Paleodistribution modeling in archaeology and paleoanthropology

abstract: Species distribution modeling (SDM) is a methodology that has been widely used in the past two decades for developing quantitative, empirical, predictive models of species–environment relationships. SDM methods could be more broadly applied than they currently are to address research questions in archaeology and paleoanthropology. Specifically, SDM can be used to hindcast paleodistributions of species and ecological communities (paleo-SDM) for time periods and locations of prehistoric human occupation. Paleo-SDM may be a powerful tool for understanding human prehistory if used to hindcast the distributions of plants, animals and ecological communities that were key resources for prehistoric humans and to use this information to reconstruct the resource landscapes (paleoscapes) of prehistoric people. Components of the resource paleoscape include species (game animals, food plants), habitats, and geologic features and landforms associated with stone materials for tools, pigments, and so forth. We first review recent advances in SDM as it has been used to hindcast paleodistributions of plants and animals in the field of paleobiology. We then compare the paleo-SDM approach to paleoenvironmental reconstructions modeled from zooarchaeological and archaeobotanical records, widely used in archaeology and paleoanthropology. Next, we describe the less well developed but promising approach of using paleo-SDM methods to reconstruct resource paleoscapes. We argue that paleo-SDM offers an explicitly deductive strategy that generates spatial predictions grounded in strong theoretical understandings of the relation between species, habitat distributions and environment. Because of their limited sampling of space and time, archaeobiological records may be better suited for paleo-SDM validation than directly for paleoenvironmental reconstruction. We conclude by discussing the data requirements, limitations and potential for using predictive modeling to reconstruct resource paleoscapes. There is a need for improved paleoclimate models, improved paleoclimate proxy and species paleodistribution data for model validation, attention to scale issues, and rigorous modeling methods including mechanistic models.This is the accepted author manuscript, accepted for publication 12/17/1

The Development and Evaluation of E-Management Platform for Patient-reported Outcomes Research Based on Business Process Improvement Theory

Background Patient-reported outcomes (PROs) refer to the health-related information coming directly from patients without any explanation by the doctors or others. It is of great significance for patients to participate in medical decision-making, have a higher quality of care，and have a better medical outcome. Therefore, patient-reported outcomes measurements (PROMs) have important clinical value. Patient-reported Outcomes Measurement Information System (PROMIS) is one of the most accurate PROMs led by NIH and focuses on health-related big data's scientific characteristics. PROMIS advocates cross-population, cross-region, and cross-disease studies and is widely recognized among the research community. PROMIS Health Organization (PHO) now promotes the global implementation of PROMIS by setting up PROMIS National Center (PNC) in various countries, and PNCs organize the research cooperation with many research groups to promote PROMIS. PROMIS China Center is one of the PNCs that takes charge of the PROs cooperative research with many research teams to promote PROMIS in China. Due to the diverse tasks, complex procedures, and low efficiency of the current cooperative management mode of PROMIS China Center, it cannot meet the efficient research management requirements. Therefore, it is necessary to analyze the needs, improve the process, and build an E-management platform under the guidance of business improvement theory to improve the management efficiency of the patient-reported outcome research and eventually promote PROMIS in China. Objectives The general purpose of this research is to improve the management process of patient-reported outcomes research based on the business process improvement theory and develop an E-Management platform as well as evaluate the usability of the E-management platform. Purpose one: The need analysis of the E-management platform for the patient-reported outcomes research; Purpose two: The framework construction of the E-management platform for patient-reported outcomes research; Purpose three: The development of the E-management platform for patient-reported outcomes research; Purpose four: The usability evaluation of the E-Management Platform for Patient-reported outcomes research. Methods The study was comprised of 4 parts： Part1: The need analysis of the E-management platform for the patient-reported outcomes research Based on business improvement theory (ESIA theory), the researcher conducted the semi-structured qualitative interviews, including five rounds of focus group interviews with 5 management staffs of the PROMIS China Center and one-on-one interviews with 11 cooperative team members to know the current management process of patient-reported outcomes research, the problems of current management process, and the need for the E-management platform. Part2: The framework construction of the E-management platform for patient-reported outcomes research The researcher held a brainstorming discussion with 13 management staffs to improve the current management process based on business improvement theory; Meanwhile, the researcher accomplished the literature study about the patient-reported outcomes research E-management platforms of other countries and analyzed the framework; Then, the researcher combined the results of need analysis, brainstorming, and literature study to draw the preliminary framework of the patient-reported outcomes research E-management platform; Finally, the researcher held an expert group meeting with 7 experts from the field of both nursing research and software engineering to revise the preliminary framework and make a final framework. Part3: The development of the E-management platform for patient-reported outcomes research The researchers organized and coordinated close cooperation among experts in different fields. Based on the final framework of the E-management platform formed in the early stage, the researchers adopted the human-centered concept and the agile development method to develop the E-management platform with 3 software engineers. Part4: The usability evaluation of the E-Management Platform for Patient-reported outcomes research The researcher implemented the formative usability evaluation during the process of development to find the problems about the interface, like font and module; Then the researcher implemented the summarized usability evaluation by task analysis and semi-structured interviews with 15 users，including 5 management staffs of the PROMIS China Center and 10 cooperative team members. The evaluation outcomes were reported after data analysis. Results Part1: The need analysis of the E-management platform for the patient-reported outcomes research The qualitative research results show the: ① PROMIS translation, validation, clinical application management processes, and the researcher presented them in text and flow chart. ② The current process's problems, like the current management process is tedious; the current management process involves too much paper materials; it is difficult for management staffs to supervise the process. ③ the need for the E-management: all the participants said they need the E-management platform and expressed their specific needs. Part2: The framework construction of the E-management platform for patient-reported outcomes research The brainstorming efficiently improved the management process, and the improved process was shown with text and flowchart; The literature study presented the framework of the Netherlands PROMIS E-management platform; the researcher drew a preliminary framework of the E-management platform under the guidance of need analysis, improved management process, and Netherlands PROMIS E-management platform, which contains 7 first-level modules, and 5 second-level modules. After the expert group meeting, the final framework was constructed, which includes 6 first-level modules: "Home", " Introduction ", "PROMIS Measurement", "News Center", "Resources", and " Research Cooperation", 16 second-level modules, and the content covered by the second-level modules. Part3: The development of the E-management platform for patient-reported outcomes research The researchers demonstrated the preliminary framework of the E-management platform to the software engineers, and we worked jointly to complete the development of the E-management platform after the steps of requirement clarification, design, development, testing, and release. Part4: The usability evaluation of the E-Management Platform for Patient-reported outcomes research During the formative usability evaluation, the researcher found many problems, and they were all solved by software engineers; During the summarized usability evaluation, we demonstrated the platform in terms of effectiveness, efficiency, and satisfaction. Based on the scores of the usability evaluation questionnaire after the test: system usefulness is 5.2 (from management staffs) and 5.8 (from cooperative team members), information quality is 6.8 (from management staffs) and 6.0 (from cooperative team members), interface quality is 5.4 (from management staffs) and 5.9 (from cooperative team members), and overall evaluation is 6.0 (from management staffs) and 6.2 (from cooperative team members). Through qualitative interviews, we understand the user experience of the platform. The interview data shows two topics related to usability. By combining quantitative and qualitative outcomes, the researcher thinks that the E-management platform's usability is generally good, but there are still some shortcomings. Conclusions Both the management staffs and cooperative team members of the PROMIS China Center have a high level of need for the E-management platform. The final framework based on need analysis and process improvement is good guidance for developing the E-management platform. The usability evaluation shows that the E-management platform has a good usability and can help manage the patient-reported outcomes cooperative research. It will be able to enhance the management efficiency of patients-reported outcomes research extensively and accelerate the rapid promotion of PROMIS in China

