Brian Davis | U.S. Geological Survey (original) (raw)

Papers by Brian Davis

Computerized Medical Imaging and Graphics, 2003

In the year 2000, it is estimated that over 20,000 men underwent transperineal interstitial perma... more In the year 2000, it is estimated that over 20,000 men underwent transperineal interstitial permanent prostate brachytherapy (TIPPB) for treatment of prostate cancer. Trans-urethral ultrasound (TUUS) is a new interactive, real-time 3D imaging method that may be effective in therapy-guidance during and after TIPPB. TUUS provides higher resolution than trans-rectal ultrasound (TRUS). TUUS can be used to accurately localize radioactive

Urology, 2009

tive first line treatment for low risk localised prostate cancer. We present the first long-term ... more tive first line treatment for low risk localised prostate cancer. We present the first long-term follow-up of an Australian series of patients with locally confined prostate cancer treated with LDRB as monotherapy. We also present a current cross-sectional analysis of health-related quality of life outcomes (HRQoL) using the validated RAND-36 item questionnaire. Materials and Methods: We investigate biochemical free relapse survival (BFRS) rates on 325 consecutive patients between 1997 and 2006 with localised prostate cancer treated with I 125 low dose brachytherapy in a large tertiary referral urological centre. A cross-sectional study of urinary function, sexual function and bowel toxicity were conducted using a validated HRQoL RAND-36 item questionnaire specific for radiotherapy treatments of prostate cancer. Result: Mean age of the cohort was 65 years (range 47-81 years) and mean pre treatment PSA was 7.4 ng/ml. As according to the D'Amico classification 76% of patients treated were low risk, 22% of patients treated were intermediate risk and 2% high risk. Mean length of follow-up was 45 month. The actuarial BFRS rate at 5 years was 90%. Thirty-two patients had evidence of biochemical failure as defined by the Pheonix definition. Conclusions: I 125 low dose brachytherapy results in excellent biochemical survival for patients with low risk localised prostate cancer.

European Urology Supplements, 2010

Scientific reports, 2015

Terrestrial carbon sequestration potential is widely considered as a realistic option for mitigat... more Terrestrial carbon sequestration potential is widely considered as a realistic option for mitigating greenhouse gas emissions. However, this potential may be threatened by global changes including climate, land use, and management changes such as increased corn stover harvesting for rising production of cellulosic biofuel. Therefore, it is critical to investigate the dynamics of soil organic carbon (SOC) at regional or global scale. This study simulated the corn production and spatiotemporal changes of SOC in the U.S. Temperate Prairies, which covers over one-third of the U.S. corn acreage, using a biogeochemical model with multiple climate and land-use change projections. The corn production (either grain yield or stover biomass) could reach 88.7-104.7 TgC as of 2050, 70-101% increase when compared to the base year of 2010. A removal of 50% stover at the regional scale could be a reasonable cap in view of maintaining SOC content and soil fertility especially in the beginning years....

2004 IEEE International Conference on Cluster Computing (IEEE Cat. No.04EX935), 2004

JuxtaView is a cluster-based application for viewing ultra-high-resolution images on scalable til... more JuxtaView is a cluster-based application for viewing ultra-high-resolution images on scalable tiled displays. We present in JuxtaView, a new parallel computing and distributed memory approach for out-of-core montage visualization, using LambdaRAM, a software-based networklevel cache system. The ultimate goal of JuxtaView is to enable a user to interactively roam through potentially terabytes of distributed, spatially referenced image data such as those from electron microscopes, satellites and aerial photographs. In working towards this goal, we describe our first prototype implemented over a local area network, where the image is distributed using LambdaRAM, on the memory of all nodes of a PC cluster driving a tiled display wall. Aggressive pre-fetching schemes employed by LambdaRAM help to reduce latency involved in remote memory access. We compare LambdaRAM with a more traditional memorymapped file approach for out-of-core visualization.

