bluuebunny/crossref_metadata_2025_split huggingface dataset:
Highly specific prediction of phosphorylation sites in proteins
Authors: Koenig Matthias , Grabe Niels 
Published: August 2004

Abstract
Summary: The prediction of significant short functional protein sequences has inherent problems. In predicting phosphorylation sites, problems came from the shortness of phosphorylation sites, the difficulties in maintaining many different predefined models of binding sites, and the difficulties of obtaining highly sensitive predictions and of obtaining predictions with a constant sensitivity and specificity. The algorithm presented in this paper overcomes these problems.
The proposed algorithm PHOSITE is based on the case-based sequence analysis. This enables the prediction of phosphorylation sites with constant specificity and sensitivity. Furthermore, this method leads not only to the prediction of phosphorylation sites in general but also predicts the most probable type of kinase involved.
Availability: The tool PHOSITE implementing the presented method can be evaluated under the website http://www.phosite.com
GO::TermFinder—open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
Authors: Boyle Elizabeth I. , Weng Shuai , Gollub Jeremy , Jin Heng , Botstein David , Cherry J. Michael , Sherlock Gavin 
Published: August 2004

Abstract
Summary: GO::TermFinder comprises a set of object-oriented Perl modules for accessing Gene Ontology (GO) information and evaluating and visualizing the collective annotation of a list of genes to GO terms. It can be used to draw conclusions from microarray and other biological data, calculating the statistical significance of each annotation. GO::TermFinder can be used on any system on which Perl can be run, either as a command line application, in single or batch mode, or as a web-based CGI script.
Availability: The full source code and documentation for GO::TermFinder are freely available from http://search.cpan.org/dist/GO-TermFinder/
Haploview: analysis and visualization of LD and haplotype maps
Authors: Barrett J. C. , Fry B. , Maller J. , Daly M. J. 
Published: August 2004

Abstract
Summary: Research over the last few years has revealed significant haplotype structure in the human genome. The characterization of these patterns, particularly in the context of medical genetic association studies, is becoming a routine research activity. Haploview is a software package that provides computation of linkage disequilibrium statistics and population haplotype patterns from primary genotype data in a visually appealing and interactive interface.
Availability: http://www.broad.mit.edu/mpg/haploview/
Contact: jcbarret@broad.mit.edu
Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprinting
Authors: Samuelsson Jim , Dalevi Daniel , Levander Fredrik , Rögnvaldsson Thorsteinn 
Published: August 2004

Abstract
Summary: A set of new algorithms and software tools for automatic protein identification using peptide mass fingerprinting is presented. The software is automatic, fast and modular to suit different laboratory needs, and it can be operated either via a Java user interface or called from within scripts. The software modules do peak extraction, peak filtering and protein database matching, and communicate via XML. Individual modules can therefore easily be replaced with other software if desired, and all intermediate results are available to the user. The algorithms are designed to operate without human intervention and contain several novel approaches. The performance and capabilities of the software is illustrated on spectra from different mass spectrometer manufacturers, and the factors influencing successful identification are discussed and quantified.
Motivation: Protein identification with mass spectrometric methods is a key step in modern proteomics studies. Some tools are available today for doing different steps in the analysis. Only a few commercial systems integrate all the steps in the analysis, often for only one vendor's hardware, and the details of these systems are not public.
Results: A complete system for doing protein identification with peptide mass fingerprints is presented, including everything from peak picking to matching the database protein. The details of the different algorithms are disclosed so that academic researchers can have full control of their tools.
Availability: The described software tools are available from the Halmstad University website www.hh.se/staff/bioinf/
Supplementary information: Details of the algorithms are described in supporting information available from the Halmstad University website www.hh.se/staff/bioinf/
How many samples are needed to build a classifier: a general sequential approach
Authors: Fu Wenjiang J. , Dougherty Edward R. , Mallick Bani , Carroll Raymond J. 
Published: August 2004

