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1.  Indices of Glucose Homeostasis in Cord Blood in Term and Preterm Newborns 
Objective:
According to the thrifty phenotype hypothesis, intrauterine malnutrition has a role in the etiology of type 2 diabetes. This study was planned to determine the early alterations in indices of glucose homeostasis (glucose, insulin, and cortisol) in term and preterm newborns and the correlations of glucose, insulin, and cortisol levels with insulin resistance indices.
Methods:
A descriptive study comprising 35 term and 35 preterm newborns was carried out from December 2013 to June 2015. Venous cord blood was collected and plasma glucose was analyzed by the glucose oxidase-peroxidase method in an auto analyzer. Serum insulin and cortisol levels were assessed by the enzyme-linked immunosorbent assay. Homeostasis model assessment of insulin resistance (HOMA-IR), quantitative insulin sensitivity check index and glucose insulin ratio were calculated to assess insulin resistance. The data on physical and metabolic parameters were analyzed using standard tests for statistical significance.
Results:
In term newborns, mean glucose and cortisol levels (83.6±17.4 mg/dL and 11.88±5.78 µg/dL, respectively) were significantly higher than those in preterm infants (70.4±15.8 mg/dL and 8.9±4.6 µg/dL, respectively). Insulin and HOMA-IR levels were found higher in preterm newborns (10.8±4.8 µIU/mL and 1.52±0.66, respectively) than in term newborns (7.9±2.7 µIU/mL and 1.19±0.29, respectively). Insulin was found to positively correlate with HOMA-IR, whereas cortisol was negatively correlated with HOMA-IR in both term and preterm newborns.
Conclusion:
Higher insulin levels and HOMA-IR values in the cord blood of preterm newborns support the theory of intrauterine origin of metabolic diseases.
doi:10.4274/jcrpe.2819
PMCID: PMC5096489  PMID: 27087404
cord blood; cortisol; glucose; insulin; insulin resistance
2.  Cord Blood Levels of Insulin, Cortisol and HOMA2-IR in Very Preterm, Late Preterm and Term Newborns 
Introduction
Alteration in the glucose homeostasis is still the major cause of morbidity and mortality in the newborns. Intrauterine undernutrition plays an important role in causing adult insulin resistance and diabetes but the exact cause is still unknown.
Aim
To estimate the plasma glucose, serum insulin and cortisol levels at birth in newborns at different gestational age.
Materials and Methods
The present cross-sectional study conducted from December 2014 to June 2015 included 58 newborns enrolled as per the inclusion criteria and further categorized into Group I (very preterm; n=19; gestational age < 32 weeks), Group II (late preterm; n=20; gestational age between 32-37 weeks) and Group III (full term; n=19; gestational age >37 weeks) newborns. Venous Cord Blood (VCB) was collected and plasma glucose was analysed by GOD-POD (Glucose Oxidase-Peroxidase) method in auto analyser whereas serum insulin and cortisol were analysed by ELISA (Enzyme Linked Immunosorbent Assay). HOMA2-IR (Homeostatic Model Assessment) calculator was used to assess insulin resistance. All parametric data was expressed as mean±SD and analysed using ANOVA with Tukey’s as the Post-Hoc test. Correlation analysis was done using Pearson’s correlation co-efficient with scatter plot as the graphical representation.
Results
Significantly increased insulin and HOMA2-IR levels were found in group I (13.7±4.7μIU/mL and 1.6±0.58 respectively) when compared to group II (8.3±2.9μIU/mL and 0.93±0.2 respectively) and group III (8.3±2.1μIU/mL and 1.03±0.26 respectively). A positive correlation between cortisol levels and gestational age (r = 0.6, n = 58, p < 0.001) and a negative correlation between insulin and gestational age (r = -0.654, n = 58, p < 0.001) was observed in the study population.