European Urology, 2015

Patients with lymph node (LN)-positive prostate cancer (PCa) at radical prostatectomy (RP) face a... more Patients with lymph node (LN)-positive prostate cancer (PCa) at radical prostatectomy (RP) face a high risk of cancer recurrence. Nevertheless, recurrence patterns of LN-positive PCa and their prognostic significance remain understudied in the literature. To analyze a large single-institution series with long-term follow-up to elucidate the various clinical recurrence patterns of LN-positive PCa and their association with oncologic outcomes. Years 1987-2012 of a prospectively maintained institutional RP registry were queried for men with LN-positive PCa at RP. Clinical recurrences were categorized as local, nodal, skeletal, or visceral. In addition to descriptive statistics and Kaplan-Meier analysis, univariable and multivariable Cox proportional hazards models were constructed to predict recurrence and to quantify the impact of recurrence patterns on cancer-specific mortality (CSM). Data from 1011 men with LN-positive PCa at RP were analyzed with 17.6 yr of median follow-up. The 15-yr clinical recurrence rate was 33% (95% confidence interval [CI], 31-35%) for all patients and 52.2% (95% CI, 47.3-57.1%) for patients with biochemical recurrence. The solitary locations were skeletal (n=94, 55%), nodal (n=59, 34%), local soft tissue (n=29, 17%), and visceral (n=8, 5%). Significant multivariable predictors of recurrence were Gleason score 8-10, number of positive nodes, pathologic Gleason score, and more recent year of surgery. The 15-yr CSM after clinical recurrence was 80%, with a mean overall survival of 30 mo after recurrence. On multivariable analysis, recurrences after 5 yr from RP (hazard ratio [HR]: 0.05), multiple recurrences (HR: 1.97), skeletal (HR: 3.13), and visceral metastases (HR: 7.43) were independently associated with CSM (all p&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;0.05). Recurrences after RP for LN-positive PCa are heterogeneous in terms of time from RP, location, and number of concomitant lesions. We found that impact of recurrence patterns on cancer-specific mortality varies significantly and allows these patients to be stratified for purposes of prognostication, follow-up, and therapy.

Oncology (Williston Park, N.Y.), 2013

Carbon balance and management, 2015

Climate change and the concurrent change in wildfire events and land use comprehensively affect c... more Climate change and the concurrent change in wildfire events and land use comprehensively affect carbon dynamics in both spatial and temporal dimensions. The purpose of this study was to project the spatial and temporal aspects of carbon storage in the Greater Yellowstone Ecosystem (GYE) under these changes from 2006 to 2050. We selected three emission scenarios and produced simulations with the CENTURY model using three General Circulation Models (GCMs) for each scenario. We also incorporated projected land use change and fire occurrence into the carbon accounting. The three GCMs showed increases in maximum and minimum temperature, but precipitation projections varied among GCMs. Total ecosystem carbon increased steadily from 7,942 gC/m(2) in 2006 to 10,234 gC/m(2) in 2050 with an annual rate increase of 53 gC/m(2)/year. About 56.6% and 27% of the increasing rate was attributed to total live carbon and total soil carbon, respectively. Net Primary Production (NPP) increased slightly ...

Microbiology (Reading, England), 2001

Among species of the heterobasidiomycetous yeasts, Filobasidiella neoformans is the only serious ... more Among species of the heterobasidiomycetous yeasts, Filobasidiella neoformans is the only serious pathogen that causes fatal infections in both immunocompromised as well as immunocompetent patients. Three phenotypic characteristics, including growth at 37 degrees C, extracellular polysaccharide capsule and laccase activity, of F. neoformans are known to play major roles in the pathogenicity of the fungus. Several CAP genes involved in polysaccharide capsule formation, as well as the CNLAC1 gene encoding a laccase, have previously been cloned and characterized. To analyse the presence of these Cryptococcus neoformans virulence factors in other heterobasidiomycetous yeasts, numerous species of heterobasidiomycetous yeasts were screened for the presence of laccase activity and a polysaccharide capsule. Species exhibiting laccase activity and possessing a glucuronoxylomannan (GXM) capsule were screened for homologues of both the CAP59 gene and the CNLAC1 gene of F. neoformans. Southern b...

