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Kaye M, Skidmore S, Howells K, McGeoch C, Gregson P, Spencer-Jones R, Graham N, Warren R. P19.02 The Use of a Real Time PCR for Diagnosis of Hip and Knee Prosthetic Infection: Method Development and Comparison with Histology and Bacterial Culture. J Hosp Infect 2006. [DOI: 10.1016/s0195-6701(06)60358-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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77
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Li C, Li XZ, Graham N. A study of the preparation and reactivity of potassium ferrate. CHEMOSPHERE 2005; 61:537-43. [PMID: 16202807 DOI: 10.1016/j.chemosphere.2005.02.027] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2004] [Revised: 02/07/2005] [Accepted: 02/14/2005] [Indexed: 05/04/2023]
Abstract
In the context of water treatment, the ferrate ([FeO(4)](2-)) ion has long been known for its strong oxidizing power and for producing a coagulant from its reduced form (i.e. Fe(III)). However, it has not been studied extensively owing to difficulties with its preparation and its instability in water. This paper describes an improved procedure for preparing solid phase potassium ferrate of high purity (99%) and with a high yield (50-70%). The characteristics of solid potassium ferrate were investigated and from XRD spectra it was found that samples of the solid have a tetrahedral structure with a space group of D(2h) (Pnma) and a=7.705A, b=5.863A, and c=10.36A. The aqueous stability of potassium ferrate at various pH values and different concentrations was investigated. It was found that potassium ferrate solution had a maximum stability at pH 9-10 and that ferrate solution at low concentration (0.25 mM) was more stable than at high concentration (0.51 mM). The aqueous reaction of ferrate with bisphenol A (BPA), a known endocrine disrupter compound, was also investigated with a molar ratio of Fe(VI):BPA in the range of 1:1-5:1. The optimal pH for BPA degradation was 9.4, and at this pH and a Fe(VI):BPA molar ratio of 5:1, approximately 90% of the BPA was degraded after 60s.
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Wolfson SS, Graham N. Dynamics of contrast-gain controls in pattern vision. J Vis 2005. [DOI: 10.1167/5.8.760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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79
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Lau TK, Chu W, Graham N. The degradation of endocrine disruptor di-n-butyl phthalate by UV irradiation: a photolysis and product study. CHEMOSPHERE 2005; 60:1045-53. [PMID: 15993151 DOI: 10.1016/j.chemosphere.2005.01.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2004] [Revised: 01/03/2005] [Accepted: 01/14/2005] [Indexed: 05/03/2023]
Abstract
The direct photolysis of an important endocrine disruptor compound, di-n-butyl phthalate (DBP), has been investigated under monochromatic UV irradiation at 254 nm over a wide pH range (3-11). The investigation was carried out under idealized conditions and has considered both reaction kinetics and the degradation mechanism. It was found that more than 90% of DBP can be degraded within an hour of irradiation in water. A simple model has been developed and used to predict the initial DBP photolysis rate constant at different pH values and initial DBP concentrations. The major decomposition mechanism of DBP is believed to involve the hydrolytic photolysis of the carbon in the alpha and/or beta-position of the ester chain with the production of aromatic carboxylic derivatives. Additionally, multi-degradation pathways are proposed for acid-catalyzed hydrolytic photolysis (pH 3-5), which was found to be useful in explaining the photo-degradation of DBP under acidic conditions. The use of 254 nm UV to photo-degrade DBP was found to be a relatively fast and clean process, especially in neutral to basic conditions.