Conclusion
Increased levels of insulin and HOMA2-IR as seen in the very preterm newborns signify the predisposition of these newborns to development of diabetes in later stages of life. The inverse association of cortisol and insulin with gestational age suggests that cortisol could also be responsible for impaired β cell function and insulin sensitivity.
doi:10.7860/JCDR/2016/18770.7857
PMCID: PMC4948379  PMID: 27437204
Insulin resistance; Neonates; Postnatal life
3.  Benign Lymphoepithelial Cyst of the Parotid in HIV Negative Patient 
Benign lymphoepithelial cysts are slow growing tumours commonly seen in HIV positive adults. It is rare to find them in non HIV individuals. In this article we discuss an uncommon presentation of a parotid swelling occurring in a 49-year-old non HIV male, which was diagnosed as benign lymphoepithelial cyst. The various investigative modalities and treatment options are outlined in this article.
doi:10.7860/JCDR/2016/17915.7609
PMCID: PMC4866143  PMID: 27190845
Cystic lymphoid hyperplasia; Parotidectomy; Salivary gland
4.  Evaluation of Ischemia-Modified Albumin, Malondialdehyde, and Advanced Oxidative Protein Products as Markers of Vascular Injury in Diabetic Nephropathy 
Biomarker Insights  2016;11:63-68.
AIM
This study aimed at evaluation of ischemia-modified albumin (IMA), malondialdehyde (MDA), and advanced oxidative protein products (AOPP) as markers of vascular injury in diabetic nephropathy (DN) with derivation of cutoff values for the same.
MATERIALS AND METHODS
Study population comprised 60 diabetes patients and 30 controls, with diabetes patients further categorized into three groups based on urine albumin/creatinine ratio (UACR) of <30 mg/g (diabetes without microalbuminuria), 30–300 mg/g (early DN), and >300 mg/g of creatinine (overt DN). Serum IMA, MDA, and AOPP were estimated by enzyme-linked immunosorbent assay; HbA1c, serum creatinine, urine albumin, and urine creatinine were estimated using automated analyzers. Statistical analysis was done using analysis of variance, Pearson’s correlation coefficient, and receiver-operating characteristic curve.
RESULTS
A statistically significant difference was found in the levels of IMA among patients with early DN (154 ng/mL), diabetes without nephropathy (109.4 ng/mL), and healthy controls (45.7 ng/mL), with highest levels in early DN cases. Similar increase was seen in AOPP as well. A significant correlation was observed between IMA and UACR in diabetes without nephropathy (r = 0.448).
CONCLUSION
The present study postulates serum IMA as a novel biomarker for the assessment of disease progression in diabetes even before microalbuminuria, and a cutoff point ≥99 ng/mL can be used for detection of early DN.
doi:10.4137/BMI.S39053
PMCID: PMC4854310  PMID: 27158221
advanced oxidative protein products; diabetic nephropathy; ischemia-modified albumin; malondialdehyde; vascular injury
5.  Total anomalous systemic venous drainage to coronary sinus 
BMJ Case Reports  2014;2014:bcr2013201493.
doi:10.1136/bcr-2013-201493
PMCID: PMC3902399  PMID: 24395884
6.  Alveolar ridge augmentation by connective tissue grafting using a pouch method and modified connective tissue technique: A prospective study 
Dental Research Journal  2015;12(6):548-553.
Background:
Localized alveolar ridge defect may create physiological and pathological problems. Developments in surgical techniques have made it simpler to change the configuration of a ridge to create a more aesthetic and more easily cleansable shape. The purpose of this study was to compare the efficacy of alveolar ridge augmentation using a subepithelial connective tissue graft in pouch and modified connective tissue graft technique.
Materials and Methods:
In this randomized, double blind, parallel and prospective study, 40 non-smoker individuals with 40 class III alveolar ridge defects in maxillary anterior were randomly divided in two groups. Group I received modified connective tissue graft, while group II were treated with subepithelial connective tissue graft in pouch technique. The defect size was measured in its horizontal and vertical dimension by utilizing a periodontal probe in a stone cast at base line, after 3 months, and 6 months post surgically. Analysis of variance and Bonferroni post-hoc test were used for statistical analysis. A two-tailed P < 0.05 was considered to be statistically significant.
Results:
Mean values in horizontal width after 6 months were 4.70 ± 0.87 mm, and 4.05 ± 0.89 mm for group I and II, respectively. Regarding vertical heights, obtained mean values were 4.75 ± 0.97 mm and 3.70 ± 0.92 mm for group I and group II, respectively.
