bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inverse Computational Fluid Dynamics: Influence of Discretization and Model Errors on Flows in Water Network Including Junctions
Authors: Waeytens Julien , Chatellier Patrice , Bourquin Frédéric 
Published: April 2015

AbstractWe address the reconstruction of relevant two-dimensional (2D) flows in drinking water networks, especially in key elements such as pipe junctions, in view of representative water quality simulations. From the optimal control theory, a specific inverse technique using few sensors and computational fluid dynamics (CFD) models has been developed. First, we determine the boundary velocities, i.e., the control parameters, by minimizing a data misfit functional. Then, knowing the boundary velocities, a direct solve of the flow model is performed to get the space–time cartography of the water flow. To reduce the number of control parameters to be determined and thus restrict the number of sensors, the spatial shape of the boundary velocities is considered as an a priori information given by the water pipes engineering literature. Thus, only the time evolution of the boundary velocities has to be determined. The whole numerical procedure proposed in this paper easily fits in a general purpose finite element software, featuring user's friendliness for a wide engineering audience. Two ways are investigated to reduce the computation time associated to the flow reconstruction. The adjoint framework is used in the minimization process. The reconstruction of the flow using coarse discretizations and simple flow models, instead of 2D Navier–Stokes equations, is studied. The influence of the flow modeling and of the dicretization on the quality of the reconstructed velocity is studied on two examples: a water pipe junction and a 200 m subsection from a French water network. In the water pipe junction, we show that at a Reynolds number of 200 a hybrid approach combining an unsteady Stokes reconstruction and a single direct Navier–Stokes simulation outperforms the algorithms based on a single model. In the network subsection, we obtain an L2 error less than 1% between the reference velocity based on Navier–Stokes equations (Reynolds number of 200) and the velocity reconstructed from Stokes equation. In this case, the reconstruction lasts less than 1 min. Stokes based reconstruction of a Navier–Stokes flow in junctions at Reynolds number up to 100 yields the same accuracy and proves fast.
Noninvasive hemodynamic assessment, treatment outcome prediction and follow‐up of aortic coarctation from MR imaging
Authors: Ralovich Kristóf , Itu Lucian , Vitanovski Dime , Sharma Puneet , Ionasec Razvan , Mihalef Viorel , Krawtschuk Waldemar , Zheng Yefeng , Everett Allen , Pongiglione Giacomo , Leonardi Benedetta , Ringel Richard , Navab Nassir , Heimann Tobias , Comaniciu Dorin 
Published: April 2015

Purpose:Coarctation of the aorta (CoA) is a congenital heart disease characterized by an abnormal narrowing of the proximal descending aorta. Severity of this pathology is quantified by the blood pressure drop (△P) across the stenotic coarctation lesion. In order to evaluate the physiological significance of the preoperative coarctation and to assess the postoperative results, the hemodynamic analysis is routinely performed by measuring the △P across the coarctation site via invasive cardiac catheterization. The focus of this work is to present an alternative, noninvasive measurement of blood pressure drop △P through the introduction of a fast, image‐based workflow for personalized computational modeling of the CoA hemodynamics.Methods:The authors propose an end‐to‐end system comprised of shape and computational models, their personalization setup using MR imaging, and a fast, noninvasive method based on computational fluid dynamics (CFD) to estimate the pre‐ and postoperative hemodynamics for coarctation patients. A virtual treatment method is investigated to assess the predictive power of our approach.Results:Automatic thoracic aorta segmentation was applied on a population of 212 3D MR volumes, with mean symmetric point‐to‐mesh error of 3.00 ± 1.58 mm and average computation time of 8 s. Through quantitative evaluation of 6 CoA patients, good agreement between computed blood pressure drop and catheter measurements is shown: average differences are 2.38 ± 0.82 mm Hg (pre‐), 1.10 ± 0.63 mm Hg (postoperative), and 4.99 ± 3.00 mm Hg (virtual stenting), respectively.Conclusions:The complete workflow is realized in a fast, mostly‐automated system that is integrable in the clinical setting. To the best of our knowledge, this is the first time that three different settings (preoperative—severity assessment, poststenting—follow‐up, and virtual stenting—treatment outcome prediction) of CoA are investigated on multiple subjects. We believe that in future—given wider clinical validation—our noninvasive in‐silico method could replace invasive pressure catheterization for CoA.
Noncoplanar VMAT for nasopharyngeal tumors: Plan quality versus treatment time
Authors: Wild Esther , Bangert Mark , Nill Simeon , Oelfke Uwe 
Published: April 2015

