Structural Analysis and Epitope Prediction of S2 Domain of SARS-CoV-2, Conservation Analysis Among Major Variants

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic. There are four structural proteins of the virus: spike, envelope, membrane, and nucleocapsid proteins. Various vaccines were designed and are effectively being used against the spike protein of the virus. However, several vaccine-related complications have been reported worldwide. Assuming that the structural integrity of the whole protein might be contributing to these complications, this study was performed to design epitopes using the S2 domain of the spike protein, which could trigger a strong immune response. We have also predicted antigenic and allergenic properties of the selected epitopes. A total of 49 B cell epitopes passing antigenicity and other assessment filters were found using three methods. Among them, RDLICAQ had the highest antigenicity score (1.1443). However, only one cytotoxic T lymphocyte epitope, RSFIEDLLF, passed the essential filters with an antigenicity score of 0.5782 to show an appropriate immune response for T cells, while among 21 helper T cell lymphocyte epitopes that were filtered, FAMQMAYRFNGIGVT showed the highest (1.3688) antigenicity score. Conservation analysis revealed that the S2 domain is significantly conserved, thus making it an ideal candidate for vaccine development. We have also designed a vaccine construct based on the best suiting components found during the whole study. This construct and S2 domain solely can be future subjects of interest or might be included in a subunit cocktail formulation for attaining unabridged immunogenicity.

Magseed placement before neoadjuvant chemotherapy to facilitate subsequent breastconserving surgery - a single-centre audit

BACKGROUND

A radio-opaque clip is placed in all patients planned for breast-conserving surgery (BCS) receiving neoadjuvant chemotherapy (NACT) to localise the tumour bed in case response to chemotherapy makes later localisation impossible. A tumour that was localised with a radio-opaque clip before NACT will then need a second localisation procedure, after the completion of NACT to aid BCS. The two most commonly used methods are hookwire and radioguided occult lesion localisation. Magseed^®, a newly available technology consisting of a small magnetic seed, has now become available. The seed is placed instead of a radio-opaque clip before the start of or during NACT and can remain in place until the time of BCS.

METHODS

A retrospective cohort study was performed, collecting data on patients who had a Magseed placed before or during NACT from December 2018 to February 2020.

RESULTS

Twenty-one Magseed devices were placed into the breasts of 20 patients, 18 under ultrasound guidance, and three under stereotactic guidance. The average breast volume of individuals who had seeds placed was 1 532 g ± 869 g. The duration that the seeds were in situ was 138 days ± 45 days. All preoperatively placed seeds were retrieved at the surgery with no observed migration outside the tumour bed.

CONCLUSION

Magseed placement before NACT is a safe and technically simple technique that can be done under ultrasound guidance in the majority of cases. It has the advantage of being a single procedure with an associated reduction in time off work and travel cost to the patient, as well as flexibility in terms of the time of placement.

Magseed placement before neoadjuvant chemotherapy to facilitate subsequent breast-conserving surgery – a single-centre audit

BACKGROUND: A radio-opaque clip is placed in all patients planned for breast-conserving surgery (BCS) receiving neoadjuvant chemotherapy (NACT) to localise the tumour bed in case response to chemotherapy makes later localisation impossible. A tumour that was localised with a radio-opaque clip before NACT will then need a second localisation procedure, after the completion of NACT to aid BCS. The two most commonly used methods are hookwire and radio-guided occult lesion localisation. Magseed®, a newly available technology consisting of a small magnetic seed, has now become available. The seed is placed instead of a radio-opaque clip before the start of or during NACT and can remain in place until the time of BCS. METHODS: A retrospective cohort study was performed, collecting data on patients who had a Magseed placed before or during NACT from December 2018 to February 2020. RESULTS: Twenty-one Magseed devices were placed into the breasts of 20 patients, 18 under ultrasound guidance, and three under stereotactic guidance. The average breast volume of individuals who had seeds placed was 1 532 g ± 869 g. The duration that the seeds were in situ was 138 days ± 45 days. All preoperatively placed seeds were retrieved at the surgery with no observed migration outside the tumour bed. CONCLUSION: Magseed placement before NACT is a safe and technically simple technique that can be done under ultrasound guidance in the majority of cases. It has the advantage of being a single procedure with an associated reduction in time off work and travel cost to the patient, as well as flexibility in terms of the time of placement.

