k mer

Motivation: De novo transcriptome assembly is an integral part for many RNA-seq workflows. Common applications include sequencing of non-model organisms, cancer or meta transcriptomes. Most de novo transcriptome assemblers use the de Bruijn graph (DBG) as the underlying data structure. The quality of the assemblies produced by such assemblers is highly influenced by the exact word length k. As such no single kmer value leads to optimal results. Instead, DBGs over different kmer values are built and the assemblies are merged to improve sensitivity. However, no studies have investigated thoroughly the problem of automatically learning at which kmer value to stop the assembly. Instead a suboptimal selection of kmer values is often used in practice. Results: Here we investigate the contribution of a single kmer value in a multi-kmer based assembly approach. We find that a comparative clustering of related assemblies can be used to estimate the importance of an additional kmer assembly. Using a model fit based algorithm we predict the kmer value at which no further assemblies are necessary. Our approach is tested with different de novo assemblers for datasets with different coverage values and read lengths. Further, we suggest a simple post processing step that significantly improves the quality of multi-kmer assemblies. Conclusion: We provide an automatic method for limiting the number of kmer values without a significant loss in assembly quality but with savings in assembly time. This is a step forward to making multi-kmer methods more reliable and easier to use. Availability and Implementation:A general implementation of our approach can be found under: https://github.com/SchulzLab/KREATION. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: [email protected]

A numerically efficient technique for the analysis of slots in multilayer media

Cataloged from PDF version of article.A numerically efficient technique for the analysis of slot geometries in multilayer media is presented using closed-form Green's functions in spatial domain in conjunction with the method of moments (MoM). The slot is represented by an equivalent magnetic-current distribution, which is then used to determine the total power crossing through the slot and the input impedance. In order to calculate power and current distribution, spatial domain closed form Green's functions are expanded as power series of the radial distance rho, which makes the analytical evaluation of the spatial domain integrals possible, saving a considerable amount of computation time

Supply Chain Performance Measurement Practices of Indian Industries

In any Industry the Supply chain performance plays a crucial role and it is vital in growth of the industry. Through this study an attempt is made to find some insight to the supply chain performance measurement practices of Indian industries through an exploratory survey. The study reveals almost all the respondents (84%) felt that supply chain performance measurement system employed in their organisation has a clear purpose. Also the study reveals that most supply chain performance measurement system provides high importance to quality measurements and includes both financial and non-financial indicators. The study gave clarity in understanding the objectives of implementing supply chain performance measurement systems and metrics (measures) used in supply chain performance measurement systems The Multivariate analysis revealed three factors emerged from this study are ‘Strategic Orientation’ followed by ‘Internal Focus’ and ‘Motivation and Control’

Comparitive study of onlay and preperitoneal mesh repair in the management of ventral hernia

BRIEF RESUME OF INTENDED WORK: Ventral hernia in the anterior abdominal wall includes both spontaneous and, most commonly, incisional hernias after an abdominal operation. . Hernia recurrence is distressing to patient and embarrassing to surgeons. Mesh repair can be pre- peritoneal or onlay. Controversy exists among the surgeons regarding the use of type of either meshoplasty, due to differences in ease in performing the surgery, time of surgery, complications occurring in the post operative period and the recurrence. Only few institution do preperitoneal mesh repair due to the need of skilled surgeon, so we are comparing onlay and preperitoneal mesh repair. AIMS AND OBJECTIVES OF THE STUDY: To compare outcome of onlay and preperitoneal mesh repair in the management of ventral hernia. MATERIALS AND METHODS: METHOD OF COLLECTION OF DATA Patient admitted with ventral hernia are included in the study with details of cases, clinical examination and symptoms are included in the study after confirming the diagnosis by ultrasonography and are divided randomly into onlay and preperitoneal group with 25 patient in each group. Patient are followed for six months to study the outcome reccurence. PERIOD OF STUDY : November 2014 to April 2015 TYPE OF STUDY : Randomized control study. SOURCE OF DATA : Patient diagnosed as ventral hernia in department of general surgery, Royapettah hospital and kilpauk medical college hospital. 50 of them are to be selected on basis of non probability (purposive) sampling method. INCLUSION CRITERIA : Patient with ventral hernia including • Umbilical hernia, • Paraumblical hernia, • Epigastric hernia • Incisional hernia. EXCLUSION CRITERIA : Patient admitted with • Groin hernia , • Divarication of recti, • Recurrent hernia, • Patient medically unfit for surgery, • Obstructed and strangulated hernias. CONCLUSION : By analyzing the outcome of seroma, wound infection, flap necrosis and recurrence in both groups the final result will be submitted in my dissertation

