Identification of cancer types from gene expressions using learning techniques.

Tumor is the major cause of death all around the world in recent days. Early detection and prediction of a cancer type are important for a patient's well-being. Functional genomic data has recently been used in the effective and early detection of cancer. According to previous research, the use of microarray data in cancer prediction has evidenced two main problems as high dimensionality and limited sample size. Several researchers have used numerous statistical and machine learning-based methods to classify cancer types but still, limitations are there which makes cancer classification a difficult job. Deep Learning (DL) and Convolutional Neural Networks (CNN) have been proven with effective analyses of unstructured data including gene expression data. In the proposed method gene expression data for five types of cancer is collected from The Cancer Genome Atlas (TCGA). Prominent features are selected using a hybrid Particle Swarm Optimization (PSO) and Random Forest (RF) algorithm followed by the use of Principal Component Analysis (PCA) for dimensionality reduction. Finally, for classification blend of Convolutional Neural Network (CNN) and Bi-directional Long Short Term Memory (Bi-LSTM) is used to predict the target type of cancer. Experimental results demonstrate that accuracy of the proposed method is 96.89%. As compared to existing work, our method outperformed with better results.

Study of Extramedullary Lymphoblastic Lymphoma (LBL) Diagnosed by Flowcytometric Immunophenotyping (FCI) on Fine Needle Aspirate (FNA) Sample-A Case Series of 18 Cases.

Background: Lymphoblastic lymphoma (LBL) accounts for about 2% of all lymphomas. Recognition of T/B-LBL albeit of their rareness is very important as they present as localized diseases with low tumor burden. They can present both at nodal and extranodal sites. Limitation of diagnosis and classification of lymphoma on fine needle aspirate (FNA) can be minimized by clubbing it with flowcytometric immunophenotyping (FCI) to ensure diagnostic accuracy rapidly. Aim: Study of a series of 18 cases of LBL to assess the utility of FCI on FNA and effusion samples in extramedullary LBL. Methods and Material: FCI was done on FNA and effusion samples from 130 morphologically diagnosed/suspicious cases of lymphoreticular malignancy, followed by peripheral blood and bone marrow (BM) examination. The patients diagnosed to have B/T LBL, based on WHO 2017 classification, were selected for further analyses. Results: FCI of 130 cases showed 91 mature and 18 precursor lymphoid neoplasms. These 18 cases were from lymph nodes (11), pleural fluid (03), and soft tissue masses (04). Peripheral blood and BM of 15/18 cases were normal of which FCI revealed T-LBL (11) and B-LBL (04). Two cases (both T LBL) showed BM involvement (<25%), while one case of B-LBL which was misdiagnosed as mature lymphoma by immunohistochemistry (IHC) evolved as B ALL. Conclusions: Diagnosis of extramedullary B/T-LBL needs comprehensive evaluation of clinical presentation, cytomorphology, and immunophenotyping. Rapid and accurate diagnosis by FCI on FNA and effusion samples allows early therapeutic decisions, thereby avoiding leukemic dissemination.

Molecular cloning and characterization of a 3-hydroxy-3-methylglutaryl-coenzyme A reductase 1 (hmgr1) gene from rubber tree (Hevea brasiliensis Muell. Arg.): A key gene involved in isoprenoid biosynthesis.

Natural rubber (cis-1,4-polyisoprene) is a secondary metabolite produced in the laticiferous tissue of Hevea tree. Mevalonate synthesis, which is the first step in isoprenoid biosynthesis, is catalyzed by the enzyme 3-hydroxy-3-methylglutarylcoenzyme A reductase 1 (hmgr1). We have cloned and characterized a full-length cDNA as well as genomic DNA for hmgr1 gene from an elite Indian rubber clone (RRII 105). The nucleotide sequence of the genomic clone comprises 4 exons and 3 introns, giving a total length of 2440 bp. The sequences of 42 bp 5' UTR and 69 bp of the 3' UTR were also determined. The hmgr1 cDNA contained an open reading frame of 1838 bp coding for 575 amino acid protein with a theoretical pI value of 6.6 and the calculated protein M W was 61.6 kDa. The deduced amino acid sequence showed high identity with other plant hmgr1 sequences. The amino acid sequence of the Hevea hmgr1 revealed several motifs which are highly conserved and common to the other plant species. These sequence conservations suggest a strong evolutionary pressure to maintain amino acid residues at specific positions, indicating that the conserved motifs might play important roles in the structural and/or catalytic properties of the enzyme. Southern blot analysis of genomic DNA from Hevea probed with a genomic fragment indicated that there were at least three isoforms of hmgr in Hevea. This result reveals that hmgr1 is one of the members of a small gene family. (Northern blot analysis showed that hmgr1 mRNA transcripts were noticed in all tissues - latex, leaf, immature leaf, and seedlings), however, the abundance of transcript level was higher in latex cells. As one step towards a better understanding of the role that this enzyme plays in coordinating isoprenoid biosynthesis in plants, hmgr1 cDNA was over expressed in transgenic Arabidopsis plants. Transgenic plants were morphologically distinguishable from control wild-type plants and an increased expression level of hmgr1 mRNA was detected. These data suggest that hmgr1 gene expression is playing an important role in isoprenoid biosynthesis.

