bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fitting NTCP models to SBRT dose and carotid blowout syndrome data
Authors: Mavroidis Panayiotis , Grimm Jimm , Cengiz Mustafa , Das Shiva , Tan Xianming , Yazici Gozde , Ozyigit Gokhan 
Published: August 2018

PurposeTo estimate the radiobiological parameters of three popular NTCP models, which describe the dose–response relations of carotid blowout syndrome (CBOS) after stereotactic body radiotherapy (SBRT). To evaluate the goodness‐of‐fit and the correlation of those models with CBOS.MethodsThe study included 61 patients with inoperable locally recurrent head and neck cancer treated with SBRT using CyberKnife (Accuray, Sunnyvale, CA) at the Department of Radiation Oncology, Hacettepe University, Ankara, Turkey between June 2007 and March 2011. The dose‐volume histograms of the internal carotid were exported from the plans of all the patients. The follow‐up results regarding the end point of carotid blowout syndrome were collected retrospectively. Initially, univariable analyses (Wilcoxon rank‐sum or Chi‐square tests) and a multivariate logistic regression analysis were performed between the outcome data and a list of clinical and treatment factors to identify significant correlations. Additionally, the Lyman–Kutcher–Burman (LKB), Relative Seriality (RS), and Logit NTCP models were used to fit the clinical data. The fitting of the different models was assessed through the area under the receiver operating characteristic curve (AUC), Akaike information criterion (AIC), and Odds Ratio methods.ResultsThe clinical/treatment factors that were found to have a significant or close to significant correlations with acute CBOS were Age at the time of CK (P‐value = 0.03), Maximum carotid dose (P‐value = 0.06), and CK prescription dose (P‐value = 0.08). Using Dmax, physical DVH, and EQD2 Gy‐DVH as the dosimetric metrics in the NTCP models, the derived LKB model parameters were: (a) D50 = 45.8 Gy, m = 0.24, n = n/a; (b) D50 = 44.8 Gy, m = 0.28, n = 0.01; and (c) D50 = 115.8 Gy, m = 0.45, n = 0.01, respectively. The AUC values for the dosimetric metrics were 0.70, 0.68, and 0.61, respectively. The differences in AIC between the different models were less than 2 and ranged within ±0.9.ConclusionThe maximum dose to the internal carotid less than 34 Gy appears to significantly reduce the risk for CBOS. Age at the time of CK, Maximum carotid dose, and CK prescription dose were also found to correlate with CBOS. The values of the parameters of three NTCP models were determined for this endpoint. A threshold of gEUD <34.5 Gy appears to be significantly associated with lower risks of CBOS.
Feedback regulation by trehalose 6‐phosphate slows down starch mobilization below the rate that would exhaust starch reserves at dawn in Arabidopsis leaves
Authors: dos Anjos Letícia , Pandey Prashant Kumar , Moraes Thiago Alexandre , Feil Regina , Lunn John E. , Stitt Mark 
Published: August 2018

AbstractTrehalose 6‐phosphate (Tre6P), a sucrose signaling metabolite, inhibits transitory starch breakdown in Arabidopsis (Arabidopsis thaliana) leaves and potentially links starch turnover to leaf sucrose status and demand from sink organs (Plant Physiology, 163, 2013, 1142). To investigate this relationship further, we compared diel patterns of starch turnover in ethanol‐inducible Tre6P synthase (iTPS) lines, which have high Tre6P and low sucrose after induction, with those in sweet11;12 sucrose export mutants, which accumulate sucrose in their leaves and were predicted to have high Tre6P. Short‐term changes in irradiance were used to investigate whether the strength of inhibition by Tre6P depends on starch levels. sweet11;12 mutants had twofold higher levels of Tre6P and restricted starch mobilization. The relationship between Tre6P and starch mobilization was recapitulated in iTPS lines, pointing to a dominant role for Tre6P in feedback regulation of starch mobilization. Tre6P restricted mobilization across a wide range of conditions. However, there was no correlation between the level of Tre6P and the absolute rate of starch mobilization. Rather, Tre6P depressed the rate of mobilization below that required to exhaust starch at dawn, leading to incomplete use of starch. It is discussed how Tre6P interacts with the clock to set the rate of starch mobilization.
Failure prediction with reporting delay
Authors: Kann Lennart , Sobotta Benjamin , Göb Rainer 
Published: August 2018

