bluuebunny/crossref_metadata_2025_split huggingface dataset:
ATF for cell culture harvest clarification: mechanistic modelling and comparison with TFF
Authors: Hadpe Sandeep Ramesh , Sharma Abhishek Kumar , Mohite Vipin Vilas , Rathore Anurag S 
Published: December 2016

AbstractBACKGROUNDExtracellular expression of proteins in mammalian cell culture systems requires clarification in order to separate the cell mass from soluble expressed protein. This task is typically accomplished by membrane based separations. This paper explores the use of alternating tangential flow (ATF) filtration for clarification.RESULTSThe superiority of ATF over the conventional tangential flow filtration (TFF) has been demonstrated with respect to the required sizing of the filter and both processes have been modeled. Modeling of TFF is based on assumptions of constant conditions of pressure, concentration of foulant, or flux. Modeling of ATF involved simultaneous variations in all three parameters and hence the traditional models that describe fouling of membranes under constant pressure filtration were appropriately modified to incorporate these variations. The resulting models are amenable to ‘exponent analysis’ and allow identification of the mechanism of ATF fouling among pore blocking, intermediate pore blocking, pore constriction, and cake formation. Complete pore blocking has been identified as the dominant mechanism for the system at hand involving clarification of mammalian cell culture harvests using ATF as well as TFF.CONCLUSIONSATF has been implemented and successfully demonstrated to be superior to TFF for mammalian cell culture clarification. The mechanism of fouling with ATF as well as TFF has been identified successfully. The modeling approach proposed here can be applied to a variety of industrial systems to determine the mode of fouling and to mitigate it. Also, sizing predictions based on mechanistic modeling can be useful for process optimization. © 2016 Society of Chemical Industry
ZNF208 polymorphisms associated with ischemic stroke in a southern Chinese Han population
Authors: Yu Jianzhong , Zhou Feng , Luo Dong , Wang Nianzhen , Zhang Chong , Jin Tianbo , Liang Xiongfei , Yu Dan 
Published: December 2016

AbstractBackgroundIschemic stroke is one of the most common diseases with a high burden of neurological deficits, disability and death. Zinc finger protein 208 (ZNF208) was found to be involved in coronary heart disease, although little information is available about its association with ischemic stroke. We performed the present case–control study to clarify the association between single‐nucleotide polymorphisms (SNPs) within ZNF208 and the risk of ischemic stroke in a southern Chinese Han population.MethodsA total of 799 subjects (400 cases and 399 healthy controls) were enrolled in the present study. Five SNPs within ZNF208 gene were selected and genotyped using Sequenom MassARRY technology (Sequenom, Inc., San Diego, CA, USA). Data management and statistical analyses were conducted using Sequenom Typer, version 4.0, and a chi‐squared test, as well as unconditional logistic regression.ResultsStatistical results showed that three variants were associated with the risk of ischemic stroke under allele models (rs2188971, rs2188972, rs8103163 and rs7248488). The variant rs2188972 was also associated with the risk of ischemic stroke in a recessive model after adjustment for age and sex. Haplotype analysis suggested that a significant difference existed between the Ars2188972 Trs2188971 Ars8103163 Ars7248488 haplotype and the risk of ischemic stroke, although this disappeared after adjustment for sex and age.ConclusionsThe results obtained in the present study indicate a potential association between ZNF208 variants and the risk of ischemic risk in a southern Chinese Han population.
Testing the Modified Sediment Delivery Model (MOSEDD) at SPA2 Experimental Basin, Sicily (Italy)
Authors: Di Stefano Costanza , Ferro Vito 
Published: December 2016

