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1.  Suitability of self-collected vaginal samples for cervical cancer screening in peri-urban villages in Andhra Pradesh, India 
Objectives:
Our aim was to determine if (1) Hybrid Capture 2 and a PCR-based method were comparable for detection of high-risk HPVs, (2) clinician-collected and self-collected samples were equally efficient to detect HPV and cervical cancer precursor lesions and (3) if participation rates improved with home-based vs. clinic-based self collection.
Methods:
Samples were selected from women participating in a cervical cancer screening study according to human papillomavirus (HPV), visual inspection with acetic acid (VIA), or Pap smear screening results. From 432 of 892 selected women, split sample aliquots were tested for HPV DNA using both the Hybrid Capture 2 assay and the Roche prototype line blot assay. Women from a subset of villages were recruited at two separate time points for clinic-based self-collection and home-based self-collection, and participation rates were compared.
Results:
Pairwise agreement between self- and clinician-collected samples was high by both hc2 (90.8% agreement, kappa=0.7) and PCR (92.6% agreement, kappa=0.8), with significantly increased high-risk HPV detection in clinician-collected specimens (McNemar's p<0.01). Ability to detect precursor lesions was highest by PCR testing of clinician-collected samples and lowest by Hybrid Capture 2 testing of self-collected samples (11/11 and 9/11 cases of cervical intraepithelial neoplasia grade 2/3 and cancer detected, respectively). Participation in home-based screening was significantly higher than clinic-based screening (71.5% and 53.8%, respectively; p<0.001) among women 30-45 years old.
Conclusion:
The combination of improved screening coverage and a high single test sensitivity afforded by HPV DNA testing of home-based self-collected swabs may have a greater programmatic impact on cervical cancer mortality reduction compared to programs requiring a pelvic exam.
doi:10.1158/1055-9965.EPI-08-1171
PMCID: PMC2762740  PMID: 19423518
2.  Purification and characterization of cysteine protease from germinating cotyledons of horse gram 
BMC Biochemistry  2009;10:28.
Background
Proteolytic enzymes play central role in the biochemical mechanism of germination and intricately involved in many aspects of plant physiology and development. To study the mechanism of protein mobilization, undertaken the task of purifying and characterizing proteases, which occur transiently in germinating seeds of horse gram.
Results
Cysteine protease (CPRHG) was purified to homogeneity with 118 fold by four step procedure comprising Crude extract, (NH4)2SO4 fractionation, DEAE-Cellulose and CM-sephacel chromatography from the 2 day germinating cotyledons of horse gram (Macrotyloma uniflorum (Lam.) Verdc.). CPRHG is a monomer with molecular mass of 30 k Da, was determined by SDS-PAGE and gel filtration. The purified enzyme on IEF showed two isoforms having pI values of 5.85 and 6.1. CPRHG composed of high content of aspartic acid, glutamic acid and serine. The enzyme activity was completely inhibited by pCMB, iodoacetate and DEPC indicating cysteine and histidine residues at the active site. However, on addition of sulfhydryl reagents (cysteine, dithiothreitol, glutathione and beta-ME) reverse the strong inhibition by pCMB. The enzyme is fairly stable toward pH and temperature. Immunoblot analysis shows that the enzyme synthesized as zymogen (preproenzyme with 81 kDa) and processed to a 40 kDa proenzyme which was further degraded to give 30 kDa active enzyme.
Conclusion
It appears that the newly synthesized protease is inactive, and activation takes place during germination. CPRHG has a broad substrate specificity and stability in pH, temperature, etc. therefore, this protease may turn out to be an efficient choice for the pharmaceutical, medicinal, food, and biotechnology industry.
doi:10.1186/1471-2091-10-28
PMCID: PMC2784799  PMID: 19919695
3.  Hyperkalemia masking left ventricular hypertrophy in electrocardiogram in a patient with end-stage renal disease 
Indian Journal of Nephrology  2008;18(1):22-23.
A patient of severe chronic renal failure presented with hyperkalemic electrocardiographic (ECG) changes and hyperkalemia. Following a session of hemodialysis, when he reverted to normokalemia, the repeat ECG revealed left ventricular hypertrophy (LVH). Thus we confronted with a situation of hyperkalemia, masking the LVH on ECG initially and when the hyperkalemia was corrected with dialysis the LVH showed in ECG. The plausible explanation for this electrophysiological behaviour was offered.
doi:10.4103/0971-4065.41284
PMCID: PMC2847725  PMID: 20368916
Electrocardiography; end stage renal disease; hyperkalemia; left ventricular enlargement
4.  Perturbing the Cellular Levels of Steroid Receptor Coactivator-2 Impairs Murine Endometrial Function 
PLoS ONE  2014;9(6):e98664.
