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author:("Khan, imra")
1.  Data Mining Strategies to Improve Multiplex Microbead Immunoassay Tolerance in a Mouse Model of Infectious Diseases 
PLoS ONE  2015;10(1):e0116262.
Multiplex methodologies, especially those with high-throughput capabilities generate large volumes of data. Accumulation of such data (e.g., genomics, proteomics, metabolomics etc.) is fast becoming more common and thus requires the development and implementation of effective data mining strategies designed for biological and clinical applications. Multiplex microbead immunoassay (MMIA), on xMAP or MagPix platform (Luminex), which is amenable to automation, offers a major advantage over conventional methods such as Western blot or ELISA, for increasing the efficiencies in serodiagnosis of infectious diseases. MMIA allows detection of antibodies and/or antigens efficiently for a wide range of infectious agents simultaneously in host blood samples, in one reaction vessel. In the process, MMIA generates large volumes of data. In this report we demonstrate the application of data mining tools on how the inherent large volume data can improve the assay tolerance (measured in terms of sensitivity and specificity) by analysis of experimental data accumulated over a span of two years. The combination of prior knowledge with machine learning tools provides an efficient approach to improve the diagnostic power of the assay in a continuous basis. Furthermore, this study provides an in-depth knowledge base to study pathological trends of infectious agents in mouse colonies on a multivariate scale. Data mining techniques using serodetection of infections in mice, developed in this study, can be used as a general model for more complex applications in epidemiology and clinical translational research.
doi:10.1371/journal.pone.0116262
PMCID: PMC4304816  PMID: 25614982
2.  Influence of Adiposity-Related Genetic Markers in a Population of Saudi Arabians Where Other Variables Influencing Obesity May Be Reduced 
Disease Markers  2014;2014:758232.
Large scale studies in Europeans have clearly identified common polymorphism affecting BMI and obesity. We undertook a genotype study to examine the impact of variants, known to influence obesity, in a sample from the Saudi Arabian population, notable for its profound combination of low mean physical activity indices and high energy intake. Anthropometry measures and genotypes were obtained for 367 Saudis, taken from King Saud University and Biomarker Screening Project in Riyadh (Riyadh Cohort). We observed large effect sizes with obesity for rs10767664 (BDNF) (OR = 1.923, P = 0.00072) and rs3751812 (FTO) (OR = 1.523, P = 0.016) in our sample and, using weighted genetic risk scores, we found strong evidence of a cumulative effect using 11 SNPs taken predominantly from loci principally affecting appetite (OR = 2.57, P = 0.00092). We used conditional analyses to discern which of our three highly correlated FTO SNPs were responsible for the observed signal, although we were unable to determine with confidence which best marked the causal site. Our analysis indicates that markers located in loci known to influence fat mass through increased appetite affect obesity in Saudi Arabians to an extent possibly greater than in Europeans. Larger scale studies will be necessary to obtain a precise comparison.
doi:10.1155/2014/758232
PMCID: PMC4251424  PMID: 25484485
3.  Enhancement of an anti-tumor immune response by transient blockade of central T cell tolerance 
Modulation of central tolerance through RANKL alters thymic output and enhances anti-tumor immunity.
Thymic central tolerance is a critical process that prevents autoimmunity but also presents a challenge to the generation of anti-tumor immune responses. Medullary thymic epithelial cells (mTECs) eliminate self-reactive T cells by displaying a diverse repertoire of tissue-specific antigens (TSAs) that are also shared by tumors. Therefore, while protecting against autoimmunity, mTECs simultaneously limit the generation of tumor-specific effector T cells by expressing tumor self-antigens. This ectopic expression of TSAs largely depends on autoimmune regulator (Aire), which is expressed in mature mTECs. Thus, therapies to deplete Aire-expressing mTECs represent an attractive strategy to increase the pool of tumor-specific effector T cells. Recent work has implicated the TNF family members RANK and RANK-Ligand (RANKL) in the development of Aire-expressing mTECs. We show that in vivo RANKL blockade selectively and transiently depletes Aire and TSA expression in the thymus to create a window of defective negative selection. Furthermore, we demonstrate that RANKL blockade can rescue melanoma-specific T cells from thymic deletion and that persistence of these tumor-specific effector T cells promoted increased host survival in response to tumor challenge. These results indicate that modulating central tolerance through RANKL can alter thymic output and potentially provide therapeutic benefit by enhancing anti-tumor immunity.
doi:10.1084/jem.20131889
PMCID: PMC4010907  PMID: 24752296
4.  Lineage tracing and cell ablation identifies a post-Aire expressing thymic epithelial cell population 
Cell reports  2013;5(1):10.1016/j.celrep.2013.08.038.
