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The diagnosis of novel coronavirus (COVID-19) has gained the spotlight of the world's scientific community since December 2019 and it remains an important issue due to the emergence of novel variants around the globe. Early diagnosis of coronavirus is captious to prevent and hard to control. This pandemic can be eradicated by implementing suppressing strategies which can lead to better outcomes and more lives being saved. Therefore, the analysis showed that COVID-19 can only be managed by adopting public health measures, such as testing, isolation and social distancing. Much work has been done to diagnose coronavirus. Various testing technologies have been developed, opted and modified for rapid and accurate detection. The advanced molecular diagnosis relies on the detection of SARS-CoV-2 as it has been considered the main causative agent of this pandemic. Studies have shown that several molecular tests are considered essential for the confirmation of coronavirus infection. Various serology-based tests are also used in the detection and diagnosis of coronavirus including point-of-care assays and high-throughput enzyme immunoassays that aid in the diagnosis of COVID-19. Both these assays are time-consuming and have less diagnostic accuracy. Nanotechnology has the potential to develop new strategies to combat COVID-19 by developing diagnostics and therapeutics. In this review, we have focused on the nanotechnology-based detection techniques including nanoparticles and biosensors to obstruct the spread of SARS-CoV-2.

Image encryption algorithms based on Chaotic approach are becoming increasingly popular for remotely sensed images using parallel techniques. It has been demonstrated that the most efficient image encryption algorithms are based on Chaos. Previous research using chaos-based cryptosystems has resulted in poor performance when using a single computer, compromising privacy, security, and reliability. Furthermore, there were issues when vulnerable satellite images were processed. This paper describes a novel chaos-based encryption technique that employs an external secret key and Henon, Logistic, and Gauss iterated maps. The proposed encryption algorithm is capable of efficiently encrypting a large number of images. When the number of images increases, however, these images become very small, and the technology becomes inefficient or impractical. This paper investigates the parallel method of image encryption on a large number of remotely sensed images in Hadoop. Hadoop's file visit method has been enhanced so that it can treat the entire Tiff file as a single unit. Furthermore, the file format is being extended to be supported by Hadoop in order to support GeoTiff in Hadoop. The results of the experiments show that the proposed parallel method for encryption is effective and scalable to a large number of images when compared to other well-known methods.

Over the past decades, nanomedicine, the medical application of nanotechnology, has been extensively investigated as a promising approach in treating different inflammatory disorders and conditions. Nanomedicine provides a wide range of engineered nanomaterials, such as polymeric nanoparticles (NPs), lipid-based NPs, liposomes, silica NPs, metallic NPs, etc. Nanomaterial-based drug delivery systems exhibit multiple advantages such as the ability to pass through different physiological barriers within the body and specifically deliver drugs to the required sites without affecting healthy cells and tissues. Enormous amounts of in-vitro and in-vivo researches were previously conducted by many research groups to validate the positive contribution that nanomedicine has regarding the treatment of inflammation and its associated illnesses. The scope of this review paper is to overview the current status of using nanomaterials in the treatment of inflammatory diseases, with an emphasis on asthma, rheumatoid arthritis, inflammatory bowel disease, gout and atherosclerosis. The future prospects of using nanomaterials for inflammatory diseases were also briefly discussed.

Clostridium botulinum is Gram-positive anaerobic spore-forming bacterium that produces very potent neurotoxins that have a potential to be used as bioweapon. In this study, we utilized applications of pan genome to develop drug targets for 51 strains of Clostridium botulinum. From the total 8756 core proteins, there were 422 non-host homologous proteins from which we selected 7 essential proteins by applying 2 thresholds that are identity > 35 and e-value = 0.001. These 7 proteins were selected as drug targets and docked against 105 anti-bacterial compounds. After docking, against each protein, top 10 compounds were selected based on the binding affinity and number of interactions and from these 10 compounds, the most promising compound was ranked on top for all target proteins. Furthermore, we also identified some compounds that have shown highest binding energies with more than one protein. From the 105 anti-bacterial compounds, we got 39 compounds on the basis of their binding energies with all target proteins. These compounds can be further validated by in vitro analysis and can proceed for clinical trials.