AbstractMotivation: The standard paradigm for a classifier design is to obtain a sample of feature-label pairs and then to apply a classification rule to derive a classifier from the sample data. Typically in laboratory situations the sample size is limited by cost, time or availability of sample material. Thus, an investigator may wish to consider a sequential approach in which there is a sufficient number of patients to train a classifier in order to make a sound decision for diagnosis while at the same time keeping the number of patients as small as possible to make the studies affordable.Results: A sequential classification procedure is studied via the martingale central limit theorem. It updates the classification rule at each step and provides stopping criteria to ensure with a certain confidence that at stopping a future subject will have misclassification probability smaller than a predetermined threshold. Simulation studies and applications to microarray data analysis are provided. The procedure possesses several attractive properties: (1) it updates the classification rule sequentially and thus does not rely on distributions of primary measurements from other studies; (2) it assesses the stopping criteria at each sequential step and thus can substantially reduce cost via early stopping; and (3) it is not restricted to any particular classification rule and therefore applies to any parametric or non-parametric method, including feature selection or extraction.Availability: R-code for the sequential stopping rule is available at http://stat.tamu.edu/~wfu/microarray/sequential/R-code.htmlContact: wfu@stat.tamu.edu
University decentralization as regional policy: the Swedish
experiment
Authors: Andersson Roland , Quigley John M. , Wilhelmson Mats 
Published: August 2004

Abstract
During the past 15 years, Swedish higher education policy has emphasized the spatial decentralization of post-secondary education. We investigate the economic effects of this decentralization policy on productivity and output per worker. We rely upon a 14-year panel of output and employment for Sweden's 285 municipalities, together with data on the location of university-based researchers and students, to estimate the effects of exogenous changes in educational policy upon regional development. We find important and significant effects of this policy upon the average productivity of workers, suggesting that the economic effects of the decentralization on regional development are economically important. We also find evidence of highly significant, but extremely localized, externalities in productivity. This is consistent with recent findings (e.g., Rosenthal and Strange, 2003) on agglomeration in ‘knowledge industries.’
Landscape effects on butterfly assemblages in an agricultural region
Authors: Bergman Karl‐Olof , Askling John , Ekberg Oscar , Ignell Håkan , Wahlman Henrik , Milberg Per 
Published: August 2004

We examined the butterfly fauna at 62 sites in southeastern Sweden within a region exhibiting high variation in the landscape surrounding the studied grasslands. The landscape varied from an intensively‐managed agricultural landscape with a large amount of open fields to a landscape with a high amount of deciduous forest/semi‐natural grassland. We made 12 179 observations of 57 species of butterflies. The amount of neighbouring deciduous forest/semi‐natural grassland, with >25% tree and bush cover, was the most important environmental factor explaining the variation in the butterfly assemblages. Landscape analyses at three different spatial scales showed that the variation in butterfly assemblages could be explained only at the largest scale (radius 5000 m) and not at the smaller ones (radii 500 and 2000 m).Logistic regressions were used to predict presence/absence of butterfly species. Our study indicated that there may be critical thresholds for the amount of habitat at the landscape scale for several butterfly species as well as for species richness. ForMelitaea athalia, there was a sharp increase in occupancy probability between 3 and 10% deciduous forests/semi‐natural grasslands at the 5000‐m scale. For 12 other species, the value for 50% probability of occurrence varied between 2 and 12% deciduous forest/semi‐natural grassland. Species which had high occupancy probabilities in landscapes with a low amount of surrounding deciduous forests/semi‐natural grasslands were significantly more mobile than others.Our study highlights the importance of applying a landscape perspective in conservation management, and that single‐patch management might fail in maintaining a diverse butterfly assemblage.
Serum adiponectin and metabolic parameters in HIV‐1‐infected patients after substitution of nevirapine for protease inhibitors
Authors: Petit J. M. , Duong M. , Masson D. , Buisson M. , Duvillard L. , Bour J. B. , Brindisi M. C. , Galland F. , Guiguet M. , Gambert P. , Portier H. , Vergès B. 
Published: August 2004

