Antralization at the edge of proximal gastric ulcers: Does Helicobacter pylori infection play a role?

Aim: To determine the prevalence of antralization at the edge of proximal gastric ulcers, and the effect of H. pylori eradication on the mucosal appearances. Methods: Biopsies were taken from the antrum, body and the ulcer edge of patients with benign proximal gastric ulcers before and one year after treatment. Gastric mucosa was classified as antral, transitional or body type. H. pylori positive patients received either triple therapy, or omeprazole. Results: Patients with index ulcers in the incisura, body or fundus (n=116) were analyzed. Antral-type mucosa was more prevalent at the ulcer edge in H. pylori-positive patients than H. pylori-negative patients (93 % vs 60 %, OR=8.95, 95 %CI: 2.47-32.4, P=0.001). At one year, there was a significant reduction in the prevalence of antralization (from 93 % to 61 %, P=0.004) at the ulcer edge in patients with H. pylori being eradicated. However, there was no difference in the prevalence of antralization at the ulcer edge in those with persistent infection. Conclusion: H. pylori infection is associated with antralization at the edge of proximal gastric ulcers, which may be reversible in some patients after eradication of the infection.published_or_final_versio

Composition of gut microbiota in infants in China and global comparison

published_or_final_versio

Tunable Multifunctional Topological Insulators in Ternary Heusler Compounds

Recently the Quantum Spin Hall effect (QSH) was theoretically predicted and experimentally realized in a quantum wells based on binary semiconductor HgTe[1-3]. QSH state and topological insulators are the new states of quantum matter interesting both for fundamental condensed matter physics and material science[1-11]. Many of Heusler compounds with C1b structure are ternary semiconductors which are structurally and electronically related to the binary semiconductors. The diversity of Heusler materials opens wide possibilities for tuning the band gap and setting the desired band inversion by choosing compounds with appropriate hybridization strength (by lattice parameter) and the magnitude of spin-orbit coupling (by the atomic charge). Based on the first-principle calculations we demonstrate that around fifty Heusler compounds show the band inversion similar to HgTe. The topological state in these zero-gap semiconductors can be created by applying strain or by designing an appropriate quantum well structure, similar to the case of HgTe. Many of these ternary zero-gap semiconductors (LnAuPb, LnPdBi, LnPtSb and LnPtBi) contain the rare earth element Ln which can realize additional properties ranging from superconductivity (e. g. LaPtBi[12]) to magnetism (e. g. GdPtBi[13]) and heavy-fermion behavior (e. g. YbPtBi[14]). These properties can open new research directions in realizing the quantized anomalous Hall effect and topological superconductors.Comment: 20 pages, 5 figure

Mathematical-based microbiome analytics for clinical translation

This is the final version. Available on open access from Elsevier via the DOI in this recordTraditionally, human microbiology has been strongly built on the laboratory focused culture of microbes isolated from human specimens in patients with acute or chronic infection. These approaches primarily view human disease through the lens of a single species and its relevant clinical setting however such approaches fail to account for the surrounding environment and wide microbial diversity that exists in vivo. Given the emergence of next generation sequencing technologies and advancing bioinformatic pipelines, researchers now have unprecedented capabilities to characterise the human microbiome in terms of its taxonomy, function, antibiotic resistance and even bacteriophages. Despite this, an analysis of microbial communities has largely been restricted to ordination, ecological measures, and discriminant taxa analysis. This is predominantly due to a lack of suitable computational tools to facilitate microbiome analytics. In this review, we first evaluate the key concerns related to the inherent structure of microbiome datasets which include its compositionality and batch effects. We describe the available and emerging analytical techniques including integrative analysis, machine learning, microbial association networks, topological data analysis (TDA) and mathematical modelling. We also present how these methods may translate to clinical settings including tools for implementation. Mathematical based analytics for microbiome analysis represents a promising avenue for clinical translation across a range of acute and chronic disease states.Singapore Ministry of Health’s National Medical Research CouncilNanyang Technological University, SingaporeEngineering and Physical Sciences Research Council (EPSRC

