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Biomedical subjects

Daniel Kahn

Publications and source records attributed to Daniel Kahn.

At least 19 recordsLinked to original sources
PubMed2007

Prospective assessment of dosimetric/physiologic-based models for predicting radiation pneumonitis.

PURPOSE: Clinical and 3D dosimetric parameters are associated with symptomatic radiation pneumonitis rates in retrospective studies. Such parameters include: mean lung dose (MLD), radiation (RT) dose to perfused lung (via SPECT), and pre-RT lung function. Based on prior publications, we defined pre-RT criteria hypothesized to be predictive for later development of pneumonitis. We herein prospectively test the predictive abilities of these dosimetric/functional parameters on 2 cohorts of patients from Duke and The Netherlands Cancer Institute (NKI). METHODS AND MATERIALS: For the Duke cohort, 55 eligible patients treated between 1999 and 2005 on a prospective IRB-approved study to monitor RT-induced lung injury were analyzed. A similar group of patients treated at the NKI between 1996 and 2002 were identified. Patients believed to be at high and low risk for pneumonitis were defined based on: (1) MLD; (2) OpRP (sum of predicted perfusion reduction based on regional dose-response curve); and (3) pre-RT DLCO. All doses reflected tissue density heterogeneity. The rates of grade > or =2 pneumonitis in the "presumed" high and low risk groups were compared using Fisher's exact test. RESULTS: In the Duke group, pneumonitis rates in patients prospectively deemed to be at "high" vs. "low" risk are 7 of 20 and 9 of 35, respectively; p = 0.33 one-tailed Fisher's. Similarly, comparable rates for the NKI group are 4 of 21 and 6 of 44, respectively, p = 0.41 one-tailed Fisher's. CONCLUSION: The prospective model appears unable to accurately segregate patients into high vs. low risk groups. However, considered retrospectively, these data are consistent with prior studies suggesting that dosimetric (e.g., MLD) and functional (e.g., PFTs or SPECT) parameters are predictive for RT-induced pneumonitis. Additional work is needed to better identify, and prospectively assess, predictors of RT-induced lung injury.

Adult↗
PubMed2007

New developments in the InterPro database.

InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following protein signature databases: PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs, PIRSF, SUPERFAMILY, Gene3D and PANTHER. The latter two new member databases have been integrated since the last publication in this journal. There have been several new developments in InterPro, including an additional reading field, new database links, extensions to the web interface and additional match XML files. InterPro has always provided matches to UniProtKB proteins on the website and in the match XML file on the FTP site. Additional matches to proteins in UniParc (UniProt archive) are now available for download in the new match XML files only. The latest InterPro release (13.0) contains more than 13 000 entries, covering over 78% of all proteins in UniProtKB. The database is available for text- and sequence-based searches via a webserver (http://www.ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro). The InterProScan search tool is now also available via a web service at http://www.ebi.ac.uk/Tools/webservices/WSInterProScan.html.

Databases, Protein↗
PubMed2006

Radiation-induced narrowing of the tracheobronchial tree: an in-depth analysis.

PURPOSE: Symptomatic narrowing of the tracheobronchial tree is not a common clinical problem after conventional-dose external beam radiation therapy but has been described when higher doses are utilized. This in-depth study quantifies changes in the caliber of the trachea and mainstem bronchi after high-dose external beam radiation therapy (EBRT). METHODS AND MATERIALS: As part of an IRB-approved prospective clinical trial to assess for radiation-induced lung injury, patients with thoracic malignancies had pre- and serial post-RT CT scans in the radiation oncology department. This report focuses on 18 enrolled patients who received high-dose (> or = 73.6 Gy) EBRT for NSCLC. The caliber of the trachea, right mainstem bronchus, and left mainstem bronchus were measured utilizing three-dimensional coordinates in axial and coronal planes such that multiple measurements were made of each structure. The decrease in airway caliber was tested for significance using a one-sided Wilcoxon matched-pairs signed-ranks test. The correlation between airway caliber changes, dose, and follow-up interval was tested using the Spearman rank correlation coefficient and the effect of chemotherapy on airway narrowing was evaluated with a one-sided exact Wilcoxon rank sum test. RESULTS: There was no significant narrowing of the trachea for all dose and time points. There were significant decreases in the caliber of both mainstem bronchi on axial measurements (p = 0.07 and 0.005 for right and left mainstem bronchi, respectively). Decrease in airway caliber ranged from 6 to 57% and appeared to be dose dependent (p = 0.08), progressed with increasing time post-RT (p = 0.04), and was worse in patients who also received chemotherapy (p = 0.04). CONCLUSION: High-dose EBRT (> or = 73.6 Gy) appears to cause narrowing of the mainstem bronchi as early as 3 months post radiation therapy. Additional study is needed to assess the impact of such narrowing on RT-induced pulmonary symptoms.

