Calculations of random fixed point index

AbstractIn this paper, we prove an important inequality and investigate some new calculating problems of random fixed point index, and generalize famous theorem by means of the theory of random fixed point index

The collapse of gene complement following whole genome duplication

Abstract Background Genome amplification through duplication or proliferation of transposable elements has its counterpart in genome reduction, by elimination of DNA or by gene inactivation. Whether loss is primarily due to excision of random length DNA fragments or the inactivation of one gene at a time is controversial. Reduction after whole genome duplication (WGD) represents an inexorable collapse in gene complement. Results We compare fifteen genomes descending from six eukaryotic WGD events 20-450 Mya. We characterize the collapse over time through the distribution of runs of reduced paralog pairs in duplicated segments. Descendant genomes of the same WGD event behave as replicates. Choice of paralog pairs to be reduced is random except for some resistant regions of contiguous pairs. For those paralog pairs that are reduced, conserved copies tend to concentrate on one chromosome. Conclusions Both the contiguous regions of reduction-resistant pairs and the concentration of runs of single copy genes on a single chromosome are evidence of transcriptional co-regulation, dosage sensitivity or other functional interaction constraining the reduction process. These constraints and their evolution over time show a consistent pattern across evolutionary domains and a highly reproducible pattern, as replicates, for the several descendants of a single WGD

Scaffold filling, contig fusion and comparative gene order inference

<p>Abstract</p> <p>Background</p> <p>There has been a trend in increasing the phylogenetic scope of genome sequencing without finishing the sequence of the genome. Increasing numbers of genomes are being published in scaffold or contig form. Rearrangement algorithms, however, including gene order-based phylogenetic tools, require whole genome data on gene order or syntenic block order. How then can we use rearrangement algorithms to compare genomes available in scaffold form only? Can the comparative evidence predict the location of unsequenced genes?</p> <p>Results</p> <p>Our method involves optimally filling in genes missing from the scaffolds, while incorporating the augmented scaffolds directly into the rearrangement algorithms as if they were chromosomes. This is accomplished by an exact, polynomial-time algorithm. We then correct for the number of extra fusion/fission operations required to make scaffolds comparable to full assemblies. We model the relationship between the ratio of missing genes actually absent from the genome versus merely unsequenced ones, on one hand, and the increase of genomic distance after scaffold filling, on the other. We estimate the parameters of this model through simulations and by comparing the angiosperm genomes <it>Ricinus communis </it>and <it>Vitis vinifera</it>.</p> <p>Conclusions</p> <p>The algorithm solves the comparison of genomes with 18,300 genes, including 4500 missing from one genome, in less than a minute on a MacBook, putting virtually all genomes within range of the method.</p

Optimization of Microwave Vacuum Drying and Pretreatment Methods for Polygonum cuspidatum

This study was conducted to optimize the drying process of Polygonum cuspidatum slices using an orthogonal experimental design. The combined effects of pretreatment methods, vacuum pressure and temperature of inner material, drying kinetics, color value, and retention of the indicator compounds were investigated. Seven mathematical models on thin-layer drying were used to study and analyze the drying kinetics. Pretreatment method with blanching for 30 s at 100°C increased the intensity of the red color of P. cuspidatum slices compared with other pretreatment methods and fresh P. cuspidatum slices. P. cuspidatum slices dried at 60°C retained more indicator compounds. Furthermore, microwave pretreatment methods, followed by microwave vacuum for 200 mbar at 50°C, resulted in high concentration of indicator compounds, with short drying time and less energy. This optimized condition for microwave vacuum drying and pretreatment methods would be useful for processing P. cuspidatum. The Newton, Page, and Wang and Singh models slightly fitted the microwave vacuum drying system. The logarithmic, Henderson and Pabis, two-term, and Midilli et al. models can be used to scale up the microwave vacuum drying system to a commercial scale. The two-term and Midilli et al. models were the best fitting mathematical models for the no-pretreatment case at 600 mbar and 60°C

Serum N‐glycans outperform CA19‐9 in diagnosis of extrahepatic cholangiocarcinoma

Extensive efforts have been devoted to improve the diagnosis of extrahepatic cholangiocarcinoma (ECCA) due to its silent clinical character and lack of effective diagnostic biomarkers. Specific alterations in N‐glycosylation of glycoproteins are considered a key component in cancer progression, which can serve as a distinct molecular signature for cancer detection. This study aims to find potential serum N‐glycan markers for ECCA. In total, 255 serum samples from patients with ECCA (n = 106), benign bile tract disease (BBD, n = 60) and healthy controls (HC, n = 89) were recruited. Only 2 μL of serum from individual patients was used in this assay where the N‐glycome of serum glycoproteins was profiled by DNA sequencer‐assisted fluorophore‐assisted capillary electrophoresis (DSA‐FACE) technology. Multi‐parameter models were constructed by combining the N‐glycans and carbohydrate antigen 19‐9 (CA19‐9) which is currently used clinically. Quantitative analyses showed that among 13 N‐glycan structures, the bifucosylated triantennary N‐glycan (peak10, NA3F2) presented the best diagnostic performance for distinguishing ECCA from BBD and HC. Two diagnostic models (Glycotest1 and Glycotest2) performed better than single N‐glycan or CA19‐9. Additionally, two N‐glycan structures (peak9, NA3Fb; peak12, NA4Fb) were tightly related to lymph node metastasis in ECCA patients. In conclusion, sera of ECCA showed relatively specific N‐glycome profiling patterns. Serum N‐glycan markers and models are novel, valuable and noninvasive alternatives in ECCA diagnosis and progression monitoring.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/139072/1/elps6272.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/139072/2/elps6272_am.pd

