Finding complex biological relationships in recent PubMed articles using Bio-LDA

The overwhelming amount of available scholarly literature in the life sciences poses significant challenges to scientists wishing to keep up with important developments related to their research, but also provides a useful resource for the discovery of recent information concerning genes, diseases, compounds and the interactions between them. In this paper, we describe an algorithm called Bio-LDA that uses extracted biological terminology to automatically identify latent topics, and provides a variety of measures to uncover putative relations among topics and bio-terms. Relationships identified using those approaches are combined with existing data in life science datasets to provide additional insight. Three case studies demonstrate the utility of the Bio-LDA model, including association predication, association search and connectivity map generation. This combined approach offers new opportunities for knowledge discovery in many areas of biology including target identification, lead hopping and drug repurposing.

Hypothalamic transcriptome plasticity in two rodent species reveals divergent differential gene expression but conserved pathways

We have addressed the question of how different rodent species cope with the life-threatening homeostatic challenge of dehydration at the level of transcriptome modulation in the supraoptic nucleus (SON), a specialised hypothalamic neurosecretory apparatus responsible for the production of the antidiuretic peptide hormone arginine vasopressin (AVP). AVP maintains water balance by promoting water conservation at the level of the kidney. Dehydration evokes a massive increase in the regulated release of AVP from SON axon terminals located in the posterior pituitary, and this is accompanied by a plethora of changes in the morphology, electrophysiological properties, biosynthetic and secretory activity of this structure. Microarray analysis was used to generate a definitive catalogue of the genes expressed in the mouse SON, and to describe how the gene expression profile changes in response to dehydration. Comparison of the genes differentially expressed in the mouse SON as a consequence of dehydration with those of the rat has revealed many similarities, pointing to common processes underlying the function-related plasticity in this nucleus. In addition, we have identified many genes that are differentially expressed in a species-specific manner. However, in many cases, we have found that the hyperosmotic cue can induce species-specific alterations in the expression of different genes in the same pathway. The same functional end can be served by different means, via differential modulation, in different species, of different molecules in the same pathway. We suggest that pathways, rather than specific genes, should be the focus of integrative physiological studies based on transcriptome data.

Hybrid cloud and cluster computing paradigms for life science applications

BACKGROUND

Clouds and MapReduce have shown themselves to be a broadly useful approach to scientific computing especially for parallel data intensive applications. However they have limited applicability to some areas such as data mining because MapReduce has poor performance on problems with an iterative structure present in the linear algebra that underlies much data analysis. Such problems can be run efficiently on clusters using MPI leading to a hybrid cloud and cluster environment. This motivates the design and implementation of an open source Iterative MapReduce system Twister.

RESULTS

Comparisons of Amazon, Azure, and traditional Linux and Windows environments on common applications have shown encouraging performance and usability comparisons in several important non iterative cases. These are linked to MPI applications for final stages of the data analysis. Further we have released the open source Twister Iterative MapReduce and benchmarked it against basic MapReduce (Hadoop) and MPI in information retrieval and life sciences applications.

CONCLUSIONS

The hybrid cloud (MapReduce) and cluster (MPI) approach offers an attractive production environment while Twister promises a uniform programming environment for many Life Sciences applications.

METHODS

We used commercial clouds Amazon and Azure and the NSF resource FutureGrid to perform detailed comparisons and evaluations of different approaches to data intensive computing. Several applications were developed in MPI, MapReduce and Twister in these different environments.

The effects of subinhibitory concentrations of costus oil on virulence factor production in Staphylococcus aureus

AIM

To determine the antimicrobial activity of costus (Saussurea lappa) oil against Staphylococcus aureus, and to evaluate the influence of subinhibitory concentrations of costus oil on virulence-related exoprotein production in staph. aureus.

METHODS AND RESULTS

Minimal inhibitory concentrations (MICs) were determined using a broth microdilution method, and the MICs of costus oil against 32 Staph. aureus strains ranged from 0.15 to 0.6 μl ml(-1) . The MIC(50) and MIC(90) were 0.3 and 0.6 μl ml(-1) , respectively. Western blot, haemolytic, tumour necrosis factor (TNF) release and real-time RT-PCR assays were performed to evaluate the effects of subinhibitory concentrations of costus oil on virulence-associated exoprotein production in Staph. aureus. The data presented here show that costus oil dose dependently decreased the production of α-toxin, toxic shock syndrome toxin 1 (TSST-1) and enterotoxins A and B in both methicillin-sensitive Staph. aureus (MSSA) and methicillin-resistant Staph. aureus (MRSA).

