CRISPR-Cas9 Targeted Enrichment and Next-Generation Sequencing for Mutation Detection

Despite the rapid application of next-generation sequencing (NGS) technologies, target sequencing in regions of the genome is often required to diagnose many genetic diseases. Target enrichment can be an effective factor in reducing the cost of sequencing and the duration of sequencing. Recently, several clustered system regularly interspaced short palindromic repeats (CRISPR)-based methods (amplification-free sequencing) have been developed to target enrichment in combination with one of the NGS platforms. CRISPR-based target enrichment strategies act as an auxiliary tool to improve NGS analytical performance, thereby indirectly facilitating nucleic acid detection. The direct DNA cleavage approach by CRISPR-Cas at genome-specific sites enhances the possibility of separating native large fragments from disease-related genomic regions. The CRISPR-Cas can isolate the target region without any amplification; subsequently, long-read sequencing technologies were also implemented. These methods, as promising tools, have the ability to assess genetic and epigenetic composition for clinical application and treatment responses in cancer precision medicine. By modifying CRISPR-based enrichment protocols, it was possible to identify different types of mutations, including structural variants, short tandem repeats, fusion genes, and mobile elements. The Cas9 can specifically eliminate wild-type sequences, and it also enables the enrichment and detection of small amounts of tumor DNA fragments among the highly heterogeneous fragments of wild-type DNA.

Alternative Medical Interventions Versus Conventional Treatment of Renal Colic: An Updated Systematic Review and Network Meta-Analysis

PURPOSE

To systematically review the recent alternative medical interventions on renal colic pain and compare their efficiency with conventional treatments.

MATERIALS AND METHODS

This was a systematic review and network meta-analysis (NMA) study, based on the PRISMA guidelines on online databases of PubMed, Scopus, and web of science. We quarried these databases with relevant keywords for clinical trial studies that aimed at reducing renal colic pain in patients refereeing to the ED from after January 2011 to February 2022. Randomized clinical trials that used the Visual Analogue Scale (VAS) for assessment of renal colic pain before and after medical interventions in adult patients were included in this study. NMA was conducted based on the continuous values of the mean difference of the pain after 30 and 60 minutes of the medication administration.

RESULTS

Twenty-four studies that were meeting the inclusion criteria were included in our review with 2724 adult participants who were mostly male. Study arms included conventional medications (NSAID, Opioid, paracetamol), ketamine, MgSo4, desmopressin, and lidocaine. Based on the qualitative synthesis, ten studies (41.7%) did not find significant differences between conventional and alternative treatments. Also, there is no agreement on some more recent medications like using ketamine or desmopressin while MgSO4 and lidocaine use are supported by most studies. NMA revealed that desmopressin is significantly having worse pain reduction properties. NMA did not show any difference between ketamine, lidocaine, and MgSo4, versus the conventional treatment.

CONCLUSION

To conclude, lidocaine and MgSo4 might be good alternative treatments for renal colic when conventional treatments are contraindicated or pain is not responding to those. Ketamine might be indicated in patient-based circumstances. Desmopressin may be agreeably avoided in further research or clinics.

Evaluation of the effect of melatonin in patients with COVID-19-induced pneumonia admitted to the Intensive Care Unit: A structured summary of a study protocol for a randomized controlled trial

OBJECTIVES

We investigate the effects of melatonin, compared to the usual therapeutic regimen on clinical symptoms and laboratory signs in severely ill patients with confirmed COVID-19 who are admitted to the Intensive Care Unit (ICU).

TRIAL DESIGN

This is a single-center, open-label, randomized, clinical trial with a parallel-group design. This study is being conducted at Shahid Mohammadi Hospital, Bandar Abbas, Iran.