Spinal Cord Regeneration using Stem Cell Transplantation and Other Novel Techniques

This thesis was an explorative study to evaluate potential possibilities for spinal cord regeneration. At present there is no medical treatment available to cure spinal cord injury and the person remain paralysed and incontinent for life. Based on the literature three major strategies were evaluated namely cell therapy, administration of growth factor and enzyme. All these studies were conducted in rat model of spinal cord injury. Rat olfactory mucosa isolated from the posterior region of nasal septum, and lamina propria was enzymatically separated from the epithelium. Lamina propria was enzymatically dissociated to yield olfactory ensheathing cells (OEC) and olfactory nerve fibroblast (OEC). The cells were cultured, characterized by IHC and flow cytometry to test p75NTR (OEC), fibronectin (ONF). Fresh second passage cells were labeled with lentiviral-GFP and transplanted on the 9th day following spinal cord injury with different dosage/combination into injured cord. Olfactory epithelium enzymatic digested to yield cells. These cells were cultured and Globose basal stem cells (GBC) were isolated by GBC III antibody and characterized immunohistochemically and flow cytometry methods for expression of neural stem cell marker (nestin, SOX2, NCAM), bone marrow MSC marker (CD90, CD54, CD29,CD105, CD73) and haematopoietic marker (CD45, CD34). The result showed that GBC has the properties of both neural stem cell and mesenchymal stem cell. In addition, GBC formed neurosphere in culture condition, which is the characteristic of neural stem cell in brain. These cells were neuronally induced and characterized for neuronal marker (βIII-tubulin, MAP2, NeuN, Neurofilament). The result showed invitro differentiation of GBC into neurons, and its multipotency. So this is considered as an alternative source of transplantation for spinal cord injury. Second passage GBCwere transplanted into spinal cord on day 9 following injury. Bone marrow collected from rat femur and tibia, and then isolated MSC were cultured. Cultured MSC were characterized for MSC marker (CD90, CD54, CD29, CD105, CD73) and haematopoietic marker (CD45,CD14, CD34) by flow cytometry and IHC to prove purity of MSC, not contaminated with haematopoietic cells. These cells neuronally induced and characterized for positive marker of neurons and glia (MAP2, NF, NeuN,βIII tubulin, O4 and GFAP). Mature neuron express voltage-gated sodium channel, which is the hallmark of functional excitable cells. To address this issue, voltage-gated sodium channel (Nav1.1) expression was seen by IHC and patch-clamp studies was done to prove the existence of gated sodium channel; but only K+ channel was expressed. Multipotent bone marrow mesenchymal stem cells (MSC) were lentiviral GFP labeled and then transplanted on 9th day after spinal cord injury in rat. Acidic fibroblast growth factor was administered to minimize the initial damage after spinal cord injury and inhibit secondary inflammatory cascade. The results show neuroprotective effects of aFGF. Hence, it is concluded that the combinatorial treatment for CNS injury, taking into consideration of the therapeutic value of each stem cell type tried in this study, may not provide complete cure as expected. Nevertheless, cell therapy could give a definite relief to the patient suffering from spinal cord injury. Prolonged assessment of motor recovery for a year or so after cell transplantation is beyond the scope of this study. Importantly; OEC, olfactory epithelial cells can provide an accessible source compared to intra-cranially located neural stem/progenitors for autologous neurotransplantation, eliminating the need for immunosuppression thus reducing GVHD problems. While olfactory bulb derived OECs shows remarkable regenerative potential, but practically olfactory bulb tissue harvesting is invasive for therapeutic autologous transplantation strategies. Bone marrow mesenchymal stem cell can also be isolated less invasively from iliac crest and could be a source of stem cell. Autologous neurotransplantation for spinal cord injury should be preceded by further studies in larger animals models for future clinical practice

