Integrated genomic view of SARS-CoV-2 in India

India first detected SARS-CoV-2, causal agent of COVID-19 in late January-2020, imported from Wuhan, China. March-2020 onwards; importation of cases from rest of the countries followed by seeding of local transmission triggered further outbreaks in India. We used ARTIC protocol based tiling amplicon sequencing of SARS-CoV-2 (n=104) from different states of India using a combination of MinION and MinIT from Oxford Nanopore Technology to understand introduction and local transmission. The analyses revealed multiple introductions of SARS-CoV-2 from Europe and Asia following local transmission. The most prevalent genomes with patterns of variance (confined in a cluster) remain unclassified, here, proposed as A4-clade based on its divergence within A-cluster. The viral haplotypes may link their persistence to geo-climatic conditions and host response. Despite the effectiveness of non-therapeutic interventions in India, multipronged strategies including molecular surveillance based on real-time viral genomic data is of paramount importance for a timely management of the pandemic.

Intelligent Handheld Expert System (HES) For Diagnosis Of Autism Spectrum Disorder And Its Severity Level

@#Objective: Autism Spectrum Disorder (ASD) is a complex neurological developmental disorder that could be diagnosed early usually before the age of 3 years and the diagnosis is the most important determining factor for the treatment of ASD. The aim of present work is to design and implement a Handheld Expert System (HES) based on Diagnostic and Statistical Manual of Mental Disorder, fifth edition (DSM-V) for the diagnosis and severity assessment of ASD. The hand-held device was trained by artificial neural network to correctly diagnosis ASD and identifies its severity level. Methods: The learning of HES for ASD diagnosis was performed by a back propagation neural network algorithm with data set created based on DSM-V. The ability of Artificial Intelligence (AI) based HES was measured in terms of epochs, training/testing data, and statistical stability on the basis of accuracy, losses, mean squared error, and execution time to validate the performance of the system. The HES was designed to consume less training/testing time with more efficient and accurate AI approach. The stability of HES was validated for the data set of 40 ASD and Typically Developed (TD) subjects (20 ASD and 20 TD). Results: The implementation of HES for diagnosis of 40 subjects (20 ASD and 20 TD) based on the proposed expert system has provided 100% accuracy in reference with DSM-V. The results were also validated by statistical analysis. Conclusion: Since AI based HES for diagnosis of ASD and determination of its severity provided accurate results in reference to DSM-V criteria, the possibility of the use of proposed HES for diagnosis of ASD is very high.

Advanced MRI Techniques in the Evaluation of Complex Cystic Breast Lesions.

OBJECTIVE: The purpose of this research work was to evaluate complex cystic breast lesions by advanced MRI techniques and correlating imaging with histologic findings. METHODS AND MATERIALS: In a cross-sectional design from September 2013 to August 2015, 50 patients having sonographically detected complex cystic lesions of the breast were included in the study. Morphological characteristics were assessed. Dynamic contrast-enhanced MRI along with diffusion-weighted imaging and MR spectroscopy were used to further classify lesions into benign and malignant categories. All the findings were correlated with histopathology. RESULTS: Of the 50 complex cystic lesions, 32 proved to be benign and 18 were malignant on histopathology. MRI features of heterogeneous enhancement on CE-MRI (13/18), Type III kinetic curve (13/18), reduced apparent diffusion coefficient (18/18), and tall choline peak (17/18) were strong predictors of malignancy. Thirteen of the 18 lesions showed a combination of Type III curve, reduced apparent diffusion coefficient value, and tall choline peak. CONCLUSIONS: Advanced MRI techniques like dynamic imaging, diffusion-weighted sequences, and MR spectroscopy provide a high level of diagnostic confidence in the characterization of complex cystic breast lesion, thus allowing early diagnosis and significantly reducing patient morbidity and mortality. From our study, lesions showing heterogeneous contrast enhancement, Type III kinetic curve, diffusion restriction, and tall choline peak were significantly associated with malignant complex cystic lesions of the breast.

Evaluation of Traumatic Spine by Magnetic Resonance Imaging and Correlation with Neurological Recovery

STUDY DESIGN: Prospective study. PURPOSE: To compare magnetic resonance imaging (MRI) findings with clinical profile and neurological status of the patient and to correlate the MRI findings with neurological recovery of the patients and predict the outcome. OVERVIEW OF LITERATURE: Previous studies have reported poor neurological recovery in patients with cord hemorrhage, as compared to cord edema in spine injury patients. High canal compromise, cord compression along with higher extent of cord injury also carries poor prognostic value. METHODS: Neurological status of patients was assessed at the time of admission and discharge in as accordance with the American Spine Injury Association (ASIA) impairment scale. Mean stay in hospital was 14.11+/-5.74 days. Neurological status at admission and neurological recovery at discharge was compared with various qualitative cord findings and quantitative parameters on MRI. In 27 patients, long-term follow-up was done at mean time of 285.9+/-43.94 days comparing same parameters. RESULTS: Cord edema and normal cord was associated with favorable neurological outcome. Cord contusion showed lesser neurological recovery, as compared to cord edema. Cord hemorrhage was associated with worst neurological status at admission and poor neurological recovery. Mean canal compromise (MCC), mean spinal cord compression (MSCC) and lesion length values were higher in patients presenting with ASIA A impairment scale injury and showed decreasing trends towards ASIA E impairment scale injury. Patients showing neurological recovery had lower mean MCC, MSCC, and lesion length, as compared to patients showing no neurological recovery (p<0.05). CONCLUSIONS: Cord hemorrhage, higher MCC, MSCC, and lesion length values have poor prognostic value in spine injury patients.

