bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of patients with chronic obstructive pulmonary disease (COPD) by measurement of plasma biomarkers
Authors: Shaker Saher B. , von Wachenfeldt Karin A. , Larsson Susanne , Mile Iréne , Persdotter Sofia , Dahlbäck Magnus , Broberg Per , Stoel Berend , Bach Karen S. , Hestad Marianne , Fehniger Thomas E. , Dirksen Asger 
Published: October 2007

AbstractIntroduction:  Inflammation is an important constituent of the pathology of chronic obstructive pulmonary disease (COPD), leading to alveolar destruction and airway remodelling.Objective:  The aim of this study was to assess the difference in plasma biomarkers of inflammation between asymptomatic smokers and patients with COPD.Methods:  We used commercially available enzyme‐linked immunosorbent assay kits to measure the plasma levels of tumour necrosis factor‐α (TNF‐α), interleukin‐8 (IL‐8), matrix metalloproteinase‐9 (MMP‐9), monocyte chemotactic protein‐1 (MCP‐1), tissue inhibitor of metalloproteinase‐1 (TIMP‐1) and tissue inhibitor of metalloproteinase‐2 (TIMP‐2) on two occasions with a 2‐week interval in patients with COPD (n = 20), asymptomatic smokers (n = 10) and healthy lifelong non‐smokers (n = 10). The participants were characterised clinically, physiologically and by quantitative computed tomography by measuring the relative area of emphysema below −910 Hounsfield units (RA‐910).Results:  The results of the biomarker measurements on the two occasions were highly reproducible. Patients with COPD had significantly higher plasma levels of IL‐8 (P = 0.004) and significantly lower levels of TIMP‐1 (P = 0.02) than smokers and non‐smokers. There was no statistically significant difference between the three groups in the level of TNF‐α, MMP‐9, MCP‐1 and TIMP‐2. The IL‐8/TIMP‐1 ratio correlated significantly with the degree of airway obstruction measured as forced expiratory volume in 1 second (FEV1) % predicted (r = −0.47, P < 0.01); with the diffusion capacity (r = −0.41, P < 0.01); and with the grade of emphysema measured as RA‐910 (r = 0.39, P = 0.01).Conclusion:  These findings suggest that the measurement of plasma biomarkers, such as IL‐8/TIMP‐1, may aid to discriminate patients with COPD from smokers at lower risk of developing COPD.Please cite this paper as: Shaker SB, von Wachenfeldt KA, Larsson S, Mile I, Persdotter S, Dahlbäck M, Broberg P, Stoel B, Bach KS, Hestad M, Fehniger TE and Dirksen A. Identification of patients with chronic obstructive pulmonary disease (COPD) by measurement of plasma biomarkers. The Clinical Respiratory Journal 2008; 2: 17–25.
Impact of home mechanical ventilation on health‐related quality of life in patients with chronic alveolar hypoventilation: a prospective study
Authors: Dellborg Catharina , Olofson Jan , Midgren Bengt , Caro Oscar , Bergman Bengt , Skoogh Bengt‐Eric , Sullivan Marianne 
Published: October 2007

AbstractBackground:  Nocturnal ventilatory support by nasal positive pressure ventilation (NPPV) is an established treatment method in patients with chronic alveolar hypoventilation (CAH). The knowledge about its long‐term effects on health‐related quality of life (HRQL) is limited.Methods:  In a prospective, longitudinal, single‐strand study, patients with CAH caused by non‐COPD conditions, consecutively recruited among referral patients in three Swedish university hospital pulmonary departments, were examined at baseline and after 9 months (n = 35) and 8 years (n = 11) on NPPV treatment. Both volume pre‐set and pressure pre‐set ventilators were used. Patients completed a battery of condition‐specific and generic HRQL questionnaires at baseline and follow‐up. Spirometry and blood gases were measured. Compliance with treatment, side effects and patient satisfaction were evaluated.Results:  After 9 months of NPPV, improvements were seen primarily not only in sleep‐related domains, but also in emotional behaviour, ambulation and sleep/rest functioning as measured with the Sickness Impact Profile (SIP). Improvements in sleep‐related symptoms were related to effectiveness in ventilation, evaluated by morning PaCO2, and remained by 8 years. Mental well‐being was stable over time, while emotional distress improved by 8 years. Satisfaction with treatment was high in spite of frequent side effects.Conclusion:  NPPV improves HRQL, particularly in condition‐specific areas. Improvements are related to effectiveness in ventilation. Side effects are common, but compliance is good and patient satisfaction is high.Please cite this paper as: Dellborg C, Olofson J, Midgren B, Caro O, Bergman B, Skoogh B‐E and Sullivan M. Impact of home mechanical ventilation on health‐related quality of life in patients with chronic alveolar hypoventilation: a prospective study. The Clinical Respiratory Journal 2008; 2: 26–35.
Simultanagnosia: When a Rose Is Not Red
Authors: Coslett H. Branch , Lie Grace 
Published: October 2007

