Analysis of the Genome Sequence of Strain GiC-126 of Gloeostereum incarnatum with Genetic Linkage Map

Gloeostereum incarnatum has edible and medicinal value and was first cultivated and domesticated in China. We sequenced the G. incarnatum monokaryotic strain GiC-126 on an Illumina HiSeq X Ten system and obtained a 34.52-Mb genome assembly sequence that encoded 16,895 predicted genes. We combined the GiC-126 genome with the published genome of G. incarnatum strain CCMJ2665 to construct a genetic linkage map (GiC-126 genome) that had 10 linkage groups (LGs), and the 15 assembly sequences of CCMJ2665 were integrated into 8 LGs. We identified 1912 simple sequence repeat (SSR) loci and detected 700 genes containing 768 SSRs in the genome; 65 and 100 of them were annotated with gene ontology (GO) terms and KEGG pathways, respectively. Carbohydrate-active enzymes (CAZymes) were identified in 20 fungal genomes and annotated; among them, 144 CAZymes were annotated in the GiC-126 genome. The A mating-type locus (MAT-A) of G. incarnatum was located on scaffold885 at 38.9 cM of LG1 and was flanked by two homeodomain (HD1) genes, mip and beta-fg. Fourteen segregation distortion markers were detected in the genetic linkage map, all of which were skewed toward the parent GiC-126. They formed three segregation distortion regions (SDR1–SDR3), and 22 predictive genes were found in scaffold1920 where three segregation distortion markers were located in SDR1. In this study, we corrected and updated the genomic information of G. incarnatum. Our results will provide a theoretical basis for fine gene mapping, functional gene cloning, and genetic breeding the follow-up of G. incarnatum.

Analysis of the Genome Sequence of Strain GiC-126 of Gloeostereum incarnatum with Genetic Linkage Map

Gloeostereum incarnatum has edible and medicinal value and was first cultivated and domesticated in China. We sequenced the G. incarnatum monokaryotic strain GiC-126 on an Illumina HiSeq X Ten system and obtained a 34.52-Mb genome assembly sequence that encoded 16,895 predicted genes. We combined the GiC-126 genome with the published genome of G. incarnatum strain CCMJ2665 to construct a genetic linkage map (GiC-126 genome) that had 10 linkage groups (LGs), and the 15 assembly sequences of CCMJ2665 were integrated into 8 LGs. We identified 1912 simple sequence repeat (SSR) loci and detected 700 genes containing 768 SSRs in the genome; 65 and 100 of them were annotated with gene ontology (GO) terms and KEGG pathways, respectively. Carbohydrate-active enzymes (CAZymes) were identified in 20 fungal genomes and annotated; among them, 144 CAZymes were annotated in the GiC-126 genome. The A mating-type locus (MAT-A) of G. incarnatum was located on scaffold885 at 38.9 cM of LG1 and was flanked by two homeodomain (HD1) genes, mip and beta-fg. Fourteen segregation distortion markers were detected in the genetic linkage map, all of which were skewed toward the parent GiC-126. They formed three segregation distortion regions (SDR1–SDR3), and 22 predictive genes were found in scaffold1920 where three segregation distortion markers were located in SDR1. In this study, we corrected and updated the genomic information of G. incarnatum. Our results will provide a theoretical basis for fine gene mapping, functional gene cloning, and genetic breeding the follow-up of G. incarnatum.

Treatment of Mandibular Second Molar with S-shaped Root Canal

Unusual root canal anatomy always poses challenge in successful endodontic management. One such case report is of S-shaped or Bayonet shaped root canal. It is always demanding to manage root canal with double curvature. The study is an attempt to focus on the significant work involved to manage root canal with double curvature.

