bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacteria associated with iron seeps in a sulfur-rich, neutral pH, freshwater ecosystem
Authors: Haaijer Suzanne C M , Harhangi Harry R , Meijerink Bas B , Strous Marc , Pol Arjan , Smolders Alfons J P , Verwegen Karin , Jetten Mike S M , Op den Camp Huub J M 
Published: August 2008

Abstract
The freshwater nature reserve De Bruuk is an iron- and sulfur-rich minerotrophic peatland containing many iron seeps and forms a suitable habitat for iron and sulfur cycle bacteria. Analysis of 16S rRNA gene-based clone libraries showed a striking correlation of the bacterial population of samples from this freshwater ecosystem with the processes of iron reduction (genus Geobacter), iron oxidation (genera Leptothrix and Gallionella) and sulfur oxidation (genus Sulfuricurvum). Results from fluorescence in situ hybridization analyses with a probe specific for the beta-1 subgroup of Proteobacteria, to which the genera Leptothrix and Gallionella belong, and newly developed probes specific for the genera Geobacter and Sulfuricurvum, supported the clone library data. Molecular data suggested members of the epsilonproteobacterial genus Sulfuricurvum as contributors to the oxidation of reduced sulfur compounds in the iron seeps of De Bruuk. In an evaluation of anaerobic dimethyl sulfide (DMS)-degrading activity of sediment, incubations with the electron acceptors sulfate, ferric iron and nitrate were performed. The fastest conversion of DMS was observed with nitrate. Further, a DMS-oxidizing, nitrate-reducing enrichment culture was established with sediment material from De Bruuk. This culture was dominated by dimorphic, prosthecate bacteria, and the 16S rRNA gene sequence obtained from this enrichment was closely affiliated with Hyphomicrobium facile, which indicates that the Hyphomicrobium species are capable of both aerobic and nitrate-driven DMS degradation.
A semiparametric test to detect associations between quantitative traits and candidate genes in structured populations
Authors: Li Meijuan , Reilly Cavan , Hanson Timothy 
Published: August 2008

Abstract
Motivation: Although population-based association mapping may be subject to the bias caused by population stratification, alternative methods that are robust to population stratification such as family-based linkage analysis have lower mapping resolution. Recently, various statistical methods robust to population stratification were proposed for association studies, using unrelated individuals to identify associations between candidate genes and traits of interest. The association between a candidate gene and a quantitative trait is often evaluated via a regression model with inferred population structure variables as covariates, where the residual distribution is customarily assumed to be from a symmetric and unimodal parametric family, such as a Gaussian, although this may be inappropriate for the analysis of many real-life datasets.
Results: In this article, we proposed a new structured association (SA) test. Our method corrects for continuous population stratification by first deriving population structure and kinship matrices through a set of random genetic markers and then modeling the relationship between trait values, genotypic scores at a candidate marker and genetic background variables through a semiparametric model, where the error distribution is modeled as a mixture of Polya trees centered around a normal family of distributions. We compared our model to the existing SA tests in terms of model fit, type I error rate, power, precision and accuracy by application to a real dataset as well as simulated datasets.
Contact: meijuanl@biostat.umn.edu
Supervised principal component analysis for gene set enrichment of microarray data with continuous or survival outcomes
Authors: Chen Xi , Wang Lily , Smith Jonathan D. , Zhang Bing 
Published: August 2008

AbstractMotivation: Gene set analysis allows formal testing of subtle but coordinated changes in a group of genes, such as those defined by Gene Ontology (GO) or KEGG Pathway databases. We propose a new method for gene set analysis that is based on principal component analysis (PCA) of genes expression values in the gene set. PCA is an effective method for reducing high dimensionality and capture variations in gene expression values. However, one limitation with PCA is that the latent variable identified by the first PC may be unrelated to outcome.Results: In the proposed supervised PCA (SPCA) model for gene set analysis, the PCs are estimated from a selected subset of genes that are associated with outcome. As outcome information is used in the gene selection step, this method is supervised, thus called the Supervised PCA model. Because of the gene selection step, test statistic in SPCA model can no longer be approximated well using t-distribution. We propose a two-component mixture distribution based on Gumbel exteme value distributions to account for the gene selection step. We show the proposed method compares favorably to currently available gene set analysis methods using simulated and real microarray data.Software: The R code for the analysis used in this article are available upon request, we are currently working on implementing the proposed method in an R package.Contact: chenx3@ccf.org.
Melvin Calvin. 8 April 1911 — 8 January 1997
Authors: Seaborg Glenn T. , Benson Andrew A. 
Published: August 2008

