Map Library Research Articles

Forward Genetics in Apicomplexa Biology: The Host Side of the Story.

Forward genetic approaches have been widely used in parasitology and have proven their power to reveal the complexities of host-parasite interactions in an unbiased fashion. Many aspects of the parasite’s biology, including the identification of virulence factors, replication determinants, antibiotic resistance genes, and other factors required for parasitic life, have been discovered using such strategies. Forward genetic approaches have also been employed to understand host resistance mechanisms to parasitic infection. Here, we will introduce and review all forward genetic approaches that have been used to identify host factors involved with Apicomplexa infections, which include classical genetic screens and QTL mapping, GWAS, ENU mutagenesis, overexpression, RNAi and CRISPR-Cas9 library screens. Collectively, these screens have improved our understanding of host resistance mechanisms, immune regulation, vaccine and drug designs for Apicomplexa parasites. We will also discuss how recent advances in molecular genetics give present opportunities to further explore host-parasite relationships.

Mapping Prejudice: The Map Library as a Hub for Community Co-Creation and Social Change

The John R. Borchert Map Library was the ideal incubator for an experiment that has changed how a wide range of people are thinking about structural racism and the history of race in American urban environments. Mapping Prejudice used a cartographic visualization of racial covenants as the intellectual nexus of a project that transcended disciplinary boundaries and invited community members into cutting-edge research work. The Map Library provided the physical space, resources, and geospatial expertise necessary for community-driven mapping work. It also served as an intersectional hub necessary for this transformative research initiative, illustrating the synergies between map librarianship and other disciplines. The work depended on the unique contributions of the map librarian: project management; experience networking with researchers, campus departments, and community groups; and knowledge of best practices surrounding data management, curation, and reuse. This article explains how Mapping Prejudice changed academic scholarship and public understandings by engaging volunteers in meaningful research. It concludes by providing a description of future directions for this project and calls on librarians to lead more work of this kind. The example of Mapping Prejudice suggests ways that map librarians can be leading new modes of inclusive, equitable and community-responsive research.

Developing a Collaborative Diversity, Equity, and Inclusion (DEI) Guide: A Library-Department Partnership in the Earth Sciences

Earth Science is one of the least diverse scientific fields, but libraries can play a role in assisting their liaison departments’ diversity, equity, and inclusion (DEI) efforts by diversifying our collections and supporting research practices that promote their use. In 2020, the University of California, Berkeley’s Earth & Planetary Science Department graduate students created an impressive Call to Action directed toward the faculty of the department. The Call to Action included a plan for advancing the department’s diversity, equity, inclusion, and accessibility, particularly important in a department with only 17% of students from underserved backgrounds enrolled in the graduate program. Stemming from this effort, the Earth Sciences & Map Library at UC Berkeley, developed a guide (https://guides.lib.berkeley.edu/geo_dei) to provide resources to further educate departmental faculty, staff, and students on the topic of DEI. The guide encourages researchers to expand their engagement with scholarship and citation practices intentionally while working on these DEI efforts. Although Earth Science is highlighted in this particular LibGuide, the strategies are universal, especially as applied to science, technology, engineering, math (STEM) fields. The development of this guide, as well as partnerships with active student groups, can serve as a tool for other academic departments creating and promoting DEI efforts.

Air- and dustborne fungi in repositories of the National Archive of the Republic of Cuba.