As pleiotropic coregulators, members of the p160/steroid receptor coactivator (SRC) family control a broad spectrum of transcriptional responses that underpin a diverse array of physiological and pathophysiological processes. Because of their potent coregulator properties, strict controls on SRC expression levels are required to maintain normal tissue functionality. Accordingly, an unwarranted increase in the cellular levels of SRC members has been causally linked to the initiation and/or progression of a number of clinical disorders. Although knockout mouse models have underscored the critical non-redundant roles for each SRC member in vivo, there are surprisingly few mouse models that have been engineered to overexpress SRCs. This deficiency is significant since SRC involvement in many of these disorders is based on unscheduled increases in the levels (rather than the absence) of SRC expression. To address this deficiency, we used recent mouse technology that allows for the targeted expression of human SRC-2 in cells which express the progesterone receptor. Through cre-loxP recombination driven by the endogenous progesterone receptor promoter, a marked elevation in expression levels of human SRC-2 was achieved in endometrial cells that are positive for the progesterone receptor. As a result of this increase in coregulator expression, female mice are severely subfertile due to a dysfunctional uterus, which exhibits a hypersensitivity to estrogen exposure. Our findings strongly support the proposal from clinical observations that increased levels of SRC-2 are causal for a number of endometrial disorders which compromise fertility. Future studies will use this mouse model to decipher the molecular mechanisms that underpin the endometrial defect. We believe such mechanistic insight may provide new molecular descriptors for diagnosis, prognosis, and/or therapy in the clinical management of female infertility.
doi:10.1371/journal.pone.0098664
PMCID: PMC4048228  PMID: 24905738
5.  Rapid assays for Gaucher and Hurler diseases in dried blood spots using digital microfluidics 
Molecular genetics and metabolism  2013;109(2):218-220.
Objective
Easy tool for newborn screening of Gaucher and Hurler diseases.
Methods
Method comparison between fluorometric enzymatic activity assay on a digital microfluidic platform and micro-titer plate bench assay was performed on normal (n=100), Gaucher (n=10) and Hurler (n=7) dried blood spot samples.
Results
Enzymatic activity analysis of glucocerebrosidase (Gaucher) and α-L-iduronidase (Hurler) revealed similar discrimination between normal and affected samples on both platforms.
Conclusions
Digital microfluidics is suitable for Gaucher and Hurler newborn screening.
doi:10.1016/j.ymgme.2013.03.010
PMCID: PMC3926749  PMID: 23578771
Newborn screening; lysosomal storage disease; digital microfluidics; dried blood spot; Gaucher disease; Hurler disease
6.  Differences in testing, stigma, and perceived consequences of stigmatization among heterosexual men and women living with HIV in Bengaluru, India 
AIDS care  2013;26(3):396-403.
Approximately 2.4 million people in India are living with HIV. Gender inequality affects HIV prevention, detection, and management. The purpose of this paper was to describe gender differences in the experience of living with HIV in Bengaluru, India. A subsample of n = 313 (159 men and 154 women) from a larger cohort was used for these analyses. Participants were recruited through AIDS service organizations. They completed an interviewer-administered survey assessing HIV testing experience, types of stigma, and perceived consequences of stigmatization. The majority of men (67%) reported getting HIV tested because of illness, while women were more likely to be tested after learning their spouse’s HIV-positive status (42%). More men (59%) than women (45%, p <0.05) were tested in private care settings. Men reported significantly higher mean levels of internalized stigma (men: M = 0.71, SD = 0.63; women: M = 0.46, SD=0.55; p<0.001), whereas the women reported significantly higher scores for enacted stigma (men: M = 1.30, SD = 1.69; women: M = 2.10, SD = 2.17; p <0.001). These differences remained significant after controlling for potential socio-demographic covariates. Following their diagnosis, more women reported moving out of their homes (men: 16%; women: 26%; p <0.05). More men (89%) than women (66%; p <0.001) reported to have modified their sexual behavior after being diagnosed. These findings suggest that the experience of living with HIV and HIV stigma varies by gender in this population. Suggestions for a gender-based approach to HIV prevention and stigma reduction are provided.
