bluuebunny/crossref_metadata_2025_split huggingface dataset:
GenMAPP 2: new features and resources for pathway analysis
Authors: Salomonis Nathan , Hanspers Kristina , Zambon Alexander C , Vranizan Karen , Lawlor Steven C , Dahlquist Kam D , Doniger Scott W , Stuart Josh , Conklin Bruce R , Pico Alexander R 
Published: June 2007

Abstract

Background
Microarray technologies have evolved rapidly, enabling biologists to quantify genome-wide levels of gene expression, alternative splicing, and sequence variations for a variety of species. Analyzing and displaying these data present a significant challenge. Pathway-based approaches for analyzing microarray data have proven useful for presenting data and for generating testable hypotheses.

Results
To address the growing needs of the microarray community we have released version 2 of Gene Map Annotator and Pathway Profiler (GenMAPP), a new GenMAPP database schema, and integrated resources for pathway analysis. We have redesigned the GenMAPP database to support multiple gene annotations and species as well as custom species database creation for a potentially unlimited number of species. We have expanded our pathway resources by utilizing homology information to translate pathway content between species and extending existing pathways with data derived from conserved protein interactions and coexpression. We have implemented a new mode of data visualization to support analysis of complex data, including time-course, single nucleotide polymorphism (SNP), and splicing. GenMAPP version 2 also offers innovative ways to display and share data by incorporating HTML export of analyses for entire sets of pathways as organized web pages.

Conclusion
GenMAPP version 2 provides a means to rapidly interrogate complex experimental data for pathway-level changes in a diverse range of organisms.
Normalization and experimental design for ChIP-chip data
Authors: Peng Shouyong , Alekseyenko Artyom A , Larschan Erica , Kuroda Mitzi I , Park Peter J 
Published: June 2007

Abstract

Background
Chromatin immunoprecipitation on tiling arrays (ChIP-chip) has been widely used to investigate the DNA binding sites for a variety of proteins on a genome-wide scale. However, several issues in the processing and analysis of ChIP-chip data have not been resolved fully, including the effect of background (mock control) subtraction and normalization within and across arrays.

Results
The binding profiles of Drosophila male-specific lethal (MSL) complex on a tiling array provide a unique opportunity for investigating these topics, as it is known to bind on the X chromosome but not on the autosomes. These large bound and control regions on the same array allow clear evaluation of analytical methods.
We introduce a novel normalization scheme specifically designed for ChIP-chip data from dual-channel arrays and demonstrate that this step is critical for correcting systematic dye-bias that may exist in the data. Subtraction of the mock (non-specific antibody or no antibody) control data is generally needed to eliminate the bias, but appropriate normalization obviates the need for mock experiments and increases the correlation among replicates. The idea underlying the normalization can be used subsequently to estimate the background noise level in each array for normalization across arrays. We demonstrate the effectiveness of the methods with the MSL complex binding data and other publicly available data.

Conclusion
Proper normalization is essential for ChIP-chip experiments. The proposed normalization technique can correct systematic errors and compensate for the lack of mock control data, thus reducing the experimental cost and producing more accurate results.
Microarray for serotyping of Bartonella species
Authors: Bonhomme Cyrille J , Nappez Claude , Raoult Didier 
Published: June 2007

AbstractBackgroundBacteria of the genusBartonellaare responsible for a large variety of human and animal diseases. Serological typing ofBartonellais a method that can be used for differentiation and identification ofBartonellasubspecies.ResultsWe have developed a novel multiple antigenic microarray to serotypeBartonellastrains and to select poly and monoclonal antibodies. It was validated using mouse polyclonal antibodies against 29Bartonellastrains. We then tested the microarray for serotyping ofBartonellastrains and defining the profile of monoclonal antibodies.Bartonellastrains gave a strong positive signal and all were correctly identified. Screening of monoclonal antibodies towards the Gro EL protein ofB. clarridgeiaeidentified 3 groups of antibodies, which were observed with variable affinities againstBartonellastrains.ConclusionWe demonstrated that microarray of spotted bacteria can be a practical tool for serotyping of unidentified strains or species (and also for affinity determination) by polyclonal and monoclonal antibodies. This could be used in research and for identification of bacterial strains.
Interaction of Salivary alpha-Amylase and Amylase-Binding-Protein A (AbpA) of Streptococcus gordonii with Glucosyltransferase of S. gordonii and Streptococcus mutans
Authors: Chaudhuri Biswendu , Rojek Jennifer , Vickerman M Margaret , Tanzer Jason M , Scannapieco Frank A 
Published: June 2007

