Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence for divalent cation (Ca2+)-stabilized oligomeric proteins and covalently bound protein-peptidoglycan complexes in the outer membrane of Rhizobium leguminosarum

Two unusual characteristics of some outer membrane proteins of Rhizobium leguminosarum are described. First, most of the major outer membrane proteins could only be visualized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis after lysozyme treatment of the isolated cell envelopes, suggesting a very strong, possibly covalent, interaction of these proteins with the peptidoglycan. These peptidoglycan-associated outer membrane proteins belonged to two distinct groups of immunologically related proteins, groups II and III, as defined by typing with monoclonal antibodies. As members of both groups of proteins could be radioactively labeled by growing cells in the presence of N-[3H]acetylglucosamine, we propose that variation in the apparent molecular weight of the antigens within each group is caused by varying numbers of peptidoglycan subunit residues on only two or three different outer membrane proteins. Second, group III outer membrane proteins, with masses of 35 to 46 kilodaltons, formed oligomers stabilized by divalent cations which resisted complete denaturation in 2% sodium dodecyl sulfate at 100 degrees C. Reconstitution experiments showed that of the divalent cations tested, Ca2+ and, to a lesser extent, Mn2+ and Sr2+ were the best stabilizers.
Monte Carlo without chains

Monte Carlo without Chains Alexandre J. Chorin Department of Mathematics, University of California and Lawrence Berkeley National Laboratory Berkeley, CA 94720 Abstract A sampling method for spin systems is presented. The spin lattice is written as the union of a nested sequence of sublattices, all but the last with conditionally independent spins, which are sampled in succession using their marginals. The marginals are computed concurrently by a fast algorithm; errors in the evaluation of the marginals are oﬀset by weights. There are no Markov chains and each sample is independent of the previous ones; the cost of a sample is proportional to the number of spins (but the number of samples needed for good statistics may grow with array size). The examples include the Edwards-Anderson spin glass in three dimensions. Keywords: Monte Carlo, no Markov chains, marginals, spin glass Introduction. Monte Carlo sampling in physics is synonymous with Markov chain Monte Carlo (MCMC) for good reasons which are too well-known to need repeating (see e.g. [2],[17]). Yet there are problems where the free energy landscape exhibits multi- ple minima and the number of MCMC steps needed to produce an independent sample is huge; this happens for example in spin glass models (see e.g. [13],[16]). It is therefore worthwhile to consider alternatives, and the purpose of the present paper is to propose one. An overview of the proposal is as follows: Consider a set of variables (“spins”) located at the nodes of a lattice L with a probability density P that one wishes to sample. Suppose one can construct a nested sequences of subsets L 0 ⊃ L 1 ⊃ · · · ⊃ L n with the following properties: L 0 = L; L n contains few points; the marginal density of the variables in each L i is known, and given values of the spins in L i+1 , the remaining variables in L i are independent. Then the following is an eﬀective sampling strategy for the spins in L: First sample the spins in L n so that each conﬁguration is sampled with a frequency equal to its probability by ﬁrst listing all the states of the spins in L n and calculating their probabilities. Then sample the variables in each L i−1 as i decreases from n − 1 to zero using the independence of these variables, making sure that each state is visited with a frequency equal to its probability. Each state of L = L 0 is then
Making Histories ‘Ngapartji-ngapartji Way’: Exploring Collaboration, Exchange and Intercultural Histories in a Colonised Settler Nation

History assumes a particular significance in contemporary colonised settler Australia. The epistemological and political challenges that persist for those historians wanting to explore an intercultural historical understanding of Australia continue to prompt questions about the nature of the discipline of History itself. This paper explores how my own intercultural, historical research seeks to actively and creatively engage with some of these epistemological and political challenges. An encounter with an unusual ethnography, set in a Central Australian cattle station and based upon the observations of the Aboriginal people who lived there, has led to an engagement of my research with archives of two very different kinds. By critically and actively engaging with the documents in the Rose archive and with Ara Irititja, an Aboriginal owned, interactive digital archival project, I hope to work with Anangu to create a collaborative and participatory research space. In exploring the use of digital media, this research project seeks to engage with the visual, oral, spatial and experiential nature of Aboriginal histories and ways of knowing and in doing so explore new and non-textual methods for historical thinking, writing and representation. Reciprocity and exchange, or doing research ngapartji-ngapartji1 way as a Pitjantjatjara speaking person might say, are foundational to my methodological approach. Anangu are not my informants. I do not want to merely observe. In seeking an intercultural and participatory engagement, this research project seeks to create a collaborative space that can tell the history of a Central Australian landscape and its people that engages Aboriginal people in history making and knowledge exchange.
Resistance, Resilience and Social Identities: Reframing ‘Problem Youth’ and the Problem of Schooling

