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1.
PeerJ Comput Sci ; 10: e1949, 2024.
Article in English | MEDLINE | ID: mdl-38660151

ABSTRACT

Background: Computational intelligence (CI) based prediction models increase the efficient and effective utilization of resources for wind prediction. However, the traditional recurrent neural networks (RNN) are difficult to train on data having long-term temporal dependencies, thus susceptible to an inherent problem of vanishing gradient. This work proposed a method based on an advanced version of RNN known as long short-term memory (LSTM) architecture, which updates recurrent weights to overcome the vanishing gradient problem. This, in turn, improves training performance. Methods: The RNN model is developed based on stack LSTM and bidirectional LSTM. The parameters like mean absolute error (MAE), standard deviation error (SDE), and root mean squared error (RMSE) are utilized as performance measures for comparison with recent state-of-the-art techniques. Results: Results showed that the proposed technique outperformed the existing techniques in terms of RMSE and MAE against all the used wind farm datasets. Whereas, a reduction in SDE is observed for larger wind farm datasets. The proposed RNN approach performed better than the existing models despite fewer parameters. In addition, the approach requires minimum processing power to achieve compatible results.

3.
Article in English | MEDLINE | ID: mdl-37037599

ABSTRACT

While the worldwide trend in life expectancy continues to increase slightly overall, the trend for the last few decades in developed countries is that more people are spending more years in poor health with multiple chronic comorbidities. These chronic conditions in aging populations consume high proportions of national healthcare budgets. The relatively young field of longevity research, after accumulating insights into the mechanisms of aging and producing dramatic laboratory demonstrations of life extension in some organisms, is entering the translational phase. This phase, through clinical trials, will confirm or refute the "geroscience hypothesis" that drugs can change the trajectory of the processes of aging within cells, and ultimately in living humans. At the same time, traditional funding patterns do not favor such visionary "moonshot" research, which, despite the potential for ultimately providing benefits for everyone, offers little prospect for rapid return on investment and high probabilities for early phase failure. New radical funding strategies incentivizing innovation will have to be called into play.

5.
PLoS One ; 17(1): e0260480, 2022.
Article in English | MEDLINE | ID: mdl-35051183

ABSTRACT

The increasing energy demand and the target to reduce environmental pollution make it essential to use efficient and environment-friendly renewable energy systems. One of these systems is the Photovoltaic (PV) system which generates energy subject to variation in environmental conditions such as temperature and solar radiations. In the presence of these variations, it is necessary to extract the maximum power via the maximum power point tracking (MPPT) controller. This paper presents a nonlinear generalized global sliding mode controller (GGSMC) to harvest maximum power from a PV array using a DC-DC buck-boost converter. A feed-forward neural network (FFNN) is used to provide a reference voltage. A GGSMC is designed to track the FFNN generated reference subject to varying temperature and sunlight. The proposed control strategy, along with a modified sliding mode control, eliminates the reaching phase so that the sliding mode exists throughout the time. The system response observes no chattering and harmonic distortions. Finally, the simulation results using MATLAB/Simulink environment demonstrate the effectiveness, accuracy, and rapid tracking of the proposed control strategy. The results are compared with standard results of the nonlinear backstepping controller under abrupt changes in environmental conditions for further validation.


Subject(s)
Neural Networks, Computer
6.
Environ Sci Pollut Res Int ; 28(11): 13697-13711, 2021 Mar.
Article in English | MEDLINE | ID: mdl-33200383

ABSTRACT

Solar radiation (SR) is essential for yield improvement in lentil, which is a crop of marginal environments. Herein, experiments were conducted over 2 years under a semi-arid environment to study the radiation interception (RI), efficiency, growth, and development of three lentil genotypes (Punjab Masoor-2009 (PM-2009), NIAB Masoor-2006 (NM-2006), and NIAB Masoor-2002 (NM-2002)) in relation to three nitrogen rates (13, 19, and 25 kg ha-1). Seasonal dynamics of intercepted photoactive radiation (IPAR) and cumulated photosynthetic photon flux density were highly associated with seasonal dynamics of leaf area index (LAI), with a high value of R2 (0.93 and 0.89) across all nitrogen rates and genotypes in both years. Nitrogen application promoted growth, and maximum LAI (3.97 and 3.57) and RI (324 and 301 MJ m-2) were attained for the first and second years of study, respectively. Biomass and yield were positively associated with IPAR. Variation in radiation absorption (RA) among genotypes was due to different patterns of LAI development. In both years, yield (23% and 25%) and radiation use efficiency (RUE) for grain yield (0.44 and 0.37 g MJ-1) were respectively higher for PM-2009 than for the other genotypes. Genotype PM-2009 had 15 days shorter crop cycle than others while 14% higher GDDs accumulated in the first year compared with the second due to the higher temperature. High nitrogen (25 kg ha-1) application resulted in higher dry matter (DM), and grain yield (GY), while RUE and PAR were not statistically different under 19 kg N ha-1 application across years. Genotypes PM-2009 and NM-2006 may perform reasonably well under arid to semi-arid regions at farmer field. These findings may assist researchers and crop modelers to optimize the lentil ideotype for efficient light utilization.


