Second harmonic generation and birefringence of some ternary pnictide semiconductors

A first-principles study of the birefringence and the frequency dependent second harmonic generation (SHG) coefficients of the ternary pnictide semiconductors with formula ABC$_2$ (A = Zn, Cd; B = Si, Ge; C = As, P) with the chalcopyrite structures was carried out. We show that a simple empirical observation that a smaller value of the gap is correlated with larger value of SHG is qualitatively true. However, simple inverse power scaling laws between gaps and SHG were not found. Instead, the real value of the nonlinear response is a result of a very delicate balance between different intraband and interband terms.Comment: 13 pages, 12 figure

Evolution of multiple cell clones over a 29-year period of a CLL patient

Chronic lymphocytic leukaemia (CLL) is a frequent B-cell malignancy, characterized by recurrent somatic chromosome alterations and a low level of point mutations. Here we present single-nucleotide polymorphism microarray analyses of a single CLL patient over 29 years of observation and treatment, and transcriptome and whole-genome sequencing at selected time points. We identify chromosome alterations 13q14−, 6q− and 12q+ in early cell clones, elimination of clonal populations following therapy, and subsequent appearance of a clone containing trisomy 12 and chromosome 10 copy-neutral loss of heterogeneity that marks a major population dominant at death. Serial single-cell RNA sequencing reveals an expression pattern with high FOS, JUN and KLF4 at disease acceleration, which resolves following therapy, but reoccurs following relapse and death. Transcriptome evolution indicates complex changes in expression occur over time. In conclusion, CLL can evolve gradually during indolent phases, and undergo rapid changes following therapy

Identification of Gene Signatures Used to Recognize Biological Characteristics of Gastric Cancer upon Gene Expression Data

High-throughput gene expression microarrays can be examined by machine-learning algorithms to identify gene signatures that recognize the biological characteristics of specific human diseases, including cancer, with high sensitivity and specificity. A previous study compared 20 gastric cancer (GC) samples against 20 normal tissue (NT) samples and identified 1,519 differentially expressed genes (DEGs). In this study, Classification Information Index (CII), Information Gain Index (IGI), and RELIEF algorithms are used to mine the previously reported gene expression profiling data. In all, 29 of these genes are identified by all three algorithms and are treated as GC candidate biomarkers. Three biomarkers, COL1A2, ATP4B, and HADHSC, are selected and further examined using quantitative real-time polymerase chain reaction (qRT-PCR) and immunohistochemistry (IHC) staining in two independent sets of GC and normal adjacent tissue (NAT) samples. Our study shows that COL1A2 and HADHSC are the two best biomarkers from the microarray data, distinguishing all GC from the NT, whereas ATP4B is diagnostically significant in lab tests because of its wider range of fold-changes in expression. Herein, a data-mining model applicable for small sample sizes is presented and discussed. Our result suggested that this mining model may be useful in small sample-size studies to identify putative biomarkers and potential biological features of GC

Concurrent alterations in TERT, KDM6A, and the BRCA pathway in bladder cancer

Purpose: Genetic analysis of bladder cancer has revealed a number of frequently altered genes, including frequent alterations of the telomerase (TERT) gene promoter, although few altered genes have been functionally evaluated. Our objective is to characterize alterations observed by exome sequencing and sequencing of the TERT promoter, and to examine the functional relevance of histone lysine (K)-specific demethylase 6A (KDM6A/UTX), a frequently mutated histone demethylase, in bladder cancer.Experimental Design: We analyzed bladder cancer samples from 54 U.S. patients by exome and targeted sequencing and confirmed somatic variants using normal tissue from the same patient. We examined the biologic function of KDM6A using in vivo and in vitro assays.Results: We observed frequent somatic alterations in BRCA1 associated protein-1 (BAP1) in 15% of tumors, including deleterious alterations to the deubiquitinase active site and the nuclear localization signal. BAP1 mutations contribute to a high frequency of tumors with breast cancer (BRCA) DNA repair pathway alterations and were significantly associated with papillary histologic features in tumors. BAP1 and KDM6A mutations significantly co-occurred in tumors. Somatic variants altering the TERT promoter were found in 69% of tumors but were not correlated with alterations in other bladder cancer genes. We examined the function of KDM6A, altered in 24% of tumors, and show depletion in human bladder cancer cells, enhanced in vitro proliferation, in vivo tumor growth, and cell migration.Conclusions: This study is the first to identify frequent BAP1 and BRCA pathway alterations in bladder cancer, show TERT promoter alterations are independent of other bladder cancer gene alterations, and show KDM6A loss is a driver of the bladder cancer phenotype. (C) 2014 AACR

Thigh-length compression stockings and DVT after stroke

Controversy exists as to whether neoadjuvant chemotherapy improves survival in patients with invasive bladder cancer, despite randomised controlled trials of more than 3000 patients. We undertook a systematic review and meta-analysis to assess the effect of such treatment on survival in patients with this disease

Development of a Nanobody–Alkaline Phosphatase Fusion Protein and Its Application in a Highly Sensitive Direct Competitive Fluorescence Enzyme Immunoassay for Detection of Ochratoxin A in Cereal

A rapid and sensitive direct competitive fluorescence enzyme immunoassay (dc-FEIA) for ochratoxin A (OTA) based on a nanobody (Nb)–alkaline phosphatase (AP) fusion protein was developed. The VHH (variable domain of heavy chain antibody) gene of Nb28 was subcloned into the expression vector pecan45 containing the AP double-mutant gene. The Nb28–AP construct was transformed into Escherichia coli BL21­(DE3)­plysS, and soluble expression in bacteria was confirmed by sodium dodecyl sulfate–polyacrylamide gel electrophoresis and Western blot. Both the Nb properties and AP enzymatic activity were validated by colorimetric and fluorometric analysis. The 50% inhibitory concentration and the detection limit of the dc-FEIA were 0.13 and 0.04 ng/mL, respectively, with a linear range of 0.06–0.43 ng/mL. This assay was compared with LC–MS/MS, and the results indicated the reliability of Nb–AP fusion protein-based dc-FEIA for monitoring OTA contamination in cereal

Promotion of Ceria Catalysts by Precious Metals: Changes in Nature of the Interaction under Reducing and Oxidizing Conditions

By depositing ceria over supported precious metal (PM) catalysts and characterizing them with in situ diffuse reflectance UV (DR UV) and in situ Raman spectroscopy, we have been able to prove a direct correlation between a decrease in ceria band gap and the work function of the metal under reducing conditions. The PM–ceria interaction results in changes on the ceria side of the metal–ceria interface, such that the degree of oxygen vacancy formation on the ceria surface also correlates with the precious metal work function. Nevertheless, conclusive evidence for a purely electronic interaction could not be provided by X-ray photoelectron spectroscopy (XPS) analysis. On the contrary, the results highlight the complexity of the PM–ceria interaction by supporting a spillover mechanism resulting from the electronic interaction under reducing conditions. Under oxidizing conditions, another effect has been observed, namely, a structural modification of ceria induced by the presence of PM cations. In particular, we have been able to demonstrate by in situ Raman spectroscopy that, depending on the PM ionic radius, it is possible to create PM–ceria solid solutions. We observed that this structural modification prevails under an oxidizing atmosphere, whereas electronic and chemical interactions take place under reducing conditions