CONCLUSION

Costus oil has potent antimicrobial activity against Staph. aureus, and the production of α-toxin, TSST-1 and enterotoxins A and B in Staph. aureus was decreased by costus oil.

SIGNIFICANCE AND IMPACT OF THE STUDY

The data suggest that costus oil may deserve further investigation for its potential therapeutic value in treating Staph. aureus infections. Furthermore, costus oil could be rationally applied in food products as a novel food preservative both to inhibit the growth of Staph. aureus and to repress the production of exotoxins, particularly staphylococcal enterotoxins.

Meta-analysis: polymorphisms in TNF-alpha gene promoter and Crohn's disease

BACKGROUND

Tumour necrosis factor alpha (TNF-alpha) is involved in the pathogenesis of Crohn's disease (CD). However, results on the association between the polymorphisms in TNF-alpha promoter and the risk of CD are inconsistent.

AIM

To perform a quantitative synthesis for the genetic polymorphisms in TNF-alpha promoter and CD risk.

METHODS

Databases were searched (up to 2009) and 31 studies were included. Risks of CD associated with the polymorphisms in TNF-alpha promoter were assessed.

RESULTS

Overall, individuals with -1031 TC+CC genotype had a slightly increased risk to develop CD compared with individuals with -1031 TT genotype (OR, 1.32; 95% CI, 1.03-1.70). In the further stratified analysis, we found Asians with the -1031T>C, -863 C>A and -857 C>T variant polymorphisms have almost one and a half CD risk compared with other genotypes (OR, 1.58; 95% CI, 1.16-2.15; OR, 1.55; 95% CI, 1.18-2.02; OR, 1.54; 95% CI, 1.19-1.99 respectively). We did not find -308 G>A variant associated with CD location and disease behaviours in stratified analysis.

CONCLUSIONS

TNF-alpha polymorphisms in the promoter region might be used as a biomarker for CD risk prediction. Larger studies with mixed ethnicity subjects and stratified by clinical and sub clinical characteristics are needed to validate our findings.

Persistent expression of biologically active anti-HER2 antibody by AAVrh.10-mediated gene transfer

Trastuzumab (Herceptin) is a recombinant humanized monoclonal antibody directed against an extracellular region of the HER2 protein. We hypothesized that a single adeno-associated virus mediated genetic delivery of an anti-HER2 antibody should be effective in mediating long term production of anti-HER2 and in suppressing the growth of human tumors in a xenograft model in nude mice. The adeno-associated virus gene transfer vector AAVrh.10αHER2 was constructed based on non-human primate AAV serotype rh.10 to express the cDNAs for the heavy and light chains of monoclonal antibody 4D5, the murine precursor to trastuzumab. The data demonstrates that genetically transferred anti-HER2 selectively bound human HER2 protein and suppressed proliferation of HER2 positive tumor cell lines. A single administration of AAVrh.10αHER2 provided long term therapeutic levels of anti-HER2 antibody expression without inducing anti-idiotype response, suppressed the growth of HER2 positive tumors and increased survival of the tumor-bearing mice. In the context that trastuzumab therapy requires frequent, repeated administration, this strategy might be developed as an alternate platform for delivery anti-HER2 therapy.