Over-expression of 3-hydroxy-3- methylglutaryl-coenzyme A reductase 1 (hmgr1) gene under super-promoter for enhanced latex biosynthesis in rubber tree (Hevea brasiliensis Muell. Arg.).

Natural rubber (cis-1, 4-polyisoprene) is being produced from bark laticifer cells of Hevea brasiliensis and the popular high latex yielding Indian rubber clones are easily prone to onset of tapping panel dryness syndrome (TPD) which is considered as a physiological syndrome affecting latex production either partially or completely. This report describes an efficient protocol for development of transgenic rubber plants by over-expression of 3-hydroxy 3-methylglutaryl Co-enzyme A reductase 1 (hmgr1) gene which is considered as rate limiting factor for latex biosynthesis via Agrobacterium-mediated transformation. The pBIB plasmid vector containing hmgr1 gene cloned under the control of a super-promoter was used for genetic transformation using embryogenic callus. Putatively transgenic cell lines were obtained on selection medium and produced plantlets with 44% regeneration efficiency. Transgene integration was confirmed by PCR amplification of 1.8 kb hmgr1 and 0.6 kb hpt genes from all putatively transformed callus lines as well as transgenic plants. Southern blot analysis showed the stable integration and presence of transgene in the transgenic plants. Over expression of hmgr1 transgene was determined by Northern blot hybridization, semi-quantitative PCR and real-time PCR (qRT-PCR) analysis. Accumulation of hmgr1 mRNA transcripts was more abundant in transgenic plants than control. Increased level of photosynthetic pigments, protein contents and HMGR enzyme activity was also noticed in transgenic plants over control. Interestingly, the latex yield was significantly enhanced in all transgenic plants compared to the control. The qRT-PCR results exhibit that the hmgr1 mRNA transcript levels was 160-fold more abundance in transgenic plants over untransformed control. These results altogether suggest that there is a positive correlation between latex yield and accumulation of mRNA transcripts level as well as HMGR enzyme activity in transgenic rubber plants. It is presumed that there is a possibility for enhanced level of latex biosynthesis in transgenic plants as the level of mRNA transcripts and HMGR enzyme activity is directly correlated with latex yield in rubber tree. Further, the present results clearly suggest that the quantification of HMGR enzyme activity in young seedlings will be highly beneficial for early selection of high latex yielding plants in rubber breeding programs.

Lipid metabolic perturbation is an early-onset phenotype in adult spinster mutants: a Drosophila model for lysosomal storage disorders.

Intracellular accumulation of lipids and swollen dysfunctional lysosomes are linked to several neurodegenerative diseases, including lysosomal storage disorders (LSD). Detailed characterization of lipid metabolic changes in relation to the onset and progression of neurodegeneration is currently missing. We systematically analyzed lipid perturbations in spinster (spin) mutants, a Drosophila model of LSD-like neurodegeneration. Our results highlight an imbalance in brain ceramide and sphingosine in the early stages of neurodegeneration, preceding the accumulation of endomembranous structures, manifestation of altered behavior, and buildup of lipofuscin. Manipulating levels of ceramidase and altering these lipids in spin mutants allowed us to conclude that ceramide homeostasis is the driving force in disease progression and is integral to spin function in the adult nervous system. We identified 29 novel physical interaction partners of Spin and focused on the lipid carrier protein, Lipophorin (Lpp). A subset of Lpp and Spin colocalize in the brain and within organs specialized for lipid metabolism (fat bodies and oenocytes). Reduced Lpp protein was observed in spin mutant tissues. Finally, increased levels of lipid metabolites produced by oenocytes in spin mutants allude to a functional interaction between Spin and Lpp, underscoring the systemic nature of lipid perturbation in LSD.

C-Peptide responses to glucose load in maturity-onset diabetes of the young (MODY).

