bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regularized Logistic Models for Probabilistic Forecasting and Diagnostics
Authors: Bröcker Jochen 
Published: August 2009

AbstractLogistic models are studied as a tool to convert dynamical forecast information (deterministic and ensemble) into probability forecasts. A logistic model is obtained by setting the logarithmic odds ratio equal to a linear combination of the inputs. As with any statistical model, logistic models will suffer from overfitting if the number of inputs is comparable to the number of forecast instances. Computational approaches to avoid overfitting by regularization are discussed, and efficient techniques for model assessment and selection are presented. A logit version of the lasso (originally a linear regression technique), is discussed. In lasso models, less important inputs are identified and the corresponding coefficient is set to zero, providing an efficient and automatic model reduction procedure. For the same reason, lasso models are particularly appealing for diagnostic purposes.
Development and first validation of the COPD Assessment Test
Authors: Jones P. W. , Harding G. , Berry P. , Wiklund I. , Chen W-H. , Kline Leidy N. 
Published: August 2009

There is need for a validated short, simple instrument to quantify chronic obstructive pulmonary disease (COPD) impact in routine practice to aid health status assessment and communication between patient and physician. Current health-related quality of life questionnaires provide valid assessment of COPD, but are complex, which limits routine use.The aim of the present study was to develop a short validated patient-completed questionnaire, the COPD Assessment Test (CAT), assessing the impact of COPD on health status.21 candidate items identified through qualitative research with COPD patients were used in three prospective international studies (Europe and the USA, n = 1,503). Psychometric and Rasch analyses identified eight items fitting a unidimensional model to form the CAT. Items were tested for differential functioning between countries. Internal consistency was excellent: Cronbach's α = 0.88. Test re-test in stable patients (n = 53) was very good (intra-class correlation coefficient 0.8). In the sample from the USA, the correlation with the COPD-specific version of the St George’s Respiratory Questionnaire was r = 0.80. The difference between stable (n = 229) and exacerbation patients (n = 67) was five units of the 40-point scale (12%; p<0.0001).The CAT is a short, simple questionnaire for assessing and monitoring COPD. It has good measurement properties, is sensitive to differences in state and should provide a valid, reliable and standardised measure of COPD health status with worldwide relevance.
Medicines used in respiratory diseases only seen in children
Authors: Lenney W. , Boner A. L. , Bont L. , Bush A. , Carlsen K-H. , Eber E. , Fauroux B. , Götz M. , Greenough A. , Grigg J. , Hull J. , Kimpen J. , Sánchez Luna M. , de Benedictis F. M. 
Published: August 2009

Detailed literature searches were carried out in seven respiratory disease areas. Therapeutic evidence for efficacy of medicinal products was assessed using the Grades of Recommendation, Assessment and Evaluation (GRADE) methodology, as well as an assessment of safety and side-effects.Systemic corticosteroids may reduce the development of bronchopulmonary dysplasia but have serious side-effects. Antioxidants need further study to demonstrate whether they have long-term benefits. Treatments for acute bronchiolitis have shown little benefit but new antiviral and monoclonal antibodies need further assessment. Well-constructed studies are needed to confirm the value of inhaled corticosteroids and/or montelukast in the management of viral-induced wheeze. Corticosteroids are the treatment of choice in croup. Minimal or no information is available for the treatment of congenital lung abnormalities, bronchiolitis obliterans and interstitial lung disease.
What defines airflow obstruction in asthma?
Authors: Cerveri I. , Corsico A. G. , Accordini S. , Cervio G. , Ansaldo E. , Grosso A. , Niniano R. , Tsana Tegomo E. , Antó J. M. , Künzli N. , Janson C. , Sunyer J. , Svanes C. , Heinrich J. , Schouten J. P. , Wjst M. , Pozzi E. , de Marco R. 
Published: August 2009

