CriSNPr, a single interface for the curated and de novo design of gRNAs for CRISPR diagnostics using diverse Cas systems

CRISPR-based diagnostics (CRISPRDx) have improved clinical decision-making, especially during the COVID-19 pandemic, by detecting nucleic acids and identifying variants. This has been accelerated by the discovery of new and engineered CRISPR effectors, which have expanded the portfolio of diagnostic applications to include a broad range of pathogenic and non-pathogenic conditions. However, each diagnostic CRISPR pipeline necessitates customized detection schemes based on the fundamental principles of the Cas protein used, its guide RNA (gRNA) design parameters, and the assay readout. This is especially relevant for variant detection, a low-cost alternative to sequencing-based approaches for which no in silico pipeline for the ready-to-use design of CRISPRDx currently exists. In this manuscript, we fill this lacuna using a unified web server, CriSNPr (CRISPR-based SNP recognition), which provides the user with the opportunity to de novo design gRNAs based on six CRISPRDx proteins of choice (Fn/enFnCas9, LwCas13a, LbCas12a, AaCas12b, and Cas14a) and query for ready-to-use oligonucleotide sequences for validation on relevant samples. Furthermore, we provide a database of curated pre-designed gRNAs as well as target/off-target for all human and SARS-CoV-2 variants reported thus far. CriSNPr has been validated on multiple Cas proteins, demonstrating its broad and immediate applicability across multiple detection platforms. CriSNPr can be found at http://crisnpr.igib.res.in/.

FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip

The COVID-19 pandemic originating in the Wuhan province of China in late 2019 has impacted global health, causing increased mortality among elderly patients and individuals with comorbid conditions. During the passage of the virus through affected populations, it has undergone mutations, some of which have recently been linked with increased viral load and prognostic complexities. Several of these variants are point mutations that are difficult to diagnose using the gold standard quantitative real-time PCR (qRT-PCR) method and necessitates widespread sequencing which is expensive, has long turn-around times, and requires high viral load for calling mutations accurately. Here, we repurpose the high specificity of Francisella novicida Cas9 (FnCas9) to identify mismatches in the target for developing a lateral flow assay that can be successfully adapted for the simultaneous detection of SARS-CoV-2 infection as well as for detecting point mutations in the sequence of the virus obtained from patient samples. We report the detection of the S gene mutation N501Y (present across multiple variant lineages of SARS-CoV-2) within an hour using lateral flow paper strip chemistry. The results were corroborated using deep sequencing on multiple wild-type (n = 37) and mutant (n = 22) virus infected patient samples with a sensitivity of 87% and specificity of 97%. The design principle can be rapidly adapted for other mutations (as shown also for E484K and T716I) highlighting the advantages of quick optimization and roll-out of CRISPR diagnostics (CRISPRDx) for disease surveillance even beyond COVID-19. This study was funded by Council for Scientific and Industrial Research, India.

Melanosis of bladder: A rare entity

Melanosis of the bladder, also known as melanosis vesicae, refers to presence of pigment in bladder mucosa. A rare phenomenon, however, it can be confused with the primary or metastatic melanoma of the bladder. Therefore, knowledge of the entity can prevent over diagnosis of this benign entity.

We are reporting a case of melanosis of bladder in a 69 year old male with prolonged history of LUTS and bladder diverticulae. Cystoscopic examination showed black patches and biopsy revealed pigmentation in the epithelium and underlying lamina propria. Special stains identified the pigment to be melanin. No malignant cells were identified.

Improved neonatal seizure detection using adaptive learning

In neonatal intensive care units performing continuous EEG monitoring, there is an unmet need for around-the-clock interpretation of EEG, especially for recognizing seizures. In recent years, a few automated seizure detection algorithms have been proposed. However, these are suboptimal in detecting brief-duration seizures (<; 30s), which frequently occur in neonates with severe neurological problems. Recently, a multi-stage neonatal seizure detector, composed of a heuristic and a data-driven classifier was proposed by our group and showed improved detection of brief seizures. In the present work, we propose to add a third stage to the detector in order to use feedback of the Clinical Neurophysiologist and adaptively retune a threshold of the second stage to improve the performance of detection of brief seizures. As a result, the false alarm rate (FAR) of the brief seizure detections decreased by 50% and the positive predictive value (PPV) increased by 18%. At the same time, for all detections, the FAR decreased by 35% and PPV increased by 5% while the good detection rate remained unchanged.