Abstract
Information regarding object identity (“what”) and spatial location (“where/how to”) is largely segregated in visual processing. Under most circumstances, however, object identity and location are linked. We report data from a simultanagnosic patient (K.E.) with bilateral posterior parietal infarcts who was unable to “see” more than one object in an array despite relatively preserved object processing and normal preattentive processing. K.E. also demonstrated a finding that has not, to our knowledge, been reported: He was unable to report more than one attribute of a single object. For example, he was unable to name the color of the ink in which words were written despite naming the word correctly. Several experiments demonstrated, however, that perceptual attributes that he was unable to report influenced his performance. We suggest that binding of object identity and location is a limited-capacity operation that is essential for conscious awareness for which the posterior parietal lobe is crucial.
Linking Cortical Spike Pattern Codes to Auditory Perception
Authors: Walker Kerry M. M. , Ahmed Bashir , Schnupp Jan W. H. 
Published: October 2007

Abstract
Neurometric analysis has proven to be a powerful tool for studying links between neural activity and perception, especially in visual and somatosensory cortices, but conventional neurometrics are based on a simplistic rate-coding hypothesis that is clearly at odds with the rich and complex temporal spiking patterns evoked by many natural stimuli. In this study, we investigated the possible relationships between temporal spike pattern codes in the primary auditory cortex (A1) and the perceptual detection of subtle changes in the temporal structure of a natural sound. Using a two-alternative forced-choice oddity task, we measured the ability of human listeners to detect local time reversals in a marmoset twitter call. We also recorded responses of neurons in A1 of anesthetized and awake ferrets to these stimuli, and analyzed these responses using a novel neurometric approach that is sensitive to temporal discharge patterns. We found that although spike count-based neurometrics were inadequate to account for behavioral performance on this auditory task, neurometrics based on the temporal discharge patterns of populations of A1 units closely matched the psychometric performance curve, but only if the spiking patterns were resolved at temporal resolutions of 20 msec or better. These results demonstrate that neurometric discrimination curves can be calculated for temporal spiking patterns, and they suggest that such an extension of previous spike count-based approaches is likely to be essential for understanding the neural correlates of the perception of stimuli with a complex temporal structure.
Neuroimaging Studies of Mental Rotation: A Meta-analysis and Review
Authors: Zacks Jeffrey M. 
Published: October 2007

Abstract
Mental rotation is a hypothesized imagery process that has inspired controversy regarding the substrate of human spatial reasoning. Two central questions about mental rotation remain: Does mental rotation depend on analog spatial representations, and does mental rotation depend on motor simulation? A review and meta-analysis of neuroimaging studies help answer these questions. Mental rotation is accompanied by increased activity in the intraparietal sulcus and adjacent regions. These areas contain spatially mapped representations, and activity in these areas is modulated by parametric manipulations of mental rotation tasks, supporting the view that mental rotation depends on analog representations. Mental rotation also is accompanied by activity in the medial superior precentral cortex, particularly under conditions that favor motor simulation, supporting the view that mental rotation depends on motor simulation in some situations. The relationship between mental rotation and motor simulation can be understood in terms of how these two processes update spatial reference frames.
qPIPSA: Relating enzymatic kinetic parameters and interaction fields
Authors: Gabdoulline Razif R , Stein Matthias , Wade Rebecca C 
Published: October 2007

Abstract

Background
The simulation of metabolic networks in quantitative systems biology requires the assignment of enzymatic kinetic parameters. Experimentally determined values are often not available and therefore computational methods to estimate these parameters are needed. It is possible to use the three-dimensional structure of an enzyme to perform simulations of a reaction and derive kinetic parameters. However, this is computationally demanding and requires detailed knowledge of the enzyme mechanism. We have therefore sought to develop a general, simple and computationally efficient procedure to relate protein structural information to enzymatic kinetic parameters that allows consistency between the kinetic and structural information to be checked and estimation of kinetic constants for structurally and mechanistically similar enzymes.

