Miracle-dz/UniFAR-FTUs huggingface dataset:
Temperature dependent mistranslation in a hyperthermophile adapts proteins to lower temperatures

All organisms universally encode, synthesize and utilize proteins that function optimally within a subset of growth conditions. While healthy cells are thought to maintain high translational fidelity within their natural habitats, natural environments can easily fluctuate outside the optimal functional range of genetically encoded proteins. The hyperthermophilic archaeon Aeropyrum pernix (A. pernix) can grow throughout temperature variations ranging from 70 to 100°C, although the specific factors facilitating such adaptability are unknown. Here, we show that A. pernix undergoes constitutive leucine to methionine mistranslation at low growth temperatures. Low-temperature mistranslation is facilitated by the misacylation of tRNALeu with methionine by the methionyl-tRNA synthetase (MetRS). At low growth temperatures, the A. pernix MetRS undergoes a temperature dependent shift in tRNA charging fidelity, allowing the enzyme to conditionally charge tRNALeu with methionine. We demonstrate enhanced low-temperature activity for A. pernix citrate synthase that is synthesized during leucine to methionine mistranslation at low-temperature growth compared to its high-fidelity counterpart synthesized at high-temperature. Our results show that conditional leucine to methionine mistranslation can make protein adjustments capable of improving the low-temperature activity of hyperthermophilic proteins, likely by facilitating the increasing flexibility required for greater protein function at lower physiological temperatures.
A Comparison of Principles of Technology and High School Physics Student Achievement Using a Principles of Technology Achievement Test

Society has traditionally taken the position that education is a primary means of achieving national goals. Unfortunately, we have never collectively agreed upon “what kind” of education is needed--general or vocational. The present K-12 public educational system in the United States is comprised of general and vocational education tracts. Historically, one of the goals of vocational education has been to provide entry-level job skills. In contrast, general education, as the title implies, has attempted to equip students for living or for further education. In preparing students to enter the workforce, vocational education can provide an opportunity to obtain hands-on experiences with many of the theoretical concepts presented within the general education classes. Many secondary education students, however, never take vocational courses because they do not view them as relevant to college preparation (Meier, 1991). Conversely, many vocational education students are not taught the theoretical mathematics and science concepts that are needed to cope with a rapidly changing society. Vocational education has been considered a separate discipline within the broad context of education and has been in continuous competition with general education for students and resources. Vocational education has been concerned with providing people with gainful employment after graduation. A “Blue Collar” affiliation is considered undesirable by those students wanting to attend college or obtain further education. The unfortunate outcome is that the average high school graduate is “nonfunctional” in our modern society (Cummins, 1989). If education is designed to help the individual attain selffulfillment in a technologically complex, work-oriented society, then education must be a synthesis of both general and vocational education. Anything less jeopardizes the individual's opportunity for self-fulfillment.
Transcriptional Regulation of the Cellobiose Operon of Streptococcus mutans

ABSTRACT The ability of Streptococcus mutans to catabolize cellobiose, a β-linked glucoside generated during the hydrolysis of cellulose, is shown to be regulated by a transcriptional regulator, CelR, which is encoded by an operon with a phospho-β-glucosidase (CelA) and a cellobiose-specific sugar phosphotransferase system (PTS) permease (EIICel). The roles of CelR, EIICel components, and certain fructose/mannose-PTS permeases in the transcriptional regulation of the cel locus were analyzed. The results revealed that (i) the celA and celB (EIIBCel) gene promoters require CelR for transcriptional activation in response to cellobiose, but read-through from the celA promoter contributes to expression of the EIICel genes; (ii) the EIICel subunits were required for growth on cellobiose and for transcriptional activation of the cel genes; (iii) CcpA plays little direct role in catabolite repression of the cel regulon, but loss of specific PTS permeases alleviated repression of cel genes in the presence of preferred carbohydrates; and (iv) glucose could induce transcription of the cel regulon when transported by EIICel. CelR derivatives containing amino acid substitutions for five conserved histidine residues in two PTS regulatory domains and an EIIA-like domain also provided important insights regarding the function of this regulator. Based on these data, a model for the involvement of PTS permeases and the general PTS proteins enzyme I and HPr was developed that reveals a critical role for the PTS in CcpA-independent catabolite repression and induction of cel gene expression in S. mutans.
Effects of hyperthyroidism on delayed rectifier potassium currents in left and right murine atrium