Language Resources and Evaluation, 2008

An increasing number of enterprises are beginning to include semantic web ontologies into their I... more An increasing number of enterprises are beginning to include semantic web ontologies into their Information Extraction (IE) and Text Analytics (TA) applications. This can be challenging for a TA group wishing to avail of semantic web ontologies due to the manual effort of retargeting and tailoring language resources within the TA system to a new domain to meet customer needs.

2008 International Multiconference on Computer Science and Information Technology, 2008

Semantic web ontologies are being increasingly used in modern text analytics applications and Ont... more Semantic web ontologies are being increasingly used in modern text analytics applications and Ontology-Based Information Extraction(OBIE) as a means to provide a semantic backbone either for modelling the internal conceptual data structures of the Text Analytics(TA) engine or to model the Knowledge base to drive the analysis of unstructured information in raw text and subsequent Knowledge acquisition and population. Creating and targeting Language Resources(LR)s from a TA to an Ontology can be time consuming and costly. In [1] the authors describe a user-friendly method for Ontology engineers to augment an ontologies with a lexical layer which provides a flexible framework to identify term mentions of ontology concepts in raw text. In this paper we explore multilinguality in these lexical layers using the same framework. We discuss a number of potential issues for the "linguistic light" Lexical Extensions for Ontologies (LEON) approach when looking at languages more morphologically rich and which have more complex linguistic constraints than English. We show how the LEON approach can cope with these phenomena once the morphological normaliser used in the lexical analysis process is able to generalise sufficiently well for the language concerned.

Analytical Proceedings, 1989

Lecture Notes in Computer Science, 2007

This paper presents a controlled language for ontology editing and a software implementation, bas... more This paper presents a controlled language for ontology editing and a software implementation, based partly on standard NLP tools, for processing that language and manipulating an ontology. The input sentences are analysed deterministically and compositionally with respect to a given ontology, which the software consults in order to interpret the input's semantics; this allows the user to learn fewer syntactic structures since some of them can be used to refer to either classes or instances, for example. A repeated-measures, task-based evaluation has been carried out in comparison with a well-known ontology editor; our software received favourable results for basic tasks. The paper also discusses work in progress and future plans for developing this language and tool.

Journal of Urology, 2000

Transperineal interstitial prostate brachytherapy is increasingly used as a definitive treatment ... more Transperineal interstitial prostate brachytherapy is increasingly used as a definitive treatment for early prostate cancer. After this treatment, seed migration to the heart is rarely frequently observed. The patient was experienced seed migration to the right ventricle after the treatment, it was difficult to diagnose in posteroanterior chest radiograph, but we were able to demonstrate it in multi-detector row computed tomography (MDCT).

Semantic Knowledge Management, 2009

A tension exists between the increasingly rich semantic models in knowledge management systems an... more A tension exists between the increasingly rich semantic models in knowledge management systems and the continuing prevalence of human language materials in large organisations. The process of tying semantic models and natural language together is referred to as semantic annotation, which may also be characterized as the dynamic creation of bidirectional relationships between ontologies and unstructured and semi-structured documents.

D Trans-Urethral Ultrasound (TUUS) imaging is a new imaging technique for the diagnosis and treat... more D Trans-Urethral Ultrasound (TUUS) imaging is a new imaging technique for the diagnosis and treatment of prostate disease. Our current research focuses on the potential of TUUS in therapy guidance during transperineal interstitial permanent prostate brachytherapy (TIPPB). TUUS may complement or potentially replace x-ray fluoroscopy and TRUS in providing data for determining the prostate boundary and radiation source locations. Prostate boundary detection and source localization using TUUS were tested on an ultrasound-equivalent prostate phantom and in a patient during TIPPB. Data collection was conducted with a 10 French, 10 MHz ultrasound catheter controlled by an Acuson Sequoia workstation. 2D and 3D TUUS scans were acquired after radioactive seeds were placed in the phantom and in the patient. Data was reconstructed, processed, and analyzed using Analyze software. Segmentation of the prostate boundary was performed semi-automatically, and seed segmentation was performed manually. Image artifacts in TUUS data resulted in incorrect reconstruction of the seeds. Intelligent processing of the seed data improved reconstruction. Comparison to the CT data suggests that TUUS data provides: 1) greater spatial resolution, 2) greater temporal resolution and 3) better contrast for soft tissue differentiation. The reconstructed source sizes and locations were measured and found accurate. Placement of the TUUS catheter into the urethra provides excellent 2D sections which can be used to acquire volumetric data for 3D analysis of the prostate and radioactive sources. Preliminary results suggest that TUUS will be useful for guidance of seed placement, post-implant seed localization, and intra-operative dosimetry.

