bluuebunny/crossref_metadata_2025_split huggingface dataset:
Linking denitrification with ecosystem respiration in mountain streams
Authors: Madinger Hilary L. , Hall Robert O. 
Published: July 2019

AbstractRivers denitrify a portion of their nitrate () load, but estimates are difficult using microcosm or reach‐scale measurements that require specific biogeochemical and hydrologic conditions. Measuring reach‐scale oxygen (O2) respiration fluxes is easier than nitrogen (N2) fluxes, thus we paired microcosm estimates of denitrification by N2 production with estimates of aerobic respiration. The median molar ratio of ΔN2:−ΔO2 from 13 streams was 0.011 (95% credible interval 0.0002–0.027 mol:mol). We then measured diel O2 concentrations from 11 streams and converted to ecosystem respiration (ER) using a multiday oxygen model. Given reach‐scale ER of −160 mmol O2 m−2 d−1, the estimated median denitrification was 1.5 mmol N2 m−2 d−1 (credible interval (CI): 0.18–4.21) across our streams. Our estimates of denitrification constituted 19% of gross uptake (CI: 0–51%). In streams, ΔN2:−ΔO2 was lower than in estuarine and marine ecosystems. Despite multiple sources of error, this approach estimates reach‐scale denitrification and variation with concentrations.
An Injectable, Bifunctional Hydrogel with Photothermal Effects for Tumor Therapy and Bone Regeneration
Authors: Luo Shiyu , Wu Juan , Jia Zhanrong , Tang Pengfei , Sheng Jun , Xie Chaoming , Liu Chen , Gan Donglin , Hu Dong , Zheng Wei , Lu Xiong 
Published: July 2019

AbstractSignificant attention has been focused on bone tumor therapy recently. At present, the treatment in clinic typically requires surgical intervention. However, a few tumor cells remain around bone defects after surgery and subsequently proliferate within several days. Thus, fabrication of biomaterials with dual functions of tumor therapy and bone regeneration is significant. Herein, the injectable hydrogel containing cisplatin (DDP) and polydopamine‐decorated nano‐hydroxyapatite is prepared via Schiff base reaction between the aldehyde groups on oxidized sodium alginate and amino groups on chitosan. The hydrogel exhibits sustained release properties for DDP due to the immobilization of DDP via abundant functional groups on polydopamine (PDA). Additionally, given the intense absorption of PDA in the near‐infrared region, the hydrogel exhibits excellent photothermal effects when exposed to the NIR laser (808 nm). Based on the properties, the hydrogel effectively ablates tumor cells (4T1 cells) in vitro and suppresses tumor growth in vivo. Furthermore, the hydrogel promotes the adhesion and proliferation of bone mesenchymal stem cells in vitro due to the abundant functional groups on PDA and further induces bone regeneration in vivo. Therefore, the study extends research on novel biomaterials with dual functions of tumor therapy and bone regeneration.
Studying the Potential Application of Electrospun Polyethylene Terephthalate/Graphene Oxide Nanofibers as Electroconductive Cardiac Patch
Authors: Ghasemi Azin , Imani Rana , Yousefzadeh Maryam , Bonakdar Shahin , Solouk Atefeh , Fakhrzadeh Hossein 
Published: July 2019

AbstractNowadays, engineering‐based cardiac patches aim to accelerate cardiac regeneration in myocardial infarcted tissues. Considering the fundamental role of cardiac electrophysiology in myocardial function, this study aims to investigate graphene oxide (GO) incorporation in the polyethylene terephthalate (PET) nanofibrous scaffold, as a conductive cardiac patch. The PET/GO nanocomposites are prepared using the uniaxial nozzle and coaxial nozzle electrospinning processes and comprehensively evaluated. The morphological observation indicates a uniform beaded free morphology with an average diameter of 147 ± 38 and 253 ± 67 nm for solid and core–shell nanocomposite fibers, respectively. Addition of GO to the PET nanofibers in a concentration of 0.05 wt% remarkably increases the Young modulus of mats from 30 ± 0.03 to 60 ± 0.02 and 69 ± 0.08 MPa for solid and core–shell nanofibers, respectively. Also, the electroconductivity is improved from 0.7 × 10−6 to 1.175 × 10−6 and 1.3 × 10−6 S cm−1 for solid and core–shell nanofibers, which are in the range of cardiac electroactivity values. PET/GO substrate interestingly supports human umbilical vein endothelial cells’ spreading morphology and cardiomyocyte elongated morphology, mainly where the GO nanosheets are distributed near the surface of nanofibers. In conclusion, the core–shell electrospun PET/GO nanocomposite fibers are suggested as a potential electroactive cardiac patch to improve cardiac cell attachment and proliferation.
Preparation of Polyetheramine‐Grafted Lignin and Its Application in UV‐Resistant Polyurea Coatings
Authors: Fang Chang , Liu Weifeng , Qiu Xueqing 
Published: July 2019

