a scenic and biological treasure located right in the middle of Long Island Sound  It is home to a rich assortment of rare plant and animal species that need to be walled off from human interference ”
The statement continued, “Nearly everyone involved in this issue agrees that it should be preserved as a natural sanctuary – not sold off to the highest bidder for development ” Presumptive Republican Presidential nominee Donald Trump had shown interest in the property at one time 
In 2008, the federal government announced plans to close the research facility on Plum Island and relocate to Manhattan, Kansas  Current law states that Plum Island must be sold publicly to help finance the new research facility 
Aerial view of Plum Island 
The lawmakers joint statement explained, “The amendment will prevent the federal agency in charge of the island from moving forward with a sale by prohibiting it from using any of its operational funding provided by Congress for that purpose,” concluding, ” This will not be the end of the fight to preserve Plum Island, but this will provide us with more time to find a permanent solution for protecting the Island for generations to come ”
For several years, members from both sides of Long Island Sound have been working in a bipartisan manner to delay and, ultimately, repeal the mandated sale of this ecological treasure  Earlier this year, the representatives, along with the whole Connecticut delegation, cosponsored legislation that passed the House unanimously to delay the sale of Plum Island 
Filed Under: Outdoors July 1 Update: Aquatic Treatment Planned for Rogers Lake, July 5 July 1, 2016 by admin Leave a Comment We received this updated information from the Old Lyme Selectman’s office at 11:05 a m  this morning:
Filed Under: Lyme, Old Lyme, Outdoors, Town Hall They’re Everywhere! All About Gypsy Moth Caterpillars — Advice from CT Agricultural Experiment Station June 2, 2016 by Adina Ripin Leave a Comment Gypsy moth caterpillars – photo by Peter Trenchard, CAES 
The potential for gypsy moth outbreak exists every year in our community 
Dr  Kirby Stafford III, head of the Department of Entomology at the Connecticut Agricultural Experiment Station, has written a fact sheet on the gypsy moth available on the CAES website  The following information is from this fact sheet 
The gypsy moth, Lymantria dispar, was introduced into the US (Massachusetts) by Etienne Leopold Trouvelot in about 1860  The escaped larvae led to small outbreaks in the area in 1882, increasing rapidly  It was first detected in Connecticut in 1905  By 1952, it had spread to 169 towns  In 1981, 1 5 million acres were defoliated in Connecticut  During the outbreak of 1989, CAES scientists discovered that an entomopathogenic fungus, Entomophaga maimaiga, was killing the caterpillars  Since then the fungus has been the most important agent suppressing gypsy moth activity 
The fungus, however, cannot prevent all outbreaks and hotspots have been reported in some areas, in 2005-06 and again in 2015 
The life cycle of the gypsy moth is one generation a year  Caterpillars hatch from buff-colored egg masses in late April to early May  An egg mass may contain 100 to more than 1000 eggs and are laid in several layers  The caterpillars (larvae) hatch a few days later and ascend the host trees and begin to feed on new leaves  The young caterpillars, buff to black-colored, lay down silk safety lines as they crawl and, as they drop from branches on these threads, they may be picked up on the wind and spread 
There are four or five larval stages (instars) each lasting 4-10 days  Instars 1-3 remain in the trees  The fourth instar caterpillars, with distinctive double rows of blue and red spots, crawl up and down the tree trunks feeding mainly at night  They seek cool, shaded protective sites during the day, often on the ground  If the outbreak is dense, caterpillars may feed continuously and crawl at any time 
With the feeding completed late June to early July, caterpillars seek a protected place to pupate and transform into a moth in about 10-14 days  Male moths are brown and fly  Female moths are white and cannot fly despite having wings  They do not feed and live for only 6-10 days  After mating, the female will lay a single egg mass and die  The egg masses can be laid anywhere: trees, fence posts, brick/rock walls, outdoor furniture, cars, recreational vehicles, firewood  The egg masses are hard  The eggs will survive the winter and larvae hatch the following spring during late April through early May 
The impact of the gypsy moth can be extensive since the caterpillar will feed on a wide diversity of trees and shrubs  Oak trees are their preferred food  Other favored tree species include apple, birch, poplar and willow  If the infestation is heavy, they will also attack certain conifers and other less favored species  The feeding causes extensive defoliation 
Healthy trees can generally withstand one or two partial to one complete defoliation  Trees will regrow leaves before the end of the summer  Nonetheless, there can be die-back of branches  Older trees may become more vulnerable to stress after defoliation  Weakened trees can also be attacked by other organisms or lack energy reserves for winter dormancy and growth during the following spring  Three years of heavy defoliation may result in high oak mortality 
The gypsy moth caterpillars drop leaf fragments and frass (droppings) while feeding creating a mess for decks, patios, outdoor furniture, cars and driveways  Crawling caterpillars can be a nuisance and their hairs irritating  The egg masses can be transported by vehicles to areas where the moth is not yet established  Under state quarantine laws, the CAES inspects certain plant shipments destined to areas free of the gypsy moth, particularly for egg masses 
There are several ways to manage the gypsy moth: biological, physical and chemical 
Biologically, the major gypsy moth control agent has been the fungus E  maimaiga  This fungus can provide complete control of the gypsy moth but is dependent on early season moisture from rains in May and June to achieve effective infection rates and propagation of the fungus to other caterpillars



ground_truth: Technological limitations, resistance to exposing data to scrutiny, and desire to hold onto data for personal use.

prompt_front: Now, answer the following question based on the text below, only give me the answer and do not output any other words.

