Nutritional and neuroprotective characterization of 'Tadanishiki' yuzu according to harvesting period or extraction condition

The present study investigated the phenolic profile, antioxidant activity, and neuroprotective properties of ‘Tadanishiki’ yuzu (Citrus junos, a seedless variety of yuzu) according to harvesting period and extraction condition. High-performance liquid chromatography (HPLC) was used to identify the functional components. To evaluate the neuroprotective properties, scopolamine was used to induce cholinergic dysfunction in human neuroblastoma SH-SY5Y cells pretreated with yuzu extracts. Among the harvesting periods, September provided the optimum fruit weight of yuzu and relatively high amounts of total phenolics (3.67 mg/g DW), flavonoids (10.13 mg/g DW), and 2,2-diphenyl-1-picrylhydrazyl (DPPH) scavenging activity (29.10 μg Vit. C eq.). Of the functional compounds, hesperidin (13.57 mg/100 g DW) and naringin (5.84 mg/100 g DW) were the highest in 5% (w/v) yuzu extracted with 80% ethanol and this extract showed the highest DPPH (289.2 μg Vit. C eq.) scavenging activity. This same extract showed the highest cell viability and lowest cortisol or acetylcholinesterase content in scopolamine-treated SH-SY5Y cells. These results indicate that ‘Tadanishiki’ yuzu harvested in September should be extracted at 5% (w/v) yuzu with 80% EtOH, and this extract might be useful for application as a natural functional additive

Multidimensional Scaling by Deterministic Annealing with Iterative Majorization Algorithm

Abstract—Multidimensional Scaling (MDS) is a dimension reduction method for information visualization, which is set up as a non-linear optimization problem. It is applicable to many data intensive scientific problems including studies of DNA sequences but tends to get trapped in local minima. Deterministic Annealing (DA) has been applied to many optimization problems to avoid local minima. We apply DA approach to MDS problem in this paper and show that our proposed DA approach improves the mapping quality and shows high reliability in a variety of experimental results. Further its execution time is similar to that of the un-annealed approach. We use different data sets for comparing the proposed DA approach with both a well known algorithm called SMACOF and a MDS with distance smoothing method which aims to avoid local optima. Our proposed DA method outperforms SMACOF algorithm and the distance smoothing MDS algorithm in terms of the mapping quality and shows much less sensitivity with respect to initial configurations and stopping condition. We also investigate various temperature cooling parameters for our deterministic annealing method within an exponential cooling scheme. I

Light-chain amyloidosis presenting with rapidly progressive submucosal hemorrhage of the stomach

SummaryThe gastrointestinal tract is frequently in involved light-chain (AL) amyloidosis, but significant hemorrhagic complications are rare. A 71-year-old man presented to our hospital with dyspepsia and heartburn for 1 month. Gastroscopy revealed a large submucosal hematoma at the gastric fundus. Two days later, a follow-up gastroscopy indicated extensive expansion of the hematoma throughout the upper half of the stomach. The hematoma displayed ongoing expansion during the endoscopic examination, suggesting that rupture was imminent. Emergency total gastrectomy was performed, and amyloidosis was confirmed after examining the surgical specimen. Bone marrow examination revealed multiple myeloma, and serum immunoglobulin assay confirmed the diagnosis of myeloma-associated AL amyloidosis. At manuscript submission, the patient was doing well and was undergoing chemotherapy

PwRn1, a novel Ty3/gypsy-like retrotransposon of Paragonimus westermani: molecular characters and its differentially preserved mobile potential according to host chromosomal polyploidy

