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.

Exploring care relations in later life: disentangling notions of care and choice

The experience of later life varies widely and is often framed in terms of the active lifestyles of the Third Age and the frailty and abjection of the Fourth Age. This thesis sought to understand how the concepts of care and choice are enacted, experienced and interrelated in the context of both informal and formal care in later life and how older people themselves, their families and significant others understand and experience these concepts. The discourse of personalisation that dominates care services has led to an emphasis on individual choice, control and independence so that those in need of care are faced with what has been described as the ‘logic of choice’, a focus on individual responsibility rather than care. Adopting a Feminist Foucauldian theoretical approach and drawing on Tronto’s (1993) ethic of care, this thesis explores the experiences of older people and their informal carers through dialogical narrative analysis. The stories begin with the recognition by individuals that there is a need for care and how this need is met through negotiations with families and significant others. As needs increase the physical and logistical limits of informal care by individuals are reached, often leading to a need to ‘choose’ formal care. Rather than impacting solely on the care recipient, formal care is shown as being an experience that is shared with informal carers. Indeed, the participants depict how informal care continues alongside formal care and how the boundaries between them become blurred. I argue that a binary division between actively making choices and being a passive recipient are not appropriate to understandings of care. By disentangling the notions of care and choice this thesis explores the extent to which these concepts are relevant to the experience of older people in specific care situations.

Co-ordination and public administration in a global economy — A Hungarian point of view

The purpose of social co-ordination mechanisms is to co-ordinate the activities of individuals and organisations specialised in the distribution of work. The paper reviews five basic types of mechanisms: market, bureaucratic, ethical, aggressive and co-operative co-ordination. Today’s world operates on the basis of a duality: international cooperation is based on nation states, in which the public administrations work according to bureaucratic coordination. However, the increasingly globalised market responds to the logic of market coordination. The article argues that in terms of understanding the working of public administration, the various coordination mechanisms are of crucial importance, especially where various mechanisms meet, such as the relationship between nation states and multinational corporations.

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.

Tanulás és innováció – Elméleti dilemmák és gyakorlati nézőpontok (Learning and innovation – Theoretical dilemmas and practical point of views)

A tanulmány egy nemrég lezárt TÁMOP-kutatás keretébe illeszkedik.1 A kutatás célja, hogy átfogó képet nyújtson az innovációról, tisztázza az innovációval kapcsolatos fogalmakat, bemutassa az innovációs trendeket és – egy empirikus felmérés nyomán – számot adjon arról, hogy ezek hogyan jelentkeznek Magyarország sajátos viszonyai között. Az innovációs fogalomkör megvilágításához hozzátartozik a tanulás és az innováció kapcsolatának tisztázása. Bár a témáról a menedzsment-szakirodalomban számtalan mű jelenik meg, a szerző saját diszciplináris elkötelezettségének megfelelően közgazdasági nézőpontból igyekszik megközelíteni a problémakört. Végül megkísérli Magyarországot elhelyezni a tanulás nemzetközi térképén. _______ This research aims to provide a comprehensive view on innovation, to clarify innovation concepts, to present innovation trends, and – based on an empirical survey – to give an account about how they appear specific conditions of Hungary. The refining of innovation category includes clarification of the relationship between learning and innovation. While many works have been published in this topic of management literature, the author in accordance his own disciplinary engagement tries to approach the problem area from economic point of view. Finally he attempts to place Hungary on the international map of learning.

A felsőoktatási képzések munkaerő-piaci szempontból (Higher education programs from point of view of labor market)

A munkaerő-piaci követelményeknek megfelelően kialakított képzések versenyképesebbek a társaiknál. A napjainkban is zajló magyar felsőoktatási reform központi elemét alkotja a képzések ennek megfelelően történő átalakítása. Mindez létjogosultságot ad egy olyan rendszernek, amely a Budapesti Corvinus Egyetem gazdaságinformatikus BSc-képzésének kompetenciaelemeit kívánja vizsgálni az állásajánlatokban megnyilvánuló munkaerő-piaci igények tükrében. Az ontológiaalapú módszertan egy egységes fogalmi kört biztosít a munkaerőpiac eltérő szemléletű oldalán kifejlesztett modellek egységesítésére és összehasonlítására. ____ Tendencies can be observed on international and domestic levels that call for restructuring of higher education according to the needs of labor market. This paper presents an information system that can investigate the compliance of education programs and current labor market needs. Competences serve as a basis for this compliance checking, which is built on ontologybased approach. Having examined the distribution of roles (developer, operator etc.) appeared in IT job offers in time and space, a prototype of this system will be showed, related to Business Informatics degree program at Corvinus University of Budapest.

