Metrology Computer Redesign

We are M[EE]2 and our project is to redesign Micro-Vu’s metrology computer (the Q16) with modern components and updated firmware. Metrology machines take high precision and high accuracy measurements, and a computer attached to each machine reads out the measurements. We will be redesigning the logic and display circuit boards on the Q16. The ports and communication methods with the machine will stay the same as it must be a drop-in replacement. The motivation behind the redesign stems from the age of the current design. The current design was created in 1986, and has not had significant modifications since. As technology has improved in the last 30 years, the current design is now expensive, obsolete, and time consuming to fabricate. The stakeholders include Natalie Lizama (our primary contact with the sponsor), Melinda Ong, Mitchell Aiken, Micro-Vu, Micro-Vu’s consumers, and Karla Carichner. The Micro-Vu sponsor is Zack Reinman. Our faculty advisor is Karla Carichner. Our goal is to successfully deliver a functional design in which its assembly can be further automated and streamlined

Chloroplast genome sequencing analysis of Heterosigma akashiwo CCMP452 (West Atlantic) and NIES293 (West Pacific) strains

Background: Heterokont algae form a monophyletic group within the stramenopile branch of the tree of life. These organisms display wide morphological diversity, ranging from minute unicells to massive, bladed forms. Surprisingly, chloroplast genome sequences are available only for diatoms, representing two (Coscinodiscophyceae and Bacillariophyceae) of approximately 18 classes of algae that comprise this taxonomic cluster. A universal challenge to chloroplast genome sequencing studies is the retrieval of highly purified DNA in quantities sufficient for analytical processing. To circumvent this problem, we have developed a simplified method for sequencing chloroplast genomes, using fosmids selected from a total cellular DNA library. The technique has been used to sequence chloroplast DNA of two Heterosigma akashiwo strains. This raphidophyte has served as a model system for studies of stramenopile chloroplast biogenesis and evolution. Results: H. akashiwo strain CCMP452 (West Atlantic) chloroplast DNA is 160,149 bp in size with a 21,822-bp inverted repeat, whereas NIES293 (West Pacific) chloroplast DNA is 159,370 bp in size and has an inverted repeat of 21,665 bp. The fosmid cloning technique reveals that both strains contain an isomeric chloroplast DNA population resulting from an inversion of their single copy domains. Both strains contain multiple small inverted and tandem repeats, non-randomly distributed within the genomes. Although both CCMP452 and NIES293 chloroplast DNAs contains 197 genes, multiple nucleotide polymorphisms are present in both coding and intergenic regions. Several protein-coding genes contain large, in-frame inserts relative to orthologous genes in other plastids. These inserts are maintained in mRNA products. Two genes of interest in H. akashiwo, not previously reported in any chloroplast genome, include tyrC, a tyrosine recombinase, which we hypothesize may be a result of a lateral gene transfer event, and an unidentified 456 amino acid protein, which we hypothesize serves as a G-protein-coupled receptor. The H. akashiwo chloroplast genomes share little synteny with other algal chloroplast genomes sequenced to date. Conclusion: The fosmid cloning technique eliminates chloroplast isolation, does not require chloroplast DNA purification, and reduces sequencing processing time. Application of this method has provided new insights into chloroplast genome architecture, gene content and evolution within the stramenopile cluster

Genome-wide analysis identifies genetic effects on reproductive success and ongoing natural selection at the FADS locus

: Identifying genetic determinants of reproductive success may highlight mechanisms underlying fertility and identify alleles under present-day selection. Using data in 785,604 individuals of European ancestry, we identified 43 genomic loci associated with either number of children ever born (NEB) or childlessness. These loci span diverse aspects of reproductive biology, including puberty timing, age at first birth, sex hormone regulation, endometriosis and age at menopause. Missense variants in ARHGAP27 were associated with higher NEB but shorter reproductive lifespan, suggesting a trade-off at this locus between reproductive ageing and intensity. Other genes implicated by coding variants include PIK3IP1, ZFP82 and LRP4, and our results suggest a new role for the melanocortin 1 receptor (MC1R) in reproductive biology. As NEB is one component of evolutionary fitness, our identified associations indicate loci under present-day natural selection. Integration with data from historical selection scans highlighted an allele in the FADS1/2 gene locus that has been under selection for thousands of years and remains so today. Collectively, our findings demonstrate that a broad range of biological mechanisms contribute to reproductive success

Genome-wide analysis identifies 12 loci influencing human reproductive behavior.

The genetic architecture of human reproductive behavior-age at first birth (AFB) and number of children ever born (NEB)-has a strong relationship with fitness, human development, infertility and risk of neuropsychiatric disorders. However, very few genetic loci have been identified, and the underlying mechanisms of AFB and NEB are poorly understood. We report a large genome-wide association study of both sexes including 251,151 individuals for AFB and 343,072 individuals for NEB. We identified 12 independent loci that are significantly associated with AFB and/or NEB in a SNP-based genome-wide association study and 4 additional loci associated in a gene-based effort. These loci harbor genes that are likely to have a role, either directly or by affecting non-local gene expression, in human reproduction and infertility, thereby increasing understanding of these complex traits

Adjunctive rifampicin for Staphylococcus aureus bacteraemia (ARREST): a multicentre, randomised, double-blind, placebo-controlled trial.