This study has as objectives to determine the concentration and diversity of the air- and dustborne mycobiota in seven National Archive of the Republic of Cuba repositories, and to assess the potential risk of biodeterioration that isolated taxa may have. In the indoor and outdoor environmental microbiological samplings a SAS biocollector was used and the indoor/outdoor (I/O) ratio was determined for each repository. The settled dust was collected during six months. Sørensen's coefficient of similarity (QS) was calculated to compare the isolated taxa among the three studied niches (indoor air, dust, outdoor air). The biodegradation potential of the isolated taxa was determined by semi-quantitative tests. The concentrations in the air of repositories with natural cross-ventilation ranged from 225.2-750.3 CFU m-3, while in the Map library with air-conditioning the concentration was significantly lower. The I/O ratios ranged from 0.1-1.7 revealing different environmental qualities. The maximum settled dust load was 22.8 mg/m2/day with a top fungal concentration of 6000 CFU g-1. 14 and eleven genera were detected in the air and dust respectively with predominance of the genera Aspergillus, Cladosporium and Penicillium. A QS of 0.8 was obtained between the indoor and the outdoor environments with eleven taxa similar evidencing the incidence of outdoors on the indoor mycobiota. The isolated taxa showed several biodeteriogenic attributes highlighting twelve and 14 taxa from indoor air and dust respectively with positive results for the five tests performed. This demonstrates the potential risk that fungal environmental represent for the preserved documentary heritage.

Rapid prediction of flood inundation by interpolation between flood library maps for real-time applications

It is important that real-time flood forecasting provides information on inundation extents and depths to emergency responders for flood mitigation planning, warning and rescue operations. Conventional hydrodynamic flood inundation modelling is generally not suited for real-time operations because of its large computational demand. The most widely adopted industry practice is to link a pre-canned library of flood maps with river levels and use an interpolation approach to derive flood surfaces and depths based on selected model inputs. However, there is surprisingly scant information in the literature on the procedures and performance of the library interpolation approach. In this study, we describe the library interpolation approach, introduce univariate and multivariate interpolation schemes, and investigate their performance through a case study of a river in Port Fairy, Australia. The MIKE 11/21 hydrodynamic model was used to construct a pre-canned flood inundation library of design events. The hydrodynamic model was also used to generate outputs for four test cases to evaluate the performance of the library interpolation approach. It is found that the accuracy of the library interpolation approach relies heavily on how the map library was constructed, selection of flood drivers, and shape and timing of hydrographs. The widely deployed univariate interpolation scheme based on a single primary flood driver yields results of varied accuracy, depending on the validity of assumptions, often made implicitly, about the inputs of the non-primary drivers. A newly developed multivariate interpolation scheme overcomes this problem. Overall, it is found that the results obtained using the map library interpolation schemes are generally satisfactory, achieving a hit rate of 0.85-0.99 and a critical success index of 0.85-0.99. However, a major limitation of the library interpolation approach is that the shape and timing of the input hydrographs need to be similar to that used in constructing the map library. Further research is needed to mitigate this limitation.

Inversion Attacks against CNN Models Based on Timing Attack

Model confidentiality attacks on convolutional neural networks (CNN) are becoming more and more common. At present, model reverse attack is an important means of model confidentiality attacks, but all of these attacks require strong attack ability, meanwhile, the success rates of these attacks are low. We study the time leakage of CNN running on the SoC (system on-chip) system and propose a reverse method based on side-channel attack. It uses the SDK tool-profiler to collect the time leakage of different networks of various CNNs. According to the linear relationship between time leakage, calculation, and memory usage parameters, we take the profiling attack to establish a mapping library of time and the different networks. After that, the smallest difference between the measured time of unknown models and the theoretical time in the mapping library is considered to be the real parameters of the unknown models. Finally, we can reverse other layers even the entire model. Based on the experiments, the reverse success rate of common convolutional layers is above 78.5%, and the reverse success rates of different CNNs (such as AlexNet, ConvNet, LeNet, etc.) are all above 67.67%. Moreover, the results show that the success rate of our method is 10% higher than the traditional methods on average. In the adversarial sample attack, the success rate reached 97%.

A Comparison of Global Brain Volumetrics Obtained from CT versus MRI Using 2 Publicly Available Software Packages.