The Butler wears Prada. A Hungarian case-study based on the analysis of the uniform and hotel industry from the point of sustainability

What is the connection between the hotel and fashion industry? The authors aim to answer this question approaching from different aspects. It can be stated that both of these industries are harmful for the environment from the point of sustainability. On the other hand there is a common solution from the viewpoint of sustainability: the uniforms and the primary materials, which are used during the production, such as the man-made and natural fibres. In our research the authors introduce the main problems which are related to the fashion industry, especially focusing on producing fibres from the viewpoint of sustainability. We introduce the solution for the fashion industry based on the literature and also present the emerging problems and solutions of the hotel industry based on the best practices. As a part of it, we are introducing the best practices from the hotel industry, where environmentally friendly uniforms are used. Finally, as a primary research part of our paper, we interpret the results of a Hungarian case-study.

The impact of selected factors in nurses' attitudes toward bedside computers

The purpose of this study was to determine the impact of selected factors on nurses' attitudes toward bedside computers. Bedside computer systems, also referred to as point-of-care systems, are clinical information systems that allow documentation of patient care and retrieval of data at the patient's bedside, or in close proximity to where care is delivered. The adoption of bedside computer systems appears to be increasing among U.S. institutions. As healthcare institutions undertake automation projects, they face many challenges associated with implementing large-scale change. ^ The study explored four factors and their relationship to nurses' attitudes toward bedside computers. A pre-bedside implementation survey of 184 staff nurses did not demonstrate a relationship between previous computer experience and nurses' attitudes toward bedside computers (p > .05). The data did not indicate a relationship between nurses' formal education and their attitude toward bedside computers (p > .05). The data did support a relationship between nurses' previous computer experience and their comfort in the use of bedside computers (p < .0005). Using a quasi-experimental control group design, attitudes of nurses were studied over an 18 month period. The Pre versus Post Survey data indicated that nurses who used bedside computers, the experimental group, had more positive attitudes than the nurses who did not use bedside computers, the control group (p < .0005). ^ The findings are significant to institutions implementing bedside computers, to the human resource development staff overseeing bedside computer training, and to the practice of clinical nursing. ^

Think before you eat: Calories and exercise equivalents presented on menus at point-of-choice

Although calorie information at the point-of-purchase at fast food restaurants is proposed as a method to decrease calorie choices and combat obesity, research results have been mixed. Much of the supportive research has weak methodology, and is limited. There is a demonstrated need to develop better techniques to assist consumers to make lower calorie food choices. Eating at fast food restaurants has been positively associated with weight gain. The current study explored the possibility of adding exercise equivalents (EE) (physical activity required to burn off the calories in the food), along with calorie information as a possible way to facilitate lower calorie choice at the point-of-choice in fast food restaurants. This three-group experimental study, in 18-34 year old, overweight and obese women, examines whether presenting caloric information in the form of EE at the point-of-choice at fast food restaurants, will lead to lower calorie food choices compared to presenting simple caloric information or no information at all. Methods. A randomized repeated measures experiment was conducted. Participants ordered a fast food meal from Burger King with menus that contained only the names of the food choices (Lunch 1). One week later (Lunch 2), study participants were given one of three menus that varied: no information, calorie information, or calorie information and EE. Study participants included 62 college aged students. Additionally, the study controlled for dietary restraint by blocking participants, before randomization, to the three groups. Results. A repeated measures analysis of variance was conducted. The study was not sufficiently powered, and while the study was designed to determine large effect sizes, a small effect size of .026, was determined. No significant differences were found in the foods ordered among the various menu conditions. Conclusion. Menu labeling alone might not be enough to reduce calories at the point-of-choice at restaurants. Additional research is necessary to determine if calorie information and EE at the point-of-choice would lead to fewer calories chosen at a meal. Studies should also look at long-term, repeated exposure to determine the effectiveness of calories and or EE at the point-of-choice at fast food restaurants.