Hyperthyroidism has been associated with atrial fibrillation (AF), however, hyperthyroidism induced ion channel changes which may predispose to AF have not been fully elucidated. To understand the electrophysiological changes occurring in left and right atrium with hyperthyroidism, the patch-clamp technique was utilized to compare action potential duration (APD) and whole cell currents in myocytes from left and right atria from both control and hyperthyroid mice. Additionally, RNase protection assays and immunoblotting were performed to evaluate the mRNA and protein expression levels of potassium channel alpha subunits in left and right atrium. The results showed that: (1) In control mice, the APD was shorter and the ultra-rapid delayed rectifier potassium conductance (I Kur) and the sustained delayed rectifier potassium conductance (I SS) were larger in the left atrium than in the right. The mRNA and protein expression levels of Kv1.5 and Kv2.1 were also higher in the left atrium. (2) In hyperthyroid mice, the APD was shortened and I Kur and I SS were increased in both left and right atrial myocytes. The protein expression levels of Kv1.5 and Kv2.1 were increased significantly in both atria from hyperthyroid mice. (3) The influence of hyperthyroidism on APD and delayed rectifier potassium currents was more prominent in right atrium than in the left, which minimized the inter-atrial APD difference. In conclusion, hyperthyroidism resulted in a more significant APD shortening and greater delayed rectifier potassium current increases in the right versus the left atrium, which can contribute to the propensity for atrial arrhythmia in the hyperthyroid heart.
Remote Sensing Based Spatial Statistics to Document Tropical Rainforest Transition Pathways

In this paper, grid cell based spatial statistics were used to quantify the drivers of land-cover and land-use change (LCLUC) and habitat degradation in a tropical rainforest in Madagascar. First, a spectral database of various land-cover and land-use information was compiled using multi-year field campaign data and photointerpretation of satellite images. Next, residential areas were extracted from IKONOS-2 and GeoEye-1 images using object oriented feature extraction (OBIA). Then, Landsat Thematic Mapper (TM) and Enhanced Thematic Mapper Plus (ETM+) data were used to generate land-cover and land-use maps from 1990 to 2011, and LCLUC maps were developed with decadal intervals and converted to 100 m vector grid cells. Finally, the causal associations between LCLUC were quantified using ordinary least square regression analysis and Moran’s I, and a forest disturbance index derived from the time series Landsat data were used to further confirm LCLUC drivers. The results showed that (1) local spatial statistical approaches were most effective at quantifying the drivers of LCLUC, and (2) the combined threats of habitat degradation in and around the reserve and increasing encroachment of invasive plant species lead to the expansion of shrubland and mixed forest within the former primary forest, which was echoed by the forest disturbance index derived from the Landsat data.
Bioactive Secondary Metabolites from the Red Sea Marine Verongid Sponge Suberea Species

In a continuation of our efforts to identify bioactive compounds from Red Sea Verongid sponges, the organic extract of the sponge Suberea species afforded seven compounds including two new dibrominated alkaloids, subereamollines C and D (1 and 2), together with the known compounds aerothionin (3), homoaerothionin (4), aeroplysinin-1 (5), aeroplysinin-2 (6) and a revised subereaphenol C (7) as ethyl 2-(2,4-dibromo-3,6-dihydroxyphenyl)acetate. The structures of the isolated compounds were assigned by different spectral data including optical rotations, 1D (1H and 13C) and 2D (COSY, multiplicity-edited HSQC, and HMBC) NMR and high-resolution mass spectroscopy. Aerothionin (3) and subereaphenol C (7) displayed potent cytotoxic activity against HeLa cell line with IC50 values of 29 and 13.3 µM, respectively. In addition, aeroplysinin-2 (6) showed potent antimigratory activity against the human breast cancer cell line MDA-MB-231 with IC50 of 18 µM. Subereamollines C and D are new congeners of the previously reported compounds subereamollines A and B with methyl ester functionalities on the side chain. These findings provide further insight into the biosynthetic capabilities of members of the genus Suberea and the chemical diversity as well as the biological activity of these compounds.
Semantic Interoperability in Electronic Business

