Wavelet analysis of DNA sequences

Using wavelet transform as a core signal processing technique, this thesis work provides a new insight into understanding the DNA sequences, specifically genes with variable protein coding capabilities. The GC-rich region of gene tends to show a universal pattern when analyzed using three different kinds of wavelet transforms and to verify this approach, various model organisms and genes with different biological importance are chosen for analysis. Two different types of input signal were created from DNA sequence using Voss representation and Z-curve. The three existing variants of wavelet transform applied are discrete, complex and wavelet packets. Thus, a total of six plots were obtained from DNA sequence (genes) of each model species. The discrete and complex wavelet techniques were also applied to longer versions of DNA sequence (chromosomes and isochores). The uniformity of results for these techniques in all chosen species confirms and validates the research idea

Steganography based image compression

The intention of image compression is to discard worthless data from image so as to shrink the quantity of data bits favored for image depiction, to lessen the storage space, broadcast bandwidth and time. Likewise, data hiding convenes scenarios by implanting the unfamiliar data into a picture in invisibility manner. The review offers, a method of image compression approaches by using DWT transform employing steganography scheme together in combination of SPIHT to compress an image

Abdominal tuberculosis: a surgical emergency

Background: To study and assess the clinico-pathologic profile, intra-operative findings, surgical intervention performed and outcome in terms of morbidity and mortality of the patients included in the study group.Methods: This study was carried out at Lok Nayak Hospital and Maulana Azad Medical College, New Delhi, a tertiary care hospital between November 2011 to March 2015. It was a retrospective study in which the records of the patients operated upon in the emergency department as peritonitis or acute intestinal obstruction and whose diagnosis was later confirmed as tuberculosis on histopathology were analysed with regards clinic-pathologic profile, intra-operative findings, surgical intervention performed and outcome in terms of morbidity and mortality.Results: The mean age of our study group was 28.7 years. 70% of our patients were found to be in the underweight category and 30% were in the normal category. Fourty three (56.6%) presented to the hospital with features suggestive of peritonitis and thirty-three (43.4) were suffering from acute intestinal obstruction. The commonest intra-operative finding encountered was ileal perforation followed by multiple small bowel perforations, solitary stricture of the small bowel with perforation, ileo-cecal mass, adhesions or bands, single or multiple strictures, stricture with impending small bowel perforation and jejunal perforation. The frequently performed surgical procedures were ilesotomy, resection and anastamosis of the involved bowel, primary repair of thr perforation, right hemicolectomy, adhesiolysis, stricturoplasty (done in case of single stricture, mostly), jejunostomy and peritoneal and omental biopsy.Conclusions: Tuberculosis is a very grave disease, studies with larger number of patients need to be conducted to standardise its surgical management as at present there is no standardised surgical management protocol

Evaluating serum bilirubin levels in acute appendicitis and appendiceal perforation

Background: Acute appendicitis is one of the commonest surgical emergencies. Authors undertook this study to evaluate serum bilirubin levels in acute appendicitis and appendiceal perforation.Methods: A retrospective study evaluating the serum bilirubin levels in acute appendicitis and appendiceal perforation was carried out for 6 years at three tertiary care hospitals at India from 2014 to 2019. Patients having acute appendicitis and appendiceal perforation, confirmed on histopathology, with no other medical or surgical comorbidity were included in the study.Results: The total number of our study subjects was 927. 306 patients had appendiceal perforation, amongst these, 226 (74%) had hyperbilirubinemia. Out of the 621 patients having acute appendicitis only 186 (30%) had hyperbilirubinemia. The lowest and the highest serum bilirubin levels of this study group were 0.6 and 3.1 mg/dl, respectively, with an average of 1.6 mg/dl. In patients diagnosed to be having acute appendicitis, the lowest and highest serum bilirubin levels were 0.6 and 2.4 mg/dl, respectively, with an average of 1.3 mg/dl. As for the patients having appendiceal perforation the lowest and highest serum bilirubin levels were 0.8 and 3.1 mg/dl, respectively, with an average of 1.8 mg/dl.Conclusions: Hyperbilirubinemia is seen in acute appendicitis but predominantly in appendiceal perforation, so serum bilirubin estimation may help us in diagnosing appendiceal perforation pre-operatively if and when used in conjunction with other available diagnostic modalities

Prognostic implications of double J ureteral stenting in patients with renal stones undergoing extracorporeal shockwave lithotripsy