Haematological Abnormalities in Decompensated Chronic Liver Disease

In our prevalence study, 100 patients admitted as inpatients at Government General Hospital are taken for our study to assess the hematological profile and the hemostatic profile. All the patients were evaluated for the diagnosis of cirrhosis. Then patients were subjected to investigations for the hematological profile and hemostatic profile. Patients were done liver biopsy, upper GI endoscopy, USG abdomen and clinical signs for the diagnosis of cirrhosis. Blood investigations were done to assess the anaemia, nature of anemia, WBCs total count and differential count, platelet count, prothrombin time and APTT. All the investigations were collected and tabulated. According to the study, the most common anemia in cirrhotics is normochromic normocytic anaemia. Microcytosis occur in patients with bleeding tendencies and macrocytosis occur mostly in alcoholics. Leucopenia occurs in a small fraction of patients and leucocytosis occurs in patients with history of repeated paracentesis and peritonitis. Eosinophilia is associated with parasitic infections. Thrombocytopenia is present in most of the cirrhosis patients and are associated with increased bleeding tendencies. Most of the patients had increased prothrombin time and APTT due to decreased synthesis of clotting factors. Thus in cirrhosis patients most of them had abnormalities in haematological parameters and hemostasis

Reactivation of Hepatitis B Virus in Cancer Patients receiving Chemotherapy

INTRODUCTION: Nearly one third of the world's population have been infected with hepatitis B and the virus is endemic in many Asian countries. In India 4-4.75 per cent carry the virus. Hepatitis B, the cause of serum hepatits,is the most versatile of hepatotropic viruses. HBV can produce (1) Acute hepatitis, (2) Chronic non progressive hepatitis, (3) Progressive chronic disease ending in cirrhosis, (4) Fulminant hepatitis with massive liver necrosis, (5) An asymptomatic carrier state. HBV is present in the blood for the last stages of incubation period of 30-180 days and during the active episodes of acute and chronic hepetits and is present in all physiological and pathological body fluids with the exception of stools. HBV is a hardy virus and can withstand extremes of temperature and humidity. Thus although blood and body fluids are the primary vehicles of transmission, virus may also spread by contact with body secretions such as semen, saliva, sweat, tears, breast milk and pathological effusions. Tansfusions, blood products, dialysis, needle stick accidents among the health care workers, intravenous drug abuse and sexual constitute the primary risk categories for HBV infection. In one third of the patient source of infection is unknown. AIM OF THE STUDY: In this study 1. To determine the hepatitis B virus carrier state in patients receiving chemotherapy. 2. To determine the incidence of reactivation of chronic carrier HBsAg positive patients who underwent chemotherapy. 3. To assess the possibility of follow up of the carrier patients with serological and liver function tests for reactivation of Hepatitis B virus. SUBJECTS AND METHODS: Inclusion criteria: 1. Among the patients reported at medical oncology department, • Pathogically confirmed malignancy either by FNAC or biopsy histopathology report. • patients with hepatocellular carcinoma- confirmed by image guided FNAC or USG/ CT imaging suggestive of HCC with elevated S.AFP. • patients with malignancy planned for chemotherapy: - neoadjuvant chemotherapy, -adjuvant chemotherapy, - palliative chemotherapy- for metastatic and recurrent lesions. 2. Performance status ECOG- 2{zubrod score}. 3. complete hemogram with in normal limits. WBC Tc- > 1,500cells/mm3, Platelets >1,00,000cells/mm3, Hemoglobin> 10gm% (or corrected with packed cell transfusion). 4. Renal function: Blood urea : < 40 mg%, S. Creatinine: < 1.2mg%, 5 Liver function test: Total bilirubin <2 mg%, SGOT/SGPT: < 1.5 times the upper limit of normal, S.ALP : < 1.5 times the upper limit of normal, Cardiac function ECHO: ejection fraction > 60%, ECG: within normal limits. 6. Age > 18 yrs. 7. Viral markers : HBs Ag positive. 8. Signed specific consent form prior to study. EXCLUSION CRITERIA: 1. known case of HBs antigen positive without proof of malignancy 2. patients with proof of malignancy and HBs antigen positivity but not on chemotherapy as per the study protocol. 