Miracle-dz/UniFAR-FTUs huggingface dataset:
Accommodating Protein Flexibility in Computational Drug Design 1 , 2

The need to account for the dynamic behavior of a receptor has long been recognized as a complicating factor in computational drug design. The use of a single, rigid protein structure—usually from a high-quality X-ray crystal structure— still is the standard in most applications (Zheng and Kyle, 1997; Walters et al., 1998). The choice to use a single protein structure is usually based on speed. For example, if a large database of compounds is to be screened for binding affinity, several conformers of each compound will be compared with each protein configuration. Although it is more accurate to use many representative protein configurations, it quickly becomes a very slow process to screen each conformer of each ligand against each protein configuration. It is usually impractical to attempt such prohibitively slow calculations because there is an unfortunate but necessary trade-off between speed and accuracy in computer modeling. Only recently have advanced methods been introduced to aid in a more accurate description of protein flexibility and its influence on ligand recognition. This has been aided by the exponential growth in the speed of computer processors, available RAM, and disk capacity—all of which are rapidly becoming less expensive. Here, we explain the need for accommodating an ensemble of protein configurations in drug design and the computational methods available for generating and manipulating that dynamic information. Most of the applications discussed below are improvements in liganddocking or in the generation of pharmacophore models for database searching. Protein Flexibility and Its Influence on Ligand Binding
A framework for assessing the exchange costs in the flax fibre supply chain

II ACKNOWLEDGEMENTS . IV TABLE OF CONTENTS . V LIST OF FIGURES. IX LIST OF TABLES . X 1.0 INTRODUCTION . 1 1.1 Background.1 1.2 Problem Statement . 2 1.3 Objectives.3 1.4 Focus of the Thesis.5 1.5 Organization of the Thesis.5 2.0 INDUSTRY BACKGROUND.7 2.
Flapping frequency and resonant frequency of insect wings

In this study, we experimentally studied the relationship between wingbeat frequency and resonant frequency of 30 individuals of eight insect species from five families: Odonata (Sympetrum flaveolum), Lepidoptera (Pieris rapae, Plusia gamma and Ochlodes), Hymenoptera (Xylocopa pubescens and Bombus rupestric), Hemiptera (Tibicen linnei) and Coleoptera (Allomyrina dichotoma). We found that wingbeat frequency does not have a strong relation with resonance frequency: in other words, insects have not been evolved sufficiently to flap at their wings' structural resonant frequency. This contradicts the general conclusion of other reports-that insects flap at their wings' resonant frequency to take advantage of passive deformation to save energy.
Effect of prenatal exposure to bisphenol a on the vagina of albino rats: immunohistochemical and ultrastructural study.

BACKGROUND Bisphenol-A (BPA) is an industrial chemical, used to manufacture polycarbonate and numerous plastic articles. It has been found to cause biological effects, mimic that of oestrogen. It belongs to a group of chemicals termed "endocrine disruptors" able to disrupt the chemical messenger system in the body. Aim of the study was to demonstrate the biological effects of BPA on the vagina of female rats, with the prediction of the neoplastic changes in relation to its potential impact. MATERIALS AND METHODS Sprague-Dawley gravid dams were divided into three groups (10 per group): G1 - control group had an equivalent volume of sesame oil to that taken in the treated groups, G2 - group was administered by gavage 0.1 mg BPA/kg body weight (low-dose group) per day, and G3 - group was administered 50 mg BPA/kg body weight (high-dose group) per day, dissolved in sesame oil. Treatment was carried out on gestation days 10 through 20. The female offsprings of each group were weaned at day 21 and the vagina was dissected when became 3 months old for histological, immunohistochemical analysis (for detection of oestrogen receptors a [ERa], and the proliferation marker Ki-67), and ultrastructural study. RESULTS The low dose group showed degeneration of the epithelial lining with focal patches of decreased epithelial layers. The high dose group revealed cytoplasmic hydropic degeneration, and the pyknotic nuclei of epithelial cells. Oestrogen receptors demonstrated a significant decrease of positive cells in low dose treated group and this decrease markedly accentuated in the high dose one. Positive nuclei for Ki-67 were markedly increased with increasing doses of BPA. Electron microscopic study revealed cytoplasmic degeneration, vacuolation and mitochondrial degeneration in both treated groups. CONCLUSIONS BPA showed an obvious mix of degenerative and proliferative histological changes and clear damage of the cellular organelles. This stressful condition may predispose to neoplastic changes of the vagina.
A novel mismatching elimination algorithm based on distribution of features

