bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two-dimensional image fusion of planar bone scintigraphy and radiographs in patients with clinical scaphoid fracture: An imaging study
Authors: Henriksen O. M. , Lonsdale M. N. , Jensen T. D. , Weikop K. L. , Holm O. , Duus B. , Friberg L. 
Published: December 2008

Background: Although magnetic resonance imaging (MRI) is now considered the gold standard in second-line imaging of patients with suspected scaphoid fracture and negative radiographs, bone scintigraphy can be used in patients with pacemakers, metallic implants, or other contraindications to MRI. Bone scintigraphy is highly sensitive for the detection of fractures, but exact localization of scintigraphic lesions may be difficult and can negatively affect diagnostic accuracy. Purpose: To investigate the influence of image fusion of planar bone scintigraphy and radiographs on image interpretation in patients with suspected scaphoid fracture. Material and Methods: In 24 consecutive patients with suspected scaphoid fracture, a standard planar bone scintigraphy of both hands was supplemented with fusion imaging of the injured wrist. Standard and fusion images were evaluated independently by three experienced nuclear medicine physicians. In addition to the diagnosis, the degree of diagnostic confidence was scored in each case. Results: The addition of fusion images changed the interpretation of each of the three observers in seven, four, and two cases, respectively, reducing the number of positive interpretations of two of the observers from 11 and nine cases to six and seven cases, respectively. The degree of diagnostic confidence increased significantly in two observers, and interobserver agreement increased in all three pairs of observers from 0.83, 0.57, and 0.73 to 0.89, 0.8, and 0.9, respectively. Conclusion: Image fusion of planar bone scintigrams and radiographs has a significant influence on image interpretation and increases both diagnostic confidence and interobserver agreement.
Personal Healthcare Worker (HCW) and Work-Site Characteristics That Affect HCWs' Use of Respiratory-Infection Control Measures in Ambulatory Healthcare Settings
Authors: Turnberg Wayne , Daniell William , Simpson Terri , Van Buren Jude , Seixas Noah , Lipkin Edward , Duchin Jeffery 
Published: December 2008

Objectives.To identify healthcare worker (HCW) and work-site characteristics associated with HCWs' reported use of recommended respiratory-infection control practices in primary and emergency care settings.Design.A cross-sectional study using a self-administered questionnaire for HCWs during the summer and fall of 2005.Setting.Primary and emergency care clinics at 5 medical centers in King County, Seattle, Washington.Results.Nurse professionals who reported receiving training (odds ratio [OR], 2.5 [confidence interval {CI}, 1.1–5.9]; P = .029), instructional feedback from supervisors (OR, 3.0 [CI, 1.5–5.9]; P = .002), and management support for implementing safe work practices had a higher odds of also reporting adherence to recommended respiratory precautions, compared with nurses who did not. Training was the only important determinant for adherence to respiratory precaution measures among medical practitioners (OR, 5.5 [CI, 1.2–25.8]; P = .031). The reported rate of adherence to hand hygiene practices was higher among nurse professionals who were male (OR, 2.2 [CI, 1.0–4.9]; P = .045), had infants, small children, or older adults living at home (OR, 2.2 [CI, 1.2–3.9]; P = .007), reported cleanliness and orderliness of the establishment where they worked (OR, 2.0 [CI, 1.1–3.5]; P = .019), had received respiratory-infection control training (OR, 3.2 [CI, 1.8–6.0]; P<.001), and reported fears about catching a dangerous respiratory infection at work (OR, 2.3 [CI, 1.2–4.5]; P= .011).Conclusion.A number of HCW and work-site characteristics associated with HCWs' use of recommended respiratory-infection control measures have been identified. These potentially influential characteristics should be considered as targets or guides for further investigation, which should include the evaluation of intervention strategies.
Reference alignment of SNP microarray signals for copy number analysis of tumors
Authors: Pounds Stan , Cheng Cheng , Mullighan Charles , Raimondi Susana C. , Shurtleff Sheila , Downing James R. 
Published: December 2008