AbstractLignin‐containing polyurea coating with good ultraviolet (UV) resistance is prepared by partially substituting polyetheramine with enzymatic hydrolysis lignin. Lignin is first grafted by polyetheramine chains via Mannich reaction, which improves its interfacial compatibility with polyurea matrix. The influences of the modified lignin on the chemical and corrosion resistance, UV‐aging property, and thermal stability of the polyurea coatings are studied. It is demonstrated that lignin‐containing polyurea coatings exhibit excellent UV‐aging properties. Aminating lignin with polyetheramine improves its dispersion in the polymer matrix. This work offers a novel method for the high‐value utilization of biomass lignin in anti‐UV polyurea coatings.
“Missing mutations” in MPS I: Identification of two novel copy number variations by an IDUA‐specific in house MLPA assay
Authors: Jahic Amir , Günther Sven , Muschol Nicole , Fossøy Stadheim Barbro , Braaten Øivind , Kjensli Hyldebrandt Hanne , Kuiper Gé‐Ann , Tylee Karen , Wijburg Frits A. , Beetz Christian 
Published: July 2019

AbstractBackgroundMucopolysaccharidosis type I (MPS I) is a rare, recessively inherited lysosomal storage disorder, characterized by progressive multi‐systemic disease. It is caused by a reduced or absent alpha‐l iduronidase (IDUA) enzyme activity secondary to biallelic loss‐of‐function variants in the IDUA. Over 200 causative variants in IDUA have been identified. Nevertheless, there is a fraction of MPS I patients with only a single mutated IDUA allele detectable.MethodsAs genetic testing of MPS I is usually based on sequencing methods, copy number variations (CNVs) in IDUA can be missed and therefore presumably remain underdiagnosed. The aim of this study was the detection of CNVs using an IDUA‐specific in house multiplex ligation‐dependent probe amplification (MLPA) assay.ResultsA total of five unrelated MPS I patient samples were re‐analyzed after only a single heterozygous IDUA mutation c.979G>C (p.A327P), c.1469T>C (p.L490P), c.1598C>G (p.P533R), c.1205G>A (p.W402X), c.973‐7C>G (p.?) could be identified. We detected a novel splice site variant c.973‐7C>G (p.?), as well as two novel CNVs, a large deletion of IDUA exon 14 and 3’UTR c.(1828 + 1_1829‐1)_(*1963_?)del, and a large duplication extending from IDUA exon 2 to intron 12 c.(157 + 1_158‐1)_(1727 + 1_1728‐1)dup.ConclusionTogether with the CNVs we previously identified, a total of four pathogenic IDUA CNVs have now been reported.
Relationships between SNPs and prognosis of breast cancer and pathogenic mechanism
Authors: He Yaning , Liu Hui , Chen Qi , Shao Yingbo , Luo Suxia 
Published: July 2019