Question: What is the group's request to the Connecticut DEEP Commissioner?

Read the following text and answer briefly.

Context 2:  The dry spring of 2015 resulted in little or no apparent fungal inoculation or spread until it killed late-stage caterpillars in some areas of the state, after most defoliation 
Infected caterpillars hang vertically from the tree trunk, head down  Some die in an upside down “V” position, a characteristic of caterpillars killed by the less common gypsy moth nucleopolyhedrosis virus (NPV)  This was not detected in caterpillars examined in 2015 
Physical controls include removing and destroying egg masses, which can be drowned in a soapy water and disposed of  Another method is to use burlap refuge/barrier bands wrapped around tree trunks so that migrating caterpillars will crawl into or under the folded burlap or be trapped by the sticky band 
There are a number of crop protection chemicals labeled for the control of gypsy moth on ornamental trees and shrubs  There are treatments for egg masses, larvae and adult moths  Detailed information about these chemical treatments is available in the CAES factsheet 
For complete information about the gypsy moth and its management, visit the CAES website and look for the fact sheet on gypsy moth 
Filed Under: News, Outdoors East Lyme Public Trust Invites Community to Celebrate Boardwalk Re-dedication May 25, 2016 by admin Leave a Comment On Saturday, May 28, at 11 a m , the East Lyme Public Trust Foundation, in co-operation with East Lyme Parks and Recreation Department, will sponsor A Dream Fulfilled, the official re-dedication of the East Lyme Boardwalk  The re-dedication ceremony, which will be held on the Boardwalk, will feature keynote speaker, Sen  Paul Formica, former First Selectman of East Lyme 
Other speakers will include East Lyme First Selectman Mark Nickerson, Public Trust President Joe Legg, Public Trust Past-President Bob DeSanto, Public Trust Vice-President John Hoye, and Parks and Recreation Director Dave Putnam; all the speakers will recognize the many people who have helped made this dream a reality 
The East Lyme Public Trust Foundation would like to invite the general public to witness this historic occasion  In addition, the members would especially like to encourage the participation of the 200 people who dedicated benches and the innumerable people who sponsored plaques  They would also love to welcome all members of the Trust – past and present – and all those who originally helped make the Boardwalk a reality 
Participants should enter the Boardwalk at Hole-in-the Wall on Baptist Lane, Niantic  Then, there will be a short walk to the area of the monument where the ceremony will take place  At the entrance to Hole-in-the Wall, the Public Trust will have a display of historical information and memorabilia related to the construction and re-construction of the Boardwalk  Public Trust members, Pat and Jack Lewis will be on hand to host the exhibit titled Before and After and to welcome participants  After the ceremony, participants will have the opportunity to visit “their bench” and re-visit “their plaque ” During and after the dedication, music will be provided by Trust member, Bill Rinoski, who is a “D J  for all occasions ” Rinoski will feature “Boardwalk-related” music and Oldies plus Top 40 selections  This historic occasion will be videotaped as a public service by Mike Rydene of Media Potions of East Lyme  High school volunteers will be on hand to greet participants and help with directions 
The organizing committee is chaired by Michelle Maitland  Her committee consists of Joe Legg, President of the East Lyme Public Trust, Carol Marelli, Bob and Polly DeSanto, June Hoye, and Kathie Cassidy 
Visit Facebook – East Lyme Public Trust Foundation – for more information on the re-dedication ceremony  For more information on the Boardwalk, explore this website 
Filed Under: Outdoors Lyme Land Trust Seeks to Preserve Whalebone Cove Headwaters May 8, 2016 by admin Leave a Comment Lyme Land Trust Preservation Vice President Don Gerber stands with Chairman Anthony Irving (kneeling) next to Whalebone Creek in the proposed Hawthorne Preserve in Hadlyme 
The Lyme Land Conservation Trust has announced a fund raising drive to protect 82 acres of ecologically strategic upland forest and swamp wildlife habitat in Hadlyme on the headwaters of Whalebone Cove, one of the freshwater tidal wetlands that comprises the internationally celebrated Connecticut River estuary complex 
The new proposed preserve is part of a forested landscape just south of Hadlyme Four Corners and Ferry Road (Rt  148), and forms a large part of the watershed for Whalebone Creek, a key tributary feeding Whalebone Cove, most of which is a national wildlife refuge under the management of the US Fish & Wildlife Service 
The Land Trust said it hopes to name the new nature refuge in honor of William Hawthorne of Hadlyme, whose family has owned the property for several generations and who has agreed to sell the property to the Land Trust at a discount from its market value if the rest of the money necessary for the purchase can be raised by the Land Trust 
“This new wildlife preserve will represent a triple play for habitat conservation,” said Anthony Irving, chairman of the Land Trust’s Preservation Committee 
