A simplified strategy for molecular formula determination of chemical constituents in traditional Chinese medicines based on accurate mass, A + 1 and A + 2 isotopic peaks using Fourier transform ion cyclotron resonance mass spectrometry.

RATIONALE: Recently, isotopic fine structures derived from Fourier transform ion cyclotron resonance mass spectrometry have been used to determine the molecular formula for unknown compounds in many complex systems. However, a simplified strategy for molecular formula determination of chemical constituents in traditional Chinese medicines (TCMs) based on accurate mass, A + 1 and A + 2 isotopic peaks is necessary. METHODS: Salviae miltiorrhizae was selected as a representative species. First, the chemical constituents were chromatographically separated and their accurate masses were obtained. The A + 1 and A + 2 isotopic peaks of all chemical constituents were then also acquired. Finally, the chemical formulae of the chemical constituents were determined. RESULTS: In the sample of Salviae miltiorrhizae, the formulae of 38 CHO-containing chemical constituents were quickly determined, and all chemical constituents were identified using their tandem mass spectrometric data. Moreover, the method was validated by comparison of the A + 1 and A + 2 isotopic peaks, their fragmentation patterns and the retention times of six selected standard substances. CONCLUSIONS: The results demonstrate that the described strategy performs well for molecular formula determination of chemical constituents in TCMs. This also indicates that this method will be meaningful for the structural identification of chemical constituents of TCMs.

Brain metabolomics study for the protective effects of Rhodiola crenulata extract on Alzheimer's disease by HPLC coupled with Fourier transform-ion cyclotron resonance mass spectrometry.

In order to investigate the protective effects of Rhodiola crenulata extract on Alzheimer's disease, a brain metabolomics study in rats was conducted by high performance liquid chromatography coupled with Fourier transform ion cyclotron resonance mass spectrometry. Rat model was constructed by bilateral hippocampal injection of amyloid-ß peptide and immunohistochemistry was performed to evaluate the pharmacological effect of Rhodiola crenulata extract. Multivariate statistical analysis was used to discover potential biomarkers in rat brain and related metabolic pathways analysis was conducted to elucidate the action mechanism of Rhodiola crenulata extract. As a result, a total of 19 metabolites contributing to Alzheimer's disease progress were identified and nine of them were restored to the normal levels after drug administration. Pathway analysis revealed that the protective effects of Rhodiola crenulata extract are related to the regulation of glutathione metabolism and arachidonic acid metabolism in rat brain. In conclusion, this work demonstrates that the developed metabolomics method is useful to investigate the protective effects of Rhodiola crenulata extract against Alzheimer's disease. These outcomes may further provide reliable evidence to illuminate the intervention mechanism of other traditional Chinese medicines on Alzheimer's disease.

G-BLASTN: accelerating nucleotide alignment by graphics processors.

MOTIVATION: Since 1990, the basic local alignment search tool (BLAST) has become one of the most popular and fundamental bioinformatics tools for sequence similarity searching, receiving extensive attention from the research community. The two pioneering papers on BLAST have received over 96 000 citations. Given the huge population of BLAST users and the increasing size of sequence databases, an urgent topic of study is how to improve the speed. Recently, graphics processing units (GPUs) have been widely used as low-cost, high-performance computing platforms. The existing GPU-BLAST is a promising software tool that uses a GPU to accelerate protein sequence alignment. Unfortunately, there is still no GPU-accelerated software tool for BLAST-based nucleotide sequence alignment. RESULTS: We developed G-BLASTN, a GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST. G-BLASTN can produce exactly the same results as NCBI-BLAST, and it has very similar user commands. Compared with the sequential NCBI-BLAST, G-BLASTN can achieve an overall speedup of 14.80X under 'megablast' mode. More impressively, it achieves an overall speedup of 7.15X over the multithreaded NCBI-BLAST running on 4 CPU cores. When running under 'blastn' mode, the overall speedups are 4.32X (against 1-core) and 1.56X (against 4-core). G-BLASTN also supports a pipeline mode that further improves the overall performance by up to 44% when handling a batch of queries as a whole. Currently G-BLASTN is best optimized for databases with long sequences. We plan to optimize its performance on short database sequences in our future work. AVAILABILITY: http://www.comp.hkbu.edu.hk/∼chxw/software/G-BLASTN.html CONTACT: chxw@comp.hkbu.edu.hk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Accelerating the scoring module of mass spectrometry-based peptide identification using GPUs.

