GBParsy: A GenBank flatfile parser library with high speed

<p>Abstract</p> <p>Background</p> <p>GenBank flatfile (GBF) format is one of the most popular sequence file formats because of its detailed sequence features and ease of readability. To use the data in the file by a computer, a parsing process is required and is performed according to a given grammar for the sequence and the description in a GBF. Currently, several parser libraries for the GBF have been developed. However, with the accumulation of DNA sequence information from eukaryotic chromosomes, parsing a eukaryotic genome sequence with these libraries inevitably takes a long time, due to the large GBF file and its correspondingly large genomic nucleotide sequence and related feature information. Thus, there is significant need to develop a parsing program with high speed and efficient use of system memory.</p> <p>Results</p> <p>We developed a library, GBParsy, which was C language-based and parses GBF files. The parsing speed was maximized by using content-specified functions in place of regular expressions that are flexible but slow. In addition, we optimized an algorithm related to memory usage so that it also increased parsing performance and efficiency of memory usage. GBParsy is at least 5 - 100× faster than current parsers in benchmark tests.</p> <p>Conclusion</p> <p>GBParsy is estimated to extract annotated information from almost 100 Mb of a GenBank flatfile for chromosomal sequence information within a second. Thus, it should be used for a variety of applications such as on-time visualization of a genome at a web site.</p

Testing a priority-based queue model with Linux command histories

We study human dynamics by analyzing Linux history files. The goodness-of-fit test shows that most of the collected datasets belong to the universality class suggested in the literature by a variable-length queueing process based on priority. In order to check the validity of this model, we design two tests based on mutual information between time intervals and a mathematical relationship known as the arcsine law. Since the previously suggested queueing process fails to pass these tests, the result suggests that the modelling of human dynamics should properly consider the statistical dependency in the temporal dimension.Comment: 17 pages, 17 figure

Enhanced Electrokinetic Transport of Sulfate in Saline Soil

The electrokinetic transport of sulfate was investigated as a means of treating and restoring a sulfate-accumulating saline soil. The electrokinetic treatment decreased the electrical conductivity of the soil, an indicator of soil salinity, to 58.6%, 73.1%, and 83.5% for 7, 14 and 21 days, respectively. More than 96% of the chloride and nitrate were removed within 7 days. However, the removal of sulfate was highly influenced by the anode material. An iron anode removed sulfate effectively, whereas, sulfate was hyper-accumulated in the anodic region when an inert anode was used. The iron anode was oxidized in a sacrificial anodic reaction, which competed with the electrolysis reaction of water at the anode, and finally the reaction prevented the severe acidification of the soil in the anodic region. However, the competing reactions produced hydrogen ions at the anode, and the ions were transported toward the cathode, which, in turn, acidified the soil, especially, in the anodic region. The acidification switched the surface charge of the soil from negative to positive, increasing the interaction between the soil surface and sulfate, and thus inhibiting the transport of sulfate under the electric field. The zeta potential analysis of the soil provided an explanation. The results indicate that preventing severe acidification is an important factor which influences the transport of anions and iron anode for the enhanced removal of anionic pollutants by electrokinetic remediation

Enhancement of phase separation in the InGaN layer for self-assembled In-rich quantum dots

The enhancement of phase separation in the InGaN layer grown on a GaN layer with a rough surface was investigated for the formation of self-assembled In-rich quantum dots(QDs) in the InGaN layer. Transmission electron microscopy images showed that In-rich QDs with a size of 2–5 nm were formed even in an InGaN layer with a low indium content, and a layer thickness less than the critical thickness. The room-temperature photoluminescence(PL) spectrum of this layer showed emission peaks corresponding to In-rich QDs. The temperature-dependent PL spectra showed dominant peak shifts to the lower energy side, indicating that the self-assembled In-rich QDs are formed in the InGaN layer grown on a rough GaNsurface and that the carriers are localized in In-rich QDs

Immunization Dynamics on a 2-layer Network Model

We introduce a 2-layer network model for the study of the immunization dynamics in epidemics. Spreading of an epidemic is modeled as an excitatory process in a small-world network (body layer) while immunization by prevention for the disease as a dynamic process in a scale-free network (head layer). It is shown that prevention indeed turns periodic rages of an epidemic into small fluctuation. The study also reveals that, in a certain situation, prevention actually plays an adverse role and helps the disease survive. We argue that the presence of two different characteristic time scales contributes to the immunization dynamics observed.Comment: 5 pages, 7 figure

Assessment of Soil Washing for Simultaneous Removal of Heavy Metals and Low-Level Petroleum Hydrocarbons Using Various Washing Solutions

Bench-scale soil washing experiments were conducted for simultaneous removal of heavy metals (Pb, Cu, Zn) and low-level petroleum hydrocarbon contaminants from soils. Various washing solutions including hydrochloric acid (HCl), nitric acid (HNO3), sulfuric acid (H2SO4), tartaric acid (C4H6O6) and ethylenediaminetetraacetic acid (C10H16N2O8, EDTA) were used. The concentration of the washing solutions ranged from 0.1 to 3M with a liquid-to-solid ratio of 10. The soil washing results showed that hydrochloric acid (HCl) was the best washing solution at 3M for heavy metal removal. Other washing solutions also showed a significant removal of heavy metals, except for sulfuric acid (H2SO4). Sulfuric acid (H2SO4) exhibited the worst performance among all washing solutions used with respect to Pb removal. 1M HCl and HNO3were sufficient for effective Pb and Cu removal, and all of the tested washing solutions at a concentration of 0.1M produced results compliant with the Korean warning standard for Zn removal. In the case of total petroleum hydrocarbons (TPH), tartaric acid (C4H6O6) produced the highest removals at all concentration levels compared with other washing solutions. More specifically, TPH removal efficiencies exceeded 33 and 82 % at the lowest (0.1M) and highest (3M) tartaric acid (TA) concentrations, respectively. Overall, TA could be a viable washing solution for the removal of both heavy metals (Pb, Cu, Zn) and TPH from contaminated soils