Insidious sensorineural hearing loss in chronic suppurative otitis media

Background: Sensorineural hearing loss may be one of the outcome of chronic suppurative otitis media

Objective: To evaluate the association of chronic suppurative otitis media with sensorineural hearing loss and also to find out whether the disease duration had any impact on hearing

Methodology: This was a cross sectional study conducted at Aga Khan University Hospital. Charts of all patients who underwent surgery for chronic suppurative otitis media from 1stJanuary 2004 to 31stDecember 2009 were reviewed. One hundred and fifty five patients out of 562 met our inclusion criteria and were included in the study. The contralateral ear was taken as control. History record and audiograms were reviewed from the patient charts for the duration of disease and evidence of SNHL at three speech frequencies [[500, 1000, and 2000 Hz]. The data was entered and analyzed by SPSS version 16

Results: Of 155 patients, 46 [29.6%] had SNHL. In a group of patients with epithelial disease[cholesteatoma] 16 out of 45 patients had SNHL whereas in the group of patients with mucosal disease [formerly known as tubotympanic type] 30 out of 110 patients had SNHL. This hearing loss found to be worsening with the duration of disease in both groups [p=0.000]

Conclusion: A significant association of SNHL was found with CSOM and disease duration. Early surgicaltreatment should be offered in order to prevent irreversible SNHL

Safety of fenbendazole in common peafowl [Pavo cristatus]

The present study was undertaken to find out the safety levels of fenbendazole in common peafowl. This bird, raised on aviaries and zoos, can be severely parasitized with Ascaridia galli [enteric worms] and Syngamus trachea [gapeworm] along with other parasitic worms. Fenbendazole is a highly effective benzimidazole-class anthelmintic in animals. The objective of this work was to provide target animal safety data in young peafowl and to demonstrate reproductive safety in adult birds. During the experimental study, diets containing fenbendazole at 0, 100, 200 and 300 ppm were fed for 21 days [three times the normal treatment duration]. Data for feed consumption, feed conversion rate, and body weights were recorded for each bird in each group. Drug concentrations in different tissues of birds were determined to correlate concentrations with clinical observations, clinical pathology, and histologic findings. There were no morbidities or mortalities after study day 21. Additionally, there were no statistically significant treatment-related differences among above mentioned parameters. Analysis of fenbendazole concentrations in kidney, liver, leg/thigh, and breast muscle and skin with associated fat revealed that, even at the highest dose level used and with no feed withdrawal, fenbendazole concentrations were relatively low in these tissues. These findings indicate that fenbendazole has a relatively wide margin of safety in young peafowl and that the proposed dose of 100 ppm in the feed for 7 consecutive days is well within the margin of safety. In the reproductive safety study, five breeder peafowl farms fed fendbendazole at 100ppm for 7 days and collected data on hatching percentage of peahen eggs before and after treatment. Reproductive performance in peahen was not adversely affected

Teaching microscopy effectively through a combined Peyton's fourstep approach and Gagne's instructional model

Objective: To design a lesson plan for teaching microscopy using a combined Peyton's and Gagne's model

Study Design: Qualitative study with scoping review

Place and Duration of Study: Khyber Medical University, Peshawar from April-September 2017

Material and Methods: We searched Pub Med through a variety of search strategies. The purpose of the search was to identify relevant articles [using an inclusion and exclusion criteria] on making a lesson plan for a psychomotor skill. After selection of articles, the evidence was synthesized including author's name, year of publication, country, key findings, model used to make a lesson plan and limitations of the study. From the synthesised evidence, a lesson plan was designed on microscopy. This is a qualitative study with scoping review, therefore, no quantitative analysis or software was used

Results: In total, 130 articles were identified but after screening and assessment for eligibility five articles were selected. The synthesized evidence suggested that four articles had used Gagne's model, while one article had used a combined Gagne's and Peyton's model to design a lesson plan to teach psychomotor skills. We used the combined model to design a lesson plan for pathology students on microscopy. The microscopy skill was broken down into different parts and each learning step was integrated into the nine events of Gagne's model. The Peyton's model was combined to teach the actual microscopy skill for better learning and executing the skill

Conclusion: The model combined Gagne's and Peyton's model, which was used to design an effective lesson plan to teach microscopy. This model could also help in delivering better teaching sessions for other psychomotor skills

Body mass index in medical students and its association with gender and academic year

Background: Students are generally prone to weight related problems due to sedentary lifestyle and disordered eating habits. The objective of current study was to evaluate the body mass index among MBBS and Physiotherapy students of Peshawar and to see its association with gender and academic year