Thymic epithelial cells in the medulla (mTECs) play a critical role in enforcing central tolerance through expression and presentation of tissue-specific antigens (TSAs) and deletion of autoreactive thymocytes. TSA expression requires autoimmune regulator (Aire), a transcriptional activator present in a subset of mTECs characterized by high CD80 and MHC II expression and a lack of potential for differentiation or proliferation. Here, using an Aire-DTR transgenic line, we show that short-term ablation specifically targets Aire+ mTECs, which quickly undergo RANK-dependent recovery. Repeated ablation also affects Aire− mTECs, and using an inducible Aire-Cre fate-mapping system, we find that this results from the loss of a subset of mTECs that showed prior expression of Aire, maintains intermediate TSA expression, and preferentially migrates towards the center of the medulla. These results clearly identify a distinct stage of mTEC development and underscore the diversity of mTECs that play a key role in maintaining tolerance.
doi:10.1016/j.celrep.2013.08.038
PMCID: PMC3820422  PMID: 24095736
5.  Mammalian keratin associated proteins (KRTAPs) subgenomes: disentangling hair diversity and adaptation to terrestrial and aquatic environments 
BMC Genomics  2014;15(1):779.
Background
Adaptation of mammals to terrestrial life was facilitated by the unique vertebrate trait of body hair, which occurs in a range of morphological patterns. Keratin associated proteins (KRTAPs), the major structural hair shaft proteins, are largely responsible for hair variation.
Results
We exhaustively characterized the KRTAP gene family in 22 mammalian genomes, confirming the existence of 30 KRTAP subfamilies evolving at different rates with varying degrees of diversification and homogenization. Within the two major classes of KRTAPs, the high cysteine (HS) subfamily experienced strong concerted evolution, high rates of gene conversion/recombination and high GC content. In contrast, high glycine-tyrosine (HGT) KRTAPs showed evidence of positive selection and low rates of gene conversion/recombination. Species with more hair and of higher complexity tended to have more KRATP genes (gene expansion). The sloth, with long and coarse hair, had the most KRTAP genes (175 with 141 being intact). By contrast, the “hairless” dolphin had 35 KRTAPs and the highest pseudogenization rate (74% relative to the 19% mammalian average). Unique hair-related phenotypes, such as scales (armadillo) and spines (hedgehog), were correlated with changes in KRTAPs. Gene expression variation probably also influences hair diversification patterns, for example human have an identical KRTAP repertoire as apes, but much less hair.
Conclusions
We hypothesize that differences in KRTAP gene repertoire and gene expression, together with distinct rates of gene conversion/recombination, pseudogenization and positive selection, are likely responsible for micro and macro-phenotypic hair diversification among mammals in response to adaptations to ecological pressures.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-779) contains supplementary material, which is available to authorized users.
doi:10.1186/1471-2164-15-779
PMCID: PMC4180150  PMID: 25208914
Concerted evolution; Gene family; Keratin Associated Proteins; Keratin; Hair; Gene conversion; Recombination; Positive selection
6.  Combination of hepatocyte specific delivery and transformation dependent expression of shRNA inducing transcriptional gene silencing of c-Myc promoter in hepatocellular carcinoma cells 
BMC Cancer  2014;14(1):582.
Background
A specific targeting modality for hepatocellular carcinoma (HCC) could ideally encompass a liver cell specific delivery system of a transcriptional unit that is active only in neoplastic cells. Sendai virosomes, derived from Sendai viral envelopes, home to hepatocytes based on the liver specific expression of asialoglycoprotein receptors (ASGPRs) which are recognized by the Sendai virosomal fusion (F) proteins. As reported earlier by us and other groups, transcriptional gene silencing (TGS) does not require continuous presence of the effector siRNA/shRNA molecule and is heritable, involving epigenetic modifications, leading to long term transcriptional repression. This could be advantageous over conventional gene therapy approaches, since continuous c-Myc inactivation is required to suppress hepatocarcinoma cells.
Methods
Exploiting such virosomal delivery, the alpha-fetoprotein (AFP) promoter, in combination with various tumour specific enhancers, was used to drive the expression of shRNA directed against ME1a1 binding site of the proto-oncogene c-Myc P2 promoter, in order to induce TGS in neoplastic liver cells.
Results
The dual specificity achieved by the Sendai virosomal delivery system and the promoter/enhancer guided expression ensured that the shRNA inducing TGS was active only in liver cells that had undergone malignant transformation. Our results indicate that such a bimodal therapeutic system induced specific activation of apoptosis in hepatocarcinoma cells due to heterochromatization and increased DNA methylation of the CpG islands around the target loci.