doi:10.1080/09540121.2013.819409
PMCID: PMC4033403  PMID: 23869716
gender differences; HIV; stigma; India
7.  Interaction of gelatin with polyenes modulates antifungal activity and biocompatibility of electrospun fiber mats 
Topical application of antifungals does not have predictable or well-controlled release characteristics and requires reapplication to achieve therapeutic local concentration in a reasonable time period. In this article, the efficacy of five different US Food and Drug Administration-approved antifungal-loaded (amphotericin B, natamycin, terbinafine, fluconazole, and itraconazole) electrospun gelatin fiber mats were compared. Morphological studies show that incorporation of polyenes resulted in a two-fold increase in fiber diameter and the mats inhibit the growth of yeasts and filamentous fungal pathogens. Terbinafine-loaded mats were effective against three filamentous fungal species. Among the two azole antifungals compared, the itraconazole-loaded mat was potent against Aspergillus strains. However, activity loss was observed for fluconazole-loaded mats against all of the test organisms. The polyene-loaded mats displayed rapid candidacidal activities as well. Biophysical and rheological measurements indicate strong interactions between polyene antifungals and gelatin matrix. As a result, the polyenes stabilized the triple helical conformation of gelatin and the presence of gelatin decreased the hemolytic activity of polyenes. The polyene-loaded fiber mats were noncytotoxic to primary human corneal and sclera fibroblasts. The reduction of toxicity with complete retention of activity of the polyene antifungal-loaded gelatin fiber mats can provide new opportunities in the management of superficial skin infections.
doi:10.2147/IJN.S58487
PMCID: PMC4043707  PMID: 24920895
fungal infections; electrospinning; antifungals; controlled release; drug–matrix interactions
8.  The distinctive germinal center phase of IgE+ B lymphocytes limits their contribution to the classical memory response 
The Journal of Experimental Medicine  2013;210(12):2755-2771.
Direct class switching to IgE generates IgE+ GC cells that are highly apoptotic and do not contribute to the memory compartment, while sequential switching through an IgG+ intermediate results in the generation of long-lived IgE+ plasma cells.
The mechanisms involved in the maintenance of memory IgE responses are poorly understood, and the role played by germinal center (GC) IgE+ cells in memory responses is particularly unclear. IgE+ B cell differentiation is characterized by a transient GC phase, a bias toward the plasma cell (PC) fate, and dependence on sequential switching for the production of high-affinity IgE. We show here that IgE+ GC B cells are unfit to undergo the conventional GC differentiation program due to impaired B cell receptor function and increased apoptosis. IgE+ GC cells fail to populate the GC light zone and are unable to contribute to the memory and long-lived PC compartments. Furthermore, we demonstrate that direct and sequential switching are linked to distinct B cell differentiation fates: direct switching generates IgE+ GC cells, whereas sequential switching gives rise to IgE+ PCs. We propose a comprehensive model for the generation and memory of IgE responses.
doi:10.1084/jem.20131539
PMCID: PMC3832920  PMID: 24218137
9.  Identification of sources of low frequency variability of arterial blood pressure: cardiac output acts as a buffer and not as a source 
Arterial blood pressure (ABP) short term variability is due to beat-by-beat fluctuations in cardiac output (CO) and total peripheral resistance (TPR), which have distinct effects at low and high frequencies. In particular, it was shown that CO is able to buffer TPR slow oscillations in the LF band, but it has not been addressed if CO can contribute to oscillations of ABP in this band. In this paper, we propose a model for the identification of ABP variability sources, in order to show evidence that CO fluctuations are not a source of ABP LF oscillations, but they only buffer ABP variability of vasomotor origin.
doi:10.1109/IEMBS.2010.5627826
PMCID: PMC3979347  PMID: 21097024
10.  Studies on soft centered coated snacks 
Roasted groundnut seeds, amaranth and dates pulp formed the center filling which was coated with sugar, breadings, desiccated coconut and roasted Bengalgram flour (BGF) to get 4 coated snacks. Physicochemical characteristics, microbiological profile, sorption behaviour and sensory quality of 4 coated snacks were determined. Centre filling to coating ratio of the products were in the range of 3:2–7:1, the product having BGF coating had the thinnest coating. Center filling had soft texture and the moisture content was 10.2–16.2% coating had lower moisture content (4.4–8.6%) except for Bengal gram coating, which had 11.1% moisture. Sugar coated snack has lowest fat (11.6%) and protein (7.2%) contents. Desiccated coconut coated snack has highest fat (25.4%) and Bengal gram flour coated snack had highest protein content (15.4%). Sorption studies showed that the coated snack had critical moisture content of 11.2–13.5%. The products were moisture sensitive and hence require packaging in films having higher moisture barrier property. In freshly prepared snacks coliforms, yeast and mold were absent. Mesophillic aerobes count did not show significant change during 90 days of storage at 27 °C and 37 °C. Sensory analysis showed that products had a unique texture due to combined effect of fairly hard coating and soft center. Flavour and overall quality of all the products were rated as very good.
