Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences

Motivation: In any macromolecular polyprotic system - for example protein, DNA or RNA - the isoelectric point - commonly referred to as the pI - can be defined as the point of singularity in a titration curve, corresponding to the solution pH value at which the net overall surface charge - and thus the electrophoretic mobility - of the ampholyte sums to zero. Different modern analytical biochemistry and proteomics methods depend on the isoelectric point as a principal feature for protein and peptide characterization. Protein separation by isoelectric point is a critical part of 2-D gel electrophoresis, a key precursor of proteomics, where discrete spots can be digested in-gel, and proteins subsequently identified by analytical mass spectrometry. Peptide fractionation according to their pI is also widely used in current proteomics sample preparation procedures previous to the LC-MS/MS analysis. Therefore accurate theoretical prediction of pI would expedite such analysis. While such pI calculation is widely used, it remains largely untested, motivating our efforts to benchmark pI prediction methods. Results: Using data from the database PIP-DB and one publically available dataset as our reference gold standard, we have undertaken the benchmarking of pI calculation methods. We find that methods vary in their accuracy and are highly sensitive to the choice of basis set. The machine-learning algorithms, especially the SVM-based algorithm, showed a superior performance when studying peptide mixtures. In general, learning-based pI prediction methods (such as Cofactor, SVM and Branca) require a large training dataset and their resulting performance will strongly depend of the quality of that data. In contrast with Iterative methods, machine-learning algorithms have the advantage of being able to add new features to improve the accuracy of prediction. Contact: yperez@ebi.ac.uk Availability and Implementation: The software and data are freely available at https://github.com/ypriverol/pIR. Supplementary information: Supplementary data are available at Bioinformatics online.

A lean termelési rendszer munkásokra gyakorolt hatása (Effects of lean production on quality of working life from workers’ point of view)

A lean termelési rendszer munkásokra gyakorolt hatásaival foglalkozó irodalomban nincsen egyetértés annak megítélésében, hogy a hatásokban a negatív vagy pozitív hatások dominálnak-e. A szerző tanulmánya ehhez a vitához a pszichológiai, egészségügyi, munkahelyi jellemzőkre és a dolgozói elégedettségre vonatkozó eredmények áttekintésével kapcsolódik. A munkások elégedettségének vizsgálata arra utal, hogy a lean termelési rendszer egyszerre növeli és csökkenti is az elégedettséget, így az összességében nem változik más termelési rendszerekhez képest. A lean termelés kritikusai azt hangsúlyozzák, hogy a többi tényező negatívan hat a munkásokra. Megállapításaik megalapozottsága a nagyon kevés empirikus munka miatt megkérdőjelezhető. Ugyanakkor a tevékenységmenedzsment kutatói érdemben nem tudják cáfolni a stressz, a sérülések és betegségek kockázatának növekedését és a munka intenzívebbé válását. A negatív hatások és a várt pozitív hatások hiányának kiemelése felveti, hogy a munkavállalók bevonásán alapuló lean termelési rendszer nehezen ültethető át a gyakorlatba, illetve hogy a lean termelés intenzifikáción alapuló modellje is elterjedt. _____________ This literature review contributes to the debate related to the effects of lean production on workers. The study reviews different dimensions of the debate and focuses on issues like worker’s satisfaction, psychological effects, health and safety aspects, and workplace characteristics. Findings of researches reviewed in this paper cannot confirm that from workers’ point of view lean production is better than other production initiatives. Lean production enhances and decreases worker’s satisfaction at the same time, altogether, the satisfaction of workers does not change significantly compared to other systems. The negative impact of the other factors (psychological etc.) on workers is usually emphasized in the critique of lean production. Although, the limited number of (empirical) studies doubts these critical voices. However, Operations Management can not reject negative effects like increasing level of stress, increased risks of health and safety problems or intensification of work. The emphasis of the negative effects and the lack of positive effects can refer to the difficult employment of lean involvement system, or simply reflect that the model of lean intensification system is widely spread.