Methods: This was a cross-sectional study conducted among MBBS and Physiotherapy students in Peshawar, from Sep 2016 to Sep 2017. A self-administered questionnaire was distributed among 250 students of different institutes, 213 filled questionnaires were returned. Body mass index [BMI] was used to classify underweight, overweight, and obesity grade I and grade II. Data was analyzed using SPSS-20

Results: Mean age of participants was 21.77+/-1.45. Females were 137 [64.3%] while males were 76 [35.7%]. Unmarried participants were 192 [90.1%], while 21[9.9%] were married. Mean height, weight and BMI of the participants were 1.654 meter, 61.1 Kg, and 22.8 respectively. One hundred and thirty [61.0%] were MBBS, and 83 [39.0%] were Physiotherapy students. Out of 213 respondents, 109 [51.2%] had normal BMI, 21[9.9%] were underweight, 41 [19.2%] were overweight, 31 [14.6%] were grade I obese and 11 [5.2%] were grade II obese. Majority of 1[st] year [68.0%] and 4[th] year [72.7%] students had normal BMI. BMI was not associated with gender or academic year [p>0.05]. Mean BMI in MBBS students was higher than the physiotherapy students [23.3 vs 22.1 Kg/M[2], p=0.03]

Conclusion: The prevalence of obesity appears higher in our students

systematic translation of biomarkers research into clinical practice

Background: The rapid gains in science and technology during the last century resulted in an epidemiological shift from infectious diseases to non-communicable diseases like cancer, diabetes mellitus, and cardiovascular diseases. However, despite the large funding put into the understanding of etiology of cancer, identification of novel diagnostic markers, and advancing cancer treatment, the translation of research findings into clinical practice leaves much to be desired for

Methods and Results: The translation of cancer biomarkers into clinical practice is a great challenge that needs to be promptly addressed for better cancer outcomes. This review discusses the characteristics of clinically useful cancer biomarkers, and how biomarkers identified by research can be used for the improved cancer management and patient outcomes. We also explored the underlying reasons for the less than an optimal translation of biomarkers research into clinical practice, how basic medical sciences can undertake more clinically relevant research, and provide suggestions on how to improve the clinical translation of research findings from such studies. The reason delaying the clinical translation of biomarkers are: lack of systematic analyses on existing cancer biomarkers; inadequate sample size; lack of an optimal scoring system and threshold; limited use of panels of biomarkers; technical differences between laboratories; and the need for well-designed validation studies [biomarker clinical trials]

Conclusion: Clinical translation of biomarkers could potentially be facilitated through a systematic approach taking into account the reasons highlighted in the current study

Evaluation of hepatotoxic and nephrotoxic effects of piroxicam sulfonated derivatives

Background: Pain management requires new pharmacotherapy with good efficacy and less side effects. Piroxicam is used routinely in clinical practice but it is associated with side effects. To minimize the chances of adverse effects, sulfonated piroxicam derivatives [SPD] have been introduced. We sought to find hepatotoxic and nephrotoxic effects of SPD in Albino rats

Methods: An experimental study on SPD was carried out at the Institute of Basic Medical Sciences, Khyber Medical University, Peshawar. Healthy 24 albino rats were divided into 5 groups. One control group and four experimental groups [compound I and II, each with a dose of 10mg/kg and 20mg/kg] received treatment for 7 days. Liver function tests [LFTs], renal function tests [RFTs] and histology of liver and kidney specimens was performed after culling rats. The difference between median values of samples was assessed using Kruskal-Wallis test with post-hoc [for LFTs and RFTs]. SPSS-21 was used for all statistical analysis and p?0.05 was considered statistically significant

