scholarly journals Mycobiome analysis in fungal Infected formalin-fixed and paraffin-embedded tissues for identification of pathogenic fungi: A pilot study

2020 ◽  
Author(s):  
Taebum Lee ◽  
Hee Young Na ◽  
Kyoung-Mee Kim ◽  
Hey Seung Lee ◽  
Sung-Hye Park ◽  
...  
Keyword(s):  
Pilot Study ◽  
Pathogenic Fungi ◽  
Sequencing Method ◽  
Fungal Organisms ◽  
Ffpe Tissues ◽  
Ncbi Refseq ◽  
Fungal Dna ◽  
Multiplex Sequencing ◽  
Formalin Fixed

ABSTRACTBackgroundFungal organisms are frequently observed in surgical pathological diagnosis. In order to more accurately identify fungi in formalin-fixed and paraffin-embedded (FFPE) tissues, it is necessary to use genomic information. The purpose of our pilot study is to identify the factors to be considered for the identification of pathogenic fungi using mycobiome analysis in FFPE tissues.MethodsWe selected 49 cases in five hospitals. In each case, FFPE tissue was cut into 50 µm and DNA was extracted. Multiplex PCR with four primers (ITS1, ITS2, ITS3 and ITS4) was performed. Multiplex sequencing was performed using MinION device according to the manufacturer’s protocol. Sequences of each case were searched using BLASTN with an ITS database from NCBI RefSeq Targeted Loci Project with default parameter.ResultsA total of 2,526 DNA nucleotides were sequenced. We were able to identify 342 fungal nucleotides in 24 (49.0%, 24/49) cases. The median value of the detected fungal DNA per case was 3 (1Q: 1 and 3Q: 14.25). The 215 (62.87%) fungal DNA contained the entire region of ITS1 or ITS2. The remaining 127 fungal DNAs were identified as fungi using partial sequence of ITS1, ITS2, 5.8S, LSU or SSU.ConclusionIn conclusion, we have identified the possibility of finding pathogenic fungi through mycobiome analysis in fungal infected FFPE tissues using nanopore sequencing method. However, we have also found several limitations to be solved for further studies. If we develop a method to characterize pathogenic fungi in FFPE tissues in a follow-up study, we think it will help patients to use appropriate antifungal agents.

scholarly journals Mycobiome analysis in fungal infected formalin-fixed and paraffin-embedded tissues for identification of pathogenic fungi: a pilot study

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 758
Author(s):  
Taebum Lee ◽  
Hee Young Na ◽  
Sun-ju Byeon ◽  
Kyoung-Mee Kim ◽  
Hey Seung Lee ◽  
...  
Keyword(s):  
Pilot Study ◽  
Dna Sequences ◽  
Pathogenic Fungi ◽  
Median Number ◽  
Fungal Organisms ◽  
Ffpe Tissues ◽  
Ncbi Refseq ◽  
Fungal Dna ◽  
Multiplex Sequencing ◽  
Formalin Fixed

Background: Fungal organisms are frequently observed in surgical pathological diagnosis. In order to more accurately identify fungi in formalin-fixed and paraffin-embedded (FFPE) tissues, it is necessary to use genomic information. The purpose of our pilot study is to identify the factors to be considered for the identification of pathogenic fungi using mycobiome analysis in FFPE tissues. Methods: We selected 49 cases in five hospitals. In each case, FFPE tissue was cut into 50 µm and DNA was extracted. Multiplex PCR with four primers (ITS1, ITS2, ITS3 and ITS4) was performed. Multiplex sequencing was performed using a MinION device according to the manufacturer’s protocol. Sequences of each case were searched using BLASTN with an ITS database from NCBI RefSeq Targeted Loci Project with default parameters. Results: A total of 2,526 DNA sequences were sequenced. We were able to identify 342 fungal sequences in 24 (49.0%, 24/49) cases. The median number of detected fungal sequences per case was 3 (1Q: 1 and 3Q: 14.25). Of the fungal DNA sequences, 215 (62.87%) contained the entire region of ITS1 or ITS2. The remaining 127 fungal DNA sequences were identified as fungi using a partial sequence of ITS1, ITS2, 5.8S, LSU or SSU. Conclusion: In conclusion, we have identified the possibility of finding pathogenic fungi through mycobiome analysis in fungal infected FFPE tissues using nanopore sequencing. However, we have also found several limitations to be solved for further studies. If we develop a method to characterize pathogenic fungi in FFPE tissues in a follow-up study, we think it will help patients to use appropriate antifungal agents.

scholarly journals Molecular identification of pathogenic fungi in formalin-fixed and paraffin-embedded tissues