Liver dysfunction is a major health problem worldwide. Stem cells therapy has opened up new avenues for researches to treat liver diseases due to their multi lineage differentiation. As mesenchymal stem cells (MSCs) can be differentiated into hepatic lineages in the presence of different exogenous factors, the current study aimed to investigate the impact of carbon tetrachloride (CCl4) induced liver injured mice serum on MSCs differentiation toward hepatocytes in vitro. Male Balb/c mice were treated for liver injury with CCl4 as determined through biochemical tests spectrophotometrically and different growth factors (EGF, HGF) quantification through Sandwich ELISA in both normal and CCl4-induced liver injured mice serum. Mice bone marrow derived-MSCs at second passage were treated with normal and CCl4-induced liver injured mice serum. After 7 days, serum treated MSCs were investigated for hepatocytes like characteristics through RT-PCR. Serum biochemical tests (Bilirubin, ALT and ALP) and sandwich ELISA results of EGF and HGF showed marked increase in CCl4 treated mice serum as compared to normal mice serum. Periodic acid Schiff’s staining and urea assay kit confirmed high level of glycogen storage and urea production in cells treated with CCl4-induced liver injured mice serum. RT-PCR results of CCl4-induced liver injured mice serum treated cells also showed expression of hepatic markers (Albumin, Cyto-8, Cyto-18, and Cyto-19). This study confirmed that CCl4-induced liver injured serum treatment can differentiate MSCs into hepatocyte-like cells in vitro.

In the current research, we have investigated the antioxidant and cholinesterase inhibitory potentials of Rosa moschata Herrm. leaves and fruits methanolic extract (RmL.Ext and RmF.Ext) for the first time. To determine the rough estimate of phytochemical composition of extracts, the total phenolic and flavonoid contents were determined using standard methods. Moreover, the phenolic compounds present in the extracts were identified by HPLC-UV analysis. The cholinesterase activities were determined following the Ellman’s assay. The antioxidant activities of extracts were investigated using DPPH and ABTS assays. Significant anticholinesterase potentials were exhibited by RmL.Ext with IC50 of 40 and 110 µg/ml against AChE and BChE respectively. In addition, RmL.Ext also scavenged the DPPH (IC50 = 360 µg/ml) and ABTS (IC50 = 105 µg/ml) free radicals. Comparatively, the leaves extract was more potent than fruits extract. Malic acid, chlorogenic acid, quercetin, rutin, pyrogallol, mandelic acid, hydroxybenzoic acid, and morin were identified as the possible potent antioxidants present in extract. Based on the current results of the study, it may be inferred that RmL.Ext and RmF.Ext of R. moschata are rich in bioactive compounds responsible for the free radicals scavenging and cholinesterases inhibition and this plant may be a valuable candidate for the treatment of neurodegenerative disorders, like Alzheimer’s disease. However, further investigation in terms of isolation of bioactive compounds and their screening of toxicological effects in animal models are needed to validate the observed results.

For several decades air pollution has been recognized to hit drastically the skin of human body. Air pollutants predominantly accountable for aging, oxidative damage, and inflammatory allergic reactions led to psoriasis, dermatitis, acne, and skin cancer owing to the impaired functions of DNA, proteins, and lipid biomolecules. Elevated air pollution and its detrimental effects along with variations in physiological parameters of the skin are verily the scaffold for anti-pollution assertions and could be recognized as markers. The present article encompasses the salient features of air pollution and UV radiations besides dreadful effects on human skin physiological parameters and some anti-pollution approaches.

