bluuebunny/crossref_metadata_2025_split huggingface dataset:
‘Life communication’ after the 2011 Fukushima nuclear disaster: what experts need to learn from residential non-scientific rationality
Authors: Ochi Sae 
Published: December 2020

ABSTRACT
After chemical, biological, radiological, nuclear or explosive (CBRNE) disasters, trepidation and infodemics about invisible hazards may cause indirect casualties in the affected society. Effective communication regarding technical issues between disaster experts and the residents is key to averting such secondary impacts. However, misconceptions about scientific issues and mistrust in experts frequently occur even with intensive and sincere communications. This miscommunication is usually attributed to residents’ conflicts with illiteracy, emotion, value depositions and ideologies. However, considering that communication is an interactive process, there are likely to be additional factors attributable to experts. This article aims to summarize the gaps in rationality between experts and residents observed after the 2011 Fukushima nuclear disaster to describe how residents perceived experts. There were discrepancies in the perception of ‘facts’, the perception of probability, the interpretation of risk comparison, what were included as risk trade-offs, the view of the disaster, whose behavior would be changed by the communication and whether risk should be considered a science. These findings suggest that there was a non-scientific rationality among residents, which often exercised a potent influence on everyday decision-making. It might not be residents but experts who need to change their behavior. The discrepancies described in this article are likely to apply to communications following any CBRNE disasters that affect people’s lives, such as the current COVID-19 pandemic. Therefore, our experiences in Fukushima may provide clues to averting mutual mistrust between experts and achieving better public health outcomes during and after a crisis.
Comprehensive analysis for detecting radiation-specific molecules expressed during radiation-induced rat thyroid carcinogenesis
Authors: Kurohama Hirokazu , Matsuda Katsuya , Kishino Mio , Yoshino Miruki , Yamaguchi Yuka , Matsuu-Matsuyama Mutsumi , Kondo Hisayoshi , Mitsutake Norisato , Kinoshita Akira , Yoshiura Ko-ichiro , Nakashima Masahiro 
Published: December 2020

ABSTRACTAlthough the association between radiation exposure and thyroid carcinogenesis is epidemiologically evident, ’true’ radiation-induced cancers cannot be identified from biological evidence of radiation-associated cases. To assess the individual risk for thyroid cancer due to radiation exposure, we aimed to identify biomarkers that are specifically altered during thyroid carcinogenesis after irradiation in a time-dependent manner in an animal model. Thyroid glands were obtained from rats (n = 175) at 6–16 months after local X-ray (0.1–4 Gy) irradiation of the neck at 7 weeks of age. The gene expression profile in thyroid glands was comprehensively analyzed using RNA microarray. Subsequently, the expression levels of the genes of interest were verified using droplet digital PCR (ddPCR). The expression level of candidate genes as biomarkers for irradiated thyroid was examined in a randomized, controlled, double-blind validation study (n = 19) using ddPCR. The incidence of thyroid cancer increased in a dose- and time-dependent manner and was 33% at 16 months after irradiation with 4 Gy. The Ki-67 labeling index in non-tumorous thyroid was significantly higher in the exposed group than in the control. Comprehensive analysis identified radiation-dependent alteration in 3329 genes. Among them, ddPCR revealed a stepwise increase in CDKN1A expression from early pre-cancerous phase in irradiated thyroid compared to that in the control. The irradiated thyroids were accurately distinguished (positive predictive value 100%, negative predictive value 69%) using 11.69 as the cut-off value for CDKN1A/β-actin. Thus, CDKN1A expression can be used as a biomarker for irradiated thyroid glands at the pre-cancerous phase.
Thoracoabdominal flap reconstruction after resection of superficial soft-tissue sarcomas in the chest wall
Authors: Sakamoto Akio , Noguchi Takashi , Matsuda Shuichi 
Published: December 2020

