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Asthma is a complex, heterogeneous disease that necessitates a proper patient evaluation to choose the most appropriate treatment and optimize disease control. The recent introduction of new target therapies for the most severe form of the disease has heralded a new era of treatment options, targeting specific molecular pathways in asthma pathophysiology. Many factors could contribute to lack of disease control and several biological markers (e.g. blood eosinophils, IgE, FeNO) have been identified that are associated with disease subtypes or disease activity. However, we still do not have accurate clinically available biomarkers to distinguish different immunoprofiles of asthma patients and guide proper and personalized treatment. Therefore, a better refinement of phenotypes and biomarkers is necessary. Understanding the molecular mechanisms behind the heterogeneity of asthma phenotypes is essential for the identification of novel biomarkers that are reliable and easy to measure. The thesis is divided into 4 parts: the first part is the introduction of this thesis, and provides an overview of the current role of precision medicine in asthma, with a specific focus on new technologies such as the analysis of exhaled breath through the eNose ( Chapters 1 and 2 ). The second part ( Chapters 3-5 ) focuses the identification of potential new asthma biomarkers, such as exhaled breath profiles and surfactant protein D (SP-D) in blood. The third part ( Chapters 6 and 7 ) addresses currently available anti-IL5 biologic therapies for severe asthma and predictive markers of response or non response to biologics. It also investigates the potential discrepancies between the population studied in clinical trials and the population that uses biologics in routine clinical care. The fourth part ( Chapter 8 ) includes the general discussion of this thesis. New technologies (eNose) and biomarkers (SP-D) might be applicable in a future real-life setting, this thesis explore their potential and their limitations, as well as the future directions and treatment perspective in asthma research.

The topic of the essay is the relationship between time and pure practical reason in the Kant’s Theory of the free determination of the will. We ask if the orientation of the free will to the moral law implies a specific orientation in time, in which the subject can get the sense of the absolute and urgent rational obbligation to the freedom. We analyse the dinamical aspect of the pure reason on the intermediete normative level of the maxims. We research in which kind of reference points in time are the conditions of possibility of the subversion of the empirical causality, of the turn of the subjective principles’ order, of the Revolution in Conduct of Thought. Furthermore temporal references are required in order to understand thr historical continuity in which evolves the intelligible character, the qualitative modifications of the self as a moral improvement and the infinite duration of the Personality.

26th European Photovoltaic Solar Energy Conference and Exhibition; 676-680, In this paper we report the experimental results obtained from the manufacturing and characterization of III-V solar cells based on single junction, dual junction and triple junction structures. The main solar cell materials are GaAs and (Al)InGaP compounds. A test plan for qualification of “bare” solar cells for concentration systems is presented with its results. The test plan was derived from the space experience and it is based on the European Standards ECSS-E ST20-08, modified keeping into account the terrestrial standard for CPV modules (IEC 62108). The solar cells performances and their reliability is discussed with emphasis to the particular operation conditions induced by the CPV approach. These solar cells were then used and tested in two different CPV approaches: one based on standard concentrators and the other based on spectrum splitting concentrators. The systems, designed for standard concentration, need very high efficiency solar cells, therefore triple junction solar cells InGaP/GaAs/Ge are preferable. HCPV (High Concentration Photovoltaic) systems, based on this approach, have demonstrated efficiencies as high as 29%. The limit of this approach is that the multi junction solar cell structure is optimised for a specified incident spectrum (generally AM1.5D). During the day the spectrum is changing and the efficiency cannot be maintained, especially in the early morning and in the late afternoon. Spectrum splitting systems divide the light in several wavelength regions and use single or dual junction solar cells, optimised on each wavelength region. In this case a very high efficient system can be obtained that is less affected by spectrum variation. The use of standard concentrator and spectrum splitting systems is compared from a theoretical, experimental and economical point of view. The first results of outdoor performances are presented and discussed.