doi:10.1007/s13197-011-0340-1
PMCID: PMC3550923  PMID: 24425933
Snacks; Soft centered; Coated snacks; Center filling; Coating material
11.  Importance of Serum Copper and Vascular Endothelial Growth Factor (VEGF-A) Levels in Postmenopausal Bleeding 
The main aim of this study is association of serum copper and vascular endothelial growth factor (VEGF-A) in postmenopausal bleeding (PMB) patients. Blood samples were collected from female patients suffering with postmenopausal bleeding (n = 50) as well as healthy females as controls (n = 50). Serum copper levels were estimated by spectrophotometric method and serum VEGF-A by ELISA technique and compared with ultrasonographic measurement of endometrial thickness in both patients and controls. A significant increase in serum copper levels and an almost twofold increase in serum VEGF-A was observed in DUB patients when compared with controls. Correlation (r) between serum VEGF-A levels and endometrial thickness was 0.96. Odds ratio for copper, VEGF-A and combination of copper and VEGF-A was 0.0426, 0.0947 and 0.0313 respectively, in all these cases odds ratio was <1. The abnormal angiogenesis in PMB could be due to increased serum copper levels,which in turn stimulates factors like VEGF-A, thereby causing an increase in endometrial growth.
doi:10.1007/s12291-012-0240-9
PMCID: PMC3613505  PMID: 24426200
Vascular endothelial growth factor; Postmenopausal bleeding; Serum copper; ELISA; VEGF-A
12.  Predictive Factors for Conversion of Laparoscopic Cholecystectomy 
doi:10.1007/s12262-012-0503-y
PMCID: PMC3644161  PMID: 24426415
13.  Association between heat shock protein 70 gene polymorphisms and clinical outcomes in intensive care unit patients with sepsis 
Objective:
The objective of the following study is to evaluate the associations between single nucleotide polymorphisms (SNPs) in the Heat Shock Protein 70 (HSP70) gene, gene expression of interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-α) and medical intensive care unit (MICU) stay and organ failure in sepsis.
Materials and Methods:
MICU patients with sepsis were genotyped for rs1061581, rs2227956, rs1008438 and rs1043618 polymorphisms in HSP70 gene using polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis or allele-specific PCR. Messenger ribonucleic acid (mRNA) expression of IL-6 and TNF-α were quantitated in peripheral blood lymphocytes. Outcomes were recorded.
Results:
108 patients (48 male) aged 40.7 ± 16.0 (mean ± standard deviation) years included H1N1 infection (36), scrub typhus (29) and urosepsis (12). Seventy-one (65.7%) had dysfunction of three or more organ systems, 66 patients (61.1%) were treated by mechanical ventilation, 21 (19.4%) needed dialysis. ICU stay was 9.3 ± 7.3 days. Mortality was 38.9%. One or more SNPs were noted in 101/108 (93.5%) and organ failure was noted in only 1/7 patients without a single SNP. The A allelotypes of rs1061581 and rs1008438 were associated with hematological dysfunction (P = 0.03 and 0.07) and longer ICU stay (P = 0.05 and 0.04), whereas IL-6 and TNF-α mRNA levels were associated with central nervous system dysfunction.
Conclusions:
HSP70 genotypes may determine some adverse outcomes in patients with sepsis.
doi:10.4103/0972-5229.130571
PMCID: PMC4033853  PMID: 24872649
Inflammatory response; innate immunity; interleukin-6; tumor necrosis factor-alpha
14.  RAG-mediated recombination is the predominant driver of oncogenic rearrangement in ETV6-RUNX1 acute lymphoblastic leukemia 
Nature genetics  2014;46(2):116-125.
The ETV6-RUNX1 fusion gene, found in 25% of childhood acute lymphoblastic leukemia (ALL), is acquired in utero but requires additional somatic mutations for overt leukemia. We used exome and low-coverage whole-genome sequencing to characterize secondary events associated with leukemic transformation. RAG-mediated deletions emerge as the dominant mutational process, characterized by recombination signal sequence motifs near the breakpoints; incorporation of non-templated sequence at the junction; ~30-fold enrichment at promoters and enhancers of genes actively transcribed in B-cell development and an unexpectedly high ratio of recurrent to non-recurrent structural variants. Single cell tracking shows that this mechanism is active throughout leukemic evolution with evidence of localized clustering and re-iterated deletions. Integration of point mutation and rearrangement data identifies ATF7IP and MGA as two new tumor suppressor genes in ALL. Thus, a remarkably parsimonious mutational process transforms ETV6-RUNX1 lymphoblasts, targeting the promoters, enhancers and first exons of genes that normally regulate B-cell differentiation.
doi:10.1038/ng.2874
PMCID: PMC3960636  PMID: 24413735
15.  Prevalence of rheumatic and congenital heart disease in school children of Andhra Pradesh, South India 
Objective
To determine the prevalence of rheumatic heart disease (RHD) and congenital heart disease (CHD) using clinical and echocardiographic criteria in rural and urban school children in Andhra Pradesh, South India.
