Miracle-dz/UniFAR-FTUs huggingface dataset:
Prediction of Enzyme Classification from Protein Sequence without the Use of Sequence Similarity

We describe a novel approach for predicting the function of a protein from its amino-acid sequence. Given features that can be computed from the amino-acid sequence in a straightforward fashion (such as pI, molecular weight, and amino-acid composition), the technique allows us to answer questions such as: Is the protein an enzyme? If so, in which Enzyme Commission (EC) class does it belong? Our approach uses machine learning (ML) techniques to induce classifiers that predict the EC class of an enzyme from features extracted from its primary sequence. We report on a variety of experiments in which we explored the use of three different ML techniques in conjunction with training datasets derived from PDB and from Swiss-Prot. We also explored the use of several different feature sets. Our method is able to predict the first EC number of an enzyme with 74% accuracy (thereby assigning the enzyme to one of six broad categories of enzyme function), and to predict the second EC number of an enzyme with 68% accuracy (thereby assigning the enzyme to one of 57 subcategories of enzyme function). This technique could be a valuable complement to sequence-similarity searches and to pathway-analysis methods.
New rfp- and pES213-Derived Tools for Analyzing Symbiotic Vibrio fischeri Reveal Patterns of Infection and lux Expression In Situ

ABSTRACT Genetically altered or tagged Vibrio fischeri strains can be observed in association with their mutualistic host Euprymna scolopes, providing powerful experimental approaches for studying this symbiosis. Two limitations to such in situ analyses are the lack of suitably stable plasmids and the need for a fluorescent tag that can be used in tandem with green fluorescent protein (GFP). Vectors previously used in V. fischeri contain the p15A replication origin; however, we found that this replicon is not stable during growth in the host and is retained by fewer than 20% of symbionts within a day after infection. In contrast, derivatives of V. fischeri plasmid pES213 were retained by ∼99% of symbionts even 3 days after infection. We therefore constructed pES213-derived shuttle vectors with a variety of selectable and visual markers. To include a visual tag that can be used in conjunction with GFP, we compared seven variants of the DsRed2 red fluorescent protein (RFP): mRFP1, tdimer2(12), DsRed.T3, DsRed.T4, DsRed.M1, DsRed.T3_S4T, and DsRed.T3(DNT). The last variant was brightest, displaying >20-fold more fluorescence than DsRed2 in V. fischeri. RFP expression did not detectably affect the fitness of V. fischeri, and cells were readily visualized in combination with GFP-expressing cells in mixed infections. Interestingly, even when inocula were dense enough that most E. scolopes hatchlings were infected by two strains, there was little mixing of the strains in the light organ crypts. We also used constitutive RFP in combination with the luxICDABEG promoter driving expression of GFP to visualize the spatial and temporal induction of this bioluminescence operon during symbiotic infection. Our results demonstrate the utility of pES213-based vectors and RFP for in situ experimental approaches in studies of the V. fischeri-E. scolopes symbiosis.
Object recognition using tactile and image information

Camera provides rich information about objects and therefore becomes the mainstream sensors in robots. However, it often fails when the objects are not visual-distinguished. As a complementary, tactile sensors in the robotic fingertips can be used to capture multiple object properties such as texture, roughness, spatial features, compliance or friction and therefore becomes a very important sense modality for intelligent robot. Nevertheless, how to effective fuse both modality is still a challenging problem. In this paper, we developed tactile-image fusion framework for object recognition task. The multivariate times series model is used to represent the tactile sequence and the covariance descriptor is used to characterize the image. We also develop a practical dataset which includes 18 household object for verification and the experimental results shows that the performance of tactile-image is obviously better than using single modality.
Verifiability and Traceability in a Linked Data Based Messaging System

When linked data applications communicate, they commonly use messaging technologies in which the message exchange itself is not represented as linked data, since it takes place on a different architectural level. When a message cannot be verified and traced on the linked data level, trust in data is moved from message originators to service providers. However, there are use cases in which the actual message exchange and its verifiability are of importance. In such situations, the separation between application data and communication data is not desirable. To address this, we propose messaging based on linked data, where communicating entities and their messages are represented as interconnected Web resources, and we show how conversations can be made verifiable using digital signatures.
AulaNet Technologies: Future Trends

In this paper we present AulaNet, an environment for the creation and maintenance of Web-based courses. It differs from other Web-based instruction environments because it lacks the physical elements of the traditional schools, lying over the trivet communication - coordination - cooperation. We also present some future trends in the development of this learning environment, focusing the creation of knowledge communities.
Analysis of Vietnamese tones to optimize database in speech synthesis using unit selection method