Conclusions
The Sendai virosomal delivery system, combined with AFP promoter/enhancer expression machinery, could serve as a generalized mechanism for the expression of genes deleterious to transformed hepatocarcinoma cells. In this system, the epigenetic suppression of c-Myc could have an added advantage for inducing cell death in the targeted cells.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2407-14-582) contains supplementary material, which is available to authorized users.
doi:10.1186/1471-2407-14-582
PMCID: PMC4153911  PMID: 25108398
Hepatocellular carcinoma; Sendai virosome; Asialoglycoprotein receptors; Transcriptional gene silencing; shRNA; c-Myc; Alpha-fetoprotein; Heterochromatization; DNA methylation
7.  Primary Omental Torsion Is a Diagnostic Challenge in Acute Abdomen—a Case Report and Literature Review 
The Indian Journal of Surgery  2013;75(4):255-257.
Torsion of greater omentum is a rare cause of acute abdominal pain. It can be primary or secondary. Secondary omental torsions are associated with a number of preexisting conditions like inguinal hernia (most common), tumours, cysts, internal or external herniation, foci of intra-abdominal inflammation and postsurgical wound or scarring. Torsion of omentum causes twisting along its long axis resulting in impaired blood supply. This condition is rare and predominant in males. Most patients are middle-aged adults. It clinically mimics acute appendicitis. If evaluated properly and diagnosed in time, good results can be achieved. We are presenting herewith a case of primary greater omental torsion and review of available literature.
doi:10.1007/s12262-013-0807-6
PMCID: PMC3726828  PMID: 24426445
Omental torsion; Greater omental torsion; Primary omental torsion; Secondary omental torsion
8.  An Energy Efficient Simultaneous-Node Repositioning Algorithm for Mobile Sensor Networks 
The Scientific World Journal  2014;2014:785305.
Recently, wireless sensor network (WSN) applications have seen an increase in interest. In search and rescue, battlefield reconnaissance, and some other such applications, so that a survey of the area of interest can be made collectively, a set of mobile nodes is deployed. Keeping the network nodes connected is vital for WSNs to be effective. The provision of connectivity can be made at the time of startup and can be maintained by carefully coordinating the nodes when they move. However, if a node suddenly fails, the network could be partitioned to cause communication problems. Recently, several methods that use the relocation of nodes for connectivity restoration have been proposed. However, these methods have the tendency to not consider the potential coverage loss in some locations. This paper addresses the concerns of both connectivity and coverage in an integrated way so that this gap can be filled. A novel algorithm for simultaneous-node repositioning is introduced. In this approach, each neighbour of the failed node, one by one, moves in for a certain amount of time to take the place of the failed node, after which it returns to its original location in the network. The effectiveness of this algorithm has been verified by the simulation results.
doi:10.1155/2014/785305
PMCID: PMC4134831  PMID: 25152924
9.  Competent statistical programmer: Need of business process outsourcing industry 
Over the last two decades Business Process Outsourcing (BPO) has evolved as much mature practice. India is looked as preferred destination for pharmaceutical outsourcing over a cost arbitrage. Among the biometrics outsourcing, statistical programming and analysis required very niche skill for service delivery. The demand and supply ratios are imbalance due to high churn out rate and less supply of competent programmer. Industry is moving from task delivery to ownership and accountability. The paradigm shift from an outsourcing to consulting is triggering the need for competent statistical programmer. Programmers should be trained in technical, analytical, problem solving, decision making and soft skill as the expectations from the customer are changing from task delivery to accountability of the project. This paper will highlight the common issue SAS programming service industry is facing and skills the programmers need to develop to cope up with these changes.
doi:10.4103/2229-3485.134300
PMCID: PMC4073556  PMID: 24987578
Business process outsourcing; statistical programmer; skill
10.  Renal allograft transplant recipient with ruptured hydatid native kidney 
Urology Annals  2014;6(3):267-269.
