Comparative proteomics and global genome-wide expression data implicate role of ARMC8 in lung cancer

Amin, Asif,Bukhari, Shoiab,Mokhdomi, Taseem A,Anjum, Naveed,Wafai, Asrar H,Wani, Zubair,Manzoor, Saima,Koul, Aabid M,Amin, Basit,Qurat-ul-Ain, Qurat-ul-Ain,Qazi, Hilal,Tyub, Sumira,Lone, Ghulam Nabi,Q Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.9

Background: Cancer loci comprise heterogeneous cell populations with diverse cellular secretions. Therefore, disseminating cancer-specific or cancer-associated protein antigens from tissue lysates could only be marginally correct, if otherwise not validated against precise standards. Materials and Methods: In this study, 2DE proteomic profiles were examined from lysates of 13 lung-adenocarcinoma tissue samples and matched against the A549 cell line proteome. A549 matched-cancer-specific hits were analyzed and characterized by MALDI-TOF/MS. Results: Comparative analysis identified a total of 13 protein spots with differential expression. These proteins were found to be involved in critical cellular functions regulating pyrimidine metabolism, pentose phosphate pathway and integrin signaling. Gene ontology based analysis classified majority of protein hits responsible for metabolic processes. Among these, only a single non-predictive protein spot was found to be a cancer cell specific hit, identified as Armadillo repeat-containing protein 8 (ARMC8). Pathway reconstruction studies showed that ARMC8 lies at the centre of cancer metabolic pathways. Conclusions: The findings in this report are suggestive of a regulatory role of ARMC8 in control of proliferation and differentiation in lung adenocarcinomas.

Antiproliferative Activity of Lavatera cashmeriana- Protease Inhibitors towards Human Cancer Cells

Rakashanda, Syed,Qazi, Asif Khurshid,Majeed, Rabiya,Rafiq, Shaista,Dar, Ishaq Mohammad,Masood, Akbar,Hamid, Abid,Amin, Shajrul Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.6

Background: Proteases play a regulatory role in a variety of pathologies including cancer, pancreatitis, thromboembolic disorders, viral infections and many others. One of the possible strategies to combat these pathologies seems to be the use of protease inhibitors. LC-pi I, II, III and IV (Lavatera cashmerian-protease inhibitors) have been found in vitro to strongly inhibit trypsin, chymotrypsin and elastase, proteases contributing to tumour invasion and metastasis, indicated possible anticancer effects. The purpose of this study was to check in vitro anticancer activity of these four inhibitors on human lung cancer cell lines. Material and Methods: In order to assess whether these inhibitors induced in vitro cytoxicity, SRB assay was conducted with THP-1 (leukemia), NCIH322 (lung) and Colo205, HCT-116 (colon) lines. Results: LC-pi I significantly inhibited the cell proliferation of all cells tested and also LC-pi II was active in all except HCT-116. Inhibition of cell growth by LC-pi III and IV was negligible. $IC_{50}$ values of LC-pi I and II for NCIH322, were less compared to other cell lines suggesting that lung cancer cells are more inhibited. Conclusion: These investigations might point to future preventive as well as curative solutions using plant protease inhibitors for various cancers, especially in the lung, hence warranting their further investigation.

Simultaneous feature selection and discretization based on mutual information

Sharmin, Sadia,Shoyaib, Mohammad,Ali, Amin Ahsan,Khan, Muhammad Asif Hossain,Chae, Oksam Elsevier 2019 Pattern recognition Vol.91 No.-