Subject(s)
Lens Plant , Biomass , Lens Plant/genetics , Nitrogen , Photosynthesis , Plant Leaves
7.
Cureus ; 11(10): e5909, 2019 Oct 15.
Article in English | MEDLINE | ID: mdl-31788369

ABSTRACT

Breast tuberculosis (TB) is rare among extrapulmonary tuberculosis cases, and the diagnosis is usually preceded by a high index of suspicion and findings of granulomatous lesions. We conducted this study to evaluate different clinical presentations of breast TB, including its diagnosis and association with lactation. We also examined the association of breast TB with TB elsewhere in the body and contact history. This prospective, descriptive study was conducted at a tertiary care hospital in Karachi, Pakistan from March 2017 to March 2019. The study population consisted of 100 women of age ranging from 30 to 39 years after 10 patients were lost to follow-up. After providing informed written consent and a histopathology or culture report, participants completed a proforma. We used IBM SPSS Statistics for Windows, Version 22.0 (IBM Corp., Armonk, NY) to analyze the data, which were kept confidential. Twenty-four patients had diabetes, while 36 patients had no comorbidities. The most consistent symptoms were breast pain (98%), breast lump (89%), fever (83%), and discharge (45%). Of the 100 women, 34 were diagnosed with TB, while 66 women had nonspecific inflammation. Sixty-nine women were lactating, and 31 were nonlactating. Of the 69 lactating women, 21 had been diagnosed with TB while 48 had nonspecific inflammation. TB represents a great burden in underdeveloped countries like Pakistan. Therefore, concerned departments must take necessary action to facilitate early diagnosis and prompt treatment.

8.
World J Surg Oncol ; 15(1): 116, 2017 Jun 26.
Article in English | MEDLINE | ID: mdl-28651545

ABSTRACT

BACKGROUND: Microsatellite instability (MSI) operates as the second major pathway in the colorectal carcinogenesis. Although genetic testing remains the gold standard for the detection of MSI, the College of American Pathologists (CAP) recommends an initial immunohistochemical workup with a four-antibody panel (MLH1, PMS2, MSH2, and MSH6) to screen for a defective mismatch repair system. An increased trend towards young age colorectal carcinoma (CRC) has been noticed in our population over recent years; however, neither screening for MSI by immunohistochemistry (IHC)/genetic testing was done nor were its morphological features studied. We aimed to determine the frequency of mismatch repair deficiency (dMMR) by loss of IHC expression of the aforementioned enzymes in CRC patients and its correlatation with clinicopathologic parameters. METHODS: This was a retrospective study conducted at Liaquat National Hospital, Karachi, between 2012 and 2015. A total of 100 cases of CRC were included in the study that underwent surgical resection. IHC stains using antibodies MLH1, PMS2, MSH2, and MSH6 were performed by DAKO EnVision method on representative tissue blocks. The results were interpreted by senior histopathologists and correlated with clinico-pathological parameters. RESULTS: A total of 100 cases of CRC were studied that included 51 males and 49 females. Thirty-four percent (n = 34) of the patients showed loss of IHC staining for MMR markers. Combined loss of expression for MLH1/PMS2 were observed in 16% (n = 16) of the cases. Loss of MSH2/MSH6 were seen in 6% (n = 6) of the cases. Loss of expression for all markers were noted in 7% (n = 7) of the cases. There were 5% (n = 5) of the cases that showed isolated loss of MLH1 only. The tumors with dMMR status were significantly associated with right-sided location (p = 0.013), exhibited intra-tumoral lymphocytosis (p = 0.007), and lymphovascular invasion (p = 0.043). No significant association was seen with gender, age, tumor stage, grade, or other morphological features. CONCLUSION: The frequency of mismatch repair deficiency in CRC patients was found to be 34% in Pakistani population which warrants further genetic testing to exclude Lynch syndrome. Moreover, right-sided location and intra-tumoral lymphocyte count may be used to identify patients who may need further workup.


