Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimation of variation for high-throughput molecular biological experiments with small sample size

Yu, Danni Ph.D., Purdue University, December 2013. Estimation of Variation For Highthroughput Molecular Biological Experiments With Small Sample Size. Major Professor: Olga Vitek. Motivation: In the quantification of molecular components, a large variation can affect and even potentially mislead the biological conclusions. Meanwhile, the high-throughput experiments often involve a small number of samples due to the limitation of cost and time. In such cases, the stochastic information may dominate the outcome of an experiment because there may not be enough samples to present the true biological information. It is challenging to distinguish the changes in phenotype from the stochastic variation. Methods: Since the biological molecules have been quantified with different technologies, different statistical methods are required. Focusing on three types of important highthroughput experiments, this thesis proposes novel solutions to reduce noise and increase the accuracy of molecular discovery. i) In the large-scale perturbation screens, thousands of mutant strains on hundreds of plates are separately profiled in hundreds of days (or batches). For each mutant strain, only a small number of samples are profiled. The artificial noise mainly consists of additive and multiplicative effects due to plates and batches. We propose a linear mixed-effect modeling framework based on experimental designs with at least two control samples. These are involved in a normalization and variance estimation procedure for the purpose of reducing the noise from data and scoring the true biological phenotype. ii) In the RNA-seq experiments, fragments of greater than thousands of genes in 4∼8 samples on a flow cell can be sequenced in one day. The additive and no-additive effects due to the large number of plates do not typically present in the data. The gene-wise variance between samples consists of both the expectation and dispersion of gene counts. Due to
Motion compensated interpolation for subband coding of moving images

With emergence of multimedia, CD-ROMS, and high speed networks there is a need for reducing the data rate for transmission and storage of images without severe loss of quality. An image compression system is presented based on motion compensated interpolation using multiframe matching techniques and subband analysis of keyframes and residual (error) frames, followed by vector quantization and arithmetic coding. Multiframe matching differs from conventional block matching in that the intermediate frames are used in addition to the keyframes for motion estimation. Multiframe matching significantly improves the efficiency of motion compensated interpolation. Keyframes and residuals are coded using a quad-split pyramid. The subbands are then coded using variance-normalized, error limited vector quantization. The vector fields, vector quantization codebooks, and look up tables are losslessly coded using arithmetic coding. In computer simulations, bit rates below 2.5 megabits per second are achieved with high quality reconstruction at the receiver. All simulation computations are carried out using integer precision arithmetic. Thesis Advisor: Bernd Girod Assistant Professor, Media Laboratory
Virtual Muse: Experiments In Computer Poetry

In this engaging, accessible memoir, Charles Hartman shows how computer programming has helped him probe poetry's aesthetic possibilities. He discusses the nature of poetry itself and his experiences with primitive computer-generated poetry programs and -- illustrated with sample computer-produced verses -- traces the development of more advanced hardware and software. The central question about this cyber-partnership, Hartman says, "isn't exactly whether a poet or a computer writes the poem, but what kinds of collaboration might be interesting. " He examines the effects of randomness, arbitrariness, and contingency on poetic composition, concluding that "the tidy dance among poet and text and reader creates a game of hesitation. In this game, a properly programmed computer has a chance to slip in some interesting moves. "
Confiabilidade do teste da caminhada de seis minutos em pacientes com miastenia gravis generalizada

Este estudo objetivou determinar a confiabilidade do teste da caminhada de seis minutos (TC6M) como um teste de capacidade funcional em pacientes com miastenia gravis generalizada (MG). Foram selecionados 11 pacientes com MG - 5 homens, 6 mulheres - com idade de 55±9 anos, avaliados inicialmente quanto a funcao fulmonar, que se submeteram a tres TC6M em dias diferentes. Durante e/ou apos cada teste foram medidas frequencia cardiaca e saturacao de oxigenio (por oximetro portatil), sensacao de dispneia (pela escala de Borg) e distância percorrida. Nos tres testes as distâncias percorridas foram 498 m, 517 m e 520 m (respectivamente 99%, 103% e 104% do valor predito). Em media, a frequencia cardiaca, dispneia e saturacao de oxigenio mostraram comportamento constante nos tres testes. Foram encontradas alta confiabilidade relativa, com coeficiente de correlacao interclasse maior que 0,90 entre os testes (TC6M1-TC6M2, 0,960; TC6M1-TC6M3, 0,945; e TC6M2-TC6M3, 0,970) e confiabilidade absoluta de 4%, 3,5% e 4,8%, com reprodutibilidade de 11%, 9,8% e 13,4%, respectivamente para o primeiro, segundo e terceiro testes. Os limites superiores e inferiores de concordância e o valor medio das medias das diferencas (bias) calculados pelo teste de Bland-Altman mostraram-se clinicamente aceitaveis. Conclui-se que o TC6M se mostrou seguro, confiavel e reprodutivel, podendo ser aplicado para avaliacao e seguimento da tolerância ao exercicio em pacientes com MG generalizada.
Five Cases of Pre-operative radiotherapy for Primary huge liver cancer

