Simulation‐based evaluation of the linear‐mixed model in the presence of an increasing proportion of singletons

Data in medical sciences often have a hierarchical structure with lower level units (e.g. children) nested in higher level units (e.g. departments). Several specific but frequently studied settings, mainly in longitudinal and family research, involve a large number of units that tend to be quite small, with units containing only one element referred to as singletons. Regardless of sparseness, hierarchical data should be analyzed with appropriate methodology such as, for example linear‐mixed models. Using a simulation study, based on the structure of a data example on Ceftriaxone consumption in hospitalized children, we assess the impact of an increasing proportion of singletons (0–95%), in data with a low, medium, or high intracluster correlation, on the stability of linear‐mixed models parameter estimates, confidence interval coverage and F test performance. Some techniques that are frequently used in the presence of singletons include ignoring clustering, dropping the singletons from the analysis and grouping the singletons into an artificial unit. We show that both the fixed and random effects estimates and their standard errors are stable in the presence of an increasing proportion of singletons. We demonstrate that ignoring clustering and dropping singletons should be avoided as they come with biased standard error estimates. Grouping the singletons into an artificial unit might be considered, although the linear‐mixed model performs better even when the proportion of singletons is high. We conclude that the linear‐mixed model is stable in the presence of singletons when both lower‐ and higher level sample sizes are fixed. In this setting, the use of remedial measures, such as ignoring clustering and grouping or removing singletons, should be dissuaded.     

Individual and interactive effects of warming and nitrogen supply on CO2 fluxes and carbon allocation in subarctic grassland

Climate warming has been suggested to impact high latitude grasslands severely, potentially causing considerable carbon (C) losses from soil. Warming can also stimulate nitrogen (N) turnover, but it is largely unclear whether and how altered N availability impacts belowground C dynamics. Even less is known about the individual and interactive effects of warming and N availability on the fate of recently photosynthesized C in soil. On a 10-year geothermal warming gradient in Iceland, we studied the effects of soil warming and N addition on CO₂ fluxes and the fate of recently photosynthesized C through CO₂ flux measurements and a ¹³CO₂ pulse-labeling experiment. Under warming, ecosystem respiration exceeded maximum gross primary productivity, causing increased net CO₂ emissions. N addition treatments revealed that, surprisingly, the plants in the warmed soil were N limited, which constrained primary productivity and decreased recently assimilated C in shoots and roots. In soil, microbes were increasingly C limited under warming and increased microbial uptake of recent C. Soil respiration was increased by warming and was fueled by increased belowground inputs and turnover of recently photosynthesized C. Our findings suggest that a decade of warming seemed to have induced a N limitation in plants and a C limitation by soil microbes. This caused a decrease in net ecosystem CO₂ uptake and accelerated the respiratory release of photosynthesized C, which decreased the C sequestration potential of the grassland. Our study highlights the importance of belowground C allocation and C-N interactions in the C dynamics of subarctic ecosystems in a warmer world.     

Restriction maps of human adenovirus types 2, 5, and 3 for BstEII, MluI, NdeI, NruI and SfiI endonucleases

The positions of cleavage sites for BstEII, MluI, NdeI, NruI and SfiI restriction endonucleases in the DNA from human adenovirus (Ad) serotypes 2, 5 and 3 were determined. In addition, the sites of cleavage for BglII in Ad3 DNA were located. All these enzymes possess a narrow specificity and generated a small number of discrete DNA fragments. Ad3 DNA was not cleaved by MluI and SfiI. It was the first observation of the absence of cleavage of an adenovirus DNA by a restriction endonuclease.     

Comparative biological activities of the four synthetic (5,6)-dihete isomers

(5,6)-dihydroxy-7,9-trans-11,14-cis-eicosatetraenoic acids [5,6)-DiHETEs) were synthesized and separated into four pure diastereoisomers. They were tested for comparative binding affinities to leukotriene receptors (LTC4, LTD4, LTB4) in guinea pig lung membranes. Only (5S,6R)-DiHETE was recognized by the LTD4 receptor, the other receptors interacted with neither of the four isomers. (5S,6R)-DiHETE also contracted ileum in vitro and this effect was inhibited by the LTD4 receptor antagonists ICI 198,615 and SKF104,353. These data suggest that the bioproduct (5S,6R)-DiHETE generated by enzymatic conversion of LTA4 could have some LTD4-like activity when produced in large concentrations.     