Subject(s)
Biomarkers, Tumor/metabolism , Colorectal Neoplasms/diagnosis , DNA-Binding Proteins/metabolism , Early Detection of Cancer , Mismatch Repair Endonuclease PMS2/metabolism , MutL Protein Homolog 1/metabolism , MutS Homolog 2 Protein/metabolism , Adenocarcinoma, Mucinous/metabolism , Adenocarcinoma, Mucinous/secondary , Adult , Aged , Aged, 80 and over , Carcinoma, Medullary/metabolism , Carcinoma, Medullary/secondary , Carcinoma, Signet Ring Cell/metabolism , Carcinoma, Signet Ring Cell/secondary , Colorectal Neoplasms/metabolism , Female , Follow-Up Studies , Humans , Immunoenzyme Techniques , Lymphatic Metastasis , Male , Middle Aged , Neoplasm Grading , Neoplasm Invasiveness , Neoplasm Staging , Prognosis , Retrospective Studies , Survival Rate , Young Adult
9.
World J Surg Oncol ; 15(1): 89, 2017 Apr 20.
Article in English | MEDLINE | ID: mdl-28427406

ABSTRACT

BACKGROUND: Hodgkin lymphoma is one of the most prevalent lymphoproliferative disorders in Pakistan; however, no risk factors for this disease have yet to be established in our population. Epstein-Barr virus (EBV) is a well-known risk factor for Hodgkin lymphoma in endemic regions of the world; however, frequency of its association in our population has not been widely studied. Latent membrane protein 1 (LMP1) expression by immunohistochemistry (IHC) is a surrogate marker of EBV in Hodgkin lymphoma. Therefore, we aimed to evaluate the frequency of expression of LMP1 in cases of Hodgkin lymphoma at our institute and its correlation with other clinical and histologic parameters. METHODS: The study included 66 cases of Hodgkin lymphoma diagnosed at Liaquat National Hospital over a duration of 2 years from January 2014 to December 2015. The slides and blocks of all cases were retrieved, and representative blocks were selected for LMP1 by IHC. LMP1 expression of >10% of cells was considered as positive expression and correlated with histologic subtypes and clinical parameters like age, gender, and site of involvement. RESULTS: The mean age of patients was 35.11 (+20.22). LMP1 expression was found in 68.1% (45/66) of cases of Hodgkin lymphoma. Mean age of the patients with LMP1 expression was 32.04 (+21.02). LMP1 expression was found in 40% cases of lymphocyte-rich, 66.7% of lymphocyte-depleted, 73.9% of mixed cellularity, 66.7% of nodular sclerosis, and 73.7% of classic Hodgkin lymphoma, NOS. No significant correlation of LMP1 expression with any clinical or histological parameter could be established in our studied patient population. CONCLUSIONS: A high frequency of expression of LMP1 is seen in cases of Hodgkin lymphoma at our setup comparable to endemic regions of the world; therefore, preventive and treatment protocols should be designed accordingly.


Subject(s)
Biomarkers, Tumor/metabolism , Epstein-Barr Virus Infections/complications , Herpesvirus 4, Human , Hodgkin Disease/diagnosis , Viral Matrix Proteins/metabolism , Adult , Epstein-Barr Virus Infections/metabolism , Epstein-Barr Virus Infections/virology , Female , Follow-Up Studies , Hodgkin Disease/metabolism , Hodgkin Disease/virology , Humans , Male , Neoplasm Staging , Pakistan , Prognosis , Survival Rate
10.
BMC Res Notes ; 10(1): 49, 2017 Jan 18.
Article in English | MEDLINE | ID: mdl-28100266

ABSTRACT

BACKGROUND: Cross matched blood is frequently ordered based on a subjective anticipation of blood loss for a procedure. Excessive blood arrangement and wastage overburdens the blood bank in terms of work load and storage of blood, increases cost of medical care and results in injudicious use of a limited resource. The aim of this short report is to assess the current practice for arranging cross matched blood in elective thyroid surgeries by comparing cross match to blood transfused ratio. FINDINGS: Medical records for all patients from January 2009 to December 2014 undergoing thyroid surgery were retrieved and reviewed through electronic health information management system (HIMS). A total of 91 patients were included in the study, out of which 18 (19.7%) were male and 73 (80.2%) were female. A total of 107 units of blood were arranged and only 9 were transfused. 47 patients underwent a total thyroidectomy, while 44 underwent a hemithyroidectomy. The cross match to transfusion ratio came out to be 11.88. CONCLUSIONS: Routine arrangement of cross matched blood is not required in elective thyroid surgeries. All institutions should have a maximum blood ordering schedule planned for elective procedures, and blood products should be arranged accordingly to avoid unnecessary cross matching.


