AimsThe aim of this guide is to provide practical help for ecologists who analyze data from biodiversity–ecosystem functioning experiments. Our approach differs from others in the use of least squares-based linear models (LMs) together with restricted maximum likelihood-based mixed models (MMs) for the analysis of hierarchical data. An original data set containing diameter and height of young trees grown in monocultures, 2- or 4-species mixtures under ambient light or shade is used as an example.MethodsStarting with a simple LM, basic features of model fitting and the subsequent analysis of variance (ANOVA) for significance tests are summarized. From this, more complex models are developed. We use the statistical software R for model fitting and to demonstrate similarities and complementarities between LMs and MMs. The formation of contrasts and the use of error (LMs) or random-effects (MMs) terms to account for hierarchical data structure in ANOVAs are explained.Important FindingsData from biodiversity experiments can be analyzed at the level of entire plant communities (plots) and plant individuals. The basic explanatory term is species composition, which can be divided into contrasts in many ways depending on specific biological hypotheses. Typically, these contrasts code for aspects of species richness or the presence of particular species. For significance tests in ANOVAs, contrast terms generally are compared with remaining variation of the explanatory terms from which they have been ‘carved out’. Once a final model has been selected, parameters (e.g. means or slopes for fixed-effects terms and variance components for error or random-effects terms) can be estimated to indicate the direction and size of effects.
BACKGROUND: Whether habitual coffee consumption interacts with the genetic predisposition to obesity in relation to body mass index (BMI) and obesity is unknown. METHODS: We analyzed the interactions between genetic predisposition and habitual coffee consumption in relation to BMI and obesity risk in 5116 men from the Health Professionals Follow-up Study (HPFS), in 9841 women from the Nurses' Health Study (NHS), and in 5648 women from the Women's Health Initiative (WHI). The genetic risk score was calculated based on 77 BMI-associated loci. Coffee consumption was examined prospectively in relation to BMI. RESULTS: The genetic association with BMI was attenuated among participants with higher consumption of coffee than among those with lower consumption in the HPFS (P interaction = 0.023) and NHS (P interaction = 0.039); similar results were replicated in the WHI (P interaction = 0.044). In the combined data of all cohorts, differences in BMI per increment of 10-risk allele were 1.38 (standard error (SE), 0.28), 1.02 (SE, 0.10), and 0.95 (SE, 0.12) kg/m(2) for coffee consumption of < 1, 1-3 and > 3 cup(s)/day, respectively (P interaction < 0.001). Such interaction was partly due to slightly higher BMI with higher coffee consumption among participants at lower genetic risk and slightly lower BMI with higher coffee consumption among those at higher genetic risk. Each increment of 10-risk allele was associated with 78% (95% confidence interval (CI), 59-99%), 48% (95% CI, 36-62%), and 43% (95% CI, 28-59%) increased risk for obesity across these subgroups of coffee consumption (P interaction = 0.008). From another perspective, differences in BMI per increment of 1 cup/day coffee consumption were 0.02 (SE, 0.09), -0.02 (SE, 0.04), and -0.14 (SE, 0.04) kg/m(2) across tertiles of the genetic risk score. CONCLUSIONS: Higher coffee consumption might attenuate the genetic associations with BMI and obesity risk, and individuals with greater genetic predisposition to obesity appeared to have lower BMI associated with higher coffee consumption.
Naturally occurring nucleos(t)ide analogue resistance (NUCr) substitution frequencies in the reverse transcriptase (RT) of the hepatitis B virus (HBV) were studied extensively after the clinical approval of nucleos(t)ide analogues (NUCs; year of approval 1998). We aimed to study NUCr substitutions in HBV RT sequences obtained before 1998 and better understand the evolution of RT sequences without NUC pressures. Our strategy was to retrieve HBV sequences from GenBank deposited before 1998. The initial search used the keywords "hepatitis B virus" or "HBV" and 1139 sequences were found. Data analyses included information extraction: sequence quality control and amino acid substitution analysis on 8 primary NUCr and 3 secondary substitution codons. Three hundred and ninety-four RT-containing sequences of 8 genotypes from 25 countries in 4 continents were selected. Twenty-seven (6.9%) sequences were found to harbor substitutions at NUCr-related codons. Secondary substitutions (rtL80V and rtV173G/A/L) occurred more frequently than primary NUCr substitutions (rtI169L; rtA181G; T184A/S; rtS202T/R; rtM204L and rtM250K). Typical amino acid substitutions associated with NUCr were of rtL80V, rtV173L and rtT184A/S. We confirm the presence of naturally occurring typical HBV NUCr substitutions with very low frequencies, and secondary substitutions are more likely to occur than primary NUCr substitutions without the selective pressure of NUCs.
Keywords: hepatitis B virus; naturally occurring; nucleos(t)ides analogue resistance; pre-existing; reverse transcriptase; substitution.
