Identifying DNA-binding proteins by combining support vector machine and PSSM distance transformation

Background: DNA-binding proteins play a pivotal role in various intra- and extra-cellular activities ranging from DNA replication to gene expression control. Identification of DNA-binding proteins is one of the major challenges in the field of genome annotation. There have been several computational methods proposed in the literature to deal with the DNA-binding protein identification. However, most of them can't provide an invaluable knowledge base for our understanding of DNA-protein interactions. Results: We firstly presented a new protein sequence encoding method called PSSM Distance Transformation, and then constructed a DNA-binding protein identification method (SVM-PSSM-DT) by combining PSSM Distance Transformation with support vector machine (SVM). First, the PSSM profiles are generated by using the PSI-BLAST program to search the non-redundant (NR) database. Next, the PSSM profiles are transformed into uniform numeric representations appropriately by distance transformation scheme. Lastly, the resulting uniform numeric representations are inputted into a SVM classifier for prediction. Thus whether a sequence can bind to DNA or not can be determined. In benchmark test on 525 DNA-binding and 550 non DNA-binding proteins using jackknife validation, the present model achieved an ACC of 79.96%, MCC of 0.622 and AUC of 86.50%. This performance is considerably better than most of the existing state-of-the-art predictive methods. When tested on a recently constructed independent dataset PDB186, SVM-PSSM-DT also achieved the best performance with ACC of 80.00%, MCC of 0.647 and AUC of 87.40%, and outperformed some existing state-of-the-art methods. Conclusions: The experiment results demonstrate that PSSM Distance Transformation is an available protein sequence encoding method and SVM-PSSM-DT is a useful tool for identifying the DNA-binding proteins. A user-friendly web-server of SVM-PSSM-DT was constructed, which is freely accessible to the public at the web-site on http://bioinformatics.hitsz.edu.cn/PSSM-DT/.

A szovjetológiától az új intézményi közgazdaságtanig - töprengések két évtized távlatából = From Sovietology to the new institutional economics - meditations from a distance of two decades

A következőkben arra teszünk kísérletet, hogy összegezzük a közép- és a kelet-európai rendszerváltozások és az ezt tanulmányozók fordulatos történetét az elmúlt két évtizedben. Bemutatjuk, hogy a közgazdaságtan egy kevéssé fejlett ága miképp szembesült a tudományág egésze szempontjából is talán legnehezebb értelmezési és alkalmazási kérdéseket fölvető történelmi folyamattal. Megpróbáljuk feloldani azt a rejtvényt, hogy a főáramú megközelítés megismerése és alkalmazása miért nem hozott átütő eredményt sem a térség gazdaságainak, sem magának a tudományszaknak. Megvizsgáljuk a fokozatosság és a reformok kritikus tömege viszonyát. Végül kísérletet teszünk arra, hogy e sajátos szakterület elemzéséből adódó, tartósnak bizonyuló tételeket beépítsük a fenntartható fejlődés szélesebben értelmezett, immár főáramú megközelítéseibe. ___________ The article attempts to give an account of the changes of system in Central and Eastern Europe and of those who studied them in the last two decades. It shows how a less devel-oped branch of economics faced a historical process that posed possibly the most difficult questions of interpretation and application for the whole discipline. An attempt is made to discover why recognition and application of the mainstream approach failed to bring resounding success for the economies of the region or for economics itself. The author examines the relation between continuity and the critical weight of reforms. Finally, an attempt is made to advance durable propositions based on analysis of this specific field through now mainstream approaches in terms of sustainable development.

Hatalmi távolság és intézményi kollektivizmus – a versenyképesség előrejelzése szövegelemzéssel (Power distance and institutional collectivism – Forecast of competitiveness by text analysis)

A tárgyalófelek elé kitett mobiltelefon alkalmazása előrejelzi a beszélgetőpartnerek versenyképességét a versenyképesség-mutatók alapján, javaslatokat adva a tárgyalás további menetére. Ez a vízió nyilván még futurisztikus, ám a csúcsvezetői nyilatkozatok rejtett szövegtartalma alapján következtetéseket levonni a képviselt szervezetek versenyképességi orientációira – ez már ma lehetőség. A GLOBE-projekt kultúrakutatási módszertanával, valamint szövegelemzési módszerekkel sikerült kimutatni a versenyképességet előrejelző hatalmi távolság és az intézményi kollektivizmus szövegbeli jeleit. Mindez eszközt jelenthet egyebek mellett a szervezetfejlesztéssel, hírszerzéssel, HR-gazdálkodással foglalkozó szakembereknek is. _______ The use of the mobile telephones laid in front of the negotiators during their conversations forecasts their indicators of competitiveness and gives suggestions for the further course of negotiation. This is obviously a futuristic vision, but drawing conclusions from the hidden content of top management narratives concerning the competitive cultural orientations of the represented organizations is a possibility that is already available. Using the culture research methodology of the GLOBE project as well as text analysis methods, it was possible to reveal narrative patterns both of the power distance, forecasting competitiveness, and of institutional collectivism. These findings may be useful tools for professionals, among others of organizational development, intelligence service and HR management.