Echinococcosis of the kidneys in a renal transplant recipient is extremely rare and its occurrence being related to immunosuppression is a possibility which needs further characterisation. Ruptured renal hydatid in a renal transplant recipient is not reported so far to our best knowledge. We present a 42-year-old renal allograft receipient who presented one year after transplant with left flank pain, palpable left lumbar mass and gross hydatiduria. Investigations revealed a ruptured native hydatid kidney. Patient was managed with a combination of chemotherapy and left native nephrectomy and discharged in a satisfactory condition.
doi:10.4103/0974-7796.134302
PMCID: PMC4127872  PMID: 25125908
Hydatid cyst; hydatiduria; renal transplant
11.  Polycythemia, increased erythropoietin levels in a patient with renal lymphoma 
A young male presented to our clinic with 3 months history of shortness of breathness and progressive distension of abdomen. On investigations, patient had renal failure, polycythemia and nephromegaly. A diagnosis of non-Hodgkin's lymphoma was made on renal and lymph node biopsy. Serum erythropoietin concentrations were physiologically inappropriate. – Erythropoietin immunohistochemistry on renal tissue samples demonstrated positive staining for tumor cells. This patient was managed as a case of infiltrative lymphoproliferative disorder with kidney involvement having polycythemia owing to paraneoplastic Erythropoietin production and possibly local hypoxia produced by tumor cells. With maximum efforts, we could not find such an association in the literature.
doi:10.4103/2277-9175.135417
PMCID: PMC4139984  PMID: 25161994
Lymphoma; polycythemia; renal failure
12.  Application of Ethnobotanical Indices on the Use of Traditional Medicines against Common Diseases 
The present study was aimed at documenting the detailed ethnomedicinal knowledge of an unexplored area of Pakistan. Semistructured interviews were taken with 55 informants randomly chosen regarding detailed ethnomedicinal and sociocultural information. The study exposed 67 medicinal plant species used to prepare 110 recipes and the major modes of herbal formulation were decoction and powdering (20% each). The disease categories with the highest Fic values were gastrointestinal and dermatological (0.87 each). The study determined 3 plant species, i.e., Acacia modesta Wall., Caralluma tuberculata R.Br., and Withania somnifera (L.) Dunal with a FL of 100%. DMR results showed that Olea ferruginea (Sol.) Steud. ranked first, Morus alba L. ranked second, and Melia azedarach L. ranked third. Among the 55 informants, the male concentration was high (61%) and most of them were over 40 years old while a leading quantity of respondents (45%) was uneducated. There is a dire need to take necessary steps for the conservation of important medicinal plants by inhibiting overgrazing and providing alternate fuel resources. Young generations should be educated regarding the importance of ethnomedicinal knowledge and plants with high Fic and FL values should be further checked chemically and pharmacologically for future exploration of modern medicine.
doi:10.1155/2014/635371
PMCID: PMC4055084  PMID: 24963328
13.  Investigation of Calpain 10 (rs2975760) gene polymorphism in Asian Indians with Gestational Diabetes Mellitus 
Meta Gene  2014;2:299-306.
Background
Type 2 Diabetes Mellitus (T2DM) and Gestational Diabetes Mellitus (GDM) are part of a heterogeneous and complex metabolic group of disorders that share common pathophysiological circumstances, including β-cell dysfunction and insulin resistance. The protein Calpain 10 (CAPN10) plays a role in glucose metabolism, pancreatic β-cell insulin secretion, and thermogenesis.
Objective
Polymerase Chain Reaction–Restriction Fragment Length Polymorphism (PCR–RFLP) based genotyping of CAPN10 (rs2975760) polymorphism was carried out in T2DM and GDM with suitable controls for each of the pathologies from the same population. Genomic DNA was isolated from 787 participants, including 250 cases of T2DM, 287 pregnant women, of which 137 were identified as having GDM and the remaining 150 were confirmed as non-GDM, and 250 healthy control volunteers, and association analysis was carried out for genotypes and alleles.
Results
In the present study, T2DM was compared with healthy controls and was not found to be associated with the CAPN10 C allele (odds ratio, OR: 1.09; 95% CI = 0.8011–1.484; p = 0.5821). GDM also did not show any association when compared with non-GDM (OR: 1.124; 95% CI = 0.7585–1.667; p = 0.5606) respectively.
Conclusion
Our study suggests that the CAPN10 (rs2975760) polymorphism scrutinized in this study is not associated with T2DM and GDM.
Highlights
•In this study Calpain 10 (CAPN10) gene was carried out with Type 2 Diabetes Mellitus (T2DM) and Gestational Diabetes Mellitus (GDM). T2DM and GDM are different etiologies of the same complex diseases, frequently coexisting disorders and major components of metabolic syndrome that cause a substantial public health and economic burden worldwide.•In this study T2DM, GDM are subsequently studied with rs2975760 polymorphism in CAPN10 gene.•Molecular Analysis were performed by PCR-RFLP analysis.•A total of 787 samples were included.
doi:10.1016/j.mgene.2014.03.001
PMCID: PMC4287813  PMID: 25606412
Type 2 Diabetes Mellitus (T2DM); Gestational Diabetes Mellitus (GDM); CAPN10; PCR–RFLP; Asian Indians
14.  A54T polymorphism in the fatty acid binding protein 2 studies in a Saudi population with type 2 diabetes mellitus 
Background
Fatty acid-binding protein 2 (FABP2) is an intracellular protein expressed exclusively in the enterocytes of proximal small intestine. FABP2 has a high affinity for saturated and unsaturated long-chain fatty acids and is believed to be involved in the absorption and transport of dietary fatty acids.
