Miracle-dz/UniFAR-FTUs huggingface dataset:
Interactions and structure of the nuclear pore complex revealed by cryo- electron microscopy

Nuclear pore complexes (NPCs) play a central role in mediating nucleocytoplasmic transport and exchange processes in eukaryotic cells. The arrangement and interactions of NPCs within amphibian nuclear envelopes have been studied using cryo-electron microscopy of unfixed and frozen hydrated specimens. The nuclear lamina in Necturus forms an orthogonal network with crossover distances which vary between 1,600 and 4,000 A and which may be related to the basic filament repeat of lamins. Furthermore, the NPCs are attached randomly within the confines of the lamin network, presumably by their nucleoplasmic rings. Image analysis of edge-on and en face projections of detergent-extracted NPCs has been combined with data on the coaxial thin rings to provide a quantitative evaluation of the triple ring model of NPC architecture proposed previously (Unwin, P. N. T., and R. Milligan. 1982. J. Cell Biol. 93:63-75). Additional details of the complex have been visualized including an intimate association of the inner spoke domains as an inner spoke ring, extensive domains within the spokes and coaxial thin rings, and interestingly, a central channel-like feature. Membrane- associated NPCs and detergent-extracted NPCs both possess peripherally located radial arms resulting in an effective diameter of approximately 1,450-1,500 A. In projection, the radial arms possess approximate mirror symmetry suggesting that they originate from both sides of the assembly. Moreover, membrane-associated NPCs are asymmetric at most radii and right-handed as viewed from the cytoplasm; detergent- extracted NPCs appear to be symmetric and have approximately 822 symmetry. Taken together, the data suggests that the framework of membrane-associated NPCs is perturbed from a symmetrical configuration, either during isolation of nuclei or by interactions with the lamina and the nuclear envelope in vivo. However, detergent extraction of nuclei appears to result in a more symmetrical alignment of components in apposing halves of the assembly.
Comparative Evaluation of Collocation Extraction Metrics

Corpus-based automatic extraction of collocations is typically carried out employing some statistic indicating concurrency in order to identify words that co-occur more often than expected by chance. In this paper we are concerned with some typical measures such as the t-score, Pearson’s χ-square test, log-likelihood ratio, pointwise mutual information and a novel information theoretic measure, namely mutual dependency. Apart from some theoretical discussion about their correlation, we perform comparative evaluation experiments judging performance by their ability to identify lexically associated bigrams. We use two different gold standards: WordNet and lists of named-entities. Besides discovering that a frequency-biased version of mutual dependency performs the best, followed close by likelihood ratio, we point out some implications that usage of available electronic dictionaries such as the WordNet for evaluation of collocation extraction encompasses.
Deletion of cagA gene of Helicobacter pylori by PCR products.

AIM Cytotoxin-associated protein (antigen) A (CagA) plays an important role in Helicobacter pylori (H pylori) pathogenesis. Our aim was to obtain cagA- mutant strains by a new mutation method so as to better understand the mechanism of CagA in epithelial cells. METHODS In contrast with the traditional method using suicide plasmid, we constructed cagA- mutant strains directly with PCR products. The constructed mutant clones grew on selective media and allelic exchange was confirmed by Southern blot. Furthermore, two different transformation methods, electroporation, and natural transformation, were compared with regard to the efficiency of recombination. RESULTS The mutation by PCR products could be completed within 3-5 d, and the recombination rate by electroporation and natural transformation was 4.02 x 10(-8) and 1.03 x 10(-9) respectively. Mutation rate by electroporation (4.02 x 10(-8)) was far higher than by natural transformation (1.03 x 10(-9)) (P = 0.000<0.005). CONCLUSION cagA- mutant strains have been constructed, which is important for further study on the function of CagA in epithelial cells. A mutation method by directly using PCR products has been proved successful with a much higher mutation rate, and is easier, especially when in combination with electroporation. This method could be widely used in gene deletion of H pylori.
Changing Interaction of Compiler and Architecture

Program optimizations that have been exclusively done by either the architecture or the compiler are now being done by both. This blurred distinction offers opportunities to optimize performance and redefine the compiler-architecture interface. We describe an optimization continuum with compile time and post run time as end points and show how different classes of optimizations fall within it. Most current commercial compilers are still at the compile-time end point, and only a few research efforts are venturing beyond it. As the gap between architecture and compiler closes, there are also attempts to completely redefine the architecture-compiler interface to increase both performance and architectural flexibility.
Monsoon-Induced Biases of Climate Models over the Tropical Indian Ocean*

