cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4557973.v1
title: Supplementary Material for: Exacerbating Factors Induce Different Gene Expression Profiles in Peripheral Blood Mononuclear Cells from Asthmatics, Patients with Chronic Obstructive Pulmonary Disease and Healthy Subjects

description: <b><i>Background:</i></b> Despite several common phenotypic features, chronic obstructive pulmonary disease (COPD) and severe asthma differ with regard to their causative factors and pathophysiology. Both diseases may be exacerbated by environmental factors, however, the molecular profiles of disease episodes have not been comprehensively studied. We identified differences in gene and protein expression profiles expressed by peripheral blood mononuclear cells (PBMC) of COPD patients, patients with atopic asthma and healthy subjects when challenged with exacerbating factors in vitro: lipopolysaccharide (LPS), house dust mite (HDM) and cat allergen. <b><i>Methods:</i></b> PBMC isolated from patients with severe atopic asthma and COPD, as well as healthy subjects were stimulated with rDer p 1 DG, rFel d 1 DG and LPS. The changes in the expression of 47 genes belonging to five groups (phospholipase A<sub>2</sub>, eicosanoids, transcription factors, cytokines and airway remodeling) were studied using TaqMan low density array cards. Immunoblotting was used to study relative protein expression. <b><i>Results:</i></b> rDer p 1 significantly up-regulated the expression of <i>PLA2G4A, PLA2G6, PLA2G15, CYSLTR1, LB4R2, PTGS1, PTGS2</i>, <i>FOXP1</i>, <i>GATA3</i>, <i>HDAC2</i>, <i>IREB2</i>, <i>PPARG</i>, <i>STAT4</i>, <i>TSLP </i>and<i> CHI3L1</i> genes in asthmatics in comparison to healthy subjects. LPS induced significant expression of <i>ANXA1</i> and<i> LTA4H </i>in asthmatics when compared to COPD patients and healthy subjects. <i>SOX6,</i><i>STAT4 </i>and <i>IL1RL1 </i>were induced in COPD after LPS stimulation. Analysis of protein expression revealed a pattern similar to mRNA expression. <b><i>Conclusions:</i></b> LPS-induced exacerbation of asthma and COPD is characterized by differential expression of selected genes in PBMC. HDM allergen changed the expression profile of inflammatory genes between patients with asthma of atopic origin and healthy controls.
DOI: 10.6084/m9.figshare.4557994.v1
title: Supplementary Material for: Endoscopic Evaluation and Dissection of the Anterior Vitreous Base

description: The specific concept of pathological anterior vitreous base (AVB) and of its endoscopy-assisted dissection was elaborated during our 20 years' experience with endoscopy for observing the ‘in vivo' anatomy and pathoanatomy of the AVB, and for dissecting the anterior vitreous cortex in over 2,000 consecutive eyes. Endoscopy provides a 360° view of the entire vitreous cavity akin to the surgeon's eye being inside the operated eye. Evaluation of the capsulozonular complex, ciliary body, and AVB is not only independent of anterior media transparency, but unimpeded by scleral depression and magnified. High magnification dissection of the AVB gel can be conducted in an individualized and unmatched fashion.
DOI: 10.6084/m9.figshare.4557955
title: Supplementary Material for: Lactic Acid Bacteria as a Surface Display Platform for Campylobacter jejuni Antigens

description: <b><i>Background:</i></b> Food poisoning and diarrheal diseases continue to pose serious health care and socioeconomic problems worldwide. <i>Campylobacter</i> spp. is a very widespread cause of gastroenteritis. Over the past decade there has been increasing interest in the use of lactic acid bacteria (LAB) as mucosal delivery vehicles. They represent an attractive opportunity for vaccination in addition to vaccination with attenuated bacterial pathogens. <b><i>Methods:</i></b> We examined the binding ability of hybrid proteins to nontreated or trichloroacetic acid (TCA)-pretreated LAB cells by immunofluorescence and Western blot analysis. <b><i>Results:</i></b> In this study we evaluated the possibility of using GEM (Gram-positive enhancer matrix) particles of <i>Lactobacillus salivarius</i> as a binding platform for 2 conserved, immunodominant, extracytoplasmic <i>Campylobacter jejuni</i> proteins: CjaA and CjaD. We analyzed the binding ability of recombinant proteins that contain <i>C. jejuni</i> antigens (CjaA or CjaD) fused with the protein anchor (PA) of the <i>L. lactis </i>peptidoglycan hydrolase AcmA, which comprises 3 LysM motifs and determines noncovalent binding to the cell wall peptidoglycan. Both fused proteins, i.e. 6HisxCjaAx3LysM and 6HisxCjaDx3LysM, were able to bind to nontreated or TCA-pretreated <i>L. salivarius</i> cells. <b><i>Conclusion:</i></b> Our results documented that the LysM-mediated binding system allows us to construct GEM particles that present 2 <i>C. jejuni</i> antigens.
DOI: 10.6084/m9.figshare.4557967.v1
title: Supplementary Material for: Bilateral Pedunculopontine Nucleus Stimulation for Progressive Supranuclear Palsy