Social network structure as a critical success condition for open source software project communities

In recent years, a surprising new phenomenon has emerged in which globally-distributed online communities collaborate to create useful and sophisticated computer software. These open source software groups are comprised of generally unaffiliated individuals and organizations who work in a seemingly chaotic fashion and who participate on a voluntary basis without direct financial incentive. ^ The purpose of this research is to investigate the relationship between the social network structure of these intriguing groups and their level of output and activity, where social network structure is defined as (1) closure or connectedness within the group, (2) bridging ties which extend outside of the group, and (3) leader centrality within the group. Based on well-tested theories of social capital and centrality in teams, propositions were formulated which suggest that social network structures associated with successful open source software project communities will exhibit high levels of bridging and moderate levels of closure and leader centrality. ^ The research setting was the SourceForge hosting organization and a study population of 143 project communities was identified. Independent variables included measures of closure and leader centrality defined over conversational ties, along with measures of bridging defined over membership ties. Dependent variables included source code commits and software releases for community output, and software downloads and project site page views for community activity. A cross-sectional study design was used and archival data were extracted and aggregated for the two-year period following the first release of project software. The resulting compiled variables were analyzed using multiple linear and quadratic regressions, controlling for group size and conversational volume. ^ Contrary to theory-based expectations, the surprising results showed that successful project groups exhibited low levels of closure and that the levels of bridging and leader centrality were not important factors of success. These findings suggest that the creation and use of open source software may represent a fundamentally new socio-technical development process which disrupts the team paradigm and which triggers the need for building new theories of collaborative development. These new theories could point towards the broader application of open source methods for the creation of knowledge-based products other than software. ^

The relationship between classroom interactions and exclusionary discipline as a social practice: A critical microethnograhy

Exclusionary school discipline results in students being removed from classrooms as a consequence of their disruptive behavior and may lead to subsequent suspension and/or expulsion. Literature documents that nondominant students, particularly Black males, are disproportionately impacted by exclusionary discipline, to the point that researchers from a variety of critical perspectives consider exclusionary school discipline an oppressive educational practice and condition. Little or no research examines specific teacher-student social interactions within classrooms that influence teachers’ decisions to use or not use exclusionary discipline. Therefore, this study set forth the central research question: In relation to classroom interactions in alternative education settings, what accounts for teachers’ use or non-use of exclusionary discipline with students? A critical social practice theory of learning served as the framework for exploring this question, and a critical microethnographic methodology informed the data collection and analysis. ^ Criterion sampling was used to select four classrooms in the same alternative education school with two teachers who frequently and two who rarely used exclusionary discipline. Nine stages of data collection and reconstructive data analysis were conducted. Data collection involved video recorded classroom observations, digitally recorded interviews of teachers and students discussing selected video segments, and individual teacher interviews. Reconstructive data analysis procedures involved hermeneutic inferencing of possible underlying meanings, critical discourse analysis, interactive power analysis and role analysis, thematic analysis of the interactions in each classroom, and a final comparative analysis of the four classrooms. ^ Four predominant themes of social interaction (resistance, conformism, accommodation, and negotiation) emerged with terminology adapted from Giroux’s (2001) theory of resistance in education and Third Space theory (Gutiérrez, 2008). Four types of power (normative, coercive, interactively established contracts, and charm), based on Carspecken’s (1996) typology, were found in the interactions between teacher and students in varying degrees for different purposes. ^ This research contributes to the knowledge base on teacher-student classroom interactions, specifically in relation to exclusionary discipline. Understanding how the themes and varying power relations influence their decisions and actions may enable teachers to reduce use of exclusionary discipline and remain focused on positive teacher-student academic interactions. ^

Social Network Structure as a Critical Success Condition for Open Source Software Project Communities

In recent years, a surprising new phenomenon has emerged in which globally-distributed online communities collaborate to create useful and sophisticated computer software. These open source software groups are comprised of generally unaffiliated individuals and organizations who work in a seemingly chaotic fashion and who participate on a voluntary basis without direct financial incentive. The purpose of this research is to investigate the relationship between the social network structure of these intriguing groups and their level of output and activity, where social network structure is defined as 1) closure or connectedness within the group, 2) bridging ties which extend outside of the group, and 3) leader centrality within the group. Based on well-tested theories of social capital and centrality in teams, propositions were formulated which suggest that social network structures associated with successful open source software project communities will exhibit high levels of bridging and moderate levels of closure and leader centrality. The research setting was the SourceForge hosting organization and a study population of 143 project communities was identified. Independent variables included measures of closure and leader centrality defined over conversational ties, along with measures of bridging defined over membership ties. Dependent variables included source code commits and software releases for community output, and software downloads and project site page views for community activity. A cross-sectional study design was used and archival data were extracted and aggregated for the two-year period following the first release of project software. The resulting compiled variables were analyzed using multiple linear and quadratic regressions, controlling for group size and conversational volume. Contrary to theory-based expectations, the surprising results showed that successful project groups exhibited low levels of closure and that the levels of bridging and leader centrality were not important factors of success. These findings suggest that the creation and use of open source software may represent a fundamentally new socio-technical development process which disrupts the team paradigm and which triggers the need for building new theories of collaborative development. These new theories could point towards the broader application of open source methods for the creation of knowledge-based products other than software.

