bluuebunny/crossref_metadata_2025_split huggingface dataset:
Toward 7T breast MRI clinical study: safety assessment using simulation of heterogeneous breast models in RF exposure
Authors: Li Xin , Rispoli Joseph V. 
Published: September 2018

PurposeTo facilitate assessment of RF power deposition and temperature rise within the breast, we present a method to seamlessly join heterogeneous breast models with standard whole‐body models and demonstrate simulations at 7 T.MethodsFinite‐difference time‐domain electromagnetic and bioheat simulations are performed to analyze the specific absorption rate (SAR) and temperature rise distributions in 36 Breast Imaging Reporting and Data System (BI‐RADS) categorized breast models fused to 2 female whole‐body models while transmitting from a 7T breast volume coil. The breast models are uncompressed in the prone position and feature heterogeneous tissue contents; fusion with human models uses affine transformation and the level‐set method.ResultsThe fusion method produces a continuous transient from the chest region to the posterior portion of breast models while preserving the original volume and shape of breast models. Simulation results of both Ella and Hanako models indicate that the maximum local SAR, partial body SAR, and local tissue temperature rise are positively correlated with both breast density and the highest BI‐RADS density classification. Additionally, maximum local tissue temperature rise is positively correlated with maximum 10‐g SAR values.ConclusionFibroglandular tissue content plays an important role in the distribution of SAR and temperature rise within breast tissue. The combined body‐breast models preserve the integrity of breast models while concurrently exhibiting the loading of whole‐body human models. The procedures presented in this simulation study facilitate safety assessments for breast MRI across the population at both clinical and ultrahigh field strengths.
Fast quantitative MRI using controlled saturation magnetization transfer
Authors: A.G. Teixeira Rui Pedro , Malik Shaihan J. , Hajnal Joseph V. 
Published: September 2018

PurposeThis study demonstrates magnetization transfer (MT) effects directly affect relaxometry measurements and develops a framework that allows single‐pool models to be valid in 2‐pool MT systems.MethodsA theoretical framework is developed in which a 2‐pool MT system effectively behaves as a single‐pool if the RMS RF magnetic field ({\text{B}}_{1}^{{{\text{rms}}}}) is kept fixed across all measurements. A practical method for achieving controlled saturation magnetization transfer (CSMT) using multiband RF pulses is proposed. Numerical, Phantom, and in vivo validations were performed directly comparing steady state (SS) estimation approaches that under correct single‐pool assumptions would be expected to vary in precision but not accuracy.ResultsNumerical simulations predict single‐pool estimates obtained from MT model generated data are not consistent for different SS estimation methods, and a systematic underestimation of T2 is expected. Neither effect occurs under the proposed CSMT approach. Both phantom and in vivo experiments corroborate the numerical predictions. Experimental data highlights that even when using the same relaxometry method, different estimates are obtained depending on which combination of flip angles (FAs) and TRs are used if the CSMT approach is not used. Using CSMT, stable measurements of both T1 and T2 are obtained. The measured T1 ) depends on {\text{B}}_{1}^{{{\text{rms}}}}, which is therefore an important parameter to specify.ConclusionThis work demonstrates that conventional single pool relaxometry, which is highly efficient for human studies, results in unreliable parameter estimates in biological tissues because of MT effects. The proposed CSMT framework is shown to allow single‐pool assumptions to be valid, enabling reliable and efficient quantitative imaging to be performed.
Caval to pulmonary 3D flow distribution in patients with Fontan circulation and impact of potential 4D flow MRI error sources
Authors: Jarvis Kelly , Schnell Susanne , Barker Alex J. , Rose Michael , Robinson Joshua D. , Rigsby Cynthia K. , Markl Michael 
Published: September 2018