Brain volumetrics have historically been obtained from MR imaging data. However, advances in CT, along with refined publicly available software packages, may support tissue-level segmentations of clinical CT images. Here, brain volumetrics obtained by applying two publicly available software packages to paired CT-MR data are compared. In a group of patients (n = 69; 35 men) who underwent both MR imaging and CT brain scans within 12 months of one another, brain tissue was segmented into WM, GM, and CSF compartments using 2 publicly available software packages: Statistical Parametric Mapping and FMRIB Software Library. A subset of patients with repeat imaging sessions was used to assess the repeatability of each segmentation. Regression analysis and Bland-Altman limits of agreement were used to determine the level of agreement between segmented volumes. Regression analysis showed good agreement between volumes derived from MR images versus those from CT. The correlation coefficients between the 2 methods were 0.93 and 0.98 for Statistical Parametric Mapping and FMRIB Software Library, respectively. Differences between global volumes were significant (P < .05) for all volumes compared within a given segmentation pipeline. WM bias was 36% (SD, 38%) and 18% (SD, 18%) for Statistical Parametric Mapping and FMRIB Software Library, respectively, and 10% (SD, 30%) and 6% (SD, 20%) for GM (bias ± limits of agreement), with CT overestimating WM and underestimating GM compared with MR imaging. Repeatability was good for all segmentations, with coefficients of variation of <10% for all volumes. The repeatability of CT segmentations using publicly available software is good, with good correlation with MR imaging. With careful study design and acknowledgment of measurement biases, CT may be a viable alternative to MR imaging in certain settings.

A symbols library and development environment for Earth and Planetary geologic mapping

A symbols library and development environment for Earth and Planetary geologic mapping

An Electric Equipment Analysis Method based on Knowledge Reasoning

Facing the increasingly complex power grid architecture and high equipment failure risk, a comprehensive equipment condition analysis method based on knowledge reasoning is proposed in this paper, mainly using the large amount of characteristic information to realize the condition evaluation, fault detection and early warning. Firstly, it statistically analyzes the historical data, extracts the characteristic information of equipment health status and builds a knowledge mapping library of key factors for equipment-centered status analysis; secondly, it establishes an intelligent early warning library of equipment index data, and gets the probability of equipment defects and fault risks through induction-based knowledge reasoning method; finally, it gets the equipment status rating through logic and rule-based knowledge reasoning method and the closed-loop system of equipment status evaluation is established. The reasonableness of the evaluation method is verified by the examples, which realizes supervision equipment operation status mining early warning, sensing equipment operation status in advance and reducing potential operation risk of power grid.

Fast and Robust 3D Reconstruction Solution from Permissive Open-Source Code

With the growth of access to faster computers and more powerful cameras, the 3D reconstruction of objects has become one of the public's main topics of research and demand. This task is vigorously applied in creating virtual environments, creating object models, and other activities. One of the techniques for obtaining 3D features is photogrammetry, mapping objects and scenarios using only images. However, this process is very costly and can be pretty time-consuming for large datasets. This paper proposes a robust, efficient reconstruction pipeline with a low runtime in batch processing and permissive code. It is even possible to commercialize it without the need to keep the code open. We mix an improved structure from motion algorithm and a recurrent multi-view stereo reconstruction. We also use the Point Cloud Library for normal estimation, surface reconstruction, and texture mapping. We compare our results with state-of-the-art techniques using benchmarks and our datasets. The results showed a decrease of 69.4% in the average execution time, with high quality but a greater need for more images to achieve complete reconstruction.

Cartographers Seen and Unseen

Glen Creason, the longtime Map Librarian of the Los Angeles Public Library, acquaints readers with six cartographers, most of them little-known today, whose work between the 1840s and 1940s shaped Los Angeles, preserved its history, and made the city accessible to visitors and Angelenos alike.

News Related to the Association of Canadian Map Libraries and Archives

News about the Association, including AGM minutes, Awards and Carto Conference abstracts

Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case.