The use of a metabolically structured model in the study of growth, nitrification, and denitrification by Thiosphaera pantotropha

Thiosphaera pantotropha is capable of aerobic heterotrophic nitrification and both aerobic and anaerobic denitrification. These phenomena have been studied in acetate-limited aerobic and anaerobic continuous cultures supplied with ammonia and nitrate. The internal reaction rates were defined, based on biochemical knowledge. The observable external conversion rates are related through a linear equation on the basis of the specified internal reaction rates. The linear equation is a Pirt relation extended for microbial systems with multiple electron donors (acetate and ammonia) and electron acceptors (oxygen and nitrate). The coefficients in this equation were estimated from the continuous culture measurements, and are composed of parameters involved in ATP production and consumption by the microorganism. It is shown that with realistic values for these parameters, the metabolically structured model describes the aerobic as well as the anaerobic experiments.     

Accounting for apparent deviations between calorimetric and van't Hoff enthalpies

Background

In theory, binding enthalpies directly obtained from calorimetry (such as ITC) and the temperature dependence of the binding free energy (van't Hoff method) should agree. However, previous studies have often found them to be discrepant.

RASSF1A and DOK1 Promoter Methylation Levels in Hepatocellular Carcinoma,Cirrhotic and Non-Cirrhotic Liver,and Correlation with Liver Cancer in Brazilian Patients

Hepatocellular carcinoma (HCC) is the second most common cause of cancer mortality worldwide. Most cases of HCC are associated with cirrhosis related to chronic hepatitis B virus or hepatitis C virus infections. Hypermethylation of promoter regions is the main epigenetic mechanism of gene silencing and has been involved in HCC development. The aim of this study was to determine whether aberrant methylation of RASSF1A and DOK1 gene promoters is associated with the progression of liver disease in Brazilian patients. Methylation levels were measured by pyrosequencing in 41 (20 HCC, 9 cirrhotic, and 12 non-cirrhotic) liver tissue samples. Mean rates of methylation in RASSF1A and DOK1 were 16.2% and 12.0% in non-cirrhotic, 26.1% and 19.6% in cirrhotic, and 59.1% and 56.0% in HCC tissues, respectively, showing a gradual increase according to the progression of the disease, with significantly higher levels in tumor tissues. In addition, hypermethylation of RASSF1A and DOK1 was found in the vast majority (88%) of the HCC cases. Interestingly, DOK1 methylation levels in HCC samples were significantly higher in the group of younger (<40 years) patients, and higher in moderately differentiated than in poorly differentiated tumors (p < 0.05). Our results reinforce the hypothesis that hypermethylation of RASSF1A and DOK1 contributes to hepatocarcinogenesis and is associated to clinicopathological characteristics. RASSF1A and DOK1 promoter hypermethylation may be a valuable biomarker for early diagnosis of HCC and a potential molecular target for epigenetic-based therapy.     

A note on the apparent absence of azotobacter in soils

Summary It is shown that soils which fail to give Azotobacter growth when inoculated in the original elective medium may still contain viable Azotobacter cells. These develop into normal cultures when 0.00005% Na₂MoO₄ is added to the liquid medium.This phenomenon is explained as a result of the low molybdenum content of the soils used.In view of the possible influence of molybdenum on soil fertility the soil plaque method was tried successfully for the demonstration of a molybdenum deficiency. of soil samples.     

Cirolana songkhla,a new species of brackish-water cirolanid isopod (Crustacea,Isopoda, Cirolanidae) from the lower Gulf of Thailand

Cirolana songkhla sp. n. was collected from brackish-water habitats including lagoons and estuaries in the coastal zone of the lower Gulf of Thailand. C. songkhla sp. n. is described and fully illustrated; C. songkhla sp. n. can be recognized by the presence of abundant chromatophores dorsally, lack of ornamentation on the posterior pereonites, pleonites and pleotelson, the number of robust setae on the uropodal and pleotelson margins (uropod exopod lateral margin with 12–14 RS, mesial margin with 5–8 RS; endopod lateral margin with 8–10 RS, mesial margin with 11–13 RS; pleotelson with 12–15 RS) and lack of setae on the endopods of pleopods 3–5. A dichotomous key of brackish Cirolana species in Thailand is given.