bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated intensity modulated treatment planning: The expedited constrained hierarchical optimization (ECHO) system
Authors: Zarepisheh Masoud , Hong Linda , Zhou Ying , Oh Jung Hun , Mechalakos James G. , Hunt Margie A. , Mageras Gig S. , Deasy Joseph O. 
Published: May 2019

PurposeTo develop and implement a fully automated approach to intensity modulated radiation therapy (IMRT) treatment planning.MethodThe optimization algorithm is developed based on a hierarchical constrained optimization technique and is referred internally at our institution as expedited constrained hierarchical optimization (ECHO). Beamlet contributions to regions‐of‐interest are precomputed and captured in the influence matrix. Planning goals are of two classes: hard constraints that are strictly enforced from the first step (e.g., maximum dose to spinal cord), and desirable goals that are sequentially introduced in three constrained optimization problems (better planning target volume (PTV) coverage, lower organ at risk (OAR) doses, and smoother fluence map). After solving the optimization problems using external commercial optimization engines, the optimal fluence map is imported into an FDA‐approved treatment planning system (TPS) for leaf sequencing and accurate full dose calculation. The dose‐discrepancy between the optimization and TPS dose calculation is then calculated and incorporated into optimization by a novel dose correction loop technique using Lagrange multipliers. The correction loop incorporates the leaf sequencing and scattering effects into optimization to improve the plan quality and reduce the calculation time. The resultant optimal fluence map is again imported into TPS for leaf sequencing and final dose calculation for plan evaluation and delivery. The workflow is automated using application program interface (API) scripting, requiring user interaction solely to prepare the contours and beam arrangement prior to launching the ECHO plug‐in from the TPS. For each site, parameters and objective functions are chosen to represent clinical priorities. The first site chosen for clinical implementation was metastatic paraspinal lesions treated with stereotactic body radiotherapy (SBRT). As a first step, 75 ECHO paraspinal plans were generated retrospectively and compared with clinically treated plans generated by planners using VMAT (volumetric modulated arc therapy) with 4 to 6 partial arcs. Subsequently, clinical deployment began in April, 2017.ResultsIn retrospective study, ECHO plans were found to be dosimetrically superior with respect to tumor coverage, plan conformity, and OAR sparing. For example, the average PTV D95%, cord and esophagus max doses, and Paddick Conformity Index were improved, respectively, by 1%, 6%, 14%, and 15%, at a negligible 3% cost of the average skin D10cc dose.ConclusionHierarchical constrained optimization is a powerful and flexible tool for automated IMRT treatment planning. The dosimetric correction step accurately accounts for detailed dosimetric multileaf collimator and scattering effects. The system produces high‐quality, Pareto optimal plans and avoids the time‐consuming trial‐and‐error planning process.
Diagnostic and therapeutic musculoskeletal ultrasound applications of the shoulder
Authors: Strakowski Jeffrey A. , Visco Christopher J. 
Published: May 2019

ABSTRACTHigh frequency ultrasound is a valuable tool for assessing soft tissue injuries about the shoulder. It has advantages over other imaging modalities including relatively low cost, portability, and dynamic real‐time visualization. It has a high sensitivity for identifying tendon degeneration, bursitis, and rotator cuff tears. Ultrasound is also an excellent modality for diagnostic and therapeutic needle‐guided procedures. A detailed knowledge of shoulder anatomy and transducer positioning is required for obtaining adequate diagnostic value from ultrasound. This Monograph is designed to help develop scanning protocols for optimizing image acquisition for musculoskeletal assessment of the shoulder. Muscle Nerve, 2019
Rainbow Trout Migration and Use of a Nature-Like Fishway at a Great Lakes Tributary
Authors: Bunt Christopher , Jacobson Bailey 
Published: May 2019

Abstract
Rainbow Trout Oncorhynchus mykiss were monitored over two consecutive vernal migration periods at a nature-like fishway on the Beaver River, Ontario, to assess attraction efficiency, passage efficiency, multiple fish passage metrics, and interannual return rates from Georgian Bay, Lake Huron. Fishway evaluations have shifted to fill knowledge gaps related to the passage of nonsalmonids; however, surprisingly little work has been conducted with Rainbow Trout, with no known study assessing attraction or passage at a nature-like fishway. Attraction efficiency was 53% and passage efficiency was 100% in 2017; only two of the radio-tagged fish returned to the fishway in 2018. Upstream passage through the fishway required an average time of 152 ± 122 min. Fish spent 19–43 d upstream before returning to Lake Huron, where downstream passage required as little as 15 min. Overall, there were no significant relationships between any of the fish passage metrics and fish size or condition. These results can be used as a foundation for anadromous O. mykiss subspecies passage research and suggest that fisheries managers may need to adjust annual fishway counts. Future research should focus on developing methods to directly integrate temporal passage metrics into estimates of fishway efficiency.
Morphological aspects of crack growth in rock materials with various flaws
Authors: Lee Jooeun , Hong Jung‐Wuk 
Published: May 2019

