46 results on '"Md. Zulfikar Ali"'
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2. Analytical approximate solutions of some fractional nonlinear evolution equations through AFVI method
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Md. Asaduzzaman, Faruk Özger, and Md. Zulfikar Ali
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AFVI method ,Fractional nonlinear evolution equations ,Caputo fractional order derivative ,Analytical approximate solution ,Convergence analysis ,Applied mathematics. Quantitative methods ,T57-57.97 - Abstract
In this article, we construct and investigate a new fractional variational iteration technique which is named as AFVI method. After that, we formulate some IVPs corresponding to the fractional nonlinear evolution equations NLTFFWE, mNLTFFWE, TFmCHE and TFmDPE. The Caputo fractional order derivative has been used to fractionalize the considered NLEEs. Then, we solve the considered IVPs by applying the formulated AFVI method. Lastly, we check the accuracy of the attained AASs by making some graphical and numerical comparisons with their corresponding exact solutions and other existing equivalent AASs. The result of this article confirm that the efficiency, appropriateness and time spent capability of the newly constructed AFVI method are better than that of the other existing analogous fractional analytical approximation methods. Here, we apply the Maple 2021 programming software to obtain the AASs of the formulated IVPs and drawing the 3D graphs of the attained AASs. Finally, in this article we validate the applicability of the Caputo fractional order derivative to form a novel analytical approximation method as well as to fractionalize some essential NLEEs of Mathematical physics.
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- 2024
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3. Effect of distinct drying approach on bioactive compounds and nutritional profiling of Ulva intestinalis and Padina tetrastromatica from the Bay of Bengal, Bangladesh
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Abu Bakker Siddique Khan, Md. Rahamat Ullah, Mousumi Akhter, Md. Monjurul Hasan, Farhana Yasmin, Aovijite Bosu, Mohammed Ashraful Haque, Md. Mohidul Islam, Al-Amin, Md. Amirul Islam, and Md. Zulfikar Ali
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Marine macroalgae ,Drying ,TPC ,TFC ,Nutritional chemicals ,Freeze drying ,Food processing and manufacture ,TP368-456 - Abstract
Marine algae have been visualized as fostering a prevalent actuation of bioactive substances that have noteworthy therapeutic effects. The current investigations deployed a trio of separate drying methods, i.e., oven drying, freeze drying, and sun drying, to quantify the total phenolic content (TPC), total flavonoid content (TFC), and dietary vitality of Ulva intestinalis and Padina tetrastromatica. By mining and scrutinizing it to the quercetin and gallic acid standards, TPC and TFC were derived. Among three drying techniques, freeze drying asserted higher TPC (12.59 ± 1.07 in U. intestinalis and 68.74 ± 1.95 mg of GA/g in P. tetrastromatica) and TFC (7.92 ± 0.97 in U. intestinalis and 58.15 ± 2.05 mg of quercetin/g in P. tetrastromatica) values. Ulva intestinalis and P. tetrastromatica also contain a high amount of protein (18.34% and 8.7%, respectively). The findings demonstrated that green seaweed possessed higher levels of potassium (2.20%) and molybdenum (2.41%) and brown seaweed showed higher amounts of potassium (2.41%) and calcium (1.11%). Where rapid drying methods are recommended to enhance constituent levels, freeze-drying could be an attractive alternative to oven and sun drying, as it addresses the drawbacks associated with prolonged drying periods.
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- 2024
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4. Population dynamics of spotted scat, Scatophagus argus (Linnaeus 1766) from the Sundarbans of Bangladesh
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Md. Hashmi Sakib, Shawon Ahmmed, Md. Reaz Morshed Ranju, Md. Moshiur Rahman, Md. Masudur Rahman, Md. Latiful Islam, and Md. Zulfikar Ali
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Fish stock ,Mortality ,Expitation ,Assessment ,Management ,Conservation ,Science (General) ,Q1-390 ,Social sciences (General) ,H1-99 - Abstract
In Bangladesh, the mangrove areas of the Sundarbans are a hotspot for the spotted scat (Scatophagus argus), as the estuarine tributeries are significant zones for fishing, local marketing and foreign trading. Due to the widespread capture of spotted scats in the wild for a variety of uses, parameters of population were estimated using length-frequency and body weight data gathered from various sites in the southwestern forest areas of the country to comprehend the stock's status. Between May 2022 and April 2023, 1280 S. argus individuals were sampled from Khulna, Bagerhat and Satkhira. To gain insight into the population dynamics of S. argus, estimations of the growth parameters, recruitment pattern, mortalities, and level of exploitation (E) were made. For S. argus, a bit of negetive allomentric growth (b = 2.95) was observed. Moreover, the growth performance index (φ′), the asymptotic length (TL∝) and the growth coefficient (K) were 2.83, 34.65, cm and 0.56 yr−1, respectively. Natural mortality (1.08 yr−1) was lower than fishing mortality (1.12 yr−1). In the wild, this species recruits throughout the year, reaching its peak between October and January. By fishing gear, 50 % of the S. argus were caught between 7.71 cm and 9.43 cm. Moreover, high fishing mortality was assumed in both the small group (11–15 cm) and the large group (29–33 cm) of S. argus by virtual population analysis (VPA). It was discovered that the E for S. argus was 0.51, over the maximum permissible limit (Emax = 0.48). In summary, it is discovered that the S. argus population is overexploited. Therefore, in order to preserve this popular fish species and avoid local extinction, spotted scat resources should be taken into account under appropriate fisheries management guidelines. These findings will guide policymakers to manage the species accordingly.
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- 2024
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5. A review on commercially important seaweed resources from the Bangladesh coast
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Mohammad Khairul Alam Sobuj, Shafiqur Rahman, and Md. Zulfikar Ali
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Commercially important seaweeds ,Production ,Availability ,Abundance ,Uses ,Bangladesh ,Food processing and manufacture ,TP368-456 - Abstract
Seaweeds have emerged as promising marine living resources globally. With a distribution of over 20,000 species worldwide, only a tiny fraction, approximately 1.1 %, are commercially utilized. Among these, 145 species are used for food purposes, while 110 species are utilized for phycocolloid production. Seaweeds’ wide range of applications and benefits highlight their immense potential in various sectors. Based on the availability, abundance, and use, 26 seaweed species are recorded from Bangladesh's coastal area with commercial significance. Of these, red seaweed (Rhodophyceae) with 10 species (38.46 %), green seaweed (Chlorophyceae) with 08 species (30.77 %), and brown seaweed (Phaeophyceae) with 08 species (30.77 %). Seaweed species like Caulerpa sp., Ulva sp., Padina sp., Sargassum sp., Hypnea sp., and Gracilaria sp. offer numerous benefits and applications in pharmaceuticals, food, animal feed, cosmetic industry, waste water treatment, biofuel production, bioremediation, and agriculture due to their bioactive components, antimicrobial, and antioxidant properties. The development of sustainable cultivation techniques and investment in seaweed-based industries can unlock the immense potential of these marine resources and contribute to the growth of a sustainable blue economy. Harnessing the vast array of seaweed species and their commercial applications can lead to economic development while promoting sustainable practices.
