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Erdemir E, Hoffmann K, Walczak A, Dashkoff N, Iyer V, Gopal A. SU-FF-I-125: Accuracy and Reliability of Manual Vessel Sizing Measurements Among Different Users and Systems. Med Phys 2007. [DOI: 10.1118/1.2760501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Vining C, Iyer V, Bhatnagar S. Intracerebroventricular administration of corticotrophin-releasing hormone receptor antagonists produces different effects on hypothalamic pituitary adrenal responses to novel restraint depending on the stress history of the animal. J Neuroendocrinol 2007; 19:198-207. [PMID: 17280593 DOI: 10.1111/j.1365-2826.2006.01522.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Corticotrophin-releasing hormone (CRH) regulates acute stress-induced changes in neuroendocrine function and behaviour. However, little is known about CRH functions in animals that have prior experience with repeated stress. Repeatedly-stressed rats exhibit a habituated hypothalamic-pituitary-adrenal (HPA) response to a familiar, homotypic stressor but exhibit maintained or enhanced HPA responses to a novel, heterotypic stressor. We examined the effects of intracerebroventricular (i.c.v.) administration of two different nonselective CRH receptor antagonists, alpha-helical CRH(9-41) (ahCRH) or D-Phe CRH(12-41) (D-PheCRH), on HPA responses to acute restraint in rats previously exposed to repeated cold stress (i.e. facilitated responses). Antagonists were administered as single i.c.v. injections prior to restraint to provide a general index of CRH function in control versus repeatedly-stressed rats. CRH receptor blockade with either ahCRH or D-PheCRH produced different effects on HPA responses to novel restraint depending on whether the animal had been previously cold stressed or not. Interestingly, some agonist-type effects were observed but only in repeatedly-stressed rats. In summary, these results indicate that manipulations of the CRH receptor have different effects on HPA activity depending on the stress history of the animal.
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Kuchi P, Iyer V, Hiremagalur R, Panchanathan S. Characteristics of gait of humans with incomplete spinal cord injury. CONFERENCE PROCEEDINGS : ... ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL CONFERENCE 2007; 2006:586-9. [PMID: 17271744 DOI: 10.1109/iembs.2004.1403225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Epidural spinal cord stimulation has been demonstrated to help the recovery of walking abilities of patients with incomplete spinal cord injury when combined with partial weight bearing therapy. However, no work has been done in studying the dynamics of these signals generated with and without stimulation. We show that the underlying dynamics of such signals is chaotic. We also estimate the correlation dimension of these signals and show the difference in the dynamics of gait with and without stimulation using the kinematic data of right knee and right hip. The correlation dimension thus estimated can be used to evaluate the efficiency of epidural spinal cord stimulation in patients.
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Bosiers M, Iyer V, Deloose K, Verbist J, Peeters P. Flemish experience using the Advanta V12 stent-graft for the treatment of iliac artery occlusive disease. THE JOURNAL OF CARDIOVASCULAR SURGERY 2007; 48:7-12. [PMID: 17308516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
AIM The aim of this study was to evaluate the technical feasibility and safety of implanting a polytetrafluoroethylene (PTFE) covered balloon expandable stent to treat iliac artery stenoses and occlusions. Additionally, the primary patency and clinical and hemodynamic efficacy at 1 year were analysed. METHODS This nonrandomized, prospective study involved patients with claudication and iliac artery occlusive disease at 2 participating centres. Patients with suitable lesions determined by clinical examination, ankle-brachial indices (ABIs), colour-flow duplex ultrasound (CFDU), magnetic resonance angiogram (MRA) and confirmed with biplanar digital subtraction angiography (DSA) were treated with PTFE-covered stainless steel stents. Procedural and 30-day periprocedural complications were recorded prospectively. According to in-hospital standards, follow-up with clinical ischemia category determination, ABI and CFDU was performed at 1, 6 and 12 months to determine treatment efficacy and primary limb patency. RESULTS In total, 91 limbs were treated in 65 patients (51 male; mean age 65 years). Stent-graft deployment was successful in 91 (100%) limbs. There were no limbs with residual stenosis >30%. There were no procedural or 30-day complications. The clinical ischemia category distribution improved significantly at 1, 6 and 12 months. The mean ABI rose significantly from 0.59 before treatment to 0.98, 0.98 and 0.99 at 1, 6 and 12 months after the procedure. Primary limb patency at 1-year was 91.1% CONCLUSIONS Implantation of Advanta V12 PTFE-covered stent for iliac occlusive disease shows to be safe and feasible with excellent clinical results at 1 year in the investigated patient cohort.