AbstractA new procedure to align single nucleotide polymorphism (SNP) microarray signals for copy number analysis is proposed. For each individual array, this reference alignment procedure (RAP) uses a set of selected markers as internal references to direct the signal alignment. RAP aligns the signals so that each array has a similar signal distribution among its reference markers. An accompanying reference selection algorithm (RSA) uses genotype calls and initial signal intensities to choose two-copy markers as the internal references for each array. After RSA and RAP are applied, each array has a similar distribution of signals of two-copy markers so that across-array signal comparisons are biologically meaningful. An upper bound for a statistical metric of signal misalignment is derived and provides a theoretical basis to choose RSA-RAP over other alignment procedures for copy number analysis of cancers. In our study of acute lymphoblastic leukemia, RSA-RAP gives copy number analysis results that show substantially better concordance with cytogenetics than do two other alignment procedures.Availability: Documented R code is freely available from www.stjuderesearch.org/depts/biostats/refnorm.Contact: stanley.pounds@stjude.orgSupplementary information: Supplementary data are available at Bioinformatics online.
Australia’s deep-water reserve network: implications of false homogeneity for classifying abiotic surrogates of biodiversity
Authors: Williams Alan , Bax Nicholas J. , Kloser Rudy J. , Althaus Franziska , Barker Bruce , Keith Gordon 
Published: December 2008

Abstract
Williams, A., Bax, N. J., Kloser, R. J., Althaus, F., Barker, B., and Keith G. 2009. Australia’s deep-water reserve network: implications of false homogeneity for classifying abiotic surrogates of biodiversity. – ICES Journal of Marine Science, 66: 214–224. Australia’s southeast network of deep-water marine reserves, declared in July 2007, was designed using a hierarchy that represented the distribution of marine biodiversity as a nested set of bioregions. In this hierarchy, geomorphic units, individual or aggregations of seabed geomorphic features, are the finest scale used in the design process. We evaluated the interaction between two hierarchical levels (depth and geomorphic features), using video survey data on seamounts and submarine canyons. False within-class homogeneity indicated that depth, size, complexity, configuration, and anthropogenic impact need to be added as modifiers to allow geomorphic features to act as surrogates for biodiversity distribution. A consequence of using unmodified geomorphic surrogates, and of not correctly nesting geomorphic features within depth, is the diminished recognition of the importance and comparative rarity of megafaunal biodiversity of the continental margin (<1500-m depths). We call this area the zone of importance, because it is where targeted marine impacts coincide with the greatest megafaunal biodiversity. Refining the geomorphic classification is desirable for future biodiversity characterization, but an alternative approach is to define patterns in biodiversity and abiotic variables jointly, and to utilize finer scale information and provide a classification that preserves the maximum information of both datasets.
Using the Nucleic Acid Programmable Protein Array (NAPPA) for Identifying Protein-Protein Interactions: General Guidelines
Authors: Link Andrew J. , LaBaer Joshua 
Published: December 2008

INTRODUCTIONThe Nucleic Acid Programmable Protein Array (NAPPA) approach for producing protein microarrays uses cell-free extracts to transcribe and translate cDNAs encoding target proteins directly onto glass slides. Following array preparation, the identification of protein interactions using NAPPA can be accomplished by either of two general schemas. The first is to probe an expressed NAPPA slide with a purified protein of interest (the query protein) and look for interactors. Signals of these interactions can be detected either by directly labeling the query protein or by using a labeled antibody either to the protein itself or to a tag on the protein. This approach works well when there is access to the purified protein, and it has the advantage that users can test query protein binding with and without post-translational modifications or under a variety of binding conditions. The second schema entails coexpressing the query protein on the NAPPA slide at the same time that all the target proteins are expressed. This article describes the advantages of using a coexpressed query protein and provides advice on choosing a suitable epitope tag.
Whole-Mount In Situ Hybridization in Amphimedon
Authors: Larroux Claire , Fahey Bryony , Adamska Maja , Richards Gemma S. , Gauthier Marie , Green Kathryn , Lovas Erica , Degnan Bernard M. 
Published: December 2008

INTRODUCTIONDevelopmental gene expression is analyzed predominantly via whole-mount in situ hybridization using digoxigenin-labeled RNA probes. This protocol describes how to perform this procedure in Amphimedon queenslandica, including fixation, hybridization, and sectioning of embryonic, larval, and post-larval juvenile stages.
Cultures of Cerebellar Granule Neurons
Authors: Bilimoria Parizad M. , Bonni Azad 
Published: December 2008

INTRODUCTIONPrimary cultures of granule neurons from the post-natal rat cerebellum provide an excellent model system for molecular and cell biological studies of neuronal development and function. The cerebellar cortex, with its highly organized structure and few neuronal subtypes, offers a well-characterized neural circuitry. Many fundamental insights into the processes of neuronal apoptosis, migration, and differentiation in the mammalian central nervous system have come from investigating granule neurons in vitro. Granule neurons are the most abundant type of neurons in the brain. In addition to the sheer volume of granule neurons, the homogeneity of the population and the fact that they can be transfected with ease render them ideal for elucidating the molecular basis of neuronal development. This protocol for isolating granule neurons from post-natal rats is relatively straightforward and quick, making use of standard enzymatic and mechanical dissociation methods. In a serum-based medium containing an inhibitor of mitosis, cerebellar granule neurons can be maintained with high purity. Axons and dendrites can be clearly distinguished on the basis of morphology and markers. For even greater versatility, this protocol for culturing granule neurons can be combined with knockout or transgenic technologies, or used in cerebellar slice overlay assays.
Chicken Erythrocyte Histone Octamer Preparation
Authors: Peterson Craig L. , Hansen Jeffrey C. 
Published: December 2008