Continuous contact of air pollutants on human skin has produced early ageing and led to roughness, dryness, poor elasticity, increased wrinkling and irregular pigmentation of the skin. The present study was carried out to fabricate an anti-pollution cosmetic-based w/o/w multiple emulsion containing D-biotin, prepared by a one-step formation as protection for the skin against the effects of air pollutants and further used for in vitro and in vivo evaluation. A similar multiple emulsion without D-biotin was also prepared in the same way. Each of the tested multiple emulsions (CB2 and CF2) was applied to the cheeks of 15 human volunteers for a testing period of 90 days. Both emulsions were assessed for skin melanin, erythema, hydration and elasticity values. The droplet sizes of CB2 and CF2 stored in the dark were 10.92 ± 0.23 and 15.4 ± 0.12 μm, respectively. The size distributions of CB2 and CF2 ranged from 4.55 ± 0.1 to 26.056 ± 0.34 μm and from 1.97.16 ± 1.2 to 45.13 ± 2.17 μm, respectively. The rheological parameters showed non-Newtonian, pseudo-plastic and shear thinning behaviour, while pH remained within an acceptable range. No considerable physical changes were observed. The skin irritation testing indicated that CB2 and CF2 were safe after application and did not cause any skin irritation. The skin melanin, erythema, moisture and elasticity values of both the right and left cheeks of the volunteers were measured at baseline visits: 15, 30, 45, 60, 75 and 90 days of time intervals. While CB2 showed insignificant effects, therefore, it was demonstrated that CF2 decreased skin erythema content and increased skin elasticity and hydration significantly but had an insignificant effect on skin melanin content with respect to time. Good sensory attributes were also achieved. Therefore, CF2 is a promising new approach for protection of the skin from the deleterious effects of air pollutants.

A 70% ethanol extract from the root portion of Reynoutria japonica afforded one new and three known juglone derivatives, namely, 2-methoxy-6-acetyl-7-methyljuglone (1), 2-ethoxy-6-acetyl-7-methyljuglone (2), 2-methoxy-7-acetonyljuglone (3), and 3-acetyl-7-methoxy-2-methyljuglone (4) together with two phenolics (5 and 6), an anthraquinone (7), a stilbene (8) and a phthalide (9). Their structures were elucidated on the basis of comprehensive spectroscopic studies including IR, MS, and 1H, 13C, 2D NMR spectra. Compound 3 is a new compound in nature, and compounds 4–6 have been isolated for the first time from R. japonica. The isolates were evaluated for their antibacterial activity against three strains (43504, 51, and 26695) of Helicobacter pylori. The four isolated juglone derivatives (1–4) showed potent growth inhibitory activity. Among them, compounds 1–3 exhibited stronger inhibitory activity than those of the positive controls, juglone and metronidazole, for the three strains and that of another reference, clarithromycin, for the 43504 and 51 strains. Specifically, the new juglone compound 3 displayed the most potent antibacterial activity against all three strains, 43504, 51, and 26695, with MIC values of 0.06, 0.06 and 0.13 μM, respectively, and MIC50 values of 0.14, 0.11 and 0.15 μM, respectively.

Background Epidermal growth factor receptor (EGFR) is a cellular oncoprotein which is overexpressed in many human cancers including a subset of endometrial cancers. Immunohistochemical (IHC) expression of EGFR has been investigated in previous studies; Role of EGFR in endometrial carcinoma as a prognostic biomarker has not been studied in our population; therefore we aimed to evaluate the expression of EGFR in cases of endometrial carcinoma in loco-regional population and its association with histologic variables. Methods Total 89 cases of endometrial carcinoma were selected from records of pathology department archives. All patients underwent surgeries at Liaquat National hospital, Karachi from January 2012 till December 2017 over a period of 6 years. Slides of all cases were retrieved and reviewed by two senior histopathologists and pathologic characteristics were evaluated. Moreover, representative tissue blocks of all 89 cases were selected for EGFR immunohistochemistry. Results 73% (65 cases) showed no EGFR expression, while 21.3% (19 cases) showed low EGFR expression and 5.6% (5 cases) revealed high EGFR expression. Significant association of EGFR expression was noted with histologic type. Serous carcinoma and carcinosarcoma showed high expression of EGFR. On the other hand, no significant association of EGFR with other histopathologic parameters was found. Conclusion Overall, we found a low EGFR expression in endometrial carcinoma in our population without any significant pathological association except for its high expression in serous carcinoma and carcinosarcoma; however, more large scale studies are warranted to validate these findings.

