Prevalence of mycosis fungoides and its association with EBV and HTLV-1 in Pakistanian patients

Mycosis fungoides (MF) is an indolent T cell lymphoma that is distinguished from other lymphomas by its initial appearance on the skin. The histologic diagnosis of MF may be difficult because there is significant overlap in the histologic features of neoplastic T-cell infiltrates and inflammatory dermatoses. This T-cell neoplasm commonly occurs in a mixed, reactive background and can show only a subtle degree of cytologic atypia, rendering histologic diagnosis difficult. In this study MF constituted 0.86% of all non-Hodgkin’s lymphoma (NHL) both T and B, as compared to the Western studies which have reported 0.5% prevalence for MF of all NHL. Polymerase chain reaction (PCR) technique was used to assess T-cell clonality in paraffinembedded skin biopsies clinically and pathologically suspicious for early MF. Out of the 14 cases diagnosed as MF, amplifiable DNA was isolated from 6 cases, which were further studied for T-cell receptor (TcR)-β, γ, and δ chain gene rearrangements. Clonal product was seen in 4 out of 6 cases for β, γ, and δ TcR chain genes. Association for Epstein Barr virus (EBV) was observed in 3 out of 6 cases (50%) of MF. Although these 3 cases were positive for EBV by PCR, but were negative by in-situ hybridization (ISH). No heterogeneity was noted in these 3 cases of MF for BainHI E, K, N, and Z regions of EBV. All six cases were negative for HTLV-1 (tax region) by PCR. It was concluded that the prevalence of MF in Pakistani population is comparable to the Western data, and that EBV association to MF cases was higher than in Western studies

Ewing\u27s sarcoma arising from the adrenal gland in a young male: a case report

Background: Ewing\u27s sarcoma uncommonly arises from extraosseous soft tissue or parenchymal organs. Primary adrenal Ewing\u27s Sarcoma, although very rare, is extremely aggressive and commonly fatal. CASE PRESENTATION: A 17 year old Pakistani male was referred to the outpatient oncology clinic at our center with a three month history of concomitant pain, swelling and dragging sensation in the right hypochondrium. Abdominal examination revealed a large, firm mass in the right hypochondrium extending into the right lumbar region and epigastrium. His genital exam was unremarkable and there were no stigmata of hepatic or adrenal disease.Computed tomography scans revealed a large peripherally enhancing mass in the hepatorenal area, biopsy of which showed a neoplastic lesion composed of small round blue cells which exhibited abundance of glycogen and stained diffusely positive for CD99 (MIC2 antigen). Fluorescence in situ hybridization demonstrated gene rearrangement at chromosome 22q12 which confirmed the diagnosis of Ewing\u27s sarcoma. Staging scans revealed pulmonary metastasis and hence he was commenced on systemic chemotherapy. CONCLUSION: This case report highlights the importance of keeping Ewing\u27s sarcoma in mind when a young patient presents with a large non-functional adrenal mass

Automatic Detection of Offensive Language for Urdu and Roman Urdu

In recent years, unethical behavior in the cyber-environment has been revealed. The presence of offensive language on social media platforms and automatic detection of such language is becoming a major challenge in modern society. The complexity of natural language constructs makes this task even more challenging. Until now, most of the research has focused on resource-rich languages like English. Roman Urdu and Urdu are two scripts of writing the Urdu language on social media. The Roman script uses the English language characters while the Urdu script uses Urdu language characters. Urdu and Hindi languages are similar with the only difference in their writing script but the Roman scripts of both languages are similar. This study is about the detection of offensive language from the user's comments presented in a resource-poor language Urdu. We propose the first offensive dataset of Urdu containing user-generated comments from social media. We use individual and combined n-grams techniques to extract features at character-level and word-level. We apply seventeen classifiers from seven machine learning techniques to detect offensive language from both Urdu and Roman Urdu text comments. Experiments show that the regression-based models using character n-grams show superior performance to process the Urdu language. Character-level tri-gram outperforms the other word and character n-grams. LogitBoost and SimpleLogistic outperform the other models and achieve 99.2% and 95.9% values of F-measure on Roman Urdu and Urdu datasets respectively. Our designed dataset is publically available on GitHub for future research

Challenges and pitfalls in diagnosis of parosteal Osteosarcoma: a clinicopathologic study of 23 cases