Catadioptric panoramic image's application to computer visual field gains its popularity in recent years. However, due to its complicated imaging relationship, most existing mismatching elimination algorithms cannot directly operate on the unprocessed panoramic images. Those above algorithms usually need to unwarp the panoramic images before further processing. In order to solve the above problems, based on the distribution characteristics of features in the panoramic image, a novel mismatching elimination algorithm is proposed in this paper. Under different scene conditions, the novel algorithm can eliminate the mismatching features and improve the matching accuracy effectively. Experiments on the image databases confirm its effectiveness.
Tncs' Technology Linkages with Domestic Firms: An Investigation of the Ict Industry in Suzhou, China

On the basis of a comprehensive survey in the information and communication technology industry in China's Suzhou municipality, we examine the determinants of the technology linkages that transnational corporations (TNCs) make with domestic firms. We found that TNCs' domestic supply and client linkages and their decentralization of decision making had a significant and positive effect on technological interactions between domestic firms and TNCs. However, such linkages were constrained by the technology gap between TNCs and domestic firms and they are focused on new product developments for the domestic Chinese market. The results highlight the challenges that domestic Chinese firms face in establishing ‘global pipelines’ of knowledge exchange. The implications of the findings on technology and foreign direct investment policies in China are also assessed, and we argue that China has potential to pave a new way of technology development by taking advantage of its indigenous capacity and sizable domestic market.
Degradation Analysis and Mitigation in FPGAs

FPGAs are powerful platforms for investigating impending challenges associated with process scaling, such as variation and degradation. Their versatility allows us to gather empirical data and evaluate novel solutions. We carried out accelerated-life tests on modern FPGA devices and obtained a useful characterisation of the ageing processes that afflict them. We also quantified the potential benefits of three degradation mitigation strategies based on exploiting spare logic and interconnect resources. The work helps cement the role of reconfigurable logic as a vitally-important technology in the face of the uncertainties of future process scaling.
Center for International Securities and Derivatives Markets Hedge Fund Strategy Performance : Using Conditional Approaches October 2003

The search for methodologies that accurately measure performance and performance persistence continues to evolve. This is especially true for investment strategies such as hedge funds, which have been shown, in several instances, to not be normally distributed. In this article, we evaluate performance of hedge funds using conditional approaches and GMM. Unlike the Sharpe ratio or Jensen’s alpha, our results would still be valid even if hedge funds were not normally distributed. We use the CISDM hedge fund database for this study. We create three portfolios to measure performance: an Active portfolio (which consists of funds in the active database), a Dead portfolio (which consists of funds in the defunct database) and an All portfolio (which consists of funds in both the active and defunct databases). We find that while the Active portfolios show evidence of positive risk-adjusted returns in most cases, the Dead portfolios do not and only some of the All portfolios show evidence of positive risk-adjusted returns. The results are similar irrespective of whether we use Jensen’s alpha or conditional approaches. Our results point to two conclusions: one the explanatory variables used in this paper may not be able to capture the type of trading strategies followed by hedge fund strategies and two the estimated alphas are good estimates of the true alphas which are mostly due to managers’ skills and hence cannot be explained by naïve static or dynamic trading strategies. In our analysis of market timing models, we show that hedge fund managers in general lack market timing ability and fund level analysis is required to determine the few that do have market timing ability. The results also suggest that hedge fund returns have option-like properties and future research should include option-based factors in performance evaluation.
Validation of a Commercially Available Indirect Elisa Using a Nucleocapside Recombinant Protein for Detection of Schmallenberg Virus Antibodies