BACKGROUND: Tandem mass spectrometry-based database searching is currently the main method for protein identification in shotgun proteomics. The explosive growth of protein and peptide databases, which is a result of genome translations, enzymatic digestions, and post-translational modifications (PTMs), is making computational efficiency in database searching a serious challenge. Profile analysis shows that most search engines spend 50%-90% of their total time on the scoring module, and that the spectrum dot product (SDP) based scoring module is the most widely used. As a general purpose and high performance parallel hardware, graphics processing units (GPUs) are promising platforms for speeding up database searches in the protein identification process. RESULTS: We designed and implemented a parallel SDP-based scoring module on GPUs that exploits the efficient use of GPU registers, constant memory and shared memory. Compared with the CPU-based version, we achieved a 30 to 60 times speedup using a single GPU. We also implemented our algorithm on a GPU cluster and achieved an approximately favorable speedup. CONCLUSIONS: Our GPU-based SDP algorithm can significantly improve the speed of the scoring module in mass spectrometry-based protein identification. The algorithm can be easily implemented in many database search engines such as X!Tandem, SEQUEST, and pFind. A software tool implementing this algorithm is available at http://www.comp.hkbu.edu.hk/~youli/ProteinByGPU.html.

SOAP3: ultra-fast GPU-based parallel alignment tool for short reads.

SOAP3 is the first short read alignment tool that leverages the multi-processors in a graphic processing unit (GPU) to achieve a drastic improvement in speed. We adapted the compressed full-text index (BWT) used by SOAP2 in view of the advantages and disadvantages of GPU. When tested with millions of Illumina Hiseq 2000 length-100 bp reads, SOAP3 takes < 30 s to align a million read pairs onto the human reference genome and is at least 7.5 and 20 times faster than BWA and Bowtie, respectively. For aligning reads with up to four mismatches, SOAP3 aligns slightly more reads than BWA and Bowtie; this is because SOAP3, unlike BWA and Bowtie, is not heuristic-based and always reports all answers.

"Barcode" cell sensor microfluidic system: Rapid and sample-to-answer antimicrobial susceptibility testing applicable in resource-limited conditions.

Many rapid antimicrobial susceptibility testing (AST) methods have been proposed to contain clinical antimicrobial resistance (AMR) and preserve the effectiveness of remaining antimicrobials. However, far fewer methods have been proposed to test AMR in resource-limited conditions, such as for frequent safety screenings of water/food/public facilities, urgent surveys of massive samples during a pandemic, or AMR tests in low-income countries. Rapid AST methods realized thus far have a variety of drawbacks when used for such surveys, e.g., high cost and the requirement of expensive instruments such as microscopy. A more reasonable strategy would be to screen samples via onsite testing first, and then send any sample suspected to contain AMR bacteria for advanced testing. Accordingly, a cost-efficient AST is demanded, which can rapidly process a large number of samples without using expensive equipment. To this end, current work demonstrates a novel "barcode" cell sensor based on an adaptive linear filter array as a fully automatic and microscope-free method for counting very small volumes of cells (~1.00 × 104 cells without pre-incubation), wherein suspended cells concentrate into microbars with length proportional to the number of cells. We combined this sensor with an on-chip culture approach we had demonstrated for rapid and automated drug exposure and realized a low-cost and resource-independent platform for portable AST, from which results can be obtained simply through a cell phone. This method has a much shorter turnaround time (2-3 h) than that of standard methods (16-24 h). Thanks to its microscopy-free analysis, affordability, portability, high throughput, and user-friendliness, our "barcode" AST system has the potential to fulfill the various demands of AST when advanced facilities are not available, making it a promising new tool in the fight against AMR.

Serum lipidomics study reveals protective effects of Rhodiola crenulata extract on Alzheimer's disease rats.

Alzheimer's disease (AD) is a chronic and progressive neurodegenerative disorder. Rhodiola crenulata extract (RCE) has shown its protective effects on AD, however, the underlying mechanism is still unclear. In this work, serum lipidomics was conducted to reveal the action mechanism of RCE on AD by HPLC coupled with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). The animal model of AD was reproduced by intrahippocampal injection of Aß1-42 in rats. The novel object recognition test and passive avoidance test were performed to evaluate the protective effects of RCE on AD rats. The differences of lipid metabolism profiles in rats were evaluated by multivariate statistical analysis. Then, the potential lipid biomarkers were identified and the possible mechanism of RCE on AD was elucidated by metabolic pathways analysis. As a result, twenty-eight lipids with significant differences between the control group and the model group were screened out. With the treatment of RCE, 19 lipids in AD rats showed a trend of callback to the normal levels. The results of pathway analysis indicated that the protective effects of RCE on AD might be closely related to the regulation of linoleic acid metabolism, α-linoleic acid metabolism, sphingolipid metabolism and ether lipid metabolism. In conclusion, this study provides a new perspective on the potential intervention mechanism of RCE for AD treatment.