Aged↗
PubMed2005

Preliminary report of the 6-minute walk test as a predictor of radiation-induced pulmonary toxicity.

PURPOSE: To assess the 6-minute walk test (6MWT) as a predictor of radiation therapy-induced lung injury (RTLI). METHODS AND MATERIALS: The 6MWT is a simple, economical, and reproducible test that measures both how far a person can walk in 6 min and any associated changes in vital signs. As part of a prospective trial to study RTLI, a pre-RT 6MWT was performed in 41 patients. The predictive capacities of pre-RT 6MWT, forced expiratory volume in 1 s (FEV1), and single-breath diffusing capacity for carbon monoxide (DLCO) for the development of RTLI were assessed with receiver operating curve (ROC) techniques. To evaluate the 6MWT, alone or with mean lung dose (MLD) of radiation, as a predictor of RTLI, the rates of RTLI in patient subgroups defined by 6MWT results were compared by using Fisher's exact test. RESULTS: Thirty-one patients with > or =3 months' follow-up were evaluable. The median baseline 6MWT result was 1400 ft. Of 31 patients, 7 developed Grade > or =2 RTLI. Of 15 patients with an MLD >18 Gy (the median), 5 developed RTLI, compared with 2 of 16 with MLD < or =18 Gy (p = 0.22). Among those with an MLD < or =18 Gy, the RTLI rates were 0 of 8 and 2 of 8 for 6MWT results > or =1400 ft or <1400 ft, respectively, p = 0.46. The ROC area under the curve for individual metrics was as follows: FEV1 0.66, MLD 0.70, DLCO 0.61, and 6MWT 0.47. Combining FEV1 with 6MWT increased the ROC to 0.71, suggesting that the ratio might be a better predictor than the individual values. Patients with a high 6MWT/FEV1 ratio had a lower rate of RTLI than those with a relatively low ratio. CONCLUSIONS: The 6MWT might provide prognostic information beyond pulmonary function tests and dosimetric parameters in predicting RTLI. Additional work is needed to better assess the utility of these functional metrics.

Adult↗
PubMed2005

"Anatomically-correct" dosimetric parameters may be better predictors for esophageal toxicity than are traditional CT-based metrics.

PURPOSE: Incidental esophageal irradiation during lung cancer therapy often causes morbidity. There is interest in trying to relate esophageal dosimetric parameters to the risk of injury. These parameters typically rely on CT-defined esophageal contours, and thus systematic limitations in esophageal contouring will influence these parameters. We herein assess the ability of a correction method, based on physiologic principles, to improve the predictive power of dosimetric parameters for radiation-induced esophageal injury. METHODS AND MATERIALS: Esophageal contours for 236 patients treated for lung cancer were quantitatively analyzed. All patients received three-dimensional planning, and all contours were generated by the same physician on axial CT images. Traditional dose-volume histogram (DVH)-based dosimetric parameters were extracted from the three-dimensional data set. A second set of "anatomically correct" dosimetric parameters was derived by adjusting the contours to reflect the known shape of the esophagus. Each patient was scored for acute and late toxicity using ROTG criteria. Univariate analysis was used to assess the predictive power of corrected and uncorrected dosimetric parameters (e.g., mean dose, V(50), and V(60)) for toxicity. The p values were taken as a measure of their significance. RESULTS: The univariate results indicate that both corrected and uncorrected dosimetric parameters are generally predictors for toxicity. The corrected parameters are more highly correlated (lower p value) with outcomes than the uncorrected metrics. CONCLUSIONS: The inclusion of corrections, based on anatomic realities, to DVH-based dosimetric parameters may provide dosimetric parameters that are better correlated with clinical outcomes than are traditional DVH-based metrics.

