MCL-CAw: A refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure

Abstract Background The reconstruction of protein complexes from the physical interactome of organisms serves as a building block towards understanding the higher level organization of the cell. Over the past few years, several independent high-throughput experiments have helped to catalogue enormous amount of physical protein interaction data from organisms such as yeast. However, these individual datasets show lack of correlation with each other and also contain substantial number of false positives (noise). Over these years, several affinity scoring schemes have also been devised to improve the qualities of these datasets. Therefore, the challenge now is to detect meaningful as well as novel complexes from protein interaction (PPI) networks derived by combining datasets from multiple sources and by making use of these affinity scoring schemes. In the attempt towards tackling this challenge, the Markov Clustering algorithm (MCL) has proved to be a popular and reasonably successful method, mainly due to its scalability, robustness, and ability to work on scored (weighted) networks. However, MCL produces many noisy clusters, which either do not match known complexes or have additional proteins that reduce the accuracies of correctly predicted complexes. Results Inspired by recent experimental observations by Gavin and colleagues on the modularity structure in yeast complexes and the distinctive properties of "core" and "attachment" proteins, we develop a core-attachment based refinement method coupled to MCL for reconstruction of yeast complexes from scored (weighted) PPI networks. We combine physical interactions from two recent "pull-down" experiments to generate an unscored PPI network. We then score this network using available affinity scoring schemes to generate multiple scored PPI networks. The evaluation of our method (called MCL-CAw) on these networks shows that: (i) MCL-CAw derives larger number of yeast complexes and with better accuracies than MCL, particularly in the presence of natural noise; (ii) Affinity scoring can effectively reduce the impact of noise on MCL-CAw and thereby improve the quality (precision and recall) of its predicted complexes; (iii) MCL-CAw responds well to most available scoring schemes. We discuss several instances where MCL-CAw was successful in deriving meaningful complexes, and where it missed a few proteins or whole complexes due to affinity scoring of the networks. We compare MCL-CAw with several recent complex detection algorithms on unscored and scored networks, and assess the relative performance of the algorithms on these networks. Further, we study the impact of augmenting physical datasets with computationally inferred interactions for complex detection. Finally, we analyse the essentiality of proteins within predicted complexes to understand a possible correlation between protein essentiality and their ability to form complexes. Conclusions We demonstrate that core-attachment based refinement in MCL-CAw improves the predictions of MCL on yeast PPI networks. We show that affinity scoring improves the performance of MCL-CAw.http://deepblue.lib.umich.edu/bitstream/2027.42/78256/1/1471-2105-11-504.xmlhttp://deepblue.lib.umich.edu/bitstream/2027.42/78256/2/1471-2105-11-504-S1.PDFhttp://deepblue.lib.umich.edu/bitstream/2027.42/78256/3/1471-2105-11-504-S2.ZIPhttp://deepblue.lib.umich.edu/bitstream/2027.42/78256/4/1471-2105-11-504.pdfPeer Reviewe

Efecto de la fecha de siembra, el genotipo y la fertilidad sobre el llenado del grano de trigo pan (Triticum aestivum L.) en la región semiárida pampeana

Los componentes importantes en la determinación del peso final de los granos en los cereales son la tasa y la duración del llenado. La primera de ellas indica cuanta materia seca se deposita en los granos en crecimiento por unidad de tiempo y la otra, la cantidad de días entre floración y madurez fisiológica. Las condiciones ambientales modifican estas variables por separado, la relación entre ambas y su relación con el rendimiento de grano. En el siguiente trabajo se planteó que un atraso en la fecha de siembra provocará una disminución de la duración y un aumento de la tasa de llenado de los granos de los distintos genotipos de trigo. Además, la fertilización aumentaría la duración y disminuiría la tasa de llenado de los granos. Se sembraron 4 genotipos de trigo pan, todos ellos de ciclo semejante, provenientes de distintos criaderos. Se incorporó un tratamiento de fertilidad (fertilizado y testigo). Se tomaron muestras de 5 espigas de cada tratamiento en 8 fechas de muestreo, realizándose una por semana desde el comienzo del llenado de los granos. Se observaron diferencias altamente significativas en cuanto al genotipo, la fertilidad y además hubo interacción entre las variables. En la Región Semiárida Pampeana el atraso de la fecha de siembra provocó una disminución de la duración del llenado de los granos, sin una clara tendencia en el comportamiento de la tasa de llenado. Es así, que en el tratamiento testigo en la segunda época mostró una mayor tasa de llenado que la primera tal como se planteó en la hipótesis. Por el contrario, en el tratamiento fertilizado la tasa disminuyó en la segunda época exceptuando una variedad. El agregado de fertilizante hizo disminuir el porcentaje de panza blanca, factor importante en la comercialización, mientras que el peso hectolítrico de todos los tratamientos lograron un valor adecuado para la comercialización