Purpose:The authors investigated the potential of optimized noncoplanar irradiation trajectories for volumetric modulated arc therapy (VMAT) treatments of nasopharyngeal patients and studied the trade‐off between treatment plan quality and delivery time in radiation therapy.Methods:For three nasopharyngeal patients, the authors generated treatment plans for nine different delivery scenarios using dedicated optimization methods. They compared these scenarios according to dose characteristics, number of beam directions, and estimated delivery times. In particular, the authors generated the following treatment plans: (1) a 4π plan, which is a not sequenced, fluence optimized plan that uses beam directions from approximately 1400 noncoplanar directions and marks a theoretical upper limit of the treatment plan quality, (2) a coplanar 2π plan with 72 coplanar beam directions as pendant to the noncoplanar 4π plan, (3) a coplanar VMAT plan, (4) a coplanar step and shoot (SnS) plan, (5) a beam angle optimized (BAO) coplanar SnS IMRT plan, (6) a noncoplanar BAO SnS plan, (7) a VMAT plan with rotated treatment couch, (8) a noncoplanar VMAT plan with an optimized great circle around the patient, and (9) a noncoplanar BAO VMAT plan with an arbitrary trajectory around the patient.Results:VMAT using optimized noncoplanar irradiation trajectories reduced the mean and maximum doses in organs at risk compared to coplanar VMAT plans by 19% on average while the target coverage remains constant. A coplanar BAO SnS plan was superior to coplanar SnS or VMAT; however, noncoplanar plans like a noncoplanar BAO SnS plan or noncoplanar VMAT yielded a better plan quality than the best coplanar 2π plan. The treatment plan quality of VMAT plans depended on the length of the trajectory. The delivery times of noncoplanar VMAT plans were estimated to be 6.5 min in average; 1.6 min longer than a coplanar plan but on average 2.8 min faster than a noncoplanar SnS plan with comparable treatment plan quality.Conclusions:The authors’ study reconfirms the dosimetric benefits of noncoplanar irradiation of nasopharyngeal tumors. Both SnS using optimized noncoplanar beam ensembles and VMAT using an optimized, arbitrary, noncoplanar trajectory enabled dose reductions in organs at risk compared to coplanar SnS and VMAT. Using great circles or simple couch rotations to implement noncoplanar VMAT, however, was not sufficient to yield meaningful improvements in treatment plan quality. The authors estimate that noncoplanar VMAT using arbitrary optimized irradiation trajectories comes at an increased delivery time compared to coplanar VMAT yet at a decreased delivery time compared to noncoplanar SnS IMRT.
Novel magnetic heating probe for multimodal cancer treatment
Authors: Kan‐Dapaah Kwabena , Rahbar Nima , Soboyejo Wole 
Published: April 2015

Purpose:Multifunctional materials consisting of polymers and magnetic nanoparticles (MNPs) are highly sought after in the field of biomedical engineering. These materials offer new opportunities for the development of novel cancer treatment modalities that can increase the efficacy of cancer therapy. In this paper, a novel probe for multimodal cancer treatment is proposed and analyzed. The probe is essentially a cannula with two main parts: a distal heat generating tip made of a magnetic nanocomposite and a proximal insulated shaft.Methods:A description of the concept and functional operations of the probe is presented. In an effort to assess its feasibility, the authors evaluated the ability of probe tip (made of PMMA‐Fe3O4 nanocomposite) to generate heat in biological tissue using alternating magnetic field (AMF) parameters (field strength and frequency) that are acceptable for human use. Heat generation by MNPs was determined using the linear response theory. The effects of Fe3O4 volume fraction on heat generation as well as treatment time on the thermal dose were studied. The finite element method model was tested for its validity using an analytical model.Results:Lesions were revealed to have an ellipsoidal shape and their sizes were affected by treatment time. However, their shapes remained unchanged. The comparison with the analytical model showed reasonably a good agreement to within 2%. Furthermore, the authors’ numerical predictions also showed reasonable agreement with the experimental results previously reported in the literature.Conclusions:The authors’ predictions demonstrate the feasibility of their novel probe to achieve reasonable lesion sizes, during hyperthermic or ablative heating using AMF parameters (field strength and frequency) that are acceptable for human use.
Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained
In Situ
U(VI) Reduction
Authors: Zhang Ping , Wu Wei-Min , Van Nostrand Joy D. , Deng Ye , He Zhili , Gihring Thomas , Zhang Gengxin , Schadt Chris W. , Watson David , Jardine Phil , Criddle Craig S. , Brooks Scott , Marsh Terence L. , Tiedje James M. , Arkin Adam P. , Zhou Jizhong 
Published: April 2015