Results: The alanine aminotransferase [ALT] values were significantly high in the 20 mg/Kg group than control for both compounds [p=0.03, p=0.001 respectively]. The aspartate aminotransferase [AST] values were significantly high in the 10 mg/Kg and 20 mg/Kg group than control for compounds II [p=0.01, p=0.0001 respectively]. The alkaline phosphatase [ALP] values were significantly high in the 20 mg/Kg group than control for compounds II [p=0.002]. The blood urea values were significantly high in the 20 mg/Kg group than control for compounds II [p=0.008]. The mean final score of liver injury in all experimental groups [mean range 5-7] was less suggesting that the damage in liver was less pronounced. Renal injury was more pronounced in the 20 mg/Kg dose for both compound I and compound II [mean score 7] compared to 10 mg/Kg dose [mean score 4]

Conclusion: Piroxicam sulfonated derivatives can cause focal changes in liver and kidney which might be reversible. The changes are less pronounced for compound I with a low dose

Attributes of a good medical school: faculty perspective in local context

Background: Medical schools and institutions are required to meet the standards of national and international accreditation bodies. These standards guide the attributes of a good medical school. The current study was designed to identify the attributes of a good medical school from a local perspective

Methods: For this qualitative study based upon grounded theory, 25 participants were recruited through purposive sampling who underwent a workshop to get an insight about the attributes of a good medical school. They were asked to provide the faculty perspectives of a good medical school. The participant responses were put in online software 'Worditout' to look for the repetitions of words, followed by open coding technique. Initial coding was followed by a second phase of axial coding of the data in order to identify themes and thematic analyses of all the data were performed

Results: The teaching experience of the participants in medical schools varied from 2 to 20 years. In total, 198 responses/comments from all the participants were recorded. After doing the open and axial coding all the responses were summarized into four themes. The themes highlighted in order of the response frequency were: 1] improved learning strategies and opportunities; 2] modification and improvements in teaching methodologies; 3] standardised and programmatic assessment methods and 4] parameters of quality assurance and management

Conclusion: The attributes of a good medical school are guided by the national and international standards. However, some of the standards are contextual and our study showed these standards as attributes of a good medical school. It includes provision of better learning opportunities, teaching methodologies, standardised assessment and quality assurance

Malaria in dengue patients

Objective: To determine frequency of malaria in dengue patients

Study Design: Cross sectional study

Place and Duration of Study: The study was carried out in the Department of Medicine, Civil Hospital Karachi from June 2008 to December 2008

Materials and Methods: 274 dengue patients with Ig M antibody positive results were included in the study after informed consent Malaria parasite peripheral film and malarial ICT [immunochromatography] test of all these dengue patients were performed in order to detect the presence of co-infection with malaria. Age and sex of the patients were also noted

Results: In the study, out of 274 dengue patients, 189 [69%] were males and 85 [31%] were females. Mean age was 31.01 +/- 14.83 years. 41 [15%] dengue patients had concomitant malarial infection. Out of these 41 dengue-malaria co-infected patients, 29 [10.6%] had plasmodium vivax; 8 [2.9%] had plasmodium falciparum and 4 [1.5%] had both falciparum + vivax

Conclusion: Patients with dengue fever are predisposed to have concomitant malarial infection. Hence, these must be investigated for malaria as undiagnosed and untreated malaria can increase the morbidity and mortality of the dengue patients

Frequency of non-alcoholic steatohepatitis on histopathology in patients of type 2 diabetes mellitus with duration of more than 5 years

Objective: to determine the frequency of non-alcoholic steatohepatitis [NASH] on histopathology in patients of type 2 diabetes mellitus with duration of more than 5 years

Study Design: descriptive, cross-sectional study

Place and Duration of Study: department of Medicine, Dow Medical College, Civil Hospital, Karachi, from November 2013 to April 2014

Methodology: patients with type 2 diabetes mellitus of more than 5 years duration having raised alanine transaminases level and fatty liver on ultrasonography were selected. Informed consent was obtained and liver biopsy was performed in all patients by experienced physician of Civil Hospital Karachi. All samples of biopsy were sent for histopathology. Those patients with hepatitis B, C and D and steatosis like alcoholic and hypertriglyceridemia were excluded from the study. Descriptive statistics were calculated on SPSS version 17

