bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary conservation and over-representation of functionally enriched network patterns in the yeast regulatory network
Authors: Meshi Ofer , Shlomi Tomer , Ruppin Eytan 
Published: January 2007

Abstract

Background
Localized network patterns are assumed to represent an optimal design principle in different biological networks. A widely used method for identifying functional components in biological networks is looking for network motifs – over-represented network patterns. A number of recent studies have undermined the claim that these over-represented patterns are indicative of optimal design principles and question whether localized network patterns are indeed of functional significance. This paper examines the functional significance of regulatory network patterns via their biological annotation and evolutionary conservation.

Results
We enumerate all 3-node network patterns in the regulatory network of the yeast S. cerevisiae and examine the biological GO annotation and evolutionary conservation of their constituent genes. Specific 3-node patterns are found to be functionally enriched in different exogenous cellular conditions and thus may represent significant functional components. These functionally enriched patterns are composed mainly of recently evolved genes suggesting that there is no evolutionary pressure acting to preserve such functionally enriched patterns. No correlation is found between over-representation of network patterns and functional enrichment.

Conclusion
The findings of functional enrichment support the view that network patterns constitute an important design principle in regulatory networks. However, the wildly used method of over-representation for detecting motifs is not suitable for identifying functionally enriched patterns.
Accurate, precise modeling of cell proliferation kinetics from time-lapse imaging and automated image analysis of agar yeast culture arrays
Authors: Shah Najaf A , Laws Richard J , Wardman Bradley , Zhao Lue Ping , Hartman John L 
Published: January 2007

Abstract

Background
Genome-wide mutant strain collections have increased demand for high throughput cellular phenotyping (HTCP). For example, investigators use HTCP to investigate interactions between gene deletion mutations and additional chemical or genetic perturbations by assessing differences in cell proliferation among the collection of 5000 S. cerevisiae gene deletion strains. Such studies have thus far been predominantly qualitative, using agar cell arrays to subjectively score growth differences. Quantitative systems level analysis of gene interactions would be enabled by more precise HTCP methods, such as kinetic analysis of cell proliferation in liquid culture by optical density. However, requirements for processing liquid cultures make them relatively cumbersome and low throughput compared to agar. To improve HTCP performance and advance capabilities for quantifying interactions, YeastXtract software was developed for automated analysis of cell array images.

Results
YeastXtract software was developed for kinetic growth curve analysis of spotted agar cultures. The accuracy and precision for image analysis of agar culture arrays was comparable to OD measurements of liquid cultures. Using YeastXtract, image intensity vs. biomass of spot cultures was linearly correlated over two orders of magnitude. Thus cell proliferation could be measured over about seven generations, including four to five generations of relatively constant exponential phase growth. Spot area normalization reduced the variation in measurements of total growth efficiency. A growth model, based on the logistic function, increased precision and accuracy of maximum specific rate measurements, compared to empirical methods. The logistic function model was also more robust against data sparseness, meaning that less data was required to obtain accurate, precise, quantitative growth phenotypes.

Conclusion
Microbial cultures spotted onto agar media are widely used for genotype-phenotype analysis, however quantitative HTCP methods capable of measuring kinetic growth rates have not been available previously. YeastXtract provides objective, automated, quantitative, image analysis of agar cell culture arrays. Fitting the resulting data to a logistic equation-based growth model yields robust, accurate growth rate information. These methods allow the incorporation of imaging and automated image analysis of cell arrays, grown on solid agar media, into HTCP-driven experimental approaches, such as global, quantitative analysis of gene interaction networks.
Incidence of low central venous oxygen saturation during unplanned admissions in a multidisciplinary intensive care unit: an observational study
Authors: Bracht Hendrik , Hänggi Matthias , Jeker Barbara , Wegmüller Ninja , Porta Francesca , Tüller David , Takala Jukka , Jakob Stephan M 
Published: January 2007

Abstract
Introduction
It has been shown that early central venous oxygen saturation (ScvO2)-guided optimization of hemodynamics can improve outcome in septic patients. The early ScvO2 profile of other patient groups is unknown. The aim of this study was to characterize unplanned admissions in a multidisciplinary intensive care unit (ICU) with respect to ScvO2 and outcome.

Methods
Ninety-eight consecutive unplanned admissions to a multidisciplinary ICU (median age 63 [range 19 to 83] years, median Simplified Acute Physiology Score [SAPS II] 43 [range 11 to 92]) with a clinical indication for a central venous catheter were included in the study. ScvO2 was assessed at ICU arrival and six hours later but was not used to guide treatment. Length of stay in ICU (LOSICU) and in hospital (LOShospital) and 28-day mortality were recorded.