PurposeUneven flow distribution in patients with Fontan circulation is suspected to lead to complications. 4D flow MRI offers evaluation using time‐resolved pathlines; however, the potential error is not well understood. The aim of this study was to systematically assess variability in flow distribution caused by well‐known sources of error.Methods4D flow MRI was acquired in 14 patients with Fontan circulation. Flow distribution was quantified by the % of caval venous flow pathlines reaching the left and right pulmonary arteries. Impact of data acquisition and data processing uncertainties were investigated by (1) probabilistic 4D blood flow tracking at varying noise levels, (2) down‐sampling to mimic acquisition at different spatial resolutions, (3) pathline calculation with and without eddy current correction, and (4) varied segmentation of the Fontan geometry to mimic analysis errors.ResultsAveraged among the cohort, uncertainties accounted for flow distribution errors from noise ≤3.2%, low spatial resolution ≤2.3% to 3.8%, eddy currents ≤6.4%, and inaccurate segmentation ≤3.9% to 9.1% (dilation and erosion, respectively). In a worst‐case scenario (maximum additive errors for all 4 sources), flow distribution errors were as high as 22.5%.ConclusionInaccuracies related to postprocessing (segmentation, eddy currents) resulted in the largest potential error (≤15.5% combined) whereas errors related to data acquisition (noise, low spatial resolution) had a lower impact (≤5.5%‐7.0% combined). Whereas it is unlikely that these errors will be additive or affect the identification of severe asymmetry, these results illustrate the importance of eddy current correction and accurate segmentation to minimize Fontan flow distribution errors.
Ultrasound in the management of iatrogenic spinal accessory nerve palsy at the posterior cervical triangle area
Authors: Shen Jun , Chen Weimin , Ye Xuan , Qiu Yanqun , Xu Jing , Zhu Yi , Shen Yundong , Xu Wendong 
Published: September 2018

ABSTRACT
Introduction: The purpose of this study was to evaluate the application of ultrasound in the management of iatrogenic spinal accessory nerve palsy at the posterior cervical triangle area. Methods: In this retrospective study, we compared ultrasonographic results with intraoperative findings in patients with iatrogenic spinal accessory nerve palsy during the time period from 2014 to 2018 at our hospital. Results: Eleven patients were included. Ultrasound detected nerve transections in 9 patients and continuities in 2 patients. The ultrasonographic results were consistent with the intraoperative findings. Furthermore, ultrasound was able to accurately reveal lesion location in 8 of 9 patients with nerve transections. Discussion: Ultrasound provides direct images about nerve lesions contributing to the diagnosis of iatrogenic spinal accessory nerve palsy at the posterior cervical triangle area and also reveals lesion location, assisting in formulating suitable surgical plans preoperatively. We recommend that ultrasound be integrated into the preoperative evaluation. Muscle Nerve 59:64–69, 2019
Novel Feed from Invasive Species is Beneficial to Walleye Aquaculture
Authors: Mejri Sahar , Tremblay Réjean , Vandenberg Grant , Audet Céline 
Published: September 2018

Abstract
Carnivorous fishes, such as the Walleye Sander vitreus, are nutritionally demanding for fish meal. A promising alternative to marine-origin fish meal, the supply of which has been stagnant in recent decades, is fish meal derived from undesirable freshwater species, such as the White Sucker Catostomus commersonii. To evaluate the relative value of such ingredients, we examined the growth performance of Walleye juveniles. Two dietary treatments were tested: an experimental (EXP) diet that was manufactured using White Sucker as fish meal in comparison with a commercial (COM) diet, EWOS Micro (EWOS Canada, Ltd.). Dietary lipid content was 15.1% and 16.8% for EXP and COM diets, respectively. The protein content was 50.4% and 57.6% for EXP and COM diets, respectively. The energy content was 5,098.76 ± 9.23 cal/g (mean ± SD) for the EXP diet and 5,134.47 ± 10.95 cal/g for the COM diet. Starting at 27 d posthatch, Walleye juveniles (initial weight [mean ± SD] = 0.03 ± 0.008 g; initial length = 15.7 ± 1.5 mm) were reared for 6 weeks in three replicate tanks for each treatment. Condition factor (0.83), final weight (1.12 ± 0.3 g), and weight gain (1.09 ± 0.06 g) were higher in fish that were fed the EXP diet. Similarly, the energetic lipid content of fish in the EXP treatment group (mean ± SD = 5.01 ± 0.45 g/kg) was also higher than that of fish fed the COM diet (3.30 ± 0.53 g/kg). Although the polar lipid content (membrane lipids) was similar in fish from the two treatments, the nutritional ratio for COM juveniles was over 1.5 for arachidonic acid and docosahexaenoic acid, indicating selective incorporation by juveniles and suggesting a potential dietary imbalance of these fatty acids. Furthermore, the higher observed selective incorporation of oleic acid in juveniles fed the EXP diet suggested that a higher value of this fatty acid in the EXP feed could have increased Walleye growth performance. Threonine was the main essential amino acid (AA; &gt;18.5% of total AAs), while serine and glycine contributed the highest percentages of the nonessential AAs (&gt;31% and 8.5% of total AAs, respectively). All three AAs, often considered limiting ingredients, are important to support growth and are involved in metabolic processes in some fish species. Our results demonstrate that feed pellets made with White Sucker fish meal improved growth in Walleye juveniles and can serve as a suitable and probably lower-cost regional alternative to marine fish meal in feeds for carnivorous fishes.
Effects of Different Levels of Marine Snail Shells in the Diets of Juvenile Kuruma Shrimps Marsupenaeus japonicus as a Source of Calcium
Authors: Moss Amina S , Ishikawa Manabu , Koshio Shunsuke , Yokoyama Saichiro , Dawood Mahmoud A O 
Published: September 2018