La leucemia mieloide cronica (LMC) è una neoplasia causata da una traslocazione reciproca non bilanciata tra il braccio lungo del cromosoma 9 e quello del cromosoma 22. Tale traslocazione determina la formazione dell’oncogene di fusione bcr-abl codificante per un’oncoproteina con attività tirosin-chinasica costitutiva. Le conoscenze dei meccanismi molecolari alla base della neoplasia, acquisite negli ultimi anni, hanno permesso di sviluppare terapie volte all’inibizione dell’attività chinasica della chimera BCR-ABL. Tra queste, l’imatinib mesilato (IM), inibitore selettivo della protein chinasi, ha rivoluzionato le terapie per la LMC. Sebbene numerosi pazienti in fase cronica, trattati con IM, abbiano raggiunto la remissione completa della neoplasia, in diversi casi si è avuto ricaduta e/o progressione in fase accelerata o blastica. Da qui la necessità di individuare nuovi farmaci che agiscano su bersagli differenti. Il carbossiamidotriazolo (CAI) è un nuovo farmaco citostatico anticancro in fase II dei clinical trials al NCI. Tale farmaco è un inibitore dei canali del Ca2+ non voltaggio dipendenti dunque agisce inibendo la proliferazione, la motilità e la sopravvivenza di numerose linee tumorali. Il nostro gruppo di ricerca ha dimostrato che dosi sub-tossiche di CAI inibiscono la proliferazione di cellule LMC IM-resistenti (LAMA84R, K562R e KCL22R) ed inducono apoptosi. Tali effetti sono associati alla capacità di questo farmaco di determinare un drastico decremento dei livelli generali di fosforilazione in tirosina, inibendo vie di trasduzione del segnale BCR/ABL-dipendenti ed indipendenti, ma anche un drastico decremento dei livelli totali dell’ oncoproteina (Alessandro et al., 2008). Al fine di comprendere in modo più approfondito il meccanismo molecolare d’azione del CAI, abbiamo utilizzato, come modello sperimentale, linee cellulari mieloidi murine (32D) trasfettate con plasmidi codificanti per BCR/ABL-p210 (Full lenght), BCR/ABL-T315I e BCR/ABL-E255K. T315I ed E255K sono mutazioni in Bcr-Abl tra le più rappresentate nella popolazione di pazienti affetti da LMC IM-resistenti. I nostri risultati hanno mostrato che il CAI riduce sia la proliferazione delle tre linee cellulari, in modo dose e tempo dipendente, sia la fosforilazione di Bcr-Abl, ma soprattutto i livelli totali di proteina; il CAI agisce anche sul mutante T315I, su cui persino i farmaci di nuova generazione non hanno mostrato alcuna efficacia. Poiché il CAI non sembra agire sui livelli di proteina totale tramite una prematura degradazione ubiquitina-proteasoma dipendente né sembra regolare in modo significativo il ciclo cellulare, abbiamo ipotizzato che possa agire inducendo un aumento delle specie reattive dell’ossigeno (ROS) all’interno della cellula. A tale scopo abbiamo sottoposto le linee LAMA84R, 32D p210 e 32D T315I a trattamenti con dosi e tempi crescenti di CAI per valutare in tali cellule i livelli di ROS. I risultati ottenuti consentono di concludere che il CAI induce sulle cellule Bcr-Abl+ ed IM-resistenti un aumento della produzione di ROS, in grado di indurre uno stress cellulare. Poiché il CAI è già in fase II di sperimentazione clinica, per il trattamento di altre neoplasie, questi risultati forniscono indicazioni rilevanti per un uso razionale di questo farmaco nel trattamento di pazienti affetti da LMC che non rispondono alla monoterapia con IM.

