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Imaging and Molecular Annotation of Xenographs and Tumours (IMAXT): High throughput data and analysis infrastructure
- Eduardo A. González-Solares, Ali Dariush, Carlos González-Fernández, Aybüke Küpcü Yoldaş, Alireza Molaeinezhad, Mohammad Al Sa’d, Leigh Smith, Tristan Whitmarsh, Neil Millar, Nicholas Chornay, Ilaria Falciatori, Atefeh Fatemi, Daniel Goodwin, Laura Kuett, Claire M. Mulvey, Marta Páez Ribes, Fatime Qosaj, Andrew Roth, Ignacio Vázquez-García, Spencer S. Watson, Jonas Windhager, Samuel Aparicio, Bernd Bodenmiller, Ed Boyden, Carlos Caldas, Owen Harris, Sohrab P. Shah, Simon Tavaré, CRUK IMAXT Grand Challenge Team, Dario Bressan, Gregory J. Hannon, Nicholas A. Walton
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- Biological Imaging / Volume 3 / 2023
- Published online by Cambridge University Press:
- 14 April 2023, e11
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With the aim of producing a 3D representation of tumors, imaging and molecular annotation of xenografts and tumors (IMAXT) uses a large variety of modalities in order to acquire tumor samples and produce a map of every cell in the tumor and its host environment. With the large volume and variety of data produced in the project, we developed automatic data workflows and analysis pipelines. We introduce a research methodology where scientists connect to a cloud environment to perform analysis close to where data are located, instead of bringing data to their local computers. Here, we present the data and analysis infrastructure, discuss the unique computational challenges and describe the analysis chains developed and deployed to generate molecularly annotated tumor models. Registration is achieved by use of a novel technique involving spherical fiducial marks that are visible in all imaging modalities used within IMAXT. The automatic pipelines are highly optimized and allow to obtain processed datasets several times quicker than current solutions narrowing the gap between data acquisition and scientific exploitation.
10 - Acquiring archives
- from PART II - ARCHIVAL PRACTICES
- Laura A. Millar
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One cannot collect all the beautiful shells on the beach; one can collect only a few, and they are more beautiful if they are few.
Anne Morrow Lindbergh (1906–2001) Gift from the Sea, 1955How does an archivist decide which archives to acquire? How does she decide which specific items within a particular acquisition should be kept? Whatever an archivist decides to keep becomes valuable in large part because it has been kept. And whatever is not kept is, in the normal course of events, gone forever. Appraisal decisions can be daunting, to say the very least.
This is one reason appraisal is considered the most important and the most difficult aspect of archival work. If every record were valuable, and if every archivist had all the money and space in the world, there would, in theory, be no need for appraisal. The archivist could pack up all the documents in her care, put them in acid-free boxes or store them on a stack of computer hard drives and tell researchers to come and get them. Many archivists and digital experts are arguing this very idea, suggesting that with the unlimited capacity of cloud computing systems and the tremendous potential for research into ‘big data’, keeping more – in theory, keeping all – is easier and potentially more fruitful than ever before.
Others, and I count myself among them, prefer to think about Anne Lindbergh's seashells. What is the point in keeping everything? What is the point in trying? If archivists and society decide just to keep everything, how can we actually know which bit of information is core evidence and which is just dross that clutters our hard drives and our minds?
In order to cope with the challenge of deciding what to keep and what to reject, archivists have invented (and rejected and redefined and reinvented) a range of theories and principles surrounding the appraisal and acquisition of archival materials. Some of these approaches are highly objective, others exceedingly subjective.
3 - Archival history and theory
- from PART I - ARCHIVAL PRINCIPLES
- Laura A. Millar
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No theory is good except on condition that one uses it to go beyond.