Subject(s)
Blood Grouping and Crossmatching/methods , Blood Transfusion/methods , Thyroid Gland/surgery , Thyroidectomy , Adult , Blood Banks , Developing Countries , Elective Surgical Procedures , Electronic Health Records , Female , Humans , Male , Middle Aged , Retrospective Studies
11.
Patient Saf Surg ; 10(1): 19, 2016.
Article in English | MEDLINE | ID: mdl-27610201

ABSTRACT

BACKGROUND: Needle stick injuries (NSIs) have the potential of causing Hepatitis B and Hepatitis C, which is constantly adding to the burden of chronic liver disease in our country. It poses a risk to Health Care Workers (HCWs) and the patients they deal with. In order to limit the spread of these viruses, it is imperative that these HCWs be fully equipped with knowledge regarding prevention of NSIs and dealing with one, regardless of their designation. We therefore aimed to assess and compare the level of awareness about precautions for needle stick injuries amongst all those greatest at risk. METHODS: This was a cross- sectional study carried out at Liaquat National Hospital, Karachi, Pakistan. A 23 itemed self-administered questionnaire was given to hospital staff including doctors, lab technicians and nurses via convenience sampling, in various departments. Data was analyzed via SPSS 18 software and a p-value of <0.05 was considered significant. RESULTS: A total of 198 responses were taken for this study, out of which 70 (35.4 %) were doctors, 70 (35.4 %) nursing staff and 58 (29.3 %) laboratory technicians. Of all HCWs, 101 (51 %) knew that the standard method of discarding needles is without recapping. 159 (80.3 %) were still recapping needles. 180 (90.9 %) HCWs were vaccinated against Hepatitis B. 36 (18.2 %) were aware that blood should be allowed to flow after an NSI and site of prick should be washed with an antiseptic. CONCLUSION: The awareness was found to be very low amongst all HCWs. It should therefore be made compulsory for all HCWs to attend proper preparatory classes by the infection control department at the time of employment in order to improve the level of awareness and ensure safe practices.

12.
BMC Res Notes ; 9: 357, 2016 Jul 22.
Article in English | MEDLINE | ID: mdl-27448602

ABSTRACT

BACKGROUND: Gorlin syndrome is a rare autosomal dominant syndrome characterized by multiple basal cell carcinomas, keratocystic odontogenic tumors (KOT) and falx cerebral calcifications, which occur due to mutation in PTCH gene. CASE PRESENTATION: A 36 year old Asian patient presented with jaw swelling and pain. Radiographic examination revealed six cysts in maxilla and mandible which were excised and histologically were compatable with keratocystic odontogenic tumors. CT scan also revealed falx cerebral calcification which led to the diagnosis of Gorlin syndrome confirmed on genetic testing. There was no evidence of basal cell carcinoma and other manifestations of Gorlin syndrome were absent. CONCLUSIONS: Multiple KCOT are hallmark of Gorlin syndrome and should always leads to its suspicion even in the absence of other manifestations and late presentation. Moreover, keratocystic odontogenic tumors have a particularly higher risk of recurrence and patients with Gorlin syndrome are prone to develop additional keratocystic odontogenic tumors from basal cells of oral epithelium. Therefore we suggest a stepwise approach to manage such patients which include a preoperative biopsy to establish a definitive diagnosis and complete removal of all keratocystic odontogenic tumors to prevent recurrence followed by close clinical follow up and early removal of any newly developed or recurrent cyst. Additionally thorough clinical examination is necessary to rule out the possibility of Gorlin syndrome in any patient with keratocystic odontogenic tumors as there are only subtle differences in histology of those cysts with a syndromic association and clinical features of Gorlin syndrome are markedly variable. Hence late occurrence of keratocystic odontogenic tumors and absence of skin manifestations like basal cell carcinoma should not preclude a diagnosis of Gorlin syndrome.


Subject(s)
Basal Cell Nevus Syndrome/diagnosis , Edema/diagnosis , Odontogenic Cysts/diagnosis , Pain/diagnosis , Adult , Basal Cell Nevus Syndrome/pathology , Basal Cell Nevus Syndrome/surgery , Edema/pathology , Edema/surgery , Humans , Immunohistochemistry , Jaw/pathology , Male , Odontogenic Cysts/pathology , Odontogenic Cysts/surgery , Orthognathic Surgical Procedures , Pain/pathology , Pain/surgery
13.
World J Surg Oncol ; 14: 91, 2016 Mar 31.
Article in English | MEDLINE | ID: mdl-27029917