Asthma guidelines from the Global Initiative for Asthma (GINA) and from the National Heart, Lung, and Blood Institute provide conflicting definitions of airflow obstruction, suggesting a fixed forced expiratory volume in 1 s (FEV1)/forced vital capacity (FVC) cut-off point and the lower limit of normality (LLN), respectively. The LLN was recommended by the recent American Thoracic Society/European Respiratory Society guidelines on lung function testing. The problem in using fixed cut-off points is that they are set regardless of age and sex in an attempt to simplify diagnosis at the expense of misclassification.The sensitivity and specificity of fixed FEV1/FVC ratios of 0.70, 0.75 and 0.80versusthe LLN were evaluated in 815 subjects (aged 20–44 yrs) with a diagnosis of asthma within the framework of the European Community Respiratory Health Survey.In males, the 0.70 ratio showed 76.5% sensitivity and 100.0% specificity, the 0.75 ratio 100.0% sensitivity and 92.4% specificity, and the 0.80 ratio 100.0% sensitivity but 58.1% specificity. In females, the 0.70 ratio showed 57.3% sensitivity and 100.0% specificity, the 0.75 ratio 91.5% sensitivity and 95.9% specificity, and the 0.80 ratio 100.0% sensitivity but 72.9% specificity.The fixed cut-off points cause a lot of misidentification of airflow obstruction in young adults, with overestimation with the 0.80 ratio and underestimation with the 0.70 ratio. In conclusion, the GINA guidelines should change their criteria for defining airflow obstruction.
Fatal dissection of the pulmonary artery in pulmonary arterial hypertension
Authors: Degano B. , Prevot G. , Têtu L. , Sitbon O. , Simonneau G. , Humbert M. 
Published: August 2009

A 41-yr-old patient with chronic stable idiopathic pulmonary arterial hypertension (PAH) presented with sudden chest pain and unusual dyspnoea during physical exertion. The patient had been diagnosed with PAH at the age of 12 yrs and was in New York Heart Association functional class I/II. The patient was being treated with an anticoagulant regimen, low-dose diuretics and continuous intravenous epoprostenol therapy.A computed tomography scan showed ancient massive thrombi in dilated central pulmonary arteries, which were not haemodynamically significant (perfusion lung scans did not demonstrate segmental or larger defects), and extensive dissection of the right pulmonary artery starting from the intermediate branch. Due to the extensiveness of the dissection, the patient was immediately considered for heart–lung transplantation, but died 72 h after the onset of symptoms. Permission forpost mortemexamination was denied.Pulmonary artery dissection should be suspected in PAH patients presenting with chest pain and worsening dyspnoea. In the current case, the factors possibly associated with increased risk for dissection may include dilatation of the pulmonary artery, local inflammation favoured byin situthrombosis, and acute increase of pulmonary pressure secondary to physical exertion. Extensive pulmonary artery dissection is a life-threatening complication of PAH, and urgent heart/lung transplantation might be the treatment of choice in eligible patients. In addition, better identification of the risk factors for pulmonary artery dissection may help in considering transplantation for selected patients at risk.
Unusual presentation for a patent ductus arteriosus
Authors: Vizza C. D. , Badagliacca R. , Poscia R. , Gambardella C. , Pezzuto B. , Crescenzi E. , Papa S. , Fedele F. 
Published: August 2009

A 63-yr-old black female, with a 1-yr history of hepatitis C and ascites was referred to an expert centre with suspicion of portopulmonary hypertension (PPHTN). Her poor condition made a rapid diagnosis imperative and precluded a normal diagnostic work-up.Echocardiography confirmed severe pulmonary hypertension (PH). A hepatic scintigraphy and an abdominal echo-Doppler study excluded liver cirrhosis and portal hypertension. Cardiac magnetic resonance imaging showed marked dilation of the right ventricle with significant hypertrophy of the free wall, a finding that is uncommon in idiopathic pulmonary arterial hypertension or PPHTN. Right heart catheterisation demonstrated severe pre-capillary PH without response to acute vasodilator testing. Finally the patient underwent computed tomography angiography, which showed marked dilation of the pulmonary artery without thromboembolic disease and, unexpectedly, a partially calcified large patent ductus arteriosus.The correct diagnosis of the underlying cause of pulmonary arterial hypertension is essential. Patients with underlying heart defects may have an atypical presentation and be referred to expert centres with an incorrect diagnosis. A full investigation is necessary; careful examination of right ventricular anatomy can provide clues about the aetiology of PH, and it is important to exclude intra- and extracardiac shunts during haemodynamic studies.
Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database
Authors: Hendrickson Erik L , Xia Qiangwei , Wang Tiansong , Lamont Richard J , Hackett Murray 
Published: September 2009

