Beef Cattle Lesson Plans: For use in the education of school-age children in the beef cattle industry

This project was initially created for use at Fort Hope in Arroyo Grande, California. It designs lesson plans created to teach children about the beef cattle industry. The project consists of lesson plans for three age groups: 7-9, 10-12, and 13-15. Each age group will learn various aspects about beef cattle, and lessons will increase in complexity as the children advance age groups. The groups will spend six days in lecture completing worksheets and activities, and on the seventh day, after completion of a review game, the children receive certificates. While the project was created specifically for the Fort Hope curriculum, it may be adapted for other uses

Photolithographic micromolding of ceramics using plasma etched polyimide patterns

Features as fine as 4 μm with high aspect ratio were produced from ceria‐zirconia ceramic using a thick plasma‐etched polyimide layer as a micromold.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/70009/2/APPLAB-63-24-3379-1.pd

FluTE, a Publicly Available Stochastic Influenza Epidemic Simulation Model

Mathematical and computer models of epidemics have contributed to our understanding of the spread of infectious disease and the measures needed to contain or mitigate them. To help prepare for future influenza seasonal epidemics or pandemics, we developed a new stochastic model of the spread of influenza across a large population. Individuals in this model have realistic social contact networks, and transmission and infections are based on the current state of knowledge of the natural history of influenza. The model has been calibrated so that outcomes are consistent with the 1957/1958 Asian A(H2N2) and 2009 pandemic A(H1N1) influenza viruses. We present examples of how this model can be used to study the dynamics of influenza epidemics in the United States and simulate how to mitigate or delay them using pharmaceutical interventions and social distancing measures. Computer simulation models play an essential role in informing public policy and evaluating pandemic preparedness plans. We have made the source code of this model publicly available to encourage its use and further development

CRISPR-UnLOCK: Multipurpose Cas9-Based Strategies for Conversion of Yeast Libraries and Strains

Citation: Roggenkamp E, Giersch RM, Wedeman E, Eaton M, Turnquist E, Schrock MN, Alkotami L, Jirakittisonthon T, Schluter-Pascua SE, Bayne GH, Wasko C, Halloran M and Finnigan GC (2017) CRISPR-UnLOCK: Multipurpose Cas9-Based Strategies for Conversion of Yeast Libraries and Strains. Front. Microbiol. 8:1773. doi: 10.3389/fmicb.2017.01773Saccharomyces cerevisiae continues to serve as a powerful model system for both basic biological research and industrial application. The development of genome-wide collections of individually manipulated strains (libraries) has allowed for high-throughput genetic screens and an emerging global view of this single-celled Eukaryote. The success of strain construction has relied on the innate ability of budding yeast to accept foreign DNA and perform homologous recombination, allowing for efficient plasmid construction (in vivo) and integration of desired sequences into the genome. The development of molecular toolkits and “integration cassettes” have provided fungal systems with a collection of strategies for tagging, deleting, or over-expressing target genes; typically, these consist of a C-terminal tag (epitope or fluorescent protein), a universal terminator sequence, and a selectable marker cassette to allow for convenient screening. However, there are logistical and technical obstacles to using these traditional genetic modules for complex strain construction (manipulation of many genomic targets in a single cell) or for the generation of entire genome-wide libraries. The recent introduction of the CRISPR/Cas gene editing technology has provided a powerful methodology for multiplexed editing in many biological systems including yeast. We have developed four distinct uses of the CRISPR biotechnology to generate yeast strains that utilizes the conversion of existing, commonly-used yeast libraries or strains. We present Cas9-based, marker-less methodologies for (i) N-terminal tagging, (ii) C-terminally tagging yeast genes with 18 unique fusions, (iii) conversion of fluorescently-tagged strains into newly engineered (or codon optimized) variants, and finally, (iv) use of a Cas9 “gene drive” system to rapidly achieve a homozygous state for a hypomorphic query allele in a diploid strain. These CRISPR-based methods demonstrate use of targeting universal sequences previously introduced into a genome

Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia

BACKGROUND: Colombia was the second most affected country during the American Zika virus (ZIKV) epidemic, with over 109,000 reported cases. Despite the scale of the outbreak, limited genomic sequence data were available from Colombia. We sought to sequence additional samples and use genomic epidemiology to describe ZIKV dynamics in Colombia. METHODS: We sequenced ZIKV genomes directly from clinical diagnostic specimens and infected Aedes aegypti samples selected to cover the temporal and geographic breadth of the Colombian outbreak. We performed phylogeographic analysis of these genomes, along with other publicly-available ZIKV genomes from the Americas, to estimate the frequency and timing of ZIKV introductions to Colombia. RESULTS: We attempted PCR amplification on 184 samples; 19 samples amplified sufficiently to perform sequencing. Of these, 8 samples yielded sequences with at least 50% coverage. Our phylogeographic reconstruction indicates two separate introductions of ZIKV to Colombia, one of which was previously unrecognized. We find that ZIKV was first introduced to Colombia in February 2015 (95%CI: Jan 2015 - Apr 2015), corresponding to 5 to 8 months of cryptic ZIKV transmission prior to confirmation in September 2015. Despite the presence of multiple introductions, we find that the majority of Colombian ZIKV diversity descends from a single introduction. We find evidence for movement of ZIKV from Colombia into bordering countries, including Peru, Ecuador, Panama, and Venezuela. CONCLUSIONS: Similarly to genomic epidemiological studies of ZIKV dynamics in other countries, we find that ZIKV circulated cryptically in Colombia. More accurately dating when ZIKV was circulating refines our definition of the population at risk. Additionally, our finding that the majority of ZIKV transmission within Colombia was attributable to transmission between individuals, rather than repeated travel-related importations, indicates that improved detection and control might have succeeded in limiting the scale of the outbreak within Colombia

Extracting key information from historical data to quantify the transmission dynamics of smallpox

<p>Abstract</p> <p>Background</p> <p>Quantification of the transmission dynamics of smallpox is crucial for optimizing intervention strategies in the event of a bioterrorist attack. This article reviews basic methods and findings in mathematical and statistical studies of smallpox which estimate key transmission parameters from historical data.</p> <p>Main findings</p> <p>First, critically important aspects in extracting key information from historical data are briefly summarized. We mention different sources of heterogeneity and potential pitfalls in utilizing historical records. Second, we discuss how smallpox spreads in the absence of interventions and how the optimal timing of quarantine and isolation measures can be determined. Case studies demonstrate the following. (1) The upper confidence limit of the 99th percentile of the incubation period is 22.2 days, suggesting that quarantine should last 23 days. (2) The highest frequency (61.8%) of secondary transmissions occurs 3–5 days after onset of fever so that infected individuals should be isolated before the appearance of rash. (3) The U-shaped age-specific case fatality implies a vulnerability of infants and elderly among non-immune individuals. Estimates of the transmission potential are subsequently reviewed, followed by an assessment of vaccination effects and of the expected effectiveness of interventions.</p> <p>Conclusion</p> <p>Current debates on bio-terrorism preparedness indicate that public health decision making must account for the complex interplay and balance between vaccination strategies and other public health measures (e.g. case isolation and contact tracing) taking into account the frequency of adverse events to vaccination. In this review, we summarize what has already been clarified and point out needs to analyze previous smallpox outbreaks systematically.</p

A Syndemic of Psychosocial Problems Places the MSM (Men Who Have Sex with Men) Population at Greater Risk of HIV Infection

Background: The MSM (Men who have sex with men) population suffers from very high rates of concurrent psychosocial problems. Together, these problems comprise a syndemic that increases the risk of HIV infection for this community. The precise mechanisms through which this syndemic can raise the likelihood of HIV infection warrant further exploration. Methodology/Principal Findings: A total of 522 MSM were enrolled via a multiframe sampling approach and were asked to report psychosocial problems, risky sexual behaviors and HIV test results. A count of psychosocial health problems was calculated to test the additive relationship of these factors on HIV risk. Adjusting analysis and restriction analysis were used to determine a proposed intermediate pathway. Psychosocial health problems are highly concurrent and intercorrelated among urban MSM. Greater numbers of health problems are significantly and positively associated with HIV infection, which is mediated, at least partially, by risky sexual behaviors. Conclusions/Significance: MSM experience concurrent psychosocial health problems that correlate with HIV infection in this community. We recommend the development of coping strategies for this population to deal with these psychosocial problems, both in prevention research and health policy

Formation of a simple cubic antiferromagnet through charge ordering in a double Dirac material

