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Deep Learning Technology: Sebastian Arnold, Betty van Aken, Paul Grundmann, Felix A. Gers and Alexander Löser. Learning Contextualized Document Representations for Healthcare Answer Retrieval. The Web Conference 2020 (WWW'20)
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A total of 400 Iranian military trainees with clinical diagnostic criteria for respiratory infection were enrolled in the survey. All participants were male, with a mean age of 21.69 ± 4.9 years (range from 18 to 57 years). Most prevalent complaints of patients referred to the military medical clinic center were sore throat (n=302; 75.5%), rhinorrhea (n=253; 63.2%), cough (n=237; 59.2%), fever (n=237; 59.2%), and nasal congestion (n=202; 50.5%) (Fig. 1). Of the 400 samples, 124 (31%) were positive for respiratory viruses. Human rhinovirus (n=29; 7.2%), human respiratory syncytial virus A (n=29; 7.2%), and influenza B virus (n=24; 6%) were the most frequently detected respiratory viruses in our study, followed by bocavirus (n=12; 3%), influenza A H1N1 (n=9; 2.2%), influenza A H3N2 (n=6; 1.5%), human respiratory syncytial virus B (n=6; 1.5%), adenovirus (n=6; 1.5%), and human coronavirus 229E (n=3; 0.7%). Other viruses including influenza C virus, human parainfluenza viruses, metapneumovirus, and echovirus have not been detected in any of the samples (Table 1, Fig. 2). It's worth noting that no co-infections were detected in our study. The most cases of dyspnea (n=5; 62.5%) were in the group of patients with respiratory syncytial viruses A and B, followed by influenza B (n=2; 25%) and coronavirus 229E (n=1; 12.5%). Sore throat and rhinorrhea were the most frequent symptoms in rhinovirus infection. The most cases of myalgia were seen in influenza B (n=5; 62.5%) and influenza A H1N1 (n=3; 37.5%) infections, respectively (Table 1).
Data and swabs result from a surveillance system that received regulatory approvals, including the CNIL (National Commission for Information Technology and Civil Liberties Number 1592205) approval in July 2012. All the patients have received oral information and gave their consent for swab and data collection. Data were collected for surveillance purpose and are totally anonymous.
The Senegalese National Ethical Committee of the Ministry of Health approved the surveillance protocol as less than minimal risk research, and written consent forms were not required. Throughout the study, the database was shared with the Epidemiology Department at the Senegalese Ministry of Health and Prevention for appropriate public health action.
Respiratory syncytial virus positivity was found in 6.8% (13/192) of the samples among the group of asymptomatic caregivers. Mean age of RSV‐positive cases was 34.3 years (20‐64 years); 11 (84,6%) of them living at home with symptomatic children tested positive for RSV in this study. In this case, living with an RSV‐infected child at home was 22 times more likely to be infected with RSV [OR 22.6 (95% CI 4.8‐106.7)]. RSV viral load of the 13 samples varied from 0.1 to 5.4‐log copies/mL (mean 2.1 log copies/mL).
Statistical analysis was performed using IBM SPSS version 18 (Inc., Chicago, USA) and Microsoft Office 2013 (Excel). Descriptive analysis was carried out using percentage and simple frequencies. Data was reported as count and percentage. Clinical signs and symptoms were counted, and the corresponding empirical proportions were calculated with 95% confidence intervals (CIs) to measure the overall symptom load.
Statistical analyses were performed with Stata® and Excel®. Two seasons were defined to identify possible seasonal trends in circulation of the viruses: winter season during weeks 23 to 39 between June and September and summer season during the rest of the year.
Out of 369 swab specimens collected and analysed, 172 (46.6%) were positive for one or more respiratory agents. The most frequently-detected respiratory virus amongst all study participants was influenza A (n = 71, 19.2%). Others were adenovirus (n = 32, 8.7%), rhinovirus A (n = 29, 7.9%) and coronavirus OC43 (n = 16, 4.3%). The least-detected respiratory viruses were parainfluenza virus 2 (n = 2, 0.5%) and coronavirus 229E (n = 2, 0.5%) (Table 2). Approximately 63.0% of all viral detections, including all the parainfluenza viruses (1, 2 and 3) and 78.1% of adenovirus and 75.0% of coronavirus OC43, were detected from study participants who were aged 10 years or less. Only Rhinovirus A and all influenza viruses were detected across all ages.
Data analysis was performed by using SPSS (version 22.0; IBM). Differences in the distribution of categorical variables were compared using chi-square or Fisher's exact tests. A P value of ≤0.05 was considered significant.
Fisher’s exact test was used to verify whether the associated proportions were statistically supported and a p-value < 0.05 was considered statistically significant. We used the 50-64 year’ old group as the reference. The R.15.1 tool was used to perform the analyses.
The samples were collected from the patients for laboratory investigation includingdetection of MERS-CoV, who had respiratory illness and epidemiological link as an emergency response where ethical clearance is exempted. Informed written consent was taken from all patients or patient’s guardian in case of minor prior to sample collection for MERS-CoV testing.