2020 ◽  
Author(s):  
Joseph Jillwin ◽  
Shivaprakash M. Rudramurthy ◽  
Shreya Singh ◽  
Amanjit Bal ◽  
Ashim Das ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Molecular Identification ◽  
Nested Pcr ◽  
18S Rdna ◽  
Test Accuracy ◽  
Fungal Identification ◽  
Ffpe Tissues ◽  
Fungal Dna ◽  
Pcr Targeting ◽  
Formalin Fixed

Introduction. Histopathological examination (HPE) of tissue helps in the diagnosis of invasive fungal infections (IFIs) but cannot identify the fungus to the genus/species level Gap Statement Available protocols for the molecular identification of fungi from formalin-fixed and paraffin-embedded (FFPE) tissues have limitations in terms of extraction and target selection, and standardisation. Aim. Development of sequence-based fungal identification protocol after extraction of DNA from formalin-fixed and paraffin-embedded (FFPE) tissues. Methodology. A total of 63 FFPE tissues from histopathology proven IFI cases were used to standardize the DNA extraction (commercial QIAamp kit-based extraction and conventional phenol-chloroform-isoamyl alcohol [PCI] method) and sequence-based fungal identification protocols. The PCR targeted different ribosomal DNA (rDNA) regions including complete internal transcribed spacer (ITS1-5.8S-ITS2), separate ITS1 and ITS2, 18S and D1/D2 of 28S regions. Semi-nested PCR targeting Mucorales-specific 18S rDNA region was performed in tissues having aseptate hyphae. The optimized ITS1-PCR protocol was evaluated in 119 FFPE tissues containing septate hyphae or yeast, and Mucorales-specific semi-nested PCR in 126 FFPE tissues containing aseptate hyphae. Results. The DNA yield by conventional PCI method was significantly higher (P<0.0001) than commercial kit, though the quality of DNA was similar by both protocols. The test accuracy was best while using ITS1 (61.9 %) as the target compared to 7.9, 29.9 and 22.2 % on targeting ITS1-5.8S-ITS2, ITS2, the D1/D2 region of 28S, respectively. The test accuracies of ITS1-PCR in tissues containing septate hyphae, aseptate hyphae and yeasts were 75.5, 18.7 and 100 %, respectively. The amplification (targeting ITS1 region) improved by increasing the thickness of tissue section (up to 50 µm) used for DNA extraction. ITS1-PCR protocol could amplify fungal DNA in 76 (63.8 %) tissues and Mucorales-specific semi-nested PCR in 86 (68.3 %) tissues. Conclusion. Conventional PCI-based DNA extraction from thick tissue (50 µm) may be used until optimal commercial fungal DNA extraction kit is developed. Subsequent ITS1-PCR for septate fungi and yeast, and semi-nested PCR targeting 18S rDNA for Mucorales are recommended to identify the fungus in FFPE tissues.

A Pilot Study of Mobile Telephone Message Interventions with Suicide Attempters in China

Crisis ◽  
2010 ◽  
Vol 31 (2) ◽  
pp. 109-112 ◽  
Author(s):  
Hui Chen ◽  
Brian L. Mishara ◽  
Xiao Xian Liu
Keyword(s):  
Pilot Study ◽  
Effective Means ◽  
Text Message ◽  
Text Messages ◽  
Mobile Telephone ◽  
Future Research ◽  
Quick Method ◽  
Suicide Attempters ◽  
To Receive

Background: In China, where follow-up with hospitalized attempters is generally lacking, there is a great need for inexpensive and effective means of maintaining contact and decreasing recidivism. Aims: Our objective was to test whether mobile telephone message contacts after discharge would be feasible and acceptable to suicide attempters in China. Methods: Fifteen participants were recruited from suicide attempters seen in the Emergency Department in Wuhan, China, to participate in a pilot study to receive mobile telephone messages after discharge. All participants have access to a mobile telephone, and there is no charge for the user to receive text messages. Results: Most participants (12) considered the text message contacts an acceptable and useful form of help and would like to continue to receive them for a longer period of time. Conclusions: This suggests that, as a low-cost and quick method of intervention in areas where more intensive follow-up is not practical or available, telephone messages contacts are accessible, feasible, and acceptable to suicide attempters. We hope that this will inspire future research on regular and long-term message interventions to prevent recidivism in suicide attempters.