AbstractBackgroundAssociation between several single‐nucleotide polymorphisms (SNPs) and breast cancer risk has been identified through genome‐wide association studies (GWAS), but little is known about their significance in patients’ prognosis. We screened SNPs which were related to the prognosis of breast cancer in Henan Han population, analyzed relevant genes by bioinformatics in database, and further constructed the genetic regulatory network involved in the pathogenesis of breast cancer.MethodsWe evaluated five SNPs in 232 cases of breast cancer at the Affiliated Tumor Hospital of Zhengzhou University. Relationships between five SNPs, clinical prognostic indicators, and disease‐free survival (DFS) were evaluated by Kaplan–Meier analysis and Cox proportional hazards model. Gene ontology (GO) functional annotation and Kyoto Encyclopedia of genes and Genome (KEGG) analysis were carried out to preliminarily establish genetic regulation network model of breast cancer. Bayesian algorithm was used to optimize the model.ResultsThe multivariate Cox proportional hazards model confirmed that SNP rs3803662 (TOX3/TNRC9) had correlation with DFS independently. In the multivariate Cox proportional hazards model, compared with GA/AA, GG increased the recurrent risk of breast cancer (p = .021, hazard ratio [HR] = 2.914). GO analysis showed that the function of TOX3/TNRC9 included biological_process, molecular_function, and cellular_component. According to KEGG signaling pathway database, the map of breast cancer‐related gene regulatory network was obtained. IGF‐IGF1R‐PI3K‐Akt‐mTOR‐S6K was the best possible pathway for the differentiation of breast cancer cells in this network and ER‐TOX3/TNRC9 was the best possible pathway for the survival of tumor cells in this network by Bayesian theorem optimization.ConclusionsSNP rs3803662 (TOX3/TNRC9) is an independent prognostic factor for breast cancer in Henan Han Population. ER‐TOX3/TNRC9 is the best possible pathway involved in the pathogenesis of breast cancer.
Whole‐exome sequencing and immunohistochemistry findings in von Hippel–Lindau disease
Authors: Guo Xiaopeng , Gao Lu , Hong Xiafei , Guo Dan , Di Wenyu , Wang Xiaoman , Xu Zhiqin , Xing Bing 
Published: July 2019

AbstractBackgroundvon Hippel–Lindau (VHL) disease has a hereditary, autosomal dominant pattern, and multiple tumors can develop in multiple organs of a single patient. However, the exact mechanisms of tumorigenesis are unclear, and further studies are needed to clarify whether the same signaling pathways are involved in different VHL‐related tumors.MethodsWhole‐exome sequencing (WES) of tumor and paired peripheral blood samples were performed for a VHL disease pedigree. A bioinformatics analysis was conducted to identify candidate somatic single‐nucleotide variants (SNVs) present in all tumor tissues. Sanger sequencing was then used to validate the SNVs identified using WES. Immunohistochemistry was performed to analyze components of the mTOR pathway, which was abnormally activated in tumor tissues.ResultsTwo hemangioblastomas and two renal cell carcinomas were sequenced. The bioinformatics analysis revealed a VHL somatic variant in all tumors; no other SNV was detected. Immunohistochemistry showed the abnormal expression of the phospho‐S6 ribosomal protein in the hemangioblastomas, but not in the renal clear cell carcinomas.ConclusionExcept for a SNV in the VHL gene, no other somatic SNVs were detected using WES. The phospho‐S6 ribosomal protein in the mTOR pathway is a potential target in VHL‐related cerebellum hemangioblastomas.
Propeller flap donor site closure by means of another propeller flap: A case report and literature review
Authors: Scaglioni Mario F. , Franchi Alberto , Fritsche Elmar 
Published: July 2019

AbstractDespite some ongoing criticisms, propeller flaps are still gaining popularity among plastic surgeons. The need of skin grafting of the donor site is one of those limitations that sometime affect the beauty and the efficacy of this reconstructive technique. Similar to a classic bi‐lobed skin flap in which the second lobe of the same flap is mobilized to cover the donor site defect of the first lobe, a second, discrete propeller flap can be harvested adjacent to the first, in order to close the first donor site defect, thus avoiding the need for a skin graft. We applied this concept of “sequential” propeller flaps to cover a 4.5 × 4 cm full thickness soft tissue defect at the level of the heel in a 54‐year‐old patient who underwent melanoma excision and sentinel node biopsy.The first and second propeller flaps of 10 × 4.5 cm respectively were rotated on a distal and on a more proximal perforator of the posterior tibial artery (PTA) respectively, obtaining a tension free closure along the entire wound. The post‐operative course was uneventful and the patient returned to full normal activities after 4 weeks. Follow up at 6 months showed a stable reconstruction with no functional deficit. This option, that relies on two separate perforator propeller flaps performed in sequence to obtain complete wound closure, may be kept in mind when dealing with soft tissue defects eligible for propeller flap reconstruction, as long as sizeable perforators in a favorable position are available. Moreover, a brief literature review on propeller flap use in flap donor site closure is also provided.
Grating lobe suppression using grid cover structures on horn arrays with linear and circular polarizations
Authors: Ordek Sezgin , Yamac Yunus E. , Kizilay Ahmet 
Published: July 2019