“First, it helps to protect the watershed feeding the fragile Whalebone Cove eco-system, which is listed as one of North America’s important freshwater tidal marshes in international treaties that cite the Connecticut River estuary as a wetland complex of global importance  Whalebone Creek, one of the primary streams feeding Whalebone Cove, originates from vernal pools and upland swamps just south of the Hawthorne tract on the Land Trust’s Ravine Trail Preserve and adjacent conservation easements and flows through the proposed preserve  Virtually all of the Hawthorne property comprises much of the watershed for Whalebone Creek 
“Second, the 82 acres we are hoping to acquire with this fund raising effort represents a large block of wetlands and forested wildlife habitat between Brush Hill and Joshuatown roads, which in itself is home to a kaleidoscope of animals from amphibians and reptiles that thrive in several vernal pools and swamp land, to turkey, coyote, bobcat and fisher  It also serves as seasonal nesting and migratory stops for several species of deep woods birds, which are losing habitat all over Connecticut due to forest fragmentation 
“Third, this particular preserve will also conserve a key link in the wildlife corridors that connects more than 1,000 acres of protected woodland and swamp habitat in the Hadlyme area ” Irving explained that the preserve is at the center of a landscape-scale wildlife habitat greenway that includes Selden Island State Park, property of the US Fish & Wild Life’s Silvio O Conte Wildlife Refuge, The Nature Conservancy’s Selden Preserve, and several other properties protected by the Lyme Land Conservation Trust 
“Because of its central location as a hub between these protected habitat refuges,” said Irving, “this preserve will protect forever the uninterrupted access that wildlife throughout the Hadlyme landscape now has for migration and breeding between otherwise isolated communities and families of many terrestrial species that are important to the continued robust bio-diversity of southeastern Connecticut and the Connecticut River estuary ”
Irving noted that the Hawthorne property is the largest parcel targeted for conservation in the Whalebone Cove watershed by the recently developed US Fish & Wildlife Service Silvio O Conte Wildlife Refuge Comprehensive Conservation Plan  Irving said the Land Trust hopes to create a network of hiking trails on the property with access from both Brush Hill Road on the east and Joshuatown Road on the west and connection to the Land Trust’s Ravine Trail to the south and the network of trails on the Nature Conservancy’s Selden Preserve 
Irving said there is strong support for the Land Trust’s proposal to preserve the property both within the Hadlyme and Lyme communities and among regional and state conservation groups  He noted letters of support have come from the Hadlyme Garden Club, the Hadlyme Public Hall Association, the Lyme Inland Wetlands & Watercourses Agency, the Lyme Planning and Zoning Commission, the Lyme Open Space Committee, the Lower Connecticut River Valley Council of Governments, the Lyme Garden Club, the Lyme Public Hall, The Nature Conservancy, The Silvio O Conte Refuge, the Connecticut River Watershed Council, and the Friends of Whalebone Cove, Inc 
He reported that between Hawthorne’s gift and several other pledges the Land Trust has already received commitments of 25 percent of the cost of the property 
Filed Under: Lyme, Outdoors, Top Story, vnn Old Lyme Tree Commission Celebrates Arbor Day April 29, 2016 by admin Leave a Comment Members of the three groups gather around the new oak tree  From left to right are Kathy Burton, Joanne DiCamillo, Joan Flynn  Anne Bing, Emily Griswold and Barbara Rayel 
Filed Under: Old Lyme, Outdoors, Top Story, Town Hall Enjoy a Tour of Private Gardens in Essex, June 4 April 28, 2016 by Adina Ripin Leave a Comment See this beautiful private garden in Essex on June 4 
ESSEX – On Saturday, June 4, from 10 a m  to 3 p m , plan to stroll through eight of the loveliest and most unusual private gardens in Essex  Some are in the heart of Essex Village while others are hidden along lanes most visitors never see  While exploring, you will find both formal and informal settings, lovely sweeping lawns and panoramic views of the Connecticut River or its coves  One garden you will visit is considered to be a ‘laboratory’ for cultivation of native plants  Master Gardeners will be available to point out specific features, offer gardening tips, and answer questions 
The garden tour is sponsored by the Friends of the Essex Library  Tickets are $25 in advance and $30 at the Essex Library the day of the event  Cash, checks, Visa or Master Card will be accepted  Tickets can be reserved by visiting the library or by completing the form included in flyers available at the library and throughout Essex beginning May 2  Completed forms can be mailed to the library  Confirmations will be sent to the email addresses on the completed forms 
Your ticket will be a booklet containing a brief description of each garden along with a map of the tour and designated parking  Tickets must be picked up at the library beginning at 9:45 a m  the day of the event 
Richard Conroy, library director, has said, “The Essex Library receives only about half of its operating revenue from the Town  The financial assistance we receive each year from the Friends is critical  It enables us to provide important resources such as Ancestry com and museum passes, as well as practical improvements like the automatic front doors that were recently installed  I urge you to help your Library by helping our Friends make this event a success! Thank you for your support ”