目的 评价巨大肝癌患者术前放疗采用全肝移动条野放疗、缩野技术和分阶段放疗，剂量递增至 60Gy 的移动条野放射综合治疗方案的长期随访疗效。 方法 : 回顾性分析 1987 年 9 月～ 1993 年 8 月江门市中心医院巨大肝癌 5 例术前放疗采用全肝移动条野放射 18 ～ 36Gy 控制亚临床病灶，再缩野对准原发病灶，放射剂量递增至 50 ～ 60Gy 。 待原发病灶明显缩小后，利于二期切除。 结果 长期随访至 2014 年 5 月， 5 年生存率 100% ， 10 年生存率 40% ， 20 年生存率 40% ，最长生存期 27 年无瘤健在。 结论 术前放疗长期临床实践首次发现了传统放疗和三维适形放疗概念所未知的事实 : ⑴国际上首次报道经长期随访的巨大肝癌术前放疗，采用全肝移动条野放疗 18 ～ 36Gy 、缩野技术和分阶段放疗，剂量递增至 50~60Gy 的移动条野放射综合治疗方案，安全有效，肿瘤由大变小，其缩小率 57.1% ～ 72.2%( 平均 62.45%) ，二期切除术顺利，放疗周期从 94 天～ 153 天 ( 平均 124 天 ) 完成，治疗周期适当，长期随访疗效令人鼓舞，最长生存期 27 年，健在无复发。 ⑵病理检查 5 例均为肝细胞癌，肿瘤组织呈大片坏死并有明显的纤维化，伴纤维包膜形成，镜下均见有残癌细胞。 提示巨大肝癌放疗 60Gy 未能根治，尚有残癌细胞，说明二期手术切除的重要性。 ⑶移动条野技术理论详细阐明移动条野放射杀癌原理，有其本身的适应证对肿瘤边界在影像学上无法确认者，提高肿瘤的生物效应，改善正常组织的耐受量为全肝移动条野放疗 30Gy ，局部缩野剂量递增至 60Gy 的应用价值，正是移动条野技术的优点。 ⑷病例少，是当前能治疗肝癌亚临床病灶的新技术，有值得探索的一丝曙光，期待有关学者组织多中心循证深入研究。
Maximum Likelihood CFO Estimation in OFDM Based Communication Systems

Orthogonal Frequency Division Multiplexing (OFDM) is a promising technique for the next generation (3G/4G and beyond) wireless communication systems. These systems are very sensitive to the carrier frequency offset (CFO) that destroys the orthogonality property of the OFDM sub-carriers and introduces inter-carrier interference (ICI) which degrades the bit error rate (BER) performance. However, Inter Symbol Interference (ISI) that occurs during transmission can be totally averted by adding cyclic prefix (CP) to the OFDM symbol. Also adding CP reduces the level of CFO introduced during transmission. Nonetheless adding CP cannot protect ICI from occurring and distorting the transmitted symbol data at the receiver side. In this paper, we set the CP to vary in length depending on the channel conditions and obtained a better performance. We have also proposed a novel bandwidth efficient ML estimation technique that has a better bit error rate compared to that of conjugate cancellation method. We have also simulated and discussed bit-error-rate (BER) of the system against SNR under different channel conditions and comparedit with other existing ICI mitigation techniques and found it better.
Effect of the corn grain storage method on saccharification and ethanol fermentation field

