Giving RSEs a Larger Stage through the Better Scientific Software Fellowship

The Better Scientific Software Fellowship (BSSwF) was launched in 2018 to foster and promote practices, processes, and tools to improve developer productivity and software sustainability of scientific codes. BSSwF's vision is to grow the community with practitioners, leaders, mentors, and consultants to increase the visibility of scientific software production and sustainability. Over the last five years, many fellowship recipients and honorable mentions have identified as research software engineers (RSEs). This paper provides case studies from several of the program's participants to illustrate some of the diverse ways BSSwF has benefited both the RSE and scientific communities. In an environment where the contributions of RSEs are too often undervalued, we believe that programs such as BSSwF can be a valuable means to recognize and encourage community members to step outside of their regular commitments and expand on their work, collaborations and ideas for a larger audience.Comment: submitted to Computing in Science & Engineering (CiSE), Special Issue on the Future of Research Software Engineers in the U

Overexpression of Prothymosin Alpha Predicts Poor Disease Outcome in Head and Neck Cancer

In our recent study, tissue proteomic analysis of oral pre-malignant lesions (OPLs) and normal oral mucosa led to the identification of a panel of biomarkers, including prothymosin alpha (PTMA), to distinguish OPLs from histologically normal oral tissues. This study aimed to determine the clinical significance of PTMA overexpression in oral squamous cell hyperplasia, dysplasia and head and neck squamous cell carcinoma (HNSCC).Immunohistochemistry of PTMA protein was performed in HNSCCs (n = 100), squamous cell hyperplasia (n = 116), dysplasia (n = 50) and histologically normal oral tissues (n = 100). Statistical analysis was carried out to determine the association of PTMA overexpression with clinicopathological parameters and disease prognosis over 7 years for HNSCC patients.<0.001). Chi-square analysis showed significant association of nuclear PTMA with advanced tumor stages (III+IV). Kaplan Meier survival analysis indicated reduced disease free survival (DFS) in HNSCC patients (p<0.001; median survival 11 months). Notably, Cox-multivariate analysis revealed nuclear PTMA as an independent predictor of poor prognosis of HNSCC patients (p<0.001, Hazard's ratio, HR = 5.2, 95% CI = 2.3–11.8) in comparison with the histological grade, T-stage, nodal status and tumor stage.Nuclear PTMA may serve as prognostic marker in HNSCC to determine the subset of patients that are likely to show recurrence of the disease

Nuclear S100A7 Is Associated with Poor Prognosis in Head and Neck Cancer

Tissue proteomic analysis of head and neck squamous cell carcinoma (HNSCC) and normal oral mucosa using iTRAQ (isobaric tag for relative and absolute quantitation) labeling and liquid chromatography-mass spectrometry, led to the identification of a panel of biomarkers including S100A7. In the multi-step process of head and neck tumorigenesis, the presence of dysplastic areas in the epithelium is proposed to be associated with a likely progression to cancer; however there are no established biomarkers to predict their potential of malignant transformation. This study aimed to determine the clinical significance of S100A7 overexpression in HNSCC.Immunohistochemical analysis of S100A7 expression in HNSCC (100 cases), oral lesions (166 cases) and 100 histologically normal tissues was carried out and correlated with clinicopathological parameters and disease prognosis over 7 years for HNSCC patients. Overexpression of S100A7 protein was significant in oral lesions (squamous cell hyperplasia/dysplasia) and sustained in HNSCC in comparison with oral normal mucosa (p(trend)<0.001). Significant increase in nuclear S100A7 was observed in HNSCC as compared to dysplastic lesions (p = 0.005) and associated with well differentiated squamous cell carcinoma (p = 0.031). Notably, nuclear accumulation of S100A7 also emerged as an independent predictor of reduced disease free survival (p = 0.006, Hazard ratio (HR = 7.6), 95% CI = 1.3-5.1) in multivariate analysis underscoring its relevance as a poor prognosticator of HNSCC patients.Our study demonstrated nuclear accumulation of S100A7 may serve as predictor of poor prognosis in HNSCC patients. Further, increased nuclear accumulation of S100A7 in HNSCC as compared to dysplastic lesions warrants a large-scale longitudinal study of patients with dysplasia to evaluate its potential as a determinant of increased risk of transformation of oral premalignant lesions

