Systematically testing human HMBS missense variants to reveal mechanism and pathogenic variation.

Defects in hydroxymethylbilane synthase (HMBS) can cause acute intermittent porphyria (AIP), an acute neurological disease. Although sequencing-based diagnosis can be definitive, ∼⅓ of clinical HMBS variants are missense variants, and most clinically reported HMBS missense variants are designated as "variants of uncertain significance" (VUSs). Using saturation mutagenesis, en masse selection, and sequencing, we applied a multiplexed validated assay to both the erythroid-specific and ubiquitous isoforms of HMBS, obtaining confident functional impact scores for >84% of all possible amino acid substitutions. The resulting variant effect maps generally agreed with biochemical expectations and provide further evidence that HMBS can function as a monomer. Additionally, the maps implicated specific residues as having roles in active site dynamics, which was further supported by molecular dynamics simulations. Most importantly, these maps can help discriminate pathogenic from benign HMBS variants, proactively providing evidence even for yet-to-be-observed clinical missense variants.

Systematically testing human HMBS missense variants to reveal mechanism and pathogenic variation.

Defects in hydroxymethylbilane synthase (HMBS) can cause Acute Intermittent Porphyria (AIP), an acute neurological disease. Although sequencing-based diagnosis can be definitive, ~⅓ of clinical HMBS variants are missense variants, and most clinically-reported HMBS missense variants are designated as "variants of uncertain significance" (VUS). Using saturation mutagenesis, en masse selection, and sequencing, we applied a multiplexed validated assay to both the erythroid-specific and ubiquitous isoforms of HMBS, obtaining confident functional impact scores for >84% of all possible amino-acid substitutions. The resulting variant effect maps generally agreed with biochemical expectation. However, the maps showed variants at the dimerization interface to be unexpectedly well tolerated, and suggested residue roles in active site dynamics that were supported by molecular dynamics simulations. Most importantly, these HMBS variant effect maps can help discriminate pathogenic from benign variants, proactively providing evidence even for yet-to-be-observed clinical missense variants.

A pilot study to show that asymptomatic sexually transmitted infections alter the foreskin epithelial proteome.

There is limited data on the role of asymptomatic STIs (aSTIs) on the risk of human immunodeficiency virus (HIV) acquisition in the male genital tract (MGT). The impact of foreskin removal on lowering HIV acquisition is well described, but molecular events leading to HIV acquisition are unclear. Here, in this pilot study, we show that asymptomatic urethral infection with Chlamydia trachomatis (CT) significantly impacts the foreskin proteome composition. We developed and optimized a shotgun liquid chromatography coupled tandem mass spectrometry (MS)-based proteomics approach and utilized this on foreskins collected at medical male circumcision (MMC) from 16 aSTI+ men and 10 age-matched STI- controls. We used a novel bioinformatic metaproteomic pipeline to detect differentially expressed (DE) proteins. Gene enrichment ontology analysis revealed proteins associated with inflammatory and immune activation function in both inner and outer foreskin from men with an aSTI. Neutrophil activation/degranulation and viral-evasion proteins were significantly enriched in foreskins from men with aSTI, whereas homotypic cell-cell adhesion proteins were enriched in foreskin tissue from men without an aSTI. Collectively, our data show that asymptomatic urethral sexually transmitted infections result in profound alterations in epithelial tissue that are associated with depletion of barrier integrity and immune activation.

Diaphragmatic rupture in case of COVID-19 pneumonia- A rare presentation.

We describe the case of a male patient admitted to our emergency department during the COVID-19 pandemic with complaints of fever, severe breathlessness and dry cough associated with symptoms of gastric reflux for 5 days. Chest HRCT showed subtle multiple areas of diffuse patchy opacities with ground-glass haze with associated left subdiaphragmatic hernia and atelectasis of the left pulmonary lobe. Barium meal revealed subdiaphragmatic hernia. A nasopharyngeal swab for 2019-nCoV was positive. A diagnosis of diaphragmatic hernia in COVID-19 pneumonia was made. To our knowledge, spontaneous herniation of the diaphragm is a rare entity. Treatment for COVID-19 and empiric antibiotic therapy were promptly started and a decision of elective surgery was made.

Mycobacterium W. - An unusual side effect.