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Gupte T, Iyer V, Damle SG, Malik N, Halbe A. Osteogenesis imperfecta. J Indian Soc Pedod Prev Dent 2006; 24 Suppl 1:S44-6. [PMID: 16891753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
Osteogenesis imperfecta is an inherited disorder of the connective tissue. The extreme bone fragility seen in patients suffering from osteogenesis imperfecta pose a series of problems with regard to behavior management and rendering of quality dental treatment. Presented here a case of a four year old child suffering from osteogenesis imperfecta.
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Birney E, Andrews D, Caccamo M, Chen Y, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez-Suarez XM, Flicek P, Gräf S, Hammond M, Herrero J, Howe K, Iyer V, Jekosch K, Kähäri A, Kasprzyk A, Keefe D, Kokocinski F, Kulesha E, London D, Longden I, Melsopp C, Meidl P, Overduin B, Parker A, Proctor G, Prlic A, Rae M, Rios D, Redmond S, Schuster M, Sealy I, Searle S, Severin J, Slater G, Smedley D, Smith J, Stabenau A, Stalker J, Trevanion S, Ureta-Vidal A, Vogel J, White S, Woodwark C, Hubbard TJP. Ensembl 2006. Nucleic Acids Res 2006; 34:D556-61. [PMID: 16381931 PMCID: PMC1347495 DOI: 10.1093/nar/gkj133] [Citation(s) in RCA: 323] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The Ensembl () project provides a comprehensive and integrated source of annotation of large genome sequences. Over the last year the number of genomes available from the Ensembl site has increased from 4 to 19, with the addition of the mammalian genomes of Rhesus macaque and Opossum, the chordate genome of Ciona intestinalis and the import and integration of the yeast genome. The year has also seen extensive improvements to both data analysis and presentation, with the introduction of a redesigned website, the addition of RNA gene and regulatory annotation and substantial improvements to the integration of human genome variation data.
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Bhatnagar S, Vining C, Iyer V, Kinni V. Changes in hypothalamic-pituitary-adrenal function, body temperature, body weight and food intake with repeated social stress exposure in rats. J Neuroendocrinol 2006; 18:13-24. [PMID: 16451216 DOI: 10.1111/j.1365-2826.2005.01375.x] [Citation(s) in RCA: 149] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
These present studies aimed to compare changes in hypothalamic-pituitary-adrenal (HPA) activity and body temperature in response to acute social defeat, to repeated social stress and to novel restraint after repeated stress, as well as to assess effects on metabolic parameters by measuring body weight gain and food and water intake. We found that social defeat produced a marked increase in both adrenocorticotrophic hormone and corticosterone compared to placement in a novel cage. Similarly, body temperature was also increased during social defeat and during 30 min of recovery from defeat. We then examined the effects of 6 days of repeated social stress and observed minimal HPA responses to repeated social stress compared to control rats. These neuroendocrine responses were contrasted by robust increases in body temperature during stress and during recovery from stress during 6 days of repeated stress. However, in response to novel restraint, repeatedly stressed rats displayed facilitated body temperature responses compared to controls, similar to our previous findings with HPA activity. Food intake was increased during the light period during which defeat took place, but later intake during the dark period was not affected. Repeated stress decreased body weight gain in the dark period but food intake was increased overall during the 6 days of repeated stress in the light period. As a result, repeated stress increased cumulative food intake during the light period in the stressed rats but these relatively small increases in food intake were unable to prevent the diminished total weight gain in repeatedly stressed rats. Overall, the results demonstrate that, although acute social defeat has similar effects on temperature and HPA activity, repeated exposure to social stress has divergent effects on HPA activity compared to body temperature and that dampened weight gain produced by repeated social stress cannot be fully explained by changes in food intake.