[Characterization of atherosclerotic plaque in patients with unstable angina pectoris and stable angina pectoris by optical coherence tomography].

OBJECTIVE: To compare the characterization of coronary atherosclerotic plaques in patients with unstable angina pectoris (UAP) and stable angina pectoris (SAP) by optical coherence tomography (OCT). METHODS: OCT was performed in 47 patients (23 UAP and 24 SAP) undergoing coronary angiography. Lipid-rich plaque (defined by > or = 2 quadrants of the cross-section area), thin cap fibroatheroma (TCFA), thickness of fibrous cap, plaque rupture, calcification and thrombus visualized by OCT were compared between UAP and SAP patients. RESULTS: OCT imaging was successfully in 44 out of 47 patients (22 UAP, 22 SAP). Proportion of lipid-rich plaques was similar between UAP and SAP groups [91% (20/22) vs. 73% (16/22), P = 0.741]. The minimum thickness of fibrous cap in the UAP group was significantly thinner than that in SAP group [(69.5 +/- 34.7) microm vs. (141.1 +/- 68.5) microm, P = 0.000] and the rate of fibrous cap erosion in the UAP group was significantly higher than that in the SAP group [59% (13/22) vs. 9% (2/22), P = 0.000]. Percents of TCFA [73% (16/22) vs. 14% (3/22), P = 0.000] and plaque rupture [50% (11/22) vs. 9% (2/22), P = 0.003] were significantly higher in UAP group compared those in SAP group. Incidence of thrombus and calcification were similar between two groups. CONCLUSIONS: OCT imaging can clearly define plaque characterization of coronary atherosclerosis. UAP patients have thinner fibrous cap, higher incidences of fibrous cap erosion, plaque rupture and TCFA compared patients with SAP.

Deep learning identifies accurate burst locations in water distribution networks.

Pipe bursts in water distribution networks lead to considerable water loss and pose risks of bacteria and pollutant contamination. Pipe burst localisation methods help water service providers repair the burst pipes and restore water supply timely and efficiently. Although methods have been reported on burst detection and localisation, there is a lack of studies on accurate localisation of a burst within a potential district by accessible meters. To address this, a novel Burst Location Identification Framework by Fully-linear DenseNet (BLIFF) is proposed. In this framework, additional pressure meters are placed at limited, optimised places for a short period (minutes to hours) to monitor system behaviour after the burst. The fully-linear DenseNet (FL-DenseNet) newly developed in this study modifies the state-of-the-art deep learning algorithm to effectively extract features in the limited pressure signals for accurate burst localisation. BLIFF was tested on a benchmark network with different parameter settings, which showed that accurate burst localisation results can be achieved even with high model uncertainties. The framework was also applied to a real-life network, in which 57 of the total 58 synthetic bursts in the potential burst district were correctly located when the top five most possible pipes are considered and among them, 37 were successfully located when considering only the top one. Only one failed because of the very small pipe diameter and remote location. Comparisons with DenseNet and the traditional fully linear neural network demonstrate that the framework can effectively narrow the potential burst district to one or several pipes with good robustness and applicability. Codes are available at https://github.com/wizard1203/waternn.

Neuroprotective effects of a Rhodiola crenulata extract on amyloid-ß peptides (Aß1-42) -induced cognitive deficits in rat models of Alzheimer's disease.