Abstract

Background
Glucosyltransferases (Gtfs), enzymes that produce extracellular glucans from dietary sucrose, contribute to dental plaque formation by Streptococcus gordonii and Streptococcus mutans. The alpha-amylase-binding protein A (AbpA) of S. gordonii, an early colonizing bacterium in dental plaque, interacts with salivary amylase and may influence dental plaque formation by this organism. We examined the interaction of amylase and recombinant AbpA (rAbpA), together with Gtfs of S. gordonii and S. mutans.

Results
The addition of salivary alpha-amylase to culture supernatants of S. gordonii precipitated a protein complex containing amylase, AbpA, amylase-binding protein B (AbpB), and the glucosyltransferase produced by S. gordonii (Gtf-G). rAbpA was expressed from an inducible plasmid, purified from Escherichia coli and characterized. Purified rAbpA, along with purified amylase, interacted with and precipitated Gtfs from culture supernatants of both S. gordonii and S. mutans. The presence of amylase and/or rAbpA increased both the sucrase and transferase component activities of S. mutans Gtf-B. Enzyme-linked immunosorbent assay (ELISA) using anti-Gtf-B antibody verified the interaction of rAbpA and amylase with Gtf-B. A S. gordonii abp A-deficient mutant showed greater biofilm growth under static conditions than wild-type in the presence of sucrose. Interestingly, biofilm formation by every strain was inhibited in the presence of saliva.

Conclusion
The results suggest that an extracellular protein network of AbpA-amylase-Gtf may influence the ecology of oral biofilms, likely during initial phases of colonization.
Outcome measurement in clinical trials for ulcerative colitis: towards standardisation
Authors: Cooney Rachel M , Warren Bryan F , Altman Douglas G , Abreu Maria T , Travis Simon PL 
Published: June 2007

Abstract
Clinical trials on novel drug therapies require clear criteria for patient selection and agreed definitions of disease remission. This principle has been successfully applied in the field of rheumatology where agreed disease scoring systems have allowed multi-centre collaborations and facilitated audit across treatment centres. Unfortunately in ulcerative colitis this consensus is lacking. Thirteen scoring systems have been developed but none have been properly validated. Most trials choose different endpoints and activity indices, making comparison of results from different trials extremely difficult. International consensus on endoscopic, clinical and histological scoring systems is essential as these are the key components used to determine entry criteria and outcome measurements in clinical trials on ulcerative colitis. With multiple new therapies under development, there is a pressing need for consensus to be reached.
Changes in the incidence and outcome for early acute kidney injury in a cohort of Australian intensive care units
Authors: Bagshaw Sean M , George Carol , Bellomo Rinaldo ,   the ANZICS Database Management Committee
Published: June 2007

Abstract
Introduction
There is limited information on whether the incidence of acute kidney injury (AKI) in critically ill patients has changed over time and there is controversy on whether its outcome has improved.

Methods
We interrogated the Australian New Zealand Intensive Care Society Adult Patient Database to obtain data on all adult admissions to 20 Australian intensive care units (ICUs) for ≥ 24 hours from 1 January 1996 to 31 December 2005. Trends in incidence and mortality for ICU admissions associated with early AKI were assessed.

Results
There were 91,254 patient admissions to the 20 study ICUs, with 4,754 cases of AKI, for an estimated crude cumulative incidence of 5.2% (95% confidence interval, 5.1 to 5.4). The incidence of AKI increased during the study period, with an estimated annual increment of 2.8% (95% confidence interval, 1.0 to 5.6, P = 0.04). The crude hospital mortality was significantly higher for patients with AKI than those without (42.7% versus 13.4%; odds ratio, 4.8; 95% confidence interval, 4.5 to 5.1; P < 0.0001). There was also a decrease in AKI crude mortality (annual percentage change, -3.4%; 95% confidence interval, -4.7 to -2.12; P < 0.001), however, which was not seen in patients without AKI. After covariate adjustment, AKI remained associated with a higher mortality (odds ratio, 1.23; 95% confidence interval, 1.14 to 1.32; P < 0.001) and there was a declining trend in the odds ratio for hospital mortality.