Organic matter provenance and depositional environment of marine-to-continental mudstones and coals in eastern Ordos Basin, China—Evidence from molecular geochemistry and petrology

Cyclothems, composed of interbedded mudstone, coal and sandstone layers, make up the Taiyuan and Shanxi Formations in the Late Carboniferous to Early Permian in North China under a marine-to-continental depositional environment. The cyclothems act as important fossil energy hosts, such as coalbeds, hydrocarbon source rocks and unconventional natural gas reservoirs. Organic geochemistry and petrology of mudstones and coals in the Taiyuan and Shanxi Formations in the eastern Ordos Basin were studied to reveal the organic matter sources and paleoenvironments. Total organic carbon (TOC) contents vary from 1.1 wt% (mudstone) to 72.6 wt% (coal). The samples are mainly within the oil window, with the Tmax values ranging from 433 to 469 °C. Organic petrology and source biomarkers indicate that the mudstones were sourced from a mixed organic matter input, and terrigenous organic matter predominates over aquatic organic matter. The coals are mostly sourced by terrigenous organic matter inputs. High concentrations of hopanes argue for a strong bacterial input. Some m/z 217 mass chromatograms have peaks at the hopanes' retention times as a result of high hopane to sterane ratios. These hopane-derived peaks do not interfere the identification of the steranes because the hopanes and the steranes have different retention times. Maturity-dependent biomarkers demonstrate that the samples have been thermally mature, which agree with the Tmax values. Anomalously low C29 20S/(20S + 20R) and C29 ββ/(ββ + αα) sterane ratios are present in all the samples, and are interpreted as due to the terrigenous organic matter input or the coal-related depositional environment. In addition, biomarkers and iron sulfide morphology indicate that the organic matter of the mudstones deposited in a proximal setting with shallow, brackish/fresh water bodies. With consideration of preservation of organic matter, the redox conditions are dysoxic. Redox oscillations resulted in the records of oxic conditions in some samples. Finally, the coals and the mudstones mainly generate gas and have poor oil generative potential

AENet: attention efficient network for cross-view image geo-localization

To address the problem that task-irrelevant objects such as cars, pedestrians and sky, will interfere with the extracted feature descriptors in cross-view image geo-localization, this paper proposes a novel method for cross-view image geo-localization, named as AENet. The method includes two main parts: an attention efficient network fusing channel and spatial attention mechanisms and a triplet loss function based on a multiple hard samples weighting strategy. In the first part, the EfficientNetV2 network is used to extract features from the images and preliminarily filter irrelevant features from the channel dimension, then the Triplet Attention layer is applied to further filter irrelevant features from the spatial dimension. In the second part, a multiple hard samples weighting strategy is proposed to enhance the learning of hard samples. Experimental results show that our proposed method significantly outperforms the state-of-the-art method on two existing benchmark datasets

Prediction of steady-state plasma concentrations of olanzapine in Chinese Han in patients based on a retrospective population pharmacokinetic model

Purpose: To develop robust methods of establishing a population pharmacokinetics (Pop-PK) model of olanzapine, using existing hospital in-patient information, in order to predict the steady-state plasma concentration of olanzapine tablets in Chinese Han inpatients, thus providing guidance for individualized therapy for mental disorders.Methods: A retrospective study analyzing and predicting the steady-state plasma olanzapineconcentration was performed using nonlinear mixed-effect modeling (Phoenix® NLME8). The effects of ten potential covariates, including age, gender, Body Mass Index, fasting lipid, family history, alcohol and smoking status in 107 Chinese Han patients with steady-state plasma olanzapine concentration were collected from the hospital information system (HIS) in Wuhan Mental Health Center from Feb 2017 to Jul 2019.Results: The final model was validated using bootstrap and visual predictive check (VPC) and was found to fit the one-compartment mixed error model. Smoking status was found to be the only factor affecting olanzapine tablets clearance. The standard Pop-PK parameters apparent volume of distribution (VL/F) and clearance (CL/F) were 223 L and 12.4 Lꞏh-1, respectively.Conclusion: The Pop-PK model for olanzapine established with the data from HIS is effective inpredicting the plasma olanzapine tablets concentration of individual Chinese in-patients. This Pop-PK model approach can now be adapted to optimize other antipsychotic drugs