Improvement of an automated neonatal seizure detector using a post-processing technique

Visual recognition of neonatal seizures during continuous EEG monitoring in neonatal intensive care units (NICUs) is labor-intensive, has low inter-rater agreement and requires special expertise that is not available around the clock. Development of an accurate automated seizure detection system with a low false alarm rate will support clinical decision making and alleviate significantly the workload. However, this is an ongoing difficult challenge for engineers as the neonatal EEG signal is non-stationary and often includes complex patterns of seizures and artifacts. In this study, we show an improvement of our previously developed neonatal seizure detector (developed using heuristic if-then rules). In order to improve the detection accuracy, mean phase coherence as a new feature is used to characterize artifacts and also support vector machine is applied to perform the post-processing step to remove false detections. As a result, the false alarm rate drops 42% (from 2.6 h(-1) to 1.5 h(-1)), whereas the good detection rate reduces only by 4%.

Effect of sub-maximal exercise stress on cold pressor pain: a gender based study

BACKGROUND

Analgesic effect of exercise is a well established fact; however available reports are contradictory on gender differences in pain perception following exercise stress test.

OBJECTIVE

The current study is prospectively designed to evaluate and compare the effect of acute bout of sub-maximal exercise stress on cold pressor pain in normal adult males and females.

METHOD

The experimental study design involved healthy adults (n= 41); females (n = 18) and males (n=23) aged between 18 to 25 years and included them into four sets of experiments: SET I (Control), "resting blood pressure, radial pulse and respiratory rate were recorded after 15 minutes of complete supine relaxation. SET II (Cold Pressor Pain Test): Pain Threshold, Pain Tolerance, and Pain Duration in seconds were taken. SET III (Exercise Stress Test): Sub-maximal exercise of 70 to 75% of maximum predicted heart rate was given for 6 minutes. SET IV (Cold Pressor Pain Test immediately after Exercise Stress Test): At 0 minute of recovery again the pain parameters; Pain Threshold, Pain Tolerance, and Pain Duration in seconds were taken. SET I, SET II were performed in order on the first day and SET III and SET IV on the second day to ensure only a single Cold Pressor Pain Test is performed in each day.

RESULT

The data (Mean ± SD) analysis showed significant increased in pain threshold (males: 14.36 ± 10.6 Vs 21.47 ± 13 seconds, p< 0.001, females: 14.1 ± 11.5 Vs 23.81 ± 20.22 seconds, p<0.001) and pain tolerance time (males: 41.3 ± 19.31 Vs 54.1 ± 21.7 seconds, p<0.001) in both sexes after 6 min of acute bout of sub-maximal exercise stress test with comparable age, BMI and baseline resting values of pain parameters and pulse rate and blood pressure. The percentage increment pain tolerance time following the exercise stress in female is higher than male (78.6 Vs 68.9%).

CONCLUSION

The result suggests that pain sensation decreases immediately after a brief period of exercise challenge irrespective of gender, and the analgesic effect of the acute bout of exercise in terms of pain tolerant time is more enhanced in females than males.

Ibn nafis - a forgotten genius in the discovery of pulmonary blood circulation

Scientific theories take centuries to come into existence and they keep on evolving. Uncountable intellectual minds work on these theories; some fail to do anything about it; some add a little after tremendous efforts, and some people give remarkable and unforgettable contribution.As far as credit is concerned, the person who is able to prove the theory by his facts and who clears the maximum doubts by his observations, experimentations, facts and reasoning, gets the credit for that theory, and this should be done with honesty.The theory of pulmonary circulation took more than 2000 years to come into existence as we know it today. With the passage of time different people were given credit. Some say that it was given to Galen; some say it was Michael Servetus; others say that Realdus Columbus was the real discoverer; some gave the credit to Ibn Nafis, and finally people gave the credit to William Harvey. But after the rediscovery of Ibn Nafis' manuscript no.62243 titled Sharah al Tashreeh al Qanoon, or "Commentary on the anatomy of Canon of Avicenna" in 1924 AD in Europe, it became clear that Ibn Nafis had described the pulmonary circulation almost 300 years before Harvey, and the historians like Aldo Mieli, Max Mayrhoff, Edward Coppola etc. clearly state that Ibn Nafis is the real discoverer of the pulmonary circulation and that he should be given the credit for the discovery of the pulmonary circulation.

Predictive value of dobutamine stress echocardiography for coronary artery disease detection in liver transplant candidates

Patients with obstructive coronary artery disease (CAD) undergoing orthotopic liver transplantation (OLT) are at increased risk of poor outcomes. The accuracy of dobutamine stress echocardiography (DSE) to detect obstructive CAD is not well established in this population. We retrospectively identified patients with end-stage liver disease who underwent both DSE and coronary angiography as part of risk stratification prior to OLT. One hundred and five patients had both DSE and angiography, of whom 14 had known CAD and 27 failed to reach target heart rate during DSE. Among the remaining 64 patients (45 men; average age 61 +/- 8 years) DSE had a low sensitivity (13%), high specificity (85%), low positive predictive value (PPV) (22%) and intermediate negative predictive value (NPV) (75%) for obstructive CAD. DSE as a screening test for obstructive CAD in OLT candidates has a poor sensitivity. The frequent chronotropic incompetence and low sensitivity in patients who achieve target heart rate, even in those with multiple cardiovascular disease risk factors, suggest that alternative or additional methods of risk stratification are necessary.

