bluuebunny/crossref_metadata_2025_split huggingface dataset:
ACPYPE - AnteChamber PYthon Parser interfacE
Authors: Sousa da Silva Alan W , Vranken Wim F 
Published: July 2012

AbstractBackgroundACPYPE (or AnteChamber PYthon Parser interfacE) is a wrapper script around the ANTECHAMBER software that simplifies the generation of small molecule topologies and parameters for a variety of molecular dynamics programmes like GROMACS, CHARMM and CNS. It is written in the Python programming language and was developed as a tool for interfacing with other Python based applications such as the CCPN software suite (for NMR data analysis) and ARIA (for structure calculations from NMR data). ACPYPE is open source code, under GNU GPL v3, and is available as a stand-alone application athttp://www.ccpn.ac.uk/acpypeand as a web portal application athttp://webapps.ccpn.ac.uk/acpype.FindingsWe verified the topologies generated by ACPYPE in three ways: by comparing with default AMBER topologies for standard amino acids; by generating and verifying topologies for a large set of ligands from the PDB; and by recalculating the structures for 5 protein–ligand complexes from the PDB.ConclusionsACPYPE is a tool that simplifies the automatic generation of topology and parameters indifferent formatsfordifferentmolecular mechanics programmes, includingcalculation of partial charges, while beingobject orientedfor integration with other applications.
Consultation performance of general practitioners when supported by an asthma/COPDC-service
Authors: Annelies Lucas EM , Emmy Derckx WCC , Marianne Meulepas A , Ivo Smeele JM , Frank Smeenk WJM , Onno van Schayck P 
Published: July 2012

Abstract

Background
General practitioners (GPs) can refer patients to an asthma/COPD service (AC-service) for diagnostic assessment of spirometry and medical history and for asthma or COPD monitoring. The AC-service reports diagnostic results and additional information about disease burden (BORG-score for complaints, MRC-dyspnoea score, exacerbation rate), life style, medication and compliance, to the patient’s GP. This study explores how GPs use this additional information when discussing the patient’s disease burden and how this influences GPs’ information and education provision during consultations with asthma/COPD patients.

Method
Patients with (a suspicion of) asthma or COPD were referred to an AC-service and consulted their GPs after they had received a report from the AC-service. Retrospectively patients answered questions about their GPs’ performance during these consultations. Performances were compared with performances of the same GPs during consultations without support of the AC-service (usual care), earlier that year.

Results
Of consultations not initiated by an AC-service check-up, 91% focussed on complaints, the initial reason for the consultation. In AC-service supported follow-up consultations, GPs explored disease burden when the (BORG-)score for complaints was high - as reported by the AC-service - even when patients themselves thought it was irrelevant. GPs put significantly less effort in exploring disease burden when the Borg-score was low (BORG 3–4: 69%; BORG1-2: 51%, p = 0,01). GPs mostly ignored MRC-dyspnoea scores: attention to dyspnoea was 18% for MRC-score <3 and 25% for MRC-score ≥3 (p = 0,63). GPs encouraged physical fitness in 13% of patients. Smoking behaviour was discussed with 66% of the actual smokers but only 14% remembered a stop smoking advice. Furthermore, pharmacotherapeutic management education in AC-service supported consultations did not differ from performance in usual care according to patient evaluations.

Conclusion
Other than taking into account the severity of complaints, there was no difference between GPs’ performance in AC-service supported and in usual care consultations. AC-service reports are thus not effective by themselves. GPs should be encouraged to use the information better and systematically check all relevant aspects that characterize the disease burden of their patients.
Lack of association between the rs2294008 polymorphism in the prostate stem cell antigen gene and colorectal neoplasia: a case-control and immunohistochemical study
Authors: Smith Christopher , Lochhead Paul , Basavaraju Umesh , Hold Georgina L , Fyfe Nicky , Murray Graeme I , El-Omar Emad M 
Published: July 2012

Abstract

Background
Prostate stem cell antigen (PSCA) has been implicated in the pathogenesis of several solid tumours, either due to changes in protein expression, or through association with the rs2294008 polymorphism in the PSCA gene. To our knowledge, the role of PSCA in the development of colorectal neoplasia has not been explored. We performed a genotyping study to assess for associations between the rs2294008 polymorphism and risk of adenomatous polyps and colorectal cancer. DNA samples were available from 388 individuals with colorectal neoplasia and 496 controls, all of whom had undergone screening colonoscopy. In addition, we performed immunohistochemical staining for PSCA in colonic tissue representing all stages of the adenoma-carcinoma sequence.

