Network-based identification of diagnosis-specific trans-omic biomarkers via integration of multiple omics data

The integration of multiple omics data promises to reveal new insights into the pathogenic mechanisms of complex human diseases, with the potential to identify avenues for the development of targeted therapies for disease subtypes. However, the extraction of diagnostic/disease-specific biomarkers from multiple omics data with biological pathway knowledge is a challenging issue in precision medicine. In this paper, we present a novel computational method to identify diagnosis-specific trans-omic biomarkers from multiple omics data. In the algorithm, we integrated multi-class sparse canonical correlation analysis (MSCCA) and molecular pathway analysis in order to derive discriminative molecular features that are correlated across different omics layers. We applied our proposed method to analyzing proteome and metabolome data of heart failure (HF), and extracted trans-omic biomarkers for HF subtypes; specifically, ischemic cardiomyopathy (ICM) and dilated cardiomyopathy (DCM). We were able to detect not only individual proteins that were previously reported from single-omics studies but also correlated protein-metabolite pairs characteristic of HF disease subtypes. For example, we identified hexokinase1(HK1)-d-fructose-6-phosphate as a paired trans-omic biomarker for DCM, which could significantly perturb amino-sugar metabolism. Our proposed method is expected to be useful for various applications in precision medicine.

Biomarker Discovery for Hepatocellular Carcinoma in Patients with Liver Cirrhosis Using Untargeted Metabolomics and Lipidomics Studies

Hepatocellular carcinoma (HCC), the most prevalent form of liver cancer, is the third leading cause of mortality globally. Patients with HCC have a poor prognosis due to the fact that the emergence of symptoms typically occurs at a late stage of the disease. In addition, conventional biomarkers perform suboptimally when identifying HCC in its early stages, heightening the need for the identification of new and more effective biomarkers. Using metabolomics and lipidomics approaches, this study aims to identify serum biomarkers for identification of HCC in patients with liver cirrhosis (LC). Serum samples from 20 HCC cases and 20 patients with LC were analyzed using ultra-high-performance liquid chromatography-Q Exactive mass spectrometry (UHPLC-Q-Exactive-MS). Metabolites and lipids that are significantly altered between HCC cases and patients with LC were identified. These include organic acids, amino acids, TCA cycle intermediates, fatty acids, bile acids, glycerophospholipids, sphingolipids, and glycerolipids. The most significant variability was observed in the concentrations of bile acids, fatty acids, and glycerophospholipids. In the context of HCC cases, there was a notable increase in the levels of phosphatidylethanolamine and triglycerides, but the levels of fatty acids and phosphatidylcholine exhibited a substantial decrease. In addition, it was observed that all of the identified metabolites exhibited a superior area under the receiver operating characteristic (ROC) curve in comparison to alpha-fetoprotein (AFP). The pathway analysis of these metabolites revealed fatty acid, lipid, and energy metabolism as the most impacted pathways. Putative biomarkers identified in this study will be validated in future studies via targeted quantification.

Systemic Delivery of Divalent Europium from Ligand Screening with Implications to Direct Imaging of Hypoxia

Hypoxia is a hallmark of many diseases, including cancer, arthritis, heart and kidney diseases, and diabetes, and it is often associated with disease aggressiveness and poor prognosis. Consequently, there is a critical need for imaging hypoxia in a noninvasive and direct way to diagnose, stage, and monitor the treatment and development of new therapies for these diseases. Eu-containing contrast agents for magnetic resonance imaging have demonstrated potential for in vivo imaging of hypoxia via changes in metal oxidation state from +2 to +3, but rapid oxidation in blood limits EuII-containing complexes to studies compatible with direct injection to sites. Here, we report a new EuII-containing complex that persists in oxygenated environments and is capable of persisting in blood long enough for imaging by magnetic resonance imaging. We describe the screening of a library of ligands that led to the discovery of the complex as well as a pH-dependent mechanism that hinders oxidation to enable usefulness in vivo. These studies of the first divalent lanthanide complex that persists in oxygenated solutions open the door to the use of EuII-based contrast agents for imaging hypoxia in a wide range of diseases.

Surgical Outcome of EDH in Children: Our Observation in DMCH

Background:Epidural hematoma (EDH) is accumulation of blood between the inner table of the skull and thedural membrane due to trauma and predominantly consists of venous blood in case ofchildren.Children with extradural hematoma (EDH) present differently than adults and outcome would also be different. Methods and Materials: This is a prospective interventional study done in the Department of Neurosurgery, Dhaka Medical College and Hospital (DMCH) in between period of January 2016 to December 2019. Children of both sex below 12 years of age with EDH were included after fulfilling inclusion and exclusion criteria. Follow up period was 1 month after surgery. Results: Among 90 patients, 73.3% were male and 26.7% were female. Age 5 - 12 years is most commonly affected among all age groups, attributing to 58.9%, fall from height was the most common cause (58.9%) followed by road traffic accident (32.2%), fall of heavy object over head (7.8%) etc. The most common symptom was vomiting which was present in 85.6% of patients followed by altered consciousness in 72.2%, headache in 60% and scalp swelling in 25.6% of patients. The follow-up of our patients was 1 month after surgery. Most of our patients made good recovery. Among them 73 patients (81.1%) were neurologically intact (GOS 5), 10 (11.1%) patients had some deficit but could do their daily activity independently (GOS 4), 03 patients (3.3%) was dependant on other for daily activity with cognitive deficit (GOS 3) and 4 patients (4.4%) died. Conclusion:EDH in children can be managed by surgery with good outcomes. Even in the presence of poor initial clinical and radiologic conditions, timely intervention can lead to a good recovery. Bangladesh Journal of Medical Science Vol. 21 No. 04 October’22 Page : 865-874

Association of Aortic Valve Sclerosis with Angiographic Severity of Coronary Artery Disease in Patients with Acute Coronary Syndrome, Aged ≤65 Years

Aortic valve sclerosis (AVS) represents a degenerative process that progresses with advancing age. The study was intended to find out the association between aortic valve sclerosis and the severity of CAD in patient's age ≤65 years with acute coronary syndrome. This cross-sectional analytical study was carried out in the department of cardiology, National Institute of Cardiovascular Diseases (NICVD), Dhaka, Bangladesh during a period of October 2017 to September 2018. A total of 140 Acute coronary syndrome (ACS) patients undergoing coronary angiogram during index hospitalization were included in the study. Study patients were divided into two groups on the basis of echocardiographic presence or absence of Aortic valve sclerosis (AVS), with 70 patients in each group. Group I was patients with aortic valve sclerosis and Group II was patients without aortic valve sclerosis. All patients underwent transthoracic echocardiography before they underwent coronary angiography on different days. Severity of CAD was determined by Gensini score and Vessel score. Association of traditional risk factors (smoking habit, hypertension, diabetes mellitus, dyslipidaemia and family history of CAD) with severity of CAD was investigated. Coronary angiography showed that AVS group had a higher positive rate of CAD (82.9% vs. 54.3%, p<0.001) and incidence rate of triple vessel CAD (40% vs. 14.3%, p<0.001) than non-AVS group. Gensini score had higher in AVS group than non AVS group (37.9±27.8 vs. 12.5±14.2; p<0.001). Multivariate analysis showed that AVS (p=0.01) and age (p=0.04) were independent predictors of the presence of significant coronary artery disease. The study concluded that echocardiographically detected AVS is an independent predictor of coronary artery disease severity. There is positive correlation between severity of AVS and severity of CAD in patient's age ≤65 years with ACS.

Block-HPCT: Blockchain Enabled Digital Health Passports and Contact Tracing of Infectious Diseases like COVID-19

Due to its significant global impact, both domestic and international efforts are underway to cure the infection and stop the COVID-19 virus from spreading further. In resource-limited environments, overwhelmed healthcare institutions and surveillance systems are struggling to cope with this epidemic, necessitating a specific strategic response. In this study, we looked into the COVID-19 situation and to establish trust, accountability, and transparency, we employed blockchain's immutable and tamper-proof properties. We offered a smart contract (SC)-based solution (Block-HPCT) that has been successfully tested to preserve a digital health passport (DHP) for vaccine recipients; also, for contact tracing (CT) we employed proof of location concept, which aids in a swift and credible response directly from the appropriate healthcare authorities. To connect on-chain and off-chain data, trusted and registered oracles were integrated and to provide a double layer of security along with symmetric key encryption; both Interplanetary File System (IPFS) and Hyperledger Fabric were merged as storage center. We also provided a full description of the suggested solution's system design, implementation, experiment results, and evaluation (privacy and cost analysis). As per the findings, the suggested approach performed satisfactorily across all significant assessment criteria, implying that it can lead the way for practical implementations and also can be used for similar types of situations where contact tracing of infectious can be crucial.