Materials and methods
A total of 4213 school children between 5 and 16 years of age were screened. 1177 were from rural schools and 3036 from urban schools. Prevalence of RHD and CHD was estimated.
Results
Clinically RHD was present in 3 (prevalence 0.7/1000). Using echocardiography RHD was detected in 32 (7.6/1000), 11 (7.3/1000) from rural and 21 (7/1000) from urban schools. (P = 0.000, O.R = 0.093 and C.I. = 0.023–0.317). Total prevalence of RHD is 8.3/1000.
Clinically CHD was present in 39 (9.2/1000) children, rural 9 (7.6/1000) and urban 30 (9.9/1000). Using echocardiography CHD was detected in 44 (10.4/1000) children, rural 11 (9.3/1000) and urban 33 (10.8/1000).
Conclusion
RHD was detected several fold using echocardiographic screening than by clinical examination alone. Longitudinal follow-up of children with echocardiographically diagnosed subclinical RHD is needed.
doi:10.1016/j.jcdr.2012.11.003
PMCID: PMC3758100  PMID: 24023464
Congenital heart disease (CHD); Echocardiography; Rheumatic heart disease (RHD)
16.  Stigma is Associated with Delays in Seeking Care Among HIV-Infected People in India 
Background
Stigma shapes the lives of people living with HIV and may affect their willingness to seek medical care. But treatment delays can compromise health and increase the risk of transmission to others.
Purpose
To examine whether four stigma manifestations—enacted (discrimination), vicarious (hearing stories of discrimination), felt normative (perceptions of stigma’s prevalence) and internalized (personal endorsement of stigma beliefs)—were linked with delays in seeking care among HIV-infected people in India.
Methods
A cross-sectional survey was conducted with 961 HIV-positive men and women in Mumbai and Bengaluru.
Results
Enacted and internalized stigmas were correlated with delays in seeking care after testing HIV-positive. Depression symptoms mediated the associations of enacted and internalized stigmas with care seeking delays, whereas efforts to avoiding disclosing HIV status mediated only the association between internalized stigma and care seeking delays.
Conclusions
It is vital to develop stigma reduction interventions to ensure timely receipt of care.
doi:10.1177/1545109711432315
PMCID: PMC3482419  PMID: 22282878
HIV/AIDS; stigma; HIV care
17.  Primary treatments for clinically localized prostate cancer: a comprehensive lifetime cost-utility analysis 
BJU international  2012;111(3):437-450.
Objectives
To characterize the costs and outcomes associated with radical prostatectomy (open, laparoscopic, or robot-assisted) and radiation therapy (dose-escalated 3-dimensional conformal radiation, intensity-modulated radiation, brachytherapy, or combination), using a comprehensive, lifetime decision analytic model.
Patients and Methods
A Markov model was constructed to follow hypothetical men with low-, intermediate-, and high-risk prostate cancer over their lifetimes following primary treatment; probabilities of outcomes were based on an exhaustive literature search yielding 232 unique publications.
Patients could experience remission, recurrence, salvage treatment, metastasis, death from prostate cancer, and death from other causes.
Utilities for each health state were determined, and disutilities were applied for complications and toxicities of treatment.
Costs were determined from the U.S. payer perspective, with incorporation of patient costs in a sensitivity analysis.
Results
Differences in quality-adjusted life years across modalities were modest, ranging from 10.3 to 11.3 for low-risk patients, 9.6 to 10.5 for intermediate-risk patients, and 7.8 to 9.3 for high-risk patients.
There were no statistically significant differences among surgical modalities, which tended to be more effective than radiation modalities, with the exception of combination external beam + brachytherapy for high-risk disease.
Radiation modalities were consistently more expensive than surgical modalities; costs ranged from $19,901 (robot-assisted prostatectomy for low-risk disease) to $50,276 (combination radiation for high-risk disease).
These findings were robust to an extensive set of sensitivity analyses.
Conclusions
Our analysis found small differences in outcomes and substantial differences in payer and patient costs across treatment alternatives.