BACKGROUND: Staphylococcus aureus bacteraemia is a common cause of severe community-acquired and hospital-acquired infection worldwide. We tested the hypothesis that adjunctive rifampicin would reduce bacteriologically confirmed treatment failure or disease recurrence, or death, by enhancing early S aureus killing, sterilising infected foci and blood faster, and reducing risks of dissemination and metastatic infection. METHODS: In this multicentre, randomised, double-blind, placebo-controlled trial, adults (≥18 years) with S aureus bacteraemia who had received ≤96 h of active antibiotic therapy were recruited from 29 UK hospitals. Patients were randomly assigned (1:1) via a computer-generated sequential randomisation list to receive 2 weeks of adjunctive rifampicin (600 mg or 900 mg per day according to weight, oral or intravenous) versus identical placebo, together with standard antibiotic therapy. Randomisation was stratified by centre. Patients, investigators, and those caring for the patients were masked to group allocation. The primary outcome was time to bacteriologically confirmed treatment failure or disease recurrence, or death (all-cause), from randomisation to 12 weeks, adjudicated by an independent review committee masked to the treatment. Analysis was intention to treat. This trial was registered, number ISRCTN37666216, and is closed to new participants. FINDINGS: Between Dec 10, 2012, and Oct 25, 2016, 758 eligible participants were randomly assigned: 370 to rifampicin and 388 to placebo. 485 (64%) participants had community-acquired S aureus infections, and 132 (17%) had nosocomial S aureus infections. 47 (6%) had meticillin-resistant infections. 301 (40%) participants had an initial deep infection focus. Standard antibiotics were given for 29 (IQR 18-45) days; 619 (82%) participants received flucloxacillin. By week 12, 62 (17%) of participants who received rifampicin versus 71 (18%) who received placebo experienced treatment failure or disease recurrence, or died (absolute risk difference -1·4%, 95% CI -7·0 to 4·3; hazard ratio 0·96, 0·68-1·35, p=0·81). From randomisation to 12 weeks, no evidence of differences in serious (p=0·17) or grade 3-4 (p=0·36) adverse events were observed; however, 63 (17%) participants in the rifampicin group versus 39 (10%) in the placebo group had antibiotic or trial drug-modifying adverse events (p=0·004), and 24 (6%) versus six (2%) had drug interactions (p=0·0005). INTERPRETATION: Adjunctive rifampicin provided no overall benefit over standard antibiotic therapy in adults with S aureus bacteraemia. FUNDING: UK National Institute for Health Research Health Technology Assessment

PREDICTION OF FLU EPIDEMIC PEAKS IN ST. PETERSBURG THROUGH POPULATION-BASED MATHEMATICAL MODELS

The paper presents two methods of predicting the peak of influenza epidemics using population-based mathematical models: Baroyan-Rvachev and modified Kermack-McKendrick model, proposed by the authors. We perform the comparison of the prediction accuracy of time and the value of epidemics peaks on long-term data of ARI incidence in the city of St. Petersburg. The methodology of comparison is based on three criteria of accuracy conventionally named as "square", "vertical stripe" and "horizontal stripe", and two variants of the model parameters estimation. In the first variant we calibrate the model on the data of the first city impacted by the epidemic, and use these parameters in the future for the other cities, that allows taking into account the spatial characteristics of the epidemic in the country. In the second case, we only use historical data available at the time of the prediction for a given city. The advantage of this approach is the lack of need for additional, not always available, external data to predict the epidemic. The results of test calculations have demonstrated that the first method shows good results in the case of significant delays between the peaks of epidemics in different cities. If the outbreak in St. Petersburg started soon after the registration of the first outbreaks in the other cities of the Russian Federation, the second method shows comparable results to an accuracy of 90% to predict the peak of the epidemic. In most cases, it is sufficient for the use of the results of calculations for planning antiviral activities. The lead time of the peak prediction is still at a relatively low level, that seems to be associated with a variety of patterns of virus spread and permanent changes in transport communications within the country

Is There an Association between Health Risk Behaviours and Academic Achievement among University Students?

University students have high rates of health risk behaviours, and these may be predictive of academic success. This cross-sectional study aimed to determine the association between individual and multiple health risk behaviours and academic achievement in a sample of Australian university students. Data from the University of Newcastle Student Healthy Lifestyle Survey 2019 were used. Health risk behaviours (diet, physical activity, sitting time, sleep, alcohol consumption, smoking) were assessed, and total number of risk factors calculated. Academic achievement was assessed using self-reported grade point average (GPA). The association between health risk behaviours and GPA was explored using linear regression, adjusted for socio-demographic and student characteristics. The sample included 1543 students (mean age 25.0 ± 7.9 years, 70.6% female). Lower GPA was associated with not meeting fruit consumption recommendations (β = −0.203), consuming >1 cup of soft drink/week (β = −0.307), having takeaway foods ≥1 time/week (β = −0.130), not consuming breakfast daily (β = −0.261), not meeting sleep recommendations (β = −0.163), exceeding single occasion alcohol consumption risk (β = −0.277), smoking (β = −0.393), and having a higher number of risk factors (β = −0.105). This study identified modest associations between GPA and health risk behaviours, suggesting that further research is warranted into whether strategies to improve university students’ health could modestly improve their academic achievement