scholarly journals Rapid identification of pathogens associated with ventilator-associated pneumonia by Nanopore sequencing

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Nan Wu ◽  
Piyush Ranjan ◽  
Changyu Tao ◽  
Chao Liu ◽  
Ence Yang ◽  
...  
Keyword(s):  
Data Analysis ◽  
Bacterial Genome ◽  
Pcr Amplification ◽  
Rapid Identification ◽  
Ventilator Associated Pneumonia ◽  
Metagenomic Sequencing ◽  
Nanopore Sequencing ◽  
Average Sensitivity ◽  
Amplification Method ◽  
Significant Difference

Abstract Background Aetiology detection is crucial in the diagnosis and treatment of ventilator-associated pneumonia (VAP). However, the detection method needs improvement. In this study, we used Nanopore sequencing to build a quick detection protocol and compared the efficiency of different methods for detecting 7 VAP pathogens. Methods The endotracheal aspirate (ETA) of 83 patients with suspected VAP from Peking University Third Hospital (PUTH) was collected, saponins were used to deplete host genomes, and PCR- or non-PCR-amplified library construction methods were used and compared. Sequence was performed with MinION equipment and local data analysis methods were used for sequencing and data analysis. Results Saponin depletion effectively removed 11 of 12 human genomes, while most pathogenic bacterial genome results showed no significant difference except for S. pneumoniae. Moreover, the average sequence time decreased from 19.6 h to 3.62 h. The non-PCR amplification method and PCR amplification method for library build has a similar average sensitivity (85.8% vs. 86.35%), but the non-PCR amplification method has a better average specificity (100% VS 91.15%), and required less time. The whole method takes 5–6 h from ETA extraction to pathogen classification. After analysing the 7 pathogens enrolled in our study, the average sensitivity of metagenomic sequencing was approximately 2.4 times higher than that of clinical culture (89.15% vs. 37.77%), and the average specificity was 98.8%. Conclusions Using saponins to remove the human genome and a non-PCR amplification method to build libraries can be used for the identification of pathogens in the ETA of VAP patients within 6 h by MinION, which provides a new approach for the rapid identification of pathogens in clinical departments.

scholarly journals Rapid Identification of Pathogens Associated With Ventilator-Associated Pneumonia By Nanopore Sequencing

2021 ◽  
Author(s):  
Nan Wu ◽  
Piyush Ranjan ◽  
Changyu Tao ◽  
Chao Liu ◽  
Ence Yang ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Rapid Identification ◽  
Construction Method ◽  
Ventilator Associated Pneumonia ◽  
Metagenomic Sequencing ◽  
Average Sensitivity ◽  
Local Data ◽  
Library Construction ◽  
Peking University ◽  
Pcr Method

Abstract BACKGROUND: Etiology detection is crucial in diagnose and treatment of ventilator associated pneumonia (VAP). However, the detection method is in need of improvement. In this study, we used Nanopore sequence to build a quick detection protocol and compared the efficiency of different methods on 7 common VAP pathogens.METHODS: Endotracheal aspirate (ETA) of 83 patients with suspected VAP from Peking University Third Hospital were collected, saponin were used to deplete host genomes, and PCR or non-PCR library construction method were used and compared for sequencing. MinION and local data analysis methods were used for sequencing and data analysis.RESULTS: Saponin depletion effectively removed 11 of 12 human genomes, while most pathogenic bacteria genome results showed no statistical difference except for S.pneumoniae who had a 0.31 times depletion. Meanwhile, the average sequence time reduced from 19.2hrs to 1.73hrs. Compared with PCR library construction method, the non-PCR method has a better average sensitivity (84.17% VS 81.35%) and specificity (97.42% VS 88.52%), while the non-PCR costs less time. The whole method takes 5-6hrs from ETA extraction to pathogen classification. After analyzed the 7 pathogens enrolled, the average sensitivity of metagenomic sequencing were about 2.4 times higher than that of clinical culture (91.79%VS 37.92%), and the average specificity was 98.08%.CONCLUSIONS: Using saponin to remove human genome and non-PCR method to build library can be used for identification of pathogens in ETA of VAP patients within 6 hours by MinION, which provides a new approach for rapid identification of pathogens in clinical departments.