The chemical conservation was chosen in the study as the method for preserv- ing fresh corn grain for distilleries. Five types of preserved corn samples were prepared. The control (with no additives) and four preserved with the preparation, based on formic and propionic acids (KemiSile 2000 Plus), at different levels. All the samples were stored for two months. Ethanol fermentations of low-temperature-cooked and pressure-cooked corn starch were carried out using commercial distillery yeast. The yeast strain, after starch hydrolysis with two enzymes, was able to produce 86-93% of theoretical ethanol yield from low-temperature-cooked corn. The ethanol production was almost equal to that produced from pressure-cooked corn starch (121°C), which was 87-94% of theoretical etha- nol yield. The quality of distillates was also investigated. The most common by-products found were: acetaldehyde, ethyl acetate, propanol, isobutanol and 3-metylo-1-butanol. There were no important differences of spirits chemical composition between low-temperature- -cooking and pressure-cooking method as well as between the kind of corn sample.
Urban sustainable development: Indicators for a Co-evolution of the Economy, the Community and the Environment

This paper wiU deal with the notion of sustainable &wlmpmksthg from a general mefa-lme2 of analysis and arriv Central premises of conventional economics ace: the m a x i m i ~ a k premise, the weighting premise and the fixed content premise. The maximisation and the weighting premises lead to the use of mmeWy evaluation methods, thus assuming complete commensurability between different viewpoints. The fixed content premise leads to the well known optimistic attitude towards economic growth. The Pearce and Turner approach in order to be operationalised, also needs a valuation of resource stocks in money terms. Ecological economics explicitely recognises that incommensurabilitiy and multidimensionality are normal features of economic-environmental processes. Thus instead of the ”maximisation premise” and the “weighting premise”, a holistic OY incizrcionist approach to economic and policy-making is emphasised, going in the direction of disaggregated approaches to decision making and resource management rather than aggregated ones. Thus an “economic axiomatization” of multicriteria evaluation methods can be found in the framework of ecological economics. to arc c p ? r a h l k e l .
Effect of steam blanching on lycopene and total phenolics in pink guava puree industry by-products

Lycopene and total phenolics of pink guava puree industry by-products (refiner, siever and decanter) were evaluated after steam blanching at selected temperatures and times. Lycopene content was in the order of decanter > siever > refiner (7.3, 6.3 and 1.5 mg/100 g, respectively), and the content of total phenolics was in the order of refiner > siever > decanter (4434.1, 2881.3 and 1529.3 mg GAE/100 g, respectively). Regression coefficients for temperatures (x1) and times (x2) from multiple linear regression models of siever and decanter showed significant (p<0.05) negative relationships with lycopene (y1) and total phenolics (y2). Nevertheless, lycopene content in decanter increased significantly about 13% from the control when steam blanching at 60 °C for 20-60 min. More than 27% of total phenolics were lost in blanched refiner. Regression analysis revealed the increasing loss of lycopene and total phenolics during steam blanching could occur when increasing in temperature and time.
Stingray diversification across the end-Cretaceous extinctions

Bertozzi, T. , Lee, M.S.Y. and Donnellan, S.C. 2016. Stingray diversification across the end-Cretaceous extinctions. Memoirs of Museum Victoria 74: 379–390. The evolution of stingrays (Myliobatiformes) is assessed using a new phylogeny with near-complete genus-level sampling, and additional molecular data. Stingrays diversified into three primary clades: (A) river stingrays, round rays and typical stingrays, (B) butterfly rays and stingarees and (C) eagle and manta rays. The enigmatic sixgill and deepwater rays (Hexatrygon and Plesiobatis) are not basal stingrays, but are part of the second clade. There is extensive clade-specific variation in molecular evolutionary rates across chondrichthyans: the most appropriate (autocorrelated) divergence dating methods indicate that the extant stingray radiation commenced in the late Cretaceous and continued across the K-Pg boundary. This is highly consistent with the fossil record, and suggests that Cretaceous stingrays, being primarily benthic taxa, were less affected by the K-Pg event than taxa inhabiting the water column. The largest pelagic radiation of stingrays (myliobatids: eagle and manta rays) evolved very shortly after the K-Pg boundary, consistent with rapid ecological expansion into newly-vacated pelagic niches.
Experimental Study on the Influence of Oxygen Fraction in the Combustion Air on the Combustion Characteristics

