Bioinformatics is a fast-growing interdisciplinary field in which the demand for quality education exceeds the supply, especially in developing regions and countries. A massive open online course (MOOC) is a new model for education that delivers videotaped lectures and other course materials over the Internet for all interested persons around the globe to learn for free. Here we present our MOOC “Bioinformatics: Introduction and Methods,” which is the second bioinformatics MOOC in the world and one of the first batch of seven MOOCs from China. In the first two runs of this bilingual MOOC, more than 30,000 students with diverse backgrounds registered from 110 countries and regions. In this manuscript, we present the content design of the MOOC, the demographic profiles and learning patterns of the students, the requirement for English support, and feedback from on-campus students. We offer a few suggestions to other scientists who may be interested in creating a MOOC. We also remember the S* course, a successful open online bioinformatics course that ran from 2001 to 2007, long before the current wave of MOOCs. We believe that MOOC education has great potential to enhance global bioinformatics education.
Ambient volatile organic compounds (VOCs) were measured intensively using an online gas chromatography–mass spectrometry/flame ionization detector (GC–MS/FID) at Ziyang in the Chengdu–Chongqing Region (CCR) from 6 December 2012 to 4 January 2013. Alkanes contributed the most (59%) to mixing ratios of measured non-methane hydrocarbons (NMHCs), while aromatics contributed the least (7%). Methanol was the most abundant oxygenated VOC (OVOC), contributing 42% to the total amount of OVOCs. Significantly elevated VOC levels occurred during three pollution events, but the chemical composition of VOCs did not differ between polluted and clean days. The OH loss rates of VOCs were calculated to estimate their chemical reactivity. Alkenes played a predominant role in VOC reactivity, among which ethylene and propene were the largest contributors; the contributions of formaldehyde and acetaldehyde were also considerable. Biomass burning had a significant influence on ambient VOCs during our study. We chose acetonitrile as a tracer and used enhancement ratio to estimate the contribution of biomass burning to ambient VOCs. Biomass burning contributed 9.4%–36.8% to the mixing ratios of selected VOC species, and contributed most (>30% each) to aromatics, formaldehyde, and acetaldehyde.
Black carbon (BC) mass emission factors (EFBC; g BC (kg fuel)(-1)) from a variety of ocean-going vessels have been determined from measurements of BC and carbon dioxide (CO2) concentrations in ship plumes intercepted by the R/V Atlantis during the 2010 California Nexus (CalNex) campaign. The ships encountered were all operating within 24 nautical miles of the California coast and were utilizing relatively low sulphur fuels (average fuel sulphur content of 0.4%, 0.09% and 0.03% for vessels operating slow-speed, medium-speed and high-speed diesel engines, respectively). Black carbon concentrations within the plumes, from which EFBC values are determined, were measured using four independent instruments: a photoacoustic spectrometer and a particle soot absorption photometer, which measure light absorption, and a single particle soot photometer and soot particle aerosol mass spectrometer, which measure the mass concentration of refractory BC directly. These measurements have been used to assess the level of agreement between these different techniques for the determination of BC emission factors from ship plumes. Also, these measurements greatly expand upon the number of individual ships for which BC emission factors have been determined during real-world operation. The measured EFBC's have been divided into vessel type categories and engine type categories, from which averages have been determined. The geometric average EFBC (excluding outliers) determined from over 71 vessels and 135 plumes encountered was 0.31 +/- 0.31 gBC (kg fuel)(-1), where the standard deviation represents the variability between individual vessels. The most frequent engine type encountered was the slow-speed diesel (SSD), and the most frequent SSD vessel type was the cargo ship sub-category. Average and median EFBC values from the SSD category are compared with previous observations from the Texas Air Quality Study (TexAQS) in 2006, during which the ships encountered were predominately operating on high-sulphur fuels (average fuel sulphur content of 1.6 %). There is a statistically significant difference between the EFBC values from CalNex and TexAQS for SSD vessels and for the cargo and tanker ship types within this engine category. The CalNex EFBC values are lower than those from TexAQS, suggesting that operation on lower sulphur fuels is associated with smaller EFBC values.
