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Background: The King's Sarcoidosis Questionnaire (KSQ) is a brief questionnaire assessing health status using five modules (General Health Status, Lung, Medication, Skin, Eyes) in patients with sarcoidosis. The KSQ was only validated in one English sarcoidosis cohort. Objective: The aim of this study was to validate the KSQ in a Dutch sarcoidosis population. Methods: The KSQ was translated according to international guidelines and tested in interviews with patients. Consecutive outpatients completed multiple questionnaires twice, two weeks apart. Construct validity, internal consistency and repeatability were determined. Results: Of the 98 patients included 85 had lung, 22 skin and 24 eye disease. There was good construct validity of the KSQ General Health Status module against the World Health Organization Quality of Life-BREF questionnaire. The Medication module correlated weak to moderate with most questionnaires. The correlations with organ-specific questionnaires varied from strong for Eyes (r=0.75), Skin (r=-0.62) to moderate for Lung (r=-0.45 with MRC breathlessness scale). Internal consistency was good for all KSQ modules (Cronbach's a 0.72-0.93). Intraclass correlation coefficients (0.70-0.90) and Bland-Altman plots showed good repeatability of the KSQ. Conclusion: The Dutch KSQ is the first translation of the English KSQ, validated in a Dutch sarcoidosis population.

Gaucher disease (GD), a lysosomal storage disorder, may result in end-stage lung disease. We report successful bilateral lung transplantation in a 49-year-old woman with GD complicated by severe pulmonary hypertension and fibrotic changes in the lungs. Before receiving the lung transplant, the patient was undergoing both enzyme replacement therapy (imiglucerase) and triple pulmonary hypertension treatment (epoprostenol, bosentan, and sildenafil). She had a history of splenectomy, severe bone disease, and renal involvement, all of which were related to GD and considered as relative contraindications for a lung transplantation. In the literature, lung transplantation has been suggested for severe pulmonary involvement in GD but has been reported only once in a child. To our knowledge, until now, no successful procedure has been reported in adults, and no reports deal with the severe potential posttransplantation complications specifically related to GD.

Coronary atherosclerosis represents the major cause of death in Western societies. As atherosclerosis typically progresses over years without giving rise to clinical symptoms, biomarkers are urgently needed to identify patients at risk. Over the past decade, evidence has accumulated suggesting cross-talk between the diseased vasculature and cells of the innate immune system. We therefore employed proteomics to search for biomarkers associated with severe atherosclerotic coronary lumen stenosis in circulating leukocytes. In a two-phase approach, we first performed in-depth quantitative profiling of the granulocyte proteome on a small pooled cohort of patients suffering from chronic (sub)total coronary occlusion and matched control patients using stable isotope peptide labeling, two-dimensional LC-MS/MS and data-dependent decision tree fragmentation. Over 3000 proteins were quantified, among which 57 candidate biomarker proteins remained after stringent filtering. The most promising biomarker candidates were subsequently verified in the individual samples of the discovery cohort using label-free, single-run LC-MS/MS analysis, as well as in an independent verification cohort of 25 patients with total coronary occlusion (CTO) and 19 matched controls. Our data reveal bactericidal/permeability-increasing protein (BPI) as a promising biomarker for severe atherosclerotic coronary stenosis, being down-regulated in circulating granulocytes of CTO patients.

The original PRIDE Converter tool greatly simplified the process of submitting mass spectrometry (MS)-based proteomics data to the PRIDE database. However, after much user feedback, it was noted that the tool had some limitations and could not handle several user requirements that were now becoming commonplace. This prompted us to design and implement a whole new suite of tools that would build on the successes of the original PRIDE Converter and allow users to generate submission-ready, well-annotated PRIDE XML files. The PRIDE Converter 2 tool suite allows users to convert search result files into PRIDE XML (the format needed for performing submissions to the PRIDE database), generate mzTab skeleton files that can be used as a basis to submit quantitative and gel-based MS data, and post-process PRIDE XML files by filtering out contaminants and empty spectra, or by merging several PRIDE XML files together. All the tools have both a graphical user interface that provides a dialog-based, user-friendly way to convert and prepare files for submission, as well as a command-line interface that can be used to integrate the tools into existing or novel pipelines, for batch processing and power users. The PRIDE Converter 2 tool suite will thus become a cornerstone in the submission process to PRIDE and, by extension, to the ProteomeXchange consortium of MS-proteomics data repositories. publishedVersion