E-business refers to the utilization of information and communication technologies (ICT) in support of all the activities of business. The standards developed for e-business help to facilitate the deployment of e-business. In particular, several organizations in e-business sector have produced standards and representation forms using XML. It serves as an interchange format for exchanging data between communicating applications. However, XML says nothing about the semantics of the used tags. XML is merely a standard notation for markup languages, which provides a means for structuring documents. Therefore the XML-based e-business software is developed by hard-coding. Hard-coding is proven to be a valuable and powerful way for exchanging structured and persistent business documents. However, if we use hard-coding in the case of non- persistent documents and non-static environments we will encounter problems in deploying new document types as it requires a long lasting standardization process. Replacing existing hard-coded ebusiness systems by open systems that support semantic interoperability, and which are easily extensible, is the topic of this article. We first consider XML-based technologies and standards developed for B2B interoperation. Then, we consider electronic auctions, which represent a form of e-business. In particular, we represent how semantic interoperability can be achieved in electronic auctions.
A novel EAP-moderate weight Extensible Authentication Protocol

Wireless Local Area Networks WLAN based on wireless technology, i.e., no physically connection exists. Therefore, security is always a major concern for WLAN development and one of the major problems in WLAN security issue is authentication. EAP (Extensible Authentication Protocol) is a framework of authentication that uses several methods of authentication such as TLS, TTLS, PEAP and LEAP. EAP-LEAP (EAP-Lightweight Extensible Authentication Protocol) is widely used in WLAN (Wi- Fi /802.11 and Wi-MAX/802.16) as solution of authentication problem. This paper presents an assessment to the security of EAP-LEAP in details and explores many weakness points. As a solution to the presented flaws, we present a new proposal EAP- MEAP in details to overcome these shortage points. Finally we present an security assessment to our proposed protocol compared with EAP-LEAP.
The CD81 Partner EWI-2wint Inhibits Hepatitis C Virus Entry

Two to three percent of the world's population is chronically infected with hepatitis C virus (HCV) and thus at risk of developing liver cancer. Although precise mechanisms regulating HCV entry into hepatic cells are still unknown, several cell surface proteins have been identified as entry factors for this virus. Among these molecules, the tetraspanin CD81 is essential for HCV entry. Here, we have identified a partner of CD81, EWI-2wint, which is expressed in several cell lines but not in hepatocytes. Ectopic expression of EWI-2wint in a hepatoma cell line susceptible to HCV infection blocked viral entry by inhibiting the interaction between the HCV envelope glycoproteins and CD81. This finding suggests that, in addition to the presence of specific entry factors in the hepatocytes, the lack of a specific inhibitor can contribute to the hepatotropism of HCV. This is the first example of a pathogen gaining entry into host cells that lack a specific inhibitory factor.
The Role of Assimilation and Multiculturalism for the Relation Between Social Dominance Orientation and Prejudice: The Case of Anglophones and Francophones in Québec

Research on national diversity policies show that cultural norms promoted by the government such as multiculturalism and assimilation play an important role in predicting the majority group members’ prejudice toward immigrants. However, the extent to which minority groups can share these cultural norms with majority group members is largely unknown. The first goal of the current research is to determine if majority and minority groups perceive similar national diversity policies and have comparable support for these policies. The second goal is to contrast, between majority and minority groups, the relationship between social dominance orientation (SDO) and prejudice toward immigrants while considering the mediation effect of national diversity policies. To reach these goals, 225 Francophones (nonimmigrant majority) and 207 Anglophones (nonimmigrant minority) living in the province of Québec answered a questionnaire. Analyses performed to satisfy the first goal indicate that Francophones and Anglophones perceive Quebecers’ support toward national diversity policies in similar ways despite the fact that Francophones show more personal support for assimilation than Anglophones while the reverse is true for multiculturalism. Regarding the second goal, results reveal that, when norms are salient, personal support for assimilation is a stronger mediator of the link between SDO and prejudice especially for Anglophones whereas the mediating role of personal support for multiculturalism is significant among Francophones only. The importance of considering majority and minority groups when elaborating national diversity policies is discussed.
WYSIWYT testing in the spreadsheet paradigm : an empirical study of end users

This paper reports on an empirical study involving end users that addresses t h e question of whether it is possible to provide the benefits of formal testing within the informal spreadsheet paradigm. We have developed a “What You See Is What You Test” (WYSIWYT) methodology that brings the benefits of formal testing in a way that does not require the users to learn the underlying software engineering theory about esting. Our WYSIWYT methodology attempts to d o this by supplementing the immediate visual feedback about the values in cells with feedback about their “testedness”. A previous controlled experiment us ing computer science students showed that the subjects who used the methodology were significantly more effective and more efficient in their testing a n d significantly less overconfident about the correctness of their spreadsheets t h a n subjects who did not use the methodology. The results were obtained wi thout providing any training in the theory of tes ting or test adequacy that t h e methodology implements. In this paper we report the results of a similar experiment that investigated whether spreadsheet nd users with little or n o programming experience would obtain the same benefits using the methodology.
Applying linked data approaches to pharmacology: Architectural decisions and implementation