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- 2024
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6. Existence of positive solution to the boundary value problems for coupled system of nonlinear fractional differential equations
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Md. Asaduzzaman and Md. Zulfikar Ali
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coupled system of Riemann-Liouville type fractional differential equations ,three-point boundary value condition ,positive solution ,Schauder’s fixed point theorem ,Mathematics ,QA1-939 - Abstract
In this paper, we investigate the existence criteria of at least one positive solution to the three-point boundary value problems with coupled system of Riemann-Liouville type nonlinear fractional order differential equations. The analysis of this study is based on the well-known Schauder’s fixed point theorem. Some new existence and multiplicity results for coupled system of Riemann-Liouville type nonlinear fractional order differential equation with three-point boundary value conditions are obtained.
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- 2019
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7. Fixed Point Theorem Based Solvability of 2-Dimensional Dissipative Cubic Nonlinear Klein-Gordon Equation
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Md. Asaduzzaman, Adem Kilicman, Md. Zulfikar Ali, and Siti Hasana Sapar
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2-Dimensional dissipative cubic nonlinear Klein-Gordon equation ,periodic solution ,GLK method ,LS fixed point theorem ,Mathematics ,QA1-939 - Abstract
The purpose of this article is to establish the solvability of the 2-Dimensional dissipative cubic nonlinear Klein-Gordon equation (2DDCNLKGE) through periodic boundary value conditions (PBVCs). The analysis of this study is founded on the Galerkin’s method (GLK) and the Leray-Schauder’s fixed point theorem (LS). First, the GLK method is used to construct some uniform priori estimates of approximate solution to the corresponding equation of 2DDCNLKGE. Finally, the LS fixed point theorem is applied to obtain the efficient and straightforward existence and uniqueness criteria of time periodic solution to the 2DDCNLKGE.
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- 2020
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8. A Persistence Detector for Metabolic Network Rewiring in an Animal
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Jote T. Bulcha, Gabrielle E. Giese, Md. Zulfikar Ali, Yong-Uk Lee, Melissa D. Walker, Amy D. Holdorf, L. Safak Yilmaz, Robert C. Brewster, and Albertha J.M. Walhout
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Biology (General) ,QH301-705.5 - Abstract
Summary: Biological systems must possess mechanisms that prevent inappropriate responses to spurious environmental inputs. Caenorhabditis elegans has two breakdown pathways for the short-chain fatty acid propionate: a canonical, vitamin B12-dependent pathway and a propionate shunt that is used when vitamin B12 levels are low. The shunt pathway is kept off when there is sufficient flux through the canonical pathway, likely to avoid generating shunt-specific toxic intermediates. Here, we discovered a transcriptional regulatory circuit that activates shunt gene expression upon propionate buildup. Nuclear hormone receptor 10 (NHR-10) and NHR-68 function together as a “persistence detector” in a type 1, coherent feed-forward loop with an AND-logic gate to delay shunt activation upon propionate accumulation and to avoid spurious shunt activation in response to a non-sustained pulse of propionate. Together, our findings identify a persistence detector in an animal, which transcriptionally rewires propionate metabolism to maintain homeostasis. : Bulcha et al. discover a transcriptional persistence detector composed of a type 1 coherent feed-forward loop with an AND-logic gate that rewires propionate metabolism in C. elegans. Keywords: persistence detector, feed-forward loop, AND-logic gate, transcription factor, gene regulatory network, C. elegans, vitamin B12, propionate, metabolism
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- 2019
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9. Regulatory properties of transcription factors with diverse mechanistic function.
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Md Zulfikar Ali, Sunil Guharajan, Vinuselvi Parisutham, and Robert C. Brewster
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- 2024
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10. Controlling gene expression timing through gene regulatory architecture.
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Md Zulfikar Ali and Robert C. Brewster
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- 2022
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11. TCTAP C-181 Pulmonary Valve Balloon Dilation and Transcatheter Closure of Atrial Septal Defect in a Teenaged Cyanotic Girl
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Abdul Momen, Ashraf Ur Rahman, Lima Asrin Sayami, ABM Abm Nurunnobi, Md Saqif Shahriar, and Md Zulfikar Ali
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Cardiology and Cardiovascular Medicine - Published
- 2023
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12. Bangla Version of Lymphedema Life Impact Scale Version 2: Reliability and Validity
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null Mohammed Emran, null Md Israt Hasan, null Md Nazmul Alam, null Neelufar Rahman, and null Md Zulfikar Ali
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General Medicine - Abstract
Background: The use of disease-specific scales would be more valuable for the evaluation of the effects of lymphedema. To manage accordingly, and maintain the optimum quality of life of lymphedema patient, a validated outcome measure is helpful.Objective: To investigate the reliability and validity of Bangla Version of Lymphedema Life Impact Scale Version 2 (B-LLIS V2).Materials and Methods: A structured process that included translation, verification, compromise assessment, reverse translation, feedback, and final correction. B-LLIS V2 reliability and validity were conducted on 52 lymphedema patients. The reliability was evaluated by performing internal consistency and test–retest analyses. Its validity was assessed by comparing the B-LLIS V2 with other scales implying Pearson’s correlation.Results: Internal consistency with Cronbach’s alpha was 0.92 for total score and 0.79, 0.82, 0.80 and 0.78 for physical, psychosocial, functional, and infection respectively. The calculated overall tool score in Intra-class correlation co-efficient (ICC) for test-retest reliability was 0.94 and among subscales, the scores were 0.92, 0.95, 0.91 and 0.93 for physical, Psychosocial, functional, and infection respectively, which signified substantial reliability. The overall values of Pearson’s correlation coefficient for the construct validity were 0.91, 0.78 and 0.86 against reference standard Bengali SF-36 Health Survey, Bangla version of the Boston Carpal Tunnel Questionnaire and Bangla Start Back Screening Tool, and they all were statistically significant.Conclusions: B-LLIS V2 is a valid and reliable tool for the assessment of impairment due to lymphedema. KYAMC Journal Vol. 13, No. 04, January 2023: 198-203
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- 2023
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13. Association of Waist and Hip Ratio with the Angiographic Severity of Coronary Artery Disease in Patients with Non ST Segment Elevation Myocardial Infarction
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Md Mozammel Haque, Md Mamunur Rashid, Md Zulfikar Ali, Iftekhar Alam, Md Sukur Ahmed, Al Mamun, Tapan Chandra Shil, Golam Rahman Mallick, Mahbubur Rahman Khan, Tamal Peter Ghosh, Zahidul Islam Khan, Shahriar Azad, Debabrata Halder, Pijus Biswas, and ABM Nurun Nobi
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General Medicine - Abstract