Maintenance Plan for 1956 Vintage Storage Tank Facility

In early 1997, Lakehead Pipe Line Company, Inc. (LPL) purchased the Hartsdale Terminal to better serve customers in the Chicago area by providing additional crude oil storage facilities. This terminal is located adjacent to Lakehead’s Griffith, Indiana Terminal and consists of nine crude oil tanks totaling 900,000 barrels of storage capacity. All nine of the Hartsdale tanks were constructed in 1956, are 134 ft. in diameter, and are open top with double deck style floaters. This report describes the integrity analysis of the facility and the corresponding maintenance plan that was developed. The analysis portion of this report describes the inspections that were done on the tanks, covering aspects such as weld spacing; tank settlement; interior and exterior coating failure; tank shell, bottom, and pontoon corrosion; seal wear and performance; roof drain integrity; and other OSHA and API mandates. The resulting maintenance plan is approximately a five-year window and is currently in its first year. The five-year duration was based on issues both operational and financial. A portion of the discussion is focused on the challenge of combining these two components into an overall comprehensive plan. In addition, aspects affecting the maintenance plan such as risk assessment, OSHA and API standards, and budgeting issues are described.</jats:p

Efecto de la fecha de siembra, el genotipo y la fertilidad sobre el llenado del grano de trigo pan (Triticum aestivum L.) en la región semiárida pampeana

Los componentes importantes en la determinación del peso final de los granos en los cereales son la tasa y la duración del llenado. La primera de ellas indica cuanta materia seca se deposita en los granos en crecimiento por unidad de tiempo y la otra, la cantidad de días entre floración y madurez fisiológica. Las condiciones ambientales modifican estas variables por separado, la relación entre ambas y su relación con el rendimiento de grano. En el siguiente trabajo se planteó que un atraso en la fecha de siembra provocará una disminución de la duración y un aumento de la tasa de llenado de los granos de los distintos genotipos de trigo. Además, la fertilización aumentaría la duración y disminuiría la tasa de llenado de los granos. Se sembraron 4 genotipos de trigo pan, todos ellos de ciclo semejante, provenientes de distintos criaderos. Se incorporó un tratamiento de fertilidad (fertilizado y testigo). Se tomaron muestras de 5 espigas de cada tratamiento en 8 fechas de muestreo, realizándose una por semana desde el comienzo del llenado de los granos. Se observaron diferencias altamente significativas en cuanto al genotipo, la fertilidad y además hubo interacción entre las variables. En la Región Semiárida Pampeana el atraso de la fecha de siembra provocó una disminución de la duración del llenado de los granos, sin una clara tendencia en el comportamiento de la tasa de llenado. Es así, que en el tratamiento testigo en la segunda época mostró una mayor tasa de llenado que la primera tal como se planteó en la hipótesis. Por el contrario, en el tratamiento fertilizado la tasa disminuyó en la segunda época exceptuando una variedad. El agregado de fertilizante hizo disminuir el porcentaje de panza blanca, factor importante en la comercialización, mientras que el peso hectolítrico de todos los tratamientos lograron un valor adecuado para la comercialización

Cross-cultural ageism: ageism and attitudes toward aging among Jews and Arabs in Israel