Abstract

Background

Porphyromonas gingivalis is a Gram-negative intracellular pathogen associated with periodontal disease. We have previously reported on whole-cell quantitative proteomic analyses to investigate the differential expression of virulence factors as the organism transitions from an extracellular to intracellular lifestyle. The original results with the invasive strain P. gingivalis ATCC 33277 were obtained using the genome sequence available at the time, strain W83 [GenBank: AE015924]. We present here a re-processed dataset using the recently published genome annotation specific for strain ATCC 33277 [GenBank: AP009380] and an analysis of differential abundance based on metabolic pathways rather than individual proteins.

Results
Qualitative detection was observed for 1266 proteins using the strain ATCC 33277 annotation for 18 hour internalized P. gingivalis within human gingival epithelial cells and controls exposed to gingival cell culture medium, an improvement of 7% over the W83 annotation. Internalized cells showed increased abundance of proteins in the energy pathway from asparagine/aspartate amino acids to ATP. The pathway producing one short chain fatty acid, propionate, showed increased abundance, while that of another, butyrate, trended towards decreased abundance. The translational machinery, including ribosomal proteins and tRNA synthetases, showed a significant increase in protein relative abundance, as did proteins responsible for transcription.

Conclusion
Use of the ATCC 33277 specific genome annotation resulted in improved proteome coverage with respect to the number of proteins observed both qualitatively in terms of protein identifications and quantitatively in terms of the number of calculated abundance ratios. Pathway analysis showed a significant increase in overall protein synthetic and transcriptional machinery in the absence of significant growth. These results suggest that the interior of host cells provides a more energy rich environment compared to the extracellular milieu. Shifts in the production of cytotoxic fatty acids by intracellular P. gingivalis may play a role in virulence. Moreover, despite extensive genomic re-arrangements between strains W83 and 33277, there is sufficient sequence similarity at the peptide level for proteomic abundance trends to be largely accurate when using the heterologous strain annotated genome as the reference for database searching.
Improved hospital-level risk adjustment for surveillance of healthcare-associated bloodstream infections: a retrospective cohort study
Authors: Tong ENC , Clements ACA , Haynes MA , Jones MA , Morton AP , Whitby M 
Published: September 2009

Abstract

Background
To allow direct comparison of bloodstream infection (BSI) rates between hospitals for performance measurement, observed rates need to be risk adjusted according to the types of patients cared for by the hospital. However, attribute data on all individual patients are often unavailable and hospital-level risk adjustment needs to be done using indirect indicator variables of patient case mix, such as hospital level. We aimed to identify medical services associated with high or low BSI rates, and to evaluate the services provided by the hospital as indicators that can be used for more objective hospital-level risk adjustment.

Methods
From February 2001-December 2007, 1719 monthly BSI counts were available from 18 hospitals in Queensland, Australia. BSI outcomes were stratified into four groups: overall BSI (OBSI), Staphylococcus aureus BSI (STAPH), intravascular device-related S. aureus BSI (IVD-STAPH) and methicillin-resistant S. aureus BSI (MRSA). Twelve services were considered as candidate risk-adjustment variables. For OBSI, STAPH and IVD-STAPH, we developed generalized estimating equation Poisson regression models that accounted for autocorrelation in longitudinal counts. Due to a lack of autocorrelation, a standard logistic regression model was specified for MRSA.

Results
Four risk services were identified for OBSI: AIDS (IRR 2.14, 95% CI 1.20 to 3.82), infectious diseases (IRR 2.72, 95% CI 1.97 to 3.76), oncology (IRR 1.60, 95% CI 1.29 to 1.98) and bone marrow transplants (IRR 1.52, 95% CI 1.14 to 2.03). Four protective services were also found. A similar but smaller group of risk and protective services were found for the other outcomes. Acceptable agreement between observed and fitted values was found for the OBSI and STAPH models but not for the IVD-STAPH and MRSA models. However, the IVD-STAPH and MRSA models successfully discriminated between hospitals with higher and lower BSI rates.