Background: Obesity is a proven independent risk factor for coronary artery disease. There are different Methods for evaluation of obesity. The aim of this study is to evaluate the association between waist hip ratio and the severity of CAD in non-ST-segment elevation myocardial infarction patients. Methods: This cross-sectional observational study was done at the National Institute of Cardiovascular Diseases (NICVD), Dhaka. A total of 100 patients with NSTEMI who underwent coronary angiogram during the indexed hospitalization period were included in this study. On the basis of WHR, study patients were divided into two groups 50 patients of NSTEMI with normal WHR (Male
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- 2022
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14. Evaluate of Angiographic Severity of Coronary Artery Disease in Patients with NSTEMI by Gensini Score and Vessel Score
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Md. Mozammel Haque, Dr. Md. Zulfikar Ali, Dr. Tapan Chandra Shil, Dr. Md. Humayun Kabir, Dr. Debabrata Halder, Dr. Sharmin Ali, Dr. Al Mamun, and Dr. Iftequar Alam
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General Medicine - Abstract
Background: Cardiovascular disease is leading cause of mortality and morbidity in developed and developing countries. Metabolic syndrome (MS) is a risk factor for coronary artery disease (CAD). Objective: The aim of this study is to evaluate the angiographic severity of coronary artery disease in patients with NSTEMI by Gensini score and \Vessel score. Methods: This cross-sectional observational study was done at the National Institute of Cardiovascular Diseases (NICVD), Dhaka. A total of 100 patients with NSTEMI underwent coronary angiography were included in the study. Coronary angiogram was done during index hospital admission. On the basis of WHR, study patients were divided into two groups: 50 patients of NSTEMI with normal WHR (Male
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- 2022
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15. Effect of skip-feeding and re-feeding regimes on compensatory growth, body composition, feed utilization, feeding cost and survival of monosex tilapia (Oreochromis niloticus) in pond aquaculture system
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MD. RASHEDUL ISLAM, MD. ZULFIKAR ALI, A.F.M. HASANUZZAMAN, and MD. RONY GOLDER
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Monosex tilapia has great acceptability particularly among the lower income people due to its lower price. However, due to increased feed price the price of tilapia has been increased in recent years. Compensatory growth (CG) of fish that is achieved after a period of feed deprivation can potentially reduce the feed cost. The present study aimed to get CG in tilapia farming so as to reduce the production cost of this popular fish. Tilapia fry of 0.54 g body weight were nursed in hapa for one month and then stocked in earthen ponds where two different restricted feeding regimes were imposed for next two months followed by one month feeding at satiation level. Sampling was done fortnightly to record average weight gain in control and treatment groups. Average individual weight in restricted feeding group (T1) reached to 170.11±4.6 g in a three months experimental period and it did not significantly (p>0.05) differ with the weight gained in control group (182.79±5.32 g) where fish were fed on regular basis. The specific growth rate (SGR) also showed no significant difference (p>0.05) between T1 (SGR 2.66±0.011 % day-1) and control group (SGR 2.69±0.012 % day-1). Feed Conversion Ratio (FCR) in T1 (1.26) was found significantly (p
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- 2022
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16. Irritable Bowel Syndrome is Comorbid with Psychiatric Disorders and is Associated with Psychosocial Stressors
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Anupam Das, Md Abdus Salam, Sultana Algin, Mohammed SI Mullick, Chanchal Kumar Ghosh, and Md Zulfikar Ali
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Background: Irritable Bowel Syndrome (IBS) is a functional disorder. Invariably it is co-morbid with psychiatric disorder and is associated with psychosocial stressors. Objectives: To see the association of types of IBS with psychiatric disorders and to assess the association of psychosocial stressors. Materials and methods: It was descriptive, cross-sectional study carried out in the Department of Gastroenterology, Bangabandhu Sheikh Mujib Medical University, Dhaka from January 2014 to December 2014. Total 250 samples were included in this study those were diagnosed as IBS. Respondents were above 18 years of age of either sex. Sampling technique was consecutive. Results: The patients with psychiatric disorders among IBS patients were 86.4%. Maximum (35.2%) were IBS-D followed by 32.8% IBS-C and 32% IBS-M. Majority (93.2%) presented with stressful life events. Common stressful life events were changing eating habit (25.2%), change in sleeping habit (20.8%) and financial loss or problem (18.8%). Conclusion: Many people remain troubled by symptoms for long term. So, proper psychiatric evaluation is necessary for successful alleviation of the bothering symptoms of such incurable functional illness. KYAMC Journal. 2022;12(04): 200-204
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- 2022
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17. Efficacy of information transmission in cellular communication
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Sumantra Sarkar, Md Zulfikar Ali, and Sandeep Choubey
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General Physics and Astronomy - Published
- 2023
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18. Effects of Stressful Life Events on Somatoform and Dissociative Disorders
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Anupam Das, Arpan Kumar Basak, Choity Malakar, and Md Zulfikar Ali
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Background: Somatoform and dissociative disorder categories have emerged from a common root, there was no apparent anatomical and physiological basis and which had a temporal relationship to a precipitating event. Objectives: To evaluate and compare of stressful life events of the patients of somatoform disorders and dissociative disorders. Materials and methods: This was a comparative cross-sectional study carried out in the outpatient department of Psychiatry, Khwaja Yunus Ali Medical College, Sirajganj. The study populations were 100 somatoform disorder and 100 dissociative disorder patients. Data were collected by pre-designed data collection sheet. Then data were edited, cleaned and analyzed. Results: Stressful life events were observed to be significantly more frequent in both the groups. Family conflicts (29%) and sexual problem (16%) were more common in the somatoform disorder group of patients but marital conflict (26%) and death of the close family member (11%) were more common in the dissociative disorder group of patients. This study shows that dissociative disorder patients were observed to experience a variety of life events more than somatoform disorder group of patients. Conclusion: The stressful life events were reported more in dissociative disorder. The results suggest a substantial involvement of stressful life events in genesis of somatoform disorders and dissociative disorders, although no significant difference is noticed. KYAMC Journal Vol. 13, No. 02, July 2022: 63-65
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- 2022
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19. Evaluation of lab scale cultivation to assess the growth performance of Spirulina platensis using different substrates
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Nur-A-Raushon, Md. Hashibur Rahman, Durin Akhter Jahan, and Md. Zulfikar Ali
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Spirulina (genus) ,Fish meal ,biology ,Fish farming ,Lab scale ,%22">Fish ,Biomass ,Context (language use) ,Food science ,biology.organism_classification - Abstract
