Software Engineering for Science

Software Engineering for Science provides an in-depth collection of peer-reviewed chapters that describe experiences with applying software engineering practices to the development of scientific software. It provides a better understanding of how software engineering is and should be practiced, and which software engineering practices are effective for scientific software. The book starts with a detailed overview of the Scientific Software Lifecycle, and a general overview of the scientific software development process. It highlights key issues commonly arising during scientific software development, as well as solutions to these problems. The second part of the book provides examples of the use of testing in scientific software development, including key issues and challenges. The chapters then describe solutions and case studies aimed at applying testing to scientific software development efforts. The final part of the book provides examples of applying software engineering techniques to scientific software, including not only computational modeling, but also software for data management and analysis. The authors describe their experiences and lessons learned from developing complex scientific software in different domains

Wireless transfer of power by a 35-GHz metamaterial split-ring resonator rectenna

Wireless transfer of power via high frequency microwave radiation using a miniature split ring resonator rectenna is reported. RF power is converted into DC power by integrating a rectification circuit with the split ring resonator. The near-field behavior of the rectenna is investigated with microwave radiation in the frequency range between 20-40 GHz with a maximum power level of 17 dBm. The observed resonance peaks match those predicted by simulation. Polarization studies show the expected maximum in signal when the electric field is polarized along the edge of the split ring resonator with the gap and minimum for perpendicular orientation. The efficiency of the rectenna is on the order of 1% for a frequency of 37.2 GHz. By using a cascading array of 9 split ring resonators the output power was increased by a factor of 20

Retreatment with anti-EGFR based therapies in metastatic colorectal cancer: impact of intervening time interval and prior anti-EGFR response.

BackgroundThis retrospective study aims to investigate the activity of retreatment with anti-EGFR-based therapies in order to explore the concept of clonal evolution by evaluating the impact of prior activity and intervening time interval.MethodsEighty-nine KRAS exon 2-wild-type metastatic colorectal patients were retreated on phase I/II clinical trials containing anti-EGFR therapies after progressing on prior cetuximab or panitumumab. Response on prior anti-EGFR therapy was defined retrospectively per physician-records as response or stable disease ≥6 months. Multivariable statistical methods included a multiple logistic regression model for response, and Cox proportional hazards model for progression-free survival.ResultsRetreatment anti-EGFR agents were cetuximab (n = 76) or cetuximab plus erlotinib (n = 13). The median interval time between prior and retreatment regimens was 4.57 months (range: 0.46-58.7). Patients who responded to the prior cetuximab or panitumumab were more likely to obtain clinical benefit to the retreatment compared to the non-responders in both univariate (p = 0.007) and multivariate analyses (OR: 3.38, 95 % CI: 1.27, 9.31, p = 0.019). The clinical benefit rate on retreatment also showed a marginally significant association with interval time between the two anti-EGFR based therapies (p = 0.053). Median progression-free survival on retreatment was increased in prior responders (4.9 months, 95 % CI: 3.6, 6.2) compared to prior non-responders (2.5 months, 95 % CI, 1.58, 3.42) in univariate (p = 0.064) and multivariate analysis (HR: 0.70, 95 % CI: 0.43-1.15, p = 0.156).ConclusionOur data lends support to the concept of clonal evolution, though the clinical impact appears less robust than previously reported. Further work to determine which patients benefit from retreatment post progression is needed

Correspondence principle for a brane in Minkowski space and vector mesons

We consider a 3-brane of positive cosmological constant (de Sitter) in D-dimensional Minkowski space. We show that the Poincare algebra in the bulk yields a SO(4,2) algebra when restricted to the brane. In the limit of zero cosmological constant (flat brane), this algebra turns into the conformal algebra on the brane. We derive a correspondence principle for Minkowski space analogous to the AdS/CFT correspondence. We discuss explicitly the cases of scalar and gravitational fields. For a 3-brane of finite thickness in the transverse directions, we obtain a spectrum for vector gravitational perturbations which correspond to vector mesons. The spectrum agrees with the one obtained in truncated AdS space by de Teramond and Brodsky provided D=10 and the bulk mass scale M is of order the geometric mean of the Planck mass ($\bar M$) on the brane and $\Lambda_{QCD}$ ($M \sim (\bar M \Lambda_{QCD})^{1/2} \sim 10^9$ GeV).Comment: 8 pages in two-column ReVTeX

Examination of Fluconazole-Induced Alopecia in an Animal Model and Human Cohort.

