bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel method for the determination of field output factors and output correction factors for small static fields for six diodes and a microdiamond detector in megavoltage photon beams
Authors: Casar Božidar , Gershkevitsh Eduard , Mendez Ignasi , Jurković Slaven , Huq M. Saiful 
Published: December 2018

PurposeThe goal of this work is to provide a large and consistent set of data for detector‐specific output correction factors, , for small static fields for seven solid‐state detectors and to determine field output factors, , using EBT3 radiochromic films and W1 plastic scintillator as reference detectors on two different linear accelerators and four megavoltage photon beams. Consistent measurement conditions and recommendations given in the International Code of Practice TRS‐483 for small‐field dosimetry were followed throughout the study.Methods were determined on two linacs, Elekta Versa HD and Varian TrueBeam, for 6 and 10 MV beams with and without flattening filter and for nine fields ranging from 0.5 × 0.5 cm2 to 10 × 10 cm2. Signal readings obtained with EBT3 radiochromic films and W1 plastic scintillator were fitted by an analytical function. Volume averaging correction factors, determined from two‐dimensional (2D) dose matrices obtained with EBT3 films and fitted to bivariate Gaussian function, were used to correct measured signals. were determined empirically for six diodes, IBA SFD, IBA Razor, PTW 60008 P, PTW 60012 E, PTW 60018 SRS, and SN EDGE, and a PTW 60019 microDiamond detector.ResultsField output factors and detector‐specific are presented in the form of analytical functions as well as in the form of discrete values. It is found that in general, for a given linac, small‐field output factors need to be determined for every combination of beam energy and filtration (WFF or FFF) and field size as the differences between them can be statistically significant (P < 0.05). For different beam energies, the present data for are found to differ significantly (P < 0.05) from the corresponding data published in TRS‐483 mostly for the smallest fields (<1.5 cm). For the PTW microDiamond detector, statistically significant differences (P < 0.05) between values were found for all investigated beams on an Elekta Versa HD linac for field sizes 0.5 × 0.5 cm2 and 0.8 × 0.8 cm2. Significant differences in between beams of a given energy but with and without flattening filters are found for measurements made in small fields (<1.5 cm) at a given linac. Differences in are also found when measurements are made at different linacs using the same beam energy filtration combination; for the PTW microDiamond detector, these differences were found to be around 6% and were considered as significant.ConclusionsSelection of two reference detectors, EBT3 films and W1 plastic scintillator, and use of an analytical function, is a novel approach for the determination of for small static fields in megavoltage photon beams. Large set of data for seven solid‐state detectors and four beam energies determined on two linacs by a single group of researchers can be considered a valuable supplement to the literature and the TRS‐483 dataset.
Performance of Diploid and Triploid Westslope Cutthroat Trout Fry Stocked into Idaho Alpine Lakes
Authors: Cassinelli John D. , Meyer Kevin A. , Koenig Martin K. , Vu Ninh V. , Campbell Matthew R. 
Published: December 2018

Abstract
Anglers value alpine lakes as providing a scenic, backcountry fishing experience that is seldom found in other fisheries. However, trout introduced into alpine lakes often pose a risk to native salmonids in downstream habitats by establishing source populations in headwater locations. Although the stocking of sterile triploid trout can reduce this risk, poststocking performance should be equivalent to that of diploid fish before fisheries managers and anglers consider triploid stocking to be ideal. In this study, three different mechanical pressure treatments were tested to create mixed-sex triploid Westslope Cutthroat Trout Oncorhynchus clarkii lewisi; at 65,500.19 kPa (9,500 psi) applied for 5 min at 300 Celsius-minutes after fertilization, triploid induction rates were 100%, and egg survival to eye-up was only 8% lower than that for diploids. Fry were stocked into 51 alpine lakes (25 with triploids and 26 with diploids), and fish were sampled 3 years later. Gill-net catch rates, growth, and condition did not differ between stocked diploid and triploid fish. General linear models revealed that test fish were larger and in better condition in lakes with fewer total fish (indicating a density-dependent influence on growth and condition) and were also in better condition in lower-elevation lakes containing a higher percentage of shallow habitat. Ploidy level was not included in the most plausible model for any of the response variables. Our results indicate that triploid Westslope Cutthroat Trout can easily be created by using pressure treatment of fertilized eggs and appear to be a suitable alternative to diploids in alpine lake stocking programs. Our study suggests that the use of triploid Westslope Cutthroat Trout in alpine lakes similar to those we studied would prevent hybridization with native salmonids in adjacent habitats without reducing the abundance, size, or condition of fish available to anglers in the lakes where they are stocked.
Consistently High Trophic Overlap between Invasive White Perch and Native Black Crappies in Southeastern Reservoirs
Authors: Feiner Zachary S. , Brey Marybeth K. , Burgett Caroline 
Published: December 2018