ABSTRACT

BACKGROUND: Ovarian neoplasms are a heterogeneous group of tumors including surface epithelial, germ cell and sex cord stromal tumors with a subset having low malignant potential (borderline tumors). While the surgical management plan differs in different categories of tumors, preoperative diagnosis is seldom available. In these circumstances, the role of frozen section becomes invaluable. In the current study, we aimed to evaluate the accuracy of the frozen section of ovarian tumors in our setup. METHODS: It was a retrospective study involving 141 cases of ovarian tumors undergoing surgical resection with frozen section evaluation from January 2009 to December 2014. After gross examination, one to five blocks were prepared on the frozen section depending upon the size of the specimen. After frozen section reporting, specimens were processed routinely for final paraffin section evaluation. Results of frozen and paraffin sections were categorized in benign, borderline, and malignant, and accuracy of frozen section was determined. RESULTS: Out of 141 cases, 107 were diagnosed as benign on final (paraffin) examination, while 6 were borderline and 28 were malignant. Out of 107 benign cases, 45 were non-neoplastic cystic lesions of the ovary including endometriotic, follicular, and corpus luteal cysts. The most common benign neoplastic tumor was mature cystic teratoma (20 cases) followed by mucinous cystadenoma (19 cases), serous cystadenoma (14 cases), sex cord stromal tumors (8 cases), and Brenner tumor (1 case). Among borderline cases, four cases were serous and two of mucinous neoplasms. The most common malignant neoplasm was serous carcinoma (11 cases) followed by mucinous carcinoma (6 cases). The overall accuracy of frozen section diagnosis is above 99 %. The sensitivity and specificity for benign tumors were found to be 100 and 97 %, respectively. The sensitivity and specificity for borderline tumors was 83 and 99 %, respectively, while for malignant tumors, it was 96 and 100 %, respectively. CONCLUSIONS: We found a high sensitivity and specificity of frozen section for the diagnosis of ovarian tumors and to determine its malignant potential. Therefore, it should always be used when the preoperative diagnosis is not definite to govern extent of surgical resection. However, under-diagnosis can occur in tumors of borderline category which can be minimized by increased sampling on the frozen section.


Subject(s)
Adenocarcinoma, Mucinous/diagnosis , Cystadenocarcinoma, Serous/diagnosis , Cystadenoma, Mucinous/diagnosis , Frozen Sections/methods , Ovarian Neoplasms/diagnosis , Adenocarcinoma, Mucinous/surgery , Cystadenocarcinoma, Serous/surgery , Cystadenoma, Mucinous/surgery , Female , Follow-Up Studies , Humans , Intraoperative Period , Neoplasm Staging , Ovarian Neoplasms/surgery , Predictive Value of Tests , Prognosis , Retrospective Studies
14.
BMC Res Notes ; 9: 205, 2016 Apr 06.
Article in English | MEDLINE | ID: mdl-27052022

ABSTRACT

BACKGROUND: Ovarian cancer is the most lethal gynecologic malignancy and it represents third most common malignancy in Karachi (after breast and oral cancer). Due to lack of well established cancer registry in our country, changing trends of ovarian tumors has not been determined. Therefore we aimed to establish the current trends and classification of ovarian tumors in our setup according to latest WHO guidelines. METHODS: We retrospectively analyzed 162 cases of ovarian tumors that underwent surgical resection from January 2009 till December 2014. Specimens were received in histopathology department, Liaquat National hospital and cases were examined by senior histopathologists and classified according to latest WHO guidelines. Various histopathologic parameters including capsular invasion, omental and lymph node meatstasis along with uterine and fallopian tube involvement were determined apart from tumor type and grade. RESULTS: Mean age at diagnosis was 35.8 years (± 15.5). surface epithelial tumors were most common, 109 cases (67.2%) followed by germ cell tumors, 44 cases (27.1%) and sex cord stromal tumors, 8 cases (4.9%). Serous tumors were most common surface epithelial tumors with 90% benign morphology. On the other hand, mucinous tumors showed a higher percentage of borderline and malignant features (16.7 and 14.6% respectively). Higher incidence of capsular invasion and omental metastasis was noted in endometroid and serous carcinoma compared to mucinous tumors. CONCLUSIONS: We noted a higher frequency of young age ovarian cancers in our set up. Serous and endometroid carcinomas were found to be associated with adverse prognostic factors like capsular invasion and omental metastasis. Moreover a significantly higher proportion of ovarian tumors constitute mucinous histology including borderline tumors. Whether this represents a changing trend towards biology of these tumors in this part of the world needs to be uncovered by further studies.