Background: Most patients with uncomplicated kidney stones can be successfully treated with extracorporeal shockwave lithotripsy (ESWL). Double-J ureteral stent is used to facilitate stone clearance, however double-J ureteral stents themselves may cause complications. Study conducted the study to know the exact role of double J stent in ESWL.Methods: 80 patients undergoing ESWL were divided into two groups, group A (n=40) double J stenting and group B (n=40) without double J stenting. Both groups were compared for stone fragmentation, stone clearance, number of shockwaves required for fragmentation, time required for passing through ureter, steinstrasse, Urinary Tract Infection.Results: Both the groups were comparable for age, sex, stone size and stone location distribution. There was no significant difference in clearance of stone and no. of shockwaves received for clearance in both the groups. The overall incidence of steinstrasse between the two groups was insignificant with a p value of 0.644. The incidence of UTI was significantly higher in stented group (p value 0.032).Conclusions: Study recommend ESWL without double J stent in patients having solitary renal calculus of size < 2 cm. Double J stent predisposes the patient to multiple complications including urinary tract infection which increases the morbidity of the patient. Based on our study we conclude that double J stenting in patients of renal calculus of size < 2cm, prior to ESWL is not beneficial

HIF-1α contributing to COVID-19 infections and poor prognosis in cancer patients – A hypothesis

In 2019, a new coronavirus (SARS-CoV-2) infecting Humans first identified in Wuhan, China, has caused the worst pandemic of the 21st century. This virus infection leads to the clinical symptoms that may range from asymptomatic condition to life-threatening illness. The insights from the recent studies suggest that SARS-CoV-2 requires a host enzyme, Furin to activate receptor-binding domain (RBD) of its S protein. Upon binding of RBD to host cell membrane-bound Angiotensin Convertase Enzyme 2 (ACE2), it facilitates the entry of virus in the host cell. Evidence from the literature also suggests that HIF-1α (Hypoxia-inducible factor 1-α) is one of the factors regulating the expression of Furin. In addition, it is also well documented that the interior of solid tumours, which grow very fast, leads to the hypoxic tumour microenvironment, resulting in overexpression and release of HIF-1α. The SARS-CoV-2 infected patients with severe tissue damage and inflammatory injury also suffer from tissue hypoxia. So, we hypothesize that hypoxic condition due to tumour microenvironment in cancer patients upregulates the HIF-1α, leading to increased expression of Furin. Upon infection of cancer patients with SARS-CoV-2 having increased Furin expression in the cells due to upregulation of HIF-1α, leads to the entry of a greater number of SARS-CoV-2 virus in these cells resulting in severe infection. The vicious cycle of the virus infection in which virus is more easily invaded into surrounding tissue leads to the involvement of multiple organs and ultimately poor prognosis in the disease outcome. Therefore, we suggest evaluating the expression of HIF-1α in SARS-CoV-2 infections at an early phase of infection particularly in patients with comorbidities like solid malignancies as well as patients having signs and symptoms of hypoxia. It is also suggested that continuous monitoring of the SpO2 level and early institution of preventive O2 therapy at an early stage in these patients may lead to lesser morbidity as well as mortality in COVID-19 patients

HIF-1α contributing to COVID-19 infections and poor prognosis in cancer patients – A hypothesis

670-675In 2019, a new coronavirus (SARS-CoV-2) infecting Humans first identified in Wuhan, China, has caused the worst pandemic of the 21st century. This virus infection leads to the clinical symptoms that may range from asymptomatic condition to life-threatening illness. The insights from the recent studies suggest that SARS-CoV-2 requires a host enzyme, Furin to activate receptor-binding domain (RBD) of its S protein. Upon binding of RBD to host cell membrane-bound Angiotensin Convertase Enzyme 2 (ACE2), it facilitates the entry of virus in the host cell. Evidence from the literature also suggests that HIF-1α (Hypoxia-inducible factor 1-α) is one of the factors regulating the expression of Furin. In addition, it is also well documented that the interior of solid tumours, which grow very fast, leads to the hypoxic tumour microenvironment, resulting in overexpression and release of HIF-1α. The SARS-CoV-2 infected patients with severe tissue damage and inflammatory injury also suffer from tissue hypoxia. So, we hypothesize that hypoxic condition due to tumour microenvironment in cancer patients upregulates the HIF-1α, leading to increased expression of Furin. Upon infection of cancer patients with SARS-CoV-2 having increased Furin expression in the cells due to upregulation of HIF-1α, leads to the entry of a greater number of SARS-CoV-2 virus in these cells resulting in severe infection. The vicious cycle of the virus infection in which virus is more easily invaded into surrounding tissue leads to the involvement of multiple organs and ultimately poor prognosis in the disease outcome. Therefore, we suggest evaluating the expression of HIF-1α in SARS-CoV-2 infections at an early phase of infection particularly in patients with comorbidities like solid malignancies as well as patients having signs and symptoms of hypoxia. It is also suggested that continuous monitoring of the SpO2 level and early institution of preventive O2 therapy at an early stage in these patients may lead to lesser morbidity as well as mortality in COVID-19 patients