Andre Gide (1869–1951) Journals, 5 August 1931While the concept of archives as evidence is considered a central component of archival theory and practice today, it was not always thus. Across the centuries, the reasons archives were valued and ways in which they were preserved varied according to local custom or inclination. No doubt, future generations will define archives and evidence differently; such is the nature of a discipline that manages the products of information and communications. As information and communications change, society's sense of the worth of documentary products must also change. I have no ability to predict the future, but I believe strongly that we can learn from the past. So in this chapter I offer an extremely brief overview of the history of archival development, summarizing ideas captured in countless archival texts. Then I introduce central archival theories and principles and place them within that historical framework. I end the chapter by considering how archival theories and principles are being challenged today.
Trends in archival history
We have had archives – documentary evidence – since before we have had records as we define them today. Pictographs have evidential value, as do stone stele, clay tablets and totem poles, if one can read the visual or symbolic content and capture the meaning. With such a long past, tracing the evolution of archival milestones over several centuries can only offer a whisper of the deep and complex history of the materials themselves and the people who manage them. But this overview, concise as it must be, will help orient the reader to the changing perception of the role and use of archives in different times and places.
Archives for church and crown
For millennia, archives were considered the sole property of the agency that created them, be it church, state or sovereign. Whether on papyrus, leather or bone, early records were preserved for their owner and most assuredly not for the public. The discovery of hundreds and thousands of clay tablets from as early as the 2nd millennium BC in archaeological sites in Syria, Egypt and Turkey provide clear evidence of the desire by ancient societies to create and preserve records, whether for short-term use or later reference.
Introduction to the second edition
- Laura A. Millar
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Habit is either the best of servants or the worst of masters.
Nathaniel Emmons (1745–1840)I began the first edition with a story that bears repeating, which goes as follows. A young woman asked her mother why she always cut the end off her roast before putting it in the oven. ‘You have to’, her mother replied. ‘It's the only way to cook a roast. That's what my mother taught me’. Not satisfied with this explanation, the woman posed the same question to her grandmother. ‘Cutting the end off is critical’, said the grandmother. ‘If you don't, the roast comes out tough and flavourless. That's how my mother did it, and that's the way it is done’. Still unsatisfied, the woman asked her great-grandmother, a matriarch of 90-plus years, if she always cut the end off her roast before cooking it. ‘Absolutely’, replied the great-grandmother, ‘Without fail’. ‘But why?’ begged the young woman, looking for some logic behind the tradition. Her great-grandmother looked puzzled. ‘Well, dear’, she finally said, ‘I had to. My roasting pan was too small’.
My point then and now is that much of what we do in life comes from habit and tradition. Our parents did it that way, and so do we; our supervisor showed us that method, and we adopted it on as our own; our teacher insisted on that approach, and we have never tried another. Individual and group behaviour – from cooking food to building houses to communicating and documenting ideas and information – are as much a result of the repetition of habits and traditions as the application of theories and principles. We do it that way because ‘that's the way it is done’.
From time to time, though, we need to step back and ask why we do something in a particular way, especially if other options are available. Why do we build houses out of wood or brick or stone? Why do some of us prefer Apple Mac computers and some only use PCs? Why do Americans use letter-size paper, while the English use A4 paper? Why do we cut the end off our roast?
6 - The principles of archival service
- from PART I - ARCHIVAL PRINCIPLES
- Laura A. Millar
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When a man assumes a public trust, he should consider himself as public property.
Thomas Jefferson (1743–1826) quoted in B.L. Rayner, Life of Jefferson, 1834While the nature of a particular archival institution will influence the nature and scope of its holdings and operations, the central principle of accountable and trustworthy archival service must be to make certain that archives are captured and protected with their evidential value intact, and then to ensure that those archives are made available as fully as possible, so that they may benefit the widest possible constituency. If archives are collected but stored away in the basement of the repository and never cleaned of dust, insects or mould, then they have not been protected for posterity. If they are acquired and preserved but never made available to anyone but the person who collected them, then they do not support a society's quest for evidence, information and knowledge.