Subject(s)
Carcinoma, Endometrioid/pathology , Cystadenocarcinoma, Serous/pathology , Ovarian Neoplasms/pathology , Pathology, Clinical/methods , Adult , Carcinoma, Endometrioid/surgery , Cystadenocarcinoma, Serous/surgery , Fallopian Tubes/pathology , Female , Humans , Lymphatic Metastasis , Middle Aged , Ovarian Neoplasms/surgery , Pakistan , Precancerous Conditions/pathology , Prognosis , Retrospective Studies , Uterus/pathology , Young Adult
15.
BMC Res Notes ; 9: 73, 2016 Feb 08.
Article in English | MEDLINE | ID: mdl-26856980

ABSTRACT

BACKGROUND: Idiopathic nephrotic syndrome encompasses diverse histogenetic patterns and depicts socioeconomic and demographic differences attributable to genetic profile, environmental factors and prevalence of infectious diseases. A lack of renal registry in our country necessitates a need to document changing histologic patterns of nephrotic syndrome as noted in different parts of the world. METHODS: We retrospectively analyzed 140 patients who underwent renal biopsy at Liaquat National Hospital from January 2009 to December 2013 over a period of 3 years. On the basis of clinical profile cases were segregated into nephritic and nephrotic syndrome and histologic and immunoflourescence findings were analyzed. RESULTS: Among 140 cases of glomerulonephritis diagnosed in the study period, 98 cases (70 %) were those of primary glomerulonephritis and 42 were of secondary glomerulopathy (30 %). Membranous glomerulonephritis was the most common primary glomerulonephritis (33.6 %) followed by focal segmental glomerulosclerosis FSGS (20.4 %), whereas lupus nephritis is the most common secondary glomerulopathy (47.6 %) followed by amyloidosis and diabetic glomerulosclerosis (16.6 % each). CONCLUSION: We found a considerable high incidence of membranous glomerulonephritis and FSGS in our population that entails a need to investigate prevalence of associated factors like Hepatitis B and HIV infections in population at risk. Moreover, renal biopsy registry would be instrumental in this regard to record changing disease pattern in this part of the world.


Subject(s)
Kidney Diseases/pathology , Kidney Glomerulus/pathology , Adult , Age Distribution , Female , Fluorescent Antibody Technique , Humans , Male , Middle Aged , Pakistan
16.
BMC Bioinformatics ; 17(Suppl 14): 431, 2016 Nov 11.
Article in English | MEDLINE | ID: mdl-28185583

ABSTRACT

BACKGROUND: Lateral gene transfer (LGT) is an evolutionary process that has an important role in biology. It challenges the traditional binary tree-like evolution of species and is attracting increasing attention of the molecular biologists due to its involvement in antibiotic resistance. A number of attempts have been made to model LGT in the presence of gene duplication and loss, but reliably placing LGT events in the species tree has remained a challenge. RESULTS: In this paper, we propose probabilistic methods that samples reconciliations of the gene tree with a dated species tree and computes maximum a posteriori probabilities. The MCMC-based method uses the probabilistic model DLTRS, that integrates LGT, gene duplication, gene loss, and sequence evolution under a relaxed molecular clock for substitution rates. We can estimate posterior distributions on gene trees and, in contrast to previous work, the actual placement of potential LGT, which can be used to, e.g., identify "highways" of LGT. CONCLUSIONS: Based on a simulation study, we conclude that the method is able to infer the true LGT events on gene tree and reconcile it to the correct edges on the species tree in most cases. Applied to two biological datasets, containing gene families from Cyanobacteria and Molicutes, we find potential LGTs highways that corroborate other studies as well as previously undetected examples.


Subject(s)
Gene Transfer, Horizontal/genetics , Models, Genetic , Biological Evolution , Entomoplasmataceae/classification , Entomoplasmataceae/genetics , Phylogeny
17.
World J Surg Oncol ; 13: 315, 2015 Nov 10.
Article in English | MEDLINE | ID: mdl-26556439

