bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Circulating Free Tumor Cells in the Peripheral Blood of Colorectal Cancer Patients during Laparoscopic Surgery
Authors: Chen Wei‐Shone , Chung Ming‐yi , Liu Jin‐Hwang , Liu Jacqueline Ming , Lin Jen‐Kou 
Published: May 2004

AbstractDespite widespread use of laparoscopic surgery for colorectal operations, its application for curative resection of colorectal cancer is still controversial. One of the major concerns is the impact of the laparoscopic procedure on dissemination of tumor cells. The main purpose of this study was to investigate the impact of laparoscopic surgery on circulating tumor cells in colorectal cancer patients. Quantitation of circulating free tumor cells (FTCs) was performed preoperatively, during the operation, and 14 days later by means of real‐time quantitative reverse transcriptase‐polymerase chain reaction (RT‐PCR) targeting guanylyl cyclase C (GCC) mRNA in 42 colorectal cancer patients undergoing laparoscopic resections. Despite an increasing trend of FTC detection in patients with advancing stage, there is no significant difference in the preoperative FTC level by disease stage. No elevation in FTC level was found during the laparoscopic procedure in most patients compared with their preoperative FTC value. Patients with a persistently high FTC load [per nucleated blood cells (NBCs)] (> 102 FTCs/106 NBCs) 2 weeks postoperatively portends a poor prognosis regarding disease recurrence and tumor‐related mortality when compared to those with an undetectable or low FTC load (≤ 102 FTCs/106 NBCs). We concluded that the laparoscopic procedure itself had no significantly deleterious effect on circulating FTCs and that the detection of FTCs by real‐time qRT‐PCR might be of clinical importance during the postoperative follow‐up for colorectal cancer patients.
Using large‐scale climate indices in climate change ecology studies
Authors: Forchhammer Mads C. , Post Eric 
Published: May 2004

AbstractRecently, climate change research in ecology has embraced the use of large‐scale climate indices in long‐term, retrospective studies. In most instances, these indices are related to large‐scale teleconnection and atmospheric patterns of which over a dozen have been identified. Although most of these relate to different geographical areas, many are related and interact. Consequently, even the simple task of selecting one to use in ecological research has become complicated, despite our ability to disentangle the results from analyses involving large‐scale climate indices. Leaning upon recent reviews of the definition and functioning of large‐scale climate indices, as well as reviews on the relationship between these and concomitant changes in ecological variables, we focus here on the usefulness of large‐scale climate indices in different aspects of climate change ecology. By providing a general framework for using climate indices, we illustrate the potential advantages of their utility by integrating three case histories focusing on two groups of evolutionarily distinct organisms: birds and mammals.
The Decision to Test in Women Receiving Genetic Counseling for BRCA1 and BRCA2 Mutations
Authors: Kelly Kimberly , Leventhal Howard , Andrykowski Michael , Toppmeyer Deborah , Much Judie , Dermody James , Marvin Monica , Baran Jill , Schwalb Marvin 
Published: May 2004

AbstractFunctions of genetic counseling include provision of risk information and provision of support in an effort to assist with decision making. This study examines (1) the relationship among intentions to test, self‐reported provision of blood sample, and receipt of test results; (2) the impact of genetic counseling on distress specific to gene status, perceived risk of developing breast and ovarian cancer in the context having BRCA1/2 mutations (mutations predisposing to increased risk of breast–ovarian cancer), and perceived risk factors for breast cancer; and (3) the clinical profile of those receiving/not receiving results. Intentions to test for BRCA1/2 mutations, self‐reported provision of blood sample immediately after counseling, and receipt of test results were statistically different but highly correlated, and intentions to test increased from pre‐ to postcounseling. A repeated measures ANOVA found distress specific to gene status and perceived risk factors decreased from pre‐ to postcounseling. Further, two clinical profiles of consultands emerged: (1) those receiving results with change in intentions to test having lower levels of distress and (2) those not receiving results and those receiving results with no change in intentions to test with higher levels of distress. Our findings are consistent with the function of genetic counseling—to provide information and support to those with familial cancer, as well as to assist in decision making. The provision of support is important as distress specific to gene status may impede flexible decision making about genetic testing.
How well do Australian women comply with dietary guidelines?
Authors: Ball Kylie , Mishra Gita D , Thane Christopher W , Hodge Allison 
Published: May 2004

