bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultrasound prostate segmentation based on multidirectional deeply supervised V‐Net
Authors: Lei Yang , Tian Sibo , He Xiuxiu , Wang Tonghe , Wang Bo , Patel Pretesh , Jani Ashesh B. , Mao Hui , Curran Walter J. , Liu Tian , Yang Xiaofeng 
Published: May 2019

PurposeTransrectal ultrasound (TRUS) is a versatile and real‐time imaging modality that is commonly used in image‐guided prostate cancer interventions (e.g., biopsy and brachytherapy). Accurate segmentation of the prostate is key to biopsy needle placement, brachytherapy treatment planning, and motion management. Manual segmentation during these interventions is time‐consuming and subject to inter‐ and intraobserver variation. To address these drawbacks, we aimed to develop a deep learning‐based method which integrates deep supervision into a three‐dimensional (3D) patch‐based V‐Net for prostate segmentation.Methods and materialsWe developed a multidirectional deep‐learning‐based method to automatically segment the prostate for ultrasound‐guided radiation therapy. A 3D supervision mechanism is integrated into the V‐Net stages to deal with the optimization difficulties when training a deep network with limited training data. We combine a binary cross‐entropy (BCE) loss and a batch‐based Dice loss into the stage‐wise hybrid loss function for a deep supervision training. During the segmentation stage, the patches are extracted from the newly acquired ultrasound image as the input of the well‐trained network and the well‐trained network adaptively labels the prostate tissue. The final segmented prostate volume is reconstructed using patch fusion and further refined through a contour refinement processing.ResultsForty‐four patients' TRUS images were used to test our segmentation method. Our segmentation results were compared with the manually segmented contours (ground truth). The mean prostate volume Dice similarity coefficient (DSC), Hausdorff distance (HD), mean surface distance (MSD), and residual mean surface distance (RMSD) were 0.92 ± 0.03, 3.94 ± 1.55, 0.60 ± 0.23, and 0.90 ± 0.38 mm, respectively.ConclusionWe developed a novel deeply supervised deep learning‐based approach with reliable contour refinement to automatically segment the TRUS prostate, demonstrated its clinical feasibility, and validated its accuracy compared to manual segmentation. The proposed technique could be a useful tool for diagnostic and therapeutic applications in prostate cancer.
Comparison of planned dose on different CT image sets to four‐dimensional Monte Carlo dose recalculation using the patient's actual breathing trace for lung stereotactic body radiation therapy
Authors: Freislederer Philipp , von Münchow Asmus , Kamp Florian , Heinz Christian , Gerum Sabine , Corradini Stefanie , Söhn Matthias , Reiner Michael , Roeder Falk , Floca Ralf , Alber Markus , Belka Claus , Parodi Katia 
Published: May 2019

PurposeThe need for four‐dimensional (4D) treatment planning becomes indispensable when it comes to radiation therapy for moving tumors in the thoracic and abdominal regions. The primary purpose of this study is to combine the actual breathing trace during each individual treatment fraction with the Linac's log file information and Monte Carlo 4D dose calculations. We investigated this workflow on multiple computed tomography (CT) datasets in a clinical environment for stereotactic body radiation therapy (SBRT) treatment planning.
Methods
We have developed a workflow, which allows us to recalculate absorbed dose to a 4DCT dataset using Monte Carlo calculation methods and accumulate all 4D doses in order to compare them to the planned dose using the Linac's log file, a 4DCT dataset, and the patient's actual breathing curve for each individual fraction. For five lung patients, three‐dimensional‐conformal radiation therapy (3D‐CRT) and volumetric modulated arc treatment (VMAT) treatment plans were generated on four different CT image datasets: a native free‐breathing 3DCT, an average intensity projection (AIP) and a maximum intensity projection (MIP) CT both obtained from a 4DCT, and a 3DCT with density overrides based on the 3DCT (DO). The Monte Carlo 4D dose has been calculated on each 4DCT phase using the Linac's log file and the patient's breathing trace as a surrogate for tumor motion and dose was accumulated to the gross tumor volume (GTV) at the 50% breathing phase (end of exhale) using deformable image registration.Results and between 4D dose and planned dose differed largely for 3DCT‐based planning and also for DO in three patients. Least dose differences between planned and recalculated dose have been found for AIP and MIP treatment planning which both tend to be superior to DO, but the results indicate a dependency on the breathing variability, tumor motion, and size. An interplay effect has not been observed in the small patient cohort.ConclusionsWe have developed a workflow which, to our best knowledge, is the first incorporation of the patient breathing trace over the course of all individual treatment fractions with the Linac's log file information and 4D Monte Carlo recalculations of the actual treated dose. Due to the small patient cohort, no clear recommendation on which CT can be used for SBRT treatment planning can be given, but the developed workflow, after adaption for clinical use, could be used to enhance a priori 4D Monte Carlo treatment planning in the future and help with the decision on which CT dataset treatment planning should be carried out.
Academy of Nutrition and Dietetics/American Society for Parenteral and Enteral Nutrition Consensus Malnutrition Characteristics: Usability and Association With Outcomes
Authors: Mogensen Kris M. , Malone Ainsley , Becker Patricia , Cutrell Stephanie , Frank Laura , Gonzales Kelly , Hudson Lauren , Miller Sarah , Guenter Peggi ,   Malnutrition Committee of the American Society for Parenteral and Enteral Nutrition (ASPEN)
Published: May 2019