Abstract
The thoracoabdominal flap is a rotation flap, and is well known for reconstruction of defects following resections for breast cancer, but the flap is not well known for reconstructing defects following resections of soft-tissue sarcomas involving the chest wall. Here we present two patients with superficial chest wall sarcomas consisting of a dermatofibrosarcoma protuberans in a 42-year-old man and a recurrent myxofibrosarcoma in a 76-year-old man. The tumors were resected with the surrounding tissue. The defect was reconstructed with a thoracoabdominal flap elevated from the ipsilateral thorax (medially-based flap). Neither case developed necrosis of the flap or reduced shoulder range of motion. The chest wall presents few options for a donor vessel. The thoracoabdominal flap has an axial blood supply and does not require a microsurgical procedure. A thoracoabdominal flap is a suitable reconstruction option for a defect after the resection of a superficial soft-tissue sarcoma in the chest wall.
Temperature and evaporative demand drive variation in stomatal and hydraulic traits across grape cultivars
Authors: Bartlett Megan K , Sinclair Gabriela 
Published: December 2020

AbstractSelection for crop cultivars has largely focused on reproductive traits, while the impacts of global change on crop productivity are expected to depend strongly on the vegetative physiology traits that drive plant resource use and stress tolerance. We evaluated relationships between physiology traits and growing season climate across wine grape cultivars to characterize trait variation across European growing regions. We compiled values from the literature for seven water use and drought tolerance traits and growing season climate. Cultivars with a lower maximum stomatal conductance were associated with regions with a higher mean temperature and mean and maximum vapor pressure deficit (r2=0.39–0.65, P&lt;0.05, n=14–29). Cultivars with greater stem embolism resistance and more anisohydric stomatal behavior (i.e. a more negative water potential threshold for 50% stomatal closure) were associated with cooler regions (r2=0.48–0.72, P&lt;0.03, n=10–29). Overall, cultivars grown in warmer, drier regions exhibited traits that would reduce transpiration and conserve soil water longer into the growing season, but potentially increase stomatal and temperature limitations on photosynthesis under future, hotter conditions.
Restriction of cytosolic sucrose hydrolysis profoundly alters development, metabolism, and gene expression in Arabidopsis roots
Authors: Pignocchi Cristina , Ivakov Alexander , Feil Regina , Trick Martin , Pike Marilyn , Wang Trevor L , Lunn John E , Smith Alison M 
Published: December 2020

AbstractPlant roots depend on sucrose imported from leaves as the substrate for metabolism and growth. Sucrose and hexoses derived from it are also signalling molecules that modulate growth and development, but the importance for signalling of endogenous changes in sugar levels is poorly understood. We report that reduced activity of cytosolic invertase, which converts sucrose to hexoses, leads to pronounced metabolic, growth, and developmental defects in roots of Arabidopsis (Arabidopsis thaliana) seedlings. In addition to altered sugar and downstream metabolite levels, roots of cinv1 cinv2 mutants have reduced elongation rates, cell and meristem size, abnormal meristematic cell division patterns, and altered expression of thousands of genes of diverse functions. Provision of exogenous glucose to mutant roots repairs relatively few of the defects. The extensive transcriptional differences between mutant and wild-type roots have hallmarks of both high sucrose and low hexose signalling. We conclude that the mutant phenotype reflects both low carbon availability for metabolism and growth and complex sugar signals derived from elevated sucrose and depressed hexose levels in the cytosol of mutant roots. Such reciprocal changes in endogenous sucrose and hexose levels potentially provide rich information about sugar status that translates into flexible adjustments of growth and development.
Excitation of decayless kink oscillations by random motion
Authors: Ruderman M S , Petrukhin N S 
Published: December 2020

Abstract
We study kink oscillations of a straight magnetic tube with a transitional region at its boundary. The tube is homogeneous in the axial direction. The plasma density monotonically decreases in the transitional region from its value inside the tube to that in the surrounding plasma. The plasma motion is described by the linear magnetohydrodynamic equations in the cold plasma approximation. We use the ideal equations inside the tube and in the surrounding plasma, but take viscosity into account in the transitional region. We also use the thin tube and thin transitional or boundary layer (TTTB) approximation. Kink oscillations are assumed to be driven by a driver at the tube footpoint. We derive the equation describing the displacement in the fundamental mode and overtones. We use this equation to study kink oscillations both in the case of harmonic as well as random driving. In the case of random driving we assume that the driver is described by a stationary random function. The displacements in the fundamental mode and overtones are also described by stationary random functions. We derive the relation between the power spectra of the fundamental mode and all overtones and the power spectrum of the driver. We suggest a new method of obtaining information on the internal structure of coronal magnetic loops based on the shape of graphs of the power spectrum of the fundamental mode.
On the azimuthal alignment of quasars spin vector in large quasar groups and cosmic strings
Authors: Slagter Reinoud J , Miedema Pieter G 
Published: December 2020