Analysis of Variance↗
PubMed2005

Dosimetric and clinical predictors for radiation-induced esophageal injury.

PURPOSE: To evaluate the clinical and three-dimensional dosimetric parameters associated with esophageal injury after radiotherapy (RT) for non-small-cell lung cancer. METHODS AND MATERIALS: The records of 254 patients treated for non-small-cell lung cancer between 1992 and 2001 were reviewed. A variety of metrics describing the esophageal dose were extracted. The Radiation Therapy Oncology Group toxicity criteria for grading of esophageal injury were used. The median follow-up time for all patients was 43 months (range, 0.5-120 months). Logistic regression analysis, contingency table analyses, and Fisher's exact tests were used for statistical analysis. RESULTS: Acute toxicity occurred in 199 (78%) of 254 patients. For acute toxicity of Grade 2 or worse, twice-daily RT, age, nodal stage of N2 or worse, and most dosimetric parameters were predictive. Late toxicity occurred in 17 (7%) of 238 patients. The median and maximal time to the onset of late toxicity was 5 and 40 months after RT, respectively. Late toxicity occurred in 2%, 3%, 17%, 26%, and 100% of patients with acute Grade 0, 1, 2, 3, and 4 toxicity, respectively. For late toxicity, the severity of acute toxicity was most predictive. CONCLUSION: A variety of dosimetric parameters are predictive of acute and late esophageal injury. A strong correlation between the dosimetric parameters prevented a comparison between the predictive abilities of these metrics. The presence of acute injury was the most predictive factor for the development of late injury. Additional studies to define better the predictors of RT-induced esophageal injury are needed.

Adult↗
PubMed2005

The ProDom database of protein domain families: more emphasis on 3D.

ProDom is a comprehensive database of protein domain families generated from the global comparison of all available protein sequences. Recent improvements include the use of three-dimensional (3D) information from the SCOP database; a completely redesigned web interface (http://www.toulouse.inra.fr/prodom.html); visualization of ProDom domains on 3D structures; coupling of ProDom analysis with the Geno3D homology modelling server; Bayesian inference of evolutionary scenarios for ProDom families. In addition, we have developed ProDom-SG, a ProDom-based server dedicated to the selection of candidate proteins for structural genomics.

Computer Graphics↗
PubMed2005

InterPro, progress and status in 2005.

InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam, PRINTS, ProDom, SMART, TIGRFAMs, PIRSF and SUPERFAMILY. Signatures are manually integrated into InterPro entries that are curated to provide biological and functional information. Annotation is provided in an abstract, Gene Ontology mapping and links to specialized databases. New features of InterPro include extended protein match views, taxonomic range information and protein 3D structure data. One of the new match views is the InterPro Domain Architecture view, which shows the domain composition of protein matches. Two new entry types were introduced to better describe InterPro entries: these are active site and binding site. PIRSF and the structure-based SUPERFAMILY are the latest member databases to join InterPro, and CATH and PANTHER are soon to be integrated. InterPro release 8.0 contains 11 007 entries, representing 2573 domains, 8166 families, 201 repeats, 26 active sites, 21 binding sites and 20 post-translational modification sites. InterPro covers over 78% of all proteins in the Swiss-Prot and TrEMBL components of UniProt. The database is available for text- and sequence-based searches via a webserver (http://www.ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro).

Databases, Protein↗
PubMed2004

Nitrogen regulation in Sinorhizobium meliloti probed with whole genome arrays.