INTRODUCTIONCore histones can be purified from a variety of cell sources, including Drosophila embryos, HeLa tissue culture cells, calf thymus, or chicken erythrocytes. Chick erythrocytes are an excellent source of cellular histones: Large quantities of source material are readily obtainable, the purified histones have low levels of post-translational modifications, and linker histones can also be purified from the same cell sample. Also, avian histones have an amino acid sequence identical to that of human histones. Histone stocks can be stored successfully for more than a year at 4°C and for several years at −20°C. With this protocol, 200 mL of blood usually yields in excess of 50 mg of purified histone octamers. Additional optional procedures are also presented for the purification of H1 and H5 linker histones, as well as for the preparation of H3/H4 tetramers and H2A/H2B dimers.
Analysis of theNicotiana tabacumStigma/Style Transcriptome Reveals Gene Expression Differences between Wet and Dry Stigma Species
Authors: Quiapim Andréa C. , Brito Michael S. , Bernardes Luciano A.S. , daSilva Idalete , Malavazi Iran , DePaoli Henrique C. , Molfetta-Machado Jeanne B. , Giuliatti Silvana , Goldman Gustavo H. , Goldman Maria Helena S. 
Published: December 2008

AbstractThe success of plant reproduction depends on pollen-pistil interactions occurring at the stigma/style. These interactions vary depending on the stigma type: wet or dry. Tobacco (Nicotiana tabacum) represents a model of wet stigma, and its stigmas/styles express genes to accomplish the appropriate functions. For a large-scale study of gene expression during tobacco pistil development and preparation for pollination, we generated 11,216 high-quality expressed sequence tags (ESTs) from stigmas/styles and created the TOBEST database. These ESTs were assembled in 6,177 clusters, from which 52.1% are pistil transcripts/genes of unknown function. The 21 clusters with the highest number of ESTs (putative higher expression levels) correspond to genes associated with defense mechanisms or pollen-pistil interactions. The database analysis unraveled tobacco sequences homologous to the Arabidopsis (Arabidopsis thaliana) genes involved in specifying pistil identity or determining normal pistil morphology and function. Additionally, 782 independent clusters were examined by macroarray, revealing 46 stigma/style preferentially expressed genes. Real-time reverse transcription-polymerase chain reaction experiments validated the pistil-preferential expression for nine out of 10 genes tested. A search for these 46 genes in the Arabidopsis pistil data sets demonstrated that only 11 sequences, with putative equivalent molecular functions, are expressed in this dry stigma species. The reverse search for the Arabidopsis pistil genes in the TOBEST exposed a partial overlap between these dry and wet stigma transcriptomes. The TOBEST represents the most extensive survey of gene expression in the stigmas/styles of wet stigma plants, and our results indicate that wet and dry stigmas/styles express common as well as distinct genes in preparation for the pollination process.
The t(X;7)(q22;q34) in paediatric T‐cell acute lymphoblastic leukaemia results in overexpression of the insulin receptor substrate 4 gene through illegitimate recombination with the T‐cell receptor beta locus
Authors: Karrman Kristina , Kjeldsen Eigil , Lassen Carin , Isaksson Margareth , Davidsson Josef , Andersson Anna , Hasle Henrik , Fioretos Thoas , Johansson Bertil 
Published: December 2008