Incredible affinity of Kattosh with PPAR-γ receptors attenuates STZ-induced pancreas and kidney lesions evidenced in chemicobiological interactions

Since ancient times, plants have been used as green bioresources to ensure a healthier life by recovering from different diseases. Kattosh (Lasia spinosa L. Thwaites) is a local plant with various traditional uses, especially for arthritis, constipation and coughs. This research investigated the effect of Kattosh stem extract (LSES) on streptozotocin-induced damage to the pancreas, kidney, and liver using in vitro, in vivo and in silico methods. In vitro phytochemical, antioxidative and anti-inflammatory effects of LSES were accomplished by established methods followed by antidiabetic actions in in vivo randomized controlled intervention in STZ-induced animal models for four weeks. In an in silico study, LSES phytocompounds interacted with antidiabetic receptors of peroxisome proliferator-activated receptor-gamma (PPAR, PDB ID: 3G9E), AMP-activated protein kinase (AMPK, PDB ID: 4CFH) and α-amylase enzyme (PDB ID: 1PPI) to verify the in vivo results. In addition, LSES showed promising in vitro antioxidative and anti-inflammatory effects. In contrast, it showed a decrease in weekly blood glucose level, normalized lipid profile, ameliorated liver and cardiac markers, managed serum AST and ALT levels, and increased glucose tolerance ability in the animal model study. Restoration of pancreatic and kidney damage was reflected by improving histopathological images. In ligand-receptor interaction, ethyl α-d-glucopyranoside of Kattosh showed the highest affinity for the α-amylase enzyme, PPAR, and AMPK receptors. Results demonstrate that the affinity of Kattosh phytocompounds potentially attenuates pancreatic and kidney lesions and could be approached as an alternative antidiabetic source with further clarification.

p53 Modulation of Autophagy Signaling in Cancer Therapies: Perspectives Mechanism and Therapeutic Targets

The key tumor suppressor protein p53, additionally known as p53, represents an attractive target for the development and management of anti-cancer therapies. p53 has been implicated as a tumor suppressor protein that has multiple aspects of biological function comprising energy metabolism, cell cycle arrest, apoptosis, growth and differentiation, senescence, oxidative stress, angiogenesis, and cancer biology. Autophagy, a cellular self-defense system, is an evolutionarily conserved catabolic process involved in various physiological processes that maintain cellular homeostasis. Numerous studies have found that p53 modulates autophagy, although the relationship between p53 and autophagy is relatively complex and not well understood. Recently, several experimental studies have been reported that p53 can act both an inhibitor and an activator of autophagy which depend on its cellular localization as well as its mode of action. Emerging evidences have been suggested that the dual role of p53 which suppresses and stimulates autophagy in various cencer cells. It has been found that p53 suppression and activation are important to modulate autophagy for tumor promotion and cancer treatment. On the other hand, activation of autophagy by p53 has been recommended as a protective function of p53. Therefore, elucidation of the new functions of p53 and autophagy could contribute to the development of novel therapeutic approaches in cancer biology. However, the underlying molecular mechanisms of p53 and autophagy shows reciprocal functional interaction that is a major importance for cancer treatment and manegement. Additionally, several synthetic drugs and phytochemicals have been targeted to modulate p53 signaling via regulation of autophagy pathway in cancer cells. This review emphasizes the current perspectives and the role of p53 as the main regulator of autophagy-mediated novel therapeutic approaches against cancer treatment and managements.

Proportion and Pattern of Central Nervous System Involvement in Acute Leukemia on Diagnosis

The most common malignant neoplasm in Childhood is Leukemia which is about 41% of all malignancies. Incidence of CNS involvement is less than 5% in Acute Lymphoblastic Leukemia and 6-29% in Acute Myeloblastic Leukemia at Diagnosis. For Successful treatment of childhood leukemia it is mandatory, to give sufficient therapy directed to the CNS to treat sub clinical or overt CNS Leukemia. Without Central Nervous System- Directed therapy, relapses originating from the CNS in up to 75% cases. For this purpose it is crucial to find out the CNS involvement in acute leukemia at diagnosis. This study was conducted to find proportion and pattern of central nervous system involvement (central nervous system manifestation and/or cerebrospinal fluid findings) in acute leukemia at diagnosis in Bangladesh. A cross sectional study was conducted from May 2012 to November 2012 in the Department of Pediatric Hematology and Oncology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh. Total 50 samples were included those having age <15 years newly diagnosed with acute leukemia by purposive sampling. Common age group 1-5 years (48%), 32 patients (64%) were male and 18 patients (36%) were female. Out of 32 male patients 4 patients presented with CNS manifestation and among 18 female patients 2 patients presented with CNS manifestation. There is no association between sex and CNS presentation (P value 0.89). 25 (50%) patients had total leukocyte count >11,000-1,00,000. Twelve (24%) patients had total leukocyte count <4,000. Eight (16%) patients had total leukocyte count 4,000-11,000, and rest 05(10%) patients had leukocyte count >1,00,000. Proportion of CNS manifestation was found 6/50 patients. Eight (8) patients were suffering from AML and 42 patients were suffering form ALL. Among 8 AML patients 1 (11.1%) patient had CNS manifestation and Among 42 ALL patients 5(11.1%) patients had CNS manifestation. Out of 6 patients with CNS manifestation, 2 (04%) patients presented with clinical manifestation, and 5(10%) had positive CSF findings. Pattern of CSF finding of 50 leukemic children CNS-1 90%, CNS-2 02%, CNS-3 08%, and no patients had traumatic lumber puncture with concomitant presence of blasts cells. There is significant association was found between hyper leukocytosis and CNS manifestation (p=0.138) but there is no statistically significant association between positive CSF findings and neurological findings (p=0.082). At conclusion, CNS manifestation is not uncommon (6/50 patients) was found in acute leukemia at diagnosis. So, every patient of acute leukemia should be examined carefully for CNS involvement along with CSF cytospin.

Epiphytic Acampe ochracea orchid relieves paracetamol-induced hepatotoxicity by inhibiting oxidative stress and upregulating antioxidant genes in in vivo and virtual screening

Orchids are basically ornamental, and biological functions are seldom evaluated. This research investigated the effects of Acampe ochracea methanol extract (AOME) in ameliorating the paracetamol (PCM) induced liver injury in Wistar albino rats, evaluating its phytochemical status through UPLC-qTOF-MS analysis. With molecular docking and network pharmacology, virtual screening verified the inevitable interactions between the UPLC-qTOF-MS-characterized compounds and hepatoprotective drug receptors. The AOME has explicit a dose-dependent decrease of liver enzymes acid phosphatase (ACP), aspartate aminotransferase (AST), alanine aminotransferase (ALT), alkaline phosphatase (ALP), gamma-glutamyl transferase (GGT), lactate dehydrogenase (LDH), total bilirubin, as well as an increase of serum total protein and antioxidant enzymes catalase (CAT), superoxide dismutase (SOD), glutathione reductase (GSH) with a virtual normalization (p < 0.05-p < 0.001) and the values were almost equivalent to the reference drug silymarin. After pretreatment with AOME, PCM-induced malondialdehyde (MDA) levels were considerably decreased (p < 0.001). Histopathological examinations corroborated the functional and biochemical findings. The AOME upregulated the genes involved in antioxidative (CAT, SOD, β-actin, PON1, and PFK1) and hepatoprotective mechanisms in PCM intoxicated rats. An array of 103 compounds has been identified from AOME through UPLC-qTOF-MS analysis. The detected compounds were substantially related to the targets of several liver proteins and antioxidative enzymes, according to an in silico study. Virtual prediction by SwissADME and admetSAR showed that AOME has drug-like, non-toxic, and potential pharmacological activities in hepatic damage. Furthermore, VEGFA, CYP19A1, MAPK14, ESR1, and PPARG genes interact with target compounds impacting the significant biological actions to recover PCM-induced liver damage.

Are safe haven assets really safe during the 2008 global financial crisis and COVID-19 pandemic?

