Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein secondary structure prediction with high accuracy using Support Vector Machine

Mining bioinformatics data is an emerging area of research. Proteomics is one of the largest areas of focus in bioinformatics and data mining research. Protein structure prediction is one of the most crucial and decisive problem in all the areas of research. Protein secondary structure can be used for the determination of the tertiary structure via the fold recognition method. Hence, predicting the secondary structures from the proteinpsilas primary sequences has attracted the attention of many researchers. Experimental methods have proved to be complex and expensive. So to develop a simple and accurate method for structure prediction is of great importance. In this paper, a new method has been proposed based on the machine learning technique. The first step of this proposal is to find out frequent patterns of consecutive amino acids in a protein database. After this, a set of frequent words (feature set) is found. Then support vector machine (SVM) is used as a binary/tertiary classifier for the classification of protein secondary structure with these frequent words.
Choosing among alternative technological strategies : an empirical analysis of formal sources of innovation

This work aims to fulfil the lack of a detailed conceptual and empirical analysis of the interfirm differences in deciding the composition of their technological efforts. Using data for Spanish firms in the period 1990-96, the study departs from the standard analysis of the determinants of innovative investment, follows with the less analysed question of the determinants of the generate versus import alternative and ends with a completely novel analysis of the firms’ characteristics that lead them to organise research internally as compared to the possibility of contracting R&D services externally. Contrasting with the standard practice, the econometric approach takes into account the existence of non-linearities in the used data.
Statistical mechanics of dictionary learning

Finding a basis matrix (dictionary) by which objective signals are represented sparsely is of major relevance in various scientific and technological fields. We consider a problem to learn a dictionary from a set of training signals. We employ techniques of statistical mechanics of disordered systems to evaluate the size of the training set necessary to typically succeed in the dictionary learning. The results indicate that the necessary size is much smaller than previously estimated, which theoretically supports and/or encourages the use of dictionary learning in practical situations.
Data characteristics that determine classifier performance

We study the relationship between the distribution of data, on the one hand, and classifier performance, on the other, for non-parametric classifiers. It is shown that predictable factors such as the available amount of training data (relative to the dimensionality of the feature space), the spatial variability of the effective average distance between data samples, and the type and amount of noise in the data set influence such classifiers to a significant degree. The methods developed here can be used to gain a detailed understanding of classifier design and selection.
VLSI Architecture Design and Implementation for Application Specific CORDIC Processor

COordinate Rotation DIgital Computer (CORDIC) algorithm has become widely researched topic in the field of vector rotated Digital Signal Processing (DSP) applications due to its simplicity. In this paper, we have represented the design of pipelined architecture for the computation of Sine and Cosine values based on application specific CORDIC processor. The design of CORDIC in the circular rotation mode gives a high system throughput due to its pipelined architecture by reducing latency in each individual pipelined stage. Saving area on silicon substrate is essential to the design of pipelined CORDIC and that can be achieved through the optimization in the number of micro rotations. The computed quantization error is also minimized using required number of iterations. The pipelined architecture can be easily integrated in VLSI technology due to its regularity and modularity.
Multichannel Brain Recordings in Behaving Drosophila Reveal Oscillatory Activity and 1 Local Coherence in Response to Sensory Stimulation and Circuit Activation. 2 3 Running Head: Multichannel Brain Recordings in Behaving Flies. 4 5

Multichannel brain recordings in behaving Drosophila reveal oscillatory activity and 1 local coherence in response to sensory stimulation and circuit activation. 2 3 Running head: Multichannel brain recordings in behaving flies. 4 5 Angelique C Paulk, Yanqiong Zhou, Peter Stratton, Li Liu, Bruno van Swinderen 6 1. Queensland Brain Institute, The University of Queensland, Brisbane, Australia 7 2. Institute of Biophysics, Chinese Academy of Sciences, Beijing, China 8 9 Corresponding author: Bruno van Swinderen 10 Email: b.vanswinderen@uq.edu. au 11 Queensland Brain Institute, The University of Queensland, Brisbane, Australia 4072 12 13 Number of pages: 41 14 15 Number of figures and tables: 1 Movie 16 1 Table 17 10 Figures 18 19 Number of words for Abstract: 247 20 Number of words for Introduction: 528 21 Number of words for Discussion: 1803 22 23 Conflict of Interest: The authors declare no competing financial interests. 24 25 Acknowledgements: We would like to thank Andrew Dacks, Wulfila Gronenberg, and 26 Joshua Martin for feedback on the manuscript. Funding for this research was provided by the 27 Australian Research Council and the Queensland Brain Institute. 28 Articles in PresS. J Neurophysiol (July 17, 2013). doi:10.1152/jn.00414. 2013
Nutritional manipulation of primate retinas, III: Effects of lutein or zeaxanthin supplementation on adipose tissue and retina of xanthophyll-free monkeys.

