Miracle-dz/UniFAR-FTUs huggingface dataset:
Removing near-neighbour redundancy from large protein sequence collections

MOTIVATION To maximize the chances of biological discovery, homology searching must use an up-to-date collection of sequences. However, the available sequence databases are growing rapidly and are partially redundant in content. This leads to increasing strain on CPU resources and decreasing density of first-hand annotation. RESULTS These problems are addressed by clustering closely similar sequences to yield a covering of sequence space by a representative subset of sequences. No pair of sequences in the representative set has >90% mutual sequence identity. The representative set is derived by an exhaustive search for close similarities in the sequence database in which the need for explicit sequence alignment is significantly reduced by applying deca- and pentapeptide composition filters. The algorithm was applied to the union of the Swissprot, Swissnew, Trembl, Tremblnew, Genbank, PIR, Wormpep and PDB databases. The all-against-all comparison required to generate a representative set at 90% sequence identity was accomplished in 2 days CPU time, and the removal of fragments and close similarities yielded a size reduction of 46%, from 260 000 unique sequences to 140 000 representative sequences. The practical implications are (i) faster homology searches using, for example, Fasta or Blast, and (ii) unified annotation for all sequences clustered around a representative. As tens of thousands of sequence searches are performed daily world-wide, appropriate use of the non-redundant database can lead to major savings in computer resources, without loss of efficacy. AVAILABILITY A regularly updated non-redundant protein sequence database (nrdb90), a server for homology searches against nrdb90, and a Perl script (nrdb90.pl) implementing the algorithm are available for academic use from http://www.embl-ebi.ac. uk/holm/nrdb90. CONTACT holm@embl-ebi.ac. uk
A GPU-driven algorithm for accurate interactive reflections on curved objects

We present a GPU-driven method for the fast computation of specular reflections on curved objects. For every reflector of the scene, our method computes a virtual object for every other object reflected in it. This virtual reflected object is then rendered and blended with the scene. For each vertex of each virtual object, a reflection point is found on the reflector's surface. This point is used to find the reflected virtual vertex, enabling the reflected virtual scene to be rendered. Our method renders the 3D points and normals of the reflector into textures, and uses a local search in a fragment program on the GPU to find the reflection points. By reorganizing the data and the computation in this manner, and correctly treating special cases, we make excellent use of the parallelism and stream-processing power of the GPU. In our results we show that, with our method, we can display high-quality reflections of nearby objects interactively.
An Evidence Ontology for Use in Pathway/Genome Databases

An important emerging need in Model Organism Databases (MODs) and other bioinformatics databases (DBs) is that of capturing the scientific evidence that supports the information within a DB. This need has become particularly acute as more DB content consists of computationally predicted information, such as predicted gene functions, operons, metabolic pathways, and protein properties. This paper presents an ontology for encoding the type of support and the degree of support for DB assertions, and for encoding the literature source in which that support is reported. The ontology includes a hierarchy of 35 evidence codes for modeling different types of wet-lab and computational evidence for the existence of operons and metabolic pathways, and for gene functions. We also describe an implementation of the ontology within the Pathway Tools software environment, which is used to query and update Pathway/Genome DBs such as EcoCyc, MetaCyc, and HumanCyc.
Developmental regulation of cryptdin, a corticostatin/defensin precursor mRNA in mouse small intestinal crypt epithelium

Cryptdin mRNA codes for the apparent precursor to a corticostatin/defensin-related peptide that accumulates to high levels in mouse intestinal crypt epithelium during postnatal development. The primary structure, intestinal cell distribution, and developmental appearance of cryptdin mRNA have been determined. Cryptdin mRNA is 450- 480 nucleotides long. Translation of the partial cryptdin cDNA sequence reveals a 70-amino acid open reading frame that includes 32 carboxy- terminal residues that align with those in the consensus sequence, C.CR. C.ER. G.C. CCR, which is a common feature of leukocyte defensins and lung corticostatins (Selsted, M. E., D. M. Brown, R. J. DeLange, S. S. L. Harwig, and R. I. Lehrer. 1985. J. Biol. Chem. 260:4579-4584; Zhu, Q., J. Hu, S. Mulay, F. Esch, S. Shimasaki, and S. Solomon. 1988. Proc. Natl. Acad. Sci. USA. 85:592-596). In situ hybridization of cryptdin cDNA to paraformaldehyde-fixed, frozen sections of adult jejunum and ileum showed intense and specific labeling of epithelial cells in the base of all crypts. Analysis of sections from suckling mice showed that cryptdin mRNA is detectable in 10-20% of crypts in 10-d-old mice, in approximately 80% of crypts in 16- d-old mice, and in all crypts of mice 20 d and older. During the fourth week, the sequence accumulates in crypts to the maximal adult level. Cryptdin mRNA content in adult small intestine is independent both of T cell involvement and luminal bacteria. The role of cryptdin in small bowel physiology remains to be determined: cryptdin may inhibit bacterial translocation, modulate intestinal hormone synthesis, influence hormonal sensitivity of the intestinal epithelium, or exhibit a multiplicity of related activities.
Query Refinement based on Topical Term Clustering