This study evaluates the safe-haven role of twelve assets against the US stock market during the 2008 global financial crisis (GFC) and the COVID-19 pandemic. Our results show that silver and the Islamic stock index were safe havens during the 2008 GFC, and the Islamic stock index and Tether have been safe havens during COVID-19. We observe that the Islamic stock index and Tether have emerged as strong new safe havens. However, our supplementary analysis reveals that gold and Bitcoin still exhibit safe-haven behavior during severe market downturns. Overall, our findings suggest that safe-haven assets may vary over time.

Surgical Outcome of CSF Drainage in Paediatric Obstructive Hydrocephalus

Hydrocephalus (HCP) is occurred when there is inequality in the formation and absorption of CSF to such a level which causes accumulation of fluid and causing raised intracranial pressure. Hydrocephalus is the most frequent neurosurgical problem encountered in the paediatric age group. CSF diversion surgically is needed as treatment for certain condition. Endoscopic third ventriculostomy (ETV) and Ventriculo-peritoneal shunt (VPS) are most widely used CSF diversion procedure. Therefore, this study was conducted for comparing the surgical outcome of ETV and VP shunt in obstructive hydrocephalus. This is a prospective experimental study conducted in the Department of Neurosurgery, Dhaka Medical College and Hospital (DMCH) and Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh from January 2017 to December 2019. Paediatric patients of both sex and 6 months to 18 years of age with obstructive hydrocephalus undergone endoscopic third ventriculostomy (ETV) or ventriculo-peritoneal shunt (VP shunt) were included after fulfilling inclusion and exclusion criteria. The patients divided into two groups (Group A and Group B). The Group A included 30 patients who treated by Endoscopic third ventriculostomy and the Group B include 30 patients, who was treated by Ventriculo-peritoneal shunt. Surgical outcome was analyzed in two procedures separately. In Group A (ETV group) symptomatic improvement, GCS score improves earlier and post-operative complications relatively less than Group B (VP shunt group). But in VP shunt group 3 months follow up reveals- improvement of papilledema, Occipital frontal circumference (OFC) regression and fontanelle size improvement was more than that of ETV group. This study concluded with suggesting that Endoscopic third ventriculostomy (ETV) is technologically superior surgical technique than VP shunt. Though ETV showed relatively more immediate procedural failure and intraventricular hemorrhage but long-term outcome is better and also associated with lower incidence of infection and re-operation in comparison to VP shunt.

Myocardial tuberculosis and beyond: A rare form of extra pulmonary TB in a young boy

Myocardial tuberculosis is an exceptionally rare form of extra-pulmonary TB. Few cases were reported world-wide. Here a young snake charmer who had skin tuberculosis 5 yrs back admitted into National institute of diseases of Chest and hospital (NIDCH), Dhaka with the complaints of cough, palpitation and breathlessness for 2 months. He had right axillary firm matted lymphadenopathy, left sided large pleural effusion, left ventricular and septal hypertrophy with band and mass inside the ventricle (evident on CT scan of heart and echocardiography). His ESR was 95 mm in1st hr, Mantaux test was 15mm, Pleural fluid was exudative lymphocyte predominant with adenosin deaminase (ADA) 68.6 U/L. Fine needle aspirates from right axillary LNs showed Mycobacterium tuberculosis on GeneXpert for MTB/RIF testing and caseous granuloma on cytopathological study. Whole Body F18 FDG PET-CT revealed numerous low FDG avid size significant lymph nodes in right side of neck, mediastinum and right axilla with cardiomegaly with focal FDG avid within the left ventricular cavity likely to be prominent papillary muscle. MRI of heart or Myocardial biopsy for histology was not done due to their cost and invasiveness and also for that there was sufficient evidence of having tuberculosis in lymph node, pleura nas myocardium. This patient was treated with anti tubercular medications (3HRZE2S/5HRE) with prednisolone for six months. After treatment, myocardial lesions, pleural effusion and lymphadenopathy were found resolved. Thus a case of fatal and serious tuberculosis was explored and managed successfully.

Comparative metabolomics and lipidomics study to evaluate the metabolic differences between first- and second-generation mammalian or mechanistic target of rapamycin inhibitors

Mammalian or mechanistic target of rapamycin (mTOR) drives its fundamental cellular functions through two distinct catalytic subunits, mTORC1 and mTORC2, and is frequently dysregulated in most cancers. To treat cancers, developed mTOR inhibitors have been classified into first and second generations based on their ability to inhibit single (first-generation) and dual (second-generation) mTOR subunits. However, the underlying metabolic differences due to the effects of first- and second-generation mTOR inhibitors have not been clearly evaluated. In this study, rapamycin (sirolimus) and AZD8055 and PP242 were selected as first- and second-generation mTOR inhibitors, respectively, to evaluate the metabolic differences due to these two generations of mTOR inhibitors after a single oral dose using untargeted metabolomics and lipidomics approaches. The metabolic differences at each time point were compared using multivariate analysis. The multivariate and data analyses showed that metabolic disparity was more prominent within 8 h after drug administration and a broad class of metabolites were affected by the administration of both generations of mTOR inhibitors. Among the metabolite classes, changes in the pattern of fatty acids and glycerophospholipids were opposite, specifically at 4 and 8 h between the two generations of mTOR inhibitors. We speculate that the inhibition of the mTORC2 subunit by the second-generation mTOR inhibitor may have resulted in a distinct metabolic pattern between the first- and second-generation inhibitors. Finally, the findings of this study could assist in a more detailed understanding of the key metabolic differences caused by first- and second-generation mTOR inhibitors.

Pancreatobiliary Diseases: Evaluation by Transabdominal and Endoscopic Ultrasound

Pancreaticobiliary diseases are the important causes of morbidity and mortality worldwide. Among the imaging modalities, Transabdominal ultrasound (TUS) is cheap, available, and noninvasive but it has some limitations. Endoscopic ultrasound (EUS) is invasive but it has some diagnostic and therapeutic advantages over TUS. This study was aimed to see the diagnostic yields of EUS and TUS in the pancreatobiliary diseases. This cross sectional study was conducted in Sir Salimullah Medical College Mitford Hospital (SSMC&MH), Dhaka, Bangladesh from March 2017 to February 2019. All (n=222) patients were evaluated clinically and with relevant investigations. TUS and EUS were done in all patients. Endoscopic retrograde cholangiopancreatography (ERCP) was done in 60 patients. Among 222 patients 56.8% were males; mean age was 46±16 years; the main presenting symptoms were abdominal pain and jaundice. In diseases of biliary tree, EUS showed dilated CBD alone or in combination with stone in 50 and 67 cases and TUS showed 37, 63 patients respectively. The difference between the findings of EUS and TUS was statistically significant (p=0.00). In gall bladder, EUS found microlithiasis in 6(2.6%) and sludges in 24(10.8%) cases whereas TUS found microlithiasis in 1(0.5%) and sludges in 17(7.7%) cases respectively (p=0.00). Both EUS and TUS detected cholelithiasis in equal number of patients 46(20.3%). On pancreatic evaluation, EUS and TUS detected pancreatic parenchymal abnormalities in 24(10.8%) and 12(5.5%) patients respectively with significant p value (0.00). In cases of pancreatic and cholangiocarcinoma the difference between the findings of EUS and TUS were statistically significant (p<0.05). EUS detected 7 cases of ampullary/peri-ampullary neoplasms whereas TUS detected only 2 cases. The sensitivity of EUS for detecting CBD dilatation, CBD stones, CBD SOL and pancreatic SOL was 85%, 91%, 93%, and 92% respectively. The sensitivity of TUS for detecting CBD dilatation, CBD stones, CBD SOL and pancreatic SOL was 42%, 52%, 40%, and 37% respectively. EUS is more sensitive than TUS in diagnosing pancreaticobiliary disorders. It is of paramount importance in patients in diagnosing CBD dilatation, choledocholithiasis, biliary microlithiasis and pancreaticobiliary neoplasm. EUS has important role before proceeding to further management by more invasive techniques like ERCP or surgery.

Impact of LFGD (Ar+O2) plasma on seed surface, germination, plant growth, productivity and nutritional composition of maize (Zea mays L.)