The effects of the ethic of care in an all-boys school from 1903 to 1974

Nel Noddings’ 1984 publication, Caring: A Feminine Approach to Ethics and Moral Education was the first formal introduction of the concept of an “ethic of care”. It is a concept that stresses the importance of compassion in any relationship. For the purpose of this dissertation, the ethic of care was studied in a specific educational community. ^ This research focused on the role of care ethics in a secondary school (The Ransom School for Boys) from 1903 to 1974. The researcher identified this school as one that operated with an ethic of care and collected and analyzed data from historical school documents as well as from 60–90 minute individual interviews with six alumni, five retired faculty, and two administrators. ^ The case study addressed how students and faculty experienced care ethics within the school and how it has been maintained throughout the adult lives of alumni. An a priori coding rubric was used to examine the presence of care ethics at the Ransom School for Boys and in the adult lives of its alumni. This rubric was generated using information taken from the literature review and encompasses 36 different words to identify the presence of care ethics. ^ The primary research question was: How have alumni incorporated care ethics into their personal and professional lives? Secondary questions included: (1) How did the ethic of care present itself over the span of 71 years? (2) Was character education part of the formal curriculum at the Ransom School? (3) Was character education part of the hidden curriculum at the Ransom School? (4) Did the presence of care ethics support the values being taught in the home? ^ While there has been research done on the importance of care ethics in an educational institution, the research is void of direct evidence associated with care ethics in a school community, specifically, an all-boys, private school. Through deductive analysis, care ethics was found to be present and utilized at the school. The interviews and historical documents suggested that moral education was an integral part of the informal curriculum and helped to integrate the ethic of care within the community.^

Effect of child care subsidies on price and quality of care for low -income families

This dissertation examines the effect of regulations, resource and referral agencies, and subsidies on price and quality of care in child care centers. This research is based on a carefully developed conceptual framework that incorporates the factors affecting the demand and supply of child care. The first step in developing this framework is sketching out the structural equations. The structural equations help us understand the underlying behavior of individuals and firms making a decision. The exogenous variables are vector of attributes relating to family characteristics, child characteristics, regulations, subsidy, community characteristics and prices of inputs. Based on the structural equations, reduced form equations are estimated to find the effect of each of the exogenous variables on each of the endogenous variables. Reduced form equations help us answer public policy questions. The sample for this study is from the 1990 Profile of Child Care Settings (PCCS) data in which 2,089 center based programs were interviewed.^ Child/Staff Ratio (Group Level). Results indicate that among subsidies, only the state subsidy per child in poverty has a significant effect on the child/staff ratio at the group level. Presence of resource and referral agencies also increase the child/staff ratio at the group level. Also when the maximum center group size regulation for 25-36 months becomes more stringent, the child/staff ratio at the group level decreases.^ Child/Staff Ratio (Center Level). When the regulations for the maximum child/staff ratio for age groups 13-24 months and 37-60 months become lax, the child/staff ratio for the center increases. As the regulation for maximum group size for infants becomes stringent, the child/staff ratio decreases. An interesting finding is that as the regulations for maximum group size for age groups 13-24 months and 25-36 months become stringent, the child/staff ratio for the center increases. Another significant finding is that when a center is located in a rural area the child/staff ratio is significantly lower.^ Center Weighted Average Hourly Fees. Maximum group size regulations for age groups 25-36 months and 37-60 months have a negative effect on center hourly fee. Maximum child staff regulations for age groups 13-24 months and 37-60 months have a negative effect on center hourly fee. Maximum child staff regulations for age groups 0-12 months and 25-36 months have a positive effect on center hourly fee. Findings also indicate that the center average hourly price is lower when there is a resource and referral agency present. Cost adjusted prekindergarten funds and JOBS child care subsidies have a negative effect on average hourly fee. Cost adjusted social services block grant and state subsidy per child in poverty have a positive effect on the average hourly price. A major finding of this dissertation is the interaction of subsidy and regulatory variables.^ Another major finding is that child/staff ratio at the group level is lower when there is an interaction between geographic location and nature of center sponsorship. ^

Think Before You Eat: Calories and Exercise Equivalents Presented on Menus at Point-of-Choice