AbstractA new version of a spatially distributed sediment delivery model taking into account the hillslope sediment transport efficiency, named MOSEDD, is presented. This model gives estimates of basin sediment yield at event scale, which are more reliable than those obtained by the original SEDD. For SPA2 basin discretized into morphological units, four different calculation schemes of MOSEDD, including the original SEDD version, were applied. All parameterization schemes of the model were calibrated using 15 events measured at the outlet of the experimental basin in the period February 2005–February 2010. The model calibration was used to determine a relationship between the coefficient βe of the model and the erosivity factor. For the model validation, other six measured events, collected in the period March 2010–February 2014, were used. At event scale, the comparison between measured sediment yield values and calculated ones showed that the three calculation schemes of MOSEDD using a rainfall–runoff erosivity factor (MODB, MODC and MODD) have the best performance in estimating sediment yield with respect to the original version of SEDD. The analysis was also developed at annual scale, for the period 2005–2014, and a relationship between the annual value of the coefficient, βa, of the model and the corresponding erosivity factor was established. This last analysis showed that the sediment delivery distributed approach has also a good predictive ability at annual scale. Copyright © 2016 John Wiley & Sons, Ltd.
On the potential for RF heating in MRI to affect metabolic rates and 18FDG signal in PET/MR: simulations of long‐duration, maximum normal mode heating
Authors: Carluccio Giuseppe , Ding Yu‐Shin , Logan Jean , Collins Christopher M. 
Published: December 2016

PurposeTo examine the possibility that MR‐induced RF power deposition (SAR) and the resulting effects on temperature‐dependent metabolic rates or perfusion rates might affect observed 18FDG signal in PET/MR.MethodsUsing numerical simulations of the SAR, consequent temperature increase, effect on rates of metabolism or perfusion, and [18FDG] throughout the body, we simulated the potential effect of maximum‐allowable whole‐body SAR for the entire duration of an hour‐long PET/MR scan on observed PET signal for two different 18FDG injection times: one hour before onset of imaging and concurrent with the beginning of imaging. This was all repeated three times with the head, the heart, and the abdomen (kidneys) at the center of the RF coil.ResultsQualitatively, little effect of MR‐induced heating is observed on simulated PET images. Maximum relative increases in PET signal (26% and 31% increase, respectively, for the uptake models based on metabolism and the perfusion) occur in regions of low baseline metabolic rate (also associated with low perfusion and, thus, greater potential temperature increase due to high local SAR), such that PET signal in these areas remains comparatively low. Maximum relative increases in regions of high metabolic rate (and also high perfusion: heart, thyroid, brain, etc.) are affected mostly by the relatively small increase in core body temperature and thus are not affected greatly (10% maximum increase).ConclusionsEven for worst‐case heating, little effect of MR‐induced heating is expected on 18FDG PET images during PET/MR for many clinically relevant applications. For quantitative, dynamic MR/PET studies requiring high SAR for extended periods, it is hoped that methods like those introduced here can help account for such potential effects in design of a given study, including selection of reference locations that should not experience notable increase in temperature.
Direct diffusion tensor estimation using a model‐based method with spatial and parametric constraints
Authors: Zhu Yanjie , Peng Xi , Wu Yin , Wu Ed X. , Ying Leslie , Liu Xin , Zheng Hairong , Liang Dong 
Published: December 2016

PurposeTo develop a new model‐based method with spatial and parametric constraints (MB‐SPC) aimed at accelerating diffusion tensor imaging (DTI) by directly estimating the diffusion tensor from highly undersampled k‐space data.MethodsThe MB‐SPC method effectively incorporates the prior information on the joint sparsity of different diffusion‐weighted images using an L1–L2 norm and the smoothness of the diffusion tensor using a total variation seminorm. The undersampled k‐space datasets were obtained from fully sampled DTI datasets of a simulated phantom and an ex‐vivo experimental rat heart with acceleration factors ranging from 2 to 4. The diffusion tensor was directly reconstructed by solving a minimization problem with a nonlinear conjugate gradient descent algorithm. The reconstruction performance was quantitatively assessed using the normalized root mean square error (nRMSE) of the DTI indices.ResultsThe MB‐SPC method achieves acceptable DTI measures at an acceleration factor up to 4. Experimental results demonstrate that the proposed method can estimate the diffusion tensor more accurately than most existing methods operating at higher net acceleration factors.ConclusionThe proposed method can significantly reduce artifact, particularly at higher acceleration factors or lower SNRs. This method can easily be adapted to MR relaxometry parameter mapping and is thus useful in the characterization of biological tissue such as nerves, muscle, and heart tissue.
Converting computed tomography images into photon interaction coefficients by using stoichiometric calibration and parametric fit models
Authors: Shih Cheng‐Ting , Wu Jay 
Published: December 2016