The tour will take place rain or shine  For more information, call 860-767-1560  All proceeds will benefit Friends of the Essex Library 
Filed Under: Outdoors Potapaug Presents Plum Island Program April 7, 2016 by admin Leave a Comment Potapaug Audubon presents “Preserving Plum Island” on Thursday, April 7, at 7 p m  at Old Lyme Town Hall, 52 Lyme St , Old Lyme, with guest speaker Chris Cryder, from the Preserve Plum Island Coalition 
Cryder will discuss the efforts to protect the island, which provides vital habitat for threatened and endangered birds 
This is a free program and all are welcome 
Filed Under: Old Lyme, Outdoors CT Legislators Support Study to Preserve Plum Island From Commercial Development March 28, 2016 by Jerome Wilson 1 Comment Aerial view of Plum Island lighthouse  (From Preserve Plum Island website)
Last Thursday, March 24, at a press conference in Old Saybrook, a triumvirate of Congressional legislators from Connecticut, State Senator Richard Blumenthal and US Representatives Joe Courtney (D-2nd District) and Rosa DeLauro (D-3rd District) confirmed their support for a study to determine the future of Plum Island located in Long Island Sound 
Members of the Plum Island Coalition — which has some 65 member organizations all dedicated to preserving the island — were in attendance to hear the good news 
The island still houses a high-security, federal animal disease research facility, but the decision has already been taken to move the facility to a new location in Kansas with an opening slated for 2022  The current facility takes up only a small percentage of the land on the island and significantly for environmentalists, the remainder of the island has for years been left to nature in the wild 
In supporting a federal study on the future of Plum Island, Sen  Blumenthal said, “This study is a step towards saving a precious, irreplaceable national treasure from developers and polluters  It will provide the science and fact-based evidence to make our case for stopping the current Congressional plan to sell Plum Island to the highest bidder ” He continued, “The stark truth is the sale of Plum Island is no longer necessary to build a new bioresearch facility because Congress has fully appropriated the funds  There is no need for this sale – and in fact, Congress needs to rescind the sale ” Congress, however, still has a law on the books that authorizes the sale of Plum Island land to the highest bidder  Therefore, opponents of the sale will have the burden of convincing Congress to change a law that is currently in place 
Filed Under: Old Lyme, Outdoors, Top Story, vnn Land Trusts’ Photo Contest Winners Announced March 24, 2016 by admin Leave a Comment Winner of the top prize, the John G  Mitchell Environmental Conservation Award – Hank Golet
The 10th Annual Land Trust’s Photo Contest winners were announced at a March 11 reception highlighting the winning photos and displaying all entered photos  Land trusts in Lyme, Old Lyme, Salem, Essex and East Haddam jointly sponsor the annual amateur photo contest to celebrate the scenic countryside and diverse wildlife and plants in these towns  The ages of the photographers ranged from children to senior citizens 
Hank Golet won the top prize, the John G  Mitchell Environmental Conservation Award, with his beautiful photograph of a juvenile yellow crowned night heron in the Black Hall River in Old Lyme  Alison Mitchell personally presented the award, created in memory of her late husband John G  Mitchell, an editor at National Geographic, who championed the cause of the environment 
William Burt, a naturalist and acclaimed wildlife photographer, who has been a contest judge for ten years, received a special mention  Judges Burt; Amy Kurtz Lansing, an accomplished art historian and curator at the Florence Griswold Museum; and Skip Broom, a respected, award-winning local photographer and antique house restoration housewright, chose the winning photographs from 219 entries 
The sponsoring land trusts – Lyme Land Conservation Trust, Essex Land Trust, the Old Lyme Land Trust, Salem Land Trust, and East Haddam Land Trust – thank the judges as well as generous supporters RiverQuest/ CT River Expeditions, Lorensen Auto Group, the Oakley Wing Group at Morgan Stanley, Evan Griswold at Coldwell Banker, Ballek’s Garden Center, Essex Savings Bank, Chelsea Groton Bank, and Alison Mitchell in honor of her late husband John G  Mitchell  Big Y and Fromage Fine Foods & Coffee provided support for the reception 
The winning photographers are:
John G  Mitchell Environmental Award, Hank Golet, Old Lyme
1st: Patrick Burns, East Haddam
2nd: Judah Waldo, Old Lyme
3rd: James Beckman, Ivoryton
Honorable Mention Gabriel Waldo, Old Lyme
Honorable Mention Sarah Gada, East Haddam
Honorable Mention Shawn Parent, East Haddam
Cultural/Historic
1st: Marcus Maronne, Mystic
2nd: Normand L  Charlette, Manchester
3rd: Tammy Marseli, Rocky Hill
Honorable Mention Jud Perkins, Salem
Honorable Mention Pat Duncan, Norwalk
Honorable Mention John Kolb, Essex
Landscapes/Waterscapes
1st: Cheryl Philopena, Salem
2nd: Marian Morrissette, New London
3rd: Harcourt Davis, Old Lyme
Honorable Mention Cynthia Kovak, Old Lyme
Honorable Mention Bopha Smith, Salem
1st: Mary Waldron, Old Lyme
2nd: Courtney Briggs, Old Saybrook
3rd: Linda Waters, Salem
Honorable Mention Pete Govert, East Haddam
Honorable Mention Marcus Maronne, Mystic
Honorable Mention Marian Morrissette, New London
First place winner of the Wildlife category – Chris Pimley
1st: Chris Pimley, Essex
2nd: Harcourt Davis, Old Lyme
Honorable Mention Thomas Nemeth, Salem