The act of acquiring and preserving archives is a service that must be performed in an accountable and structured fashion, with respect not only for the documentary evidence itself but also for the individuals and groups who created that evidence and for the people who may wish to access that evidence now and in the future. To understand the nature of archival service, it is necessary to outline the core duties and skills of the archivist and then to examine a central challenge the archivist faces: balancing the rights of some to access and use archival materials for any manner of research with the rights of others to ensure their own personal information is protected from illegitimate use. This chapter looks at the principles that guide the work of the archivist in providing archival services to society. Chapter 7 is devoted to a discussion of the specific challenge of balancing access and privacy.
Archival obligations
Irrespective of the scope of the archival institution, the archivist working in that institution, or the archivist working as an independent consultant for a number of clients, has a responsibility to perform certain core duties. Her ultimate goal is to support the effective care of archival materials, so that they are preserved and managed as authentic and reliable documentary evidence and then available for the widest possible use. How does she do that?
PART II - ARCHIVAL PRACTICES
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Part II of this book puts into action the principles, theories and concepts introduced in Part I. The following topics are addressed: how does the archivist manage the institution, or understand how it is managed if she is not the decision maker? How should archival materials be preserved so that they remain stable, authentic and reliable over decades and centuries? What issues need to be considered when acquiring archives, and how should those archives be arranged and described? Finally, how should the archivist make those materials available for use: what is involved in providing equitable reference services and in engaging actively with the research community and the wider public? These questions are considered in the following chapters:
Chapter 8: Managing the institution
Chapter 9: Preserving archives
Chapter 10: Acquiring archives
Chapter 11: Arranging and describing archives
Chapter 12: Making archives available.
7 - Balancing access and privacy
- from PART I - ARCHIVAL PRINCIPLES
- Laura A. Millar
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Historically, privacy was almost implicit, because it was hard to find and gather information. But in the digital world, whether it's digital cameras or satellites or just what you click on, we need to have more explicit rules – not just for governments but for private companies.
Bill Gates (1955–) Wired.com, 12 November 2013When an archivist receives archival materials into her care her first interest is, almost inevitably, to make the documentary treasures available for use. What a thrill it is to hold in your hands an original letter written by your favourite artist, or to see the name of a former mayor among the rolls of students in your local high school. As someone once said, archivists get paid to read other people's mail. We love the opportunity to see into the lives of other people and, through them, to understand the way our communities functioned in years past.
But the artist and the mayor have rights too. And these rights do not vanish when documents created or owned by them move into archival custody. The need to balance access and privacy and the need to respect intellectual property rights are perhaps the greatest source of tension for the archivist, especially given the ubiquity of digital technologies today.
The requirements of access, privacy and copyright laws can throw obstacles in the way of achieving the goal of archival service, which, as stated many times already, is to support the acquisition, preservation and management of archival materials so that they can be made available for use. But the creators of documentary materials – the people who kept personal diaries, wrote letters to their sister, took photographs on their holiday, prepared financial reports for their business – did not create those records for posterity. The fact that those records ended up in an archival repository, perhaps decades after their creation, does not mean that the creators of those records have lost all right to control the ways in which those materials may be used.
4 - The uses of archives
- from PART I - ARCHIVAL PRINCIPLES
- Laura A. Millar
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To be ignorant of what occurred before you were born is to remain always a child. For what is the worth of human life, unless it is woven into the life of our ancestors by the records of history?
Marcus Tullius Cicero (106–43 BC) Orator, 46 BCWhy should societies keep archives at all? Who cares about preserving the documentary remains of anyone's life or work or keeping the evidence of government or corporate decisions? Why do we bother recording our activities and experiences at the time they happen, and why should anyone bother committing the resources needed to keep those accounts for the indefinite future?
Archives are not just ‘neat old stuff’. As discussed already, archivists today define archival materials first and foremost as sources of documentary evidence. Archives prove rights, confirm obligations, verify events and substantiate claims. They help us remember the past, and they safeguard us against inaccurate recollections or intentional deceit. A written contract reminds two parties of their agreements, but it also prevents one or the other party from avoiding their obligations, because the document exists as proof of the original accord. A photograph of the family at sunset on the beach helps us remember a wonderful holiday, but it also serves as proof that we were on that trip at that specific time. One of the first steps in deciding whether or not to keep archives, then, is to consider their potential value as evidence, which allows the archivist to ensure that, at the very least, she has captured those archives that can be used as proof.