BACKGROUND: Rhodiola crenulata has been wildly used as a healthy food, antidepressant and antifatigue for many years in China. Recent studies suggested that Rhodiola crenulata extract (RCE) has cognitive protective effects in the treatment of Alzheimer's disease (AD). PURPOSE: To assess the protective effects of RCE on cognitive deficits and clarify its therapeutic mechanisms in Aß1-42 -induced rat models of AD. STUDY DESIGN: RCE was prepared by freeze-drying technology. Their protective effects on Aß1-42-induced rat models of AD and the preliminary therapeutic mechanisms were studied. METHODS: The Y maze test and Morris water maze (MWM) test were conducted to evaluate the learning and memory abilities of the rats. Subsequently, biochemical assays, hematoxylin-eosin staining, immunohistochemistry and Western blotting were performed to elucidate the mechanisms. RESULTS: RCE significantly increased the spontaneous alternation (F (6, 111) = 8.165, p < 0.001), prolonged the swimming time (F (6, 111) = 20.143, p < 0.001) and decreased the escape latency in rat models of AD. In addition, RCE significantly increased the acetylcholine (Ach) level and the choline acetyl transferase (ChAT) activity (F (6, 34) = 6.033, p < 0.001; F (6, 34) = 6.958, p < 0.001, respectively), repaired the damage of hippocampus neurons and prevented Aß formation in the hippocampus in Aß1-42 injected rats. Moreover, RCE increased the superoxide dismutase (SOD) activity and decreased the malondialdehyde (MDA) level in cortex of Aß1-42 injected rats (F (6, 34) = 5.097, p < 0.01; F (6, 34) = 2.907, p < 0.05, respectively), significantly reduced the expressions of p-tau (ser396) and induced the expressions of p-GSK3ß (ser9) in hippocampus (F (6, 34) = 15.297, p < 0.001; F (6, 34) = 9.652, p < 0.001, respectively). CONCLUSION: Our findings demonstrated that RCE significantly alleviated the learning and memory deficits in the Aß1-42-induced rat models of AD. The mechanisms involved its protection effects against cholinergic system deficiency, oxidative stress damage and GSK3ß activation. RCE may be a potential therapeutic medicine with multi-targets to prevent the progression of cognitive deterioration in AD.

An available strategy for elemental composition determination of organic impurities in commercial preparations based on accurate mass and peak ratio of isotopic fine structures (IFSs) by dual mode combined-FT-ICR-MS and fraction collection technology.

A strategy to determine the elemental composition of organic impurities in commercial preparations was established by combining high-performance liquid chromatography (HPLC)-Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and fraction collector with direct infusion-FT-ICR-MS (DI-FT-ICR-MS). Under HPLC-FT-ICR-MS mode, all impurities in model sample were chromatographically separated and collected by fraction collector according to their retention time. The accurate mass of each impurity and their candidate formulae under 1 ppm mass tolerance were calculated. Subsequently, theoretical isotopic fine structures (IFSs) of the candidate formulae were generated. Furthermore, the collected fractions were tested and the experimental IFSs of impurities were acquired by DI-FT-ICR-MS mode. Finally, the elemental composition of all impurities was decisively determined by comparing the experimental and theoretical IFSs. Our results demonstrate that the combined strategy is effective in separating impurities and acquiring accurate mass by HPLC-FT-ICR-MS, obtaining the appropriate samples by fraction collection technology for DI-FT-ICR-MS, and acquiring the IFSs of impurities by DI-FT-ICR-MS. It could be concluded that the strategy is an accurate and standard independent approach to determine the elemental composition of organic impurities in commercial preparations.

Trade-offs between longevity and pathogen resistance in Drosophila melanogaster are mediated by NFkappaB signaling.

The innate immune response protects numerous organisms, including humans, from the universe of pathogenic molecules, viruses and micro-organisms. Despite its role in promoting pathogen resistance, inappropriate activation and expression of NFkappaB and other immunity-related effector molecules can lead to cancer, inflammation, and other diseases of aging. Understanding the mechanisms leading to immune system activation as well as the short- and long-term consequences of such activation on health and lifespan is therefore critical for the development of beneficial immuno-modulating and longevity-promoting interventions. Mechanisms of innate immunity are highly conserved across species, and we take advantage of genetic tools in the model organism, Drosophila melanogaster, to study the effects of acute and chronic activation of immunity pathways on pathogen resistance and general fitness of adult flies. Our findings indicate that fat body specific overexpression of a putative pathogen recognition molecule, peptidoglycan recognition protein (PGRP-LE), is sufficient for constitutive up-regulation of the immune response and for enhanced pathogen resistance. Primary components of fitness are unaffected by acute activation, but chronic activation leads to an inflammatory state and reduced lifespan. These phenotypes are dependent on the NFkappaB-related transcriptional factor, Relish, and they establish a mechanistic basis for a link between immunity, inflammation, and longevity.

[Visualization of intimal proliferation of drug-eluting stent and bare mental stent by use of optical coherence tomography].