PARTICIPANTS

All patients admitted to the ICU of Shahid Mohammadi Hospital, Bandar Abbas, Iran, will be screened for the following criteria. Inclusion criteria 1. Age >20 years 2. Definitive diagnosis of COVID-19 based on RT-PCR or/and serological testing 3. Severe pneumonia and lung involvement in imaging 4. Signing informed consent Exclusion criteria 1. Underlying diseases, including convulsive disorders, chronic hepatic and renal diseases 2. Use of mechanical ventilation 3. History of known allergy to Melatonin 4. Pregnancy and breastfeeding INTERVENTION AND COMPARATOR: Intervention group: The standard treatment regimen for COVID-19, according to the Iranian Ministry of Health and Medical Education's protocol, along with Melatonin soft gelatin capsule (Danna Pharmaceutical Company) at a dose of 5 mg twice a day for a period of seven days.

CONTROL GROUP

The standard treatment for COVID-19 based on the Iranian Ministry of Health and Medical Education's protocol for a period of seven days.

MAIN OUTCOMES

The primary outcomes are the recovery rate of clinical symptoms and checking arterial blood gas (ABG), C-reactive protein (C-RP), Ferritin, Lactate dehydrogenase (LDH) within seven days of randomization. The secondary outcomes are time to improvement of clinical and paraclinical features and length of stay in the ICU, need for mechanical ventilation, and mortality rate within seven days of randomization.

RANDOMIZATION

Included patients will be allocated to one of the study arms using block randomization in a 1:1 ratio (each block consists of 6 patients). This randomization method ensures a balanced allocation between the arms during the study. A web-based system will generate random numbers for the allocation sequence and concealment of participants. Each number relates to one of the study arms.

BLINDING (MASKING)

This is an open-label trial without blinding and placebo control.

NUMBERS TO BE RANDOMIZED (SAMPLE SIZE)

A total of 60 participants randomizes (30 patients allocated to the intervention group and 30 patients allocated to the control group).

TRIAL STATUS

The protocol is Version 1.0, February 16, 2021. Recruitment began February 28, 2021, and is anticipated to be completed by July 31, 2021.

TRIAL REGISTRATION

The trial protocol has been registered in the Iranian Registry of Clinical Trials (IRCT). The registration number is " IRCT20200506047323N7 ". The registration date was February 16, 2021.

FULL PROTOCOL

The full protocol is attached as an additional file, accessible from the Trials website (Additional file 1). In the interest of expediting the dissemination of this material, the familiar formatting has been eliminated; this Letter serves as a summary of the key elements of the full protocol.

CRISPR-based biosensing systems: a way to rapidly diagnose COVID-19

The outbreak of the emerging SARS-CoV-2 virus has highlighted the challenges of detecting viral infections, especially in resource-limited settings. The SARS-CoV-2 virus transmission chain is interrupted when screening and diagnosis can be performed on a large scale by identifying asymptomatic or moderately symptomatic patients. Diagnosis of COVID-19 with reverse transcription polymerase chain reaction (RT-PCR) has been limited due to inadequate access to complex, expensive equipment and reagents, which has impeded efforts to reduce the spread of virus transmission. Recently, the development of several diagnostic platforms based on the CRISPR-Cas system has reduced the dependence on RT-PCR. The first CRISPR-based diagnostic test for SARS-CoV-2 was recently approved by the U.S. Food and Drug Administration. The biosensing systems have several important features that make them suitable for point-of-care tests, including the speed of design and synthesis of each platform in less than a few days, an assay time of 1-2 h, and the cost of materials and reagents less than one dollar per test. The HUDSON-SHERLOCK and STOPCovid biosensing systems, as field-deployable and rapid diagnostic tests, can detect low-copy viruses in body fluids without nucleic acid extraction and with minimal equipment. In addition, Cas13-based treatment strategies could potentially be an effective antiviral strategy for the prevention and treatment of emerging pandemic viruses such as SARS-CoV-2. In this review, we describe recent advances in CRISPR-based diagnostic platforms with an emphasis on their use in the rapid diagnosis and potential treatment of COVID-19.