Manipulating infrared photons using plasmons in transparent graphene superlattices

Superlattices are artificial periodic nanostructures which can control the flow of electrons. Their operation typically relies on the periodic modulation of the electric potential in the direction of electron wave propagation. Here we demonstrate transparent graphene superlattices which can manipulate infrared photons utilizing the collective oscillations of carriers, i.e., plasmons of the ensemble of multiple graphene layers. The superlattice is formed by depositing alternating wafer-scale graphene sheets and thin insulating layers, followed by patterning them all together into 3-dimensional photonic-crystal-like structures. We demonstrate experimentally that the collective oscillation of Dirac fermions in such graphene superlattices is unambiguously nonclassical: compared to doping single layer graphene, distributing carriers into multiple graphene layers strongly enhances the plasmonic resonance frequency and magnitude, which is fundamentally different from that in a conventional semiconductor superlattice. This property allows us to construct widely tunable far-infrared notch filters with 8.2 dB rejection ratio and terahertz linear polarizers with 9.5 dB extinction ratio, using a superlattice with merely five graphene atomic layers. Moreover, an unpatterned superlattice shields up to 97.5% of the electromagnetic radiations below 1.2 terahertz. This demonstration also opens an avenue for the realization of other transparent mid- and far-infrared photonic devices such as detectors, modulators, and 3-dimensional meta-material systems.Comment: under revie

Exciton properties in zincblende InGaN-GaN quantum wells under the effects of intense laser fields

ABSTRACT: In this work, we study the exciton states in a zincblende InGaN/GaN quantum well using a variational technique. The system is considered under the action of intense laser fields with the incorporation of a direct current electric field as an additional external probe. The effects of these external influences as well as of the changes in the geometry of the heterostructure on the exciton binding energy are discussed in detail

A transient homotypic interaction model for the influenza A virus NS1 protein effector domain

Influenza A virus NS1 protein is a multifunctional virulence factor consisting of an RNA binding domain (RBD), a short linker, an effector domain (ED), and a C-terminal 'tail'. Although poorly understood, NS1 multimerization may autoregulate its actions. While RBD dimerization seems functionally conserved, two possible apo ED dimers have been proposed (helix-helix and strand-strand). Here, we analyze all available RBD, ED, and full-length NS1 structures, including four novel crystal structures obtained using EDs from divergent human and avian viruses, as well as two forms of a monomeric ED mutant. The data reveal the helix-helix interface as the only strictly conserved ED homodimeric contact. Furthermore, a mutant NS1 unable to form the helix-helix dimer is compromised in its ability to bind dsRNA efficiently, implying that ED multimerization influences RBD activity. Our bioinformatical work also suggests that the helix-helix interface is variable and transient, thereby allowing two ED monomers to twist relative to one another and possibly separate. In this regard, we found a mAb that recognizes NS1 via a residue completely buried within the ED helix-helix interface, and which may help highlight potential different conformational populations of NS1 (putatively termed 'helix-closed' and 'helix-open') in virus-infected cells. 'Helix-closed' conformations appear to enhance dsRNA binding, and 'helix-open' conformations allow otherwise inaccessible interactions with host factors. Our data support a new model of NS1 regulation in which the RBD remains dimeric throughout infection, while the ED switches between several quaternary states in order to expand its functional space. Such a concept may be applicable to other small multifunctional proteins

Compromised BRCA1-PALB2 interaction is associated with breast cancer risk.

