bluuebunny/crossref_metadata_2025 huggingface dataset:
Prediction of flexible/rigid regions from protein sequences using k-spaced amino acid pairs
Authors: Chen Ke , Kurgan Lukasz A , Ruan Jishou
Published: April 2007

Background

Traditionally, it is believed that the native structure of a protein corresponds to a global minimum of its free energy. However, with the growing number of known tertiary (3D) protein structures, researchers have discovered that some proteins can alter their structures in response to a change in their surroundings or with the help of other proteins or ligands. Such structural shifts play a crucial role with respect to the protein function. To this end, we propose a machine learning method for the prediction of the flexible/rigid regions of proteins (referred to as FlexRP); the method is based on a novel sequence representation and feature selection. Knowledge of the flexible/rigid regions may provide insights into the protein folding process and the 3D structure prediction.

Results

The flexible/rigid regions were defined based on a dataset, which includes protein sequences that have multiple experimental structures, and which was previously used to study the structural conservation of proteins. Sequences drawn from this dataset were represented based on feature sets that were proposed in prior research, such as PSI-BLAST profiles, composition vector and binary sequence encoding, and a newly proposed representation based on frequencies of k-spaced amino acid pairs. These representations were processed by feature selection to reduce the dimensionality. Several machine learning methods for the prediction of flexible/rigid regions and two recently proposed methods for the prediction of conformational changes and unstructured regions were compared with the proposed method. The FlexRP method, which applies Logistic Regression and collocation-based representation with 95 features, obtained 79.5% accuracy. The two runner-up methods, which apply the same sequence representation and Support Vector Machines (SVM) and Naïve Bayes classifiers, obtained 79.2% and 78.4% accuracy, respectively. The remaining considered methods are characterized by accuracies below 70%. Finally, the Naïve Bayes method is shown to provide the highest sensitivity for the prediction of flexible regions, while FlexRP and SVM give the highest sensitivity for rigid regions.

Conclusion

A new sequence representation that uses k-spaced amino acid pairs is shown to be the most efficient in the prediction of the flexible/rigid regions of protein sequences. The proposed FlexRP method provides the highest prediction accuracy of about 80%. The experimental tests show that the FlexRP and SVM methods achieved high overall accuracy and the highest sensitivity for rigid regions, while the best quality of the predictions for flexible regions is achieved by the Naïve Bayes method.
When "no" might not quite mean "no"; the importance of informed and meaningful non-consent: results from a survey of individuals refusing participation in a health-related research project
Authors: Williams Brian , Irvine Linda , McGinnis Alison R , McMurdo Marion ET , Crombie Iain K
Published: April 2007

Background

Low participation rates can lead to sampling bias, delays in completion and increased costs. Strategies to improve participation rates should address reasons for non-participation. However, most empirical research has focused on participants' motives rather than the reasons why non-participants refuse to take part. In this study we investigated the reasons why older people choose not to participate in a research project.

Methods

Follow-up study of people living in Tayside, Scotland who had opted-out of a cross-sectional survey on activities in retirement. Eight hundred and eighty seven people aged 65–84 years were invited to take part in a home-based cross-sectional survey. Of these, 471 refused to take part. Permission was obtained to follow-up 417 of the refusers. Demographic characteristics of people who refused to take part and the reasons they gave for not taking part were collected.

Results

54% of those invited to take part in the original cross-sectional survey refused to do so. However, 61% of these individuals went on to participate in the follow-up study and provided reasons for their original refusal. For the vast majority of people initial non-participation did not reflect an objection to participating in research in principle but frequently stemmed from barriers or misunderstandings about the nature or process of the project itself. Only 28% indicated that they were "not interested in research". The meaningfulness of expressions of non-consent may therefore be called into question. Hierarchical log-linear modelling showed that refusal was independently influenced by age, gender and social class. However, this response pattern was different for the follow-up study in which reasons for non-participation in the first survey were sought. This difference in pattern and response rates supports the likely importance of recruitment issues that are research and context specific.

Conclusion

An expression of non-consent does not necessarily mean that a fully informed evaluation of the pros and cons of participation and non-participation has taken place. The meaningfulness of expressions of non-consent may therefore be a cause for concern and should be subject to further research. Many reasons for non-participation may be specific to a particular research topic or population. Information sheets should reflect this by going beyond standardised guidelines for their design and instead proactively seek out and address areas of concern or potential misunderstanding. The use of established behavioural theory in their design could also be considered.
The Consumer Quality Index Hip Knee Questionnaire measuring patients' experiences with quality of care after a total hip or knee arthroplasty
Authors: Stubbe Janine H , Gelsema Tanya , Delnoij Diana MJ
Published: April 2007

Background

The Dutch Consumer Quality Index Hip Knee Questionnaire (CQI Hip Knee) was used to assess patients' experiences with and evaluations of quality of care after a total hip (THA) or total knee arthroplasty (TKA). The aim of this study is to evaluate the construct validity and internal consistency reliability of this new instrument and to assess its ability to measure differences in quality of care between hospitals.

Methods

Survey data of 1,675 subjects who underwent a THA or TKA were used to evaluate the psychometric properties. Exploratory factor analyses were performed and item-total correlations and inter-factor correlations were calculated to assess the construct validity of the instrument. Reliability analyses included tests of internal consistency (Cronbach's alpha coefficients). Finally, multilevel analyses were performed to assess the ability of the instrument to discriminate between hospitals in quality of care.