DMA, a Bisbenzimidazole, Offers Radioprotection by Promoting NFκB Transactivation through NIK/IKK in Human Glioma Cells

BACKGROUND: Ionizing radiation (IR) exposure often occurs for human beings through occupational, medical, environmental, accidental and/or other sources. Thus, the role of radioprotector is essential to overcome the complex series of overlapping responses to radiation induced DNA damage. METHODS AND RESULTS: Treatment of human glioma U87 cells with DMA (5- {4-methylpiperazin-1-yl}-2-[2'-(3, 4-dimethoxyphenyl)-5'-benzimidazolyl] in the presence or absence of radiation uncovered differential regulation of an array of genes and proteins using microarray and 2D PAGE techniques. Pathway construction followed by relative quantitation of gene expression of the identified proteins and their interacting partners led to the identification of MAP3K14 (NFκB inducing kinase, NIK) as the candidate gene affected in response to DMA. Subsequently, over expression and knock down of NIK suggested that DMA affects NFκB inducing kinase mediated phosphorylation of IKKα and IKKβ both alone and in the presence of ionizing radiation (IR). The TNF-α induced NFκB dependent luciferase reporter assay demonstrated 1.65, 2.26 and 3.62 fold increase in NFκB activation at 10, 25 and 50 µM DMA concentrations respectively, compared to control cells. This activation was further increased by 5.8 fold in drug + radiation (50 µM +8.5 Gy) treated cells in comparison to control. We observed 51% radioprotection in control siRNA transfected cells that attenuated to 15% in siRNA NIK treated U87 cells, irradiated in presence of DMA at 24 h. CONCLUSIONS: Our studies show that NIK/IKK mediated NFκB activation is more intensified in cells over expressing NIK and treated with DMA, alone or in combination with ionizing radiation, indicating that DMA promotes NIK mediated NFκB signaling. This subsequently leads to the radioprotective effect exhibited by DMA

On th-Order Slant Weighted Toeplitz Operator

Let = { } ∈Z be a sequence of positive numbers with 0 = 1, 0 &lt; / +1 ≤ 1 when ≥ 0 and 0 &lt; / −1 ≤ 1 when ≤ 0. A th-order slant weighted Toeplitz operator on 2 ( ) is given by = , where is the multiplication on 2 ( ) and is an operator on 2 ( ) given by ( ) = ( / ) ( ), { ( ) = / } ∈Z being the orthonormal basis for 2 ( ). In this paper, we define a th-order slant weighted Toeplitz matrix and characterise in terms of this matrix. We further prove some properties of using this characterisation

Comparative evaluation of Jones pyrex tubes and polyethylene tubes in conjunctivo-dacryocystorhinostomy

A comparative study of the use of Pyrex glass tubes and the polyethylene tubes in con-junctivo-dacryocystorhinostomy is presented in 20 patients. The various factors contributing to the success of the surgery are discussed. The merits and demerits of the two types of tubes used are also highlighted

Dyslipidemia in pregnancy may contribute to increased risk of neural tube defects -a pilot study in north Indian population

The paper addresses the simultneous determination of goup-sparse loadings by block optimization, and the correlated problem of defining explained variance for a set of non orthogonal components. We give in both cases a comprehensive mathematical presentation of the problem, which leads to propose i) a new formulation/algorithm for group-sparse block PCA and ii) a framework for the definition of explained variance with the analysis of five definitions. The numerical results i) confirm the superiority of block optimization over deflation for the determination of group-sparse loadings, and the importance of group information when available, and ii) show that ranking of algorithms according to explained variance is essentially independant of the definition of explained variance. These results lead to propose a new optimal variance as the definition of choice for explained variance