OBJECTIVE: To present an interesting case of unusual side effect of Mycobacterium W. in an adult COVID 19 positive male and discuss its assessment and management. METHODS: - DESIGN: Case Report. SETTING: Tertiary care hospital. PATIENT: One. RESULTS: 70 years male was admitted with complaints of fever, persistent dry cough since 10-12 days and progressive breathlessness since 3-4 days. Patient was found COVID-19 RTPCR positive and is known case of Type-II Diabetes with CAD (Post PTCA). Patient was managed conservatively with Oxygen support, I/V antibiotics, I/V Steroids, oral Favipiravir and other supportive treatment. Patient was also given injection Mycobacterium W. in dose of 0.3 ml per day intradermally at 3 different sites (both deltoids) consecutively for three days. 7-8 days after administration, patient developed bright red pustules which later got converted into small punched out ulcerations on all nine local sites of administration, which were managed conservatively with oral analgesics and local steroids for 8-10 days which healed without any scar formation. CONCLUSION: Injection Mycobacterium W. is used in COVID 19 patients as an immunomodulator agent and has been proved to be safe in most of the cases but we encountered this unusual side effect of bright red pustules formation at all nine local sites of injection in our case most likely because of being administered subcutaneously instead of intradermally, making this an interesting case which is being reported to scientific fraternity.

Beware of spurious tracheo-bronchial stents.

OBJECTIVE: To present a case of accidental sheath removal of tracheo-bronchial self-expandable metallic airway stent in a patient with endotracheal tumour. METHODS: Design: Case Report; Setting: Tertiary care hospital; Patient: One. RESULTS: A 65 years male, follow up case of endotracheal tumor with tracheo-bronchial self-expandable metallic stenting done presented with dry cough and difficulty in breathing since 8-10 days and suddenly coughed out thin whitish paper-like material 2 days back (which later proved as sheath of metallic stent). Direct laryngoscopy with flexible videobronchoscopy was done which showed tracheal stent well placed and intact, coughed out sheath couldn't be replaced back. Procedure was uneventful and patient was discharged in satisfactory condition and is doing well on regular follow up. CONCLUSION: Self-expandable metallic airway stents (SEMAS) represents a standard method of airways stenting especially when employed for the management of malignant central airway obstruction. Despite the obvious stenting advantages, it may be complicated with stent migration and accidental removal or coughing out of stent especially in high tracheal stenosis. In our case, as a peculiar complication there was accidental removal of the tracheal stent sheath which couldn't be replaced back whereas stent was well in place and intact. We need to be beware of such spurious tracheo-bronchial stents.

Sjogren's syndrome-An interesting case.

OBJECTIVE: To present a case of Sjogren syndrome with pulmonary manifestations in an adult female and discuss its assessment and management. DESIGN: Case Report. SETTING: Tertiary care hospital. PATIENT: One. RESULTS: A 50 yrs female admitted with complaints of dryness of eyes with decreased salivation causing difficulty in swallowing since last 3 years, with persistent dry cough since 10-15 days and progressive dyspnea since 4-5 days. Anti-nuclear antibody (ANA) profile revealed Anti- Ro/SS-A and Anti- La/SS-B Positive. Also, sub-lingual excisional biopsy was done which was consistent with findings of Sjogren's syndrome. Patient showed significant improvement after starting oral glucocorticoids, systemic anti inflammatory agents (Tab. HCQS), artificial tear drops, oral iron supplements and other supportive treatment. CONCLUSION: Sjögren syndrome (SS) is a chronic inflammatory disorder characterized by diminished lacrimal and salivary gland function and associated with lymphocytic infiltration of exocrine glands, and can affect extraglandular organ systems including the skin, lung, heart, kidney, neural, and hematopoietic systems. We present a case of Sjogren syndrome in an adult female presenting with xerostomia and dyspnea and was diagnosed upon detection of anti-Ro and anti-La antibodies and confirmed by histopathological examination of lip biopsy. Patient was started on oral steroids and other supportive treatment, General condition improved significantly and is doing very well on regular follow-up.

Thoracoscopic practices in India-a survey by Indian chest society.

