Archeota, Spring/Summer 2021

Archeota is a platform for SJSU iSchool students to contribute to the archival conversation. It is written BY students, FOR students. It provides substantive content on archival concerns and issues, and promotes professional development in the field of archival studies. Archeota upholds the core values of the archival profession. “Documenting a Nation in Crisis: Rapid Response Collecting in the Wake of the Capitol Riot” by Kelli Roisman “Review of Survival Mode: SJSU Responds to Historic Crises” by Sara Wang “Reflections on the Roles of Archivists: Collectors, Storytellers, Gatekeepers, and Changemakers” by Alyssa Key “What is an NFT and Why Should Archivists Pay Attention” by Alison Quirion “From Print to Pixels (and Back): The Environmental Cost of Archival Digitization” by Samantha Hamilton “Farewell to our 2021 MLIS Graduates: Interviews with Departing SAASC Leaders: Alyssa Key; Alison Quirion; Sabrina Holecko; Samantha Hamilton.” Summer Reading Recommendationshttps://scholarworks.sjsu.edu/saasc_archeota/1013/thumbnail.jp

Decision‐support networks of women newly diagnosed with breast cancer

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/138904/1/cncr30848_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/138904/2/cncr30848.pd

What is a good medical decision? A research agenda guided by perspectives from multiple stakeholders

Informed and shared decision making are critical aspects of patient-centered care, which has contributed to an emphasis on decision support interventions to promote good medical decision making. However, researchers and healthcare providers have not reached a consensus on what defines a good decision, nor how to evaluate it. This position paper, informed by conference sessions featuring diverse stakeholders held at the 2015 Society of Behavioral Medicine and Society for Medical Decision Making annual meetings, describes key concepts that influence the decision making process itself and that may change what it means to make a good decision: interpersonal factors, structural constraints, affective influences, and values clarification methods. This paper also proposes specific research questions within each of these priority areas, with the goal of moving medical decision making research to a more comprehensive definition of a good medical decision, and enhancing the ability to measure and improve the decision making process

The Children's Respiratory and Environmental Workgroup (CREW) birth cohort consortium: design, methods, and study population

Background: Single birth cohort studies have been the basis for many discoveries about early life risk factors for childhood asthma but are limited in scope by sample size and characteristics of the local environment and population. The Children’s Respiratory and Environmental Workgroup (CREW) was established to integrate multiple established asthma birth cohorts and to investigate asthma phenotypes and associated causal pathways (endotypes), focusing on how they are influenced by interactions between genetics, lifestyle, and environmental exposures during the prenatal period and early childhood. Methods and results: CREW is funded by the NIH Environmental influences on Child Health Outcomes (ECHO) program, and consists of 12 individual cohorts and three additional scientific centers. The CREW study population is diverse in terms of race, ethnicity, geographical distribution, and year of recruitment. We hypothesize that there are phenotypes in childhood asthma that differ based on clinical characteristics and underlying molecular mechanisms. Furthermore, we propose that asthma endotypes and their defining biomarkers can be identified based on personal and early life environmental risk factors. CREW has three phases: 1) to pool and harmonize existing data from each cohort, 2) to collect new data using standardized procedures, and 3) to enroll new families during the prenatal period to supplement and enrich extant data and enable unified systems approaches for identifying asthma phenotypes and endotypes. Conclusions: The overall goal of CREW program is to develop a better understanding of how early life environmental exposures and host factors interact to promote the development of specific asthma endotypes.HHS/NIH [5UG3OD023282]; Columbia University [P01ES09600, R01 ES008977, P30ES09089, R01 ES013163, R827027]; Tucson Children's Respiratory Study (TCRS) [NHLBI 132523]; Infant Immune Study (IIS) [HL-56177]; Childhood Origins of Asthma Study (COAST) [P01 HL070831, U10 HL064305, R01 HL061879]; Wayne County Health, Environment, Allergy and Asthma Longitudinal Study (WHEALS) [R01 AI050681, R56 AI050681, R01 AI061774, R21 AI059415, K01 AI070606, R21 AI069271, R01 HL113010, R21 ES022321, P01 AI089473, R21 AI080066, R01 AI110450, R01 HD082147]; Fund for Henry Ford Health System; Childhood Allergy Study (CAS) [R01 AI024156, R03 HL067427, R01 AI051598]; Blue Cross Foundation Johnson; Fund for Henry Ford Hospital; Microbes, Allergy, Asthma and Pets (MAAP) [P01 AI089473]; Infant Susceptibility to Pulmonary Infections and Asthma following RSV Exposure (INSPIRE) [NIH/NIAID U19 AI 095227, NIH/NCATS UL1 TR 002243, NIH/NIAID K24 AI 077930, NIH/NHLBI R21 HD 087864, NIH/NHLBI X01 HL 134583]; Wisconsin Infant Study Cohort (WISC) [U19 AI104317, NCATS UL1TR000427]; Upper Midwest Agricultural Safety and Health Center (UMASH) [U54 OH010170]; RTI International, Research Triangle Park, North Carolina, USA; NIH [U24OD023382]; Urban Environment and Childhood Asthma Study (URECA) [NO1-AI-25482, HHSN272200900052C, HHSN272201000052I, NCRR/NIH RR00052, M01RR00533, 1UL1RR025771, M01RR00071, 1UL1RR024156, UL1TR001079, 5UL1RR024992-02, NCATS/NIH UL1TR000040]; Cincinnati Childhood Allergy and Air Pollution Study (CCAAPS) [R01 ES11170, R01 ES019890]; Epidemiology of Home Allergens and Asthma Study (EHAAS) [R01 AI035786]Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