Implementation of a digital optical matrix-vector multiplier using a holographic look-up table and residue arithmetic

The design and implementation of a digital (numerical) optical matrix-vector multiplier are presented. The objective is to demonstrate the operation of an optical processor designed to minimize computation time in performing a practical computing application. This is done by using the large array of processing elements in a Hughes liquid crystal light valve, and relying on the residue arithmetic representation, a holographic optical memory, and position coded optical look-up tables. In the design, all operations are performed in effectively one light valve response time regardless of matrix size. The features of the design allowing fast computation include the residue arithmetic representation, the mapping approach to computation, and the holographic memory. In addition, other features of the work include a practical light valve configuration for efficient polarization control, a model for recording multiple exposures in silver halides with equal reconstruction efficiency, and using light from an optical fiber for a reference beam source in constructing the hologram. The design can be extended to implement larger matrix arrays without increasing computation time

Beyond the asylum: Colonial psychiatry in French Indochina, 1880-1940

This dissertation looks beyond the asylum to consider the development of psychiatry in French Indochina as the product of everyday exchanges between lay people and experts. Drawing on archival research conducted over two years in Vietnam and France - including hundreds of patient case files - I trace the movements of patients in and out of asylums and between prisons, poor houses, youth reformatories, hospitals and family homes. Together, these individual patient itineraries challenge our notion of the colonial asylum as a closed setting where patients rarely left, run by experts who enjoyed broad and unquestioned authority. Instead, they reveal how ideas about what it meant to be abnormal, as well as normal enough to return to social life, were debated between psychiatrists, colonial authorities and the public throughout the early decades of twentieth century. By examining the dynamics of patient movements in and out of psychiatric care, this study shifts our perspective from the asylum itself to its relationship with the world beyond its walls. Colonial scholars have focused on the way psychiatry provided a new scientific discourse of racial difference and how it figured within a wider biopolitics of colonial rule. However the social histories of the asylums themselves, and how they functioned within colonial political systems, remain little explored. I argue that by situating the history of psychiatry within the local dynamics of colonial rule, the asylum emerges as less of a blunt instrument for the control and medicalization of colonial society than as a valuable historical site for reframing narratives of colonial repression and resistance