<p>Abstract</p> <p>Background</p> <p>Retrotransposons have been known to involve in the remodeling and evolution of host genome. These reverse transcribing elements, which show a complex evolutionary pathway with diverse intermediate forms, have been comprehensively analyzed from a wide range of host genomes, while the information remains limited to only a few species in the phylum Platyhelminthes.</p> <p>Results</p> <p>A LTR retrotransposon and its homologs with a strong phylogenetic affinity toward <it>CsRn1 </it>of <it>Clonorchis sinensis </it>were isolated from a trematode parasite <it>Paragonimus westermani </it>via a degenerate PCR method and from an insect species <it>Anopheles gambiae </it>by <it>in silico </it>analysis of the whole mosquito genome, respectively. These elements, designated <it>PwRn1 </it>and <it>AgCR-1 </it>– <it>AgCR-14 </it>conserved unique features including a t-RNA^Trpprimer binding site and the unusual CHCC signature of Gag proteins. Their flanking LTRs displayed >97% nucleotide identities and thus, these elements were likely to have expanded recently in the trematode and insect genomes. They evolved heterogeneous expression strategies: a single fused ORF, two separate ORFs with an identical reading frame and two ORFs overlapped by -1 frameshifting. Phylogenetic analyses suggested that the elements with the separate ORFs had evolved from an ancestral form(s) with the overlapped ORFs. The mobile potential of <it>PwRn1 </it>was likely to be maintained differentially in association with the karyotype of host genomes, as was examined by the presence/absence of intergenomic polymorphism and mRNA transcripts.</p> <p>Conclusion</p> <p>Our results on the structural diversity of <it>CsRn1</it>-like elements can provide a molecular tool to dissect a more detailed evolutionary episode of LTR retrotransposons. The <it>PwRn1</it>-associated genomic polymorphism, which is substantial in diploids, will also be informative in addressing genomic diversification following inter-/intra-specific hybridization in <it>P. westermani </it>populations.</p

Browsing large scale cheminformatics data with dimension reduction

Visualization of large-scale high dimensional data tool is highly valuable for scientific discovery in many fields. We present PubChemBrowse, a customized visualization tool for cheminformatics research. It provides a novel 3D data point browser that displays complex properties of massive data on commodity clients. As in GIS browsers for Earth and Environment data, chemical compounds with similar properties are nearby in the browser. PubChemBrowse is built around in-house high performance parallel MDS (Multi-Dimensional Scaling) and GTM (Generative Topographic Mapping) services and supports fast interaction with an external property database. These properties can be overlaid on 3D mapped compound space or queried for individual points. We prototype the use with Chem2Bio2RDF system using SPARQL query language to access over 20 publicly accessible bioinformatics databases. We describe our design and implementation of the integrated PubChemBrowse application and outline its use in drug discovery. The same core technologies can be used to develop similar high dimensional browsers in other scientific areas. 1

Parallel Data Mining on Multicore Clusters”, gcc

Abstract-The ever increasing number of cores per chip will be accompanied by a pervasive data deluge whose size will probably increase even faster than CPU core count over the next few years. This suggests the importance of parallel data analysis and data mining applications with good multicore, cluster and grid performance. This paper considers data clustering, mixture models and dimensional reduction presenting a unified framework applicable to bioinformatics, cheminformatics and demographics. Deterministic annealing is used to lessen effect of local minima. We present performance results on clusters of 2-8 core systems identifying effects from cache, runtime fluctuations, synchronization and memory bandwidth. We discuss needed programming model and compare with MPI and other approaches

Role of age and sex in determining antibiotic resistance in febrile urinary tract infections

SummaryObjectivesTo identify the age- and sex-specific antimicrobial susceptibility patterns of Gram-negative bacteria (GNB) in outpatient febrile urinary tract infections (UTIs) in Korea.MethodsA total 2262 consecutive samples collected from patients aged 1–101 years with febrile UTIs, during the period January 2012 to December 2014, were analyzed in this multicentre, retrospective cohort study.ResultsThe sensitivities to cefotaxime and cefoxitin were over 85% for females but under 75% for males. Sex played an important role in the susceptibility of GNB to cefotaxime (p<0.001) and cefoxitin (p<0.001). The sensitivity to ciprofloxacin (age >20 years) was under 75% in both sexes, and was not influenced by sex (p=0.204). Age distributions of the incidences of resistance to cefotaxime, cefoxitin, and ciprofloxacin (age >20 years) were similar to the age distribution of the incidence of GNB, which indicates that the resistance patterns to these drugs were not affected by age (Kolmogorov–Smirnov test, female/male: p=0.927/p=0.509, p=0.193/p=0.911, and p=0.077/p=0.999, respectively).ConclusionsAge is not a considerable factor in determining the antibiotic resistance in febrile UTIs. Ciprofloxacin should be withheld from both sexes until culture results indicate its use. Second- or third-generation cephalosporins such as cefoxitin and cefotaxime can be used empirically only in females