Honorable Mention Jeri Duefrene, Niantic
Honorable Mention Elizabeth Gentile, Old Lyme
The winning photos will be on display at the Lymes’ Senior Center for the month of March and Lyme Public Library in April  For more information go to lymelandtrust org 
Filed Under: Outdoors Old Lyme’s Open Space Commission Hosts Talk on Sea Level Rise, Salt Marsh Advance March 11, 2016 by admin 1 Comment The Town of Old Lyme’s Open Space Commission invites all interested parties to a workshop by Adam Whelchel, PhD, Director of Science at The Nature Conservancy’s Connecticut Chapter  The workshop will be held on Friday, March 11, at 9 a m  in the Old Lyme Town Hall 
Filed Under: Outdoors, Town Hall Inaugural Meeting of ‘Friends of Whalebone Cove’ Held, Group Plans to Protect Famous Tidal Wetland March 7, 2016 by admin Leave a Comment The newly formed ‘Friends of Whalebone Cove’ are working to preserve and protect the Cove’s fragile ecosystem 
A new community conservation group to protect Whalebone Cove, a freshwater tidal marsh along the Connecticut river in Hadlyme recognized internationally for its wildlife habitat, will hold its first organizational meeting this coming Sunday, March 6, at 4 p m 
Calling the group “Friends of Whalebone Cove” (FOWC), the organizers say their purpose is to “create a proactive, community-based constituency whose mission is to preserve and protect the habitat and fragile eco-systems of Whalebone Cove ”
Much of Whalebone Cove is a nature preserve that is part of the Silvio O  Conte National Wildlife Refuge (www fws gov/refuge/silvio_o_conte) under the jurisdiction of the U S  Fish & Wildlife Service (USFW)  The Refuge owns and manages 116 acres of marshland in Whalebone Cove and upland along its shores 
Prior to being taken over by USFW, the Whalebone Cove preserve was under the protection of The Nature Conservancy 
As part of the Connecticut River estuary, the Cove is listed in the Ramsar Convention on International Wetlands (www ramsar org) as tidal marshlands on the Connecticut River that constitute a “wetlands complex of international importance ”
The Ramsar citation specifically notes that Whalebone Cove has one of the largest stands of wild rice in the state  Except at high tide, most of the Cove is open marshland covered by wild rice stands with relatively narrow channels where Whalebone Creek winds its way through the Cove to the main stem of the Connecticut River 
Brian Slater, one of the group’s leaders who is filing the incorporation documents creating FOWC, said the creation of the organization was conceived by many of those living around the Cove and others in the Hadlyme area because of increased speeding motor boat and jet ski traffic in the Cove in recent years, damaging wetland plants and disrupting birds and other wildlife that make the Cove their home 
Slater said “Our goal is to develop a master plan for protection of the Cove through a collaborative effort involving all those who have a stake in Whalebone Cove – homeowners along its shores and those living nearby, the Silvio O  Conte Refuge, the Connecticut Department of Energy & Environmental Protection (DEEP), hunters, fishing enthusiasts, canoeing and kayaking groups, Audubon groups, the Towns of Lyme and East Haddam, The Nature Conservancy, the Connecticut River Watershed Council, the Lyme Land Conservation Trust, the Connecticut River Gateway Commission, and others who want to protect the Cove ”
“Such a plan”, said Slater, “should carefully evaluate the habitat, plants, wildlife and eco-systems of the Cove and the surrounding uplands and watershed and propose an environmental management plan that can be both implemented and enforced by those entrusted with stewarding the Cove and its fragile ecosystems for the public trust ”
FOWC has written a letter to Connecticut DEEP Commissioner Rob Klee asking that he appoint a blue ribbon commission to conduct the research and develop the management plan  FOWC also asked that Commissioner Klee either deny or defer approval on any applications for new docks in the Cove until the management plan can be developed and implemented  Currently there are no docks in the Cove 
“We are very concerned that the installation of docks permitted for motor boat use will greatly increase the amount of motorized watercraft in the Cove,” said Slater  “There’s already too much jet ski and speeding motorboat traffic in the Cove  Those living on the Cove have even seen boats towing water skiers crisscrossing the wild rice plants at high tide  Something has to be done to protect the birds and marine life that give birth and raise their young in the Cove ”
Slater urged all those “who treasure Whalebone Cove and the many species of birds, turtles, fish, reptiles, amphibians, beaver, and rare flora and fauna that make their home in it to attend the meeting, whether they live in the Hadlyme area or beyond ”
Expected to be at the meeting will be representatives from USFW, DEEP, the Connecticut River Watershed Council, and several other conservation organizations 
The meeting will be held at Hadlyme Public Hall, 1 Day Hill Rd , in Lyme, which is at the intersection of Ferry Rd  (Rte  148), Joshuatown Rd , and Day Hill Rd  Representatives from the Silvio O  Conte Refuge will make a short presentation on the history and mission of the Conte Refuge system, which includes nature preserves throughout the Connecticut River Valley in four states 
For more information, call 860-322-4021 or email fowchadlyme@gmail com
Filed Under: Lyme, News, Outdoors Next Page »
Context 3: Paper Info