Methods
This is a case–control study conceded in 438 T2DM cases and 460 subjects with normal glucose levels and non-obese considered as healthy controls. Allelic discrimination was performed using TaqMan single-nucleotide polymorphism was carried out by real time-polymerase chain reaction (RT-PCR) assays using purified DNA.
Results
Clinical data and anthropometric measurements except age, glucose levels and lipid profile of the patients were significantly different from those of the controls (p < 0.05). Statistical analyses failed to show any type of significant association of the polymorphism between cases and controls. However logistic regression analyses was suggests that the TT genotype is significantly associated with male patients (p = 0.001). None of the allele or genotypes of FABP2 A54T was associated with T2DM cases versus the controls (AT genotype, OR = 0.85 (0.64-1.12), p = 0.25; TT genotype, OR = 0.66 (0.39-1.11), p = 0.11; T allele, 0.82 (0.67-1.02), p = 0.08).
Conclusion
In conclusion, this study suggests that the above named variant in FABP2 gene is not potential contributor to the risk of T2DM and related traits in a Saudi population. However TT genotype is a risk factor for the disease in males.
doi:10.1186/1476-511X-13-61
PMCID: PMC4032166  PMID: 24690233
A54T polymorphism; FABP2 gene; Type 2 diabetes mellitus; Saudi population
15.  Epidemiological Factors in Gall Bladder Cancer in Eastern India-A Single Centre Study 
India has high incidence of Gallbladder carcinoma with regional variation in incidence possibly due to environmental factors. Prospective study of all the gall bladder cancer in our hospital over 18 months analysing how the epidemiological factors are influencing the disease. Incidence-Four cases per 100,000 populations per year. The peak incidence was in 41 to 50 years group (49.20 %). Male to female ratio was 1:3.8. Majority (69.84 %) were in lower socio-economic group. 61 out of 63 patients (96.62 %) were non-vegetarians. 60.34 % and 19.04 % patients weighed between 50 and 55 kg and 55and 60 kg respectively (p = 0.003). Male smokers had significantly higher risk (p = 0.000 1). Gall stones were present in 45 out of 63 cases(71.42 %).45 out of 63 patients were typhoid carriers (p < 0.05). Pain abdomen was the commonest complaint (87.30 %), followed by pallor, lump in right upper quadrant, nausea & vomiting and jaundice in 71.42 %, 69.84 %, 66.66 %, 31.74 % patients respectively. This data highlights high prevalence of gall bladder carcinoma in Eastern India. Better hygiene and water supply to prevent typhoid carriers, prevention of malnutrition, early intervention for cholelithiasis, importance of balanced diet, increase in awareness about risk of tobacco and alcohol consumption-all are highlighted as significant modifiable factors.
doi:10.1007/s13193-012-0203-x
PMCID: PMC3578539  PMID: 24426702
Gallbladder carcinoma; Epidemiology; Cholelithiasis
16.  Insulin Receptor Substrate-1 (IRS-1) Gly927Arg: Correlation with Gestational Diabetes Mellitus in Saudi Women 
BioMed Research International  2014;2014:146495.
Pregnant women with gestational diabetes mellitus (GDM) and type 2 diabetes mellitus (T2DM) share a common pathophysiology associated with similar risk factors. Genetic variants used to determine the risk of developing T2DM might also be associated with the prevalence of GDM. The aim of the present study was to scrutinize the relationship between the G972R polymorphism of the insulin receptor substrate-1 (IRS-1) gene with GDM in the Saudi female population. This is a case-control study that monitored 500 Saudi women. Subjects with GDM (n = 200) were compared with non-GDM (n = 300) controls. We opted to evaluate rs1801278 polymorphism in the IRS1 gene, which plays a critical role in the insulin-signaling pathway. Genotyping was performed with the Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) method. The frequency of the rs1801278 polymorphism was significantly higher in women with GDM than in women with non-GDM (for TT + CT versus CC: P = 0.02). Additionally, there was a significant increase in the frequency of the Arg-encoding mutant allele from GDM to non-GDM (for T versus C: P = 0.01). Our results suggest that the rs1801278 polymorphism in the IRS-1 gene is involved in the occurrence of GDM in the Saudi population.