Objectives T/E fusion results in constitutive expression of ERG oncoprotein resulting in enhanced proliferation and invasive potential of prostatic cancer cells. In the present study we aimed to evaluate the ERG overexpression in 78 cases prostate acinar adenocarcinoma and its association with other prognostic parameters. Results ERG protein expression was noted in 39.7% (31 cases), out of which 3 cases (3.8%) showed low ERG expression, 10 cases (12.8%) showed intermediate expression and 18 cases (23.1%) revealed high ERG expression. Significant association of ERG expression was noted with gleason score (p = 0.009), WHO grade group (p = 0.008) and perineural invasion (p = 0.043). We found a significant proportion of our patients of prostatic acinar adenocarcinoma to over-express ERG protein which can help in devising therapeutic protocols. Significant association of ERG protein expression with gleason score and perineural invasion signifies its prognostic significance in prostatic carcinoma. Moreover, we also suggest that molecular studies should be performed in patients with prostatic carcinoma to look for T/E fusion gene and its correlation with ERG protein expression.

Background Epidermal growth factor receptor (EGFR) is potential prognostic biomarker expressed in many human cancers. Prognostic significance of EGFR immunohistochemical expression has not been established in prostatic acinar adenocarcinoma, therefore we aimed to evaluate the frequency of expression of EGFR in prostatic adenocarcinoma and its association with other prognostic parameters. Methods The study included 123 cases of biopsy proven prostatic acinar adenocarcinoma treated at Liaquat National hospital, Karachi from January 2013 till December 2017. Paraffin blocks of all cases were retrieved; sections were cut and stained with haematoxylin and eosin. Pathologic characteristics including tumor quantification, WHO grade group, gleason score, perineural and lymphovascular invasion were evaluated. EGFR immunohistochemistry (IHC) was performed on all tissue blocks. Results Mean age of the patients included in the study was 69.05 ± 8.68 years. High gleason scores i.e. 8 & 9 were noted in 22% (27 cases) and 22.8% (28 cases) respectively. Similarly, 22.8% (28 cases) showed WHO grade group 5. 52.8% (65 cases) had > 50% tissue involvement by carcinoma and perineural invasion was seen in 37.4% (46 cases). Positive EGFR expression was noted in 18.7% (23 cases), while 81.3% (100 cases) showed negative EGFR expression. Significant association of EGFR expression was noted with gleason score (p-value =

A yttria-stabilized zirconia (YSZ, 8 mol % $${{Y}_{2} {O}_{3}}$$ ) membrane was prepared employing zirconium n-propoxide as a precursor via sol–gel method. Unlike conventional methods, hydrolyzing water was slowly released in this method through esterification of 1-propanol and glacial acetic acid. X-ray diffraction verified that YSZ membrane was partially transformed to the tetragonal phase. Ten times dip-coated membrane thickness was about 742 nm, determined by field emission scanning electron microscopy (FE-SEM) micrograph. Brunauer–Emmet–Teller measured average pore size of unsupported YSZ from gas adsorption and desorption indicating two modes centered at 2.66 and 2.38 nm. Crystallite size (D) as calculated from Scherrer’s equation was 6.8, 12.23, and 13.61 nm for unsupported YSZ powder before and after calcination, respectively, at 25, 500, and $${600\,^{\circ} {C}}$$ . Thermogravimetric analysis showed that the mass loss of the samples calcined at temperatures higher than $${600\,^{\circ} {C}}$$ had no significant differences indicating the completion of loss of organics. Supported YSZ membrane was tested by a gas permeation apparatus. The single gas permeance of YSZ membrane including $${\alpha-{Al}_{2} {O}_{3}}$$ was measured as $${14.89\times10^{-6}}$$ and $${1.75\times10^{-6} \,{ mol m}^{-2} { s}^{-1} { Pa}^{-1}}$$ for $${{\rm{H}}_{2}}$$ and $${{\rm {CO}}_{2}}$$ at $${300\,^{\circ} {C}}$$ , respectively. Permeance of $${{\rm{H}}_{2}}$$ and $${{\rm {CO}}_{2}}$$ through YSZ in 75:25 $${{\rm{H}}_{2}}$$ / $${{\rm {CO}}_{2}}$$ binary feed mixture was $${9.696\times10^{-6}}$$ and $${0.97\times10^{-6} \,{ mol\,m}^{-2} { s}^{-1} \,{ Pa}^{-1}}$$ , respectively, at $${300\,^{\circ} {C}}$$ . The selectivity of hydrogen in YSZ was 10. It was concluded that the membrane was highly promising for the separation of $${{\rm{H}}_{2}/{\rm {CO}}_{2}}$$ mixture from various $${{\rm{H}}_{2}}$$ -containing process streams under steam environment for high-temperature separation.