Association of Body Mass Index and Blood Pressure with Age: A Cross Sectional Study in Elderly Male

The aim of the study was to assess the status of body mass index (BMI) and blood pressure in elderly male in comparison to younger male and to study the association of BMI and blood pressure with age. This analytical type of cross-sectional study was carried out in the Department of Physiology, Mymensingh Medical College, Mymensingh, Bangladesh from January 2019 to December 2019. A total number of 140 male subjects were included in this study. Among them seventy (70) younger males were taken as control group (Group I) and seventy (70) elderly males were taken as study group (Group II). Body mass index (BMI) was calculated as the weight in kilograms divided by the square of the height in meters (kg/m²). Systolic and diastolic blood pressure was measured by aneroid sphygmomanometer (ALPK2, Japan). Data were expressed as Mean±SD and statistical significance of difference among the group was calculated by unpaired student's 't' test. Pearson's correlation coefficient test was done to find the correlation of BMI, systolic blood pressure (SBP) & diastolic blood pressure (DBP) with age. In this study we found that mean BMI, systolic blood pressure & diastolic blood pressure were significantly higher in elderly male persons in comparison to younger male. Although the magnitude of correlation differed, we found that BMI, systolic blood pressure & diastolic blood pressure were positively correlated with age of the subjects. Based on the study carried out it can be concluded that due to aging process geriatric populations are more prone to development of hypertension and other cardiovascular complications than younger individuals.

Evaluation of Change of Peak Expiratory Flow Rate (PEFR) in Male Chronic Obstructive Pulmonary Diseased (COPD) Patients

Chronic obstructive pulmonary disease (COPD) is a major public health problem which causes high health care utilizations, poor health-related quality of life, and substantial cost burden and deaths in worldwide. This study was done to evaluate the changes of peak expiratory flow rate (PEFR) in COPD patients in comparison to healthy person. This analytical type of cross sectional study was carried out in the Department of Physiology, Mymensingh Medical College, Mymensingh, Bangladesh from July 2018 to June 2019. A total number of 160 male subjects, age ranged from 30-70 years was included in this study. Among them, eighty (80) male COPD subjects were taken as study group (Group II) and eighty (80) age matched male healthy subjects were taken as control group (Group I). PEFR was assessed by peak flow meter. Data were expressed as mean ±SD and statistical significance of difference among the group was calculated by unpaired students' 't' test. The mean ±SD of PEFR of Group I and Group II were 432.75±30.23 L/min & 203.5±20.81 L/min respectively. The mean ±SD of PEFR significantly lower in study group in comparison with control group. Patients with COPD with greater changes in PEFR causes more frequent hospitalization and increased mortality and morbidity due to COPD related complications. So, assessment of this parameter is important for early detection and prevention of complications related to COPD for leading a healthy life.

Prospect of microbial food borne diseases in Pakistan: a review

Nowadays food borne illness is most common in people due to their epidemic nature. These diseases affect the human digestive system through bacteria, viruses and parasites. The agents of illness are transmitted in our body through various types of food items, water and uncooked. Pathogens show drastic changes in immunosuppressant people. This review gives general insights to harmful microbial life. Pakistan is a developed country and because of its improper food management, a lot of gastrointestinal problems are noted in many patients. Bacteria are most common agents to spread diarrhoea, villi infection, constipation and dysenteric disease in human and induce the rejection of organ transplant. Enhancement of their lifestyle, properly cooked food should be used and to overcome the outbreak of the diseases.