Results: out of the 262 cases, 56.49% [148/262] showed non-alcoholic steatohepatitis on the basis of histopathology. The mean age of the patients was 50.72 +/-8.48 years. Median [interquartile] duration of diabetes mellitus of the cases was 9 years [15 - 4]. Out of 148 NASH cases, 56.1% [83/148] were males and 43.9% [65/148] were females

Conclusion: nonalcoholic steatohepatitis is an increasingly important and unrecognized spectrum of chronic liver disease associated with high prevalence of diabetes that is often overlooked and diagnosed with complications. So early recognition of these patients can prevent further complications

Alzheimer and vascular dementia in the elderly patients

Objectives: To find out the frequency of Alzheimer's and Vascular dementia in the elderly patients

Methods:This cross sectional descriptive study was conducted in Department of Medicine, Ziauddin Hospital Karachi from 1[st] October 2013 to 31[st] March 2014. Patients with symptoms of dementia for more than 6 months duration, and Mini Mental State Examination score <24 were included in this study. Patients who fell in category of dementia were assessed for duration of symptoms. Patients underwent CT scan of brain. Patients with generalized atrophy of brain on CT scanning of brain were labeled as Alzheimer's dementia, while patients with ischemic or hemorrhagic stroke on CT scan of brain were labeled as vascular dementia

Results:Four hundred twenty two patients were included in this study. There were 232 [54.98 %] male and 190 [45.02 %] were female. The mean age +/- SD of the patients was 72.58+/-5.34 years [95%CI: 72.07 to 73.09], similarly average duration of symptoms was 10.14+/-2.85 months. About 18.96% of patients were illiterate, 32.23% were matric, 28.44% were intermediate and 20.33% were graduate and post graduate. Hypertension and diabetes were the commonest co-morbid i.e. 81.3% and 73.7%, hyperlipedimia and smoking were 38.2% and 45% respectively. Frequency of Alzheimer's disease and vascular dementia in the elderly was observed in 3.79% [16/422] and 2.61% [11/422] cases

Conclusion:A good number of patients, 27 out of 422, in this hospital based study were suffering from Alzheimer's disease and vascular dementia. Early detection and prompt treatment can reduce the burden of the disease in our population

Resection of posterior mediastinal tumors by video assisted thoracic surgery

This case report illustrates successful Video Assisted Thoracic Surgery [VATS] performed on a 45-year-old woman and 52-year-old man presenting with a mass in left and right paravertebral space on the CT scan respectively. VATS has many benefits over traditional open operation [thoracotomy], resulting in less pain and shorten recovery time. However, VATS has higher equipment cost but when an experienced surgeon performs the surgery, better outcomes are achieved. VATS is not common in Pakistan's surgical setup as it is an expensive method of eradicating mediastinal pathologies and not every patient undergoes VATS. The primary objective of presenting these cases is to promote the use of VATS specifically for removal of posterior mediastinal tumors and improve the surgical outcomes

Treatment of mycosis fungoides with total skin electron beam therapy using modified stanford technique

A retrospective review of three patients with mycosis fungoides treated with total skin electron beam therapy, from the year 2007 to 2009, at the Oncology department, Ziauddin University Hospital

Hepatocellular carcinoma first presenting as a tumor of the oral cavity

Hepatocellular carcinoma [HCC] is the sixth most common neoplasm worldwide; HCC metastasis is common affecting 50% of cases. However, metastasis to the oral cavity is extremely infrequent. We present a case of hepatocellular cancer first presenting as a mass lesion at the upper alveolus and review metastatic hepatocellular carcinoma to the oral cavity in 73-year-old male patient

Association of airborne Aspergillus with asthma exacerbation in Southern Pakistan

