bluuebunny/crossref_metadata_2025_split huggingface dataset:
TMDL Balance: A Model for Coastal Water Pollutant Loadings
Authors: Johnson Stephanie L. , Maidment David R. , Kirisits Mary J. 
Published: March 2013

AbstractBacterial contamination accounts for more than 60% of the impairments included on the 2008 Texas 303(d) List. Many of these bacterial impairments are along the Texas Gulf Coast because coastal waters often are regulated for oyster harvesting, which have strict water quality standards. Under the Clean Water Act, each one of these impaired waterbodies requires a total maximum daily load (TMDL) study to be performed. A recent, statewide study recommended the development and application of simple modeling approaches to address the majority of Texas's bacteria TMDLs, including “… simple load duration curve, GIS [geographic information systems], and/or mass balance models.” We developed the TMDL Balance model in response to this recommendation. TMDL Balance is a steady state, mass balance, GIS‐based model for simulating pollutant loads and concentrations in coastal systems. The model uses plug‐flow reactor and continuously‐stirred tank reactor equations to route spatially distributed point and nonpoint source loads through a watershed via overland flow, non‐tidal flow, and tidal flow, decaying the loads via first‐order kinetics. In this paper, we explain the development of the watershed loading portion of the TMDL Balance model, demonstrating the methodology through a case study: computing bacterial loads in the Copano Bay watershed of southeast Texas. The application highlights an example of distributing bacterial sources spatially based on land use data.
Site‐specific deformable imaging registration algorithm selection using patient‐based simulated deformations
Authors: Nie Ke , Chuang Cynthia , Kirby Neil , Braunstein Steve , Pouliot Jean 
Published: March 2013

Purpose:The accuracy of deformable image registration could have a significant dosimetric impact in radiation treatment planning. Various image registration algorithms have been developed for clinical application. However, validation of these algorithms in the current clinical setting remains subjective, relying on visual assessment and lacking a comparison to the ground‐truth deformation. In this study, the authors propose a framework to quantitatively validate various image registration solutions by using patient‐based synthetic quality assurance (QA) phantoms, which can be applied on a site‐by‐site basis.Methods:The computer‐simulated deformation was first generated with virtual deformation QA software and further benchmarked using a physical pelvic phantom that was modeled after real patient CT images. After the validity of the virtual deformation was confirmed, a set of synthetic deformable images was produced to simulate various anatomical movements during radiotherapy based on real patient CT images. Three patients with head‐and‐neck, prostate, and spine cancer were included. The transformations included bladder filling, soft tissue deformation, mandible, and vertebral body movement, etc., which provided various ground‐truth images to validate deformable registration. Several clinically available deformable registration algorithms were tested on these images with multiple registration setups, such as global or regional and single‐pass or multipass optimization. The generated deformation fields and the ground‐truth deformation are compared using voxel‐by‐voxel based analysis as well as regional based analysis.Results:Performance of registration algorithms varies with clinical sites. The voxel‐by‐voxel analysis showed the intensity‐based free‐form deformation by MIM generated the greatest accuracy for low‐contrast small regions that underwent significant deformation, such as bladder expansion for prostate. However, for large field deformations with strong contrast, this approach may increase errors, which is especially evident in the cranial spinal irradiation (CSI) case. Both single‐pass and multipass B‐spline registrations performed well for the head‐and‐neck patient and CSI patients.Conclusions:QA for deformable image registration is essential to verify the cumulated dose for accurate adaptive radiotherapy. In this study, the authors develop a workflow that can validate image registration techniques for several different clinical sites and for various types of deformations using patient‐based simulated deformations. This work could provide a reference for clinicians and radiation physicists on how to choose appropriate image registration algorithms for different situations.
Automated knowledge‐based detection of nonobstructive and obstructive arterial lesions from coronary CT angiography
Authors: Kang Dongwoo , Slomka Piotr J. , Nakazato Ryo , Arsanjani Reza , Cheng Victor Y. , Min James K. , Li Debiao , Berman Daniel S. , Jay Kuo C.‐C. , Dey Damini 
Published: March 2013

