Deep ocean disposal of sewage sludge off Orange County, California: a research plan

Even though the discharge of sludge into the ocean via an outfall is not now permitted, this research plan has been prepared to show what could be learned with a full scale experimental sludge discharge of 150 dry tons/day by the County Sanitation Districts of Orange County into deep water (over 1000 feet). To provide a wide range of inputs and evaluation, a broad-based Research Planning Committee was established to advise the Environmental Quality Laboratory on the overall content and details of the research plan. Two meetings were held at EQL on: March 4-5, 1982: The entire Committee July 19-20, 1982: A working subgroup of the Committee The entire Committee is listed in Appendix B, with footnotes to indicate meeting attendance. Those unable to come to a meeting were asked to comment on the drafts by mail or telephone. We gratefully acknowledge the members of the Research Planning Committee for their generous help in formulating the research tasks and reviewing report drafts

The Forest Products Industry in Montana

Paper published as Bulletin 31 in the UM Bulletin Forestry Series.https://scholarworks.umt.edu/umforestrybulletin/1015/thumbnail.jp

Bidirectional Representation Learning from Transformers using Multimodal Electronic Health Record Data to Predict Depression

Advancements in machine learning algorithms have had a beneficial impact on representation learning, classification, and prediction models built using electronic health record (EHR) data. Effort has been put both on increasing models' overall performance as well as improving their interpretability, particularly regarding the decision-making process. In this study, we present a temporal deep learning model to perform bidirectional representation learning on EHR sequences with a transformer architecture to predict future diagnosis of depression. This model is able to aggregate five heterogenous and high-dimensional data sources from the EHR and process them in a temporal manner for chronic disease prediction at various prediction windows. We applied the current trend of pretraining and fine-tuning on EHR data to outperform the current state-of-the-art in chronic disease prediction, and to demonstrate the underlying relation between EHR codes in the sequence. The model generated the highest increases of precision-recall area under the curve (PRAUC) from 0.70 to 0.76 in depression prediction compared to the best baseline model. Furthermore, the self-attention weights in each sequence quantitatively demonstrated the inner relationship between various codes, which improved the model's interpretability. These results demonstrate the model's ability to utilize heterogeneous EHR data to predict depression while achieving high accuracy and interpretability, which may facilitate constructing clinical decision support systems in the future for chronic disease screening and early detection.Comment: in IEEE Journal of Biomedical and Health Informatics (2021

Apparent Role for \u3cem\u3eBorrelia burgdorferi\u3c/em\u3e LuxS During Mammalian Infection

The Lyme disease spirochete, Borrelia burgdorferi, controls protein expression patterns during its tick-mammal infection cycle. Earlier studies demonstrated that B. burgdorferi synthesizes 4,5-dihydroxy-2,3-pentanedione (autoinducer-2 [AI-2]) and responds to AI-2 by measurably changing production of several infection-associated proteins. luxS mutants, which are unable to produce AI-2, exhibit altered production of several proteins. B. burgdorferi cannot utilize the other product of LuxS, homocysteine, indicating that phenotypes of luxS mutants are not due to the absence of that molecule. Although a previous study found that a luxS mutant was capable of infecting mice, a critical caveat to those results is that bacterial loads were not quantified. To more precisely determine whether LuxS serves a role in mammalian infection, mice were simultaneously inoculated with congenic wild-type and luxS strains, and bacterial numbers were assessed using quantitative PCR. The wild-type bacteria substantially outcompeted the mutants, suggesting that LuxS performs a significant function during mammalian infection. These data also provide further evidence that nonquantitative infection studies do not necessarily provide conclusive results and that regulatory factors may not make all-or-none, black-or-white contributions to infectivity

Quaternary Ammonia Compounds in Disinfectant Products: Evaluating the Potential for Promoting Antibiotic Resistance and Disrupting Wastewater Treatment Plant Performance

Quaternary ammonium compounds (QACs) are a class of compounds that were widely used as disinfectants during the COVID-19 pandemic and continue to be used as disinfecting agents. After consumer usage, QAC concentrations are diluted in wastewater as they enter wastewater treatment plants. At sub-inhibitory concentrations, QACs may have unintended repercussions, including increased antibiotic resistance and inhibition of process performance in wastewater treatment plants. This review first summarizes how QACs inhibit bacteria and then highlights the mechanisms by which QACs can promote antibiotic resistance in general. Reported environmental concentrations of QACs are compared to concentrations that are suspected to impact antibiotic resistance, and the role QACs may have on antibiotic resistance proliferation in wastewater treatment is addressed. Finally, the specific impacts that QACs can have on biological wastewater processes (activated sludge and anaerobic digestion) are reviewed. We highlight key research gaps along with recommendations for future research. Of particular interest, research is needed to elucidate the relationship between the chemical structure of QACs and impacts on antibiotic resistance as well as process performance in wastewater treatment plants. Finally, the ability to mitigate (reverse) these impacts if QACs are removed needs to be determined

Effect of Microscopic Damage Events on Static and Ballistic Impact Strength of Triaxial Braid Composites