Transmissible spongiform encephalopathies (TSEs) are neurodegenerative disorders characterized by the accumulation, principally in the central nervous system (CNS), of the abnormal form (PrPTSE) of a host encoded protein, the cellular prion protein (PrPC). In humans some forms of TSEs have a genetic etiology, as they are associated to mutations in the PrP gene: thus it is extremely important to elucidate the role played by the altered residue in the pathological conversion of the protein. Aim of our work was to deduce the involvement of the mutated residue in the molecular mechanisms underlying genetic TSE pathogenesis by means of a quantitative mass spectrometry analysis of the PrPTSE allotypes accumulated in the brains of genetic Creutzfeldt-Jakob disease (gCJD) affected individuals. We have integrated our previous data on the gCJD patient carrying the R208H mutation with those regarding V210I gCJD patients in order to verify if diverse mutations regulate in a different fashion the process of molecular pathogenesis. The LC/MS (liquid chromatography/mass spectrometry) protocol developed by us (Schininà M.E. et al., 2003. Pure Appl. Chem., 75: 317-323) has been implemented in order to set up, by means of appropriate synthetic deuterated (internal standards) and non-deuterated (calibrants) peptides, a quantitative analysis of the pathological PrP allotypes. In all cases the amount of the mutant allotype is higher than the wild-type counterpart: in the R208H subject the mutant/wild-type ratio has been again estimated and it was around 3/1, while in all the V210I individuals it was lower than 2/1. These results demonstrate that the presence of the mutation is partially involved in favouring the pathological conversion of PrP, but it is not the only factor implicated in the pathogenesis of TSEs as the ratio of the two allotypes does not reveal a significantly higher amount of the mutant allotype compared to the wild-type one. Further investigations are needed in order to elucidate the molecular mechanisms underlying the pathogenesis of genetic human TSEs.

Transmissible spongiform encephalopathies (TSEs), or prion diseases, are neurodegenerative disorders affecting both humans and animals. TSEs are caused by the infectious agent 'prion', which is poorly characterized and is believed to be composed of the pathological isoform--TSE-associated prion protein (PrP(TSE))--of a physiological, host-encoded protein called cellular prion protein (PrPC). Whereas it is certain that the process of PrP(TSE) formation has a fundamental role in the development of TSE, other aspects, including the mechanism of this process, the nature and the role of the factors involved (related or unrelated to PrP), and the relationship between PrP(TSE) conformations and disease phenotypes remain poorly defined. Different proteomic strategies have been utilized to address these issues. In this ambit, mass spectrometry (MS) has gained a prominent position, with applications that range from the investigation of the molecular pathogenesis to the development of new diagnostic tools. The aim of this review is to outline these advances and to highlight promising avenues to prion research that have been opened by novel MS applications.

Objective: Severe asthma is considered a risk factor for SARS-Coronavirus 2 (SARS-CoV-2) infection but scientific evidences are lacking. Methods: we performed a literature search and review based on PubMed database national, international recommendations as well as papers on severe asthmatic patients and their management during SARS-CoV-2 pandemic. Results: the majority of international recommendations, expert panels and editorials provide indications about management of severe asthmatic patients. No published studies evaluated the effects of biologic agents on severe asthmatic patients during SARS-CoV-2 pandemic. Conclusions: the relationship between SARS-CoV-2 and asthma is variable worldwide and severe asthmatic patients were seldom reported in published cohorts. International recommendations suggest maintaining asthma under control to limit exacerbations occurrence, by using all available treatment. The minimum steroid dosage effective to control symptoms should be maintained to avoid exacerbations; biologic agents administration should be regularly scheduled encouraging patient support programmes.