Results

Exploratory factor analyses indicated that the survey consisted of 21 items measuring five aspects of care (i.e. communication with nurses, communication with doctors, communication with general practitioner, communication about new medication, and pain control). Cronbach's alpha coefficients ranged from 0.76 to 0.90 indicating good internal consistency. The survey's ability to discriminate between hospitals was partly supported by multilevel analysis. Two scales (i.e. communication with nurses and communication with doctors) were able to measure differences between hospitals with respect to patients' experiences with quality of care. Logistic multilevel analyses indicated that hospitals explained part of the variation between patients in receiving information.

Conclusion

These findings suggest that the CQI Hip Knee is reliable and valid for use in Dutch health care. Health care providers or health plans can use this survey to measure patients' experiences with hospital care and to identify variations in care between hospitals.
An exploratory study of community factors relevant for participatory malaria control on Rusinga Island, western Kenya
Authors: Opiyo Pamela , Mukabana W Richard , Kiche Ibrahim , Mathenge Evan , Killeen Gerry F , Fillinger Ulrike
Published: April 2007

Background

Capacity strengthening of rural communities, and the various actors that support them, is needed to enable them to lead their own malaria control programmes. Here the existing capacity of a rural community in western Kenya was evaluated in preparation for a larger intervention.

Methods

Focus group discussions and semi-structured individual interviews were carried out in 1,451 households to determine (1) demographics of respondent and household; (2) socio-economic status of the household; (3) knowledge and beliefs about malaria (symptoms, prevention methods, mosquito life cycle); (4) typical practices used for malaria prevention; (5) the treatment-seeking behaviour and household expenditure for malaria treatment; and (6) the willingness to prepare and implement community-based vector control.

Results

Malaria was considered a major threat to life but relevant knowledge was a chimera of scientific knowledge and traditional beliefs, which combined with socio-economic circumstances, leads to ineffective malaria prevention. The actual malaria prevention behaviour practiced by community members differed significantly from methods known to the respondents. Beside bednet use, the major interventions implemented were bush clearing and various hygienic measures, even though these are ineffective for malaria prevention. Encouragingly, most respondents believed malaria could be controlled and were willing to contribute to a community-based malaria control program but felt they needed outside assistance.

Conclusion

Culturally sensitive but evidence-based education interventions, utilizing participatory tools, are urgently required which consider traditional beliefs and enable understanding of causal connections between mosquito ecology, parasite transmission and the diagnosis, treatment and prevention of disease. Community-based organizations and schools need to be equipped with knowledge through partnerships with national and international research and tertiary education institutions so that evidence-based research can be applied at the grassroots level.
Polymeric nanoparticle-encapsulated curcumin ("nanocurcumin"): a novel strategy for human cancer therapy
Authors: Bisht Savita , Feldmann Georg , Soni Sheetal , Ravi Rajani , Karikar Collins , Maitra Amarnath , Maitra Anirban
Published: April 2007

Background

Curcumin, a yellow polyphenol extracted from the rhizome of turmeric (Curcuma longa), has potent anti-cancer properties as demonstrated in a plethora of human cancer cell line and animal carcinogenesis models. Nevertheless, widespread clinical application of this relatively efficacious agent in cancer and other diseases has been limited due to poor aqueous solubility, and consequently, minimal systemic bioavailability. Nanoparticle-based drug delivery approaches have the potential for rendering hydrophobic agents like curcumin dispersible in aqueous media, thus circumventing the pitfalls of poor solubility.

Results

We have synthesized polymeric nanoparticle encapsulated formulation of curcumin – nanocurcumin – utilizing the micellar aggregates of cross-linked and random copolymers of N-isopropylacrylamide (NIPAAM), with N-vinyl-2-pyrrolidone (VP) and poly(ethyleneglycol)monoacrylate (PEG-A). Physico-chemical characterization of the polymeric nanoparticles by dynamic laser light scattering and transmission electron microscopy confirms a narrow size distribution in the 50 nm range. Nanocurcumin, unlike free curcumin, is readily dispersed in aqueous media. Nanocurcumin demonstrates comparablein vitrotherapeutic efficacy to free curcumin against a panel of human pancreatic cancer cell lines, as assessed by cell viability and clonogenicity assays in soft agar. Further, nanocurcumin's mechanisms of action on pancreatic cancer cells mirror that of free curcumin, including induction of cellular apoptosis, blockade of nuclear factor kappa B (NFκB) activation, and downregulation of steady state levels of multiple pro-inflammatory cytokines (IL-6, IL-8, and TNFα).

Conclusion

Nanocurcumin provides an opportunity to expand the clinical repertoire of this efficacious agent by enabling ready aqueous dispersion. Future studies utilizing nanocurcumin are warranted in pre-clinicalin vivomodels of cancer and other diseases that might benefit from the effects of curcumin.
Imprint cytology on microcalcifications excised by Vacuum-Assisted Breast Biopsy: A rapid preliminary diagnosis
Authors: Fotou Maria , Oikonomou Vassiliki , Zagouri Flora , Sergentanis Theodoros N , Nonni Afroditi , Athanassiadou Pauline , Drouveli Theodora , atsouris Efstratios , Kotzia Evagelia , Zografos George C
Published: April 2007

Background

To evaluate imprint cytology in the context of specimens with microcalcifications derived from Vacuum-Assisted Breast Biopsy (VABB).