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Iyer V, Kato Y, Sano H, Yoneda M, Kaito T, Kanno T. Clip reconstruction for a case of peripheral posterior inferior cerebellar artery aneurysm: case report. MINIMALLY INVASIVE NEUROSURGERY : MIN 2005; 48:244-6. [PMID: 16172972 DOI: 10.1055/s-2005-870902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The authors report an unusual surgical treatment for an aneurysm on the left peripheral posterior inferior cerebellar artery (PICA). The computed tomographic scan showed subarachnoid haemorrhage and a haematoma in the left cerebellar region close to the fourth ventricle. The 3D CT angiography demonstrated an aneurysm on the left peripheral PICA which was confirmed on four-vessel angiography. The aneurysm was approached through a posterior suboccipital craniotomy and the PICA was reconstructed with multiple clips. The literature concerning peripheral PICA aneurysms and their treatment is reviewed and discussed.
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Hubbard T, Andrews D, Caccamo M, Cameron G, Chen Y, Clamp M, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez-Suarez XM, Gilbert J, Hammond M, Herrero J, Hotz H, Howe K, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Keenan S, Kokocinsci F, London D, Longden I, McVicker G, Melsopp C, Meidl P, Potter S, Proctor G, Rae M, Rios D, Schuster M, Searle S, Severin J, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Trevanion S, Ureta-Vidal A, Vogel J, White S, Woodwark C, Birney E. Ensembl 2005. Nucleic Acids Res 2005; 33:D447-53. [PMID: 15608235 PMCID: PMC540092 DOI: 10.1093/nar/gki138] [Citation(s) in RCA: 354] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2004] [Revised: 11/01/2004] [Accepted: 11/01/2004] [Indexed: 11/17/2022] Open
Abstract
The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of large genome sequences. Over the last year the number of genomes available from the Ensembl site has increased by 7 to 16, with the addition of the six vertebrate genomes of chimpanzee, dog, cow, chicken, tetraodon and frog and the insect genome of honeybee. The majority have been annotated automatically using the Ensembl gene build system, showing its flexibility to reliably annotate a wide variety of genomes. With the increased number of vertebrate genomes, the comparative analysis provided to users has been greatly improved, with new website interfaces allowing annotation of different genomes to be directly compared. The Ensembl software system is being increasingly widely reused in different projects showing the benefits of a completely open approach to software development and distribution.
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Birney E, Andrews D, Bevan P, Caccamo M, Cameron G, Chen Y, Clarke L, Coates G, Cox T, Cuff J, Curwen V, Cutts T, Down T, Durbin R, Eyras E, Fernandez-Suarez XM, Gane P, Gibbins B, Gilbert J, Hammond M, Hotz H, Iyer V, Kahari A, Jekosch K, Kasprzyk A, Keefe D, Keenan S, Lehvaslaiho H, McVicker G, Melsopp C, Meidl P, Mongin E, Pettett R, Potter S, Proctor G, Rae M, Searle S, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Ureta-Vidal A, Woodwark C, Clamp M, Hubbard T. Ensembl 2004. Nucleic Acids Res 2004; 32:D468-70. [PMID: 14681459 PMCID: PMC308772 DOI: 10.1093/nar/gkh038] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organize biology around the sequences of large genomes. It is a comprehensive and integrated source of annotation of large genome sequences, available via interactive website, web services or flat files. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. The facilities of the system range from sequence analysis to data storage and visualization and installations exist around the world both in companies and at academic sites. With a total of nine genome sequences available from Ensembl and more genomes to follow, recent developments have focused mainly on closer integration between genomes and external data.
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Reid KH, Paskitti M, Guo SZ, Schmelzer T, Iyer V. Experience with ketamine and sodium pentobarbital as anesthetics in a rat model of cardiac arrest and resuscitation. Resuscitation 2003; 57:201-10. [PMID: 12745189 DOI: 10.1016/s0300-9572(03)00025-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We review 7 years experience with the chest compression model of cardiac arrest and resuscitation, comparing two different anesthetics. Ketamine stimulates cardiac function and only mildly depresses respiration; of the two it provides easier resuscitation. However, ketamine severely depresses brain protein synthesis; in studies using this measure ketamine is unsuitable and another agent must be used. Sodium pentobarbital mildly depresses brain protein synthesis, but depresses both cardiac and respiratory function, making resuscitation more difficult. Use of alternate chest/abdominal pumping (Babbs resuscitation technique), with judicious use of intra-cardiac epinephrine (adrenaline), made resuscitation reliable under sodium pentobarbital as well.