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McMurtrie A, McClelland D, Graham N. Response to paper by T Ibrahim, SM Ong, GJStC Taylor the new consent form: is it any better? Ann R Coll Surg Engl 2004; 86: 206-9: response 2. Ann R Coll Surg Engl 2004; 86:466; author reply 467. [PMID: 15527595 PMCID: PMC1964269 DOI: 10.1308/1478708041145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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81
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Wolfson SS, Graham N, Slinin O. Normalization and uncertainty effects in three objective tasks using first-order and second-order textures. J Vis 2004. [DOI: 10.1167/4.8.534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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82
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Trinh KV, Kay TM, Graham N, Gross AR, Goldsmith CH, Cameron I, Wang E, Radylovic Z. Acupuncture for neck disorders. Hippokratia 2003. [DOI: 10.1002/14651858.cd004870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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83
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Chen X, Jeyaseelan S, Graham N. Physical and chemical properties study of the activated carbon made from sewage sludge. WASTE MANAGEMENT (NEW YORK, N.Y.) 2002; 22:755-60. [PMID: 12365778 DOI: 10.1016/s0956-053x(02)00057-0] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Preparation of activated carbon from sewage sludge is a promising way to produce a useful adsorbent for pollutants removal as well as to dispose of sewage sludge. The objective of this study was to investigate the physical and chemical properties of the activated carbon made from sewage sludge so as to give a basic understanding of its structure. The activated carbon was prepared by activating anaerobically digested sewage sludge with 5 M ZnCl2 and thereafter pyrolyzing it at 500 degrees C for 2 h under nitrogen atmosphere. The properties investigated in the present study included its surface area and pore size distribution, its elemental composition and ash content, its surface chemistry structure and its surface physical morphology. Furthermore, its adsorption capacities for aqueous phenol and carbontetrachloride were examined. The results indicated that the activated carbon made from sewage sludge had remarkable micropore and mesopore surface areas and notable adsorption capacities for phenol and carbon-tetrachloride. In comparison with commercial activated carbons, it displayed distinctive physical and chemical properties.
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85
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Wolfson SS, Graham N. Processing in the probed-sinewave paradigm is likely retinal. Vis Neurosci 2001; 18:1003-10. [PMID: 12020074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
In the probed-sinewave paradigm-used to study the dynamics of light adaptation-a small probe of light is superimposed on a sinusoidally flickering background. Detection threshold for the probe is measured at various times with respect to the flickering background. Here we present such stimuli using three methods: monoptic (the probe and the flickering background are presented to the same eye), dichoptic (the probe is presented to one eye and the flickering background is presented to the other eye), and binocular (the probe and the flickering background are both presented to both eyes). The results suggest that the processing associated with detecting the probe is primarily in the retina (or any place with monocular input). However, the results also suggest a slight amount of processing in the cortex (or any place with binocular input), particularly at the higher frequency of flickering background used here (9.4 Hz vs. 1.2 Hz). A simple schematic model with three ocular-dominance channels is consistent with the results.
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Graham N, Jaffe RL, Quandt M, Weigel H. Quantum energies of interfaces. PHYSICAL REVIEW LETTERS 2001; 87:131601. [PMID: 11580574 DOI: 10.1103/physrevlett.87.131601] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2001] [Indexed: 05/23/2023]
Abstract
We present a method for computing the one-loop, renormalized quantum energies of symmetrical interfaces of arbitrary dimension and codimension using elementary scattering data. Internal consistency requires finite-energy sum rules relating phase shifts to bound state energies.
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87
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Graham N, Wolfson SS. A note about preferred orientations at the first and second stages of complex (second-order) texture channels. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2001; 18:2273-2281. [PMID: 11551062 DOI: 10.1364/josaa.18.002273] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Complex (second-order) channels have been useful in explaining many of the phenomena of perceived texture segregation. These channels contain two stages of linear filtering with an intermediate pointwise nonlinearity. One unanswered question about these hypothetical channels is that of the relationship between the preferred orientations of the two stages of filtering. Is a particular orientation at the second stage equally likely to occur with all orientations at the first stage, or is there a bias in the "mapping" between the two stages' preferred orientations? In this study we consider two possible mappings: that where the orientations at the two stages are identical (called "consistent" here) and that where the orientations at the two stages are perpendicular ("inconsistent"). We explore these mappings using a texture-segregation task with textures composed of arrangements of grating-patch elements. The results imply that, to explain perceived texture segregation, complex channels with a consistent orientation mapping must be either somewhat more prevalent or more effective than those with an inconsistent mapping.