ABSTRACT

A pilot-scale field experiment demonstrated that a one-time amendment of emulsified vegetable oil (EVO) reduced groundwater U(VI) concentrations for 1 year in a fast-flowing aquifer. However, little is known about how EVO amendment stimulates the functional gene composition, structure, and dynamics of groundwater microbial communities toward prolonged U(VI) reduction. In this study, we hypothesized that EVO amendment would shift the functional gene composition and structure of groundwater microbial communities and stimulate key functional genes/groups involved in EVO biodegradation and reduction of electron acceptors in the aquifer. To test these hypotheses, groundwater microbial communities after EVO amendment were analyzed using a comprehensive functional gene microarray. Our results showed that EVO amendment stimulated sequential shifts in the functional composition and structure of groundwater microbial communities. Particularly, the relative abundance of key functional genes/groups involved in EVO biodegradation and the reduction of NO
3
−
, Mn(IV), Fe(III), U(VI), and SO
4
2−
significantly increased, especially during the active U(VI) reduction period. The relative abundance for some of these key functional genes/groups remained elevated over 9 months. Montel tests suggested that the dynamics in the abundance, composition, and structure of these key functional genes/groups were significantly correlated with groundwater concentrations of acetate, NO
3
−
, Mn(II), Fe(II), U(VI), and SO
4
2−
. Our results suggest that EVO amendment stimulated dynamic succession of key functional microbial communities. This study improves our understanding of the composition, structure, and function changes needed for groundwater microbial communities to sustain a long-term U(VI) reduction.
Validation of Reference Genes for Transcriptional Analyses in Pleurotus ostreatus by Using Reverse Transcription-Quantitative PCR
Authors: Castanera Raúl , López-Varas Leticia , Pisabarro Antonio G. , Ramírez Lucía 
Published: April 2015

ABSTRACT

Recently, the lignin-degrading basidiomycete
Pleurotus ostreatus
has become a widely used model organism for fungal genomic and transcriptomic analyses. The increasing interest in this species has led to an increasing number of studies analyzing the transcriptional regulation of multigene families that encode extracellular enzymes. Reverse transcription (RT) followed by real-time PCR is the most suitable technique for analyzing the expression of gene sets under multiple culture conditions. In this work, we tested the suitability of 13 candidate genes for their use as reference genes in
P. ostreatus
time course cultures for enzyme production. We applied three different statistical algorithms and obtained a combination of stable reference genes for optimal normalization of RT-quantitative PCR assays. This reference index can be used for future transcriptomic analyses and validation of transcriptome sequencing or microarray data. Moreover, we analyzed the expression patterns of a laccase and a manganese peroxidase (
lacc10
and
mnp3
, respectively) in lignocellulose and glucose-based media using submerged, semisolid, and solid-state fermentation. By testing different normalization strategies, we demonstrate that the use of nonvalidated reference genes as internal controls leads to biased results and misinterpretations of the biological responses underlying expression changes.
Resistance Genes and Genetic Elements Associated with Antibiotic Resistance in Clinical and Commensal Isolates of Streptococcus salivarius
Authors: Chaffanel Fanny , Charron-Bourgoin Florence , Libante Virginie , Leblond-Bourget Nathalie , Payot Sophie 
Published: April 2015