The discovery of new medicines requires pharmacologists to interact with a number of information sources ranging from tabular data to scientific papers, and other specialized formats. In this application report, we describe a linked data platform for integrating multiple pharmacology datasets that form the basis for several drug discovery applications. The functionality offered by the platform has been drawn from a collection of prioritised drug discovery business questions created as part of the Open PHACTS project, a collaboration of research institutions and major pharmaceutical companies. We describe the architecture of the platform focusing on seven design decisions that drove its development with the aim of informing others developing similar software in this or other domains. The utility of the platform is demonstrated by the variety of drug discovery applications being built to access the integrated data.An alpha version of the OPS platform is currently available to the Open PHACTS consortium and a first public release will be made in late 2012, see http://www.openphacts. org/ for details.
Under Consideration for Publication in Theory and Practice of Logic Programming (co)recursion in Logic Programming: Lazy Vs Eager *

CoAlgebraic Logic Programming (CoALP) is a dialect of Logic Programming designed to bring a more precise compile-time and run-time analysis of termination and productivity for recursive and corecursive functions in Logic Programming. Its second goal is to introduce guarded lazy (co)recursion akin to functional theorem provers into logic programming. In this paper, we explain lazy features of CoALP, and compare them with the loop-analysis and eager execution in Coinductive Logic Programming (CoLP). We conclude by outlining the future directions in developing the guarded (co)recursion in logic programming.
Homotopy algorithm for the symmetric diagonal-plus-semiseparable eigenvalue problem

A dense symmetric matrix can be reduced into a similar diagonalplus-semiseparable one by means of orthogonal similarity transformations. This makes such a diagonal-plus-semiseparable representation a good alternative to the tridiagonal one when solving dense linear algebra problems. For symmetric tridiagonal matrices there have been developed different homotopy eigensolvers. We present a homotopy method combined with a divide-andconquer approach to find all the eigenvalues and eigenvectors of a diagonal-plus-semiseparable matrix. The basic mathematical theory behind this algorithm is reviewed and is followed by a discussion of the numerical considerations of the actual implementation. First, we split the original matrix into two smaller matrices of the same structure, and later we join the eigendecompositions of these smaller matrices. On this way a complete eigenvalue problem for a diagonal plus rank-one matrix is solved by a homotopy method. Deflation techniques are implemented, leading to a fast convergence of the homotopy method. Accuracy of the computed eigenvalues and orthogonality of the computed eigenvectors are illustrated by numerical experiments.
Two parallel alignment algorithms for big number of strings

This poster paper deals with algorithmic solutions for the alignment of a large number of data strings, which is a challenging and computationally demanding task, belonging to the class of NP-hard problems. In order to get practical and time-acceptable solutions, the development of heuristic approaches and the employment of parallelism are inevitable. Two parallel algorithms are presented for solving the alignment problem in the context of extraction of data from webpages. Both algorithms have their sequential counterpart, which represents an efficient heuristic approach, based on the estimation of local parameters for symbol distances. The algorithms are characterized by different assignments of data to processors of the parallel system: In the first one the processed data sets are distributed according to symbols, in the second one by columns. The algorithms are formulated in pseudocode and implemented with MPI. Their computational and space complexities are estimated and compared. Moreover, they are examined on a parallel cluster with multi-core nodes for a pool of test data coming from web-pages. The results of experiments show that the variant with distribution by columns is less efficient because of high communication costs. The algorithm with the data distribution according to symbols delivers acceptable timings, especially when the matrix of string data is long and thin.
Implementing Agent Interoperability between Language-Heterogeneous Platforms

One of the most important feature of a MAS (Multi-Agent System) is the cooperation and the coordination among agents placed in distributed environments. Due to the high heterogeneity of agents and platforms, interoperability has become a key issue for the use of MASs in academic and industrial fields. Several approaches to interoperability proposed so far are based on the JAVA technology exploiting the homogeneity of the programming language and technology. In this paper we introduce a new middleware that enables the interoperability among agents execution in different platforms, implemented with different programming languages. Our approach is FIPA-IEEE compliant and programming-language independent.