Using whole genome arrays, we systematically investigated nitrogen regulation in the plant symbiotic bacterium Sinorhizobium meliloti. The use of glutamate instead of ammonium as a nitrogen source induced nitrogen catabolic genes independently of the carbon source, including two glutamine synthetase genes, various aminoacid transporters and the glnKamtB operon. These responses depended on both the ntrC and glnB nitrogen regulators. Glutamate repressible genes included glutamate synthase and a H+-translocating pyrophosphate synthase. The smc01041-ntrBC operon was negatively autoregulated in a glnB-dependent fashion, indicating an involvement of phosphorylated NtrC. In addition to the nitrogen response, glutamate remodelled expression of carbon metabolism by inhibiting expression of the Entner-Doudoroff and pentose phosphate pathways, and by stimulating gluconeogenetic genes independently of ntrC.

Bacterial Proteins↗
PubMed2004

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype.

Tetraodon nigroviridis is a freshwater puffer fish with the smallest known vertebrate genome. Here, we report a draft genome sequence with long-range linkage and substantial anchoring to the 21 Tetraodon chromosomes. Genome analysis provides a greatly improved fish gene catalogue, including identifying key genes previously thought to be absent in fish. Comparison with other vertebrates and a urochordate indicates that fish proteins have diverged markedly faster than their mammalian homologues. Comparison with the human genome suggests approximately 900 previously unannotated human genes. Analysis of the Tetraodon and human genomes shows that whole-genome duplication occurred in the teleost fish lineage, subsequent to its divergence from mammals. The analysis also makes it possible to infer the basic structure of the ancestral bony vertebrate genome, which was composed of 12 chromosomes, and to reconstruct much of the evolutionary history of ancient and recent chromosome rearrangements leading to the modern human karyotype.

Animals↗
PubMed2004

Effects of intravenous amino acid administration with Y-90 DOTA-Phe1-Tyr3-Octreotide (SMT487[OctreoTher) treatment.

Y-90-DOTA-Phe1-Tyr3-Octreotide (90Y-SMT 487, OctreoTher) has shown potential for effectively treating patients with neuroendocrine tumors. The dose-limiting organ for this agent is the kidney. The purpose of this work is to assess the effectiveness of a commercially available amino acid solution on reducing renal uptake of 90Y-SMT 487 and determine the safety profile of this solution. Subjects with In-111 pentetreotide positive tumors and normal creatinine levels were treated with 3 cycles of 90Y-SMT 487, 120 mCi/cycle, at 6-9 week intervals. During each treatment two liters of an amino acid solution containing arginine and lysine (Aminosyn II 7%, Abbott Laboratories, Abbott Park, IL) were infused IV over 4 hours. Adverse events were recorded. To assess the effect of Aminosyn II on renal uptake of 90Y-SMT 487, a subgroup of subjects underwent bremsstrahlung imaging 24 hours following infusion. Kidney to liver (K/L) count density ratios were generated from the baseline In-111 pentetreotide images (performed without amino acid infusion) and the 90Y bremsstrahlung images. Follow-up creatinine levels were obtained. Thirty-seven subjects received a total of 89 90Y-SMT 487 treatments. The number of amino-acid infusions associated with one or more episodes of emesis was 53 (62%). During 13 (15%) of these infusions, the Aminosyn II rate had to be reduced because of severe nausea and vomiting. Symptomatic flushing occurred during 16 (18%) of the infusions. One subject experienced a near syncopal event shortly after completing the infusion. Creatinine levels remained normal in 34 of 36 subjects during a mean follow-up period of 9.8 months. Fourteen subjects underwent bremsstrahlung imaging following infusion of 90Y-SMT 487. Kidney uptake appeared to decrease with administration of the amino acid solution in 13 of 14 subjects. For the 28 individual kidneys, the mean percent decrease in the Kidney/Liver uptake ratio with the amino acid solution was found to be 32%. We conclude that 2 L of Aminosyn II 7% infused over 4 hours appears to notably reduce renal uptake of 90Y-SMT 487. Aminosyn is generally well tolerated, particularly at lower infusion rates with occasional moderate to severe nausea and vomiting at higher rates.

Adult↗
PubMed2004

Global changes in gene expression in Sinorhizobium meliloti 1021 under microoxic and symbiotic conditions.