SummaryThe t(X;7)(q22;q34), a translocation not previously reported in a neoplastic disorder, was identified and molecularly characterised in a paediatric T‐cell acute lymphoblastic leukaemia (T‐ALL), subsequently shown also to harbour a deletion of 6q, a STIL/TAL1 fusion and an activating NOTCH1 mutation. The t(X;7) was further investigated using fluorescence in situ hybridisation (FISH), real‐time quantitative polymerase chain reaction (RQ‐PCR) and Western blot analyses. FISH revealed a breakpoint at the T‐cell receptor beta locus at 7q34 and mapped the corresponding breakpoint to Xq22.3. The latter region contains only two known genes, namely insulin receptor substrate 4 (IRS4) and collagen, type IV, alpha 5 (COL4A5), the expressions of which were analysed by the use of RQ‐PCR. COL4A5 was not differentially expressed in the t(X;7)‐positive sample compared to five T‐ALL controls. However, a marked, 1000‐fold overexpression of IRS4 was identified. Western blot analysis with a monoclonal antibody against IRS4 showed overexpression also at the protein level. Considering that forced expression of several members of the IRS family has been shown to result in increased cell proliferation, for example in haematopoietic cells, we hypothesise that the IRS4 up‐regulation in T‐ALL is pathogenetically important as a mitogenic stimulus.
Epstein‐Barr virus and cytomegalovirus are differentially associated with numbers of cytokine‐producing cells and early atopy
Authors: Nilsson C. , Larsson Sigfrinius A.‐K. , Montgomery S. M. , Sverremark‐Ekström E. , Linde A. , Lilja G. , Blomberg M. T. 
Published: December 2008

SummaryBackground
We have previously shown that Epstein‐Barr virus (EBV) seropositivity, at 2 years of age, was inversely related to IgE‐sensitization and that this effect was enhanced when EBV is combined with cytomegalovirus (CMV) seropositivity. We hypothesize that early exposure to EBV or CMV will affect the cytokine balance in the individual.Objective
The aim of this study was to relate the cytokine profile in peripheral blood mononuclear cells (PBMC) to the EBV and CMV serostatus and IgE‐sensitization in children at 2 years of age.Methods
Seventy‐five children were followed prospectively from birth until 2 years of age. Their EBV and CMV serostatus was correlated to the numbers of IFN‐γ, IL‐4, IL‐10 and IL‐12‐producing PBMC following PHA stimulation in vitro. Skin prick tests and allergen‐specific IgE antibodies were used to assess IgE‐sensitization.Results
In the study cohort, there was an inverse association between EBV seropositivity and IgE‐sensitization but not with CMV seropositivity. Following linear regression analysis, we did not detect any statistically significant associations between children with IgG antibodies against EBV at 2 years of age and the investigated cytokines. However, there was a non‐significant tendency to a positive association between high numbers of all individual cytokine‐producing cells and EBV seropositivity. Children who were CMV seropositive had significantly higher numbers of IFN‐γ and lower numbers of IL‐4‐producing cells compared with CMV negative children. There was a significant, positive association between the number of IL‐4‐producing cells and IgE‐sensitization.Conclusion
Taken together our results indicate that infections with EBV and CMV in different ways will interact with the immune system and may protect children from developing early atopy.
CD26/dipeptidyl peptidase 4-deficiency alters thymic emigration patterns and leukcocyte subsets in F344-rats age-dependently
Authors: Klemann C , Schade J , Pabst R , Leitner S , Stiller J , Von Hörsten S , Stephan M 
Published: December 2008

SummaryAs CD26 (dipeptidyl peptidase 4/DPP4) rapidly truncates incretins N-terminally, including glucagon-like peptide-1, DPP4-inhibitors have been developed for treatment of diabetes type 2. To some extent this is surprising, as CD26/DPP4 is also deeply involved in immune regulation. Long-term pharmacological studies are hampered by off-target inhibition of DPP4-homologues. Therefore, we studied the effects of genetic CD26/DPP4-deficiency by investigating blood, spleen and thymus leucocyte subpopulations of wild-type and CD26-deficient F344-rats at different ages. In young animals at 1 and 3 months of age, there were no differences in leucocyte subsets, while in older animals the T cell composition was changed significantly. From the age of 6 months onwards, reduced numbers of recent thymic emigrants and memory T cells, and consequently an increased amount of naive T cells were observed in CD26-deficient rats. In addition, the architecture of the thymus was altered, as observed by a reduced density of lymphocytes in the medulla. Furthermore, the number of proliferating cells in the thymus was decreased in CD26-deficient rats at a higher age. Moreover, CD26-deficiency resulted in markedly reduced numbers of B cells in later life. Additionally, an age- but not CD26-dependent increase of regulatory T cells and a decrease of natural killer cell numbers were detected in the blood and spleen. Our findings indicate an important role of CD26 in maintaining lymphocyte composition, memory T cell generation and thymic emigration patterns during immunosenescence, with possible implications for using DPP4-inhibitors.
FAMILIAL BENIGN HYPERCALCAEMIA: HYPERCALCIURIA AND HYPOCALCIURIA IN AFFECTED MEMBERS OF A SMALL KINDRED
Authors: PASIEKA JANICE L. , ANDERSEN MEL A. , HANLEY DAVID A. 
Published: December 2008