Bio-inspired Model of Humanoid Robot for Ascending Movement

Stair climbing is one of the important daily life activities that biped robots have to carry out. However, the number of researches study the ascending movement mechanisms and its stability is low. In this study, we have inspired by human ascending movement underlying mechanisms and developed a new control law based on the nature of the human motor behavior. This model has been developed in phase space using an intermittent sliding mode controller to give stable control and eliminate the effect of the system's uncertainty. A planar five-link biped model has been used to test the model. The embedded space and controller has been formed for each joint separately. Therefore, in this case, the position of each angle in embedded space gets compared along time with its corresponding desired dynamic. The position of each angle in space regarding its corresponding reference trajectory made the error signal. Results show that the designed sliding mode controllers successfully keeps the trajectory near the desired dynamics, and the output follows the desired dynamic very well.

Better Hemodynamic Profile of Laryngeal Mask Airway Insertion Compared to Laryngoscopy and Tracheal Intubation

Background:

Laryngoscopy and tracheal intubation can cause serious cardiovascular responses in patients such as hypertension, tachycardia, and arrhythmias. Alternative airway maintenance techniques may attenuate these hemodynamic stress responses.

Objectives:

This study aimed to compare the immediate hemodynamic effects of the insertion of laryngeal mask airway supreme (LMA-S) and classic (LMA-C) with laryngoscopy and Endotracheal Intubation (ETT).

Patients and Methods:

This study was a prospective, double-blind, and randomized clinical trial conducted on 150 patients aged 18 to 50 years with ASA I (American Society of Anesthesiologists), in the general operating room of Shahid Mohammadi hospital, Hormozgan university of medical sciences, Bandar Abbas, Iran. In the ETT group, endotracheal intubation was performed using the Macintosh laryngoscope; while for the LMA-C and LMA-S groups, LMA Classic and LMA Supreme were inserted, respectively. The induction and maintenance of anesthesia were similar in all patients. The hemodynamic parameters such as heart rate (HR), systolic blood pressure (SBP), and diastolic blood pressure (DBP) were measured before (baseline) and after induction of anesthesia at 4 different time points. The statistical analysis was done and P value less than 0.05 was considered significant.

Results:

Participants in all groups were similar in terms of gender, age, weight, height, and Mallampati class. The mean ± SD of SBPs (105.62 ± 12.12, 112.90 ± 12.2, and 112.48 ± 15.14 mm Hg, respectively for ETT, LMA-C, and LMA-S) and DBPs (64.64 ± 10.23, 73.78 ± 9.70, and 71.20 ± 12.27 mm Hg, respectively for ETT, LMA-C, and LMA-S) were significantly lower in the ETT group compared to LMA groups 5 minutes after device insertion (P < 0.01 for SBPs and P < 0.001 for DBPs); however these values were lower than the baseline values in all groups. There were no differences in the mean SBP and DBPs between the three groups at the other time points. The mean ± SD heart rates in the ETT group, compared to the LMA-C and LMA-S groups, were considerably higher in the first minute (100.06 ± 18.27, 82.50 ± 10.52, and 82.00 ± 13.60 bpm, respectively for ETT, LMA-C, and LMA-S), third minute (91.04 ± 17.12, 78.84 ± 11.23, and 78.90 ± 13.41 bpm, respectively for ETT, LMA-C, and LMA-S) and fifth minute (85.82 ± 16.01, 75.78 ± 11.73, and 75.04 ± 13.90 bpm, respectively for ETT, LMA-C, and LMA-S) after intubation (P < 0.001). There were no significant differences between the LMA-C and LMA-S groups in terms of hemodynamic parameters.

Conclusions:

Maintaining the airway using laryngeal mask airway is associated with less cardiovascular responses compared to direct laryngoscopy and tracheal intubation.

Seizure Duration and Hemodynamic State During Electroconvulsive Therapy: Sodium Thiopental Versus Propofol

Introduction:

General anesthesia is required for Electroconvulsive Therapy (ECT) and it is usually provided by a hypnotic agent. The seizure duration is important for the treatment, and it is usually accompanied by severe hemodynamic changes. The aim of this study was to compare the effects of sodium thiopental versus Propofol on seizure duration and hemodynamic variables during ECT.