Sinorhizobium meliloti is an alpha-proteobacterium that alternates between a free-living phase in bulk soil or in the rhizosphere of plants and a symbiotic phase within the host plant cells, where the bacteria ultimately differentiate into nitrogen-fixing organelle-like cells, called bacteroids. As a step toward understanding the physiology of S. meliloti in its free-living and symbiotic forms and the transition between the two, gene expression profiles were determined under two sets of biological conditions: growth under oxic versus microoxic conditions, and in free-living versus symbiotic state. Data acquisition was based on both macro- and microarrays. Transcriptome profiles highlighted a profound modification of gene expression during bacteroid differentiation, with 16% of genes being altered. The data are consistent with an overall slow down of bacteroid metabolism during adaptation to symbiotic life and acquisition of nitrogen fixation capability. A large number of genes of unknown function, including potential regulators, that may play a role in symbiosis were identified. Transcriptome profiling in response to oxygen limitation indicated that up to 5% of the genes were oxygen regulated. However, the microoxic and bacteroid transcriptomes only partially overlap, implying that oxygen contributes to a limited extent to the control of symbiotic gene expression.

Adaptation, Biological↗
PubMed2004

99mTc-depreotide tumour uptake in patients with non-Hodgkin's lymphoma.

BACKGROUND: 99mTc-depreotide (NeoTect) is a synthetic somatostatin analogue, which binds to somatostatin receptor (SSTR) subtypes 2, 3 and 5. Imaging patients with non-Hodgkin's lymphoma (NHL) using the somatostatin analogue In-pentetreotide (Octreoscan) has demonstrated the feasibility of identifying lymphoma sites with this class of peptide radiopharmaceutical. SSTR peptides can be labelled with beta emitters and, if sufficient tumour uptake relative to normal organs can be demonstrated, therapeutic applications can be considered. METHODS: In this prospective Institutional Review Board (IRB)-approved study, patients with NHL and a recent computed tomography (CT) examination were eligible. Whole-body and selected single-photon emission computed tomography (SPECT) imaging was performed 1 h after intravenous injection of 99mTc-depreotide. Images were compared with CT scan findings. The radioactivity concentration of 99mTc-depreotide in abdominal/pelvic tumour sites, together with normal organs, was determined and expressed as the percentage of injected activity per gram of tissue (%IA x g). RESULTS: Paired CT and 99mTc-depreotide images for three patients with indolent and six with aggressive NHL revealed abnormal 99mTc-depreotide uptake corresponding to the tumour seen on CT in seven of these patients. In three of the patients, all known tumour sites were detected on 99mTc-depreotide images. The mean %IA x g for nine abdominal/pelvic tumour foci from four patients was found to be 0.004% (range, 0.001-0.007%). The mean tumour to bone marrow activity concentration ratio in these four patients was found to be 0.94 (range, 0.33-1.40), whereas the tumour to kidney ratio was 0.53 (range, 0.16-0.80). CONCLUSIONS: Levels of 99mTc-depreotide in tumour suggest at least the possibility of potential therapy with beta emitter-labelled SSTR peptides; however, depreotide itself appears not to be a suitable candidate as a targeting agent due to the relatively high bone marrow concentration.

Humans↗
PubMed2004

FixJ-regulated genes evolved through promoter duplication in Sinorhizobium meliloti.

The FixLJ two-component system of Sinorhizobium meliloti is a global regulator, turning on nitrogen-fixation genes in microaerobiosis. Up to now, nifA and fixK were the only genes known to be directly regulated by FixJ. We used a genomic SELEX approach in order to isolate new FixJ targets in the genome. This led to the identification of 22 FixJ binding sites, including the known sites in the fixK1 and fixK2 promoters. FixJ binding sites are unevenly distributed among the three replicons constituting the S. meliloti genome: a majority are carried either by pSymA or by a short chromosomal region of non-chromosomal origin. Thus FixJ binding sites appear to be preferentially associated with the pSymA replicon, which carries the fixJ gene. Functional analysis of FixJ targets led to the discovery of two new FixJ-regulated genes, smc03253 and proB2. This FixJ-dependent regulation appears to be mediated by a duplication of the whole fixK promoter region, including the beginning of the fixK gene. Similar duplications were previously reported for the nifH promoter. By systematic comparison of all promoter regions we found 17 such duplications throughout the genome, indicating that promoter duplication is a common mechanism for the evolution of regulatory pathways in S. meliloti.