Abstract
The detrimental impacts of invasive species often occur through deleterious trophic interactions (e.g., competition) with native species. However, the potential for competitive interactions between species may vary among systems, among seasons, or throughout the species’ ontogeny, requiring a thorough examination of trophic niches to determine whether overlap exists and to elucidate the likelihood of competition. The Black Crappie Pomoxis nigromaculatus is a popular game fish species across the United States, but recent invasions of White Perch Morone americana, which exploit a similar trophic niche, into southern reservoirs represent a major concern for the continued sustainability of Black Crappie fisheries. We examined the trophic niches of these species throughout their ontogeny in two North Carolina reservoirs during 2009 and 2010 using a combination of diet content and stable isotope analyses. Extensive and significant similarities in diet composition and isotopic niche overlap existed between Black Crappies and White Perch throughout their ontogeny and across seasons in both systems. Overlap was particularly high between smaller (&lt;200-mm), invertivorous Black Crappies and all sizes of White Perch. This overlap suggests that if invertebrate resources become limited, competition during the juvenile stage could reduce growth rates and survival of young Black Crappies. By evaluating variation in the trophic niches of each species among seasons, body sizes, and reservoirs, we conclude that the potential for competitive interactions between White Perch and Black Crappie is high in southern reservoirs. Management options to either reduce White Perch abundance or prevent their spread to novel habitats may be necessary to sustain native and supplemented Black Crappie populations that are potentially vulnerable to White Perch invasions.
Discovery of Novel Molecular Frameworks of Farnesoid X Receptor Modulators by Ensemble Machine Learning
Authors: Merk Daniel , Grisoni Francesca , Schaller Kay , Friedrich Lukas , Schneider Gisbert 
Published: December 2018

AbstractInvited for this month's cover picture is the group of Prof. Dr. Gisbert Schneider from the Swiss Federal Institute of Technology (ETH) Zurich (Switzerland). The cover picture illustrates the application of machine‐learning methods to expand the chemical space of farnesoid X receptor (FXR)‐targeting small molecules, by employing an ensemble of three complementary machine‐learning approaches (counter‐propagation artificial neural network, k‐nearest neighbor learner, and three‐dimensional pharmacophore model). Read the full text of their Full Paper at 10.1002/open.201800156.
Chemical modification of cellulose nanocrystals and their application in thermoplastic starch (TPS) and poly(3‐hydroxybutyrate) (P3HB) nanocomposites
Authors: Ribeiro Paulo Leonardo Lima , Figueiredo Tamiris Vilas Boas , Moura Lívia Eloy , Druzian Janice Izabel 
Published: December 2018

The effect of sulfated (original), carboxylated (oxidized), and Jeffamines M2005‐grafted cellulose nanocrystals (CNCs) on the barrier and mechanical properties of thermoplastic starch (TPS) and poly(3‐hydroxybutyrate) (P(3HB)) matrices was investigated. CNCs were first oxidized via a catalytic reaction using NaClO as an oxidant and then grafted with an amine‐terminated ethylene oxide (EO)/propylene oxide (PO) copolymer (Jeffamine) by an amine‐acid coupling reaction. A degree of oxidation (DO) of 0.108 (mol/mol of anhydroglucose) was attempted for the carboxylated CNCs, whereas a degree of substitution (DS) of 0.04 (mol/mol of anhydroglucose) was determined for the M2005‐grafted CNCs. These values indicated satisfactory reactive process, with yields of 68% and 47.3% for the carboxylation and peptide coupling reactions, respectively. Fourier‐transform infrared spectroscopy (FTIR) analysis showed bands at 1643 cm−1 and 1550 cm−1 in the spectrum of M2005‐grafted CNCs, which qualitatively indicated the amide bond formation. In addition, the morphology and the zeta potential of modified CNCs ensured their homogeneity, stability, and surface degree of charge. In spite of a decrease in the solubility in water of the modified crystals, the procedure of chemical modification used avoided any variation in their crystalline structure and thermal stability. Then, the incorporation of sulfated, oxidized, or M2005‐grafted CNCs in matrices of TPS and P(3HB) allowed to produce reinforced nanocomposite films, with excellent barrier properties. Therefore, the chemical compatibility between CNCs and the polymer matrices is essential to produce attractive nanocomposites with improved mechanical properties for industrial applications.
Neural correlates of the effect of implementation intention on prospective memory
Authors: Chen Xing‐Jie , Liu Lu‐Lu , Wang Ya , Yang Tian‐Xiao , Huang Jia , Li Ke , Zeng Ya‐Wei , Cheung Eric F.C. , Shum David H.K. , van Amelsvoort Therese , Chan Raymond C.K. 
Published: December 2018