ABSTRACT

The diversity of clinical (
n
= 92) and oral and digestive commensal (
n
= 120) isolates of
Streptococcus salivarius
was analyzed by multilocus sequence typing (MLST). No clustering of clinical or commensal strains can be observed in the phylogenetic tree. Selected strains (92 clinical and 46 commensal strains) were then examined for their susceptibilities to tetracyclines, macrolides, lincosamides, aminoglycosides, and phenicol antibiotics. The presence of resistance genes
tet
(M),
tet
(O),
erm
(A),
erm
(B),
mef
(A/E), and
catQ
and associated genetic elements was investigated by PCR, as was the genetic linkage of resistance genes. High rates of erythromycin and tetracycline resistance were observed among the strains. Clinical strains displayed either the
erm
(B) (macrolide-lincosamide-streptogramin B [MLS
B
] phenotype) or
mef
(A/E) (M phenotype) resistance determinant, whereas almost all the commensal strains harbored the
mef
(A/E) resistance gene, carried by a macrolide efflux genetic assembly (MEGA) element. A genetic linkage between a macrolide resistance gene and genes of Tn
916
was detected in 23 clinical strains and 5 commensal strains, with a predominance of Tn
3872
elements (
n
= 13), followed by Tn
6002
(
n
= 11) and Tn
2009
(
n
= 4) elements. Four strains harboring a
mef
(A/E) gene were also resistant to chloramphenicol and carried a
catQ
gene. Sequencing of the genome of one of these strains revealed that these genes colocalized on an IQ-like element, as already described for other viridans group streptococci. ICE
St3
-related elements were also detected in half of the isolates. This work highlights the potential role of
S. salivarius
in the spread of antibiotic resistance genes both in the oral sphere and in the gut.
Impact of Protein Palmitoylation on the Virulence Potential of Cryptococcus neoformans
Authors: Nichols Connie B. , Ost Kyla S. , Grogan Dayton P. , Pianalto Kaila , Hasan Shirin , Alspaugh J. Andrew 
Published: April 2015

ABSTRACT

The localization and specialized function of Ras-like proteins are largely determined by posttranslational processing events. In a highly regulated process, palmitoyl groups may be added to C-terminal cysteine residues, targeting these proteins to specific membranes. In the human fungal pathogen
Cryptococcus neoformans
, Ras1 protein palmitoylation is essential for growth at high temperature but is dispensable for sexual differentiation. Ras1 palmitoylation is also required for localization of this protein on the plasma membrane. Together, these results support a model in which specific Ras functions are mediated from different subcellular locations. We therefore hypothesize that proteins that activate Ras1 or mediate Ras1 localization to the plasma membrane will be important for
C. neoformans
pathogenesis. To further characterize the Ras1 signaling cascade mediating high-temperature growth, we have identified a family of protein
S
-acyltransferases (PATs), enzymes that mediate palmitoylation, in the
C. neoformans
genome database. Deletion strains for each candidate gene were generated by homogenous recombination, and each mutant strain was assessed for Ras1-mediated phenotypes, including high-temperature growth, morphogenesis, and sexual development. We found that full Ras1 palmitoylation and function required one particular PAT, Pfa4, and deletion of the
PFA4
gene in
C. neoformans
resulted in altered Ras1 localization to membranes, impaired growth at 37°C, and reduced virulence.
Innovation in immediate neonatal care: development of the Bedside Assessment, Stabilisation and Initial Cardiorespiratory Support (BASICS) trolley
Authors: Weeks A D , Watt P , Yoxall C W , Gallagher A , Burleigh A , Bewley S , Heuchan A M , Duley L 
Published: April 2015

ObjectiveBabies receive oxygen through their umbilical cord while in the uterus and for a few minutes after birth. Currently, if the baby is not breathing well at birth, the cord is cut so as to transfer the newborn to a resuscitation unit. We sought to develop a mobile resuscitation trolley on which newly born babies can be resuscitated while still receiving oxygenated blood and the ‘placental transfusion’ through the umbilical cord. This would also prevent separation of the mother and baby in the first minutes after birth.DesignMultidisciplinary iterative product development.SettingClinical Engineering Department of a University Teaching Hospital.MethodsFollowing an initial design meeting, a series of prototypes were developed. At each stage, the prototype was reviewed by a team of experts in the laboratory and in the hospital delivery suite to determine ease of use and fitness for purpose. A commercial company was identified to collaborate on the trolley's development and secure marking with the Conformité Européenne mark, allowing the trolley to be introduced into clinical practice.ResultsThe trolley is a small mobile resuscitation unit based on the concept of an overbed hospital table. It can be manoeuvred to within 50 cm of the mother's pelvis so that the umbilical cord can remain intact during resuscitation, irrespective of whether the baby is born naturally, by instrumental delivery or by caesarean section. Warmth for the newborn comes from a heated mattress and the trolley has the facility to provide suction, oxygen and air.ConclusionsThis is the first mobile resuscitation device designed specifically to facilitate newborn resuscitation at the bedside and with an intact cord. The next step is to assess its safety, its acceptability to clinicians and parents, and to determine whether it allows resuscitation with an intact cord.
Brain Penetration and Efficacy of Different Mebendazole Polymorphs in a Mouse Brain Tumor Model
Authors: Bai Ren-Yuan , Staedtke Verena , Wanjiku Teresia , Rudek Michelle A. , Joshi Avadhut , Gallia Gary L. , Riggins Gregory J. 
Published: April 2015