The Relationship between Classroom Interactions and Exclusionary Discipline as a Social Practice: A Critical Microethnography

Exclusionary school discipline results in students being removed from classrooms as a consequence of their disruptive behavior and may lead to subsequent suspension and/or expulsion. Literature documents that nondominant students, particularly Black males, are disproportionately impacted by exclusionary discipline, to the point that researchers from a variety of critical perspectives consider exclusionary school discipline an oppressive educational practice and condition. Little or no research examines specific teacher-student social interactions within classrooms that influence teachers’ decisions to use or not use exclusionary discipline. Therefore, this study set forth the central research question: In relation to classroom interactions in alternative education settings, what accounts for teachers’ use or non-use of exclusionary discipline with students? A critical social practice theory of learning served as the framework for exploring this question, and a critical microethnographic methodology informed the data collection and analysis. Criterion sampling was used to select four classrooms in the same alternative education school with two teachers who frequently and two who rarely used exclusionary discipline. Nine stages of data collection and reconstructive data analysis were conducted. Data collection involved video recorded classroom observations, digitally recorded interviews of teachers and students discussing selected video segments, and individual teacher interviews. Reconstructive data analysis procedures involved hermeneutic inferencing of possible underlying meanings, critical discourse analysis, interactive power analysis and role analysis, thematic analysis of the interactions in each classroom, and a final comparative analysis of the four classrooms. Four predominant themes of social interaction (resistance, conformism, accommodation, and negotiation) emerged with terminology adapted from Giroux’s (2001) theory of resistance in education and Third Space theory (Gutiérrez, 2008). Four types of power (normative, coercive, interactively established contracts, and charm), based on Carspecken’s (1996) typology, were found in the interactions between teacher and students in varying degrees for different purposes. This research contributes to the knowledge base on teacher-student classroom interactions, specifically in relation to exclusionary discipline. Understanding how the themes and varying power relations influence their decisions and actions may enable teachers to reduce use of exclusionary discipline and remain focused on positive teacher-student academic interactions.

2003 Habitat Maps derived from Grey Nurse Shark (GNS) Project of Wolf Rock, Double Island Point, Queensland, Australia

Surveying habitats critical to the survival of grey nurse sharks in South-East Queensland has mapped critical habitats, gathered species inventories and developed protocols for ecological monitoring of critical habitats in southern Queensland. This information has assisted stakeholders with habitat definition and effective management. In 2002 members of UniDive applied successfully for World Wide Fund for Nature, Threatened Species Network funds to map the critical Grey Nurse Shark Habitats in south east Queensland. UniDive members used the funding to survey, from the boats of local dive operators, Wolf Rock at Double Island Point, Gotham, Cherub's Cave, Henderson's Rock and China Wall at North Moreton and Flat Rock at Point Look Out during 2002 and 2003. These sites are situated along the south east Queensland coast and are known to be key Grey Nurse Shark aggregation sites. During the project UniDive members were trained in mapping and survey techniques that include identification of fish, invertebrates and substrate types. Training was conducted by experts from the University of Queensland (Centre of Marine Studies, Biophysical Remote Sensing) and the Queensland Parks and Wildlife Service who are also UniDive members. The monitoring methods (see methods) are based upon results of the UniDive Coastcare project from 2002, the international established Reef Check program and research conducted by Biophysical Remote Sensing and the Centre of Marine Studies. Habitats were mapped using a combination of towed GPS photo transects, aerial photography, bathymetry surveys and expert knowledge. This data provides georeferenced information regarding the major features of each of Sites mapped including Wolf Rock

"Sub Tiberio quies"? Judaea’s Political Situation under the Prefects (6-41 c.e.), between Reality and Ideology

Deeply conflicting views on the political situation of Judaea under the Roman prefects (6-41 c.e.) have been offered. According to some scholars, this was a period of persistent political unrest and agitation, whilst according to a widespread view it was a quiescent period of political calm (reflected in Tacitus’ phrase sub Tiberio quies). The present article critically examines again the main available sources –particularly Josephus, the canonical Gospels and Tacitus– in order to offer a more reliable historical reconstruction. The conclusions drawn by this survey calls into question some widespread and insufficiently nuanced views on the period. This, in turn, allows a reflection on the non-epistemic factors which might contribute to explain the origin of such views.

Plato’s Parmenides and understanding the One in the philosophy of Plotinus: an oversight by Heidegger?