Objectives The purpose of this study was to determine the frequency of in-hospital mortality in 351 patients who developed cardiogenic shock after acute myocardial infarction and by determining this; we might find that how efficiently we could manage this serious condition in our population by knowing the factors which are associated with high mortality after cardiogenic shock. Moreover impact of early revascularization like thrombolytic therapy or angioplasty was also evaluated. Results Mean age was 65.41 ± 7.78 years in our study. In-hospital mortality with cardiogenic shock after acute myocardial infarction was found to be 44.73%. Significant association of in-hospital mortality was noted with age, hypertension, diabetes mellitus and BMI. Patients receiving early revascularization were noted to have lower in-hospital mortality compared to those in whom revascularization was not done due to delayed presentation. This study concluded that there is a high frequency (44.73%) of in-hospital mortality in patients with cardiogenic shock after acute myocardial in our population. So, we recommend that for achieving a good outcome and to reduce in-hospital mortality; in addition to rapid diagnosis of this condition, underlying risk factors like hypertension and diabetes should be evaluated and managed accordingly and early revascularization should be done when possible.

Background p16 and p53 genes are frequently mutated in triple negative breast cancer & prognostic value of these mutations have been shown; however, their role as immunohistochemical overexpression has not been fully validated. Therefore we aimed to evaluate the association of p16 and p53 overexpression in triple negative breast cancer with various prognostic parameters. Methods Total 150 cases of triple negative breast cancers were selected from records of pathology department archives that underwent surgeries at Liaquat National hospital, Karachi from January 2008 till December 2013. ER, PR and Her2neu immunohistochemistry were re-performed to confirm triple negative status. p16 & p53 immunohistochemistry was performed on all cases and association with various clinicopathologic parameters was determined. Results Mean age of the patients involved in the study was 48.9 years. Most of the patients presented at stage T2 with a high mean ki67 index i.e. 46.9%. 42.7% of cases had nodal metastasis. Although 84% cases were of invasive ductal carcinoma; however a significant proportion of cases were of metaplastic histology (9.3%). Fifty-one percent (76 cases) of cases showed positive p53 expression while 49% (74 cases) were negative. Higher percentage of p53 expression was found to correlate with higher T stage, high ki67 index and higher nodal stage. On the other hand, strong intensity of p53 expression was positively correlated with higher tumor grade and ki67 index. Seventy-one percent (98 cases) of cases showed positive p16 expression, whereas 24.8% (34 cases) were negative and 3.6% (5 cases) showed focal positive p16 expression. However, no significant association was found between p16 expression and various clinical and pathologic parameters. Similarly, no significant association of either p16 or p53 over-expression was noted with recurrence status of patients. Conclusion On the basis of significant association of p53 over-expression with worse prognostic factors in triple negative breast cancer, therefore we suggest that more large scale studies are needed to validate this finding in loco-regional population. Moreover, high expression of p16 in triple negative breast cancer suggests a potential role of this biomarker in triple negative breast cancer pathogenesis which should be investigated with molecular based research in our population.

Objectives Gastrointestinal stromal tumors (GISTs) are rare tumors of gastrointestinal tract, prognosis of which largely depends upon histopathologic characteristics of resection specimens, which were not widely studied in our population. Therefore we aimed to evaluate the histopathologic characteristics of GISTs in our population and their prognostic grouping according to college of American pathologist’s guidelines. Results Mean age of patients was 53.4 years (18–71 years). 92% of cases were of primary GISTs and stomach was the most common site (57.7%). 75% of cases were of spindle cell morphology and 53.8% belonged to high risk prognostic group. Comparison of stomach and intestinal GISTs showed that intestinal GISTs were found to be of high grade (70%) and of high risk prognostic group (75 and 80%) compared to stomach GISTs (43% were of high risk prognostic group), however this finding was not statistically significant. GISTs are infrequent gastrointestinal tumors but early diagnosis and identification of adverse histological features are key to successful treatment. We found a large majority of GISTs to be located in stomach, however intestinal GISTs were found more likely to be associated with adverse prognostic parameters. However more large scale studies are warranted to establish this finding. Electronic supplementary material The online version of this article (10.1186/s13104-018-3562-8) contains supplementary material, which is available to authorized users.