AbstractMalnutrition has been documented in approximately one‐third of patients in developed countries on hospital admission and is associated with negative clinical outcomes. The need to identify and intervene in at‐risk patients is critical to minimize these negative outcomes. A consensus approach for diagnosing and documenting malnutrition in hospitalized adult and pediatric patients was published jointly by the Academy of Nutrition and Dietetics (Academy) and the American Society for Parenteral and Enteral Nutrition (ASPEN) in 2012 and 2014, respectively. The purpose of this paper is to review the available literature on the usability, feasibility, validity, and reliability of both the adult and pediatric consensus malnutrition diagnostic approaches, as well as to evaluate their use in studying clinical outcomes. In adults, abstracts and published studies have shown the diagnostic tool is a usable, feasible, and reliable method for the identification of severe and non‐severe or moderate malnutrition. In pediatrics, only 1 published study to date used the pediatric malnutrition indicators, indicating the need to demonstrate that the tool is feasible, valid, and reliable. Both the adult and pediatric tools have shown significant correlation with negative clinical outcomes in malnourished patients, including increased mortality, increased hospital length of stay (adults), increased complications (pediatrics), and increased hospital readmissions. Further large‐scale studies are needed to evaluate the feasibility, usability, validity, and reliability of both the adult and pediatric malnutrition diagnostic approaches.
Spontaneous Restoration of Nutrition Autonomy in a Case of Intestinal Failure Secondary to a Gastrointestinal Neuromuscular Disease
Authors: McCulloch Adam , Malhi Hardip , Parkinson Sharmalie , Martin Joanne E. , Cooper Sheldon C. 
Published: May 2019

AbstractPolyglucosan inclusion body myopathy (PIBM) is a recently described gastrointestinal neuromuscular disease. Given its rarity, very little is known of its natural history and prognosis. In this case report, we present the first case of PIBM and resultant intestinal failure in which, following 7 years of home parenteral nutrition, gastrointestinal symptoms subsided and nutrition autonomy was restored.
Using a vibratory source at Mt. Etna (Italy) to investigate the wavefield polarization at Pernicana Fault
Authors: Di Giulio Giuseppe , Punzo Michele , Bruno Pier Paolo , Cara Fabrizio , Rovelli Antonio 
Published: May 2019