Abstract
We find evidence of the alignment of the azimuthal angle of the spin vectors of quasars in their host galaxy in large quasar groups of different redshift. This effect could be explained by symmetry breaking of the scalar-gauge field of cosmic strings in the early universe. It is expected that this effect will be more profound for higher red shift.
Metformin: a novel promising option for fertility preservation during cyclophosphamide-based chemotherapy
Authors: Huang Chu-Chun , Chou Chia-Hung , Yang Yu-Shih , Ho Hong-Nerng , Shun Chia-Tung , Wen Wen-Fen , Chen Shee-Uan , Chen Mei-Jou 
Published: December 2020

Abstract
Cyclophosphamide (CP) could cause severe gonadotoxicity via imbalanced activation of primordial follicles through PI3K/AKT/mTOR activation. Whether metformin, a widely prescribed anti-diabetes agent with mTOR inhibitory effect, could preserve ovarian function against CP toxicity is unknown. Female C57BL/6 mice were randomized into seven groups (n = 11), including control, CP-alone, CP + metformin, CP + sirolimus or everolimus, metformin-alone and sirolimus-alone groups. The duration of pharmaceutical treatment was 4 weeks. CP treatment significantly impaired ovarian function and fertility in mice. CP + metformin treatment significantly attenuated the gonadotoxicity comparing to CP-alone treatment (primordial follicle count: 17.6 ± 4.2 versus 10.3 ± 2.7 follicles/high-power field; P = 0.027). CP + metformin treatment also tended to increase antral follicular count (5.4 ± 1.1 versus 2.5 ± 1.6 follicles/section), serum AMH levels (4.6 ± 1.2 versus 2.0 ± 0.8 ng/ml) and the litter size (4.2 ± 1.3 versus 1.5 ± 1.0 mice per pregnancy), compared with CP-alone group. Expression of phospho-mTOR and the number of TUNEL-positive granulosa cells increased after CP treatment and decreased in the CP + metformin groups, suggesting the mTOR inhibitory and anti-apoptotic effects of metformin. In in-vitro granulosa cell experiments, the anti-apoptotic effect of metformin was blocked after inhibiting p53 or p21 function, and the expression of p53 mRNA was blocked with AMPK inhibitor, suggesting that the anti-apoptotic effect was AMPK/p53/p21-mediated. In conclusion, concurrent metformin treatment during CP therapy could significantly preserve ovarian function and fertility and could be a promising novel fertility preserving agent during chemotherapy. The relatively acceptable cost and well-established long-term safety profiles of this old drug might prompt its further clinical application at a faster pace.
Identification of lysine isobutyrylation as a new histone modification mark
Authors: Zhu Zhesi , Han Zhen , Halabelian Levon , Yang Xiangkun , Ding Jun , Zhang Nawei , Ngo Liza , Song Jiabao , Zeng Hong , He Maomao , Zhao Yingming , Arrowsmith Cheryl H , Luo Minkui , Bartlett Michael G , Zheng Y George 
Published: December 2020