Spirulina has been so popular in the present world’s context due to its high nutritional value. Due to its primitive and good quality protein, vitamins, essential fatty acids contents, antioxidant pigments, antimicrobial activity, and anticancer properties Spirulina which is a fast-growing cyanobacteria have been used as a possible alternative source of protein for the fish culture. As it is known that, the biomass of Spirulina is nutritionally rich in protein it may be used as a splendid alternative to fish protein to reduce the cost of feed. It has its tremendous attributes to replenish the required amount of protein dwindling the excessive cost as 70% of the total operating costs belongs to the feed supplement in terms of whole culture period. The study was conducted on the feasibility of Spirulina culture assessing its growth pattern through lab scale culture. The experiment was carried out to evaluate the lab scale cultivation of Spirulina by using different substrates having different concentration of Fish Meal Medium (FMM) each with the three replications T1 (15% FMM), T2 (20% FMM), T3 (25% FMM) & T4 (Kosaric medium), respectively. The growth rate of S. platensis was significantly higher in T4 (p
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- 2021
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20. Presence and diversity of positive solutions for a Caputo-type fractional order nonlinear differential equation with an advanced argument
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Adem Kilicman, Md. Asaduzzaman, and Md. Zulfikar Ali
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Computational Mathematics ,Argument ,General Mathematics ,Computational Mechanics ,Applied mathematics ,Order (group theory) ,Type (model theory) ,Nonlinear differential equations ,Computer Science Applications ,Diversity (business) ,Mathematics - Published
- 2020
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21. Existence of Solution to Fractional Order Impulsive Partial Hyperbolic Differential Equations with Infinite Delay
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Md. Zulfikar Ali and Md. Asaduzzaman
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Differential equation ,Applied Mathematics ,lcsh:Mathematics ,foiphdes ,Order (group theory) ,Applied mathematics ,FOIPHDEs,Burton-Krik fixed point theorem ,burton-kirk fixed point theorem ,lcsh:QA1-939 ,Analysis ,Mathematics - Abstract
In this paper, we investigate the existence of solutions to a class of initial value problem for fractional order impulsive partial hyperbolic differential equations (for short FOIPHDEs) with infinite delay. Here we use Mixed Riemann-Liouville fractional derivative to construct the considered FOIPHDEs. The analysis of this paper is based on Burton-Krik fixed point theorem. A new existence result for FOIPHDEs with infinite delay has been obtained. To support the analytic proof, we give an illustrative example.
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- 2020
22. Tunable transcription factor library for robust quantification of regulatory properties in Escherichia coli
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Vinuselvi Parisutham, Shivani Chhabra, Md Zulfikar Ali, and Robert C Brewster
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Zinc ,Computational Theory and Mathematics ,General Immunology and Microbiology ,Applied Mathematics ,Escherichia coli Proteins ,Escherichia coli ,Gene Regulatory Networks ,Gene Expression Regulation, Bacterial ,General Agricultural and Biological Sciences ,General Biochemistry, Genetics and Molecular Biology ,Information Systems ,Transcription Factors - Abstract
Predicting the quantitative regulatory function of transcription factors (TFs) based on factors such as binding sequence, binding location, and promoter type is not possible. The interconnected nature of gene networks and the difficulty in tuning individual TF concentrations make the isolated study of TF function challenging. Here, we present a library of Escherichia coli strains designed to allow for precise control of the concentration of individual TFs enabling the study of the role of TF concentration on physiology and regulation. We demonstrate the usefulness of this resource by measuring the regulatory function of the zinc-responsive TF, ZntR, and the paralogous TF pair, GalR/GalS. For ZntR, we find that zinc alters ZntR regulatory function in a way that enables activation of the regulated gene to be robust with respect to ZntR concentration. For GalR and GalS, we are able to demonstrate that these paralogous TFs have fundamentally distinct regulatory roles beyond differences in binding affinity.
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- 2022
23. Controlling gene expression timing through gene regulatory architecture
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Md Zulfikar Ali and Robert C. Brewster
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Metabolic Processes ,Cell Binding ,Computer and Information Sciences ,Cell Physiology ,QH301-705.5 ,DNA transcription ,Gene Identification and Analysis ,Gene Expression ,Genetic Networks ,Computational biology ,Biology ,Biochemistry ,Cellular and Molecular Neuroscience ,Genes, Regulator ,Gene expression ,Genetics ,Transcriptional regulation ,Computer Simulation ,Gene Regulatory Networks ,Gene Regulation ,Cell Cycle and Cell Division ,Biology (General) ,Molecular Biology ,Gene ,Ecology, Evolution, Behavior and Systematics ,Models, Genetic ,Ecology ,Messenger RNA ,Biology and Life Sciences ,Proteins ,Cell Biology ,Auto regulation ,Nucleic acids ,Metabolism ,Gene Expression Regulation ,Computational Theory and Mathematics ,Cell Processes ,Modeling and Simulation ,Proteolysis ,RNA ,Preprint ,Network Analysis ,Protein Binding ,Transcription Factors ,Research Article - Abstract
Gene networks typically involve the regulatory control of multiple genes with related function. This connectivity enables correlated control of the levels and timing of gene expression. Here we study how gene expression timing in the single-input module motif can be encoded in the regulatory DNA of a gene. Using stochastic simulations, we examine the role of binding affinity, TF regulatory function and network size in controlling the mean first-passage time to reach a fixed fraction of steady-state expression for both an auto-regulated TF gene and a target gene. We also examine how the variability in first-passage time depends on these factors. We find that both network size and binding affinity can dramatically speed up or slow down the response time of network genes, in some cases predicting more than a 100-fold change compared to that for a constitutive gene. Furthermore, these factors can also significantly impact the fidelity of this response. Importantly, these effects do not occur at “extremes” of network size or binding affinity, but rather in an intermediate window of either quantity., Author summary Regulated genes are able to respond to stimuli in order to ramp up or down production of specific proteins. Although there is considerable focus on the magnitude (or fold-change) of the response and how that depends on the architectural details of the regulatory DNA, the dynamics, which dictates the response time of the gene, is another key feature of a gene that is encoded within the DNA. Unraveling the rules that dictate both the response time of a gene and the precision of that response encoded in the DNA poses a fundamental problem. In this manuscript, we systematically investigate how the response time of genes in auto-regulatory networks is controlled by the molecular details of the network. In particular, we find that network size and TF-binding affinity are key parameters that can slow, in the case of auto-activation, or speed up, in the case of auto-repression, the response time of not only the auto-regulated gene but also the genes that are controlled by the auto-regulated TF. In addition, we find that the precision of the response depends crucially on these characteristics.