AbstractObjective:To investigate the proportion of middle-aged Australian women meeting national dietary recommendations and its variation according to selected sociodemographic and behavioural characteristics.Design:This cross-sectional population-based study used a food-frequency questionnaire to investigate dietary patterns and compliance with 13 commonly promoted dietary guidelines among a cohort of middle-aged women participating in the Australian Longitudinal Study on Women's Health.Setting:Nation-wide community-based survey.Subjects:A total of 10 561 women aged 50–55 years at the time of the survey in 2001.Results:Only about one-third of women complied with more than half of the guidelines, and only two women in the entire sample met all 13 guidelines examined. While guidelines for meat/fish/poultry/eggs/nuts/legumes and ‘extra’ foods (e.g. ice cream, chocolate, cakes, potatoes, pizza, hamburgers and wine) were met well, large percentages of women (68–88%) did not meet guidelines relating to the consumption of breads, cereal-based foods and dairy products, and intakes of total and saturated fat and iron. Women working in lower socio-economic status occupations, and women living alone or with people other than a partner and/or children, were at significantly increased risk of not meeting guidelines.Conclusions:The present results indicate that a large proportion of middle-aged Australian women are not meeting dietary guidelines. Without substantial changes in their diets, and help in making these changes, current national guidelines appear unachievable for many women.
Homocysteine and cobalamin status in German vegans
Authors: Waldmann Annika , Koschizke Jochen W , Leitzmann Claus , Hahn Andreas 
Published: May 2004

AbstractObjective:The study aimed to evaluate the homocysteine and cobalamin status of German vegans and determine whether the intake of very small amounts of foods of animal origin can improve this status.Design and setting:Cross-sectional study, Germany.Subjects:The dietary and nutritional intakes of 131 vegans (73 women, 58 men; a range: 20.2–82.1 years) were evaluated using a general questionnaire and two food–frequency questionnaires.Results:The prevalence of inadequate cobalamin status in volunteers of the German Vegan Study was 28.2%, and that of hyperhomocysteinaemia, 38.1%. Moderate vegans were affected to a lesser extent than were strict vegans. Duration of veganism and cobalamin concentration were inversely correlated (Spearman'sr= -0.175,P= 0.047). Folate concentration and erythrocyte aspartic acid aminotransferase activity were not correlated with plasma homocysteine concentration, but duration of veganism correlated positively with homocysteine concentration (Spearman'sr= 0.319,P< 0.001). Cobalamin and homocysteine concentrations were inversely correlated (when controlling for duration of veganism;r= -0.602,P< 0.001).Conclusion:Cobalamin status needs to be improved in order to minimise the risk of hyperhomocysteinaemia.
Factors to consider in Micronesian food-based interventions: a case study of preventing vitamin A deficiency
Authors: Englberger L , Marks GC , Fitzgerald MH 
Published: May 2004

AbstractBackground:Many factors need to be considered in a food-based intervention. Vitamin A deficiency and chronic diseases, such as diabetes, heart disease and cancer, have become serious problems in the Federated States of Micronesia (FSM) following the decreased production and consumption of locally grown foods. However, agricultural and social conditions are still favourable for local food production.Aim:To identify key factors to consider in a Micronesian food-based intervention focusing on increased production and consumption of four major Micronesian staple foods: banana, breadfruit, giant swamp taro and pandanus.Methods:Ethnographic methods including key informant interviews and a literature review.Results:Pacific and Micronesian values, concepts of food and disease, and food classifications differ sharply from Western concepts. There are few FSM professionals with nutrition expertise. Traditional foods and food cultivars vary in nutrient content, consumption level, cost, availability, status, convenience in growing, storing and cooking, and organoleptic factors.Conclusions:A systematic consideration of the factors that relate to a food-based intervention is critical to its success. The evaluation of which food and cultivar of that food that might be most effectively promoted is also critical. Regional differences, for example FSM inter-island differences between the staple foods and cultivars, must be considered carefully. The evaluation framework presented here may be relevant to Pacific Island and other countries with similar foods where food-based interventions are being planned. An ethnographic approach was found to be essential in understanding the cultural context and in data collection and analysis.
Why the Bush administration and the global sugar industry are determined to demolish the 2004 WHO global strategy on diet, physical activity and health
Authors: Cannon Geoffrey 
Published: May 2004