The present article focuses on the study of the exegesis by Plotinus with regard to the meaning of the ineffability of the one provided in Plato’s Parmenides in the first hypothesis. He places this first ineffable one at the very centre of his system, which would have important implications from both an ontological point of view and with regard to understanding the language. The conception of reality that derives from the ineffability of the first principle and the implications for the nature of philosophical language that this postulate raises will be the centre of our reflections. To shed light on the position set down in the Enneads, we will review the key points based on the original texts that deal with this issue and related critical works. We will also look at the contemporary relevance of this position and its ability to go beyond the Heideggerian critique of metaphysics.

The perception of the African-American community through the eyes of the Hispanic media in the U.S.: a critical discourse analysis of the reporting of the death of Michael Brown

In this paper, 36 English and 38 Spanish news articles were selected from English and Spanish newspapers and magazines published in the U.S.A. from August 2014 to November 2014. All articles discuss the death of Michael Brown, the ensuing protests and police investigations. A discourse analysis shows that there are few differences between reporting by the mainstream and the Hispanic media. Like the mainstream media, the Hispanic media adopts a neutral point of view with regard to the African-American minority. However, it presents a negative opinion with regard to the police. It appears that the Hispanic media does not explicitly side with the African-American community, but rather agrees more with the mainstream media’s opinion and is substantially influenced by it.

What is the Point of Copyright History?:Reflections on Copyright at Common law in 1774 by H. Tomás Gómez-Arostegui

Copyright history has long been a subject of intense and contested enquiry. Historical narratives about the early development of copyright were first prominently mobilised in eighteenth century British legal discourse, during the so-called Battle of the Booksellers between Scottish and London publishers. The two landmark copyright decisions of that time – Millar v. Taylor (1769) and Donaldson v. Becket (1774) – continue to provoke debate today. The orthodox reading of Millar and Donaldson presents copyright as a natural proprietary right at common law inherent in authors. Revisionist accounts dispute that traditional analysis. These conflicting perspectives have, once again, become the subject of critical scrutiny with the publication of Copyright at Common Law in 1774 by Prof Tomas Gomez-Arostegui in 2014, in the Connecticut Law Review ((2014) 47 Conn. L. Rev. 1) and as a CREATe Working Paper (No. 2014/16, 3 November 2014).

Taking Prof Gomez-Arostegui’s extraordinary work in this area as a point of departure, Dr Elena Cooper and Professor Ronan Deazley (then both academics at CREATe) organised an event, held at the University of Glasgow on 26th and 27th March 2015, to consider the interplay between copyright history and contemporary copyright policy. Is Donaldson still relevant, and, if so, why? What justificatory goals are served by historical investigation, and what might be learned from the history of the history of copyright? Does the study of copyright history still have any currency within an evidence-based policy context that is increasingly preoccupied with economic impact analysis?

This paper provides a lasting record of these discussions, including an editorial introduction, written comments by each of the panelists and Prof. Gomez-Arostegui and an edited transcript of the Symposium debate.

What is the Point of Copyright History?

Copyright history has long been a subject of intense and contested enquiry, and has once again become the subject of critical scrutiny with the publication of "Copyright at Common Law in 1774" by Prof Tomas Gomez-Arostegui in the Connecticut Law Review ((2014) 47 Conn. L. Rev. 1).
This online resource documents two events organised to explore the impact of "Copyright at Common Law in 1774". It incorporates a public lecture by Prof Gomez-Arostegui, and the full record of a one-day symposium of international experts debating the implications of Gomez-Arostegui's scholarship in this domain.

Ultrasound in undergraduate medical education: A systematic and critical review

Introduction: Point-of-care ultrasound (POCUS) use in clinical care is growing rapidly, and advocates have recently proposed the integration of ultrasound into undergraduate medical education (UME). The evidentiary basis for this integration has not been evaluated critically or systematically. In this study, we conducted a critical and systematic review framed by the rationales enumerated by advocates of ultrasound in UME in academic publications.

Methods: This research was conducted in two phases. First, the dominant discursive rationales for the integration of ultrasound in UME were identified using techniques from Foucauldian critical discourse analysis (CDA) from an archive of 403 academic publications. We then sought empirical evidence in support of theses rationales, using a critical synthesis methodology also adapted from CDA.

Results: We identified four dominant discursive rationales, with different levels of evidentiary support. Ultrasound was not demonstrated to improve students’ understanding of anatomy. The benefit of ultrasound in teaching physical examination was inconsistent,and rests on minimal evidence. With POCUS, students’ diagnostic accuracy was improved for certain pathologies, but findings were inconsistent for others. Finally, the rationale that ultrasound training in UME will improve quality of patient care was difficult to evaluate.