Pancreatic beta cell responses were measured in obese and nonobese maturity-onset diabetes of the young (MODY) patients by estimating serum immunoreactive insulin (IRI) and C-peptide (CP) during oral glucose tolerance testing (OGTT). The serum CP responses were generally low in MODY patients and more pronounced in obese patients. The IRI responses were heterogenous; some patients had normal and others low responses. It was observed that in several patients there was a relatively higher IRI concentration in comparison with the CP values, as indicated by low CP and normal IRI values. This is suggestive of altered metabolic fates of insulin and CP in the MODY patients.

Pancreatic beta-cell function in tropical pancreatic diabetes.

Individuals with tropical pancreatic diabetes (TPD) have features of malnutrition and insulin-dependent diabetes but do not exhibit ketosis on withdrawal of insulin. Fasting and postglucose C-peptide responses were assessed in TPD and compared with noninsulin-dependent (NIDDM), insulin-dependent (IDDM), and control groups, matched for body weight. The C-peptide concentrations were lower in TPD in comparison with the controls and NIDDM patients but were significantly higher than in classical IDDM. It is likely that the higher C-peptide is responsible for the ketosis resistance in these patients.

Serum uric acid concentrations in offspring of conjugal diabetic parents.

Serum uric acid concentrations were measured in offspring of conjugal diabetic parents, in diabetic patients, and in matched nondiabetic controls. The mean uric acid level in offspring of conjugal diabetic parents was significantly higher than in the controls and diabetic patients (P less than 0.001 in the nonobese and P less than 0.05 in the obese). Diabetic patients did not show significant differences in the serum uric acid concentration compared to the controls. The elevated level of serum uric acid in offspring of conjugal diabetic parents could possibly be an early biochemical marker of diabetes.

Prevalence of overweight and obesity in affluent adolescent girls in Chennai in 1981 and 1998.

This study was conducted to assess the prevalence of obesity and overweight in adolescent public school girls ( 10-15 years of age) of Chennai in 1981 and 1998. The first part of the study done in the year 1981 (Group I; n = 707) was compared with the second part in 1998 (Group II; I = 610). Overweight and obesity were denoted by body mass index (BMI) above 85th and 95th percentile respectively. The prevalence of overweight (9.6 per cent in 1981 and 9.7 per cent in 1998) and obesity (5. 9 per cent in 1981 and 6.2 per cent in 1998) was comparable in both studies. It was also observed that the BMI for the corresponding age showed an increase front 1981 to 1998.

Management of febrile neutropenia in solid organ malignancies following chemotherapy.

BACKGROUND: Febrile neutropenia is a medical emergency and it requires immediate hospitalization for evaluation and administration of empiric broad-spectrum antibiotics. The present study was undertaken to analyze the infectious agents, choice of empiric antibiotics, and outcome in high-risk febrile neutropenia in the solid organ malignancies. MATERIALS AND METHODS: In this study, 92 high risk febrile neutropenic episodes were analyzed in 72 patients with solid organ malignancies. We used cefoperazone-sulbactum as an initial empiric antibiotic. Piperacillin/tazobactum or carbapenems were added to the patients who did not respond to initial antibiotic. RESULTS: Among the 92 episodes treated, most patients received first-line chemotherapy for locally advanced disease. Microbes were isolated in 25% of febrile neutropenic episodes. Gram-negative organism (61.70%) constituted the most common isolates. The most common microbes identified were E. coli and Staphylococcus aureus in blood, Klebsiella pneumonia in sputum and E. coli in urine culture. Patients who had been treated with cefoperazone-sulbactum improved clinically in 70.6% of febrile neutropenic episodes. Second- line antibiotics (piperacillin-tazobactum with amikacin) were required in 24% episodes, while another 5.4% episodes required third-line antibiotics (carbapenems). In this study, mortality was seen in 12% of febrile neutropenic episodes. Staphylococcus aureus was 100% sensitive to linezolid, teicoplanin, and vancomycin, whereas Gram-negative organisms were 100% sensitive to imepenem and meropenem. CONCLUSION: Cephaperazone-sulbactum is a reasonable initial choice for empirical therapy in high risk febrile neutropenic patients in solid organ malignancies.

Clinical and microbiological profile of febrile neutropenia in solid tumors and hematological malignancies at a tertiary cancer care center in South India.