ABSTRACTBackground: While it is generally agreed that traditional societies are more favorable toward their elders, research findings have been inconsistent. Accordingly, this study presents a cultural comparison between Jews and Arabs in Israel in attitudes toward older adults and personal views regarding one's own aging. It was assumed that Arabs would rate their culture as more tolerant toward older adults, would report spending more time with them, and express lower ageism and aging anxieties.Method: We examined 154 native Israeli citizens, 86 Jewish and 68 Muslim Arabs, who completed measures of ageism, aging anxieties, and cultural views of older adults.Results: Arabs rated their culture as more tolerant toward their elders, perceived older adults as significantly more contributing to society, and reported engaging in less avoiding behaviors toward them. Arabs also exhibited less general fears of growing old and concerns over one's physical appearance in old age. But it was interesting to note that Arab women reported higher scores of aging anxieties and ageist attitudes in comparison to Arab men, whereas no such differences were found among Jews.Conclusions: Our findings point that the cultural importance of elders for the Arab cohort transcends beyond Westernization processes which affect the Arab society in Israel, and reflect the demanding role of Arab women as primary caregivers for the elders in the family. Limitations and implications of the study are discussed.</jats:p

Perceived quality of life and ageism among elderly people living in sheltered housing and in the community

IntroductionAlthough there are studies on ageist attitudes and perceptions of quality of life (QoL) among elderly people, no publications exist that compare ageist attitudes and QoL perceptions among elderly people who live in private sector sheltered housing (PRSSH) and in the community.ObjectivesTo map the differences and understand the relations between QoL and negative social perceptions of one’s own age group among older adults, living in PRSSH and in the community.Aims(1) To examine if there are differences in ageist attitudes and perceptions of quality of life (QoL), and(2) to understand the role of QoL in explaining ageist attitudes among these two groups of elderly people.MethodsThe sample included 126 participants, aged 64–94, who live in PRSSH or in the community. The participants completed Fraboni et al. scale of ageism, a QoL inventory (SF-36 inventory), which provides scores on measures such as physical functioning, mental health and social functioning, and answered demographic questions.ResultsMultivariate analyses of covariance (MANCOVA) partially supported our hypotheses that elderly people who live in PRSSH will demonstrate more ageist attitudes towards people of their own age, and report a lower QoL than elderly people who live in the community.Gender also had a distinctive effect on ageism and QoL among individuals in PRSSH. These findings were supported by regression analyses.ConclusionsAlthough PRSSH may offer luxurious living conditions, the current study shows that living in an age segregated environment, may trigger negative self-perceptions of old age and decrease QoL.</jats:sec

Staff attitudes towards patients with borderline personality disorder

IntroductionBDP is a common diagnosis in hospitals and community settings, estimated at 20% and 11%, respectively. Nevertheless, the attitudes and skills of all mental health professionals regarding the treatment of these patients had hardly been studied.ObjectivesDevelop tools and use them to understand staff attitudes towards BDP patients.Aims(1)To develop two inventories for the measurement of cognitive and emotional attitudes towards borderline personality disorder (BPD) patients and their treatment;(2)To use these tools to understand and compare attitudes of psychiatrists, psychologists and nurses toward BPD patients.MethodTwo lists of items referring to cognitive and emotional attitudes towards BPD patients were formulated. Nurses, psychologists and psychiatrist (n = 57), working in public psychiatric institutions rated their level of agreement with each item. Both lists of attitudes yielded three factors (cognitive: required treatment, suicidal tendencies, and antagonistic judgment, and emotional: negative emotions, experienced difficulties in treatment, and empathy, respectively).ResultsPsychologists scored lower than psychiatrists and nurses on antagonistic judgments. Nurses scored lower than psychiatrists and psychologists on empathy. Regression stepwise analyses on the three emotional attitudes separately showed that suicidal tendencies of BPD patients mainly explained negative emotions and difficulties in treating these patients. All groups were interested in learning more about the treatment of these patients.ConclusionsSuicidal tendencies of BPD patients provoke antagonistic judgments among the three professions. Psychiatrists, psychologists and nurses hold distinctive cognitive and emotional attitudes towards these patients. Staff training programs regarding BDP patients should consider these differences and concerns.</jats:sec