Conclusion
Over the past decade, in a large cohort of critically ill patients admitted to 20 Australian ICUs, there has been a significant rise in the incidence of early AKI while the mortality associated with AKI has declined.
Toxicogenomic analysis of Caenorhabditis elegans reveals novel genes and pathways involved in the resistance to cadmium toxicity
Authors: Cui Yuxia , McBride Sandra J , Boyd Windy A , Alper Scott , Freedman Jonathan H 
Published: June 2007

Abstract
Background
Exposure to cadmium is associated with a variety of human diseases. At low concentrations, cadmium activates the transcription of stress-responsive genes, which can prevent or repair the adverse effects caused by this metal.

Results
Using Caenorhabditis elegans, 290 genes were identified that are differentially expressed (>1.5-fold) following a 4 or 24 hour exposure to cadmium. Several of these genes are known to be involved in metal detoxification, including mtl-1, mtl-2, cdr-1 and ttm-1, confirming the efficacy of the study. The majority, however, were not previously associated with metal-responsiveness and are novel. Gene Ontology analysis mapped these genes to cellular/ion trafficking, metabolic enzymes and proteolysis categories. RNA interference-mediated inhibition of 50 cadmium-responsive genes resulted in an increased sensitivity to cadmium toxicity, demonstrating that these genes are involved in the resistance to cadmium toxicity. Several functional protein interacting networks were identified by interactome analysis. Within one network, the signaling protein KEL-8 was identified. Kel-8 protects C. elegans from cadmium toxicity in a mek-1 (MAPKK)-dependent manner.

Conclusion
Because many C. elegans genes and signal transduction pathways are evolutionarily conserved, these results may contribute to the understanding of the functional roles of various genes in cadmium toxicity in higher organisms.
Measuring the accuracy of genome-size multiple alignments
Authors: Prakash Amol , Tompa Martin 
Published: June 2007

AbstractWhole-genome alignments are invaluable for comparative genomics. Before doing any comparative analysis on a region of interest, one must have confidence in that region's alignment. We provide a methodology to measure the accuracy of arbitrary regions of these alignments, and apply it to the UCSC Genome Browser's 17-vertebrate alignment. We identify 9.7% (21 Mbp) of the human chromosome 1 alignment as suspiciously aligned. We present independent evidence that many of these suspicious regions represent misalignments.
Splitting the Difference
Authors: KNUTSON BRIAN , WIMMER G. ELLIOTT 
Published: June 2007

So, nat'ralists observe, a flea Hath smaller fleas that on him prey; And these have smaller still to bite 'em; And so proceedad infinitum. —Jonathan Swift,On Poetry: A Rhapsody, 1733Abstract: Animal research and human brain imaging findings suggest that reward processing involves distinct anticipation and outcome phases. Error terms in popular models of reward learning (such as the temporal difference [TD] model) do not distinguish between the updating of expectations in response to reward cues and outcomes. Thus, correlating a single error term with neural activation assumes recruitment of similar neural substrates at each update. Here, we split the error term to separately model reward prediction and prediction errors, and compare the fit of single versus split error terms to functional magnetic resonance imaging (FMRI) data acquired during a monetary incentive delay task. We speculate and find that while the nucleus accumbens computes gain prediction in response to cues, the mesial prefrontal cortex (MPFC) computes gain prediction errors in response to outcomes. In addition to offering a more comprehensive and anatomically situated view of reward processing, split error terms generate novel predictions about psychiatric symptoms and lesion‐induced deficits.
Fusion of Metabolic Function and Morphology: Sequential [18F]Fluorodeoxyglucose Positron-Emission Tomography/Computed Tomography Studies Yield New Insights Into the Natural History of Bone Metastases in Breast Cancer
Authors: Du Yong , Cullum Ian , Illidge Tim M. , Ell Peter J. 
Published: June 2007