ABSTRACTThe paper presents the results of a controlled‐source seismic experiment performed using a vibratory source capable of producing harmonic vibrations. The survey aimed at investigating the horizontal directional amplification mechanism observed at the Pernicana Fault (Mt. Etna in Sicily, Italy) along an N150°/N330° orientation. With the vibratory source (a shaker truck) working in shear‐wave mode in the frequency range 5–40 Hz, we recorded seismic data using both three‐component velocimeters and 4.5 Hz geophones. These two types of receivers were arranged in linear configuration along two orthogonal orientations: radial and transverse to the direction of the main polarization observed within the fault zone. The two lines of seismic stations allowed us to investigate the polarization evolution as a function of the distance from the source. Results show that when the shear excitation induced by the source is parallel to the direction of observed polarization of the ground motion, the seismic signal propagates efficiently, maintaining the same horizontal polarization induced by the active source. This polarization is well recorded up to distances as large as 300 m from the source. On the contrary, when the shear excitation is orthogonal to the predominant site polarization, the ground excitation loses its initial polarization in less than 50 m away from the source position. At larger distances, the transmitted energy propagates with the natural site polarization independently from the original source polarization. The observations in terms of polarization were combined with surface‐wave analysis, aimed at investigating the dispersion characteristics of the wavefield on the geophone lines. The data suggest that the experimental Rayleigh‐wave dispersion spectra show a more coherent signal over the frequency range along the same orientation of the observed site polarization, supporting a preferential direction in the propagation of surface waves. From inversion of the Rayleigh dispersion curves, we inferred the shear‐wave velocity (Vs) to be in the range of 120–450 m/s in the first 30 m deep of Quaternary volcanic sediments. The dispersion curves are not constant along transverse and radial directions, suggesting the presence of fracture‐induced seismic anisotropy in the near surface.
Policy entrepreneurship in developing countries: A systematic review of the literature
Authors: Frisch Aviram Neomi , Cohen Nissim , Beeri Itai 
Published: May 2019

SummaryWhat can be learned from two decades of studies on policy entrepreneurship in developing countries? Policy entrepreneurship is a rapidly evolving analytical concept. A growing number of studies exploring public policy in developing countries use policy entrepreneurship as an explanatory theoretical concept. However, a substantial part of this research relies on qualitative case study analysis, lacking a comprehensive overview of the concept of policy entrepreneurship. This paper conducts a systematic review of the literature on policy entrepreneurship in developing countries. A total of 47 papers addressing policy entrepreneurship in the developing world, published between 1993 and 2017, have been analysed. The purpose and contribution of this paper are to offer a clearer picture of policy entrepreneurship in the developing world by concentrating on two aspects. First, we describe the characteristics of the studies on policy entrepreneurship in the developing world. Second, we analyse such studies, identifying the lessons that can be drawn on the phenomenon of policy entrepreneurship in the developing world. We conclude with an agenda for future studies, examining new theoretical, methodological, and empirical opportunities to advance the understanding of policy entrepreneurship in developing countries.
Use of real‐world evidence from healthcare utilization data to evaluate drug safety during pregnancy
Authors: Huybrechts Krista F. , Bateman Brian T. , Hernández‐Díaz Sonia 
Published: May 2019

AbstractPurposeBecause preapproval clinical trials typically exclude pregnant women, the evidence on drug safety during pregnancy required to inform drug labeling must come from postapproval controlled observational studies. Common designs have included pregnancy registries and case‐control studies. Recently, pregnancy cohorts nested within healthcare utilization databases are increasingly being used. Despite clear advantages, these databases share some important limitations that may threaten the validity of studies emerging from them.MethodsThis paper describes the distinctive methodological aspects of conducting drug safety studies in healthcare utilization databases with special emphasis on design and analytic approaches to minimize biases.ResultsWe describe considerations for study design, cohort definition, and follow‐up. We then address issues related to exposure ascertainment based on prescription fills, including the importance of the etiologically relevant window and of properly accounting for preterm births. This is followed by a discussion of advantages and challenges when ascertaining maternal and infant outcomes based on secondary data. We then explore useful approaches to address confounding within the context of pregnancy research and of the potential for selection bias when restricting the cohort to live births. Finally, we consider issues related to external validity and statistical significance. The examples are mainly drawn from a pregnancy cohort nested in the Medicaid Analytic Extract.ConclusionsThe approaches presented provide guidance regarding the important methodological considerations that need to be attended to in order to generate valid, minimally biased risk when using large healthcare utilization databases for drug safety surveillance in pregnancy.
Substrate selection by the proteasome through initiation regions
Authors: Tomita Takuya , Matouschek Andreas 
Published: May 2019