AbstractLong-standing biases of climate models limit the skills of climate prediction and projection. Overlooked are tropical Indian Ocean (IO) errors. Based on the phase 5 of the Coupled Model Intercomparison Project (CMIP5) multimodel ensemble, the present study identifies a common error pattern in climate models that resembles the IO dipole (IOD) mode of interannual variability in nature, with a strong equatorial easterly wind bias during boreal autumn accompanied by physically consistent biases in precipitation, sea surface temperature (SST), and subsurface ocean temperature. The analyses show that such IOD-like biases can be traced back to errors in the South Asian summer monsoon. A southwest summer monsoon that is too weak over the Arabian Sea generates a warm SST bias over the western equatorial IO. In boreal autumn, Bjerknes feedback helps amplify the error into an IOD-like bias pattern in wind, precipitation, SST, and subsurface ocean temperature. Such mean state biases result in an interannual I.
Building a predictive model from data in high dimensions with application to analysis of microarray experiments

This work presents a comparative study of methods for building predictive models from data in high dimensionality spaces, i.e. where the number of features describing items to be classified is high as compared with the available number of items used to build the model and test its predictive performance. Application of such methods may be quite diverse, ranging from data analysis in life sciences (e.g., analysis of data from experiments generating thousands of feature-numbers per tested case, such a microarray or RT-PCR techniques), to analysis of monitoring data from a complex, highly reliable technical system, where the relationship is being sought between the monitoring data and the relatively infrequent occurrences of some event (such as a faulty or somewhat untypical state of the system). This latter case may be of special interest in early prediction of abnormal conditions in systems focused on dependability. The multidimensional data analysis challenges and generic methods are described in this paper using a very problem specific language of life sciences, namely classification of samples based on gene expression profiles obtained using DNA microarrays. We concentrate on feature selection methods (which in the context are gene selection methods). We also propose a method to evaluate performance of feature (gene) selection methods by looking at predictive power of classifiers based on selected features.
Decreased Resistance to Bacterial Infection and Granulocyte Defects in IAP-Deficient Mice

Granulocyte [polymorphonuclear leucocyte (PMN)] migration to sites of infection and subsequent activation is essential for host defense. Gene-targeted mice deficient for integrin-associated protein (IAP, also termed CD47) succumbed to Escherichia coli peritonitis at inoccula survived by heterozygous littermates. In vivo, they had an early defect in PMN accumulation at the site of infection. In vitro, IAP−/− PMNs were deficient in β3 integrin-dependent ligand binding, activation of an oxidative burst, and Fc receptor-mediated phagocytosis. Thus, IAP plays a key role in host defense by participating both in PMN migration in response to bacterial infection and in PMN activation at extravascular sites.
Generalized constrained energy minimization approach to subpixel detection for multispectral imagery

Subpixel detection for multispectral imagery presents a challenging problem due to relatively low spectral resolution. This paper proposes a Generalized Constrained Energy Minimization (GCEM) approach to detecting objects in multispectral imagery at subpixel level. GCEM is a combination of a dimensionality expansion (DE) approach resulting from a generalized orthogonal subspace projection (GOSP) developed for multispectral image classification and a CEM method developed for hyperspectral image classification. DE allows us to generate additional bands from original multispectral images while CEM is used for subpixel detection to extract objects embedded in multispectral images. CEM has been successfully applied to hyperspectral target detection and image classification. Its applicability to multispectral imagery has not been investigated. A potential limitation of CEM on multispectral imagery is the effectiveness of interference elimination due to the lack of sufficient dimensionality. DE is introduced to mitigate this problem. Experiments have shown that the proposed GCEM detects objects more effectively than CEM without dimensionality expansion and GOSP.
Analysis of denoising filters for photo response non uniformity noise extraction in source camera identification

Identification of the source that has generated a digital content is considered one of the main open issues in multimedia forensics community. The extraction of photo-response non-uniformity (PRNU) noise has been so far indicated as a mean to identify sensor fingerprint. Such a fingerprint can be estimated from multiple images taken by the same camera by means of a denoising filtering operation. This paper presents an analysis of the performances of different denoising filters based on diverse noise models when applied for digital camera tracking. In particular, a digital filter, based on a signal-dependent noise model, is introduced and compared with others commonly adopted for this purpose. A theoretical framework and experimental results are provided and discussed.
Auditory fovea based speech enchancement and its application to human-robot dialog system

This paper presents an active direction-pass ﬁlter (ADPF) that separates sound from a speciﬁed direction by using a pair of microphones. Its application to front-end processing for speech recognition is also reported. The ADPF improves sound source separation by accurate sound direction obtained by multi-modal integration and active motor control that keeps the robot facing to a sound source, because the resolution of the center direction is much higher than that of peripherals, indicating similar property of visual fovea. In order to recognize separated sound streams, a Hidden Markov Model (HMM) based automatic speech recognition is built with multiple acoustic models trained by the output of the ADPF under various conditions. The experimental results by a preliminary dialog system prove that it works well even when two speakers speak simultaneously.
On the geometry of impulsive gravitational waves