Results
No genotypic associations were found between the rs2294008 polymorphism and the risk of colorectal adenomata or cancer. Immunohistochemical staining did not reveal any alteration in PSCA expression accompanying the adenoma-carcinoma sequence.

Conclusion
From these data it seems unlikely that PSCA has a role in the initiation or progression of colorectal neoplasia.
A study of a population of Nyssomyia trapidoi (Diptera: Psychodidae) caught on the Pacific coast of Ecuador
Authors: S Zapata , L Mejía , F Le Pont , R León , B Pesson , C Ravel , L Bichaud , R Charrel , C Cruaud , G Trueba , J Depaquit 
Published: July 2012

Abstract

Background
Cutaneous leishmaniasis is endemic to the Pacific coast of Ecuador, and Nyssomyia trapidoi is considered to be its main vector. Dujardin et al. [1] recorded some differences in body pigmentation and isoenzymatic profiles in sympatric populations of Ny. trapidoi from the Pacific coast of Ecuador and suggested the existence of two cryptic species.

Methods
Entomological collections were performed in November 2008 and March 2011 in the locality of Paraíso Escondido using CDC miniature light traps and human bait. Morphological, isoenzymatical and molecular (sequencing of cytochome b and cytochrome c oxidase 1 of the mitochondrial DNA) analyses, such as detection of Leishmania DNA and phlebovirus RNA in some females, were performed.

Results
Neighbor-joining trees from mitochondrial sequences grouped all of Ecuadorian Ny. trapidoi (including the two color variants) in one cluster, except for two specimens which clustered separately in both genes. Isoenzymatic characterization confirmed that the color variants belong to the same population. Additionally, 11.5% of females were found by PCR to contain Endotrypanum monterogeii kinetoplastid DNA. All pools of Ny. trapidoi were negative for phlebovirus RNA.

Conclusion
Analysis of mitochondrial gene sequences and isoenzymes was unable to support the existence of two sibling species within Ny. trapidoi, which is a probable vector of Endotrypanum monterogeii.
Electrocardiographic and enzymatic correlations with outcome in neonates with hypoxic-ischemic encephalopathy
Authors: Agrawal Jyoti , Shah Gauri S , Poudel Prakash , Baral Nirmal , Agrawal Ajay , Mishra Om P 
Published: July 2012

Abstract

Background
Perinatal asphyxia leading to hypoxic-ischemic encephalopathy (HIE) is a common problem causing multi organ dysfunction including myocardial involvement which can affect the outcome.

Objective
To evaluate the myocardial dysfunction in neonates having HIE by electrocardiographic(ECG) and cardiac enzymes (CK Total, CK-MB and Troponin I) and find out the relationship with HIE and outcome.

Design/Methods
This was a hospital based prospective study. Sixty term neonates who had suffered perinatal asphyxia and developed HIE were enrolled. Myocardial involvement was assessed by clinical, ECG, and CK Total, CK-MB and Troponin I measurements.

Results
Of 60 cases, 13(21.7%) were in mild, 27(45%) in moderate and 20(33.3%) belonged to severe,HIE. ECG was abnormal in 46 (76.7%); of these 19 (41.3%) had grade I, 13 (28.2%) grades II and III each and 1 (2.1%) with grade IV changes. Serum levels of CK Total, CK- MB and Troponin I were raised in 54 (90%), 52 (86.6%) and 48 (80%) neonates, respectively. ECG changes and enzymatic levels showed increasing abnormalities with severity of HIE, and the differences among different grades were significant (p = 0.002, 0.02, <0.001 and 0.004, respectively). Nineteen (32%) cases died during hospital stay. The non- survivors had high proportion of abnormal ECG (p = 0.024), raised levels of CK-MB (p = 0.018) and Troponin I (p = 0.008) in comparison to survivors.

Conclusions
Abnormal ECG and cardiac enzymes levels are found in HIE and can lead to poor outcome due to myocardial damage Early detection can help in better management and survival of these neonates.
The effect of smoking and alcohol consumption on markers of systemic inflammation, immunoglobulin levels and immune response following pneumococcal vaccination in patients with arthritis
Authors: Roseman Carmen , Truedsson Lennart , Kapetanovic Meliha Crnkic 
Published: July 2012

Abstract
Introduction
The purpose of this research was to study the influence of cigarette smoking and alcohol consumption on immune response to heptavalent pneumococcal conjugate vaccine, immunoglobulin levels (Ig) and markers of systemic inflammation in patients with rheumatoid arthritis (RA) or spondylarthropathy (SpA).