Simple SummaryReconstructing plant genomes is a difficult task due to their often large sizes, unusual ploidy, and large numbers of repeated elements. However, the field of sequencing is changing very rapidly, with new and improved methods released every year. The ultimate goal of this study is to provide readers with insights into techniques that currently exist for obtaining high-quality and chromosome-scale assemblies of plant genomes. In this work, we presented the advanced techniques already existing in the field and illustrated their application to reconstruct the genome of the yellow sarson, Brassica rapa cv. Z1.With the rise of long-read sequencers and long-range technologies, delivering high-quality plant genome assemblies is no longer reserved to large consortia. Not only sequencing techniques, but also computer algorithms have reached a point where the reconstruction of assemblies at the chromosome scale is now feasible at the laboratory scale. Current technologies, in particular long-range technologies, are numerous, and selecting the most promising one for the genome of interest is crucial to obtain optimal results. In this study, we resequenced the genome of the yellow sarson, Brassica rapa cv. Z1, using the Oxford Nanopore PromethION sequencer and assembled the sequenced data using current assemblers. To reconstruct complete chromosomes, we used and compared three long-range scaffolding techniques, optical mapping, Omni-C, and Pore-C sequencing libraries, commercialized by Bionano Genomics, Dovetail Genomics, and Oxford Nanopore Technologies, respectively, or a combination of the three, in order to evaluate the capability of each technology.

Use of infographics as a technology-based information dissemination tool: the perspective of Egyptian public university libraries library staff

PurposeThis study aims to explore the potential use of infographics as a technology-based information dissemination tool in Egyptian public university libraries.Design/methodology/approachA quantitative approach was used in the form of a survey conducted in February 202. The survey tool was a self-administrated questionnaire. The study sample consisted of valid responses from 231 library staff. Of this number, 173 (74.9%) were infographics users, and 58 (25.1%) were infographics users.FindingsInfographics users tended to be males between 31 and 45 years of age, mostly BA holders, librarians, with work experience ranging from 11 to 25 years. On the other hand, infographics nonusers tended to be also males between 31 and 45 years of age, mostly BA holders, librarians, with work experience ranging from 11 to 25 years. The majority of library staff used infographics mainly to provide information about the library's map, news, services, events, contact, working hours, policies and activities, to provide guidance, instructions on the library use, explain its classification scheme and provide statistical data. The largest number of library staff indicated that their use of informational infographics ranged from “Completely used” to “Most used”, followed by statistical infographics and timeline infographics The use of informational infographics and statistical infographics described to be at least fairly easy to them. In addition, the use of timeline infographics, statistical infographics and informational infographics has also been described to at least fairly useful to them. A very large number of infographics users indicated that these means are attractive, effective, persuasive, focused, easy to embed, easy to read, artistic, easy to track, highly digestible data, easily shareable, easily rememberable, informative and understandable. About two-thirds of infographics users showed that they provided infographics through a computer-based format, followed by both printed and computer-based formats, and printed format. Barriers, such as lack of awareness of infographics, lack of knowledge about infographics, lack of time needed and lack of necessary technical skills, have been described as the greatest barriers to the use of infographics by library staff.Originality/valueThis study is one of the very few studies concerned with the potential role of using infographics in Egyptian public university libraries, which relates to the presentation of information in the library environment.

News Related to the Association of Canadian Map Libraries and Archives

News Related to the Association of Canadian Map Libraries and Archives

Implementation of serverless cloud GIS platform for land valuation

ABSTRACT Cloud computing enables performing computations and analysis tasks and sharing services in web-based computer centres instead of local desktop systems. One of the most used areas of cloud computing is geographic information systems (GIS) applications. Although Desktop GIS products are still used in the community frequently, Web GIS and Cloud GIS applications have drawn attention and have become more efficient for users. In this study, a serverless Cloud GIS framework is implemented for the land valuation platform. In order to store, analyse, and share geospatial data, the Aurora Serverless PostgreSQL database is created on Amazon Web Services (AWS). While adopting Aurora Serverless PostgreSQL as a database management system, a simple point in polygon analysis conducted to compare the performances with Amazon Relational Database Service (RDS) instance. Results showed that the serverless database responded to the query faster and scaled up during high workload to decrease latency. Hence, parcel vector data, which conveys ownership information and land values attributes, is shared directly from the PostGIS database as vector tiles. Besides S3 and AWS Lambda services are used for storing and disseminating raster-based land value map tiles. To visualize all shared data and maps through a web browser, open source web mapping library Mapbox GL JS is used.