AbstractIn this letter, a 2 × 2 pyramidal horn antenna array is presented to accomplish linear and circular polarizations with suppressed grating lobes using removable grid cover structures (GCSs) mounted on the top of the antenna array. The spacing between the unit cells becomes farther than a wavelength due to electrically large pyramidal horns and the feeding network. The proposed GCSs, called linear and circular GCS, in this arrangement act as a spacing reducer between the apertures of the horn antennas without the need of physical change of the spacings. Thereby, the desired array factor with newly created apertures can be realized. Although using both GCSs benefit to suppress the highest‐level grating lobe, the circular GCS also converts the polarization to circular. The feeding network, which also prevents a formal array factor due to its massive structure, is made up of equal power dividers with T‐junction waveguides. The proposed horn arrays, the feeding network, and both GCSs are fabricated, and the total antenna is measured to validate the simulation results. A good agreement is achieved between simulations and measurements.
Automatic large quantity landmark pairs detection in 4DCT lung images
Authors: Fu Yabo , Wu Xue , Thomas Allan M. , Li Harold H. , Yang Deshan 
Published: July 2019

PurposeTo automatically and precisely detect a large quantity of landmark pairs between two lung computed tomography (CT) images to support evaluation of deformable image registration (DIR). We expect that the generated landmark pairs will significantly augment the current lung CT benchmark datasets in both quantity and positional accuracy.MethodsA large number of landmark pairs were detected within the lung between the end‐exhalation (EE) and end‐inhalation (EI) phases of the lung four‐dimensional computed tomography (4DCT) datasets. Thousands of landmarks were detected by applying the Harris‐Stephens corner detection algorithm on the probability maps of the lung vasculature tree. A parametric image registration method (pTVreg) was used to establish initial landmark correspondence by registering the images at EE and EI phases. A multi‐stream pseudo‐siamese (MSPS) network was then developed to further improve the landmark pair positional accuracy by directly predicting three‐dimensional (3D) shifts to optimally align the landmarks in EE to their counterparts in EI. Positional accuracies of the detected landmark pairs were evaluated using both digital phantoms and publicly available landmark pairs.ResultsDense sets of landmark pairs were detected for 10 4DCT lung datasets, with an average of 1886 landmark pairs per case. The mean and standard deviation of target registration error (TRE) were 0.47 ± 0.45 mm with 98% of landmark pairs having a TRE smaller than 2 mm for 10 digital phantom cases. Tests using 300 manually labeled landmark pairs in 10 lung 4DCT benchmark datasets (DIRLAB) produced TRE results of 0.73 ± 0.53 mm with 97% of landmark pairs having a TRE smaller than 2 mm.ConclusionA new method was developed to automatically and precisely detect a large quantity of landmark pairs between lung CT image pairs. The detected landmark pairs could be used as benchmark datasets for more accurate and informative quantitative evaluation of DIR algorithms.
Investigation of the influence of B0 drift on the performance of the PLANET method and an algorithm for drift correction
Authors: Shcherbakova Yulia , van den Berg Cornelis A.T. , Moonen Chrit T.W. , Bartels Lambertus W. 
Published: July 2019

PurposeThe PLANET method was designed to simultaneously reconstruct maps of T1 and T2, the off‐resonance, the RF phase, and the banding free signal magnitude. The method requires a stationary B0 field over the course of a phase‐cycled balanced SSFP acquisition. In this work we investigated the influence of B0 drift on the performance of the PLANET method for single‐component and two‐component signal models, and we propose a strategy for drift correction.MethodsThe complex phase‐cycled balanced SSFP signal was modeled with and without frequency drift. The behavior of the signal influenced by drift was mathematically interpreted as a sum of drift‐dependent displacement of the data points along an ellipse and drift‐dependent rotation around the origin. The influence of drift on parameter estimates was investigated experimentally on a phantom and on the brain of healthy volunteers and was verified by numerical simulations. A drift correction algorithm was proposed and tested on a phantom and in vivo.ResultsDrift can be assumed to be linear over the typical duration of a PLANET acquisition. In a phantom (a single‐component signal model), drift induced errors of 4% and 8% in the estimated T1 and T2 values. In the brain, where multiple components are present, drift only had a minor effect. For both single‐component and two‐component signal models, drift‐induced errors were successfully corrected by applying the proposed drift correction algorithm.ConclusionWe have demonstrated theoretically and experimentally the sensitivity of the PLANET method to B0 drift and have proposed a drift correction method.
Spatially regularized estimation of the tissue homogeneity model parameters in DCE‐MRI using proximal minimization
Authors: Bartoš Michal , Rajmic Pavel , Šorel Michal , Mangová Marie , Keunen Olivier , Jiřík Radovan 
Published: July 2019