Results
We describe qPIPSA: quantitative Protein Interaction Property Similarity Analysis. In this analysis, molecular interaction fields, for example, electrostatic potentials, are computed from the enzyme structures. Differences in molecular interaction fields between enzymes are then related to the ratios of their kinetic parameters. This procedure can be used to estimate unknown kinetic parameters when enzyme structural information is available and kinetic parameters have been measured for related enzymes or were obtained under different conditions. The detailed interaction of the enzyme with substrate or cofactors is not modeled and is assumed to be similar for all the proteins compared. The protein structure modeling protocol employed ensures that differences between models reflect genuine differences between the protein sequences, rather than random fluctuations in protein structure.

Conclusion
Provided that the experimental conditions and the protein structural models refer to the same protein state or conformation, correlations between interaction fields and kinetic parameters can be established for sets of related enzymes. Outliers may arise due to variation in the importance of different contributions to the kinetic parameters, such as protein stability and conformational changes. The qPIPSA approach can assist in the validation as well as estimation of kinetic parameters, and provide insights into enzyme mechanism.
Family expansion and gene rearrangements contributed to the functional specialization of PRDM genes in vertebrates
Authors: Fumasoni Irene , Meani Natalia , Rambaldi Davide , Scafetta Gaia , Alcalay Myriam , Ciccarelli Francesca D 
Published: October 2007

Abstract

Background
Progressive diversification of paralogs after gene expansion is essential to increase their functional specialization. However, mode and tempo of this divergence remain mostly unclear. Here we report the comparative analysis of PRDM genes, a family of putative transcriptional regulators involved in human tumorigenesis.

Results
Our analysis assessed that the PRDM genes originated in metazoans, expanded in vertebrates and further duplicated in primates. We experimentally showed that fast-evolving paralogs are poorly expressed, and that the most recent duplicates, such as primate-specific PRDM7, acquire tissue-specificity. PRDM7 underwent major structural rearrangements that decreased the number of encoded Zn-Fingers and modified gene splicing. Through internal duplication and activation of a non-canonical splice site (GC-AG), PRDM7 can acquire a novel intron. We also detected an alternative isoform that can retain the intron in the mature transcript and that is predominantly expressed in human melanocytes.

Conclusion
Our findings show that (a) molecular evolution of paralogs correlates with their expression pattern; (b) gene diversification is obtained through massive genomic rearrangements; and (c) splicing modification contributes to the functional specialization of novel genes.
Androgen-induced masculinization in rainbow trout results in a marked dysregulation of early gonadal gene expression profiles
Authors: Baron Daniel , Montfort Jérôme , Houlgatte Rémi , Fostier Alexis , Guiguen Yann 
Published: October 2007