Objective Immunohistochemical over expression of p53 is considered as a marker of poor prognosis in many cancers. Therefore, we aimed to evaluate immunohistochemical overexpression of p53 in 121 cases of head and neck Squamous cell carcinoma and its association with various clinicopathologic features and survival. Results Total 66.1% (80 cases) expressed positive p53 expression, 34% (29 cases) revealed no p53 expression, while focal positive p53 expression was noted in 9.9% (12 Cases). Moreover, high p53 expression (> 70%) was noted in 26.4% (32 cases), while 19% (23 cases) showed 51–70% p53 expression. On the basis of intensity of p53 staining; strong p53 expression was noted in 39.7% (48 cases), while 24.8% (30 cases) and 10.7% (13 cases) revealed intermediate and weak p53 expression respectively. Significant association of p53 intensity of expression with extranodal extension and higher tumor grade (grades II and III) was noted. p53 is useful prognostic biomarker in head and neck Squamous cell carcinoma and therefore we suggest that more large scale studies are needed to evaluate its prognostic significance in our population. Electronic supplementary material The online version of this article (10.1186/s13104-018-3547-7) contains supplementary material, which is available to authorized users.

Objectives A rising frequency of colorectal carcinoma has been noted in recent years in Pakistan. In the present study, we aimed to evaluate clinicopathologic features of colorectal carcinoma in our population so that protocols could be developed to stratify patients that may require further biomarker/molecular testing. Furthermore, histological features which predict higher T and N stage were also evaluated. Results Median age at diagnosis was 54.5 (19–85) years. 79% cases were of conventional adenocarcinoma while 13% cases were of mucinous carcinoma. Most of the cases were at T3 stage (81%), while 27 and 68% of cases revealed lymphovascular invasion and nodal metastasis respectively. Mucinous and signet ring tumors were associated with a higher N stage. Pre-existing polyp was associated with lower T and N stage. We found a high proportion of our cases to present at advanced T-stage. Tumor grade and lymphovascular invasion were found to be associated with higher N-stage while tumor infiltrating lymphocytes was associated with lower T and N-stage. Moreover, a high frequency of mucinous differentiation may be linked to microsatellite instability in our cases of colorectal carcinoma; therefore, we suggest that microsatellite instability testing in colorectal carcinoma should be evaluated in our setup.

Background Prognosis of breast cancer and success of therapeutic interventions largely rely on the clinico-pathologic and biological characteristics of the tumor and vary due to the heterogeneous nature of breast cancers. The aim of this study was to determine the frequency and prognostic parameters of luminal breast cancers in our population to devise targeted and personalized therapeutic regimens tailored to the needs of the loco-regional population. Methods A retrospective cross-sectional study including 1951 cases of primary breast cancer treated at Liaquat National Hospital Karachi was conducted during the year 2011–2016. The clinico-pathologic characteristics were observed and semiquantitative immunohistochemical analysis was performed to study the luminal subtypes A and B. The cross-tabulated statistics of the observed characteristics were performed between the two subtypes. The significance level of each characteristic was estimated utilizing the chi-square test. Results Luminal cancers comprised 62.7% of the total number of cases diagnosed with breast cancers in the study period. Out of these 1224 cases of luminal cancers, 845 cases (69%) were luminal B, while 379 (31%) cases were of luminal A. Luminal B cancers were significantly more common in younger age groups as compared to luminal A cancers. Comparison of the two subtypes of luminal breast cancers revealed significant differences. Luminal B cancers were associated with higher grade (26% grade III in luminal B compared to 8% in luminal A), micropapillary histology, and high frequency of nodal metastasis (54 vs. 43%). Conclusions Luminal B comprised the most frequent subtype of breast cancer in our study and they were found more constantly in a younger age group. Moreover, they were associated with adverse clinico-histologic parameters like higher grade and nodal metastasis. Therefore, we suggest that, despite lack of widespread availability of molecular studies in our setup, IHC-based typing should be done in every case of breast cancer to individualize therapy.