We describe impulsive gravitational pp-waves entirely in the distributional picture. Applying Colombeau's nonlinear framework of generalized functions we handle the formally ill-defined products of distributions which enter the geodesic as well as the geodesic deviation equation. Using a universal regularization procedure we explicitly derive regularization independent distributional limits. In the special case of impulsive plane waves we compare our results with the particle motion derived from the continuous form of the metric.
Varieties of Political Process During Systems Development

This study uses a longitudinal research design with multiple data collection methods on a systems development project. Five theoretical perspectives about power have been used to evaluate the case: zero sum, processual, organizational, structurally constrained, and social shaping/social construction. Our working assumption is that power is multidimensional and therefore that any attempt to understand systems development must simultaneously use several complementary perspectives. Studies of information systems development have in the past often been based on a view of power as zero sum with winners and losers from systems development and of power as based on information. We will attempt to show that expansion from this narrow definition of power has much to offer information systems research. The paper will attempt to identify what unique and essential insights about the relationship between power and systems development are surfaced by each perspective.
Proteome-wide analysis reveals an age-associated cellular phenotype of in situ aged human fibroblasts

We analyzed an ex vivo model of in situ aged human dermal fibroblasts, obtained from 15 adult healthy donors from three different age groups using an unbiased quantitative proteome-wide approach applying label-free mass spectrometry. Thereby, we identified 2409 proteins, including 43 proteins with an age-associated abundance change. Most of the differentially abundant proteins have not been described in the context of fibroblasts’ aging before, but the deduced biological processes confirmed known hallmarks of aging and led to a consistent picture of eight biological categories involved in fibroblast aging, namely proteostasis, cell cycle and proliferation, development and differentiation, cell death, cell organization and cytoskeleton, response to stress, cell communication and signal transduction, as well as RNA metabolism and translation. The exhaustive analysis of protein and mRNA data revealed that 77% of the age-associated proteins were not linked to expression changes of the corresponding transcripts. This is in line with an associated miRNA study and led us to the conclusion that most of the age-associated alterations detected at the proteome level are likely caused post-transcriptionally rather than by differential gene expression. In summary, our findings led to the characterization of novel proteins potentially associated with fibroblast aging and revealed that primary cultures of in situ aged fibroblasts are characterized by moderate age-related proteomic changes comprising the multifactorial process of aging.
Private and Flexible Proximity Detection Based on Geohash

Proximity detection is one of the critical components in Location-based Social Networks (LBSNS), which has attracted much attention recently. With the advent of LBSNS, more and more users' location information will be collected by the service providers. However, with a potentially untrusted server, such a proximity detection service may threaten the privacy of users. In this paper, aiming at achieving enhanced privacy against the untrusted service providers in LBSNS, we introduce a new architecture with dual-servers for the first time and propose a privacy-preserving proximity detection method based on Geohash. In our architecture, the location coordinates of users are converted into a bit-string by dichotomy approximation, and divided into two subsets: prefix and suffix. The social network server firstly selects the candidate neighbors only in the light of the prefix, and then a third-party server is introduced to compute the relative distance of candidate neighbors according to the suffix. Each server can only get a subset of location code, instead of the whole location information of users as the previous work. We also prove that the new construction is secure under the untrusted server model with enhanced privacy. Finally, we provide extensive experimental results to demonstrate the efficiency of our proposed construction.
Interactive Multiresolution Editing of Arbitrary Meshes

This paper presents a novel approach to multiresolution editing of a triangular mesh. The basic idea is to embed an editing area of a mesh onto a 2D rectangle and interpolate the user‐specified editing information over the 2D rectangle. The result of the interpolation is mapped back to the editing area and then used to update the mesh. We adopt harmonic maps for the embedding and multilevel B‐splines for the interpolation. The proposed mesh editing technique can handle an arbitrary mesh without any preprocessing such as remeshing. It runs fast enough to support interactive editing and produces intuitive editing results.
The Architecture of the Language Faculty