Patients and methods

A total of 93 women with microcalcifications BI-RADS 3 and 4 underwent VABB and imprint samples were examined. VABB was performed on Fischer's table using 11-gauge Mammotome vacuum probes. A mammogram of the cores after the procedure confirmed the excision of microcalcifications. For the application of imprint cytology, the cores with microcalcifications confirmed by mammogram were gently rolled against glass microscope slides and thus imprint smears were made. For rapid preliminary diagnosis Diff-Quick stain, modified Papanicolaou stain and May Grunwald Giemsa were used. Afterwards, the core was dipped into a CytoRich Red Collection fluid for a few seconds in order to obtain samples with the use of the specimen wash. After the completion of cytological procedures, the core was prepared for routine histological study. The pathologist was blind to the preliminary cytological results. The cytological and pathological diagnoses were comparatively evaluated.

Results

According to the pathological examination, 73 lesions were benign, 15 lesions were carcinomas (12 ductal carcinomas in situ, 3 invasive ductal carcinomas), and 5 lesions were precursor: 3 cases of atypical ductal hyperplasia (ADH) and 2 cases of lobular neoplasia (LN). The observed sensitivity and specificity of the cytological imprints for cancer were 100% (one-sided, 97.5% CI: 78.2%–100%). Only one case of ADH could be detected by imprint cytology. Neither of the two LN cases was detected by the imprints. The imprints were uninformative in 11 out of 93 cases (11.8%). There was no uninformative case among women with malignancy.

Conclusion

Imprint cytology provides a rapid, accurate preliminary diagnosis in a few minutes. This method might contribute to the diagnosis of early breast cancer and possibly attenuates patients' anxiety.
Xanthogranulomatous osteomyelitis of ulna mimicking neoplasm
Authors: Vankalakunti Mahesha , Saikia Uma N , Mathew Manoj , Kang Mandeep
Published: April 2007

Background

Xanthogranulomatous osteomyelitis often presents as a severe chronic inflammation associated with pain, fever, and leukocytosis. It may mimic carcinoma in the involved organs.

Case presentation

A 50-year-old post-menopausal woman presented with a 2 year history of increasing swelling in the extensor aspect of her right forearm. Plain X-ray revealed an ill-defined expansile osteolytic lesion in the diaphysis of ulna. The gross, microscopic and ultrastructure findings of the curettage specimen was consistent with xanthogranulomatous osteomyelitis.

Conclusion

This case highlights the rare occurrence of xanthogranulomatous osteomyelitis involving ulna, which can mimic as a primary or secondary bone tumors. A correct diagnosis can only be made on histopathological examination.
Monocyte-derived dendritic cells loaded with a mixture of apoptotic/necrotic melanoma cells efficiently cross-present gp100 and MART-1 antigens to specific CD8+ T lymphocytes
Authors: von Euw Erika M , Barrio María M , Furman David , Bianchini Michele , Levy Estrella M , Yee Cassian , Li Yongqing , Wainstok Rosa , Mordoh José
Published: April 2007

Background

In the present study, we demonstrate, in rigorous fashion, that human monocyte-derived immature dendritic cells (DCs) can efficiently cross-present tumor-associated antigens when co-cultured with a mixture of human melanoma cells rendered apoptotic/necrotic by γ irradiation (Apo-Nec cells).

Methods

We evaluated the phagocytosis of Apo-Nec cells by FACS after PKH26 and PKH67 staining of DCs and Apo-Nec cells at different times of coculture. The kinetics of the process was also followed by electron microscopy. DCs maturation was also studied monitoring the expression of specific markers, migration towards specific chemokines and the ability to cross-presentin vitrothe native melanoma-associated Ags MelanA/MART-1 and gp100.

Results

Apo-Nec cells were efficiently phagocytosed by immature DCs (iDC) (55 ± 10.5%) at 12 hs of coculture. By 12–24 hs we observed digested Apo-Nec cells inside DCs and large empty vacuoles as part of the cellular processing. Loading with Apo-Nec cells induced DCs maturation to levels achieved using LPS treatment, as measured by: i) the decrease in FITC – Dextran uptake (iDC: 81 ± 5%; DC/Apo-Nec 33 ± 12%); ii) the cell surface up-regulation of CD80, CD86, CD83, CCR7, CD40, HLA-I and HLA-II and iii) an increasedin vitromigration towards MIP-3β. DC/Apo-Nec isolated from HLA-A*0201 donors were able to induce >600 pg/ml IFN-γ secretion of CTL clones specific for MelanA/MART-1 and gp100 Ags after 6 hs and up to 48 hs of coculture, demonstrating efficient cross-presentation of the native Ags. Intracellular IL-12 was detected in DC/Apo-Nec 24 hs post-coculture while IL-10 did not change.

Conclusion

We conclude that the use of a mixture of four apoptotic/necrotic melanoma cell lines is a suitable source of native melanoma Ags that provides maturation signals for DCs, increases migration to MIP-3β and allows Ag cross-presentation. This strategy could be exploited for vaccination of melanoma patients.
Promoting childbirth companions in South Africa: a randomised pilot study
Authors: Brown Heather , Hofmeyr G Justus , Nikodem V Cheryl , Smith Helen , Garner Paul
Published: April 2007

Background

Most women delivering in South African State Maternity Hospitals do not have a childbirth companion; in addition, the quality of care could be better, and at times women are treated inhumanely. We piloted a multi-faceted intervention to encourage uptake of childbirth companions in state hospitals, and hypothesised that lay carers would improve the behaviour of health professionals.