Purpose By monitoring bone metastases with sequential [18F]fluorodeoxyglucose positron-emission tomography/computed tomography ([18F]FDG-PET/CT) imaging, this study investigates the clinical relevance of [18F]FDG uptake features of bone metastases with various radiographic appearances. Patients and Methods Bone metastases were found in 67 of 408 consecutive patients with known/suspected recurrent breast cancer on [18F]FDG-PET/CT, characterized by CT morphology changes and/or bony [18F]FDG uptake. Twenty-five of the patients had sequential [18F]FDG-PET/CT examinations (86 studies) over an average follow-up period of 23 months. The temporal changes in [18F]FDG uptake and corresponding CT morphology features of 146 bone lesions identified in these 25 patients were followed up and correlated with therapeutic outcome retrospectively. Results The 146 lesions were classified as osteolytic (77), osteoblastic (41), mixed-pattern (11), or no change/negative (17) on CT. The majority of the osteolytic (72; 93.5%) and mixed-pattern lesions (nine; 81.8%), but fewer of the osteoblastic lesions (25; 61%), showed increased [18F]FDG uptake. After treatment, 58 osteolytic lesions (80.5%) became [18F]FDG negative and osteoblastic on CT and only 14 relatively large lesions (19.5%) remained [18F]FDG avid. Of the 25 [18F]FDG-avid osteoblastic lesions, 13 (52%) became [18F]FDG negative, but 12 (48%) remained [18F]FDG avid and increased in size on CT. Five of the mixed-pattern lesions remained [18F]FDG avid after treatment. All 17 CT-negative lesions became [18F]FDG negative; however, nine of them became osteoblastic. None of the initially [18F]FDG-negative lesions showed [18F]FDG avidity during follow-up. Conclusion [18F]FDG uptake reflects the immediate tumor activity of bone metastases, whereas the radiographic morphology changes vary greatly with time among patients.
The effect of strain rate on the plastic flow characteristics of steel and aluminium sheet
Authors: Bramley A N , Mellor P B 
Published: June 2007

Work-hardening characteristics for sheet steel and aluminium have been obtained experimentally over a range of strain rates from 10−4 to 102/s. Use of the diaphragm test enables work-hardening characteristics to be obtained to much higher plastic strains than is possible in uniaxial tension. Results for killed steel show that the slope of the work-hardening characteristics decreases with increase in strain rate. Tentative extrapolation of the results suggests that if similar tests could be carried out at a strain rate of 104 then the work hardening characteristic would be that of an ideally plastic solid. In the case of aluminium the above phenomenon is not so marked and it is not possible to make even a tentative extrapolation to higher strain rates.
Toxoplasmosis
Authors: Fulton J. D. 
Published: June 2007

Summary Toxoplasma is unique among protozoa in its wide distribution and lack of host or tissue specificity. It is a successful parasite in so far as it rarely causes death of the host. The infection is frequently inapparent and this type of infection may be passed from mother to foetus with disastrous results. In domestic animals, it is a cause of serious economic losses, especially among lambs in this country and New Zealand. It may be associated with concomitant infections such as distemper in dogs and helminth infection in cats. In man lymphadenopathy is the commonest clinical manifestation; various affections of the eye and pneumonia also occur. The means of transmission in nature is still unknown apart from the congenital form. It is, however, regarded as a zoonosis and women should take special care where sick animals are concerned. They should be excluded from experimental work on toxoplasmosis. The reaction of the parasite to drugs is unlike that of most protozoa, but curative treatment is possible.
Mycoplasmas and Their Role as Rodent Pathogens
Authors: Fallon R. J. 
Published: June 2007

Summary Mycoplasmas are the smallest known free-living form of life, and differ from bacteria in a number of characteristics. They are widely distributed in the animal kingdom and may give rise to both acute and latent infections as well as being present as normal flora. The three principal rodent pathogens so far described are Mycoplasma pulmonis, Mycoplasma arthritidis and Mycoplasma neuroiyticum. The diseases associated with these organisms are discussed.
The Histology of The Oral Mucosa of Macaca Irus
Authors: Cohen Lawrence 
Published: June 2007