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Ross L, Scarsella A, Raffanti S, Henry K, Becker S, Fisher R, Liao Q, Hirani A, Graham N, St Clair M, Hernandez J. Thymidine analog and multinucleoside resistance mutations are associated with decreased phenotypic susceptibility to stavudine in HIV type 1 isolated from zidovudine-naive patients experiencing viremia on stavudine-containing regimens. AIDS Res Hum Retroviruses 2001; 17:1107-15. [PMID: 11522180 DOI: 10.1089/088922201316912718] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Studies have demonstrated that HIV-1 isolated from subjects experiencing virologic failure on stavudine (d4T)-containing regimens often contains thymidine analog mutations (TAMs), consisting of reverse transcriptase (RT) mutations M41L, D67N, K70R, L210W, T215Y/F, and K219Q/E, previously associated only with zidovudine (ZDV) resistance. In clinical study NZT40012, HIV-1 was isolated from 86 ZDV-naive subjects experiencing viremia on d4T-based therapies (plasma HIV-1 RNA > or =1000 copies/ml) and analyzed to examine the association between RT mutations and phenotypic resistance to d4T. Resistance-associated mutations were analyzed from HIV-1 isolated from 85 subjects. Of these, 24 samples (28%) had TAMs, and 30 samples (35%) had either TAMs and/or the Q151M multinucleoside resistance (MNR) mutation. Phenotypic susceptibility to d4T was determined by two commercially available methods. Statistically significant increases (p < 0.001) in phenotypic fold resistance to d4T were observed in virus with at least one TAM or MNR mutation. However, the mean increases in phenotypic resistance were 4-fold for the Antivirogram assay and 3-fold for the Phenosense HIV assay, only slightly above the levels used to designate decreased susceptibility to d4T. Subjects can experience viremia on d4T-containing regimens with virus exhibiting only small increases in IC(50), suggesting that relatively small changes in viral susceptibility to d4T may influence drug efficacy.
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Tay JH, Chen XG, Jeyaseelan S, Graham N. A comparative study of anaerobically digested and undigested sewage sludges in preparation of activated carbons. CHEMOSPHERE 2001; 44:53-57. [PMID: 11419759 DOI: 10.1016/s0045-6535(00)00384-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Disposal of sewage sludge is an increasingly expensive and environmentally sensitive problem throughout the world. Preparation of activated carbon from sewage sludge offers an attractive re-use alternative to the traditional disposal routes. The objective of this research work was to compare anaerobically digested sewage sludge (DS) and undigested sewage sludge (US) as source materials in the preparation of activated carbons. Prior to the preparation the properties of the two types of sewage sludges were determined and compared. Subsequently the sludge samples were activated with 5 M ZnCl2 solution and thereafter pyrolysed at heating temperature of 650 degrees C for 2 h with the heating rate of 15 degrees C/min under a nitrogen atmosphere. The produced activated carbons were characterised by surface area and porosity analysis, CHN elemental composition and ash contents determination, and aqueous phase phenol adsorption tests. The results indicate that in comparison with the DS, the US had a higher carbon content and lower ash content, and accordingly yielded a better activated carbon with a higher BET surface area, pore volume, carbon content and phenol adsorption capacity.
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Tay JH, Chen XG, Jeyaseelan S, Graham N. Optimising the preparation of activated carbon from digested sewage sludge and coconut husk. CHEMOSPHERE 2001; 44:45-51. [PMID: 11419758 DOI: 10.1016/s0045-6535(00)00383-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Preparation of activated carbon from sewage sludge is a promising way to dispose of sewage sludge as well as to produce a low-cost adsorbent for pollutant removal. This research work aimed to optimise the condition for activated carbon preparation from anaerobically digested sewage sludge with the additive coconut husk. The sewage sludge sample was mixed with the additive coconut husk. The preparation condition variables investigated involved the concentration of the ZnCl2 solutions, heating temperature, dwell time and heating rate in pyrolysis and the mixing ratio of coconut husk to sewage sludge. Surface area, pore size distribution, aqueous phenol adsorption capacity and the production yield of the final products were determined and compared. Experimental results revealed that low concentrations of ZnCl2 solution tended to improve the microporosity of the final product. Heating temperature had a considerable impact on the surface area, pore size distribution and phenol adsorption capacity of the final products, whereas dwell time and heating rate performed comparatively insignificantly. The effect of increasing the mixing ratio of coconut husk to sewage sludge was principally to increase the microporosity of the final products. The activated carbon with the highest BET surface area was produced with the activation of 5 M ZnCl2 solution and, thereafter, pyrolysis at a heating temperature of 500 degrees C for 2 h with a heating rate of 10 degrees C/min. The mixing ratio of 1:4 in terms of coconut husk to sewage sludge based on their dried weights was found to be most cost effective.