AbstractBackground  In the context of HIV infection and antiretroviral therapy, adiponectin concentrations have been shown to be related to lipodystrophy, metabolic alterations and HIV‐protease inhibitor (PI) use. The replacement of PI by nevirapine has improved the lipid profile of patients under antiretroviral therapy. The aim of the present study was to examine whether adiponectin concentration or insulin sensitivity level correlate with the modifications of lipid parameters after the switch of PI by nevirapine.Material and methods  The evolution of metabolic parameters before and after 6 months of substitution of nevirapine for protease inhibitors was evaluated in a cohort of 55 HIV‐1 infected patients. Adiponectin concentration, insulin sensitivity, lipid profile, cholesterol ester transfer protein (CETP) mass concentration and triglyceride enrichment of HDL were determined before and after the replacement of PI by nevirapine. Insulin sensitivity was evaluated by the HOMA model assessment.Results  Twenty‐four weeks of treatment with nevirapine improved significantly the lipid profile with a significant reduction of apoB (from 0·98 to 0·92 g L−1; P = 0·005) and triglyceride (from 2·02 to 1·66 mmol L−1; P = 0·02). HDL cholesterol and apoA1 increased significantly (from 0·99 to 1·19 mmol L−1; P = 0·001 and from 1·40 to 1·57 g L−1; P < 0·001, respectively). The triglyceride enrichment of HDL significantly decreased after the replacement of PI by nevirapine (from 0·248 ± 0·092 to 0·213 ± 0·093; P = 0·003). At baseline, and after 24 weeks of nevirapine treatment, we observed significant correlations between adiponectin level and lipid parameters [(HDL‐cholesterol (r = 0·66, P = 0·001 and r = 0·69, P = 0·001); triglycerides (r = −0·42, P = 0·002 and r =−0·57, P = 0·001), and triglyceride enrichment of HDL (r = −0·43, P = 0·005 and r = −0·53, P = 0·005)]. Twenty‐four weeks of treatment with nevirapine did not significantly change adiponectin concentrations (from 984 to 1086 µg L−1, P = 0·22), CETP mass and insulin sensitivity.Conclusion  This study shows that even though a strong correlation was found between adiponectin and some metabolic parameters at baseline and after 24 weeks of treatment by nevirapine, the improvement of lipid profile observed after the replacement of PI by nevirapine was not in relation to the change of plasma adiponectin concentration. The significant decrease of triglyceride enrichment of HDL after the replacement of PI by nevirapine probably leads to a decreased catabolism of HDL lipoprotein, and consequently explains the increase of plasma HDL concentration observed in this study.
Low‐dose growth hormone and human immunodeficiency virus‐associated lipodystrophy syndrome: a pilot study
Authors: Andersen O. , Haugaard S. B. , Flyvbjerg A. , Andersen U. B. , Ørskov H. , Madsbad S. , Nielsen J. O. , Iversen J. 
Published: August 2004

AbstractBackground  Treatment with high doses (2–6 mg day−1) of human growth hormone (hGH) in patients with human immunodeficiency virus (HIV)‐associated lipodystrophy syndrome (HALS) has been shown to increase concentrations of total insulin‐like growth‐factor‐I (IGF‐I) more than twofold greater than the normal upper range and is accompanied by adverse effects such as joint pain and glucose intolerance.Materials and methods  We performed a 16‐week open‐labelled prospective pilot study in six male HALS patients using a s.c. low‐dose hGH, 0·7 mg day−1, aiming to examine the impact on total and free IGF‐I and fat distribution. Glucose metabolism was examined by oral glucose tolerance tests and hyperinsulinaemic euglycaemic clamps.Results  Total IGF‐I increased twofold (P < 0·01) and free IGF‐I increased 2·5‐fold (P < 0·01) to the level of the normal upper range. HDL‐cholesterol increased (P = 0·01). Patients reported improvements of lipodystrophy, which was supported by a decreased waist‐to‐thigh ratio (P = 0·01), and waist‐to‐hip ratio (P = 0·06). Ratio of peripheral to trunk soft tissue mass increased (P = 0·01, measured by dual‐energy X‐ray absorptiometry scans) and a trend towards reduction in percentage of trunk fat was suggested (P = 0·12). Total fat mass, exercise capacity, glucose tolerance, glucose disposal rate and immune status, respectively, did not change (all P > 0·5). The patients did not complain of arthralgia or other known GH‐related side‐effects.Conclusions  Sixteen weeks’ treatment of lipodystrophic HIV‐infected patients with hGH, 0·7 mg day−1, increased total and free IGF‐I twofold and appeared safe and tolerable. The potential of low‐dose hGH in the treatment of HIV‐lipodystrophy awaits examination by placebo‐controlled, randomized trials.
Impact of laparoscopic adjustable gastric banding on plasma ghrelin, eating behaviour and body weight
Authors: Schindler K. , Prager G. , Ballaban T. , Kretschmer S. , Riener R. , Buranyi B. , Maier C. , Luger A. , Ludvik B. 
Published: August 2004