BACKGROUND: Diagnostic thoracentesis is the initial diagnostic investigation in the workup of an undiagnosed Pleural effusion. However, a significant percentage of pleural effusions remain undiagnosed after this step and after closed pleural biopsy. Medical thoracoscopy (MT) has a high diagnostic yield in these patients. MT is now widely practised in India. This survey endeavours to study the practice of this technique by respiratory physicians in India. METHODS: An electronic survey called 'Indian Thoracoscopy survey' was prepared and conducted under the aegis of Indian Chest Society. In all there were 63 Questions in English prepared and disseminated as a "Google Form" to conduct this survey. The subjects were recruited from the e-mail lists of the three major professional surgeries that serve the interests of the respiratory physicians. The participation in the survey was voluntary and no incentive of any sort was offered to the participants. The survey link was kept open for a 3-month period. RESULTS: There were total 659 respondents, whose mean age was 41.5 years and majority of them were males (n = 564, 85.6%). The largest group of respondents practiced in corporate/private hospitals (n = 315, 47.8%). Only 311 (47.2%) respondents performed MT. Of these, 190 (61.1%) used flex-rigid/semi rigid thoracoscopes. Undiagnosed pleural effusions (N = 194; 62.4%) and recurrent pleural effusions (N = 117; 37.6%) were the most common indications for performing MT. Majority of the thoracoscopists (222, 71.4%) used conscious sedation and a combination of Midazolam and Fentanyl was the most preferred combination (n = 238; 76.5%). Most follow the manufacturer's recommendation for thoracoscope cleaning and disinfection and had safety check lists in place. CONCLUSION: Our survey captures the practice of MT in India. MT seems to be increasing in popularity with significant numbers of respiratory physicians performing the procedure. Respondents felt that MT was a valuable investigation that was underused and more of them wanted to learn. It is safe to perform MT under conscious sedation and local anaesthesia and a boon to patients who required surgical procedures for evaluation of difficult to diagnose pleural diseases. The setup cost is significant and would not justify installation in all centres. The lack of opportunities for training is something that needs to be looked in to.

Impact of training on use of inhalational techniques of different inhaler devices: A single institutional cross sectional observation study.

OBJECTIVE: To assess the impact of training on use of inhalational techniques of different inhaler devices in spirometry proved cases of COPD and Bronchial Asthma in a tertiary care centre. METHODS: A total of 128 spirometry proved cases of Asthma and COPD were enrolled. They were equally distributed in four groups comprising of 32 patients each according to their inhalation devices namely pMDI, Rotahaler, Accuhaler and Turbohaler. Patients were asked to demonstrate their inhalation technique and errors were noted according to their inhaler specific checklist. Patients were also interviewed regarding their knowledge about inhalation devices. Training about proper inhalation techniques was given to every participant. Rechecking of inhalation technique was again done at the second visit after 2 wks in the similar manner. Correct and incorrect steps of inhalation technique again evaluated by filling the checklist of the individual device to see post training improvement. RESULT: In our study, out of total cases more than one third of the patients were >60 yrs of age (41.4%) and most of the patients were males (62.5%). During the interview at first visit, almost 92% patients claimed to know how to use the inhalation device correctly but in reality most of the patients (around 96.1%) had committed at least one mistakes in their inhalation technique among all the inhalation steps. Errors were noted in different steps of inhalation including the essential steps among all the four devices. Statistically significant improvement in inhalation techniques including the essential steps were found among all the four devices after educational intervention and demonstration of sequential steps involved in particular inhaler. CONCLUSION: Our study confirmed a significant increase in the percentage of improvement in inhalation technique after proper demonstration and training about the inhalation devices. Inhalation technique including essential steps of inhalation significantly improved in all the four devices used.

Opaque hemithorax - An interesting case.

OBJECTIVE: To present an interesting case of left opaque hemithorax in an adult female and discuss its assessment and management. METHODS: Design: Case Report. SETTING: Tertiary care hospital. PATIENT: One. RESULTS: 44yrs retropositive female admitted with complaints of acute onset dry cough since 15-20 days, sudden breathlesness since 5 days which was progressive in nature, left sided heaviness in chest since 5 days. CECT Thorax showed complete collapse of left lung with cut off of left main bronchus while video bronchoscopy showed left main bronchus completely blocked with very thick necrotic mass and was difficult to dislodge. Debulking with cryo probe was done and left main bronchus was completely cleared off. Allergen panel showed very high serum IgE, high S.IgE against aspergillus and high specific S.IgG against aspergillus. Patient and her Chest X-ray showed significant improvement post cryo debulking and was discharged satisfactorily on oral voriconazole therapy. CONCLUSION: Endobronchial aspergillosis is characterized by massive intrabronchial overgrowth of the aspergillus species, mainly aspergillus fumigatus. Most patients with chronic pulmonary aspergillosis, including those with simple aspergillomas and Aspergillus nodules, have positive Aspergillus IgG antibodies in the blood. We hereby present a case of 44 yrs female presenting with complaints of dry cough and dyspnea and was diagnosed with endobronchial aspergillosis with complete obliteration of left main bronchus by fungal debris in which cryo debulking was done which relieved the symptoms significantly and was discharged in satisfactory condition on oral voriconazole therapy.