Relationship of BMI and Fasting Serum Glucose with Hypertension

Hypertension is an important worldwide public-health challenge because of its high frequency and concomitant risks of cardiovascular and kidney disease. It is recognized as a major contributor to the disease burden globally. Aim of the study was to evaluate body mass index and fasting serum glucose level in male hypertensive patients in order to compare these parameters with male normotensive subjects. This analytical type of cross sectional study was carried out in the Department of Physiology, Mymensingh Medical College, Bangladesh from July 2018 to June 2019. Total 200 male subjects, age range was from 30-65 years were included in this study. Among them, 100 hypertensive subjects were taken as study group (Group II) and 100 ages matched normotensive male subjects were taken as control group (Group I). Quantitative data were expressed as mean (±SD) and statistical significance of difference among the group was calculated by unpaired student's 't' test. In this study we found that body mass index was significantly (p<0.001) increased in study group (29.52±2.46) in comparison with control group (22.91±1.04). Fasting serum glucose level was also significantly (p<0.001) increased in study group (6.35±0.47) in comparison with control group (4.52±0.50). Based on the study carried out it is concluded that there is definite relationship of body mass index and fasting serum glucose level with hypertension. Therefore, basic measurement of weight and height to determine the body mass index and fasting serum glucose level as routine assessment during hospital visitation with appropriate lifestyle modification would help in controlling hypertension as well as its devastating consequences.

Body Mass Index and Serum Thyroid Stimulating Hormone in Third Trimester of Pregnancy

Pregnancy is a natural physiological state with hormonal and metabolic changes that helps the growth and survival of the fetus. Adequate body mass index (BMI) in pregnancy is important for securing, protecting and promoting the health of women and newborns. High or low maternal body mass index is associated with adverse outcome. Thyroid physiology plays a major role in pregnancy and thyroid disorders constitute one of the most common endocrine disorders in pregnancy. To assess the levels of body mass index and serum thyroid stimulating hormone (TSH) in third trimester of pregnancy in order to compare these parameters with non-pregnant women of same age range. This analytical type of cross sectional study was carried out in the Department of Physiology, Mymensingh Medical College, Bangladesh from January 2019 to December 2019. A total number of 140 subjects, age range between 20-35 years were included in this study. Among them, 70 healthy subjects were taken as control group (Group I) and 70 pregnant women of third trimester were taken as study group (Group II). The results were calculated and analyzed by using SPSS. Quantitative data were expressed as mean (±SE) and statistical significance of difference among the group was calculated by unpaired student's 't' test. In this study we found that BMI was 27.87±1.9kg/m² and serum TSH level was 2.27±1.18μIU/ml in study group. Both (BMI & TSH) are significantly increased in study groups in comparison with control group. Therefore, by this study we recommended that routine estimation of these parameters is important for prevention of complication related to pregnancy.

Thyroid Function Status in Elderly Male

With the advancement of age, the production, metabolism and action of thyroid hormone are also changed. The incidence of thyroid dysfunction is increased greatly with age. Aim of the study was to assess the age-related change in thyroid function status in elderly male in order to compare it with younger male. This analytical type of cross-sectional study was carried out in the Department of Physiology, Mymensingh Medical College, Mymensingh, Bangladesh from January 2019 to December 2019. A total number of 140 male subjects were included in this study. Among them seventy (70) younger male were taken as control group (Group I) and seventy (70) elderly male were taken as study group (Group II). For assessment of thyroid function, serum free tri-iodothyronine (FT₃), free thyroxine (FT₄) and thyroid stimulating hormone (TSH) levels were estimated by RIA method. Data were expressed as mean (±SD) and statistical significance of difference among the group was calculated by unpaired student's t-test. Pearson's correlation coefficient test was done to find the correlation of serum FT₃, FT₄ & TSH with age. In this study we found that mean serum free tri-iodothyronine (FT₃) & free thyroxine (FT₄) levels were significantly lower and serum thyroid stimulating hormone (TSH) level was significantly higher in elderly male persons in comparison to younger male. Again, serum FT₃, FT₄ was negatively correlated with age of the subjects whereas serum TSH level was positively correlated with age of the subjects. Based on the study carried out it is concluded that there is a progressive decrease in thyroid function with advancement of age.