Abstract
Shells derived from marine mollusks represent over 80% of shellfish waste. Therefore, a 42-d feeding trial was conducted to assess the effects of different levels of snail shells (SS) in the diets of kuruma shrimps Marsupenaeus japonicus as a source of calcium (Ca). An evaluation of the ability of SS to replace Ca was done by applying principles from a previously researched condition index to quantify the external characteristics of juvenile kuruma shrimps (initial body weight, 0.12 ± 0.01 g each [mean ± SD]) with relation to their growth performance. Five diets were formulated to include increasing levels of SS at 0, 2, 5, 10, and 0% (D1, D2, D3, D4, and D5, respectively); D1 was the positive control with Ca and no SS, and D5 was the negative control with no SS and no Ca included in the diet. Each diet was randomly allocated to triplicate groups of 15 shrimps per tank in a flow-through system. Survival, body weight gain, specific growth rate, feed efficiency ratio, individual dry weight, total body length, condition index, freshwater stress resistance, and fatty acid composition were evaluated. Results indicated that shrimps fed 2% and 10% SS had significantly higher stress resistance than those fed the other diets (P &lt; 0.05). Generally, dietary SS supplementation improved growth performances (such as final body weight, percent weight gain, specific growth rate, feed efficiency ratio), and the significantly highest performance was found in shrimps fed 10% SS (D4). Shrimps fed diets with ≤2% SS supplementation (D1, D2, and D5) had significantly lower condition index and hepatosomatic index. Under the present experimental conditions, using the condition index as a tool to evaluate the fitness of kuruma shrimps was beneficial; however, it was a poor indication of freshwater stress resistance. Instead, the ratio of n-3:n-6 in the shrimps’ bodies seemed to be correlated with stress resistance. Additionally, supplementing 10% SS in kuruma shrimp diets is recommended for better growth performance.
Very long‐term molecular follow‐up of minimal residual disease in patients with neuroblastoma
Authors: Tchirkov Andrei , Greze Victoria , Plantaz Dominique , Rouel Nadège , Vago Philippe , Kanold Justyna 
Published: September 2018

AbstractIn high‐risk neuroblastoma (HR‐NB), the clinical significance of long‐term minimal residual disease (MRD) monitoring using quantitative reverse transcription‐polymerase chain reaction (qRT‐PCR) for neuroblastoma mRNAs has not been investigated. We report long‐term MRD follow‐ups of four patients with HR‐NB throughout the disease (diagnosis, remission, and relapse) and treatment course (chemotherapy, autologous and allogeneic stem cell transplantation, and donor lymphocyte and natural killer cell infusions). The results showed the stability of mRNA marker expression after different treatments and demonstrated their validity to predict relapse and assess therapeutic response. This opens up the possibility of investigating the utility of long‐term molecular monitoring of MRD in prospective multicenter studies.
Formation of Heterotypic Amyloids: α‐Synuclein in Co‐Aggregation
Authors: Bhasne Karishma , Mukhopadhyay Samrat 
Published: September 2018

AbstractProtein misfolding resulting in the formation of ordered amyloid aggregates is associated with a number of devastating human diseases. Intrinsically disordered proteins (IDPs) do not autonomously fold up into a unique stable conformation and remain as an ensemble of rapidly fluctuating conformers. Many IDPs are prone to convert into the β‐rich amyloid state. One such amyloidogenic IDP is α‐synuclein that is involved in Parkinson's disease. Recent studies have indicated that other neuronal proteins, especially IDPs, can co‐aggregate with α‐synuclein in many pathological ailments. This article describes several such observations highlighting the role of heterotypic protein–protein interactions in the formation of hetero‐amyloids. It is believed that the characterizations of molecular cross talks between amyloidogenic proteins as well as the mechanistic studies of heterotypic protein aggregation will allow us to decipher the role of the interacting proteins in amyloid proteomics.
All Cats are Gray in the Dark: Enrichment/Depletion Approaches for Biomarker Discovery on Felis catus Plasma
Authors: Carcangiu Laura , Pisanu Salvatore , Tore Silvia , Addis Maria Filippa , Zini Eric , Uzzau Sergio , Pagnozzi Daniela 
Published: September 2018