Methods

We conducted a pilot randomised controlled trial of an intervention to promote childbirth companions in hospital deliveries. We promoted evidence-based information for maternity staff at 10 hospitals through access to the World Health Organization Reproductive Health Library (RHL), computer hardware and training to all ten hospitals. We surveyed 200 women at each site, measuring companionship, and indicators of good obstetric practice and humanity of care. Five hospitals were then randomly allocated to receive an educational intervention to promote childbirth companions, and we surveyed all hospitals again at eight months through a repeat survey of postnatal women. Changes in median values between intervention and control hospitals were examined.

Results

At baseline, the majority of hospitals did not allow a companion, or access to food or fluids. A third of women were given an episiotomy. Some women were shouted at (17.7%, N = 2085), and a few reported being slapped or struck (4.3%, N = 2080). Despite an initial positive response from staff to the childbirth companion intervention, we detected no difference between intervention and control hospitals in relation to whether a companion was allowed by nursing staff, good obstetric practice or humanity of care.

Conclusion

The quality and humanity of care in these state hospitals needs to improve. Introducing childbirth companions was more difficult than we anticipated, particularly in under-resourced health care systems with frequent staff changes. We were unable to determine whether the presence of a lay carer impacted on the humanity of care provided by health professionals.

Trial registration: Current Controlled Trials ISRCTN33728802
Pathological cell-cell interactions are necessary for striatal pathogenesis in a conditional mouse model of Huntington's disease
Authors: Gu Xiaofeng , André Véronique M , Cepeda Carlos , Li Shi-Hua , Li Xiao-Jiang , Levine Michael S , Yang X William
Published: April 2007

A critical issue in understanding Huntington's disease (HD) pathogenesis is how the ubiquitously expressed mutant huntingtin (mhtt) with an expanded polyglutamine repeat can cause selective toxicity of striatal and cortical neurons. Two potential cellular models may contribute to such specificity: expression of mhtt in these vulnerable neurons alone may be sufficient to result in their dysfunction and/or degeneration (cell-autonomous model); or mhtt in other cell types can elicit pathological cell-cell interactions to cause the vulnerable neurons to become dysfunctional and be at risk for degeneration (cell-cell interaction model). To distinguish between these two models, we have selectively expressed a neuropathogenic fragment of mhtt-exon1 in striatal medium spiny neurons (MSNs) by crossing a conditional mouse model of HD with a striatal-specific Cre mouse line. In this striatal model of HD, we observed progressive and cell-autonomous nuclear accumulation of mhtt aggregates in MSNs. Surprisingly, unlike the mouse model expressing mhtt-exon1 in all the neurons in the brain, the striatal model lacks significant locomotor deficits and striatal neuropathology including gliosis and dark degenerating neurons. Electrophysiological findings from acutely dissociated MSNs revealed a cell-autonomous deficit in N-methyl-d-aspartate (NMDA) receptor sensitivity to Mg2+, a deficit also present in other mouse models of HD. In conclusion, this study provides the first in vivo genetic evidence that pathological cell-cell interactions are necessary for striatal pathogenesis in a conditional mouse model of HD, and suggests a ''two-hit'' hypothesis in which both cell-autonomous toxicity and pathological cell-cell interactions are critical to HD pathogenesis.
Replication of the genetic effects of IFN regulatory factor 5 (IRF5) on systemic lupus erythematosus in a Korean population
Authors: Shin Hyoung Doo , Sung Yoon-Kyoung , Choi Chan-Bum , Lee Soo Ok , Lee Hye Won , Bae Sang-Cheol
Published: April 2007

Recently, two studies provided convincing evidence that IFN regulatory factor 5 (IRF5) gene polymorphisms are significantly associated with systemic lupus erythematosus (SLE) in several white populations. To replicate the association with SLE in an Asian population, we examined the genetic effects in our SLE cohort from a Korean population. A total of 1,565 subjects, composed of 593 cases and 972 controls, were genotyped using the TaqMan® (Applied Biosystems, Foster City, CA, USA) method. The genetic effects of polymorphisms on the risk of SLE were evaluated using χ2 tests and a Mantel–Haenszel meta-analysis. Statistical analysis revealed results in the Korean population were similar to the previous reports from white populations. The rs2004640 T allele had a higher frequency in SLE cases (0.385) than controls (0.321; odds ratio (OR) = 1.32, P = 0.0003). In combined analysis, including all seven independent cohorts from the three studies so far, robust and consistent associations of the rs2004640 T allele with SLE were observed. The estimate of risk was OR = 1.44 (range, 1.34–1.55), with an overall P = 1.85 × 10-23 for the rs2004640 T allele. The haplotype (rs2004640T–rs2280714T) involved in both the alternative splice donor site and the elevated expression of IRF5 also had a highly significant association with SLE (pooled, P = 2.11 × 10-16). Our results indicate that the genetic effect on the risk of SLE mediated by IRF5 variants can be generally accepted in both white and Asian populations.
Microenvironmental changes during differentiation of mesenchymal stem cells towards chondrocytes
Authors: Djouad Farida , Delorme Bruno , Maurice Marielle , Bony Claire , Apparailly Florence , Louis-Plence Pascale , Canovas François , Charbord Pierre , Noël Danièle , Jorgensen Christian
Published: April 2007