Feasibility and Safety of Chorionic Villus Sampling (CVS) for Prenatal Diagnosis of Thalassemia in Bangladesh

Thalassaemia is one of the commonest inherited disorders in Bangladesh. Since population is rapidly increasing in Bangladesh, therefore birth of large number of new cases is expected every year. Chorionic villus sampling (CVS) is an invasive diagnostic procedure done in early pregnancy to obtain fetal cells for the prenatal diagnosis of chromosomal and genetic disorders like thalassemia. To investigate the feasibility, safety, and outcome of transabdominal Chorionic Villus Sampling (CVS) for prenatal diagnosis of Beta Thalassemia, this retrospective analytical study was carried out on women who had undergone transabdominal CVS for prenatal diagnosis of Beta thalassemia. All CVS are done at Fetal Medicine Centre, Family Foundation, Green Road, Dhaka, Bangladesh from June 2013 to December 2016. A total of 236 couples who were referred for prenatal diagnosis of thalassemia (Beta thalassemia & Hb-E beta thalassemia) were studied. Transabdominal CVS was done under local anesthesia and real-time ultrasound guidance. A 18G/88mm Spinal Needle (B Braun, Germany) was used. Most procedures were done between 11 and 13 weeks (range 11-14 weeks). All CVS were performed with the "2 operators" technique. The samples were sent for prenatal diagnosis by genetic analysis. Results were recorded and analyzed for descriptive statistics. Out of 236, 123 (52.1%) fetuses were diagnosed as trait (Beta trait or HbE trait), 64 (27.1%) as healthy fetuses and 49 (20.7%) as affected fetuses. A total of 236 CVSs were performed as outdoor basis. Most aspirations (95.1%) were easy; however, in 4.8% cases the aspiration was difficult due to a variety of factors. The overall success rate was 100%. Minor complications like placental hematoma and pervaginal (P/V) bleeding occurred in 2% & 1.3% respectively which were subsided by conservative management. The procedure related miscarriage within three weeks not occurred in any cases. Transabdominal CVS under real-time sonography is a useful outdoor procedure for prenatal diagnosis of beta thalassaemia in early pregnancy without significant risk to the mother and the fetus.

Study on Clinical Presentation and Outcome of Septic Abortion and Its Relationship with Person Inducing Abortion

Abortion is a global problem. Maternal mortality and morbidity is still high due to uncontrolled abortion mainly induced abortion which may turn to septic abortion. A total of 50 cases of septic abortion cases admitted in Dhaka Medical College Hospital were included in this study. This cross sectional study was designed to find out the clinical presentation and outcome of septic abortion from January 2010 to January 2011. Out of 50 cases of septic abortion admitted where 44(88%) were induced abortion. Majority of the cases were parous (2-3 parity 32%; 4-6 parity 38%; and 6+ parity 4%) and housewives 42(84%), living with their husbands 49(98%), hailing from urban, semi urban and urban slums. Nineteen (38%) having no education and 21(42%) had primary education. Most of the women 20(45.45%) wanted no more child, decided to terminate pregnancy not to overburden their families or due to disturbed marital relationship. The termination of pregnancy was carried out in first trimester 20(40%) and between (13-16) weeks it was 17(34%). Complications of septic abortion still remain a lethal threat to the life and health of women. The death rate was found 6(12%). And the leading causes of death were generalized peritonitis with septicaemia 3(50%), septicaemia with renal failure 2(33.30%), septic abortion with Disseminated Intravascular Coagulation 1(16.70%). Effective and widespread contraceptive use and continuing health and sex education remain pivotal if the incidence of septic abortion and their complications are to be reduced.