Methods
In total, 505 patients were vaccinated. Six pre-specified groups were enrolled: RA on methotrexate (MTX) treatment in some cases other disease-modifying antirheumatic drugs (DMARDs) (I); RA on anti-tumour necrosis factor (TNF) as monotherapy (II); RA on anti-TNF+MTX+ possibly other DMARDs (III); SpA on anti-TNF as monotherapy (IV); SpA on anti-TNF+MTX+ possibly other DMARDs (V); and SpA on nonsteroidal anti-inflammatory drugs (NSAIDs) and/or analgesics (VI). Smoking (pack-years) and alcohol consumption (g/week) were calculated from patient questionnaires. Ig, C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR) were determined at vaccination. IgG antibodies against serotypes 23F and 6B were measured at vaccination and after four to six weeks using standard ELISA. Immune response (ratio between post- and pre-vaccination antibodies; immune response (IR)) and positive immune response (≥2-fold increase in pre-vaccination antibodies; posIR) were calculated.

Results
Eighty-eight patients (17.4%) were current smokers. Smokers had higher CRP and ESR, lower IgG and lower IR for both serotypes (P between 0.012 and 0.045). RA patients on MTX who smoked ≥1pack-year had lower posIR for both serotypes (P = 0.021; OR 0.29; CI 0.1 to 0.7) compared to never-smokers. Alcohol consumption was associated with lower CRP (P = 0.05) and ESR (P = 0.003) but did not influence IR or Ig levels.

Conclusion
Smoking predicted impaired immune response to pneumococcal conjugate vaccine in RA patients on MTX. Smokers with arthritis had higher inflammatory markers and lower IgG regardless of diagnosis and treatment. Low to moderate alcohol consumption was related to lower levels of inflammation markers but had no impact on immune response.

Trial registration
EudraCT EU 2007-006539-29 and NCT00828997
Analysis of IgG4 class switch-related molecules in IgG4-related disease
Authors: Tsuboi Hiroto , Matsuo Naomi , Iizuka Mana , Tsuzuki Sayaka , Kondo Yuya , Tanaka Akihiko , Moriyama Masafumi , Matsumoto Isao , Nakamura Seiji , Sumida Takayuki 
Published: July 2012

Abstract

Introduction

Immunoglobulin G4 (IgG4)-related disease (IgG4-RD) is a new disease entity characterized by high serum IgG4 levels, IgG4-positive plasmacytic infiltration, and fibrosis in various organs. The purpose of this study was to determine the mechanism of upregulation of IgG4 class switch recombination in IgG4-RD.

Methods

We extracted RNA from peripheral blood mononuclear cells (PBMCs) of patients with IgG4-RD (n = 6), Sjögren syndrome (SS) (n = 6), and healthy controls (n = 8), from CD3-positive T cells and CD20-positive B cells sorted from PBMCs of patients with IgG4-RD (n = 3), SS (n = 4), and healthy controls (n = 4), as well as from labial salivary glands (LSGs) of patients with IgG4-RD (n = 11), SS (n = 13), and healthy controls (n = 3). The mRNA expression levels of IgG4-specific class switch-related molecules, such as Th2 cytokines (IL-4 and IL-13), Treg cytokines (IL-10 and TGF-β), and transcriptional factors (GATA3 and Foxp3) were examined with quantitative polymerase chain reaction (PCR). IgG4-nonspecific class switch-related molecules, such as CD40, CD154, BAFF, APRIL, IRF4, and AID, were also examined.

Results

The expression levels of Treg cytokines (IL-10 and TGF-β) and AID were significantly higher in LSGs of IgG4-RD than in SS and the controls (P < 0.05, each). In contrast, those of CD40 and CD154 were significantly lower in PBMCs of IgG4-RD than in SS (P < 0.05, each), whereas CD40 in CD20-positive B cells and CD154 in CD3-positive T cells were comparable in the three groups.