SummaryCrack evolution is initiated by the occurrence of tensile wing cracks and is then further promoted due to the crack coalescence caused by the extension of a central tensile crack segment between two relatively adjacent flaws. To understand such progressive failures in rock, a parallelized peridynamics coupled with a finite element method is utilized. Through this method, the initiation position of tensile wing cracks is observed with respect to varying inclination angles of a flaw, and then its corresponding shifting mechanism is investigated. In addition, the phenomenon of the position shifting being sensitive to various flaw shapes is discussed. Moreover, it is observed that the inclination angle of a central flaw affects the initiation position of other flaws; therefore, the initiation positions of tensile wing crack emanating from other neighboring flaws are analyzed with their angles. Following tensile wing cracks, a central tensile crack segment occurs in the bridging region between a central flaw and other neighboring flaws; the developmental patterns caused by the crack segment are discussed as well. Finally, the role a central tensile crack segment plays in the formation of crack coalescence and specimen failure is investigated in detail. The numerical results in this paper demonstrate good fidelity with established physical test results and complement them, thereby expanding the understanding of fracturing morphology in rock specimens with various flaws.
Evaluation of resistivity anisotropy parameters in the Eastern Mitidja basin, Algeria, using azimuthal electrical resistivity tomography
Authors: Aissaoui Roza , Bounif Abdallah , Zeyen Hermann , Messaoudi Sid‐Ali 
Published: May 2019

ABSTRACTWe study electrical anisotropy using azimuthal electrical resistivity tomography (A‐ERT) for identifying geological layers and determining the preferential aquifer flow direction. The work presented in this paper aims at calculating the anisotropy coefficient from the inverted resistivity measurements, relating the geophysical results to the site geology and water flow direction, and comparing the results with those obtained from prior studies using hydrogeological approaches. The study area is located in the Eastern Mitidja basin, about 15 km east of Algiers. The work carried out includes three measurement points, totalling 24 ERT profiles. For each point, eight A‐ERT profiles, using Wenner–Schlumberger array configuration, were performed every 22.5° around a fixed central point. The data processing includes two‐dimensional inversion of each profile, representation of the inverted resistivities at the central points as a function of the azimuth in polar diagrams, and implementation of an inversion program to determine the best fitting azimuthal anisotropy parameters. The origin of electrical anisotropy is probably due to grain alignment, which is often observed in fine‐grained sediments such as clays and some sands. This alignment creates a higher electrical resistivity perpendicular to the alignment than parallel to it, which is an indicator for higher hydraulic permeability in the minimum resistivity direction, which corresponds to the preferential groundwater flow direction.
Are Liquid Sugars Different from Solid Sugar in Their Ability to Cause Metabolic Syndrome?
Authors: Sundborn Gerhard , Thornley Simon , Merriman Tony R. , Lang Bodo , King Christopher , Lanaspa Miguel A. , Johnson Richard J. 
Published: May 2019

ObjectiveIntake of sugary drinks, especially soft drinks, carries increased risk for obesity and diabetes. This article reviews whether sugary drinks carry different risks for metabolic syndrome compared with foods that contain natural or added sugars.MethodsA narrative review was performed to evaluate differences between liquid and solid sugars in their ability to induce metabolic syndrome and to discuss potential mechanisms to account for the differences.ResultsEpidemiological studies support liquid added sugars, such as soft drinks, as carrying greater risk for development of metabolic syndrome compared with solid sugar. Some studies suggest that fruit juice may also confer relatively higher risk for weight gain and insulin resistance compared with natural fruits. Experimental evidence suggests this may be due to differences in how fructose is metabolized. Fructose induces metabolic disease by reducing the energy levels in liver cells, mediated by the concentration of fructose to which the cells are exposed. The concentration relates to the quantity and speed at which fructose is ingested, absorbed, and metabolized.ConclusionsAlthough reduced intake of added sugars (sucrose and high‐fructose corn syrup) remains a general recommendation, there is evidence that sugary soft drinks may provide greater health risks relative to sugar‐containing foods.
Identification of structurally diverse alkaloids in Talguenea quinquinervia (gill. Et hook) by liquid chromatography/electrospray ionisation tandem mass spectroscopy and insecticidal activity
Authors: Quiroz‐Carreño Soledad , Céspedes‐Acuña Carlos L. , Seigler David S. , Alarcón‐Enos Julio 
Published: May 2019