This paper presents a novel approach to optimize data in Vietnameses speech synthesis using Unit Selection method. First, we conduct analysis of Vietnamese tone using Fujisaki model to find out the parameters of fundamental frequency contours (F0 contours) influencing on Vietnamese vowels while speech is expressed. Next, analysis, testing, and evaluation of the effects on the vowel are performed. After that, the data of unit selection speech synthesis system is optimized by recording the vowel with a level tone. As a result, when a Vietnamese word is synthesized, it will be synthesized with a level vowel first followed by being adjusted the parameter of F0 contour to create a word with appropriate tone. With this approach, recorded data can be reduced up to 64,44% while sound quality is insignificantly affected.
Type Erasure in C + + : The Glue between Object-Oriented and Generic Programming Presentation

C++ is a multi-paradigm language. The two main paradigms in C++ are object-oriented programming and generic programming. Many real-world C++ software projects use these two paradigms side by side. This creates considerable tension due to the fact that object-oriented programming is largely based on the judicious choice of types and hierarchies, while generic programming tends to cause an abundance of unrelated types. We show how type erasure can reconcile these conflicting tendencies. We present iterator type erasure as a concrete example that we have implemented and that is being used in production code at Zephyr Associates, Inc.
Developmental toxicity study in rats and rabbits administered an emulsion containing medium chain triglycerides as an alternative caloric source.

Triglyceride-containing lipid emulsions have been designed as caloric sources that can be administered intravenously to patients that cannot meet their nutritional needs by conventional parenteral therapies. In their study, we evaluate the developmental toxicity of a 20% lipid emulsion that contains a 3:1 ratio of medium chain triglyceride (MCT) to one long chain containing lipid emulsion (LCT). This emulsion was administered by intravenous infusion to rats and rabbits at dosages of 1 and 4.28 g lipid/kg body weight (g lipid/kg) at dose volumes of 5 and 21.4 mL/kg, respectively, once daily during organogenesis to assess the potential developmental toxicity of the test article. The control group received 0.9% saline at a dose volume of 21.4 mL/kg. Animals were observed for clinical signs of toxicity and adverse effects on body weights and feed consumption. On Day 20 (rats) or Day 29 (rabbits), females were necropsied and examined for maternal and embryo/fetal toxicity. Fetuses were removed, weighed, and examined for external, soft tissue, and skeletal abnormalities. Dosages of 4.28 g lipid/kg resulted in lower feed consumption for rats and rabbits, an expected finding based on the high-caloric nature of the test article. Potentially test article-related gross necropsy findings, including enlarged lymph nodes and spleen, small thymus, and enlarged renal pelvis, for rats given 4.28 g lipid/kg were present at a low incidence. There were no adverse effects on fetal parameters for rats even in the presence of some maternal toxicity. However, embryo and fetal toxicity (i.e., resorptions) and skeletal abnormalities were present for rabbits given 4.28 g lipid/kg. Under the conditions of this study, the no-observable-effect level for developmental toxicity was greater than or equal to 4.28 g lipid/kg for rats and greater than or equal to 1 g lipid/kg but less than 4.28 g lipid/kg for rabbits.
Modal /spl mu/-types for processes

Introduces a new paradigm for concurrency, called behaviours-as-types. In this paradigm, types are used to convey information about the behaviour of processes: while terms correspond to processes, types correspond to behaviours. We apply this paradigm to Winskel's (1994) process algebra. Its types are similar to Kozen's (1983) modal /spl mu/-calculus; hence, they are called modal /spl mu/-types. We prove that two terms having the same type denote two processes which behave in the some way, that is, they are bisimilar. We give a sound and complete compositional typing system for this language. Such a system naturally also recovers the notion of bisimulation on open terms, allowing us to deal with processes with undefined parts in a compositional manner.
Prevalence and Determinants of Metabolic Health in Subjects with Obesity in Chinese Population

Background: The study was to investigate the prevalence of metabolic health in subjects with obesity in the Chinese population and to identify the determinants related to metabolic abnormality in obese individuals. Methods: 5013 subjects were recruited from seven provincial capitals in China. The obesity and metabolic status were classified based on body mass index (BMI) and the number of abnormalities in common components of metabolic syndrome. Results: 27.9% of individuals with obesity were metabolically healthy. The prevalence of the metabolically healthy obese (MHO) phenotype was significantly decreased with age in women (p trend < 0.001), but not significantly in men (p trend = 0.349). Central obesity (odds ratio [OR] = 4.07, 95% confidence interval [CI] = 1.93–8.59), longer sedentary time (OR = 1.97, 95%CI = 1.27–3.06), and with a family history of obesity related diseases (hypertension, diabetes, dyslipidemia) (OR = 1.85, 95%CI = 1.26–2.71) were significantly associated with having metabolic abnormality in obese individuals. Higher levels of physical activity and more fruit/vegetable intake had decreased ORs of 0.67 (95%CI = 0.45–0.98) and 0.44 (95%CI = 0.28–0.70), respectively. Conclusion: 27.9% of obese participants are in metabolic health. Central obesity, physical activity, sedentary time, fruits/vegetables intake and family history of diseases are the determinants associated with metabolic status in obesity.
: A Computational Perspective (cid:3)