AbstractBackground  Plasma ghrelin, an orexigenic peptide derived from the stomach and duodenum, increases following weight loss and might contribute to weight regain. The aim of the present study was to evaluate the effect of laparoscopic adjustable gastric banding (LAGB) on body weight and body composition as well as plasma ghrelin in relation to eating behaviour in morbidly obese patients.Materials and methods  This study was performed in 23 morbidly obese subjects who underwent standardized LAGB. Fasting plasma ghrelin was measured before and 6 months after surgery and was correlated with body weight, body composition, and eating behaviour.Results  Six months after LAGB, body weight decreased significantly by −15·7 ± 1·4 kg (mean ± SEM, P = 0·0001) which was accompanied by an increased cognitive restraint of eating (P = 0·001), and by a decreased disinhibition of eating and susceptibility to hunger (P = 0·0001). Plasma ghrelin increased (P = 0·016) by 27·2% from 100·39 ± 12·90 to 127·22 ± 13·15 fmol mL−1. The change in plasma ghrelin correlated with changes in body weight (r = −0·49, P = 0·02), BMI (r = −0·42, P = 0.048) and fat mass (r = −0·519, P = 0·013), but not with changes of fat‐free mass and of the three dimensions of eating behaviour.Conclusion  Weight loss following LAGB leads to an increase in fasting plasma ghrelin and is accompanied by a decrease in hunger, disinhibition of eating and an increase in cognitive restraint. Thus, changes in eating behaviour, which promote reduction of food intake and not fasting ghrelin, determines weight loss achieved by LAGB.
Free fatty acids exert a greater effect on ocular and skin blood flow than triglycerides in healthy subjects
Authors: Bayerle‐Eder M. , Polska E. , Kopf A. , Roden M. , Waldhäusl W. , Pleiner H. , Wipler B. , Wolzt M. , Schmetterer L. 
Published: August 2004

AbstractBackground  Free fatty acids (FFAs) and triglycerides (TGs) can cause vascular dysfunction and arteriosclerosis. Acute elevation of plasma FFA and TG concentration strongly increase ocular and skin blood flow. This study was designed to discriminate whether FFA or TG independently induce hyperperfusion by measuring regional and systemic haemodynamics.Methods  In a balanced, randomized, placebo‐controlled, double‐blind, three‐way, crossover study nine healthy subjects received either Intralipid® (Pharmacia and Upjohn, Vienna, Austria) with heparin, Intralipid® alone or placebo control. Pulsatile choroidal blood flow was measured with laser interferometry, retinal blood flow and retinal red blood cell velocity with laser Doppler velocimetry, and skin blood flow with laser Doppler flowmetry during an euglycaemic insulin clamp.Results  A sevenfold increase of FFA during Intralipid®/heparin infusion was paralleled by enhanced choriodal, retinal, and skin blood flow by 17 ± 4%, 26 ± 5% (P < 0·001), and 47 ± 19% (P = 0·03) from baseline, respectively. In contrast, a mere threefold increase of FFA by infusion of Intralipid® alone did not affect outcome parameters, despite the presence of plasma TG levels of 250–700 mg dL−1; similar to those obtained during combined Intralipid®/heparin infusion. Systemic haemodynamics were not affected by drug infusion.Conclusions  Present findings demonstrate a concentration‐dependent increase in ocular and skin blood flow by FFA independently of elevated TG plasma concentrations. As vasodilation of resistance vessels occur rapidly, FFA may play a role in the development of continued regional hyperperfusion and deteriorate microvascular function.
Humming‐induced release of nasal nitric oxide for assessment of sinus obstruction in allergic rhinitis: pilot study
Authors: Maniscalco M. , Sofia M. , Weitzberg E. , De Laurentiis G. , Stanziola A. , Rossillo V. , Lundberg J. O. 
Published: August 2004