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Clamp M, Andrews D, Barker D, Bevan P, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Hubbard T, Kasprzyk A, Keefe D, Lehvaslaiho H, Iyer V, Melsopp C, Mongin E, Pettett R, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, Birney E. Ensembl 2002: accommodating comparative genomics. Nucleic Acids Res 2003; 31:38-42. [PMID: 12519943 PMCID: PMC165530 DOI: 10.1093/nar/gkg083] [Citation(s) in RCA: 180] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of human, mouse and other genome sequences, available as either an interactive web site or as flat files. Ensembl also integrates manually annotated gene structures from external sources where available. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. These range from sequence analysis to data storage and visualisation and installations exist around the world in both companies and at academic sites. With both human and mouse genome sequences available and more vertebrate sequences to follow, many of the recent developments in Ensembl have focusing on developing automatic comparative genome analysis and visualisation.
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Sousa J, Iyer V, Roberts G. 'Mirror image' distal anterior cerebral artery aneurysms. A case report of two patients with review of literature. Acta Neurochir (Wien) 2002; 144:933-5; discussion 935. [PMID: 12376776 DOI: 10.1007/s00701-002-0986-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We report two cases of patients with bilateral 'mirror image' or 'kissing' aneurysms at the distal anterior cerebral arteries who presented with subarachnoid haemorrhage and frontal intracerebral haematoma.
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Turner JA, Iyer V, McEwen RS, Herz W. Structure of the products resulting from photochemically induced hydrogen transfers in the levopimaric acid-cyclopentenedione adduct. J Org Chem 2002. [DOI: 10.1021/jo00915a034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Morgan BLG, Chao CR, Iyer V, Ross MG. Correlation between fetal scalp blood samples and intravascular blood pH, pO2 and oxygen saturation measurements. J Matern Fetal Neonatal Med 2002; 11:325-8. [PMID: 12389674 DOI: 10.1080/jmf.11.5.325.328] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
OBJECTIVE This study was designed to compare the values of blood gases in local scalp blood, obtained by scalp blood sampling, with direct measurements of fetal preductal arterial blood in fetal sheep. METHODS Six fetal lambs were catheterized in the brachial artery and vein. Maternal oxygenation was reduced in steps from a fractional inspired oxygen concentration (FiO2) of 20 to 5% by addition of nitrogen to the inhaled gas mixture. Fetal scalp and arterial blood were sampled simultaneously at maternal FiO2 step intervals after maternal FiO2 and oxygen were stable for > 5 min. Blood pH, pO2 and oxygen saturation were measured and linear regression was performed to determine the correlation between these values. RESULTS Scalp pH correlated well with arterial pH, whereas scalp pO2, pCO2 and oxygen saturation did not. However, when a secondary analysis was performed taking into account the effects of aerobic contamination, scalp pCO2, pO2 and oxygen saturation became highly correlated with arterial values. CONCLUSIONS Local scalp blood oxygen saturation correlates highly with fetal preductal arterial values, when physiological artifacts are eliminated. The technique of scalp blood sampling introduces error into oxygenation saturation measurements, owing to difficulties in anaerobic sample collection. These results suggest that continuous measurement of fetal scalp oxygenation by noninvasive oximetry may be superior to direct sampling of scalp blood.