BACKGROUND: Exposure to airborne fungi has been related with exacerbation of asthma in adults and children leading to increased outpatient, emergency room visits, and hospitalizations. Hypersensitivity to these airborne fungi may be an important initial predisposing factor in the development and exacerbation of asthma. OBJECTIVE: This study was conducted to determine an association between fungal types and spore concentrations with the risk of asthma exacerbation in adults. METHODS: This cross-sectional study was conducted from May 2008 to August 2009 at the Aga Khan University Hospital Karachi, Pakistan. All adult (age≥16 years) patients presenting to the hospital with acute asthma exacerbation were enrolled after informed consent. A home survey was conducted for each patient to assess their environmental characteristics. Indoor air samples were also obtained from the patient's home to determine the type and spore concentration of fungi within the week of their enrollment in the study. RESULTS: Three hundred and ninety-one patients with an acute asthma exacerbation were enrolled during the study period. The mean age of participants was 46 years (standard deviation, ±18 years) and 247 (63.2%) were females. A trend of higher asthma enrollment associated with higher Aspergillus concentrations was found in two consecutive summers. A total of nineteen types of fungi were found in air samples. Aspergillus spp. was the most frequently isolated fungus with acute asthma exacerbation. CONCLUSION: An association of higher concentration of indoor Aspergillus spp. with asthma exacerbation in adults was observed in this study.

Aortic aneurysm: a rare cause of Ortner's syndrome

A young man presented with hoarseness of voice and was found to have left vocal cord paralysis and a large opacity on chest X-ray in the left upper zone. CT angiography showed a giant aneurysm of the aortic arch involving the left subclavian artery. Using a dual perfusion system, with the femoral bypass circuit taking care of the spinal protection and the aortic bypass circuit providing the cerebral protection, the aneurysm was excised and a 16 mm Dacron [registered] graft was anastomosed to the aortic arch and the left subclavian artery was anastomosed to the interposition graft. He had a smooth postoperative course and his hoarseness subsided in next 6 months.

Pathological findings of chronic supparative otitis media in tertiary care hospital

Objectives: To see the clinico-pathological pattern of findings in the chronic supparative otitis media [CSOM] during surgery

Study Design: A prospective observational study

Place And Duration: This study was conducted in Karachi Medical and Dental College and Abbasi Shaheed Hospital during the period of October 2006 to October 2010

Methodology: For this study, 288 patients were selected. After complete history, examination and relevant investigations surgery was performed and intra-operative findings of middle ear cleft were noted

Results: Total number of patients selected were 288, in which female were dominating slightly with 54.1%. Maximum incidence was noted between the ages of 16-30 years of age in 180 patients [62.5%]. 140 cases [48.61%] had no ossicles damage while 148 cases[51.38%] had one or more ossicles damage. Granulation tissue found in 99 patients [34.37%], while cholesteatoma found in 77 patients [26.73%]

Conclusion: Pathological changes varies from simple mucosal edema to extensive destruction of the middle ear cleft

Frequency of dyslipidaemia in young patients with acute myocardial infarction

To study the frequency of dyslipidaemia in young patients aged between 20-40 years, with Acute Myocardial Infarction in our population. Descriptive study. Coronary Care Unit [CCU] of Armed Forces Institute of Cardiology [AFIC]/ National Institute of Heart Diseases [NIHD], Rawalpindi from December 2008 to May 2009. One hundred patients of acute myocardial infarction [AMI] fulfilling the World Health Organization [WHO] diagnostic criteria of AMI, having ages between 20-40 years, were included in the study after full informed consent using non-probability consecutive sampling. Blood samples for serum lipid profile were taken after 12 hours fasting [within 24 hours of presentation], and analyzed in laboratory of AFIC. Individual patients' results were compiled with respect to age, gender, serum total cholesterol, serum triglycerides, serum low density lipoprotein [LDL] cholesterol, serum very low density lipoprotein [VLDL] cholesterol and serum high density lipoprotein [HDL] cholesterol. The data was entered in SPSS [version 11.0] and analyzed. Of the 100 patients with AMI, 47 were found to have dyslipidaemia. Hypertriglyceridaemia was the most common lipid abnormality as it was found in 32 [68.1%] patients; followed by raised serum VLDL, hypercholesterolemia, raised serum LDL and low serum HDL found in 25 [53.2%], 16 [34.0%], 4 [8.5%] and 2 [4.3%] patients respectively. Out of 47 patients with dyslipidaemia, 28 [59.6%] had more than one lipid abnormality. Frequency of dyslipidaemia in young patients with AMI in our population is high.