In flat areas, transport of dissolved nutrients by water through the soil matrix to groundwater and drains is assumed to be the dominant pathway for nutrient losses to ground- and surface waters. However, long-term data on the losses of nutrients to surface water and the contribution of various pathways is limited. We studied nutrient losses and pathways on a heavy clay soil in a fluvial plain in The Netherlands during a 5-yr period. Average annual nitrogen (N) and phosphorus (P) losses to surface water were 15.1 and 3.0 kg ha(-1) yr(-1), respectively. Losses were dominated by particulate N (50%) and P (70%) forms. Rapid discharge through trenches was the dominant pathway (60-90%) for water and nutrient transport. The contribution of pipe drains to the total discharge of water and nutrients was strongly related to the length of the dry period in the preceding summer. This relationship can be explained by the very low conductivity of the soil matrix and the formation of shrinkage cracks during summer. Losses of dissolved reactive P through pipe drains appear to be dominated by preferential flow based on the low dissolved reactive P concentration in the soil matrix at this depth. Rainfall occurring after manure application played an important role with respect to the annual losses of N and P in spring when heavy rainfall occurred within 2 wk after manure application.

Electron transfer dissociation (ETD) of peptide ions has been introduced as a tool for mass spectrometry based peptide sequencing, complementary to the commonly used collision induced dissociation (CID). It has been proposed that ETD may have better performance than CID for more highly charged and/or larger peptides. Here, we compare the performance of ETD and CID on data generated in a large-scale proteomics experiment. First, tryptic proteolytic peptides of Drosophila melanogaster oocytes were off-line separated based on their insolution net charge state using strong cation exchange chromatography (SCX), followed by an on-line reversephase (RP) liquid chromatography separation coupled to an ion trap mass spectrometer with ETD capabilities. The mass spectrometer selected MS peaks were subjected to both ETD and CID thus allowing a fair comparison. Around 2300 peptides were exclusively identified by CID and similarly more than 3000 by ETD with approximately 1400 by both ETD and CID. In total nearly 7,000 peptides were identified with a very conservative Mascot peptide cut-off score of 60 clearly verifying that ETD and CID are complementary techniques. In the early SCX fractions, which contain peptides with a ‘low’ net charge, more than 90% of the peptides could be successfully identified by CID whereas in the later SCX fractions more than 90% of the identified peptides could be successfully identified by using ETD only. The chosen strategy, with a combination of SCX and RP-LC-MS/MS, allows the user to make targeted decisions on whether to optimally use CID and/or ETD. Analysis of the sequence and amino acid contents of all identified peptides clearly revealed that the impressive performance of ETD for peptides possessing charge states above three do not require CID based sequencing which, at best, would be solely confirmatory.

Background Nasal nitric oxide (nNO) values are reduced in patients with cystic fibrosis (CF). Humming during nNO measurement increases nNO values in healthy subjects. Nasal NO is reduced in patients with CF, sinus disease or nasal polyps. Humming nNO values have not been reported in CF patients yet. Our aim was to explore humming nNO values in CF patients and assess whether nNO during humming is a better discriminator than silent nNO measurements in this patient group. Materials and methods In a cross sectional study we measured nNO concentrations in healthy controls (HC) and in CF patients (n = 23 and 31, respectively). The participants held their breath for 10 s while air was passively extracted from one nostril with 700 mL min−1 for direct NO measurements (NIOX chemiluminescence analyser). Subsequently nNO was measured during humming with the mouth closed for 10 s. Results Mean nNO in parts per billion (p.p.b.) (SD) during breath hold was 499 (164) and 240 (139), respectively. The median nNO peak (p.p.b., minimum–maximum) during humming was 1500 (425–4100) for HC and 120 (23–500) for CF. There was a highly significant difference between nNO both with and without humming between CF and HC (P