Identification of replicative senescence-associated genes in human umbilical vein endothelial cells by an annealing control primer system

Cellular senescence is regulated by specific genes in many organisms. The identification and functional analysis of senescence-associated genes could provide valuable insights into the senescence process. Here, we employed a new and improved differential display reverse transcription-polymerase chain reaction (DDRT-PCR) method that involves annealing control primers (ACPs) to identify genes that are differentially expressed in human umbilical endothelial cells during replicative senescence. Using 120 ACPs, we identified 31 differentially expressed genes (DEGs). Basic local alignment search tool (BLAST) search revealed 29 known genes and two unknown genes. Expression levels of the 29 known genes were confirmed by real-time quantitative RT-RCR and by Western blotting for eight of these genes. CD9 antigen, MHC class I chain-related sequence A (MICA) and cell division cycle 37 homolog (CDC37) were up-regulated, and bone morphogenetic protein 4 (BMP4), dickkopf-1 (DKK1), and transcription factor 7-like 1 (TCF7L1) were down-regulated in old cells. Treatment with recombinant human MICA caused a decrease in cell proliferation and an increase in senescence-associated beta-galactosidase staining. Further analysis of differentially expressed genes may provide insights into the molecular basis of replicative senescence and vascular diseases associated with cellular senescence

Safety and Effectiveness of the Novel Catheter 3.0 System for Diagnostic Cerebral Angiography: A Pilot Study

Purpose The purpose of this study was to evaluate the safety and effectiveness of a new angiographic system (Catheter 3.0 system) using a 5 French (Fr), large-bore angiography catheter, a 0.032-inch stiff guidewire, and a continuous flushing system in diagnostic cerebral angiography. Materials and Methods This retrospective study included 30 consecutive patients who underwent transfemoral cerebral angiography using the Catheter 3.0 system from October 2019 to March 2020. As the control group, we included 30 consecutive patients examined before the Catheter 3.0 system was introduced. Procedural outcomes, including technical success, procedure time, dose metrics, procedure-related complications, and image quality were reviewed and analyzed. Results All transfemoral cerebral angiographies were performed for a diagnosis of unruptured intracranial aneurysms. The Catheter 3.0 system showed a significantly shorter fluoroscopy time (6.2 vs. 9.7 minutes, P=0.008) and lower fluoroscopy dose (387.2 vs. 614.4, P=0.002) compared with the conventional 4-Fr catheter system. The Catheter 3.0 system also showed better results in terms of procedural time (21.0 vs. 22.5 minutes, P=0.072) and technical success rate (98.1% vs. 94.0%, P=0.078), although a statistical significance was not reached. The complication rate and qualitative assessment of the digital subtraction angiography (DSA) image quality were similar between the two groups. Conclusion The Catheter 3.0 system using a 5 Fr catheter with a large inner diameter was convenient, effective, and safe compared with the conventional system in diagnostic cerebrovascular angiography

Combined effects of aerobic exercise and 40-Hz light flicker exposure on early cognitive impairments in Alzheimer’s disease of 3×Tg mice

Alzheimer’s disease (AD) is a progressive degenerative brain disease and the primary cause of dementia. At an early stage, AD is generally characterized by short-term memory impairment, owing to dysfunctions of the cortex and hippocampus. We previously reported that a combination of exercise and 40-Hz light flickering can protect against AD-related neuroinflammation, gamma oscillations, reduction in Aβ, and cognitive decline. Therefore, we sought to extend our previous findings to the 5-mo-old 3×Tg-AD mouse model to examine whether the same favorable effects occur in earlier stages of cognitive dysfunction. We investigated the effects of 12 wk of exercise combined with 40-Hz light flickering on cognitive function by analyzing neuroinflammation, mitochondrial function, and neuroplasticity in the hippocampus in a 3×Tg-AD mouse model. Five-month-old 3×Tg-AD mice performed 12 wk of exercise with 40-Hz light flickering administered independently and in combination. Spatial learning and memory, long-term memory, hippocampal Aβ, tau, neuroinflammation, proinflammatory cytokine expression, mitochondrial function, and neuroplasticity were analyzed. Aβ and tau proteins levels were significantly reduced in the early stage of AD, resulting in protection against cognitive decline by reducing neuroinflammation and proinflammatory cytokines. Furthermore, mitochondrial function improved, apoptosis was reduced, and synapse-related protein expression increased. Overall, exercise with 40-Hz light flickering was significantly more effective than exercise or 40-Hz light flickering alone, and the improvement was comparable to the levels in the nontransgenic aged-match control group. Our results indicate a synergistic effect of exercise and 40-Hz light flickering on pathological improvements in the hippocampus during early AD-associated cognitive impairment