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Nijland MJ, Shankar U, Iyer V, Ross MG. Assessment of fetal scalp oxygen saturation determination in the sheep by transmission pulse oximetry. Am J Obstet Gynecol 2000; 183:1549-53. [PMID: 11120526 DOI: 10.1067/mob.2000.107736] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
OBJECTIVE Electronic fetal heart rate monitoring has an unacceptable false-positive nonreassuring rate, which results in an excess of operative interventions. As a more objective measure of fetal oxygenation, fetal scalp pulse oximetry has been used to assess fetal blood oxygen saturation (SO (2)). The current devices use reflectance oximetry, which has inherent limitations. These include varying depths of signal penetration, variation with position, and potential for optical interference. In this study we evaluated a newly developed transmission pulse oximetry device consisting of transmitter and receiver diodes mounted within the coil of a standard scalp electrode (Spiral O(2)CTG; Respironics Inc, Marietta, Ga). STUDY DESIGN Six pregnant ewes at 127 to 135 days' gestation (term, 145 days' gestation) were anesthetized, intubated, and prepared with a femoral artery catheter. Fetuses were prepared with brachial artery and jugular vein catheters. Maternal inspired oxygen fraction was titrated from 21% to 3%. Oximetry O(2)CTG devices were positioned on the fetal scalp, and recordings were compared with directly determined fetal arterial pH, PO (2), and SO (2) values. RESULTS Maternal SaO (2) and PaO (2) ranged from 102% to 16% and 110 to 18 mm Hg, respectively. Fetal SaO (2) and PaO (2) ranged from 76% to 12% and 28 to 8 mm Hg, respectively. There was excellent correlation between direct fetal SaO (2) and scalp SO (2) (r (2) = 0.90; scalp SO (2) = 0.79 SaO (2) + 6.89). With an SaO (2) of <30% as the cutoff point for assessment of fetal compromise, scalp SO (2) measurements had a 94% +/- 10% specificity and a 94% +/- 10% positive predictive value. CONCLUSION (1) Preliminary studies of the Spiral O(2)CTG sensor demonstrated high correlation of scalp SO (2) with fetal SaO (2). (2) Although potential inaccuracies remain, transmission oximetry may offer potential advantages in consistency, ease of application, and technology with respect to the current reflection oximeter devices.
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Eisler T, Svensson O, Iyer V, Wejkner B, Schmalholz A, Larsson H, Elmstedt E. Revision total hip arthroplasty using third-generation cementing technique. J Arthroplasty 2000; 15:974-81. [PMID: 11112190 DOI: 10.1054/arth.2000.9825] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
A total of 83 consecutive first-revision total hip arthroplasties were performed in 83 patients using pressurized vacuum-mixed cement, a third-generation cementing technique. At a median follow-up of 3.6 years (range, 1.5-6.3 years), the overall failure rates (radiographic loosening, re-revision, or both) were 39% for the femoral components and 30% for the acetabular components. With definite radiographic loosening as an endpoint, the cement-bone interface achieved was the only significant factor to predict stem durability, with an adjusted odds ratio of 1.8 (95% confidence interval, 1.1-3.0). On the acetabular side, bone stock was the only significant factor, with an adjusted odds ratio of 5.3 (95% confidence interval, 4.0-27.7). In this retrospective cohort study, femoral cement pressurization per se did not appear to improve the results over those of other studies using second-generation techniques.
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Ross DT, Scherf U, Eisen MB, Perou CM, Rees C, Spellman P, Iyer V, Jeffrey SS, Van de Rijn M, Waltham M, Pergamenschikov A, Lee JC, Lashkari D, Shalon D, Myers TG, Weinstein JN, Botstein D, Brown PO. Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet 2000; 24:227-35. [PMID: 10700174 DOI: 10.1038/73432] [Citation(s) in RCA: 1573] [Impact Index Per Article: 65.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We used cDNA microarrays to explore the variation in expression of approximately 8,000 unique genes among the 60 cell lines used in the National Cancer Institute's screen for anti-cancer drugs. Classification of the cell lines based solely on the observed patterns of gene expression revealed a correspondence to the ostensible origins of the tumours from which the cell lines were derived. The consistent relationship between the gene expression patterns and the tissue of origin allowed us to recognize outliers whose previous classification appeared incorrect. Specific features of the gene expression patterns appeared to be related to physiological properties of the cell lines, such as their doubling time in culture, drug metabolism or the interferon response. Comparison of gene expression patterns in the cell lines to those observed in normal breast tissue or in breast tumour specimens revealed features of the expression patterns in the tumours that had recognizable counterparts in specific cell lines, reflecting the tumour, stromal and inflammatory components of the tumour tissue. These results provided a novel molecular characterization of this important group of human cell lines and their relationships to tumours in vivo.