Previous studies have investigated the associations between exposure to ambient air pollution and biomarkers of physiological pathways, yet little has been done on the comparison across biomarkers of different pathways to establish the temporal pattern of biological response. In the current study, we aim to compare the relative temporal patterns in responses of candidate pathways to different pollutants. Four biomarkers of pulmonary inflammation and oxidative stress, five biomarkers of systemic inflammation and oxidative stress, ten parameters of autonomic function, and three biomarkers of hemostasis were repeatedly measured in 125 young adults, along with daily concentrations of ambient CO, PM2.5, NO2, SO2, EC, OC, and sulfate, before, during, and after the Beijing Olympics. We used a two-stage modeling approach, including Stage I models to estimate the association between each biomarker and pollutant over each of 7 lags, and Stage II mixed-effect models to describe temporal patterns in the associations when grouping the biomarkers into the four physiological pathways. Our results show that candidate pathway groupings of biomarkers explained a significant amount of variation in the associations for each pollutant, and the temporal patterns of the biomarker-pollutant-lag associations varied across candidate pathways (p<0.0001) and were not linear (from lag 0 to lag 3: p = 0.0629, from lag 3 to lag 6: p = 0.0005). These findings suggest that, among this healthy young adult population, the pulmonary inflammation and oxidative stress pathway is the first to respond to ambient air pollution exposure (within 24 hours) and the hemostasis pathway responds gradually over a 2-3 day period. The initial pulmonary response may contribute to the more gradual systemic changes that likely ultimately involve the cardiovascular system.
Emissions factors (EFs) for gas and sub-micron particle-phase species were measured in intercepted plumes as a function of vessel speed from an underway research vessel, the NOAA ship Miller Freeman, operating a medium-speed diesel engine on low-sulfur marine gas oil (fuel sulfur content similar to 0.1% by weight). The low-sulfur fuel in use conforms to the MARPOL fuel sulfur limit within emission control areas set to take effect in 2015 and to California-specific limits set to take effect in 2014. For many of the particle-phase species, EFs were determined using multiple measurement methodologies, allowing for an assessment of how well EFs from different techniques agree. The total sub-micron PM (PM1) was dominated by particulate black carbon (BC) and particulate organic matter (POM), with an average POM/BC ratio of 1.3. Consideration of the POM/BC ratios observed here with literature studies suggests that laboratory and in-stack measurement methods may overestimate primary POM EFs relative to those observed in emitted plumes. Comparison of four different methods for black carbon measurement indicates that careful attention must be paid to instrument limitations and biases when assessing EFBC. Particulate sulfate (SO42-) EFs were extremely small and the particles emitted by Miller Freeman were inefficient as cloud condensation nuclei (CCN), even at high super saturations, consistent with the use of very low-sulfur fuel and the overall small emitted particle sizes. All measurement methodologies consistently demonstrate that the measured EFs (fuel mass basis) for PM1 mass, BC and POM decreased as the ship slowed. Particle number EFs were approximately constant across the speed change, with a shift towards smaller particles being emitted at slower speeds. Emissions factors for gas-phase CO and formaldehyde (HCHO) both increased as the vessel slowed, while EFs for NOx decreased and SO2 EFs were approximately constant.
To track the chemical characteristics and formation mechanism of biomass burning pollution, the hourly variations of meteorological factors and pollutant concentrations during a heavy pollution on 18–21 May, 2012 in Chengdu are presented in this study. The episode was the heaviest and most long-lasting pollution event in the historical record of Chengdu caused by a combination of stagnant dispersion conditions and enhanced PM2.5 emission from intensive biomass burning, with peak values surpassing 500 μg m− 3. The event was characterized by three nighttime peaks, relating to the burning practice and decreased boundary layer height at night. The prevailing northeasterly wind during nighttime preferentially brought more pollutants to the urban regions from northern suburbs of Chengdu, where dense fire spots were observed. Due to the obstruction of hilly topography and weak wind speed, minor regional features were reflected from the PM10 variations in nearby cities, whereas the long-distance transport of the plume impacted extensive regions in northern and eastern China. Carbon monoxide (CO) concentrations increased by more than 200%, while exceptionally high PM2.5 levels of 190.1 and 268.4 μg m− 3 on 17 May and 18 May, were observed and showed high correlation with CO (r = 0.75). The relative contribution of biomass burning smoke to organic carbon was estimated from OC/EC ratios (organic carbon/elemental carbon) and elevated to 81.3% during the episode, indicating a significant impact on urban aerosol levels. The occurrence of high PM2.5/PM10 ratios (> 0.80) and K+/EC ratios (> 1.0), along with the increased carbonaceous concentrations and their fraction in PM2.5 (> 40%) and high OC/EC ratios (about 8), could be used as immediate indicators for biomass burning pollution in cities. In addition, the heavy pollution involved a mixture of anthropogenic sources, reflected from the high SOR and NOR values and increases in the EFs (enrichment factors) of Mo, Zn, Cd, and Pb.