Conclusion:
Within the limitations of this study, connective tissue graft proposed significantly more improvement as compare to connective tissue graft in pouch.
PMCID: PMC4696357  PMID: 26759591
Alveolar ridge augmentation; connective tissue graft; periodontal plastic surgery
7.  Ganglioneuroblastoma of Skull Base 
Neuroblastic tumours are common in childhood and adrenal glands are the most common site. Head and neck ganglioneuroblastomas are extremely rare and nose is a very uncommon site for a ganglioneuroblastoma. The management of this primitive sympathogonic tumour may vary depending on the age of the patient and stage of the tumour. We present a middle-aged man with a ganglioneuroblastoma of skull base, management of this tumour and a review of literature.
doi:10.7860/JCDR/2015/14135.6334
PMCID: PMC4576567  PMID: 26435974
Lateral rhinotomy; Medial maxillectomy; Neuroblastoma
8.  Ancient schwannoma mimicking a thyroid mass with retrosternal extension 
BMJ Case Reports  2013;2013:bcr2013200608.
We report the case of a middle-aged hypothyroid woman presenting with a neck swelling, voice change and breathing difficulty. On evaluation, she was diagnosed to have goitre with retrosternal extension. The mass was surgically excised and a histopathological report of ancient schwannoma was obtained. A review of literature on schwannomas of the head and neck was carried out. An ancient schwannoma should be considered as one of the differential diagnosis of a cervical mass, even though the clinical presentation point towards a thyroid swelling. At 6 months follow-up, the patient was found to be asymptomatic except for a hoarse voice.
doi:10.1136/bcr-2013-200608
PMCID: PMC3794216  PMID: 24001735
9.  Dancing vegetations: Kocuria rosea endocarditis 
BMJ Case Reports  2013;2013:bcr2013010339.
doi:10.1136/bcr-2013-010339
PMCID: PMC3703028  PMID: 23814223
10.  Combination of bone allograft, barrier membrane and doxycycline in the treatment of infrabony periodontal defects: A comparative trial 
The Saudi Dental Journal  2015;27(3):155-160.
Aim
The purpose of the present study was to compare the regenerative potential of noncontained periodontal infrabony defects treated with decalcified freeze-dried bone allograft (DFDBA) and barrier membrane with or without local doxycycline.
Methods
This study included 48 one- or two-wall infrabony defects from 24 patients (age: 30–65 years) seeking treatment for chronic periodontitis. Defects were randomly divided into two groups and were treated with a combination of DFDBA and barrier membrane, either alone (combined treatment group) or with local doxycycline (combined treatment + doxycycline group). At baseline (before surgery) and 3 and 6 months after surgery, the pocket probing depth (PPD), clinical attachment level (CAL), radiological bone fill (RBF), and alveolar height reduction (AHR) were recorded. Analysis of variance and the Newman–Keuls post hoc test were used for statistical analysis. A two-tailed p-value of less than 0.05 was considered to be statistically significant.
Results
In the combined treatment group, the PPD reduction was 2.00 ± 0.38 mm (32%), CAL gain was 1.25 ± 0.31 mm (17.9%), and RBF was 0.75 ± 0.31 mm (20.7%) after 6 months. In the combined treatment + doxycycline group, these values were 2.75 ± 0.37 mm (44%), 1.5 ± 0.27 mm (21.1%), and 1.13 ± 0.23 mm (28.1%), respectively. AHR values for the groups without and with doxycycline were 12.5% and 9.4%, respectively.
Conclusion
There was no significant difference in the regeneration of noncontained periodontal infrabony defects between groups treated with DFDBA and barrier membrane with or without doxycycline.
doi:10.1016/j.sdentj.2015.01.003
PMCID: PMC4501465  PMID: 26236130
Bone grafting; Doxycycline; Guided tissue regeneration
11.  Retrospective analysis of perioperative factors on outcome of patients undergoing surgery for Moyamoya disease 
Background:
The short term outcome of patients undergoing surgery for Moyamoya disease can be affected by various perioperative factors. However, due to lesser prevalence of this disease in our country, data relating the effect of perioperative factors on the overall neurological outcomes of these patients is lacking.