AbstractProspective memory (PM) refers to the ability to remember to do something in the future. Implementation intention refers to a self‐regulatory strategy in the form of “If …, then …” planning that can improve PM performance. However, the neural basis of the effect of implementation intention on PM remains unclear, as do the phases of PM that are affected by implementation intention. This study aimed to address these issues. Healthy participants were randomly assigned to the implementation intention (n = 18) and typical instruction (n = 20) conditions. All of them underwent functional magnetic resonance imaging (fMRI) scanning when performing a PM task, which differentiated encoding, maintenance, and execution phases. Results demonstrated that participants in the implementation intention group showed different brain activations compared to participants in the typical instruction group. During the encoding phase, the implementation intention group showed increased activations in the inferior frontal gyrus (BA 10) and supramarginal gyrus (BA 40) compared to the typical instruction group; during the maintenance phase, the typical instruction group showed stronger activations in the inferior frontal gyrus (BA 46) than the implementation intention group; during the execution phase, the typical instruction group showed increased activations in the precentral gyrus (BA 6) and middle frontal gyrus (BA 8) than the implementation intention group. These results demonstrated the neural correlates of implementation intention on PM in different phases, and support the conclusion of our previous review based on fMRI evidence that implementation intention's improvement of PM performance is not fully automatic.
Identification of Saliva Proteins of the Spider Mite Tetranychus evansi by Transcriptome and LC–MS/MS Analyses
Authors: Huang Hai‐Jian , Cui Jia‐Rong , Chen Lei , Zhu Yu‐Xi , Hong Xiao‐Yue 
Published: December 2018

AbstractThe spider mite Tetranychus evansi has a remarkable ability to suppress and manipulate plant defenses, which makes it an ideal model to investigate plant–herbivores interactions. In this study, a de novo assembly of the transcriptome of T. evansi is performed and the proteins in its secreted saliva by LC–MS/MS are characterized. A total of 29 365 unigenes are assembled and 136 saliva proteins are identified. Comparative analysis of the saliva proteins in T. evansi, T. truncatus, and T. urticae shows that 64 protein groups are shared by at least two Tetranychus species, and 52 protein groups are specifically identified in T. evansi. In addition, some saliva proteins are common in arthropod species, while others are species‐specific. These results will help to elucidate the molecular mechanisms by which T. evansi modulates plant defenses.
Cytomine: Toward an Open and Collaborative Software Platform for Digital Pathology Bridged to Molecular Investigations
Authors: Rubens Ulysse , Hoyoux Renaud , Vanosmael Laurent , Ouras Mehdy , Tasset Maxime , Hamilton Christopher , Longuespée Rémi , Marée Raphaël 
Published: December 2018

