Isomorphism and Similarity for 2-Generation Pedigrees

We consider the emerging problem of comparing the similarity between (unlabeled) pedigrees. More specifically, we focus on the simplest pedigrees, namely, the 2-generation pedigrees. We show that the isomorphism testing for two 2-generation pedigrees is GI-hard. If the 2-generation pedigrees are monogamous (i.e., each individual at level-1 can mate with exactly one partner) then the isomorphism testing problem can be solved in polynomial time. We then consider the problem by relaxing it into an NP-complete decomposition problem which can be formulated as the Minimum Common Integer Pair Partition (MCIPP) problem, which we show to be FPT by exploiting a property of the optimal solution. While there is still some difficulty to overcome, this lays down a solid foundation for this research

Ontogenetic development of gonads and external sexual characters of the protandric simultaneous hermaphrodite peppermint shrimp, Lysmata vittata (Caridea: Hippolytidae)

© 2019 Chen et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The peppermint shrimp Lysmata vittata (Caridea: Hippolytidae) is a marine caridean shrimp popular in marine aquarium trade. The species is known to display the sexual system of protandric simultaneous hermaphrodite. In this study, based on captive bred specimens, the complete ontogenetic gonad development of L. vittata was studied both morphologically and histologically, from newly settled juveniles until they reached euhermaphrodite phase. It was found that in all specimens examined (carapace length: 1.8-8.5 mm), including the newly settled juveniles, possessed ovotestes, which comprised of an anterior ovarian and a posterior testicular part. Based on both morphological (e.g., size, color and shape) and histological features (e.g., oogenesis and spermatogenesis), four gonadal development stages were defined and described for L. vittata. From Stage I to III, the testicular part of the gonad became gradually mature but the ovarian part was still immature, which is defined as the male phase. At the male phase, cincinulli (5-8 hooks) presented at the tips of the appendix interna on the first pair of pleopods while appendices masculinae (AM), in a form of a stick structure with spines, presented at the inner edge of the appendix interna (AI) on the second pair of pleopods. At Stage IV, both the testicular part and the ovarian part were mature and hence is defined as euhermaphrodite phase. At the euhermaphrodite phase, most individuals lacked cincinulli and appendices masculinae on the first and second pair of pleopods respectively. This is the first time that complete ontogenetic gonadal and external sexual character development have been described and staged for a species from the genus Lysmata from newly settled juveniles to euhermaphrodite phase

Computational identification of rare codons of Escherichia coli based on codon pairs preference

<p>Abstract</p> <p>Background</p> <p>Codon bias is believed to play an important role in the control of gene expression. In <it>Escherichia coli</it>, some rare codons, which can limit the expression level of exogenous protein, have been defined by gene engineering operations. Previous studies have confirmed the existence of codon pair's preference in many genomes, but the underlying cause of this bias has not been well established. Here we focus on the patterns of rarely-used synonymous codons. A novel method was introduced to identify the rare codons merely by codon pair bias in <it>Escherichia coli</it>.</p> <p>Results</p> <p>In <it>Escherichia coli</it>, we defined the "rare codon pairs" by calculating the frequency of occurrence of all codon pairs in coding sequences. Rare codons which are disliked in genes could make great contributions to forming rare codon pairs. Meanwhile our investigation showed that many of these rare codon pairs contain termination codons and the recognized sites of restriction enzymes. Furthermore, a new index (F_rare) was developed. Through comparison with the classical indices we found a significant negative correlation between F_rareand the indices which depend on reference datasets.</p> <p>Conclusions</p> <p>Our approach suggests that we can identify rare codons by studying the context in which a codon lies. Also, the frequency of rare codons (F_rare) could be a useful index of codon bias regardless of the lack of expression abundance information.</p

Non-ideal optical isotropy of blue phase liquid crystal

Since 1981, blue phase liquid crystal (BPLC) was regarded as optical isotropy and high contrast ratio (CR) should be achieved easily. However, low CR of BPLC display was reported in all literatures. Here, we show BPLC is non-ideal optical isotropy which leads to poor CR. In our report, BPLC not only revealed primary structure of double-twist cylinder and secondary structure of lattice but also revealed tertiary structure of self-alignment on electrode surface. This finding will be useful to improve CR and inspire researches in display industry and academics

Optical rotatory power of polymer-stabilized blue phase liquid crystals

Macroscopically, a polymer-stabilized blue phase liquid crystal (BPLC) is assumed to be an optically isotropic medium. Our experiment challenges this assumption. Our results indicate that the optical rotatory power (ORP) of some nano-scale double-twist cylinders in a BPLC composite causes the polarization axis of the transmitted light to rotate a small angle, which in turn leaks through the crossed polarizers. Rotating the analyzer in azimuthal direction to correct this ORP can greatly improve the contrast ratio. A modified De Vries equation based on a thin twisted-nematic layer is proposed to explain the observed phenomena

Utilization of BIM in the construction of a submarine tunnel: a case study in Xiamen city, China