Aims:
To analyze the effect of perioperative factors on the duration of postoperative hospital stay in patients undergoing surgery for Moyamoya disease.
Settings and Design:
It is a retrospective study analyzing various perioperative factors influencing the overall outcome of patients undergoing surgery for Moyamoya disease at a tertiary care centre in North India.
Methods and Material:
The medical records of all patients who underwent revascularization surgeries for Moyamoya disease from 2007 to till January 2014 were included for retrospective analysis. Various preoperative, intraoperative, and postoperative data were recorded. The data was statistically compared for short and prolonged hospital stay for various perioperative factors. The duration of post operative hospital stay was categorized as short (<5 days) and prolonged (>5 days).
Statistical Analysis:
Kolmogrov Smirnov test was applied to see the normality of continuous data. The association of various categorically classified data with 2 groups was found using Fisher Exact test. The trends in intraoperative hemodynamics were analysed using 2 way repeated measure Anova test. T-test was used for comparing two group means for various parameters.
Results:
A total of 15 patients were included in the study. One patient underwent surgery twice on two different occasions. Thirteen patients belonged to paediatric age group (<18 years). The type of anaesthetics used for induction and maintenance had no effect on patient outcome. Mean duration of anaesthesia was 2.45 (1.3-4.0) hours. The mean duration of hospital stay was 5.13 (3-10) days. Most of the parameters did not have significant effect on postoperative hospital stay. Patients with mean value of intraoperative end tidal carbon dioxide (EtCO2) either less than 31 mmHg or more than 35 mmHg had statistically significant prolongation of hospital stay.
Conclusion:
Maintaining the intraoperative EtCO2 between 31-35 mmHg may be associated with short hospital stay when compared to those who have intraoperative EtCO2 either less than 31 mmHg or more than 35 mmHg.
doi:10.4103/0976-3147.150313
PMCID: PMC4387829  PMID: 25883498
Moyamoya disease; perioperative factors; postoperative hospital stay
13.  Pulmonary hypertension due to presence of isolated partial anomalous pulmonary venous connection: A case report 
Anomalous pulmonary venous return is an uncommon congenital malformation which can be broadly categorized into partial or total, of which the former is more common. The anomaly is considered to be partial if some of the pulmonary veins drain into the systemic circulation and total if all the pulmonary veins drain into systemic circulation. Isolated partial anomalous pulmonary venous return (PAPVC) is an uncommon finding and is a very uncommon cause of pulmonary arterial hypertension. Whilst many patients with PAPVC remain asymptomatic, some may present at a later age with symptoms related to left-to-right shunt, pulmonary hypertension and right heart failure. We are presenting an interesting case report of an 18 years old patient who presented with exertional dyspnea and fatigue conforming to NYHA class II symptom status. Trans-esophageal echocardiography revealed isolated obstructive PAPVC as the cause for pulmonary hypertension without other demonstrable left-to-right shunts.
doi:10.1016/j.jcdr.2014.01.002
PMCID: PMC3953709  PMID: 24653588
Partial anomalous pulmonary venous connection; Pulmonary hypertension; Trans-esophageal echocardiography
14.  Large vegetation in a case of bacterial endocarditis by a rare commensal organism: Kocura rosea 
Heart Asia  2014;6(1):17.
doi:10.1136/heartasia-2014-010499
PMCID: PMC4832732  PMID: 27326156
LV aneurysm; heart in heart
15.  Coronary artery disease in patients undergoing cardiac surgery for non-coronary lesions in a tertiary care centre 
Indian Heart Journal  2014;66(1):52-56.
Background
The objective of the present study was to determine the prevalence of coronary artery disease (CAD) in patients undergoing surgery for various valvular as well as non-valvular cardiac pathologies.
Methods
Patients with various valvular and non-valvular pathologies were selected. All patients with age ≥40 years and an indication for open heart surgery underwent pre-operative coronary angiogram and were included in the study.