EFEKTIVITAS STRATEGI CLOZE STORY MAPPING TERHADAP KEMAMPUAN MEMBACA PEMAHAMAN PADA SISWA KELAS V DI SD 2 PADOKAN KASIHAN BANTUL

2018 ◽  
Vol 5 (1) ◽  
Author(s):  
Danuri Danuri ◽  
Dwendha Lahitani
Keyword(s):  
Data Analysis ◽  
Learning Strategy ◽  
T Test ◽  
Effective Learning ◽  
Average Value ◽  
Story Mapping ◽  
Analysis Technique ◽  
Significant Difference ◽  
Quasi Experimental ◽  
Class Average

This study aims to determine the effectiveness of CSM strategies on comprehension reading skills in classes V Padokan 2 Elementary School. The research method used is a quasi-experimental method. In this study the subjects of the study were VA class students as the control class and V C as the experimental class with 28 VA and VC class students. Quantitative data analysis technique used is the calculation of independent sample t-test. Based on data analysis and discussion, researchers can conclude that CSM strategies are more effective than conventional methods of reading comprehension learning. The results of this study indicate that there is a significant difference between the experimental class and the control class as evidenced by the results of the independent sample t-test obtained by the value of Asymp. Sig (2-Tailed) 0.014 <0.05. CSM strategy is an effective learning strategy seen from the average value of the experimental class posstest which is 81.61 higher than the control class average value of 72.96.

Household and Population-Level Behavioural Changes Due to COVID-19 Pandemic: A Smart Thermostat Based Comparative Data Analysis

2021 ◽  
Vol 10 (1) ◽  
pp. 1-6
Author(s):  
Kirti Sundar Sahu ◽  
Arlene Oetomo ◽  
Niloofar Jalali ◽  
Plinio P. Morita
Keyword(s):  
Data Analysis ◽  
Population Level ◽  
World Health ◽  
Motion Sensors ◽  
Household Level ◽  
Work From Home ◽  
Significant Difference ◽  
Health Organization ◽  
Smart Thermostat ◽  
The Impact

The World Health Organization declared the coronavirus outbreak as a pandemic on March 11, 2020. To inhibit the spread of COVID-19, governments around the globe, including Canada, have implemented physical distancing and lockdown measures, including a work-from-home policy. Canada in 2020 has developed a 24-Hour Movement Guideline for all ages laying guidance on the ideal amount of physical activity, sedentary behaviour, and sleep (PASS) for an individual in a day. The purpose of this study was to investigate changes on the household and population-level in lifestyle behaviours (PASS) and time spent indoors at the household level, following the implementation of physical distancing protocols and stay-at-home guidelines. For this study, we used 2019 and 2020 data from ecobee, a Canadian smart Wi-Fi thermostat company, through the Donate Your Data (DYD) program. Using motion sensors data, we quantified the amount of sleep by using the absence of movement, and similarly, increased sensor activation to show a longer duration of household occupancy. The key findings of this study were; during the COVID-19 pandemic, overall household-level activity increased significantly compared to pre-pandemic times, there was no significant difference between household-level behaviours between weekdays and weekends during the pandemic, average sleep duration has not changed, but the pattern of sleep behaviour significantly changed, specifically, bedtime and wake up time delayed, indoor time spent has been increased and outdoor time significantly reduced. Our data analysis shows the feasibility of using big data to monitor the impact of the COVID-19 pandemic on the household and population-level behaviours and patterns of change.

scholarly journals Diversity of Epibionts Associated with Lepidochelys olivacea (Eschscholtz 1829) Sea Turtles Nesting in the Mexican South Pacific

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1734
Author(s):  
Brenda Sarahí Ramos-Rivera ◽  
Himmer Castro-Mondragon ◽  
José Gabriel Kuk-Dzul ◽  
Pedro Flores-Rodríguez ◽  
Rafael Flores-Garza
Keyword(s):  
Data Analysis ◽  
Sea Turtles ◽  
South Pacific ◽  
First Record ◽  
Abundant Species ◽  
Interspecific Relationships ◽  
Lepidochelys Olivacea ◽  
Significant Difference ◽  
The Relationship ◽  
Head Neck