Abstract
Purpose: Mebendazole (MBZ), first used as an antiparasitic drug, shows preclinical efficacy in models of glioblastoma and medulloblastoma. Three different mebendazole polymorphs (A, B, and C) exist, and a detailed assessment of the brain penetration, pharmacokinetics, and antitumor properties of each individual mebendazole polymorph is necessary to improve mebendazole-based brain cancer therapy.
Experimental Design and Results: In this study, various marketed and custom-formulated mebendazole tablets were analyzed for their polymorph content by IR spectroscopy and subsequently tested in an orthotopic GL261 mouse glioma model for efficacy and tolerability. The pharmacokinetics and brain concentration of mebendazole polymorphs and two main metabolites were analyzed by LC/MS. We found that polymorph B and C both increased survival in a GL261 glioma model, as B exhibited greater toxicity. Polymorph A showed no benefit. Polymorph B and C both reached concentrations in the brain that exceeded the IC50 in GL261 cells 29-fold. In addition, polymorph C demonstrated an AUC0–24h brain-to-plasma (B/P) ratio of 0.82, whereas B showed higher plasma AUC and lower B/P ratio. In contrast, polymorph A presented markedly lower levels in the plasma and brain. Furthermore, the combination with elacridar was able to significantly improve the efficacy of polymorph C in GL261 glioma and D425 medulloblastoma models in mice.
Conclusions: Among mebendazole polymorphs, C reaches therapeutically effective concentrations in the brain tissue and tumor with fewer side effects, and is the better choice for brain cancer therapy. Its efficacy can be further enhanced by combination with elacridar. Clin Cancer Res; 21(15); 3462–70. ©2015 AACR.
Blood Pressure, Sex, and Female Sex Hormones Influence Renal Inner Medullary Nitric Oxide Synthase Activity and Expression in Spontaneously Hypertensive Rats
Authors: Sasser Jennifer M. , Brinson Krystal N. , Tipton Ashlee J. , Crislip G. Ryan , Sullivan Jennifer C. 
Published: April 2015

Background

We previously reported that sexually mature female spontaneously hypertensive rats (
SHRs
) have greater nitric oxide (
NO
) synthase (
NOS
) enzymatic activity in the renal inner medulla (
IM
), compared to age‐matched males. However, the mechanisms responsible for this sexual dimorphism are unknown. The current study tested the hypothesis that sex differences in renal
IM NOS
activity and
NOS
1 expression in adult
SHRs
develop with sexual maturation and increases in blood pressure (BP) in a female sex hormone‐dependent manner.

Methods and Results

Renal
IM
were isolated from sexually immature 5‐week‐old and sexually mature 13‐week‐old male and female
SHRs
. Whereas
NOS
activity and
NOS
1 expression were comparable in 5‐ and 13‐week‐old male
SHRs
and 5‐week‐old female
SHRs
, 13‐week‐old females had greater
NOS
activity and
NOS
1 expression, compared to 5‐week‐old female
SHRs
and age‐matched males.
NOS
3 expression was greater in 5‐week‐old than 13‐week‐old
SHRs
regardless of sex. Treatment with antihypertensive therapy (hydrochlorothiazide and reserpine) from 6 to 12 weeks of age to attenuate age‐related increases in BP abolished the sex difference in
NOS
activity and
NOS
1 expression between sexually mature
SHR
males and females. To assess the role of female sex hormones in age‐related increases in
NOS
, additional females were ovariectomized (
OVX
), and
NOS
activity was studied 8 weeks post‐
OVX
.
OVX
decreased
NOS
activity and
NOS
1 expression.

Conclusions

The sex difference in renal
IM NOS
in
SHR
is mediated by a sex hormone‐ and BP‐dependent increase in
NOS
1 expression and
NOS
activity exclusively in females.