Assessment of Postnatal Depression by Edinburgh Postnatal Depression Scale in a Tertiary Care Hospital of Bangladesh

The objective of the study was to estimate the prevalence of post partum depression and its associated risk factors among the mothers in their immediate post natal period. This cross sectional study was carried out in the Department of Obstetrics & Gynaecology, Bangabandhu Sheikh Mujib Medical University (BSMMU) and a tertiary care centre in Dhaka, Bangladesh from July 2015 to December 2015. Total 145 post natal mothers were screened for postnatal depression from day 5-7 following caesarean section by the validated Bangla version of Edinburgh Postnatal Depression Scale. To find out the risk factors for depression baseline data included age, parity, socioeconomic conditions, educational level, and occupation, history of depression, social support, and marital support, gestational age at the time of delivery, weight and sex of the baby. Postpartum depression was noted among 12.4% cases. Maternal age, history of depression, lack of social support was found to be significantly associated with maternal depression. This small study reflected the facts that many of the postnatal mothers of our circumstances suffer from postpartum depression and needs medical attention. Screening of postpartum depression can be considered as a routine part of postpartum care.

Current Trend of Using Anti-Hypertensives in Pregnancy and Postpartum Period in a Tertiary Level Hospital

Hypertensive disorders are one of the most common disorders in pregnancy. They are amongst the major cause of maternal and perinatal morbidity and mortality. Incidence is increasing in developing countries like Bangladesh. This cross sectional descriptive study has done to observe the utilization of antihypertensive drugs in hypertensive disorders of pregnancy and conducted from January 2016 to December 2016 in the department of Pharmacology in collaboration with department of Gynecology and Obstetrics in Mymensingh Medical College Hospital, Mymensingh, Bangladesh. Non random purposive sampling technique was used. Total of 300 patients participated in the study, 281 anti partum and 19 postpartum. Age distribution showed 42% patients were in 21-25 years age group. Majority of the participants (91%) were housewife and majority (79%) came from poor socioeconomic status with below SSC education (68%). About 82% patients lived in rural area. Trimester and gravida wise distribution showed most of the participants were 3rd trimester (61%) and primigravida (57%) and only 6% patients belong to postpartum period. In this study preeclampsia was highest (63.8%) among all other types of hypertensive diseases in pregnancy. Majority of the patient were preferred for dual therapy (53%), mono therapy was used in 29% of cases. Most frequently given drug in pregnancy associated hypertension was methyldopa that is 88.33% (single 22.3%, combination 66%). Second most commonly used drug was nifidipine consisting of 47.6% but used in combination in all cases. Average number of anti hypertensive drugs prescribed per prescription was 1.87 and majorities (92%) were from essential drug list but used as trade name. Preeclampsia and eclampsia were more common among the hypertensive disorders in tertiary level hospital cases. Methyldopa was found to be the commonest prescribed antihypertensive in monotherapy and in combination.

Fluorescence based cell counting in collagen monolayer cultures of primary hepatocytes

Accurate determination of cell number is essential for the quantitative description of biological processes. The changes should be related to a measurable reference e.g. in the case of cell culture, the viable cell number is a very valuable reference parameter. Indirect methods of cell number/viability measurements may have up to 10 % standard deviation. This can lead to undesirable large deviations in the analysis of "-omics" data as well as time course studies. Such data should be preferably normalized to the exact viable cell number at a given time to allow meaningful interpretation and understanding of the biological processes. Manual counting of cell number is very laborious and not possible in certain experimental setups. We therefore, developed a simple and reliable fluorescence based method with an accuracy of 95-98 % for the determination of the viable cell number in situ. We optimized the seeding cell densities for primary rat hepatocytes for optimal cell adhesion. This will help in efficient use of primary cells which are usually limited in availability. The method will be very useful in the application of "-omics" techniques, especially metabolome analysis where the specific rates of uptake/production of metabolites can be reliably calculated.