Breast Positioning during Mammography: Mistakes to be Avoided.

AIMS AND OBJECTIVES: Breast positioning is the key factor affecting a mammogram. If care is taken during positioning, it maximizes the amount of breast tissue being imaged, eliminates most of the artifacts, and increases sensitivity of the mammogram. This retrospective study was carried out in our department to assess correctness, and also the incorrectness of breast positioning, which need to be avoided to obtain an ideal mammogram. MATERIAL AND METHODS: A total of 1369 female patients were included in this study. Mammography was performed on full field detector digital mammography equipment. Craniocaudal (CC) view and mediolateral oblique (MLO) view were carried out for each breast. Four views were done for 1322 patients. The remaining 47 patients had undergone a mastectomy and underwent two views for the other breast. Mistakes in improperly positioned mammogram were assessed with respect to proper visualization of nipple, position of pectoralis major, pectoral-nipple distance (PND), inframammary fold, and adequate coverage of all breast quadrants. RESULTS: As per prescribed guidelines, mistakes in positioning were recognized in 2.879% of total mammograms. Improper positioning of the nipple was the commonest problem, seen in 3.827% of mammograms, CC view. On MLO view, bilaterally, pectoralis shadow was not seen in 0.520% mammograms, its margin was not straight/convex in 0.706%, lower edge of pectoralis was above pectoralis-nipple line in 2.081%, and inframammary fold was not seen in 1.189%. There was inadequate coverage of lower quadrants in 2.787%, and mismatch in PND was seen in 3.864%. In few of the patients, the shortcomings as a result of improper positioning were noted on one view, the rest being normal. CONCLUSION: Positioning is the most important factor affecting the resultant mammography image. During mammography, many cases are improperly positioned and as a result the examination is inconclusive, which reduces the sensitivity of mammography.

Utility of gray-scale ultrasound to differentiate benign from malignant thyroid nodules.

OBJECTIVE: The objective was to assess the utility of gray-scale USG to identify patterns of thyroid nodules and to correlate the characteristics of benign and malignant nodules with pathological diagnosis. MATERIALS AND METHODS: From September 2009 to August 2010, a total of 203 patients (17 males and 186 females), with 240 nodules detected at USG, were included in this study. The characteristics of each nodule were determined. The results were then compared with fine needle aspiration (FNA)/histopathological diagnosis. RESULTS: Of the 240 nodules examined, 44 (18.33%) were found to be malignant on cytopathology. The malignant nodules demonstrated solid or predominantly solid composition (sensitivity 88.6%, specificity 53.5%); presence of microcalcification (sensitivity 65.9%, specificity 97.9%); irregular or poorly defined margins (sensitivity 84%, specificity 88.7%); anteroposterior (AP) diameter > transverse diameter (sensitivity 77.2%, specificity 80.1%); absent or thick incomplete halo (sensitivity 70.4%, specificity 65.8%); and markedly hypoechoic character (sensitivity 65.9%, specificity 84.6%). Among males, malignant nodules were found in 36.8%, whereas in females the occurrence was 16.7%. CONCLUSION: Gray-scale USG features of thyroid nodules are useful to distinguish patients with clinically significant thyroid nodules from those with innocuous nodules despite the overlap of findings. From our study, it is apparent that the USG findings of poorly defined margins, marked hypoechogenicity, microcalcifications, and a taller-than-wider shape have a high diagnostic accuracy for identifying malignant thyroid nodules.

Evaluation of sentinel node biopsy in locally advanced breast cancer patients who become clinically node-negative after neoadjuvant chemotherapy: a preliminary study.

Introduction. Controversy continues over the appropriate timing of sentinel lymph node (SLN) biopsy in locally advanced breast cancer (LABC) patients receiving neoadjuvant chemotherapy. We evaluated the feasibility and accuracy of SLN biopsy in LABC patients with cytology-proven axillary nodal metastasis who become clinically node-negative after neoadjuvant chemotherapy. Materials. 30 consecutive patients with LABC, who had become clinically node-negative after 3 cycles of neoadjuvant chemotherapy, were included in the study. They were then subjected to SLN biopsy, axillary lymph node dissection, and breast surgery. Results. Sentinel nodes were successfully identified in 26 of the 30 patients, resulting in an identification rate of 86.67%, sensitivity of 83.33%, false negative rate of 20%, negative predictive value of 72.73%, and an overall accuracy of 88.46%. No complications were observed as a result of dye injection. Conclusions. SLN biopsy is feasible and safe in LABC patients with cytology-positive nodes who become clinically node-negative after neoadjuvant chemotherapy. Our accuracy rate, identification rate, and false negative rate are comparable to those in node-negative LABC patients. SLN biopsy as a therapeutic option in LABC after neoadjuvant chemotherapy is a promising option which should be further investigated.

Pictorial essay: Mammography of the male breast.

Mammography is an imaging modality that is widely perceived to be of use only in women for the detection and diagnosis of breast pathologies. Here, we present a pictorial essay on the mammographic spectrum of male breast pathologies.