Conclusion

Overexpression of IL-10, TGF-β, and AID in LSGs might play important roles in the pathogenesis of IgG4-RD, such as IgG4-specific class-switch recombination and fibrosis. IgG4 class-switch recombination seems to be mainly upregulated in affected organs.
Plasma suPAR levels are associated with mortality, admission time, and Charlson Comorbidity Index in the acutely admitted medical patient: a prospective observational study
Authors: Haupt Thomas Huneck , Petersen Janne , Ellekilde Gertrude , Klausen Henrik Hedegaard , Thorball Christian Wandall , Eugen-Olsen Jesper , Andersen Ove 
Published: July 2012

Abstract
Introduction
Soluble urokinase plasminogen activator receptor (suPAR) is the soluble form of the membrane-bound receptor (uPAR) expressed predominantly on various immune cells. Elevated plasma suPAR concentration is associated with increased mortality in various patient groups, and it is speculated that suPAR is a low-grade inflammation marker reflecting on disease severity. The aim of this prospective observational study was to determine if the plasma concentration of suPAR is associated with admission time, re-admission, disease severity/Charlson Comorbidity Index Score, and mortality.

Methods
We included 543 patients with various diseases from a Danish Acute Medical Unit during a two month period. A triage unit ensured that only medical patients were admitted to the Acute Medical Unit. SuPAR was measured on plasma samples drawn upon admission. Patients were followed-up for three months after inclusion by their unique civil registry number and using Danish registries to determine admission times, readmissions, International Classification of Diseases, 10th Edition (ICD-10) diagnoses, and mortality. Statistical analysis was used to determine suPAR's association with these endpoints.

Results
Increased suPAR was significantly associated with 90-day mortality (4.87 ng/ml in survivors versus 7.29 ng/ml in non-survivors, P < 0.0001), higher Charlson Score (P < 0.0001), and longer admission time (P < 0.0001), but not with readmissions. The association with mortality remained when adjusting for age, sex, C-reactive protein (CRP), and Charlson Score. Furthermore, among the various Charlson Score disease groups, suPAR was significantly higher in those with diabetes, cancer, cardiovascular disease, and liver disease compared to those without comorbidities.

Conclusions
SuPAR is a marker of disease severity, admission time, and risk of mortality in a heterogeneous cohort of patients with a variety of diseases. The independent value of suPAR suggests it could be of value in prognostic algorithms.
Regulation of alternative splicing by the circadian clock and food related cues
Authors: McGlincy Nicholas J , Valomon Amandine , Chesham Johanna E , Maywood Elizabeth S , Hastings Michael H , Ule Jernej 
Published: July 2012

Abstract
Background
The circadian clock orchestrates daily rhythms in metabolism, physiology and behaviour that allow organisms to anticipate regular changes in their environment, increasing their adaptation. Such circadian phenotypes are underpinned by daily rhythms in gene expression. Little is known, however, about the contribution of post-transcriptional processes, particularly alternative splicing.

Results
Using Affymetrix mouse exon-arrays, we identified exons with circadian alternative splicing in the liver. Validated circadian exons were regulated in a tissue-dependent manner and were present in genes with circadian transcript abundance. Furthermore, an analysis of circadian mutant Vipr2
-/-
mice revealed the existence of distinct physiological pathways controlling circadian alternative splicing and RNA binding protein expression, with contrasting dependence on Vipr2-mediated physiological signals. This view was corroborated by the analysis of the effect of fasting on circadian alternative splicing. Feeding is an important circadian stimulus, and we found that fasting both modulates hepatic circadian alternative splicing in an exon-dependent manner and changes the temporal relationship with transcript-level expression.

Conclusions
The circadian clock regulates alternative splicing in a manner that is both tissue-dependent and concurrent with circadian transcript abundance. This adds a novel temporal dimension to the regulation of mammalian alternative splicing. Moreover, our results demonstrate that circadian alternative splicing is regulated by the interaction between distinct physiological cues, and illustrates the capability of single genes to integrate circadian signals at different levels of regulation.
Verbesserung modellbasierter Überschlagserkennung mittels Schätzung relevanter Fahrzeugparameter
Authors: Ertlmeier Rudolf , Mühlfeld Florian , Faisst Holger , Jumar Ulrich , Brandmeier Thomas 
Published: July 2012

Zusammenfassung
Passive Rückhaltemittel wie Airbags können Fahrzeuginsassen während eines Überschlags vor Verletzungen schützen. Der Beladungszustand eines Pkws ist jedoch entscheidend für dessen Kippverhalten, wodurch auch die Detektion eines Überschlags beeinflusst wird. Dieser Beitrag zeigt eine Schätzung relevanter Fahrzeugkennwerte und die damit mögliche Optimierung eines modellbasierten Überschlagserkennungssystems.
Transient Behaviour of Synchronised Agents
Authors: Lunze Jan 
Published: July 2012