Distance-based accessibility indices

The paper attempts to develop a suitable accessibility index for networks where each link has a value such that a smaller number is preferred like distance, cost, or travel time. A measure called distance sum is characterized by three independent properties: anonymity, an appropriately chosen independence axiom, and dominance preservation, which requires that a node not far to any other is at least as accessible. We argue for the need of eliminating the independence property in certain applications. Therefore generalized distance sum, a family of accessibility indices, will be suggested. It is linear, considers the accessibility of vertices besides their distances and depends on a parameter in order to control its deviation from distance sum. Generalized distance sum is anonymous and satisfies dominance preservation if its parameter meets a sufficient condition. Two detailed examples demonstrate its ability to reflect the vulnerability of accessibility to link disruptions.

A földrajzi távolság, a kulturális hasonlóság és a szabadkereskedelem hatása a borkereskedelemre = Effects on the global wine trade of geographical distance, cultural and linguistic similarity, and free trade

A globalizálódó világgazdaságban a vezető bortermelő országok egyre jelentősebb borkereskedelmet bonyolítanak le egymás között. Míg Európában a fogyasztók egyre kevesebb bort vásárolnak, addig Amerikában és Ázsiában a bor iránti kereslet folyamatosan bővül: a borkereskedelem földrajzi átrendeződése zajlik. A kulturális hasonlóság és a földrajzi távolság kereskedelemre gyakorolt hatását gyakran a kereskedelemelméletek gravitációs modelljével elemzik. E tanulmány azt vizsgálja, hogy a fő borexportáló országok közötti földrajzi távolság, kulturális hasonlóság és szabadkereskedelem milyen hatással van a nemzetközi borkereskedelemre, annak költségeire. A regressziós becslés eredményei alátámasztják, hogy a borkereskedelem költségei alacsonyabbak, ha a kereskedelmi partnerek kulturálisan hasonlók, földrajzilag közel helyezkednek el egymáshoz, vagy van tengeri kikötőjük, tagjai a WTO-nak, illetve ha kötöttek egymással regionális kereskedelmi megállapodást. Ezenkívül megállapítható, hogy az angolszász, a latin-amerikai és az európai kulturális klaszterek elsősorban egymással kereskednek. A kutatás számos kulturális változó alkalmazásával és több ökonometriai modell, illetve becslési eljárás nagymintás tesztelésével gazdagítja a szakirodalmat. ____ In a globalizing world, major wine-producing countries export considerable quantities to the global wine market and turn over a notable trade, but in what happens European wine regions differ markedly from the New World. Here major wine producers suffered a remarkable fall in domestic wine consumption in recent decades, while New World wine producers increased their production potential and generated new foreign demand. The changes have been joined by geographical relocation of wine consumption and exports. The gravity equation can be derived from demand-side or supply-side theory-consistent estimation methods that suggest relationships between the size of the economies, geographical distances, cultural similarities, and size of their trade. The paper analyses the effects of cultural and geographical proximity, free trade, and linguistic similarity on bilateral trade in the main wine-producing countries, using a cross-section gravity model for 2012. The results suggest that larger countries export more wine, while transport costs rise in line with geographical distance and are higher for landlocked trading partners. Wine export costs are lower if trading partners are culturally similar, share a dominant religion, or are both WTO members with regional trade agreements. Anglo-Saxon, Germanic, Latin American and Latin European countries mainly trade wines within their groups. The paper looks to extend the number of trading partners, investigate the effect of language clusters, and confirm that the results are robust by different econometric methodologies.