This paper explores the experiences of young people on a public housing estate in inner-city Sydney. Their relations to schooling, truancy and participation in the illicit activities of the local youth network are framed as resistances, as necessary identity work, given the context of their marginalisation. In their explication of the dynamics of schooling, the network and the neighbourhood, young people claim the margins, as an alternative ‘centre’ where they obtain status, positive reputation, and a sense of belonging to their people. Social identity is central to their experiences and cultural management. The argument is made for two distinct forms of belonging to identifiable groups: that which is ‘chosen’, claimed and desired; as well as ‘unchosen’, ascribed and positioned, identity. How outsiders see them is largely an unchosen identity which young people resist. Chosen identity is mainly associated with the norms and values of the margins. In their transgressions of dominant norms, attempts to counter negative stereotypes, and social critiques, young people's strengths despite adversity are evident. Resistances are thus reframed as resilience.
Clustering for semi-supervised spam filtering

We present a novel investigation of email clustering, demonstrating that clustering can be a powerful tool for email spam filtering. We first extend the well-known notion that ham and spam emails can be divided into clusters, showing the striking result that almost any reasonable clustering algorithm will naturally partition an email dataset into almost entirely spam and entirely spam clusters. We then consider the specific semi-supervised spam filtering scenario of filtering when a large amount of training data is available, but only a few true labels can be obtained for that data. We present two spam filtering approaches for this scenario, both of which start with a clustering of training email. Our first approach uses the true labels of the medoids of each cluster to train a spam filter; our second approach functions similar to the first, except that the true label of each cluster's medoid is used as the label of every email within the cluster, giving a much larger set of labels for training, while still only requiring only a few labels. We evaluate our approaches using the TREC2005 and CEAS2008 spam email datasets. For a large range of different numbers of true labels, we show that both of our approaches significantly outperform training on the same number of randomly selected email messages. The results of our second approach are also better than those of a previously published state-of-the-art semi-supervised small sample spam filtering approach.
Device authentication mechanism for Smart Energy Home Area Networks

Smart Energy Home Area Networks (SE-HAN) enable two-way communication between utility companies and HAN devices. Due to multifaceted nature of SE-HAN, securely managing SE-HAN is very challenging. In this paper, we propose a device authentication mechanism for smart energy home area network. The proposed mechanism is more robust and secure than the existing one.
Criticising images: critical discourse analysis of visual semiosis in picture news

Abstract The author of this article aimed to conduct a holistic study on the critical discourse analysis (CDA) of visual semiosis in picture news. Integrating various theories within the field of CDA and multimodal studies, a theoretical framework of critical visual analysis is postulated to facilitate empirical study. Theoretically, the research sets out to help establish the academic identity of the critical multimodal discourse analysis, as discussed in Theo van Leeuwen (2012), and attempts to construct a holistic theoretical framework of critical visual discourse studies.
Endosomal Sorting of Amyloid Precursor Protein‐P‐Selectin Chimeras Influences Secretase Processing

Amyloid β protein, the major component of the senile plaques in Alzheimer's disease, is generated by secretory and endocytic processing of amyloid precursor protein. Internalized amyloid precursor protein either recycles to the plasma membrane, where α‐secretase resides, or moves to acidic compartment(s) for β‐secretase exposure. While the trans‐Golgi network contains β‐secretase activity, recent examination of the subcellular distribution of this proteinase, called BACE, has led to the suggestion that β‐secretase activity might also reside at the plasma membrane and in endosomes. To examine the role of endocytic compartments in β‐secretase processing of amyloid precursor protein, the wild‐type and endosomal sorting mutant P‐selectin cytoplasmic domains were used to control movement of amyloid precursor protein through endosomes. Amyloid precursor protein/P‐selectin, which is sorted from early to late endosomes, undergoes significantly less α‐secretase cleavage, and more β‐secretase cleavage, than amyloid precursor protein/P‐selectin768A, a mutant that recycles more efficiently to the cell surface. Our results demonstrate that endosomal sorting influences relative exposure of the amyloid precursor protein/P‐selectin chimeras to α‐ and β‐secretase activities, and suggest that, because delivery to late endocytic compartments favors β‐secretase processing of amyloid precursor protein, there is likely limited β‐secretase activity in early endosomes or at the cell surface. We propose that the trans‐Golgi network may be involved in both secretory and endocytic generation of amyloid β protein.
Disulfide bond structure of glycoprotein D of herpes simplex virus types 1 and 2

