bluuebunny/crossref_metadata_2025_split huggingface dataset:
Feast and famine: Socioeconomic disparities in global nutrition and health
Authors: Darnton-Hill I , Coyne ET 
Published: December 2005

AbstractObjective:To review current information on under- and over-malnutrition and the consequences of socioeconomic disparities on global nutrition and health.Design:Malnutrition, both under and over, can no longer be addressed without considering global food insecurity, socioeconomic disparity, both globally and nationally, and global cultural, social and epidemiological transitions.Setting:The economic gap between the more and less affluent nations is growing. At the same time income disparity is growing within most countries, both developed and developing. Concurrently, epidemiological, demographic and nutrition transitions are taking place in many countries.Results:Fully one-third of young children in the world's low-income countries are stunted because of malnutrition. One-half of all deaths among young children are, in part, a consequence of malnutrition. Forty per cent of women in the developing world suffer from iron deficiency anaemia, a major cause of maternal mortality and low birth weight infants. Despite such worrying trends, there have been significant increases in life expectancy in nearly all countries of the world, and continuing improvements in infant mortality rates. The proportion of children malnourished has generally decreased, although actual numbers have not in sub-Saharan Africa and south Asia. Inequalities are increasing between the richest developed countries and the poorest developing countries. Social inequality is an important factor in differential mortality in both developed and developing countries. Many countries have significant pockets of malnutrition and increased mortality of children, while obesity and non-communicable disease (NCDs) prevalences are increasing. Not infrequently it is the poor and relatively disadvantaged sectors of the population who are suffering both. In the industrialized countries. cardiovascular disease incidence has declined, but less so in the poorer socioeconomic strata.conclusions:The apparent contradicitions found represent a particular point in time (population responses generally lag behind social and environmental transitions). They do also show encouraging evidence that interventions can have a positive impact, sometimes despite disadvantageous circumstances. However, it seems increasingly unlikely that food production will continue to keep up with population growth. It is also unlikely present goals for reducing protein-energy malnutrition prevalence will be reached. The coexistence of diseases of undernutrition and NCDs will have an impact on allocation of resources. Action needs to be continued and maintained at the international, national and individual level.
Mortality in vegetarians and non-vegetarians: a collaborative analysis of 8300 deaths among 76,000 men and women in five prospective studies
Authors: Key Timothy J , Fraser Gary E , Thorogood Margaret , Appleby Paul N , Beral Valerie , Reeves Gillian , Burr Michael L , Chang-Claude Jenny , Frentzel-Beyme Rainer , Kuzma Jan W , Mann Jim , McPherson Klim 
Published: December 2005

AbstractObjective:To compare the mortality rates of vegetarians and non-vegetarians.Design:Collaborative analysis using original data from five prospective studies. Death rate ratios for vegetarians compared to non-vegetarians were calculated for ischaemic heart disease, cerebrovascular disease, cancers of the stomach, large bowel, lung, breast and prostate, and for all causes of death. All results were adjusted for age, sex and smoking. A random effects model was used to calculate pooled estimates of effect for all studies combined.Setting:USA, UK and Germany.Subjects:76, 172 men and women aged 16–89 years at recruitment. Vegetarians were those who did not eat any meat or fish (n = 27,808). Non-vegetarians were from a similar background to the vegetarians within each study.Results:After a mean of 10.6 years of follow-up there were 8330 deaths before the age of 90 years, including 2264 deaths from ischaemic heart disease. In comparison with non-vegetarians, vegetarians had a 24% reduction in mortality from ischaemic heart disease (death rate ratio 0.76, 95% CI 0.62–0.94). The reduction in mortality among vegetarians varied significantly with age at death: rate ratios for vegetarians compared to non-vegetarians were 0.55 (95% CI 0.35—0.85), 0.69 (95% CI 0.53–0.90) and 0.92 (95% CI 0.73–1.16) for deaths from ischaemic heart disease at ages <65, 65–79 and 80–89 years, respectively. When the non-vegetarians were divided into regular meat eaters (who ate meat at least once a week) and semi-vegetarians (who ate fish only or ate meat less than once a week), the ischaemic heart disease death rate ratios compared to regular meat eaters were 0.78 (95% CI 0.68–0.89) in semi-vegetarians and 0.66 (95% CI 0.53–0.83) in vegetarians (test for trend P<0.001). There were no significant differences between vegetarians and non-vegetarians in mortality from the other causes of death examined.Conclusion:Vegetarians have a lower risk of dying from ischaemic heart disease than non-vegetarians.
Schoolchildren's diets and participation in school feeding programmes in Jamaica
Authors: Walker Susan P , Powell Christine A , Hutchinson Sharmaine E , Chang Susan M , Grantham-McGregor Sally M 
Published: December 2005