Background Intraoperative consultation is an important tool for the evaluation of the upper aerodigestive tract (UAT) malignancies. Although frozen section analysis is a preferred method of intra-operative consultation, however in resource limited countries like Pakistan, this facility is not available in most institutes; therefore, we aimed to evaluate the diagnostic accuracy of touch imprint cytology for UAT malignancies using histopathology of the same tissue as gold standard. Methods The study involved 70 cases of UAT lesions operated during the study period. Intraoperatively, after obtaining the fresh biopsy specimen and prior to placing them in fixative, each specimen was imprinted on 4-6 glass slides, fixed immediately in 95% alcohol and stained with Hematoxylin and Eosin stain. After completion of the cytological procedure, the surgical biopsy specimen was processed. The slides of both touch Imprint cytology and histopathology were examined by two consultant histopathologists. Results The result of touch imprint cytology showed that touch imprint cytology was diagnostic in 68 cases (97.1%), 55 (78.6%) being malignant, 2 cases (2.9%) were suspicious for malignancy, 11 cases (15.7%) were negative for malignancy while 2 cases (2.9%) were false negative. Amongst the 70 cases, 55 cases (78.6%) were malignant showing squamous cell carcinoma in 49 cases (70%), adenoid cystic carcinoma in 2 cases (2.9%), non-Hodgkin lymphoma 2 cases (2.9%), Mucoepidermoid carcinoma 1 case (1.4%), spindle cell sarcoma in 1 case (1.4%). Two cases (2.9%) were suspicious of malignancy showing atypical squamoid cells on touch imprint cytology, while 13 cases (18.6%) were negative for malignancy, which also included 2 false negative cases. The overall diagnostic accuracy of touch imprint cytology came out to be 96.7% with a sensitivity and specificity of 96 and 100%, respectively while PPV and NPV of touch imprint cytology was found to be 100 and 84%, respectively. Conclusion Our experience in this study has demonstrated that touch imprint cytology provides reliable specific diagnoses and can be used as an adjunct to histopathology, particularly in developing countries, where the facility of frozen section is often not available, since a rapid preliminary diagnosis may help in the surgical management planning.

Background Despite advances in the gene-set enrichment analysis methods; inadequate definitions of gene-sets cause a major limitation in the discovery of novel biological processes from the transcriptomic datasets. Typically, gene-sets are obtained from publicly available pathway databases, which contain generalized definitions frequently derived by manual curation. Recently unsupervised clustering algorithms have been proposed to identify gene-sets from transcriptomics datasets deposited in public domain. These data-driven definitions of the gene-sets can be context-specific revealing novel biological mechanisms. However, the previously proposed algorithms for identification of data-driven gene-sets are based on hard clustering which do not allow overlap across clusters, a characteristic that is predominantly observed across biological pathways. Results We developed a pipeline using fuzzy-C-means (FCM) soft clustering approach to identify gene-sets which recapitulates topological characteristics of biological pathways. Specifically, we apply our pipeline to derive gene-sets from transcriptomic data measuring response of monocyte derived dendritic cells and A549 epithelial cells to influenza infections. Our approach apply Ward’s method for the selection of initial conditions, optimize parameters of FCM algorithm for human cell-specific transcriptomic data and identify robust gene-sets along with versatile viral responsive genes. Conclusion We validate our gene-sets and demonstrate that by identifying genes associated with multiple gene-sets, FCM clustering algorithm significantly improves interpretation of transcriptomic data facilitating investigation of novel biological processes by leveraging on transcriptomic data available in the public domain. We develop an interactive ‘Fuzzy Inference of Gene-sets (FIGS)’ package (GitHub: https://github.com/Thakar-Lab/FIGS) to facilitate use of of pipeline. Future extension of FIGS across different immune cell-types will improve mechanistic investigation followed by high-throughput omics studies. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1669-x) contains supplementary material, which is available to authorized users.