Asthma is a chronic respiratory disease that can lead to exacerbations, defined as acute episodes of worsening respiratory symptoms and lung function. Predicting the occurrence of these exacerbations is an important goal in asthma management. The measurement of exhaled breath by electronic nose (eNose) may allow for the monitoring of clinically unstable asthma and exacerbations. However, data on its ability to perform this is lacking. We aimed to evaluate whether eNose could identify patients that recently had asthma exacerbations. We performed a cross-sectional study, measuring exhaled breath using the SpiroNose in adults with a physician-reported diagnosis of asthma. Patients were randomly divided into a training (n = 252) and validation (n = 109) set. For the analysis of eNose signals, principal component (PC) and linear discriminant analysis (LDA) were performed. LDA, based on PC1-4, reliably discriminated between patients who had a recent exacerbation from those who had not (training receiver operating characteristic (ROC)–area under the curve (AUC) = 0.76,95% CI 0.69–0.82), (validation AUC = 0.76, 95% CI 0.64–0.87). Our study showed that, exhaled breath analysis using eNose could accurately identify asthma patients who recently had an exacerbation, and could indicate that asthma exacerbations have a specific exhaled breath pattern detectable by eNose.

Severe asthma is a heterogeneous disease with different phenotypes based on clinical, functional or inflammatory parameters. In particular, the eosinophilic phenotype is associated with type 2 inflammation and increased levels of interleukin (IL)‐4, IL‐5 and IL‐13). Monoclonal antibodies that target the eosinophilic inflammatory pathways (IL‐5R and IL‐5), namely mepolizumab, reslizumab, and benralizumab, are effective and safe for severe eosinophilic asthma. Eosinophils threshold represents the most indicative biomarker for response to treatment with all three monoclonal antibodies. Improvement in asthma symptoms scores, lung function, the number of exacerbations, history of late‐onset asthma, chronic rhinosinusitis with nasal polyposis, low oral corticosteroids use and low body mass index represent predictive clinical markers of response. Novel Omics studies are emerging with proteomics data and exhaled breath analyses. These may prove useful as biomarkers of response and non‐response biologics. Moreover, future biomarker studies need to be undertaken in paediatric patients affected by severe asthma. The choice of appropriate biologic therapy for severe asthma remains challenging. The importance of finding biomarkers that can predict response continuous an open issue that needs to be further explored. This review describes the clinical effects of targeting the IL‐5 pathway in severe asthma in adult and paediatric patients, focusing on predictors of response and non‐response.

SARS-CoV-2 pandemic has contributed to implement telemedicine, allowing clinicians to follow the patient remotely, therefore minimizing the risk of any exposure to positive COVID-19 patients. We summarize the approaches adopted to treat and monitor severe asthmatic patients during the lockdown phase of the pandemic. Our experience supports the strategy that every effort should be made to minimize patient contact with the health-care system, planning a pathway that allows patients to receive appropriate medical care and continue the biological therapies, thus preventing the loss of disease control and acute severe exacerbations.

Background The SARS-CoV-2 pandemic has changed the health-care systems around the world in a remarkable way. We describe the strategies adopted to cope with the limitations imposed by the pandemic to the access to health care by patients diagnosed with idiopathic Pulmonary Fibrosis (IPF). Material and methods We conducted a retrospective observational analysis including IPF patients under antifibrotic drugs (nintedanib and pirfenidone) that accessed to the Outpatient clinic of the University of Palermo, Italy. Patients received a phone number and an email address in case of any urgency and a virtual meeting was settled up monthly. Results 40 patients (M/F: 30/10) were followed up, 33 under nintedanib treatment, 7 under pirfenidone . Among patients under nintedanib, 1 patient reported high fever (T max 39 °C) and purulent sputum with no sign of infections, 1 had hemoptysis that was spontaneously resolved. 2 patients accessed to the emergency department for the worsening of dyspnea; 5 patients had diarrhea that resolved with symptomatic drugs in few days. 3 patients had an increase of alkaline phosphatase levels, leading to the withdrawal of the antifibrotic drug for 15 days, and subsequent normalization of the plasmatic levels. Among patients under pirfenidone, one subject had an increase of ferritin serum levels with no symptoms. The remaining subjects were in stable clinical conditions. None of the patients reported hospitalization or exacerbations, and did not experience antifibrotic withdrawal. Conclusions We were able to demonstrate that by implementing alternative ways to monitor the disease, patients did not incur in increased rates of acute exacerbations or higher frequency of side effects and antifibrotic treatment withdrawal.