Introduction: Stress, depression, anxiety and fatigue are major problems in sarcoidosis. Little is known about the etiology of psychological distress in sarcoidosis. Serum and saliva cortisol tests are commonly used to monitor acute stress. Scalp hair cortisol is a novel biomarker of long-term cortisol levels, and may reveal biological stress and its relationship with psychopathology in sarcoidosis patients. Aim: To study the relationships between hair cortisol concentrations (HCC) and psychological and fatigue measures in patients with sarcoidosis. Methods: We measured HCC using liquid chromatography–tandem mass spectrometry in glucocorticoid naive sarcoidosis patients. All patients completed the Hospital Anxiety and Depression Scale (HADS), Fatigue Assessment Scale (FAS), Perceived Stress Scale (PSS) and Short Form 36 (SF-36). Results: We included 32 patients with sarcoidosis (14 male). Mean (ranges) questionnaire scores were respectively PSS 26 (4-55), FAS 29 (10-46), HADS anxiety 6 (0-19), HADS depression 7 (0-21) and SF-36 mental field 60 (36-75); no significant sex differences were observed. In women, elevated HCC were associated with decreased psychological wellbeing, as measured by PSS (r=0.588, p=0.01), SF-36 mental (r=-0.553, p=0.017) and HADS anxiety (r=0.716, p=0.001), HADS depression (r=0.655,p=0.003). No significant correlations were found in men. HCC did not correlate with the FAS. Conclusion: Long-term increased cortisol measured in scalp hair is associated with decreased psychological wellbeing in women with sarcoidosis, but not with fatigue. Hair cortisol analysis seems a promising non-invasive biomarker of distress in sarcoidosis. Sex differences need further evaluation.

Background: Optimization of first-line prednisone therapy for sarcoidosis is warranted, since side effects can be severe and long-term benefits debated. Prospective data on the early response towards prednisone treatment is lacking. We initiated a prospective study to evaluate the early lung function response to prednisone treatment and tapering, using a calibrated hand-held spirometer at a daily basis. Methods: Treatment naive sarcoidosis patients in whom prednisone therapy is initiated for a pulmonary indication are eligible. Prednisone treatment is protocolled for the first three months (mo). Lung function parameters are shown as mean %predicted(± SD). sIL2 is shown in pg/ml. Results: Up to date, 10 patients are included. Baseline FVC was 68.05(±11.56) and DLCO(csb) 53.41(±16.17). MRC score was 2.71(±0.95), FAS score 29.71(±7.50), and sIL2R was 13196(±10696). Upon treatment, FVC increased to 86.01(±11.08) at 1-mo and 86.37(±9.05) at 3-mo. DLCO increased to 70.23 (±11.08) at 1-mo and 70.90 (±8.43) at 3-mo. MRC score decreased to 1.0(±1.23) at 1-mo and 1.25(±0.96) at 3-mo. FAS score decreased to 20.30(±7.84) at 1-mo and 23.75(±5.19) at 3-mo. sIL2 decreased to 4292(±3444) at 1-mo and 4664(±2552) at 3-mo. Interestingly, already at 10 days(±12.16) the largest proportion(>95%) of FVC increase at 3-mo was reached. Similarly, at day 14 MRC score decreased to 1.6(± 1.34), which was preserved for 3-mo. Conclusion: These results show that in newly-treated sarcoidosis patients the majority of the prednisone effect is reached within 2 weeks. Daily monitoring of the pulmonary function can help individualize first-line prednisone therapy in pulmonary sarcoidosis patients, aiming at early dose tapering and reducing side-effects.

