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We propose a modified alternating positive semidefinite splitting (MAPSS) preconditioner for solving block three-by-three saddle point problems that arise in linear programming and the finite element discretization of Maxwell equations. Spectral properties of the MAPSS-preconditioned matrix are discussed and analyzed in detail. As the efficiency of the MAPSS preconditioner depends on its parameters, we derive fast and effective formulas to compute the quasi-optimal values of these parameters. Numerical examples show that the MAPSS preconditioner performs better than the APSS preconditioner.

Transcription factor 21 (TCF21) has been identified as a candidate tumor suppressor gene which was epigenetically inactivated in a variety of human cancers. However, TCF21 methylation pattern remains unknown in hematologic malignancies. The aim of this study was to investigate TCF21 methylation and its clinical relevance in myelodysplastic syndrome (MDS) and non-M3 acute myeloid leukemia (AML). A total cohort of 33 MDS patients, 100 non-M3 AML patients and 25 healthy donors were enrolled in the study. Targeted bisulfite sequencing assay was performed to identify the methylation pattern of CpG islands within the promoter of TCF21 gene. The bioinformatics analyses were based on The Cancer Genome Atlas (TCGA) database and Gene Expression Omnibus (GEO). The results showed that there were significant differences in the methylation levels of TCF21 between MDS, non-M3 AML and controls (P = 0.003 and < 0.001, respectively). TCF21 hypermethylation might be served as a promising biomarker which could distinguish MDS/AML from normal controls (P < 0.001 and = 0.003, respectively). There was a significant difference in cytogenetic risk categories between TCF21 hypermethylation and non-hypermethylation AML patients (P = 0.032). Notably, TCF21 hypermethylation occurred frequently in AML patients with adverse risk category, compared with those with favorable and intermediate categories, respectively (67% vs 44% and 29%). TCF21 non-hypermethylation AML patients showed a higher probability of normal karyotype than abnormal karyotype (P = 0.003). The rate of DNMT3A gene mutation was significantly higher in the non-hypermethylation AML patients than that in the hypermethylation (8/44 vs 0/34, P = 0.020). These results suggested that aberrant DNA promoter methylation of TCF21 was frequent event in MDS and non-M3 AML, and TCF21 hypermathylation was associated with adverse risk karyotype in AML.

Majorana zero modes are usually attributed to topological superconductors. We study a class of two-dimensional topologically trivial superconductors without chiral edge modes, which nevertheless host robust Majorana zero modes in topological defects. The construction of this minimal single-band model is facilitated by the Hopf map and the Hopf invariant. This work will stimulate investigations of Majorana zero modes in superconductors in the topologically trivial regime., 15 pages, 6 figures, including supplemental material. The published version is slightly shortened

In topological semimetals, the valence band and conduction band meet at zero-dimensional nodal points or one-dimensional nodal rings, which are protected by band topology and symmetries. In this Rapid Communication, we introduce "nodal-link semimetals", which host linked nodal rings in the Brillouin zone. We put forward a general recipe based on the Hopf map for constructing models of nodal-link semimetal. The consequences of nodal ring linking in the Landau levels and Floquet properties are investigated., Comment: 12 pages, 5 figures, including supplemental material. Published version

Topological nodal-line semimetals are characterized by one-dimensional lines of band crossing in the Brillouin zone. In contrast to nodal points, nodal lines can be in topologically nontrivial configurations. In this paper, we study the simplest topologically nontrivial forms of nodal line, namely, a single nodal line taking the shape of a knot in the Brillouin zone. We introduce a generic construction for various "nodal-knot semimetals", which yields the simplest trefoil nodal knot and other more complicated nodal knots in the Brillouin zone. The knotted-unknotted transitions by nodal-line reconnections are also studied. Our work brings the knot theory to the subject of topological semimetals., Comment: 7 pages, 5 figures. Figure quality improved.

Backscattering-immune chiral modes arise along certain line defects in three-dimensional materials. In this paper, we study Floquet chiral modes along Floquet topological defects, namely, the defects come entirely from spatial modulations of periodic driving. We define a precise topological invariant that counts the number of Floquet chiral modes, which is expressed as an integral on a five-dimensional torus parameterized by $(k_x,k_y,k_z,\theta,t)$. This work demonstrates the possibility of creating chiral modes in three-dimensional bulk materials by modulated driving. We hope that it will stimulate further studies of Floquet topological defects., Comment: 11 pages, 7 figures, including supplemental material. Published version

Unidirectional transports have been observed in two-dimensional systems, however, so far they have not been experimentally observed in three-dimensional bulk materials. In this theoretical work we show that the recently discovered Weyl materials provide a platform for unidirectional transports inside bulk materials. With high experimental feasibility, a complex Dirac mass can be generated and manipulated in the photonic Weyl crystals, creating unidirectionally propagating modes observable in transmission experiments. Possible realization in (electronic) Weyl semimetals is also studied. We show in a lattice model that, with a short-range interaction, the desired form of the Dirac mass can be spontaneously generated in a first-order transition., 9 pages, with supplemental material