AbstractIntroductionTalguenea quinquinervia has been used in folk medicine and to dye wool, and the main constituents are alkaloids and triterpenes. Identification of these type of compounds in this specie is a necessary step to understand the biological properties.ObjectiveTo evaluate the relationship between the chemical composition of root from T. quinquinervia and its insecticidal properties using liquid chromatography electrospray ionisation tandem mass spectrometry (LC‐ESI‐MS/MS).MethodsAlkaloids were extracted using Soxhlet extraction with methanol. Total extract was partitioned at pH 2 and 12 to enrich alkaloid constituents and to remove interferences. The separation of alkaloids in the Talguenea extract was performed on a C18 column using gradient elution and their tandem mass spectra were obtained by quadrupole time‐of‐flight tandem mass spectrometry (QTOF‐MS/MS) to perform accurate mass measurements of fragment ions for the alkaloid constituents.ResultsSeveral types of alkaloids were separated and identified by LC‐ESI‐MS/MS. The structural assignment of individual alkaloids was performed based on convergence of MS/MS spectral data, pH partitioning behaviour, LC retention behaviour, and accurate mass measurements. The pH partition of the extract provided structural information about unknown alkaloids extracted from T. quinquinervia. A total of 20 compounds were identified and tentatively characterised, and of these 15 alkaloids were reported for the first time in the investigated T. quinquinervia.ConclusionThe chemical profiling of alkaloids in T. quinquinervia with different origins was performed for the first time and provided diagnostic ions for diverse alkaloids in T. quinquinervia. Insecticidal activity observed can be explain by the presence of alkaloid and pentacyclic triterpenes on the fractions assayed.
Enhancing the durability of poly(lactic acid) composites by nucleated modification
Authors: Sun Ce , Li Changxin , Tan Haiyan , Zhang Yanhua 
Published: May 2019

AbstractBiodegradable poly(lactic acid) (PLA) composites were prepared using an innovative combination of wood fiber (WF) and 1,3,2,4‐bis(3,4‐dimethylobenzylideno)sorbitol (DMDBS). DMDBS acted as an effective nucleating agent, which improved the mechanical properties and slowed down the degradation of the WF/PLA composites. The enzymatic degradation of the composites was examined by immersing in proteinase K or cellulase buffer. The presence of DMDBS resulted in a 26.7% increase of the crystallinity compared to the WF/PLA composites. The increase in crystallinity enhanced the thermal stability and tensile strength of the WF/DMDBS/PLA composites by 8.5%. The durability of the WF/DMDBS/PLA composites after nucleated modification was enhanced after enzymolysis. After nucleated modification, the surface of the WF/PLA composites showed clear cracks due to degradation, while these appeared about 2 weeks later in the case of the WF/DMDBS/PLA composites. The results revealed that the introduction of cellulase degraded WF in the composites, which increased hydrolysis or enzymolysis sites. The combination of nucleated modification and enzyme buffer gave an expanded downstream application of WF/PLA composites in packaging and agricultural materials. © 2019 Society of Chemical Industry
Overexpression of a Monocot Acyl‐CoA‐Binding Protein Confers Broad‐Spectrum Pathogen Protection in a Dicot
Authors: Panthapulakkal Narayanan Saritha , Liao Pan , Taylor Paul W. J. , Lo Clive , Chye Mee‐Len 
Published: May 2019