AbstractObjective:To describe food consumption during the school day of rural Jamaican children and participation in two government school feeding programmes. To determine factors which were related to these.Design:Cross sectional.Setting:16 primary schools in rural Jamaica.Subjects:415 children in grades 2 and 5 (ages 7 and 10 years).Results:Consumption of sweets, sweet drinks and snacks was high. Mean intakes at lunch were: energy 1537 kJ (SD 756), protein 10.4 g (SD 7.6) and iron 1.5 mg (SD 1.2). The mean energy intake was 17–20% of the daily requirement for this age group. Two types of school feeding programmes were available in the schools, one provided a cooked meal and the other a bun and milk. Median availability of school meals (as a percentage of children enrolled in the schools) over three terms was 24.6% (range 0–85.4%). Twenty per cent of the children participated in one or other programme. Poorer children were more likely to participate in the bun and milk programme (odds ratio 2.1, 95% C1 1.3–3.5) but children with more money to purchase food participated in the more costly cooked meal programme (odds ratio 2.4, 95% CI 1.3–4.6).Conclusions:Energy intakes at lunch in Jamaican children were somewhat below optimal levels and the reliance on sweets and snacks is an area of concern. Programme characteristics such as meal cost, may affect access to school feeding by poor children.
Mycotoxins in ruminants
Authors: Lancaster M. C. 
Published: December 2005

Mycotoxins have for long been associated with disease and death in animals,
but because of the great variety of fungi present in animal feedstuffs and
the detailed investigations needed to establish a causal relationship
between mycotoxin and a clinical disease, few disease syndromes have been
identified.In this paper, it is proposed to consider three confirmed clinical diseases
caused by mycotoxins, to review briefly their history and identification and
to consider their biological effects in ruminants.
TRAP: automated classification, quantification and annotation of tandemly repeated sequences
Authors: Sobreira Tiago José P. , Durham Alan M. , Gruber Arthur 
Published: December 2005

Abstract
Summary: TRAP, the Tandem Repeats Analysis Program, is a Perl program that provides a unified set of analyses for the selection, classification, quantification and automated annotation of tandemly repeated sequences. TRAP uses the results of the Tandem Repeats Finder program to perform a global analysis of the satellite content of DNA sequences, permitting researchers to easily assess the tandem repeat content for both individual sequences and whole genomes. The results can be generated in convenient formats such as HTML and comma-separated values. TRAP can also be used to automatically generate annotation data in the format of feature table and GFF files.
Availability: TRAP is available under the GNU General Public License at
Contact: argruber@usp.br
Supplementary Information: Supplementary data are available at
A support vector machine-based method for predicting the propensity of a protein to be soluble or to form inclusion body on overexpression in Escherichia coli
Authors: Idicula-Thomas Susan , Kulkarni Abhijit J. , Kulkarni Bhaskar D. , Jayaraman Valadi K. , Balaji Petety V. 
Published: December 2005

Abstract
Motivation: Inclusion body formation has been a major deterrent for overexpression studies since a large number of proteins form insoluble inclusion bodies when overexpressed in Escherichia coli. The formation of inclusion bodies is known to be an outcome of improper protein folding; thus the composition and arrangement of amino acids in the proteins would be a major influencing factor in deciding its aggregation propensity. There is a significant need for a prediction algorithm that would enable the rational identification of both mutants and also the ideal protein candidates for mutations that would confer higher solubility-on-overexpression instead of the presently used trial-and-error procedures.
Results: Six physicochemical properties together with residue and dipeptide-compositions have been used to develop a support vector machine-based classifier to predict the overexpression status in E.coli. The prediction accuracy is ∼72% suggesting that it performs reasonably well in predicting the propensity of a protein to be soluble or to form inclusion bodies. The algorithm could also correctly predict the change in solubility for most of the point mutations reported in literature. This algorithm can be a useful tool in screening protein libraries to identify soluble variants of proteins.
Avalibility: Software is available on request from the authors.
Contact: balaji@iitcb.ac.in; vk.jayaraman@ncl.res.in
Supplementary information: Supplementary data are available at Bioinformatics Online web site.
In silico sequence evolution with site-specific interactions along phylogenetic trees
Authors: Gesell Tanja , von Haeseler Arndt 
Published: December 2005