The major breast cancer suppressor proteins BRCA1 and BRCA2 play essential roles in homologous recombination (HR)-mediated DNA repair, which is thought to be critical for tumor suppression. The two BRCA proteins are linked by a third tumor suppressor, PALB2, in the HR pathway. While truncating mutations in these genes are generally pathogenic, interpretation of missense variants remains a challenge. To date, patient-derived missense variants that disrupt PALB2 binding have been identified in BRCA1 and BRCA2; however, there has not been sufficient evidence to prove their pathogenicity in humans, and no variants in PALB2 that disrupt either its BRCA1 or BRCA2 binding have been reported. Here we report on the identification of a novel PALB2 variant, c.104T>C (p.L35P), that segregates in a family with a strong history of breast cancer. Functional analyses showed that L35P abrogates the PALB2-BRCA1 interaction and completely disables its abilities to promote HR and confer resistance to platinum salts and PARP inhibitors. Whole-exome sequencing of a breast cancer from a c.104T>C carrier revealed a second, somatic, truncating mutation affecting PALB2, and the tumor displays hallmark genomic features of tumors with BRCA mutations and HR defects, cementing the pathogenicity of L35P. Parallel analyses of other germline variants in the PALB2 N-terminal BRCA1-binding domain identified multiple variants that affect HR function to varying degrees, suggesting their possible contribution to cancer development. Our findings establish L35P as the first pathogenic missense mutation in PALB2 and directly demonstrate the requirement of the PALB2-BRCA1 interaction for breast cancer suppression

The incidence of liver injury in Uyghur patients treated for TB in Xinjiang Uyghur autonomous region, China, and its association with hepatic enzyme polymorphisms nat2, cyp2e1, gstm1 and gstt1.

BACKGROUND AND OBJECTIVE: Of three first-line anti-tuberculosis (anti-TB) drugs, isoniazid is most commonly associated with hepatotoxicity. Differences in INH-induced toxicity have been attributed to genetic variability at several loci, NAT2, CYP2E1, GSTM1and GSTT1, that code for drug-metabolizing enzymes. This study evaluated whether the polymorphisms in these enzymes were associated with an increased risk of anti-TB drug-induced hepatitis in patients and could potentially be used to identify patients at risk of liver injury. METHODS AND DESIGN: In a cross-sectional study, 2244 tuberculosis patients were assessed two months after the start of treatment. Anti-TB drug-induced liver injury (ATLI) was defined as an ALT, AST or bilirubin value more than twice the upper limit of normal. NAT2, CYP2E1, GSTM1 and GSTT1 genotypes were determined using the PCR/ligase detection reaction assays. RESULTS: 2244 patients were evaluated, there were 89 cases of ATLI, a prevalence of 4% 9 patients (0.4%) had ALT levels more than 5 times the upper limit of normal. The prevalence of ATLI was greater among men than women, and there was a weak association with NAT2*5 genotypes, with ATLI more common among patients with the NAT2*5*CT genotype. The sensitivity of the CT genotype for identifying patients with ATLI was 42% and the positive predictive value 5.9%. CT ATLI was more common among slow acetylators (prevalence ratio 2.0 (95% CI 0.95,4.20) )compared to rapid acetylators. There was no evidence that ATLI was associated with CYP2E1 RsaIc1/c1genotype, CYP2E1 RsaIc1/c2 or c2/c2 genotypes, or GSTM1/GSTT1 null genotypes. CONCLUSIONS: In Xinjiang Uyghur TB patients, liver injury was associated with the genetic variant NAT2*5, however the genetic markers studied are unlikely to be useful for screening patients due to the low sensitivity and low positive predictive values for identifying persons at risk of liver injury

Study on Resistance Switching Properties of Na0.5Bi0.5TiO3Thin Films Using Impedance Spectroscopy

The Na0.5Bi0.5TiO3(NBT) thin films sandwiched between Au electrodes and fluorine-doped tin oxide (FTO) conducting glass were deposited using a sol–gel method. Based on electrochemical workstation measurements, reproducible resistance switching characteristics and negative differential resistances were obtained at room temperature. A local impedance spectroscopy measurement of Au/NBT was performed to reveal the interface-related electrical characteristics. The DC-bias-dependent impedance spectra suggested the occurrence of charge and mass transfer at the interface of the Au/NBT/FTO device. It was proposed that the first and the second ionization of oxygen vacancies are responsible for the conduction in the low- and high-resistance states, respectively. The experimental results showed high potential for nonvolatile memory applications in NBT thin films