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- 2021
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24. Day Care Coronary Angiogram in Bangladesh- Our Experience with 100 cases
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Mir Jamal Uddin, Saqif Shahriar, Sabina Hashem, Lima Asrin Sayami, Md Abul Alam, Mohammad Ali, Shudhakor Sarker, Iftequar Alam, Md Monsurul Haque, ABM Nurunnabi, Reaz Mahmud Huda, Ashraf Ur Rahman, Md Zulfikar Ali, and Abdul Momen
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General Medicine - Abstract
Background: In conventional coronary angiography (CAG) by transfemoral approach patients usually need to stay at least one night in hospital. CAG by transradial approach gives the opportunity for same day hospital discharge. The objective of this study was to assess the safety and feasibly of day case CAG in Bangladesh. Methods: This is a single operator observational study where patients admitted for CAG through transradial (conventional and distal radial) approach were included. Patients were admitted at least 2 hours before the procedure. Hemostasis was done with manual compression followed by tight gauge-rolled bandage. Predischarge criteria had been set and applied to all patients. An emergency telephone number was given to the patient and they were contacted on the next day over telephone. Results: 30 (30%) female and 70 (70%) male were included with mean age 53±9SD years. Patients were discharged from the hospital on an average after 3.3±1.1 hours of the procedure. Only 4(4%) patients contacted to the emergency number. No bleeding complication was noted and 16(16%) patients complained about of some puncture site pain. Radial artery patency was was maintained in 96% of the patient on subsequent follow up. Conclusion: Same day hospital discharge is a feasible and safe alternative with similar radial artery patency rate. It will reduce the hospital cost and bed occupancy rate in a busy center in Bangladesh. Cardiovasc. j. 2019; 11(2): 152-158
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- 2019
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25. Evaluation of Selected Dietary Probiotics on Growth Performance, Nutrient Utilization and Body Carcass Composition of Mystus Cavasius (Hamilton, 1822) Fry
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Prasanta Jana, Md. Khalilur Rahman, Yahia Mahmud, Md. Zulfikar Ali, and Mritunjoy Paul
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Mystus cavasius ,Nutrient ,Animal science ,Biology ,Carcass composition - Published
- 2018
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26. Extended Cubic Method and Its Convergence Analysis for Generalized Equations
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Mohammed Harunor Rashid, Md. Zulfikar Ali, and Alain Piétrus
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Convergence (routing) ,Applied mathematics ,Mathematics - Published
- 2018
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27. Modified Double Sub-equation Method for Finding Complexiton Solutions to the ( $$1+1$$ 1 + 1 ) Dimensional Nonlinear Evolution Equations
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Harun-Or Roshid, Md. Belal Hossen, and Md. Zulfikar Ali
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Applied Mathematics ,One-dimensional space ,Hyperbolic function ,Mathematical analysis ,01 natural sciences ,010305 fluids & plasmas ,Burgers' equation ,Computational Mathematics ,Nonlinear system ,Nonlinear Sciences::Exactly Solvable and Integrable Systems ,0103 physical sciences ,Trigonometry ,010306 general physics ,Gardner's relation ,Nonlinear evolution ,Korteweg–de Vries equation ,Nonlinear Sciences::Pattern Formation and Solitons ,Mathematics - Abstract
This paper reflects the execution of a reliable technique which we proposed as a modified double sub-equation method for solving nonlinear evolution equations. The proposed scheme has been successfully hardened on a very important evolution equation namely the ( $$1+1$$ )-dimensional Burger equation and the ( $$1+1$$ )-dimensional Gardner equation (or combined KdV–mKdV). As a results, we found more complexiton solutions in-terms of trigonometric, hyperbolic functions. Finally, the interaction phenomena of the achieved complexiton solutions between solitary waves and/or periodic waves are presented with in depth derivation. The outcome can be used to enhance the dynamical activities of higher dimensional nonlinear wave field areas.
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- 2017
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28. Probing mechanisms of transcription elongation through cell-to-cell variability of RNA polymerase
- Author
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Md. Zulfikar Ali, Robert C. Brewster, Sandeep Choubey, and Dipjyoti Das
- Subjects
Transcription, Genetic ,Transcription elongation ,Saccharomyces cerevisiae ,Cell ,Biophysics ,Computational biology ,Biology ,Transcription initiation ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,RNA polymerase ,Gene expression ,Escherichia coli ,Transcriptional regulation ,medicine ,Gene ,030304 developmental biology ,Regulation of gene expression ,0303 health sciences ,DNA-Directed RNA Polymerases ,Articles ,Ribosomal RNA ,biology.organism_classification ,Cell biology ,Kinetics ,medicine.anatomical_structure ,Gene Expression Regulation ,chemistry ,Elongation ,030217 neurology & neurosurgery - Abstract
The process of transcription initiation and elongation are primary points of control in the regulation of gene expression. While biochemical studies have uncovered the mechanisms involved in controlling transcription at each step, how these mechanisms manifestin vivoat the level of individual genes is still unclear. Recent experimental advances have enabled single-cell measurements of RNAP molecules engaged in the process of transcribing a gene of interest. In this manuscript, we use Gillespie simulations to show that measurements of cell-to-cell variability of RNAP numbers and inter-polymerase distances can reveal the prevailing mode of regulation of a given gene. Mechanisms of regulation at each step, from initiation to elongation dynamics, produce qualitatively distinct signatures which can further be used to discern between them. Intriguingly, depending on the initiation kinetics, stochastic elongation can either enhance or suppress cell-to-cell variability at the RNAP level. To demonstrate the value of this framework, we analyze RNAP number distribution data for ribosomal genes in S. cerevisiae from three previously published studies and show that this approach provides crucial mechanistic insights into the transcriptional regulation of these genes.Author SummaryThe process of transcription comprises many distinct steps and understanding the regulation of each of these steps provides insight into how the levels of gene expression are controlled in the cell. In this manuscript, we use stochastic simulations to explore how regulation at the level of elongation and initiation together influences the distribution of actively transcribing RNAP on a gene. We find that each of these steps of regulation leaves a distinct imprint on the gene-to-gene variability of number of actively transcribing RNAP on the gene and their inter-RNAP distances. Using these results, we analyze recent experimental data of transcribing RNAP distributions and find that the perturbations in these studies primarily impact the transcription initiation dynamics of the genes.