ABSTRACT

BACKGROUND: Peritoneal dissemination of ovarian tumors is a major prognostic parameter in ovarian malignancies. Analysis of peritoneal washing cytology serves as a useful predictor of ovarian surface involvement and peritoneal metastasis even in the absence of clinical omental spread. The aim of the current study is to correlate peritoneal cytology with various histologic features of ovarian cancers in our setup. METHODS: A total of 60 cases of ovarian tumors were included in the study that underwent total abdominal hysterectomy with bilateral salpingo-oophorectomy and omental and lymph node sampling during 2009 till 2014 at the Liaquat National Hospital, Karachi. Any free abdominal fluid was aspirated at the time of surgery. In the absence of free fluid, peritoneal washing was done with 50-100 ml of normal saline. Four cytospin preparations were done along with a cell block preparation. Correlation of peritoneal cytology with various histologic parameters was performed. RESULTS: Out of the 60 cases of ovarian tumors involved in the study, 56 were surface epithelial tumors, 2 germ cell tumors, and 2 metastatic carcinomas. The mean tumor size was 9.6 cm. Capsular invasion was seen in 61 % of the cases, and omental metastasis in 51 % of the cases. Serous carcinoma was found to have a significantly higher frequency of positive peritoneal cytology (76.9 %) compared to endometrioid and mucinous carcinomas (44 and 25 %, respectively). A significant positive correlation was seen between positive peritoneal cytology and capsular invasion and omental metastasis with a p value of <0.001. CONCLUSIONS: Positive peritoneal washing cytology has been implemented in ovarian cancer guidelines because of its prognostic significance in ovarian tumors. In addition to being an indicator of peritoneal metastasis, positive cytology also correlates with capsular invasion and histologic type in ovarian tumors. Therefore, it should always be used as an adjunctive tool in the surgical management of ovarian tumors.


Subject(s)
Carcinoma/secondary , Ovarian Neoplasms/pathology , Peritoneal Cavity/pathology , Peritoneal Lavage , Peritoneal Neoplasms/secondary , Adult , Carcinoma/surgery , Cohort Studies , Female , Humans , Hysterectomy , Middle Aged , Ovarian Neoplasms/surgery , Prognosis
18.
Patient Saf Surg ; 9: 31, 2015.
Article in English | MEDLINE | ID: mdl-26379780

ABSTRACT

BACKGROUND: Symptomatic gallstone disease is one of the most common problem attended by a general surgeon. The application of minimally invasive surgical techniques for the removal of gallbladder is now an accepted and preferred method for treating this condition. The avoidance of a subcostal incision and minimal bowel handling leads to decreased postoperative pain, early returning to function and overall shorter duration of hospital stay. Nevertheless, patients do have significant postoperative pain, and newer techniques to further reduce this pain are the subject of many ongoing studies. Many intraoperative techniques for reducing postoperative pain have been described. The current practice at many institutions, including ours, is to discharge the patient on the first postoperative day on oral analgesics. Better control of postoperative pain may help establishing laparoscopic cholecystectomy as a day care procedure in selected patients. The aim of this study is to determine the effect of 0.5 % bupivacaine soaked oxidized regenerated cellulose surgical versus normal saline soaked surgical applied at the gallbladder bed on postoperative mean pain score after laparoscopic cholecystectomy for symptomatic gallstones. PATIENTS AND METHODS: Patients scheduled for laparoscopic cholecystectomy were enrolled in the study after meeting the inclusion criteria. Relevant history was taken and clinical examination was done. Necessary investigations were carried out. All patients were divided to receive either 0.5 % bupivacaine soaked surgicel or normal saline soaked surgicel after laparoscopic cholecystectomy with each group having equal number of patients. The pain score was measured with a visual analogue scale (VAS) at 4, 12 and 24 h after the procedure in both groups. All data was recorded on performa and SPSS-19 was used for analysis. RESULTS: The demographic characteristic of the two groups has shown that studied patients were matched as regarding gender, age, weight, ASA status and duration of surgery. Post-operative abdominal pain was significantly lower in bupivacaine Group than Saline group. This difference was reported from 4 h till 12 h post-operatively. Bradycardia, Hypotension and Urinary retention were the most common perioperative symptoms reported, with an incidence of 28.3 % in the saline Group and 15 % in the bupivacaine group with no significant differences. Evaluation of postoperative details such as oral intake, time to walk and length of hospital stay revealed that bupivacaine group reported better outcomes as compared to saline group. CONCLUSION: Placing bupivacaine soaked surgicel has been shown to decrease the mean postoperative pain score in patients. No significant complication was noticed with the use of surgicel. Because adequate pain control requires intravenous medications, additional methods for pain control need to be studied before laparoscopic cholecystectomy can be routinely performed as a day care case.