AbstractProteins in the cell have to be eliminated once their function is no longer desired or they become damaged. Most regulated protein degradation is achieved by a large enzymatic complex called the proteasome. Many proteasome substrates are targeted for degradation by the covalent attachment of ubiquitin molecules. Ubiquitinated proteins can be bound by the proteasome, but for proteolysis to occur the proteasome needs to find a disordered tail somewhere in the target at which it initiates degradation. The initiation step contributes to the specificity of proteasomal degradation. Here, we review how the proteasome selects initiation sites within its substrates and discuss how the initiation step affects physiological processes.
Selection and analyses of variants of a designed protein suggest importance of hydrophobicity of partially buried sidechains for protein stability at high temperatures
Authors: Han Mingjie , Liao Sanhui , Peng Xiong , Zhou Xiaoqun , Chen Quan , Liu Haiyan 
Published: May 2019

AbstractComputationally designed proteins of high stability provide specimen in addition to natural proteins for the study of sequence‐structure stability relationships at the very high end of protein stability spectrum. The melting temperature of E_1r26, a protein we previously designed using the A Backbone‐based Amino aCid Usage Survey (ABACUS) sequence design program, is above 110 °C, more than 50 °C higher than that of the natural thioredoxin protein whose backbone (PDB ID 1R26) has been used as the design target. Using an experimental selection approach, we obtained variants of E_1r26 that remain folded but are of reduced stability, including one whose unfolding temperature and denaturing guanidine concentration are similar to those of 1r26. The mutant unfolds with a certain degree of cooperativity. Its structure solved by X‐ray crystallography agrees with that of 1r26 by a root mean square deviation of 1.3 Å, adding supports to the accuracy of the ABACUS method. Analyses of intermediate mutants indicate that the substitution of two partially buried hydrophobic residues (isoleucine and leucine) by polar residues (threonine and serine, respectively) are responsible for the dramatic change in the unfolding temperature. It is suggested that the effects of mutations located in rigid secondary structure regions, but not those in loops, may be well predicted through ABACUS mutation energy analysis. The results also suggest that hydrophobic effects involving intermediately buried sidechains can be critically important for protein stability at high temperatures.
Schisandra chinensis extract ameliorates age‐related muscle wasting and bone loss in ovariectomized rats
Authors: Kim Jeong‐Seok , Takanche Jyoti Shrestha , Kim Ji‐Eun , Jeong Seon‐Hwa , Han Sin‐Hee , Yi Ho‐Keun 
Published: May 2019

Exercise and healthy diet consumption support healthy aging. Schisandra chinensis (Turcz.) also known as “Baill.” has anti‐inflammatory and antioxidant properties. However, the role of S. chinensis as an antiaging compound has yet to be demonstrated. This study elucidated the antiaging effect of S. chinensis ethanol–hexane extract (C1) and the effect of C1 treatment on muscle and bone following physical exercise in ovariectomized (OVX) rats. RAW 264.7, human diploid fibroblasts (HDFs), C2C12 myoblasts, bone marrow macrophages, and MC3T3‐E1 cells were used for in vitro, and muscle and bone of OVX rats were used for in vivo study to demonstrate the effect of C1. The C1 significantly inhibited the expression of inflammatory molecules, β‐galactosidase activity, and improved antioxidant activity via down‐regulation of reactive oxygen species in RAW 264.7 and aged HDF cells. The C1 with exercise improved muscle regeneration in skeletal muscle of OVX rats by promoting mitochondrial biogenesis and autophagy. C1 induced osteoblast differentiation, and C1 + exercise modulated the bone formation and bone resorption in OVX rats. C1 exhibited anti‐inflammatory, antioxidant, myogenic, and osteogenic effects. C1 with exercise improved age‐related muscle wasting and bone loss. Therefore, S. chinensis may be a potential prevent agent for age‐related diseases such as sarcopenia and osteoporosis.
Theoretical study on ionic liquids based on DBUH+: Molecular engineering and hydrogen bond evaluation
Authors: Rezaeian Mojtaba , Izadyar Mohammad 
Published: May 2019