Purpose:Visual analysis of three‐dimensional (3D) coronary computed tomography angiography (CCTA) remains challenging due to large number of image slices and tortuous character of the vessels. The authors aimed to develop a robust, automated algorithm for unsupervised computer detection of coronary artery lesions.Methods:The authors’ knowledge‐based algorithm consists of centerline extraction, vessel classification, vessel linearization, lumen segmentation with scan‐specific lumen attenuation ranges, and lesion location detection. Presence and location of lesions are identified using a multi‐pass algorithm which considers expected or “normal” vessel tapering and luminal stenosis from the segmented vessel. Expected luminal diameter is derived from the scan by automated piecewise least squares line fitting over proximal and mid segments (67%) of the coronary artery considering the locations of the small branches attached to the main coronary arteries.Results:The authors applied this algorithm to 42 CCTA patient datasets, acquired with dual‐source CT, where 21 datasets had 45 lesions with stenosis ≥25%. The reference standard was provided by visual and quantitative identification of lesions with any stenosis ≥25% by three expert readers using consensus reading. The authors algorithm identified 42 lesions (93%) confirmed by the expert readers. There were 46 additional lesions detected; 23 out of 39 (59%) of these were less‐stenosed lesions. When the artery was divided into 15 coronary segments according to standard cardiology reporting guidelines, per‐segment basis, sensitivity was 93% and per‐segment specificity was 81% using 10‐fold cross‐validation.Conclusions:The authors’ algorithm shows promising results in the detection of both obstructive and nonobstructive CCTA lesions.
Needle segmentation using 3D Hough transform in 3D TRUS guided prostate transperineal therapy
Authors: Qiu Wu , Yuchi Ming , Ding Mingyue , Tessier David , Fenster Aaron 
Published: March 2013

Purpose:Prostate adenocarcinoma is the most common noncutaneous malignancy in American men with over 200 000 new cases diagnosed each year. Prostate interventional therapy, such as cryotherapy and brachytherapy, is an effective treatment for prostate cancer. Its success relies on the correct needle implant position. This paper proposes a robust and efficient needle segmentation method, which acts as an aid to localize the needle in three‐dimensional (3D) transrectal ultrasound (TRUS) guided prostate therapy.Methods:The procedure of locating the needle in a 3D TRUS image is a three‐step process. First, the original 3D ultrasound image containing a needle is cropped; the cropped image is then converted to a binary format based on its histogram. Second, a 3D Hough transform based needle segmentation method is applied to the 3D binary image in order to locate the needle axis. The position of the needle endpoint is finally determined by an optimal threshold based analysis of the intensity probability distribution. The overall efficiency is improved through implementing a coarse‐fine searching strategy. The proposed method was validated in tissue‐mimicking agar phantoms, chicken breast phantoms, and 3D TRUS patient images from prostate brachytherapy and cryotherapy procedures by comparison to the manual segmentation. The robustness of the proposed approach was tested by means of varying parameters such as needle insertion angle, needle insertion length, binarization threshold level, and cropping size.Results:The validation results indicate that the proposed Hough transform based method is accurate and robust, with an achieved endpoint localization accuracy of 0.5 mm for agar phantom images, 0.7 mm for chicken breast phantom images, and 1 mm forin vivo patient cryotherapy and brachytherapy images. The mean execution time of needle segmentation algorithm was 2 s for a 3D TRUS image with size of 264 × 376 × 630 voxels.Conclusions:The proposed needle segmentation algorithm is accurate, robust, and suitable for 3D TRUS guided prostate transperineal therapy.
Complete Genome Sequence of the Avian Pathogenic Escherichia coli Strain APEC O78
Authors: Mangiamele Paul , Nicholson Bryon , Wannemuehler Yvonne , Seemann Torsten , Logue Catherine M. , Li Ganwu , Tivendale Kelly A. , Nolan Lisa K. 
Published: March 2013

ABSTRACT

Colibacillosis, caused by avian pathogenic
Escherichia coli
(APEC), is a significant disease, causing extensive animal and financial losses globally. Because of the significance of this disease, more knowledge is needed regarding APEC's mechanisms of virulence. Here, we present the fully closed genome sequence of a typical avian pathogenic
E. coli
strain belonging to the serogroup O78.
Draft Genome of Pseudomonas stutzeri Strain NF13, a Nitrogen Fixer Isolated from the Galapagos Rift Hydrothermal Vent
Authors: Peña Arantxa , Busquets Antonio , Gomila Margarita , Mayol Joan , Bosch Rafael , Nogales Balbina , García-Valdés Elena , Bennasar Antonio , Lalucat Jorge 
Published: March 2013