Conclusion
The high model goodness-of-fit and the higher frequency of OBSI and STAPH outcomes indicated that hospital-specific risk adjustment based on medical services provided would be useful for these outcomes in Queensland. The low frequency of IVD-STAPH and MRSA outcomes indicated that development of a hospital-level risk score was a more valid method of risk adjustment for these outcomes.
HIV-associated bladder cancer: a case series evaluating difficulties in diagnosis and management
Authors: Gaughan Elizabeth M , Dezube Bruce J , Bower Mark , Aboulafia David M , Bohac Gerry , Cooley Timothy P , Pantanowitz Liron 
Published: September 2009

Abstract

Background
Chronic human immunodeficiency virus (HIV) infection is associated with an increased incidence of Non-Acquired Immunodeficiency Syndrome (non-AIDS) defining cancers. To date, only a limited number of cases of bladder cancer have been linked with HIV infection. We sought to describe the clinical characteristics of HIV-associated bladder cancer.

Methods
A retrospective study was performed involving HIV-positive patients with bladder cancer, combining cases from multiple institutions with published case reports. Data regarding patient demographics, HIV status, clinical presentation, pathology, cancer treatment, and outcome were analyzed using descriptive statistics.

Results
Eleven patients were identified with a median age of 55 years (range, 33 - 67). The median CD4+ count at cancer diagnosis was 280 cells/mm3 (range, 106 - 572 cells/mm3). Six patients (55%) had a known risk factor for bladder cancer, and nine (82%) presented with hematuria. Ten patients had transitional cell carcinoma, and most had superficial disease at presentation. Treatment included mainly transurethral resection of bladder tumor followed by a combination of local and systemic therapies. One patient received intravesical bacillus Calmette-Guèrin (BCG) without complication. Several patients (55%) were alive following therapy, although many (64%) suffered from local relapse and metastatic disease.

Conclusion
Bladder cancer is part of the growing list of cancers that may be encountered in patients living longer with chronic HIV-infection. Our patients presented at a younger age and with only mild immunosuppression, however, they experienced an expected course for their bladder cancer. Hematuria in an HIV-infected patient warrants a complete evaluation.
Dichloroacetate alleviates development of collagen II-induced arthritis in female DBA/1 mice
Authors: Bian Li , Josefsson Elisabet , Jonsson Ing-Marie , Verdrengh Margareta , Ohlsson Claes , Bokarewa Maria , Tarkowski Andrej , Magnusson Mattias 
Published: September 2009

Abstract
Introduction
Dichloroacetate (DCA) has been in clinical use for the treatment of lactacidosis and inherited mitochondrial disorders. It has potent anti-tumor effects both in vivo and in vitro, facilitating apoptosis and inhibiting proliferation. The pro-apoptotic and anti-proliferative properties of DCA prompted us to investigate the effects of this compound in arthritis.

Methods
In the present study, we used DCA to treat murine collagen type II (CII)-induced arthritis (CIA), an experimental model of rheumatoid arthritis. DBA/1 mice were treated with DCA given in drinking water.

Results
Mice treated with DCA displayed much slower onset of CIA and significantly lower severity (P < 0.0001) and much lower frequency (36% in DCA group vs. 86% in control group) of arthritis. Also, cartilage and joint destruction was significantly decreased following DCA treatment (P = 0.005). Moreover, DCA prevented arthritis-induced cortical bone mineral loss. This clinical picture was also reflected by lower levels of anti-CII antibodies in DCA-treated versus control mice, indicating that DCA affected the humoral response. In contrast, DCA had no effect on T cell- or granulocyte-mediated responses. The beneficial effect of DCA was present in female DBA/1 mice only. This was due in part to the effect of estrogen, since ovariectomized mice did not benefit from DCA treatment to the same extent as sham-operated controls (day 30, 38.7% of ovarectomized mice had arthritis vs. only 3.4% in sham-operated group).

