Quantifying design exclusion

This part of the book aims to convince a designer that inclusive design is a realistic goal.

Quantifying the effectiveness of SiO2/Au light trapping nanoshells for thin film poly-Si solar cells

In order to enhance light absorption of thin film poly-crystalline silicon (TF poly-Si) solar cells over a broad spectral range, and quantify the effectiveness of nanoshell light trapping structure over the full solar spectrum in theory, the effective photon trapping flux (EPTF) and effective photon trapping efficiency (EPTE) were firstly proposed by considering both the external quantum efficiency of TF poly-Si solar cell and scattering properties of light trapping structures. The EPTF, EPTE and scattering spectrum exhibit different behaviors depending on the geometric size and density of nanoshells that form the light trapping layer. With an optimum size and density of SiO2/Au nanoshell light trapping layer, the EPTE could reach up to 40% due to the enhancement of light trapping over a broad spectral range, especially from 500 to 800 nm.

中国砂鼠利什曼原虫（Leishmania gerbilli）的细微结构及动质体碱性昼白的细胞化学特性的初步研究

本文以中国砂鼠利会曼原虫（Leishmanina grbilli）为材料，对动质体的细微结构及动质体碱性蛋白的细胞化学特性作了研究。已知真细菌类染色质体中有碱性的HU蛋白与DNA结合着，动质体中是否也有碱性蛋白与DNA相结合，一直是有争议的问题。de Souza等（1978-83）证明锥虫的动质体中确有碱性蛋白存在，但迄今止，国际上还没有关于利会曼原虫动质体碱性蛋白的报导。用热三氯醋酸-偶氮洋红G法、热三氯醋酸-固绿法、碱性比布列希猩法、碳酸氨银反应（AS反应）、经亚硝酸处理后作AS反应和经碱性蛋白不同成份抽提后作AS反应等光学显微细胞化学方法以及酒精钨酸染色（E-PTA）、用乙醇-醋酸固定、DNA酶处理后作E-PTA染色和碳酸氨银反应等电镜水平的细胞化学方法进行了研究。得到了如下的结果：（1）L.gerbilli的动质体中确实含有大量的酸溶性碱性蛋白。（2）对用E—PTA染色后，动质体只有周边着色的现象作了探讨，认为是假期象。动质体中碱性蛋白与DNA的分布是一致的。（3）动质体碱性蛋白对热三氯醋酸（TCA）处理的耐受性比HU蛋白的强比组慢白的弱；动质体碱性蛋白对亚硝酸处理的耐受性和与AS液的亲和力也比组蛋白弱。（4）可以抽提富含精氨酸的组蛋白的80%Alc-0.18NHCl，和可以抽抻富含赖氨酸的组蛋白的10%Alc-0.18NHCl，都不能把动质体碱性昼白全部抽提掉。（5）与真细菌类的HU蛋白相比较。L.gerbilli的动质体的碱性蛋白看来含有较多的精氨酸成份。作超薄切片，用电镜观察了L.gerbilli的质膜及质膜下微管、鞭毛、细胞核、动质体、线粒体、复片层结构等，发现：①与其它利会曼原虫和锥虫的鞭毛基部的结构不同，L.gerbilli的鞭毛基部没有基板存在。②L.gerbilli的复片层结构特别发达，是由膜组成的同心圆或同心椭圆结构。③L.gerbilli的动质体在通常情况下作“棒”状，但我们发现它实际上是一个环状结构。这在细胞膨胀时表现得非常突出。

Quantifying intrinsic specificity: A potential complement to affinity in drug screening

We report here the investigation of a novel description of specificity in protein-ligand binding based on energy landscape theory. We define a new term, intrinsic specificity ratio (ISR), which describes the level of discrimination in binding free energies of the native basin for a protein-ligand complex from the weaker binding states of the same ligand. We discuss the relationship between the intrinsic specificity we defined here and the conventional definition of specificity. In a docking study of molecules with the enzyme COX-2, we demonstrate a statistical correspondence between ISR value and geometrical shapes of the small molecules binding to COX-2. We further observe that the known selective (nonselective) inhibitors of COX-2 have higher (lower) ISR values. We suggest that intrinsic specificity ratio may be a useful new criterion and a complement to affinity in drug screening and in searching for potential drug lead compounds.

Quantifying robustness and dissipation cost of yeast cell cycle network: The funneled energy landscape perspectives

We study the origin of robustness of yeast cell cycle cellular network through uncovering its underlying energy landscape. This is realized from the information of the steady-state probabilities by solving a discrete set of kinetic master equations for the network. We discovered that the potential landscape of yeast cell cycle network is funneled toward the global minimum, G1 state. The ratio of the energy gap between G1 and average versus roughness of the landscape termed as robustness ratio ( RR) becomes a quantitative measure of the robustness and stability for the network. The funneled landscape is quite robust against random perturbations from the inherent wiring or connections of the network. There exists a global phase transition between the more sensitive response or less self-degradation phase leading to underlying funneled global landscape with large RR, and insensitive response or more self-degradation phase leading to shallower underlying landscape of the network with small RR. Furthermore, we show that the more robust landscape also leads to less dissipation cost of the network. Least dissipation and robust landscape might be a realization of Darwinian principle of natural selection at cellular network level. It may provide an optimal criterion for network wiring connections and design.