<P><B>Abstract</B></P> <P>Recently mutual information based feature selection criteria have gained popularity for their superior performances in different applications of pattern recognition and machine learning areas. However, these methods do not consider the correction while computing mutual information for finite samples. Again, finding appropriate discretization of features is often a necessary step prior to feature selection. However, existing researches rarely discuss both discretization and feature selection simultaneously. To solve these issues, Joint Bias corrected Mutual Information (JBMI) is firstly proposed in this paper for feature selection. Secondly, a framework namely modified discretization and feature selection based on mutual information is proposed that incorporates JBMI based feature selection and dynamic discretization, both of which use a <I>χ</I> <SUP>2</SUP> based searching method. Experimental results on thirty benchmark datasets show that in most of the cases, the proposed methods outperform the state-of-the-art methods.</P> <P><B>Highlights</B></P> <P> <UL> <LI> We address discretization and feature selection jointly with a single criteria. </LI> <LI> The proposed discretization method is dynamic and independent of classification algorithms. </LI> <LI> The amount of errors introduced for Relevancy, Redundancy and Complementary Information are derived analytically. </LI> <LI> It is also analytically shown that Relevancy, Redundancy and Complementary follows χ<SUP>2</SUP>-distribution. </LI> <LI> A χ<SUP>2</SUP>-based search is introduced to select a small set of features and to discretize them with small number of intervals. </LI> </UL> </P>

Electrophoretic deposition of PVA coated hydroxyapatite on 316L stainless steel

Nida Iqbal,Rabia Nazir,Anila Asif,Aqif Anwar Chaudhry,Muhammad Akram,Goh Yi Fan,Aftab Akram,Rashid Amin,박성하,Rafaqat Hussain 한국물리학회 2012 Current Applied Physics Vol.12 No.3

Polyvinyl alcohol (PVA) coated hydroxyapatite was deposited onto a 316L stainless steel substrate by electrophoretic deposition. Deposition was carried out in a methanol suspension at pH 5.5 using a graphite rod as an anode. Parameters such as PVA concentration, deposition voltage and time were optimized to achieve a homogeneous, crack-free adhesive coating. Techniques such as X-ray diffraction and Fourier transform infrared spectroscopy were used to study the phase composition of the coated materials and the stability of hydroxyapatite in the presence of PVA.

First-principles investigation of structural, elastic, electronic and magnetic properties of Be0.75Co0.25Y (Y=S, Se and Te) compounds

W. Tanveer,M.A. Faridi,N.A. Noor,Asif Mahmood,B. Amin 한국물리학회 2015 Current Applied Physics Vol.15 No.11

We have theoretically investigated the structural, elastic, electronic and magnetic properties of Be0.75Co0.25Y (Y=S, Se and Te) alloys, in their zinc-blend phase. This study is carried out by using the fullpotential augmented plane wave plus local orbitals method within the density functional theory. Foe computing the exchange-correlation potential, the Wu and Cohen generalized gradient approximation is employed to calculate structural and elastic properties whereas the modified Becke and Johnson potential local density approximation is utilized to examine electronic and magnetic properties. By minimizing the total energy in paramagnetic (PM) and ferromagnetic (FM) phases, it is found the studied compounds are stable in FM structure. The mechanical behavior of the studied compounds is reported with the calculation of shear modulus, Young's modulus, and Poisson's ratio provides. Such mechanical aspects might be useful for the experimentalists to study the mechanical properties upon alloying BeY compounds with Co. We also compute electronic structures, density of states (total and partial), pdexchange splitting and magnetic moments. Moreover, bond nature is studied by estimating the spin polarized charge densities of Be0.75Co0.25Y (Y=S, Se and Te).

Relative Expression of Apocarotenoid Biosynthetic Genes in Developing Stigmas of Crocus sativus L.

IqbaLMzr, Javid,Ahmed, Nazeer,Mokhdomi, Tassem Ahmad,Wafai, Asrar Hussain,Wani, Sajad Hassan,Bukhari, Shoiab,Amin, Asif,Qadri, Raies Ahmad 한국작물학회 2013 Journal of crop science and biotechnology Vol.16 No.3

Saffron, the desiccated stigmas of Crocus sativus, is recognized for its attractive color, flavor, and aroma which are due to the accumulation of crocin, picrocrocin, and safranal, respectively. HPLC analysis demonstrated maximum apocarotenoid accumulation during the fully developed scarlet stage of stigma development followed by the orange and yellow stages of stigma development. Reverse Transcription-PCR analysis revealed a concurrent expression pattern of CsZCD and CsLYC genes in a developmental stage-specific manner. However, CsBCH and CsGT2 genes were specifically expressed during the mature, scarlet stage of stigma development. Real-Time PCR analysis showed a sharp increase in gene expression of CsLYC gene during stigma development indicative of its possible regulatory role in apocarotenoid biosynthesis or stigma development. Results suggest that genetic manipulation of this gene can help to improve the quality of stigma in saffron; besides highlighting its potential to monitor stigma development during in vitro experimentation.