ABSTRACT

Pseudomonas stutzeri
strain NF13 was isolated from a water sample taken at a hydrothermal vent in the Galapagos rift. It was selected for its ability to metabolize sulfur compounds and to grow diazotrophically. Here, we report the first draft genome of a member of genomovar 19 of the species.
Lack of Invariant Natural Killer T Cells Affects Lipid Metabolism in Adipose Tissue of Diet-Induced Obese Mice
Authors: Strodthoff Daniela , Lundberg Anna M. , Agardh Hanna E. , Ketelhuth Daniel F.J. , Paulsson-Berne Gabrielle , Arner Peter , Hansson Göran K. , Gerdes Norbert 
Published: March 2013

Objective—
Obesity promotes a chronic inflammatory condition in adipose tissue (AT). Impairment of insulin sensitivity coincides with infiltration of T cells into AT in early stages of obesity, when macrophages are not yet present. Here, we examine the role of invariant natural killer T (iNKT) cells, a subtype of T cells activated by lipid antigens, on glucose and lipid metabolism in obesity.

Approach and Results—

Jα18
−/−
mice, specifically lacking iNKT cells, and wild-type mice consumed a chow or high-fat diet for 10 weeks. One third of all T lymphocytes in the liver of wild-type mice were iNKT cells, whereas few were detected in AT. Diet-induced obesity increased blood glucose in both genotypes of mice, whereas glucose tolerance test revealed similar kinetics of glucose clearance in
Jα18
−/−
and wild-type mice. Under obese conditions, expression of inflammatory cytokines in AT did not differ between the groups, although the number of T cells and macrophages was lower in
Jα18
−/−
mice. Nonetheless, AT homeostasis in
Jα18
−/−
mice was altered evidenced by lower AT weight, smaller adipocytes, accelerated lipogenesis, increased expression of hormone-sensitive lipase, and accelerated basal lipolysis.

Conclusions—
iNKT cells do not affect glucose clearance but rather modulate lipid metabolism in both liver and AT. Only few iNKT cells are found in AT under lean and obese conditions, suggesting that their effects on lipid metabolism are mainly mediated in the liver, their primary host organ.
Paradoxical Association of Enhanced Cholesterol Efflux With Increased Incident Cardiovascular Risks
Authors: Li Xin-Min , Tang Wai Hong Wilson , Mosior Marian K. , Huang Ying , Wu Yuping , Matter William , Gao Vivian , Schmitt David , DiDonato Joseph A. , Fisher Edward A. , Smith Jonathan D. , Hazen Stanley L. 
Published: March 2013

Objective—
Diminished cholesterol efflux activity of apolipoprotein B (apoB)–depleted serum is associated with prevalent coronary artery disease, but its prognostic value for incident cardiovascular events is unclear. We investigated the relationship of cholesterol efflux activity with both prevalent coronary artery disease and incident development of major adverse cardiovascular events (death, myocardial infarction, or stroke).

Approach and Results—

Cholesterol efflux activity from free cholesterol–enriched macrophages was measured in 2 case–control cohorts: (1) an angiographic cohort (n=1150) comprising stable subjects undergoing elective diagnostic coronary angiography and (2) an outpatient cohort (n=577). Analysis of media from cholesterol efflux assays revealed that the high-density lipoprotein fraction (1.063<
d
<1.21) contained only a minority (≈40%) of [
14
C]cholesterol released, with the majority found within the lipoprotein particle–depleted fraction, where ≈60% was recovered after apolipoprotein A1 immunoprecipitation. Albumin immunoprecipitation recovered another ≈30% of radiolabeled cholesterol within this fraction. Enhanced cholesterol efflux activity from ATP-binding cassette transporter A1–stimulated macrophages was associated with reduced risk of prevalent coronary artery disease in unadjusted models within both cohorts; however, the inverse risk relationship remained significant after adjustment for traditional coronary artery disease risk factors only within the outpatient cohort. Surprisingly, higher cholesterol efflux activity was associated with increase in prospective (3 years) risk of myocardial infarction/stroke (adjusted hazard ratio, 2.19; 95% confidence interval, 1.02–4.74) and major adverse cardiovascular events (adjusted hazard ratio, 1.85; 95% confidence interval, 1.11–3.06).