Summary The histology of the oral mucosa of Macaca irus was studied in nineteen monkeys. It was found that the oral mucosa of this monkey is identical with that of man. No single specimen of M. irus had orthokeratinization of the gingivae in all regions. In addition, those sections of gingiva which exhibited orthokeratosis had a poorly developed granular layer. Thus it seems unlikely that keratohyalin granules contribute towards keratinization; they probably represent cytoplasmic debris.
Parasites of Laboratory Animals Transmissible to Man
Authors: Gibson T. E. 
Published: June 2007

Summary An assessment is made of the hazards to man from parasites of laboratory animals. The chief danger arises from gastrointestinal helminths and protozoa of primates and tapeworms of rodents and prevention of infection depends on the adoption of normal hygienic measures for disposal of the faeces and bedding of experimental animals. Simian malaria constitutes a possible danger in those parts of the world where suitable vectors exist and in these areas the screening of animal houses against mosquitoes is necessary. Many ectoparasites of laboratory animals are capable of establishing themselves on human beings but their tenure is usually short. Infestation of man can be prevented only by control of the ectoparasites in the laboratory animals and this is desirable for the welfare of the animals themselves. The possibility of human infection with the parasites of laboratory animals can be greatly reduced by a period of quarantine immediately following arrival, during which examination is made for the presence of parasites and appropriate treatment given to remove any found to be present.
The Relationship Between A Rodent Mycoplasma, Mycoplasma Pulmonis, and Certain Mycoplasmas Isolated From Tissue Cultures Inoculated with Material from Patients With Leukaemia
Authors: Fallon R. J. , Jackson D. K. 
Published: June 2007

Summary The relationship between Negroni and strain 880 mycoplasmas, isolated from tissue cultures inoculated with material from leukaemic patients, and a rodent pathogen, Mycoplasma polmonis, were studied in detail. The close relationship previously reported between these strains was confirmed but some serological differences were noted. The importance of these differences in the classification of the organisms is discussed.
Rat-Bite Fever in Laboratory Personnel
Authors: Gledhill A. W. 
Published: June 2007

Summary A few cases of rat-bite fever due to Streptobacillus moniliformis have been reported in laboratory workers. Since many laboratory rats carry the aetiological agent in the upper respiratory tract, the opportunity for human infections is high, and undiagnosed infections are probably commoner than is supposed. The symptoms and means of diagnosis of human cases are described, together with a brief account of the infection in laboratory animals. The human disease is also compared with rat-bite fever due to Spirillum minus, which on current evidence appears to be rarer than that due to Streptobacillus moniliformis.
Urine marking of cages and visual isolation as possible sources of error in behavioural studies of small mammals
Authors: Dagg Anne I. , Bell W. L. , Windsor D. E. 
Published: June 2007

Chipmunks ( Tamias striatus), jumping mice ( Zapus hudsonius), voles ( Microtus pennsylvanicus), deer mice ( Peromyscus maniculalus), hamsters ( Mesocricetus auratus), house mice ( Mus musculus) and gerbils ( Meriones unguiculalus) were individually confined in dark cages. A corner of each cage had been marked with dried urine. Animals tended (311 of 461 tests) to urinate in the marked corner. Animals did not usually urinate (except adult gerbils) or defecate (except hamsters) in their nests. The effect of visual isolation of individual mice was not apparent in organ weights, but did lead to altered behaviour.
The production of experimental vitamin A deficiency in rats and mice
Authors: Moore T. , Holmes P. D. 
Published: June 2007

Vitamin A deficiency in rats and mice was induced by restricting dams and litters from parturition to a pelleted diet made mainly from white flour. Young rats usually developed clear signs of avitaminosis A within 60 days from birth. Mice were more resistant, and some survived for periods up to 150 days from birth. Retention of traces of vitamin A in the liver was no more prolonged in mice than in rats. In mice, enlargement of the prostates and seminal vesicles, and atrophy of the testes, were usually the most prominent pathological features. In rats, timely treatment with vitamin A acid (retinoic acid) cured xerophthalmia and restored growth. Signs of deficiency reappeared soon after its administration was stopped. This procedure allows supplies of animals to be kept in good general health, but ready for the production of acute deficiency at short notice. Retinoic acid was also effective in curing deficient mice. Incidental observations on the eyes and reproductive powers of mice or rats dosed with retinoic acid, and on the response of rats to variations in the casein contents of their diet, are recorded.