PurposeThe Tofts and the extended Tofts models are the pharmacokinetic models commonly used in dynamic contrast‐enhanced MRI (DCE‐MRI) perfusion analysis, although they do not provide two important biological markers, namely, the plasma flow and the permeability‐surface area product. Estimates of such markers are possible using advanced pharmacokinetic models describing the vascular distribution phase, such as the tissue homogeneity model. However, the disadvantage of the advanced models lies in biased and uncertain estimates, especially when the estimates are computed voxelwise. The goal of this work is to improve the reliability of the estimates by including information from neighboring voxels.Theory and MethodsInformation from the neighboring voxels is incorporated in the estimation process through spatial regularization in the form of total variation. The spatial regularization is applied on five maps of perfusion parameters estimated using the tissue homogeneity model. Since the total variation is not differentiable, two proximal techniques of convex optimization are used to solve the problem numerically.ResultsThe proposed algorithm helps to reduce noise in the estimated perfusion‐parameter maps together with improving accuracy of the estimates. These conclusions are proved using a numerical phantom. In addition, experiments on real data show improved spatial consistency and readability of perfusion maps without considerable lowering of the quality of fit.ConclusionThe reliability of the DCE‐MRI perfusion analysis using the tissue homogeneity model can be improved by employing spatial regularization. The proposed utilization of modern optimization techniques implies only slightly higher computational costs compared to the standard approach without spatial regularization.
Understanding the physical relations governing the noise navigator
Authors: Navest R. J. M. , Mandija S. , Andreychenko A. , Raaijmakers A. J. E. , Lagendijk J. J. W. , van den Berg C. A. T. 
Published: July 2019

PurposeThe noise navigator is a passive way to detect physiological motion occurring in a patient through thermal noise modulations measured by standard clinical radiofrequency receive coils. The aim is to gain a deeper understanding of the potential and applications of physiologically induced thermal noise modulations.MethodsNumerical electromagnetic simulations and MR measurements were performed to investigate the relative contribution of tissue displacement versus modulation of the dielectric lung properties over the respiratory cycle, the impact of coil diameter and position with respect to the body. Furthermore, the spatial motion sensitivity of specific noise covariance matrix elements of a receive array was investigated.ResultsThe influence of dielectric lung property variations on the noise variance is negligible compared to tissue displacement. Coil size affected the thermal noise variance modulation, but the location of the coil with respect to the body had a larger impact. The modulation depth of a 15 cm diameter stationary coil approximately 3 cm away from the chest (i.e. radiotherapy setup) was 39.7% compared to 4.2% for a coil of the same size on the chest, moving along with respiratory motion. A combination of particular noise covariance matrix elements creates a specific spatial sensitivity for motion.ConclusionsThe insight gained on the physical relations governing the noise navigator will allow for optimized use and development of new applications. An optimized combination of elements from the noise covariance matrix offer new ways of performing, e.g. motion tracking.
Nonsingular systems of generalized Sylvester equations: An algorithmic approach
Authors: De Terán Fernando , Iannazzo Bruno , Poloni Federico , Robol Leonardo 
Published: July 2019

SummaryWe consider the uniqueness of solution (i.e., nonsingularity) of systems of r generalized Sylvester and ⋆‐Sylvester equations with n×n coefficients. After several reductions, we show that it is sufficient to analyze periodic systems having, at most, one generalized ⋆‐Sylvester equation. We provide characterizations for the nonsingularity in terms of spectral properties of either matrix pencils or formal matrix products, both constructed from the coefficients of the system. The proposed approach uses the periodic Schur decomposition and leads to a backward stable O(n3r) algorithm for computing the (unique) solution.