These findings may inform future policy discussions regarding strategies to improve efficiency of treatment selection for localized prostate cancer.
doi:10.1111/j.1464-410X.2012.11597.x
PMCID: PMC3587031  PMID: 23279038
prostate neoplasms; decision analysis; comparative effectiveness; surgery; radiation
18.  Signatures of mutational processes in human cancer 
Alexandrov, Ludmil B. | Nik-Zainal, Serena | Wedge, David C. | Aparicio, Samuel A.J.R. | Behjati, Sam | Biankin, Andrew V. | Bignell, Graham R. | Bolli, Niccolo | Borg, Ake | Børresen-Dale, Anne-Lise | Boyault, Sandrine | Burkhardt, Birgit | Butler, Adam P. | Caldas, Carlos | Davies, Helen R. | Desmedt, Christine | Eils, Roland | Eyfjörd, Jórunn Erla | Foekens, John A. | Greaves, Mel | Hosoda, Fumie | Hutter, Barbara | Ilicic, Tomislav | Imbeaud, Sandrine | Imielinsk, Marcin | Jäger, Natalie | Jones, David T.W. | Jones, David | Knappskog, Stian | Kool, Marcel | Lakhani, Sunil R. | López-Otín, Carlos | Martin, Sancha | Munshi, Nikhil C. | Nakamura, Hiromi | Northcott, Paul A. | Pajic, Marina | Papaemmanuil, Elli | Paradiso, Angelo | Pearson, John V. | Puente, Xose S. | Raine, Keiran | Ramakrishna, Manasa | Richardson, Andrea L. | Richter, Julia | Rosenstiel, Philip | Schlesner, Matthias | Schumacher, Ton N. | Span, Paul N. | Teague, Jon W. | Totoki, Yasushi | Tutt, Andrew N.J. | Valdés-Mas, Rafael | van Buuren, Marit M. | van ’t Veer, Laura | Vincent-Salomon, Anne | Waddell, Nicola | Yates, Lucy R. | Zucman-Rossi, Jessica | Futreal, P. Andrew | McDermott, Ultan | Lichter, Peter | Meyerson, Matthew | Grimmond, Sean M. | Siebert, Reiner | Campo, Elías | Shibata, Tatsuhiro | Pfister, Stefan M. | Campbell, Peter J. | Stratton, Michael R.
Nature  2013;500(7463):415-421.
All cancers are caused by somatic mutations. However, understanding of the biological processes generating these mutations is limited. The catalogue of somatic mutations from a cancer genome bears the signatures of the mutational processes that have been operative. Here, we analysed 4,938,362 mutations from 7,042 cancers and extracted more than 20 distinct mutational signatures. Some are present in many cancer types, notably a signature attributed to the APOBEC family of cytidine deaminases, whereas others are confined to a single class. Certain signatures are associated with age of the patient at cancer diagnosis, known mutagenic exposures or defects in DNA maintenance, but many are of cryptic origin. In addition to these genome-wide mutational signatures, hypermutation localized to small genomic regions, kataegis, is found in many cancer types. The results reveal the diversity of mutational processes underlying the development of cancer with potential implications for understanding of cancer etiology, prevention and therapy.
doi:10.1038/nature12477
PMCID: PMC3776390  PMID: 23945592
19.  Distribution of Capillary Transit Times in Isolated Lungs of Oxygen-Tolerant Rats 
Annals of biomedical engineering  2010;38(11):3449-3465.
Rats pre-exposed to 85% O2 for 5–7 days tolerate the otherwise lethal effects of 100% O2. The objective was to evaluate the effect of rat exposure to 85% O2 for 7 days on lung capillary mean transit time (t̄c) and distribution of capillary transit times (hc(t)). This information is important for subsequent evaluation of the effect of this hyperoxia model on the redox metabolic functions of the pulmonary capillary endothelium. The venous concentration vs. time outflow curves of fluorescein isothiocyanate labeled dextran (FITC-dex), an intravascular indicator, and coenzyme Q1 hydroquinone (CoQ1H2), a compound which rapidly equilibrates between blood and tissue on passage through the pulmonary circulation, were measured following their bolus injection into the pulmonary artery of isolated perfused lungs from rats exposed to room air (normoxic) or 85% O2 for 7 days (hyperoxic). The moments (mean transit time and variance) of the measured FITC-dex and CoQ1H2 outflow curves were determined for each lung, and were then used in a mathematical model [Audi et al. J. Appl. Physiol. 77: 332–351, 1994] to estimate t̄c and the relative dispersion (RDc) of hc(t). Data analysis reveals that exposure to hyperoxia decreases lung t̄c by 42% and increases RDc, a measure hc(t) heterogeneity, by 40%.