Objective: Parosteal Osteosarcoma (PO) is an uncommon variant of osteosarcoma. Diagnosing PO is important due to its malignant nature but the diversity of histologic features makes it challenging by adding a number of soft tissue, bony and cartilaginous lesions into the list of differential diagnosis. Our aim was to study the clinicopathologic and histological features of PO with emphasis on features helpful in its discrimination from other mimicking lesions. Methods: We reviewed 23 cases of PO diagnosed in our institution between January 2001 and August 2015. Results: Femur was the most commonly involved bone (68.2%) along with other long bones and rib in a single case. Soft tissue component was graded as Grade1 in 9(39%), Grade2 in 8(34.7%) and Grade3 in 4(17.3%) cases. Bony component was seen either in combination of or exclusively as parallel streams and interconnected trabeculae (mosaic-pattern). Out of 9 cases with cartilage component, 3 showed a cartilage cap. 2(8.6%) cases showed dedifferentiation into osteosarcoma. Conclusion: PO should always be considered in the differential diagnosis of every lesion arising from the bone surface. Knowledge of the variations in histologic features helps to reach the correct diagnosis which should never be made without radiological correlation

Conceptual framework for a cardiac surgery simulation laboratory and competency-based curriculum in Pakistan - a short innovation report

Simulation is a commonly utilized technique in healthcare education as it provides trainees a realistic, but safe, environment to learn a variety of skills. Trainees belonging to fields known for high stakes with low margins for error, such as cardiac surgery, can greatly benefit from simulation-based education. We propose the establishment of the first multi-tier high fidelity cardiac surgery simulation lab with a structured curriculum that will eventually provide multidisciplinary training to promising cardiac surgeons across Pakistan. The simulation lab may also be used for research, grant acquisition and patent development. Our setup will include the following levels of simulation: a simple bench model, a virtual reality simulator and a unique human performance simulator. Our multitiered approach allows for appropriate sequential trainee skill progression. Finally, we hope that our model inspires the development of similar curricula and modules for trainees belonging to other surgica

The accuracy of protein structure alignment servers

Background: Protein structural alignment is one of the most fundamental and crucial areas of research in the domain of computational structural biology. Comparison of a protein structure with known structures helps to classify it as a new or belonging to a known group of proteins. This, in turn, is useful to determine the function of protein, its evolutionary relationship with other protein molecules and grasping principles underlying protein architecture and folding. Results: A large number of protein structure alignment methods are available. Each protein structure alignment tool has its own strengths andweaknesses that need to be highlighted.We compared and presented results of six most popular and publically available servers for protein structure comparison. These web-based servers were compared with the respect to functionality (features provided by these servers) and accuracy (how well the structural comparison is performed). The CATH was used as a reference. The results showed that overall CE was top performer. DALI and PhyreStorm showed similar results whereas PDBeFold showed the lowest performance. In case of few secondary structural elements, CE, DALI and PhyreStorm gave 100% success rate. Conclusion: Overall none of the structural alignment servers showed 100% success rate. Studies of overall performance, effect of mainly alpha and effect of mainly beta showed consistent performance. CE, DALI, FatCat and PhyreStorm showed more than 90% success rate

An Integrated Framework for Analysis and Prediction of Impact of Single Nucleotide Polymorphism Associated with Human Diseases

Single nucleotide polymorphisms are most common type of genetic variation in human genome. Analyzing genetic variants can help us better understand the genetic basis of diseases and develop predictive models which are useful to identify individuals who are at increased risk for certain diseases. Several SNP analysis tools have already been developed. For running these tools, the user needs to collect data from various databases. Secondly, often researchers have to use multiple variant analysis tools for cross validating their results and increase confidence in their findings. Extracting data from multiple databases and running multiple tools at a time, increases complexity and time required for analysis. There are some web-based tools that integrate multiple genetic variant databases and provide variant annotations for a few tools. These approaches have some limitations such as retrieving annotation information, filtering common pathogenic variants. The proposed web-based tool, namely IPSNP: An Integrated Platform for Predicting Impact of SNPs is written in Django which is a python-based framework. It uses RESTful API of MyVariant.info to extract annotation information of variants associated with a given gene, rsID, HGVS format variants specified in a VCF file for 29 tools. The results are in the form of a CSV file of predictions (1) derived from the consensus decision, (2) a file having annotations for the variants associated with the given gene, (3) a file showing variants declared as pathogenic commonly by the selected tools, and (4) a CSV file containing chromosome coordinates based on GRCh37 and GRCh38 genome assemblies, rsIDs and proteomic data, so that users may use tools of their choice and avoiding manual parameter collection for each tool. IPSNP is a valuable resource for researchers and clinicians and it can help to save time and effort in discovering the novel disease-associated variants and the development of personalized treatments

Histopathology of bone and soft tissue

Bone and soft tissue pathology is considered to be one of the most challenging areas of diagnostic pathology. It requires not only radiologic films at hand but also frequent use of ancillary tests like special and immunohistochemical (IHC) stains. Many chromosomal translocations and other chromosomal abnormalities are hallmark of several of these tumours which require molecular genetic testing usually by using techniques as FISH. Hence an attempt is made to encompass not only light microscopic features and pattern analysis but also judicious use of special and IHC stains as well as FISH to describe and diagnose a distinct entity compatible with clinical presentation and radiologic findings