- Published
- 2019
- Full Text
- View/download PDF
29. Ebola
- Author
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Md Zulfikar Ali
- Abstract
not availableKYAMC Journal Vol. 5, No.-2, Jan 2015, Page 494-496
- Published
- 2017
- Full Text
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30. A Persistence Detector for Metabolic Network Rewiring in an Animal
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Robert C. Brewster, L. Safak Yilmaz, Md. Zulfikar Ali, Gabrielle E. Giese, Jote T. Bulcha, Melissa D. Walker, Yong-Uk Lee, Amy D. Holdorf, and Albertha J.M. Walhout
- Subjects
0301 basic medicine ,Persistence (psychology) ,Gene regulatory network ,Receptors, Cytoplasmic and Nuclear ,Metabolic network ,Computational biology ,Biology ,General Biochemistry, Genetics and Molecular Biology ,Article ,03 medical and health sciences ,0302 clinical medicine ,Animals ,Homeostasis ,Caenorhabditis elegans ,lcsh:QH301-705.5 ,Transcription factor ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,Chemistry ,Detector ,biology.organism_classification ,Cell biology ,Vitamin B 12 ,030104 developmental biology ,lcsh:Biology (General) ,Nuclear receptor ,Propionate ,Preprint ,Propionates ,Transcriptome ,Flux (metabolism) ,Shunt (electrical) ,Metabolic Networks and Pathways ,030217 neurology & neurosurgery - Abstract
SUMMARY Biological systems must possess mechanisms that prevent inappropriate responses to spurious environmental inputs. Caenorhabditis elegans has two breakdown pathways for the short-chain fatty acid propionate: a canonical, vitamin B12-dependent pathway and a propionate shunt that is used when vitamin B12 levels are low. The shunt pathway is kept off when there is sufficient flux through the canonical pathway, likely to avoid generating shunt-specific toxic intermediates. Here, we discovered a transcriptional regulatory circuit that activates shunt gene expression upon propionate buildup. Nuclear hormone receptor 10 (NHR-10) and NHR-68 function together as a “persistence detector” in a type 1, coherent feed-forward loop with an AND-logic gate to delay shunt activation upon propionate accumulation and to avoid spurious shunt activation in response to a non-sustained pulse of propionate. Together, our findings identify a persistence detector in an animal, which transcriptionally rewires propionate metabolism to maintain homeostasis., Graphical Abstract, In Brief Bulcha et al. discover a transcriptional persistence detector composed of a type 1 coherent feed-forward loop with an AND-logic gate that rewires propionate metabolism in C. elegans.
- Published
- 2018
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31. ON NEW THREE-STEP ITERATIVE SCHEME FOR APPROXIMATING THE FIXED POINTS OF NON-EXPANSIVE MAPPINGS
- Author
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M. Saleha Khatun, Md. Zulfikar Ali, and Md. Asaduzzaman
- Subjects
Discrete mathematics ,Computer science ,Scheme (mathematics) ,Applied mathematics ,Fixed point ,Expansive - Published
- 2016
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32. Data Dependence For Noor Iterative Scheme Dealing With Contractive-Like Operators
- Author
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Md. Asaduzzaman and Md. Zulfikar Ali
- Subjects
Operator (computer programming) ,Scheme (mathematics) ,Data dependence ,Convergence (routing) ,Calculus ,Applied mathematics ,Fixed point ,Mathematics - Abstract
In this paper, we have established the convergence result and the data dependence for Noor iterative scheme dealing with contractive-like operators. A numerical example has also given, in which instead of computing the fixed point of an operator, we have approximated the operator with a contractive-like one. GANIT J. Bangladesh Math. Soc. Vol. 33 (2013) 13-24 DOI: http://dx.doi.org/10.3329/ganit.v33i0.17651
- Published
- 2014
- Full Text
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33. Outcome of Urgent Hemodialysis in Chronic Kidney Disease in a Rural Tertiary Care Hospital
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Sheik Salahuddin Ahmed, Moniruzzaman, Md. Zulfikar Ali, and Tarafdar Runa Laila
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Nephrology ,medicine.medical_specialty ,Hyperkalemia ,business.industry ,medicine.medical_treatment ,Encephalopathy ,Metabolic acidosis ,Disease ,medicine.disease ,Internal medicine ,medicine ,Hemodialysis ,medicine.symptom ,business ,Intensive care medicine ,Dialysis ,Kidney disease - Abstract
Chronic kidney disease is a worldwide public health problem with an increasing incidence and prevalence. Outcomes of chronic kidney disease include not only complications of decreased kidney function and cardiovascular disease but also end stage renal failure causing increased morbidity and mortality. The development of acute but serious uremic complications in advanced kidney disease may put the patient's life at risk requiring immediate dialysis. The objective of this study was to find out the outcomes of urgent hemodialysis in advanced kidney disease, the minimum number of hemodialysis required for satisfactory clinical improvement, and to detect uremic emergencies associated with those patients. Twenty two patients with end stage renal failure admitted in a rural tertiary care private hospital of Bangladesh for emergency and short term dialysis were included in this study. For each patient hemodialysis was done at one day interval three times in a week in a dialysis unit. Results show that two sessions of hemodialysis produced 72 % and three sessions, almost 100% clinical recovery at satisfactory level. Urgent hemodialysis was found to be life saving in observed uremic emergencies like acute pulmonary edema, cerebral encephalopathy, metabolic acidosis, hyperkalemia, gross fluid overload and pericardial effusion. Dialysis therapy ameliorates many of the clinical manifestations of renal failure and postpones otherwise imminent death and for these logical reasons it is recommended that dialysis should not be delayed in uremic emergencies for the best interest of clinical outcomes. KYAMC Journal Vol. 3, No.-2, January 2013, Page 277-281 DOI: http://dx.doi.org/10.3329/kyamcj.v3i2.15167
- Published
- 2013
- Full Text
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34. Hidden long evolutionary memory in a model biochemical network
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Md. Zulfikar Ali, Ned S. Wingreen, and Ranjan Mukhopadhyay
- Subjects