Recurrent pregnancy loss. An update

OBJECTIVE

To comprehensively review causes of recurrent pregnancy loss and the currently applied methodologies for their diagnosis and management.

STUDY DESIGN

A review article addressing pertinent issues on the subject of recurrent pregnancy loss, which, by definition, is three consecutive pregnancy losses prior to the 20th week of gestation.

RESULTS AND CONCLUSION

Diagnostic workup and treatment of recurrent abortion often poses a special challenge as numerous conclusive and nonconclusive causes have been described with varied and often controversial approaches for their management. While a definitive cause may not be discovered in a significant number of cases, among those with an identifiable cause, anatomic disorders are by far the most conclusively diagnosable and effectively treatable conditions, making their exclusion or inclusion an essential part of the evaluation. That up to 60% of these cases may achieve successful pregnancy without any intervention should receive serious consideration when analyzing results of studies that claim therapeutic benefits from treatment modalities.

Sperm transmigration as a cause of ectopic pregnancy

This case represents the phenomenon of contralateral sperm transperitoneal migration: sperm gaining access to the left oviduct after entering the peritoneal cavity via the right oviduct. The ovum from the left ovary after being successfully fertilized could not be transported into the uterine cavity due to the previous segmental resection, ultimately resulting in an ectopic pregnancy.

Transcutaneous electrical nerve stimulation for reducing narcotic use after cesarean section

This study evaluated the potential efficacy of transcutaneous electrical nerve stimulation in reducing narcotic requirements following cesarean section. The total required dose of postoperative analgesic (meperidine) was found to be 511 mg in the experimental group and 456 mg in the control group. There was no significant difference in narcotic use or hospital stay between the experimental and control groups.

Cervical incompetence. A review

Cervical incompetence is one of the main contributors to repeated pregnancy loss, accounting for approximately 25% of the cases. Typically it results in progressive cervical dilatation, leading to a painless second- or early-third-trimester abortion. In most instances cervical incompetence is the result of previous obstetric or gynecologic trauma; a congenital etiology is unusual. Despite the various reported diagnostic procedures, the obstetric history and frequent visual and digital examinations during pregnancy remain the most important factors in arriving at the correct diagnosis. In spite of the fact that numerous procedures have been advocated as treatment, the McDonald purse string closure technique is by far the most simple and effective corrective surgical technique, yielding an overwhelming number of successful pregnancies.

Successful management of post-cesarean-section acute pseudoobstruction of the colon (Ogilvie's syndrome) with colonoscopic decompression. A case report

Although acute pseudoobstruction of the colon is a rare entity, a large percentage of the reported cases have occurred following obstetric and gynecologic surgical procedures. Early recognition is mandatory to avoid severe and potentially fatal complications and can allow successful decompression by means of colonoscopy, thus avoiding surgical intervention, as in the case reported on here.

Contraception and the cervix

In the human and subhuman primates the uterine cervix plays an important role in the reproductive process by its permissive and inhibitory action on sperm migration from the vaginal pool into the cervical canal, the uterine cavity and the fallopian tube, the site of gamete unification and fertilization. This is accomplished through physico-chemical (amount, clarity, viscosity, pH, electrolyte composition, etc.) alteration of the cervical mucus in response to the circulating sex steroids. In an ovulatory cycle, shortly prior to and at the time of ovulation the cervical mucus becomes most receptive to the spermatozoa whereas at other times, specifically following ovulation, it becomes hostile to the spermatozoa and virtually impenetrable. This unique property of the cervical mucus may, in addition to the presently available techniques (diaphragm, cervical cap and intracervical devices), allow identification of such potential contraceptive modalities as: pH modifier - changing the pH of the cervical mucus from alkaline to acid around the time of ovulation; Electrolyte modifier - changing electrolyte composition of the cervical mucus to produce a mesh impenetrable to spermatozoa. Finally, development of a temporary localized tissue-fixed immune antibody to spermatozoa in the cervical mucus is within the realm of reality and deserves the necessary attention.

Chemical alteration of cervical mucus by electrolytes

Scanning electron microscopy and energy-dispersive x-ray analysis have been used, together with conventional light microscopy and sperm penetration tests, to evaluate the alteration of cervical mucus composition and properties during the menstrual cycle and subsequent to exposure of cervical mucus to electrolytes in vitro and in vivo. Alteration of the electrolyte content of cervical mucus appears to offer a means for the predictable control of cervical properties and penetrability by sperm. This method may have clinical application in both reduction and enhancement of fertility in the human.

