Third generation sequencing technologies such as Pacific Biosciences and Oxford Nanopore provide faster, cost-effective and simpler assembly process generating longer reads than the ones in the next generation sequencing. However, the error rates of these long reads are higher than those of the short reads, resulting in an error correcting process before the assembly such as using the Circular Consensus Sequencing (CCS) reads in PacBio sequencing machines. In this paper, we propose a probabilistic model for the error occurrence along the CCS reads. We obtain the error probability of any arbitrary nucleotide as well as the base calling Phred quality score of the nucleotides along the CCS reads in terms of the number of sub-reads. Furthermore, we derive the error rate distribution of the reads in relation to the pass number. It follows the binomial distribution which can be approximated by the normal distribution for long reads. Finally, we evaluate our proposed model by comparing it with three real PacBio datasets, namely, Lambda, and E. coli genomes, and Alzheimer's disease targeted experiment.
Escherichia coli , High-Throughput Nucleotide Sequencing , Sequence Analysis, DNA/methods , Escherichia coli/genetics , High-Throughput Nucleotide Sequencing/methods , Genome , Nucleotides
Nasal swab tests are widely used to screen for coronavirus disease 2019 (COVID-19). Pain, discomfort, and the urge to sneeze are the most common complications of this screening method. We report a case of a 55-year-old female patient with beta-thalassemia major suffering from a nasal septal abscess (NSA) as a complication of a COVID-19 nasal swab test. Following the test, the patient only had mild nasal congestion. However, three days later, her clinical condition deteriorated, and she developed fever, and her level of consciousness decreased to lethargy and drowsiness. Physical examinations revealed a bilateral nasal abscess. She underwent surgical intervention, and the abscess was removed. For the first time in Iran, a case of NSA after a COVID-19 nasal swab test is reported. It is strongly recommended to exercise caution while performing nasal swab tests, especially in the elderly and patients at risk of bleeding or hemoglobinopathy.
COVID-19 , Paranasal Sinus Diseases , Respiratory Tract Infections , Humans , Female , Aged , Middle Aged , Abscess/diagnosis , Abscess/etiology , Nasal Septum/surgery , COVID-19/complications , Paranasal Sinus Diseases/complications , Respiratory Tract Infections/complications , Cellulitis/complications
Hydatid cysts in the neck area are considered as very rare and few cases have been reported in endemic areas. In the present study, we reported a 38-year-old female that underwent surgical operation for extraction of simple cyst in the submandibular area and the diagnosis of hydatid cyst was established by laboratory examinations. The patient was later diagnosed with hepatic hydatid cyst and received systemic treatments. We recommend that physicians should pay more attention to the possibilities of hydatid cysts in unusual areas in endemic regions especially Middle East.
INTRODUCTION: Intratympanic therapy, as a widely used treatment for inner ear diseases, is regarded as a therapeutic method in controlling the vertigo of the patients with Meniere's disease. This study was designed to evaluate the effect of the Intratympanic dexamethasone-hyaluronic acid combination on patients suffering from Meniere's disease. MATERIALS AND METHODS: This study was a clinical trial on patients with Meniere's disease during 2016-2017. Patients received two Intratympanic injections of dexamethasone plus hyaluronic acid as a mixture within a month. Before and 2 weeks after the intervention, pure tone average (PTA) at 0.5, 1, 2, and 4 KHz frequencies, speech discrimination score (SDS), dizziness handicap inventory (DHI), and tinnitus handicap inventory (THI) scores were evaluated for each patient. The obtained scores were statistically analyzed. RESULTS: This study was conducted on a total number of 25 patients with Meniere's disease. The mean age of participants in this study was 44.71±4.92 years. Gender distribution among participants revealed that 36% of patients were male. The mean values of PTA, SDS, and THI were not significantly different before and after the intervention. However, the mean score of DHI decreased significantly after the intervention (P<0.001). CONCLUSION: Intratympanic dexamethasone/hyaluronic acid had a positive effect on the vertigo of the investigated patients without any significant improvement in hearing impairment and tinnitus in the short term.
PURPOSE: To evaluate the effects of subthreshold diode micropulse laser photocoagulation on treating patients with refractory diabetic macular edema (DME). METHODS: This randomized clinical trial recruited patients with DME in both eyes that were resistant to treatment with intravitreal bevacizumab (IVB). The eyes were randomly divided into two groups who received laser therapy and IVB, or IVB alone. Subthreshold diode micropulse laser photocoagulation and IVB injection were administered in one eye, and an IVB injection was administered in the second eye. IVB injections were repeated in both eyes within one month and two months after the first injection. Best corrected visual acuity (BCVA) logarithm of the minimum angle of resolution (logMAR) and central macular thickness (CMT) were measured before, within a month, and three months after start of intervention. RESULTS: In this study, 42 eyes of 21 patients were evaluated. The mean age of patients was 60.86 ± 8.57 years. Ten patients (47.6%) were male. Within-group analysis showed a significant decreased in BCVA logMAR in the laser + IVB group reflecting improvement in visual acuity (VA) (P < 0.001); it increased in the control group during study reflecting more vision loss (P = 0.01). In the laser + IVB group, a significant decrease in mean ± standard deviation (SD) CMT at 3 months compared to baseline was observed (baseline: 513 ± 126.29 vs. three months: 408.1 ± 95.28; P < 0.001). The mean ± SD CMT was significantly lower in the laser + IVB group of eyes than in the control group three months after intervention (P = 0.02). CONCLUSION: Using subthreshold diode micropulse laser photocoagulation in combination with IVB can significantly reduce CMT and improve BCVA in patients with refractory DME.
