Cloud Computing-Based TagSNP Selection Algorithm for Human Genome Data

Single nucleotide polymorphisms (SNPs) play a fundamental role in human genetic variation and are used in medical diagnostics, phylogeny construction, and drug design. They provide the highest-resolution genetic fingerprint for identifying disease associations and human features. Haplotypes are regions of linked genetic variants that are closely spaced on the genome and tend to be inherited together. Genetics research has revealed SNPs within certain haplotype blocks that introduce few distinct common haplotypes into most of the population. Haplotype block structures are used in association-based methods to map disease genes. In this paper, we propose an efficient algorithm for identifying haplotype blocks in the genome. In chromosomal haplotype data retrieved from the HapMap project website, the proposed algorithm identified longer haplotype blocks than an existing algorithm. To enhance its performance, we extended the proposed algorithm into a parallel algorithm that copies data in parallel via the Hadoop MapReduce framework. The proposed MapReduce-paralleled combinatorial algorithm performed well on real-world data obtained from the HapMap dataset; the improvement in computational efficiency was proportional to the number of processors used

Preparation and Evaluation of Novel Transfersomes Combined with the Natural Antioxidant Resveratrol

Resveratrol (tran-3,5,4′-trihydroxystibene, RSV) is a kind of polyphenol which has anti-inflammatory, antioxidant, anti-allergy, and anti-cancer properties, as well as being a scavenger of free radicals and preventing cardiovascular diseases. However, it is quite unstable in light, heat, and other conditions, and decays easily due to environmental factors. For these reasons, this study used a new type of carrier, transfersome, to encapsulate RSV. Transfersome consists of phosphatidyl choline (PC) from a liposomal system and non-ionic edge activators (EA). EA are an important ingredient in the formulation of transfersome; they can enhance the flexibility of the lipid bimolecular membrane of transfersome. Due to its ultradeformability, it also allows drugs to penetrate the skin, even through the stratum corneum. We hope that this new encapsulation technique will improve the stability and enhance the permeability of RSV. Concluding all the tested parameters, the best production condition was 5% PC/EA (3:1) and 5% ethanol in distilled water, with an ultrasonic bath and stirring at 500 rpm, followed by high pressure homogenization. The optimal particle size was 40.13 ± 0.51 nm and the entrapment efficiency (EE) was 59.93 ± 0.99%. The results of antioxidant activity analysis showed that transfersomes were comparable to the RSV group (unencapsulated). During in vitro transdermal delivery analysis, after 6 h, D1-20(W) increased 27.59% by accumulation. Cell viability assay showed that the cytotoxicity of D3-80(W) was reduced by 34.45% compared with the same concentration of RSV. Therefore, we successfully prepared RSV transfersomes and also improved the stability, solubility, and safety of RSV

Composition Analysis and Feature Selection of the Oral Microbiota Associated with Periodontal Disease

Periodontitis is an inflammatory disease involving complex interactions between oral microorganisms and the host immune response. Understanding the structure of the microbiota community associated with periodontitis is essential for improving classifications and diagnoses of various types of periodontal diseases and will facilitate clinical decision-making. In this study, we used a 16S rRNA metagenomics approach to investigate and compare the compositions of the microbiota communities from 76 subgingival plagues samples, including 26 from healthy individuals and 50 from patients with periodontitis. Furthermore, we propose a novel feature selection algorithm for selecting features with more information from many variables with a combination of these features and machine learning methods were used to construct prediction models for predicting the health status of patients with periodontal disease. We identified a total of 12 phyla, 124 genera, and 355 species and observed differences between health- and periodontitis-associated bacterial communities at all phylogenetic levels. We discovered that the genera Porphyromonas, Treponema, Tannerella, Filifactor, and Aggregatibacter were more abundant in patients with periodontal disease, whereas Streptococcus, Haemophilus, Capnocytophaga, Gemella, Campylobacter, and Granulicatella were found at higher levels in healthy controls. Using our feature selection algorithm, random forests performed better in terms of predictive power than other methods and consumed the least amount of computational time

An observational study of extending FOLFOX chemotherapy, lengthening the interval between radiotherapy and surgery, and enhancing pathological complete response rates in rectal cancer patients following preoperative chemoradiotherapy