In this present study conducted with the LFGD (Low-Frequency Glow Discharge) (Ar + O₂) plasma treated maize seeds, to inspect the effect on seed surface modifications, seed germination, growth, development, productivity and nutritional compositions of maize plants. This study reported that LFGD (Ar + O₂) plasma treated maize seeds have a potential effect to change its smooth seed surfaces and, it becomes rougher. It also enhances the seed germination rate up to (15.88%), which might help to increase the shoot length (33.42%), root length (10.67%), stem diameter (13.37%), total chlorophyll content (46.93%), total soluble protein (52.48%), total soluble phenol (21.68%) and sugar (1.62%) concentrations in respect controls of our experimental plants. For this reason, the acceptable treatment duration for maize seeds were 30sec, 60sec, 90sec and 120sec. After treatment, the plants exhibited a significant increase in CAT, SOD, APX and GR activities in the leaves and roots, and also significantly changes in H₂O₂ (208.33 ± 5.87μ molg^-1 FW) in the leaves and (61.13 ± 1.72μ molg^-1 FW) in the roots, NO was (369.24 ± 213.19μ molg^-1FW) and (1094.23 ± 135.44μ molg^-1FW) in the leaves and roots. LFGD plasma treatment also contributed to enhancement of productivity (1.27%), nutritional (moisture, ash, fat, and crude fiber) compositions, and iron and zinc micro-nutrition concentrations of maize. From this research, LFGD (Ar + O₂) plasma treatment showed a potential impact on the maize cultivation system, which is very effective tools and both in nationally and internationally alter the conventional cultivation system of maize. Because it promotes seed surface modification, improved germination rate, shoot length, root length, chlorophyll content, some of the growths related enzymatic activity, nutrient composition, iron, and zinc micro-nutrients and the productivity of maize.

Cyberattacks Detection in IoT-Based Smart City Applications Using Machine Learning Techniques

In recent years, the widespread deployment of the Internet of Things (IoT) applications has contributed to the development of smart cities. A smart city utilizes IoT-enabled technologies, communications and applications to maximize operational efficiency and enhance both the service providers’ quality of services and people’s wellbeing and quality of life. With the growth of smart city networks, however, comes the increased risk of cybersecurity threats and attacks. IoT devices within a smart city network are connected to sensors linked to large cloud servers and are exposed to malicious attacks and threats. Thus, it is important to devise approaches to prevent such attacks and protect IoT devices from failure. In this paper, we explore an attack and anomaly detection technique based on machine learning algorithms (LR, SVM, DT, RF, ANN and KNN) to defend against and mitigate IoT cybersecurity threats in a smart city. Contrary to existing works that have focused on single classifiers, we also explore ensemble methods such as bagging, boosting and stacking to enhance the performance of the detection system. Additionally, we consider an integration of feature selection, cross-validation and multi-class classification for the discussed domain, which has not been well considered in the existing literature. Experimental results with the recent attack dataset demonstrate that the proposed technique can effectively identify cyberattacks and the stacking ensemble model outperforms comparable models in terms of accuracy, precision, recall and F1-Score, implying the promise of stacking in this domain.

Evaluation of the antitumor effects of PP242 in a colon cancer xenograft mouse model using comprehensive metabolomics and lipidomics

PP242, an inhibitor of mechanistic target of rapamycin (mTOR), displays potent anticancer effects against various cancer types. However, the underlying metabolic mechanism associated with the PP242 effects is not clearly understood. In this study, comprehensive metabolomics and lipidomics investigations were performed using ultra-high-performance chromatography-Orbitrap-mass spectrometry (UHPLC-Orbitrap-MS) in plasma and tumor tissue to reveal the metabolic mechanism of PP242 in an LS174T cell-induced colon cancer xenograft mouse model. After 3 weeks of PP242 treatment, a reduction in tumor size and weight was observed without any critical toxicities. According to results, metabolic changes due to the effects of PP242 were not significant in plasma. In contrast, metabolic changes in tumor tissues were very significant in the PP242-treated group compared to the xenograft control (XC) group, and revealed that energy and lipid metabolism were mainly altered by PP242 treatment like other cancer inhibitors. Additionally, in this study, it was discovered that not only TCA cycle but also fatty acid β-oxidation (β-FAO) for energy metabolism was inhibited and clear reduction in glycerophospholipid was observed. This study reveals new insights into the underlying anticancer mechanism of the dual mTOR inhibitor PP242, and could help further to facilitate the understanding of PP242 effects in the clinical application.

Coupling protocol of interlocked feedback oscillators in circadian clocks

Circadian rhythms (approx. 24 h) show the robustness of key oscillatory features such as phase, period and amplitude against external and internal variations. The robustness of Drosophila circadian clocks can be generated by interlocked transcriptional-translational feedback loops, where two negative feedback loops are coupled through mutual activations. The mechanisms by which such coupling protocols have survived out of many possible protocols remain to be revealed. To address this question, we investigated two distinct coupling protocols: activator-coupled oscillators (ACO) and repressor-coupled oscillators (RCO). We focused on the two coupling parameters: coupling dissociation constant and coupling time-delay. Interestingly, the ACO was able to produce anti-phase or morning-evening cycles, whereas the RCO produced in-phase ones. Deterministic and stochastic analyses demonstrated that the anti-phase ACO provided greater fluctuations in amplitude not only with respect to changes in coupling parameters but also to random parameter perturbations than the in-phase RCO. Moreover, the ACO deteriorated the entrainability to the day-night master clock, whereas the RCO produced high entrainability. Considering that the real, interlocked feedback loops have evolved as the ACO, instead of the RCO, we first proposed a hypothesis that the morning-evening or anti-phase cycle is more essential for Drosophila than achieving robustness and entrainability.

Outcome of Surgically Treated 79 Patients of Hepatic Hydatidosis: A Single Center Tertiary Care Hospital Experience in Bangladesh

Background: Proper patient selection for most appropriate treatment option for hepatic hydatid is crucial to ensure successful treatment outcome. Chemotherapy, newer approaches, like PAIR procedure, (puncture, aspiration, injection and reaspiration) laparoscopy are available. As the indications for these approaches are restricted, surgery remains the key treatment strategy with hope for complete cure. Radical surgical excision coupled with chemotherapy and long-term aggressive chemotherapy for partially resected ensures lowest morbidity and mortality. Methods: This cross sectional observational study of 15-year single-institution experience, intended to further validate different surgical procedures in management of hydatid disease of liver and its outcome. Patients were randomly selected irrespective of their age, sex and mode of presentation. Different preferred surgical treatment modalities, perioperative complications, recurrences, and length of hospital stay were retrospectively analyzed. Result: The study was carried out on 79 Bangladeshi patients diagnosed hepatic hydatidosis, treated surgically from January 2002 to December 2017 in BIRDEM General Hospital. Among them was no anastomotic leakage or mortality in the immediate postoperative period in our series. Conclusion: This study revealed, proper case selection and consideration of risks-benefits, indicationscontraindications for each case of Hydatid cyst of liver, for making a decision for type and timing of surgery is key to successful outcome. Surgery is the mainstay of treatment strategy. Radical surgery is key to effective and successful outcome, ensures better quality of life and prevents recurrence of the disease. Journal of Surgical Sciences (2018) Vol. 22 (2) : 118-124

Effects of DBD air plasma treatment on the enhancement of black gram (Vigna mungo l.) seed germination and growth

Effects of black gram (vigna mungo L.cv. Barimash 3) seed treatments with 400 torr dielectric barrier discharge (DBD) air plasma on seed surface morphology, seed germination, seedling growth and antioxidant enzyme activities in the roots, shoots and leaves were investigated. The plasma discharge voltage, frequency, electrode spacing, gas temperature and power were 5kV, 4.5kHz, 60mm, 310K and 45W, respectively. The seeds were treated for the duration ranging from 20 to 180 s. Seed germination rate, seedling growth, total chlorophyll content, total soluble protein and sugar concentrations in the seedlings grown from the treated seeds were found to increase 13.67%, 37.13%, 37.26%,53.60% and 51.71%, respectively, with respect to control. This study reveals that the DBD air plasma was involved in the enhancement of nitrogen complex in the seed coat of black gram which upregulated the protein through nitrogen conversion that was ultimately responsible for the increased seed germination and seedling growth of black gram.