Five field isolates of infectious bronchitis virus (IBV) were isolated from chicken flocks in the Hubei province of China. The IBVs were characterized by RT-PCR and phylogenetic analysis. The S1 gene sequence of the spike glycoprotein was compared with previously published gene sequences of IBV strains. Analysis of the nucleotide and deduced amino acid sequences revealed that the five isolated strains shared greater than 79% nucleotide and 73% amino acid homology within the S1 region. The nucleotide similarity of the S1 protein gene between the five Chinese IBV isolates and 15 strains of other IBVs varied from 73 to 97%. The identity of the S1 protein gene between the five Chinese IBV isolates and 15 strains of other IBVs varied from 71 to 98%. Most of the sequence variations were observed between amino acids 51-96, 123-156, 218-314, 361-397, and 427-497. Phylogenetic analysis suggested that the five IBV isolates were divided into two genotypes. Four isolates including JS, JZ, XT, and XG formed a cluster together with other Chinese strains with a 99% nucleotide sequence identity and 97% amino acid sequence identity. These isolates belong to group C of IBVs, which was not related to conventional vaccines strains. This group likely represents strains indigenous to China. By contrast, the HP strain was a member of group B, which showed a close relationship with H120 (95% nucleotide similarity and 98% amino acid sequence identities). In conclusion, this study clearly demonstrates that there are at least four groups of IBVs prevailing in China and variant IBV strains continue to emerge. The disease outbreaks might have been caused by infection of multiple strains of IBV. Key words: Infectious bronchitis virus; identification; S1 gene; molecular characteristics; sequencing; phylogenetic analysis.

The nonstructural genes (NS1) of nine H9N2 subtype avian influenza viruses isolated from diseased chickens on different farms during 1998-2005 were amplified by RT-PCR and completely sequenced. The nucleotide and deduced amino acid sequences of NS1 genes of these isolates were compared. The results showed that NS1 genes of all H9N2 isolates contained 654 bp and encoded 217 amino acids. The homologies of the nucleotide and deduced amino sequences of the isolates were 95.4%-99.8% and 93.6%-100%, respectively. Comparison of the amino acid sequences of NS1 proteins of these isolates with other H9N2 viruses demonstrated that NS1 proteins of the nine strains had a deletion of 13 amino acid residues at the carboxyl terminus, which may be the molecule mark of the isolates in mainland China. Phylogenetic analysis revealed that the NS1 genes of these isolates fell into the same lineage and belonged to allele A. Eight out of nine isolates belonged to the CK/SH/F/98-like lineage while only Ck/HN/A3/98 strain belonged to the Ck/HK/Y280/97-like linease. All the isolates were derived from Ck/BJ/1/94 strain which was the first isolate is mainland China in 1994. The results indicated that H9N2 subtype AIV appeared differentiation following the passage of time and the viruses belonging to Ck/SH/F/98-like acquired an epidemic spread advantage in chicken population in mainland China.

NS1 protein is the only non-structural protein of influenza A virus, which is encoded by the collinear mRNA transcribed from the viral RNA segment 8. It is a RNA-banding protein which has important posttranscriptional regulatory activity. It accumulates in the nucleus of the infected cell at early times but is also present in the cytoplasm later in the infection, Two functional domains have been identified in the NS1 protein: a RNA-binding domain at the N-terminus, and an effector domain at the C-terminus, which are associated with the inhibiting host celluar protein synthesis, inducing apoptosis and resisting the production of interferon-alpha/beta. In addition, NS1 protein could provide a means for the distinction between vaccinated and virus-infected poultry and act as a vaccine vector because it can tolerate large inserts of foreign sequences. Moreover, it might be an attractive target for antiviral drug design. All of these demonstrate that NS1 protein have the potential application benefits.

S-layer protein CTC surface display system of Bacillus thuringiensis (Bt) was used to test the possibility of displaying avian influenza virus nucleoprotein (NP) on Bt cell surface. Four recombinant plasmids were constructed by replacing 3'-terminal or central part below the surface anchor sequence slh of S-layer protein gene ctc with full length of np gene or part np gene (npp). The four resulting plasmids were pSNP (harboring fusion gene ctc-np), pCSA-SNP (harboring fusion gene csa-ctc-up, csa represents csaAB operon which is very important to the anchoring of S-layer protein on the bacterial cell surface), pCTC-NPP (harboring fusion gene ctc-npp) and pCSNPP (harboring fusion gene csa-ctc-npp). Five recombinant Bt strains were constructed by electro-transferring recombinant plasmids to Bt plasmid-free derivative strain BMB171. The resulting strains were BN (harboring pSNP), BCN (harboring pSNP as well as the plasmid pMIL-CSA which carried csaAB operon), C-S (harboring pCSA-SNP), BCCN (harboring pCTC-NPP and pMIL-CSA) and CN (harboring pCSNPP). The vegetative cells of five recombinant strains were used as agglutinogens of slide agglutination assay. Slide agglutination assay showed recombinant NP proteins were successfully displayed on the surface of five recombinant strains, respectively. After immunizing mice with vegetative cells of five recombinant strains respectively, five recombinant strains all elicited humoral respones to NP and exhibited immunogenicity as assayed by enzyme-linked immunosorbent assay (ELISA). Meanwhile these assays showed recombinant strain CN (harboring fusion gene csa-ctc-npp) exhibited the highest immunogenicity among five recombinant strains. That means the best way of constructing S-layer fusion gene is csa-ctc-* (* denotes heterologous antigen gene) which means the central part of S-layer protein gene ctc replaced by the heterologous antigen gene and csaAB operon located on the upstream of fusion gene. The strategy developed in this study gives a possibility to generate heat stable,oral, veterinary vaccine with Bt S-layer protein CTC surface display system.