doi:10.1155/2014/146495
PMCID: PMC3948357  PMID: 24695443
17.  Exploratory Study on Plasma Immunomodulator and Antibody Profiles in Tuberculosis Patients 
Host immune responses to Mycobacterium tuberculosis are generally able to contain infection and maintain a delicate balance between protection and immunopathology. A shift in this balance appears to underlie active disease observed in about 10% of infected individuals. Effects of local inflammation, combined with anti-M. tuberculosis systemic immune responses, are directly detectable in peripheral circulation, without ex vivo stimulation of blood cells or biopsy of the affected organs. We studied plasma immunomodulator and antibody biomarkers in patients with active pulmonary tuberculosis (TB) by a combination of multiplex microbead immunoassays and computational tools for data analysis. Plasma profiles of 10 immunomodulators and antibodies against eight M. tuberculosis antigens (previously reported by us) were examined in active pulmonary TB patients in a country where TB is endemic, Pakistan. Multiplex analyses were performed on samples from apparently healthy individuals without active TB from the same community as the TB patients to establish the assay baselines for all analytes. Over 3,000 data points were collected from patients (n = 135) and controls (n = 37). The data were analyzed by multivariate and computer-assisted cluster analyses to reveal patterns of plasma immunomodulators and antibodies. This study shows plasma profiles that in most patients represented either strong antibody or strong immunomodulator biomarkers. Profiling of a combination of both immunomodulators and antibodies described here may be valuable for the analysis of host immune responses in active TB in countries where the disease is endemic.
doi:10.1128/CVI.00213-13
PMCID: PMC3754529  PMID: 23761664
18.  Defining the Limits of Normal Conjunctival Fornix Anatomy in a Healthy South Asian Population 
Ophthalmology  2014;121(2):492-497.
Purpose
Quantifying the extent of conjunctival fibrosis for documentation of progression in conjunctival scarring disease is a clinical challenge. Measurement of forniceal foreshortening facilitates monitoring of these disorders. This study aims (1) to define the limits of the normal human conjunctival fornices and how these alter with age and (2) to provide normative data for upper and lower fornix depths (FDs) and fornix intercanthal distance (FICD) within a healthy South Asian, racially distinct population.
Design
Epidemiologic, cross-sectional study.
Participants
A total of 240 subjects with national origins from South Asia, with no known ocular history and normal adnexal and conjunctival examination, aged 20 to 80 years.
Methods
An FICD modification of a custom-designed fornix depth measurer (FDM) was validated and used for measurement of both lower and upper FDs together with FICDs in 480 healthy eyes with no ocular comorbidities. Data were analyzed using repeated-measures analysis of variance and presented as means with 95% confidence intervals (CIs).
Main Outcome Measures
Mean lower and upper FDs and FICD for the entire cohort, stratified according to age decade and sex.
Results
For this South Asian population, the overall upper and lower FDs were 15.3 mm (95% CI, 14.9–15.6) and 10.9 mm (95% CI, 10.7–11.1), respectively, with FICD defined as 32.9 mm (95% CI, 32.5–33.4) (upper) and 31.7 mm (95% CI, 31.3–32.1) (lower). With increasing age, a progressive reduction of all measured parameters (P < 0.001) was noted, with female subjects having significantly shallower fornices (upper FD, P < 0.001; lower FD, P < 0.001; upper FICD, P = 0.081; and lower FICD, P = 0.015).
Conclusions
This is the first study to define the limits of normal upper FD and FICDs in any population group. Our study demonstrates sex variations and progressive conjunctival shrinkage with age. Although it provides important, objective data for normal forniceal anatomy, further study is recommended in other populations to confirm the generalizability of these data or to enable normal comparative datasets for the assessment of conjunctival scarring disorders among all anthropological groups.
doi:10.1016/j.ophtha.2013.09.033
PMCID: PMC3991394  PMID: 24314841
19.  Comparison between short- and long-acting erythropoiesis-stimulating agents in hemodialysis patients: target hemoglobin, variability, and outcome 
Purpose
Maintaining target hemoglobin (Hb) with minimal variability is a challenge in hemodialysis (HD) patients. The aim of this study is to compare the long- and short-acting erythropoietin-stimulating agents such as Aranesp and Eprex in achieving these targets.
Methods
Randomized, prospective, open-labeled study of 24 weeks includes stable patients on HD >3 months, age >18 years, and on Eprex for >3 months. Patients were randomized into two groups: A-(Aranesp group):HD patients on Eprex Q TIW or BIW were converted to Aranesp Q weekly, by using the conversion factor of 200:1 and those on Eprex Q weekly to Aranesp Q 2 weeks; B-(Eprex group):patients continued on Eprex treatment. Hemoglobin target was set at (105–125 g/l). Primary end points were percentage of patients achieving target Hb, hemoglobin variability, and number of dose changes in each group.