PurposeX ray and γ‐ray are widely applied in radiology, radiotherapy, and nuclear medicine. Linear attenuation coefficients and linear energy absorption coefficients are essential for dose calculation and image correction. In this study, a method that entails combining the stoichiometric calibration and parametric physical models was developed to convert computed tomography (CT) images into the linear attenuation coefficients and linear energy absorption coefficients.MethodsA calibration scan was performed using standard tissue‐equivalent materials to obtain the characteristics of the x‐ray energy spectrum. Subsequently, relationships between CT numbers and tissue parameters were established using standard soft tissue and bone tissue data adopted from the literature. The linear attenuation coefficient and linear energy absorption coefficient were calculated using the parametric fit model.ResultsThe results showed a linear relationship between CT numbers and tissue parameters. The tissue‐equivalent materials differed from real human tissues, leading to considerable errors in estimation of mass attenuation coefficients when the photon energy was lower than 50 keV. Mass attenuation coefficients and mass energy transfer coefficients of five tissues were calculated and validated using clinical CT images. The error was less than ± 5% and ± 8%, compared with the values of the International Commission on Radiation Units (ICRU) 46 report.ConclusionsThe probability of photon interaction with tissues and physical characteristics of tissues can be accurately evaluated by using the proposed method and applied in various clinical applications.
Examining the influence of humidity on reference ionization chamber performance
Authors: McEwen Malcolm R. , Taank Jaswinder 
Published: December 2016

PurposeInternational dosimetry protocols require measurements made with a vented ionization chamber to be corrected for the influence of air density by using the standard temperature‐pressure correction factor. The effect of humidity, on the other hand, is generally ignored with the provision that the relative humidity (RH) is within certain limits (typically 20% to 80%). However, there is little experimental data in the published literature as to the true effect of humidity on modern reference‐class ionization chambers. This investigation used two different radiation beams – a Co‐60 irradiator and an Sr‐90 check source – to examine the effect of humidity on several Farmer‐type ionization chambers.MethodsAn environmental cabinet controlled the humidity. For the Co‐60 beam, the irradiation was external, whereas for the Sr‐90 measurements, the source itself was placed within the cabinet. Extensive measurements were carried out to ensure that the experimental setup provided reproducible readings. Four chamber types were investigated: IBA FC65‐G, IBA FC65‐P, PTW 30013 and Exradin A19. The different wall materials provided potentially different mechanical responses (i.e., in terms of expansion/contraction) to the water content in the air. The relative humidity was varied between 8% and 98% and measurements were made with both increasing and decreasing humidity to investigate any possible hysteresis effects.ResultsMeasurements in Co‐60 were consistent with the published data obtained with primary standard cavity chambers in ICRU Report 31 (i.e., a very small variation <0.1% for RH >10%). The measurements in the Sr‐90 field showed no dependence with the relative humidity, within the measurement uncertainties (0.05%, k = 1). Very good repeatability of the ionization current was obtained over successive wet/dry cycles, no hysteresis was observed, and there was no dependence on chamber type.ConclusionThese results indicate that humidity has no significant effect on these particular types of ionization chambers, consistent with recommendations in current megavoltage dosimetry protocols.
A 2D silicon detector array for quality assurance in small field dosimetry: DUO
Authors: Shukaili Khalsa Al , Petasecca Marco , Newall Matthew , Espinoza Anthony , Perevertaylo Vladimir L. , Corde Stéphanie , Lerch Michael , Rosenfeld Anatoly B. 
Published: December 2016