Quantifying the kinetic paths of flexible biomolecular recognition

Biomolecular recognition often involves large conformational changes, sometimes even local unfolding. The identification of kinetic pathways has become a central issue in understanding the nature of binding. A new approach is proposed here to study the dynamics of this binding-folding process through the establishment of a path-integral framework on the underlying energy landscape. The dominant kinetic paths of binding and folding can be determined and quantified. The significant coupling between the binding and folding of biomolecules often exists in many important cellular processes. In this case, the corresponding kinetic paths of binding are shown to be intimately correlated with those of folding and the dynamics becomes quite cooperative. This implies that binding and folding happen concurrently. When the coupling between binding and folding is weak (strong), the kinetic process usually starts with significant folding (binding) first, with the binding (folding) later proceeding to the end. The kinetic rate can be obtained through the contributions from the dominant paths. The rate is shown to have a bell-shaped dependence on temperature in the concentration-saturated regime consistent with experiment. The changes of the kinetics that occur upon changing the parameters of the underlying binding-folding energy landscape are studied.

Quantifying the value of improved wind energy forecasts in a pool-based electricity market

This work illustrates the influence of wind forecast errors on system costs, wind curtailment and generator dispatch in a system with high wind penetration. Realistic wind forecasts of different specified accuracy levels are created using an auto-regressive moving average model and these are then used in the creation of day-ahead unit commitment schedules. The schedules are generated for a model of the 2020 Irish electricity system with 33% wind penetration using both stochastic and deterministic approaches. Improvements in wind forecast accuracy are demonstrated to deliver: (i) clear savings in total system costs for deterministic and, to a lesser extent, stochastic scheduling; (ii) a decrease in the level of wind curtailment, with close agreement between stochastic and deterministic scheduling; and (iii) a decrease in the dispatch of open cycle gas turbine generation, evident with deterministic, and to a lesser extent, with stochastic scheduling.

Quantifying data quality for clinical trials using electronic data capture.

BACKGROUND: Historically, only partial assessments of data quality have been performed in clinical trials, for which the most common method of measuring database error rates has been to compare the case report form (CRF) to database entries and count discrepancies. Importantly, errors arising from medical record abstraction and transcription are rarely evaluated as part of such quality assessments. Electronic Data Capture (EDC) technology has had a further impact, as paper CRFs typically leveraged for quality measurement are not used in EDC processes. METHODS AND PRINCIPAL FINDINGS: The National Institute on Drug Abuse Treatment Clinical Trials Network has developed, implemented, and evaluated methodology for holistically assessing data quality on EDC trials. We characterize the average source-to-database error rate (14.3 errors per 10,000 fields) for the first year of use of the new evaluation method. This error rate was significantly lower than the average of published error rates for source-to-database audits, and was similar to CRF-to-database error rates reported in the published literature. We attribute this largely to an absence of medical record abstraction on the trials we examined, and to an outpatient setting characterized by less acute patient conditions. CONCLUSIONS: Historically, medical record abstraction is the most significant source of error by an order of magnitude, and should be measured and managed during the course of clinical trials. Source-to-database error rates are highly dependent on the amount of structured data collection in the clinical setting and on the complexity of the medical record, dependencies that should be considered when developing data quality benchmarks.

Cohabitation: quantifying an equitable share

Discusses the House of Lords judgment in Stack v Dowden on the factors the courts may consider when determining whether to rebut the presumption that former cohabitees, who were registered as joint legal owners of a property, were also joint beneficial owners with equal shares in the property. [From the Legal Journals Index]

Quantifying the beneficial interests of cohabitees

Discusses entitlements to a share of the sale proceeds of the family home where partners are cohabiting but not married and the property is registered in the name of one person only. Explains the obligation to establish that a cohabitee has an equitable interest in the property under the principles of constructive or resulting trusts. Considers how the court is able to quantify the respective shares, both before and after Oxley v Hiscock. [From the Legal Journals Index]

Induction of apoptosis in host cells: a survival mechanism for Leishmania parasites?

Leishmania parasites invade host macrophages, causing infections that are either limited to skin or spread to internal organs. In this study, 3 species causing cutaneous leishmaniasis, L. major, L. aethiopica and L. tropica, were tested for their ability to interfere with apoptosis in host macrophages in 2 different lines of human monocyte-derived macrophages (cell lines THP-1 and U937) and the results confirmed in peripheral blood mononuclear cells (PBMC). All 3 species induced early apoptosis 48 h after infection (expression of phosphatidyl serine on the outer membrane). There were significant increases in the percentage of apoptotic cells both for U937 and PBMC following infection with each of the 3 species. Early apoptotic events were confirmed by mitochondrial membrane permeabilization detection and caspase activation 48 and 72 h after infection. Moreover, the percentage of infected THP-1 and U937 macrophages increased significantly (up to 100%) following treatment with an apoptosis inducer. Since phosphatidyl serine externalization on apoptosing cells acts as a signal for engulfment by macrophages, induction of apoptosis in the parasitized cells could actively participate in spreading the infection. In summary, parasite-containing apoptotic bodies with intact membranes could be released and phagocytosed by uninfected macrophages.