Conclusion
Our results indicate that DCA delays the onset and alleviates the progression of CIA in an estrogen-dependent manner.
Early-onset dementia
Authors: Jefferies Kate , Agrawal Niruj 
Published: August 2009

SummaryDementia is is stereotypically associated with older people. However, in a significant minority it can affect people in their 40s and 50s, or even younger. Currently there is a lack of awareness, even among healthcare professionals, and there is a dearth of appropriate services for such patients. Despite the attention given to this condition by National Institute for Health and Clinical Excellence guidelines, provision of specialist early-onset dementia services in the UK remains patchy. Carers and patients often find themselves being passed ‘from pillar to post’ between psychiatry and neurology, and also between adult, old age and liaison psychiatry. The responsibility for identifying available and appropriate help is often left with carers. This leads to unnecessary delays, causes undue distress to patients and places an added burden on carers.
Risk assessment and management in obsessive–compulsive disorder
Authors: Veale David , Freeston Mark , Krebs Georgina , Heyman Isobel , Salkovskis Paul 
Published: August 2009

SummarySome people with obsessive–compulsive disorder (OCD) experience recurrent intrusive sexual, aggressive or death-related thoughts and as a result may be subjected to lengthy or inappropriate risk assessments. These apparent ‘primary’ risks can be dealt with relatively easily through a careful understanding of the disorder's phenomenology. However, there are other, less obvious ‘secondary’ risks, which require more careful consideration. This article discusses the differentiation of intrusive thoughts and urges in people with OCD from those experienced by sexual or violent offenders; assessing the risk of self-harm and suicide; discussing the nature of repugnant obsessions with a patient; assessing risk of harm and violence to the dependents and family living with someone with the disorder; and assessing the lack of insight and the use of the Mental Health Act. Issues specifically related to children and young people with OCD are also highlighted.
Depression in schizophrenia and early psychosis: implications for assessment and treatment
Authors: Upthegrove Rachel 
Published: August 2009

SummaryDepression in schizophrenia has been a neglected field for some time, but much evidence exists as to the common occurrence of affective disturbance in so-called non-affective psychosis. Depression is related to poor outcome in terms of functional recovery, relapse rate and suicide, and there is increasing evidence that it also precedes the onset of first-episode psychosis for many individuals. This article reviews recent steps forward in the evidence base for depression in schizophrenia in terms of prevalence, importance, assessment and treatment implications, with the aim of providing useful information for practising psychiatrists.
Clinical judgement and individual patients: Invited Commentary on … In Defence of Professional Judgement
Authors: Thornton Tim 
Published: August 2009

SummaryAlthough in agreement with their conclusions about the importance of clinical judgement, this commentary criticises the way that Downie & Macnaughton defend it in their article. I argue that their defence is both overly limited in its account of the role of judgement and that it employs unnecessarily contentious arguments. I outline the ineliminable role that judgement plays in determining which general diagnostic concepts fit individual patients given their individuality and specificity.
Emotional side-effects of selective serotonin reuptake
inhibitors: qualitative study
Authors: Price Jonathan , Cole Victoria , Goodwin Guy M. 
Published: August 2009

BackgroundSome people who take selective serotonin reuptake inhibitor (SSRI)
antidepressants report that their experience of emotions is ‘blunted’.
This phenomenon is poorly understood.AimsTo understand patients' experiences of this phenomenon.MethodQualitative study, gathering data through individual interviews, a group
interview and validation interviews; and searching patient websites for
relevant posts.ResultsThere was strong evidence that some people taking SSRIs experience
significant emotional symptoms that they strongly attribute to their
antidepressant. These emotional symptoms can be described within six key
themes. A seventh theme represents the impact of these side-effects on
everyday life, and an eighth represents participants' reasons for
attributing these symptoms to their antidepressant. Most participants
felt able to distinguish between emotional side-effects of
antidepressants and emotional symptoms of their depression or other
illness.ConclusionsEmotional side-effects of SSRIs are a robust phenomenon, prominent in
some people's thoughts about their medication, having a demonstrable
impact on their functioning and playing a role in their decision-making
about antidepressant adherence.