The Sichuan Basin is a low visibility area in southwest China, where the hilly and basin topography, plus humid and stagnant weather, lead to unique pollution patterns. To identify the characteristics and sources of carbonaceous aerosols, one-year record of 24-h PM2.5samples were analyzed for organic carbon (OC) and elemental carbon (EC) content following the thermal/optical transmission protocol at three cities (Chengdu (CD), Neijiang (NJ), and Chongqing (CQ)) in the region during May 2012 to April 2013. The annual average concentrations were 19.0 ± 13.3 μg OC m−3 and 4.6 ± 2.6 μg EC m−3 in CD, 18.3 ± 8.4 μg OC m−3 and 4.1 ± 1.8 μg EC m−3 in NJ, and 15.2 ± 8.4 μg OC m−3 and 4.0 ± 1.6 μg EC m−3 in CQ, respectively. Organic matter (1.6OC) plus EC contributed about 40% of PM2.5 mass and displayed weak regional uniformity. Relatively high ratios of OC to EC were observed in the region with 4.3 for CD, 4.6 for NJ, and 3.8 for CQ, respectively. OC and EC pollution in the region exhibited interesting season-dependent characteristics with the lowest concentrations and OC/EC ratios in summer, but higher levels in other seasons. Higher OC/EC ratios in spring and autumn resulted from biomass burning, and in winter were from the enhanced secondary organic aerosol formation under favorable conditions. The exceptionally high OC and EC levels in May and October, mostly notable in CD, resulted from the burning of agricultural residues during harvest period. The high K+concentrations and the high Kexcess/EC ratios implied the persistent influence of biomass burning throughout the year. Using a novel technique combing the EC tracer method and potassium mass balance in the aerosols, a K/EC ratio of 1.22 was used to retrieve the OC from biomass burning and the estimated contributions were 30.8%, 28.3%, and 21.9% in CD, NJ, and CQ, respectively, while secondary OC contributions to OC were 26.7%, 24.6%, and 25.7% in CD, NJ, and CQ, respectively.
Field campaigns monitoring the aerosol optical properties and chemical components of PM10 were carried out in Beijing in 2006 summer. The average light extinction coefficient b(ext), dry aerosol scattering coefficient b(sp) and aerosol absorption coefficient b(ap) were 895.0 +/- 820.8 Mm(-1), 364.0 +/- 324.3 Mm(-1) and 57.8 +/- 31.1 Mm(-1), respectively. b(ext), b(sp) and b(ap) had the similar increasing trend during the formation process of haze. Pronounced diurnal cycles were observed for omega(550) (aerosol single scattering albedo at 550 nm), b(sp), b(ap) and b(ext). The dry b(sp) was elevated during the daytime with a maximum mean value of 475.8 Mm(-1) (LST 06:00). b(ext), PM2.5 mass concentration and PM2.5/PM10 ratio increased at night due to continuous emissions of pollutants to the lower nocturnal boundary layer, and decreased during the daytime due to convective mixing. b(ap) increased at night, and decreased during the daytime and reached the minimum (37 Mm(-1)) at LST 16:00. The single scattering albedo reached its maximum (0.87) at LST 11:00. This trend was consistent with the SNA (sulfate, nitrate, and ammonium)/PM10 ratio and was contrary to the BC (black carbon)/PM10 ratio, which demonstrated that secondary pollution largely influenced the scattering ability of aerosols. Ammonium sulfate, ammonium nitrate, organic mass, elemental carbon and coarse mass contributed 26.5%, 15.2%, 21.8%, 16.1% and 20.4% to the total extinction coefficient during clean days, and 44.6%, 22.3%, 13.6%, 10.8% and 8.7% during hazy days. The fractional contributions of ammonium sulfate and ammonium nitrate were significantly higher during the hazy time than those during the clean days. While the fractional contributions of organic mass, elemental carbon and coarse mass were lower during the haze time than those during the clean days.