Discussion: Our analysis has shown that the frequently repeated rationales for the integration of ultrasound in UME are not supported by a sufficient base of empirical research. The repetition of these dominant discursive rationales in academic publications legitimizes them and may preclude further primary research. Since the value of clinical ultrasound use by medical students remains unproven, educators must consider whether the associated financial and temporal costs are justified or whether more research is required.

Exploring critical literacy in Swedish education : Introductory notes

This article is an introductory note to The thematic section in this issue of Education Inquiry has its background in the need for research interpreting literacy from a critical perspective. Teaching literacy is not solely about technical reading skills but is also about understanding and the making of meaning. From that point of view, teaching must also consider the use of language, the context within which language is used, and issues of power. The thematic section includes five articles about critical literacy in Swedish education. The contributions were developed after a workshop conducted by Professor Hilary Janks, University of the Witwatersrand, Johannesburg. She introduces the framework of a critical literacy theory in the first article of the issue. Further, the contributions of Swedish scholars are united in their interest in applying a mode of critical literacy designed by Janks to different practices, sites and speech-events, for example policy documents, home reading, teaching and learning practices. The articles offer a wide perspective of critical literacy in education and further understanding of the complex processes in teaching.

Power relations and good governance: a social network analysis of the evolution of the integrity in public office act in the Commonwealth of Dominica

La Banque mondiale propose la bonne gouvernance comme la stratégie visant à corriger les maux de la mauvaise gouvernance et de faciliter le développement dans les pays en développement (Carayannis, Pirzadeh, Popescu & 2012; & Hilyard Wilks 1998; Leftwich 1993; Banque mondiale, 1989). Dans cette perspective, la réforme institutionnelle et une arène de la politique publique plus inclusive sont deux stratégies critiques qui visent à établir la bonne gouvernance, selon la Banque et d’autres institutions de Bretton Woods. Le problème, c’est que beaucoup de ces pays en voie de développement ne possèdent pas l’architecture institutionnelle préalable à ces nouvelles mesures. Cette thèse étudie et explique comment un état en voie de développement, le Commonwealth de la Dominique, s’est lancé dans un projet de loi visant l’intégrité dans la fonction publique. Cette loi, la Loi sur l’intégrité dans la fonction publique (IPO) a été adoptée en 2003 et mis en œuvre en 2008. Cette thèse analyse les relations de pouvoir entre les acteurs dominants autour de évolution de la loi et donc, elle emploie une combinaison de technique de l’analyse des réseaux sociaux et de la recherche qualitative pour répondre à la question principale: Pourquoi l’État a-t-il développé et mis en œuvre la conception actuelle de la IPO (2003)? Cette question est d’autant plus significative quand nous considérons que contrairement à la recherche existante sur le sujet, l’IPO dominiquaise diverge considérablement dans la structure du l’IPO type idéal. Nous affirmons que les acteurs "rationnels," conscients de leur position structurelle dans un réseau d’acteurs, ont utilisé leurs ressources de pouvoir pour façonner l’institution afin qu’elle serve leurs intérêts et ceux et leurs alliés. De plus, nous émettons l’hypothèse que: d’abord, le choix d’une agence spécialisée contre la corruption et la conception ultérieure de cette institution reflètent les préférences des acteurs dominants qui ont participé à la création de ladite institution et la seconde, notre hypothèse rivale, les caractéristiques des modèles alternatifs d’institutions de l’intégrité publique sont celles des acteurs non dominants. Nos résultats sont mitigés. Le jeu de pouvoir a été limité à un petit groupe d’acteurs dominants qui ont cherché à utiliser la création de la loi pour assurer leur légitimité et la survie politique. Sans surprise, aucun acteur n’a avancé un modèle alternatif. Nous avons conclu donc que la loi est la conséquence d’un jeu de pouvoir partisan. Cette recherche répond à la pénurie de recherche sur la conception des institutions de l’intégrité publique, qui semblent privilégier en grande partie un biais organisationnel et structurel. De plus, en étudiant le sujet du point de vue des relations de pouvoir (le pouvoir, lui-même, vu sous l’angle actanciel et structurel), la thèse apporte de la rigueur conceptuelle, méthodologique, et analytique au discours sur la création de ces institutions par l’étude de leur genèse des perspectives tant actancielles que structurelles. En outre, les résultats renforcent notre capacité de prédire quand et avec quelle intensité un acteur déploierait ses ressources de pouvoir.