A method integrating simulation and reinforcement learning for operation scheduling in container terminals

The objective of operation scheduling in container terminals is to determine a schedule that minimizes time for loading or unloading a given set of containers. This paper presents a method integrating reinforcement learning and simulation to optimize operation scheduling in container terminals. The introduced method uses a simulation model to construct the system environment while the Q-learning algorithm (reinforcement learning algorithm) is applied to learn optimal dispatching rules for different equipment (e.g. yard cranes, yard trailers). The optimal scheduling scheme is obtained by the interaction of the Q-learning algorithm and simulation environment. To evaluate the effectiveness of the proposed method, a lower bound is calculated considering the characteristics of the scheduling problem in container terminals. Finally, numerical experiments are provided to illustrate the validity of the proposed method

Investigation of the STR loci noise distributions of PowerSeq Auto System

AimTo characterize the noise and stutter distribution of 23 short tandem repeats (STRs) included in the PowerSeqTM Auto System. MethodsRaw FASTQ files were analyzed using STRait Razor v2s to display alleles and coverage. The sequence noise was divided into several categories: noise at allele position, noise at -1 repeat position, and artifact. The average relative percentages of locus coverage for each noise, stutter, and allele were calculated from the samples used for this locus noise analysis. ResultsStutter products could be routinely observed at the -2 repeat position, -1 repeat position, and +1 repeat position of alleles. Sequence noise at the allele position ranged from 10.22% to 28.81% of the total locus coverage. At the allele position, individual noise reads were relatively low. ConclusionThe data indicate that noise generally will be low. In addition, the PowerSeqTM Auto System could capture nine flanking region single nucleotide polymorphisms (SNPs) that would not be observed by other current kits for massively parallel sequencing (MPS) of STRs

Aqueous extract of Sargentodoxa cuneata alleviates ulcerative colitis and its associated liver injuries in mice through the modulation of intestinal flora and related metabolites

BackgroundUlcerative colitis (UC) is a refractory disease worldwide. Liver injury can be found clinically with UC, and now, it is found that gut dysbiosis is an important mechanism in the pathogenesis of UC. Sargentodoxa cuneata has been used as a traditional Chinese medicine and is commonly used clinically for the treatment of UC. The main objective of this study was to investigate the intrinsic mechanisms of Sargentodoxa cuneata in the treatment of UC and its associated liver injuries from the perspective of intestinal flora and related metabolites.MethodsUltra-performance liquid chromatography-mass spectrometry was used to identify the components in the aqueous extract of Sargentodoxa cuneata (AESc). Mice with UC induced by dextran sulfate sodium were used to study the effects of AESc on UC and its associated liver injuries. Furthermore, 16S rRNA gene sequencing and analysis were performed on intestinal contents, and correlation analysis of intestinal flora with short-chain fatty acids (SCFAs) and organic acids was performed.ResultsA total of 114 compounds were identified in AESc. AESc improved disease activity index scores, liver index, and colon length in mice with UC and had a good protective effect on intestine and liver injuries. Moreover, the administration of AESc regulated gut microbiota dysbiosis and the levels of a few SCFAs and organic acids in mice with UC. In addition, the correlation analysis results showed that the Megamonas and Bifidobacterium were the key intestinal flora related to the levels of differential SCFAs and organic acids in mice with UC after AESc intervention.ConclusionAESc has a good protective effect on UC and UC related liver injuries. Modulation of the intestinal flora and its metabolites (SCFAs and a few organic acids) is an important pathway for AESc in the treatment of UC and also provides a rationale for the clinical use of Sargentodoxa cuneata in the treatment of UC

Underlying Data for Sequencing the Mitochondrial Genome with the Massively Parallel Sequencing Platform Ion Torrent (TM) PGM (TM)

Background: Massively parallel sequencing (MPS) technologies have the capacity to sequence targeted regions or whole genomes of multiple nucleic acid samples with high coverage by sequencing millions of DNA fragments simultaneously. Compared with Sanger sequencing, MPS also can reduce labor and cost on a per nucleotide basis and indeed on a per sample basis. In this study, whole genomes of human mitochondria (mtGenome) were sequenced on the Personal Genome Machine (PGM (TM)) (Life Technologies, San Francisco, CA), the out data were assessed, and the results were compared with data previously generated on the MiSeq (TM) (Illumina, San Diego, CA). The objectives of this paper were to determine the feasibility, accuracy, and reliability of sequence data obtained from the PGM. Results: 24 samples were multiplexed (in groups of six) and sequenced on the at least 10 megabase throughput 314 chip. The depth of coverage pattern was similar among all 24 samples; however the coverage across the genome varied. For strand bias, the average ratio of coverage between the forward and reverse strands at each nucleotide position indicated that two-thirds of the positions of the genome had ratios that were greater than 0.5. A few sites had more extreme strand bias. Another observation was that 156 positions had a false deletion rate greater than 0.15 in one or more individuals. There were 31-98 (SNP) mtGenome variants observed per sample for the 24 samples analyzed. The total 1237 (SNP) variants were concordant between the results from the PGM and MiSeq. The quality scores for haplogroup assignment for all 24 samples ranged between 88.8%-100%. Conclusions: In this study, mtDNA sequence data generated from the PGM were analyzed and the output evaluated. Depth of coverage variation and strand bias were identified but generally were infrequent and did not impact reliability of variant calls. Multiplexing of samples was demonstrated which can improve throughput and reduce cost per sample analyzed. Overall, the results of this study, based on orthogonal concordance testing and phylogenetic scrutiny, supported that whole mtGenome sequence data with high accuracy can be obtained using the PGM platform.Peer reviewe