Results
The mean age was 51.5 ± 9.02 years. 178 (59.3%) patients were males and 122 (40.7%) patients were females. Out of 300 patients, 270 (90%) patients had valvular heart disease (VHD) and 30 (10%) patients had non-valvular heart disease. Rheumatic heart disease (RHD), mitral valve prolapse (MVP), degenerative aortic valve disease (DAVD) and bicuspid aortic valve (BAV) was present in 161 (53.7%), 17 (5.7%), 60 (20%) and 32 (10.7%) patients respectively. Overall, 26 (8.7%) patients were found to have significant CAD. CAD was significantly more common in patients with VHD as compared to patients with other etiologies (1 patient, 3.3%, p < 0.05). In the valvular group, DAVD patients had maximum prevalence of CAD (14 patients, 23.4%, p < 0.05). In the group with CAD, the presence of variables such as age >60 years, male sex, typical angina, HT, dyslipidemia and smoking were significantly greater as compared to those with normal coronaries.
Conclusion
The overall prevalence of CAD among patients undergoing non-coronary cardiac surgery is 8.7%. Coronary artery disease is relatively uncommon in patients with rheumatic VHD (4.9%), while its prevalence is highest in DAVD (23.4%).
doi:10.1016/j.ihj.2013.12.014
PMCID: PMC3946445  PMID: 24581096
Coronary artery disease; Prevalence; Preoperative coronary angiogram
18.  Dothiepin-induced transient hypomania and extrapyramidal syndrome 
Indian Journal of Psychiatry  2013;55(4):383-385.
A case has been reported here, who developed transient hypomanic symptoms as well as extrapyramidal symptoms after being switched from sertraline to dothiepin therapy. The possible mechanisms and clinical implications of the same are discussed.
doi:10.4103/0019-5545.120549
PMCID: PMC3890912  PMID: 24459312
Dothiepin; extrapyramidal syndrome; hypomania
19.  Pleiotropy of chemically modified tetracycline in periodontitis 
doi:10.4103/0975-7406.116831
PMCID: PMC3778596  PMID: 24082703
20.  Comparative evaluation of decalcified freeze dried bone allograft with and without local doxycycline in non-contained human periodontal infrabony defects 
Background:
Doxycycline has been advocated as useful adjuncts in periodontal therapy not only due to their antimicrobial actions, but also to their recently recognized anti-collagenolytic, anti-inflammatory, osteoclast inhibitory and fibroblast stimulating property. The purpose of the present cohort study was to evaluate the regenerative outcomes of bone graft with or without local doxycycline in non-contained infrabony periodontal defects.
Materials and Methods:
16 one or two wall infrabony defects, in 11 patients suffering from moderate to severe chronic periodontitis, aged 35-60 years, were randomly divided for bone graft, alone (control) and with doxycycline (test) for the study. At baseline, after 3 months and after 6 months of post-operative period, pocket probing depth (PPD), clinical attachment level (CAL), radiological bone fill (RBF) and alveolar height reduction were recorded. Analysis of variance and Newman-Keuls post-hoc test were used or statistical analysis. A two-tailed probability (P) value P < 0.05 was considered to be statistically significant.
Results:
For the control group PPD reduction 2.00 ± 0.18 mm, CAL gain 1.38 ± 0.17 mm, RBF 0.63 ± 0.27 mm (18.0%) was observed while in the test group PPD reduction 2.00 ± 0.38 mm, CAL gain 1.25 ± 0.31 mm, RBF 0.75 ± 0.31 mm (20.7%) was evaluated. While alveolar height reduction for the control group and test group was 13% and 12.5% respectively.
Conclusion:
The study confirmed no added benefits of local doxycycline, as compared with bone graft alone, for regeneration of non-contained human periodontal infrabony defects.
doi:10.4103/0972-124X.118322
PMCID: PMC3800413  PMID: 24174730
Decalcified freeze dried bone allograft; doxycycline; infrabony defects and periodontal regeneration
21.  A validated regulatory network for Th17 cell specification 
Cell  2012;151(2):289-303.