BACKGROUND: Febrile neutropenia (FN) is a common but serious complication of chemotherapy in patients with solid tumors (ST) and hematological malignancies (HM). The epidemiology of FN keeps changing. OBJECTIVE: The objective was to study the epidemiology of FN in adult patients with ST and HM at Kidwai Memorial Institute of Oncology, Bangalore - A tertiary cancer care center. MATERIALS AND METHODS: Data of all episodes of FN that occurred during the period July 2011 to December 2011 were collected prospectively and analyzed. RESULTS: A total of 75 episodes of FN was observed during study period involving 55 patients. Febrile neutropenic episodes were more frequent in HM than in ST (57% vs. 43%). The rate of bloodstream infection was 14.7%. Gram-negative organisms were the predominant isolates (56.25%). Overall mortality rate was 13.3%. Presence of medical co-morbidity and positive culture predicted high mortality. Mortality rate did not differ significantly between HM and ST (14% vs. 12.5%; P = 1.0). Gram-positive bacteremia was associated with greater mortality than Gram-negative bacteremia (P = 0.02). CONCLUSION: Empiric antibiotic treatment for FN should be tailored to the locally prevalent pathogens and their susceptibility patterns.

Effect of the integrated approach of yoga therapy on platelet count and uric acid in pregnancy: A multicenter stratified randomized single-blind study.

BACKGROUND: Yoga improves maternal and fetal outcomes in pregnancy. Platelet Count and Uric acid (Ua) are valuable screening measures in high-risk pregnancy. AIM: To examine the effect of yoga on platelet counts and serum Ua in high-risk pregnancy. MATERIALS AND METHODS: This stratified randomized controlled trial, conducted by S-VYASA University at St. John's Medical College Hospital and Gunasheela Maternity Hospital, recruited 68 women with high-risk pregnancy (30 yoga and 38 controls) in the twelfth week of pregnancy. The inclusion criteria were: Bad obstetrics history, twin pregnancies, maternal age < 20 or > 35 years, obesity (BMI > 30), and genetic history of pregnancy complications. Those with normal pregnancy, anemia (< 10 grams%dl), h/o clotting disorders; renal, hepatic or heart disease; seizure disorder; or structural abnormalities in the pelvis, were excluded. The yoga group practiced simple meditative yoga (three days / week for three months). RESULTS: At baseline, all women had normal platelet counts (> 150×10(9)/L) with a decrease as pregnancy advanced. Ua (normal at baseline) increased in both groups. No one developed abnormal thrombocytopenia or hyperuricemia. Healthy reduction in platelet count (twelfth to twentieth week) occurred in a higher (P < 0.001, Chi(2) test) number of women in the yoga group than the control group. A similar trend was found in uric acid. Significantly lesser number of women in the yoga group (n = 3) developed pregnancy-induced hypertension (PIH) / pre-eclampsia (PE) than those in the control group (n = 12), with absolute risk reduction (ARR) by 21%. CONCLUSION: Antenatal integrated yoga from the twelfth week is safe and effective in promoting a healthy progression of platelets and uric acid in women with high-risk pregnancy, pointing to healthy hemodilution and better physiological adaptation.

Photodermatoses in India.

Photodermatoses are a group of disorders resulting from abnormal cutaneous reactions to solar radiation. They include idiopathic photosensitive disorders, drug or chemical induced photosensitivity reactions, DNA repair-deficiency photodermatoses and photoaggravated dermatoses. The pathophysiology differs in these disorders but photoprotection is the most integral part of their management. Photoprotection includes wearing photoprotective clothing, applying broad spectrum sunscreens and avoiding photosensitizing drugs and chemicals.

Persistence and distribution of endosulfan under field condition.

Rapid increase in industrialization and agricultural activities to meet the population need has led to environmental pollution. The major revolution in agricultural production is mainly due to increased use of pesticides and fertilizers. Soil act as a major sink for majority of pesticides applied on agricultural crops. Among the organochlorines, endosulfan is the most commonly used pesticide, hence this study concentrates on the persistence and distribution behaviour of endosulfan under field conditions. The result showed that the alpha endosulfan concentrations were very minimum (0.98 mg/kg of soil) in all the four fields under study (Nazarath, Othikadu, Ekkadu and Ekkadukandigai of Thiruvallur district, Tamil Nadu). Where as beta endosulfan concentration at the time of application was 6.39 mg/kg and declined to 0.8 mg/kg on soil at 150th day. The endosulfan sulfate concentration was 11.8 mg/kg in soil at 15th day and then concentration declined to 2.2 mg/kg at 150th day. Field run-off samples showed maximum residue levels (0.024 mg/l) at the early irrigation period. While plant foliar parts showed maximum concentrations of alpha-endosulfan (43.4 mg/kg), beta-endosulfan (40.6 mg/kg) and endosulfan sulfate (20.1 mg/kg). At harvest stage, rice grain and husk also had lower concentrations of endosulfan sulfate (2.2 and 0.09 mg/kg), respectively.

