Empirical correction of a toy climate model

Improving the accuracy of forecast models for physical systems such as the atmosphere is a crucial ongoing effort. Errors in state estimation for these often highly nonlinear systems has been the primary focus of recent research, but as that error has been successfully diminished, the role of model error in forecast uncertainty has duly increased. The present study is an investigation of a particular empirical correction procedure that is of special interest because it considers the model a "black box", and therefore can be applied widely with little modification. The procedure involves the comparison of short model forecasts with a reference "truth" system during a training period in order to calculate systematic (1) state-independent model bias and (2) state-dependent error patterns. An estimate of the likelihood of the latter error component is computed from the current state at every timestep of model integration. The effectiveness of this technique is explored in two experiments: (1) a perfect model scenario, in which models have the same structure and dynamics as the true system, differing only in parameter values; and (2) a more realistic scenario, in which models are structurally different (in dynamics, dimension, and parameterization) from the target system. In each case, the results suggest that the correction procedure is more effective for reducing error and prolonging forecast usefulness than parameter tuning. However, the cost of this increase in average forecast accuracy is the creation of substantial qualitative differences between the dynamics of the corrected model and the true system. A method to mitigate the structural damage caused by empirical correction and further increase forecast accuracy is presented.Comment: 16 pages, 12 figure

The Mass Distributions of Starless and Protostellar Cores in Gould Belt Clouds

Using data from the SCUBA Legacy Catalogue (850 um) and Spitzer Space Telescope (3.6 - 70 um), we explore dense cores in the Ophiuchus, Taurus, Perseus, Serpens, and Orion molecular clouds. We develop a new method to discriminate submillimeter cores found by SCUBA as starless or protostellar, using point source photometry from Spitzer wide field surveys. First, we identify infrared sources with red colors associated with embedded young stellar objects (YSOs). Second, we compare the positions of these YSO-candidates to our submillimeter cores. With these identifications, we construct new, self-consistent starless and protostellar core mass functions (CMFs) for the five clouds. We find best fit slopes to the high-mass end of the CMFs of -1.26 +/- 0.20, -1.22 +/- 0.06, -0.95 +/- 0.20, and -1.67 +/- 0.72 for Ophiuchus, Taurus, Perseus, and Orion, respectively. Broadly, these slopes are each consistent with the -1.35 power-law slope of the Salpeter IMF at higher masses, but suggest some differences. We examine a variety of trends between these CMF shapes and their parent cloud properties, potentially finding a correlation between the high-mass slope and core temperature. We also find a trend between core mass and effective size, but we are very limited by sensitivity. We make similar comparisons between core mass and size with visual extinction (for A_V >= 3) and find no obvious trends. We also predict the numbers and mass distributions of cores that future surveys with SCUBA-2 may detect in each of these clouds.Comment: 56 pages, 18 figures, fixed typo in Eq 1, results in paper remain unchange

Global distribution and diversity of marine Verrucomicrobia

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of Nature Publishing Group for personal use, not for redistribution. The definitive version was published in The ISME Journal 6 (2012): 1499-1505, doi:10.1038/ismej.2012.3.Verrucomicrobia is a bacterial phylum that is commonly detected in soil but little is known about the distribution and diversity of this phylum in the marine environment. To address this, we analyzed the marine microbial community composition in 506 samples from the International Census of Marine Microbes as well as eleven coastal samples taken from the California Current. These samples from both the water column and sediments covered a wide range of environmental conditions. Verrucomicrobia were present in 98% of the analyzed samples and thus appeared nearly ubiquitous in the ocean. Based on the occurrence of amplified 16S rRNA sequences, Verrucomicrobia constituted on average 2% of the water column and 1.4% of the sediment bacterial communities. The diversity of Verrucomicrobia displayed a biogeography at multiple taxonomic levels and thus, specific lineages appeared to have clear habitat preference. We found that Subdivision 1 and 4 generally dominated marine bacterial communities, whereas Subdivision 2 was confined to low salinity waters. Within the subdivisions, Verrucomicrobia community composition were significantly different in the water column compared to sediment as well as within the water column along gradients of salinity, temperature, nitrate, depth, and overall water column depth. Although we still know little about the ecophysiology of Verrucomicrobia lineages, the ubiquity of this phylum suggests that it may be important for the biogeochemical cycle of carbon in the ocean.We would like to thank the UCI Undergraduate Research Opportunity Program (S.F.), the National Science Foundation (OCE-0928544 and OCE-1046297, A.C.M.) and the Alfred P. Sloan Foundation (S.H., D.M.W., M.S.) for supporting the work

Somatostatin receptor in human hepatocellular carcinomas: Biological, patient and tumor characteristics

Background/Aim: The evidence on the efficacy of somatostatin analogues in the treatment of hepatocellular carcinoma (HCC) in humans is conflicting. A variety of human tumors demonstrate somatostatin receptors. All subtypes bind human somatostatin with high affinity, while somatostatin analogues bind with high affinity to somatostatin receptor subtype 2 (sst2). We investigated the sst2 expression in HCC and examined whether HCCs expressing sst2 are a distinct subgroup. Patients and Methods: Forty-five human HCCs were tested for sst2 expression and biological alterations. The proliferative capacity was determined with Ki67 immunostaining and the DNA ploidy status was measured by fluorescent in situ hybridization with a chromosome 1-specific repetitive DNA probe. Expression of tumor suppressor genes (p16, p53 and Rb1) was measured by immunohistochemistry. Results: sst2 expression was detected in 30 tumors (67%). No correlation existed between sst2 expression and the immunoprofiles of the tumor suppressor genes, aneuploidy, proliferation, age, gender, α-fetoprotein levels, tumor size, tumor grade and underlying liver disease. Conclusion: In 67% of the patients with HCC, sst2 could be detected in the tumor. No clinical, pathological or biological characteristics were specific for sst2-positive tumors. Copyrigh

