Dyno-Mite Redesign

The Cal Poly Mechanical Control Systems Laboratory currently employs an outdated device, known as the Motomatic, to teach students about various motor characteristics and control methods. These include open-loop vs. closed-loop control, speed vs. position control, and DC motor response curves. The current device does not function properly and produces unreliable data due to overwhelming non-linear effects such as stiction and shaft misalignment. Our team was tasked with designing a replacement device that retains many of the same educational goals as the original lab procedure, while also adding new educational goals pertaining to the device system dynamics. The new apparatus, dubbed the Dyno-Mite is a one tenth scale tire testing machine, incorporating two DC brushed motors, adjustable mechanisms, and load cell measuring devices. The design will also pay special attention to modularity so that future adjustments and modifications can be made to the lab apparatus, allowing for instructors to tailor the machine to meet their specific educational goals

Berkeley Supernova Ia Program I: Observations, Data Reduction, and Spectroscopic Sample of 582 Low-Redshift Type Ia Supernovae

In this first paper in a series we present 1298 low-redshift (z\leq0.2) optical spectra of 582 Type Ia supernovae (SNe Ia) observed from 1989 through 2008 as part of the Berkeley SN Ia Program (BSNIP). 584 spectra of 199 SNe Ia have well-calibrated light curves with measured distance moduli, and many of the spectra have been corrected for host-galaxy contamination. Most of the data were obtained using the Kast double spectrograph mounted on the Shane 3 m telescope at Lick Observatory and have a typical wavelength range of 3300-10,400 Ang., roughly twice as wide as spectra from most previously published datasets. We present our observing and reduction procedures, and we describe the resulting SN Database (SNDB), which will be an online, public, searchable database containing all of our fully reduced spectra and companion photometry. In addition, we discuss our spectral classification scheme (using the SuperNova IDentification code, SNID; Blondin & Tonry 2007), utilising our newly constructed set of SNID spectral templates. These templates allow us to accurately classify our entire dataset, and by doing so we are able to reclassify a handful of objects as bona fide SNe Ia and a few other objects as members of some of the peculiar SN Ia subtypes. In fact, our dataset includes spectra of nearly 90 spectroscopically peculiar SNe Ia. We also present spectroscopic host-galaxy redshifts of some SNe Ia where these values were previously unknown. [Abridged]Comment: 34 pages, 11 figures, 11 tables, revised version, re-submitted to MNRAS. Spectra will be released in January 2013. The SN Database homepage (http://hercules.berkeley.edu/database/index_public.html) contains the full tables, plots of all spectra, and our new SNID template

Constraints on the Progenitor System of the Type Ia Supernova SN 2011fe/PTF11kly

Type Ia supernovae (SNe) serve as a fundamental pillar of modern cosmology, owing to their large luminosity and a well-defined relationship between light-curve shape and peak brightness. The precision distance measurements enabled by SNe Ia first revealed the accelerating expansion of the universe, now widely believed (though hardly understood) to require the presence of a mysterious "dark" energy. General consensus holds that Type Ia SNe result from thermonuclear explosions of a white dwarf (WD) in a binary system; however, little is known of the precise nature of the companion star and the physical properties of the progenitor system. Here we make use of extensive historical imaging obtained at the location of SN 2011fe/PTF11kly, the closest SN Ia discovered in the digital imaging era, to constrain the visible-light luminosity of the progenitor to be 10-100 times fainter than previous limits on other SN Ia progenitors. This directly rules out luminous red giants and the vast majority of helium stars as the mass-donating companion to the exploding white dwarf. Any evolved red companion must have been born with mass less than 3.5 times the mass of the Sun. These observations favour a scenario where the exploding WD of SN 2011fe/PTF11kly, accreted matter either from another WD, or by Roche-lobe overflow from a subgiant or main-sequence companion star.Comment: 22 pages, 6 figures, submitte

DLK induces developmental neuronal degeneration via selective regulation of proapoptotic JNK activity

DLK is part of a specialized JNK signaling complex in axons that promotes apoptosis via c-Jun but axon degeneration via distinct JNK substrates

Inflammatory Genital Infections Mitigate a Severe Genetic Bottleneck in Heterosexual Transmission of Subtype A and C HIV-1