We propose a method for supporting query refinement using topical term clusters. First, we propose a new term weighting method that can extract terms strongly related to a specific topic, because a document set retrieved with an ambiguous query may include divergent topics. Our formulation of term weighting is based on the statistics of term co-occurrence. Then, we generate term clusters using extracted terms, and rerank the documents in the search results by using each term cluster as a query. This clustering procedure is intended to isolate each topic as a set of related terms. In our experiments, we evaluated our term weighting method by checking: 1) whether each of the top-ranked document sets corresponds to one topic; and 2) whether some of the top-ranked document sets cover all the topics included in the synthesized document set. The results of our experiment show our method outperforms the existing term weighting methods MI, KLD, CHI-square and RSV.
Restarted Generalized Second-Order Krylov Subspace Methods for Solving Quadratic Eigenvalue Problems

This article is devoted to the numerical solution of large-scale quadratic eigenvalue problems. Such problems arise in a wide variety of applications, such as the dynamic analysis of structural mechanical systems, acoustic systems, fluid mechanics, and signal processing. We first introduce a generalized second-order Krylov subspace based on a pair of square matrices and two initial vectors and present a generalized second-order Arnoldi process for constructing an orthonormal basis of the generalized second-order Krylov subspace. Then, by using the projection technique and the refined projection technique, we propose a restarted generalized second-order Arnoldi method and a restarted refined generalized second-order Arnoldi method for computing some eigenpairs of largescale quadratic eigenvalue problems. Some theoretical results are also presented. Some numerical examples are presented to illustrate the effectiveness of the proposed methods. Keywords—Quadratic eigenvalue problem, Generalized secondorder Krylov subspace, Generalized second-order Arnoldi process, Projection technique, Refined technique, Restarting.
Exploiting Transport-Level Characteristics of Spam

We present a spam detection technique that relies on neither content nor reputation analysis. Instead, this work investigates the discriminatory power of the email TCP packet stream. From a corpus of packet flows and their corresponding messages, we extract per-email transport-layer features. While legitimate mail traffic is well-behaved, we observe small congestion windows, retransmissions, loss and large latencies in spam flows. To identify the most selective flow properties, thereby adapting to different networks and users, we build “SpamFlow. ” On our data, SpamFlow achieves greater than 90% classification accuracy while correctly identifying 78% of the false negatives from a popular content filter. By capitalizing on spam’s fundamental requirement to source large quantities of mail, often from resource constrained hosts and networks, SpamFlow promises a unique and difficult-to-subvert complement to existing spam defenses.
Misconceptions in Astronomy Digital Full-domes: the Future of Virtual Astronomy Education

Although digital video full-dome theaters have the potential for showing a wide range of content, debate continues on how appropriate they are for astronomy education [1]. Such debate is not new. More than twenty years ago, Charles Hagar decried the fact that planetariums displaying video within their domes were trying to compete against first class Holly-wood productions, and failing at it [2]. Given the expense involved in converting to full-dome theaters and the work necessary to create new visitor programming, operators and managers at traditional optical-mechanical planetariums may wonder whether the positives outweigh the negatives when taking the digital plunge. Since the main focus of planetariums has historically been that of astronomy education , what are the educational benefits of a digital system over its analog counterpart? Is the new technology actually worth it from an astronomy instructional point of view? Before addressing how digital domes can be of use, it must be acknowledged that astronomy is a subject that has historically been difficult to teach. Although U.S. education standards identify astronomy topics as being important for K—12 science literacy [3, 4], most college students including many preservice teachers retain misconceptions that are not easily changed by standard classroom instruction (e.g., [5-8]). The difficulty of understanding astronomy is due in part to concepts involving geometries and orientations of celestial bodies in three dimensions. Students have to build conceptual knowledge about a three-dimensional (3D) physical space while being taught using two-dimensional (2D) textbook materials. Many educational researchers have therefore advocated the use of 3D models as being crucial for astronomy learning [9, 10]. A suite of technologies especially appropriate for creating representational 3D models of physical phenomenon are the artificial realities or virtual environments. Virtual environments (VEs) are computer-generated, 3D environments that a user can interact with and navigate through. A carefully constructed VE allow users to gain direct experience about a place or phenomenon that would otherwise be difficult or impossible to observe in real life. When astronomy VE software 1 is run immersively in a full-dome theater, the illusion of the artificial reality is further enhanced by the wrap-around projection that surrounds the user with imagery on all sides. As the following review will show, the combination of VE and full-dome technologies result in a unique opportunity for astronomy instruction that is not possible in any other milieu. Many involved in astronomy education are aware of the video A …
Development of Microsatellite Markers Derived from Expressed Sequence Tags of Polyporales for Genetic Diversity Analysis of Endangered Polyporus umbellatus