Influenza-like illness (ILI) surveillance was conducted in thirteen sentinels' public health center across 13 Indonesia provinces in 2012 in Figure 1. The WHO case definitions were used to determine the ILI cases: fever ≥ 38°C and a cough or a sore throat. Demographic and clinical data were obtained from questionnaires that are filled out by trained staff. Throat swab and nasal swabs from 1,692 patients were collected in viral transport medium (VTM), which were then sent to the Virology Laboratory, National Institute of Health Research and Development (NIHRD) in Jakarta. The VTM consists of bovine serum albumin, penicillin, streptomycin, and amphotericin B, according to WHO surveillance manual. Only specimens were received by the laboratory within three days after the collection was processed for molecular examinations. Specimens were stored in a −80 freezer prior to the laboratory tests. For this multiplex study, a total of three hundred thirty-four specimens were randomly selected.
An RSV rate of 24% (47/196) was obtained for children included in the study. The mean age of children who had positive samples was 2.9 years (0.25‐12 years). The mean age of children with positive samples was not statistically different from the mean age of 3.8 years among children with RSV‐negative samples (P = .17). The average time from onset of symptoms until the date of sample collection was 3.4 days (range 1‐7 days).The average viral load for the samples was 4.6‐log copies/mL, ranging from 1.2 to 8.4‐log copies/mL. We found significantly higher viral load for children younger than 2 years of age compared with children older than 2 years of age (P = .0077). The average values for viral load found in the different age groups of children are listed in Table 2.
During the outbreak of the disease, 21 pharynx swab specimens and 21 acute-phase sera samples were collected from 21 patients; and 12 returning patients gave convalescent-phase sera. The pharynx swab specimens were collected and transferred to 1 ml viral transport medium.
The ELISA for HAdV IgA was performed using the 21 serum samples from the acute phase collected from 21 patients. Six samples had positives and three suspension positive (which the OD value is closed to the cut-off) results for IgA. We used the entire virion of the HAdV-7 strain isolated and used the identified strain HAdV7-HZ0901 as the neutralization virus. The CCID50 was determined to be approximately 105.0 CCID50s/50 μ.
Conventional neutralization tests were performed using 12 pairs of paired serum samples. We found the neutralization titers of the convalescent-phase samples were four times higher than those of the acute-phase samples in nine pairs (Table 1). We noticed that there was not a good correlation between detection of IgA and fourfold rise in neutralizing antibody titer as neutralization test detection relies mainly on IgG rather than IgM or IgA, it is quite possible that during the early onset period of the disease as the serum specimen is collected, IgG has not appeared for some cases.
Respiratory virus samples were collected from patients presenting to hospital for the first time with symptoms of respiratory infection or within 7 days of admission. The time frame included for the sampling criteria was based on the incubation periods of these viruses [26, 27].
Patient samples collected after 7 days from the date of admission were excluded from the study, as these samples were considered nosocomial infections.
The descriptive statistics were used to analyse demographics, clinical, and laboratory data using Microsoft Excel (Microsoft Corporation, Washington, US). To compare between single and multiple infection, two paired tests were used.
Between August and December 2008, a total of 369 study participants presenting with ILI at the two study centres were recruited. Of these, 286 (77.5%) participants were from Entebbe Hospital and 83 (22.5%) participants were from Kiswa Health Centre (Table 1). Both genders were represented in almost equal proportions (52.3% females and 47.7% males) and the median age was 6 years (range: 1–70). Over half of the study participants (61.5%) were aged 10 years or less, and had low or no form of education (74.5%).
All patients were seen at the outpatient departments of the two study sites and none required hospital admission at the time of enrolment. Apart from fever, the most common clinical symptoms were cough (98.4%), shortness of breath (43.1%) and headache (29.0%). Only 3.8% (n = 14) of the study participants reported the presence of a chronic condition or illness such as active tuberculosis, chronic cough and chest pain. Almost all of the participants (94.5%) reported to the clinic within three days (range: 1–31) of the onset of symptoms.
Nucleic acid was extracted and purified from samples according to manufacturer’s instruction (Viral RNA/DNA mini kit, PureLink, life technologies, CA, USA). Real time qRT-PCR assays for detection of MERS-CoV RNA was performed by using TaqMan technology. Primers and probes for upstream of the envelope (UpE) and non-structural protein 2 (N2) gene were used, provided by Centers for Disease Control (CDC), USA (CDC, catalog # KT0136). The sensitivity and specificity of the RT-PCR assay kit is 100%. In addition RT-PCR was done for detection of nucleic acid of other respiratory viruses such asinfluenza A with subtype, influenza B, respiratory syncytial virus (RSV), parainfluenza virus types 1–4, human metapneumovirus, and adenoviruses. Primers and probes for theserespiratory viruses were also supplied by CDC, Atlanta, USA. Ribonucleoprotein (RP) was used as internal control.