Breath analysis using eNose technology can be used to discriminate between asthma and COPD patients, but it remains unclear whether results are influenced by smoking status. We aim to study whether eNose can discriminate between ever- vs. never-smokers and smoking &lt, 24 vs. &gt, 24 h before the exhaled breath, and if smoking can be considered a confounder that influences eNose results. We performed a cross-sectional analysis in adults with asthma or chronic obstructive pulmonary disease (COPD), and healthy controls. Ever-smokers were defined as patients with current or past smoking habits. eNose measurements were performed by using the SpiroNose. The principal component (PC) described the eNose signals, and linear discriminant analysis determined if PCs classified ever-smokers vs. never-smokers and smoking &lt, 24 h. The area under the receiver–operator characteristic curve (AUC) assessed the accuracy of the models. We selected 593 ever-smokers (167 smoked &lt, 24 h before measurement) and 303 never-smokers and measured the exhaled breath profiles of discriminated ever- and never-smokers (AUC: 0.74, 95% CI: 0.66–0.81), and no cigarette consumption &lt, 24h (AUC 0.54, 95% CI: 0.43–0.65). In healthy controls, the eNose did not discriminate between ever or never-smokers (AUC 0.54, 95% CI: 0.49–0.60) and recent cigarette consumption (AUC 0.60, 95% CI: 0.50–0.69). The eNose could distinguish between ever and never-smokers in asthma and COPD patients, but not recent smokers. Recent smoking is not a confounding factor of eNose breath profiles.

The spread of the SARS-CoV-2 infection among population has imposed a re-organization of healthcare services, aiming at stratifying patients and dedicating specific areas where patients with suspected COVID-related respiratory disease could receive the necessary health care assistance while waiting for the confirmation of the diagnosis of COVID-19 disease. In this scenario, the pathway defined as a “grey zone” is strongly advocated. We describe the application of rules and pathways in a regional context with low diffusion of the infection among the general population in the attempt to provide the best care to respiratory patients with suspected COVID-19. To date, this process has avoided the worst-case scenario of intra-hospital epidemic outbreak.

A 65-year-old man was referred for evaluation of acute onset of fever, productive cough and dyspnoea. He had previously received a diagnosis of laryngeal carcinoma, which had been treated with laryngectomy and bilateral laterocervical lymphadenectomy, followed by chemotherapy. He underwent plastic surgery of the laryngocutaneous fistula, and a positron emission tomography (PET)- computed tomography (CT) examination performed during follow-up showed 18-FDG (2-fluoro-2-deoxyd- glucose) lung uptake in the apical right portion. He had a smoking history and his regular medications included dexamethasone, metoclopramide, omeprazole, furosemide, cholecalciferol and pregabalin. He had a history of chronic kidney failure and thyroid goitre, no family history of pulmonary disease or malignancy, nor of drug allergies.

Objective: Management of asthma includes monitoring of inhaler technique and level of adherence to treatment. Both factors could be influenced by high frequency of switching inhaler devices. We explored whether switching inhalers is an independent predictive factor of exacerbations. Methods: Data were collected from 2015 to 2017 from the outpatient clinic of asthma at the University of Palermo, Italy. This observational study consisted of two phases: Phase 1 included subjects of at least three visits in the previous year who reported the frequency of inhalers switched; Phase 2 included subjects of at least two visits during the second year, and the rate of switches and exacerbations was recorded. We included adult (24–84 years old) mild/moderate asthmatics under regular inhaled treatment; uncontrolled asthma was defined as poor symptom control, exacerbations (≥2/year) requiring oral corticosteroids (OCS), or serious exacerbations (≥1/year) requiring hospitalization. Results: A total of 109 records were retrieved for the analysis. A significant correlation between the rate of switches in Phase 1 and exacerbations in Phase 2 was found (p = 0.001). Age and the rates of exacerbations in Phase 1 were also independently associated with a higher number of exacerbations in Phase 2 (p < 0.0001). The multivariate regression model showed that the numbers of switches, as well as exacerbations in Phase 1, were independently correlated to the number of exacerbations in Phase 2 (p = 0.003). Conclusions: The frequency of switching inhalers independently affects the risk of exacerbations in asthma. These results imply that changing inhaler requires careful management in clinical practice.