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Abstract
Using the probed-sinewave paradigm, we explore the differences between increment and decrement probes across a range of frequencies (approx. 1-19 Hz). In this paradigm, detection threshold is measured for a small test probe presented on a large sinusoidally flickering background (at eight different phases). Probe thresholds are very similar for increment and decrement probes, but there is a very small (and systematic) difference: increment thresholds are usually slightly higher relative to decrement thresholds during the part of the cycle when the background's intensity is increasing. Although Wilson's (1997, Vis. Neuro., 14, 403-423) model substantially underestimates the size of this difference, it predicts some phase dependency. However, the existence of On- and Off-pathways in Wilson's model is not important for these predictions. A recent model by Snippe, Poot, and van Hateren (2000, Vis. Neuro., 17, 449-462) may be able to predict this result by using explicit contrast-gain control rather than separate On- and Off-pathways. Auxiliary experiments measuring the perceived polarity of the probe provide a further argument suggesting that separate On- and Off-pathways are not useful in explaining increment and decrement probe thresholds.
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Casimiro I, Marchant A, Bhalerao RP, Beeckman T, Dhooge S, Swarup R, Graham N, Inzé D, Sandberg G, Casero PJ, Bennett M. Auxin transport promotes Arabidopsis lateral root initiation. THE PLANT CELL 2001; 13:843-52. [PMID: 11283340 PMCID: PMC135543 DOI: 10.1105/tpc.13.4.843] [Citation(s) in RCA: 668] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Lateral root development in Arabidopsis provides a model for the study of hormonal signals that regulate postembryonic organogenesis in higher plants. Lateral roots originate from pairs of pericycle cells, in several cell files positioned opposite the xylem pole, that initiate a series of asymmetric, transverse divisions. The auxin transport inhibitor N-1-naphthylphthalamic acid (NPA) arrests lateral root development by blocking the first transverse division(s). We investigated the basis of NPA action by using a cell-specific reporter to demonstrate that xylem pole pericycle cells retain their identity in the presence of the auxin transport inhibitor. However, NPA causes indoleacetic acid (IAA) to accumulate in the root apex while reducing levels in basal tissues critical for lateral root initiation. This pattern of IAA redistribution is consistent with NPA blocking basipetal IAA movement from the root tip. Characterization of lateral root development in the shoot meristemless1 mutant demonstrates that root basipetal and leaf acropetal auxin transport activities are required during the initiation and emergence phases, respectively, of lateral root development.
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93
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Scott T, Garris C, Rogers M, Graham N, Garrett L, Pedneault L. Safety profile and tolerability of amprenavir in patients enrolled in an early access program. Clin Ther 2001; 23:252-9. [PMID: 11293558 DOI: 10.1016/s0149-2918(01)80007-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
BACKGROUND The amprenavir (APV) early or expanded access program was designed to provide open-label APV to patients who would potentially receive benefit beyond that expected from currently available protease inhibitors (PIs) and who were at risk of disease progression before the drug's expected time of regulatory approval. OBJECTIVE This study was conducted as part of an early access program to assess the safety profile and tolerability of APV in adults and children (> or =4 years of age) who were either intolerant to or, in the opinion of the patient's physician, virologically failing a previous PI-containing antiretroviral regimen. Specific CD4+ cell count and viral load limits were not imposed by this early access protocol. METHODS This open-label, nonrandomized study was conducted at multiple sites throughout the United States. Adults received APV at a dosage of 1200 mg BID. Patients weighing <50 kg received APV at a dosage of 20 mg/kg BID for the solid formulation or 1.5 mL/kg BID for the liquid formulation. RESULTS A total of 489 physicians registered for this program; 364 (74.4%) enrolled patients. The safety population of 2217 patients (2048 males [92.4%] and 169 females [7.6%] aged 2 to 74 years) received APV for a median duration of 85 days (range, 2-218 days). Patients in the intent-to-treat population (n = 1427) had extensive experience with antiretroviral therapy. Drug-related treatment-emergent adverse events reported in >3% of patients in the safety population were nausea in 279 patients (12.6%), diarrhea in 197 patients (8.9%), rash in 177 patients (8.0%), vomiting in 148 patients (6.7%), and fatigue in 89 patients (4.0%). Adverse events and laboratory test abnormalities were graded for severity on a scale of 1 to 4 in accordance with AIDS Clinical Trials Group guidelines. Grade 3 treatment-emergent abnormal laboratory values regardless of causality occurring in >3% of patients were neutropenia in 69 of 1887 patients (3.7%; grade 3 toxicity = 500-749/mm3) and elevated triglycerides in 80 of 1593 patients (5.0%; grade 3 toxicity = 751-1200 mg/dL). Most common grade 4 treatment-emergent laboratory abnormalities were elevated serum creatine phosphokinase levels in 36 of 1266 patients (2.8%; grade 4 = >6 times upper normal limit), elevated triglycerides in 39 of 1593 patients (2.4%), and neutropenia in 41 of 1887 patients (2.2%). CONCLUSIONS The results of this large cohort of patients support the data from the phase II/III clinical development program and suggest that APV has an acceptable safety profile and is generally well tolerated when used in combination with other antiretroviral drugs in a heavily treatment-experienced, heterogeneous patient population.
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Graham N, Chen XG, Jayaseelan S. The potential application of activated carbon from sewage sludge to organic dyes removal. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2001; 43:245-252. [PMID: 11380186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The objective of this research work was to study the potential application of activated carbon from sewage sludge to organic dye removal. Methylene blue and crystal violet were the two dyes investigated in the present study. Three activated carbons were produced from the exclusive sewage sludge (referred to as DS), the sludge with the additive of coconut husk (DC) and sludge with the additive of peanut shell (DP) respectively. They were characterized by their surface area and porosity and their surface chemistry structure. Adsorption studies were performed by the batch technique to obtain kinetic and equilibrium data. The results show that the three sludge-derived activated carbons had a developed porosity and marked content of surface functional groups. They exhibited a rapid three-stage adsorption process for both methylene blue and crystal violet. Their adsorption capacities for the two dyes were high, the carbon DP performed best in the adsorption whereas the carbon DC performed worst. It is therefore concluded that the activated carbons made from sewage sludge and its mixtures are promising for dye removal from aqueous streams.
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Graham N, Sutter A. Normalization: contrast-gain control in simple (Fourier) and complex (non-Fourier) pathways of pattern vision. Vision Res 2000; 40:2737-61. [PMID: 10960649 DOI: 10.1016/s0042-6989(00)00123-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Results from two types of texture-segregation experiments considered jointly demonstrate that the heavily-compressive intensive nonlinearity acting in static pattern vision is not a relatively early, local gain control like light adaptation in the retina or LGN. Nor can it be a late, within-channel contrast-gain control. All the results suggest that it is inhibition among channels as in a normalization network. The normalization pool affects the complex-channel (second-order, non-Fourier) pathway in the same manner in which it affects the simple-channel (first-order, Fourier) pathway, but it is not yet known whether complex channels' outputs are part of the normalization pool.
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Wolfson SS, Graham N. Exploring the dynamics of light adaptation: the effects of varying the flickering background's duration in the probed-sinewave paradigm. Vision Res 2000; 40:2277-89. [PMID: 10927115 DOI: 10.1016/s0042-6989(00)00088-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In the probed-sinewave paradigm, threshold for detecting a probe is measured at various phases with respect to a sinusoidally-flickering background. Here we vary the duration of the flickering background before (and after) the test probe is presented. The adaptation is rapid; after approximately 10-30 ms of the flickering background, probe threshold is the same as that on a continually-flickering background. It is interesting that this result holds at both low (1. 2 Hz) and middle (9.4 Hz) frequencies because at middle frequencies (but not at low) there is a dc-shift, i.e. probe threshold is elevated at all phases relative to that on a steady background (of the same mean luminance). We compare our results to predictions from Wilson's model [Wilson (1997), Visual Neuroscience, 14, 403-423; Hood & Graham (1998), Visual Neuroscience, 15, 957-967] of light adaptation. The model predicts the rapid adaptation, and the dc-shift, but not the detailed shape of the probe-threshold-versus-phase curve at middle frequencies.