PurposeDigital histology is being increasingly used in research and clinical applications. In parallel, new tissue imaging methods (e.g., imaging mass spectrometry) are currently regarded as very promising approaches for better molecular diagnosis in pathology. However, these new data sources are still often underexploited because of the lack of collaborative software to share and correlate information for multimodal analysis.Experimental designThe open science paradigm is followed to develop new features in the web‐based Cytomine software to support next‐generation digital pathology bridged to molecular investigations.ResultsNew open‐source developments allow to explore whole‐slide classical histology with Matrix Assisted Laser Desorption Ionisation (MALDI) imaging and to support preprocessing for biomarker discovery using laser microdissection‐based microproteomics.Conclusions and clinical relevanceThe updated version of Cytomine is the first open and web‐based tool to enable sharing data from classical histology, molecular imaging, and cell counting for proteomics preprocessing. It holds good promise to fulfill imminent needs in molecular histopathology.
Ex vivo treatment of prostate tumor tissue recapitulates in vivo therapy response
Authors: Zhang Wenhao , van Weerden Wytske M. , de Ridder Corrina M. A. , Erkens‐Schulze Sigrun , Schönfeld Edgar , Meijer Titia G. , Kanaar Roland , van Gent Dik C. , Nonnekens Julie 
Published: December 2018

BackgroundIn vitro models of prostate cancer (PCa) are not always reliable to evaluate anticancer treatment efficacy. This limitation may be overcome by using viable tumor slice material. Here we report on the establishment of an optimized ex vivo method to culture tissue slices from patient‐derived xenografts (PDX) of prostate cancer (PCa), to assess responses to PCa treatments.MethodsThree PDX models were used that are characterized by different androgen receptor (AR) expression and different homology directed DNA repair capacities, due to a breast cancer associated two (BRCA2) wild‐type or mutated status. Tumors were removed from mice, sliced using a vibratome and cultured for a maximum of 6 days. To test the sensitivity to androgen antagonist, tumor slices from the AR‐expressing and AR‐negative PDX tumors were treated with the anti‐androgen enzalutamide. For sensitivity to DNA repair intervention, tumors slices from BRCA2 wild‐type and mutated PDXs were treated with the poly (ADP‐ribose) polymerase‐1 inhibitor olaparib. Treatment response in these tumor slices was determined by measuring slice morphology, cell proliferation, apoptosis, AR expression level, and secretion of prostate specific antigen (PSA).ResultsWe compared various culture conditions (support materials, growth media, and use of a 3D smooth rocking platform) to define the optimal condition to maintain tissue viability and proliferative capacity up to least 6 days. Under optimized conditions, enzalutamide treatment significantly decreased proliferation, increased apoptosis, and reduced AR‐expression and PSA secretion of AR‐expressing tumor slices compared to AR‐negative slices, that did not respond to the intervention. Olaparib treatment significantly increased cell death in BRCA2 mutated tumors slices as compared to slices from BRCA2 wild type tumors.ConclusionsEx vivo treatment of PCa PDX tumor slices with enzalutamide and olaparib recapitulates responses previously observed in vivo. The faithful retention of tissue structure and function in this ex vivo model offers an ideal opportunity for treatment efficacy screening, thereby reducing costs and numbers of experimental animals.
Residue‐level determinants of angiopoietin‐2 interactions with its receptor Tie2
Authors: Bakhman Anna , Rabinovich Eitan , Shlamkovich Tomer , Papo Niv , Kosloff Mickey 
Published: December 2018

AbstractWe combined computational and experimental methods to interrogate the binding determinants of angiopoietin‐2 (Ang2) to its receptor tyrosine kinase (RTK) Tie2—a central signaling system in angiogenesis, inflammation, and tumorigenesis. We used physics‐based electrostatic and surface‐area calculations to identify the subset of interfacial Ang2 and Tie2 residues that can affect binding directly. Using random and site‐directed mutagenesis and yeast surface display (YSD), we validated these predictions and identified additional Ang2 positions that affected receptor binding. We then used burial‐based calculations to classify the larger set of Ang2 residues that are buried in the Ang2 core, whose mutations can perturb the Ang2 structure and thereby affect interactions with Tie2 indirectly. Our analysis showed that the Ang2‐Tie2 interface is dominated by nonpolar contributions, with only three Ang2 and two Tie2 residues that contribute electrostatically to intermolecular interactions. Individual interfacial residues contributed only moderately to binding, suggesting that engineering of this interface will require multiple mutations to reach major effects. Conversely, substitutions in substantially buried Ang2 residues were more prevalent in our experimental screen, reduced binding substantially, and are therefore more likely to have a deleterious effect that might contribute to oncogenesis. Computational analysis of additional RTK‐ligand complexes, c‐Kit‐SCF and M‐CSF‐c‐FMS, and comparison to previous YSD results, further show the utility of our combined methodology.
Structure and function insights garnered from in silico modeling of the thrombospondin type‐1 domain‐containing 7A antigen
Authors: Stoddard Shana V. , Welsh Colin L. , Palopoli Maggie M. , Stoddard Serena D. , Aramandla Mounika P. , Patel Riya M. , Ma Hong , Beck Laurence H. 
Published: December 2018