DISPOSABLE COVID BOX - A new invention.

OBJECTIVE: To introduce a new method to do safe bronchoscopy, a highly aerosol generating procedure through disposable COVID box in this difficult COVID time. METHODS: We have introduced an unbelievably cheap and effective method "DISPOSABLE COVID BOX". We took an acrylic board 70 × 20 cm and attached 3 bars 32 cm long and slide it under the side of the patient. A similar contraption is used on the other side. Then, it is covered by a polypropylene sheet 2' × 2'. It makes a completely disposable airtight chamber with the polypropylene sheet. We make a 1 cm nick in the sheet and introduce the video-bronchoscope, which is further navigated into the patient without any discomfort either to the patient or Bronchoscopist. When the procedure is finished, scope is withdrawn from the patient and the polypropylene sheet is squeezed out. The polypropylene sheet is removed and disposed off with all precautions, and the acrylic boards and the bars are cleaned with 1% Sodium hypochlorite solution. This way, the cost is only of polypropylene sheet which is negligible. RESULTS: Videobronchoscopies in indicated patients were done using this novel disposable covid box. This new invention called Disposable COVID box has been practiced for the first time, it's an innovative technique about which we want the world to be known. CONCLUSION: To conclude, there are no aerosols released in atmosphere after the procedure, making it absolutely safe for bronchoscopist and at same time patient also remains safe. We are ready again in no time with fresh polypropylene sheet to do the next bronchoscopy.

Radiology quiz- dancing ball.

We are presenting an interesting case of Pneumonia, who after good initial response deteriorated with recurrent hemoptysis. On culture of bronchial aspirate, patient had coexisting fungal infection and on repeat bronchoscopy showed a unique and rare picture. There was a dancing ball in RUL which was moving. Patient was initially managed conservatively but finally had to undergo lobectomy to achieve permanent cure.

Transbronchial lung cryobiopsy by twin bronchoscopes (kissing technique).

OBJECTIVE: To introduce a new & novel method of obtaining big lung tissue samples by transbronchial lung cryobiopsy by twin bronchoscopes (kissing technique) in an advanced interventional pulmonology suite. METHODS: In patients of diffuse parenchymal lung diseases, transbronchial lung cryobiopsy were taken using this novel approach using simultaneously two bronchoscopes under C- arm guidance under conscious sedation. First, a standard fibreoptic bronchoscope was inserted intranasally and fixed just above the area to be biopsied, then fogarty's catheter was introduced through FOB's suction channel and protruded it at the biopsy site. Second, another video bronchoscope was introduced orally by the side of FOB and cryobiopsy were taken using cryobiopsy forceps. Immediately, Fogarty's catheter was inflated and sealed the opening from where biopsy was taken to stop the bleeding. Third Video bronchoscope was also used which went up to larynx to take photograph of two bronchoscopes kissing each other and entering the vocal cords only, after which it was withdrawn. RESULTS: Transbronchial lung cryobiopsy in patients of diffuse parenchymal lung diseases were taken using this novel approach. This new technique called twin bronchoscopy (Kissing technique) has been practiced for the first time, it's a technique about which we want the world to be known. CONCLUSION: This new and novel two scope kissing bronchoscopy technique for TBLC under conscious sedation can be an alternative and fruitful method, especially the use of Fogarty's catheter to contain intra-bronchial bleeding. There is no deleterious effect on the patient and the patient can be discharged on the same day.

Predictors of success and failure of non-invasive ventilation use in type-2 respiratory failure.