Although calorie information at the point-of-purchase at fast food restaurants is proposed as a method to decrease calorie choices and combat obesity, research results have been mixed. Much of the supportive research has weak methodology, and is limited. There is a demonstrated need to develop better techniques to assist consumers to make lower calorie food choices. Eating at fast food restaurants has been positively associated with weight gain. The current study explored the possibility of adding exercise equivalents (EE) (physical activity required to burn off the calories in the food), along with calorie information as a possible way to facilitate lower calorie choice at the point-of-choice in fast food restaurants. This three-group experimental study, in 18-34 year old, overweight and obese women, examines whether presenting caloric information in the form of EE at the point-of-choice at fast food restaurants, will lead to lower calorie food choices compared to presenting simple caloric information or no information at all. Methods: A randomized repeated measures experiment was conducted. Participants ordered a fast food meal from Burger King with menus that contained only the names of the food choices (Lunch 1). One week later (Lunch 2), study participants were given one of three menus that varied: no information, calorie information, or calorie information and EE. Study participants included 62 college aged students. Additionally, the study controlled for dietary restraint by blocking participants, before randomization, to the three groups. Results: A repeated measures analysis of variance was conducted. The study was not sufficiently powered, and while the study was designed to determine large effect sizes, a small effect size of .026, was determined. No significant differences were found in the foods ordered among the various menu conditions. Conclusion: Menu labeling alone might not be enough to reduce calories at the point-of-choice at restaurants. Additional research is necessary to determine if calorie information and EE at the point-of-choice would lead to fewer calories chosen at a meal. Studies should also look at long-term, repeated exposure to determine the effectiveness of calories and or EE at the point-of-choice at fast food restaurants.

Effect of child care subsidies on price and quality of care for low -income families

This dissertation examines the effect of regulations, resource and referral agencies, and subsidies on price and quality of care in child care centers. This research is based on a carefully developed conceptual framework that incorporates the factors affecting the demand and supply of child care. The first step in developing this framework is sketching out the structural equations. The structural equations help us understand the underlying behavior of individuals and firms making a decision. The exogenous variables are vector of attributes relating to family characteristics, child characteristics, regulations, subsidy, community characteristics and prices of inputs. Based on the structural equations, reduced form equations are estimated to find the effect of each of the exogenous variables on each of the endogenous variables. Reduced form equations help us answer public policy questions. The sample for this study is from the 1990 Profile of Child Care Settings (PCCS) data in which 2,089 center based programs were interviewed. Child/Staff Ratio (Group Level): Results indicate that among subsidies, only the state subsidy per child in poverty has a significant effect on the child/staff ratio at the group level. Presence of resource and referral agencies also increase the child/staff ratio at the group level. Also when the maximum center group size regulation for 25-36 months becomes more stringent, the child/staff ratio at the group level decreases. Child/Staff Ratio (Center Level): When the regulations for the maximum child/staff ratio for age groups 13-24 months and 37-60 months become lax, the child/staff ratio for the center increases. As the regulation for maximum group size for infants becomes stringent, the child/staff ratio decreases. An interesting finding is that as the regulations for maximum group size for age groups 13-24 months and 25-36 months become stringent, the child/staff ratio for the center increases. Another significant finding is that when a center is located in a rural area the child/staff ratio is significantly lower. Center Weighted Average Hourly Fees: Maximum group size regulations for age groups 25-36 months and 37-60 months have a negative effect on center hourly fee. Maximum child staff regulations for age groups 13-24 months and 37-60 months have a negative effect on center hourly fee. Maximum child staff regulations for age groups 0-12 months and 25-36 months have a positive effect on center hourly fee. Findings also indicate that the center average hourly price is lower when there is a resource and referral agency present. Cost adjusted prekindergarten funds and JOBS child care subsidies have a negative effect on average hourly fee. Cost adjusted social services block grant and state subsidy per child in poverty have a positive effect on the average hourly price. A major finding of this dissertation is the interaction of subsidy and regulatory variables. Another major finding is that child/staff ratio at the group level is lower when there is an interaction between geographic location and nature of center sponsorship.

22 years of Predictive Testing for Huntington’s Disease : The Experience of the UK Huntington’s Prediction Consortium

Peer reviewed