Graph algorithms for the haplotyping problem

Evidence from investigations of genetic differences among human beings shows that genetic diseases are often the results of genetic mutations. The most common form of these mutations is single nucleotide polymorphism (SNP). A complete map of all SNPs in the human genome will be extremely valuable for studying the relationships between specific haplotypes and specific genetic diseases. Some recent discoveries show that the DNA sequence of human beings can be partitioned into long blocks where genetic recombination has been rare. Then, inferring both haplotypes from chromosome sequences is a biologically meaningful research topic, which has compounded mathematical and computational problems.;We are interested in the algorithmic implications to infer haplotypes from long blocks of DNA that have not undergone recombination in populations. The assumption justifies a model of haplotype evolution---haplotypes in a population evolves along a coalescent, based on the standard population-genetic assumption of infinite sites, which as a rooted tree is a perfect phylogeny. The Perfect Phylogeny Haplotyping (PPH) Problem was introduced by Daniel Gusfield in 2002. A nearly linear-time solution to the PPH problem (O( nmalpha(nm)), where alpha is the extremely slowly growing inverse Ackerman function) is provided. However, it is very complex and difficult to implement. So far, even the best practical solution to the PPH problem has the worst-case running time of O( nm2). D. Gusfield conjectured that a linear-time ( O(nm)) solution to the PPH problem should be possible.;We solve the conjecture of Gusfield by introducing a linear-time algorithm for the PPH problem. Different kinds of posets for haplotype matrices and genotype matrices are designed and the relationships between them are studied. Since redundant calculations can be avoided by the transitivity of partial ordering in posets, we design a linear-time (O(nm )) algorithm for the PPH problem that provides all the possible solutions from an input. The algorithm is fully implemented and the simulation shows that it is much faster than previous methods

Interaction of Avelox with Bovine Serum Albumin and Effect of the Coexistent Drugs on the Reaction

The interaction between Avelox and bovine serum albumin (BSA) was investigated at different temperatures by fluorescence spectroscopy. Results showed that Avelox could quench the intrinsic fluorescence of BSA strongly, and the quenching mechanism was a static quenching process with Förester spectroscopy energy transfer. The electrostatic force played an important role on the conjugation reaction between BSA and Avelox. The order of magnitude of binding constants (Ka) was 104, and the number of binding site (n) in the binary system was approximately equal to 1. The binding distance (r) was less than 3 nm and the primary binding site for Avelox was located in subdomain IIA of BSA. Synchronous fluorescence spectra clearly revealed that the microenvironment of amino acid residues and the conformation of BSA were changed during the binding reaction. In addition, the effect of some antibiotics on the binding constant of Avelox with BSA was also studied

Linear Gaussian Bounding Box Representation and Ring-Shaped Rotated Convolution for Oriented Object Detection

In oriented object detection, current representations of oriented bounding boxes (OBBs) often suffer from boundary discontinuity problem. Methods of designing continuous regression losses do not essentially solve this problem. Although Gaussian bounding box (GBB) representation avoids this problem, directly regressing GBB is susceptible to numerical instability. We propose linear GBB (LGBB), a novel OBB representation. By linearly transforming the elements of GBB, LGBB avoids the boundary discontinuity problem and has high numerical stability. In addition, existing convolution-based rotation-sensitive feature extraction methods only have local receptive fields, resulting in slow feature aggregation. We propose ring-shaped rotated convolution (RRC), which adaptively rotates feature maps to arbitrary orientations to extract rotation-sensitive features under a ring-shaped receptive field, rapidly aggregating features and contextual information. Experimental results demonstrate that LGBB and RRC achieve state-of-the-art performance. Furthermore, integrating LGBB and RRC into various models effectively improves detection accuracy

Adaptation of Rice to the Nordic Climate Yields Potential for Rice Cultivation at Most Northerly Site and the Organic Production of Low-Arsenic and High-Protein Rice

There is an urgent demand for low-arsenic rice in the global market, particularly for consumption by small children. Soils in Uppsala, Sweden, contain low concentrations of arsenic (As). We hypothesize that if certain japonica paddy rice varieties can adapt to the cold climate and long day length in Uppsala and produce normal grains, such a variety could be used for organic production of low-arsenic rice for safe rice consumption. A japonica paddy rice variety, "Heijing 5," can be cultivated in Uppsala, Sweden, after several years' adaptation, provided that the rice plants are kept under a simple plastic cover when the temperature is below 10 degrees C. Uppsala-adapted "Heijing 5" has a low concentration of 0.1 mg per kg and high protein content of 12.6% per dry weight in brown rice grain, meaning that it thus complies with all dietary requirements determined by the EU and other countries for small children. The high protein content is particularly good for small children in terms of nutrition. Theoretically, Uppsala-adapted "Heijing 5" can produce a yield of around 5100 kg per ha, and it has a potential for organic production. In addition, we speculate that cultivation of paddy rice can remove nitrogen and phosphorus from Swedish river water and reduce nutrient loads to the Baltic Sea and associated algae blooms

Mechanism of liver regeneration: 20-year bibliometric analyses

Objectives: The study aims to explore the most influential countries, institutions, journals, authors, “research hotspots,” and trends in the study of the mechanism of liver regeneration (MoLR) in the last 20 years using bibliometric analyses.Methods: The literature associated with the MoLR was retrieved from the Web of Science Core Collection on 11 October 2022. CiteSpace 6.1.R6 (64-bit) and VOSviewer 1.6.18 were used for bibliometric analyses.Results: A total of 18,956 authors from 2,900 institutions in 71 countries/regions published 3,563 studies in different academic journals on the MoLR. The United States was the most influential country. The University of Pittsburgh was the institution from which most articles on the MoLR were published. Cunshuan Xu published the most articles on the MoLR, and George K. Michalopoulos was the most frequently co-cited author. Hepatology was the journal in which most articles on the MoLR were published and the most frequently co-cited journal in this field. The research hotspots for the MoLR were origin and subsets of hepatocytes during LR; new factors and pathways in LR regulation; cell therapy for LR; interactions between liver cells in LR; mechanism of the proliferation of residual hepatocytes and trans-differentiation between cells; and prognosis of LR. The emerging topic was the mechanism of regeneration of a severely injured liver.Conclusion: Our bibliometric analyses provide (i) a comprehensive overview of the MoLR; (ii) important clues and ideas for scholars in this field