Evaluating Bioinformatic Pipeline Performance for Forensic Microbiome Analysis*,†,‡

Microbial communities have potential evidential utility for forensic applications. However, bioinformatic analysis of high‐throughput sequencing data varies widely among laboratories. These differences can potentially affect microbial community composition and downstream analyses. To illustrate the importance of standardizing methodology, we compared analyses of postmortem microbiome samples using several bioinformatic pipelines, varying minimum library size or minimum number of sequences per sample, and sample size. Using the same input sequence data, we found that three open‐source bioinformatic pipelines, MG‐RAST, mothur, and QIIME2, had significant differences in relative abundance, alpha‐diversity, and beta‐diversity, despite the same input data. Increasing minimum library size and sample size increased the number of low‐abundant and infrequent taxa detected. Our results show that bioinformatic pipeline and parameter choice affect results in important ways. Given the growing potential application of forensic microbiology to the criminal justice system, continued research on standardizing computational methodology will be important for downstream applications.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154468/1/jfo14213_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154468/2/jfo14213.pd

A Nonword Repetition Task for Speakers with Misarticulations: The Syllable Repetition Task (SRT)

Purpose. Conceptual and methodological confounds occur when non(sense) repetition tasks are administered to speakers who do not have the target speech sounds in their phonetic inventories or who habitually misarticulate targeted speech sounds. We describe a nonword repetition task, the Syllable Repetiton Task (SRT) that eliminates this confound and report findings from three validity studies. Method. Ninety-five preschool children with Speech Delay and 63 with Typical Speech, completed an assessment battery that included the Nonword Repetition Task (NRT: Dollaghan & Campbell, 1998) and the SRT. SRT stimuli include only four of the earliest occurring consonants and one early occurring vowel. Results. Study 1 findings indicated that the SRT eliminated the speech confound in nonword testing with speakers who misarticulate. Study 2 findings indicated that the accuracy of the SRT to identify expressive language impairment was comparable to findings for the NRT. Study 3 findings illustrated the SRT’s potential to interrogate speech processing constraints underlying poor nonword repetition accuracy. Results supported both memorial and auditory-perceptual encoding constraints underlying nonword repetition errors in children with speech-language impairment. Conclusion. The SRT appears to be a psychometrically stable and substantively informative nonword repetition task for emerging genetic and other research with speakers who misarticulate

CitDet: A Benchmark Dataset for Citrus Fruit Detection

In this letter, we present a new dataset to advance the state of the art in detecting citrus fruit and accurately estimate yield on trees affected by the Huanglongbing (HLB) disease in orchard environments via imaging. Despite the fact that significant progress has been made in solving the fruit detection problem, the lack of publicly available datasets has complicated direct comparison of results. For instance, citrus detection has long been of interest in the agricultural research community, yet there is an absence of work, particularly involving public datasets of citrus affected by HLB. To address this issue, we enhance state-of-the-art object detection methods for use in typical orchard settings. Concretely, we provide high-resolution images of citrus trees located in an area known to be highly affected by HLB, along with high-quality bounding box annotations of citrus fruit. Fruit on both the trees and the ground are labeled to allow for identification of fruit location, which contributes to advancements in yield estimation and potential measure of HLB impact via fruit drop. The dataset consists of over 32,000 bounding box annotations for fruit instances contained in 579 high-resolution images. In summary, our contributions are the following: (i) we introduce a novel dataset along with baseline performance benchmarks on multiple contemporary object detection algorithms, (ii) we show the ability to accurately capture fruit location on tree or on ground, and finally (ii) we present a correlation of our results with yield estimations.Comment: Submitted to IEEE Robotics and Automation Letters (RA-L

Adolescent Perceptions of Animation Violence as an Indication of Aggressive Attitudes and Behaviors