AbstractThe new generation of the ionic liquids (ILs) based on 1,8‐diazobicylo [5,4,0] undec‐7‐ene (DBU) are applied as the solvent in organic reactions. In this work, by using a theoretical procedure, the most probable interactions between the ion pairs of DBUH+ based ILs, including 10 functionalized imidazole anions were investigated. For this purpose, the electrostatic potential surfaces were analyzed to detect the most probable interaction sites of DBUH+. On the basis of the obtained results, hydrogen bond formation between the anions and DBUH+ is influenced by the electronic effect of the substituted functional groups. This means that electron donating groups, such as phenyl has a stabilizing effect on the ion pairs, while electron‐withdrawing groups, such as nitro, induces a destabilizing effect. These behaviors are described based on the interaction energy values (ΔEint). To investigate the dispersion interaction effects in ILs formation, M06‐2X‐D3 functional was applied in energy analysis. The solvent reaction field was investigated by the polarizable continuum model in ethanol and chloroform as the solvent. The results showed that ethanol has a greater effect on the interaction energy of the ILs. Finally, to have a comprehensive understanding of the charge transfer effect on the stability of the studied ILs and to characterize the most probable interactions, natural bond orbital and quantum theory of atoms in molecules analyses were applied and the obtained results were analyzed.
Optimal control of a linear system subject to partially specified input noise
Authors: Erreygers Alexander , De Bock Jasper , de Cooman Gert , Van Camp Arthur 
Published: May 2019

SummaryOne of the most basic problems in control theory is that of controlling a discrete‐time linear system subject to uncertain noise with the objective of minimizing the expectation of a quadratic cost. If one assumes the noise to be white, then solving this problem is relatively straightforward. However, white noise is arguably unrealistic: noise is not necessarily independent, and one does not always precisely know its expectation. We first recall the optimal control policy without assuming independence and show that, in this case, computing the optimal control inputs becomes infeasible. In the next step, we assume only the knowledge of lower and upper bounds on the conditional expectation of the noise and prove that this approach leads to tight lower and upper bounds on the optimal control inputs. The analytical expressions that determine these bounds are strikingly similar to the usual expressions for the case of white noise.
Robust nonovershooting tracking control for fractional‐order systems
Authors: Xavier Nithin , Babu Praveen S , Bandyopadhyay Bijnan , Schmid Robert 
Published: May 2019

SummaryA robust tracking control is proposed for the fractional‐order systems (FOSs) to achieve a tracking response with no overshoot, even in the presence of a class of disturbances. The control proposed makes use of a newly designed integral sliding mode technique for FOSs, which is capable of rejecting the bounded disturbances acting through the input channel. The proposed integral sliding mode control design has two components: a nominal control component and a discontinuous control component. The overshoot in the system response is avoided by the nominal control designed with the use of Moore's eigenstructure assignment algorithm. The sliding mode technique is used for the design of discontinuous part of the control that imparts the desired robustness properties.
Discovery of and Insights into DNA “Codes” for Tunable Morphologies of Metal Nanoparticles
Authors: Satyavolu Nitya Sai Reddy , Loh Kang Yong , Tan Li Huey , Lu Yi 
Published: May 2019

AbstractThe discovery and elucidation of genetic codes has profoundly changed not only biology but also many fields of science and engineering. The fundamental building blocks of life comprises of four simple deoxyribonucleotides and yet their combinations serve as the carrier of genetic information that encodes for proteins that can carry out many biological functions due to their unique functionalities. Inspired by nature, the functionalities of DNA molecules have been used as a capping ligand for controlling morphology of nanomaterials, and such a control is sequence dependent, which translates into distinct physical and chemical properties of resulting nanoparticles. Herein, an overview on the use of DNA as engineered codes for controlling the morphology of metal nanoparticles, such as gold, silver, and Pd‐Au bimetallic nanoparticles is provided. Fundamental insights into rules governing DNA controlled growth mechanisms are also summarized, based on understanding of the affinity of the DNA nucleobases to various metals, the effect of combination of nucleobases, functional modification of DNA, the secondary structures of DNA, and the properties of the seed employed. The resulting physical and chemical properties of these DNA encoded nanomaterials are also reviewed, while perspectives into the future directions of DNA‐mediated nanoparticle synthesis are provided.