The thermoplasmonic effect causing the local overheating in nanostructured metallic substrates has been recently recognized as an intriguing technological tool for the development of light-controlled active micro and nano systems. Here, we present a study of thermoplasmonic effect in Lab-on-Fiber devices, consisting in nanostructured gold layers directly integrated onto the cleaved facet of an optical fiber tip. We analyze the effect of the metallic nanostructure parameters on the temperature distribution under different (in-fiber) illumination conditions. Heating and cooling temporal dynamics are also investigated. At the steady state, a linear relationship between input optical power and temperature with a linear coefficient in the order of 10 °C/mW is found. All the experimental results are in good agreement with numerical simulations based on a finite element method. Our findings lay the groundwork for the development of light triggered active Lab-on-Fiber probes, merging the unique characteristics of the optical fiber platform and the enormous potentiality offered by thermoplasmonics.

Individuals with Chronic Obstructive Pulmonary Disease (COPD) experience sleep disturbances due to the impact of respiratory symptoms on sleep quality. We explored whether sleep disturbances in COPD are linked to heterogeneity of airway constriction.The impact of breathing problems on sleep quality was measured in consecutive COPD outpatients with the COPD and Asthma Sleep Impact Scale (CASIS) questionnaire. Impulse oscillometry technique (IOS) was employed to assess heterogeneity of airway constriction. Subjects with a previous or concomitant diagnosis of asthma or obstructive sleep apnea (OSA) were excluded.Fifty COPD subjects (M/F 40/10; age: 71 +/- 8 yrs, Body Mass Index (BMI): 26.2 +/- 4.7 kg/m(2), Forced Expiratory Volume in the first second (FEV1): 65 +/- 25% predicted; mean +/- SD) were enrolled. The mean CASIS score was 36 +/- 3.3, and the R5-R20 value was 0.2 +/- 0.15 kPa s L-1. The CASIS score was significantly higher in subjects with increased R5-R20 (>0.07 kPa s L-1) (39 +/- 24; p = 0.02) compared to normal R5-R20 (21 +/- 17). When subjects were categorized on the basis of lung function in severely versus non severely obstructed (FEV1 50% predicted) or air trappers versus non air trappers (Residual Volume, RV >= or

Urinary incontinence (UI) is defined as a loss of bladder control and is characterized by the complaint of any involuntary leakage of urine. Evidence suggests that the prevalence of UI is higher in subjects with chronic obstructive pulmonary disease (COPD) than in age-matched controls in both sexes. UI is classified as stress, urge, and mixed, and has a considerable impact on quality of life. However, the prevalence of UI in individuals with COPD is mostly unexplored in clinical research and often underestimated in clinical practice. Interestingly, although the involuntary leakage of a small amount of urine during coughing (e.g., stress UI) is among the most plausible causes of UI in patients with COPD, its importance has been questioned by some researchers. Moreover, UI as a respiratory drug-related adverse effect is largely overlooked; only a few randomized controlled trials have reported the presence of urinary symptoms, mainly as urinary retention due to anticholinergic agents. In this narrative review, we explored whether, and to what extent, UI occurs in COPD individuals, and what the proposed actions to improve this condition are. We found that the association between UI and COPD is largely unexplored, mostly because UI tends to be attributed to older age. We infer that the prevalence of UI in individuals with chronic respiratory symptoms is often underestimated in clinical practice. The misinterpretation of urinary symptoms as related to the respiratory condition can delay diagnostic and therapeutic approaches. The use of simple self-administered questionnaires to assess the presence of UI is encouraged.