Thermal Conductivity of Ordered Mesoporous Nanocrystalline Silicon Thin Films Made from Magnesium Reduction of Polymer-Templated Silica

This paper reports the cross-plane thermal conductivity of ordered mesoporous nanocrystalline silicon thin films between 25 and 315 K. The films were produced by evaporation induced self-assembly of mesoporous silica followed by magnesium reduction. The periodic ordering of pores in mesoporous silicon was characterized by X-ray diffraction and direct SEM imaging. The average crystallite size, porosity, and film thickness were about 13 nm, 25-35%, and 140-340 nm, respectively. The pores were arranged in a face-centered cubic lattice. The cross-plane thermal conductivity of the mesoporous silicon thin films was measured using the 3ω method. It was between 3 and 5 orders of magnitude smaller than that of bulk single crystal silicon in the temperature range considered. The effects of temperature, film thickness, and copolymer template on the thermal conductivity were investigated. A model based on kinetic theory was used to accurately predict the measured thermal conductivity for all temperatures. On the one hand, both the measured thermal conductivity and the model predictions showed a temperature dependence of k proportional to T2 at low temperatures, typical of amorphous and strongly disordered materials. On the other hand, at high temperatures the thermal conductivity of mesoporous silicon films reached a maximum, indicating a crystalline-like behavior. These results will be useful in designing mesoporous silicon with desired thermal conductivity by tuning its morphology for various applications

Extensive microbial and functional diversity within the chicken cecal microbiome

Chickens are major source of food and protein worldwide. Feed conversion and the health of chickens relies on the largely unexplored complex microbial community that inhabits the chicken gut, including the ceca. We have carried out deep microbial community profiling of the microbiota in twenty cecal samples via 16S rRNA gene sequences and an in-depth metagenomics analysis of a single cecal microbiota. We recovered 699 phylotypes, over half of which appear to represent previously unknown species. We obtained 648,251 environmental gene tags (EGTs), the majority of which represent new species. These were binned into over two-dozen draft genomes, which included Campylobacter jejuni and Helicobacter pullorum. We found numerous polysaccharide- and oligosaccharide-degrading enzymes encoding within the metagenome, some of which appeared to be part of polysaccharide utilization systems with genetic evidence for the co-ordination of polysaccharide degradation with sugar transport and utilization. The cecal metagenome encodes several fermentation pathways leading to the production of short-chain fatty acids, including some with novel features. We found a dozen uptake hydrogenases encoded in the metagenome and speculate that these provide major hydrogen sinks within this microbial community and might explain the high abundance of several genera within this microbiome, including Campylobacter, Helicobacter and Megamonas

Survival rate in patients with hepatocellular carcinoma: a retrospective analysis of 389 patients

Hepatocellular carcinoma (HCC) is the fifth most common cancer worldwide. However, treatment options are limited and often inefficient. The aim of this study was to determine current survival rates for patients diagnosed with HCC and to identify prognostic factors, which will help in choosing optimal therapies for individual patients. A retrospective analysis of medical records was performed on 389 patients who were identified through the central tumour registry at our institution from 1998 to 2003. Clinical parameters, treatments received and survival curves from time of diagnosis were analysed. Overall median survival was 11 months. Liver cirrhosis was diagnosed in 80.5% of all patients. A total of 170 patients received transarterial chemoembolisation (TACE) and/or percutaneous ethanol injections (PEI) with a median survival rate of 16 months for patients receiving TACE, 11 months for patients receiving PEI and 24 months for patients receiving TACE followed by PEI. Independent negative prognostic parameters for survival were the presence of portal vein thrombosis, advanced liver cirrhosis (Child–Pugh score B or C) and a score of >2. This study will help to estimate survival rates for patients with HCC according to their clinical status at diagnosis and the treatments received

Snapshot of the Eukaryotic Gene Expression in Muskoxen Rumen—A Metatranscriptomic Approach

BACKGROUND: Herbivores rely on digestive tract lignocellulolytic microorganisms, including bacteria, fungi and protozoa, to derive energy and carbon from plant cell wall polysaccharides. Culture independent metagenomic studies have been used to reveal the genetic content of the bacterial species within gut microbiomes. However, the nature of the genes encoded by eukaryotic protozoa and fungi within these environments has not been explored using metagenomic or metatranscriptomic approaches. METHODOLOGY/PRINCIPAL FINDINGS: In this study, a metatranscriptomic approach was used to investigate the functional diversity of the eukaryotic microorganisms within the rumen of muskoxen (Ovibos moschatus), with a focus on plant cell wall degrading enzymes. Polyadenylated RNA (mRNA) was sequenced on the Illumina Genome Analyzer II system and 2.8 gigabases of sequences were obtained and 59129 contigs assembled. Plant cell wall degrading enzyme modules including glycoside hydrolases, carbohydrate esterases and polysaccharide lyases were identified from over 2500 contigs. These included a number of glycoside hydrolase family 6 (GH6), GH48 and swollenin modules, which have rarely been described in previous gut metagenomic studies. CONCLUSIONS/SIGNIFICANCE: The muskoxen rumen metatranscriptome demonstrates a much higher percentage of cellulase enzyme discovery and an 8.7x higher rate of total carbohydrate active enzyme discovery per gigabase of sequence than previous rumen metagenomes. This study provides a snapshot of eukaryotic gene expression in the muskoxen rumen, and identifies a number of candidate genes coding for potentially valuable lignocellulolytic enzymes