3. known case of HBs antigen positive patients already on T.Lamivudine prophylaxis. 4. previous or present history of other immunesuppressive drugs patients already on steroids for other comorbid medical conditions and as a treatment of malignancy except dexamethasone used as antiemetic prophylaxis and treatment. • patients already on T.cyclophosphamide, azathioprine, cyclosporine, etc. 5. patients with history of autoimmune disorders are excluded. 6. patients with history of uncontrolled diabetes mellitus, and history. of congestive cardiac failure, chronic kidney disease. 7. patients with decompensated liver disease. • Total bilirubin > 2 mg%, • Elevated SGOT/SGPT > 1.5x UNL, • Elevated ALP > 1.5x UNL, • Low albumin < 4gm%, • Albumin / globulin ratio reversal (imaging suggested of cirrhosis with coexisting liver sol suggestive of hepatocellular carcinoma and elevated tumor markers with normal LFT are included in the study). 8. coexisting viral infections such as human immune deficiency virus are excluded. 9. patients with history of jaundice within 6 months previous to chemotherapy are excluded. 10. patients with coexisting HCV antibodies positive are excluded. 11. previous history of chemotherapy and radiotherapy. 12. previous history of malignancy treated surgically other than included in the study (patients with history of malignancy previously treated with surgery only but not with chemotherapy or radiotherapy now with metastatic or recurrent disease and planned for 1st line chemotherapy are included in the sudy). 13. performance status > 3. 14. patients with evidence of malignancy planned for chemotherapy with HBs antigen positive patients but with anti HBc positive patients, HBe antigen positive and HBV DNA positive are excluded from the study. 15 patients with severe and active comorbid medical and surgical conditions. 16. pregnant and nursing mothers. 17 age 65 yrs. 18. patients requiring dose modification due to renal or hepatic dysfunction are excluded from the study. RESULTS : Between June 2009 and December 2010 all the patients registered at medical oncology opd GGH were evaluated for the serological status. All the patients underwent serology tests ELISA for HIV, ELISA for HBs AG and ELISA for Anti HCV antibodies. Totally 1850 patients were examined among them 62 patients were found to be HBS antigen positive. The HBS antigen positive patients are about 3.35% of the total patients underwent serological tests. There were about 20 female patients and 42 male patients were diagnosed as hepatitis b antigen positive .Among the 62 patients one patient had coexisting HIV infection and not included in the study, one patient had coexisting HCV antibodies positive and hence not included in the study. Among the 60 patients only 43 patients had met the eligibility criteria for the study and included in the study. Those 17 patients who do not met the criteria for the study 11 patients presented with jaundice and 3 patients had chronic renal disease and 2 patients had congestive cardiac failure and not included in the study. One patient had rheumatoid arthritis and already on steroids and excluded. Among the 11 patients with jaundice 8 patients were diagnosed as hepatocellular carcinoma and 2 were carcinoma stomach with liver secondaries and one with carcinoma pancreas with liver secondaries. CONCLUSION: From the Study, we concluded that, 1. The overall incidence of chronic HBs antigen carrier state is about 3.35%. 2. The incidence of reactivation of Hepatitis B virus in chronic HBs antigen patients receiving chemotherapy is 21% as we concluded from the study. 3. Patients who are on adriamycin based chemotherapy for the solid malignancies also had increased incidence of reactivation of hepatits B virus in HBs antigen chronic carriers. 4. Since patients with solid malignancy in chronic carrier HBs antigen state had high incidence of reactivation, we suggest that those patients should be treated with prophylactic Lamivudine

Role of insulin-like growth factor binding protein-4 in prevention of colon cancer

Insulin-like growth factors (IGFs) are important for the proliferation of cancer cells. One of their binding proteins, known as insulin-like growth factor binding protein -4 (IGFBP-4) is well known for its inhibitory action on IGFs in vitro. We assessed the effect of IGFBP-4 in prevention of development of colon cancer in vivo