SUMMARYFamilial benign hypercalcaemia has also been termed familial hypocalciuric hypercalcaemia because a major feature of this condition has been a relative hypocalciuria in relation to the hypercalcaemia, such that the calcium to creatinine clearance ratio is less than 0.016. The following is a report of a small kindred of patients with familial benign hypercalcaemia in which two of the affected members have frank hypercalciuria.
FACTORS INFLUENCING URINARY 6‐SULPHATOXYMELATONIN, A MAJOR MELATONIN METABOLITE, IN NORMAL HUMAN SUBJECTS
Authors: BOJKOWSKI C. J. , ARENDT J. 
Published: December 2008

SUMMARY6‐Sulphatoxymelatonin (aMT6) has been measured, by a direct radioimmunoassay, in urine from 130 normal volunteers aged 2–80 years. Its relationship to a number of physiological parameters has been assessed. Total urinary excretion of aMT6s did not vary in a group of 40 children aged 2–20 years (24 boys and 16 girls) except when expressed as a function of body weight. In this case, total aMT6s excretion over 24 h decreased as a function of age. In 90 adult volunteers (44 men and 46 women) aged 20–80 years, there was an age‐related decline in total 24 h aMT6s excretion with significantly lower values in elderly subjects. In this same adult group no relationships were found between total aMT6s excretion and body weight or height. No sex differences were found either in the 2–20 years or the 20–80 years groups. Pineal calcification was assessed by lateral skull X‐ray in 26 adult volunteers (17 men and 9 women) aged 20–50 years. No significant differences in aMT6s excretion were found as a function of pineal calcification. In 16 of these subjects plasma melatonin and aMT6s also showed no relationship to pineal calcification. These studies confirm the usefulness of aMT6s as an index of melatonin secretion in normal volunteers.
INSULIN SECRETION, INSULIN SENSITIVITY AND GLUCOSE‐MEDIATED GLUCOSE DISPOSAL IN THYROTOXICOSIS: A MINIMAL MODEL ANALYSIS
Authors: PESTELL RICHARD , ALFORD FRANK , RAMOS ROMULUS , SAWYER STEVEN , BEST JAMES , WARD GLENN 
Published: December 2008

SUMMARYIn order to evaluate simultaneously in thyrotoxic subjects the relative contributions of insulin secretion, insulin‐sensitivity (SI) and glucose‐mediated (SG) glucose disposal to overall glucose tolerance, seven non‐obese patients with thyrotoxicosis were studied by the minimal model analysis of the frequently sampled intravenous glucose tolerance test, before and > 1 month after being rendered euthyroid, and compared with eight healthy control subjects. Basal glucose, C‐peptide and glucagon levels were similar in all groups but, in the toxic and euthyroid states, basal insulin levels were significantly elevated compared to the control group (11.2 ±2‐0 and 7.9± 1‐1 vs 5.1 ±0.6 μU/ml, mean±SE, P<0.02). FFA levels were raised in the thyrotoxic subjects prior to treatment (0.95 ±0.11 vs 0.68 ± 0.08 and 054 ± 008 mmol/1, P <0.0). Glucose tolerance (Kg) was reduced in the thyrotoxic subjects compared to the euthyroid state (1.16 ± 0.12 vs 1.44 ± 0.13 per min, P <0.025) and control group (1.44± 1.0 per min, 0.05 <P<0.1). First phase (ψ1) and second phase (ψ2) insulin release were both significantly elevated in the thyrotoxic and euthyroid states compared to the control group (ψ1), 7.10± 1.88 and 5.29± 1.03 vs 1.72 ± 0.17 μU/mg/minx 10‐2 P<0.01; ψ2 18.64 ± 3.14 and 16.74 ± 4.48 vs 9.23 ± 0.74 μU/mg/minx 10‐2 respectively, P<0.02). SG was similar in all groups but SI was significantly reduced in the thyrotoxic subjects compared to the control group (2.24 ± 0.62 vs 5.92 ± 1.50/minμU/ml × 104, P<0.02) and rose post‐treatment in the euthyroid subjects (4.23 ± 1.75/minμU/ml × 104). In the thyrotoxic subjects before and after treatment, log SI correlated negatively with basal FFA levels (r=‐0.57, P<0.05) and with ψ2 (r= ‐0.58, P<0.05). The fractional clearance rate of insulin was unaltered by the thyrotoxic state. It is concluded that in thyrotoxicosis the impairment of Kg is due to reduced insulin sensitivity in the presences of enchanced insulin secretion, but glucose‐medicated glucose disposal is unaltered by the toxic state.