The present study contributes to the knowledge of epibionts recorded on sea turtles that nested on a beach in the South Pacific of Mexico. A total of 125 Lepidochelys olivacea turtles nested on Llano Real beach, Guerrero, Mexico, were examined. We collected 450 conspicuous organisms from 8 species from 43 turtles. The corresponding data analysis was carried out to obtain the relative abundance, the relationship between turtle sizes and the presence of organisms, the similarity of species between the sampling months, and the interspecific relationships between the epibionts and the turtles observed. Chelonibia testudinaria was the most abundant species, while Remora remora was the least abundant species. The turtles were divided into six body sections, with the greatest abundance of these organisms located in the head–neck section of turtles, and there was a significant difference in the size of the turtles that presented epibionts and those that did not. C. testudinaria showed greater similarity between sampling months, and the interspecific relationships recorded were commensalism, parasitism, amensalism, and protocooperation. This research contributes the first record of epibionts in L. olivacea nesting in Guerrero, Mexico.

scholarly journals SCAPP: an algorithm for improved plasmid assembly in metagenomes

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
David Pellow ◽  
Alvah Zorea ◽  
Maraike Probst ◽  
Ori Furman ◽  
Arik Segal ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Bacterial Genome ◽  
Biological Knowledge ◽  
Assessment Procedure ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Human Gut ◽  
Double Stranded Dna ◽  
Wide Range ◽  
Python Package

Abstract Background Metagenomic sequencing has led to the identification and assembly of many new bacterial genome sequences. These bacteria often contain plasmids: usually small, circular double-stranded DNA molecules that may transfer across bacterial species and confer antibiotic resistance. These plasmids are generally less studied and understood than their bacterial hosts. Part of the reason for this is insufficient computational tools enabling the analysis of plasmids in metagenomic samples. Results We developed SCAPP (Sequence Contents-Aware Plasmid Peeler)—an algorithm and tool to assemble plasmid sequences from metagenomic sequencing. SCAPP builds on some key ideas from the Recycler algorithm while improving plasmid assemblies by integrating biological knowledge about plasmids. We compared the performance of SCAPP to Recycler and metaplasmidSPAdes on simulated metagenomes, real human gut microbiome samples, and a human gut plasmidome dataset that we generated. We also created plasmidome and metagenome data from the same cow rumen sample and used the parallel sequencing data to create a novel assessment procedure. Overall, SCAPP outperformed Recycler and metaplasmidSPAdes across this wide range of datasets. Conclusions SCAPP is an easy to use Python package that enables the assembly of full plasmid sequences from metagenomic samples. It outperformed existing metagenomic plasmid assemblers in most cases and assembled novel and clinically relevant plasmids in samples we generated such as a human gut plasmidome. SCAPP is open-source software available from: https://github.com/Shamir-Lab/SCAPP.

Multiphase Transient Slugging Flow in Subsea Oil and Gas Production

2016 ◽  
Author(s):  
Zhenhua Zhang ◽  
Longbin Tao
Keyword(s):  
Data Analysis ◽  
Temperature Distribution ◽  
Numerical Model ◽  
Slug Flow ◽  
Field Data ◽  
Oil And Gas ◽  
Gas Production ◽  
Worst Case ◽  
Oil And Gas Production ◽  
Significant Difference

Slug flow in horizontal pipelines and riser systems in deep sea has been proved as one of the challenging flow assurance issues. Large and fluctuating gas/liquid rates can severely reduce production and, in the worst case, shut down, depressurization or damage topside equipment, such as separator, vessels and compressors. Previous studies are primarily based on experimental investigations of fluid properties with air/water as working media in considerably scaled down model pipes, and the results cannot be simply extrapolated to full scale due to the significant difference in Reynolds number and other fluid conditions. In this paper, the focus is on utilizing practical shape of pipe, working conditions and fluid data for simulation and data analysis. The study aims to investigate the transient multiphase slug flow in subsea oil and gas production based on the field data, using numerical model developed by simulator OLGA and data analysis. As the first step, cases with field data have been modelled using OLGA and validated by comparing with the results obtained using PIPESYS in steady state analysis. Then, a numerical model to predict slugging flow characteristics under transient state in pipeline and riser system was set up using multiphase flow simulator OLGA. One of the highlights of the present study is the new transient model developed by OLGA with an added capacity of newly developed thermal model programmed with MATLAB in order to represent the large variable temperature distribution of the riser in deep water condition. The slug characteristics in pipelines and temperature distribution of riser are analyzed under the different temperature gradients along the water depth. Finally, the depressurization during a shut-down and then restart procedure considering hydrate formation checking is simulated. Furthermore, slug length, pressure drop and liquid hold up in the riser are predicted under the realistic field development scenarios.