The appearance of spontaneous charge order in chemical systems is often associated with the emergence of novel, and useful, properties. Here we show through single crystal diffraction that the Eu ions in the mixed valent metal EuPd$_3$S$_4$ undergo long-range charge ordering at $T_{\mathrm{CO}} = 340 \mathrm{~K}$ resulting in simple cubic lattices of Eu$^{2+}$ ($J = 7/2$) and Eu$^{3+}$ ($J = 0$) ions. As only one of the two sublattices has a non-magnetic ground state, the charge order results in the emergence of remarkably simple G-type antiferromagnetic order at $T_{\mathrm{N}} = 2.85(6) \mathrm{~K}$, observed in magnetization, specific heat, and neutron diffraction. Application of a $0.3 \mathrm{~T}$ field is sufficient to induce a spin flop transition to a magnetically polarized, but still charge ordered, state. Density functional theory calculations show that this charge order also modifies the electronic degeneracies present in the material: without charge order, EuPd$_3$S$_4$ is an example of a double Dirac material containing 8-fold degenerate electronic states, greater than the maximum degeneracy of six possible in molecular systems. The symmetry reduction from charge order transmutes 8-fold double Dirac states into 4-fold Dirac states, a degeneracy that can be preserved even in the presence of the magnetic order. Our results show not only how charge order can be used to produce interesting magnetic lattices, but also how it can be used to engineer controlled degeneracies in electronic states.Comment: 33 pages, 23 figure

European guidelines for quality assurance in colorectal cancer screening and diagnosis: overview and introduction to the full supplement publication

Population-based screening for early detection and treatment of colorectal cancer (CRC) and precursor lesions, using evidence-based methods, can be effective in populations with a significant burden of the disease provided the services are of high quality. Multidisciplinary, evidence-based guidelines for quality assurance in CRC screening and diagnosis have been developed by experts in a project co-financed by the European Union. The 450-page guidelines were published in book format by the European Commission in 2010. They include 10 chapters and over 250 recommendations, individually graded according to the strength of the recommendation and the supporting evidence. Adoption of the recommendations can improve and maintain the quality and effectiveness of an entire screening process, including identification and invitation of the target population, diagnosis and management of the disease and appropriate surveillance in people with detected lesions. To make the principles, recommendations and standards in the guidelines known to a wider professional and scientific community and to facilitate their use in the scientific literature, the original content is presented in journal format in an open-access Supplement of Endoscopy. The editors have prepared the present overview to inform readers of the comprehensive scope and content of the guidelines.Fil: Arrossi, Silvina. Centro de Estudios de Estado y Sociedad; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: von Karsa, Lawrence. International Agency for Research on Cancer; FranciaFil: Patrick, J.. NHS Cancer Screening Programmes Sheffield; Reino Unido. University of Oxford; Reino UnidoFil: Segnan, N.. International Agency for Research on Cancer; Francia. AO Città della Salute e della Scienza di Torino; ItaliaFil: Atkin, W.. Imperial College London; Reino UnidoFil: Halloran, S.. University of Surrey; Reino UnidoFil: Saito, H.. National Cancer Centre; JapónFil: Sauvaget, C.. International Agency for Research on Cancer; FranciaFil: Scharpantgen, A.. Ministry of Health; LuxemburgoFil: Schmiegel, W.. Ruhr-Universität Bochum; AlemaniaFil: Senore, C.. AO Città della Salute e della Scienza di Torino; ItaliaFil: Siddiqi, M.. Cancer Foundation of India; IndiaFil: Sighoko, D.. University of Chicago; Estados Unidos. Formerly International Agency for Research on Cancer; FranciaFil: Smith, R.. American Cancer Society; Estados UnidosFil: Smith S.. University Hospitals Coventry & Warwickshire NHS Trust; Reino UnidoFil: Suchanek, S.. Charles University; República ChecaFil: Suonio, E.. International Agency for Research on Cancer; FranciaFil: Tong, W.. Chinese Academy of Sciences; República de ChinaFil: Törnberg, S.. Stockholm Gotland Regional Cancer Centre. Department of Cancer Screening; SueciaFil: Van Cutsem, E.. Katholikie Universiteit Leuven; BélgicaFil: Vignatelli, L.. Agenzia Sanitaria e Sociale Regionale; ItaliaFil: Villain, P.. University of Oxford; Reino UnidoFil: Voti, L.. Formerly International Agency for Research on Cancer; Francia. University of Miami; Estados UnidosFil: Watanabe, H.. Niigata University; JapónFil: Watson, J.. University of Oxford; Reino UnidoFil: Winawer, S.. Memorial Sloan–Kettering Cancer Center; Estados UnidosFil: Young, G.. Flinders University. Gastrointestinal Services; AustraliaFil: Zaksas, V.. State Patient Fund; LituaniaFil: Zappa, M.. Cancer Prevention and Research Institute; ItaliaFil: Valori, R.. NHS Endoscopy; Reino Unid