Chondrogenesis is a process involving stem-cell differentiation through the coordinated effects of growth/differentiation factors and extracellular matrix (ECM) components. Recently, mesenchymal stem cells (MSCs) were found within the cartilage, which constitutes a specific niche composed of ECM proteins with unique features. Therefore, we hypothesized that the induction of MSC differentiation towards chondrocytes might be induced and/or influenced by molecules from the microenvironment. Using microarray analysis, we previously identified genes that are regulated during MSC differentiation towards chondrocytes. In this study, we wanted to precisely assess the differential expression of genes associated with the microenvironment using a large-scale real-time PCR assay, according to the simultaneous detection of up to 384 mRNAs in one sample. Chondrogenesis of bone-marrow-derived human MSCs was induced by culture in micropellet for various periods of time. Total RNA was extracted and submitted to quantitative RT-PCR. We identified molecules already known to be involved in attachment and cell migration, including syndecans, glypicans, gelsolin, decorin, fibronectin, and type II, IX and XI collagens. Importantly, we detected the expression of molecules that were not previously associated with MSCs or chondrocytes, namely metalloproteases (MMP-7 and MMP-28), molecules of the connective tissue growth factor (CTGF); cef10/cyr61 and nov (CCN) family (CCN3 and CCN4), chemokines and their receptors chemokine CXC motif ligand (CXCL1), Fms-related tyrosine kinase 3 ligand (FlT3L), chemokine CC motif receptor (CCR3 and CCR4), molecules with A Disintegrin And Metalloproteinase domain (ADAM8, ADAM9, ADAM19, ADAM23, A Disintegrin And Metalloproteinase with thrombospondin type 1 motif ADAMTS-4 and ADAMTS-5), cadherins (4 and 13) and integrins (α4, α7 and β5). Our data suggest that crosstalk between ECM components of the microenvironment and MSCs within the cartilage is responsible for the differentiation of MSCs into chondrocytes.
Relationship between physical activity and stiff or painful joints in mid-aged women and older women: a 3-year prospective study
Authors: Heesch Kristiann C , Miller Yvette D , Brown Wendy J
Published: April 2007

This prospective study examined the association between physical activity and the incidence of self-reported stiff or painful joints (SPJ) among mid-age women and older women over a 3-year period. Data were collected from cohorts of mid-age (48–55 years at Time 1; n = 4,780) and older women (72–79 years at Time 1; n = 3,970) who completed mailed surveys 3 years apart for the Australian Longitudinal Study on Women's Health. Physical activity was measured with the Active Australia questions and categorized based on metabolic equivalent value minutes per week: none (<40 MET.min/week); very low (40 to <300 MET.min/week); low (300 to <600 MET.min/week); moderate (600 to <1,200 MET.min/week); and high (1,200+ MET.min/week). Cohort-specific logistic regression models were used to examine the association between physical activity at Time 1 and SPJ 'sometimes or often' and separately 'often' at Time 2. Respondents reporting SPJ 'sometimes or often' at Time 1 were excluded from analysis. In univariate models, the odds of reporting SPJ 'sometimes or often' were lower for mid-age respondents reporting low (odds ratio (OR) = 0.77, 95% confidence interval (CI) = 0.63–0.94), moderate (OR = 0.82, 95% CI = 0.68–0.99), and high (OR = 0.75, 95% CI = 0.62–0.90) physical activity levels and for older respondents who were moderately (OR = 0.80, 95% CI = 0.65–0.98) or highly active (OR = 0.83, 95% CI = 0.69–0.99) than for those who were sedentary. After adjustment for confounders, these associations were no longer statistically significant. The odds of reporting SPJ 'often' were lower for mid-age respondents who were moderately active (OR = 0.71, 95% CI = 0.52–0.97) than for sedentary respondents in univariate but not adjusted models. Older women in the low (OR = 0.72, 95% CI = 0.55–0.96), moderate (OR = 0.54, 95% CI = 0.39–0.76), and high (OR = 0.61, 95% CI = 0.46–0.82) physical activity categories had lower odds of reporting SPJ 'often' at Time 2 than their sedentary counterparts, even after adjustment for confounders. These results are the first to show a dose–response relationship between physical activity and arthritis symptoms in older women. They suggest that advice for older women not currently experiencing SPJ should routinely include counseling on the importance of physical activity for preventing the onset of these symptoms.
FGFR1 amplification in breast carcinomas: a chromogenic in situhybridisation analysis
Authors: Elbauomy Elsheikh Somaia , Green Andrew R , Lambros Maryou BK , Turner Nicholas C , Grainge Matthew J , Powe Des , Ellis Ian O , Reis-Filho Jorge S
Published: April 2007

Background

The amplicon on 8p11.2 is reported to be found in up to 10% of breast carcinomas. It has been demonstrated recently that this amplicon has four separate cores. The second core encompasses important oncogene candidates, including the fibroblast growth factor receptor 1 (FGFR1) gene. Recent studies have demonstrated that specific FGFR1 amplification correlates with gene expression and that FGFR1 activity is required for the survival of a FGFR1 amplified breast cancer cell line.

Methods

FGFR1 amplification was analysed in tissue microarrays comprising a cohort of 880 unselected breast tumours by means of chromogenic in situ hybridisation using inhouse-generated FGFR1-specific probes. Chromogenic in situ hybridisation signals were counted in a minimum 30 morphologically unequivocal neoplastic cells. Amplification was defined as >5 signals per nucleus in more than 50% of cancer cells or when large gene copy clusters were seen.