Organochlorine pesticide residues in ground water of Thiruvallur district, India.

Modern agriculture practices reveal an increase in use of pesticides and fertilizers to meet the food demand of increasing population which results in contamination of the environment. In India crop production increased to 100% but the cropping area has increased marginally by 20%. Pesticides have played a major role in achieving the maximum crop production, but maximum usage and accumulation of pesticide residues was highly detrimental to aquatic and other ecosystem. The present study was chosen to know the level of organochlorines contamination in ground water of Thiruvallur district, Tamil Nadu, India. The samples were highly contaminated with DDT, HCH, endosulfan and their derivatives. Among the HCH derivatives, Gamma HCH residues was found maximum of 9.8 microg/l in Arumbakkam open wells. Concentrations of pp-DDT and op-DDT were 14.3 microg/l and 0.8 microg/l. The maximum residue (15.9 microg/l) of endosulfan sulfate was recorded in Kandigai village bore well. The study showed that the ground water samples were highly contaminated with organochlorine residues.

Moxifloxacin, ofloxacin, sparfloxacin, and ciprofloxacin against Mycobacterium tuberculosis: evaluation of in vitro and pharmacodynamic indices that best predict in vivo efficacy.

Members of the fluoroquinolone class are being actively evaluated for inclusion in tuberculosis chemotherapy regimens, and we sought to determine the best in vitro and pharmacodynamic predictors of in vivo efficacy in mice. MICs for Mycobacterium tuberculosis H37Rv were 0.1 mg/liter (sparfloxacin [SPX]) and 0.5 mg/liter (moxifloxacin [MXF], ciprofloxacin [CIP], and ofloxacin [OFX]). The unbound fraction in the presence of murine serum was concentration dependent for MXF, OFX, SPX, and CIP. In vitro time-kill studies revealed a time-dependent effect, with the CFU reduction on day 7 similar for all four drugs. However, with a J774A.1 murine macrophage tuberculosis infection model, CIP was ineffective at up to 32x MIC. In addition, MXF, OFX, and SPX exhibited less activity than had been seen in the in vitro time-kill study. After demonstrating that the area under the concentration-time curve (AUC) and maximum concentration of drug in plasma were proportional to the dose in vivo, dose fractionation studies with total oral doses of 37.5 to 19,200 mg/kg of body weight (MXF), 225 to 115,200 mg/kg (OFX), 30 to 50,000 mg/kg (SPX), and 38 to 100,000 mg/kg (CIP) were performed with a murine aerosol infection model. MXF was the most efficacious agent (3.0+/-0.2 log10 CFU/lung reduction), followed by SPX (1.4+/-0.1) and OFX (1.5+/-0.1). CIP showed no effect. The ratio of the AUC to the MIC was the pharmacodynamic parameter that best described the in vivo efficacy. In summary, a lack of intracellular killing predicted the lack of in vivo activity of CIP. The in vivo rank order for maximal efficacy of the three active fluoroquinolones was not clearly predicted by the in vitro assays, however.

Pancreatic beta cell function in offspring of conjugal diabetic parents. Assessment by IRI and C-peptide ratio.

Serum C-peptide and insulin responses to oral glucose load were measured in 69 offspring of conjugal diabetic parents (OCDP). The insulin responses were varied. The non obese OCDP showed higher mean insulin levels than non obese controls while the obese OCDP did not have significant differences in the mean insulin responses compared to obese controls. The C-peptide levels were, however, low in both obese and non-obese OCDP. The IRI/CP ratios were elevated in both groups of OCDP. These results suggest that OCDP have low beta cell function and also possibly a change in the metabolism of insulin at the hepatic level, which is more pronounced in non obese OCDP.

Hepatic extraction of insulin in non-insulin dependent diabetes. Comparative study of obese and non-obese patients.

Changes in the secretion and metabolism of insulin were measured by estimating serum C-peptide and insulin and their ratio during oral GTT in 30 non obese and 12 obese NIDDM patients. The mean IRI and CP responses were low in both groups of patients, compared to weight-matched controls. The reduction in CP was more marked than the reduction in IRI. The molar ratio of insulin and CP was found to be elevated in the patients, probably indicating reduced hepatic and peripheral extraction of insulin. It was noted that the elevated IRI/CP ratio was a 1) a common feature in NIDDM, irrespective of the body weight, 2) it is present even under basal conditions when the insulin levels are the lowest, 3) it appears to be independent of the concentration of insulin reaching the liver, and 4) obese patients appear to have an exaggerated defect compared to their non obese counterparts.