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Abstract
BACKGROUND Menorrhagia (heavy menstrual bleeding) is a benign yet debilitating social and health condition. The widely accepted clinical definition of menorrhagia is blood loss of 80ml or more per period. This figure is derived from population studies that have shown that the average blood loss is between 30 and 40ml, and 90% of women have blood losses of less than 80ml. Excessive menstrual bleeding is the commonest cause of iron deficiency in the United Kingdom affecting 20-25% of the fertile female population. Menorrhagia is a common problem accounting for 12% of all gynaecological referral in the UK. Ranges of medical therapies are prescribed in order to reduce excessive menstrual blood loss, including prostaglandin synthetase inhibitors, antifibrinolytics, the oral contraceptive pill and other hormones. The combined oral contraceptive pill (OCP) is claimed to have a variety of beneficial, inducing a regular shedding of a thinner endometrium and inhibiting ovulation thus having the effect of treating menorrhagia and providing contraception. OBJECTIVES To determine whether: 1. the OCP is an effective medical therapy to reduce menorrhagia in both the short term and long term. 2. the effectiveness of combined oral contraceptive pills (OCP) compared with other medical therapies for the treatment of menorrhagia. 3. OCP is a more cost effective method than any other medical treatments of menorrhagia. 4. OCP has fewer side effects than other drugs used for menorrhagia. SEARCH STRATEGY All publications which describe randomised trials of OCP for the treatment of menorrhagia were obtained using the search strategy developed by the Menstrual Disorders Group. SELECTION CRITERIA All randomised controlled comparisons of OCP versus other medical therapies, placebo or no treatment for the treatment of menorrhagia. Women of reproductive years with regular heavy periods, measured either objectively or subjectively and greater than, or equal to, two months follow up. DATA COLLECTION AND ANALYSIS All assessments of the quality of trials and data extraction were performed unblinded by at least two reviewers. Only one trial met the inclusion criteria and none were excluded. The included trial involved a total of 45 women. MAIN RESULTS As the trial used a cross-over design, only data from the first treatment period (cycles 3 and 4 ) were analysed. The results from all the three mefanamic acid groups were combined. There was no significant difference in menstrual blood loss (MBL) between those patients treated with the OCP and danazol, mefenamic acid or naproxen. REVIEWER'S CONCLUSIONS The one small study identified [Fraser 1991] found no significant difference between groups treated with OCP, mefenamic acid, low dose danazol or naproxen. Overall, the evidence from the one study identified [Fraser 1991] is not sufficient to adequately assess the effectiveness of OCP. This review was unable to achieve its stated objectives because of the paucity of the data.
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Chan SA, Reid KH, Schurr A, Miller JJ, Iyer V, Tseng MT. Fosphenytoin reduces hippocampal neuronal damage in rat following transient global ischemia. Acta Neurochir (Wien) 1999; 140:175-80. [PMID: 10398998 DOI: 10.1007/s007010050080] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Fosphenytoin, a water-soluble disodium phosphate ester of phenytoin, is a phenytoin prodrug with similar anticonvulsant properties. In this study, we evaluated its neuroprotective properties in a cardiac arrest-induced global ischemia model. After 12 minute ischemia, Long-Evans hooded rats were resuscitated, given fosphenytoin (30 mg/kg, i.m.) or saline 5 minutes after the ischemic episode, and killed on day 7. Brains were removed, fixed, and vibratome sectioned to assess the numbers of normal appearing CAI pyramidal neurons and for immunohistological staining of glial fibrillary acidic protein (GFAP). After global ischemia, the number of hippocampal CA1 pyramidal neurons decreased significantly (from 14.33 +/- 1.73 to 2.19 +/- 0.16 per 100 micron 2). Most hippocampal CA1 pyramidal neurons showed signs of injury and GFAP immunoreactivity of the region increased. With fosphenytoin treatment 5 min after ischemia, hippocampal CA1 pyramidal neurons remained at near control level (13.90 +/- 0.92), however, GFAP staining was not significantly changed. Our data, although indicating different neuronal and glial responses following fosphenytoin treatment, nevertheless, suggest that fosphenytoin is an effective neuroprotectant against ischemia-induced damage.