AbstractPlants are continuously infected by various pathogens throughout their lifecycle. Previous studies have reported that the expression of Class III acyl‐CoA‐binding proteins (ACBPs) such as the Arabidopsis ACBP3 and rice ACBP5 were induced by pathogen infection. Transgenic Arabidopsis AtACBP3‐overexpressors (AtACBP3‐OEs) displayed enhanced protection against the bacterial biotroph, Pseudomonas syringae, although they became susceptible to the fungal necrotroph Botrytis cinerea. A Class III ACBP from a monocot, rice (Oryza sativa) OsACBP5 was overexpressed in the dicot Arabidopsis. The resultant transgenic Arabidopsis lines conferred resistance not only to the bacterial biotroph P. syringae but to fungal necrotrophs (Rhizoctonia solani, B. cinerea, Alternaria brassicicola) and a hemibiotroph (Colletotrichum siamense). Changes in protein expression in R. solani‐infected Arabidopsis OsACBP5‐overexpressors (OsACBP5‐OEs) were demonstrated using proteomic analysis. Biotic stress‐related proteins including cell wall‐related proteins such as FASCILIN‐LIKE ARABINOGALACTAN‐PROTEIN10, LEUCINE‐RICH REPEAT EXTENSIN‐LIKE PROTEINS, XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE PROTEIN4, and PECTINESTERASE INHIBITOR18; proteins associated with glucosinolate degradation including GDSL‐LIKE LIPASE23, EPITHIOSPECIFIER MODIFIER1, MYROSINASE1, MYROSINASE2, and NITRILASE1; as well as a protein involved in jasmonate biosynthesis, ALLENE OXIDE CYCLASE2, were induced in OsACBP5‐OEs upon R. solani infection. These results indicated that upregulation of these proteins in OsACBP5‐OEs conferred protection against various plant pathogens.
Hip Radiograph Findings in Patients Aged 40 Years and Under with Posterior Pelvic Pain
Authors: Prather Heidi , Decker Gregory , Bonnette Michael , Simpson Scott , Hunt Devyani , Sahrmann Shirley , Cheng Abby , Nepple Jeffrey 
Published: May 2019

BackgroundSeveral sacroiliac joint (SIJ) provocative tests used to assess posterior pelvic pain involve moving and stressing the hip. It is unknown if there is a subgroup of patients with posterior pelvic pain who have underlying hip deformity that could potentially influence performance and interpretation of these tests.ObjectiveTo describe the prevalence of radiographic hip deformity and hip osteoarthritis in a group of adults 40 years old and under who met the clinical diagnostic criteria for treatment of posterior pelvic pain with an image guided intra‐articular SIJ injection.DesignRetrospective cohort study.SettingTertiary university orthopedic departmentPatients (or Participants)One hundred and forty‐eight patients were evaluated (83% (123/148) female; mean age 31.3 ± 6.2 years). All had completed a trial of comprehensive noninvasive treatment for posterior pelvic pain and had a minimum of three positive SIJ provocative tests on physical examination.MethodsRetrospective review identified patients undergoing SIJ injection for pain recommended and performed by seven physiatrists between 2011 and 2017. Hip radiographs were read by a physician with expertise in hip measurements with previously demonstrated excellent intrarater reliability.Main Outcome MeasurementsPercentage of patients with hip deformity findings.ResultsNo patients meeting the inclusion criteria had significant radiographic hip osteoarthritis (Tonnis ≥2 indicating moderate or greater radiographic hip osteoarthritis) and 4/148 (3%) were found to have mild radiographic hip osteoarthritis. Prearthritic hip disorders were identified in 123 (83%, 95% CI: 76, 89%) patients. For those patients with prearthritic hip disorders, measurements consistent with femoroacetabular impingement (FAI) were seen in 61 (41%) patients, acetabular dysplasia in 49 (33%) patients, and acetabular retroversion in 85 (57%) patients. Acetabular retroversion was identified in 43% (crossover sign) and 39% (prominent ischial spine) of patients.ConclusionsApproximately 57% of adult patients under the age of 40 years with the clinical symptom complex of SIJ pain were found to have radiographic acetabular retroversion. This is a higher percentage than the 5%‐15% found in asymptomatic people in the current literature. Further study is needed to assess links between hip structure, hip motion, and links to pelvic pain including peri and intra‐articular SIJ pain.Level of EvidenceIII
Controlling and quantifying protein concentration in Escherichia coli
Authors: Speer Shannon L. , Guseman Alex J. , Patteson Jon B. , Ehrmann Brandie M. , Pielak Gary J. 
Published: May 2019