0301 basic medicine ,Network complexity ,Sequence ,Computer science ,Molecular Networks (q-bio.MN) ,FOS: Physical sciences ,Topology ,Models, Biological ,Article ,Biochemical network ,Minimal model ,Evolution, Molecular ,03 medical and health sciences ,030104 developmental biology ,Biological Physics (physics.bio-ph) ,FOS: Biological sciences ,Core (graph theory) ,Mutation (genetic algorithm) ,Mutation ,Quantitative Biology - Molecular Networks ,Sequence space (evolution) ,Physics - Biological Physics ,Protein Interaction Maps ,Topology (chemistry) - Abstract
We introduce a minimal model for the evolution of functional protein-interaction networks using a sequence-based mutational algorithm, and apply the model to study neutral drift in networks that yield oscillatory dynamics. Starting with a functional core module, random evolutionary drift increases network complexity even in the absence of specific selective pressures. Surprisingly, we uncover a hidden order in sequence space that gives rise to long-term evolutionary memory, implying strong constraints on network evolution due to the topology of accessible sequence space., Comment: 20 Pages, 14 Figures
- Published
- 2017
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35. High Blood Pressure can be Controlled by Reducing Extra Table Salt Intake
- Author
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Akm Alamgir, Kmhs Sirajul Haque, Md. Zulfikar Ali, and Shah Mohammad Keramat Ali
- Subjects
medicine.medical_specialty ,education.field_of_study ,business.industry ,Population ,Reduced model ,Surgery ,Mean blood pressure ,Blood pressure ,Quality of life ,Lifestyle modification ,Internal medicine ,Medicine ,Salt intake ,business ,Table salt intake ,education - Abstract
Background: This quasi-experimental community trial was done through door-to-door health education to find out effect of reducing extra table salt intake on patients with high blood pressure. Material and Method: This study was conducted among 4,930 respondents out of 7,474 population (response rate was 65.96%). Respondents had age 18 years or above living in Mohammadpur area of Dhaka city in Bangladesh. Study period was from August 2005 to February 2009. Intervention was for 18 months on 282 (male 69.5% and female 30.5%) respondents with stage-I hypertension. Respondents on trial had no co-morbidity and they were neither aware about their hypertension nor were ever treated for it. The intervention was given person-to-person to quit extra table salt after signing the informed consent form. Follow-up for selected parameters were done after 6, 12 and 18 month of intervention. Data analysis and interpretation were done through SPSS. Result: Mean Blood Pressure of the respondents was found to be 121/78 mmHg. Overall prevalence of hypertension is 20.1% (JNC-7 criteria). After 18m intervention percent reduction of SBP is -7.0% and DBP is -9.9%. Blood pressure of 14.9% (n=42) went up in spite of behavioural risk reduction. Normal blood pressure was found among 7.8% respondents having stage-I hypertension while 17.7% remained at stage-I but their blood pressure is reduced. Multinominal regression analysis showed chi-square value of 25.8 df 13 p=0.018 between use of extra table salt and systolic blood pressure while the value was 28.684 df 11 p= 0.003 for diastolic blood pressure in a -2 Log Likelihood reduced model. At beginning 44% respondents used extra salt while eating. After 6m, 12m and 18m of intervention, extra salt intake was found among 20.6%, 5.0% and 1.8% respondents respectively. Quantitatively extra salt intake reduced from 63±6.5g per week at beginning to 29±4.6g per week after 18m intervention. Change of salt intake was significantly related to change of both SBP (F= 9.688; p=0.000) and DBP (F=6.544; p=0.002). Quality of life was evaluated for both subjective and objective indices. Conclusion: Reversal of hypertension was 56.7% by lifestyle modification and behavioural changes including salt intake reduction. This study confirmed relation of salt with hypertension and also confirmed reduction of blood pressure after reducing salt intake. This study recommended no extra salt intake for patients at risk or with high blood pressure. DOI: http://dx.doi.org/10.3329/kyamcj.v1i2.13314 KYAMC Journal Vol.1(2) January 2011, 48-53
- Published
- 2013
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36. Analgesic Nephropathy and Hyperparathyroidism - a case report
- Author
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Sheikh Salahuddin Ahmed, Tarafdar Runa Laila, and Md. Zulfikar Ali
- Subjects
medicine.medical_specialty ,Hyperparathyroidism ,Endocrinology ,business.industry ,Internal medicine ,medicine ,medicine.disease ,Analgesic nephropathy ,business ,Gastroenterology ,Mineral bone disease - Abstract
DOI: http://dx.doi.org/10.3329/kyamcj.v1i1.13305KYAMC Journal Vol.1(1) July 2010, 30-33
- Published
- 2013
- Full Text
- View/download PDF
37. Sinus histiocytosis with lymphadenopathy - a case report
- Author
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Sheikh Salahuddin Ahmed, Tarafdar Runa Laila, and Md. Zulfikar Ali
- Subjects
Pathology ,medicine.medical_specialty ,business.industry ,Sinus Histiocytosis with Massive Lymphadenopathy ,medicine.disease ,Histiocytosis ,Lymphatic system ,medicine.anatomical_structure ,Chronic Lymphadenitis ,medicine ,Axillary Lymphadenopathy ,business ,Lymph node ,Rosai–Dorfman disease ,Histiocyte - Abstract
Sinus histiocytosis with lymphadenopathy is a rare condition of unknown etiology that is characterized by the overproduction of histiocytes accumulating in the lymph node sinuses and in the lymphatics of extranodal sites if involved. Lymph nodes of the neck are the most common place of histiocyte accumulation, although other lymph nodes and organs may involve, as well. The common sites of the disease outside the lymph nodes are skin, soft tissues, upper respiratory tract, the sinuses, kidney, thyroid, small bowel, breast, and bone. Hepatosplenomegaly is uncommon. The symptoms of this disease vary with the site of involvement. It is often referred to as sinus histiocytosis with massive lymphadenopathy (SHML). In this article an adult male of 38 years, has been described who presented with bilateral cervical and axillary lymphadenopathy clinically suspected of infectious (tubercular-in the context of our country) or hematological malignant etiology. However on fine needle aspiration cytology, the smears showed many histiocytes, lymphocytes and plasma cells. Biopsy of cervical lymph node showed dilated sinuses filled with histiocytes and lymph node architecture showing inflammatory cells having lymphocytes and histiocytes. These findings were considered consistent with sinus histiocytosis with chronic lymphadenitis.DOI: http://dx.doi.org/10.3329/kyamcj.v2i2.13266KYAMC Journal Vol.2(2) January 2012, 205-208