Abstract
Short-chain acylations of lysine residues in eukaryotic proteins are recognized as essential posttranslational chemical modifications (PTMs) that regulate cellular processes from transcription, cell cycle, metabolism, to signal transduction. Lysine butyrylation was initially discovered as a normal straight chain butyrylation (Knbu). Here we report its structural isomer, branched chain butyrylation, i.e. lysine isobutyrylation (Kibu), existing as a new PTM on nuclear histones. Uniquely, isobutyryl-CoA is derived from valine catabolism and branched chain fatty acid oxidation which is distinct from the metabolism of n-butyryl-CoA. Several histone acetyltransferases were found to possess lysine isobutyryltransferase activity in vitro, especially p300 and HAT1. Transfection and western blot experiments showed that p300 regulated histone isobutyrylation levels in the cell. We resolved the X-ray crystal structures of HAT1 in complex with isobutyryl-CoA that gleaned an atomic level insight into HAT-catalyzed isobutyrylation. RNA-Seq profiling revealed that isobutyrate greatly affected the expression of genes associated with many pivotal biological pathways. Together, our findings identify Kibu as a novel chemical modification mark in histones and suggest its extensive role in regulating epigenetics and cellular physiology.
In vitroselections with RNAs of variable length converge on a robust catalytic core
Authors: Popović Milena , Ellingson Alexander Q , Chu Theresa P , Wei Chenyu , Pohorille Andrew , Ditzler Mark A 
Published: December 2020

AbstractIn vitro selection is a powerful tool that can be used to understand basic principles of molecular evolution. We used in vitro selection to understand how changes in length and the accumulation of point mutations enable the evolution of functional RNAs. Using RNA populations of various lengths, we performed a series of in vitro experiments to select for ribozymes with RNA ligase activity. We identified a core ribozyme structure that was robust to changes in RNA length, high levels of mutagenesis, and increased selection pressure. Elaboration on this core structure resulted in improved activity which we show is consistent with a larger trend among functional RNAs in which increasing motif size can lead to an exponential improvement in fitness. We conclude that elaboration on conserved core structures is a preferred mechanism in RNA evolution. This conclusion, drawn from selections of RNAs from random sequences, is consistent with proposed evolutionary histories of specific biological RNAs. More generally, our results indicate that modern RNA structures can be used to infer ancestral structures. Our observations also suggest a mechanism by which structural outcomes of early RNA evolution would be largely reproducible even though RNA fitness landscapes consist of disconnected clusters of functional sequences.
Catalytically inactive Cas9 impairs DNA replication fork progression to induce focal genomic instability
Authors: Doi Goro , Okada Satoshi , Yasukawa Takehiro , Sugiyama Yuki , Bala Siqin , Miyazaki Shintaro , Kang Dongchon , Ito Takashi 
Published: December 2020

AbstractCatalytically inactive Cas9 (dCas9) has become an increasingly popular tool for targeted gene activation/inactivation, live-cell imaging, and base editing. While dCas9 was reported to induce base substitutions and indels, it has not been associated with structural variations. Here, we show that dCas9 impedes replication fork progression to destabilize tandem repeats in budding yeast. When targeted to the CUP1 array comprising ∼16 repeat units, dCas9 induced its contraction in most cells, especially in the presence of nicotinamide. Replication intermediate analysis demonstrated replication fork stalling in the vicinity of dCas9-bound sites. Genetic analysis indicated that while destabilization is counteracted by the replisome progression complex components Ctf4 and Mrc1 and the accessory helicase Rrm3, it involves single-strand annealing by the recombination proteins Rad52 and Rad59. Although dCas9-mediated replication fork stalling is a potential risk in conventional applications, it may serve as a novel tool for both mechanistic studies and manipulation of genomic instability.
Circulating angiopoietin-2 and angiogenic microRNAs associate with cerebral small vessel disease and cognitive decline in older patients reaching end-stage renal disease
Authors: Bijkerk Roel , Kallenberg Marije H , Zijlstra Laurien E , van den Berg Bernard M , de Bresser Jeroen , Hammer Sebastiaan , Bron Esther E , Achterberg Hakim , van Buchem Mark A , Berkhout-Byrne Noeleen C , Bos Willem Jan W , van Heemst Diana , Rabelink Ton J , van Zonneveld Anton Jan , van Buren Marjolijn , Mooijaart Simon 
Published: December 2020

Abstract

Background
The prevalence of end-stage renal disease (ESRD) is increasing worldwide, with the majority of new ESRD cases diagnosed in patients &gt;60 years of age. These older patients are at increased risk for impaired cognitive functioning, potentially through cerebral small vessel disease (SVD). Novel markers of vascular integrity may be of clinical value for identifying patients at high risk for cognitive impairment.