NGlyAlign: an automated library building tool to align highly divergent HIV envelope sequences

BackgroundThe high variability in envelope regions of some viruses such as HIV allow the virus to establish infection and to escape subsequent immune surveillance. This variability, as well as increasing incorporation of N-linked glycosylation sites, is fundamental to this evasion. It also creates difficulties for multiple sequence alignment methods (MSA) that provide the first step in their analysis. Existing MSA tools often fail to properly align highly variable HIV envelope sequences requiring extensive manual editing that is impractical with even a moderate number of these variable sequences.ResultsWe developed an automated library building tool NGlyAlign, that organizes similar N-linked glycosylation sites as block constraints and statistically conserved global sites as single site constraints to automatically enforce partial columns in consistency-based MSA methods such as Dialign. This combined method accurately aligns variable HIV-1 envelope sequences. We tested the method on two datasets: a set of 156 founder and chronic gp160 HIV-1 subtype B sequences as well as a set of reference sequences of gp120 in the highly variable region 1. On measures such as entropy scores, sum of pair scores, column score, and similarity heat maps, NGlyAlign+Dialign proved superior against methods such as T-Coffee, ClustalOmega, ClustalW, Praline, HIValign and Muscle. The method is scalable to large sequence sets producing accurate alignments without requiring manual editing. As well as this application to HIV, our method can be used for other highly variable glycoproteins such as hepatitis C virus envelope.ConclusionsNGlyAlign is an automated tool for mapping and building glycosylation motif libraries to accurately align highly variable regions in HIV sequences. It can provide the basis for many studies reliant on single robust alignments. NGlyAlign has been developed as an open-source tool and is freely available at https://github.com/UNSW-Mathematical-Biology/NGlyAlign_v1.0 .

Examining the Background, Duties and Perceptions of Today’s Map Librarians

The traditional map library full of map drawers, aerial photographs, atlases and globes has evolved to include computer terminals and data collection equipment. Library patrons are accessing maps and geospatial data digitally. As the library has changed, so has the role of the map librarian. Historically, specialized coursework for map librarianship has been minimal in graduate library science programs. To effectively support library users of geographic information system (GIS), education is needed in this field, as well. A survey was distributed to map librarians via email listserv with a goal of observing trends in job duties and educational backgrounds of today’s map librarians. The views of 67 responding map librarians regarding training, professional development and the direction of map librarianship as a profession were also collected. The resulting data show a strong need for training opportunities for work with paper maps as well as GIS data and software.