Conclusions—
Heightened cholesterol efflux to apoB-depleted serum was paradoxically associated with increased prospective risk for myocardial infarction, stroke, and death. The majority of released radiolabeled cholesterol from macrophages in cholesterol efflux activity assays does not reside within a high-density lipoprotein particle.
Risk of Rupture of an Intracranial Aneurysm Based on Patient Characteristics
Authors: Vlak Monique H.M. , Rinkel Gabriel J.E. , Greebe Paut , Algra Ale 
Published: March 2013

Background and Purpose—
Knowledge about risk factors contributes to understanding the pathophysiological mechanisms that cause intracranial aneurysm rupture and helps to develop possible treatment strategies. We aimed to study lifestyle and personal characteristics as risk factors for the rupture of intracranial aneurysms.

Methods—
We performed a case–control study with 250 patients with an aneurysmal subarachnoid hemorrhage and 206 patients with an unruptured intracranial aneurysm. All patients with an aneurysmal subarachnoid hemorrhage and patients with a unruptured intracranial aneurysm were asked to fill in a structured questionnaire about their lifestyle and medical history. For patients with an unruptured intracranial aneurysm, we also collected data on the indication for imaging. With logistic regression analysis, we identified independent risk factors for aneurysmal rupture.

Results—
Reasons for imaging in patients with an unruptured intracranial aneurysm were atherosclerotic disease (23%), positive family history (18%), headache (8%), preventive screening (3%), and other (46%). Factors that increased risk for aneurysmal rupture were smoking (odds ratio, 1.9; 95% confidence interval, 1.2–3.0) and migraine (2.4; 1.1–5.1); hypercholesterolemia decreased this risk (0.4; 0.2–1.0), whereas a history of hypertension did not independently influence the risk.

Conclusions—
Smoking, migraine and, inversely, hypercholesterolemia are independent risk factors for aneurysmal rupture. Data from the questionnaire are insufficient to conclude whether hypercholesterolemia or its treatment with statins exerts a risk-reducing effect. The pathophysiological mechanisms through which smoking and migraine increase the risk of aneurysmal rupture should be investigated in further studies. Although a history of hypertension does not increase risk of rupture, a sudden rise in blood pressure might still trigger aneurysmal rupture.
Legal Aspects of Personalized Health Monitoring
Authors: Callens Stefaan 
Published: March 2013

Abstract
Personal health monitoring (PHM) can be defined as comprising all technical systems, processing, collecting, and storing of data linked to a person. PHM involves several legal issues that are described in this article. This article analyses firstly the short term actions that are needed at the European level to allow personal health monitoring in respect of the interests and rights of patients such as the need to have more harmonized medical liability rules at the EU level. Introducing PHM implies also legal action at the EU level on the long run. These long-term actions are related to e.g., the way in which hospitals are organized in their relation with healthcare professionals and with other hospitals or healthcare actors. The paper will finally analyse also how health monitoring projects may change the traditional (non-) relationship between patients and pharmaceutical/medical device industry. Today, the producers and distributors of medicinal products have no specific contact with patients. This situation may change when applying telemonitoring projects and may require to new legal rules.
Incremental Correction for the Dynamical Downscaling of Ensemble Mean Atmospheric Fields
Authors: Yoshimura Kei , Kanamitsu Masao 
Published: March 2013

Abstract
This research was motivated by the need for an improved method compared to the conventional brute-force approach to ensemble downscaling. That method simply applies dynamical downscaling to each ensemble member. It obtains a reliable forecast by taking the ensemble average of all the downscaled ensemble members. This approach, although straightforward, has a problem in that the computational cost is too large for an operational environment. Herein a method for downscaling ensemble mean forecasts is proposed. Although this method does not provide probabilistic forecasts, it will provide the regional-scale detail at minimum cost. In this product, all of the predicted parameters are dynamically and physically consistent (i.e., most likely to occur on a seasonal time scale). It is believed that such a product has great utility for regional climate forecast and application products. The method applies a correction to one of the global forecast members in such a way that the seasonal mean is equal to that of the ensemble mean, and it then downscales the corrected global forecast. This method was tested for a 140-yr period by using the Twentieth-Century Reanalysis dataset, which is a product of ensemble Kalman filtering data assimilation. Use of the method clearly improves the downscaling skill compared to the case of using only a single member; the skill becomes equivalent to that achieved when between two and six members are used directly.
Examination of Situation-Dependent Background Error Covariances at the Convective Scale in the Context of the Ensemble Kalman Filter
Authors: Chung Kao-Shen , Chang Weiguang , Fillion Luc , Tanguay Monique 
Published: March 2013