Results
This study consisted of 139 HD patients: 72 in the Aranesp and 67 in the Eprex—mean (SD) age 54 (16.2) years, 77 (55 %) males. About 46 % were diabetic. Target Hb achieved in 64.8 % of the Aranesp and 59.7 % in the Eprex (p = 0.006). Hb variability was less frequent in the Aranesp group (p = 0.2). Mean number of dose changes was 1.3 (0.87) in the Aranesp and 1.9 (1.2) in the Eprex (p < 0.001). There was 1 vascular access thrombosis in the Aranesp and 8 in the Eprex (p < 0.001). There was no difference in hospitalization and death number between the 2 groups.
Conclusions
Aranesp Q weekly or every 2 weeks is more efficient in achieving target Hb, with less dose changes and minor vascular access complications.
doi:10.1007/s11255-013-0640-7
PMCID: PMC3932161  PMID: 24448756
Short; Long-acting ESAs; Target hemoglobin; Hemoglobin variability; Hemodialysis
20.  Generation of Functional Thymic Epithelium from Human Embryonic Stem Cells that Supports Host T Cell Development 
Cell stem cell  2013;13(2):10.1016/j.stem.2013.04.004.
SUMMARY
Inducing immune tolerance to prevent rejection is a key step toward successful engraftment of stem-cell-derived tissue in a clinical setting. Using human pluripotent stem cells to generate thymic epithelial cells (TECs) capable of supporting T cell development represents a promising approach to reach this goal; however, progress toward generating functional TECs has been limited. Here, we describe a robust in vitro method to direct differentiation of human embryonic stem cells (hESCs) into thymic epithelial progenitors (TEPs) by precise regulation of TGFβ, BMP4, RA, Wnt, Shh, and FGF signaling. The hESC-derived TEPs further mature into functional TECs that support T cell development upon transplantation into thymus-deficient mice. Importantly, the engrafted TEPs produce T cells capable of in vitro proliferation as well as in vivo immune responses. Thus, hESC-derived TEP grafts may have broad applications for enhancing engraftment in cell-based therapies as well as restoring age-and stress-related thymic decline.
doi:10.1016/j.stem.2013.04.004
PMCID: PMC3869399  PMID: 23684540
21.  Association of angiotensin converting enzyme gene insertion/deletion polymorphism and familial hypercholesterolemia in the Saudi population 
Background
The study of the association between genotype and phenotype is of great importance for the prediction of multiple diseases and pathophysiological conditions. The relationship between angiotensin converting enzyme (ACE) Insertion/Deletion (I/D) polymorphism and Familial Hypercholesterolemia (FH) has been not fully investigated in all the ethnicities. In this study we sought to determine the frequency of I/D polymorphism genotypes of ACE gene in Saudi patients with FH.
Results
This is a case–control study carried out purely in Saudi population. Genomic DNA was isolated from 128 subjects who have participated in this study. ACE gene I/D polymorphism was analyzed by polymerase chain reaction in 64 FH cases and 64 healthy controls. There was no statistically significant difference between the groups with respect to genotype distribution. Furthermore, we did not find any significant difference in the frequency of ACE I/D polymorphism in FH subjects when stratified by gender (p = 0.43).
Conclusion
Our data suggest that ACE gene I/D polymorphism examined in this study has no role in predicting the occurrence and diagnosis of FH.
doi:10.1186/1476-511X-12-177
PMCID: PMC4220775  PMID: 24289455
Familial hypercholesterolemia; Angiotensin converting enzyme; Polymorphism
22.  EASER: Ensembl Easy Sequence Retriever 
The rapid advances in genome sequencing technologies have increased the pace at which biological sequence databases are becoming available to the broad scientific community. Thus, obtaining and preparing an appropriate sequence dataset is a crucial first step for all types of genomic analyses. Here, we present a script that can widely facilitate the easy, fast, and effortless downloading and preparation of a proper biological sequence dataset for various genomics studies. This script retrieves Ensembl defined genomic features, associated with a given Ensembl identifier. Coding (CDS) and genomic sequences can be easily retrieved based on a selected relationship from a set of relationship types, either considering all available organisms or a user specified subset of organisms. The script is very user-friendly and by default starts with an interactive mode if no command-line options are specified.
doi:10.4137/EBO.S11335
PMCID: PMC3855309  PMID: 24324324
sequence analysis; bioinformatics; molecular evolution; genomics; data curation; databases
23.  Mechanism of action of chromogranin A on catecholamine release: molecular modeling of the catestatin region reveals a β-strand/loop/β-strand structure secured by hydrophobic interactions and predictive of activity 
Regulatory peptides  1998;77(0):43-53.