Building information modeling (BIM) is an emerging technology that can effectively solve the problems of information dispersion, complex personnel management, and lack of construction supervision, which often occur during the construction of tunnel engineering. Taking the construction of Haicang Tunnel in Xiamen, China as a case study, the utilization of BIM technology in the design stage, the construction simulation and operation are demonstrated during the full-life cycle of the project. During the construction of Haicang Tunnel, the technologies of BIM 3D, BIM 4D, BIM 5D, and Cloud Platform are used to make the construction process controllable and to facilitate the implementation and deployment of construction plans. BIM 3D is a visualization method to show the detailed model in the construction. The design is optimized by the navigation collision function of BIM 3D. BIM 4D adds the time schedule into BIM 3D model to show the construction schedule. BIM 5D adds the cost into BIM 4D model to show the construction consumption. The methods of BIM 4D and BIM 5D can assist the engineering management in allocating resources and funds in the project. Cloud Platform is used to effectively implement information management

Bioactivity in silica/poly(γ-glutamic acid) sol–gel hybrids through calcium chelation

Bioactive glasses and inorganic/organic hybrids have great potential as biomedical implant materials. Sol–gel hybrids with interpenetrating networks of silica and biodegradable polymers can combine the bioactive properties of a glass with the toughness of a polymer. However, traditional calcium sources such as calcium nitrate and calcium chloride are unsuitable for hybrids. In this study calcium was incorporated by chelation to the polymer component. The calcium salt form of poly(γ-glutamic acid) (γCaPGA) was synthesized for use as both a calcium source and as the biodegradable toughening component of the hybrids. Hybrids of 40 wt.% γCaPGA were successfully formed and had fine scale integration of Ca and Si ions, according to secondary ion mass spectrometry imaging, indicating a homogeneous distribution of organic and inorganic components. 29Si magic angle spinning nuclear magnetic resonance data demonstrated that the network connectivity was unaltered with changing polymer molecular weight, as there was no perturbation to the overall Si speciation and silica network formation. Upon immersion in simulated body fluid a hydroxycarbonate apatite surface layer formed on the hybrids within 1 week. The polymer molecular weight (Mw 30–120 kDa) affected the mechanical properties of the resulting hybrids, but all hybrids had large strains to failure, >26%, and compressive strengths, in excess of 300 MPa. The large strain to failure values showed that γCaPGA hybrids exhibited non-brittle behaviour whilst also incorporating calcium. Thus calcium incorporation by chelation to the polymer component is justified as a novel approach in hybrids for biomedical materials

Hippo Signaling Suppresses Cell Ploidy and Tumorigenesis through Skp2

大多数真核生物的体细胞是二倍体，即仅含有两组染色体，分别遗传自父本和母本。而一些特定组织如心脏、肝脏等就含有多倍体细胞，特别是肝脏组织含有较高比例的四、八倍体等多倍体细胞。肝脏是人体的重要解毒器官，同时酒精、肝炎病毒等毒性物质或毒性代谢物容易诱发肝细胞的基因突变，多倍体被认为有利于提供代偿性的正常基因来维持肝脏稳态。然而肝脏受损后，多倍体细胞将会受胁迫进行增殖，再生修复受损的肝组织。因此研究机体调控多倍体细胞产生及多倍体细胞进行细胞分裂的调控机理对于理解肝癌的发病机理和肝癌的治疗至关重要。Hippo信号通路在调节组织成体干细胞的分化和增殖，调控器官再生与尺寸大小中具有重要作用。深入研究发现, Hippo信号通路下游效应分子YAP通过AKT-SKP2信号促进二倍体细胞向多倍体转化及多倍体细胞的生长增殖。本项研究阐明了Hippo缺失及YAP激活促进多倍体细胞产生及增殖作为肝癌发生发展中的一个重要机制，为肝癌诊疗提供了新的策略。 周大旺，博士，厦门大学生命科学学院教授、副院长、国家杰出青年基金获得者。【Abstract】Polyploidy can lead to aneuploidy and tumorigenesis. Here, we report that the Hippo pathway effector Yap promotes the diploid-polyploid conversion and polyploid cell growth through the Akt-Skp2 axis. Yap strongly induces the acetyltransferase p300-mediated acetylation of the E3 ligase Skp2 via Akt signaling. Acetylated Skp2 is exclusively localized to the cytosol, which causes hyper-accumulation of the cyclin-dependent kinase inhibitor p27, leading to mitotic arrest and subsequently cell polyploidy. In addition, the pro-apoptotic factors FoxO1/3 are overly degraded by acetylated Skp2, resulting in polyploid cell division, genomic instability, and oncogenesis. importantly, the depletion or inactivation of Akt or Skp2 abrogated Hippo signal deficiency-induced liver tumorigenesis, indicating their epistatic interaction. Thus, we conclude that Hippo-Yap signaling suppresses cell polyploidy and oncogenesis through Skp2.该研究工作获得了国家自然科学基金委、国家重点基础研究发展计划(973)项目、青年千人计划和中央高校基本科研基金的资助。 The Yap (S127A) transgenic mice were kindly provided by Dr. Fernando Camargo from Harvard Medical School, Boston, MA. D.Z. and L.C. were supported by the National Natural Science Foundation of China (31625010,U1505224, and J1310027 to D.Z.; 81422018, U1405225, and 81372617 to L.C.; 81472229 to L.H.), the National Basic Research Program (973) of China (2015CB910502 to L.C.), the Fundamental Research Funds for the Central Universities of China-Xiamen University (20720140551 to L.C. and 2013121034 and 20720140537 to D.Z.)