Objectives. To assess the impact of clinical selection criteria on pathologic features among pati... more Objectives. To assess the impact of clinical selection criteria on pathologic features among patients treated by radical retropubic prostatectomy and to evaluate the implications of broadening eligibility for permanent prostate brachytherapy monotherapy. Methods. A consecutive series of 423 patients with prostate cancer, who underwent diagnostic biopsy and subsequent radical retropubic prostatectomy, were selected for this study. Four subgroups were defined using the American Brachytherapy Society selection criteria, including prostate size limits (group 1), no prostate size limits (group 2A), a modified set of criteria (group 2B), and clinical Stage T1-T2 (group 3). The rates of extraprostatic extension, seminal vesicle invasion, and lymph node involvement were compared. Results. Adverse pathologic features at radical retropubic prostatectomy were noted in 8 (9.3%) of 86 patients in group 1, 11 (5.6%) of 195 patients in group 2A, 35 (12.0%) of 292 patients in group 2B, and 90 (21.8%) of 413 patients in group 3. The rates of extraprostatic extension, seminal vesicle invasion, and lymph node involvement appeared comparable among groups 1 (5.8%, 3.5%, and 0.0%, respectively), 2A (3.6%, 2.1%, and 0.0%, respectively), and 2B (6.9%, 3.8%, and 1.4%, respectively), but were greater in group 3 (9.7%, 7.8%, and 4.4%, respectively). Conclusions. Judicious broadening of the clinical selection criteria may allow a greater number of patients to be eligible for permanent prostate brachytherapy monotherapy by including patients whose risk of having adverse pathologic features is comparable to that of patients currently deemed suitable for permanent prostate brachytherapy monotherapy. Prospective assessment of oncologic outcomes of such an approach is required. UROLOGY 68: 810-814, 2006.

Interstitial transperineal cryoablation with 17-gauge cryoprobes is an accepted treatment modalit... more Interstitial transperineal cryoablation with 17-gauge cryoprobes is an accepted treatment modality for localized prostate cancer. The effectiveness of cryoablation in the treatment of local prostate cancer recurrence after radical retropubic prostatectomy (RRP) is unknown.

Effective brachytherapy procedures require precise placement of radioactive seeds in the prostate... more Effective brachytherapy procedures require precise placement of radioactive seeds in the prostate. Currently, transrectal ultrasound (TRUS) imaging is one of the main intraoperative imaging modalities to assist physicians in placement of brachytherapy seeds. However, the seed detection rate with TRUS is poor mainly because ultrasound imaging is highly sensitive to variations in seed orientation. The purpose of this study is to investigate the abilities of a new acoustic radiation force imaging modality, vibro-acoustography (VA), equipped with a 1.75D array transducer and implemented on a customized clinical ultrasound scanner, to image and localize brachytherapy seeds in prostatic tissue. To perform experiments, excised cadaver prostate specimens were implanted with dummy brachytherapy seeds, and embedded in tissue mimicking gel to simulate the properties of the surrounding soft tissues. The samples were scanned using the VA system and the resulting VA signals were used to reconstruct VA images at several depths inside the tissue. To further evaluate the performance of VA in detecting seeds, X-ray computed tomography (CT) images of the same tissue sample, were obtained and used as a gold-standard to compare the number of seeds detected by the two methods. Our results indicate that VA is capable of imaging of brachytherapy seeds with accuracy and high contrast, and can detect a large percentage of the seeds implanted within the tissue samples.