Excessive Memory Usage of the ELLPACK Sparse Matrix Storage Scheme throughout the Finite Element Computations

Sparse matrices are occasionally encountered during solution of various problems by means of numerical methods, particularly the finite element method. ELLPACK sparse matrix storage scheme, one of the most widely used methods due to its implementation ease, is investigated in this study. The scheme uses excessive memory due to its definition. For the conventional finite element method, where the node elements are used, the excessive memory caused by redundant entries in the ELLPACK sparse matrix storage scheme becomes negligible for large scale problems. On the other hand, our analyses show that the redundancy is still considerable for the occasions where facet or edge elements have to be used

Codes of Modernity: Infrastructures of Language and Chinese Scripts in an Age of Global Information Revolution

This dissertation explores the global history of Chinese script reforms—the effort to phoneticize Chinese language and/or simplify the writing system—from its inception in the 1890s to its demise in the 1980s. These reforms took place at the intersection of industrialization, colonialism, and new information technologies, such as alphabet-based telegraphy and breakthroughs in printing technologies. As these social and technological transformations put unprecedented pressure on knowledge management and the use of mental and clerical labor, many Chinese intellectuals claimed that learning Chinese characters consumed too much time and mental energy. Chinese script reforms, this dissertation argues, were an effort to increase speed in producing, transmitting, and accessing information, and thus meet the demands of the industrializing knowledge economy. The industrializing knowledge economy that this dissertation explores was built on and sustained by a psychological understanding of the human subject as a knowledge machine, and it was part of a global moment in which the optimization of labor in knowledge production was a key concern for all modernizing economies. While Chinese intellectuals were inventing new signs of inscription, American behavioral psychologists, Soviet psycho-economists, and Central Asian and Ottoman technicians were all experimenting with new scripts in order to increase mental efficiency and productivity. This dissertation reveals the intimate connections between the Chinese and non-Chinese script engineering projects that were taking place synchronically across the world. The chapters of this work demonstrate for the first time, for instance, that the simplification of Chinese characters in the 1920s and 1930s was intimately connected to the discipline of behavioral psychology in the US. The first generation of Chinese psychologists employed the American psychologists’ methods to track eye movements, count word-frequencies, and statistically analyze the speed of reading, writing, and memorizing in order to simplify and “rationalize” the Chinese writing system in an effort to discipline and optimize mental labor. Other chapters explore the issue of mental and clerical optimization by finding the origins of the Chinese Latin Alphabet (CLA), the mother of pinyin, in hitherto unknown Eurasian connections. The CLA, the pages of this work shows, was the product of a transnational exchange that involved Ottoman and Transcaucasian typographers as well as Russian engineers and Chinese communists who sought efficiency in knowledge production through inventing new scripts. Situating the Chinese script reforms at this global intersection of psychology, economy, and linguistics, this dissertation examines the global connections and forces that turned the human subject into a knowledge worker who was cognitively managed through education, literacy, propaganda, and other measures of organizing information, all of which had the script at the center. The search for efficiency and productivity—the core values of industrialism—lay at the heart of script reforms in China, but this search was inseparable from linguistic orders and political ambitions. Even if writing, transmitting, and learning a phonetic script could theoretically be easier and more efficient than the Chinese characters, the alphabet opened a veritable Pandora’s Box around the issue of selection: given the complex linguistic landscape in China, which speech was a phonetic script supposed to represent? There were myriad languages spoken throughout the empire and the subsequent nation-state, most of which were mutually incomprehensible. Mandarin as spoken in Beijing was different from that spoken in the south, and “topolects” or regional languages such as Min or Cantonese were to Mandarin what Romanian is to English. As a linguistic life-or-death issue, phonetic scripts stood for the infrastructural possibilities and limitations in the representation of speeches. Some scripts, such as Lao Naixuan’s phonetic script composed of more than a hundred signs, were capable of representing multiple Mandarin and non-Mandarin speeches; whereas others, such as Phonetic Symbols that only has thirty-seven syllabic signs, represented only one speech, i.e., Mandarin. Using Mandarin-oriented scripts to transcribe non-Mandarin speeches was like writing English with fifteen letters, hence the acrimonious disputes that fill the pages of this dissertation. Succinctly put, it was at the level of script invention that Chinese and non-Chinese actors engineered different infrastructures not only for laboring minds but also for the social world of Chinese languages. The history of information technologies and knowledge economy in China was thus inseparable from the world of speech and language, as each script offered a new potential to reassemble the written matter and the speaking mind in a different way. “Codes of Modernity” thus conceptualizes the script itself as an infrastructural medium. A script was not merely a passive carrier of information, but an existential artifact. Building on an expanding literature on infrastructures, it endorses the observation that infrastructures, technologies, and the social world around them work in a recursive loop. An infrastructure is not just the physical object that permits the flow of information, goods, ideas, and people, but a sociotechnical product that enables the experience of culture, while imposing constrains on it at the same time. Like electricity grids, transportation systems, and sewage canals, the experience of scripts as infrastructures is the experience of thought worlds. After a long tradition of structuralism and poststructuralism that sought to understand the world through the semiotic prism of language, “Codes of Modernity” argues that it is time for an infrastructuralism that excavates the indispensable media that enable the production of language and thought

Design of the Square Loop Frequency Selective Surfaces with Particle Swarm Optimization via the Equivalent Circuit Model