Title: Interpretable reduced-order modeling with time-scale separation Interpretable reduced-order modeling with time-scale separation
Publish Date: 7 March 2023
Author List: Sebastian Kaltenbach (from CSE-Lab, ETH Zurich, Harvard SEAS), Phaedon-Stelios Koutsourelakis (from CSE-Lab, ETH Zurich, Harvard SEAS), Petros Koumoutsakos (from CSE-Lab, ETH Zurich, Harvard SEAS), Harvard Seas (from CSE-Lab, ETH Zurich, Harvard SEAS)

Figure

FIG  5  Comparison between the phase-space of the reference solution (left) and the phase-space of the predictions
FIG  7  Comparison between predictions and reference solutions for a new initial condition fort = 1 25, 3 75, 7 5, 12 5, 20, 30  (from left to right and top to down) We note that with longer prediction time the uncertainty bounds increases Despite the chaotic nature of the KS equation, the predictive posterior mean is close to the reference solution for t ≤ 12 5

abstract

Partial Differential Equations (PDEs) with high dimensionality are commonly encountered in computational physics and engineering  However, finding solutions for these PDEs can be computationally expensive, making model-order reduction crucial  We propose such a data-driven scheme that automates the identification of the time-scales involved and, can produce stable predictions forward in time as well as under different initial conditions not included in the training data 
To this end, we combine a non-linear autoencoder architecture with a time-continuous model for the latent dynamics in the complex space  It readily allows for the inclusion of sparse and irregularly sampled training data  The learned, latent dynamics are interpretable and reveal the different temporal scales involved 
We show that this data-driven scheme can automatically learn the independent processes that decompose a system of linear ODEs along the eigenvectors of the system's matrix  Apart from this, we demonstrate the applicability of the proposed framework in a hidden Markov Model and the (discretized) Kuramoto-Shivashinsky (KS) equation 
Additionally, we propose a probabilistic version, which captures predictive uncertainties and further improves upon the results of the deterministic framework 

INTRODUCTION

High-fidelity simulations of critical phenomena such as ocean dynamics and epidemics have become essential for decision-making  They are based on physically-motivated PDEs expressing system dynamics that span multiple spatiotemporal scales and which necessitate cumbersome computations   In recent years there is increased attention to the development of data-driven models that can accelerate the solution of these PDEs as well as reveal salient, lower-dimensional features that control the long-term evolution 
In most cases, data-driven reduced-order models are not interpretable  In particular, models based on neural networks despite good predictive capabilities , they offer a black-box description of the system dynamics  A possible remedy is applying a symbolic regression to the learned neural network representation , but this adds additional computational cost due to the two-step procedure 
A number of frameworks such as SINDy allows to learn interpretable dynamics but it relies on the a-priori availability of lower-dimensional descriptors and of time-derivatives which can be very noisy for both simulation and experimental data  Other frameworks are tailored to specific problems such as molecular dynamics  
Here, we present a framework that only needs the value of the observables, and not their derivatives, as training data and is capable of identifying interpretable latent dynamics  The deployment of interpretable latent dynamics ensures that conservation of important properties of that are reflected in the reduced-order model  
The present method is related to approaches based on the Koopman-operator extended Dynamic Mode Decomposition (eDMD) but uses continuous complex-valued latent space dynamics and only requires one scalar variable per latent dimension to describe the latent space dynamics  Therefore we do not have to enforce any parametrizations on the Koopman matrix  
The time-continuous formulation moreover allows to incorporate sparse and irregularly sampled training data and fast generation of predictions after the training phase  By using a complex-valued latent space we can also incorporate harmonic effects and reduce the number of latent variables needed  Linear and non-linear autoencoders are used to map the observed, high-dimensional time-series to the lower-dimensional, latent representation and we identify simultaneously the autoencoder as well as the latent dynamics by optimizing a combined loss function 
Hence the to tasks of dimensionality reduction and discovery of the reduced dynamics are unified while other frameworks treat the two parts separately   Apart from using an architecture based on autoencoders to identify the latent space, projection-based methods could also be employed   We are also proposing a probabilistic version of our algorithm ) that makes use of probabilistic Slow Feature Analysis  
This allows for a latent representation that arart from being time-continuous, can quantify the predictive uncertainty and hierarchically decompose the dynamics into their pertinent scales while promoting the discovery of slow processes that control the system's evolution over long time horizons  The rest of the paper is structured as follows: We introduce the methodological framework as well as algorithmic details in section II 
Particular focus is paid on the interpretability of the inferred lower-dimensional dynamics  In section III we present three numerical illustrations, i e  a system of linear ODEs, a hidden Markov Model and the discretized KS-equation  We then present in section IV the probabilistic extension of the framework and apply it to the KS-equation 
We conclude with a summary and a short discussion about possible next steps  We introduce the autoencoders deployed in this work, followed by the interpretable latent space dynamic and discuss the training process  We consider data from high-dimensional time series x n ∈ R f with n = 1,    , T   We remark that the intervals between the different states do not need to be uniformly spaced 

Autoencoder

A core assumption of the method is that each high-dimensional state x n can be compressed to a lower-dimensional representation z n ∈ C c with c << f   We identify this lower-dimensional representation by an autoencoder consisiting of a parameterized encoder and decoder  The encoder maps the high-dimensional representation to the latent space as:
The latent space is complex-valued  The decoder reconstructs the high-dimensional representation based on the latent variables as: We denote the parameters of the encoder as well as the decoder by θ  As discussed later in Section II C, both set of parameters are optimized simultaneously during training and therefore there is no need for differentiating them 