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Ross L, Johnson M, DeMasi R, Liao Q, Graham N, Shaefer M, St Clair M. Viral genetic heterogeneity in HIV-1-infected individuals is associated with increasing use of HAART and higher viremia. AIDS 2000; 14:813-9. [PMID: 10839589 DOI: 10.1097/00002030-200005050-00007] [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: 11/26/2022]
Abstract
OBJECTIVE To assess the correlation between the outgrowth of mutant viruses (viral genetic heterogeneity), highly active antiretroviral therapy (HAART), and plasma HIV-1 RNA in a population-based observational cohort study. DESIGN The study population consisted of 42 HIV-1-infected individuals receiving at least two nucleotide reverse transcriptase (RT) inhibitors and one or more protease inhibitors at study entry. There were no restrictions on antiretroviral therapy after enrollment. METHODS Plasma samples were obtained from subjects at baseline, at therapy changes, and at quarterly intervals for quantitation of HIV-1 RNA levels and for sequence determination of the entire protease coding region and the first 235 codons of the reverse transcriptase coding region. Data were analyzed using the generalized estimating equation method for longitudinal data and using linear regression analysis. RESULTS With increased time on HAART there were significant increases in the number of total HIV-1 mutations in the regions sequenced (P = 0.010). There were significant correlations between the increases in the plasma HIV-1 RNA levels and the numbers of total mutations and reverse transcriptase mutations (P = 0.007 and 0.021, respectively). CONCLUSIONS The number of HIV-1 mutations increased over time. Failure of HAART in this study population was correlated with outgrowth of virus with numerous mutations in the reverse transcriptase and protease coding regions. Phenotypic results correlated with genotypic results, showing decreased susceptibility to antiretrovirals over time in the majority of this population during HAART. Both synonymous and non-synonymous mutations were observed, with a higher incidence of non-synonymous mutations occurring at codons associated with drug resistance.
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Boyer FE, Vara Prasad JV, Domagala JM, Ellsworth EL, Gajda C, Hagen SE, Markoski LJ, Tait BD, Lunney EA, Palovsky A, Ferguson D, Graham N, Holler T, Hupe D, Nouhan C, Tummino PJ, Urumov A, Zeikus E, Zeikus G, Gracheck SJ, Sanders JM, VanderRoest S, Brodfuehrer J, Iyer K, Sinz M, Gulnik SV. 5,6-Dihydropyran-2-ones possessing various sulfonyl functionalities: potent nonpeptidic inhibitors of HIV protease. J Med Chem 2000; 43:843-58. [PMID: 10715152 DOI: 10.1021/jm990281p] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
On the basis of previous SAR findings and molecular modeling studies, a series of compounds were synthesized which possessed various sulfonyl moieties substituted at the 4-position of the C-3 phenyl ring substituent of the dihydropyran-2-one ring system. The sulfonyl substituents were added in an attempt to fill the additional S(3)' pocket and thereby produce increasingly potent inhibitors of the target enzyme. Racemic and enantiomerically resolved varieties of selected compounds were synthesized. All analogues in the study displayed decent binding affinity to HIV protease, and several compounds were shown to possess very good antiviral efficacy and safety margins. X-ray crystallographic structures confirmed that the sulfonamide and sulfonate moieties were filling the S(3)' pocket of the enzyme. However, the additional substituent did not provide improved enzymatic inhibitory or antiviral activity as compared to the resolved unsubstituted aniline. The addition of the sulfonyl moiety substitution does not appear to provide favorable pharamacokinectic parameters. Selected inhibitors were tested for antiviral activity in clinical isolates and exhibited similar antiviral activity against all of the HIV-1 strains tested as they did against the wild-type HIV-1. In addition, the inhibitors exhibited good antiviral efficacies against HIV-1 strains that displayed resistance to the currently marketed protease inhibitors.