Introduction: Patients with rectal cancer who exhibit a pathologic complete response to preoperative concurrent chemoradiotherapy have excellent oncologic outcomes. In this study, we evaluated the potential advantages of adding oxaliplatin to preoperative fluoropyrimidine-based chemoradiotherapy administered in rectal cancer patients. Methods: A total of 78 patients with rectal cancer were enrolled. Patients were administered chemoradiotherapy, which comprised radiotherapy and chemotherapy involving a 5-fluorouracil, leucovorin, and oxaliplatin regimen every 2 weeks. Surgery was performed 10–12 weeks after radiotherapy completion. Tumor regression, adverse events, surgical complications, and short-term clinical outcomes were recorded. Results: Two patients were excluded because of incomplete radiotherapy treatment or refusal of surgery. Eventually, 76 patients underwent total mesorectal excision and no perioperative mortality was observed. Of these, 20 patients (25.6%) developed grade 3 or 4 toxicity during concurrent chemoradiotherapy. Among the 76 patients who underwent surgery, 24 (31.6%) patients achieved a pathologic complete response. The sphincter preservation rate was 96.1% (73/76) in all patients and 92.2% (39/42) in patients with tumors located less than 5 cm from the anal verge. The 2-year overall and disease-free survivals were 94% and 87.4%, respectively. Conclusion: The intensified multimodality therapy was well tolerated in our cohort and resulted in a considerably high pathologic complete response rate. Regardless of favorable short-term clinical outcomes, long-term oncologic outcomes will be closely monitored among the patients with a pathologic complete response

The Association between DNA Copy Number Aberrations at Chromosome 5q22 and Gastric Cancer

<div><p>Background</p><p>Gastric cancer is common cancer. Discovering novel genetic biomarkers might help to identify high-risk individuals. Copy number variation (CNV) has recently been shown to influence risk for several cancers. The aim of the present study was sought to test the association between copy number at a variant region and GC.</p><p>Methods</p><p>A total of 110 gastric cancer patients and 325 healthy volunteers were enrolled in this study. We searched for a CNV and found a CNV (Variation 7468) containing part of the <i>APC</i> gene, the <i>SRP19</i> gene and the <i>REEP5</i> gene. We chose four probes targeting at <i>APC-intron8</i>, <i>APC-exon9</i>, <i>SRP19</i> and <i>REEP5</i> to interrogate this CNV. Specific Taqman probes labeled by different reporter fluorophores were used in a real-time PCR platform to obtain copy number. Both the original non-integer data and transformed integer data on copy number were used for analyses.</p><p>Results</p><p>Gastric caner patients had a lower non-integer copy number than controls for the <i>APC-exon9</i> probe (Adjusted p = 0.026) and <i>SRP19</i> probe (Adjusted p = 0.002). The analysis of integer copy number yielded a similar pattern although less significant (Adjusted p = 0.07 for <i>APC-exon9</i> probe and Adjusted p = 0.02 for <i>SRP19</i> probe).</p><p>Conclusions</p><p>Losses of a CNV at 5q22, especially in the DNA region surrounding <i>APC-exon 9</i>, may be associated with a higher risk of gastric cancer.</p></div

Predictive Value of FOLFOX-Based Regimen, Long Interval, Hemoglobin Levels and Clinical Negative Nodal Status, and Postchemoradiotherapy CEA Levels for Pathological Complete Response in Patients with Locally Advanced Rectal Cancer after Neoadjuvant Chemoradiotherapy

We aimed to identify predictors of a pathological complete response (pCR) in patients with locally advanced rectal cancer (LARC) following a multimodality therapy. We retrospectively reviewed 236 patients with LARC treated with neoadjuvant chemoradiotherapy (CRT) followed by radical resection from January 2011 to December 2017. Patients were administered CRT, which comprised radiotherapy and chemotherapy with an oxaliplatin plus 5-fluorouracil- or fluoropyrimidine-based regimen. Clinical factors were correlated with treatment response. The multivariate logistic regression revealed that a negative nodal stage (odds ratio (OR) = 3.2, P=0.0135), a high hemoglobin level (>10 g/dL) during neoadjuvant CRT (OR = 3.067, P=0.0125), an oxaliplatin-containing neoadjuvant CRT (OR = 5.385, P=0.0044), a long interval (>8 weeks) between radiotherapy and surgery (OR = 1.135, P=0.0469), and a post-CRT CEA ≤2 ng/mL (OR = 2.891, P=0.0233) were the independent predictors of increased pCR rates. The prediction nomogram was developed according to the above independent variables. The concordance index was 0.74, and the calibration curve showed good agreement. In summary, negative nodal stages, high hemoglobin levels during treatment, oxaliplatin-containing neoadjuvant therapy, a long radiotherapy-surgery interval (>8 weeks), and post-CRT CEA levels ≤2 ng/mL were favorable predictors of a pCR. This prediction nomogram might be crucial for patients with LARC undergoing a multimodality therapy