Ferrihydrite, as one of the most common naturally occurring iron oxides, can sequester toxic metals through co-precipitation. In this study, using grazing-incidence small-angle X-ray scattering, the heterogeneous precipitation of pure, Ni-, and Cd-bearing ferrihydrite on quartz was quantified in 0.1 mM Fe3+ solutions in the absence and presence of 1 mM Ni2+ or Cd2+ (pH 3.8 ± 0.1). Under acidic condition, the limited hydrolysis of metal ions resulted in their small amounts of incorporation in ferrihydrite lattices (<0.1%), several orders of magnitude lower than those reported at neutral and alkaline pH conditions. The presence of Ni2+ or Cd2+ did not significantly affect the surface charges of either ferrihydrite pre-nucleation clusters (PNCs) or quartz surfaces. Therefore, with similar electrostatic interactions between PNCs and quartz, similar initial heterogeneous precipitation rates of pure and Ni- and Cd-bearing ferrihydrite on quartz were observed. Later on, continuous heterogeneous nucleation and growth of ferrihydrite nanoparticles resulted in their increased polydispersity, and the size-dependent solubility of ferrihydrite nanoparticles caused the Ostwald ripening process. The presence of Ni and Cd was found to retard the recrystallization of ferrihydrite, probably as a result of their structural incorporation, which could inhibit the dissolution of ferrihydrite. This study provided new kinetic and mechanistic insights for understanding the effects of metal ions on the heterogeneous precipitation and recrystallization processes of ferrihydrite nanoparticles on mineral surfaces, which can better predict the fate and transport of heavy metals.
The interaction between photochemical oxidants and aerosol particles has been examined in previous atmospheric pollution studies. The heterogeneous reaction can affect the concentration of gases and free radicals, as well as the morphology and properties of particles. In this report, the interaction between the photochemical oxidant peroxyacetyl nitrate (PAN) and soot particles was investigated using a flow tube system. We used real-time online monitoring equipment to track changes in PAN concentrations. Substances on the soot surface were detected using ion chromatography (IC), x-ray photoelectron spectroscopy (XPS), and other surface analysis methods. At 295 K, the upper and lower limits of the initial uptake coefficients were 1.28 × 10−5 and 9.16 × 10−9, respectively. The heterogeneous reaction of PAN on soot was a first-order reaction to PAN under both dry and wet conditions. The products formed on soot included CH3COO−, HCOO−, NO2−, and NO3−. With an increase in relative humidity, the production of all species decreased and the relative amounts changed.
Heterogeneous reactions of mineral dust aerosol with trace gases in the atmosphere could directly and indirectly affect tropospheric oxidation capacity, in addition to aerosol composition and physicochemical properties. In this article we provide a comprehensive and critical review of laboratory studies of heterogeneous uptake of OH, NO3, O-3, and their directly related species as well (including HO2, H2O2, HCHO, HONO, and N2O5) by mineral dust particles. The atmospheric importance of heterogeneous uptake as sinks for these species is assessed (i) by comparing their lifetimes with respect to heterogeneous reactions with mineral dust to lifetimes with respect to other major loss processes and (ii) by discussing relevant field and modeling studies. We have also outlined major open questions and challenges in laboratory studies of heterogeneous uptake by mineral dust and discussed research strategies to address them in order to better understand the effects of heterogeneous reactions with mineral dust on tropospheric oxidation capacity.
High-efficiency organic inorganic hybrid perovskite solar cells have experienced rapid development and attracted significant attention in recent years. Crystal growth as an important factor would significantly influence the quality of perovskite films and ultimately the device performance, which usually requires thermal annealing for 10 min or more. Herein, we demonstrate a new method to get high crystallization of perovskite film by electric current annealing for just 5 s. In contrast to conventional thermal annealing, a homogeneous perovskite film was formed with larger grains and fewer pinholes, leading to a better performance of the device with higher open-circtlit voltage and fill factor. An average power conversion efficiency of 17.02% with electric current annealing was obtained, which is higher than that of devices with a conventional thermal annealing process (16.05%). This facile electric current annealing process with legs energy loss and time consumption shows great potential in the industrial mass production of photovoltaic devices.
Development of high-peak power laser system encounters difficulties in producing the pulses with high temporal contrast. To increase the pulse temporal contrast ratio, a nonlinear filter based on crossed-polarized wave (XPW) generation is proposed. The XPW generation relies on a third-order nonlinear process occurring in a nonlinear medium, such as barium fluorite (BaF2) crystal. The XPW process is quite straightforward:a linearly polarized laser pulse is focused on BaF2 crystal positioned between two orthogonally polarizers, high power main pulses due to nonlinear polarization rotation can pass through the second polarizer, while low power unconverted pre-and post-pulses are filtered by the second polarizer. With the XPW technique, pulse contrast can be enhanced by several orders of magnitude. Furthermore, XPW spectrum can be broaden by a factor with respect to the initial spectrum. This efficient pulse cleaner presents many advantages and has proved to be a simple and reliable pulse filter operating in a double chirped pulse amplification system.Most of previous XPW experiments utilize short focal systems or work off focus due to an intensity limit in the crystal (BaF2). These drawbacks result in a lower conversion efficiency (lower than 10%) when using a single crystal. Dual crystal setup is capable of achieving efficiency more than 20%, yet the configuration restricts the crystal separation to a millimeter level. The use of long focus lens in the XPW device is capable of reaching higher efficiency, with BaF2 crystal positioned in the focal plane. Hence for milljoule pulses, the setup distance increases to tens of meters, resulting in a complicated system and cumbersome configuration.Considering these limitations, a compact, highly efficient and stable XPW generation using dual-lens system suitable for non-vacuum transmission is presented. The measured nonlinear accumulated phase shows little deterioration of pulse quality. With a compact dual lens system, we realize an excellent XPW conversion of above 22% (internal efficiency of 30%) with using double BaF2 crystals, while a femtosecond laser pulse can experience a spectrum broadening up to a factor of 1.78. The dual-lens configuration overcomes the crystal separation limit, and conversion efficiency exceeds 20% for a crystal separation from 13 cm to 22 cm, which is conducible to flexibility and robustness. The stability for the setup to generate shorter pulses with very high contrast or compensate for spectral gain narrowing in the preamplifier is ensured due to the dual-lens focusing system.