A large scale of EST sequences of Polyporales was screened in this investigation in order to identify EST-SSR markers for various applications. The distribution of EST sequences and SSRs in five families of Polyporales was analyzed, respectively. Mononucleotide was the most abundant type, followed by trinucleotide. Among five families, Ganodermataceae occupied the most SSR markers, followed by Coriolaceae. Functional prediction of SSR marker-containing EST sequences in Ganoderma lucidum obtained three main groups, namely, cellular component, biological process, and molecular function. Thirty EST-SSR primers were designed to evaluate the genetic diversity of 13 natural Polyporus umbellatus accessions. Twenty one EST-SSRs were polymorphic with average PIC value of 0.33 and transferability rate of 71%. These 13 P. umbellatus accessions showed relatively high genetic diversity. The expected heterozygosity, Nei's gene diversity, and Shannon information index were 0.41, 0.39, and 0.57, respectively. Both UPGMA dendrogram and principal coordinate analysis (PCA) showed the same cluster result that divided the 13 accessions into three or four groups.
The Microevolution of V1r Vomeronasal Receptor Genes in Mice

Vomeronasal sensitivity is important for detecting intraspecific pheromonal cues as well as environmental odorants and is involved in mating, social interaction, and other daily activities of many vertebrates. Two large families of seven-transmembrane G-protein–coupled receptors, V1rs and V2rs, bind to various ligands to initiate vomeronasal signal transduction. Although the macroevolution of V1r and V2r genes has been well characterized throughout vertebrates, especially mammals, little is known about their microevolutionary patterns, which hampers a clear understanding of the evolutionary forces behind the rapid evolutionary turnover of V1r and V2r genes and the great diversity in receptor repertoire across species. Furthermore, the role of divergent vomeronasal perception in enhancing premating isolation and maintaining species identity has not been evaluated. Here we sequenced 44 V1r genes and 25 presumably neutral noncoding regions in 14 wild-caught mice belonging to Mus musculus and M. domesticus, two closely related species with strong yet incomplete reproductive isolation. We found that nucleotide changes in V1rs are generally under weak purifying selection and that only ∼5% of V1rs may have been subject to positive selection that promotes nonsynonymous substitutions. Consistent with the low functional constraints on V1rs, 18 of the 44 V1rs have null alleles segregating in one or both species. Together, our results demonstrate that, despite occasional actions of positive selection, the evolution of V1rs is in a large part shaped by purifying selection and random drift. These findings have broad implications for understanding the driving forces of rapid gene turnovers that are often observed in the evolution of large gene families.
Development of thermoregulating textile materials with microencapsulated phase change materials (PCM). II. Preparation and application of PCM microcapsules

Melamine–formaldehyde microcapsules containing eicosane were prepared by in situ polymerization. The characterization of the microcapsules, including the particle size and size distribution, morphology, thermal properties, and stability, was carried out. The prepared microcapsules were added to polyester knit fabrics by a conventional pad–dry–cure process to develop thermoregulating textile materials. The morphology, thermal properties, and laundering properties of the treated fabrics were also investigated. The microcapsules were spherical and had melamine–formaldehyde shells containing eicosane. The microcapsules were strong enough to secure capsule stability under stirring in hot water and alkaline solutions. The heat storage capacity increased as the concentration of the microcapsules increased. The thermoregulating fabrics had heat storage capacities of 0.91–4.44 J/g, which depended on the concentration of the microcapsules. The treated fabrics retained 40% of their heat storage capacity after five launderings. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 96: 2005–2010, 2005
Reducing Resistance to Narrative Persuasion About Binge Drinking: The Role of Self-Activation and Habitual Drinking Behavior

ABSTRACT This study explores the effects of habitual health risk behaviors and self-activation on resistance to narrative persuasion. In two experiments, heavier drinkers were more resistant to an anti-binge-drinking narrative public service announcement (PSA) in which a binge drinker suffers a negative outcome. Specifically, heavier drinkers were more likely to generate counterarguments, unrealism judgments, and negative evaluations about the message compared to lighter drinkers or nondrinkers. However, activating self-concept when processing the persuasive narrative reduced unrealism judgments and negative evaluations, particularly among heavier drinkers. Self-activation also decreased perceived freedom threat among both heavier and lighter drinkers, which further led to higher perceived risk of binge drinking. Theoretical and practical implications are discussed.
Dewarping of Document Images using Coupled-Snakes