Fantastic Place and Space in China Miéville’s Fiction. Rhetorics of Emancipatory Spatial Changes in the Miévillean New Weird

This dissertation explores how the literary construction of urban space is taking place in the New Weird fiction. The study analyses how, in six books by contemporary British author China Miéville, and whether literary space can be used for emancipation as a critique of capitalism, and if so, how. The paper draws on the conceptual and terminological approaches of space studies, critical map theory and narratology to explore these six books. It aims to establish a hermeneutic model in which literary space functions as a political critique of capitalist state apparatuses and represented superstructures. The thesis scrutinises the Bas-Lag trilogy (Perdido Street Station (2000); The Scar (2002); and Iron Council (2004)). The City and The City (2009); Un Lun Dun (2007); and This Census-taker (2016). This approach links narratology through its engagement with literary narratives and perspectives, interpretation of the city, place/space, third space and cognitive mapping cognitive space. The paper also considers the political aspects of spatial arrangement between the slum and the centre in the spatial representation of ideological state apparatuses. Miéville uses the New Weird as a means of investigative arena for themes such as politics, ideology and the critique of capitalism. He utilises the framework of Marxism, in which he point out the recognition of the capacity of fantastic literature to contaminate the real with the non-real and thereby reveal to the reader the possibility of seeing the world differently, and of bringing the political aspects of urban life into the for those without power. The dissertation interprets space within the framework of Michel Foucault, Henri Lefebvre and Edward W. Soja. The thesis provides insights into the New spatial arrangements of the New Weird, drawing on the context of spatial studies, critical map theory and narratology, and narrative theories and their political aspects

Molecular and evolutionary analysis of a gene conserved in most Orthopoxviruses

Evidence is presented to show that variola and monkeypox viruses evolved independently from a common ancestor. An open reading frame (ORF), potentially coding for a protein of 341 amino acid residues, was found to be conserved in two strains of variola virus (Harvey and Somalia), but degenerate in the Denmark strain of monkeypox virus. Monkeypox virus had a deletion of 391 bp, two 24bp deletions and a single base pair deletion within the coding region of this single copy ORF. The ORF corresponds to the E5R ORF in the published sequence of the Copenhagen strain of vaccinia virus, and the DNA sequence was determined for an additional strain of vaccinia virus, Dairen. A number of other Orthopoxviruses were found to contain this ORF, strengthening confidence in its presence in an ancestral Orthopoxvirus. The equivalent DNA sequence was determined for a number of monkeypox virus strains from West and Central Africa. The Denmark strain was identical to one from Liberia, indicating that this virus probably originated from West Africa. A third virus from West Africa, Benin, was found to have >99% base similarity and the same pattern of deletions as the other two monkeypox viruses. The Zaire strains were identical to one another and different from the West African strains. Like the West African strains, they contained the two 24bp deletions and single base pair deletion. In place of the large deletion they had three smaller deletions of 5-, 9- and 127-bp as well as a single base pair insertion. They also had additional deletions of land 2-bp and an insertion of 3bp. The West African strains have the potential to code for a truncated gene product of 107 amino acid residues, whereas the Zaire strains have no significant ORF. This clearly shows that monkeypox virus has diverged into two geographically isolated groups (Zaire and West Africa). There was >99% base similarity between the two groups, suggesting that the divergence occurred recently. Phylogenetic analysis, by the neighbour-joining method, was undertaken on the corresponding DNA sequences from variola (2 strains), monkeypox (6 strains), vaccinia (1 strain + 2 published sequences), cowpox (2 strains), taterapox, camel pox and ectromelia viruses. For every species gerbilpox virus was the nearest neighbour, suggesting that taterapox virus may be the species most closely related to the common ancestral Orthopoxvirus. Within the variola and cowpox virus species there was >99% DNA sequence conservation. Between species, camelpox virus was the most closely related species to gerbilpox virus, with variola virus, and, more distantly, vaccinia virus, falling into the same group. Cowpox virus was the most diverged species examined. Ectromelia virus shared a branch with cowpox virus. A comparison was made of the intergenic DNA sequence between this ORF and the adjacent downstream ORF. Variation was found, both within and between species, in the form of insertions and deletions. The interrelationships between the different Orthopoxvirus species more or less parallels that of the E5R-equivalent comparison. Some of the viruses had clusters of direct repeats. A pentameric repeated unit was found in 2, 10 and 17 copies in camelpox, gerbilpox and ectromelia viruses respectively. Raccoon poxvirus had a 7bp unit in 13 adjacent copies. The two cowpox viruses had a more complex arrangement of repeated sequences. It was thought that the ESR ORF may prove to be nonessential for virus replication. This was tested by interruption of the E5R gene in vaccinia virus; this did not affect the ability of the virus to form plaques in cell culture, but appeared to reduce the pathogenicity of the 'virus for rabbits. The deduced amino acid sequences were analysed for conserved and variable regions within the gene, to which no specific function has yet been assigned