Results

FGFR1 amplification was observed in 8.7% of the tumours and was significantly more prevalent in patients >50 years of age and in tumours that lacked HER2 expression. No association was found with other histological parameters. Survival analysis revealed FGFR1 amplification as an independent prognostic factor for overall survival in the whole cohort. Subgroup analysis demonstrated that the independent prognostic impact of FGFR1 amplification was only seen in patients with oestrogen-receptor-positive tumours, where FGFR1 amplification was the strongest independent predictor of poor outcome.

Conclusion

Given that up to 8.7% of all breast cancers harbour FGFR1 amplification and that this amplification is an independent predictor of overall survival, further studies analysing the FGFR1 as a potential therapeutic target for breast cancer patients are warranted.
Inhibitory effects of estrogen receptor beta on specific hormone-responsive gene expression and association with disease outcome in primary breast cancer
Authors: Lin Chin-Yo , Ström Anders , Li Kong Say , Kietz Silke , Thomsen Jane S , Tee Jason BS , Vega Vinsensius B , Miller Lance D , Smeds Johanna , Bergh Jonas , Gustafsson Jan-Åke , Liu Edison T
Published: April 2007

Introduction

The impact of interactions between the two estrogen receptor (ER) subtypes, ERα and ERβ, on gene expression in breast cancer biology is not clear. The goal of this study was to examine transcriptomic alterations in cancer cells co-expressing both receptors and the association of gene expression signatures with disease outcome.

Methods

Transcriptional effects of ERβ overexpression were determined in a stably transfected cell line derived from ERα-positive T-47D cells. Microarray analysis was carried out to identify differential gene expression in the cell line, and expression of key genes was validated by quantitative polymerase chain reaction. Microarray and clinical data from patient samples were then assessed to determine the in vivo relevance of the expression profiles observed in the cell line.

Results

A subset of 14 DNA replication and cell cycle-related genes was found to be specifically downregulated by ERβ. Expression profiles of four genes, CDC2, CDC6, CKS2, and DNA2L, were significantly inversely correlated with ERβ transcript levels in patient samples, consistent with in vitro observations. Kaplan-Meier analysis revealed better disease outcome for the patient group with an expression signature linked to higher ERβ expression as compared to the lower ERβ-expressing group for both disease-free survival (p = 0.00165) and disease-specific survival (p = 0.0268). These findings were further validated in an independent cohort.

Conclusion

Our findings revealed a transcriptionally regulated mechanism for the previously described growth inhibitory effects of ERβ in ERα-positive breast tumor cells and provide evidence for a functional and beneficial impact of ERβ in primary breast tumors.
Use of plasma C-reactive protein, procalcitonin, neutrophils, macrophage migration inhibitory factor, soluble urokinase-type plasminogen activator receptor, and soluble triggering receptor expressed on myeloid cells-1 in combination to diagnose infections: a prospective study
Authors: Kofoed Kristian , Andersen Ove , Kronborg Gitte , Tvede Michael , Petersen Janne , Eugen-Olsen Jesper , Larsen Klaus
Published: April 2007

Introduction

Accurate and timely diagnosis of community-acquired bacterial infections in patients with systemic inflammation remains challenging both for clinician and laboratory. Combinations of markers, as opposed to single ones, may improve diagnosis and thereby survival. We therefore compared the diagnostic characteristics of novel and routinely used biomarkers of sepsis alone and in combination.

Methods

This prospective cohort study included patients with systemic inflammatory response syndrome who were suspected of having community-acquired infections. It was conducted in a medical emergency department and department of infectious diseases at a university hospital. A multiplex immunoassay measuring soluble urokinase-type plasminogen activator (suPAR) and soluble triggering receptor expressed on myeloid cells (sTREM)-1 and macrophage migration inhibitory factor (MIF) was used in parallel with standard measurements of C-reactive protein (CRP), procalcitonin (PCT), and neutrophils. Two composite markers were constructed – one including a linear combination of the three best performing markers and another including all six – and the area under the receiver operating characteristic curve (AUC) was used to compare their performance and those of the individual markers.

Results

A total of 151 patients were eligible for analysis. Of these, 96 had bacterial infections. The AUCs for detection of a bacterial cause of inflammation were 0.50 (95% confidence interval [CI] 0.40 to 0.60) for suPAR, 0.61 (95% CI 0.52 to 0.71) for sTREM-1, 0.63 (95% CI 0.53 to 0.72) for MIF, 0.72 (95% CI 0.63 to 0.79) for PCT, 0.74 (95% CI 0.66 to 0.81) for neutrophil count, 0.81 (95% CI 0.73 to 0.86) for CRP, 0.84 (95% CI 0.71 to 0.91) for the composite three-marker test, and 0.88 (95% CI 0.81 to 0.92) for the composite six-marker test. The AUC of the six-marker test was significantly greater than that of the single markers.

Conclusion

Combining information from several markers improves diagnostic accuracy in detecting bacterial versus nonbacterial causes of inflammation. Measurements of suPAR, sTREM-1 and MIF had limited value as single markers, whereas PCT and CRP exhibited acceptable diagnostic characteristics.

Trial registration

NCT 00389337
Optimizing intensive care capacity using individual length-of-stay prediction models
Authors: Van Houdenhoven Mark , Nguyen Duy-Tien , Eijkemans Marinus J , Steyerberg Ewout W , Tilanus Hugo W , Gommers Diederik , Wullink Gerhard , Bakker Jan , Kazemier Geert
Published: April 2007

Introduction

Effective planning of elective surgical procedures requiring postoperative intensive care is important in preventing cancellations and empty intensive care unit (ICU) beds. To improve planning, we constructed, validated and tested three models designed to predict length of stay (LOS) in the ICU in individual patients.