Abstract
Motivation: A biological sequence usually has many sites whose evolution depends on other positions of the sequence, but this is not accounted for by commonly used models of sequence evolution. Here we introduce a Markov model of nucleotide sequence evolution in which the instantaneous substitution rate at a site depends on the states of other sites. Based on the concept of neighbourhood systems, our model represents a universal description of arbitrarily complex dependencies among sites.
Results: We show how to define complex models for some illustrative examples and demonstrate that our method provides a versatile resource for simulations of sequence evolution with site-specific interactions along a tree. For example, we are able to simulate the evolution of RNA taking into account both secondary structure as well as pseudoknots and other tertiary interactions. To this end, we have developed a program Simulating Site-Specific Interactions (SISSI) that simulates evolution of a nucleotide sequence along a phylogenetic tree incorporating user defined site-specific interactions. Furthermore, our method allows to simulate more complex interactions among nucleotide and other character based sequences.
Availability: We implemented our method in an ANSI C program SISSI which runs on UNIX/Linux, Windows and Mac OS systems, including Mac OS X. SISSI is available at
Contact: sissi@cs.uni-duesseldorf.de
BALLView: a tool for research and education in molecular modeling
Authors: Moll Andreas , Hildebrandt Andreas , Lenhof Hans-Peter , Kohlbacher Oliver 
Published: December 2005

Abstract
Summary: We present BALLView, a molecular viewer and modeling tool. It combines state-of-the-art visualization capabilities with powerful modeling functionality including implementations of force field methods and continuum electrostatics models. BALLView is a versatile and extensible tool for research in structural bioinformatics and molecular modeling. Furthermore, the convenient and intuitive graphical user interface offers novice users direct access to the full functionality, rendering it ideal for teaching. Through an interface to the object-oriented scripting language Python it is easily extensible.
Availability: BALLView is an open source software and runs on all major platforms (Windows, MacOS X, Linux and most Unix flavors). It is available free of charge under the GNU Public License at
Contact: amoll@bioinf.uni-saarland.de
Evaluating phylogenetic footprinting for human–rodent comparisons
Authors: Sauer Tilman , Shelest Ekaterina , Wingender Edgar 
Published: December 2005

Abstract
Motivation: ‘Phylogenetic footprinting’ is a widely applied approach to identify regulatory regions and potential transcription factor binding sites (TFBSs) using alignments of non-coding orthologous regions from two or more organisms. A systematic evaluation of its validity and usability based on known TFBSs is needed to use phylogenetic footprinting most effectively in the identification of unknown TFBSs.
Results: In this paper we use 2678 human, mouse and rat TFBSs from the TRANSFAC® database for this evaluation. To ensure the retrieval of correct orthologous sequences, we combine gene annotation and sequence homology searches. Demanding a sequence identity of at least 65% is most effective in discriminating TFBSs from non-functional sequence parts, while different alignment algorithms only have a minor influence on TFBS identification by human–rodent comparisons. With this threshold ∼72% of the known TFBSs are found conserved, a number which varies significantly between different transcription factors and also depends on the function of the regulated gene. TFBSs for certain transcription factors do not require strict sequence conservation but instead may show a high pattern conservation, limiting somewhat the validity of purely sequence-based phylogenetic footprinting.
Availability: Scripts are available from the authors upon request.
Contact: tsa@bioinf.med.uni-goettingen.de
Supplementary information:
Gene network inference from incomplete expression data: transcriptional control of hematopoietic commitment
Authors: Missal Kristin , Cross Michael A. , Drasdo Dirk 
Published: December 2005