AbstractWe consider a parametric framework for predicting the future number of failures based on censored and right truncated field data. This type of data regularly occurs in industrial field data with reporting delays. This article presents methods to account for the truncation in this prediction problem. Our simulations show the influence of truncation on the coverage of the resulting prediction interval. The coverage properties of the introduced methods are evaluated. The adjusted prediction intervals show improved coverage properties compared with the unmodified prediction interval based on the truncated data.
When Immunity Means Impunity: Lessons for Canada from Recent Cases on State Immunity from Execution
Authors: ROSE KELSEY A. 
Published: August 2018

AbstractThis article reviews recent cases from Canada, Australia, the United Kingdom, and the United States involving state immunity from execution and suggests the burden on creditors to disprove this immunity is excessively onerous. While the problem is much belaboured, few solutions have been explored or implemented. This article proposes that in the Canadian context, adjusting the evidentiary burden on parties to an execution immunity dispute would improve the ability of creditors to obtain fair payment from debtor states, without infringing state sovereignty.
DO OPEN-POLLINATED MAIZE VARIETIES PERFORM BETTER THAN HYBRIDS IN AGROFORESTRY SYSTEMS?
Authors: NDOLI ALAIN , BAUDRON FRÉDÉRIC , SIDA TESFAYE SHIFERAW , SCHUT ANTONIUS G. T. , VAN HEERWAARDEN J. , GILLER KEN E. 
Published: August 2018

SUMMARYA large body of evidence demonstrates the agronomic superiority of maize hybrids over open-pollinated varieties (OPVs) in intensive monoculture. However, comparisons of the performance of hybrids and OPVs in agroforestry systems are scarce. In this study, the performance of four maize hybrids and four OPVs is compared in sole crop and under mature trees. Experiments were conducted on-farm during four seasons in Bugesera, Rwanda and two seasons in Meki, Ethiopia. Two tree species were selected in Bugesera (Grevillea robusta and Senna spectabilis) and one in Meki (Acacia tortilis), and three farms were selected for each tree species, each including two plots with almost identical trees in their centre and two plots without tree. In Bugusera, grain yield was higher for hybrids (2 Mg ha−1) than for OPVs (1.5 Mg ha−1), and the presence of trees reduced the harvest index more in OPVs than in hybrids. In this region, the estimated reduction in grain yield due to the presence of trees was 0.9 and 1.1 Mg ha−1 in hybrids and OPVs, respectively, while estimated reduction in biomass was 1.5 and 1.7 Mg ha−1, respectively. In Meki, the grain yield of OPVs (2.08 Mg ha−1) and hybrids (2.04 Mg ha−1) did not differ and the presence of trees reduced their grain yields in the same manner. Our results showed that hybrids yielded more than OPVs under G. robusta and S. spectabilis in Bugesera but performed equally well under A. tortilis in Meki. We conclude that agroforestry farmers could benefit from growing hybrids in the equatorial savannahs of Rwanda, but that the choice between hybrid and OPV in equatorial savannahs of Ethiopia can simply be based on other factors such as seed costs and availability.
CONSIDERING THE FARM WORKFORCE AS PART OF FARMERS' INNOVATIVE BEHAVIOUR: A KEY FACTOR IN INCLUSIVE ON-FARM PROCESSES OF TECHNOLOGY AND PRACTICE ADOPTION
Authors: COFRE-BRAVO GABRIELA , ENGLER ALEJANDRA , KLERKX LAURENS , LEIVA-BIANCHI MARCELO , ADASME-BERRIOS CRISTIAN , CACERES CRISTIAN 
Published: August 2018

SUMMARYThe literature identifies multiple factors that can affect the adoption of new technologies and practices in agriculture to support farm innovation, such as farmers’ socio-economic characteristics and the characteristics of the promoted technology, among others. It has, however, scarcely contemplated the role of the farm workforce in technology and practice adoption. The objective of this study is (i) to describe innovative behaviour and its relation with farmers’ ability to collaborate with the workforce in the adoption process; and (ii) to associate this description with the level of adoption of certain technologies and practices. Structural equation modelling (bifactor model) was used to identify the components of innovative behaviour, and correlation analysis was used to determine the relationship between these components and adoption level. The results show that relevant components of innovative behaviour are farmers’ ability to generate and implement new ideas, to extend their networks and to involve the workforce in the adoption process. Worker involvement proved to be a key factor within the definition of farmers’ innovative behaviour, which additionally shows a positive and significant correlation with the level of adoption of technologies and practices. A main theoretical implication is that research on technology and practice adoption needs to move beyond looking at single owner-managers of (family) farms and incorporate workers into the unit of analysis. The practical and policy implications are that innovation support programmes should give more attention to workforce management, training and skills of owner-managers as transformative and inclusive leaders, as these are essential for technology and practice adoption, and more broadly for innovation capacity.
THE EFFECT OF GLOSS TYPE ON LEARNERS’ INTAKE OF NEW WORDS DURING READING
Authors: Warren Paul , Boers Frank , Grimshaw Gina , Siyanova-Chanturia Anna 
Published: August 2018