Methods

Retrospective data were collected from 518 consecutive patients who underwent oesophagectomy with reconstruction for carcinoma between January 1997 and April 2005. Three multivariable linear regression models for LOS, namely preoperative, postoperative and intra-ICU, were constructed using these data. Internal validation was assessed using bootstrap sampling in order to obtain validated estimates of the explained variance (r2). To determine the potential gain of the best performing model in day-to-day clinical practice, prospective data from a second cohort of 65 consecutive patients undergoing oesophagectomy between May 2005 and April 2006 were used in the model, and the predictive performance of the model was compared with prediction based on mean LOS.

Results

The intra-ICU model had an r2 of 45% after internal validation. Important prognostic variables for LOS included greater patient age, comorbidity, type of surgical approach, intraoperative respiratory minute volume and complications occurring within 72 hours in the ICU. The potential gain of the best model in day-to-day clinical practice was determined relative to mean LOS. Use of the model reduced the deficit number (underestimation) of ICU days by 65 and increased the excess number (overestimation) of ICU days by 23 for the cohort of 65 patients. A conservative analysis conducted in the second, prospective cohort of patients revealed that 7% more oesophagectomies could have been accommodated, and 15% of cancelled procedures could have been prevented.

Conclusion

Patient characteristics can be used to create models that will help in predicting LOS in the ICU. This will result in more efficient use of ICU beds and fewer cancellations.
Diagnosis of left ventricular diastolic dysfunction in the setting of acute changes in loading conditions
Authors: Vignon Philippe , Allot Vincent , Lesage Jérôme , Martaillé Jean-François , Aldigier Jean-Claude , François Bruno , Gastinne Hervé
Published: April 2007

Introduction

Conventional pulsed wave Doppler parameters are known to be preload dependent, whereas newly proposed Doppler indices may be less influenced by variations in loading conditions. The aim of the present study was to evaluate the effects of haemodialysis-induced preload reduction on both conventional and new Doppler parameters for the assessment of left ventricular (LV) diastolic function.

Methods

This prospective observational study was conducted in a medical-surgical intensive care unit (ICU) and nephrology department of a teaching hospital. In total, 37 haemodialysis patients with end-stage renal disease (age [mean ± standard deviation]: 52 ± 13 years) and eight ventilated ICU patients with acute renal failure receiving vasopressor therapy (age 57 ± 16 years; Simplified Acute Physiology Score II 51 ± 17) were studied. Echocardiography was performed before and after haemodialysis. Conventional pulsed wave Doppler indices of LV diastolic function as well as new Doppler indices, including Doppler tissue imaging early diastolic velocities (E' wave) of the septal and lateral portions of the mitral annulus, and propagation velocity of LV inflow at early diastole (Vp) were measured and compared before and after ultrafiltration.

Results

The volume of ultrafiltration was greater in haemodialysis patients than in ICU patients (3.0 ± 1.1 l versus 1.9 ± 0.9 l; P = 0.005). All conventional pulsed wave Doppler parameters were altered by haemodialysis. In haemodialysis patients, E' velocity decreased after ultrafiltration when measured at the septal mitral annulus (7.1 ± 2.5 cm/s versus 5.9 ± 1.7 cm/s; P = 0.0003), but not at its lateral portion (8.9 ± 3.1 cm/s versus 8.3 ± 2.6 cm/s; P = 0.37), whereas no significant variation was observed in ICU patients. Vp decreased uniformly after ultrafiltration, the difference being significant only in haemodialysis patients (45 ± 11 cm/s versus 41 ± 13 cm/s; P = 0.04). Although of less magnitude, ultrafiltration-induced variations in Doppler parameters were also observed in haemodialysis patients with altered LV systolic function.

Conclusion

In contrast to other Doppler parameters, Doppler tissue imaging E' maximal velocity measured at the lateral mitral annulus represents an index of LV diastolic function that is relatively insensitive to abrupt and marked preload reduction.
Changes in pulse pressure variability during cardiac resynchronization therapy in mechanically ventilated patients
Authors: Keyl Cornelius , Stockinger Jochem , Laule Sven , Staier Klaus , Schiebeling-Römer Jochen , Wiesenack Christoph
Published: April 2007

Introduction

The respiratory variation in pulse pressure (PP) has been established as a dynamic variable of cardiac preload which indicates fluid responsiveness in mechanically ventilated patients. The impact of acute changes in cardiac performance on respiratory fluctuations in PP has not been evaluated until now. We used cardiac resynchronization therapy as a model to assess the acute effects of changes in left ventricular performance on respiratory PP variability without the need of pharmacological intervention.

Methods

In 19 patients undergoing the implantation of a biventricular pacing/defibrillator device under general anesthesia, dynamic blood pressure regulation was assessed during right ventricular and biventricular pacing in the frequency domain (power spectral analysis) and in the time domain (PP variation: difference between the maximal and minimal PP values, normalized by the mean value).

Results

PP increased slightly during biventricular pacing but without statistical significance (right ventricular pacing, 33 ± 10 mm Hg; biventricular pacing, 35 ± 11 mm Hg). Respiratory PP fluctuations increased significantly (logarithmically transformed PP variability -1.27 ± 1.74 ln mm Hg2 versus -0.66 ± 1.48 ln mm Hg2; p < 0.01); the geometric mean of respiratory PP variability increased 1.8-fold during cardiac resynchronization. PP variation, assessed in the time domain and expressed as a percentage, showed comparable changes, increasing from 5.3% (3.1%; 12.3%) during right ventricular pacing to 6.9% (4.7%; 16.4%) during biventricular pacing (median [25th percentile; 75th percentile]; p < 0.01).