Background: Loss of tolerance to auto-antigens after vascular injury could trigger vascular remodeling in idiopathic pulmonary arterial hypertension (IPAH) patients. Endothelial cell-specific auto-antibodies produced by B cells could influence the early development of IPAH. Similarities with IPAH pathology have been observed in mice in which B-cell-receptor (BCR) signaling is continuously increased by Bruton9s tyrosine kinase (Btk) overexpression. Therefore, the aim of our study is to investigate if patients with IPAH have activated B cells and if Btk-Tg mice develop signs of PH after pulmonary injury. Methods: Using flow cytometry we determined Btk expression in peripheral B cells from healthy controls (HC) after stimulation with F(ab)2 anti-IgM and in different B-cell subsets in PB mononuclear cells inpatients with IPAH and HC. Finally, we assessed right ventricular weight (RVW) in Btk-Tg and wild type (WT) mice 56 days after bleomycine-induced lung injury. Results: IgM stimulation induced robust Btk protein upregulation in B-cells. IPAH patients (n=13) showed an increased Btk expression in B-cells compared with HC (P Conclusion: Our data suggest that IPAH pathogenesis in humans is driven by B-cell-dependent auto-immune responses. Interestingly, the combination of Btk overexpression in B cells and lung injury in mice could be a novel model to study IPAH and this may be a new tool to study future experimental therapies.

Gaucher disease (GD), a lysosomal storage disorder, may result in end-stage lung disease. We report successful bilateral lung transplantation in a 49-year-old woman with GD complicated by severe pulmonary hypertension and fibrotic changes in the lungs. Before receiving the lung transplant, the patient was undergoing both enzyme replacement therapy (imiglucerase) and triple pulmonary hypertension treatment (epoprostenol, bosentan, and sildenafil). She had a history of splenectomy, severe bone disease, and renal involvement, all of which were related to GD and considered as relative contraindications for a lung transplantation. In the literature, lung transplantation has been suggested for severe pulmonary involvement in GD but has been reported only once in a child. To our knowledge, until now, no successful procedure has been reported in adults, and no reports deal with the severe potential posttransplantation complications specifically related to GD.

Protein O-GlcNAcylation is a reversible post-translational signaling modification of nucleocytoplasmic proteins that is essential for embryonic development in bilateria. In a search for a reductionist model to study O-GlcNAc signaling, we discovered the presence of functional O-GlcNAc transferase (OGT), O-GlcNAcase (OGA), and nucleocytoplasmic protein O-GlcNAcylation in the most basal extant animal, the placozoan Trichoplax adhaerens. We show via enzymatic characterization of Trichoplax OGT/OGA and genetic rescue experiments in Drosophila melanogaster that these proteins possess activities/functions similar to their bilaterian counterparts. The acquisition of O-GlcNAc signaling by metazoa may have facilitated the rapid and complex signaling mechanisms required for the evolution of multicellular organisms.

Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive lung disease of unknown cause. IPF has a poor prognosis with a mean survival of 2 to 5 years after diagnosis. The diagnostic process is often complex and demands a multidisciplinary approach. To date, the only curative therapy available is lung transplant. New insights into the pathogenesis of IPF have brought about changes in standard treatment strategies. New drugs have recently become available and have been shown to slow down the decline in pulmonary function considerably and improve survival.

Subjects believed to have grown out of asthma often develop symptoms again later in life. Ongoing airway inflammation may determine the risk of relapse, although the mechanisms involved are still misunderstood. Additionally, patients with asthma during childhood may develop irreversible airflow obstruction ( airway remodeling) as a result of chronic airway inflammation. Recently, airway inflammation and remodeling could be demonstrated in bronchial biopsy specimens from young adults who considered themselves grown out of asthma. It is also shown that evidence of airway inflammation and remodeling can be obtained noninvasively, thereby providing the opportunity to monitor disease activity. If chronic airway inflammation and/or remodeling are consistent findings in asymptomatic subjects with a history of atopic asthma, the question arises whether natural history can be positively altered with prolonged antiinflammatory therapy. Benefits of long-term prognosis are, however, not yet shown. Since epidemiologic work has demonstrated that a certain percentage of subjects with apparently outgrown atopic asthma remains asymptomatic without needing therapy for the rest of their lives, it can be argued that "asthma remission does exist." The question is whether this percentage can be increased with prolonged antiinflammatory therapy and regular control.