A novel fragment of chromogranin A, known as ‘catestatin’ (bovine chromogranin A344–364), inhibits catecholamine release from chromaffin cells and noradrenergic neurons by acting as a non-competitive nicotinic cholinergic antagonist, and may therefore constitute an endogenous autocrine feedback regulator of sympathoadrenal activity. To characterize how this activity depends on the peptide’s structure, we searched for common 3-dimensional motifs for this primary structure or its homologs. Catestatin’s primary structure bore significant (29–35.5% identity, general alignment score 44–57) sequence homology to fragment sequences within three homologs of known 3-dimensional structures, based on solved X-ray crystals: 8FAB, 1PKM, and 2IG2. Each of these sequences exists in nature as a β-strand/loop/β-strand structure, stabilized by hydrophobic interactions between the β-strands. The catestatin structure was stable during molecular dynamics simulations. The catestatin loop contains three Arg residues, whose electropositive side chains form the terminus of the structure, and give rise to substantial uncompensated charge asymmetry in the molecule. A hydrophobic moment plot revealed that catestatin is the only segment of chromogranin A predicted to contain amphiphilic β-strand. Circular dichroism in the far ultraviolet showed substantial (63%) β-sheet structure, especially in a hydrophobic environment. Alanine-substitution mutants of catestatin established a crucial role for the three central arginine residues in the loop (Arg351, Arg353, and Arg358), though not for two arginine residues in the strand region toward the amino-terminus. [125I]Catestatin bound to Torpedo membranes at a site other than the nicotinic agonist binding site. When the catestatin structure was ‘docked’ with the extracellular domain of the Torpedo nicotinic cholinergic receptor, it interacted principally with the β and δ subunits, in a relatively hydrophobic region of the cation pore extracellular orifice, and the complex of ligand and receptor largely occluded the cation pore, providing a structural basis for the non-competitive nicotinic cholinergic antagonist properties of the peptide. We conclude that a homology model of catestatin correctly predicts actual features of the peptide, both physical and biological. The model suggests particular spatial and charge features of the peptide which may serve as starting points in the development of non-peptide mimetics of this endogenous nicotinic cholinergic antagonist.
PMCID: PMC3676947  PMID: 9809795
Adrenal medulla; Chromaffin; Chromogranin A; Catestatin; Nicotinic cholinergic receptor; Mutagenesis; Homology modeling; Molecular dynamics; Alanine scan; Catecholamine; Synthetic peptide; Circular dichroism
24.  The use of individually wrapped presterilized small orthopaedic implants increase operating time: a prospective experimental study 
JRSM Short Reports  2013;4(6):34.
Objective
There have been concerns about the potential increases in operating time associated with the use of individually wrapped presterilized small orthopaedic implants compared with our traditional method of screw banks. We set out to quantify this theory.
Design
Prospective experimental study.
Setting
Theatre.
Participants
Orthopaedic Surgical Trainees and Theatre Scrub team.
Main outcome measure
The time taken to complete the operation.
Results
The use of prepacked and sterilized implants added 2 min 56 s to the use of a bank with a full complement of normal screws that required tapping and 3 min 58 s if self-tapping screws were used (P < 0.001).
Conclusion
Using individually wrapped presterilized small orthopaedic implants increases operating time.
doi:10.1177/2042533313476413
PMCID: PMC3697854  PMID: 23885288
25.  Association of Human Papilloma Virus Infection and Oral Squamous Cell Carcinoma in Bangladesh 
Oral squamous cell carcinoma is the sixth most common malignancy worldwide. In Bangladesh, it comprises 20% of the whole body malignancies. Several studies found that 15% to 25% of oropharyngeal cancer cases are associated with human papilloma virus (HPV). This study is done to find the association of human papilloma virus subtypes, particularly HPV type 16 and HPV type 18, with the oral squamous cell carcinoma in Bangladeshi patients. In total, 34 diagnosed patients of oral squamous cell carcinoma were included in the study. Extracted DNA from the cancerous tissues was checked for PCR reaction to detect the subtypes of human papilloma virus. Data of the present study suggest that oral squamous cell carcinoma are almost absent in Bangladeshi patients with human papilloma virus, particularly HPV 16 and 18.
PMCID: PMC3702360  PMID: 23617206
Human papilloma virus (HPV); HPV type 16; HPV type 18; Oral cancer; Polymerase chain reaction; Bangladesh

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