AbstractThe thrombospondin type‐1 domain containing 7A (THSD7A) protein is known to be one of the antigens responsible for the autoimmune disorder idiopathic membranous nephropathy. The structure of this antigen is currently unsolved experimentally. Here we present a homology model of the extracellular portion of the THSD7A antigen. The structure was evaluated for folding patterns, epitope site prediction, and function was predicted. Results show that this protein contains 21 extracellular domains and with the exception of the first two domains, has a regular repeating pattern of TSP‐1‐like followed by F‐spondin‐like domains. Our results indicate the presence of a novel Trp‐ladder sequence of WxxxxW in the TSP‐1‐like domains. Of the 21 domains, 18 were shown to have epitope binding sites as predicted by epitopia. Several of the F‐spondin‐like domains have insertions in the canonical TSP fold, most notably the coiled coil region in domain 4, which may be utilized in protein‐protein binding interactions, suggesting that this protein functions as a heparan sulfate binding site.
Efficacy of SMTP‐7, a small‐molecule anti‐inflammatory thrombolytic, in embolic stroke in monkeys
Authors: Suzuki Eriko , Nishimura Naoko , Yoshikawa Tetsuya , Kunikiyo Yudai , Hasegawa Keiko , Hasumi Keiji 
Published: December 2018

AbstractSMTP‐7 (Stachybotrys microspora triprenyl phenol‐7) is a small molecule that promotes thrombolysis and suppresses inflammation possibly through plasminogen modulation and soluble epoxide hydrolase (sEH) inhibition, respectively. Here, we demonstrate an efficacy of SMTP‐7 in a severe embolic stroke model in monkeys. The middle cerebral artery was embolized by an autologous blood clot. Saline, SMTP‐7, or tissue‐type plasminogen activator (t‐PA) (n = 5 in each group) was given after 3 hours, and neurologic deficit scoring and infarct characterization were performed after 24 hours. Hemorrhagic infarct‐accompanied premature death was observed for two animals in t‐PA group. SMTP‐7 treatment significantly reduced the sizes of infarct by 65%, edema by 37%, and clot by 55% compared to saline treatment. Plasma levels of the products of plasminogen activation (plasmin‐α2‐antiplasmin complex) and sEH reaction (dihydroxyeicosatrienoic acid) in SMTP‐7 group were 794% (P < 0.05) and 60% (P = 0.085) compared to saline group, respectively. No significant changes in the plasma levels of MMP‐9, CRP, MCP‐1, and S100B were found. There was an inverse correlation between plasmin‐α2‐antiplasmin complex level and infarct volume (r = 0.93, P < 0.05), suggesting a role of thrombolysis in the SMTP‐7 action to limit infarct development. In conclusion, SMTP‐7 is effective in treating severe embolic stroke in monkeys under conditions where t‐PA treatment tends to cause hemorrhagic infarct‐associated premature death.
Quantum Transport Properties of an Exciton Insulator/Superconductor Hybrid Junction
Authors: Bercioux Dario , Bujnowski Bogusz , Bergeret F. Sebastián 
Published: December 2018

AbstractA theoretical study of electronic transport in a hybrid junction consisting of an excitonic insulator sandwiched between a normal and a superconducting electrode is presented. The normal region is described as a two‐band semi‐metal and the superconducting lead as a two‐band superconductor. In the excitonic insulator region, the coupling between carriers in the two bands leads to an excitonic condensate and a gap Γ in the quasi‐particle spectrum. Four different scattering processes at both interfaces are identified: Two types of normal reflection, intra‐ and inter‐band; and two different Andreev reflections, one retro‐reflective within the same band and one specular reflective between the two bands. The differential conductance of the structure is calculated and the existence of a minimum at voltages of the order of the excitonic gap is shown. The findings are useful toward the detection of the excitonic condensate and provide a plausible explanation for recent transport experiments on HgTe quantum wells and InAs/GaSb bilayer systems.