The presented paper was focused on the experimental investigation of a promising combustion technology, namely the oxygen-enhanced combustion (OEC). This technology is used in those industrial heating applications that require increased productivity, higher heat transfer efficiency, improved flame characteristics, reduced equipment cost and last but not least improved product quality. However, there are potential problems associated with the use of OEC if the system is not properly designed, e.g. refractory or burner damage, non-uniform heating and/or increased pollutant emissions. The experimental study of OEC was carried out at the large-scale burner testing facility that enables to test the gaseous fuel burners, the liquid fuel burners and the combined burners up to the thermal input of 1800 kW. The combustion tests were performed with the experimental low-NOx type burner, namely the two-gas-staged burner. The oxygen content in the combustion air was increased by means of the oxygen injection directly into the incoming airstream before entering the burner. The aim of the tests was to assess the impact of oxidizer composition (the volume fraction of oxygen in the combustion air), burner thermal input and gas-staging on the characteristic combustion parameters including the concentration of nitrogen oxides in flue gas, the flue gas temperature, the heat flux to the combustion chamber wall, and lastly the flame stability and its dimensions.
The Evolution of Business Models and Marketing Strategies in the Music Industry

This article provides a strategic analysis using a services marketing framework of 3 business models in the music industry: the traditional music industry; renegade peer-to-peer music file trading; and new, legitimate online downloading services. Key recommendations are made on how new, legitimate services can succeed using convergent marketing strategies. Finally, a conclusion is provided addressing the future of the music industry and other media-related industries.
Characterization of two dinuclear complexes of the gadolinium ion by IR and Raman

In this work, we studied by IR and Raman spectroscopy studies, the structure of dinuclear complexes of the gadolinium ion (Gd 3+ ) with the oxalic and the glycolic acid; comparing the two spectra : the free acid and its complex in the similar experimental conditions. Both complexes were formed in an aqueous solution according to the acidity of (5.50 3650cm –1 ) in α position of the glycolic acid was reduced in the case of Gd-glycolate. These results show that all the oxygen atoms of the acids studied are related to the gadolinium ion and verified that by the appearance of new peaks characteristic of the vibration Gd–O link (197 ± 10cm –1 ) and (490 ± 80cm –1 ) on the spectra of the complex Gd–acids. The absence of doubling peaks spectra of the complexes (new peaks) show that the structures are symmetrical. Gadolinium ions have been inserted in mononuclear tetradentate site (Gd-Oxalate : –COOGdOOC–) and mononuclear tridentate site (Gd-Glycolate : –C–OHGdOOC–).
Engagement in Asymmetric Markets: Causes and Consequences

This paper contributes to the emprical debate on firm heterogeneity in international trade dealing with the direction of causality from which the performance premium across destination markets originates. For this purpose, we first investigate the selection of firms into markets with asymmetric income levels exploring which firm level characteristics are associated with this selection. Once we identify movements along different statuses on a year to year basis we investigate the factors that drive these movements. We search for the heterogeneity in post-entry effects of trading with different type of markets by establishing treatment models in line with the learning by exporting hypothesis. Our results indicate self-selection mechanisms and post-entry effects differ from market to market for Turkish manufacturing firms.
Beneficial Effects of Caffeic Acid Phenethyl Ester on Formaldehyde-Induced Learning and Memory Disabilities: A Labyrinth Test Performance Study

Purpose: In this study, it was aimed to investigate the efficacy of caffeic acid phenethyl ester (CAPE) on formaldehyde (HCHO)-induced learning and memory changes in rats. Material and Methods: For this purpose, labyrinth test was performed on 21 male Wistar rats. These animals were divided into three equal groups. All groups underwent training period in the labyrinth test. At the end of this period, control rats were injected intraperitoneally with ethanol; the rats in HCHO group were injected intraperitoneally with formaldehyde, and the rats in HCHO+CAPE group were injected with CAPE along with formaldehyde. All animals, within injection period, were subjected to labyrinth test again. The time spent by each rat in reaching the target was recorded and statistically evaluated using one-way variance analysis (ANOVA) and two-way ANOVA for repeated measures. Results: Formaldehyde was observed to cause defects in learning and memory, and changes in behavior in rats. The time used by the HCHO-exposed rats in reaching the target was longer than that of control rats. This negative effect of HCHO exposure was partially alleviated by CAPE administration. Conclusion: In view of the present findings, it is suggested that caffeic acid phenethyl ester exerts beneficial effects against formaldehyde toxicity.
Forcing mechanisms of dielectric barrier discharge plasma actuators at carrier frequency of 625 Hz