description: The pedunculopontine nucleus (PPN) is a potential target for gait disorders. We report 4 cases of bilateral PPN stimulation in progressive supranuclear palsy (PSP) patients with short-term (6 months) and long-term (18 months) follow-ups. Patients with PSP who had gait disturbances, but were able to walk with or without assistance, were selected. The patients' median age was 64 years and the disease duration 3 years. Bilateral PPN deep brain stimulation (DBS) was performed. The pacemaker was programmed using a bipolar mode and lower frequencies (20-45 Hz). The PSP rating scores (PSPRS) and their gait subscores (No. 25, 26, 27 and 28) along with PSP staging scores were used as primary end points. The total Unified Parkinson's Disease Rating Scale (UPDRS), UPDRS III and the 39-item Parkinson's Disease Questionnaire were considered as secondary end points. Video recordings of the gaits were performed before surgery and at the 6- and 18-month follow-ups. These were retrospectively reviewed by a blinded neurologist for the primary end points. At the 6- and 18-month follow-ups, the median change in PSPRS was from 33 (baseline) to 37.5 and 47, respectively. Similarly, the PSP staging changed from 3 to 2.5 and 3.5, item 25 from 1.5 to 2 and 3.5, item 26 from 2.5 to 2 and 3.5, item 27 from 3.5 to 3 and 3.5 and item 28 from 1.5 to 1.5 and 3. Two patients in the study with the PSP-parkinsonism phenotype experienced improvement in their gait until the last follow-up. Bilateral PPN DBS can be safely performed in PSP patients despite mid-brain atrophy.
DOI: 10.6084/m9.figshare.4557955.v1
title: Supplementary Material for: Lactic Acid Bacteria as a Surface Display Platform for Campylobacter jejuni Antigens

description: <b><i>Background:</i></b> Food poisoning and diarrheal diseases continue to pose serious health care and socioeconomic problems worldwide. <i>Campylobacter</i> spp. is a very widespread cause of gastroenteritis. Over the past decade there has been increasing interest in the use of lactic acid bacteria (LAB) as mucosal delivery vehicles. They represent an attractive opportunity for vaccination in addition to vaccination with attenuated bacterial pathogens. <b><i>Methods:</i></b> We examined the binding ability of hybrid proteins to nontreated or trichloroacetic acid (TCA)-pretreated LAB cells by immunofluorescence and Western blot analysis. <b><i>Results:</i></b> In this study we evaluated the possibility of using GEM (Gram-positive enhancer matrix) particles of <i>Lactobacillus salivarius</i> as a binding platform for 2 conserved, immunodominant, extracytoplasmic <i>Campylobacter jejuni</i> proteins: CjaA and CjaD. We analyzed the binding ability of recombinant proteins that contain <i>C. jejuni</i> antigens (CjaA or CjaD) fused with the protein anchor (PA) of the <i>L. lactis </i>peptidoglycan hydrolase AcmA, which comprises 3 LysM motifs and determines noncovalent binding to the cell wall peptidoglycan. Both fused proteins, i.e. 6HisxCjaAx3LysM and 6HisxCjaDx3LysM, were able to bind to nontreated or TCA-pretreated <i>L. salivarius</i> cells. <b><i>Conclusion:</i></b> Our results documented that the LysM-mediated binding system allows us to construct GEM particles that present 2 <i>C. jejuni</i> antigens.
DOI: 10.6084/m9.figshare.4557946
title: Supplementary Material for: Gastroesophageal Reflux Disease Is a Risk Factor for Severity of Organizing Pneumonia