Plants have many polarized cell types, but relatively little is known about the mechanisms that establish polarity. The orc mutant was identified originally by defects in root patterning, and positional cloning revealed that the affected gene encodes STEROL METHYLTRANSFERASE1, which is required for the appropriate synthesis and composition of major membrane sterols. smt1(orc) mutants displayed several conspicuous cell polarity defects. Columella root cap cells revealed perturbed polar positioning of different organelles, and in the smt1(orc) root epidermis, polar initiation of root hairs was more randomized. Polar auxin transport and expression of the auxin reporter DR5-beta-glucuronidase were aberrant in smt1(orc). Patterning defects in smt1(orc) resembled those observed in mutants of the PIN gene family of putative auxin efflux transporters. Consistently, the membrane localization of the PIN1 and PIN3 proteins was disturbed in smt1(orc), whereas polar positioning of the influx carrier AUX1 appeared normal. Our results suggest that balanced sterol composition is a major requirement for cell polarity and auxin efflux in Arabidopsis.

Growing evidence underlines the importance of social conditions in the adoption and use of GIS, which generally takes place within organisations. The paper explores the role of culture in this respect. Cultural 'desirability' seems to depend on the extent to which GIS supports culturally desired organisational functions. The 'feasibility' of the actual introduction of GIS would then be governed largely by cultural conditions specific to the recipient organisation.

Outcomes of comparative evaluations of enrichment methods for phosphopeptides depend highly on the experimental protocols used, the operator, the source of the affinity matrix, and the samples analyzed. Here, we attempt such a comparative study exploring a very large synthetic library containing thousands of serine, threonine, and tyrosine phosphorylated peptides, being present in roughly equal abundance, along with their nonphosphorylated counterparts, and use an optimized protocol for enrichment by TiO2 and Ti(4+)-immobilized metal affinity chromatography (IMAC) by a single operator. Surprisingly, our data reveal that there are minimal differences between enrichment of phosphopeptides by TiO2 and Ti(4+)-IMAC when considering biochemical and biophysical parameters such as peptide length, sequence surrounding the site, hydrophobicity, and nature of the amino acid phosphorylated. Similar results were obtained when evaluating a tryptic digest of a cellular lysate, representing a more natural source of phosphopeptides. All the data presented are available via ProteomeXchange with the identifier PXD000759.

The regulation of columella stem cell activity in the Arabidopsis root cap by a nearby organizing centre, the quiescent centre, has been a key example of the stem cell niche paradigm in plants. Here, we investigate interactions between transcription factors that have been shown to regulate columella stem cells using a simple quantification method for stem cell activity in the root cap. Genetic and expression analyses reveal that the RETINOBLASTOMA-RELATED protein, the FEZ and SOMBRERO NAC-domain transcription factors, the ARF10 and ARF16 auxin response factors and the quiescent centre-expressed WOX5 homeodomain protein each provide independent inputs to regulate the number of columella stem cells. Given the tight control of columella development, we found that these inputs act in a surprisingly parallel manner. Nevertheless, important points of interaction exist; for example, we demonstrate the repression of SMB activity by non-autonomous action of WOX5. Our results suggest that the developmental progression of columella stem cells may be quantitatively regulated by several more broadly acting transcription factors rather than by a single intrinsic stem cell factor, which raises questions about the special nature of the stem cell state in plants.

