An effective reliability-driven technique of allocating tasks on heterogeneous cluster systems

In large-scale heterogeneous cluster computing systems, processor and network failures are inevitable and can have an adverse effect on applications executing on such systems. One way of taking failures into account is to employ a reliable scheduling algorithm. However, most existing scheduling algorithms for precedence constrained tasks in heterogeneous systems only consider scheduling length, and not efficiently satisfy the reliability requirements of task. In recognition of this problem, we build an application reliability analysis model based on Weibull distribution, which can dynamically measure the reliability of task executing on heterogeneous cluster with arbitrary networks architectures. Then, we propose a reliability-driven earliest finish time with duplication scheduling algorithm (REFTD) which incorporates task reliability overhead into scheduling. Furthermore, to improve system reliability, it duplicates task as if task hazard rate is more than threshold \(\theta \) . The comparison study, based on both randomly generated graphs and the graphs of some real applications, shows that our scheduling algorithm can shorten schedule length and improve system reliability significantly.     

Copper uptake and translocation in chicory ( Cichorium intybus L. cv. Grasslands Puna) and tomato (Lycopersicon esculentum Mill. cv. Rondy) plants grown in NFT system. I. Copper uptake and distribution in plants

The uptake and distribution of copper was examined in chicory (Cichorium intybus L. cv. Grasslands Puna) and tomato (Lycopersicon esculentumMill. cv. Rondy) plants grown in a Nutrient Film Technique System (NFT) with addition of 0.05, 5, 10 and 20 mg Cu L^-1. Biomass production of shoots and roots of both chicory and tomato was strongly depressed by Cu concentrations higher than 5 mg Cu L^-1 in the rooting media. Although Cu concentrations in both shoots and roots of both species increased with increasing Cu concentrations in the rooting media, the increase in roots was very much greater than that in shoots, in which the range of concentrations was small. A large proportion of total Cu uptake was retained by roots except when plants were grown in solution Cu concentrations of 0.05 mg Cu L^-1. Copper retention by roots limited Cu translocation to xylem and shoots. Copper adsorption by the root appears to buffer against increases of Cu in the rooting media. A cupric-sensitive electrode used in conjunction with total Cu analysis by graphite furnace atomic absorption spectrophotometry (GFAAS) indicated that more than 99.6% of total Cu in xylem sap was in a complexed form. Large differences between measured and predicted Cu accumulation by shoots of tomato (0.134–0.243 mg Cu plant^-1, 0.660–4.274 mg Cu plant^-1, respectively) and chicory (0.095–0.203 mg Cu plant^-1, 0.626–1.620 mg Cu plant^-1, respectively) suggest that some xylem transported Cu is recirculated to roots via the phloem. This revised version was published online in June 2006 with corrections to the Cover Date.     

Stem cell research in China

In the past 5 years, China has increased its efforts in the field of stem cell research and practice. Basic research mainly focuses on bone marrow and embryonic stem cells. Clinical applications of stem cells in the treatment of acute heart failure, acute liver failure and lower limb ischaemia have been reported by many hospitals. China enacted its 'Ethical Guidelines for Human Embryonic Stem Cell Research' in 2003. At present, China has the most liberal and favourable environments for human embryonic stem cell research.     

Identification of Sarcocystis cymruensis in wild Rattus flavipectus and Rattus norvegicus from Peoples Republic of China and its transmission to rats and cats

Sarcocystis cymruensis was initially identified in skeletal muscles of 22 (11.6%) of 189 wild rats (Rattus spp.) captured in 2008 in Anning and Kunming, Peoples Republic of China. Sarcocyst walls were thin (<1 μm) and smooth. Ultrastructurally, the parasitophorous vacuolar membrane had small, osmiophilic knob-like invaginations covered with numerous vesicle-like invaginations toward the interior of the cyst. Domestic cats (Felis catus) fed sarcocysts shed sporocysts measuring 10.3 (9.8-11.0) × 7.6 (7.2-9.5) μm with a prepatent period of 6 to 8 days. Sarcocysts were infective orally to Norway rats, and oocysts and sporocysts developed in the lamina propria of the small intestine of rats fed sarcocysts. Thus, rats were both intermediate and definitive hosts for S. cymruensis.     