AbstractObjective:To indicate why the world's most powerful nation state and one powerful sector of the food and drink production and manufacturing industry are determined to demolish the 2004 WHO (World Health Organization) global strategy on diet, physical activity and health, and to disassociate it from the 2003 WHO/FAO (Food and Agriculture Organization) expert report on diet, nutrition and the prevention of chronic diseases, which with its background papers is the immediate scientific basis for the strategy. To encourage representatives of nation states at the 2004 WHO World Health Assembly to support the strategy together with the report, so that the strategy is explicit and quantified, and responds to the need expressed by member states at the 2002 World Health Assembly. This is for an effective global strategy to prevent and control chronic diseases whose prevalence is increased by nutrient-poor food low in vegetables and fruits and high in energy-dense fatty, sugary and/or salty foods and drinks and also by physical inactivity. Of these diseases, obesity, diabetes, cardiovascular diseases and cancers of several sites are now the chief causes of morbidity and mortality in most countries in the world.Method:A summary of the global strategy and its roots in scientific knowledge accumulated over the last half-century. Reasons why the global strategy and the expert report are opposed by the current US government and the world sugar industry, with some reference to modern historical context. A summary of the trajectory of the global strategy since its first draft made in early 2003, and a further summary of its weaknesses, strengths and potential.Conclusion:The 2004 WHO global strategy and the 2003 WHO/FAO expert report are perceived by the current US administration as an impediment to US trade and international policy, within a general context of current US government hostility to the UN (United Nations) system as a brake on the exercise of its power as the world's dominant nation. Policy-makers throughout the world should be aware of the contexts of current pressures put on them by powerful nation states and sectors of industry whose ideologies and commercial interests are challenged by international initiatives designed to improve public health and to leave a better legacy for future generations.
Algorithms for sequence analysis via mutagenesis
Authors: Keith Jonathan M. , Adams Peter , Bryant Darryn , Cochran Duncan A. E. , Lala Gita H. , Mitchelson Keith R. 
Published: May 2004

Abstract
Motivation: Despite many successes of conventional DNA sequencing methods, some DNAs remain difficult or impossible to sequence. Unsequenceable regions occur in the genomes of many biologically important organisms, including the human genome. Such regions range in length from tens to millions of bases, and may contain valuable information such as the sequences of important genes. The authors have recently developed a technique that renders a wide range of problematic DNAs amenable to sequencing. The technique is known as sequence analysis via mutagenesis (SAM). This paper presents a number of algorithms for analysing and interpreting data generated by this technique.
Results: The essential idea of SAM is to infer the target sequence using the sequences of mutants derived from the target. We describe three algorithms used in this process. The first algorithm predicts the number of mutants that will be required to infer the target sequence with a desired level of accuracy. The second algorithm infers the target sequence itself, using the mutant sequences. The third algorithm assigns quality values to each inferred base. The algorithms are illustrated using mutant sequences generated in the laboratory.
Availability: Software will be made available upon request.
A mixture model for estimating the local false discovery rate in DNA microarray analysis
Authors: Liao J.G. , Lin Yong , Selvanayagam Zachariah E. , Shih Weichung Joe 
Published: May 2004