Results
ScvO2 was 70% ± 12% (mean ± standard deviation) at admission and 71% ± 10% six hours later (p = 0.484). Overall 28-day mortality was 18%, LOSICU was 3 (1 to 28) days, and LOShospital was 19 (1 to 28) days. Patients with an ScvO2 of less than 60% at admission had higher mortality than patients with an ScvO2 of more than 60% (29% versus 17%, p < 0.05). Changes in ScvO2 during the first six hours were not predictive of LOSICU, LOShospital, or mortality.

Conclusion
Low ScvO2 in unplanned admissions and high SAPS II are associated with increased mortality. Standard ICU treatment increased ScvO2 in patients with a low admission ScvO2, but the increase was not associated with LOSICU or LOShospital.
Splanchnic ischemia and reperfusion injury is reduced by genetic or pharmacological inhibition of TNF-α
Authors: Esposito Emanuela , Mazzon Emanuela , Muià Carmelo , Meli Rosaria , Sessa Edoardo , Cuzzocrea Salvatore 
Published: January 2007

AbstractIn the present study, we used TNF-α receptor 1 knockout (TNF-αR1KO) mice to evaluate a possible role of TNF-α on the pathogenesis of ischemia and reperfusion injury of the multivisceral organs. Ischemia and reperfusion injury was induced in mice by clamping the superior mesenteric artery and the celiac artery for 30 min, followed thereafter by reperfusion. Sixty minutes after reperfusion, animals were killed for histological examination and biochemical studies. Injured wild-type (WT) mice developed a significant increase of ileum TNF-α levels, myeloperoxidase activity, and marked histological injury and apoptosis. Ischemia and reperfusion injury of the multivisceral organs was also associated with a significant mortality. Reperfused ileum sections from injured WT mice showed positive staining for P-selectin, VCAM, ICAM-1, and E-selectin. The intensity and degree of P-selectin, E-selectin, VCAM, and ICAM-1 were reduced markedly in tissue sections from injured TNF-αR1KO mice. Ischemia and reperfusion-injured TNF-αR1KO mice also showed a significant reduction of neutrophil infiltration into the intestine, a reduction of apoptosis, an improved histological status of the intestine, and survival. In addition, we investigated the effect of Etanercept, a TNF-α soluble receptor construct, on ischemia and reperfusion injury of the multivisceral organs. Etanercept (5 mg/kg administered i.p. 5 min prior to reperfusion) significantly reduced the inflammatory response and the ileum injury. Taken together, our results clearly demonstrate that TNF-α plays an important role in the ischemia and reperfusion injury and put forward the hypothesis that modulation of TNF-α expression may represent a novel and possible strategy.
Trajectories and predictors of anxiety and depression in women during the 12 months following an acute cardiac event
Authors: Murphy Barbara M. , Elliott Peter C. , Worcester Marian U. C. , Higgins Rosemary O. , Le Grande Michael R. , Roberts Susan B. , Goble Alan J. 
Published: January 2007

Objectives. Many previous investigations of the recovery of emotional well‐being, particularly the resolution of depression, following an acute cardiac event assume that all patients follow a similar, linear trajectory. However, it is possible that there are different groups of patients who follow different trajectories. This study tested for multiple trajectories of anxiety and depression and identified the characteristics of patients most at risk for persistent or worsening anxiety and depression in the 12 months following their cardiac event.Method. A consecutive sample of 226 women was interviewed following either acute myocardial infarction (AMI) or coronary artery bypass graft surgery (CABGS). The Hospital Anxiety and Depression Scale were administered on four occasions over 12 months. Growth curve and growth mixture modelling were used to identify trajectories of change and univariate tests were employed to establish predictors of each trajectory.Results. Most women began with relatively low levels of anxiety and/or depression that improved over the 12 month period (84% women showed this trajectory for anxiety, 89% for depression). A smaller group began with relatively high levels of anxiety and/or depression that worsened over time (16% for anxiety, 11% for depression). Patients in the latter group were more likely to report high levels of loneliness, have a first language other than English, perceive their cardiac disease as more severe (anxiety group only) and have diabetes (depression group only). Trajectories were non‐linear, with most change occurring in the initial 2‐month period.Conclusion. Growth modelling techniques highlight that change in anxiety and depression following an acute event follows neither a single nor linear trajectory. Most women showed early resolution of anxiety and depression following their event, indicative of a normal bereavement or adjustment response. A minority of women reported worsening anxiety and/or depression in the year following their cardiac event, particularly those who lacked social support or were from non‐English speaking backgrounds. Intervention studies to explore support options for these women are warranted, both prior to and following their event.
The State, Private Sector Development, and Ghana's “Golden Age of Business”
Authors: Arthur Peter 
Published: January 2007