Analysis of a clonal lineage of HIV-1 envelope V2/V3 conformational epitope-specific broadly neutralizing antibodies and their inferred unmutated common ancestors

V2/V3 conformational epitope antibodies that broadly neutralize HIV-1 (PG9 and PG16) have been recently described. Since an elicitation of previously known broadly neutralizing antibodies has proven elusive, the induction of antibodies with such specificity is an important goal for HIV-1 vaccine development. A critical question is which immunogens and vaccine formulations might be used to trigger and drive the development of memory B cell precursors with V2/V3 conformational epitope specificity. In this paper we identified a clonal lineage of four V2/V3 conformational epitope broadly neutralizing antibodies (CH01 to CH04) from an African HIV-1-infected broad neutralizer and inferred their common reverted unmutated ancestor (RUA) antibodies. While conformational epitope antibodies rarely bind recombinant Env monomers, a screen of 32 recombinant envelopes for binding to the CH01 to CH04 antibodies showed monoclonal antibody (MAb) binding to the E.A244 gp120 Env and to chronic Env AE.CM243; MAbs CH01 and CH02 also bound to transmitted/founder Env B.9021. CH01 to CH04 neutralized 38% to 49% of a panel of 91 HIV-1 tier 2 pseudoviruses, while the RUAs neutralized only 16% of HIV-1 isolates. Although the reverted unmutated ancestors showed restricted neutralizing activity, they retained the ability to bind to the E.A244 gp120 HIV-1 envelope with an affinity predicted to trigger B cell development. Thus, E.A244, B.9021, and AE.CM243 Envs are three potential immunogen candidates for studies aimed at defining strategies to induce V2/V3 conformational epitope-specific antibodies.     

Characterization of NocL involved in thiopeptide nocathiacin I biosynthesis: a [4Fe-4S] cluster and the catalysis of a radical S-adenosylmethionine enzyme

The radical S-adenosylmethionine (AdoMet) enzyme superfamily is remarkable at catalyzing chemically diverse and complex reactions. We have previously shown that NosL, which is involved in forming the indole side ring of the thiopeptide nosiheptide, is a radical AdoMet enzyme that processes L-Trp to afford 3-methyl-2-indolic acid (MIA) via an unusual fragmentation-recombination mechanism. We now report the expansion of the MIA synthase family by characterization of NocL, which is involved in nocathiacin I biosynthesis. EPR and UV-visible absorbance spectroscopic analyses demonstrated the interaction between L-Trp and the [4Fe-4S] cluster of NocL, leading to the assumption of nonspecific interaction of [4Fe-4S] cluster with other nucleophiles via the unique Fe site. This notion is supported by the finding of the heterogeneity in the [4Fe-4S] cluster of NocL in the absence of AdoMet, which was revealed by the EPR study at very low temperature. Furthermore, a free radical was observed by EPR during the catalysis, which is in good agreement with the hypothesis of a glycyl radical intermediate. Combined with the mutational analysis, these studies provide new insights into the function of the [4Fe-4S] cluster of radical AdoMet enzymes as well as the mechanism of the radical-mediated complex carbon chain rearrangement catalyzed by MIA synthase.     

An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228

Klebsiella pneumoniae is a Gram-negative bacterium of the family Enterobacteriaceae that possesses diverse metabolic capabilities: many strains are leading causes of hospital-acquired infections that are often refractory to multiple antibiotics, yet other strains are metabolically engineered and used for production of commercially valuable chemicals. To study its metabolism, we constructed a genome-scale metabolic model (iYL1228) for strain MGH 78578, experimentally determined its biomass composition, experimentally determined its ability to grow on a broad range of carbon, nitrogen, phosphorus and sulfur sources, and assessed the ability of the model to accurately simulate growth versus no growth on these substrates. The model contains 1,228 genes encoding 1,188 enzymes that catalyze 1,970 reactions and accurately simulates growth on 84% of the substrates tested. Furthermore, quantitative comparison of growth rates between the model and experimental data for nine of the substrates also showed good agreement. The genome-scale metabolic reconstruction for K. pneumoniae presented here thus provides an experimentally validated in silico platform for further studies of this important industrial and biomedical organism.     