Abstract 11119: Real-Time Nanopore Sequencing for Bacterial Pneumonia After Out-of-Hospital Cardiac Arrest, a Pilot Proof-of-Concept Study

Circulation ◽  
2021 ◽  
Vol 144 (Suppl_2) ◽  
Author(s):  
Alexandra Weissman ◽  
Mariam Bramah Lawani ◽  
Thomas Rohan ◽  
Clifton W CALLAWAY
Keyword(s):  
Patient Care ◽  
Pathogen Detection ◽  
Bacterial Pathogen ◽  
Improve Patient Care ◽  
Antibiotic Administration ◽  
Nanopore Sequencing ◽  
Proof Of Concept ◽  
Chi Square ◽  
Significant Difference ◽  
Improve Patient

Introduction: Pneumonia is common after OHCA but is difficult to diagnose in the first 72 hours following ROSC, this results in early untargeted antibiotic administration based on non-specific imaging and laboratory findings. Antibiotic resistance is rising, is influenced by untargeted antibiotic administration, and can increase patient morbidity and mortality as well as healthcare costs. Precision methods of bacterial pathogen detection in OHCA patients are needed to improve patient care. This proof-of-concept pilot study aimed to assess feasibility of bacterial pathogen sequencing and comparability of sequencing results to clinical culture after OHCA. Methods: Blood and bronchoalveolar lavage (BAL) were obtained from residual clinical specimens collected within 12 hours of ROSC. Bacterial DNA was extracted using the Qiagen PowerLyzer PowerSoil DNA kit, sequenced using the MinION nanopore sequencer, and analyzed with Oxford Nanopore Technologies’ EPI2ME bioinformatics software. Sequencing results were compared to culture results using McNemar’s chi-square statistic. Study-defined pneumonia was based on presence of at least two characteristics within 72 hours of ROSC: fever (temperature ≥38°C); persistent leukocytosis >15,000 or leukopenia <3,500 for 48 hours; persistent chest radiography infiltrates for 48 hours per clinical radiology read; bacterial pathogen cultured. Results: We enrolled 38 consecutive OHCA subjects: mean age 61.8 years (18.0); 16 (42%) female; 25 (66%) White, 7 (18%) Black, 6 (16%) “Other” race; 7 subjects (18%) survived and 31 (82%) died; 16 (42%) subjects had pneumonia. Sequencing results were available in 12 hours while culture results were available in 48-72 hours after collection. There was a non-significant difference in the proportion of the same pathogens identified for each method per McNemar’s chi-square: p = 0.38, difference of 0.095 (-0.095, 0.286). Conclusions: Nanopore sequencing detects pathogenic bacteria comparable to clinical microbiologic culture and in less time. This technology can produce a paradigm shift in early bacterial pathogen detection in OHCA survivors, which can improve patient care. The technology is applicable to other patient populations and for viral and fungal pathogens.

A Cross-Sectional Study to Compare Differences on Clinical and Laboratory Findings in Children with Seropositive and Seronegative Lupus

2021 ◽  
Author(s):  
Shima Salehi ◽  
Rozita Hosseini Shamsabadi ◽  
Hassan Otukesh ◽  
Reza Shiari ◽  
Monir Sharafi
Keyword(s):  
Autoimmune Disease ◽  
Disease Diagnosis ◽  
Cross Sectional Study ◽  
Rapid Identification ◽  
The Body ◽  
Musculoskeletal Symptoms ◽  
Laboratory Findings ◽  
Cross Sectional ◽  
Significant Difference ◽  
History Of