description: <b><i>Background:</i></b> The link between organizing pneumonia (OP) and gastroesophageal reflux disease (GERD) is not well known. There is little evidence in the literature to establish a causal link between GERD and OP. <b><i>Objectives:</i></b> The aim of the study was to assess the hypothesis that OP is more severe when it is associated with GERD and that it leads to more frequent relapses. <b><i>Methods:</i></b> In a retrospective study on 44 patients suffering from OP, we compared the clinical, radiological and histological characteristics of 2 groups, 1 composed of patients with GERD (n = 20) and the other of patients without GERD (n = 24). <b><i>Results:</i></b> The GERD group was distinguished by a higher number of patients with migratory alveolar opacities on chest radiography and thoracic computerized tomography (14/20 vs. 9/24; p = 0.03 and 18/20 vs. 13/24; p = 0.01), greater hypoxemia [60 (42-80) vs. 70 (51-112) mm Hg; p = 0.03], greater bronchoalveolar lavage cellularity [0.255 (0.1-1.8) vs. 0.150 (0.05-0.4) g/l; p = 0.035] and more frequent relapses (14/20 vs. 9/24; p = 0.03). <b><i>Conclusions:</i></b> OP associated with GERD is more severe and results in more frequent relapses. Microinhalation of gastric secretions might induce lung inflammation leading to OP and relapse. We suggest that typical symptoms of GERD such as pyrosis should be investigated in OP.
DOI: 10.6084/m9.figshare.4557952
title: Stimulus set

description: Complete experiment stimulus set.<br>
DOI: 10.6084/m9.figshare.4557952.v1
title: Stimulus set

description: Complete experiment stimulus set.<br>
DOI: 10.6084/m9.figshare.4557889
title: Supplementary Material for: Multinucleated Giant Hemocytes Are Effector Cells in Cell-Mediated Immune Responses of Drosophila

description: We identified and characterized a so far unrecognized cell type<i>,</i> dubbed the multinucleated giant hemocyte (MGH), in the ananassae subgroup of Drosophilidae. Here, we describe the functional and ultrastructural characteristics of this novel blood cell type as well as its characterization with a set of discriminative immunological markers. MGHs are encapsulating cells that isolate and kill the parasite without melanization. They share some properties with but differ considerably from lamellocytes, the encapsulating cells of <i>Drosophila melanogaster</i>, the broadly used model organism in studies of innate immunity. MGHs are nonproliferative effector cells that are derived from phagocytic cells of the sessile tissue and the circulation, but do not exhibit phagocytic activity. In contrast to lamellocytes, MGHs are gigantic cells with filamentous projections and contain many nuclei, which are the result of the fusion of several cells. Although the structure of lamellocytes and MGHs differ remarkably, their function in the elimination of parasites is similar, which is potentially the result of the convergent evolution of interactions between hosts and parasites in different geographic regions. MGHs are highly motile and share several features with mammalian multinucleated giant cells, a syncytium of macrophages formed during granulomatous inflammation.
DOI: 10.6084/m9.figshare.4557913
title: Supplementary Material for: Liver Disease and Other Comorbidities in Wolcott-Rallison Syndrome: Different Phenotype and Variable Associations in a Large Cohort

description: <b><i>Background:</i></b> Wolcott-Rallison syndrome (WRS) is caused by recessive <i>EIF2AK3</i> mutations and characterized by early-onset diabetes and skeletal dysplasia. Hepatic dysfunction has been reported in 60% of patients. <b><i>Aims:</i></b> To describe a cohort of WRS patients and discuss the pattern and management of their liver disease. <b><i>Methods:</i></b> Detailed phenotyping and direct sequencing of <i>EIF2AK3</i> gene were conducted in all patients. <b><i>Results:</i></b> Twenty-eight genetically confirmed patients (67% male; mean age 4.6 years) were identified. 17 different <i>EIF2AK3</i> mutations were detected, of which 2 were novel. The p.S991N mutation was associated with prolonged survival and p.I650T with delayed onset. All patients presented before 25 months with diabetes with variation in the frequency and severity of 10 other features. Liver disease, first manifested as non-autoimmune hepatitis, was the commonest extra-pancreatic feature identified in 85.7% (24/28). 22/24 had at least one episode of acute hepatic failure which was the cause of death in all deceased patients (13/28). One child was treated by liver transplantation and had no liver disease and better diabetes control for the following 6 years. <b><i>Conclusions:</i></b> Liver disease in WRS is more frequent than previously described and carries high mortality. The first experience with liver transplantation in WRS is encouraging.
DOI: 10.6084/m9.figshare.4557946.v1
title: Supplementary Material for: Gastroesophageal Reflux Disease Is a Risk Factor for Severity of Organizing Pneumonia