Impaired thymic export and apoptosis contribute to regulatory T-cell defects in patients with chronic heart failure

Objective

Animal studies suggest that regulatory T (T_reg) cells play a beneficial role in ventricular remodeling and our previous data have demonstrated defects of T_reg cells in patients with chronic heart failure (CHF). However, the mechanisms behind T_reg-cell defects remained unknown. We here sought to elucidate the mechanism of T_reg-cell defects in CHF patients.

Methods and Results

We performed flow cytometry analysis and demonstrated reduced numbers of peripheral blood CD4⁺CD25⁺FOXP3⁺CD45RO⁻CD45RA⁺ naïve T_reg (nT_reg) cells and CD4⁺CD25⁺FOXP3⁺CD45RO⁺CD45RA⁻ memory T_reg (mT_reg) cells in CHF patients as compared with non-CHF controls. Moreover, the nT_reg/mT_reg ratio (p<0.01), CD4⁺CD25⁺FOXP3⁺CD45RO⁻ CD45RA⁺CD31⁺ recent thymic emigrant T_reg cell (RTE-T_reg) frequency (p<0.01), and T-cell receptor excision circle levels in T_reg cells (p<0.01) were lower in CHF patients than in non-CHF controls. Combined annexin-V and 7-AAD staining showed that peripheral T_reg cells from CHF patients exhibited increased spontaneous apoptosis and were more prone to interleukin (IL)-2 deprivation- and CD95 ligand-mediated apoptosis than those from non-CHF individuals. Furthermore, analyses by both flow cytometry and real-time polymerase chain reaction showed that T_reg-cell frequency in the mediastinal lymph nodes or Foxp3 expression in hearts of CHF patients was no higher than that of the non-CHF controls.

Conclusion

Our data suggested that the T_reg-cell defects of CHF patients were likely caused by decreased thymic output of nascent T_reg cells and increased susceptibility to apoptosis in the periphery.     

Transgene flow to hybrid rice and its male-sterile lines

Gene flow from genetically modified (GM) crops to the same species or wild relatives is a major concern in risk assessment. Transgenic rice with insect and/or disease resistance, herbicide, salt and/or drought tolerance and improved quality has been successfully developed. However, data on rice gene flow from environmental risk assessment studies are currently insufficient for the large-scale commercialization of GM rice. We have provided data on the gene flow frequency at 17 distances between a GM japonica line containing the bar gene as a pollen donor and two indica hybrid rice varieties and four male-sterile (ms) lines. The GM line was planted in a 640m² in an isolated experimental plot (2.4 ha), which simulates actual conditions of rice production with pollen competition. Results showed that: (1) under parallel plantation at the 0-m zone, the transgene flow frequency to the ms lines ranged from 3.145 to 36.116% and was significantly higher than that to hybrid rice cultivars (0.037–0.045%). (2) Gene flow frequency decreased as the distance increased, with a sharp cutoff point at about 1–2 m; (3) The maximum distance of transgene flow was 30–40 m to rice cultivars and 40–150 m to ms lines. We believe that these data will be useful for the risk assessment and management of transgenic rice lines, especially in Asia where 90% of world's rice is produced and hybrid rice varieties are extensively used. Shirong Jia, Feng Wang and Lei Shi contributed equally to this investigation.     

Prostate androgen receptor: immunohistological localization and mRNA characterization

Four androgen receptor (AR) specific monoclonal antibodies were used for the immunohistochemical localization of AR in the human prostate tissue. The prostate tissue consisted of alveoli embedded in fibromuscular stroma and lined with a single layer of columnar secretory epithelial cells. The immunoreactive ARs were found predominantly in the nuclei of epithelial cell, suggesting ARs, like estrogen receptors and progesterone receptors, are mainly nuclear proteins. Northern blot hybridization showed that AR mRNA is about 9 kilobases (kb) and relative abundant in the androgen-sensitive organs, such as ventral prostate, dorsolateral prostate and seminal vesicle.