Molecular chlorine (Cl-2) and nitryl chloride (GINO(2)) concentrations were measured using chemical ionization mass spectrometry at a rural site over the North China Plain during June 2014. High levels of daytime Cl-2 up to similar to 450 pptv were observed. The average diurnal Cl-2 mixing ratios showed a maximum around noon at pptv. ClNO2 exhibited a strong diurnal variation with early morning maxima reaching ppbv levels and afternoon minima sustained above 60 pptv. A moderate correlation (R-2 = 0.31) between Cl-2 and sulfur dioxide was observed, perhaps indicating a role for power plant emissions in the generation of the observed chlorine. We also observed a strong correlation (R-2 = 0.83) between daytime (10:00-20:00) Cl-2 and ClNO2, which implies that both of them were formed from a similar mechanism. In addition, Cl-2 production is likely associated with a photochemical mechanism as Cl-2 concentrations varied with ozone (O-3) levels. The impact of Cl-2 and ClNO2 as Cl atom sources is investigated using a photochemical box model. We estimated that the produced Cl atoms oxidized slightly more alkanes than OH radicals and enhanced the daily concentrations of peroxy radicals by 15% and the O-3 production rate by 19%.
The heterogeneous hydrolysis of dinitrogen pentoxide (N2O5) is important to understanding the formation of particulate nitrate (pNO(3)(-)). Measurements of N2O5 in the surface layer taken at an urban site in Beijing are presented here. N2O5 was observed with large day-to-day variability. High N2O5 concentrations were determined during pollution episodes with the co-presence of large aerosol loads. The maximum value was 1.3 ppbv (5 s average), associated with an air mass characterized by a high level of O-3. N2O5 uptake coefficients were estimated to be in the range of 0.025-0.072 using the steady-state lifetime method. As a consequence, the nocturnal pNO(3)(-) formation potential by N2O5 heterogeneous uptake was calculated to be 24-85 mu g m(-3) per night and, on average, 57 mu g m(-3) during days with pollution. This was comparable to or even higher than that formed by the partitioning of HNO3. The results highlight that N2O5 heterogeneous hydrolysis is vital in pNO(3)(-) formation in Beijing.
The heterogeneous hydrolysis of dinitrogen pentoxide (N2O5) is important to understanding the formation of particulate nitrate (pNO(3)(-)). Measurements of N2O5 in the surface layer taken at an urban site in Beijing are presented here. N2O5 was observed with large day-to-day variability. High N2O5 concentrations were determined during pollution episodes with the co-presence of large aerosol loads. The maximum value was 1.3 ppbv (5 s average), associated with an air mass characterized by a high level of O-3. N2O5 uptake coefficients were estimated to be in the range of 0.025-0.072 using the steady-state lifetime method. As a consequence, the nocturnal pNO(3)(-) formation potential by N2O5 heterogeneous uptake was calculated to be 24-85 mu g m(-3) per night and, on average, 57 mu g m(-3) during days with pollution. This was comparable to or even higher than that formed by the partitioning of HNO3. The results highlight that N2O5 heterogeneous hydrolysis is vital in pNO(3)(-) formation in Beijing.
The heterogeneous hydrolysis of dinitrogen pentoxide (N2O5) is important to understanding the formation of particulate nitrate (pNO(3)(-)). Measurements of N2O5 in the surface layer taken at an urban site in Beijing are presented here. N2O5 was observed with large day-to-day variability. High N2O5 concentrations were determined during pollution episodes with the co-presence of large aerosol loads. The maximum value was 1.3 ppbv (5 s average), associated with an air mass characterized by a high level of O-3. N2O5 uptake coefficients were estimated to be in the range of 0.025-0.072 using the steady-state lifetime method. As a consequence, the nocturnal pNO(3)(-) formation potential by N2O5 heterogeneous uptake was calculated to be 24-85 mu g m(-3) per night and, on average, 57 mu g m(-3) during days with pollution. This was comparable to or even higher than that formed by the partitioning of HNO3. The results highlight that N2O5 heterogeneous hydrolysis is vital in pNO(3)(-) formation in Beijing.