AbstractMotivation: The topology and function of gene regulation networks are commonly inferred from time series of gene expression levels in cell populations. This strategy is usually invalid if the gene expression in different cells of the population is not synchronous. A promising, though technically more demanding alternative is therefore to measure the gene expression levels in single cells individually. The inference of a gene regulation network requires knowledge of the gene expression levels at successive time points, at least before and after a network transition. However, owing to experimental limitations a complete determination of the precursor state is not possible.Results: We investigate a strategy for the inference of gene regulatory networks from incomplete expression data based on dynamic Bayesian networks. This permits prediction of the number of experiments necessary for network inference depending on parameters including noise in the data, prior knowledge and limited attainability of initial states. Our strategy combines a gradual ‘Partial Learning’ approach based solely on true experimental observations for the network topology with expectation maximization for the network parameters. We illustrate our strategy by extensive computer simulations in a high-dimensional parameter space in a simulated single-cell-based example of hematopoietic stem cell commitment and in random networks of different sizes. We find that the feasibility of network inferences increases significantly with the experimental ability to force the system into different initial network states, with prior knowledge and with noise reduction.Availability: Source code is available under:Contact: drasdo@izbi.uni-leipzig.deSupplementary information: Supplementary Data are available at Bioinformatics online.
Consenting to blood: what do patients remember?
Authors: Chan T. , Eckert K. , Venesoen P. , Leslie K. , Chin‐Yee I. 
Published: December 2005

summary.  We sought to characterize the consent process for transfusion and determine its impact on patients' knowledge and level of comfort with receiving blood.We identified all adult patients who had received blood transfusion at a tertiary care centre over 3 months. Patients who were discharged each received a survey that assessed their (1) recall of the consent process, (2) recall of information conveyed, (3) assessment of the discussion's understandability and (4) perceived knowledge of as well as comfort level with transfusion as a result of the discussion.Overall, 80% of respondents recalled discussing and signing an informed consent. Information was mostly conveyed by attending physicians (35%) and consent obtained in the patient's hospital room (38%) or the preadmission clinic (19%). Although the majority recalled the consent process, many did not recall the discussion of specific transfusion risks or alternatives to donor blood (88%). Although the majority felt the discussion was at least somewhat understandable (77%), only 35% felt better informed and more comfortable with accepting blood.Despite implementation of written informed consent for transfusion, patients' recollection and understanding of risks and alternatives remain poor. This suggests the need for improving risk communication.
Low dose erythropoietin is effective in reducing transfusion requirements following allogeneic HSCT
Authors: Fox C. P. , Pacey S. , Das‐Gupta E. P. , Russell N. H. , Byrne J. L. 
Published: December 2005

summary.  Blood transfusions are frequently required for several weeks after allogeneic transplantation due to inadequate erythropoiesis and defective erythropoietin production. Because red cell transfusion is not without complications in this setting, we sought to avoid them using recombinant human erythropoietin (rhEpo) therapy.We treated 53 patients following allogeneic transplantation for haematological malignancy, using rhEpo at a dose of 10 000 units subcutaneously twice weekly. The median time of commencement of rhEpo was 61 days post‐transplant (range 19–465 days), and the median haemoglobin (Hb) concentration was 9·4 g dL−1 (range 7·0–10·7 g dL−1). Thirty patients responded to rhEpo and required no further transfusion with a median rise in Hb after 2 weeks of therapy of 1·5 g (0·7–4·1 g dL−1). Erythropoietin (Epo) was discontinued at a median of 5 weeks (range 2–36), when the median Hb concentration was 12·3 g dL−1 (range 10·0–14·3 g dL−1). Those patients who failed to respond to rhEpo frequently had additional reasons for anaemia including cytomegalovirus (CMV) reactivation and treatment, major ABO incompatibility, disease relapse, graft rejection or other transplant‐related complications.We conclude that a short course of rhEpo is an effective treatment for anaemia arising following allogeneic hematopoietic cell transplantation, and can avoid the need for transfusion in this setting.
The marginalist approach and the making of fuel policy in France and Britain, 1945–721
Authors: CHICK MARTIN 
Published: December 2005