Background: Healthcare decisions made on the basis of insufficient evidence may potentially have ineffective or even harmful consequences. The proportion of older ages (over 65 years) in randomized controlled trials (RCTs) for severe asthma is not enough to establish whether anti-IL-5/IL-5R therapies are equally effective in the elderly as in younger subjects. Methods: In order to assess the relationship between age and the efficacy of anti-IL-5 monoclonal antibodies (mABs) with respect to the risk of exacerbations and changes in FEV1, a meta-regression analysis via random-effect method was carried out by plotting the effect estimates (outcome variables) resulting from the pairwise meta-analysis with the age of asthmatic subjects (explanatory variable). A comprehensive literature search was performed for pivotal RCTs on the effects of anti-IL-5/IL-5R in severe asthma, with the following keywords: “asthma and mepolizumab”, “asthma and reslizumab” and “asthma and benralizumab”. The study was restricted to “clinical trials”, “age over 65” and “humans”. Data were checked for age, exacerbation rates, changes from baseline in FEV1, and blood eosinophil (Eos) count. Secondary outcomes included inhaled and oral medication use, clinical scores and quality of life. Results: A total of 10 studies were analysed. Age did not modulate the efficacy of anti-IL-5/IL-5R treatment against the risk of exacerbation neither in the overall population (coefficient −0.007, P = 0.89), nor in patients with high blood Eos count (coefficient 0.075, P = 0.30). The blood Eos level drove the efficacy of anti-IL-5/IL-5R mABs against the risk of exacerbation regardless of age (coefficient −0.27, P

Bioinformatics tools are imperative for the in depth analysis of heterogeneous high-throughput data. Most of the software tools are developed by specific laboratories or groups or companies wherein they are designed to perform the required analysis for the group. However, such software tools may fail to capture "what the community needs in a tool". Here, we describe a novel community-driven approach to build a comprehensive functional enrichment analysis tool. Using the existing FunRich tool as a template, we invited researchers to request additional features and/or changes. Remarkably, with the enthusiastic participation of the community, we were able to implement 90% of the requested features. FunRich enables plugin for extracellular vesicles wherein users can download and analyse data from Vesiclepedia database. By involving researchers early through community needs software development, we believe that comprehensive analysis tools can be developed in various scientific disciplines. We would like to thank Tejaswee P. Shah for her valuable input in the development of FunRich. We would like to thank Jan Lotvall for helping us in this effort by circulating the email within his group. We thanks many other users who requested for features/changes in FunRich though the e-mail and the online forum. Suresh Mathivanan is supported by Australian Research Council DECRA (DE150101777) and Award U54- DA036134 supported by the NIH Common Fund through the Office of Strategic Coordination/Office of the NIH Director.The funders had no role in study design, data collection andanalysis, decision to publish, or preparation of the manuscript. Sí

Objective The intestinal inflammation observed in patients with ankylosing spondylitis (AS) is characterized by an overexpression of interleukin-23 (IL-23). IL-23 is known to regulate IL-22 production through lamina propria NKp44+ natural killer (NK) cells, which are thought to be involved in protective mucosal mechanisms. This study was undertaken to evaluate the frequency of NKp44+ NK cells and the expression of IL-22 in the ileum of AS patients. Methods Tissue NKp44+ NK cells, NKp46+ NK cells, and IL-22–producing cells were analyzed by flow cytometry. Quantitative gene expression analysis of IL-22, IL-23, IL-17, STAT-3, and mucin 1 (MUC-1) was performed by reverse transcriptase–polymerase chain reaction on ileal samples from 15 patients with AS, 15 patients with Crohn's disease (CD), and 15 healthy controls. NKp44, pSTAT-3, and IL-22 expression was analyzed by immunohistochemistry. Results The frequency of NKp44+ but not NKp46+ NK cells was increased in the inflamed ileum of AS patients compared to CD patients and controls. The frequency of NKp46+ NK cells was significantly increased only in CD patients. Among CD4+ lymphocytes and NKp44+ NK cell subsets, the latter were the major source of IL-22 on lamina propria mononuclear cells from AS patients. Significant up-regulation of IL-22, IL-23p19, MUC-1, and STAT-3 transcripts in the terminal ileum of patients with AS was observed. Immunohistochemical analysis confirmed the increased IL-22 and pSTAT-3 expression in inflamed mucosa from AS and CD patients. Conclusion Our findings indicate that overexpression of IL-22, together with an increased number of IL-22–producing NKp44+ NK cells, occurs in the gut of AS patients, where it appears to play a tissue-protective role.