Abstract
Motivation: Statistical methods based on controlling the false discovery rate (FDR) or positive false discovery rate (pFDR) are now well established in identifying differentially expressed genes in DNA microarray. Several authors have recently raised the important issue that FDR or pFDR may give misleading inference when specific genes are of interest because they average the genes under consideration with genes that show stronger evidence for differential expression. The paper proposes a flexible and robust mixture model for estimating the local FDR which quantifies how plausible each specific gene expresses differentially.
Results: We develop a special mixture model tailored to multiple testing by requiring the P-value distribution for the differentially expressed genes to be stochastically smaller than the P-value distribution for the non-differentially expressed genes. A smoothing mechanism is built in. The proposed model gives robust estimation of local FDR for any reasonable underlying P-value distributions. It also provides a single framework for estimating the proportion of differentially expressed genes, pFDR, negative predictive values, sensitivity and specificity. A cervical cancer study shows that the local FDR gives more specific and relevant quantification of the evidence for differential expression that can be substantially different from pFDR.
Availability: An R function implementing the proposed model is available at http://www.geocities.com/jg_liao/software
Rainbow: a toolbox for phylogenetic supertree construction and analysis
Authors: Chen D. , Eulenstein O. , Fernández-Baca D. 
Published: May 2004

Abstract
Summary: Rainbow is a program that provides a graphic user interface to construct supertrees using different methods. It also provides tools to analyze the quality of the supertrees produced. Rainbow is available for Mac OS X, Windows and Linux.
Availability: Rainbow is a free open-source software. Its binary files, source code, and manual can be downloaded from the Rainbow web page: http://genome.cs.iastate.edu/Rainbow/
A model of bovine tuberculosis in the badger Meles meles: an evaluation of different vaccination strategies
Authors: WILKINSON D. , SMITH G. C. , DELAHAY R. J. , CHEESEMAN C. L. 
Published: May 2004

Summary

In recent years bovine tuberculosis (TB) incidence in cattle has been increasing in south‐west England. The European badger Meles meles is implicated in the transmission of TB to cattle and has been the subject of culling operations in an attempt to control the disease.
An individual‐based, spatial, stochastic, simulation model was used to investigate the control of TB in the badger by various badger‐vaccination strategies. Nearly all population and epidemiological parameters were derived from a single long‐term study site. Heterogeneous carrying capacities (the maximum number of breeding females per badger social group) and different sized badger territories were used to simulate natural heterogeneity. The model included the transmission of TB from badgers to cattle to allow reactive vaccination of badgers, i.e. in response to positive cattle TB test results.
The model predicted that badger populations with reduced contiguity (e.g. natural barriers) between social group territories would have a lower TB prevalence.
In the absence of information on the true prevalence of TB in badger social groups, vaccinating 80% of groups at a low vaccine probability (10% successfully immunized) was more effective in the model at reducing prevalence of TB in badgers, than vaccinating 10% of the groups at a higher probability (80% successfully immunized).
Although a lower cost option, vaccinating badgers purely in reaction to cattle herd infections took longer to reduce badger TB prevalence to 50% than proactive strategies (7–20 years compared with 3–5 years). Simulations suggested that at least 40% of healthy badgers need to be immunized each year to eradicate TB in the badger. The model indicated that vaccination of badgers is a viable alternative to badger culling for the control of TB in cattle. Combined control policies were not investigated.
Synthesis and applications. Widespread proactive vaccination appears to be the most effective strategy for disease control. Initial proactive vaccination followed by localized reactive vaccination can lead to a greater reduction in disease prevalence for less effort. This is likely to be a global finding for the control of wildlife diseases, although the optimal duration for a proactive campaign will depend upon specific circumstances (e.g. detection rate of disease).
On the loss of saltmarshes in south‐east England and methods for their restoration
Authors: HUGHES R. G. , PARAMOR O. A. L. 
Published: May 2004