BACKGROUND: Non-invasive ventilation is widely used now a days in patients with hypercapnic respiratory failure. Non-invasive ventilation can be used in Intensive Care Unit setting and wards provided trained staff is there to monitor. METHODS: This was a prospective observational study of 100 adult patients who were admitted with hypercapnic respiratory failure. Demographic information such as Age, Sex were recorded. Clinical parameters like Respiratory Rate, Heart Rate, Oxygen saturation and Arterial Blood Gas variables like pH, PaCO2, HCO3 were measured at the time of admission and at 1st hour, 4 hours and 24 hours after start of non-invasive ventilation. Outcome was recorded as success and failure with Non invasive ventilation. RESULTS: Out of 100 patients, 76 (76%) managed successfully with non-invasive ventilation and 24 patients (24%) needed intubation and invasive mechanical ventilation in this study. Majority of patients (76%) were with clinical diagnosis of Chronic Obstructive Pulmonary Disease. Respiratory Rate and Heart Rate were significantly lower and showed significant improvement at 1st hour, 4 hours and 24 hours in patients who successfully improved with Non invasive ventilation. Oxygen saturation was found to be significantly higher among patients successfully managed with Non invasive ventilation (84.35 ± 8.55 vs 76.87 ± 7.33) as compared to patients who required intubation. pH was found to be significantly higher (7.28 ± 0.06 vs 7.23 ± 0.05) in patients showing good response to Non invasive ventilation and improvement in pH at 1st hour, 4 hours and 24 hours was observed in patients successfully managed with Non invasive ventilation. PaCO2 level was found to be significantly lower and significant improvement in PaCO2 at 1st hour, 4 hours and 24 hours was seen in patients with Non invasive ventilation success. CONCLUSION: Improvement in clinical parameters like respiratory rate, heart rate, Oxygen saturation and improvement in ABG variables like pH, PaCO2 after 1st and 4 hours of start of Non invasive ventilation and maintaining the improvement at 24 hours are predictors of success of non-invasive ventilation in hypercapnic patients.

Endobronchial capillary hemangioma a rare cause of hemoptysis.

Endobronchial capillary hemangioma is a very rare benign tumor in adults. The clinical presentation and management of adult capillary hemangiomas involving the tracheobronchial tree are not yet established. We present a case of an isolated capillary hemangioma of the right main bronchus detected during the evaluation of an adult male presented with hemoptysis.

A Comprehensive, Flexible Collection of SARS-CoV-2 Coding Regions.

The world is facing a global pandemic of COVID-19 caused by the SARS-CoV-2 coronavirus. Here we describe a collection of codon-optimized coding sequences for SARS-CoV-2 cloned into Gateway-compatible entry vectors, which enable rapid transfer into a variety of expression and tagging vectors. The collection is freely available. We hope that widespread availability of this SARS-CoV-2 resource will enable many subsequent molecular studies to better understand the viral life cycle and how to block it.

Case of urinothorax - A rare presentation.

Urinothorax (UT) is a rare and often undiagnosed condition, defined as the presence of urine in the pleural cavity due to the retroperitoneal leakage of urine (known as urinoma) into the pleural space. It is a rare cause of pleural effusion and is secondary to traumatic or obstructive reasons. UT is usually a transudate pleural effusion. Its diagnosis requires a high degree of clinical suspicion, because the respiratory symptoms tend to be absent or mild and urological signs tend to dominate. Thoracocentesis followed by measurement of creatinine in the pleural fluid is a procedure to establish the true diagnosis. The average pleural fluid-to-serum creatinine ratio is in the range of 1.09-19.8. Pleural fluid-to-serum creatinine ratio >1 is the diagnostic criterion of UT. We report a case of UT associated with trauma.

Endo-bronchial application of glue in the management of hemoptysis.

BACKGROUND: Hemoptysis from varied etiologies, often fails to respond to conservative therapy. The conventional managements of such a situation are Bronchial Artery Embolization (BAE) or thoracic surgery which is often not possible. Endoscopic application of glue may stand as a method of therapy in these circumstances. METHODS: 202 patients of hemoptysis were treated by video-bronchoscopy assisted endobronchial application of glue (n-butyl cyanoacrylate) with the help of polyethylene catheter being placed through the working channel. The details of the procedure and their 6 month follow up are presented. RESULTS: Immediate control of hemoptysis was achieved in 183 i.e. 90.59% of patients. 19 patients had a partial response, i.e., hemoptysis stopped and then recurred, endobronchial application of glue was repeated in them out of which 14 (6.9%) responded to the second procedure whereas 5 (2.47%) failed to show any response in spite of the repeated procedure. The complication rate was 0.49% in the form of glue migrating into the trachea. There was no mortality. CONCLUSION: Endobronchial application of glue for hemoptysis can be an effective, economic and alternative therapy for mild to moderate hemoptysis.