OBJECTIVE: To compare neointimal proliferation of drug-eluting stent (DES) with bare mental stent (BMS) by optical coherence tomography (OCT). METHODS: OCT images were obtained in 21 diseased coronary vessels with 23 stents in 19 patients with coronary artery disease at 5 - 93 months post DES or BMS stents. Twenty-two stents of all 23 stents were divided into three groups. Nine DES stents at 6 - 10 months post stenting were considered as group A, 8 BMS stents at 5 - 10 months post stenting as group B, and 5 BMS stents at 23 - 93 months post stenting as group C. OCT images were quantitatively analyzed to compare neointimal proliferation of three groups after stenting. RESULTS: All 21 vessels and 23 stents OCT images were successfully acquired. The maximal neointima, luminal loss in diameter and cross sectional area (CSA), and restenosis in diameter and CSA were significantly statistically different within three groups. The maximal intimal proliferations post stenting in group A were significantly lower than group B (0.20 mm +/- 0.13 mm vs 0.81 mm +/- 0.46 mm, P = 0.019) or group C (0.91 mm +/- 0.27 mm, P = 0.007), luminal loss of diameter in group A were significantly lower than group B (0.27 mm +/- 0.17 mm vs 1.12 mm +/- 0.79 mm, P = 0.009) or group C (1.20 mm +/- 0.31 mm, P = 0.013), restenosis rates in diameter in group A were significantly less than group B (8.90% +/- 4.47% vs 36.36% +/- 24.34%, P = 0.009) or group C (35.48 +/- 6.09, P = 0.017), luminal loss in CSA in group A were lower than group B (1.14 mm(2) +/- 0.9 mm(2) vs 3.96 mm(2) +/- 2.62 mm(2), P = 0.009) or group C (4.66 mm(2) +/- 1.66 mm(2), P = 0.006), and restenosis rates in CSA in group A were less than group B (15.43% +/- 7.89% vs 48.14% +/- 30.43%, P = 0.017) or group C (55.20% +/- 11.24%, P = 0.009). Almost all surfaces of 13 BMS stent struts were covered by significant neointimal coverage, surfaces of 10 DES struts were less significantly neointimal coverage, and some surfaces of DES struts were uncovered with neointima even at 29 months post stenting. CONCLUSION: OCT imaging can clearly visualize stent struts and neointimal formation of strut surfaces post DES or BMS stenting, and this new imaging modality will play important role in evaluating the efficacy of drug-eluting stent.

[Coronary artery atherosclerotic plaque and stent visualizations by optical coherence tomography].

OBJECTIVE: To evaluate coronary artery atherosclerotic plaque characteristics and changes post coronary stenting by optical coherence tomography (OCT). METHODS: OCT images were obtained in 22 diseased coronary vessels after coronary angiography or percutaneous coronary interventions (PCI) in 20 patients and in 23 stents [7 sirolimus-eluting stents (SES) follow up at 4-29 months post stenting and 8 bare mental stents (BMS) at 4-35 months post stenting, 8 stents immediately after PCI]. RESULTS: All 22 vessels and 23 stents OCT images were successfully acquired. Two thromboses, 8 fibrous, 9 lipid-rich and 3 calcium plaques as well as 3 plaque ruptures were visualized by OCT. No significant neointimal proliferation and restenosis were found in SES stents and some struts were not covered with neointima even at 29 months post stenting. Significant neointimal proliferation on surfaces of stent struts were visualized in all 8 BMS stents and restenosis was detected in 3 BMS stents. OCT images obtained immediately after PCI showed that 3 stents were well positioned, tissue prolapse between coronary stent struts occurred in 4 stents and stent dissociation with vessel wall could be seen in 1 stent. CONCLUSIONS: OCT imaging can clearly visualize different types of atherosclerotic plaques. By providing detailed information on plaque characteristics, this technique might help cardiologists in choosing suitable stents and guiding preventive therapy for patients with coronary heart disease.

Regulation of Drosophila life span by olfaction and food-derived odors.

Smell is an ancient sensory system present in organisms from bacteria to humans. In the nematode Caenorhabditis elegans, gustatory and olfactory neurons regulate aging and longevity. Using the fruit fly, Drosophila melanogaster, we showed that exposure to nutrient-derived odorants can modulate life span and partially reverse the longevity-extending effects of dietary restriction. Furthermore, mutation of odorant receptor Or83b resulted in severe olfactory defects, altered adult metabolism, enhanced stress resistance, and extended life span. Our findings indicate that olfaction affects adult physiology and aging in Drosophila, possibly through the perceived availability of nutritional resources, and that olfactory regulation of life span is evolutionarily conserved.