HEAT TRANSFER IN WAVY DUCT WITH DIFFERENT CORRUGATION ANGLE

ABSTRACT The present study investigates the effects of duct corrugation angle and flow velocity on the convective heat/mass transfer characteristics in wavy ducts applied in a primary surface heat exchanger. Local heat/mass transfer coefficients on the corrugated duct sidewall are determined using a naphthalene sublimation technique. The flow visualization technique is used to understand the overall flow structures inside the duct. The corrugation angles of the wavy ducts are 145º and 130º, and the duct aspect ratio is fixed at 7.3. The Reynolds numbers, based on the duct hydraulic diameter, vary from 1,000 to 5,000. The results show that secondary vortex flow cells, called TaylorGörtler vortices, exist periodically in the wavy duct. Therefore, non-uniform distributions of the heat/mass transfer coefficients are obtained on the duct walls. On the pressure-side wall, high heat/mass transfer cell-shaped regions appear due to the secondary vortex flows for both corrugation angles. On the suction-side wall, the heat transfer coefficients are lower than those on the pressure-side wall. The wavy duct with the corrugation angle of 130º has the stronger strength of the secondary vortex cells resulting in higher heat/mass transfer rates on the duct wall because the sharp turn enhances the development of the secondary flow cells

The socio-economic transition and health professions education in Mongolia: a qualitative study

Background Former socialist countries have undergone a socio-economic transition in recent decades. New challenges for the healthcare system have arisen in the transition economy, leading to demands for better management and development of the health professions. However, few studies have explored the effects of this transition on health professions education. Thus, we investigated the effects of the socio-economic transition on the health professions education system in Mongolia, a transition economy country, and to identify changes in requirements. Methods We used a multi-level perspective to explore the effects of the transition, including the input, process, and output levels of the health professions education system. The input level refers to planning and management, the process level refers to the actual delivery of educational services, and the output level refers to issues related to the health professionals, produced by the system. This study utilized a qualitative research design, including document review and interviews with local representatives. Content analysis and the constant comparative method were used for data analysis. Results We explored tensions in the three levels of the health professions education system. First, medical schools attained academic authority for planning and management without proper regulation and financial support. The government sets tuition fees, which are the only financial resource of medical schools; thus, medical schools attempt to enroll more students in order to adapt to the market environment. Second, the quality of educational services varies across institutions due to the absence of a core curriculum and differences in the learning environment. After the transition, the number of private medical schools rapidly increased without quality control, while hospitals started their own specialized training programs. Third, health professionals are struggling to maintain their professional values and development in the market environment. Fixed salaries lead to a lack of motivation, and quality evaluation measures more likely reflect government control than quality improvement. Conclusions Mongolia continues to face the consequences of the socio-economic transition. Medical schools lack of financial authority, the varying quality of educational services, and poor professional development are the major adverse effects. Finding external financial support, developing a core curriculum, and reforming a payment system are recommended

Interpolative multidimensional scaling techniques for the identification of clusters in very large sequence sets

<p>Abstract</p> <p>Background</p> <p>Modern pyrosequencing techniques make it possible to study complex bacterial populations, such as <it>16S rRNA</it>, directly from environmental or clinical samples without the need for laboratory purification. Alignment of sequences across the resultant large data sets (100,000+ sequences) is of particular interest for the purpose of identifying potential gene clusters and families, but such analysis represents a daunting computational task. The aim of this work is the development of an efficient pipeline for the clustering of large sequence read sets.</p> <p>Methods</p> <p>Pairwise alignment techniques are used here to calculate genetic distances between sequence pairs. These methods are pleasingly parallel and have been shown to more accurately reflect accurate genetic distances in highly variable regions of <it>rRNA </it>genes than do traditional multiple sequence alignment (MSA) approaches. By utilizing Needleman-Wunsch (NW) pairwise alignment in conjunction with novel implementations of interpolative multidimensional scaling (MDS), we have developed an effective method for visualizing massive biosequence data sets and quickly identifying potential gene clusters.</p> <p>Results</p> <p>This study demonstrates the use of interpolative MDS to obtain clustering results that are qualitatively similar to those obtained through full MDS, but with substantial cost savings. In particular, the wall clock time required to cluster a set of 100,000 sequences has been reduced from seven hours to less than one hour through the use of interpolative MDS.</p> <p>Conclusions</p> <p>Although work remains to be done in selecting the optimal training set size for interpolative MDS, substantial computational cost savings will allow us to cluster much larger sequence sets in the future.</p