doi:10.1007/s10439-010-0092-5
PMCID: PMC3932033  PMID: 20552277
Perfusion heterogeneity; Hyperoxia; Coenzyme Q1; Multiple indicator dilution; Flow-limited indicators; Angiotensin converting enzyme
20.  Oral Rehydration Therapy in the Second Decade of the Twenty-first Century 
Oral rehydration solution (ORS) was established as the cornerstone of therapy for dehydration secondary to acute infectious diarrhea approximately 40 years ago. The efficacy of ORS is based on the ability of glucose to stimulate Na and fluid absorption in the small intestine via a cyclic AMP-independent process. Despite the establishment that ORS is the primary reason for the substantial reduction in morbidity and mortality from diarrhea in children in developing countries, the use of ORS has lagged for many reasons. This review highlights efforts to establish a major reformulation of ORS following the demonstration that short-chain fatty acids (SCFA) stimulate colonic Na and fluid absorption by a cyclic AMP-independent mechanism. The addition of high-amylose maize starch (HAMS), a microbially-fermentable (or ‘resistant’) starch, to ORS results in delivery of non-absorbed carbohydrate to the colon where it is fermented to SCFA. To date, three randomized controlled trials with a HAMS-ORS in south India have demonstrated a substantial decrease in diarrhea duration in both adults and children hospitalized for acute diarrhea. Significant efforts are now underway to establish this dual-action, modified HAMS-hypoosmolar ORS solution as the standard ORS for the treatment of dehydration from acute diarrhea.
doi:10.1007/s11894-014-0376-2
PMCID: PMC3950600  PMID: 24562469
Acute diarrhea; Dual-action oral rehydration solution; Fermentable/resistant starch; Oral rehydration solution; Short-chain fatty acids
21.  A rapid method for authentication of Buffalo (Bubalus bubalis) meat by Alkaline Lysis method of DNA extraction and species specific polymerase chain reaction 
Buffalo (Bubalus bubalis) meat is a major item of export from India but export of beef i.e. meat from cattle (Bos indicus) is prohibited. Also, adulteration of buffalo meat with that of beef (meat from cattle) is a common fraudulent practice because of prohibition on cow slaughter in most states of India. Food analysts require precise identification techniques to implement such regulations. In the present study, a method of DNA extraction by Alkaline lysis from meat samples and speciation of buffalo meat using species specific Polymerase Chain Reaction (PCR) has been reported. Alkaline lysis technique is a rapid method which involves triturating meat with four volumes of 0.2N NaOH, dilution of resultant liquid extract with eight volumes of 0.2N NaOH, heating the mix 75 °C for 20 min followed by neutralization with eight volumes of 0.04N Tris HCl. Entire procedure of DNA extraction takes less than 30 min and it is economical as it involves less expensive chemicals. Method was successfully applied in animal byproducts also viz., liver, heart and kidney. For authentication of buffalo meat, pair of primers was designed based on mitochondrial D loop gene nucleotide sequence. PCR amplification using the designed primers gave amplicon of size 482 bp in buffalo and no amplification was detected in closely related species viz., cattle, sheep and goat meat samples. Results of the assay were highly repetitive and reliable. An export sample referred by export regulation authorities was also analyzed by using the Alkaline lysis method of DNA extraction and species specific PCR which enabled authentication of meat within 5 h.
doi:10.1007/s13197-011-0230-6
PMCID: PMC3550954  PMID: 24425899
Bubalus bubalis; PCR; DNA; Alkaline lysis; Mitochondrial D loop gene; Speciation
22.  Evaluation of softening ability of Xylene & Endosolv-R on three different epoxy resin based sealers within 1 to 2 minutes - an in vitro study 
Objectives
This study evaluated the efficacy of Endosolv-R and Xylene in softening epoxy resin based sealer after 1 to 2 min exposure.
Materials and Methods
Sixty Teflon molds (6 mm × 1.5 mm in inner diameter and depth) were equally divided into 3 groups of 20 each. AH 26 (Dentsply/De Trey), AH Plus (Dentsply/De Trey), Adseal (Meta-Biomed) were manipulated and placed in the molds allotted to each group and allowed to set at 37℃ in 100% humidity for 2 wk. Each group was further divided into 2 subgroups according to the solvents used, i.e. Xylene (Lobachemie) and Endosolv-R (Septodont). Specimens in each subgroup were exposed to respective solvents for 1 and 2 min and the corresponding Vicker's microhardness (HV) was assessed. Data was analysed by Mauchly's test and two-way analysis of variance (ANOVA) with repeated measures, and one-way ANOVA.
Results
Initial hardness was significantly different among the three sealers with AH Plus having the greatest and Adseal having the least. After 2 min, Xylene softened AH Plus and Adseal sealer to 11% and 25% of their initial microhardness, respectively (p < 0.001), whereas AH 26 was least affected, maintaining 89.4% of its initial microhardness. After 2 min, Endosolv-R softened AH 26, AH Plus and Adseal to 12.7, 5.6 and 8.1% of their initial microhardness, respectively (p < 0.001).