Interpretable Latent Space Dynamics

We employ a propagator in the latent space to capture the reduced-order dynamics of the system  In contrast to other time-extended variational autoencoder frameworks, our representation uses complex valued latent variables  In addition the latent variables are treated independently  The latter feature enables us to have an interpretable latent dynamics as well as a model that is especially suitable for being trained in the Small Data regime due to the small number of required parameters 
This is in contrast to temporal propagators such as LSTMs   For each dimension i of the latent variable z we are using the following continuous ODE in the complex plane: By solving this ODE, we can define the operator: Interpretable reduced-order modeling with time-scale separation Here, λ is a vector containing all the individual λ's and ∆t n indicates the time-step between the latent states 
The symbol is used to indicate a component-wise multiplication  We remark that the latent variables and the parameter governing the temporal evolution are complex numbers and their role in describing the system dynamics is similar to that of an eigenvalue  The real part is associated with growth and decay whereas the imaginary part is representing the periodic component 
This approach has similarities with the Koopman-operator based methods and the extended dynamic mode decomposition   In contrast to the methods mentioned before we are using a continuous formulation in the latent space that allows us to incorporate scarce and irregularly sampled training data and directly rely on complex numbers in the latent space 

Training and Predictions

We optimize a loss function that combines both a reconstruction loss as well as a loss associated with the error of our learned propagator in the latent space: (5) We note that we could directly incorporate mini-batch training by only taking the summation over a subset of the N available training data 
For new predictions of unseen states, we use the encoder to generate a latent representations which is then advanced in time by the learned propagator  At a designated time step we are using the decoder to reconstruct the high-dimensional solution  We applied our algorithm to three systems  First, we show that the algorithm is capable of exactly reproducing the solution of a linear ODE and to identify its eigenvalues 
Afterwards we are applying the framework to a high-dimensional process generated by a complex latent dynamics, which is correctly identified  As a final test case, we are applying the algorithm to a Kuramoto Shivashinski (KS) equation  Interpretable reduced-order modeling with time-scale separation

Linear ODE

We are considering a two-dimensional ODE system for x = y 1 y 2 : Based on the obtained training data we run our algorithm using a linear encoder and decoder structure as well as two latent variables z



ground_truth: Appointing a blue ribbon commission to conduct the research and develop the management plan and denying or defering approval on any applications for new docks in the Cove until the management plan can be developed and implemented.

prompt_front: Now, answer the following question based on the text below, only give me the answer and do not output any other words.

Question: How does the framework capture the reduced-order dynamics?

Read the following text and answer briefly.

Context 3:  The loss function was optimized using the Adam algorithm   As we consider a linear ODE we can analytically compute the eigenvalues involved and compare it with the parameters λ identified by our algorithm 
We observe in Figure that the algorithm was able to recover the correct values, i e  the eigenvalues 7 and 3 of the given linear ODE  The system does not have a periodic component and the two imaginary parts correctly go to zero, whereas the real parts converge to the reference value  Moreover we are also able to identify for the linear mapping between our latent variables z and the training data a matrix consisting of a multiple of the eigenvectors (1,1) and (1,-1) and thus the correct solution 
This example was chosen to show that the algorithm is able to quickly identify the exact solution of a linear ODE in terms of its linearly independent components 

Hidden multiscale dynamics

We consider eight-dimensional synthetic time series data produced by an underlying twodimensional complex valued process  In particular, the data points x are generated by first solving for the temporal evolution for the two complex-valued processes p 1 and p 2 and than mapping to the eight-dimensional space by using a randomly sampled linear mapping W  
One of the two processes used to generate the data is chosen to be much slower than the other one and both processes have a periodic component  dp 2 dt = (−0 9 + 1 5i)p 2 (8) As training data we consider 40 time series with 150 data points each, obtained by simulating the described processes for a maximum of t = 15 s and then sampling from the obtained data points 
Hence the training data consists of: • 40 time-series • with each consisting 150 observations of the x at a uniform time-step ∆t = 0 0025 The autoencoder obtained consists of one linear layer for both the decoder as well as the encoder  The model is trained for 5000 iterations using the Adam optimizer and a learning rate of 10 −3  
The results for the convergence of the parameters λ 1 and λ 2 can be found in Figure   We note that the process which is slower decaying and thus more responsible for the long-term evolution of the system has a higher convergence rate than the faster process  With the obtained parameters λ as well as the trained autoencoder, we compute predictions based on the last time step used for training, i e  we apply the encoder to obtain our latent representation and than use the latent dynamics to advance the latent representation in time 
Afterwards, we employ the decoder to reconstruct the full high-dimensional system  The results can be found in Figure and show very good agreement between predictions and reference data  This example shows that our model is successfully able to carry out dimensionality reduction and moreover indicates that the convergence rate between latent processes can be different 
The latter is relevant when training models as for accurate predictions all latent processes and their dynamics should be converged 