19.
Diagn Pathol ; 10: 100, 2015 Jul 14.
Article in English | MEDLINE | ID: mdl-26170201

ABSTRACT

BACKGROUND: Myoepithelial neoplasms, although sometimes encountered in soft tissues are described very rarely in mediastinum and lung. We reported a rare case of such a tumor which was very large in size and not connected to respiratory tree. CASE PRESENTATION: A 24 year old male presented with blunt chest pain and respiratory distress. A CT scan was performed which showed large heterogeneously enhancing soft tissue mass occupying the left hemithorax. It measures 18.5 X 15.8 X 7.6. Thoracotomy with excision of the tumor was done. Operative findings include multilobulated and nodular large glistening white tumor located in anterior mediastinum adherent to parietal pleura and effacing the pulmonary parenchyma. However tumor was not connected or seems to originate from trachea or lung. Microscopic sections show neoplastic lesion composed of nests, cords and trabeculae of small to medium sized cells with round nuclei and clear cytoplasm. Background showed myxoid appearance with areas of cartilaginous differentiation. Immunohistochemical expression of CKAE1/AE3, p63, ASMA, S100 and GFAP favored the diagnosis of benign myoepithelioma. CONCLUSION: Myoepithelial tumors are rare soft tissue tumors thought to arise from stem cells capable of divergent differentiation and occur anywhere in the body. Histopathologic recognition of these tumors is essential as these tumors may behave in a benign fashion despite large sizes.


Subject(s)
Mediastinal Neoplasms/pathology , Myoepithelioma/pathology , Biomarkers, Tumor/analysis , Biopsy , Chest Pain/etiology , Humans , Immunohistochemistry , Male , Mediastinal Neoplasms/chemistry , Mediastinal Neoplasms/complications , Mediastinal Neoplasms/surgery , Myoepithelioma/chemistry , Myoepithelioma/complications , Myoepithelioma/surgery , Respiration Disorders/etiology , Thoracotomy , Tomography, X-Ray Computed , Treatment Outcome , Tumor Burden , Young Adult
20.
BMC Res Notes ; 8: 101, 2015 Mar 27.
Article in English | MEDLINE | ID: mdl-25879702

ABSTRACT

BACKGROUND: Fine needle aspiration cytology (FNAC) is a cytodiagnostic method based on morphologic findings of individual and small group of cells aspirated using a fine needle. The aim of the present study is to evaluate the spectrum of salivary gland lesions in our setting and to assess the diagnostic accuracy of FNAC for salivary gland lesions. METHODS: The study involved 187 cases of parotid and submandibular swellings of patients who underwent FNAC at our institution. Thirty one (31) patients with a FNAC diagnosis of neoplastic lesion subsequently underwent excision biopsies. The results of FNAC and final histology were compared and accuracy of FNAC was determined. RESULTS: Mean age of patients was 42 (± 21) years and male to female ratio was 1:1. Chronic sialadenitis was the most common non-neoplastic lesion (33.8%) followed by acute and chronic sialadenitis (29.7%) and chronic granulomatous inflammation (27.0%). Pleomorphic adenoma was the most common benign neoplasm and non-Hodgkin's lymphoma was the most common malignant lesion (38.9%) followed by acinic cell (27.8%) and adenoid cystic carcinoma (16.7%). Total 31 patients subsequently underwent surgical excision, out of which 21 were benign and 9 were malignant, 20 cases (64.5%) were of pleomorphic adenoma, 3 cases (9.6%) of acinic cell carcinoma, 2 cases (6.4%) each of warthin tumor, adenoid cystic carcinoma and non-hodgkin lymphoma and 1 case (3.2%) each of mucoepidermoid carcinoma and mucinous adenocarcinoma. The overall accuracy of FNAC in our study was found to be 83.8% with 77.7% sensitivity and 86.3%, specificity. The revised sensitivity and specificity after adjusting verification bias were 68.5% and 91% respectively. False negative diagnosis was rendered in mucoepidermoid carcinoma and acinic cell carcinoma whereas false positive diagnosis was given in cases of pleomorphic adenoma. CONCLUSION: We found a good concordance between FNAC and histology, however pleomorphic adenoma may impart a diagnostic challenge when inadequately aspirated and therefore we advice either immunohistochemical studies (if cell block material is available) or repeat aspiration in difficult cases.


Subject(s)
Adenoma, Pleomorphic/pathology , Carcinoma, Acinar Cell/pathology , Carcinoma, Adenoid Cystic/pathology , Lymphoma, Non-Hodgkin/pathology , Salivary Gland Neoplasms/pathology , Salivary Glands/pathology , Sialadenitis/pathology , Acute Disease , Adenoma, Pleomorphic/diagnosis , Adult , Biopsy, Fine-Needle , Carcinoma, Acinar Cell/diagnosis , Carcinoma, Adenoid Cystic/diagnosis , Female , Humans , Lymphoma, Non-Hodgkin/diagnosis , Male , Middle Aged , Predictive Value of Tests , Retrospective Studies , Salivary Gland Neoplasms/diagnosis , Sialadenitis/diagnosis
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