PURPOSE Macular pigment (MP) is composed of the xanthophylls lutein (L) and zeaxanthin (Z) and may help to prevent age-related macular degeneration or retard its progression. In this study the effects of L or Z supplementation on carotenoid levels was examined in serum, adipose tissue, and retina in rhesus monkeys with no previous intake of xanthophylls. METHODS From birth to 7 to 16 years of age, 18 rhesus monkeys were fed semipurified diets containing all essential nutrients but no xanthophylls. Six were supplemented with pure L and 6 with pure Z at 3.9 micromol/kg per day for 24 to 101 weeks. At baseline and at 4- to 12-week intervals, carotenoids in adipose tissue were measured by HPLC. At study completion, carotenoids in serum and retina (central 4 mm, 8-mm annulus, and the periphery) were determined. Results were compared with data from control monkeys fed a standard laboratory diet. RESULTS Monkeys fed xanthophyll-free diets had no L or Z in serum or tissues. After L or Z supplementation, serum and adipose tissue concentrations significantly increased in the supplemented groups. Both L and 3R,3'S-Z (RSZ or meso-Z, not present in the diet) were incorporated into retinas of monkeys supplemented with L, with RSZ present only in the macula (central 4 mm). All-trans Z, but no RSZ, accumulated in retinas of monkeys supplemented with Z. CONCLUSIONS L is the precursor of RSZ, a major component of macular pigment. Xanthophyll-free monkeys can accumulate retinal xanthophylls and provide a valuable model for examining their uptake and conversion.
Optimal Algorithms for Stabbing Polygons by Monotone Chains

In this paper we present optimal algorithms to compute monotone stabbers for convex polygons. More precisely, given a set of m convex polygons with n vertices in total we want to stab the polygons with an x-monotone polygonal chain such that each polygon is entered at its leftmost point and departed at its rightmost point. Since such a stabber does not exist in general, we study two related problems. In the rst problem we want to compute a monotone stabber that stabs as many convex polygons as possible. The second problem is to compute the minimal number of x-monotone stabbers that are necessary to stab all given convex polygons. We present optimal O(m log m + n) algorithms for both problems.
Optimal redistribution of white space for wire length minimization

Existing floorplanning algorithms compact blocks to the left and bottom. Although the compaction obtains an optimal area it may not be good to meet other objectives such as minimizing total wire length which is the first-order objective. It is not known in the literature how to place blocks to obtain an optimal wire length. In this paper, we first show that the problem can be formulated as linear programming. Thereafter, instead of using the general but slow linear programming, we propose an efficient min-cost flow based approach to solve it. Our approach guarantees to obtain the minimum of total wire length in polynomial time and meanwhile keep the minimum area by distributing white space smarter for a given floorplan topology. We also show that the approach can be easily extended to handle constraints such as fixed-frame (fixed area), IO pins, pre-placed blocks, boundary blocks, range placement, alignment and abutment, rectilinear blocks, soft blocks, one-dimensional cluster placement, and bounded net delay, without loss of optimality. Practically, the algorithm is so efficient in that it finishes in less than 0.4 seconds for all MCNC benchmarks of block placement. It is also very effective. Experimental results show we can improve 4.2% of wire length even on very compact floorplans. Thus it provides an ideal way of post-floorplanning (refine floorplanning).
Human cell lines for biopharmaceutical manufacturing: history, status, and future perspectives

Abstract Biotherapeutic proteins represent a mainstay of treatment for a multitude of conditions, for example, autoimmune disorders, hematologic disorders, hormonal dysregulation, cancers, infectious diseases and genetic disorders. The technologies behind their production have changed substantially since biotherapeutic proteins were first approved in the 1980s. Although most biotherapeutic proteins developed to date have been produced using the mammalian Chinese hamster ovary and murine myeloma (NS0, Sp2/0) cell lines, there has been a recent shift toward the use of human cell lines. One of the most important advantages of using human cell lines for protein production is the greater likelihood that the resulting recombinant protein will bear post-translational modifications (PTMs) that are consistent with those seen on endogenous human proteins. Although other mammalian cell lines can produce PTMs similar to human cells, they also produce non-human PTMs, such as galactose-α1,3-galactose and N-glycolylneuraminic acid, which are potentially immunogenic. In addition, human cell lines are grown easily in a serum-free suspension culture, reproduce rapidly and have efficient protein production. A possible disadvantage of using human cell lines is the potential for human-specific viral contamination, although this risk can be mitigated with multiple viral inactivation or clearance steps. In addition, while human cell lines are currently widely used for biopharmaceutical research, vaccine production and production of some licensed protein therapeutics, there is a relative paucity of clinical experience with human cell lines because they have only recently begun to be used for the manufacture of proteins (compared with other types of cell lines). With additional research investment, human cell lines may be further optimized for routine commercial production of a broader range of biotherapeutic proteins.
Evaluation of a Mycobacterium avium subsp. paratuberculosis leuD Mutant as a Vaccine Candidate against Challenge in a Caprine Model