Melvin Calvin died in Berkeley on 8 January 1997, at the age of 85, from a heart attack following years of declining health. He was widely known for his mental intensity, skill in asking questions, and impressive presentation of his research and ideas.During the period1946–57 Calvin directed laboratories utilizing carbon–14 and other radio–isotopes in the University of California's Radiation Laboratory, founded by Ernest Orlando Lawrence. Among his achievements was the delineation of the path of carbon in photo synthesis, for which he was awarded a Nobel Prize in 1961. He was elected to the National Academy of Sciences in 1954. Among his many honours were the Priestley Medal of the American Chemical Society in 1978, the US National Medal of Science in 1989, and the Davy Medal of the Royal Society in1964.
ETHICS COMMITTEES IN WESTERN AND CENTRAL AFRICA: CONCRETE FOUNDATIONS
Authors: EFFA PIERRE , MASSOUGBODJI ACHILLE , NTOUMI FRANCINE , HIRSCH FRANÇOIS , DEBOIS HENRI , VICARI MARISSA , DERME ASSETOU , NDEMANGA‐KAMOUNE JACQUES , NGUEMBO JOSEPH , IMPOUMA BENIDO , AKUÉ JEAN‐PAUL , EHOUMAN ARMAND , DIEYE ALIOUNE , KILAMA WEN 
Published: August 2008

ABSTRACTThe involvement of developing countries in international clinical trials is necessary for the development of appropriate medicines for local populations. However, the absence of appropriate structures for ethical review represents a barrier for certain countries. Currently there is very little information available on existing structures dedicated to ethics in western and central Africa. This article briefly describes historical milestones in the development of networks dedicated to capacity building in ethical review in these regions and outlines the major conclusions of two workshops on this issue, which were held in September and October 2002 in Libreville, Gabon, and Paris, France. The workshops were the culmination of collaboration between the African Malaria Network Trust (AMANET) and the Pan African Bioethics Initiative (PABIN). They produced an update on ethics organizations with regard to mission, function, activities, members, and contact people, in eight countries within the regions discussed. As a result of the commitment of mandated delegates, a further prominent outcome followed these workshops: the creation of national structures, where none existed before, dedicated to the ethical review of clinical trials.
Is ACCTRAN better than DELTRAN?
Authors: Agnarsson Ingi , Miller Jeremy A. 
Published: August 2008

AbstractWhen parsimony ancestral character reconstruction is ambiguous, it is often resolved in favour of the more complex character state. Hence, secondary loss (secondary “absence”) of a complex feature is favoured over parallel gains of that feature as this preserves the stronger hypothesis of homology. We believe that such asymmetry in character state complexity is important information for understanding character evolution in general. However, we here point out an inappropriate link that is commonly made between this approach and the accelerated transformation (ACCTRAN) algorithm. In ACCTRAN, changes are assigned along branches of a phylogenetic tree as close to the root as possible. This has been taken to imply that ACCTRAN will minimize hypotheses of parallel origins of complex traits and thus that ACCTRAN is philosophically better justified than the alternatives, such as delayed transformation (DELTRAN), where changes are assigned along branches as close to the tips as possible. We provide simple examples to show that such views are mistaken and that neither ACCTRAN nor DELTRAN consistently minimize parallel gain of complex traits. We therefore do not see theoretical grounds for favouring the popular ACCTRAN algorithm.© The Willi Hennig Society 2008.
Adiponectin is an indicator of insulin resistance in non‐obese prepubertal children born large for gestational age (LGA) and is affected by birth weight
Authors: Darendeliler Feyza , Poyrazoglu Sukran , Sancakli Ozlem , Bas Firdevs , Gokcay Gulbin , Aki Semih , Eskiyurt Nurten 
Published: August 2008