Status of Women in Geography (SWIG) in the Southeastern Division

Status of Women in Geography (SWIG) in the Southeastern Division Heidi J.L. Lannon (bio) In honor of the women of the Southeastern Division of the American Association of Geographers (SEDAAG) and in recognition of the second consecutive female President, it is with pleasure that the cover of Southeastern Geographer is dedicated to the Status of Women in Geography (SWIG) in the Division. Women are strongly represented at the American Association of Geographers (AAG) in addition to the Southeastern Division. SEDAAG is led by President Lynn Resler of Virginia Tech, who followed Joann Mossa of the University of Florida. Women are represented on the SEDAAG Executive Board by Vice President Jennifer Rahn of Samford University, Amy Potter of Georgia Southern University as Treasurer, and Selima Sultana as Regional Councilor and Co-Editor of Southeastern Geographer. Amy Lobben of the University of Oregon served as the first virtual President of the AAG from 2020–2021. Emily T. Yeh of the University of Colorado at Boulder is serving as the second consecutive female President of the AAG from 2021–2022. The following recollections began as anecdotal observations to accompany the cover of this issue. The author was ushered to her first meeting in the early 1990s as a graduate student by her female mentor, Joann Mossa. Further research and assistance by mentors and friends Peggy Gripshover, Anne Oberhauser, and Ezra Ozdenerol (personal communications 2020) unearthed a lengthy history of female participation in SEDAAG. An exact date for the establishment of SWIG at the Division level has not been determined, and membership is not formally recorded. Meetings of women geographers have historically been over breakfast and scheduled at the uncivilized hour of 7 AM. Meetings were informal and attended by a faithful few (Figure 1). Southeastern Geographer has a tradition of publishing details of annual conference activities. From the accounts, historical activities of women in geography can be gleaned. In a 1979 report of the annual meeting, Nancy Erwin and David Lee arranged a session entitled "Questions and Answers: AAG Committee on the Status of Women" (Lineback 1980). The first acknowledgement of the SEDAAG Committee on the Status of Women in Geography was at the 1981 meeting when SWIG sponsored a discussion on "The Working Woman" (Fisher 1982). At that meeting, Jackalie Blue convened a regional meeting of the AAG Committee on the Status of Women and Susan Moorlag led two workshops on careers in geography. The award for best Ph.D. student paper that year was to a woman, Ellen Cromley of the University of Kentucky, and Jonathan Phillips of East Carolina University [End Page 281] Click for larger view View full resolution Figure 1. Enjoying breakfast together, SEDAAG meeting, Asheville, NC, 2012. Margaret "Peggy" Gripshover, Western Kentucky University; Helen Ruth Aspass, Virginia Commonwealth University (retired); Amanda Rees, Columbus State University; Heidi Lannon, Santa Fe College; Michael Brown, Northwest Florida College (retired). Image courtesy of Heidi Lannon, Eric Spears, photographer. won at the master's level. In 1982, Helen Jane Armstrong of the University of Florida led a map library workshop (Fisher 1983). At the 1984 meeting, the first Merle C. Prunty Scholarship was awarded to Jeanne Murday of the University of South Carolina. The same year Risa Palm was elected the President of AAG (Aiken 1985). She was the second female President of the AAG since 1904, after Meredith Burrill in 1965 (Wikipedia 2020). SWIG meetings are reported as being part of annual meetings beginning in 1991 (Meentemeyer 1992). At the 50th meeting of SEDAAG in Knoxville, conference highlights included that "panel sessions were organized to address current issues, including the status of women in geography" (Hartshorn 1996, 82). The 1997 meeting was reported on by Moore (1998), who wrote that two panel sessions were organized by the SWIG Committee. [End Page 282] Click for larger view View full resolution Table 1. Female Presidents of SEDAAG Click for larger view View full resolution Table 2. Female Treasurers of SEDAAG A perusal of Southeastern Geographer volumes provides a record of female participation and the activities of SWIG. Table 1 shows the six women who have served as the President (previously "Chair") of SEDAAG, since 1946, beginning with Lillian Worley Stimson of the...

Literature Mapper: A QGIS Plugin for Georeferencing Citations in Zotero

Many studies in air, soil, and water research involve observations and sampling of a specific location. Knowing where studies have been previously undertaken can be a valuable addition to future research, including understanding the geographical context of previously published literature and selecting future study sites. Here, we introduce Literature Mapper, a Python QGIS plugin that provides a method for creating a spatial bibliography manager as well as a specification for storing spatial data in a bibliography manager. Literature Mapper uses QGIS’ spatial capabilities to allow users to digitize and add location information to a Zotero library, a free and open-source bibliography manager on basemaps or other geographic data of the user’s choice. Literature Mapper enhances the citations in a user’s online Zotero database with geo-locations by storing spatial coordinates as part of traditional citation entries. Literature Mapper receives data from and sends data to the user’s online database via Zotero’s web API. Using Zotero as the backend data storage, Literature Mapper benefits from all of its features including shared citation Collections, public sharing, and an open web API usable by additional applications, such as web mapping libraries. To evaluate Literature Mapper’s ability to provide insights into the spatial distribution of published literature, we provide a case study using the tool to map the study sites described in academic publications related to the biogeomorphology of California’s coastal strand vegetation, a line of research in which air movement, soil, and water are all driving factors. The results of this exercise are presented in static and web map form. The source code for Literature Mapper is available in the corresponding author’s GitHub repository: https://github.com/MicheleTobias/LiteratureMapper