The HIV-1 epidemic in sub-Saharan Africa is driven largely by heterosexual transmission of non-subtype B viruses, of which subtypes C and A are predominant. Previous studies of subtype B and subtype C transmission pairs have suggested that a single variant from the chronically infected partner can establish infection in their newly infected partner. However, in subtype A infected individuals from a sex worker cohort and subtype B individuals from STD clinics, infection was frequently established by multiple variants. This study examined over 1750 single-genome amplified viral sequences derived from epidemiologically linked subtype C and subtype A transmission pairs very early after infection. In 90% (18/20) of the pairs, HIV-1 infection is initiated by a single viral variant that is derived from the quasispecies of the transmitting partner. In addition, the virus initiating infection in individuals who were infected by someone other than their spouse was characterized to determine if genital infections mitigated the severe genetic bottleneck observed in a majority of epidemiologically linked heterosexual HIV-1 transmission events. In nearly 50% (3/7) of individuals infected by someone other than their spouse, multiple genetic variants from a single individual established infection. A statistically significant association was observed between infection by multiple genetic variants and an inflammatory genital infection in the newly infected individual. Thus, in the vast majority of HIV-1 transmission events in cohabiting heterosexual couples, a single genetic variant establishes infection. Nevertheless, this severe genetic bottleneck can be mitigated by the presence of inflammatory genital infections in the at risk partner, suggesting that this restriction on genetic diversity is imposed in large part by the mucosal barrier

Cross-Sectional Detection of Acute HIV Infection: Timing of Transmission, Inflammation and Antiretroviral Therapy

BACKGROUND: Acute HIV infection (AHI) is a critical phase of infection when irreparable damage to the immune system occurs and subjects are very infectious. We studied subjects with AHI prospectively to develop better treatment and public health interventions. METHODS: Cross-sectional screening was employed to detect HIV RNA positive, antibody negative subjects. Date of HIV acquisition was estimated from clinical history and correlated with sequence diversity assessed by single genome amplification (SGA). Twenty-two cytokines/chemokines were measured from enrollment through week 24. RESULTS: Thirty-seven AHI subjects were studied. In 7 participants with limited exposure windows, the median exposure to HIV occurred 14 days before symptom onset. Lack of viral sequence diversification confirmed the short duration of infection. Transmission dates estimated by SGA/sequencing using molecular clock models correlated with transmission dates estimated by symptom onset in individuals infected with single HIV variants (mean of 28 versus 33 days). Only 10 of 22 cytokines/chemokines were significantly elevated among AHI participants at enrollment compared to uninfected controls, and only 4 participants remained seronegative at enrollment. DISCUSSION: The results emphasize the difficulty in recruiting subjects early in AHI. Viral sequence diversity proved accurate in estimating time of infection. Regardless of aggressive screening, peak viremia and inflammation occurred before enrollment and potential intervention. Given the personal and public health importance, improved AHI detection is urgently needed

Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution.