But in order to make a thoughtful decision about whether or not to keep any group of archival materials, it is important to remember that archives are ultimately kept in order to be used, by anyone for any reason. Researchers, scholars and average citizens refer to archives to find proof; to gather research data; to illustrate, illuminate or explain. Archives are tools that people use to look beyond the present moment and understand the wider context of a family, community or society. Like George Mallory who said he wanted to climb Mount Everest ‘because it's there’, anyone can use archives for any reason, as long as the archives ‘are there’.
Index
- Laura A. Millar
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PART I - ARCHIVAL PRINCIPLES
- Laura A. Millar
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Part I of this book looks at the principles and theories within which archival practice is situated. How do we define archives, and what types of material fall within and outside that definition? How did archival theory and practice develop throughout history, and how do we position our work today within existing theoretical frameworks? Theory notwithstanding, how do people actually use archives? What types of institutions are created to hold archival materials, and what are the similarities or differences between them? Regardless of institution, what are the guiding principles – the golden rule(s) – of effective and ethical archival service? And, especially in a world abounding with cloud computing systems, data security concerns, identity theft and 24-hour news cycles, how can the archivist balance the right of citizens to access evidence with the right of individuals to retain their privacy? These topics are addressed in the following chapters:
Chapter 1: What are archives?
Chapter 2: The nature of archives
Chapter 3: Archival history and theory
Chapter 4: The uses of archives
Chapter 5: Types of archival institution
Chapter 6: The principles of archival service
Chapter 7: Balancing access and privacy.
Conclusion
- Laura A. Millar
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There will always be a frontier when there is an open mind and a willing hand.
Charles Kettering (1876–1958), inventor and engineerAs I get older and I occasionally luxuriate in the thought that I must be getting wiser, I understand better what my psychiatrist father meant when he warned me, as a teenager, of the dangers of what he called ‘temporal chauvinism’. This, he argued, was the mistaken belief that we, in our current time and place, are the latest and greatest and best of our generation, and that our creations, inventions and ideas are right and true and good, better than anything that came before. All societies, he claimed – particularly their younger members – are prone to embrace the conceited, erroneous notion that they and theirs are better than anyone or anything that came before. (My mother, a jazz singer, was more lyrical. ‘Listen, Missy,’ she would laugh. ‘Don't forget, a lot of things happened before you were born.’)
A lot of things did happen before we were born, and a lot of things are going to happen after we move on to a new frontier. And perhaps more than many other disciplines, the work of managing the documentary evidence of a society – its archives – demands the greatest respect for this temporal reality. Every change in the technology used to create information, from a clay tablet to a piece of sheepskin to a biometric chip, changes the way in which we need to manage that information. Helping society accomplish this task of creating and managing authentic evidence is the job of the archivist. Ergo, staying on top of the changes brought by time, not thinking we have got it all figured out today, is fundamental to the success of archival work. Change is our business.
Thus, archivists need to remain nimble, agile and humble. Clinging to theories when reality slaps us in the face is just as futile as following an old habit when science proves it wrong. There was a time when archives were defined as old and linear. No more. There was a time when the archivist could wait for stuff to come to her instead of going out and finding it. No more.