Methods:

A number of 100 patient-sessions of ECT were included in this randomized clinical trial. The initial hemodynamic state of each patient was recorded. Anesthesia was induced by Sodium thiopental in the 1^st group and with Propofol in 2^nd group. All the patients received the muscle relaxant succinylcholine. The hemodynamic variables after seizure and seizure duration were recorded. The data were analyzed through SPSS 20 and independent t-test. P<0.05 was considered significant.

Results:

The mean duration of seizure in the sodium thiopental group was significantly longer than the Propofol group (40.3±16.6 sec versus 32±11.3 sec) (P=0.001). There was no statistically significant difference between the mean energy level applied in the two groups (20.5±3.81 joules in the sodium thiopental versus 20.2±3.49 joules in the Propofol group). The mean systolic and diastolic blood pressure at all times after seizure and mean heart rate at 3 and 5 minutes after seizure were significantly lower in Propofol than sodium thiopental groups.

Discussion and Conclusion:

Propofol provides a more stable hemodynamic state for the ECT procedures, and its use is highly preferred over sodium thiopental in patients with cardiovascular disease.

[Therapy of splenic injuries by freezing and fibrin gluing. Animal experiment study]

The goal of this investigation was to improve the reliability of intraoperative and postoperative hemostasis and to observe the healing process after using a combined technique of tissue freezing followed by the application of collagen fleece and fibrin glue for the treatment of splenic ruptures. Grade II lesions were inflicted on the spleens of 15 swine. The bleeding wounds were frozen for 1 min at -60 degrees C using a cryosurgical device. Immediately afterwards the frozen lesions were covered with fibrin glue and collagen fleece and kept under slight compression. In every case complete hemostasis was achieved intraoperatively. The spleens of three animals each time were collected for gross and microscopic examination after 2 days and 1, 2, 5, and 6 weeks. A visceroperitoneal adhesion was observed in only one spleen, U-shaped viscerovisceral adhesions in five spleens. Superficial coagulation necroses could be detected microscopically only after 2 days and 1 week. Organization of the wounds, indicated by granulation tissue which contained siderophages, started in the 2nd week. There was distinct formation of collagen fibers after 5 and 6 weeks; only a residue of the collagen fleece was visible and the surplus fibrin glue was encapsulated. With this combined technique complete and safe hemostasis and a good subsequent healing process was achieved.

Experimental salvage of the spleen. A combined technique of cryosurgery and tissue sealant

The goal of this investigation has been to improve the safety of intra- and post-operative haemostasis in splenic lesions by a combined technique of tissue freezing followed by the application of collagen fleece and fibrin glue in an animal study. The progression of healing was observed after different periods of time. Grade II lesions were set on the spleens of 15 pigs. The wounds were frozen for 1 m at -60 degrees C with a cryosurgical probe and afterwards sealed with fibrin glue and collagen fleece. In every case, complete haemostasis was achieved intraoperatively. The spleens of 3 animals each were examined microscopically after 2 days, 1, 2, 5 and 6 weeks, respectively. A visceroperitoneal adhesion was observed in only 1 spleen and u-shaped viscerovisceral adhesions in 5 spleens. Superficial coagulation necroses were observed only in specimens removed after 2 days and 1 week, respectively. Complete and safe haemostasis followed by acceptable subsequent healing was achieved using this combined technique.

[Primary conservative treatment of open tibial shaft fractures]

Between 1969 and 1976 104 open tibia shaft fractures were primarily conservatively treated. 85 of these fractures healed without complications. In 19 cases a late operation was necessary. In 3 cases an ostitis developed. The follow-up, after 4 1/2 years on average, of 59 exclusively conservatively treated patients, showed in 51 cases a good result. It appears that the conservative treatment of open tibia shaft fractures still provides a debatable alternative to primary osteosynthesis.