Abstract
The task of synchronising autonomous agents is solved by a networked controller that steers the agents towards a common trajectory. This paper considers the transient behaviour of completely coupled synchronised agents, which brings the agents from their initial state towards the common synchronous trajectory. An explicit relation of the transient behaviour in terms of the initial agent states is derived, which shows how the time to synchronise the agents depends upon the coupling strength. As an important phenomenon of agents with complete couplings, it is proved that groups of agents, which are initially synchronised among each other, remain synchronised during the transient phase. The results are illustrated by their application to vehicle platooning.
Entscheidung und Macht. Kondylis als Kritiker des Normativismus
Authors: Zenkert Georg 
Published: July 2012

Abstract
Despite his undeniable erudition Kondylis never made his mark on the contemporary discussions. This is not surprising, because he preferred to stay in opposition to the mainstream of normativistic thinking, as shown in a rereading of his programmatic work on “Macht und Entscheidung”. Yet this isolated position allows the deficits of normativism to be perceived in remarkable lucidity in mirror-image reversal: a restricted perception of political power and the unclear relation between deliberation and decision. Hence the consequence can be drawn that any attempt at a normative conception of life-world must clarify its relationship to a positive concept of power and the meaning of decision-making.
Philosophie Aktuell: Die gesetzliche Neuregelung der Organtransplantation
Authors: Esser Andrea , Birnbacher Dieter , Wiesemann Claudia , Stoecker Ralf , Lübbe Weyma , Quante Michael 
Published: July 2012

Abstract
Under the new heading “Philosophie aktuell” topics which are relevant in terms of public, moral, and political discourse will be discussed from a philosophical vantage point. By way of example, the explanatory capacity of philosophical reflection and critique will be demonstrated. The present issue puts the reform of the Transplantation Law under philosophical investigation. Concepts of life and death, in particular that of cerebral death, will be scrutinized. It will be asked whether these concepts are descriptive in nature or prescriptive, normatively charged ones. Are cerebrally dead persons still alive or already dead?
Drei Sitzungsprotokolle aus den Frankfurter Seminaren Theodor W. Adornos
Authors: Braunstein Dirk 
Published: July 2012

Abstract
From 1949 to 1969, Theodor W. Adorno habitually let students take minutes of his Frankfurt seminars in philosophy und sociology. More than 470 of these minutes have been retained, and three of them shall now for the first time be rendered unabridged.
Functional and Aesthetic Guidelines for Stress-Reduced Direct Posterior Composite Restorations
Authors: Deliperi S 
Published: July 2012

SUMMARY
Amalgam has been used in the restoration of structurally compromised posterior teeth for many years. When placing large amalgam restorations, replacement of weak cusps with restorative material is recommended to prevent tooth fracture. This recommendation can be modified with new guidelines using modern adhesive techniques. Semidirect and indirect inlay/onlay composite restorations have progressively replaced amalgam restorations over the past 20 years. Lately, single visit direct resin-bonded composite (RBC) restorations have also been used as a viable alternative to conventional indirect restorations. This paper is intended to introduce a step-by-step protocol for the direct restoration of structurally compromised posterior teeth using RBCs with stress-reducing protocols.
On Galilean connections and the first jet bundle
Authors: Grant James , Lackey Bradley 
Published: July 2012

Abstract
We see how the first jet bundle of curves into affine space can be realized as a homogeneous space of the Galilean group. Cartan connections with this model are precisely the geometric structure of second-order ordinary differential equations under time-preserving transformations — sometimes called KCC-theory. With certain regularity conditions, we show that any such Cartan connection induces “laboratory” coordinate systems, and the geodesic equations in this coordinates form a system of second-order ordinary differential equations. We then show the converse — the “fundamental theorem” — that given such a coordinate system, and a system of second order ordinary differential equations, there exists regular Cartan connections yielding these, and such connections are completely determined by their torsion.
Finite Element Model Updating of Reinforced Concrete Beams with Honeycomb Damage
Authors: Ismail Z. 
Published: July 2012

Abstract A method of detecting honeycombing damage in a reinforced concrete beam using the finite element model updating technique was proposed. A control beam and two finite element models representing different severity of damage were constructed using available software and the defect parameters were updated. Analyses were performed on the finite element models to approximate the modal parameters. A datum and a control finite element model to match the datum test beams with honeycombs were prepared. Results from the finite element model were corrected by updating the Young’s modulus and the damage parameters. There was a loss of stiffness of 3% for one case, and a loss of 7% for another. The more severe the damage, the higher the loss of stiffness. There was no significant loss of stiffness by doubling the volume of the honeycombs.