Medication Management System: An Approach to Reduce Medication Error In Apollo Hospitals Dhaka

Apollo Hospitals Dhaka surely stepped ahead than any other hospital of Bangladesh for reducing medication errors significantly. From the very beginning of its establishment, reducing medication errors was taken as a major challenge and effective and approved strategies were developed when no other hospital took efforts in this regard. Strategies included tracking incidents of medication errors, analyzing, reporting & arranging proper training sessions for hospital staffs etc. All four types of errors like Prescription errors, Transcription errors, Dispensing errors and Administration errors are rectified and officially reported by hospital pharmacists. Along with these, Prescription Reviewing, Medication Reconciliation, incidents of Adverse Drug Reactions (ADR) are also monitored to ensure rational drug use for patients. With all its efforts, Apollo Hospitals Dhaka was able to reduce the rate of medication errors within the internationally acceptable range. DOI: http://dx.doi.org/10.3329/pulse.v5i2.20265 Pulse Vol.5 July 2011 p.41-47

New chromogenic dipeptide substrate for continuous assay of the D-alanyl-D-alanine dipeptidase VanX required for high-level vancomycin resistance

A direct continuous UV-Vis spectrophotometric assay has been developed for VanX, a D-alanyl-D-alanine aminodipeptidase necessary for vancomycin resistance. This method is based on the hydrolysis of the alternative substrate D-alanyl-alpha-(R)-phenylthio-glycine D-Ala-D-Gly(S-Ph)-OH (H-DAla-DPsg-OH, 5a). Spontaneous decomposition of the released phenylthioglycine generates thiophenol, which is quantified using Ellman's reagent. The dipeptide behaved as an excellent substrate of VanX, exhibiting Michaelis-Menten kinetics with a kcat of 76 +/- 5/s and a KM of 0.83 +/- 0.08 mm (kcat = 46 +/- 3/s and KM = 0.11 +/- 0.01 mm for D-Ala-D-Ala). Determination of the kinetic parameters of the previously reported mechanism-based inhibitor D-Ala-D-Gly(SPhip-CHF2)-OH (H-D-Ala-DPfg-OH, 5c) [Araoz, R., Anhalt, E., René, L., Badet-Denisot, M.-A., Courvalin, P. & Badet, B. (2000) Biochemistry 39, 15971-15979] using the substrate reported in the present study yielded values of Kirr of 22 +/- 1 microM and kinact of 9.3 +/- 0.4/min in good agreement with values previously obtained in our laboratory (Kirr = 30 +/- 1 mm; kinact = 7.3 +/- 0.3/min). In addition, inhibition by the competing substrate D-Ala-D-Ala resulted in determination of a Ki = 70 +/- 6 microM close to the previously reported KM value. These results demonstrate that the present assay is a convenient, rapid and sensitive tool in the search for VanX inhibitors.

Antimicrobial activity of some commonly used herbs

In the present study some herbal extracts have been tested for their antibacterial activity using seven different strains of Gram positive and Gram negative bacteria to measure the zone of inhibition. Extracts were found devoid of activity against all the microorganisms.

Role of quinone moiety as antitumour agents: a review

Quinone antitumour agents with wide spectrum of activity have been extensively used in different forms of human cancers. Quinones have been isolated either from animals, microorganisms or plants. Extensive research on quinone compounds is going on to discover novel effective antitumour compound. We also discussed the mechanism of action, which have not been fully clarified. In this review we cover all the above-mentioned aspects to emphasize the importance of quinone moiety as antitumour agents.

Assessment of Anemone pulsatilla for some biological activities

Preliminary screening of herbal extracts employs the determination of their biological activity and the estimation of their therapeutic potential. This eliminates the unnecessary effort of fractionation and purification of constituents unimportant from the practice pharmacological point of view. It also gives a scientific basis to the herbs traditionally used in folk medicine. Thus, during the present investigation the spasmolytic effect of Anemone pulsatilla extract on isolated tissues of rabbit jejunum was evaluated. In addition the pharmacological screening of Anemone pulsatilla extract was also earned out.