SummaryBackground and objective  Being born as large for gestational age (LGA) has an increased risk of developing insulin resistance. Hypoadiponectinaemia is associated with insulin resistance. The aim of this study was to evaluate adiponectin levels and insulin resistance in association with body composition in LGA born non‐obese children at prepubertal ages.Patients and methods  Thirty‐five (17 female and 18 male) LGA born non‐obese children (mean age 4·8 ± 0·3 years) were evaluated with respect to glucose, insulin, IGFBP‐1, leptin, adiponectin levels and body composition by DEXA. Their data were compared to that of non‐obese 49 (20 female, 29 male) appropriate for gestational age (AGA) children (mean age 3·8 ± 0·1 year).Results  LGA children, who had similar body mass index standard deviation scores (BMI SDS) as AGA children, had significantly higher insulin (P = 0·043) and statistically borderline significant homeostasis model assessment‐insulin resistance (HOMA‐IR) levels (P = 0·054) than those of AGA children. Adiponectin levels were significantly lower in LGA than AGA children (P = 0·004) even after controlling for age, sex and BMI (P = 0·016). IGFBP‐1, leptin levels and body composition did not show a difference. When the LGA group was divided into subgroups according to birth weight, the analysis revealed that after controlling for BMI, being an LGA and having a higher birth weight in the upper half were associated with lower adiponectin levels (estimated marginal means of logarithmic adiponectin levels 2·6 ± 0·2 vs. 2·1 ± 0·2 µg/ml, P = 0·042).Conclusion  LGA children have higher insulin and lower adiponectin levels than AGA children in spite of similar BMI. Adiponectin is a better indicator of insulin resistance in LGA children at prepubertal ages and is affected by birth weight.
Secretion of interferon‐γ by human macrophages demonstrated at the single‐cell level after costimulation with interleukin (IL)‐12 plus IL‐18
Authors: Darwich Laila , Coma Gemma , Peña Ruth , Bellido Rocio , Blanco Ester J. J. , Este José A. , Borras Francesc E. , Clotet Bonaventura , Ruiz Lidia , Rosell Antoni , Andreo Felipe , Parkhouse R. Michael E. , Bofill Margarita 
Published: August 2008

SummaryThe interferon (IFN)‐γ component of the immune response plays an essential role in combating infectious and non‐infectious diseases. Induction of IFN‐γ secretion by human T and natural killer (NK) cells through synergistic costimulation with interleukin (IL)‐12 and IL‐18 in the adaptive immune responses against pathogens is well established, but induction of similar activity in macrophages is still controversial, with doubts largely focusing on contamination of macrophages with NK or T cells in the relevant experiments. The possible contribution of macrophages to the IFN response is, however, an important factor relevant to the pathogenesis of many diseases. To resolve this issue, we analysed the production of IFN‐γ at the single‐cell level by immunohistochemistry and by enzyme‐linked immunosorbent spot (ELISPOT) analysis and unequivocally demonstrated that human macrophages derived from monocytes in vitro through stimulation with a combination of IL‐12 and IL‐18 or with macrophage colony‐stimulating factor (M‐CSF) were able to produce IFN‐γ when further stimulated with a combination of IL‐12 and IL‐18. In addition, naturally activated alveolar macrophages immediately secreted IFN‐γ upon treatment with IL‐12 and IL‐18. Therefore, human macrophages in addition to lymphoid cells contribute to the IFN‐γ response, providing another link between the innate and acquired immune responses.
Evaluation of a community‐based intervention to enhance breast cancer screening practices in Brazil
Authors: Thuler Luiz Claudio Santos , Freitas Hilda Guimaraes 
Published: August 2008