Kuramoto-Sivashinsky

Finally, we applied our algorithm to the KS equation and aim to identify a reduced-order model for the solution u(y, t): We employed periodic boundary conditions, µ = 1 and a domain size y ∈ [0, 22]  For this domain-size, the KS-equation exhibits a structurally stable chaotic attractor as discussed in The black lines divides the area for which training data was given from the area without raining data 
;   The equation is discretized in space using a discretization step of 22 64 resulting in a state vector x of dimension 64 and a nonlinear system of coupled ODEs  This is solved using a stiff fourth-order solver  We employed a non-linear encoder and decoder with four fully-connected layers each and ReLU-activation functions as well as Dropout Layers between the fully-connected layers 
We trained the model for 200000 iterations using Adam and a learning rate of 5 • 10 4 and assuming a five-dimensional latent space  We obtained the λ's in Figure   Four latent variables have λ's close to zero and thus a slow temporal dynamic that is responsible for the long-term evolution whereas one latent variable is quickly decaying 
Based on the obtained parameters, we do predictions based on an unseen initial condition not contained in the training data  We are able to reconstruct the correct phase space based on our predictions despite only using a very limited amount of training data  The results for the phase space can be seen in Figure  
Although the small-scale fluctuations in the temporal dynamics are not well captured, the model identifies the correct manifold which has a good accuracy compared to the reference solution  All phase-spaces were obtained by using a finite-difference operator on the data or predictions  These results are in accordance Interpretable reduced-order modeling with time-scale separation with whose LSTM-based temporal dynamic model was also able to find the correct phase space but not to track the actual dynamics for long-term predictions 
Our model is not able to account for noise in the temporal evolution and thus dealing with chaotic, small-scale fluctuations is challenging  We believe that a probabilistic version of our algorithm could be advantageous here  This section contains a fully probabilistic formulation for the deterministic model discussed before 
We replace the Autoencoder with a Variational Autoencoder and the ODE in the latent space with a SDE  The loss function which we optimize is the Evidence-Lower Bound (ELBO) 

Model Structure

We postulate the following relations for our probabilistic model using an Ornstein-Uhlenbeck (OU) for each dimension i of the latent space and a Wiener process W t in the latent space: We again assume that the latent variables z t are complex-valued and a priori independent  Complex variables were chosen as their evolution includes a harmonic components which are observed in many physical systems 
We assume an initial conditions z 0,i ∼ CN (0, σ 2 0,i )  The total parameters associated with the latent space dynamics of our model are thus {σ 2 0,i , σ 2 i , λ i } c i=1 and will be denoted by θ together with all parameters responsible for the decoder mapping G (see next section)  These parameters along with the state variables z t have to be inferred from the data x t  
Based on probabilistic Slow Feature Analysis (SFA) , we set σ 2 i = 2; (λ j ) and σ 2 0,i = 1  As a consequence, a priori, the latent dynamics are stationary  A derivation and reasoning for this choice can be found in Appendix A  Hence the only independent parameters are the λ i , the imaginary part of which can account for periodic effects in the latent dynamics 

Variational Autoencoder

We employ a variational autoencoder to account for a probabilistic mappings from the lower-dimensional representation z n to the high-dimensional system x n   In particular we are employing a probabilistic decoder The encoder is used to infer the state variables z based on the given data and thus defined in the inference and learning section 

Inference and Learning

Given the probabilistic relations , our goal is to infer the latent variables z 0:T as well as all model parameters θ  We follow a hybrid Bayesian approach in which the posterior of the state variables is approximated using amortized Variational Inference and Maximum-A-Posteriori (MAP) point-estimates for θ are computed 
The application of Bayes' rule for each data sequence x 0:T leads to the following posterior: where p(θ) denotes the prior on the model parameters  In the context of variational inference, we use the following factorization of the approximate posterior i e  we infer only the mean µ and variance σ for each state variable based on the given data points 
This conditional density used for inference is the encoder-counterpart to the probabilistic decoder defined in the section before  It can be readily shown that the optimal parameter values are found by maximizing the Evidence Lower Bound (ELBO) F(q φ (z 0:T ), θ) which is derived in Appendix B  We compute Monte Carlo estimates of the gradient of the ELBO with respect to φ and θ with the help of the reparametrization trick and carry out stochastic optimization with the ADAM algorithm  

Results for the probabilistic extension

We applied our probabilistic version to the KS-equation  We used the same settings as for the deterministic approach but considered up to 10 complex latent variables  The obtained λ's are in Figure   The probabilistic model allows us to quantify the uncertainty in predictions  In Figure predictions for various time-steps and the respective uncertainty bounds are shown for an unseen initial condition 
Due to the chaotic nature of the KS-equation and the small amount of training data, the underlying linear dynamic of our model is only able to capture the full dynamics for a limited time horizon  Fortunately, due to the probabilistic approach the model is capable of capturing chaotic fluctuations with increasingly wide uncertainty bounds 
We also computed the phase space representation for the KS-equation based on the predictions obtained by our model and compare it with the reference solution  The probabilistic model identifies the correct manifold with a better accuracy than the deterministic model  As some of the small-scale fluctuations are accounted as noise, the resulting manifold is more concentrated at the origin and the obtained values are slightly smaller than the reference manifold although their shape is very similar 



ground_truth: By using a propagator in the latent space.