AbstractIn veterinary medicine, assay performance is often affected by the lack of species‐specific diagnostic tools. Reliable biomarkers might be identified by investigating biological fluids of the species of interest, but protein sequence databases are often incomplete and human‐specific devices for reducing sample complexity might fail when applied to animal plasma. Here, seven commercial methods based on different capturing agents (anti‐human antibodies, affinity ligands, mixture of antibodies and ligands, and combinatorial peptide ligand libraries) are applied to cat plasma and evaluated in terms of yield, identified proteins/ peptides, and relative abundance by high‐resolution shotgun proteomics and label‐free quantitation. As a result, anti‐human antibody‐based methods are unsatisfactory. Most fail in reducing albumin and immunoglobulins, and some lead to a substantial removal of other highly abundant proteins, probably because of nonspecific interactions. A protein A/dye ligand‐based method is efficient in reducing immunoglobulins, fibrinogen, and apolipoprotein A1 and A2, but not albumin, and protein identifications do not increase. Only peptide ligand libraries flatten the dynamic range, and increased protein identification (59.0%). Albumin and immunoglobulins are successfully depleted (60.7% and 35.9%, respectively). Although further studies will be required for reinforcing our observations, this work can provide a useful guide for cat plasma pretreatment in biomarker discovery studies.
MaSS‐Simulator: A Highly Configurable Simulator for Generating MS/MS Datasets for Benchmarking of Proteomics Algorithms
Authors: Awan Muaaz Gul , Saeed Fahad 
Published: September 2018

AbstractMass Spectrometry (MS)‐based proteomics has become an essential tool in the study of proteins. With the advent of modern MS machines huge amounts of data is being generated, which can only be processed by novel algorithmic tools. However, in the absence of data benchmarks and ground truth datasets algorithmic integrity testing and reproducibility is a challenging problem. To this end, MaSS‐Simulator has been presented, which is an easy to use simulator and can be configured to simulate MS/MS datasets for a wide variety of conditions with known ground truths. MaSS‐Simulator offers many configuration options to allow the user a great degree of control over the test datasets, which can enable rigorous and large‐ scale testing of any proteomics algorithm. MaSS‐Simulator is assessed by comparing its performance against experimentally generated spectra and spectra obtained from NIST collections of spectral library. The results show that MaSS‐Simulator generated spectra match closely with real‐spectra and have a relative‐error distribution centered around 25%. In contrast, the theoretical spectra for same peptides have relative‐error distribution centered around 150%. MaSS‐Simulator will enable developers to specifically highlight the capabilities of their algorithms and provide a strong proof of any pitfalls they might face. Source code, executables, and a user manual for MaSS‐Simulator can be downloaded from https://github.com/pcdslab/MaSS-Simulator.
A Critical Survey of Dithiocarbamate Reversible Addition‐Fragmentation Chain Transfer (RAFT) Agents in Radical Polymerization
Authors: Moad Graeme 
Published: September 2018

ABSTRACTThis article provides a critical review of the properties, synthesis, and applications of dithiocarbamates Z′Z″NC(=S)SR as mediators in reversible addition‐fragmentation chain transfer (RAFT) polymerization. These are among the most versatile RAFT agents. Through choice of substituents on nitrogen (Z′, Z″), the polymerization of most monomer types can be controlled to provide living characteristics (i.e., low dispersities, high end‐group fidelity, and access to complex architectures). These include the more activated monomers (MAMs; e.g., styrenes and acrylates) and the less activated monomers (LAMs; e.g., vinyl esters and vinylamides). Dithiocarbamates with balanced activity (e.g., 1H‐pyrazole‐1‐carbodithioates) or switchable RAFT agents [e.g., a N‐methyl‐N‐(4‐pyridinyl)dithiocarbamate] allow control MAMs and LAMs with a single RAFT agent and provide a pathway to low‐dispersity poly(MAM)‐block‐poly(LAM). © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2019, 57, 216–227
Digital PCR After MALDI–Mass Spectrometry Imaging to Combine Proteomic Mapping and Identification of Activating Mutations in Pulmonary Adenocarcinoma
Authors: Kazdal Daniel , Longuespée Rémi , Dietz Steffen , Casadonte Rita , Schwamborn Kristina , Volckmar Anna‐Lena , Kriegsmann Jörg , Kriegsmann Katharina , Fresnais Margaux , Stenzinger Albrecht , Sültmann Holger , Warth Arne , Kriegsmann Mark 
Published: September 2018