An extreme sea level indicator for the contiguous United States coastline

We develop an aggregated extreme sea level (ESL) indicator for the contiguous United States coastline, which is comprised of separate indicators for mean sea level (MSL) and storm surge climatology (SSC). We use water level data from tide gauges to estimate interannual to multi-decadal variability of MSL and SSC and identify coastline stretches where the observed changes are coherent. Both the MSL and SSC indicators show significant fluctuations. Indicators of the individual components are combined with multi-year tidal contributions into aggregated ESL indicators. The relative contribution of the different components varies considerably in time and space. Our results highlight the important role of interannual to multi-decadal variability in different sea level components in exacerbating, or reducing, the impacts of long-term MSL rise over time scales relevant for coastal planning and management. Regularly updating the proposed indicator will allow tracking changes in ESL posing a threat to many coastal communities, including the identification of periods where the likelihood of flooding is particularly large or small.

Pretreatment with Magnesium Sulfate to Alleviate Pain on Propofol Injection: A Prospective Randomized Double Blind Study

Background and aim of study: Propofol is one of the most frequently used medications for inducing and maintaining anesthesia. However, propofol injection causes pain and discomfort in more than 70% of patients. This study was performed to determine the effect of magnesium sulfate on reducing pain at the onset of anesthesia induced by propofol injection. Materials and methods: A total of 80 healthy adult patients were selected in this study with either sex, scheduled for routine elective surgical procedure under general anesthesia. The patients enrolled were divided randomly into two groups of 40 patients each. Group I received 30 mg/kg of intravenous magnesium sulfate in 5 ml. Group II (placebo group) received 5ml of 0.9% intravenous normal saline 1 minute before propofol injection. The patients were asked to report their pain during injection of propofol. For all statistical tests, p<0.05 was taken to indicate a significant difference. Results: The incidence of pain experienced in magnesium sulfate group was 30% patients and in saline group was 60% patients, which is statistically significant p<0.05. The severity of POPI was also lower in magnesium sulfate group than the saline group (p<0.05). The incidence of mild and moderate pain in groups I versus group II was 22.5% versus 37.5% and 7.5% versus 22.5% respectively p<0.05. There was no severe pain recorded in any groups. Conclusion: Magnesium sulfate can be used before induction of anesthesia to reduce pain on propofol injection. Mediscope Vol. 6, No. 2: Jul 2019, Page 73-77

Computational identification of microbial phosphorylation sites by the enhanced characteristics of sequence information

Protein phosphorylation on serine (S) and threonine (T) has emerged as a key device in the control of many biological processes. Recently phosphorylation in microbial organisms has attracted much attention for its critical roles in various cellular processes such as cell growth and cell division. Here a novel machine learning predictor, MPSite (Microbial Phosphorylation Site predictor), was developed to identify microbial phosphorylation sites using the enhanced characteristics of sequence features. The final feature vectors optimized via a Wilcoxon rank sum test. A random forest classifier was then trained using the optimum features to build the predictor. Benchmarking investigation using the 5-fold cross-validation and independent datasets test showed that the MPSite is able to achieve robust performance on the S- and T-phosphorylation site prediction. It also outperformed other existing methods on the comprehensive independent datasets. We anticipate that the MPSite is a powerful tool for proteome-wide prediction of microbial phosphorylation sites and facilitates hypothesis-driven functional interrogation of phosphorylation proteins. A web application with the curated datasets is freely available at http://kurata14.bio.kyutech.ac.jp/MPSite/.

Miltefosine Induced Reduced Male Fertility Capacity after Treatment of Post Kala-azar Dermal Leishmaniasis, Bangladesh

Post Kala-azar Dermal Leishmaniasis (PKDL) is the sequel of visceral leishmaniasis in Indian subcontinent and may appear among patients with or without previous history of visceral leishmaniasis (VL). The aim of the study is to understand the male reproductive safety profile of miltefosine used for the treatment of Post Kala-azar Dermal Leishmaniasis (PKDL) in Bangladesh. From January 2017 to March 2017, an exploratory study was carried out on male fertility capacity in Bangladesh among male patients above 14 years old with PKDL treated with miltefosine. Twenty nine male patients were included to observe the effect of miltefosine on reproductive health. All PKDL patients had history of visceral leishmaniasis (VL) in different time periods. Among them three (10.3%) patients were unable to ejaculate semen. In semen analysis, 3 patients (10.3%) were found azoospermia (sperm count & motility- 0, viscosity- good, pH- 7 to 8), microscopically there was presence of RBC (5-15/HPF), WBC (8-15/HPF). Another 3 patients (10.3%) were found oligospermia (sperm count- 4.2 to 15.3 million/ml, motility- 20 to 50%, viscosity- good, pH- 6 to 9, RBC- 4 to 15/HPF, WBC- 4 to 15/HPF). The study documented some important findings in evaluating male infertility and selection of drug regimens in treating PKDL patients with miltefosine for 12 weeks.

Development of a non-stationary Standardized Precipitation Index and its application to a South Australian climate

In a changing climate, while hydroclimatic variables such as precipitation may show non-stationary behaviour, a traditional Standardized Precipitation Index (SPI) is not capable of accurately predicting extreme meteorological droughts. In this study, we have developed a non-stationary Standardized Precipitation Index (NSPI) within the Generalized Additive Model in Location, Scale and Shape (GAMLSS) modelling framework. This incorporates various climate indices such as SOI, Niño3.4, PDO, SAM and DMI as external covariates to capture the non-stationary and nonlinear characteristics of precipitation and thereby droughts. This idea has been applied at 46 high quality rainfall stations in the state of South Australia. The results indicate that a non-stationary model that considers climate indices can reproduce the rainfall variability better than a stationary model thereby NSPI is better than a traditional stationary SPI (SSPI) at capturing drought characteristics. Bivariate frequency analysis shows that the recurrence interval of drought events exceeding any severity and duration of interest is significantly different for NSPI compared to SSPI. This study demonstrates the need to use a non-stationary drought index in a changing climate to accurately represent the drought characteristics.

Cold Injury and Flash Flood Damage in Boro Rice Cultivation in Bangladesh: A Review

Increasing population with decreasing resources and increasing climate vulnerability appeared as the great challenges to sustain food security of Bangladesh. Cold stress adversely affects growth and productivity of rice (Oryza sativa L.). Systematic studies have been carried out to improve understanding on rice cold tolerance. Two adverse conditions, such as low temperature stress at reproductive stages and flash flood at maturity affect the Boro rice in the haor areas of Bangladesh. Any deviation of these two phenomena is enough to cause disaster in haor areas. Here, we summarized different types of cold injury, rice cold injury scenario and cold tolerant rice varieties/genotypes available in different countries. Moreover, we discussed on rice cold tolerant barrier and flash flood risk in Boro rice cultivation at haor areas of Bangladesh. Based on the authors’ own research and available data, the concept of overcoming cold and flash flood damage was proposed. According to this concept there were distinguished possible ways how to improve cold tolerance and flash flood problem in Boro rice cultivation in BangladeshBangladesh Rice j. 2017, 21(1): 13-25

Metabolite identification and pharmacokinetic profiling of PP242, an ATP-competitive inhibitor of mTOR using ultra high-performance liquid chromatography and mass spectrometry

PP242 is a second generation novel selective ATP-competitive inhibitor of mTOR that displayed promising anti-cancer activity over several cancer types by inhibiting both the complexes of mTOR (mTORC1 and mTORC2). The purpose of this study is to identify the possible metabolites and to evaluate the pharmacokinetic profile of PP242 after a single oral administration to Sprague-Dawley (SD) rats. Two metabolites, including one phase I and one phase II, were identified by in vitro and in vivo studies using rat liver microsomes (RLMs) as well as rat plasma, urine and feces, respectively, through ultra high-performance liquid chromatography-linear ion trap quadrupole-orbitrap-mass spectrometry (UHPLC-LTQ-Orbitrap-MS). The major biotransformation pathways of PP242 were hydroxylation and glucuronide conjugation. Additionally, a simple and rapid quantification method was developed and validated. The method recovery was within 79.7-84.6%, whereas the matrix effect was 78.1-96.0% in all three quality control (QC) concentrations (low, medium and high) including the LLOQ. Other parameters showed acceptable results according to the US food and drug administration (FDA) guidelines for bioanalytical method validation. Afterwards, pharmacokinetic parameters were evaluated in rat plasma by successfully applying the validated method using liquid chromatography-tandem mass spectrometry (LC-MS/MS). After a single oral administration at a dose of 5mg/kg, the maximum plasma concentration (C_max) of PP242 was 0.17±0.08μg/mL, while the elimination was moderately fast (T_1/2: 172.18±45.54min). All of the obtained information on the metabolite identification and pharmacokinetic parameter elucidation could facilitate the further development of PP242.