AbstractObjectives  The primary aim of this study was to evaluate a programme called ‘Touch of Life’ (Toque de Vida in Portuguese) proposed to increase breast cancer screening awareness and provide free clinical breast examination (CBE) for asymptomatic women 40–69 years of age.Method  Evaluation of the intervention used a before‐and‐after quasi‐experimental design without control groups. A total of 11 762 women, living in three cities in the State of Mato Grosso do Sul, Brazil, were submitted to breast cancer screening by CBE. The evaluation indicators were participation rate, abnormal call rate, cancer detection rate and rate of advanced‐stage breast cancers.Results  Mean age was 42.6 years. Most women belonged to the 40–69‐year age group (56.7%) and had less than 8 years of formal education (60.9%). Mean age at menarche was 12.9 years (±1.7). The proportions of parous and nulliparous women were 85.1% and 14.8% respectively. Mean age of first pregnancy was 19.8 years (±4.4). Less than one‐third (29.3%) of the women had a history of abortion or miscarriage. History of breastfeeding was reported by 79.3% of the women, and 14.4% had used hormone replacement therapy at some time. For women between 40 and 49 years of age, the participation rate was 74.9%. The abnormal call rate for CBE was 10.7%. The main abnormalities found were breast lumps in 630 women (5.4%), thickening in 332 (2.8%) and other suspicious lesions in 316 (2.7%). The breast cancer detection rate was 1.3 per thousand, and only 20.0% of women were diagnosed with advanced‐stage disease (stages III and IV).Conclusions  The intervention was effective in detecting new cases of breast cancer. A community‐wide screening approach based on CBE may be effective to enhance breast cancer detection in vulnerable populations, especially in areas where mammography screening is not available.
Automatic seamless mosaicing of microscopic images: enhancing appearance with colour degradation compensation and wavelet‐based blending
Authors: HSU W.‐Y. , POON W.‐F. PAUL , SUN Y.‐N. 
Published: August 2008

SummaryIn order to observe the fine details of biomedical specimens, various kinds of high‐magnification microscopes are used. However, they suffer from a limited field of view when visualizing highly magnified specimens. Image mosaicing techniques are necessary to integrate two or more partially overlapping images into one and make the whole specimen visible. In this study, we propose a new system that automatically creates panoramic images by mosaicing all the microscopic images acquired from a specimen. Not only does it effectively compensate for the congenital narrowness in microscopic views, but it also results in the mosaiced image containing as little distortion with respect to the originals as possible. The system consists of four main steps: (1) feature point extraction using multiscale wavelet analysis, (2) image matching based on feature points or by projection profile alignment, (3) colour difference adjustment and optical degradation compensation with a Gaussian‐like model and (4) wavelet‐based image blending. In addition to providing a precise alignment, the proposed system also takes into account the colour deviations and degradation in image mosaicing. The visible seam lines are eliminated after image blending. The experimental results show that the system performs well on differently stained image sequences and is effective on acquired images with large colour variations and degradation. It is expected to be a practical tool for microscopic image mosaicing.
Reverse genetics screen identifies six proteins important for malaria development in the mosquito
Authors: Ecker Andrea , Bushell Ellen S. C. , Tewari Rita , Sinden Robert E. 
Published: August 2008

SummaryTransmission from the vertebrate host to the mosquito vector represents a major population bottleneck in the malaria life cycle that can successfully be targeted by intervention strategies. However, to date only about 25 parasite proteins expressed during this critical phase have been functionally analysed by gene disruption. We describe the first systematic, larger scale generation and phenotypic analysis of Plasmodium berghei knockout (KO) lines, characterizing 20 genes encoding putatively secreted proteins expressed by the ookinete, the parasite stage responsible for invasion of the mosquito midgut. Of 12 KO lines that were generated, six showed significant reductions in parasite numbers during development in the mosquito, resulting in a block in transmission of five KOs. While expression data, time point of essential function and mutant phenotype correlate well in three KOs defective in midgut invasion, in three KOs that fail at sporulation, maternal inheritance of the mutant phenotype suggests that essential function occurs during ookinete formation and thus precedes morphological abnormalities by several days.
Assays with lower detection limits: implications for epidemiological investigations
Authors: Whitcomb Brian W. , Schisterman Enrique F. 
Published: August 2008