ABSTRACT Johne's disease (JD) is prevalent worldwide and has a significant impact on the global agricultural economy. In the present study, we evaluated the protective efficacy of a leuD (Δleud) mutant and gained insight into differential immune responses after challenge with virulent M. avium subsp. paratuberculosis in a caprine colonization model. The immune response and protective efficacy were compared with those of the killed vaccine Mycopar. In vitro stimulation of peripheral blood mononuclear cells with johnin purified protein derivative showed that Mycopar and ΔleuD generated similar levels of gamma interferon (IFN-γ) but significantly higher levels than unvaccinated and challenged phosphate-buffered saline controls. However, only with ΔleuD was the IFN-γ response maintained. Flow cytometric analysis showed that the increase in IFN-γ correlated with proliferation and activation (increased expression of CD25) of CD4, CD8, and γδT cells, but this response was significantly higher in ΔleuD-vaccinated animals at some time points after challenge. Both Mycopar and ΔleuD vaccines upregulated Th1/proinflammatory and Th17 cytokines and downregulated Th2/anti-inflammatory and regulatory cytokines at similar levels at almost all time points. However, significantly higher levels of IFN-γ (at weeks 26 and 30), interleukin-2 (IL-2; week 18), IL-1b (weeks 14 and 22), IL-17 (weeks 18 and 22), and IL-23 (week 18) and a significantly lower level of IL-10 (weeks 14 and 18) and transforming growth factor β (week 18) were detected in the ΔleuD-vaccinated group. Most importantly, ΔleuD elicited an immune response that significantly limited colonization of tissues compared to Mycopar upon challenge with wild-type M. avium subsp. paratuberculosis. In conclusion, the ΔleuD mutant is a promising vaccine candidate for development of a live attenuated vaccine for JD in ruminants.
Exploiting effects of parts in fine-grained categorization of vehicles

Fine-grained categorization has become a hot topic in computer vision. Based on the theory that part information is crucial for fine-grained categorization, we proposed a part-based categorization method for vehicles, consisting vehicle parts localization, part-based vehicle representation and classification. There were three contributions we made in this work: 1) we analyzed discriminative powers of parts for fine-grained categorization; 2) we proposed a frame of how to integrate discriminative powers of parts into categorization, and proved that it can achieve better performance than treating every part equally; 3) we provided an annotated dataset with parts for vehicle categorization.
Fixed Assets and Consumer Durable Goods for 1925-2001

THIS report presents new estimates of net stocks for 2000, revised estimates for 1998-99, and a summary of previously published estimates for 1925-97. These estimates, which cover the net stock of equipment and software and of structures owned by business and government and the net stock of durable goods owned by consumers, incorporate the revised national income and product accounts estimates for 1998-2000. Tables 1-15 present the revised estimates of fixed assets and consumer durable goods. The odd-numbered tables except table 15 present current-cost estimates; the even-numbered tables present real-cost measures in terms of chain-type quantity indexes.
Automatic workarounds as failure recoveries

Mechanisms to automatically recover from problems are key elements to designing self-managed software systems. So far most research on self-managed systems focused on non-functional problems, such as architectural mismatches, performance problems and configuration incompatibilities. In our work, we focus on techniques for automatically recovering from functional failures. We aim to exploit the intrinsic redundancy of many complex software systems that can produce the same results in several ways. We are investigating techniques that, in case of failure, look for execution sequences that are equivalent to the one that leads to the failure, and can thus be executed in alternative to the failing one to produce the expected results. We refer to sequences that are equivalent to failing ones and can recover from failures as automatic workarounds. The contribution of the thesis will be the definition of techniques to automatically generate equivalent sequences from different models, and to identify automatic workarounds within sets of equivalent sequences, and a thorough evaluation of the techniques in the context of self-healing software systems.
Stabilizing BGP routing without harming convergence

RFD and MRAI are the only two built-in mechanisms in BGP router against unstable routes, they can however negatively impact the convergence. In this paper, we propose a churn aggregation approach CAGG to stabilize BGP routing without harming convergence. CAGG is based on the observation that AS PATH change is the dominant cause for BGP updates and only a small number of AS PATHs are explored by each highly active prefix. A CAGG equipped router converts the multiple AS PATHs explored by a highly active prefix into an aggregated path, and propagates the aggregated path instead to reduce the number of resulted BGP updates from AS PATH changes. Our experiments with real BGP data show that CAGG can reduce as much as 50% of BGP updates, and 60% of BGP path exploration duration in its best case, while on average 28.1% and 32% respectively across 36 RouteViews monitors. Furthermore, CAGG is shown to perform better than both RFD and PED[1] in reducing BGP updates, path exploration duration and accelerating BGP convergence, at the cost of buffering around 5,000 AS PATHs.
The role of central level staff in supporting high quality instruction