Prognostic significance of C1–C2 facet malalignment after surgical decompression in adult Chiari malformation type I: a pilot study based on the Chicago Chiari Outcome Scale

2020 ◽  
pp. 1-7
Author(s):  
Michael Lumintang Loe ◽  
Tito Vivas-Buitrago ◽  
Ricardo A. Domingo ◽  
Johan Heemskerk ◽  
Shashwat Tripathi ◽  
...  
Keyword(s):  
Pilot Study ◽  
Chiari Malformation ◽  
Prognostic Significance ◽  
Foramen Magnum ◽  
Bivariate Analysis ◽  
Type I ◽  
Foramen Magnum Decompression ◽  
Swallowing Function ◽  
Chiari Malformation Type I

OBJECTIVEThe authors assessed the prognostic significance of various clinical and radiographic characteristics, including C1–C2 facet malalignment, in terms of surgical outcomes after foramen magnum decompression of adult Chiari malformation type I.METHODSThe electronic medical records of 273 symptomatic patients with Chiari malformation type I who were treated with foramen magnum decompression, C1 laminectomy, and duraplasty at Mayo Clinic were retrospectively reviewed. Preoperative and postoperative Neurological Scoring System scores were compared using the Friedman test. Bivariate analysis was conducted to identify the preoperative variables that correlated with the patient Chicago Chiari Outcome Scale (CCOS) scores. Multiple linear regression analysis was subsequently performed using the variables with p < 0.05 on the bivariate analysis to check for independent associations with the outcome measures. Statistical software SPSS version 25.0 was used for the data analysis. Significance was defined as p < 0.05 for all analyses.RESULTSFifty-two adult patients with preoperative clinical and radiological data and a minimum follow-up of 12 months were included. Motor deficits, syrinx, and C1–C2 facet malalignment were found to have significant negative associations with the CCOS score at the 1- to 3-month follow-up (p < 0.05), while at the 9- to 12-month follow-up only swallowing function and C1–C2 facet malalignment were significantly associated with the CCOS score (p < 0.05). Multivariate analysis showed that syrinx presence and C1–C2 facet malalignment were independently associated with the CCOS score at the 1- to 3-month follow-up. Swallowing function and C1–C2 facet malalignment were found to be independently associated with the CCOS score at the 9- to 12-month follow-up.CONCLUSIONSThe observed results in this pilot study suggest a significant negative correlation between C1–C2 facet malalignment and clinical outcomes evaluated by the CCOS score at 1–3 months and 9–12 months postoperatively. Prospective studies are needed to further validate the prognostic value of C1–C2 facet malalignment and the potential role of atlantoaxial fixation as part of the treatment.

Short-Term Ultramicronized Palmitoylethanolamide Therapy in Patients with Myasthenia Gravis: a Pilot Study to Possible Future Implications of Treatment

2019 ◽  
Vol 18 (3) ◽  
pp. 232-238 ◽  
Author(s):  
Emanuela Onesti ◽  
Vittorio Frasca ◽  
Marco Ceccanti ◽  
Giorgio Tartaglia ◽  
Maria Cristina Gori ◽  
...  
Keyword(s):  
Pilot Study ◽  
Myasthenia Gravis ◽  
Repetitive Nerve Stimulation ◽  
Beneficial Effects ◽  
Antibody Titers ◽  
The Stability ◽  
Ultramicronized Palmitoylethanolamide ◽  
Open Pilot

Background: The cannabinoid system may be involved in the humoral mechanisms at the neuromuscular junction. Ultramicronized-palmitoylethanolamide (μm-PEA) has recently been shown to reduce the desensitization of Acetylcholine (ACh)-evoked currents in denervated patients modifying the stability of ACh receptor (AChR) function. <p> Objective: To analyze the possible beneficial effects of μm-PEA in patients with myasthenia gravis (MG) on muscular fatigue and neurophysiological changes. <p> Method: The duration of this open pilot study, which included an intra-individual control, was three weeks. Each patient was assigned to a 1-week treatment period with μm-PEA 600 mg twice a day. A neurophysiological examination based on repetitive nerve stimulation (RNS) of the masseteric and the axillary nerves was performed, and the quantitative MG (QMG) score was calculated in 22 MG patients every week in a three-week follow-up period. AChR antibody titer was investigated to analyze a possible immunomodulatory effect of PEA in MG patients. <p> Results: PEA had a significant effect on the QMG score (p=0.03418) and on RNS of the masseteric nerve (p=0.01763), thus indicating that PEA reduces the level of disability and decremental muscle response. Antibody titers did not change significantly after treatment. <p> Conclusion: According to our observations, μm-PEA as an add-on therapy could improve muscular response to fatigue in MG. The possible modulation of AChR currents as a means of eliciting a direct effect from PEA on the conformation of ACh receptors should be investigated. The co-role of cytokines also warrants an analysis. Given the rapidity and reversibility of the response, we suppose that PEA acts directly on AChR, though further studies are needed to confirm this hypothesis.