Although the computational perspective on cognitive tasks has always played a major role in Arti(cid:12)cial Intelligence, the interest in the precise determination of the computational costs that are required for solving typical AI problems has grown only recently. In this paper, we will describe what insights a computational complexity analysis can provide and what methods are available to deal with the complexity problem. (cid:3) This work was partially supported by the European Commissionas part of DRUMS-II, the ESPRIT Basic Research Project P6156.
OO-H Method: extending UML to model web interfaces

The mostly "creative" authoring process used to develop many Web applications during the last years has already proven unsuccessful to tackle, with its increasing complexity, both in terms of user and technical requirements. This fact has nurtured a mushrooming of proposals, most based on conceptual models, that aim at facilitating the development, maintenance and assessment of Web applications, thus improving the reliability of the Web development process.In this chapter, we will show how traditional software engineering approaches can be extended to deal with the Web idiosyncrasy, taking advantage of proven successful notation and techniques for common tasks, while adding models and constructs needed to capture the nuances of the Web environment. In this context, our proposal, the Object-Oriented Hypermedia (OO-H) Method, developed at University of Alicante, provides a set of new views that extend UML to provide a Web interface model. A code generation process is able to, departing from such diagrams and their associated tagged values, generate a Web interface capable of connecting to underlying business modules.
A Statistical Analysis of UK Academic Web Links

The analysis of web-based documents using quantitative techniques is a well-established area of research within the realm of information science. This paper builds on some of that work and presents the results of statistical analysis carried out on the web link structure text files of 111 UK universities. Summary statistics are produced using Alternative Document Models and the results of the statistical analysis are also graphically displayed, including trendline equations. Mathematical linear relationships were observed between certain bivariate data with subsequent Pearson correlation analysis revealing a number of very strong correlation relationships, particularly between site size and number of source / target directories and pages. This seems to support previous research by suggesting that the directory Alternative Document Model has some advantages over the domain Alternative Document Model.
Practical Illustration of Text: Customized Search, View Selection, and Annotation

This poster presents concepts to support authors illustrating their texts. We introduce a system which smoothly integrates the search and adaptation of appropriate illustrations into target documents. It enables the author to search for images and 3D models. To effectively support the context of the document, the view and label layout of the retrieved 3D models can be semi-automatically adjusted. Further on, we explicitly store the label layout in conjunction with the adapted illustrations. Since this information reflects the semantic and pragmatic content of illustrations, it eases the retrieval, reuse, and adaptation of illustrations in multimedia databases.
Enhancement of k-anonymity algorithm for privacy preservation in social media

In recent times, more and more social data is transmitted in different ways. Protecting the privacy of social network data has turn out to be an essential issue. Hypothetically, it is assumed that the attacker utilizes the similar information used by the genuine user. With the knowledge obtained from the users of social networks, attackers can easily attack the privacy of several victims. Thus, assuming the attacks or noise node with the similar environment information does not resemble the personalized privacy necessities, meanwhile, it loses the possibility to attain better utility by taking benefit of differences of users’ privacy necessities. The traditional research on privacy-protected data publishing can only deal with relational data and even cannot applied to the data of social networking. In this research work, K-anonymity is used for providing the security of the sensitive information from the attacker in the social network. K-anonymity provides security from attacker by making the graph and developing nodes degree. The clusters are made by grouping the similar degree into one group and the process is repeated until the noisy node is identified. For measuring the efficiency the parameters named as Average Path Length (APL) and information loss are measured. A reduction of 0.43% of the information loss is obtained.
Heterogeneity in femA in the Indian Isolates of Staphylococcus aureus Limits Its Usefulness as a Species Specific Marker

Increase in prevalence of MRSA worldwide and hence the need for rapid detection, have led to use of molecular methods for confirmation of the species and also MRSA. Species specific markers like fem or nuc along with the methicillin-resistance determinant, mecA, have been used by several investigators worldwide for the identification of MRSA. In the current study, we have screened 54 microbiologically confirmed (MRSA, MSSA and CoNS) isolates for the presence of mecA, 16S rRNA, femA and nuc markers. While mecAPCR and 16S rRNAPCR results were consistent with other studies, femA and nuc showed dramatic variation in detection rate (sensitivity) of S. aureus 29.6% and 53.7% respectively. Evidences are presented to demonstrate the absence of femA. Our attempt to amplify the complete femA gene using sequences flanking femA further confirmed these results and also indicated that variations exist even in the genomic sequences around femA. Our data reveals the need for exercising care while using primers designed on sequences of constitutive genes like femA and nuc for PCR based identification of S. aureus species. Though geographic variations in the genome of S. aureus have previously been reported from around the world, we present here evidence for the first time from India for absence of femA and also for probable variations in the sequences around the femA gene in clinical isolates of S. aureus.
NOP3 is an essential yeast protein which is required for pre-rRNA processing