A newly developed Enzym Like Immuno Sorbant Assay (ELISA) based on the recombinant nucleocapsid protein (N) of Schmallenberg virus (SBV) was evaluated and validated for the detection of SBV-specific IgG antibodies in ruminant sera by three European Reference Laboratories. Validation data sets derived from sheep, goat and bovine sera collected in France and Germany (n = 1515) in 2011 and 2012 were categorized according to the results of a virus neutralization test (VNT) or an indirect immuno-flurorescence assay (IFA). The specificity was evaluated with 1364 sera from sheep, goat and bovine collected in France and Belgium before 2009. Overall agreement between VNT and ELISA was 98.9% and 98.3% between VNT and IFA, indicating a very good concordance between the different techniques. Although cross-reactions with other Orthobunyavirus from the Simbu serogroup viruses might occur, it is a highly sensitive, specific and robust ELISA-test validated to detect anti-SBV antibodies. This test can be applied for SBV sero-diagnostics and disease-surveillance studies in ruminant species in Europe.
Fast Pyrolysis of Four Lignins from Different Isolation Processes Using Py-GC/MS

Pyrolysis is a promising approach that is being investigated to convert lignin into higher value products including biofuels and phenolic chemicals. In this study, fast pyrolysis of four types of lignin, including milled Amur linden wood lignin (MWL), enzymatic hydrolysis corn stover lignin (EHL), wheat straw alkali lignin (AL) and wheat straw sulfonate lignin (SL), were performed using pyrolysis gas-chromatography/mass spectrometry (Py-GC/MS). Thermogravimetric analysis (TGA) showed that the four lignins exhibited widely different thermolysis behaviors. The four lignins had similar functional groups according to the FTIR analysis. Syringyl, guaiacyl and p-hydroxyphenylpropane structural units were broken down during pyrolysis. Fast pyrolysis product distributions from the four lignins depended strongly on the lignin origin and isolation process. Phenols were the most abundant pyrolysis products from MWL, EHL and AL. However, SL produced a large number of furan compounds and sulfur compounds originating from kraft pulping. The effects of pyrolysis temperature and time on the product distributions from corn stover EHL were also studied. At 350 °C, EHL pyrolysis mainly produced acids and alcohols, while phenols became the main products at higher temperature. No obvious influence of pyrolysis time was observed on EHL pyrolysis product distributions.
PERILAKU BIROKRASI DALAM PELAYANAN PENDIRIAN PANTI ASUHAN DI DINAS SOSIAL PROVINSI SULAWESI SELATAN

Birokrasi adalah fenomena kehidupan yang setidaknya sejak abad 19, telah menjadi aktor sedemikian penting dalam sejarah umat manusia. Apabila orang ditanya tentang organisasi apakah yang paling mereka butuhkan dalam hidup, maka jawaban semua orang adalah hampir pasti: birokrasi. Sejak sebelum lahir, sampai dengan meninggalnya, seorang manusia yang hidup di dunia modern, akan senantiasa berurusan dengan institusi pemerintah yang kita kenal dengan nama birokrasiitu. Tujuan dari penelitian ini adalah untuk menggambarkan perilaku birokrasi dalam pelayanan pendirian panti asuhan di Dinas Sosial Provinsi Sulawesi Selatan. Metode penelitian ini penulis menggunakan pendekatan kualitatif dimana dalam penelitian yang dilakukan hanya bersifat deskriptif yaitu untuk menggambarkan kenyataan dari kejadian yang diteliti sehingga memudahkan penulis untuk mendapatkan data yang objektif dalam rangka mengetahui dan memahami perilaku birokrasi dalam pelayanan sosial di panti asuhan. Adapun dasar penelitian yang digunakan dalam penelitian ini adalah penelitian studi kasus dengan mengumpulkan data dan informasi untuk menjawab permasalahan yang ada. Hasil penelitian Kemampuan pegawai dalam melayani pihak panti asuhan sudah berjalan dengan baik. Seperti tidak melakukan kesalahan dalam pekerjaannya, mengetahui seluk beluk pekerjaannya, dan mampu berkomunikasi dengan pihak panti asuhan sebagai masyarakat yang dilayani maupun antara rekan kerjanya. Kebutuhan pegawai dapat terpenuhi dengan baik, seperti gaji yang diterima, adanya penghargaan bagi pegawai yang berpretasi dan juga ada kesempatan yang diberikan Dinas Sosial Provinsi Sulawesi Selatan bagi setiap pegawai untuk meningkatkan kemampuannya baik itu pelatihan maupun jalurpendidikan. Hierarki di Kantor Dinas Sosial Provinsi Sulawesi Selatan tercipta dengan baik. Hal ini dapat dilihat bahwa adanya penyusunan struktur jabatan serta tugas dan tanggung jawab dengan jelas dan spesifik serta tercipta komunikasi yang harmonis antara pimpinan dengan bawahannya, maupun antara sesama pegawai di Kantor Dinas Sosial dan Provinsi SulawesiSelatan.
Ordered Progression of Nematogenesis from Stem Cells through Differentiation Stages in the Tentacle Bulb of Clytia Hemisphaerica (hydrozoa, Cnidaria)