AbstractA reading experiment combining online and offline data evaluates the effect on second language learners’ reading behaviors and lexical uptake of three gloss types designed to clarify word meaning. These are (a) textual definition, (b) textual definition accompanied by picture, and (c) picture only. We recorded eye movements while intermediate learners of English read a story presented on-screen and containing six glossed pseudowords repeated three times each. Cumulative fixation counts and time spent on the pseudowords predicted posttest performance for form recall and meaning recognition, confirming findings of previous eye-tracking studies of vocabulary acquisition from reading. However, the total visual attention given to pseudowords and glosses was smallest in the condition with picture-only glosses, and yet this condition promoted best retention of word meaning. This suggests that gloss types differentially influence learners’ processing of novel words in ways that may elude the quantitative measures of attention captured by eye-tracking.
Microbial tryptophan catabolites in health and disease
Authors: Roager Henrik M. , Licht Tine R. 
Published: August 2018

AbstractAccumulating evidence implicates metabolites produced by gut microbes as crucial mediators of diet-induced host-microbial cross-talk. Here, we review emerging data suggesting that microbial tryptophan catabolites resulting from proteolysis are influencing host health. These metabolites are suggested to activate the immune system through binding to the aryl hydrocarbon receptor (AHR), enhance the intestinal epithelial barrier, stimulate gastrointestinal motility, as well as secretion of gut hormones, exert anti-inflammatory, anti-oxidative or toxic effects in systemic circulation, and putatively modulate gut microbial composition. Tryptophan catabolites thus affect various physiological processes and may contribute to intestinal and systemic homeostasis in health and disease.
Smooth tracking of visual targets distinguishes lucid REM sleep dreaming and waking perception from imagination
Authors: LaBerge Stephen , Baird Benjamin , Zimbardo Philip G. 
Published: August 2018

AbstractHumans are typically unable to engage in sustained smooth pursuit for imagined objects. However, it is unknown to what extent smooth tracking occurs for visual imagery during REM sleep dreaming. Here we examine smooth pursuit eye movements during tracking of a slow-moving visual target during lucid dreams in REM sleep. Highly similar smooth pursuit tracking was observed during both waking perception and lucid REM sleep dreaming, in contrast to the characteristically saccadic tracking observed during visuomotor imagination. Our findings suggest that, in this respect, the visual imagery that occurs during REM sleep is more similar to perception than imagination. The data also show that the neural circuitry of smooth pursuit can be driven by a visual percept in the absence of retinal stimulation and that specific voluntary shifts in the direction of experienced gaze within REM sleep dreams are accompanied by corresponding rotations of the physical eyes.
Epigenetic dysregulation of naive CD4+ T-cell activation genes in childhood food allergy
Authors: Martino David , Neeland Melanie , Dang Thanh , Cobb Joanna , Ellis Justine , Barnett Alice , Tang Mimi , Vuillermin Peter , Allen Katrina , Saffery Richard 
Published: August 2018

AbstractFood allergy poses a significant clinical and public health burden affecting 2–10% of infants. Using integrated DNA methylation and transcriptomic profiling, we found that polyclonal activation of naive CD4+ T cells through the T cell receptor results in poorer lymphoproliferative responses in children with immunoglobulin E (IgE)-mediated food allergy. Reduced expression of cell cycle-related targets of the E2F and MYC transcription factor networks, and remodeling of DNA methylation at metabolic (RPTOR,PIK3D,MAPK1,FOXO1) and inflammatory genes (IL1R,IL18RAP,CD82) underpins this suboptimal response. Infants who fail to resolve food allergy in later childhood exhibit cumulative increases in epigenetic disruption at T cell activation genes and poorer lymphoproliferative responses compared to children who resolved food allergy. Our data indicate epigenetic dysregulation in the early stages of signal transduction through the T cell receptor complex, and likely reflects pathways modified by gene–environment interactions in food allergy.
Linear mapping approximation of gene regulatory networks with stochastic dynamics
Authors: Cao Zhixing , Grima Ramon 
Published: August 2018