- Published
- 2013
- Full Text
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38. Chicken Pox
- Author
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Md Zulfikar Ali
- Abstract
not availableKYAMC Journal Vol. 5, No.-1, Jul 2014, Page 434-435
- Published
- 2017
- Full Text
- View/download PDF
39. Peptic ulcer disease
- Author
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Md. Zulfikar Ali
- Subjects
medicine.medical_specialty ,Gastrointestinal tract ,biology ,business.industry ,Stomach ,Disease ,Helicobacter pylori ,biology.organism_classification ,medicine.disease ,Gastroenterology ,humanities ,digestive system diseases ,medicine.anatomical_structure ,Internal medicine ,Peptic ulcer ,medicine ,business - Abstract
A peptic ulcer, also known as peptic ulcer disease (PUD) is the most common ulcer of an area of the gastrointestinal tract that is usually acidic and thus extremely painful. It is defined as mucosal erosions equal to or greater than 0.5 cm. As many as 70%-90% of such ulcers are associated with Helicobacter pylori, a spiral-shaped bacterium that lives in the acidic environment of the stomach. KYAMC Journal Vol. 3, No.-2, January 2013, Page 270-272 DOI: http://dx.doi.org/10.3329/kyamcj.v3i2.15164
- Published
- 2013
- Full Text
- View/download PDF
40. Nipah virus - Reemergence in Bangladesh
- Author
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Md. Zulfikar Ali
- Subjects
business.industry ,Nipah virus ,Medicine ,business ,Virology - Abstract
DOI: http://dx.doi.org/10.3329/kyamcj.v1i2.13311KYAMC Journal Vol.1(2) January 2011, 36-38
- Published
- 2013
- Full Text
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41. Remark on Kantorovich theorem and Urabe's theorem
- Author
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Md. Zulfikar, Ali and Yoshitane, SHINOHARA
- Abstract
Theoretical theorems are usually discussed on the real number system. But, in numerical computation, such system has to be approximated by real number system of a rather special type such as fixed point number system or floating point number system. Hence, when we discuss the theoretical theorems in numerical analysis, we must take care of their numerical properties.
- Published
- 1999
42. Anthrax Diseases
- Author
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Md. Zulfikar Ali
- Abstract
DOI: http://dx.doi.org/10.3329/kyamcj.v1i1.13297KYAMC Journal Vol.1(1) July 2010, 1-2
- Published
- 2013
- Full Text
- View/download PDF
43. ON CONVERGENCE OF NEWTON'S METHOD
- Author
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Md. Zulfikar, Ali, M. Majedur, Rahman, Department of Mathematics, University of Rajshahi, and Department of Mathematics, BIT Rajshahi
- Abstract
A new theorem has been given that generalizes Rall's theorem.
- Published
- 2002
44. Decoding the grammar of transcriptional regulation from RNA polymerase measurements: models and their applications.
- Author
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Md Zulfikar Ali and Sandeep Choubey
- Published
- 2019
- Full Text
- View/download PDF
45. Difficulties to enter the left ventricle during percutaneous transvenous mitral commissurotomy (PTMC)- our experiences of 80 cases with modified techniques
- Author
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Abdul Momen, Md Zulfikar Ali, Naharuma Aive Hyder Chowdhury, Reaz Mahmud Huda, ABM Nurun Nobi, Ashraf Ur Rahman, Iftequar Alam, Lima Asrin Sayami, Md Abul Alam, Md Delwar Hossain, and Samia Tasneem
- Subjects
BMV ,Inoue technique ,Mitral stenosis ,PTMC ,Surgery ,RD1-811 ,Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Abstract
Background: Percutaneous transvenous mitral commissurotomy (PTMC) is the standard of treatment for symptomatic severe rheumatic mitral stenosis (MS). PTMC has the standard Inoue technique, but we have to modify the procedure in many technically challenging cases, especially to cross the mitral valve. Methodology: Two over-the-wire strategies to enter the LV were taken in 80 complex cases of PTMC. The first one was done by exchanging the J-shaped wire from the balloon, introducing the spring wire into it, and pushing it into LV. The second one-removal of balloon keeping the spring wire in LA and the Mullin's sheath was introduced, and the tip of the wire was pushed into LV, and the balloon was introduced over the wire. We also changed the left atrium (LA) graphy in the RAO view instead of the AP view to facilitating entry into LV. Results: We succeeded in 76 (95 %) cases. Strategy one was applied to all but successful in only 25 cases (31 %), and strategy 2 was applied in the remaining. Strategy 1 required less procedural time and fluoroscopic time in comparison to strategy 2 (40 ± 10 vs 60 ± 16 min, 25 ± 7 vs 35 ± 8 min). After modification of taking the LA graphy in RAO view, our rate of facing the difficulties decreased from 21 % to 9 %. Critical MS (31 %) and the giant LA (30 %) were the topmost causes of difficulties. No major complications were recorded. Conclusion: Over-the-wire entry into LV is cost-effective, requiring no new equipment and is safe and can be used in complex cases.
- Published
- 2021
- Full Text
- View/download PDF
46. Inherent regulatory asymmetry emanating from network architecture in a prevalent autoregulatory motif
- Author
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Md Zulfikar Ali, Vinuselvi Parisutham, Sandeep Choubey, and Robert C Brewster
- Subjects
quantitative gene regulation ,synthetic biology ,systems biology ,network motifs ,stochastic simulations ,autoregulation ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Predicting gene expression from DNA sequence remains a major goal in the field of gene regulation. A challenge to this goal is the connectivity of the network, whose role in altering gene expression remains unclear. Here, we study a common autoregulatory network motif, the negative single-input module, to explore the regulatory properties inherited from the motif. Using stochastic simulations and a synthetic biology approach in E. coli, we find that the TF gene and its target genes have inherent asymmetry in regulation, even when their promoters are identical; the TF gene being more repressed than its targets. The magnitude of asymmetry depends on network features such as network size and TF-binding affinities. Intriguingly, asymmetry disappears when the growth rate is too fast or too slow and is most significant for typical growth conditions. These results highlight the importance of accounting for network architecture in quantitative models of gene expression.
- Published
- 2020
- Full Text
- View/download PDF
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