Archives
- Principles and practices
- Laura A. Millar
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- Published by:
- Facet
- Published online:
- 08 June 2018
- Print publication:
- 11 May 2017
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This new and extensively revised second edition offers an international perspective on archives management, providing authoritative guidance relevant to collections-based repositories and to organizations responsible for managing their own institutional archives. Written in clear language with lively examples, Archives: Principles and practices introduces core archival concepts, explains best-practice approaches and discusses the central activities that archivists need to know to ensure the documentary materials in their charge are cared for as effectively as possible. Topics addressed include: core archival principles and concepts archival history and the evolution of archival theories the nature and diversity of archival materials and institutions the responsibilities and duties of the archivist issues in the management of archival institutions the challenges of balancing access and privacy in archival service best practice principles and strategic approaches to central archival tasks such as acquisition, preservation, reference and access detailed comparison of custodial, fonds-oriented approaches and post-custodial, functional approaches to arrangement and description. Discussion of digital archives is woven throughout the book, including consideration of the changing role of the archivist in the digital age. In recasting her book to address the impact of digital technologies on records and archives, Millar offers us an archival manual for the twenty-first century. This book will be essential reading for archival practitioners, archival studies students and professors, librarians, museum curators, local authorities, small governments, public libraries, community museums, corporations, associations and other agencies with archival responsibility.|This new and extensively revised second edition offers an international perspective on archives management, providing authoritative guidance relevant to collections-based repositories and to organizations responsible for managing their own institutional archives.
11 - Arranging and describing archives
- from PART II - ARCHIVAL PRACTICES
- Laura A. Millar
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Watch out for the fellow who talks about putting things in order! Putting things in order always means getting other people under your control.
Denis Diderot (1713–84) Supplement to Bougainville's ‘Voyage’, 1796Arrangement and description are central to the preservation of archives as documentary evidence. Arrangement and description are also the least stable of archival activities: the ‘best’ way to arrange a collection of archives a century ago is not considered by archivists to be the best way – at all – today.
A Mesopotamian record keeper placed clay tablets into clay pots and onto clay shelves, relying on his memory to know which tablets related to what topics. No one could access the archives without his permission, and only he knew what was there. One suspects he rarely went on vacation. A librarian in 19th-century Connecticut, on the other hand, described manu script collections by writing and filing catalogue cards for each new arrival: a complete description of the materials on a ‘main entry’ card and cross-references to subjects or people in ‘added entry’ cards. Banks and banks of cards filled the archives, and if the front door was opened as the archivist was adding new entries and a stiff wind blew through, half the day was spent picking up cards off the floor and putting them back in order.
Today, the computer is king, and even the smallest and least secure of archival institutions wants to create a database of archival holdings, not put binders of paper finding aids on a bookshelf or add cards to a catalogue in the reference room. (Few institutions rely on clay tablets, though it has been suggested that they are perhaps the most stable medium around these days.) As archives themselves keep changing, the ways in which they can be arranged and described keeps changing. This is why arrangement and description is the area of archival effort most infused with theory, and why those theories can become such contentious areas of debate.
9 - Preserving archives
- from PART II - ARCHIVAL PRACTICES
- Laura A. Millar
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What boots it at one gate to make defence,
And at another to let in the foe?
John Milton (1608–74) Samson Agonistes, 1671In theory, archival materials should be safer in archival custody than they were in the basement or attic of the person who created the records. Otherwise, one could argue, the archival institution should not acquire the materials in the first place. Many archivists would refute that statement, saying that if they did not bring a particular archival collection into their institution, the documents would be lost forever: shredded by a business that did not want to pay for storage or burnt by a family that had to clear out grandfather's home immediately after his death. Both positions have merit. But even if the archivist cannot achieve quality preservation controls today, she should not be ignorant of the best scenario for archival care. This chapter addresses the ideals of preservation and the realities of achieving them.
It is critical to emphasize at the start that the profession of conservation is a recognized specialty, quite distinct from archival management. Ideally, the first course of action for any archivist needing to address matters of preservation and conservation would be to work with a professional conservator or a digital preservation specialist to identify risks and establish priorities for action. In reality, though, the vast majority of archival insti - tutions do not have the resources to employ conservators or digital preservation specialists. Compromises must be made.
Fortunately, the greatest success with preservation comes not from active repairs but from basic housekeeping efforts. Keeping the facility clean, monitoring the environment, establishing temperature and relative humidity controls and reducing the risk of disasters can be much more beneficial in the long run than spending scarce resources to get cellotape off a fading map.