Fluconazole-induced alopecia is a significant problem for patients receiving long-term therapy. We evaluated the hair cycle changes of fluconazole in a rat model and investigated potential molecular mechanisms. Plasma and tissue levels of retinoic acid were not found to be causal. Human patients with alopecia attributed to fluconazole also underwent detailed assessment and in both our murine model and human cohort fluconazole induced telogen effluvium. Future work further examining the mechanism of fluconazole-induced alopecia should be undertaken

Mutations in the paralogous human α-globin genes yielding identical hemoglobin variants

The human α-globin genes are paralogues, sharing a high degree of DNA sequence similarity and producing an identical α-globin chain. Over half of the α-globin structural variants reported to date are only characterized at the amino acid level. It is likely that a fraction of these variants, with phenotypes differing from one observation to another, may be due to the same mutation but on a different α-globin gene. There have been very few previous examples of hemoglobin variants that can be found at both HBA1 and HBA2 genes. Here, we report the results of a systematic multicenter study in a large multiethnic population to identify such variants and to analyze their differences from a functional and evolutionary perspective. We identified 14 different Hb variants resulting from identical mutations on either one of the two human α-globin paralogue genes. We also showed that the average percentage of hemoglobin variants due to a HBA2 gene mutation (α2) is higher than the percentage of hemoglobin variants due to the same HBA1 gene mutation (α1) and that the α2/α1 ratio varied between variants. These α-globin chain variants have most likely occurred via recurrent mutations, gene conversion events, or both. Based on these data, we propose a nomenclature for hemoglobin variants that fall into this category

Impurity effect on weak anti-localization in the topological insulator Bi2Te3

We study weak anti-localization (WAL) effect in topological insulator Bi2Te3 thin films at low temperatures. Two-dimensional WAL effect associated with surface carriers is revealed in the tilted magnetic field dependence of magneto-conductance. Our data demonstrates that the observed WAL is robust against deposition of non-magnetic Au impurities on the surface of the thin films. But it is quenched by deposition of magnetic Fe impurities which destroy the pi Berry's phase of the topological surface states. The magneto-conductance data of a 5 nm Bi2Te3 film suggests that a crossover from symplectic to unitary classes is observed with the deposition of Fe impurities.Comment: 4 pages, 3 figures. Corresponding author email address: [email protected]

Physical layer security jamming: Theoretical limits and practical designs in wireless networks

Physical layer security has been recently recognized as a promising new design paradigm to provide security in wireless networks. In addition to the existing conventional cryptographic methods, physical layer security exploits the dynamics of fading channels to enhance secured wireless links. In this approach, jamming plays a key role by generating noise signals to confuse the potential eavesdroppers, and significantly improves quality and reliability of secure communications between legitimate terminals. This article presents theoretical limits and practical designs of jamming approaches for physical layer security. In particular, the theoretical limits explore the achievable secrecy rates of user cooperation based jamming whilst the centralized, and game theoretic based precoding techniques are reviewed for practical implementations. In addition, the emerging wireless energy harvesting techniques are exploited to harvest the required energy to transmit jamming signals. Future directions of these approaches, and the associated research challenges are also briefly outlined

New generalized fuzzy metrics and fixed point theorem in fuzzy metric space

In this paper, in fuzzy metric spaces (in the sense of Kramosil and Michalek (Kibernetika 11:336-344, 1957)) we introduce the concept of a generalized fuzzy metric which is the extension of a fuzzy metric. First, inspired by the ideas of Grabiec (Fuzzy Sets Syst. 125:385-389, 1989), we define a new G-contraction of Banach type with respect to this generalized fuzzy metric, which is a generalization of the contraction of Banach type (introduced by M Grabiec). Next, inspired by the ideas of Gregori and Sapena (Fuzzy Sets Syst. 125:245-252, 2002), we define a new GV-contraction of Banach type with respect to this generalized fuzzy metric, which is a generalization of the contraction of Banach type (introduced by V Gregori and A Sapena). Moreover, we provide the condition guaranteeing the existence of a fixed point for these single-valued contractions. Next, we show that the generalized pseudodistance J:X×X→[0,∞) (introduced by Włodarczyk and Plebaniak (Appl. Math. Lett. 24:325-328, 2011)) may generate some generalized fuzzy metric NJ on X. The paper includes also the comparison of our results with those existing in the literature

Combined Inflammatory and Metabolic Defects Reflected by Reduced Serum Protein Levels in Patients with Buruli Ulcer Disease

Buruli ulcer is a skin disease caused by Mycobacterium ulcerans that is spreading in tropical countries, with major public health and economic implications in West Africa. Multi-analyte profiling of serum proteins in patients and endemic controls revealed that Buruli ulcer disease down-regulates the circulating levels of a large array of inflammatory mediators, without impacting on the leukocyte composition of peripheral blood. Notably, several proteins contributing to acute phase reaction, lipid metabolism, coagulation and tissue remodelling were also impacted. Their down-regulation was selective and persisted after the elimination of bacteria with antibiotic therapy. It involved proteins with various functions and origins, suggesting that M. ulcerans infection causes global and chronic defects in the host’s protein metabolism. Accordingly, patients had reduced levels of total serum proteins and blood urea, in the absence of signs of malnutrition, or functional failure of liver or kidney. Interestingly, slow healers had deeper metabolic and coagulation defects at the start of antibiotic therapy. In addition to providing novel insight into Buruli ulcer pathogenesis, our study therefore identifies a unique proteomic signature for this disease