Quantitation of thyroid-stimulating hormone receptor mRNA with real-time PCR for early diagnosis of papillary thyroid microcarcinoma

Recently, the value of thyroid-stimulating hormone receptor(TSHR) mRNA as a molecular marker in diagnosis of thyroid cancer has been greatly explored. However, its role in detecting thyroid microcarcinoma has never been reported. In this study, we aim to investigate the value of TSHR mRNA in diagnosis of papillary thyroid microcarcinoma(PTMC). To do that, TSHR mRNA levels were measured by real time PCR in 30 healthy subjects and 72 patients (benign thyroid nodules, n=38; PTMC, n=34). TSHR mRNA levels were then compared with cancer volume in surgical specimen. We found that TSHR mRNA levels in PTMC were significantly higher than benign thyroid nodules(P<0.01). At a cutoff value of 0.71 ng/microg total RNA, the TSHR mRNA correctly classified 77.8% of patients preoperatively (sensitivity= 76.5%; specificity= 79.4%). Comparatively, it performed better in larger PTMC of 0.5-1.0 cm than <0.5 cm(sensitivity, 83.4% vs 72.4%; specificity, 88.5% vs 74.1%). Combining TSHR mRNA and ultra sound examination correctly detect 97.1% of PTMC and could spared surgery in 86.8% of patients with benign thyroid nodules. Thus, TSHR mRNA measured with real time PCR enhances the preoperative detection of PTMC in patients with thyroid nodules, which dramatically reduces unnecessary surgeries.

KEYWORDS

thyroid-stimulating hormone receptor, papillary thyroid microcarcinoma, diagnosis.

Conversion from cyclosporin A to sirolimus retards the progression of chronic allograft nephropathy in the long term in a rat kidney transplantation model

In a rat renal allograft model, the long-term effect of conversion from cyclosporin A (CsA) to sirolimus on recipient kidneys and growth factor expression were compared with continuous use or withdrawal of CsA. Kidneys from Fisher 344 rats were orthotopically transplanted into Lewis rats. Four Fisher 344 to Lewis allograft groups were treated post-transplant as follows: (i) CsA (transplant to week 8) then sirolimus (weeks 8 - 24); (ii) CsA (transplant to week 24); (iii) CsA (transplant to week 8) then vehicle (weeks 8 - 24); (iv) control vehicle (transplant to week 24). A fifth group underwent syngeneic isograft (Lewis to Lewis) with no drug treatment. Proteinuria was measured every 4 weeks and grafts harvested at 24 weeks for morphological and immunohistochemical analysis. Conversion from CsA to sirolimus resulted in a significant decrease in proteinuria at 24 weeks, a lower Banff sum score and lower expression of transforming growth factor mRNA compared with continuous use or withdrawal of CsA. In conclusion, conversion from CsA to sirolimus retarded progression of chronic allograft nephropathy in the rat model.

Species differences for stereoselective metabolism of ethofumesate and its enantiomers in vitro

1. The stereoselective metabolism of ethofumesate (ETO) and its enantiomers in rabbit and rat liver microsomes have been studied by chiral high-performance liquid chromatography (HPLC) method. Two metabolites were detected in both liver microsomes in the presence of beta-nicotinamide adenine dinucleotide phosphate (NADPH). 2. The T(1/2) of (+)-ETO and (-)-ETO in rabbit liver microsomes were 12.2 and 4.7 min of rac-ETO and 25.9 and 6.7 of ETO enantiomers. However, the T(1/2) of (+)-ETO and (-)-ETO in rat liver microsomes were 5.3 and 5.9 min of rac-ETO and 7.8 and 10.6 of ETO enantiomers. The stereoselective selectivity is similar to the in vivo study. 3. After incubation of ETO enantiomers, stereoselectivity was present in the formation of ETO-OH enantiomer in rabbit liver microsomes, but stereoselectivity was not evident in rat liver microsomes. 4. There was no chiral inversion from the (+)-ETO to (-)-ETO or inversion from (-)-ETO to (+)-ETO in both rabbit and rat liver microsomes.

Evaluation of the Clinical Curative Effect of an O(2)-O(3) mixture to Treat Lumbar Disc Herniation with Different Treatment Sessions

SUMMARY

To compare the effective rates among one week, two week and four week treatment sessions of ozone therapy for lumbar disc herniation to provide a foundation for clinical decision-making. One hundred and eighty-seven lumbar disc herniation patients were divided into three groups, 103 cases for one week, 61 cases for two week and 23 cases for four week treatment sessions. The clinical curative effective rates in the three groups were 82.52%, 85.24% and 95.65% respectively. The effective rate among the three groups showed no significant difference at statistical analysis. Considering the cost-effectiveness of ozone therapy, increasing the treatment course does not enhance the curative effect.