Conclusions
Endosolv-R was a significantly more effective short term softener for all the tested sealers after 2 min whereas Xylene was an effective short term softener against AH plus and Adseal but less effective against AH 26.
doi:10.5395/rde.2014.39.1.17
PMCID: PMC3916501  PMID: 24516825
Adseal; AH 26; AH plus; Endosolv-R; Micro-hardness; Xylene
23.  Population Pharmacokinetics of Inhaled Tobramycin Powder in Cystic Fibrosis Patients 
Tobramycin powder for inhalation (TOBI Podhaler or TIP) is approved for the treatment of Pseudomonas aeruginosa airway infection in patients with cystic fibrosis (CF). A population pharmacokinetic model for tobramycin inhalation powder (TIP) in CF patients was developed to characterize the effect of covariates including body mass index (BMI) and lung function (forced expiratory volume in 1 s as percent of the predicted value (FEV1% predicted) at baseline) on the serum exposure parameters.
A two-compartment model with first-order elimination and first-order absorption was developed. Across a range of baseline demographic values in the study population, the predicted mean values for the maximum (Cmax) and trough (Ctrough) plasma concentrations at steady state were at least 7.5 and 5-fold lower, respectively, than the recommended thresholds for tobramycin toxicity (12 µg/ml for Cmax and 2 µg/ml for Ctrough). This model adequately described the tobramycin serum concentration–time course in CF patients following inhalation of TIP. The results indicate that no BMI- or FEV1-based dose adjustment is needed for use of TIP in CF patients.
doi:10.1038/psp.2013.76
PMCID: PMC3944114  PMID: 24522146
24.  Dual Targeting of MEK and PI3K Pathways Attenuates Established and Progressive Pulmonary Fibrosis 
PLoS ONE  2014;9(1):e86536.
Pulmonary fibrosis is often triggered by an epithelial injury resulting in the formation of fibrotic lesions in the lung, which progress to impair gas exchange and ultimately cause death. Recent clinical trials using drugs that target either inflammation or a specific molecule have failed, suggesting that multiple pathways and cellular processes need to be attenuated for effective reversal of established and progressive fibrosis. Although activation of MAPK and PI3K pathways have been detected in human fibrotic lung samples, the therapeutic benefits of in vivo modulation of the MAPK and PI3K pathways in combination are unknown. Overexpression of TGFα in the lung epithelium of transgenic mice results in the formation of fibrotic lesions similar to those found in human pulmonary fibrosis, and previous work from our group shows that inhibitors of either the MAPK or PI3K pathway can alter the progression of fibrosis. In this study, we sought to determine whether simultaneous inhibition of the MAPK and PI3K signaling pathways is a more effective therapeutic strategy for established and progressive pulmonary fibrosis. Our results showed that inhibiting both pathways had additive effects compared to inhibiting either pathway alone in reducing fibrotic burden, including reducing lung weight, pleural thickness, and total collagen in the lungs of TGFα mice. This study demonstrates that inhibiting MEK and PI3K in combination abolishes proliferative changes associated with fibrosis and myfibroblast accumulation and thus may serve as a therapeutic option in the treatment of human fibrotic lung disease where these pathways play a role.
doi:10.1371/journal.pone.0086536
PMCID: PMC3903543  PMID: 24475138
25.  Combined effects of prenatal inhibition of vasculogenesis and neurogenesis on rat brain development 
Neurobiology of disease  2008;32(3):499-509.
Malformations of cortical development (MCD) are one of the most common causes of neurological disabilities including autism and epilepsy. To disrupt cortical formation, methylazoxymethanol (MAM) or thalidomide (THAL) has been used to affect neurogenesis or vasculogenesis. Although previous models of MCD have been useful, these models primarily attack a single aspect of cortical development. We hypothesized that simultaneous prenatal exposure to MAM or THAL will lead to the development of a novel and specific type of brain maldevelopment. Rats were prenatally exposed to MAM and THAL. At early postnatal days, brains displayed abnormal ventricular size and hemispheric asymmetry due to altered brain water homeostasis. The postnatal brain was also characterized by gliosis in regions of focal leakage of the blood brain barrier. These morphological abnormalities gradually disappeared at adult stages. Although the adult MAM-THAL rats showed normal cortical morphology, abnormal hippocampal connectivity and mossy fiber sprouting persisted well into adulthood.
doi:10.1016/j.nbd.2008.09.007
PMCID: PMC3900291  PMID: 18930144
Blood–brain barrier; Cerebrovascular function; Angiogenesis; In utero; Epilepsy; Hydrocephalus

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