Abstract Background: Lupus is an inflammatory and autoimmune disease that involves various tissues and organs of the body. Identification of diagnostic elements to rapid identification of seronegative lupus cases is very important in order to prevent morbidity and progression of disease. This study aimed to compare clinical and laboratory findings of seropositive cases with seronegative lupus patients. Methods: This cross-sectional analytic study was performed on 43 children (17 seronegative and 26 seropositive) with lupus who were admitted to Ali Asghar Hospital during 2007-2017. Seropositive patients had anti-nuclear antibody (ANA) titration >1/80, while seronegative patients had ANA titration <1/80 (at the time of disease diagnosis). Clinical and laboratory findings were compared between two groups.Results: Serositis in patients with ANA- was significantly higher than ANA+ (41.17% vs. 23.07%; p = 0.042). ANA- group had higher autoimmune disease history than ANA+ group (42.85% vs. 15.0%; p = 0.041). The family history of the disease in the ANA- group was greater than ANA+ group (50% vs. 23.52%). The percentage of hypertensive patients in ANA- group was higher than ANA+ group (52.94% vs. 26.92%; p = 0.037). Neurologic symptoms in ANA+ and ANA- groups were 38.46% and 17.64%, respectively (p = 0.043). The frequency of patients with thrombocytopenia in ANA+ group was significantly greater than ANA- group (32% vs. 12.5%; p=0.041). There was no significant difference in other clinical and laboratory findings between two groups. Conclusion: Seronegative lupus patients had higher percentage of musculoskeletal symptoms, autoimmune disease history, familial history of disease, and hypertension, while neurological and thrombocytopenia symptoms were higher in seropositive patients compared to seronegative cases. Therefore, evaluation of these factors can be helpful to diagnosis of seronegative patients.

A modified direct PCR amplification method using the GlobalFiler™ PCR Amplification Kit on bloodstains collected using microFLOQ™ direct swabs

2019 ◽  
Vol 7 (1) ◽  
pp. 30-32
Author(s):  
Yongxun Wong ◽  
Boon Kiat Ng ◽  
Kevin Wai Yin Chong ◽  
Wei Siong Holden Lim ◽  
Afiqah Razanah Rosli ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
Direct Pcr ◽  
Amplification Method

scholarly journals Screening of epileptic seizures in children and adolescents with hydrocephalus and ventriculoperitoneal shunt

2009 ◽  
Vol 15 (3) ◽  
pp. 106-109 ◽  
Author(s):  
Raimundo Francisco de Amorim Júnior ◽  
Suerda Emiliana Cavalcanti Dantas ◽  
Rodrigo de Holanda Mendonça ◽  
Abdiel de Lira Rolim ◽  
Maria Luiza de Carvalho Jales ◽  
...  
Keyword(s):  
Retrospective Study ◽  
Data Analysis ◽  
Prospective Study ◽  
Children And Adolescents ◽  
Ventriculoperitoneal Shunt ◽  
Epileptic Seizures ◽  
Significant Difference ◽  
A Prospective Study ◽  
Larger Sample ◽  
Diagnosis Age

OBJECTIVES: To assess the occurrence of epileptic seizures (ES) in children and adolescents with hydrocephalus and their relationship with ventriculoperitoneal shunt (VPS) treatment. METHODS: Retrospective study of 45 patients from both genders, aged 0 to 18 years, with hydrocephalus and presenting with ES or not. The following variables were analyzed: gender, hydrocephalus etiology, age at diagnosis, age at initial VPS treatment, age at first ES and types of ES. RESULTS: Data analysis showed the following: 20 (44.4%) presented with ES, 13 (65%) of the girls and seven (35%) of the boys. There was a predominance of ES in the girls, but with no statistically significant difference. In total, 13 (65%) patients used VPS. Of the 13 patients with VPS and ES, it was observed that the onset of ES was after VPS in 10 (76.9%) individuals, whereas it occurred before VPS in two (15.4%). CONCLUSIONS: The results showed no association between VPS treatment and ES (ρ=0.832); however, most of the patients presented with their first ES episode after VPS, suggesting a possible relationship between this treatment and the occurrence of ES. A larger sample and a prospective study might answer this question.

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