Abstract:The promotion of the private sector has become an integral part of Ghana's economic development strategy since it embarked on its structural adjustment program (SAP) in 1983. Private sector development, which involves the improvement of the investment climate and the enhancing of basic service delivery, is considered one of the necessary factors for sustaining and expanding businesses, stimulating economic growth, and reducing poverty. This article examines the policies of Ghana's New Patriotic Party (NPP) government and its strategies for making the private sector the bedrock of economic development and for achieving what it calls the “Golden Age of Business.” It argues that while the policies and initiatives being pursued have the potential to help in the development of the private sector in Ghana, the government has to play a more central role in this process, not only by creating the enabling environment for private businesses, but also by providing business with support and protection. While the “Golden Age of Business” is a neoliberal concept, its effective implementation requires a robust statist input.
Predictors and Sequelae of Fractures in the Elderly: The Canadian Study of Health and Aging (CSHA)
Authors: Østbye Truls , Walton Ruth E. , Steenhuis Runa , Hodsman Anthony B. 
Published: January 2007

ABSTRACTThe objective of this study was to describe the incidence, type, risk factors, and sequelae of fractures experienced by community-dwelling elderly Canadians. Data are from the Canadian Study of Health and Aging (CSHA), a longitudinal cohort study, collected in three waves: baseline (1991), wave 2 (1996), and wave 3 (2001). In CSHA-2 (1996), fractures were reported by 3.7 per cent of men and 7.5 per cent of women; in CSHA-3 (2001), by 2.9 per cent of men and 7.3 per cent of women. The distribution of fracture types was similar for men and women. Risk factors for women were increased age, history of fracture, and regular alcohol use; for men, stroke, arthritis, and lack of independent bathing. Walkers or wheelchairs were needed by over 30 per cent of those with any lower body fracture. One third of subjects with any fracture and over 50 per cent with femur fractures reported moderate or severe pain. It is concluded that elderly Canadians are at high risk for fractures, and older women are at most risk. Pain and mobility problems were common sequelae. The need for primary and secondary prevention of these age-related events is paramount.
“Doing Ethics” in the Context of Sharing Patients' Personal Health Information
Authors: Somerville Margaret A. 
Published: January 2007

ABSTRACTThere are at present two inconsistencies with respect to the sharing of personal health information (PHI) among health care professionals caring for a patient whom the information concerns. First, there is an inconsistency between what is in theory the ethics and law governing the confidentiality and privacy of this information—it may only be disclosed with informed consent—and what is the actual practice of health care professionals—they share it without such consent. Second, there is an inconsistency between what ethics and law demand in theory and what all parties want: They all approve of the current practice. Ethics and law can be brought into line with what is needed to act in the patient's best interests and with what people want, without opening up any serious potential for abuse of privacy and confidentiality, by establishing a safeguarded,provision-of-careexception that allows co-caring health care professionals to share patients' PHI. The requirements for a system establishing such safeguards are proposed. The basic governing presumption is respect for the person and for rights to autonomy, self-determination, privacy, and confidentiality. Therefore, disclosure may only be made with the informed consent of the competent person to whom the information pertains, unless a defence of necessity applies. Where there is doubt about someone's competence, there should likewise be doubt about disclosure without that person's informed consent. Where the person is incompetent, such a disclosure can be made to the patient's substitute decision makers, most often the family, if that is necessary for the care of the patient and in the patient's best interests. To the extent possible, consistent with the best interests of the patient, the wishes of incompetent people should be respected.
Observations on Institutional Long-Term Care in Ontario: 1996–2002
Authors: Berta Whitney , Laporte Audrey , Valdmanis Vivian 
Published: January 2007

ABSTRACTWe provide descriptive statistics for data collected via the Residential Care Facilities Survey (RCFS), from long-term care (LTC) facilities operating in Ontario between 1996 and 2002. The LTC sector in Ontario is dominated by large, proprietary for-profit facilities. The proportion of residents receiving extended care has increased from 53 per cent in 1996 to over 61 per cent in 2002. Government-owned facilities are significantly larger than both for-profit proprietary facilities and lay non-profit facilities. Religious and lay non-profit facilities provide care to more residents 85 years of age and older than do for-profit and government-owned facilities, while government-owned facilities provide care to a greater proportion of higher needs residents. Government-owned facilities have higher nursing intensity levels and higher direct care staffing levels than other ownership types, while for-profit facilities have significantly lower levels than other facility types. Non-profit operators have higher ratios of administrative to care staff than proprietary and government-owned facilities.
Appreciating the Predicament of Housebound Older Adults with Arthritis: Portrait of a Population
Authors: Nour Kareen , Laforest Sophie , Gignac Monique , Gauvin Lise 
Published: January 2007