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists

Psychosocial interventions for supporting women to stop smoking in pregnancy

Background: Tobacco smoking remains one of the few preventable factors associated with complications in pregnancy, and has serious long-term implications for women and babies. Smoking in pregnancy is decreasing in high-income countries, but is strongly associated with poverty and is increasing in low- to middle-income countries. Objectives: To assess the effects of smoking cessation interventions during pregnancy on smoking behaviour and perinatal health outcomes. Search methods: In this sixth update, we searched the Cochrane Pregnancy and Childbirth Group's Trials Register (13 November 2015), checked reference lists of retrieved studies and contacted trial authors. Selection criteria: Randomised controlled trials, cluster-randomised trials, and quasi-randomised controlled trials of psychosocial smoking cessation interventions during pregnancy. Data collection and analysis: Two review authors independently assessed trials for inclusion and trial quality, and extracted data. Direct comparisons were conducted in RevMan, with meta-regression conducted in STATA 14. Main results: The overall quality of evidence was moderate to high, with reductions in confidence due to imprecision and heterogeneity for some outcomes. One hundred and two trials with 120 intervention arms (studies) were included, with 88 trials (involving over 28,000 women) providing data on smoking abstinence in late pregnancy. Interventions were categorised as counselling, health education, feedback, incentives, social support, exercise and dissemination. In separate comparisons, there is high-quality evidence that counselling increased smoking cessation in late pregnancy compared with usual care (30 studies; average risk ratio (RR) 1.44, 95% confidence interval (CI) 1.19 to 1.73) and less intensive interventions (18 studies; average RR 1.25, 95% CI 1.07 to 1.47). There was uncertainty whether counselling increased the chance of smoking cessation when provided as one component of a broader maternal health intervention or comparing one type of counselling with another. In studies comparing counselling and usual care (largest comparison), it was unclear whether interventions prevented smoking relapse among women who had stopped smoking spontaneously in early pregnancy. However, a clear effect was seen in smoking abstinence at zero to five months postpartum (11 studies; average RR 1.59, 95% CI 1.26 to 2.01) and 12 to 17 months (two studies, average RR 2.20, 95% CI 1.23 to 3.96), with a borderline effect at six to 11 months (six studies; average RR 1.33, 95% CI 1.00 to 1.77). In other comparisons, the effect was unclear for most secondary outcomes, but sample sizes were small. Evidence suggests a borderline effect of health education compared with usual care (five studies; average RR 1.59, 95% CI 0.99 to 2.55), but the quality was downgraded to moderate as the effect was unclear when compared with less intensive interventions (four studies; average RR 1.20, 95% CI 0.85 to 1.70), alternative interventions (one study; RR 1.88, 95% CI 0.19 to 18.60), or when smoking cessation health education was provided as one component of a broader maternal health intervention. There was evidence feedback increased smoking cessation when compared with usual care and provided in conjunction with other strategies, such as counselling (average RR 4.39, 95% CI 1.89 to 10.21), but the confidence in the quality of evidence was downgraded to moderate as this was based on only two studies and the effect was uncertain when feedback was compared to less intensive interventions (three studies; average RR 1.29, 95% CI 0.75 to 2.20). High-quality evidence suggests incentive-based interventions are effective when compared with an alternative (non-contingent incentive) intervention (four studies; RR 2.36, 95% CI 1.36 to 4.09). However pooled effects were not calculable for comparisons with usual care or less intensive interventions (substantial heterogeneity, I2 = 93%). High-quality evidence suggests the effect is unclear in social support interventions provided by peers (six studies; average RR 1.42, 95% CI 0.98 to 2.07), in a single trial of support provided by partners, or when social support for smoking cessation was provided as part of a broader intervention to improve maternal health. The effect was unclear in single interventions of exercise compared to usual care (RR 1.20, 95% CI 0.72 to 2.01) and dissemination of counselling (RR 1.63, 95% CI 0.62 to 4.32). Importantly, high-quality evidence from pooled results demonstrated that women who received psychosocial interventions had a 17% reduction in infants born with low birthweight, a significantly higher mean birthweight (mean difference (MD) 55.60 g, 95% CI 29.82 to 81.38 g higher) and a 22% reduction in neonatal intensive care admissions. However the difference in preterm births and stillbirths was unclear. There did not appear to be adverse psychological effects from the interventions. The intensity of support women received in both the intervention and comparison groups has increased over time, with higher-intensity interventions more likely to have higher-intensity comparisons, potentially explaining why no clear differences were seen with increasing intervention intensity in meta-regression analyses. Among meta-regression analyses: studies classified as having 'unclear' implementation and unequal baseline characteristics were less effective than other studies. There was no clear difference between trials implemented by researchers (efficacy studies), and those implemented by routine pregnancy staff (effectiveness studies), however there was uncertainty in the effectiveness of counselling in four dissemination trials where the focus on the intervention was at an organisational level. The pooled effects were similar in interventions provided for women classified as having predominantly low socio-economic status, compared to other women. The effect was significant in interventions among women from ethnic minority groups; however not among indigenous women. There were similar effect sizes in trials with biochemically validated smoking abstinence and those with self-reported abstinence. It was unclear whether incorporating use of self-help manuals or telephone support increased the effectiveness of interventions. Authors' conclusions: Psychosocial interventions to support women to stop smoking in pregnancy can increase the proportion of women who stop smoking in late pregnancy and the proportion of infants born low birthweight. Counselling, feedback and incentives appear to be effective, however the characteristics and context of the interventions should be carefully considered. The effect of health education and social support is less clear. New trials have been published during the preparation of this review and will be included in the next update