description: <b><i>Background:</i></b> The link between organizing pneumonia (OP) and gastroesophageal reflux disease (GERD) is not well known. There is little evidence in the literature to establish a causal link between GERD and OP. <b><i>Objectives:</i></b> The aim of the study was to assess the hypothesis that OP is more severe when it is associated with GERD and that it leads to more frequent relapses. <b><i>Methods:</i></b> In a retrospective study on 44 patients suffering from OP, we compared the clinical, radiological and histological characteristics of 2 groups, 1 composed of patients with GERD (n = 20) and the other of patients without GERD (n = 24). <b><i>Results:</i></b> The GERD group was distinguished by a higher number of patients with migratory alveolar opacities on chest radiography and thoracic computerized tomography (14/20 vs. 9/24; p = 0.03 and 18/20 vs. 13/24; p = 0.01), greater hypoxemia [60 (42-80) vs. 70 (51-112) mm Hg; p = 0.03], greater bronchoalveolar lavage cellularity [0.255 (0.1-1.8) vs. 0.150 (0.05-0.4) g/l; p = 0.035] and more frequent relapses (14/20 vs. 9/24; p = 0.03). <b><i>Conclusions:</i></b> OP associated with GERD is more severe and results in more frequent relapses. Microinhalation of gastric secretions might induce lung inflammation leading to OP and relapse. We suggest that typical symptoms of GERD such as pyrosis should be investigated in OP.
DOI: 10.6084/m9.figshare.4557814
title: Supplementary Material for: Transcriptional Analysis of Host Responses to Marek's Disease Virus Infection in Chicken Thymus

description: Marek's disease virus (MDV) is a cell-associated alpha-herpesvirus that causes T-cell lymphomas and nervous disorders in chickens. Different from other lymphoid organs, the thymus is the site of T-cell maturation and differentiation. However, the transcriptional response to MDV infection in the chicken thymus is still not known. In this study, we performed genome-wide expression analysis in thymus tissues of RB1B-infected chickens at different time points to investigate the molecular mechanisms of MDV pathogenesis. The number of differentially expressed genes with 2-fold or higher changes (&gt;2) are as follows: 1,250 genes (7 dpi), 834 genes (14 dpi), 1,958 genes (21 dpi), and 2,306 genes (28 dpi). Gene ontology enrichment analysis revealed that the upregulated genes were involved in immune and inflammatory response at 7 dpi; angiogenesis, cytoskeleton organization, cell adhesion, and signal transduction showed different expressions at 21 and 28 dpi. The expression pattern of 18 randomly selected genes was confirmed by real-time RT-PCR. Several differently expressed host genes associated with tumor development are discussed. We identified the global host-gene expression pattern in the thymus of chickens that responded to MDV infection. The present data may provide groundwork for future investigation in the biology and pathogenesis of MDV.
DOI: 10.6084/m9.figshare.4557823
title: Supplementary Material for: Blood Outgrowth Endothelial Cells Reduce Hypoxia-Mediated Fibroblast to Myofibroblast Conversion by Decreasing Proangiogenic Cytokines

description: <b><i>Purpose:</i></b> Hypoxic conditions cause fibroblasts to differentiate into alpha smooth-muscle cell actin (α -SMA)-positive cells, i.e. myofibroblasts. This process is a hallmark of venous neointimal hyperplasia (VNH) associated with hemodialysis vascular access. The purpose of this study was to determine if blood outgrowth endothelial cells (BOEC) may reduce the conversion of fibroblasts into myofibroblasts under hypoxic conditions, and to determine the potential mechanisms involved. <b><i>Methods:</i></b> An experimental model was used, in which fibroblasts and BOEC were subjected to hypoxia under contact and transwell conditions to determine if BOEC reduce the conversion of fibroblasts into myofibroblasts under hypoxic conditions. Gene expression under different conditions was performed. In addition, functional assays including cell proliferation and migration were determined. <b><i>Results:</i></b> This study demonstrates that contact needs to occur between BOEC and fibroblasts for the reduction of the hypoxia-driven conversion of fibroblasts into α-SMA. This is associated with a decrease in several proangiogenic genes including vascular endothelial growth factor A, platelet-derived growth factor, fibroblast growth factor and matrix metalloproteinase 2 in fibroblasts in contact with BOEC when compared to fibroblasts alone. In addition, migration is significantly reduced while proliferation remains unchanged. <b><i>Conclusion:</i></b> This study helps provide rationale for using BOEC delivered to the adventitia of the outflow vein of hemodialysis vascular access to reduce VNH.
DOI: 10.6084/m9.figshare.4557913.v1
title: Supplementary Material for: Liver Disease and Other Comorbidities in Wolcott-Rallison Syndrome: Different Phenotype and Variable Associations in a Large Cohort