Higher Fertilizer Inputs Increase Fitness Traits of Brown Planthopper in Rice

Rice (Oryza sativa L.) is the primary staple food source for more than half of the world's population. In many developing countries, increased use of fertilizers is a response to increase demand for rice. In this study, we investigated the effects of three principal fertilizer components (nitrogen, phosphorus and potassium) on the development of potted rice plants and their effects on fitness traits of the brown planthopper (BPH) [Nilaparvata lugens (Stål) (Homoptera: Delphacidae)], which is a major pest of rice in Bangladesh and elsewhere. Compared to low fertilizer inputs, high fertilizer treatments induced plant growth but also favored BPH development. The BPH had higher survival, developed faster, and the intrinsic rate of natural increase (r _m ) was higher on well-fertilized than under-fertilized plants. Among the fertilizer inputs, nitrogen had the strongest effect on the fitness traits of BPH. Furthermore, both the "Plant vigor hypothesis" and the "Plant stress hypothesis" were supported by the results, the former hypothesis more so than the latter. These hypotheses suggest that the most suitable/attractive hosts for insect herbivores are the most vigorous plants. Our findings emphasized that an exclusive focus on yield increases through only enhanced crop fertilization may have unforeseen, indirect, effects on crop susceptibility to pests, such as BPH.

Comparative genomics of two jute species and insight into fibre biogenesis

Jute (Corchorus sp.) is one of the most important sources of natural fibre, covering ∼80% of global bast fibre production¹. Only Corchorus olitorius and Corchorus capsularis are commercially cultivated, though there are more than 100 Corchorus species² in the Malvaceae family. Here we describe high-quality draft genomes of these two species and their comparisons at the functional genomics level to support tailor-designed breeding. The assemblies cover 91.6% and 82.2% of the estimated genome sizes for C. olitorius and C. capsularis, respectively. In total, 37,031 C. olitorius and 30,096 C. capsularis genes are identified, and most of the genes are validated by cDNA and RNA-seq data. Analyses of clustered gene families and gene collinearity show that jute underwent shared whole-genome duplication ∼18.66 million years (Myr) ago prior to speciation. RNA expression analysis from isolated fibre cells reveals the key regulatory and structural genes involved in fibre formation. This work expands our understanding of the molecular basis of fibre formation laying the foundation for the genetic improvement of jute.

Response of Adult Brown Planthopper Nilaparvata lugens (Stål) to Rice Nutrient Management

Nitrogen (N) limitation is well documented for the brown planthopper (BPH) Nilaparvata lugens (Stål), but phosphorus (P) and potassium (K) limitation is poorly studied. We studied the effects of N, P, and K application on chemical composition of rice plants and its consequences on life parameters-adult longevity, fecundity, and egg hatchability of BPH. Life parameters of BPH were regressed as function of plant chemical composition. A completely randomized design with four replicates in a factorial scheme was used considering N, P, and K levels as factors. Nitrogen application increased N and soluble proteins (SP) and decreased silicon (Si) content in the plants resulting in increased adult longevity, fecundity, and egg hatchability of BPH. Phosphorus fertilization increased P content and showed markedly increased fecundity, but not egg hatchability or adult longevity. Significant interaction between N and P was observed for fecundity of BPH. Potassium supplementation increased K content but reduced N, Si, SP, and total free sugars (TFS) content in the plants, but it had no significant effect on life parameters of BPH. The association of BPH life parameters with N, SP, TFS, and P content was significant and positive, but it was negative with the content of Si. Thus, N and P fertilization on rice plants enhanced BPH fitness. In conclusion, judicious nutrient application can be helpful in avoiding generalized infestation of BPH to rice.

Response of Adult Brown Planthopper Nilaparvata lugens (Stål) to Rice Nutrient Management

Nitrogen (N) limitation is well documented for the brown planthopper (BPH) Nilaparvata lugens (Stål), but phosphorus (P) and potassium (K) limitation is poorly studied. We studied the effects of N, P, and K application on chemical composition of rice plants and its consequences on life parameters-adult longevity, fecundity, and egg hatchability of BPH. Life parameters of BPH were regressed as function of plant chemical composition. A completely randomized design with four replicates in a factorial scheme was used considering N, P, and K levels as factors. Nitrogen application increased N and soluble proteins (SP) and decreased silicon (Si) content in the plants resulting in increased adult longevity, fecundity, and egg hatchability of BPH. Phosphorus fertilization increased P content and showed markedly increased fecundity, but not egg hatchability or adult longevity. Significant interaction between N and P was observed for fecundity of BPH. Potassium supplementation increased K content but reduced N, Si, SP, and total free sugars (TFS) content in the plants, but it had no significant effect on life parameters of BPH. The association of BPH life parameters with N, SP, TFS, and P content was significant and positive, but it was negative with the content of Si. Thus, N and P fertilization on rice plants enhanced BPH fitness. In conclusion, judicious nutrient application can be helpful in avoiding generalized infestation of BPH to rice.

Statistical downscaling of CMIP5 outputs for projecting future changes in rainfall in the Onkaparinga catchment

A generalized linear model was fitted to stochastically downscaled multi-site daily rainfall projections from CMIP5 General Circulation Models (GCMs) for the Onkaparinga catchment in South Australia to assess future changes to hydrologically relevant metrics. For this purpose three GCMs, two multi-model ensembles (one by averaging the predictors of GCMs and the other by regressing the predictors of GCMs against reanalysis datasets) and two scenarios (RCP4.5 and RCP8.5) were considered. The downscaling model was able to reasonably reproduce the observed historical rainfall statistics when the model was driven by NCEP reanalysis datasets. Significant bias was observed in the rainfall when downscaled from historical outputs of GCMs. Bias was corrected using the Frequency Adapted Quantile Mapping technique. Future changes in rainfall were computed from the bias corrected downscaled rainfall forced by GCM outputs for the period 2041-2060 and these were then compared to the base period 1961-2000. The results show that annual and seasonal rainfalls are likely to significantly decrease for all models and scenarios in the future. The number of dry days and maximum consecutive dry days will increase whereas the number of wet days and maximum consecutive wet days will decrease. Future changes of daily rainfall occurrence sequences combined with a reduction in rainfall amounts will lead to a drier catchment, thereby reducing the runoff potential. Because this is a catchment that is a significant source of Adelaide's water supply, irrigation water and water for maintaining environmental flows, an effective climate change adaptation strategy is needed in order to face future potential water shortages.

Muscle LIM protein/CSRP3: a mechanosensor with a role in autophagy

Muscle LIM protein (MLP) is a microtubule-associated protein expressed in cardiac and muscle tissues that belongs to the cysteine-rich protein (CSRP/CRP) family. MLP has a central role during muscle development and for architectural maintenance of muscle cells. However, muscle cells rely on autophagy during differentiation and for structural maintenance. To study the role of MLP in autophagy, we have used C2C12 mouse myoblasts silenced or overexpressing MLP. Our results show that MLP contributes to the correct autophagosome formation and flux by interacting with LC3 as demonstrated by co-immunoprecipitation and PLA assay. In fact, MLP silencing results in decreased LC3-II staining and absent degradation of long-lived proteins. Moreover, MLP silencing impaired myoblasts differentiation as measured by decreased expression of MyoD1, MyoG1 and myosin heavy chain. Ultrastructural analysis revealed the presence of large empty autophagosomes in myoblasts and multimembranous structures in myotubes from MLP-silenced clones. Impaired autophagy in MLP-silenced cells resulted in increased susceptibility to apoptotic cell death. In fact, treatment of MLP-silenced C2C12 myoblasts and myotubes with staurosporine resulted in increased caspase-3 and PARP cleavage as well as increased percentage of cell death. In conclusion, we propose that MLP regulates autophagy during muscle cell differentiation or maintenance through a mechanism involving MLP/LC3-II interaction and correct autophagosome formation.