AbstractBackgroundFish gonadal sex differentiation is affected by sex steroids treatments providing an efficient strategy to control the sexual phenotype of fish for aquaculture purposes. However, the biological effects of such treatments are poorly understood. The aim of this study was to identify the main effects of an androgen masculinizing treatment (11β-hydroxyandrostenedione, 11βOHΔ4, 10 mg/kg of food for 3 months) on gonadal gene expression profiles of an all-female genetic population of trout. To characterize the most important molecular features of this process, we used a large scale gene expression profiling approach using rainbow trout DNA microarrays combined with a detailed gene ontology (GO) analysis.Results2,474 genes were characterized as up-regulated or down-regulated in trout female gonads masculinized by androgen in comparison with control male or female gonads from untreated all-male and all-female genetic populations. These genes were classified in 13 k-means clusters of temporally correlated expression profiles. Gene ontology (GO) data mining revealed that androgen treatment triggers a marked down-regulation of genes potentially involved in early oogenesis processes (GO 'mitotic cell cycle', 'nucleolus'), an up-regulation of the translation machinery (GO 'ribosome') along with a down-regulation of proteolysis (GO 'proteolysis', 'peptidase' and 'metallopeptidase activity'). Genes considered as muscle fibres markers (GO 'muscle contraction') and genes annotated as structural constituents of the extracellular matrix (GO 'extracellular matrix') or related to meiosis (GO 'chromosome' and 'meiosis') were found significantly enriched in the two clusters of genes specifically up-regulated in androgen-treated female gonads. GO annotations 'Sex differentiation' and 'steroid biosynthesis' were enriched in a cluster of genes with high expression levels only in control males. Interestingly none of these genes were stimulated by the masculinizing androgen treatment.ConclusionThis study provides evidence that androgen masculinization results in a marked dysregulation of early gene expression profiles when compared to natural testicular or ovarian differentiation. Based on these results we suggest that, in our experimental conditions, androgen masculinization proceeds mainly through an early inhibition of female development.
The 2G allele of promoter region of Matrix metalloproteinase-1 as an essential pre-condition for the early onset of oral squamous cell carcinoma
Authors: Nishizawa Rishiho , Nagata Masaki , Noman Arhab A , Kitamura Nobutaka , Fujita Hajime , Hoshina Hideyuki , Kubota Takehiko , Itagaki Manami , Shingaki Susumu , Ohnishi Makoto , Kurita Hiroshi , Katsura Kouji , Saito Chikara , Yoshie Hiromasa , Takagi Ritsuo 
Published: October 2007

Abstract

Background
Matrix metalloproteinase (MMP) is known to be involved in the initial and progressive stages of cancer development, and in the aggressive phenotypes of cancer. This study examines the association of single nucleotide polymorphisms in promoter regions of MMP-1 and MMP-3 with susceptibility to oral squamous cell carcinoma (OSCC).

Methods
We compared 170 Japanese OSCC cases and 164 healthy controls for genotypes of MMP-1 and MMP-3.

Results
The frequency of the MMP-1 2G allele was higher and that of the 1G homozygote was lower in the OSCC cases (p = 0.034). A multivariate logistic regression analysis revealed that subjects who were 45 years old or older had a significantly increased (2.47-fold) risk of OSCC (95%CI 1.47–4.14, p = 0.0006), and those carrying the MMP-1 2G allele had a 2.30-fold risk (95%CI 1.15–4.58, p = 0.018), indicating independent involvement of these factors in OSCC. One of the key discoveries of this research is the apparent reduction of the MMP-1 1G/1G and 1G/2G genotype distributions among the early onset OSCC cases under the ages of 45 years. It should be noted that the tongue was the primary site in 86.2% of these early onset cases. This could suggest the specific carcinogenic mechanisms, i.e. specific carcinogenic stimulations and/or genetic factors in the tongue.

Conclusion
Since the 2G allele is a majority of the MMP-1 genotype in the general population, it seems to act as a genetic pre-condition in OSCC development. However this report suggests a crucial impact of the MMP-1 2G allele in the early onset OSCC.
Prevalence of self-reported diagnosis of diabetes mellitus and associated risk factors in a national survey in the US population: SHIELD (Study to Help Improve Early evaluation and management of risk factors Leading to Diabetes)
Authors: Bays Harold E , Bazata Debbra D , Clark Nathaniel G , Gavin James R , Green Andrew J , Lewis Sandra J , Reed Michael L , Stewart Walter , Chapman Richard H , Fox Kathleen M , Grandy Susan 
Published: October 2007

Abstract

Background
Studies derived from continuous national surveys have shown that the prevalence of diagnosed diabetes mellitus in the US is increasing. This study estimated the prevalence in 2004 of self-reported diagnosis of diabetes and other conditions in a community-based population, using data from the Study to Help Improve Early evaluation and management of risk factors Leading to Diabetes (SHIELD).

Methods
The initial screening questionnaire was mailed in 2004 to a stratified random sample of 200,000 households in the US, to identify individuals, age ≥ 18 years of age, with diabetes or risk factors associated with diabetes. Follow-up disease impact questionnaires were then mailed to a representative, stratified random sample of individuals (n = 22,001) in each subgroup of interest (those with diabetes or different numbers of risk factors for diabetes). Estimated national prevalence of diabetes and other conditions was calculated, and compared to prevalence estimates from the National Health and Nutrition Examination Survey (NHANES) 1999–2002.