Urinary expressed prostatic secretion or "EPS-urine" is proximal tissue fluid that is collected after a digital rectal exam (DRE). EPS-urine is a rich source of prostate-derived proteins that can be used for biomarker discovery for prostate cancer (PCa) and other prostatic diseases. We previously conducted a comprehensive proteome analysis of direct expressed prostatic secretions (EPS). In the current study, we defined the proteome of EPS-urine employing Multidimensional Protein Identification Technology (MudPIT) and providing a comprehensive catalogue of this body fluid for future biomarker studies. We identified 1022 unique proteins in a heterogeneous cohort of 11 EPS-urines derived from biopsy negative noncancer diagnoses with some benign prostatic diseases (BPH) and low-grade PCa, representative of secreted prostate and immune system-derived proteins in a urine background. We further applied MudPIT-based proteomics to generate and compare the differential proteome from a subset of pooled urines (pre-DRE) and EPS-urines (post-DRE) from noncancer and PCa patients. The direct proteomic comparison of these highly controlled patient sample pools enabled us to define a list of prostate-enriched proteins detectable in EPS-urine and distinguishable from a complex urine protein background. A combinatorial analysis of both proteomics data sets and systematic integration with publicly available proteomics data of related body fluids, human tissue transcriptomic data, and immunohistochemistry images from the Human Protein Atlas database allowed us to demarcate a robust panel of 49 prostate-derived proteins in EPS-urine. Finally, we validated the expression of seven of these proteins using Western blotting, supporting the likelihood that they originate from the prostate. The definition of these prostatic proteins in EPS-urine samples provides a reference for future investigations for prostatic-disease biomarker studies.

Specific antibodies are essential tools for studying proteins as well as for diagnostic research in biomedicine. The egg yolk of immunized chicken is an inexpensive source of high-quality polyclonal antibodies. The 12-kDa Parietaria judaica 2 allergen was expressed as a fusion protein and was used to immunize Leghorn chickens. In this paper, we show, using 2-dimensional gel electrophoresis and immunoblotting, that chicken antibodies raised against a recombinant allergen can be used to recognize similar proteins from a pollen raw extract. Allergen identity was confirmed by nanoLC-nanospray-tandem mass spectrometry analysis. Our data demonstrate for the first time that a synergistic combination of molecular biology, 2-dimensional PAGE, and use of nonmammalian antibodies represents a powerful tool for reliable identification of allergens.

Pulmonary surfactant is a mixture of lipids and surfactant-specific proteins that covers the alveolar surface, as well as the terminal conducting airways, lowering the surface tension at the air–liquid interface during breathing. The involvement of pulmonary surfactant in the pathophysiology of asthma has been suggested. An interesting working hypothesis is that the surface tension of the peripheral airways is altered in asthma, because the inflammatory process affects the structure and function of surfactant, leading to excessive airway narrowing and features of air trapping. We explored whether serum levels of surfactant protein D (SP-D) in asthmatics are related to the severity of the disease. In addition, we aimed to assess whether serum SP-D correlated with functional abnormalities of peripheral airways.