Dit rapport beschrijft het onderzoek dat in 2011 en 2012 is uitgevoerd aan twee pilots met onderwaterdrains in Utrecht, in Demmeriksekade (polder Groot-Wilnis) en De Keulevaart (Lopikerwaard). In het onderzoek is voornamelijk het effect van onderwaterdrains op de waterkwantiteit (debieten) en de waterkwaliteit onderzocht. De meetresultaten zijn uitgewerkt en geëvalueerd met de modellen SWAP en ANIMO. Een overzicht van eerder en lopend onderzoek naar maaivelddaling, waterkwantiteit, waterkwaliteit, bedrijfseconomische aspecten en effect op weidevogels is gegeven en betrokken in de conclusies. In de conclusies zijn ook de resultaten van een pilot in de Krimpenerwaard opgenomen (gerapporteerd in Alterra-rapport 2466). De hoeveelheden in en uit te pompen water blijken in het algemeen toe te nemen. Het effect op de waterkwaliteit is in het algemeen neutraal of gunstig. Melkveehouders zijn in het algemeen positief over de effecten van onderwaterdrains.

Symptoms of atopic asthma often decrease or even seem to disappear around puberty. The aim of this study was to investigate whether this so-called clinical remission is accompanied by remission of airway inflammation, since symptoms relapse in a substantial proportion of subjects later in life. To assess indicators of inflammation and/or structural damage of the airways, exhaled nitric oxide (eNO) and bronchial responsiveness to adenosine-5'-monophosphate (AMP) and methacholine (MCh) were determined in 21 subjects in clinical remission of atopic asthma. Clinical remission was defined as complete absence of symptoms of asthma without the use of any medication in the year preceding the study. Results were compared with those of 21 patients with current asthma and 18 healthy control subjects. We found significantly higher eNO values in the remission group than in healthy controls (geometric mean, 18.9 and 1.0 ppb, respectively; p < 0.001) whereas eNO values of the remission group and those of the subjects with current asthma (geometric mean, 21.9 ppb) were similar (p = 0.09). The responsiveness to both AMP and MCh of subjects in clinical remission was significantly higher as compared with responsiveness of healthy controls, and lower than responsiveness of subjects with current asthma. A significant correlation could be established between eNO and responsiveness to AMP, but not between eNO and responsiveness to MCh. The results of this study are suggestive of persistent airway inflammation during clinical remission of atopic asthma. We speculate that subclinical inflammation is a risk factor for asthma relapse later in life, and that eNO and responsiveness to both AMP and MCh can be used as different, noninvasive indices of the inflammatory process of the airways.

My thanks to Don Traut for his very intriguing comments on the larger role of displacement in Stravinsky's music. A strong parallel does indeed seem to exist between the metrical displacement of repeated motives and chords and the displacement of "contrapuntal lines." Especially revealing is Traut's account of a passage from Stravinsky's Piano Concerto (Ex. 3). Schenker's earlier commentary on this passage (Ex. 4) is shown to have been a good deal more savvy about the nature of Stravinsky's art than his outright rejection of it would have led one to believe. The "overlapping" of tonic and dominant harmony, pervasive in the composer's neoclassical works from the time of Pulcinella (1919), has frequently been remarked upon, of course, as have the static, non developmental implications of the practice. By way of the Piano Sonata (Ex. 8), Traut includes it as a form of displacement. The sense of motion associated with the actual progression of these chord functions is more or less cancelled out by their superimposition. Harmony is flattened out in the process. My view of the Piano Concerto is that, at least on a local scale in the first movement, many of the techniques cited by Traut derive from Bach's use of the non-harmonic, metrically accented passing tone (another from of displacement, of course). Bach's keyboard music served as a constant point of reference for Stravinsky during the 1920s, even as a kind of daily staple for a while. The anti-modernist slogan "back to Bach" dates from this era. Underscored by Traut as well is the governing role that displace ment assumes in Stravinsky's music, whatever the stylistic orientation, presumably Russian, neoclassical, or serial. Overlooked by him, however, are the "contrapuntal shifts" that result as a matter of course from strati fication. In Stravinsky's layered structures, superimposed fragments, registrally and often instrumental!/ fixed, repeat according to spans or cycles that vary independently of one another. The result is an