Th17 cells have critical roles in mucosal defense and are major contributors to inflammatory disease. Their differentiation requires the nuclear hormone receptor RORγt working with multiple other essential transcription factors (TFs). We have used an iterative systems approach, combining genome-wide TF occupancy, expression profiling of TF mutants, and expression time series to delineate the Th17 global transcriptional regulatory network. We find that cooperatively-bound BATF and IRF4 contribute to initial chromatin accessibility, and with STAT3 initiate a transcriptional program that is then globally tuned by the lineage-specifying TF RORγt, which plays a focal deterministic role at key loci. Integration of multiple datasets allowed inference of an accurate predictive model that we computationally and experimentally validated, identifying multiple new Th17 regulators, including Fosl2, a key determinant of cellular plasticity. This interconnected network can be used to investigate new therapeutic approaches to manipulate Th17 functions in the setting of inflammatory disease.
doi:10.1016/j.cell.2012.09.016
PMCID: PMC3503487  PMID: 23021777
22.  Synthesis and Bioevaluation of 125I-Labeled Gold Nanorods 
Nanotechnology  2011;22(13):135102.
A novel technique is discribed to monitor in vivo behaviors of gold nanorods (GNRs) using γ-imaging. GNRs were radiolabeled using [125I] sodium iodide in a simple and fast manner with high yield and without disturbing optical properties. Radiolabeled GNRs were successfully visualized by radioisotope tag, allowing longitudinal in vivo studies to be performed repeatedly in the same animal. The preliminary biodistribution study showed that PEGylated GNRs have much longer blood circulation times and clear out faster, while bare GNRs accumulate quickly in the liver after systematic administration. The highly efficient method reported here provides an extensively useful tool for guidance of design and development of new gold nanoparticles as target-specific agents for both diagnostics and photothermal therapy.
doi:10.1088/0957-4484/22/13/135102
PMCID: PMC3139686  PMID: 21343651
Gold nanorods; Iodine-125; γ-imaging; Radiolabeled nanoparticles; PEGylation
23.  Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project 
Gerstein, Mark B. | Lu, Zhi John | Van Nostrand, Eric L. | Cheng, Chao | Arshinoff, Bradley I. | Liu, Tao | Yip, Kevin Y. | Robilotto, Rebecca | Rechtsteiner, Andreas | Ikegami, Kohta | Alves, Pedro | Chateigner, Aurelien | Perry, Marc | Morris, Mitzi | Auerbach, Raymond K. | Feng, Xin | Leng, Jing | Vielle, Anne | Niu, Wei | Rhrissorrakrai, Kahn | Agarwal, Ashish | Alexander, Roger P. | Barber, Galt | Brdlik, Cathleen M. | Brennan, Jennifer | Brouillet, Jeremy Jean | Carr, Adrian | Cheung, Ming-Sin | Clawson, Hiram | Contrino, Sergio | Dannenberg, Luke O. | Dernburg, Abby F. | Desai, Arshad | Dick, Lindsay | Dosé, Andréa C. | Du, Jiang | Egelhofer, Thea | Ercan, Sevinc | Euskirchen, Ghia | Ewing, Brent | Feingold, Elise A. | Gassmann, Reto | Good, Peter J. | Green, Phil | Gullier, Francois | Gutwein, Michelle | Guyer, Mark S. | Habegger, Lukas | Han, Ting | Henikoff, Jorja G. | Henz, Stefan R. | Hinrichs, Angie | Holster, Heather | Hyman, Tony | Iniguez, A. Leo | Janette, Judith | Jensen, Morten | Kato, Masaomi | Kent, W. James | Kephart, Ellen | Khivansara, Vishal | Khurana, Ekta | Kim, John K. | Kolasinska-Zwierz, Paulina | Lai, Eric C. | Latorre, Isabel | Leahey, Amber | Lewis, Suzanna | Lloyd, Paul | Lochovsky, Lucas | Lowdon, Rebecca F. | Lubling, Yaniv | Lyne, Rachel | MacCoss, Michael | Mackowiak, Sebastian D. | Mangone, Marco | McKay, Sheldon | Mecenas, Desirea | Merrihew, Gennifer | Miller, David M. | Muroyama, Andrew | Murray, John I. | Ooi, Siew-Loon | Pham, Hoang | Phippen, Taryn | Preston, Elicia A. | Rajewsky, Nikolaus | Rätsch, Gunnar | Rosenbaum, Heidi | Rozowsky, Joel | Rutherford, Kim | Ruzanov, Peter | Sarov, Mihail | Sasidharan, Rajkumar | Sboner, Andrea | Scheid, Paul | Segal, Eran | Shin, Hyunjin | Shou, Chong | Slack, Frank J. | Slightam, Cindie | Smith, Richard | Spencer, William C. | Stinson, E. O. | Taing, Scott | Takasaki, Teruaki | Vafeados, Dionne | Voronina, Ksenia | Wang, Guilin | Washington, Nicole L. | Whittle, Christina M. | Wu, Beijing | Yan, Koon-Kiu | Zeller, Georg | Zha, Zheng | Zhong, Mei | Zhou, Xingliang | Ahringer, Julie | Strome, Susan | Gunsalus, Kristin C. | Micklem, Gos | Liu, X. Shirley | Reinke, Valerie | Kim, Stuart K. | Hillier, LaDeana W. | Henikoff, Steven | Piano, Fabio | Snyder, Michael | Stein, Lincoln | Lieb, Jason D. | Waterston, Robert H.