Nematogenesis, the production of stinging cells (nematocytes) in Cnidaria, can be considered as a model neurogenic process. Most molecular data concern the freshwater polyp Hydra, in which nematocyte production is scattered throughout the body column ectoderm, the mature cells then migrating to the tentacles. We have characterized tentacular nematogenesis in the Clytia hemisphaerica hydromedusa and found it to be confined to the ectoderm of the tentacle bulb, a specialized swelling at the tentacle base. Analysis by a variety of light and electron microscope techniques revealed that while cellular aspects of nematogenesis are similar to Hydra, the spatio-temporal characteristics are markedly more ordered. The tentacle bulb nematogenic ectoderm (TBE) was found to be polarized, with a clear progression of successive nematoblast stages from a proximal zone (comprising a majority of undifferentiated cells) to the distal end where the tentacle starts. Pulse-chase labelling experiments demonstrated a continuous displacement of differentiating nematoblasts towards the tentacle tip, and that nematogenesis proceeds more rapidly in Clytia than in Hydra. Compact expression domains of orthologues of known nematogenesis-associated genes (Piwi, dickkopf-3, minicollagens and NOWA) were correspondingly staggered along the TBE. These distinct characteristics make the Clytia TBE a promising experimental system for understanding the mechanisms regulating nematogenesis.
Adaptive E-learning content generation based on semantic web technology

The efficient authoring of learning content is a central problem of courseware engineering. Courseware authors will appreciate the benefits of tools which automate various authoring tasks. We describe a system, OntAWare, which provides an environment comprising a set of software tools that support learning content authoring, management and delivery. This system exploits an opportunity provided by the emerging technologies of the Semantic Web movement, most notably knowledge-representation standards and knowledge-processing techniques. The system represents a combination of these newer developments with earlier work in areas such as artificial intelligence (AI) and intelligent tutoring systems (ITS). A key feature of the authoring environment is the semi-automatic generation of standard e-learning and other courseware elements (learning objects). Widely available standardised knowledge representations (ontologies) and ontology-structured content are used as source material. Standard courseware elements are produced by the application of graph transformations to these ontologies. The resulting products can be hosted by standards-compliant delivery environments. Adaptivity is an important characteristic of the system as a whole. Authors can select and customise new or existing subject ontologies and employ an appropriate teaching/learning strategy in the generation of learning objects. Instructors can configure the delivery environment either to offer strictly sequenced presentations to students, or to allow also varying degrees of free student navigation, based on the the runtime incorporation of domain ontologies. Students in turn can take the generated courses in the preconfigured delivery environment, and this delivery is dynamically customised to the individual student's preferences and constantly monitored learning track. The combination of the semi-automatic generation of learning objects with an adaptive delivery environment is a central feature of this new system. Keywords: courseware generation, Semantic Web, ontology, learning object, adaptivity.
The Open University ’ s repository of research publications and other research outputs Alleviating data sparsity for Twitter sentiment analysis

Twitter has brought much attention recently as a hot research topic in the domain of sentiment analysis. Training sentiment classifiers from tweets data often faces the data sparsity problem partly due to the large variety of short and irregular forms introduced to tweets because of the 140-character limit. In this work we propose using two different sets of features to alleviate the data sparseness problem. One is the semantic feature set where we extract semantically hidden concepts from tweets and then incorporate them into classifier training through interpolation. Another is the sentiment-topic feature set where we extract latent topics and the associated topic sentiment from tweets, then augment the original feature space with these sentiment-topics. Experimental results on the Stanford Twitter Sentiment Dataset show that both feature sets outperform the baseline model using unigrams only. Moreover, using semantic features rivals the previously reported best result. Using sentimenttopic features achieves 86.3% sentiment classification accuracy, which outperforms existing approaches.
Microelectronic Cooling by Enhanced Pool Boiling of a Dielectric Fluorocarbon Liquid