It is also important to remember that, whatever the ideal might be, every archival institution needs to determine its own preservation needs, in keeping with its particular social and geopolitical realities. An archival institution in northern Europe faces different preservation challenges from one in sub- Saharan Africa, and the developers of a digital repository will prioritize different preservation concerns from a special collections department with a large number of medieval manuscripts. Blanket statements about what is best in theory do not necessarily translate to achievable results in practice.
5 - Types of archival institution
- from PART I - ARCHIVAL PRINCIPLES
- Laura A. Millar
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Wise and prudent men have long known that in a changing world worthy institutions can be conserved only by adjusting them to the changing time.
Franklin D. Roosevelt (1882–1945) Address at the Democratic State Convention, Syracuse, New York, 29 September 1936Today, archival institutions can be found in virtually every corner of the world, from governments, universities, corporations and clubs to historical societies, religious organizations, political groups and co-operatives. There are over 1000 self-proclaimed archival institutions in Canada, thousands in the USA and countless more around the globe. These institutions have been established to serve the needs of their society, and they are governed by the laws, cultures and priorities of that society.
Too often, archivists attempt to categorize archival institutions in relation to administrative placement rather than scope of service. For example, archivists might distinguish between church archives, government archives and university archives. But this approach does not account for the fact that one government archives might only manage the records of that government, while another government archives might also acquire private papers, or that one university archives cares only for its institutional records while another university archives has a broad responsibility for acquiring and preserving manuscripts and special collections. Ultimately, archival institutions will always represent whatever their society decides they should represent. Therefore, a more useful way to understand the different ‘types’ of institution that might exist in different societies is to focus on the services they might provide rather than on the adjective attached to the name: church archives versus special collections department versus business archives.
A distinction can be made at the start between those institutions that manage only the archives of the sponsor agency itself and those that acquire and manage non-sponsor archives (private and personal papers, the archives of other corporations or associations and so on). In practice these two services often merge and overlap; rarely can an archival institution claim it focuses on one duty to the exclusion of the other.
1 - What are archives?
- from PART I - ARCHIVAL PRINCIPLES
- Laura A. Millar
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A wise man proportions his belief to the evidence.
David Hume (1711–76) An Enquiry Concerning Human Understanding, 1748The word ‘archives’ conjures up different images. Some people picture dusty, dry storage rooms where stuffy, brown-bow-tie curators enveloped in ancient cardigans look askance at anyone who speaks above a whisper. Others imagine websites where listeners can download podcasts of radio programmes aired just hours before. Some people think of old parchments, scrolls and leather-bound volumes of medieval treatises; others imagine electronic back-up copies of a corporate report or membership database.
Two centuries ago, the majority of archival materials were twodimensional, manually created items such as papyrus scrolls, parchment codices, bound ledgers, or black and white photographs. Today, the holdings of archival institutions may include e-mail messages, relational databases, YouTube videos and interactive web pages. Digital technologies have transformed our understanding of the nature of information and commun - ications; what were considered archives a century ago are only the smallest subset of what might be defined as archives today.
Computers and the internet have also bred a growth industry in the dissemination of digital archival information. Governments, corporations, publishers, music producers, writers, performers and artists have all discovered the value of sharing information, including historical records, electronically. Newspapers reprint archived articles in print and online editions. Radio stations post copies of concerts and interviews on their websites. Music producers repackage old recordings, billing them as treasures from the vault. Entire television channels are devoted to broadcasting ‘classic’ TV shows and movies, and historical documentaries and ‘find your ancestor’ genealogical shows are among the most popular subset of reality TV on air today. Even local churches record their Sunday sermons and post them on their Facebook pages to serve home-bound parishioners.
As more and more people are exposed to digital information, both old and new, the concept of archives has become more ambiguous. The blanket depiction of archives as brittle old documents used only by scholars has been replaced by another stereotype: that archives comprise any piece of information older than yesterday that might be worth referring to again tomorrow. For those who decide to create an online repository of their favourite recipes or music or newspaper articles and call it their ‘archive’, the subtleties of language may be of little consequence.
2 - The nature of archives
- from PART I - ARCHIVAL PRINCIPLES
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