The central office manages and directs a school system. In the wake of district and school reforms, the impact of the central office on schools and quality instruction has not been fully dissected. This study explores the role of the central office in the support of high quality instruction. Further, it analyzes the perceptions of those central office staff members who support schools and school-based staff. The study was conducted using qualitative methodology to determine and describe the impact of Executive Directors and Directors on instruction in schools. Specifically, interviews were conducted with 22 central office staff members in one urban school district. Interviewees were questioned about their roles and their practice of instructional leadership. In addition, individuals were asked about the current reality of their work and asked to consider how their work could be different given different circumstances or constraints. Central office staff members also gave recommendations for how the central office could better support high quality instruction. Ten issues were identified based on the content of the interviews. One important finding was the need for better recruitment of central office staff members with a focus on the specific skill set needed for their work. A critical discovery was the lack of direct influence and involvement of central office staff with school-based principals and other school-based administrators. The level of collaboration between central office staff and school based principals was largely absent which is ironic considering the current research on the importance of the principal in the process of school reform.
ADAPTIVE ROUTING ON TRANSPUTER NETWORKS WITH TORUS 2-D TOPOLOGY

Second generation multicomputers use wormhole routing, allowing a very low channel setup time and drastically reducing the dependency between network latency and internode distance. The network routing can be deterministic or adaptive. In this paper, we present the development and implementation of a fully adaptive routing algorithm. Our work is carried out in a multicomputer with the C104 routers and the T9000 transputers. We describe several implementation details and give some simulation results. These results show the performance improvement that can be achieved using fully adaptive routing. Our simulations have been carried out on a torus 2-D topology.
Environmental Exposure Assessment of Pesticides in Farmworker Homes

Farmworkers and their families are exposed to pesticides both at work and in their homes. Environmental exposure assessment provides a means to evaluate pesticides in the environment and human contact with these chemicals through identification of sources and routes of exposure. To date, a variety of methods have been used to assess pesticide exposure among farmworker families, mostly focusing on dust and handwipe samples. While many of the methods are similar, differences in the collection, chemical analysis, and statistical analysis, can limit the comparability of results from farm-worker studies. This mini-monograph discusses the strategies used to assess pesticide exposures, presents limitations in the available data for farmworkers, and suggests research needs for future studies of pesticide exposure among farmworker families.
Penultimate predecessors of the 2004 Indian Ocean tsunami in Aceh, Sumatra: Stratigraphic, archeological, and historical evidence

We present stratigraphic, archeological and historical evidence for two closely timed predecessors of the giant 2004 tsunami on the northern coast of Aceh, northern Sumatra. This is the first direct evidence that a tsunami played a role in a fifteenth century cultural hiatus along the northern Sumatran portion of the maritime silk route. One seacliff exposure on the eastern side of the Lambaro headlands reveals two beds of tsunamigenic coral rubble within a small alluvial fan. Radiocarbon and Uranium‐Thorium disequilibrium dates indicate emplacement of the coral rubble after 1344 ± 3 C.E. Another seacliff exposure, on the western side of the peninsula, contains evidence of nearly continuous settlement from ~1240 C.E. to soon after 1366 ± 3 C.E. , terminated by tsunami destruction. At both sites, the tsunamis are likely coincident with sudden uplift of coral reefs above the Sunda megathrust 1394 ± 2 C.E. , evidence for which has been published previously. The tsunami (or tsunami pair) appears to have destroyed a vibrant port community and led to the temporary recentering of marine trade dominance to more protected locations farther east. The reestablishment of vibrant communities along the devastated coast by about 1500 CE set the stage for the 2004 disaster.
Introducing VERO: visual experiential requirements organizer

Crucial to the advancement of the User Experience field is the ability to understand product qualities as perceived by users. Therefore we would like to introduce VERO (Visual Experiential Requirements Organizer), an online tool for the structured elicitation of users' perceptions of a given stimulus such as a product, a system or a concept. Contrary to the existing elicitation methods, VERO aims to enable users to freely express opinions about qualities relevant for a given stimulus; to indicate the importance of each quality without imposing a hierarchical order and to cluster related qualities according to users' own perception regarding the strength of the link between them. In this paper we also motivate our approach in developing VERO and sketch our research agenda regarding its validation and application in the field of User Experience.