On birth single dose live attenuated OPV and BCG vaccination induces gut cathelicidin LL37 responses at 6 week of age: a natural experiment

In a cross sectional study, we show that infants who received single dose of live attenuated OPV and BCG vaccines within 48h of birth, have higher excretion of human cathelicidin LL37 (p<0.05) in stool at 6wk of age. This response remained unchanged in multivariate analysis after adjusting for sex, mode of delivery, infant age, mother age birth weight and breast milk feeding pattern. This analysis also reveals that irrespective of vaccination, girl infants have higher human-beta-defencin2 (HBD2) and exclusively breastfed infants have higher total and anti-polio specific IgA to all three subtypes in stool (p<0.05). However, vaccination induces anti-polio IgA responses only to infants who are exclusively breastfed. Thus on-birth live attenuated vaccination may provide non-specific beneficial effect against infections while exclusive breastfeeding enhance protection by boosting vaccine induced IgA. The result also suggests that in polio endemic area, exclusive breastfeeding may be sufficient for mucosal anti-polio responses during early infancy.

Effect of different levels of Dhania seed (Coriandrum sativum) on the performance of broiler

A total of 72 as hatched Cobb 500 broilers were fed ad libitum on a diet with 0 %, 0.5 %, 1.0 % and 1.5 % of coriander seed meal (CSM) to assess its feeding value. Treatment group with 1.5 % of CSM significantly (p<0.05) affected live weight of broilers at the age of 28 and 35 days. Among the dietary groups there is no significant difference in feed intake and feed efficiency. Meat yield characteristics especially abdominal fat level decreased significantly (p<0.01) at 1.5 % level of CSM. Cost of production per kg live broiler decreased when dietary inclusion level was increased. Profit per kg of live broiler was significantly (p<0.05) increased with the increase levels of dietary CSM. These results suggest that the CSM could be considered as a potential natural growth promoter for poultry, and showed the best responses at a 1.5 % level of inclusion. It was concluded that the supplementation of the coriander seed meal to broiler diet had beneficial effects on body weight gain, feed conversion ratio and carcass yield.DOI: http://dx.doi.org/10.3329/bjas.v43i1.19383 Bang. J. Anim. Sci. 2014. 43 (1): 38-44

Nonlinear programming technique for analyzing flocculent settling data

The traditional graphical approach for drawing iso-concentration curves to analyze flocculent settling data and design sedimentation basins poses difficulties for computer-based design methods. Thus, researchers have developed empirical approaches to analyze settling data. In this study, the ability of five empirical approaches to fit flocculent settling test data is compared. Particular emphasis is given to compare rule-based SETTLE and rule-based nonlinear programming (NLP) techniques as a viable alternative to the modeling methods of Berthouex and Stevens (1982), San (1989), and Ozer (1994). Published flocculent settling data are used to test the suitability of these empirical approaches. The primary objective, however, is to determine if the results of a NLP optimization technique are more reliable than those of other approaches. For this, mathematical curve fitting is conducted and the modeled concentration data are graphically compared to the observed data. The design results in terms of average solid removal efficiency as a function of detention times are also compared. Finally, the sum of squared errors values from these approaches are compared. The results indicate a strong correlation between observed and NLP modeled concentration data. The SETTLE and NLP approaches tend to be more conservative at lower retention times and less conservative at longer retention times. The SETTLE approach appears to be the most conservative. In terms of sum of squared errors values, NLP appears to be rank number one (i.e., best model) for eight data sets and number two for six data sets among 15 data sets. Therefore, NLP is recommended for analyzing flocculent settling data as a logical extension of other approaches. The NLP approach is further recommended as it is an optimization technique and uses conventional mathematical algorithms that can be solved using widely available software such as EXCEL and LINGO.

Long term cyclic heat stress influences physiological responses and blood characteristics in indigenous sheep

The present study was designed to elucidate changes in physiological and blood parameters of indigenous sheep during cyclic heat exposure. Twelve 2-4 year-old sheep with an average body weight of 10.5±0.5 kg were randomly allocated to one of three experimental heat treatments: control (21°C, stall feeding), short term (21°C to 32°C; 32°C for 4 h/d, grazing), and long term (21°C to 32°; 32°C for 8 h/d, grazing).The results have shown that sheep exposed to cyclic heat treatments exhibited higher (P=0.05) rectal temperature, body temperature, and respiratory rate compared to the control group. Cyclic heat treatments significantly decreased heart rate of sheep. There was a sharp reduction in rumination and an increase in time spent by sheep in eating during cyclic heat treatments. Long term heat treatment significantly increased RBC and WBC counts, PCV values, and hemoglobin level than that of the control and short term heat treatments. Similar responses were also observed in plasma glucose, uric acid, aspartate aminotransferase, and blood urea nitrogen levels. These results suggest that short term heat stress is tolerable but long term is physiologically detrimental to them to indigenous sheep.DOI: http://dx.doi.org/10.3329/bjas.v42i2.18486 Bang. J. Anim. Sci. 2013. 42 (2): 96-100

Histopathological Studies of Experimentally Infected Shing, Heteropneustes fossiliswith Aeromonas hydrophila Bacteria

Heteropneustes fossilis (shing) of 35g body weight were experimentally infected with Aeromonas hydrophila by two different methods: viz. intraperitonial and intramuscular injection. A standard dose of infection (6.4 × 107 CFU/ml) was selected based on predetermined LD50. Each method gave rise to the mortality of shing up to 85%. Clinical signs of fish included injury, hemorrhage and large ulcerative lesions on the body at the injected area. In kidney, liver and intestine pathologically, massive atrophy and focal necrosis were found. Hemorrhage, Vacuolation and atrophy of hepatic sinusoids represented by necrosis of the sinusoidal lining cells, degeneration of hepatic tissue and distribution of bacterial cell all over the tissue were found in liver. Atrophy, hemorrhage, villi missing and missing of epithelium were found in intestine of the experimentally infected shing. Bacterial cells were distributed in the whole hematopoietic tissue including the renal tubules. Tissue abscess characterized by focal necrosis, hemorrhage and Vacuolation were also found in the kidney of the infected shing. But the above symptoms were not found in the organs of the apparently healthy shing species.DOI: http://dx.doi.org/10.3329/pa.v19i1.17359 Progress. Agric. 19(1): 89 - 96, 2008 

Isolation of Aeromonas hydrophila from EUS Affected Shing Heteropneustes fossilis of a Fish Farm in Mymensingh

Aeromonas hydrophila bacteria was isolated from the suspected EUS-affected shing fish, Heteropneustes fossilis (Bloch). The disease investigations were primarily based on clinical signs and subsequently confirmed by the isolation of bacterial pathogen Aeromonas hydrophila from lesion of liver and kidney. The A. hydrophila isolates were identified by a series of morphological, physiological and biochemical tests. The total bacterial load in liver, intestine and kidney were 1.67 × 104 to 6.46 × 108 CFU/g, 1.71 × 103 to 1.18 × 109 CFU/g and 1.47 × 104 to 3.70 × 108 CFU/g respectively.DOI: http://dx.doi.org/10.3329/pa.v19i1.17362 Progress. Agric. 19(1): 117 - 124, 2008 

Hypersensitivity reaction to all drugs of category-1 anti-tuberculosis regime in an adult tuberculosis patient

Adverse drug reaction to tuberculous chemotherapy is not an uncommon problem. Usually it occurs to single drug and can be treated easily with minimal intervention. We follow WHO recommended guideline for National Tuberculosis Control Programs to treat these adverse reactions. Here we found an adult who has been suffering left sided pleural tuberculosis developed anaphylactic reaction to first dose of category-1 anti-TB regime. Later on it was found that he could not even tolerate smaller challenging doses of isoniazide, Ethambutol, Rifampicin and Pyrazinamide separately. It became very difficult to choose an alternate regime for this patient. Lastly a regime with levofloxacin, streptomycin and clarithromycin was give to treat him and patient was recovered with this regime successfully. This experience will help in management of unusual drug reactions to anti-tuberculosis drugs.