Science (New York, N.Y.)  2010;330(6012):1775-1787.
We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor–binding sites, and maps of chromatin organization. From this, we created more complete and accurate gene models, including alternative splice forms and candidate noncoding RNAs. We constructed hierarchical networks of transcription factor–binding and microRNA interactions and discovered chromosomal locations bound by an unusually large number of transcription factors. Different patterns of chromatin composition and histone modification were revealed between chromosome arms and centers, with similarly prominent differences between autosomes and the X chromosome. Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome.
doi:10.1126/science.1196914
PMCID: PMC3142569  PMID: 21177976
24.  The CRIT framework for identifying cross patterns in systems biology and application to chemogenomics 
Genome Biology  2011;12(3):R32.
Biological data is often tabular but finding statistically valid connections between entities in a sequence of tables can be problematic - for example, connecting particular entities in a drug property table to gene properties in a second table, using a third table associating genes with drugs. Here we present an approach (CRIT) to find connections such as these and show how it can be applied in a variety of genomic contexts including chemogenomics data.
doi:10.1186/gb-2011-12-3-r32
PMCID: PMC3129682  PMID: 21453526
25.  Detection and monitoring of the multiple inflammatory responses by photoacoustic molecular imaging using selectively targeted gold nanorods 
Biomedical Optics Express  2011;2(3):645-657.
In vitro cell experiments have been performed to detect and monitor the upregulation of intercellular adhesion molecule-1 (ICAM-1) and E-selectin simultaneously by photoacoustic molecular imaging (PMI). Human umbilical vein endothelial cells (HUVECs) were grown on gelatin-coated glass slides and stimulated with inflammatory cytokines to induce the expression of the inflammatory biomarkers, ICAM-1 and E-selectin. Gold nanorods (GNRs) of aspect ratio (AR) 1:3 with absorption centered at 715 nm conjugated to anti-ICAM-1 antibody and GNRs of AR 1:3.5 with absorption centered at 800 nm conjugated to anti-E-selectin were exposed to HUVECs with different stimulation conditions. A focused high frequency ultrasonic transducer (60 MHz, f/1.5) was used to scan the photoacoustic (PA) signal over the top surface of the cell containing slides. Averaged PA signal intensity from the stimulated cells was about 3 folds higher (~10 dB) compared to the un-stimulated cells for both ICAM-1 and E-selectin. The strong binding of GNRs to the stimulated HUVEC cells was evidenced by fluorescence imaging. Exposure of HUVEC cells to GNRs conjugated to isotype control antibodies confirms a low level non-specific binding. Also, at 0, 2, 6, and 24 hours after inflammatory stimulation, the HUVECs were exposed to GNRs conjugated anti-ICAM-1 antibody and anti-E-selectin antibody. PA intensity at each stage of inflammation compares well with fluorescence imaging and rt-PCR quantification.
doi:10.1364/BOE.2.000645
PMCID: PMC3047369  PMID: 21412469
(000.0000) General; (000.2700) General science

Results 1-25 (30)