AbstractBackground  Humming greatly increases nasal nitric oxide (NO) in healthy people by causing a rapid washout of NO from the sinuses. This increase is abolished in patients with complete sinus ostial obstruction.Objective  Allergic rhinitis is a risk factor for development of sinusitis and we wanted to study whether nasal NO measurement during humming could be used to detect sinus abnormalities in this disorder.Methods  Fifty‐nine consecutive subjects with mild to moderate allergic rhinitis were studied. Their present nasal symptoms were recorded. Then NO levels were measured by chemiluminescence during quiet single‐breath nasal exhalations and humming exhalations at a fixed exhalation flow of 0·2 L s−1. Based on the NO results the patients were divided into two groups: those with a great increase in nasal NO during humming (humming responders, n = 46) and those without a significant increase (humming nonresponders, n = 13). In 11 of the nonresponders and in 22 of the responders the passage to the osteomeatal complex area was assessed and scored by nasal endoscopy. This was carried out by an oto‐rhino‐laryngologist unaware of the NO results.Results  Among the nonresponders nine of 11 patients (80%) had endoscopic signs of bilateral sinus obstruction, compared with one of the 22 (< 5%) humming responders. Baseline nasal symptom score and NO levels during quiet exhalation were not significantly different between the groupsConclusion  Absence of a nasal NO peak during humming is associated with endoscopic findings suggestive of sinus ostial obstruction in subjects with allergic rhinitis. Measurement of nasal NO during humming may be a simple method to detect sinus abnormalities in these patients.
Type 1 diabetes is insulin −2221 MspI and CTLA‐4 +49 A/G polymorphism dependent
Authors: Haller K. , Kisand K. , Nemvalts V. , Laine A.‐P. , Ilonen J. , Uibo R. 
Published: August 2004

AbstractBackground  Several studies have demonstrated an association of type 1 diabetes with specific alleles of HLA class II molecules, as with polymorphisms of insulin gene region. The aim of our study was to evaluate the interaction of insulin −2221 MspI polymorphism to type 1 diabetes susceptibility in connection with autoimmunity associated gene – CTLA‐4 polymorphism.Materials and methods  Insulin −2221 MspI C/T and CTLA‐4 +49 A/G polymorphisms were detected by restriction fragment‐length polymorphism analysis or oligonucleotide hybridization in type 1 (n = 69), type 2 diabetes (n = 301) patients and 158 healthy controls. Regression model adjusted for age, gender and gene polymorphisms was studied.Results  C‐allele of insulin −2221 MspI and G‐allele of +49 CTLA‐4 were significant risk factors for type 1 diabetes (crude OR 3·53 and 1·59, respectively) and this impact increased in the homozygous form of both alleles. The regression model supported the idea of insulin CC and CTLA‐4 GG genotypes for an independent and clearly significant risk for developing type 1 diabetes. We could not detect any significant correlation between investigated polymorphisms and type 2 diabetes.Conclusions  There exists a significant association between the C‐allele of −2221 MspI in the insulin gene and type 1 diabetes. The CTLA‐4 G‐allele is also positively correlated with type 1 diabetes. According to the regression model the investigated gene polymorphisms are independent risk factors for development of type 1 diabetes in the Estonian population. We propose that −2221 MspI is a good marker for evaluation of risk of insulin gene haplotype in type 1 diabetes patients.
Elevated sweat sodium associated with pulmonary oedema in meningococcal sepsis
Authors: Eisenhut M. , Sidaras D. , Barton P. , Newland P. , Southern K. W. 
Published: August 2004

AbstractBackground  We observed a temporary positive sweat test with sodium and chloride levels greater than 60 mmol L−1 following meningococcal septicaemia. Objective was to investigate whether this finding is reproducible and whether this disturbance in epithelial sodium transport is related to sepsis‐induced pulmonary oedema.Materials and methods  Twenty‐four children with a diagnosis of meningococcal septicaemia and 10 controls with noninfectious critical illness admitted to the Royal Liverpool Children's Hospital were included. Sweat collection was by pilocarpine iontophoresis in the acute phase of the illness (days 1–5) and on follow up. Sodium and chloride concentrations were determined by flame photometry.Results  In patients with meningococcal septicaemia, sweat sodium and chloride concentrations were significantly higher in the acute compared with the recovery phase, with a mean (SD) of 31·0 (14·6) mmol L−1 in the acute vs. 19·6 (10·2) mmol L−1 on recovery for sodium and 21·0 (12·1) mmol L−1 in the acute vs. 11·8 (4·9) mmol L−1 on recovery for chloride (P < 0·01, t‐test, for sodium and chloride). Sweat sodium and chloride were significantly higher in patients with meningococcal disease compared with controls and in the acute phase in patients with septicaemia‐related pulmonary oedema [mean (SD) sodium: 41·0 (15·4) mmol L−1 and chloride: 28·8 (14·3) mmol L−1] compared with septic patients without [mean (SD) sodium: 24·5 (10·1) mmol L−1 and chloride: 15·3 (7·9) mmol L−1] (P < 0·01 for sodium and chloride).Conclusions  This is the first study to provide in vivo evidence of reduced epithelial sodium transport in children with septicaemia and of its association with pulmonary oedema.