Gene Structure Induced Epigenetic Modifications of pericarp color1 Alleles of Maize Result in Tissue-Specific Mosaicism

BACKGROUND: The pericarp color1 (p1) gene encodes for a myb-homologous protein that regulates the biosynthesis of brick-red flavonoid pigments called phlobahpenes. The pattern of pigmentation on the pericarp and cob glumes depends upon the allelic constitution at the p1 locus. p1 alleles have unique gene structure and copy number which have been proposed to influence the epigenetic regulation of tissue-specific gene expression. For example, the presence of tandem-repeats has been correlated with the suppression of pericarp pigmentation though a mechanism associated with increased DNA methylation. METHODOLOGY/PRINCIPAL FINDINGS: Herein, we extensively characterize a p1 allele called P1-mosaic (P1-mm) that has mosaic pericarp and light pink or colorless cob glumes pigmentation. Relative to the P1-wr (white pericarp and red cob glumes), we show that the tandem repeats of P1-mm have a modified gene structure containing a reduced number of repeats. The P1-mm has reduced DNA methylation at a distal enhancer and elevated DNA methylation downstream of the transcription start site. CONCLUSIONS/SIGNIFICANCE: Mosaic gene expression occurs in many eukaryotes. Herein we use maize p1 gene as model system to provide further insight about the mechanisms that govern expression mosaicism. We suggest that the gene structure of P1-mm is modified in some of its tandem gene repeats. It is known that repeated genes are susceptible to chromatin-mediated regulation of gene expression. We discuss how the modification to the tandem repeats of P1-mm may have disrupted the epigenetic mechanisms that stably confer tissue-specific expression

Carcinoid Klatskin tumour: A Rare Cause of Obstructive Jaundice

Carcinoid tumours of the extrahepatic biliary ducts represent an extremely rare cause of bile duct obstruction. We report a case of obstructive jaundice secondary to carcinoid tumour arising at the hilar confluence. Resection of the primary tumour was done and the patient is doing well on follow-up. This case demonstrated that surgery offers the only potential cure for biliary carcinoid and aggressive surgical therapy should be the preferred treatment in cases of potentially resectable biliary tumours

Expression of a putative \u3ci\u3eflavonoid 3\u27-hydroxylase\u3c/i\u3e in sorghum mesocotyls synthesizing 3-deoxyanthocyanidin phytoalexins

In sorghum, ingress of Cochliobolus heterostrophus stimulates the synthesis of 3-deoxyanthocyanidins that act as phytoalexins. Apigeninidin and luteolinidin are two major phytoalexins induced in the first 24 h after infection. In an attempt to understand genetic regulation of the biosynthesis of sorghum phytoalexins, we isolated a differentially expressed partial cDNA. Characterization and comparison showed that this cDNA sequence corresponds to a putative flavonoid 3’-hydroxylase. Full length sequence characterization allowed us to establish that the sorghum putative f3’h cDNA encodes a peptide of 517 amino acids that has domains conserved among cytochrome P450 proteins functioning in the flavonoid biosynthetic pathway. Heterologous expression of the putative f3’h cDNA in Escherichia coli yielded a membrane preparation that catalyzed the hydroxylation of naringenin. We show here that transcription of the flavonoid 3’-hydroxylase was coordinately regulated with that of chalcone synthase and dihydroflavonol reductase, and expression of these genes was induced within the first 24 h of fungal challenge. Synthesis of apigeninidin and luteolinidin followed the induced expression of the f3’h gene, implicating its role in fungal induced expression of sorghum phytolaexins