Efficacy of lower cut off value of serum prostate specific antigen in diagnosis of prostate cancer

Indications of prostate biopsy are high serum prostate specific antigen (PSA) value and or abnormal digital rectal examination (DRE) findings. Although serum PSA value of 4 ng/ml is the most commonly used threshold for recommending prostate biopsy, significant proportion of men harbor prostate cancer even when their serum PSA values are less than 4.0 ng/ml. Therefore present study was designed to determine the performance status of serum PSA in lower cut-off values. This hospital based prospective study was conducted in the Department of Urology of Bangabandhu Sheikh Mujib Medical University (BSMMU) and Comfort Nursing Home Pvt. Ltd, Dhaka from July 2009 to October 2010. Two hundred six male patients aged over 50 years having lower urinary tract symptoms (LUTS) and serum PSA more than 2.5 ng/ml were prepared for prostate biopsy. Trans rectal ultrasound (TRUS) guided biopsy was done. The test statistics used to analyze the data were descriptive statistics, sensitivity, specificity, positive and negative predictive value, ROC curve. For all analytical tests, the level of significance was set at 0.05 and p < 0.05 was considered significant. In 2.5-4 serum PSA range, 28.26% (13 out of 46) of all malignancy were found, which would be missed if we take cut off value 4. At 2.5 PSA cut-off, Sensitivity 91.3%, Specificity 14.37%, PPV 23.46%, NPV 85.18%, Efficacy 31.55%. At 4 PSA cut-off value, Sensitivity 71.73%, Specificity 46.25%, PPV 27.73%, NPV 85.05%, Efficacy 51.94%. So it can be concluded that, for early diagnosis of prostate cancer cut-off value of serum PSA of 2.5 ng/ml can be recommended as an indication for prostate biopsy.

Efficient mining of interesting patterns in large biological sequences

Pattern discovery in biological sequences (e.g., DNA sequences) is one of the most challenging tasks in computational biology and bioinformatics. So far, in most approaches, the number of occurrences is a major measure of determining whether a pattern is interesting or not. In computational biology, however, a pattern that is not frequent may still be considered very informative if its actual support frequency exceeds the prior expectation by a large margin. In this paper, we propose a new interesting measure that can provide meaningful biological information. We also propose an efficient index-based method for mining such interesting patterns. Experimental results show that our approach can find interesting patterns within an acceptable computation time.

An efficient approach to mining maximal contiguous frequent patterns from large DNA sequence databases

Mining interesting patterns from DNA sequences is one of the most challenging tasks in bioinformatics and computational biology. Maximal contiguous frequent patterns are preferable for expressing the function and structure of DNA sequences and hence can capture the common data characteristics among related sequences. Biologists are interested in finding frequent orderly arrangements of motifs that are responsible for similar expression of a group of genes. In order to reduce mining time and complexity, however, most existing sequence mining algorithms either focus on finding short DNA sequences or require explicit specification of sequence lengths in advance. The challenge is to find longer sequences without specifying sequence lengths in advance. In this paper, we propose an efficient approach to mining maximal contiguous frequent patterns from large DNA sequence datasets. The experimental results show that our proposed approach is memory-efficient and mines maximal contiguous frequent patterns within a reasonable time.

Comparison between prostate volume and intravesical prostatic protrusion in detecting bladder outlet obstruction due to benign prostatic hyperplasia

The objectives of this study were to determine and compare the correlation of intravesical prostatic protrusion (IPP) and prostate volume (PV) with bladder outlet obstruction (BOO). This study was conducted in the department of urology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh, between July 2009 to September 2010. Fifty benign prostatic hyperplasia (BPH) patients were included in the study. Their evaluation consisted of history along with International Prostate Symptoms Score (IPSS), digital rectal examination (DRE), transabdominal ultrasonography to measure prostate volume, intravesical prostatic protrusion & post voidal residual (PVR) urine and pressure-flow studies to detect bladder outflow obstruction (BOO). Statistical analysis included Unpaired ‘t’ test, Chisquare test and Spearman’s Rank correlation test. Receiver Operator Characteristic (ROC) curves were used to compare the correlation of PV and IPP with BOO. Mean prostate volume was significantly larger in bladder outlet obstructed patients (P<0.05). Mean IPP was significantly greater in obstructed patients (P<0.001). Area under ROC curve was 0.700 for PV and 0.821 for IPP. Prostate volume & intravesical prostatic protrusion measured through transabdominal ultrasonography are noninvasive and accessible method that significantly correlates with bladder outlet obstruction in patients with benign prostatic hyperplasia and the correlation of IPP is much more stronger than that of prostate volume. Introduction Benign prostatic hyperplasia (BPH) is one of the most common diseases in elderly men. The prevalence of histological BPH increases with age and appears in approximately 40% of men aged 50- 60 years and in approximately 90% of men aged more than 80 years1. Benign prostatic hyperplasia may lead to prostatic enlargement, bladder outlet obstruction (BOO) and lower urinary tract symptoms (LUTS). But the symptoms and obstruction do not entirely depend on prostate’s size. In contrast, intravesical prostatic protrusion (IPP) has been found to correlate with BOO2. IPP is a morphological change due to overgrowth of prostatic median and lateral lobes into the bladder and may lead to diskinetic movement of bladder during voiding. This IPP would cause more obstruction than if there were no protrusion and just enlargement of lateral lobes, as the strong bladder contraction could force open a channel between the lobes3. Several studies have previously demonstrated that the ultrasonographic measurement of IPP is able to detect BOO in BPH patients quickly and non-invasively4. This study was designed to diagnose BOO through non-invasive methods and aimed to define the correlationDOI: http://dx.doi.org/10.3329/bmrcb.v38i1.10446  Bangladesh Med Res Counc Bull 2012; 38: 14-17

Pulmonary metastases of a papillary adeno-carcinoma of ovary in a pregnant lady

A 28 years young lady admitted to National Institute of Diseases of Chest and Hospital (NIDCH), Dhaka with the complaints of respiratory distress and cough for 2 months. She was in her last trimester of first pregnancy when she becomes dyspneic on exertion and at night. Gradually it increases in time and she become unable to walk when she consulted with specialists in Barisal. She was examined clinically and radiographically and found some opacity on both lung fields. She was on several antibiotics, but got no improvement. In the meantime, an emergency caesarean section was done to have a healthy baby and patient came to NIDCH for this unexplained breathlessness and cough. She was severely dyspneic, tachypnoic, cyanosed. There were bilateral coarse crepitations, bilateral opacities predominantly on both lower and middle zones of both lungs obscuring costo-phrenic angles on chest X-rays. CT scan of chest shows bilateral reticulo-nodular shadows with a homogenous opacity on right lower lung which enhances after contrast scanning. A CT guided FNAC was done from that opacity which revealed a papillary adeno-carcinoma with psammoma bodies on cytopathological study. Thereafter, to explore the primary site, thyroid gland, abdominal organs was assessed adequately and only positive finding was raised CA-125 (706 IU/ml) which was consistent with ovarian cancer. In this way, a primary ovarian carcinoma in a pregnant young lady with normal sized ovary that metastasizes to lung causing bilateral pleural effusion and lymphangitis carcinomatosa was explored. This was an unusual presentation of ovarian papillary adeno-carcinoma with cough and breathlessness at the last trimester of pregnancy in absence of any abdominal mass.

Primary disseminated MDR-TB in a Bangladeshi man: a silent and emerging clinical problem for clinicians

A 26 years old Bangladeshi man experienced sudden gross haematuria for 10 days when he was working in Italy in June'07 that was resolved spontaneously. Six months' later he again developed haematuria and was admitted into an Italian hospital for its evaluation and management. In the mean time, he developed low grade fever, cough, back pain, spinal angulations, walking difficulty. His X-ray chest postero-anterior view revealed cavitary lesions in upper zones of both lung fields. Intravenous Urography (IVU) was done which revealed hydronephrosis and hydroureter of left kidney. Magnetic Resonance Imaging (MRI) of dorso-lumber spine revealed collapse of D10-12 and L4-5 vertebral bodies with perivertebral and epidural abscess. Sputum and urine smear for Acid-Fast-Bacilli (AFB) demonstrated the organisms on Z-N stain and AFB culture and sensitivity demonstrated that it was resistant to isoniazide, Rifampicin and streptomycin and diagnosed as primary disseminated multi-drug Resistant tuberculosis (MDR-TB). Second-line drugs were started in Italy on 15th January'08 and were continued thereafter in National Institute of Diseases of the Chest and Hospital (NIDCH). A ureteric stent which was given in Italy to get relief of hydro-ureter was removed in Dhaka. A neurosurgery (costo-transversectomy with decompression of spine) was done in Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka and patient get relief of back pain paresthesia. Lastly, his sputum and urine AFB smear and AFB culture became negative. So, primary disseminated MDR-TB with renal, spinal and pulmonary involvement was diagnosed in this Bangladeshi man who had a sputum AFB culture and sensitivity during his initial diagnostic work-up in Italy. It's an alarming case that demonstrated necessity of sputum AFB culture and sensitivity during initial diagnostic work-up.