Glycoprotein D (gD) is a structural component of the herpes simplex virus envelope which is essential for virus penetration. The function of this protein is highly dependent on its structure, and its structure is dependent on maintenance of three intact disulfide bonds. gD contains six cysteines in its ectodomain whose spacing is conserved among all its homologs in other alphaherpesviruses as well as Marek's disease virus. For other proteins, conservation of cysteine spacing correlates with conservation of disulfide bond structure. We have now solved the disulfide bond structure of gD-1 and gD-2 of herpes simplex virus types 1 and 2, respectively. Two approaches were used. First, we constructed 15 double-Cys mutants of gD-1, representing all possible disulfide pairs. In each case, codons for cysteines were changed to serine. We reasoned that if two cysteines normally form a disulfide bond, double mutations which eliminate one proper bond should be less harmful to gD structure than double mutations which eliminate two disulfide bonds. The mutated genes were cloned into a eucaryotic expression vector, and the proteins were expressed in transiently transfected cells. Three double mutations, Cys-1,5, Cys-2,6, and Cys-3,4 permitted gD-1 folding, processing, transport to the cell surface, and function in virus infection, whereas 12 other double mutations each produced a malfolded and nonfunctional protein. Thus, the three functional double-Cys mutants may represent the actual partners in disulfide bond linkages. The second approach was to define the actual disulfide bond structure of gD by biochemical means. Purified native gD-2 was cleaved by CNBr and proteases, and the peptides were separated by high-performance liquid chromatography. Disulfide-linked peptides were subjected to N-terminal amino acid sequencing. The results show that cysteine 1 (amino acid [aa] 66) is bonded to cysteine 5 (aa 189), cysteine 2 (aa 106) is bonded to cysteine 6 (aa 202), and cysteine 3 (aa 118) is bonded to cysteine 4 (aa 127). Thus, the biochemical analysis of gD-2 agrees with the genetic analysis of gD-1. A similar disulfide bond arrangement is postulated to exist in other gD homologs.
Automatic Discovery of Web Services Based on Dynamic Black-Box Testing

Most current approaches to Web Service discovery exploit description logic-based matchmaking algorithms. Until now, these Semantic Web Service technologies have not substituted for traditional search methods, because higher modeling costs, such as representing Service Annotation Ontologies and Domain Ontologies, are required. In this paper, we present an automatic testing-based approach to the discovery of Web Services. Through the automatic generation and execution of test cases based on a small amount of semantic information, Web Services are simultaneously evaluated and a decision is made on which Web Services the requestor needs. The experimental results show our technique reduces modeling costs significantly, whilst outperforming existing approaches in terms of precision. Furthermore, reliable QoS attribute values are obtained as by-products.
Nonedge-Specific Adaptive Scheme for Highly Robust Blind Motion Deblurring of Natural Imagess

Blind motion deblurring estimates a sharp image from a motion blurred image without the knowledge of the blur kernel. Although significant progress has been made on tackling this problem, existing methods, when applied to highly diverse natural images, are still far from stable. This paper focuses on the robustness of blind motion deblurring methods toward image diversity-a critical problem that has been previously neglected for years. We classify the existing methods into two schemes and analyze their robustness using an image set consisting of 1.2 million natural images. The first scheme is edge-specific, as it relies on the detection and prediction of large-scale step edges. This scheme is sensitive to the diversity of the image edges in natural images. The second scheme is nonedge-specific and explores various image statistics, such as the prior distributions. This scheme is sensitive to statistical variation over different images. Based on the analysis, we address the robustness by proposing a novel nonedge-specific adaptive scheme (NEAS), which features a new prior that is adaptive to the variety of textures in natural images. By comparing the performance of NEAS against the existing methods on a very large image set, we demonstrate its advance beyond the state-of-the-art.
Impact of Body-Thickness-Dependent Band Structure on Scaling of Double-Gate MOSFETs: A DFT/NEGF Study

First principles density functional theory has been used to calculate the 2-D band structure of Si slabs with different thicknesses. From the calculated 2-D band structure, electron longitudinal and transverse effective masses have been extracted as a function of the slab thickness. These thickness-dependent electron effective masses have then been used to simulate I D-VG characteristics of scaled, sub-10 nm double-gate (DG) MOSFETs and to compare them with the results obtained using bulk masses. The channel thickness dependence of the Si band structure starts to affect noticeably DG MOSFET performance at channel lengths below 10 nm, lowering the on-current by approximately 10, for transistors with a body thickness of 2.6 nm, and by 20, for transistors with a body thickness of 1.3 nm. On the other hand, the subthreshold swing is improved by 10, in the 6-nm-gate length DG MOSFET and by 15, in the 4-nm-gate length device. Finally, the impact of thickness-dependent effective masses has been related to the behavior of the transmission coefficients.
Developmental basis of homeosis in precociously germinating Brassica napus embryos: phase change at the shoot apex.