Abstract
A high-resolution ensemble Kalman filter (HREnKF) system at the convective scale has been developed based on the Canadian Meteorological Center's operational global ensemble Kalman filter (EnKF) system. This study focuses on the very early stage of transition from purely homogeneous isotropic background error correlations to situation-dependent correlations. It has been found that forecast error structures can develop situation-dependent features in as little as 15 min. Furthermore, the dynamic and thermodynamic variables require different periods of time to build up their own forecast error structures. Differences in these structures between regions with and without precipitation are also investigated. An examination of temperature tendencies revealed that physical processes are as important as dynamical forcing in determining the structure of convective-scale errors structures, and that once physical processes become active, these structures change rapidly before the onset of precipitation. This study is intended to be the basis for a systematic exploration in the near future of the usefulness of the HREnKF system in assimilating high-density observations such as radar data.
Patients’ and carers’ perception of needs in a Polish sample
Authors: Cialkowska-Kuzminska Magdalena , Misiak Blazej , Kiejna Andrzej 
Published: March 2013

Background: The assessment of patients’ needs is an essential element of psychiatric health care planning and evaluation. Not much interest has been paid to the study of psychiatric patients’ needs in Poland so far. Aims: To assess the relation between inpatients’ and their key carers’ perception of needs in a Polish sample. Methods: Out of 324 inpatients invited to take part in the study, 60 sets were finally included. Patients and their carers were examined by means of CANSAS to rate patients’ and carers’ perception of needs. Results: The mean number of general needs indicated by patients themselves was 7.11 (± 2.98), and those indicated by carers equalled 9.53 (± 3.92). The more unmet needs identified by the patient, the more met and general needs of the patient identified by their carer ( r = .27, p = .03; r = .38, p = .02, respectively). The more general needs perceived by the patient themself, the higher the indicator of unmet and general needs scored by their carer ( r = .32, p = .01; r = .39, p = .001, respectively). Conclusions: There is a significant association between the inpatients’ and their carers’ perception of needs. Patients’ perspective should serve as a high priority in developing treatment plans.
Operative Time and Cost of Resident Surgical Experience: Effect of Instituting an Otolaryngology Residency Program
Authors: Pollei Taylor R. , Barrs David M. , Hinni Michael L. , Bansberg Stephen F. , Walter Logan C. 
Published: March 2013

ObjectiveDescribe the procedure length difference between surgeries performed by an attending surgeon alone compared with the resident surgeon supervised by the same attending surgeon.Study DesignCase series with chart review.SettingTertiary care center and residency program.Subjects and MethodsSix common otolaryngologic procedures performed between August 1994 and May 2012 were divided into 2 cohorts: attending surgeon alone or resident surgeon. This division coincided with our July 2006 initiation of an otolaryngology–head and neck surgery residency program. Operative duration was compared between cohorts with confounding factors controlled. In addition, the direct result of increased surgical length on operating room cost was calculated and applied to departmental and published resident case log report data.ResultsFive of the 6 procedures evaluated showed a statistically significant increase in surgery length with resident involvement. Operative time increased 6.8 minutes for a cricopharyngeal myotomy (P =. 0097), 11.3 minutes for a tonsillectomy (P <. 0001), 27.4 minutes for a parotidectomy (P =. 028), 38.3 minutes for a septoplasty (P <. 0001), and 51 minutes for tympanomastoidectomy (P <. 0021). Thyroidectomy showed no operative time difference. Cost of increased surgical time was calculated per surgery and ranged from $286 (cricopharyngeal myotomy) to $2142 (mastoidectomy). When applied to reported national case log averages for graduating residents, this resulted in a significant increase of direct training‐related costs.ConclusionResident participation in the operating room results in increased surgical length and additional system cost. Although residency is a necessary part of surgical training, associated costs need to be acknowledged.