Questions, goals, assumptions - universal grammar, necessities and assumptions, syntactocentrism and perfection interfaces, representational modularity - the 'articulatory-perceptual' interfaces, the phonology-syntax interface, the 'conceptual-intentional' interface, embedding mismatches between syntactic structure and conceptual structure, the tripartite parallel architecture, representional modularity more on the syntax-semantics interface - enriched composition, aspectual coercions, reference transfer functions, arguments structure alternations, adjective-noun modification, summary, anaphora, quantification, remarks the lexical interface - lexical insertion versus lexical licensing, PIL=CIL, PIL and CIL are at S-structure, checking argument structure, remarks on processing, the lexicon in a more general mental ecology lexical entries, lexical rules - broadening the conception of the lexicon, morphosyntax versus morphophonology, inflectional versus derivational morphology, productivity versus semiproductivity, psycholinguistic considerations, 'optimal coding' of semiproductive forms, final remarks remarks on productive morphology - introduction, the place of traditional morphophonology, phonological and class-based allomorphy, suppletion of composed forms by irregulars, the status of zero inflections, why the lexicon cannot be minimalist idioms and other fixed expressions - reviews of the issues, the wheel of fortune corpus: if it isn't lexical, what is it? lexical insertion of idioms as Xos, lexical licensing of units larger than Xo, parallels between idioms and compounds, syntactic mobility of (only) some idioms, idioms that are specializations of other idiomatic constructions, relation to construction grammar, summary epilogue: how language helps us think - introduction, brain phenomena opaque to awareness, language is not thought, and vice versa, phonetic form is conscious , thought is not, the significance of consciousness again, first way language helps us think: linguistic communication, second way language helps us think: making conceptual structure available for attention, third way language helps us think: valuation of conscious percepts, summing up,
Feature Extraction Techniques for Ultrasonic Shaft Signal Classification

Discrete Wavelet Transform (DWT) coefficients of ultrasonic test signals are considered useful features for input into classifiers due to their effective time-frequency representation of non-stationary signals. However, DWT exhibits a time-variance problem that has resulted in reservations for, its wide acceptance. In this paper, a new technique to derive a preprocessing method for time-domain A-scans signal is presented. This techniques offer consistent extraction of a segment of the signal from long signals that occur in the Non Destructive Testing of shafts. We performed a comparison using artificial neural networks and evaluated classification performance of the classifier supplied with features generated by our method. We compared with other alternatives and report the results here. We established experimentally that DWT coefficients can be used as a feature extraction scheme more reliably by using our new preprocessing technique.
Adopting XP practices for teaching object oriented programming

This paper reports on an Action Research project that investigated the effect of introducing a number of Extreme Programming (XP) practices as teaching techniques to introductory programming students. The focus of the study was on using the XP practices to assist students in an introductory programming subject develop object oriented programming skills, problem solving skills and teach them to become more self-sufficient in their learning. The research is concerned with applying several of the XP practices as a means of value-adding to current pedagogical approaches. The results from this first exploratory cycle have been mixed, but there have been enough positive results to feed forward into the next action research cycle.
Nutritional Obesity and body Composition

It will be abundantly evident from other papers in this symposium that obesity is not a common feature in modem farm animals nor should it be inferred from the inclusion of this paper that nutritional obesity is an inevitable consequence of the consumption of animal products. The justification for including this subject rests entirely on the obsession with human obesity in our overnourished western world and the considerable research effort, particularly during the last 15 years, on the development and sequelae of overnutrition, using animal models. However, detailed examination of the voluminous literature reveals that most studies have used the laboratory rat and were undertaken to study food intake or energy metabolism with only a very limited number being primarily designed to examine body composition. The author has therefore been forced to be selective in terms of literature cited and acknowledges di4iculty in reaching unifying themes. It will become clear that the general principles relating to body composition of growing and adult animals which have b&n elucidated and developed during the last 40 years apply equally well during the development of obesity as during undemutrition. It is therefore fitting to begin this paper with a tribute to those who so painstakingly laid the basis of our understanding of growth and body composition and, in particular, to two research groups from Cambridge, namely the late Sir John Hammond and his colleagues (McMeekan, 1940a,b,c; Palsson & Verges, 1952; Palsson, 1955) and McCance & Widdowson and their colleagues (Spray & Widdowson, 1950; Dickerson & McCance, 1961; Cabak et al. 1962; Lister & McCance, 1967; Widdowson, 1968). Hyperphagia and consequential obesity have been induced in the laboratory rat by offering high-fat diets (Mickelsen et al. 1955), by gastric intubation (Cohn et al. I ~ J ) , by offering concentrated sugar solutions (Muto & Miyahara, 1972) or by offering a varied ‘cafeteria’ diet (Sclafani & Springer, 1976). Spontaneous obesity was observed in the squirrel monkey (Saimiri sciureus) given semi-purified diets (Ausman et al. 1981) and obesity was induced in sheep by long-term feeding of pelleted diets (Blaxter, 1976; Blaxter et al. 1982). The present paper will primarily examine the extent to which the means of inducing nutritional obesity in the laboratory rat affects chemical and anatomical aspects of body composition but will also take account of species differences where possible. In addition, consideration will be given to ( I ) the effect of dietary fat composition on the development of obesity and on the composition of body fat, and (2) variations in the energy content of weight gain during hyperalimentation or of weight loss during fasting or restricted energy intake.