Viral nucleic acids were extracted from nasal and throat swabs using RNA/DNA extraction kit «RIBO-sorb» (Interlabservice, Russia) according to the manufacturer’s instructions. The extracted viral nucleic acid was immediately used to perform the reaction of reverse transcription using commercial kit "REVERTA-L" (Interlabservice, Russia).
Detection of respiratory viruses, including HPIV 1–4, HRSV, HMPV, HCoV-OC43, HCoV-229E, HCoVNL63, HCoV-HKU1, HRV, HAdV, and HBoV was performed using a RT-PCR Kit «AmpliSens ARVI-screen-FL» (Interlabservice, Russia), and IFVA and IFVB virus detection was performed using a RT-PCR Kit « AmpliSens Influenza virus A/B-FL» (Interlabservice, Russia) according to the manufacturer's instructions. Positive and negative controls were included in each run.
Viral nucleic acids were extracted from 200 μL of sample using a commercial kit (RNeasy Mini Kit, Qiagen, Hilden, Germany), and viral RNA was reverse transcribed into cDNA with random hexamer primers (Roche, Mannheim, Germany) and RevertAid reverse transcriptase enzyme (Fermentas, St. Leon-Rot, Germany) following the manufacturers' instructions. For the detection of influenza A and B viruses, RSV, PIV 1, 2, and 3, and cDNA were amplified in two separate real-time multiplex PCRs with minor modifications. Other, slightly modified real-time PCRs were used for the detection of influenza A subtypes H1 and H3 (R. Fouchier, Rotterdam, the Netherlands, personal communication), influenza C (L. P. Nielsen, Copenhagen, Denmark, personal communication), bocavirus, metapneumovirus, and adenovirus. Real-time RT-PCR for the detection of HRV was performed as described and of enteroviruses (HEV) according to the method by Centers for Disease Control and Prevention, Atlanta, USA (W.A. Nix and D.R. Kilpatrick, personal communication). We know that the HEV test is not 100% specific but also reacts with some HRV strains (Savolainen-Kopra et al., unpublished results). Therefore, specimens yielding a positive result in the HEV test were divided into two groups, and a designated “true HEV” result was scored only for those HEV-positive specimens that were negative in the HRV test.
RVP FAST assay detects influenza A and B (INFA, INFB) including subtypes H1N1 (1977), H1N1pdm09, H3N2, respiratory syncytial virus A and B (RSVA, RSVB), enteroviruses including rhinoviruses (EV/Rhi), human parainfluenza viruses 1–4 (PIV1-4), human metapneumovirus (hMPV), adenovirus (ADV), human coronavirus NL63 (hCoV NL63), hCoV HKU1, hCoV 229E, hCoV OC43, and human bocavirus (hBoV). The assay was performed according to the manufacturer's instructions. Assay performance was controlled using bacteriophage lambda included in every run. The assay comprised two steps: a multiplex PCR amplification step and hybridization step.
This study supports the similarity between SRT-PCR and MRT-PCR for detecting influenza virus among patients seeking outpatient care for acute respiratory illnesses.
Between February 15, 2011 and January 18, 2012, 371 pediatric CAP patients from 1 year to 17 years old were enrolled in this study. CAP patients were stratified into three groups: 242 (65.2%) patients were in the pre-kindergarten group (≤3 years), 36 (9.7%) were in the kindergarten group (3–7 years) and 93 (25.1%) were in the school-age group (≥7 years). Of the patients enrolled, a fever was documented in 52.3% (194/371), 76% presented with sputum and chest pain (282/371), and 18.6% presented with lung consolidation (69/371). The clinical characteristics for each age group are shown in Table 1.
The nucleic acid was subjected to multiplex amplification for all specimens using SureX 13 Respiratory Pathogen Multiplex Detection Kit (Cat. No. 1 060 144, Ningbo Health Gene Technology) on ABI GeneAmp PCR System 9700 (Thermo Fisher Scientific). The 13 respiratory pathogens were as following: influenza A virus, influenza A virus H1N1 (2009), seasonal H3N2 influenza virus, influenza B virus, adenovirus, boca virus, rhinovirus, parainfluenza virus, chlamydia, human metapneumovirus, Mycoplasma pneumoniae, coronavirus, and respiratory syncytial virus. The PCR product was subjected to capillary electrophoresis using GenomeLab™ GeXP Genetic Analysis System (Beckman Coulter) according to the instructions. Each pathogen, if detectable, produced a distinctive fragment size after PCR amplification. The results of fragment analysis were used to determine the outcomes of testing. In brief, if the peak height of a targeted fragment size is lower than the lower peak of the signal standard, the targeted pathogen is determined negative; if the peak height of a targeted fragment size is higher than the higher peak of the signal standard, the targeted pathogen is determined positive; if the peak height of a targeted fragment size is between the higher and the lower peaks of the signal standard, the targeted pathogen is determined uncertain and the test should be repeated.