The four nucleolar proteins NOP1, SSB1, GAR1, and NSR1 of Saccharomyces cerevisiae share a repetitive domain composed of repeat units rich in glycine and arginine (GAR domain). We have cloned and sequenced a fifth member of this family, NOP3, and shown it to be essential for cell viability. The NOP3 open reading frame encodes a 415 amino acid protein with a predicted molecular mass of 45 kD, containing a GAR domain and an RNA recognition motif. NOP3-specific antibodies recognize a 60-kD protein by SDS-PAGE and decorate the nucleolus and the surrounding nucleoplasm. A conditional lethal mutation, GAL::nop3, was constructed; growth of the mutant strain in glucose medium represses NOP3 expression. In cells depleted of NOP3, production of cytoplasmic ribosomes is impaired. Northern analysis and pulse-chase labeling indicate that pre-rRNA processing is inhibited at the late steps, in which 27SB pre-rRNA is cleaved to 25S rRNA and 20S pre-rRNA to 18S rRNA.
The role of molecular chaperones in spermatogenesis and the post-testicular maturation of mammalian spermatozoa.

BACKGROUND Spermatogenesis culminates in production of one of the most highly differentiated cells in biology, the spermatozoon. The gametes that emerge from the testes are, however, functionally immature and only acquire full functionality once they have completed a process of post-testicular maturation in the epididymis and female reproductive tract. Remarkably, this acquisition of sperm function occurs while these cells are transcriptionally and translationally silent and is therefore highly dependent on post-translational modifications to their existing protein complement. In this review, we consider the emerging roles of several prominent molecular chaperone families in orchestrating both the morphological differentiation of male germ cells during spermatogenesis and their functional transformation during sperm maturation. METHODS Journal databases were searched using key words, including chaperone, heat shock protein, testes, spermatogenesis, spermatozoa, epididymal maturation, capacitation and fertilization. RESULTS In the past two decades, molecular chaperones have been acknowledged to play key roles in controlling both the morphological transformation of germ cells during spermatogenesis and the post-testicular maturation of these cells as they transit the male and female reproductive tracts. Furthermore, there is mounting evidence that aberrant chaperone expression may be a major contributing factor to the defective sperm function seen in many cases of male infertility. CONCLUSIONS Molecular chaperones are critically involved in all phases of sperm development. Targeted disruption of these proteins has the ability to arrest spermatogenesis, compromise sperm maturation and inhibit fertilization. These proteins therefore hold considerable promise as targets for novel contraceptive strategies and as diagnostic biomarkers for male infertility.
The Neural Plasticity Theory of Depression: Assessing the Roles of Adult Neurogenesis and PSA-NCAM within the Hippocampus

Depression is a devastating and prevalent disease, with profound effects on neural structure and function; however the etiology and neuropathology of depression remain poorly understood. Though antidepressant drugs exist, they are not ideal, as only a segment of patients are effectively treated, therapeutic onset is delayed, and the exact mechanism of these drugs remains to be elucidated. Several theories of depression do exist, including modulation of monoaminergic neurotransmission, alterations in neurotrophic factors, and the upregulation of adult hippocampal neurogenesis, and are briefly mentioned in the review. However none of these theories sufficiently explains the pathology and treatment of depression unto itself. Recently, neural plasticity theories of depression have postulated that multiple aspects of brain plasticity, beyond neurogenesis, may bridge the prevailing theories. The term “neural plasticity” encompasses an array of mechanisms, from the birth, survival, migration, and integration of new neurons to neurite outgrowth, synaptogenesis, and the modulation of mature synapses. This review critically assesses the role of adult hippocampal neurogenesis and the cell adhesion molecule, PSA-NCAM (which is known to be involved in many facets of neural plasticity), in depression and antidepressant treatment.
An optimized k-NN classifier based on minimum spanning tree for email filtering

In the era of internet where mailboxes are being flooded by unnecessary emails, it becomes troublesome and time consuming to organize and classify legitimate emails into folders. Although there has been extensive investigation of automatic document categorization, email classification gives rise to a number of challenges, and there has been relatively little study in this domain. This paper presents a framework for email classification using Enron email dataset based on an improved k-NN classification using a minimum spanning tree clustering algorithm considering the case where the number of clusters (email folders) are unknown initially. Such a classification can be useful in maintaining email and web directories, identifying spam and valid mails. Experimental results show that the proposed algorithm outperforms state of art classification algorithms like standard k-NN and Naïve Bayes classifiers and c4.5 decision tree classifier.