Summary

The saltmarshes of south‐east England have been eroding rapidly for about the last 50 years, at a continuing rate of about 40 ha year−1, with deleterious consequences for conservation and coastal flood defence. The possible reasons for this erosion and suitability of methods of saltmarsh restoration are discussed.
The prevailing hypothesis that the saltmarsh erosion is due to coastal squeeze, where sea walls prevent a landward migration of saltmarsh in response to sea level rise, is rejected because: (i) as the sea level rises saltmarshes accrete vertically as well, at least at the same rate, and may even extend seaward; (ii) in recent decades the rate of rise in sea level has been no higher than in the past when the saltmarshes developed; (iii) the pattern of vegetation loss, mostly of pioneer zone species, is opposite to that predicted by coastal squeeze, where the upper marsh plants should disappear first.
Alternative explanations and hypotheses are proposed that relate the recent saltmarsh erosion to changes to the intertidal biota, an increase in abundance of the infaunal polychaete Nereis diversicolor, and a decrease in abundance of intertidal seagrasses. Bioturbation and herbivory by Nereis cause the loss of pioneer zone plants, increase sediment instability and exacerbate the erosion of saltmarsh creeks. The erosion of the seaward edge of some marshes may also be due to increased wave action, and increased tidal current speeds in estuaries, following the loss of intertidal seagrasses since the 1930s through wasting disease.
Synthesis and applications. The current strategy for saltmarsh creation is based on managed realignment, where some sea walls are breached to provide new intertidal habitat. The conclusion that the causes of saltmarsh loss are not related to sea level rise calls into question this dependence on management realignment as the most appropriate means of saltmarsh creation, not least because many realignment areas are unlikely to develop vegetation. Other methods should be considered for creating new marshes and for reducing/reversing marsh erosion. These include, alone or in combinations, exclusion of the infauna, use of dredged material for strategic intertidal recharge, and transplantation of intertidal seagrasses.
The effects of bioturbation and herbivory by the polychaete Nereis diversicolor on loss of saltmarsh in south‐east England
Authors: PARAMOR O. A. L. , HUGHES R. G. 
Published: May 2004

Summary

The saltmarshes of south‐east England are eroding rapidly. Field and laboratory experiments were used to test the hypotheses that: (i) at the mudflat–saltmarsh boundary there are two alternative states, one dominated by pioneer zone vegetation that excludes burrowing infauna, and the other dominated by infaunal invertebrates that exclude vegetation; and (ii) the major cause of the loss of saltmarshes in south‐east England is internal creek erosion, which is exacerbated by bioturbation and herbivory by the infaunal polychaete Nereis diversicolor.
In laboratory experiments Nereis ate the seeds and seedlings of Salicornia spp., and Salicornia deterred burrowing by Nereis. In field experiments, at Tollesbury in Essex, UK, exclusion of Nereis from the sediment surface increased the density of Salicornia, but only when a source of seeds was close by. In the Tollesbury saltmarsh the plants and Nereis had mutually exclusive distributions within a vertical zone of overlap. The recently vegetated area of the managed realignment site at Tollesbury contained no Nereis, but Nereis colonized areas where Salicornia had been removed. These observations and data support the first hypothesis.
Much of the loss of the Tollesbury saltmarsh is by lateral erosion of the internal creeks. Physical factors alone cannot be responsible for this erosion because experimental exclusion of Nereis led to sediment accretion. These results support the second hypothesis. Creek erosion may create a positive feedback where creek enlargement leads to faster tidal currents and further erosion until creeks have widened to their new equilibrium morphology.
Synthesis and applications. We conclude that the infauna are a major cause of reduction in area of saltmarsh vegetation and this has implications for the management of saltmarsh restoration. These results call into question the assumption that saltmarsh erosion in south‐east England is due to sea level rise and coastal squeeze, and demands re‐examination of the role of management realignment in the regeneration of saltmarshes. Reducing the rates of saltmarsh creek erosion, by exclusion of the infauna, and/or by reducing current velocities in the saltmarsh creeks, would reduce the need to replace eroded marshes by managed realignment, and would reduce future erosion of existing sea walls by wave action.