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99
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Prasad JV, Boyer FE, Domagala JM, Ellsworth EL, Gajda C, Hamilton HW, Hagen SE, Markoski LJ, Steinbaugh BA, Tait BD, Humblet C, Lunney EA, Pavlovsky A, Rubin JR, Ferguson D, Graham N, Holler T, Hupe D, Nouhan C, Tummino PJ, Urumov A, Zeikus E, Zeikus G, Gracheck SJ, Erickson JW. Nonpeptidic HIV protease inhibitors possessing excellent antiviral activities and therapeutic indices. PD 178390: a lead HIV protease inhibitor. Bioorg Med Chem 1999; 7:2775-800. [PMID: 10658583 DOI: 10.1016/s0968-0896(99)00215-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
With the insight generated by the availability of X-ray crystal structures of various 5,6-dihydropyran-2-ones bound to HIV PR, inhibitors possessing various alkyl groups at the 6-position of 5,6-dihydropyran-2-one ring were synthesized. The inhibitors possessing a 6-alkyl group exhibited superior antiviral activities when compared to 6-phenyl analogues. Antiviral efficacies were further improved upon introduction of a polar group (hydroxyl or amino) on the 4-position of the phenethyl moiety as well as the polar group (hydroxymethyl) on the 3-(tert-butyl-5-methyl-phenylthio) moiety. The polar substitution is also advantageous for decreasing toxicity, providing inhibitors with higher therapeutic indices. The best inhibitor among this series, (S)-6-[2-(4-aminophenyl)-ethyl]-(3-(2-tert-butyl-5-methyl-phenylsulfa nyl)-4-hydroxy-6-isopropyl-5,6-dihydro-pyran-2-one (34S), exhibited an EC50 of 200 nM with a therapeutic index of > 1000. More importantly, these non-peptidic inhibitors, 16S and 34S, appear to offer little cross-resistance to the currently marketed peptidomimetic PR inhibitors. The selected inhibitors tested in vitro against mutant HIV PR showed a very small increase in binding affinities relative to wild-type HIV PR. Cmax and absolute bioavailability of 34S were higher and half-life and time above EC95 were longer compared to 16S. Thus 34S, also known as PD 178390, which displays good antiviral efficacy, promising pharmacokinetic characteristics and favorable activity against mutant enzymes and CYP3A4, has been chosen for further preclinical evaluation.
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Ross L, Johnson M, Graham N, Shaefer M, St Clair M. The reverse transcriptase codon 69 insertion is observed in nucleoside reverse transcriptase inhibitor-experienced HIV-1-infected individuals, including those without prior or concurrent zidovudine therapy. JOURNAL OF HUMAN VIROLOGY 1999; 2:290-5. [PMID: 10551735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
OBJECTIVES This study was undertaken to examine 6-bp insertions following codon 69 in the reverse transcriptase (RT) coding region of human immunodeficiency virus type 1 (HIV-1) mutations in terms of incidence, presence of additional RT mutations, phenotypic drug resistance, HIV-1 RNA levels, and antiretroviral treatment history. STUDY DESIGN/METHODS A retrospective study of 121 nucleoside reverse transcriptase inhibitor (NRTI)-experienced subjects infected with HIV-1 was performed. Methods included quantitation of HIV-1 RNA levels, genotypic analyses of the RT and protease coding regions, and determination of phenotypic drug resistance. RESULTS A 6-bp insertion following RT codon 69 was observed in viral isolates from 4 subjects. Two subjects had a history of zidovudine (ZDV)-based therapy, and two subjects had a history of stavudine (D4T)-based therapy without prior exposure to ZDV. The T69S mutation and the 6-bp insertion following RT codon 69 were the only RT mutations observed in the 2 subjects with a history of D4T-based therapy. CONCLUSIONS Six-basepair insertions occurred in virus from 4 of 121 (3%) NRTI-experienced subjects, including those without prior ZDV treatment, and was observed in the absence of the T215Y mutation. There was no apparent correlation between insertion incidence and HIV-1 viremia.
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