Electrolyte interactions in cervical mucus and their relationship to circulating hormone levels

The changes in electrolyte composition of cervical mucus (CM) were monitored during the menstrual cycle, using scanning electronic microscopy (SEM) and energy dispersive X-ray analysis (EDX). Correlations were sought between the electrolytes present in CM, the physical characterisitics of the CM, and circulating levels of gonadal steroids and protein hormones. The results suggest that there is a definite relationship between circulating estrogen levels and electrolyte composition of CM, and also provide information on the secretion of electrolytes during the human menstrual cycle. This information will be of use in development of methods for fertility control directed to the uterine cervix.

Sodium bicarbonate douching for improvement of the postcoital test

In the hope of improving sperm survival within the cervical mucus, 93 infertile patients with unfavorable postcoital tests were advised to douche with a solution of sodium bicarbonate 30 to 60 minutes prior to sexual intercourse. In most patients observed, the repeatedly poor postcoital test improved remarkably, and 31 pregnancies have been achieved. In the majority of patients, the postcoital test was repeated on 2 subsequent days (without and with the benefit of sodium bicarbonate douching) with astonishing differences in the test results. In addition to pH changes, sodium bicarbonate douching resulted in significant alteration of the cervical mucus electrolyte components (detected by scanning electron microscopy and energy-dispersive x-ray analysis). The possible modes of action of sodium bicarbonate douching are fully analyzed.

End-to-end tubal anastomosis using an absorbable stent

Using absorbable suture as a stent, end-to-end anastomosis of previously ligated or cauterized fallopian tubes was performed in 15 cases. Luminal patency of at least one fallopian tube has been achieved in all cases, and thus far seven pregnancies have occurred in six cases. The technique for inserting the absorbable suture into the distal and proximal portions of the tube is fully described, and the importance of repeated hydrotubations to maintain tubal patency is emphasized.

Liver tumors and oral contraceptives

A possible causal relationship between oral contraceptives and liver cell adenomas has been postulated in the recent literature. In this presentation three additional cases are reported to support the existence of such an association. The possible etiologic causes for this newly described condition and specific diagnostic procedures for its accurate diagnosis are presented.

Silicone rubber band for laparoscopic tubal sterilization

In 1974, Yoon and associates (Am J Obstet Gynecol 120:132, 1974) described a new approach in which laparoscopic tubal occlusion was accomplished by utilizing the silicone rubber band technique. Recognizing the great advantages of the new technique in eliminating potential thermal injury associated with electrocoagulation, the authors have utilized the Yoon silicone rubber band technique in these institutions over the past 20 months. Thus far the procedure has been performed in 304 patients without any major complications. In the hope of eliminating and/or reducing possible pregnancy-failure rates, in 110 cases. In addition to application of the silicone band, the tube within the band was transected with non-electrical Seigler biopsy forceps. This, we believe, should provide an interesting long-term comparative study.

Foley catheter for salpingography, pneumonography, tubal insufflation, and hydrotubation

Using a pediatric Foley catheter, salpingography, CO2 insufflation, hydrotubation, pelvic pneumography, pelvic pneumoperitoneum for laparoscopy, and pneumohysterosalpingography were performed in more than 1000 cases. The Foley catheter technic was fully described and the advantages outlined. In general, the Foley catheter proved to be a simple and atraumatic technic, eliminating some of the difficulties associated with the use of the metal cannula.

Urinary estriol for assessment of fetoplacental function

A total of 1,607 urinary estriol determinations were performed in 447 patients with normal and complicated pregnancies. In general, the test provided reliable information concerning fetal status, particularly in pregnancies complicated by toxemia, diabetes, and postmaturity. When measured consecutively, a drop of 50% or more in estriol level usually should be considered a significant index of fetal distress. Limitations of the test and several compensatory measures aimed at minimizing inaccuracy are discussed.

Pregnancy and neurofibromatosis (von Recklinghausen's disease)

A case of neurofibromatosis adversely affected by pregnancy has been presented. The large neurofibromatosis lesions in this patient increased extensively during the latter part of pregnancy, mainly as the result of massive hemorrhage within the masses. Additionally, the patient developed partial paralysis of the lower extremities resulting in inability to walk. This was thought to be due either to the development of neurofibromatosis or to enlargement of a previously existing intraspinal small neurofibromatosis lesion. In view of exacerbation of von Recklinghausen's disease during pregnancy, as reported here and recorded by others, and its hereditary transmission (autosomal dominant gene), early termination of pregnancy and sterilization are recommended.

Thyrotoxicosis in a mongol

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