Traditional OCR systems are designed for planar (dewarped) images and the accuracy is reduced when applied on warped images. Therefore, developing new OCR techniques for warped images or developing dewarping techniques are the possible solutions for improving OCR accuracy camera-captured documents. Among different types of dewarping techniques, curled textlines information based dewarping techniques are the most popular ones, but are sensitive to high degrees of curl and variable line spacing. In this paper we build a novel dewarping approach based on curled textlines information, which has been extracted using ridges based modified active contour model (coupledsnakes). Our dewarping approach is less sensitive different direction of curl and variable line spacing. Experimental results show that OCR error rate, from warped to dewarped documents, has been reduced from 5.15% to 1.92% on the dataset of CBDAR 2007 document image dewarping contest. We also report the performance of our method in comparison with other state-of-the-art methods.
RELIABILITY AND VALIDITY OF THE MODIFIED CONCONI TEST ON CONCEPT II ROWING ERGOMETERS

The purpose of this study was to assess the reliability and validity of the modified Conconi test on Concept II rowing ergometers. Twenty-eight oarsmen conducted 3 performance tests on separate days. Reliability was assessed using the break point in heart rate (HR) linearity called the Conconi test (CT) and Conconi retest (CRT) for the noninvasive measurement of anaerobic threshold (AT). Blood lactate measurement was considered the gold standard for the assessment of the AT, and the validity of the CT was assessed by blood samples taken during an incremental load test (ILT) on ergometers. According to the results, the mean power output (PO) scores for the CT, CRT, and ILT were 234.2 ± 40.3 W, 232.5 ± 39.7 W, and 229.7 ± 39.6 W, respectively. The mean HR values at the AT for the CT, CRT, and ILT were 165.4 ± 11.2 b·min, 160.4 ± 10.8 b·min, and 158.3 ± 8.8 b·min, respectively. Interclass correlation coefficient (ICC) analysis indicated a significant correlation between the 3 tests with one another. Also, Bland and Altman plots showed that there was an association between noninvasive tests and the ILT PO scores and HRs (95% confidence interval [CI]). In conclusion, this study showed that the modified CT is a reliable and valid method for determining the AT of elite men rowers.
Lizard tricks: overcoming conflicting requirements of speed versus climbing ability by altering biomechanics of the lizard stride

SUMMARY Adaptations promoting greater performance in one habitat are thought to reduce performance in others. However, there are many examples of animals in which, despite habitat differences, such predicted differences in performance do not occur. One such example is the relationship between locomotory performance to habitat for varanid lizards. To explain the lack of difference in locomotor performance we examined detailed observations of the kinematics of each lizard's stride. Differences in kinematics were greatest between climbing and non-climbing species. For terrestrial lizards, the kinematics indicated that increased femur adduction, femur rotation and ankle angle all contributed positively to changes in stride length, but they were constrained for climbing species, probably because of biomechanical restrictions on the centre of mass height (to increase stability on vertical surfaces). Despite climbing species having restricted stride length, no differences have been previously reported in sprint speed between climbing and non-climbing varanids. This is best explained by climbing varanids using an alternative speed modulation strategy of varying stride frequency to avoid the potential trade-off of speed versus stability on vertical surfaces. Thus, by measuring the relevant biomechanics for lizard strides, we have shown how kinematic differences among species can mask performance differences typically associated with habitat variation.
A Research on Mobile Cloud Computing and Future Trends

With an exploding growth of the mobile applications and emerging of cloud computing, mobile cloud computing (MCC) has become a potential technology for mobile services. MCC is the combination of cloud computing, mobile computing and wireless networks to bring rich computational resources to mobile users, network operators, as well as cloud computing providers. Despite increasing usage of mobile computing, exploiting its full potential is difficult due to its inherent problems such as resource scarcity, frequent disconnections and mobility. MCC can address these problems by executing mobile applications on the resource providers’ side. In this paper, we give a definition of mobile cloud computing and provide an overview of state-of-the-art progress, in particular, models of mobile cloud applications. We also highlight research challenges in the area of mobile cloud computing. We conclude that mobile cloud computing can help building more powerful mobile applications.
A fast kinematic-based control method for lower-limb power augmentation exoskeleton

Exoskeletons are robotic devices which are used in power augmentation and rehabilitation robotics. The exoskeleton control system is one of the most challenging issues in human-robot interaction systems. Although the rehabilitation robotic control methods are well studied, little research has been conducted on power augmenting control methods. This paper presents a novel idea in control system of exoskeletons for load carrying and power augmentation. Here, the desired linear velocity of the exoskeleton in interaction points are taken to be proportional to interaction force at the corresponding location. The introduced control method is merely based on kinematic model and thus easy to implement practically. The result of simulation on a seven segmented dynamic model of Human-Exoskeleton shows that the interaction forces tend to zero and the position tracking error of exoskeleton is less than 2° degree.