Robust Likelihood-Based Survival Modeling with Microarray Data

Gene expression data can be associated with various clinical outcomes. In particular, these data can be of importance in discovering survival-associated genes for medical applications. As alternatives to traditional statistical methods, sophisticated methods and software programs have been developed to overcome the high-dimensional difficulty of microarray data. Nevertheless, new algorithms and software programs are needed to include practical functions such as the discovery of multiple sets of survival-associated genes and the incorporation of risk factors, and to use in the R environment which many statisticians are familiar with. For survival modeling with microarray data, we have developed a software program (called rbsurv) which can be used conveniently and interactively in the R environment. This program selects survival-associated genes based on the partial likelihood of the Cox model and separates training and validation sets of samples for robustness. It can discover multiple sets of genes by iterative forward selection rather than one large set of genes. It can also allow adjustment for risk factors in microarray survival modeling. This software package, the rbsurv package, can be used to discover survival-associated genes with microarray data conveniently.

A rare case of primary malignant small cell carcinoma combined with urothelial cell carcinoma in the ureter

BACKGROUND: Extrapulmonary small cell carcinomas have been reported in a variety of organs, and their incidence in the genitourinary tract is second only to that in the gastrointestinal tract. To date, however, only a few cases of small cell carcinoma of the ureter have been reported. Because the extreme rarity of this type of carcinoma, its clinical behaviour, diagnostic methods, and effective treatment modalities have not yet been determined. CASE PRESENTATION: A 59-year-old man presented with a 1-month history of painless gross haematuria. Urine cytopathology revealed a urothelial carcinoma and computed tomography revealed left hydronephroureterosis with a distal ureteral stone and a mildly enhanced fungating mass just below the stone-impacted site. The preoperative TNM stage was T2N0M0. The patient underwent simultaneous diagnostic ureterorenoscopy and left laparoscopic nephroureterectomy with bladder cuff resection. Gross examination showed a 3.5 × 3.0 × 0.8 cm white, partly yellow mass in the left distal ureter. Light microscopy showed a small cell carcinoma, overlaid on a urothelial carcinoma in situ, invading the ureter and external lateral resection margins. The small cell carcinoma was diffusely positive for neuron-specific enolase, and exhibited focal positivity for CD 56, synaptophysin, chromogranin and cytokeratin 20. The patient was treated with adjuvant chemotherapy, consisting of cisplatin and etoposide, and radiation therapy, and has been well, without evidence of tumour recurrence or metastasis in the 10 months after surgery. CONCLUSION: Small cell carcinoma of the ureter is rare. Although its clinical behaviour and diagnostic modalities have not been determined and it has yet to be diagnosed immunohistopathologically, multimodality treatment including surgery, chemotherapy and radiotherapy may improve patient survival

Robust Likelihood-Based Survival Modeling with Microarray Data

Gene expression data can be associated with various clinical outcomes. In particular, these data can be of importance in discovering survival-associated genes for medical applications. As alternatives to traditional statistical methods, sophisticated methods and software programs have been developed to overcome the high-dimensional difficulty of microarray data. Nevertheless, new algorithms and software programs are needed to include practical functions such as the discovery of multiple sets of survival-associated genes and the incorporation of risk factors, and to use in the R environment which many statisticians are familiar with. For survival modeling with microarray data, we have developed a software program (called rbsurv) which can be used conveniently and interactively in the R environment. This program selects survival-associated genes based on the partial likelihood of the Cox model and separates training and validation sets of samples for robustness. It can discover multiple sets of genes by iterative forward selection rather than one large set of genes. It can also allow adjustment for risk factors in microarray survival modeling. This software package, the rbsurv package, can be used to discover survival-associated genes with microarray data conveniently

Sources of Value Gains in Minority Equity Investments by Private Equity Funds: Evidence from Block Share Acquisitions

Using a large sample of block share acquisitions made by private equity (PE) funds over the 1990 to 2006 period, we examine the sources of value gains in PE minority equity investments. We find that compared to non-PE acquirers, PE acquirers are more likely to place representatives with finance experience on a target’s board, particularly when the target performs poorly or when it has more pronounced agency problems. PE acquirers are also more likely to place representatives with experience in the target’s industry on the target’s board when the target has more complex operations (e.g., multiple segments or higher R&D intensity). The targets in PE acquisitions, particularly those whose boards have representatives from PE acquirers, realize both higher abnormal announcement returns and better post-acquisition operating performance than do targets in other types of acquisitions. Target announcement abnormal returns and post-acquisition operating performance are also higher when PE-appointed directors have expertise in the target’s industry, when they sit on the boards of poorly performing targets, or when they sit on the boards of targets with higher R&D intensity. Thes

Experimental observation of hidden Berry curvature in inversion-symmetric bulk 2H-WSe2

We investigate the hidden Berry curvature in bulk 2H-WSe2 by utilizing the surface sensitivity of angle resolved photoemission (ARPES). The symmetry in the electronic structure of transition metal dichalcogenides is used to uniquely determine the local orbital angular momentum (OAM) contribution to the circular dichroism (CD) in ARPES. The extracted CD signals for the K and K' valleys are almost identical but their signs, which should be determined by the valley index, are opposite. In addition, the sign is found to be the same for the two spin-split bands, indicating that it is independent of spin state. These observed CD behaviors are what are expected from Berry curvature of a monolayer of WSe2. In order to see if CD-ARPES is indeed representative of hidden Berry curvature within a layer, we use tight binding analysis as well as density functional calculation to calculate the Berry curvature and local OAM of a monolayer WSe2. We find that measured CD-ARPES is approximately proportional to the calculated Berry curvature as well as local OAM, further supporting our interpretation.Comment: 6 pages, 3 figure

B1gB_{\rm 1g} phonon anomaly driven by Fermi surface instability at intermediate temperature in YBa2_2Cu3_3O7−δ_{7-\delta}

We performed temperature- and doping-dependent high-resolution Raman spectroscopy experiments on YBa$_2$Cu$_3$O$_{7-\delta}$ to study $B$$_{\rm 1g}$ phonons. The temperature dependence of the real part of the phonon self-energy shows a distinct kink at $T=T_{\rm B1g}$ above $T$$_{\rm c}$ due to softening, in addition to the one due to the onset of the superconductivity. $T$$_{\rm B1g}$ is clearly different from the pseudogap temperature with a maximum in the underdoped region. The region between $T$$_{\rm B1g}$ and $T$$_{\rm c}$ resembles that of superconducting fluctuation or charge density wave order. While the true origin of the $B$$_{\rm 1g}$ phonon softening is not known, we can attribute it to a gap on the Fermi surface due to an electronic order. Our results may reveal the role of the $B$$_{\rm 1g}$ phonon not only in the superconducting state but also in the intertwined orders in multilayer copper oxide high-$T$$_{\rm c}$ superconductors.Comment: 5 pages, 4 figure