AbstractThe presence of protein–DNA binding reactions often leads to analytically intractable models of stochastic gene expression. Here we present the linear-mapping approximation that maps systems with protein–promoter interactions onto approximately equivalent systems with no binding reactions. This is achieved by the marriage of conditional mean-field approximation and the Magnus expansion, leading to analytic or semi-analytic expressions for the approximate time-dependent and steady-state protein number distributions. Stochastic simulations verify the method’s accuracy in capturing the changes in the protein number distributions with time for a wide variety of networks displaying auto- and mutual-regulation of gene expression and independently of the ratios of the timescales governing the dynamics. The method is also used to study the first-passage time distribution of promoter switching, the sensitivity of the size of protein number fluctuations to parameter perturbation and the stochastic bifurcation diagram characterizing the onset of multimodality in protein number distributions.
Element- and momentum-resolved electronic structure of the dilute magnetic semiconductor manganese doped gallium arsenide
Authors: Nemšák Slavomír , Gehlmann Mathias , Kuo Cheng-Tai , Lin Shih-Chieh , Schlueter Christoph , Mlynczak Ewa , Lee Tien-Lin , Plucinski Lukasz , Ebert Hubert , Di Marco Igor , Minár Ján , Schneider Claus M. , Fadley Charles S. 
Published: August 2018

AbstractThe dilute magnetic semiconductors have promise in spin-based electronics applications due to their potential for ferromagnetic order at room temperature, and various unique switching and spin-dependent conductivity properties. However, the precise mechanism by which the transition-metal doping produces ferromagnetism has been controversial. Here we have studied a dilute magnetic semiconductor (5% manganese-doped gallium arsenide) with Bragg-reflection standing-wave hard X-ray angle-resolved photoemission spectroscopy, and resolved its electronic structure into element- and momentum- resolved components. The measured valence band intensities have been projected into element-resolved components using analogous energy scans of Ga 3d, Mn 2p, and As 3d core levels, with results in excellent agreement with element-projected Bloch spectral functions and clarification of the electronic structure of this prototypical material. This technique should be broadly applicable to other multi-element materials.
Insights into degradation mechanism of N-end rule substrates by p62/SQSTM1 autophagy adapter
Authors: Kwon Do Hoon , Park Ok Hyun , Kim Leehyeon , Jung Yang Ouk , Park Yeonkyoung , Jeong Hyeongseop , Hyun Jaekyung , Kim Yoon Ki , Song Hyun Kyu 
Published: August 2018

Abstractp62/SQSTM1 is the key autophagy adapter protein and the hub of multi-cellular signaling. It was recently reported that autophagy and N-end rule pathways are linked via p62. However, the exact recognition mode of degrading substrates and regulation of p62 in the autophagic pathway remain unknown. Here, we present the complex structures between the ZZ-domain of p62 and various type-1 and type-2 N-degrons. The binding mode employed in the interaction of the ZZ-domain with N-degrons differs from that employed by classic N-recognins. It was also determined that oligomerization via the PB1 domain can control functional affinity to the R-BiP substrate. Unexpectedly, we found that self-oligomerization and disassembly of p62 are pH-dependent. These findings broaden our understanding of the functional repertoire of the N-end rule pathway and provide an insight into the regulation of p62 during the autophagic pathway.
The tumor suppressor menin prevents effector CD8 T-cell dysfunction by targeting mTORC1-dependent metabolic activation
Authors: Suzuki Junpei , Yamada Takeshi , Inoue Kazuki , Nabe Shogo , Kuwahara Makoto , Takemori Nobuaki , Takemori Ayako , Matsuda Seiji , Kanoh Makoto , Imai Yuuki , Yasukawa Masaki , Yamashita Masakatsu 
Published: August 2018