SummaryEpidemiological investigations of health effects related to chronic low‐level exposures or other circumstances often face the difficult task of dealing with levels of biomarkers that are hard to detect and/or quantify. In these cases instrumentation may not adequately measure biomarker levels. Reasons include a failure of instruments to detect levels below a certain value or, alternatively, interference by error or ‘noise’. Current laboratory practice determines a ‘limit of detection (LOD)’, or some other detection threshold, as a function of the distribution of instrument ‘noise’. Although measurements are produced above and below this threshold in many circumstances, rather than numerical data, all points observed below this threshold may be reported as ‘not detected’. The focus of this process of determination of the LOD is instrument noise and avoiding false positives. Moreover, uncertainty is assumed to apply only to the lowest values, which are treated differently from above‐threshold values, thereby potentially creating a false dichotomy.In this paper we discuss the application of thresholds to measurement of biomarkers and illustrate how conventional approaches, though appropriate for certain settings, may fail epidemiological investigations. Rather than automated procedures that subject observed data to a standard threshold, the authors advocate investigators to seek information on the measurement process and request all observed data from laboratories (including the data below the threshold) to determine appropriate treatment of those data.
PREVALENCE AND CORRELATES OF ANAEMIA IN ESSENTIAL HYPERTENSION
Authors: Paul Biju , Wilfred Neeta C , Woodman Richard , DePasquale Carmine 
Published: August 2008

SUMMARY

Anaemia is an independent predictor of mortality in pro‐atherosclerotic conditions with impaired endothelial function, such as diabetes and chronic kidney disease. However, the prevalence of anaemia in hypertension, a condition characterized by endothelial dysfunction, is unclear.
Haemoglobin concentration, renal function and echocardiographic parameters of 187 consecutive patients (M : F 83 : 104; mean (±SD) age 58 ± 15 years) who underwent ambulatory blood pressure monitoring between 2005 and 2006 were assessed in a tertiary level university hospital.
The prevalence of normocytic anaemia in our cohort of hypertensive patients was 16% and was higher in patients with uncontrolled hypertension (20%) than among those with well‐controlled hypertension (4%; P = 0.03). Red cell indices (mean corpuscular volume, mean cell haemoglobin and mean cell haemoglobin concentration) did not differ between the groups. However, the haemoglobin concentration was progressively lower between patients with well‐controlled hypertension and uncontrolled hypertension (P = 0.007). Haematological parameters did not correlate to echocardiographic indices of left ventricular size and function.
Normocytic anaemia was highly prevalent in hypertensive patients. Poor blood pressure control was associated with lower haemoglobin concentration. This may indicate a higher cardiovascular risk in uncontrolled hypertension, as in other pro‐atherosclerotic conditions. Additional studies are needed to evaluate the effect of anaemia on morbidity and mortality in hypertensive patients.
POTENTIAL ROLE OF NITRIC OXIDE IN CONTRACTION‐STIMULATED GLUCOSE UPTAKE AND MITOCHONDRIAL BIOGENESIS IN SKELETAL MUSCLE
Authors: McConell Glenn K , Wadley Glenn D 
Published: August 2008

SUMMARYThe present review discusses the potential role of nitric oxide (NO) in the: (i) regulation of skeletal muscle glucose uptake during exercise; and (ii) activation of mitochondrial biogenesis after exercise.We have shown in humans that local infusion of an NO synthase inhibitor during exercise attenuates increases in skeletal muscle glucose uptake without affecting blood flow. Recent studies from our laboratory in rodents support these findings in humans, although rodent studies from other laboratories have yielded conflicting results.There is clear evidence that NO increases mitochondrial biogenesis in non‐contracting cells and that NO influences basal skeletal muscle mitochondrial biogenesis. However, there have been few studies examining the potential role of NO in the activation of mitochondrial biogenesis following an acute bout of exercise or in response to exercise training. Early indications are that NO is not involved in regulating the increase in mitochondrial biogenesis that occurs in response to exercise.Exercise is considered the best prevention and treatment option for diabetes, but unfortunately many people with diabetes do not or cannot exercise regularly. Alternative therapies are therefore critical to effectively manage diabetes. If skeletal muscle NO is found to play an important role in regulating glucose uptake and/or mitochondrial biogenesis, pharmaceutical agents designed to mimic these effects of exercise may improve glycaemic control.