Precociously germinating Brassica napus (oilseed rape) embryos produce extra cotyledons or chimeric organs with sectors of cotyledon and leaf tissue, rather than leaves, at the shoot apex. To investigate this phenomenon in more detail, scanning electron microscopy was used to examine the development of organ primordia at the shoot apex. In situ hybridizations with molecular markers of the embryonic phase were used to assess the status of individual cells in the shoot apex with regard to the transition between embryonic and vegetative phases. The results indicate that, under conditions that support precocious germination, primordia develop at the shoot apex in the mode characteristic of postgerminative growth, i.e. they arise sequentially in a spiral phyllotaxy. Cells in the rest of the embryo, however, can continue to express molecular markers of the embryonic phase for several weeks after the start of culture. When patterns of gene expression and the fate of individual primordia were compared, a strong correlation was found between organ identity and the status of cells in the vicinity of the meristem with regard to phase. Primordia that develop in situations where neighboring cells are in the embryonic phase always produce organs with cotyledon morphology. Primordia that develop in situations where neighboring cells have exited the embryonic phase produce leaves. Based on an examination of situations where chimeric organs are produced, I propose that short range interactions or signalling are likely to be involved in communicating information about phase to developing primordia.
Dipole Source Analysis

The spatiotemporal approach of dipole source analysis is a crucial methodological advance in event-related potential research, as overlapping subcomponents of cortical evoked potentials can be separated and related to their generating structures. This enhances the reliability and validity of event-related potential parameters and facilitates the link to underlying neurochemical processes. The present paper presents methodological aspects of the dipole source analysis of auditory-evoked potentials to different stimulus intensities.
Automatic prediction of intelligibility of English words spoken with Japanese accents - comparative study of features and models used for prediction

This study investigates automatic prediction of the words in given sentences that will be unintelligible to American listeners when they are pronounced with Japanese accents. The ERJ intelligibility database [1] contains results of a large listening test, where 800 English sentences read with Japanese accents were presented to 173 American listeners and correct perception rate was obtained for each spoken word. By using this database, in our previous study [8], an intelligibility predictor was built for each word of input texts or utterances. For prediction, lexical and linguistic features were extracted from texts and pronunciation distance and word confusability were calculated from utterances. CART was used as prediction model. In this paper, new features that are related to speech prosody and three new prediction models of ensemble methods (Adaboost, Random Forest and Extremely Randomized Trees) are tested and compared to the old features and model. Finally, our new system can predict very unintelligible words and rather unintelligible words with F1-scores of 72.74% and 84.78%, respectively. Index Terms: Spoken word intelligibility, ERJ database, prosodic features, machine learning, IPA transcript, second language learning, foreign accent
The Children's Attitudes toward the Environment Scale

Abstract The authors describe the development of a scale to measure environmental attitudes of grade-school children. The scale items reflect children's knowledge of environmental issues, and the scale uses an age-appropriate format. The 25 items that make up the scale were selected through item analysis from a larger pool of items. The internal-consistency reliability of the scale (Cronbach's alpha) ranged from . 70 to . 85. Test-retest reliability was . 68. The authors discuss potential use of this scale for research and evaluation of programs.
The Apprenticeship Framework in England: a new beginning or a continuing sham?

This paper highlights critical shortcomings in the approach to apprenticeship in England and argues that the proposed Apprenticeship Framework is unlikely to fulfil its stated aims of enhancing quality and quantity. The key weaknesses identified are a clear definition of what constitutes an apprenticeship framework, an educational component, employee involvement and lack of recognition of alternative college‐based routes. Drawing on a recent cross‐national study, the authors compare the English situation with the vocational education and training systems of other leading European countries. These embody a distinctly different approach and framework, being based on social partnership and the education of young people into a broadly defined occupation. It is shown how the current proposals mark a potential step backwards and a departure from the principles of the 1944 Education Act by ignoring general and civic educational elements in young people’s formation. Above all, for any framework to be successful, it needs to take into account the longer term interests of employees, given changes in the labour market, and to address the issue of employer disengagement. The conclusions drawn suggest ways forward.
First large-scale information retrieval experiments on turkish texts

We present the results of the first large-scale Turkish information retrieval experiments performed on a TREC-like test collection. The test bed, which has been created for this study, contains 95.5 million words, 408,305 documents, 72 ad hoc queries and has a size of about 800MB. All documents come from the Turkish newspaper Milliyet. We implement and apply simple to sophisticated stemmers and various query-document matching functions and show that truncating words at a prefix length of 5 creates an effective retrieval environment in Turkish. However, a lemmatizer-based stemmer provides significantly better effectiveness over a variety of matching functions.