PurposeNowadays, there are many different applications that use small fields in radiotherapy treatments. The dosimetry of small radiation fields is not trivial due to the problems associated with lateral disequilibrium and source occlusion and requires reliable quality assurance (QA). Ideally such a QA tool should provide high spatial resolution, minimal beam perturbation and real time fast measurements. Many different types of silicon diode arrays are used for QA in radiotherapy; however, their application in small filed dosimetry is limited, in part, due to a lack of spatial resolution. The Center of Medical Radiation Physics (CMRP) has developed a new generation of a monolithic silicon diode array detector that will be useful for small field dosimetry in SRS/SRT. The objective of this study is to characterize a monolithic silicon diode array designed for dosimetry QA in SRS/SRT named DUO that is arranged as two orthogonal 1D arrays with 0.2 mm pitch.MethodsDUO is two orthogonal 1D silicon detector arrays in a monolithic crystal. Each orthogonal array contains 253 small pixels with size 0.04 × 0.8 mm2 and three central pixels are with a size of 0.18 × 0.18 mm2 each. The detector pitch is 0.2 mm and total active area is 52 × 52 mm2. The response of the DUO silicon detector was characterized in terms of dose per pulse, percentage depth dose, and spatial resolution in a radiation field incorporating high gradients. Beam profile of small fields and output factors measured on a Varian 2100EX LINAC in a 6 MV radiation fields of square dimensions and sized from 0.5 × 0.5 cm2 to 5 × 5 cm2. The DUO response was compared under the same conditions with EBT3 films and an ionization chamber.ResultsThe DUO detector shows a dose per pulse dependence of 5% for a range of dose rates from 2.7 × 10−4 to 1.2 × 10−4 Gy/pulse and 23% when the rate is further reduced to 2.8 × 10−5 Gy/pulse. The percentage depth dose measured to 25 cm depth in solid water phantom beyond the surface and for a field size of 10 × 10 cm2 agrees with that measured using a Markus IC within 1.5%. The beam profiles in both X and Y orthogonal directions showed a good match with EBT3 film, where the FWHM agreed within 1% and penumbra widths within 0.5 mm. The effect of an air gap above the DUO detector has also been studied. The output factor for field sizes ranging from 0.5 × 0.5 cm2 to 5 × 5 cm2 measured by the DUO detector with a 0.5 mm air gap above silicon surface agrees with EBT3 film and MOSkin detectors within 1.8%.ConclusionsThe CMRP's monolithic silicon detector array, DUO, is suitable for SRS/SRT dosimetry and QA because of its very high spatial resolution (0.2 mm) and real time operation.
Experimental investigation on spontaneous counter‐current imbibition in water‐wet natural reservoir sandstone core using MRI
Authors: Zhao Yuechao , Song Yongchen 
Published: December 2016

AbstractCounter‐current imbibition is a process whereby a wetting phase spontaneously imbibes into a porous media, displacing the non‐wetting phase. This process is considered an important oil recovery mechanism during water flooding in fractured oil reservoirs. In this study, the dynamic process of counter‐current imbibition for a natural reservoir sandstone core with an all‐face‐open boundary condition was monitored using magnetic resonance imaging (MRI). A series of images and relaxation time T1 spectra were acquired. The movement of water spontaneously entering the core sample while oil escapes, the spatial distribution of oil and water, and the in situ saturation change of oil and water in porous media can be accurately detected using MRI. MRI assists the direct evaluation of the basic mechanisms of imbibitions. Experimental results suggest the remaining oil was trapped in some large pores because of the capillary pressure, and the oil recovery in some large‐pore regions is lower than that in some small‐pore regions at the end of imbibition. Experimental findings show a close agreement between conventional material balance and oil recovery determined from MRI. The in situ oil recovery data agree well with the empirical models. The observations from MRI images could provide test cases to enable the development of mathematical models and to facilitate the evaluation of the proposed imbibition mechanisms. Copyright © 2016 John Wiley & Sons, Ltd.
Autocalibrating motion‐corrected wave‐encoding for highly accelerated free‐breathing abdominal MRI
Authors: Chen Feiyu , Zhang Tao , Cheng Joseph Y. , Shi Xinwei , Pauly John M. , Vasanawala Shreyas S. 
Published: December 2016