A Large Expansion of the HSFY Gene Family in Cattle Shows Dispersion across Yq and Testis-Specific Expression

Heat shock transcription factor, Y-linked (HSFY) is a member of the heat shock transcriptional factor (HSF) family that is found in multiple copies on the Y chromosome and conserved in a number of species. Its function still remains unknown but in humans it is thought to play a role in spermatogenesis. Through real time polymerase chain reaction (PCR) analyses we determined that the HSFY family is largely expanded in cattle (∼70 copies) compared with human (2 functional copies, 4 HSFY-similar copies). Unexpectedly, we found that it does not vary among individual bulls as a copy number variant (CNV). Using fluorescence in situ hybridization (FISH) we found that the copies are dispersed along the long arm of the Y chromosome (Yq). HSFY expression in cattle appears restricted to the testis and its mRNA correlates positively with mRNA markers of spermatogonial and spermatocyte cells (UCHL1 and TRPC2, respectively) which suggests that HSFY is expressed (at least in part) in early germ cells

An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome

Background: Single Nucleotide Polymorphisms (SNPs) are widely used molecular markers, and their use has increased massively since the inception of Next Generation Sequencing (NGS) technologies, which allow detection of large numbers of SNPs at low cost. However, both NGS data and their analysis are error-prone, which can lead to the generation of false positive (FP) SNPs. We explored the relationship between FP SNPs and seven factors involved in mapping-based variant calling - quality of the reference sequence, read length, choice of mapper and variant caller, mapping stringency and filtering of SNPs by read mapping quality and read depth. This resulted in 576 possible factor level combinations. We used error- and variant-free simulated reads to ensure that every SNP found was indeed a false positive. Results: The variation in the number of FP SNPs generated ranged from 0 to 36,621 for the 120 million base pairs (Mbp) genome. All of the experimental factors tested had statistically significant effects on the number of FP SNPs generated and there was a considerable amount of interaction between the different factors. Using a fragmented reference sequence led to a dramatic increase in the number of FP SNPs generated, as did relaxed read mapping and a lack of SNP filtering. The choice of reference assembler, mapper and variant caller also significantly affected the outcome. The effect of read length was more complex and suggests a possible interaction between mapping specificity and the potential for contributing more false positives as read length increases. Conclusions: The choice of tools and parameters involved in variant calling can have a dramatic effect on the number of FP SNPs produced, with particularly poor combinations of software and/or parameter settings yielding tens of thousands in this experiment. Between-factor interactions make simple recommendations difficult for a SNP discovery pipeline but the quality of the reference sequence is clearly of paramount importance. Our findings are also a stark reminder that it can be unwise to use the relaxed mismatch settings provided as defaults by some read mappers when reads are being mapped to a relatively unfinished reference sequence from e.g. a non-model organism in its early stages of genomic exploration

The genomes of two key bumblebee species with primitive eusocial organization

Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation

Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.

The QT interval, an electrocardiographic measure reflecting myocardial repolarization, is a heritable trait. QT prolongation is a risk factor for ventricular arrhythmias and sudden cardiac death (SCD) and could indicate the presence of the potentially lethal mendelian long-QT syndrome (LQTS). Using a genome-wide association and replication study in up to 100,000 individuals, we identified 35 common variant loci associated with QT interval that collectively explain ∼8-10% of QT-interval variation and highlight the importance of calcium regulation in myocardial repolarization. Rare variant analysis of 6 new QT interval-associated loci in 298 unrelated probands with LQTS identified coding variants not found in controls but of uncertain causality and therefore requiring validation. Several newly identified loci encode proteins that physically interact with other recognized repolarization proteins. Our integration of common variant association, expression and orthogonal protein-protein interaction screens provides new insights into cardiac electrophysiology and identifies new candidate genes for ventricular arrhythmias, LQTS and SCD

Emergent sustainability in open property regimes

Current theoretical models of the commons assert that common-pool resources can only be managed sustainably with clearly defined boundaries around both communities and the resources that they use. In these theoretical models, open access inevitably leads to a tragedy of the commons. However, in many open-access systems, use of common-pool resources seems to be sustainable over the long term (i.e., current resource use does not threaten use of common-pool resources for future generations). Here, we outline the conditions that support sustainable resource use in open property regimes. We use the conceptual framework of complex adaptive systems to explain how processes within and couplings between human and natural systems can lead to the emergence of efficient, equitable, and sustainable resource use. We illustrate these dynamics in eight case studies of different social–ecological systems, including mobile pastoralism, marine and freshwater fisheries, swidden agriculture, and desert foraging. Our theoretical framework identifies eight conditions that are critical for the emergence of sustainable use of common-pool resources in open property regimes. In addition, we explain how changes in boundary conditions may push open property regimes to either common property regimes or a tragedy of the commons. Our theoretical model of emergent sustainability helps us to understand the diversity and dynamics of property regimes across a wide range of social–ecological systems and explains the enigma of open access without a tragedy. We recommend that policy interventions in such self-organizing systems should focus on managing the conditions that are critical for the emergence and persistence of sustainability