In this study, Particle Swarm Optimization is applied for the design of Square Loop Frequency Selective Surfaces (the conventional Square Loop, Gridded Square Loop, and Double Square Loop) via their equivalent circuits. For this purpose, first the derivation of the equivalent circuit formulation is revisited. Then an objective function, which is based on the transmission coefficients at various frequencies at the pass/stop-bands, is defined. By means of an ANSI C++ implementation, a platform independent console application (which depends on the Equivalent Circuit Models and continuous form of Particle Swarm Optimization) is developed. The obtained results are compared to those in the literature. It is observed that the Particle Swarm Optimization is perfectly suitable for this sort of problems, and the solution accuracy is limited to and dominated by that of the Equivalent Circuit Model

Identification and functional analysis of an autophagy-related gene TdAtg8 in wild emmer wheat under biotic (fusarium culmorum) and abiotic (drought) stress conditions

Autophagy, literally self eating, is an evolutionary conserved catalytic process for vacuolar degradation of intracellular components, previously examined in yeast, mammals and plants. Abiotic stress factors, including nutrient starvation, oxidative stress, salt stress and osmotic stress have been previously reported to induce autophagy in plants. In this study, for the first time, Atg8 gene was cloned from wild emmer wheat (TdAtg8) and the role of autophagy under biotic and abiotic stress conditions was investigated. Examination of TdAtg8 expression patterns indicates that Atg8 expression was immensely upregulated under drought stress, especially in the roots. Monodansylcadaverine (MDC) and Lysotracker Red markers utilized to observe autophagosomes revealed that autophagy is constitutively active in T. dicoccoides. Moreover, autophagy was determined to be more active in plants exposed to drought stress when compared to plants grown under normal conditions. TdAtg8 gene was demonstrated to complement Atg8 yeast mutants grown under starvation conditions in a drop test assay. For further functional analysis, ATG8 protein from T. dicoccoides were expressed in yeast and analyzed with western blotting. TdAtg8 was also silenced in wild emmer wheat by virus-induced gene silencing and its role was investigated in the presence of a plant pathogen, Fusarium culmorum. This response, for the first time, showed that fungi sporulation decreased in Atg8 silenced plants in comparison to controls. Based on the data obtained, we conclude that the plants become more resistant against the plant pathogen when the autophagy was inhibited

Sub-wavelength imaging with a left-handed material flat lens

We study numerically, by means of the pseudospectral time-domain method, the unique features of imaging by a flat lens made of a left-handed metamaterial that possesses the property of negative refraction. We confirm the earlier finding that a left-handed flat lens can provide near-perfect imaging of a point source and a pair of point sources with clear evidence of the sub-wavelength resolution. We illustrate the limitation of the resolution in the time-integrated image due to the presence of surface waves.Comment: 4 pages, RevTeX, 6 figures; added references and some discussio

Eukaryotic translation initiation factor 4All contributes to microRNA-122 regulation of hepatitis C virus replication

Hepatitis C virus (HCV) is a positive sense RNA virus that persistently infects human liver, leading to cirrhosis and hepatocellular carcinoma. HCV replication requires the liver-specific microRNA-122 (miR-122). In contrast to canonical miRNA-mediated repression via 3’UTR sites, miR-122 positively regulates HCV replication by a direct interaction with the 5’ untranslated region (UTR) of the viral RNA. The protein factor requirements for this unusual miRNA regulation remain poorly understood. Here, we identify eIF4AII, previously implicated in miRNA-mediated repression via 3’UTR sites, as a host factor that is important for HCV replication. We demonstrate that eIF4AII interacts with HCV RNA and that this interaction is miR-122-dependent. We show that effective miR-122 binding to, and regulation of, HCV RNA are reduced following eIF4AII depletion. We find that the previously identified HCV co-factor CNOT1, which has also been implicated in miRNA-mediated repression via 3’UTR sites, contributes to regulation of HCV by eIF4AII. Finally, we show that eIF4AI knockdown alleviates the inhibition of HCV replication mediated by depletion of either eIF4AII or CNOT1. Our results suggest a competition effect between the eIF4A proteins to influence HCV replication by modulation of miR-122 function

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

The novel coronavirus SARS-CoV-2, the causative agent of COVID-19 respiratory disease, has infected over 2.3 million people, killed over 160,000, and caused worldwide social and economic disruption1,2. There are currently no antiviral drugs with proven clinical efficacy, nor are there vaccines for its prevention, and these efforts are hampered by limited knowledge of the molecular details of SARS-CoV-2 infection. To address this, we cloned, tagged and expressed 26 of the 29 SARS-CoV-2 proteins in human cells and identified the human proteins physically associated with each using affinity-purification mass spectrometry (AP-MS), identifying 332 high-confidence SARS-CoV-2-human protein-protein interactions (PPIs). Among these, we identify 66 druggable human proteins or host factors targeted by 69 compounds (29 FDA-approved drugs, 12 drugs in clinical trials, and 28 preclinical compounds). Screening a subset of these in multiple viral assays identified two sets of pharmacological agents that displayed antiviral activity: inhibitors of mRNA translation and predicted regulators of the Sigma1 and Sigma2 receptors. Further studies of these host factor targeting agents, including their combination with drugs that directly target viral enzymes, could lead to a therapeutic regimen to treat COVID-19