Conclusion

Changes in cardiac performance have a significant impact on respiratory hemodynamic fluctuations in ventilated patients. This influence should be taken into consideration when interpreting PP variation.
Case mix, outcome and activity for patients admitted to intensive care units requiring chronic renal dialysis: a secondary analysis of the ICNARC Case Mix Programme Database
Authors: Hutchison Colin A , Crowe Alex V , Stevens Paul E , Harrison David A , Lipkin Graham W
Published: April 2007

Introduction

This report describes the case mix, outcome and activity for admissions to intensive care units (ICUs) of patients who require prior chronic renal dialysis for end-stage renal failure (ESRF), and investigates the effect of case mix factors on outcome.

Methods

This was a secondary analysis of a high-quality clinical database, namely the Intensive Care National Audit & Research Centre (ICNARC) Case Mix Programme Database, which includes 276,731 admissions to 170 adult ICUs across England, Wales and Northern Ireland from 1995 to 2004.

Results

During the eight year study period, 1.3% (n = 3,420) of all patients admitted to ICU were receiving chronic renal dialysis before ICU admission. This represents an estimated ICU utilization of six admissions (32 bed-days) per 100 dialysis patient-years. The ESRF group was younger (mean age 57.3 years versus 59.5 years) and more likely to be male (60.2% versus 57.9%) than those without ESRF. Acute Physiology and Chronic Health Evaluation II score and Acute Physiology Score revealed greater severity of illness on admission in patients with ESRF (mean 24.7 versus 16.6 and 17.2 versus 12.6, respectively). Length of stay in ICU was comparable between groups (median 1.9 days versus 1.8 days) and ICU mortality was only slightly elevated in the ESRF group (26.3% versus 20.8%). However, the ESRF group had protracted overall hospital stay (median 25 days versus 17 days), and increased hospital mortality (45.3% versus 31.2%) and ICU readmission (9.0% vs. 4.7%). Multiple logistic regression analysis adjusted for case mix identified the increased hospital mortality to be associated with increasing age, emergency surgery and nonsurgical cases, cardiopulmonary resuscitation before ICU admission and extremes of physiological norms. The adjusted odds ratio for ultimate hospital mortality associated with chronic renal dialysis was 1.24 (95% confidence interval 1.13 to 1.37).

Conclusion

Patients with ESRF admitted to UK ICUs are more likely to be male and younger, with a medical cause of admission, and to have greater severity of illness than the non-ESRF population. Outcomes on the ICU were comparable between the two groups, but those patients with ESRF had greater readmission rates, prolonged post-ICU hospital stay and increased post-ICU hospital mortality. This study is by far the largest comparative outcome analysis to date in patients with ESRF admitted to the ICU. It may help to inform clinical decision-making and resource requirements for this patient population.
Mobilization of pro-inflammatory lipids in obese Plscr3-deficient mice
Authors: Mutch David M , O'Maille Grace , Wikoff William R , Wiedmer Therese , Sims Peter J , Siuzdak Gary
Published: April 2007

Background

The obesity epidemic has prompted the search for candidate genes capable of influencing adipose function. One such candidate, that encoding phospholipid scramblase 3 (PLSCR3), was recently identified, as genetic deletion of it led to lipid accumulation in abdominal fat pads and changes characteristic of metabolic syndrome. Because adipose tissue is increasingly recognized as an endocrine organ, capable of releasing small molecules that modulate disparate physiological processes, we examined the plasma from wild-type, Plscr1-/-, Plscr3-/- and Plscr1&3-/- mice. Using an untargeted comprehensive metabolite profiling approach coupled with targeted gene expression analyses, the perturbed biochemistry and functional redundancy of PLSCR proteins was assessed.

Results

Nineteen metabolites were differentially and similarly regulated in both Plscr3-/- and Plscr1&3-/- animals, of which five were characterized from accurate mass, tandem mass spectrometry data and their correlation to the Metlin database as lysophosphatidylcholine (LPC) species enriched with C16:1, C18:1, C20:3, C20:5 and C22:5 fatty acids. No significant changes in the plasma metabolome were detected upon elimination of PLSCR1, indicating that increases in pro-inflammatory lipids are specifically associated with the obese state of Plscr3-deficient animals. Correspondingly, increases in white adipose lipogenic gene expression confirm a role for PLSCR3 in adipose lipid metabolism.

Conclusion

The untargeted profiling of circulating metabolites suggests no detectable functional redundancies between PLSCR proteins; however, this approach simultaneously identified previously unrecognized lipid metabolites that suggest a novel molecular link between obesity, inflammation and the downstream consequences associated with PLSCR3-deficiency.
A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome
Authors: Small Kerrin S , Brudno Michael , Hill Matthew M , Sidow Arend
Published: April 2007

The sequence of Ciona savignyi was determined using a whole-genome shotgun strategy, but a high degree of polymorphism resulted in a fractured assembly wherein allelic sequences from the same genomic region assembled separately. We designed a multistep strategy to generate a nonredundant reference sequence from the original assembly by reconstructing and aligning the two 'haplomes' (haploid genomes). In the resultant 174 megabase reference sequence, each locus is represented once, misassemblies are corrected, and contiguity and continuity are dramatically improved.