ABSTRACTThis paper draws a socio-demographic, physical, psychosocial, and behavioural profile of housebound older adults with arthritis and compares older adults with rheumatoid arthritis to those with osteoarthritis. Data from 125 housebound older adults with osteoarthritis (65%) or rheumatoid arthritis (35%) were compared to published samples and to population data using appropriate weighting. Respondents were mainly women, living alone, mean age 77 years (SD = 10.50). Symptoms of stiffness, fatigue, and pain intensity were moderate to severe, and a substantial proportion (51.4%) reported depression. Participants reported low levels of health behaviours such as exercise. Overall, older adults with rheumatoid arthritis were significantly younger, reported less pain and limitations, were more optimistic and satisfied with their social life, and had a higher self-efficacy than older adults with osteoarthritis. Home-based pain self-management programs should be constructed considering the unique profiles and needs of this population.
The Quality of Life of Older Adults Living in an Urban Environment: Professional and Lay Perspectives
Authors: Richard L. , Laforest S. , Dufresne F. , Sapinski J.P. 
Published: January 2007

ABSTRACTThis study aimed to identify factors affecting older adults' quality of life in urban environments and to compare older adults' and professionals' perspectives on the issue. Eleven focus groups were conducted (eight involving older adults, three involving professionals), each discussing a wide range of issues related to determinants of health and quality of life. The most salient themes were health and independence, financial security, social integration, health care services, housing, accessibility of community services, and decision-making power. Older adults' and professionals' comments strongly converged, with specific issues also raised by each. Older adults provided the richest and most in-depth data on intrapersonal factors, such as personal growth, personal qualities, and spirituality. Professionals discussed community environment issues in greater depth. Health promotion interventions to maximize older adults' quality of life are needed. These results contribute to building a knowledge base to guide such efforts, by identifying a variety of possible intervention sectors for future programs.
Are Canadian Seniors Becoming More Active? Empirical Evidence Based on Time-Use Data
Authors: Victorino Charlemaigne C. , Gauthier Anne H. 
Published: January 2007

ABSTRACTIn this study, we examine trends in the patterns of time use of seniors in Canada since the 1980s. In particular, we ask whether today's seniors devote more, or less, time to productive activities than 20 years ago. Our inquiry is motivated by the claims that today's seniors are not engaged in ‘active aging.’ This study uses data from a series of time-use surveys carried out in Canada since 1981 to empirically test the validity of this claim. Our results suggest that some shift towards active aging has taken place in Canada since the 1980s; however, this shift involves a complex pattern of reallocation of time that varies by gender and age.
Revelation and Normativity in Visual Experience
Authors: Jakab Zoltán 
Published: January 2007

Suppose Figure 1 depicts Stimuli from an experiment on shape discrimination, where the subjects are asked to point out the best circle.Now suppose that Figure 2 shows Stimuli from a color-discrimination experiment where the subjects’ task is to pick the purest green — green that is neither yellowish nor bluish — in other words, isuniquegreen.In both these tasks there are individual differences between different subjects. However, notice that in the shape-discrimination case there is exactly one correct response: the best circle is the fourth from the left. In the color case it is not obvious, to put it mildly, that there is exactly one correct response. One color-normal subject may find that the purest green is the third from the left, whereas another may choose the fifth from the left, and still another may pick the fourth. Who is right, and who is wrong? More importantly, why is there this difference between shape perception and color perception?
Apprentissage coop�ratif et prises de parole en langue cible dans deux classes d'immersion
Authors: Mattar Cathérine , Blondin Ch 
Published: January 2007

Résumé Un des défis Ã relever en immersion linguistique, comme dans les cours de langue classiques, est de fournir aux élèves suffisamment d'occasions de parler et de communiquer en langue cible. La recherche montre que l'apprentissage coopératif, dont l'efficacité a été bien établie dans des contextes variés, constitue un outil susceptible d'aider Ã répondre Ã ce défi. Des activités d'apprentissage coopératif proposées par une des chercheuses ont été mises en place par les titulaires de deux classes de deuxième année primaire (élèves de 7 et 8 ans) en immersion partielle, l'une en allemand et l'autre en néerlandais. L'analyse des prises de parole au sein des deux groupes hétérogènes de quatre enfants par classe dont les interactions ont été enregistrées, met en évidence que chacun des enfants a pris la parole non seulement en français, mais aussi en langue cible, et que la répartition des interventions au sein des groupes est assez équitable. Abstract Providing students with enough opportunities to speak and communicate in the target language is one of the challenges faced by both linguistic immersion and conventional language courses. The study documented here shows that cooperative learning, the efficiency of which has been demonstrated in various contexts, could help educators meet this challenge. Cooperative learning activities suggested by one of the researchers were organized by the teachers of two Grade 2 classes (7- and 8-year-old students) in partial immersion (German in one case, Dutch in the other). The speech acts among two heterogeneous groups of four children per class were recorded and analysed. The article shows that every pupil spoke not only in their L1 but also in the target language and that speech acts were fairly equally distributed within each group. [End Page 225]