Comparative tolerance of two massively parallel sequencing systems to common PCR inhibitors

Human remains can be severely affected by the environment, and the DNA may be damaged, degraded, and/or inhibited. In this study, a DNA sample (at 1 ng DNA target input in triplicate) was spiked with five concentrations of five inhibitors (humic acid, melanin, hematin, collagen, and calcium) and sequenced with both the HID-Ion AmpliSeq (TM) Library Kit and ID panel on the Ion PGM (TM) System and the ForenSeq DNA Signature Prep Kit on the MiSeq FGx (TM). The objective of this study was to compare the baseline tolerance of the two sequencing chemistries and platforms to common inhibitors encountered in human remains recovered from missing person cases. The two chemistries generally were comparable but not always susceptible to the same inhibitors or at the same capacity. The HID-Ion AmpliSeq (TM) Library Kit and ID panel and the ForenSeq DNA Signature Prep Kit both were susceptible to humic acid, melanin, and collagen; however, the ForenSeq kit showed greater inhibition to melanin and collagen than the AmpliSeq (TM) kit. In contrast, the ForenSeq kit was resistant to the effects of hematin and calcium, whereas the AmpliSeq (TM) kit was highly inhibited by hematin. Short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) showed the same trend among inhibitors when using the ForenSeq kit. Generally, locus read depth, heterozygote allele balance, and the numbers of alleles typed were inversely correlated with increasing inhibitor concentration. The larger STR loci were affected more so by the presence of inhibitors compared to smaller STR amplicons and SNP loci. Additionally, it does not appear that sequence noise is affected by the inhibitors. The noise percentage, however, does increase as the inhibitor concentration increases, due to the decrease in locus read depth and not likely because of chemistry effects

Impact of Water Level Fluctuations on Landslide Deformation at Longyangxia Reservoir, Qinghai Province, China

The construction of Longyangxia Reservoir has altered the hydrogeological conditions of its banks. Infiltration and erosion caused by the periodic rise and fall of the water level leads to collapse of the reservoir banks and local deformation of the landslide. Due to heterogeneous topographic characteristics across the region, water level also varies between different location. Previous research on the influence of fluctuations in reservoir water level on landslide deformation has focused on single-point monitoring of specific slopes, and single-point water level monitoring data have often been used instead of water level data for the entire reservoir region. In addition, integrated remote sensing methods have seldom been used for regional analysis. In this study, the freely-available Landsat8 OLI and Sentinel-2 data were used to extract the water level of Longyangxia Reservoir using the NDWI method, and Sentinel-1A data were used to obtain landslide deformation time series using SBAS-InSAR technology. Taking the Chana, Chaxi, and Mangla River Estuary landslides (each having different reservoir water level depths) as typical examples, the influence of changes in reservoir water level on the deformation of three wading landslides was analyzed. Our main conclusions are as follows: First, the change in water level is the primary external factor controlling the deformation velocity and trend of landslides in the Longyangxia Reservoir, with falling water levels having the greatest influence. Second, the displacement of the Longyangxia Reservoir landslides lags water level changes by 0 to 62 days. Finally, this study provides a new method applicable other areas without water level monitoring data

Data_Sheet_1_Aqueous extract of Sargentodoxa cuneata alleviates ulcerative colitis and its associated liver injuries in mice through the modulation of intestinal flora and related metabolites.docx

BackgroundUlcerative colitis (UC) is a refractory disease worldwide. Liver injury can be found clinically with UC, and now, it is found that gut dysbiosis is an important mechanism in the pathogenesis of UC. Sargentodoxa cuneata has been used as a traditional Chinese medicine and is commonly used clinically for the treatment of UC. The main objective of this study was to investigate the intrinsic mechanisms of Sargentodoxa cuneata in the treatment of UC and its associated liver injuries from the perspective of intestinal flora and related metabolites.MethodsUltra-performance liquid chromatography-mass spectrometry was used to identify the components in the aqueous extract of Sargentodoxa cuneata (AESc). Mice with UC induced by dextran sulfate sodium were used to study the effects of AESc on UC and its associated liver injuries. Furthermore, 16S rRNA gene sequencing and analysis were performed on intestinal contents, and correlation analysis of intestinal flora with short-chain fatty acids (SCFAs) and organic acids was performed.ResultsA total of 114 compounds were identified in AESc. AESc improved disease activity index scores, liver index, and colon length in mice with UC and had a good protective effect on intestine and liver injuries. Moreover, the administration of AESc regulated gut microbiota dysbiosis and the levels of a few SCFAs and organic acids in mice with UC. In addition, the correlation analysis results showed that the Megamonas and Bifidobacterium were the key intestinal flora related to the levels of differential SCFAs and organic acids in mice with UC after AESc intervention.ConclusionAESc has a good protective effect on UC and UC related liver injuries. Modulation of the intestinal flora and its metabolites (SCFAs and a few organic acids) is an important pathway for AESc in the treatment of UC and also provides a rationale for the clinical use of Sargentodoxa cuneata in the treatment of UC.</p