Results
Response rates were 63.7% for the screening, and 71.8% for the follow-up baseline survey. The SHIELD screening survey found overall prevalence of self-reported diagnosis of diabetes (either type 1 or type 2) was 8.2%, with increased prevalence with increasing age and decreasing income. In logistic regression modeling, individuals were more likely to be diagnosed with type 2 diabetes if they had abdominal obesity (odds ratio [OR] = 3.50; p < 0.0001), BMI ≥28 kg/m2 (OR = 4.04; p < 0.0001), or had been diagnosed with dyslipidemia (OR = 3.95; p < 0.0001), hypertension (OR = 4.82; p < 0.0001), or with cardiovascular disease (OR = 3.38; p < 0.0001).

Conclusion
The SHIELD design allowed for a very large, community-based sample with broad demographic representation of the population of interest. When comparing results from the SHIELD screening survey (self-report only) to those from NHANES 1999–2002 (self-report, clinical and laboratory evaluations), the prevalence of diabetes was similar. SHIELD allows the identification of respondents with and without a current diagnosis of the illness of interest, and potential longitudinal evaluation of risk factors for future diagnosis of that illness.
Mitochondrial DNA mutations in oxyphilic and chief cell parathyroid adenomas
Authors: Costa-Guda Jessica , Tokura Takehiko , Roth Sanford I , Arnold Andrew 
Published: October 2007

Abstract

Background
The potential pathogenetic significance of mitochondrial DNA (mtDNA) mutations in tumorigenesis is controversial. We hypothesized that benign tumorigenesis of a slowly replicating tissue like the human parathyroid might constitute an especially fertile ground on which a selective advantage conferred by mtDNA mutation could be manifested and might contribute to the oxyphilic phenotype observed in a subset of parathyroid tumors.

Methods
We sought acquired mitochondrial DNA mutations by sequencing the entire 16.6 kb mitochondrial genome of each of thirty sporadic parathyroid adenomas (18 chief cell and 12 oxyphil cell), eight independent, polyclonal, parathyroid primary chief cell hyperplasias plus corresponding normal control samples, five normal parathyroid glands, and one normal thyroid gland.

Results
Twenty-seven somatic mutations were identified in 15 of 30 (9 of 12 oxyphil adenomas, 6 of 18 chief cell) parathyroid adenomas studied. No somatic mutations were observed in the hyperplastic parathyroid glands.

Conclusion
Features of the somatic mutations suggest that they may confer a selective advantage and contribute to the molecular pathogenesis of parathyroid adenomas. Importantly, the statistically significant differences in mutation prevalence in oxyphil vs. chief cell adenomas also suggest that mtDNA mutations may contribute to the oxyphil phenotype.
Acute cholecystitis – early laparoskopic surgery versus antibiotic therapy and delayed elective cholecystectomy: ACDC-study
Authors: Weigand Kilian , Köninger Jörg , Encke Jens , Büchler Markus W , Stremmel Wolfgang , Gutt Carsten N 
Published: October 2007

AbstractBackgroundAcute cholecystitis occurs frequently in the elderly and in patients with gall stones. Most cases of severe or recurrent cholecystitis eventually require surgery, usually laparoscopic cholecystectomy in the Western World. It is unclear whether an initial, conservative approach with antibiotic and symptomatic therapy followed by delayed elective surgery would result in better morbidity and outcome than immediate surgery. At present, treatment is generally determined by whether the patient first sees a surgeon or a gastroenterologist. We wish to investigate whether both approaches are equivalent. The primary endpoint is the morbidity until day 75 after inclusion into the study.DesignA multicenter, prospective, randomized non-blinded study to compare treatment outcome, complications and 75-day morbidity in patients with acute cholecystitis randomized to laparoscopic cholecystectomy within 24 hours of symptom onset or antibiotic treatment with moxifloxacin and subsequent elective cholecystectomy. For consistency in both arms moxifloxacin, a fluorquinolone with broad spectrum of activity and high bile concentration is used as antibiotic. Duration: October 2006 – November 2008Organisation/ResponsibilityThe trial was planned and is being conducted and analysed by the Departments of Gastroenterology and General Surgery at the University Hospital of Heidelberg according to the ethical, regulatory and scientific principles governing clinical research as set out in the Declaration of Helsinki (1989) and the Good Clinical Practice guideline (GCP).Trial RegistrationClinicalTrials.gov NCT00447304