Relative Expression of Apocarotenoid Biosynthetic Genes in Developing Stigmas of Crocus sativus L.

Javid IqbaLMzr,Raies Ahmad Qadri,Nazeer Ahmed,Tassem Ahmad Mokhdomi,Asrar Hussain Wafai,Sajad Hassan Wani,Shoiab Bukhari,Asif Amin 한국작물학회 2013 Journal of crop science and biotechnology Vol.16 No.3

Saffron, the desiccated stigmas of Crocus sativus, is recognized for its attractive color, flavor, and aroma which are due to the accumulation of crocin, picrocrocin, and safranal, respectively. HPLC analysis demonstrated maximum apocarotenoid accumulation during the fully developed scarlet stage of stigma development followed by the orange and yellow stages of stigma development. Reverse Transcription-PCR analysis revealed a concurrent expression pattern of CsZCD and CsLYC genes in a developmental stagespecific manner. However, CsBCH and CsGT2 genes were specifically expressed during the mature, scarlet stage of stigma development. Real-Time PCR analysis showed a sharp increase in gene expression of CsLYC gene during stigma development indicative of its possible regulatory role in apocarotenoid biosynthesis or stigma development. Results suggest that genetic manipulation of this gene can help to improve the quality of stigma in saffron; besides highlighting its potential to monitor stigma development during in vitro experimentation

iCBLS: An interactive case-based learning system for medical education

Ali, Maqbool,Han, Soyeon Caren,Bilal, Hafiz Syed Muhammad,Lee, Sungyoung,Kang, Matthew Jee Yun,Kang, Byeong Ho,Razzaq, Muhammad Asif,Amin, Muhammad Bilal Elsevier 2018 International journal of medical informatics Vol.109 No.-

<P><B>Abstract</B></P> <P>Medical students should be able to actively apply clinical reasoning skills to further their interpretative, diagnostic, and treatment skills in a non-obtrusive and scalable way. <I>Case-Based Learning</I> (CBL) approach has been receiving attention in medical education as it is a student-centered teaching methodology that exposes students to real-world scenarios that need to be solved using their reasoning skills and existing theoretical knowledge. In this paper, we propose an interactive CBL System, called iCBLS, which supports the development of collaborative clinical reasoning skills for medical students in an online environment. The iCBLS consists of three modules: (i) <I>system administration</I> (SA), (ii) <I>clinical case creation</I> (CCC) with an innovative semi-automatic approach, and (iii) <I>case formulation</I> (CF) through intervention of medical students’ and teachers’ knowledge. Two evaluations under the umbrella of the context/input/process/product (CIPP) model have been performed with a <I>Glycemia</I> study. The first focused on the system satisfaction, evaluated by 54 students. The latter aimed to evaluate the system effectiveness, simulated by 155 students. The results show a high success rate of 70% for students’ interaction, 76.4% for group learning, 72.8% for solo learning, and 74.6% for improved clinical skills.</P> <P><B>Highlights</B></P> <P> <UL> <LI> This study describes how to foster medical trainees’ collaborative learning skills with the support of online advanced learning technologies and real-world clinical cases. </LI> <LI> Designed and developed an <I>interactive Case-Based Learning System</I> (iCBLS) for practising clinical cases before and outside the class. </LI> <LI> The iCBLS supports an innovative method to create real-world clinical cases using a semi-automatic approach. </LI> <LI> Two types of evaluations under the umbrella of the CIPP model have been performed in heterogeneous environments with a <I>Glycemia</I> study. </LI> <LI> The iCBLS achieves a success rate of more than 70% for students’ interaction, group learning, solo learning, and improving clinical skills. </LI> </UL> </P>