Amino Acid Sequence↗
PubMed2004

RBCs labeled at two biotin densities permit simultaneous and repeated measurements of circulating RBC volume.

BACKGROUND: The extend potential applications of a nonradioactive method for measuring circulating RBC volume, we tested the hypothesis that RBC volume could be determined independently using two populations of RBCs labeled with low-density biotin (LDB1) and high-density biotin (HDB). STUDY DESIGN AND METHODS: In 10 healthy adults, autologous RBCs were labeled with HDB, LDB, or 51Cr. The labeled RBCs were mixed and transfused. RBC volume was measured in postinfusion peripheral venous blood by quantitating dilution of each population of labeled RBCs. RESULTS: RBC volume measured using either LDB or HDB cells agreed well with RBC volume measured using 51Cr. For the regression of RBC volume by LDB versus RBC volume by 51Cr, correlation = 0.994 and slope = 0.933. For HDB versus 51Cr, correlation = 0.982 and slope = 0.953. RBC volume measured a second time in four subjects with HDB agreed well; mean CV for the differences between HDB and 51Cr were less than 5 percent. CONCLUSIONS: Using RBCs labeled with two different densities of biotin, RBC volume can be accurately measured simultaneously and repeatedly in the same subject without radiation exposure.

Biotin↗
PubMed2004

The utility of 99mTc depreotide compared with F-18 fluorodeoxyglucose positron emission tomography and surgical staging in patients with suspected non-small cell lung cancer.

STUDY OBJECTIVES: The findings from conventional imaging modalities, such as chest CT, are frequently unreliable in patients with lung cancer. This study was designed to compare the relative diagnostic accuracies and utility of the two most widely used functional imaging examinations, F-18-2-fluoro-2-deoxyglucose (FDG) positron emission tomography (PET) and (99m)Tc depreotide scintigraphy, for the diagnosis and staging of lung cancer. DESIGN: Prospective, experimental investigation. SETTING: Academic medical center. PATIENTS: One hundred sixty-six subjects with suspected lung cancer were enrolled in the study. INTERVENTIONS: Whole-body and single-photon emission CT imaging of the chest was performed after IV administration of (99m)Tc depreotide. Attenuation-corrected FDG PET imaging was performed after IV administration of FDG. Image findings were compared with the biopsy results or clinical follow-up. MEASUREMENTS AND RESULTS: In 157 subjects with evaluable lung lesions, the sensitivities and specificities for detecting malignant disease (95% confidence intervals) of FDG PET are 96% (90 to 98%) and 71% (54 to 85%), and of (99m)Tc depreotide are 94% (88 to 98%) and 51% (34 to 68%). In the 139 subjects with available complete staging data, FDG PET correctly staged 76 of 139 patients (55%), and (99m)Tc depreotide correctly staged 63 of 139 patients (45%). CONCLUSIONS: The sensitivity for detection of lung cancer in the primary lesion is equally high for FDG PET and (99m)Tc depreotide. The specificity is superior for FDG PET. The staging accuracy of FDG PET and (99m)Tc depreotide is similar, but when read with the chest CT neither scintigraphic examination is sufficiently accurate to stage patients with non-small cell lung cancer.

Adult↗
PubMed2003

Enzyme-specific profiles for genome annotation: PRIAM.

The advent of fully sequenced genomes opens the ground for the reconstruction of metabolic pathways on the basis of the identification of enzyme-coding genes. Here we describe PRIAM, a method for automated enzyme detection in a fully sequenced genome, based on the classification of enzymes in the ENZYME database. PRIAM relies on sets of position-specific scoring matrices ('profiles') automatically tailored for each ENZYME entry. Automatically generated logical rules define which of these profiles is required in order to infer the presence of the corresponding enzyme in an organism. As an example, PRIAM was applied to identify potential metabolic pathways from the complete genome of the nitrogen-fixing bacterium Sinorhizobium meliloti. The results of this automated method were compared with the original genome annotation and visualised on KEGG graphs in order to facilitate the interpretation of metabolic pathways and to highlight potentially missing enzymes.

Bacterial Proteins↗