description: <b><i>Background:</i></b> Wolcott-Rallison syndrome (WRS) is caused by recessive <i>EIF2AK3</i> mutations and characterized by early-onset diabetes and skeletal dysplasia. Hepatic dysfunction has been reported in 60% of patients. <b><i>Aims:</i></b> To describe a cohort of WRS patients and discuss the pattern and management of their liver disease. <b><i>Methods:</i></b> Detailed phenotyping and direct sequencing of <i>EIF2AK3</i> gene were conducted in all patients. <b><i>Results:</i></b> Twenty-eight genetically confirmed patients (67% male; mean age 4.6 years) were identified. 17 different <i>EIF2AK3</i> mutations were detected, of which 2 were novel. The p.S991N mutation was associated with prolonged survival and p.I650T with delayed onset. All patients presented before 25 months with diabetes with variation in the frequency and severity of 10 other features. Liver disease, first manifested as non-autoimmune hepatitis, was the commonest extra-pancreatic feature identified in 85.7% (24/28). 22/24 had at least one episode of acute hepatic failure which was the cause of death in all deceased patients (13/28). One child was treated by liver transplantation and had no liver disease and better diabetes control for the following 6 years. <b><i>Conclusions:</i></b> Liver disease in WRS is more frequent than previously described and carries high mortality. The first experience with liver transplantation in WRS is encouraging.
DOI: 10.6084/m9.figshare.4557808
title: Inspiratory muscle training is effective to reduce postoperative pulmonary complications and length of hospital stay: a systematic review and meta-analysis

description: <b>Purpose:</b> This study systematically review and meta-analyse the effectiveness of inspiratory muscle training (IMT) to reduce postoperative pulmonary complications (PPC) and length of hospital stay (LOS), both in the preoperative and/or postoperative periods of cardiac, pulmonary, and abdominal surgical patients. Sensitive analysis was performed to examine which patients benefit more from IMT according to methodological features (quality of studies and sample size), patient’s characteristics (pulmonary risk stratification, age, and body mass index), type of surgery, period of training, and training protocols (training doses and level of supervision). <b>Methods:</b> The literature search was made in the electronic databases PubMed®, EBSCO, Web of Science<sup>®</sup>, PEDro and Scopus<sup>®</sup>. Only randomized controlled trials were included. Data extraction, quality assessment and meta-analysis were performed. <b>Results:</b> We included 17 randomized controlled trials in the systematic review, of which, 12 were included for the PPC meta-analysis and 11 for the LOS meta-analysis. IMT significantly reduced the risk of PPC (Risk Ratio (RR) = 0.50, 95%CI: 0.39, 0.64, <i>I<sup>2 </sup></i>=<i><sup> </sup></i>0.0%), and a decrease in LOS (Mean Difference = −1.41, 95%CI: −2.07, −0.75, <i>I</i><sup>2</sup> = 0.0%). <b>Conclusion:</b> IMT is effective to reduce PPC and LOS in patients undergoing surgery.Implications for RehabilitationPhysiotherapy interventions with inspiratory muscle training (IMT) are effective to reduce postoperative pulmonary complications (PPC) and length of hospital stay (LOS) after major surgery, and should start preoperatively.Rehabilitation with IMT is beneficial at all ages and risk levels, but older and high-risk patients benefit more, as well as pulmonary surgery patients.IMT is more effective if it is supervised, and prescription target at least two-week period, sessions with more than 15 minutes, with imposed load increment, and adding other exercise modes. Physiotherapy interventions with inspiratory muscle training (IMT) are effective to reduce postoperative pulmonary complications (PPC) and length of hospital stay (LOS) after major surgery, and should start preoperatively. Rehabilitation with IMT is beneficial at all ages and risk levels, but older and high-risk patients benefit more, as well as pulmonary surgery patients. IMT is more effective if it is supervised, and prescription target at least two-week period, sessions with more than 15 minutes, with imposed load increment, and adding other exercise modes.