AbstractThe cellular environment is dynamic and complex, involving thousands of different macromolecules with total concentrations of hundreds of grams per liter. However, most biochemistry is conducted in dilute buffer where the concentration of macromolecules is less than 10 g/L. High concentrations of macromolecules affect protein stability, function, and protein complex formation, but to understand these phenomena fully we need to know the concentration of the test protein in cells. Here, we quantify the concentration of an overexpressed recombinant protein, a variant of the B1 domain of protein G, in Tuner (DE3)™ Escherichia coli cells as a function of inducer concentration. We find that the protein expression level is controllable, and expression saturates at over 2 mM upon induction with 0.4 mM isopropyl β‐d‐thiogalactoside. We discuss the results in terms of what can and cannot be learned from in‐cell protein NMR studies in E. coli.
Examination of the nucleotide‐linked assembly mechanism of E. coli ClpA
Authors: Duran Elizabeth C. , Lucius Aaron L. 
Published: May 2019

AbstractEscherichia coli ClpA is a AAA+ (ATPase Associated with diverse cellular Activities) chaperone that catalyzes the ATP‐dependent unfolding and translocation of substrate proteins targeted for degradation by a protease, ClpP. ClpA hexamers associate with one or both ends of ClpP tetradecamers to form ClpAP complexes. Each ClpA protomer contains two nucleotide‐binding sites, NBD1 and NBD2, and self‐assembly into hexamers is thermodynamically linked to nucleotide binding. Despite a number of studies aimed at characterizing ClpA and ClpAP‐catalyzed substrate unfolding and degradation, respectively, to date the field is unable to quantify the concentration of ClpA hexamers available to interact with ClpP for any given nucleotide and total ClpA concentration. In this work, sedimentation velocity studies are used to quantitatively examine the self‐assembly of a ClpA Walker B variant in the presence of ATP. In addition to the hexamerization, we observe the formation of a previously unreported ClpA dodecamer in the presence of ATP. Further, we report apparent equilibrium constants for the formation of each ClpA oligomer obtained from direct boundary modeling of the sedimentation velocity data. The energetics of nucleotide binding to NBD1 and NBD2 are revealed by examining the dependence of the apparent association equilibrium constants on free nucleotide concentration.
Gauge PDE and AKSZ‐type Sigma Models
Authors: Grigoriev Maxim , Kotov Alexei 
Published: May 2019

AbstractA gauge PDE is a natural notion which arises by abstracting what physicists call a local gauge field theory defined in terms of BV‐BRST differential (not necessarily Lagrangian). We study supergeometry of gauge PDEs paying particular attention to globally well‐defined definitions and equivalences of such objects. We demonstrate that a natural geometrical language to work with gauge PDEs is that of Q‐bundles. In particular, we demonstrate that any gauge PDE can be embedded into a super‐jet bundle of the Q‐bundle. This gives a globally well‐defined version of the so‐called parent formulation. In the case of reparameterization‐invariant systems, the parent formulation takes the form of an AKSZ‐type sigma model with an infinite‐dimensional target space.
Higher Gauge Structures in Double and Exceptional Field Theory
Authors: Hohm Olaf , Samtleben Henning 
Published: May 2019

AbstractWe review the higher gauge symmetries in double and exceptional field theory from the viewpoint of an embedding tensor construction. This is based on a (typically infinite‐dimensional) Lie algebra and a choice of representation R. The embedding tensor is a map from the representation space R into satisfying a compatibility condition (‘quadratic constraint'). The Lie algebra structure on is transported to a Leibniz–Loday algebra on R, which in turn gives rise to an ‐structure. We review how the gauge structures of double and exceptional field theory fit into this framework.
Categorical Equivalence and the Renormalization Group
Authors: Sharpe Eric 
Published: May 2019

AbstractIn this article we review how categorical equivalences are realized by renormalization group flow in physical realizations of stacks, derived categories, and derived schemes. We begin by reviewing the physical realization of sigma models on stacks, as (universality classes of) gauged sigma models, and look in particular at properties of sigma models on gerbes (equivalently, sigma models with restrictions on nonperturbative sectors), and ‘decomposition,’ in which two‐dimensional sigma models on gerbes decompose into disjoint unions of ordinary theories. We also discuss stack structures on examples of moduli spaces of SCFTs, focusing on elliptic curves, and implications of subtleties there for string dualities in other dimensions. In the second part of this article, we review the physical realization of derived categories in terms of renormalization group flow (time evolution) of combinations of D‐branes, antibranes, and tachyons. In the third part of this article, we review how Landau–Ginzburg models provide a physical realization of derived schemes, and also outline an example of a derived structure on a moduli spaces of SCFTs.