The forcing behavior of a dielectric barrier discharge (DBD) actuator is investigated experimentally using a time-resolved particle image velocimetry (PIV) system in conjunction with a phase shifting technique. The spatio-temporal evolution of the induced flowfield is accurately captured within one high voltage (HV) cycle allowing the calculation of the instantaneous velocity and acceleration. Additional voltage and current measurements provide the power consumption for each case. Four different applied voltage waveform shapes are independently tested, namely, sine, square, positive sawtooth, and negative sawtooth at fixed applied voltage (10 kVpp) and carrier frequency (625 Hz). The instantaneous flowfields reveal the effect of the plasma forcing during the HV cycle. Sine waveform provides large positive forcing during the forward stroke, with minimal but still positive forcing during the backward stroke. Square waveform provides strong and concentrated positive and negative forcing at the beginning of the forward and backward stroke, respectively. Positive sawtooth provides positive but weak forcing during both strokes while the negative sawtooth case produces observable forcing only during the forward stroke. Results indicate the inherent importance of negative ions on the force production mechanisms of DBD’s. Furthermore, the revealed influence of the waveform shape on the force production can provide guidelines for the design of custom asymmetric waveforms for the improvement of the actuator’s performance.
Riemannian symmetric superspaces and their origin in random‐matrix theory

Gaussian random‐matrix ensembles defined over the tangent spaces of the large families of Cartan’s symmetric spaces are considered. Such ensembles play a central role in mesoscopic physics, as they describe the universal ergodic limit of disordered and chaotic single‐particle systems. The generating function for the spectral correlations of each ensemble is reduced to an integral over a Riemannian symmetric superspace in the limit of large matrix dimension. Such a space is defined as a pair (G/H,M r ), where G/H is a complex‐analytic graded manifold homogeneous with respect to the action of a complex Lie supergroup G, and M r is a maximal Riemannian submanifold of the support of G/H.
Heuristic 3 d Reconstruction Of Irregular Spaced Lidar 2006

As more data sources have become abundantly available, an increased interest in 3D reconstruction has emerged in the image processing academic community. Applications for 3D reconstruction of urban and residential buildings consist of urban planning, network planning for mobile communication, tourism information systems, spatial analysis of air pollution and noise nuisance, microclimate investigations, and Geographical Information Systems (GISs). Previous, classical, 3D reconstruction algorithms solely utilized aerial photography. With the advent of LIDAR systems, current algorithms explore using captured LIDAR data as an additional feasible source of information for 3D reconstruction. Preprocessing techniques are proposed for the development of an autonomous 3D Reconstruction algorithm. The algorithm is designed for autonomously deriving three dimensional models of urban and residential buildings from raw LIDAR data. First, a greedy insertion triangulation algorithm, modified with a proposed noise filtering technique, triangulates the raw LIDAR data. The normal vectors of those triangles are then passed to an unsupervised clustering algorithm – Fuzzy Simplified Adaptive Resonance Theory (Fuzzy SART). Fuzzy SART returns a rough grouping of coplanar triangles. A proposed multiple regression algorithm then further refines the coplanar grouping by further removing outliers and deriving an improved planar segmentation of the raw LIDAR data. Finally, further refinement is achieved by calculating the intersection of the best fit roof planes and moving nearby points close to that intersection to exist at the intersection, resulting in straight roof ridges. The end result of the aforementioned techniques culminates in a well defined model approximating the considered building depicted by the LIDAR data.
Development of a Collaborative Learning System for Supporting Ubiquitous Contextual Learning Activities

With the advancement and popularity of mobile and wireless communication technologies, computer-supported learning activities can be conducted without being limited by time and space. Researchers have called such an anywhere and anytime learning approach "ubiquitous learning. " In a ubiquitous contextual learning activity, students are situated in an environment that combines real-world and digital-world learning resources. Although such a learning approach is innovative and interesting, researches have pointed out the problem of lacking proper learning mechanisms that can guide or assist the students to learn collaboratively in such complicated learning contexts. To cope with this problem, in this study, a collaborative learning system is developed based on a knowledge engineering approach to supporting collaborative ubiquitous learning activities. An experiment conducted in an elementary school Natural Science course has shown the effectiveness of this system.