PO-0814 Developmental Follow Up Of Former Premature Infants: A Pilot Study In Lebanon: Abstract PO-0814 Table 1

2014 ◽  
Vol 99 (Suppl 2) ◽  
pp. A520.2-A520
Author(s):  
L Charafeddine ◽  
R El Hage ◽  
H Tamim ◽  
L Akouri-Dirani ◽  
D Sinno
Keyword(s):  
Pilot Study ◽  
Premature Infants

scholarly journals Utility of routinely collected electronic health records data to support effectiveness evaluations in inflammatory bowel disease: a pilot study of tofacitinib

2021 ◽  
Vol 28 (1) ◽  
pp. e100337
Author(s):  
Vivek Ashok Rudrapatna ◽  
Benjamin Scott Glicksberg ◽  
Atul Janardhan Butte
Keyword(s):  
Inflammatory Bowel Disease ◽  
Pilot Study ◽  
Disease Activity ◽  
Real World ◽  
Bowel Disease ◽  
P Value ◽  
Health Records ◽  
Real World Evidence ◽  
Inflammatory Bowel

ObjectivesElectronic health records (EHR) are receiving growing attention from regulators, biopharmaceuticals and payors as a potential source of real-world evidence. However, their suitability for the study of diseases with complex activity measures is unclear. We sought to evaluate the use of EHR data for estimating treatment effectiveness in inflammatory bowel disease (IBD), using tofacitinib as a use case.MethodsRecords from the University of California, San Francisco (6/2012 to 4/2019) were queried to identify tofacitinib-treated IBD patients. Disease activity variables at baseline and follow-up were manually abstracted according to a preregistered protocol. The proportion of patients meeting the endpoints of recent randomised trials in ulcerative colitis (UC) and Crohn’s disease (CD) was assessed.Results86 patients initiated tofacitinib. Baseline characteristics of the real-world and trial cohorts were similar, except for universal failure of tumour necrosis factor inhibitors in the former. 54% (UC) and 62% (CD) of patients had complete capture of disease activity at baseline (month −6 to 0), while only 32% (UC) and 69% (CD) of patients had complete follow-up data (month 2 to 8). Using data imputation, we estimated the proportion achieving the trial primary endpoints as being similar to the published estimates for both UC (16%, p value=0.5) and CD (38%, p-value=0.8).Discussion/ConclusionThis pilot study reproduced trial-based estimates of tofacitinib efficacy despite its use in a different cohort but revealed substantial missingness in routinely collected data. Future work is needed to strengthen EHR data and enable real-world evidence in complex diseases like IBD.

Does transcranial direct current stimulation affect selective visual attention in children with left-sided infantile hemiplegia? A randomized, controlled pilot study

2020 ◽  
pp. 1-13
Author(s):  
Raed A. Alharbi ◽  
Saleh A. Aloyuni ◽  
Faizan Kashoo ◽  
Mohamed I. Waly ◽  
Harpreet Singh ◽  
...  
Keyword(s):  
Pilot Study ◽  
Direct Current ◽  
Transcranial Direct Current Stimulation ◽  
Repeated Measures ◽  
Sham Group ◽  
Time Points ◽  
Selective Visual Attention ◽  
Subject Factor ◽  
And Control

Abstract Objective: Infantile hemiplegia due to brain injury is associated with poor attention span, which critically affects the learning and acquisition of new skills, especially among children with left-sided infantile hemiplegia (LSIH). This study aimed to improve the selective visual attention (SVA) of children with LSIH through transcranial direct current stimulation (tDCS). Methods: A total of 15 children participated in this randomized, double-blinded, pilot study; of them, 10 experienced LSIH, and the remaining 5 were healthy age-matched controls. All the children performed the Computerized Stroop Color-Word Test (CSCWT) at baseline, during the 5th and 10th treatment sessions, and at follow-up. The experimental (n = 5) and control groups (n = 5) received tDCS, while the sham group (n = 5) received placebo tDCS. All three groups received cognitive training on alternate days, for 3 weeks, with the aim to improve SVA. Results: Two-way repeated measures analysis of variance (ANOVA) showed a statistically significant change in the mean scores of CSCWT between time points (baseline, 5th and 10th sessions, and follow-up) within-subject factor, group (experimental, sham) between-subject factor and interaction (time points X group) (p < 0.005). Furthermore, a one-way repeated measures ANOVA showed significant differences between time point (p < 0.005) for the experimental and control group but not the sham group. Conclusion: These pilot results suggest that future research should be conducted with adequate samples to enable conclusions to be drawn.

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