The reliability of impact simulations for aircraft components made with triaxial-braided carbon-fiber composites is currently limited by inadequate material property data and lack of validated material models for analysis. Methods to characterize the material properties used in the analytical models from a systematically obtained set of test data are also lacking. A macroscopic finite element based analytical model to analyze the impact response of these materials has been developed. The stiffness and strength properties utilized in the material model are obtained from a set of quasi-static in-plane tension, compression and shear coupon level tests. Full-field optical strain measurement techniques are applied in the testing, and the results are used to help in characterizing the model. The unit cell of the braided composite is modeled as a series of shell elements, where each element is modeled as a laminated composite. The braided architecture can thus be approximated within the analytical model. The transient dynamic finite element code LS-DYNA is utilized to conduct the finite element simulations, and an internal LS-DYNA constitutive model is utilized in the analysis. Methods to obtain the stiffness and strength properties required by the constitutive model from the available test data are developed. Simulations of quasi-static coupon tests and impact tests of a represented braided composite are conducted. Overall, the developed method shows promise, but improvements that are needed in test and analysis methods for better predictive capability are examined

RNA-Seq of \u3cem\u3eBorrelia burgdorferi\u3c/em\u3e in Multiple Phases of Growth Reveals Insights into the Dynamics of Gene Expression, Transcriptome Architecture, and Noncoding RNAs

Borrelia burgdorferi, the agent of Lyme disease, differentially expresses numerous genes and proteins as it cycles between mammalian hosts and tick vectors. Insights on regulatory mechanisms have been provided by earlier studies that examined B. burgdorferi gene expression patterns during cultivation. However, prior studies examined bacteria at only a single time point of cultivation, providing only a snapshot of what is likely a dynamic transcriptional program driving B. burgdorferi adaptations to changes during culture growth phases. To address that concern, we performed RNA sequencing (RNA-Seq) analysis of B. burgdorferi cultures at early-exponential, mid-exponential, and early-stationary phases of growth. We found that expression of nearly 18% of annotated B. burgdorferi genes changed significantly during culture maturation. Moreover, genome-wide mapping of the B. burgdorferi transcriptome in different growth phases enabled insight on transcript boundaries, operon structures, and identified numerous putative non-coding RNAs. These RNA-Seq data are discussed and presented as a resource for the community of researchers seeking to better understand B. burgdorferi biology and pathogenesis

DNA Methylation by Restriction Modification Systems Affects the Global Transcriptome Profile in \u3cem\u3eBorrelia burgdorferi\u3c/em\u3e

Prokaryote restriction modification (RM) systems serve to protect bacteria from potentially detrimental foreign DNA. Recent evidence suggests that DNA methylation by the methyltransferase (MTase) components of RM systems can also have effects on transcriptome profiles. The type strain of the causative agent of Lyme disease, Borrelia burgdorferi B31, possesses two RM systems with N6-methyladenosine (m6A) MTase activity, which are encoded by the bbe02 gene located on linear plasmid lp25 and bbq67 on lp56. The specific recognition and/or methylation sequences had not been identified for either of these B. burgdorferi MTases, and it was not previously known whether these RM systems influence transcript levels. In the current study, single-molecule real-time sequencing was utilized to map genome-wide m6A sites and to identify consensus modified motifs in wild-type B. burgdorferi as well as MTase mutants lacking either the bbe02 gene alone or both bbe02 and bbq67 genes. Four novel conserved m6A motifs were identified and were fully attributable to the presence of specific MTases. Whole-genome transcriptome changes were observed in conjunction with the loss of MTase enzymes, indicating that DNA methylation by the RM systems has effects on gene expression. Genes with altered transcription in MTase mutants include those involved in vertebrate host colonization (e.g., rpoS regulon) and acquisition by/transmission from the tick vector (e.g., rrp1 and pdeB). The results of this study provide a comprehensive view of the DNA methylation pattern in B. burgdorferi, and the accompanying gene expression profiles add to the emerging body of research on RM systems and gene regulation in bacteria

Farmers Markets and the Local Food System: The Case of Gettysburg, Pennsylvania

In order to examine and obtain a better understanding of the local food system within Adams County, Pennsylvania, this study explores the characteristics and perspectives of the customers and vendors at the farmers markets in Gettysburg, Pennsylvania. Survey findings from the Gettysburg Farmers Market and the three Adams County Farmers Markets include customer demographic information, perspectives and shopping behavior as well as vendor product information, farm size and location and preference for market management. Introductory background information on the Farm Bill and the influence of agricultural practices on the environment, human health and nutrition and the relationship between farmers markets and the local economy are offered in order to emphasize the value of a well-managed local food system. Conclusions provide evidence that lower income and lower education levels are not sufficiently represented at all the markets and food stamp programs are being underutilized. This study suggests employing additional marketing to target underrepresented demographic groups, public transportation to potentially inaccessible market locations and increased advertisement and encouragement of food stamp programs at all markets in order to expand the customer base and increase access to healthy, local foods for less advantaged citizens. The results from this study are intended to offer evidence that will promote and facilitate market management, strengthen customer/vendor relationships and encourage better ties between the local community and local food systems at the farmers markets within Gettysburg in Adams County, Pennsylvania