An experimental study of boiling heat transfer from a simulated microelectronic component immersed in a stagnant pool of the dielectric Fluorinert (FC-72) is presented. Various enhancement surfaces were attached to an electrically heated copper calorimeter bar having a vertically oriented heat transfer surface area of 12.7 {times} 12.7 mm{sup 2}. A number of enhancement schemes aimed at a reduction of the incipience temperature overshoot were tested, employing various arrangement of fins, studs, grooves, and vapor-trapping cavities. Atmospheric pressure testing revealed a variation in the magnitude of boiling curve incipience temperature excursion as a function of both macro- and microcharacterization of the surface geometry and initial conditions (pressure and temperature history) prior to boiling. Increased incipience temperatures accompanied prolonged periods of nonboiling. It is assumed that this is due to vapor embryos within surface cavities collapsing to smaller radii. Large artificially created cavities (0.3 mm diameter) were found incapable of maintaining a stable vapor embryo for time periods greater than 10 min. In comparison to flat surfaces, low-profile surface geometries having a structure scale of the order of one bubble departure diameter resulted in significant enhancement of nucleate boiling while drilled surfaces had minimal effectiveness. Surface finish and artificial cavities hadmore » no effect on CHF, but levels of critical heat flux computed on base area were strongly dependent on macrogeometry, due in part to increased surface area. « less
Combinations of fungicide and cultural practices influence the incidence and impact of fusiform rust in slash pine plantations

Slush pine was grown in central Louisiana unrler,f? )ur levels c! f'culture with or without repeatc~d spmyings of the . sy.vten~ic ,fungicide triadimefhn ,fir protection against ,fusifi)rm rust. The eight treatment cornbinations were: (I) no,fungicide, weed control, or,fertilizer; (2) weeded; (3) weeded, applied irzorganic ,firtilizer, and bedded b<fi)replcrrlting; (4) weeded, bedded, and applied inorganic fertilizer in the sixth growing season (clel(.lcryedjkrtilizutioi~); (5) c~pplied fungicide but no weed control or,fertilizer; (6) applied fungicide and weeded; (7) czpplied ,fungicide plus treatment 3; and (8) applied fungicide plus treatment 4. Fungicide appliccrtions greatly reduced,fu.sijorm rust impact in 10-yr-old sla.sh pine stands. Fungicide treatments resulted in higher . survival, ,fewer trees with stem galls, fewer trees with gal1.s encircling 76%-100% c$' the . stem circumference, greater total volume/ac, and less volume/c~c among infected trees. The fungicide-treated trees had,fewer stem ga1l.s below 5 ft of tree height compared with untreated trees, indicating that the furzgicide treutmentprotectedpIc1nted seedlings through several growing seasons. Weed control increased fusiform rust incidence. The,fungicicle-treated plots receiving delayedfertilization yielded the most volume (3,018 ft3/ac) a$er 10 growing seasons because of high stocking and accelerated growth ji)llowing ,fertilization. South. J. Appl. For. (2):53-59.
Childhood in the rural areas of Chile, intergenerational and gendered perspectives

ABSTRACT This article triangulates intergenerational (childhood, adulthood, and old age) visions on the social representation of childhood in rural areas of Chile. These visions were considered within the framework of identity constructs (perceptions, social behaviours, preferences, and ambitions) and were compared against emerging transformations in the spheres of family, and gender relations. A qualitative methodology was used to analyse 68 individual interviews (41 children; 21 women old age; and 6 adult women). It was concluded that, in a context of globalization, rural boys and girls use modern, urban symbols and conform to traditional gender stereotypes. In a familial environment, rural children have acquired discursive protagonism in alliance with older women, a reality that conflicts with the conservative vision of middle-aged adults who have poor awareness regarding the participation of children. Contrasting visions exist between adult women and seniors concerning the responsibilities assigned to children in general and, particularly, to girls.