SUMMARYFocusing on the shift from coal to oil in the French and British economies between 1945 and 1972, this article analyses the influence of economists and economic concepts on fuel‐policy making in each economy. The framing of French fuel policy around marginalist principles from 1958 is examined, and the unusually direct influence of economists on policy making is ascribed to a mix of national security, industrial modernization, and political considerations.
Evaluation of intracavitary mitoxantrone and carboplatin for treatment of carcinomatosis, sarcomatosis and mesothelioma, with or without malignant effusions: A retrospective analysis of 12 cases (1997–2002)*
Authors: Charney S. C. , Bergman P. J. , McKnight J. A. , Farrelly J. , Novosad C. A. , Leibman N. F. , Camps‐Palau M. A. 
Published: December 2005

AbstractCarcinomatosis, sarcomatosis and mesothelioma, with or without malignant effusions, are difficult to treat and generally carry a poor prognosis. The purpose of this study was two‐fold; first, to determine the prognosis for dogs with carcinomatosis, sarcomatosis, or mesothelioma, with or without malignant effusions; second, to evaluate the safety and efficacy of treatment with intracavitary (IC) carboplatin and mitoxantrone in dogs with these syndromes. Nineteen dogs were evaluated. Seven were untreated and 12 were treated with IC chemotherapy (mitoxantrone and/or carboplatin), and multiple factors were analysed for significance with respect to survival time. The median survival time (MST) for untreated dogs was 25 days, whereas the MST for treated dogs was 332 days (Log Rank,P < 0.0001). Treatment with IC chemotherapy was well tolerated. This study suggests that IC chemotherapy with mitoxantrone and/or carboplatin is an effective treatment for dogs with carcinomatosis, sarcomatosis or mesothelioma, with or without malignant effusion.
Vascular‐targeted photodynamic therapy (VTP) of a canine‐transmissible venereal tumour in a murine model with Pd‐bacteriopheophorbide (WST09)
Authors: Vilensky J. , Koudinova N. V. , Harmelin A. , Scherz A. , Salomon Y. 
Published: December 2005

AbstractTreatment of canine‐transmissible venereal tumour (CTVT) with local vascular‐targeted photodynamic therapy (VTP) using Pd‐bacteriopheophorbide (WST09) as a drug is suggested as an alternative to conventional chemotherapy. Male CD1 nude mice were subcutaneously grafted with the xenograft‐transmissible canine venereal tumour (XTVT). The VTP protocol delivered once consisted of intravenous administration of WST09 (10 mg kg−1) followed by immediate local illumination with a diode laser (763 nm). Controls included animals treated with light or WST09 alone. Macroscopic and microscopic evaluations of tumour response were conducted 10, 24 and 48 h after treatment. Upon VTP, tumours underwent necrosis that lasted 8–10 days and exhibited complete healing by 25–35 days, reaching an overall long‐term cure rate (83%) by 90 days after treatment. This study suggests that VTP with WST09 can efficiently treat CTVT in a single session, as compared with 4–6 sessions of chemotherapy and thus may be feasible for common veterinary practice, particularly under ambulatory conditions.
Detection of centrosome amplification as a surrogate marker of dysfunction in the p53 pathway –p53 gene mutation or MDM2 overexpression
Authors: Kaneko N. , Okuda M. , Toyama N. , Oikawa T. , Watanabe M. , Kanaya N. , Yazawa M. , Hasegawa K. , Morimoto M. , Hayashi T. , Une S. , Nakaichi M. , Taura Y. , Tsujimoto H. , Inokuma H. 
Published: December 2005

AbstractIn human and canine cancers, the inactivation of p53 protein as well as p53 gene mutation and MDM2 overexpression result in centrosome amplification that in turn contributes to chromosomal instability. To explore the usefulness of the detection of centrosome amplification as a surrogate marker of dysfunction in the p53 pathway, we systematically analysed centrosome amplification, p53 overexpression, p53 gene mutation and MDM2 overexpression in canine tumours. Centrosome amplification was detected in 16 of 51 (31%) naturally developing tumours in dogs. All the tumour specimens with aberrations in the p53 pathway, including p53 overexpression, p53 gene mutation or MDM2 overexpression, showed centrosome amplification, suggesting that the detection of centrosome amplification could serve as a preliminary surrogate marker of dysfunction in the p53 pathway.