AbstractWhile menin plays an important role in preventing T-cell dysfunction, such as senescence and exhaustion, the regulatory mechanisms remain unclear. We found that menin prevents the induction of dysfunction in activated CD8 T cells by restricting the cellular metabolism. mTOR complex 1 (mTORC1) signaling, glycolysis, and glutaminolysis are augmented by menin deficiency. Rapamycin treatment prevents CD8 T-cell dysfunction in menin-deficient CD8 T cells. Limited glutamine availability also prevents CD8 T-cell dysfunction induced by menin deficiency, and its inhibitory effect is antagonized by α-ketoglutarate (α-KG), an intermediate metabolite of glutaminolysis. α-KG-dependent histone H3K27 demethylation seems to be involved in the dysfunction in menin-deficient CD8 T cells. We also found that α-KG activates mTORC1-dependent central carbon metabolism. These findings suggest that menin maintains the T-cell functions by limiting mTORC 1 activity and subsequent cellular metabolism.
Porous SnO2 nanoparticles based ion chromatographic determination of non-fluorescent antibiotic (chloramphenicol) in complex samples
Authors: Muhammad Nadeem , Rahman Abdul , Younis Muhammad Adnan , Subhani Qamar , Shehzad Khurram , Cui Hairong , Zhu Yan 
Published: August 2018

AbstractNowadays, there are rising concerns about the extensive use of the antibiotics such as chloramphenicol (CAP), has threatened the human life in the form of various vicious diseases. The limited selectivity and sensitivity of confirmatory techniques (UV and electrochemical) and non-fluorescence property of CAP make its determination a challenging task in the modern pharmaceutical analysis. In order to redeem the selective, sensitive and cost-effective fluorescence methodology, here by the dual role of synthesized porous SnO2 nanoparticles were exploited; (i) a porous sorbent in a µ-QuEChERS based sample preparation and as (ii) a stimulant for the transformation of non-fluorescent analytes namely CAP and p-nitrophenol (p-NP) into their respective fluorescent product. We report a green, simple, selective and cost effective ion chromatographic method for CAP sensitive determination in three complex matrices including milk, human urine and serum. The synthesized sorbent not only selectively adsorbed and degraded the matrix/interferences but also selectively reduced the non-fluorescent antibiotic CAP into a fluorescent species. This developed ion chromatographic method exhibited good selectivity, linearity (r2 ≥ 0.996) and limit of detection (LOD) was in the range 0.0201–0.0280 µg/kg. The inter- and intraday precisions were also satisfactory having a relative standard deviation (RSDs) less than 14.96% and excellent recoveries of CAP in the range of 78.3–100.2% were retrieved in various complex samples.
Time-reversal invariant resonant backscattering on a topological insulator surface driven by a time-periodic gate voltage
Authors: Deng Ming-Xun , Ma R. , Luo Wei , Shen R. , Sheng L. , Xing D. Y. 
Published: August 2018

AbstractWe study the scattering of the Dirac electrons by a point-like nonmagnetic impurity on the surface of a topological insulator, driven by a time-periodic gate voltage. It is found that, due to the doublet degenerate crossing points of different Floquet sidebands, resonant backscattering can happen for the surface electrons, even without breaking the time-reversal (TR) symmetry of the topological surface states (TSSs). The energy spectrum is reshuffled in a way quite different from that for the circularly polarized light, so that new features are exhibited in the Friedel oscillations of the local charge and spin density of states. Although the electron scattering is dramatically modified by the driving voltage, the 1/ρ scale law of the spin precession persists for the TSSs. The TR invariant backscattering provides a possible way to engineer the Dirac electronic spectrum of the TSSs, without destroying the unique property of spin-momentum interlocking of the TSSs.
Finding hens in a haystack: Consistency of movement patterns within and across individual laying hens maintained in large groups
Authors: Rufener C. , Berezowski J. , Maximiano Sousa F. , Abreu Y. , Asher L. , Toscano M. J. 
Published: August 2018

AbstractWe sought to objectively quantify and compare the recorded movement and location patterns of laying hens within a commercial system. Using a custom tracking system, we monitored the location within five zones of a commercial aviary for 13 hens within a flock of 225 animals for a contiguous period of 11 days. Most hens manifested a hen-specific pattern that was (visually) highly consistent across days, though, within that consistency, manifested stark differences between hens. Three different methods were used to classify individual daily datasets into groups based on their similarity: (i) Linear Discriminant Analysis based on six summary variables (transitions into each zone) and total transitions; (ii) Hierarchical Clustering, a naïve clustering analysis technique, applied to summary variables and iii) Hierarchical Clustering applied to dissimilarity matrices produced by Dynamic Time Warping. The three methods correctly classified more than 85% of the hen days and provided a unique means to assess behaviour of a system indicating a considerable degree of complexity and structure. We believe the current effort is the first to document these location and movement patterns within a large, complex commercial system with a large potential to influence the assessment of animal welfare, health, and productivity.