PurposeMatrix assisted laser desorption/ionization time‐of‐flight mass spectrometry imaging (MALDI–MSI) is a powerful tool to analyze the spatial distribution of peptides in tissues. Digital PCR (dPCR) is a method to reliably detect genetic mutations. Biopsy material is often limited due to minimally invasive techniques, but information on diagnosis, prognosis, and prediction is required for subsequent clinical decision making. Thus, saving tissue material during diagnostic workup is highly warranted for best patient care. The possibility to combine proteomic analysis by MALDI–MSI and mutational analysis by dPCR from the same tissue section is evaluated.Experimental designTen 0.5 × 0.5 cm formalin‐fixed paraffin embedded tissue samples of pulmonary adenocarcinomas with known EGFR or KRAS mutations are analyzed by MALDI–MSI. Subsequently, DNA is extracted from the analyzed tissue material and tested for the respective driver mutation by dPCR.ResultsDetection of driver gene mutations after MALDI MSI analysis is successful in all analyzed samples. Determined mutant allele frequencies are in good agreement with values assessed from untreated serial tissue sections with a mean absolute deviation of 0.16.Conclusion and clinical relevanceIt has been demonstrated that MALDI–MSI can be combined with genetic analysis, like dPCR. Workflows enabling the subsequent analysis of proteomic and genetic markers are particularly promising for the analysis of limited sample material such as biopsy specimen.
In MALDI–Mass Spectrometry Imaging on Formalin‐Fixed Paraffin‐Embedded Tissue Specimen Section Thickness Significantly Influences m/z Peak Intensity
Authors: Longuespée Rémi , Kriegsmann Katharina , Cremer Martin , Zgorzelski Christiane , Casadonte Rita , Kazdal Daniel , Kriegsmann Jörg , Weichert Wilko , Schwamborn Kristina , Fresnais Margaux , Schirmacher Peter , Kriegsmann Mark 
Published: September 2018

BackgroundIn matrix‐assisted laser desorption/ionization–mass spectrometry imaging (MALDI–MSI) standardized sample preparation is important to obtain reliable results. Herein, the impact of section thickness in formalin‐fixed paraffin embedded (FFPE) tissue microarrays (TMA) on spectral intensities is investigated.Patients and methodsTMAs consisting of ten different tissues represented by duplicates of ten patients (n = 200 cores) are cut at 1, 3, and 5 μm. MSI analysis is performed and mean intensities of all evaluable cores are extracted. Measurements are merged and mean m/z intensities are compared.ResultsVisual inspection of spectral intensities between 1, 3, and 5 μm reveals generally higher intensities in thinner tissue sections. Specifically, higher intensities are observed in the vast majority of peaks (98.6%, p < 0.01) in 1 μm compared with 5 μm sections. Note that 28.4% and 2.1% of m/z values exhibit a at least two‐ and threefold intensity difference (p < 0.01) in 1 μm compared to 5 μm sections, respectively.ConclusionA section thickness of 1 μm results in higher spectral intensities compared with 5 μm. The results highlight the importance of standardized protocols in light of recent efforts to identify clinically relevant biomarkers using MSI. The use of TMAs for comparative analysis seems advantageous, as section thickness displays less variability.
Prediction of GABARAP interaction with the GABA type A receptor
Authors: Irwin B.W.J. , Vukovič Siniša , Payne M.C. , ElGamacy Mohammad , Chau P.‐L. 
Published: September 2018

AbstractWe have performed docking simulations on GABARAP interacting with the GABA type A receptor using SwarmDock. We have also used a novel method to study hydration sites on the surface of these two proteins; this method identifies regions around proteins where desolvation is relatively easy, and these are possible locations where proteins can bind each other. There is a high degree of consistency between the predictions of these two methods. Moreover, we have also identified binding sites on GABARAP for other proteins, and listed possible binding sites for as yet unknown proteins on both GABARAP and the GABA type A receptor intracellular domain.