This reported study was designed to examine the beliefs and perceptions of adolescents on whether or not viewing violence on television contributes to an increase in adolescents’ abilities to learn aggressive attitudes and behaviors. It also explored the effects humor and satire used in the animated television series The Simpsons has on adolescents’ abilities to learn aggressive attitudes and behaviors. Finally, it examined to what extent the violence portrayed in The Simpsons was believed to be realistic and justified by adolescents viewing the show. Results indicate that adolescents were not affected by the violence they observed in The Simpsons animation: Further, they did not feel that it was acceptable for their favorite characters to use violence to solve problems. Youth did not have reactions to viewing the series that were violent, nor did they report becoming aggressive in response to viewing the violence on the The Simpsons. While the majority of the youth also reported that they did not use violence to solve a problem, 3.3% reported that they did. Overall, the study concluded that adolescents’ exposure to violent content by viewing it in animation in The Simpsons did not affect adolescents’ perceptions of their abilities to learn aggressive attitudes and behaviors. Youth did not perceive that the violence portrayed was realistic

Total RNA Analysis of Bacterial Community Structural and Functional Shifts Throughout Vertebrate Decomposition

Multiple methods have been proposed to provide accurate time since death estimations, and recently, the discovery of bacterial community turnover during decomposition has shown itself to have predictable patterns that may prove useful. In this study, we demonstrate the use of metatranscriptomics from the postmortem microbiome to simultaneously obtain community structure and functional data across postmortem intervals (PMIs). We found that bacterial succession patterns reveal similar trends as detected through DNA analysis, such as increasing Clostridiaceae as decomposition occurs, strengthening the reliability of total RNA community analyses. We also provide one of the first analyses of RNA transcripts to characterize bacterial metabolic pathways during decomposition. We found distinct pathways, such as amino acid metabolism, to be strongly up‐regulated with increasing PMIs. Elucidating the metabolic activity of postmortem microbial communities provides the first steps to discovering postmortem functional biomarkers since functional redundancy across bacteria may reduce host individual microbiome variability.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/152033/1/jfo14083_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152033/2/jfo14083.pd

Necrobiome framework for bridging decomposition ecology of autotrophically and heterotrophically derived organic matter

Decomposition contributes to global ecosystem function by contributing to nutrient recycling, energy flow, and limiting biomass accumulation. The decomposer organisms influencing this process form diverse, complex, and highly dynamic communities that often specialize on different plant or animal resources. Despite performing the same net role, there is a need to conceptually synthesize information on the structure and function of decomposer communities across the spectrum of dead plant and animal resources. A lack of synthesis has limited cross-disciplinary learning and research in important areas of ecosystem and community ecology. Here we expound on the “necrobiome” concept and develop a framework describing the decomposer communities and their interactions associated with plant and animal resource types within multiple ecosystems.We outline the biotic structure and ecological functions of the necrobiome, along with how the necrobiome fits into a broader landscape and ecosystem context. The expanded necrobiome model provides a set of perspectives on decomposer communities across resource types, and conceptually unifies plant and animal decomposer communities into the same framework, while acknowledging key differences in processes and mechanisms. This framework is intended to raise awareness among researchers, and advance the construction of explicit, mechanistic hypotheses that further our understanding of decomposer community contributions to biodiversity, the structure and function of ecosystems, global nutrient recycling and energy flow

NECROBIOME FRAMEWORK FOR BRIDGING DECOMPOSITION ECOLOGY OF AUTOTROPHICALLY AND HETEROTROPHICALLY DERIVED ORGANIC MATTER

Life arises from death through species that decompose dead biomass or necromass. This paper provides a synthesis of the species responsible for dead plant and animal decomposition and describes a conceptual perspective—the “necrobiome”— that defines the diverse and complex communities that interact to recycle necromass. The concept brings unification to the previously disparate fields of plant and animal decomposition by discussing the universal processes occurring across all forms of necromass. It highlights the factors that make each form of dead biomass different in a way that defines how unique necrobiomes drive decomposition and ultimately shape ecosystem structure and function

2014 Massachusetts Family Impact Seminar: A Lot On Our Plate; Chronic Health Threats in Massachusetts

A Lot on Our Plate: Chronic Health Threats in Massachusetts is the fifth Massachusetts Family Impact Seminar, and is designed to emphasize a family perspective in policymaking on issues related to childhood obesity, cardiovascular disease, and type 2 diabetes. In general, Family Impact Seminars analyze the consequences an issue, policy, or program may have for families