A comparison of a distance education and locally based course in an urban university setting

The purpose of this research was to compare the academic performance and attitudes of students at the instructor-based site of a televised course and the distant site. An earlier pilot program indicated the need for certain technical and structural interventions at the distant site such as multiple "press-to-touch" microphones, a site-administrator and participative seating arrangements. At the beginning of the class, demographic data were collected from the students at both sites through a questionnaire and supplemented with information from students' records. Factors such as age, gender, ethnicity, marital status, number of children, current class status, major, work status and CLAST scores (achievement tests) were examined. There were no significant differences between the students at the sites except ethnicity and reading CLAST scores. The instructor-based site had a higher percentage of Hispanic students and the distant site had a larger percentage of Caucasian and Black Americans. The distant site scored significantly better on the reading section of the CLAST achievement test. An evaluation instrument was distributed to both sites, at the midpoint of the semester, measuring their attitude toward the organizational, technical, and pedagogical factors of the course. A second evaluation instrument, measuring similar factors, but more in-depth, was distributed to both sites near the end of the term. Nine students at the distant site were interviewed along with the site administrator to collect additional information.^ Course completion rates, dropout rates, pass rates and final grades of students at both sites were compared. There were no significant differences in academic performance between the students at both sites, however, there were significant differences in their attitudes. Those at the instructor-based site gave better ratings to most of items in the evaluation instruments. Problems at the distant site included audio and visual clarity, lack of available assistance, too much nonrelated talking, not enough opportunities to ask questions or to interact with the instructor during class. ^

A distance education case study: A comparison of instructional delivery methods practiced by higher education faculty and emerging standards

The purpose of this research was to compare the delivery methods as practiced by higher education faculty teaching distance courses with recommended or emerging standard instructional delivery methods for distance education. Previous research shows that traditional-type instructional strategies have been used in distance education and that there has been no training to distance teach. Secondary data, however, appear to suggest emerging practices which could be pooled toward the development of standards. This is a qualitative study based on the constant comparative analysis approach of grounded theory.^ Participants (N = 5) of this study were full-time faculty teaching distance education courses. The observation method used was unobtrusive content analysis of videotaped instruction. Triangulation of data was accomplished through one-on-one in-depth interviews and from literature review. Due to the addition of non-media content being analyzed, a special time-sampling technique was designed by the researcher--influenced by content analyst theories of media-related data--to sample portions of the videotape instruction that were observed and counted. A standardized interview guide was used to collect data from in-depth interviews. Coding was done based on categories drawn from review of literature, and from Cranton and Weston's (1989) typology of instructional strategies. The data were observed, counted, tabulated, analyzed, and interpreted solely by the researcher. It should be noted however, that systematic and rigorous data collection and analysis led to credible data.^ The findings of this study supported the proposition that there are no standard instructional practices for distance teaching. Further, the findings revealed that of the emerging practices suggested by proponents and by faculty who teach distance education courses, few were practiced even minimally. A noted example was the use of lecture and questioning. Questioning, as a teaching tool was used a great deal, with students at the originating site but not with distance students. Lectures were given, but were mostly conducted in traditional fashion--long in duration and with no interactive component.^ It can be concluded from the findings that while there are no standard practices for instructional delivery for distance education, there appears to be sufficient information from secondary and empirical data to initiate some standard instructional practices. Therefore, grounded in this research data is the theory that the way to arrive at some instructional delivery standards for televised distance education is a pooling of the tacitly agreed-upon emerging practices by proponents and practicing instructors. Implicit in this theory is a need for experimental research so that these emerging practices can be tested, tried, and proven, ultimately resulting in formal standards for instructional delivery in television education. ^

The effects of cultural distance on student socialization and departure decisions

Organizational socialization theory and university student retention literature support the concept that social integration influences new recruits' level of satisfaction with the organization and their decision to remain. This three-phase study proposes and tests a Cultural Distance Model of student retention based on Tinto's (1975) Student Integration Model, Louis' (1980) Model of Newcomer Experience, and Kuh and Love's (2000) theory relating cultural distance to departure from the organization. ^ The main proposition tested in this study was that the greater the cultural distance, the greater the likelihood of early departure from the organization. Accordingly, it was inferred that new recruits entering the university culture experience some degree of social and psychological distance. The extent of the distance correspondingly influences satisfaction with the institution and intent to remain for subsequent years. ^ The model was tested through two freshman student surveys designed to examine the effects of cultural distance on non-Hispanics at a predominantly Hispanic, urban, public university. The first survey was administered eight weeks into their first Fall semester and the second at the end of their first year. Student retention was determined through their re-enrollment for the second Fall semester. Path analysis tested the viability of the hypothesis relating cultural distance to satisfaction and retention as suggested in the model. Logistic regression tested the model's predictive power. ^ Correlations among variables were significant, accounting for 54% of variance in students' decisions to return for the second year with 96% prediction accuracy. Initial feelings of high cultural distance were related to increased dissatisfaction with social interactions and institutional choice at the end of the first year and students' intention not to re-enroll. Path analysis results supported the view that the construct of culture distance incorporates both social and psychological distance, and is composed of beliefs of institutional fit with one's cultural expectations, individual comfort with the fit, and the consequent sense of “belonging” or identifying with the institution. ^