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Perry SF, Reid SG, Wankiewicz E, Iyer V, Gilmour KM. Physiological Responses of Rainbow Trout (Oncorhynchus mykiss) to Prolonged Exposure to Soft Water. ACTA ACUST UNITED AC 1996. [DOI: 10.1086/physzool.69.6.30164267] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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72
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Iyer V, Struhl K. Absolute mRNA levels and transcriptional initiation rates in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 1996; 93:5208-12. [PMID: 8643554 PMCID: PMC39223 DOI: 10.1073/pnas.93.11.5208] [Citation(s) in RCA: 146] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
We quantitate the absolute levels of individual mRNAs per yeast cell by hybridizing total yeast RNA with an excess of gene-specific 32P-oligonucleotides, and digesting the resulting RNA-DNA hybrids with S1 nuclease. By comparing the his3 hybridization signal from a known amount of yeast cells to the signal generated by a known amount of his3 RNA synthesized in vitro, we determine that yeast strain KY114 growing in yeast extract/peptone/glucose medium at 30 degrees C contains seven molecules of his3 mRNA per cell. Using a galactose shut-off procedure, we determined that the half-life of his3 mRNA is approximately 11 min under these conditions. From these observations, we calculate that one his3 mRNA molecule is synthesized every 140 s. Analysis of other his3 promoter derivatives suggests that the maximal transcriptional initiation rate in yeast cells is one mRNA molecule every 6-8 s. Using his3 as an internal standard, the number of mRNA molecules per cell have been determined for ded1, trp3, rps4, and gall under a variety of growth conditions. From these results, the absolute mRNA level of any yeast gene can be determined in a single hybridization experiment. Moreover, the rate of transcriptional initiation can be determined for mRNAs whose decay rates are known.
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Reid KH, Young C, Schurr A, Tseng M, Payne RS, Keelen P, Miller J, Iyer V. Audiogenic seizures following global ischemia induced by chest compression in Long-Evans rats. Epilepsy Res 1996; 23:195-209. [PMID: 8739123 DOI: 10.1016/0920-1211(95)00099-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Transient global ischemia was used to produce a rat model of generalized tonic-clonic epilepsy. Controlled chest compression in ketamine-anesthesized Long-Evans rats produced transient global ischemia by mechanically preventing the heart from pumping blood. Circulation was restored by standard cardiopulmonary resuscitation techniques. With a temporal muscle (skull) temperature of 35 +/- 0.4 degrees C, 75% (76/102) of the rats survived 7 min of chest compression. Generalized seizures could be evoked in 78% (59/76) of the surviving rats by a 60 s exposure to a loud sound (bell, 110 dB) beginning 24 h after the ischemic episode. The seizure patterns seen resembled those described by Maresceaux (1987) for genetically seizure-prone Wistar rats. Susceptibility to sound-induced seizures declined with time, with wide variations in recovery rate between individuals; one rat showed a daily sound-induced seizure for over 5 months. Seizures were attenuated or blocked by treatment with carbamazepine or sodium valproate. This model is similar to the great vessel occlusion model used by Kawai et al. (1995), but is less invasive. We believe it will be useful in the evaluation of therapies for acquired generalized (grand mal) seizures.
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Jagose JT, Suresh G, Iyer V, Kirpalani AL, Chitale AR. On the importance of electron microscopic evaluation of renal biopsies in glomerular disease. THE JOURNAL OF THE ASSOCIATION OF PHYSICIANS OF INDIA 1996; 44:70. [PMID: 8773105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Iyer V, Struhl K. Mechanism of differential utilization of the his3 TR and TC TATA elements. Mol Cell Biol 1995; 15:7059-66. [PMID: 8524273 PMCID: PMC230961 DOI: 10.1128/mcb.15.12.7059] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The yeast his3 promoter region contains two TATA elements, TC and TR, that are differentially utilized in constitutive his3 transcription and Gcn4-activated his3 transcription. TR contains the canonical TATAAA sequence, whereas TC is an extended region that lacks a conventional TATA sequence and does not support transcription in vitro. Surprisingly, differential his3 TATA-element utilization does not depend on specific properties of activator proteins but, rather, is determined by the overall level of his3 transcription. At low levels of transcription, the upstream TC is preferentially utilized, even though it is inherently a much weaker TATA element than TR. The TATA elements are utilized equally at intermediate levels, whereas TR is strongly preferred at high levels of transcription. This characteristic behavior can be recreated by replacing TC with moderately functional derivatives of a conventional TATA element, suggesting that TC is a collection of weak TATA elements. Analysis of promoters containing two biochemically defined TATA elements indicates that differential utilization occurs when the upstream TATA element is weaker than the downstream element. In other situations, the upstream TATA element is preferentially utilized in a manner that is independent of the overall level of transcription. Thus, in promoters containing multiple TATA elements, relative utilization not only depends on the quality and arrangement of the TATA elements but can vary with the overall level of transcriptional stimulation. We suggest that differential TATA utilization results from the combination of an intrinsic preference for the upstream element and functional saturation of weak TATA elements at low levels of transcriptional stimulation.
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