PurposeTo develop a motion‐robust wave‐encoding technique for highly accelerated free‐breathing abdominal MRI.MethodsA comprehensive 3D wave‐encoding‐based method was developed to enable fast free‐breathing abdominal imaging: (a) auto‐calibration for wave‐encoding was designed to avoid extra scan for coil sensitivity measurement; (b) intrinsic butterfly navigators were used to track respiratory motion; (c) variable‐density sampling was included to enable compressed sensing; (d) golden‐angle radial‐Cartesian hybrid view‐ordering was incorporated to improve motion robustness; and (e) localized rigid motion correction was combined with parallel imaging compressed sensing reconstruction to reconstruct the highly accelerated wave‐encoded datasets. The proposed method was tested on six subjects and image quality was compared with standard accelerated Cartesian acquisition both with and without respiratory triggering. Inverse gradient entropy and normalized gradient squared metrics were calculated, testing whether image quality was improved using paired t‐tests.ResultsFor respiratory‐triggered scans, wave‐encoding significantly reduced residual aliasing and blurring compared with standard Cartesian acquisition (metrics suggesting P < 0.05). For non‐respiratory‐triggered scans, the proposed method yielded significantly better motion correction compared with standard motion‐corrected Cartesian acquisition (metrics suggesting P < 0.01).ConclusionThe proposed methods can reduce motion artifacts and improve overall image quality of highly accelerated free‐breathing abdominal MRI. Magn Reson Med 78:1757–1766, 2017. © 2016 International Society for Magnetic Resonance in Medicine.
Prophylactic window therapy with the clinical poly(ADP‐ribose) polymerase inhibitor olaparib delays BRCA1‐deficient mammary tumour formation in mice
Authors: van de Ven Marieke , van der Burg Eline , van der Gulden Hanneke , Klarenbeek Sjoerd , Bouwman Peter , Jonkers Jos 
Published: December 2016

AbstractWomen with heterozygous germline mutations in the BRCA1 tumour suppressor gene are strongly predisposed to developing early‐onset breast cancer through loss of the remaining wild‐type BRCA1 allele and inactivation of TP53. Although tumour prevention strategies in BRCA1‐mutation carriers are still limited to prophylactic surgery, several therapeutic strategies have been developed to target the DNA repair defects (also known as ‘BRCAness’) of BRCA1‐deficient tumours. In particular, DNA‐damaging agents such as platinum drugs and poly(ADP‐ribose) polymerase (PARP) inhibitors show strong activity against BRCA1‐mutated tumours. However, it is unclear whether drugs that target BRCAness can also be used to prevent tumour formation in BRCA1‐mutation carriers, especially as loss of wild‐type BRCA1 may not be the first event in BRCA1‐associated tumourigenesis. We performed prophylactic treatments in a genetically engineered mouse model in which de novo development of BRCA1‐deficient mammary tumours is induced by stochastic loss of BRCA1 and p53. We found that prophylactic window therapy with nimustine, cisplatin or olaparib reduced the amount and size of mammary gland lesions, and significantly increased the median tumour latency. Similar results were obtained with intermittent prophylactic treatment with olaparib. Importantly, prophylactic window therapy with nimustine and cisplatin resulted in an increased fraction of BRCA1‐proficient mammary tumours, suggesting selective survival and malignant transformation of BRCA1‐proficient lesions upon prophylactic treatment with DNA‐damaging agents. Prophylactic therapy with olaparib significantly prolonged mammary tumour‐free survival without any significant increase in the fraction of BRCA1‐proficient tumours, warranting the evaluation of this PARP inhibitor in prophylactic trials in BRCA1‐mutation carriers. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
New additions to the ClusPro server motivated by CAPRI
Authors: Vajda Sandor , Yueh Christine , Beglov Dmitri , Bohnuud Tanggis , Mottarella Scott E. , Xia Bing , Hall David R. , Kozakov Dima 
Published: December 2016

ABSTRACTThe heavily used protein–protein docking server ClusPro performs three computational steps as follows: (1) rigid body docking, (2) RMSD based clustering of the 1000 lowest energy structures, and (3) the removal of steric clashes by energy minimization. In response to challenges encountered in recent CAPRI targets, we added three new options to ClusPro. These are (1) accounting for small angle X‐ray scattering data in docking; (2) considering pairwise interaction data as restraints; and (3) enabling discrimination between biological and crystallographic dimers. In addition, we have developed an extremely fast docking algorithm based on 5D rotational manifold FFT, and an algorithm for docking flexible peptides that include known sequence motifs. We feel that these developments will further improve the utility of ClusPro. However, CAPRI emphasized several shortcomings of the current server, including the problem of selecting the right energy parameters among the five options provided, and the problem of selecting the best models among the 10 generated for each parameter set. In addition, results convinced us that further development is needed for docking homology models. Finally, we discuss the difficulties we have encountered when attempting to develop a refinement algorithm that would be computationally efficient enough for inclusion in a heavily used server. Proteins 2017; 85:435–444. © 2016 Wiley Periodicals, Inc.