Methods
We aimed to associate the levels of angiopoietin-2 (Ang-2), asymmetric dimethylarginine and a selection of eight circulating angiogenic microRNAs (miRNAs) with SVD and cognitive impairment in older patients reaching ESRD that did not yet initiate renal replacement therapy (n = 129; mean age 75.3 years, mean eGFR 16.4 mL/min). We assessed brain magnetic resonance imaging changes of SVD (white matter hyperintensity volume, microbleeds and the presence of lacunes) and measures of cognition in domains of memory, psychomotor speed and executive function in a neuropsychological test battery.

Results
Older patients reaching ESRD showed an unfavourable angiogenic profile, as indicated by aberrant levels of Ang-2 and five angiogenic miRNAs (miR-27a, miR-126, miR-132, miR-223 and miR-326), compared with healthy persons and patients with diabetic nephropathy. Moreover, Ang-2 was associated with SVD and with the domains of psychomotor speed and executive function, while miR-223 and miR-29a were associated with memory function.

Conclusions
Taken together, these novel angiogenic markers might serve to identify older patients with ESRD at risk of cognitive decline, as well as provide insights into the underlying (vascular) pathophysiology.
Comprehensive Nutrient Gap Assessment (CONGA): A method for identifying the public health significance of nutrient gaps
Authors: Beal Ty , White Jessica M , Arsenault Joanne E , Okronipa Harriet , Hinnouho Guy-Marino , Morris Saul S 
Published: December 2020

AbstractIdentifying dietary nutrient gaps and interpreting their public health significance are essential for improving poor diets and reducing malnutrition. Evidence indicative of the burden of nutrient deficiencies and inadequate nutrient intake or availability exists in many countries yet is often misinterpreted or underused in decision-making. Clear guidance is lacking on how to synthesize and interpret the relevant evidence, which comes in many forms. To fill this methodological gap, an approach called Comprehensive Nutrient Gap Assessment was created to enable use of existing evidence to assess the public health significance of nutrient gaps and identify evidence gaps. Comprehensive Nutrient Gap Assessment requires ≥ 2 experts in nutritional assessment but does not require primary data collection or secondary quantitative data analysis. It can be implemented relatively quickly with low costs, for specific countries and subnational regions, and updated on the basis of new data with minimal effort. The findings from a Comprehensive Nutrient Gap Assessment are easily interpretable by nontechnical decision makers yet include clear justification for technical audiences.
Pressurized Liquid Extraction of a Phycocyanobilin Chromophore and Its Reconstitution with a Cyanobacteriochrome Photosensor for Efficient Isotopic Labeling
Authors: Kamo Takanari , Eki Toshihiko , Hirose Yuu 
Published: December 2020

Abstract
Linear tetrapyrrole compounds (bilins) are chromophores of the phytochrome and cyanobacteriochrome classes of photosensors and light-harvesting phycobiliproteins. Various spectroscopic techniques, such as resonance Raman, Fourier transform-infrared and nuclear magnetic resonance, have been used to elucidate the structures underlying their remarkable spectral diversity, in which the signals are experimentally assigned to specific structures using isotopically labeled bilin. However, current methods for isotopic labeling of bilins require specialized expertise, time-consuming procedures and/or expensive reagents. To address these shortcomings, we established a method for pressurized liquid extraction of phycocyanobilin (PCB) from the phycobiliprotein powder Lina Blue and also the cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis). PCB was efficiently cleaved in ethanol with three extractions (5 min each) under nitrogen at 125�C and 100 bars. A prewash at 75�C was effective for removing cellular pigments of Synechocystis without PCB cleavage. Liquid chromatography and mass spectrometry suggested that PCB was cleaved in the C3-E (majority) and C3-Z (partial) configurations. 15N- and 13C/15N-labeled PCBs were prepared from Synechocystis cells grown with NaH13CO3 and/or Na15NO3, the concentrations of which were optimized based on cell growth and pigmentation. Extracted PCB was reconstituted with a recombinant apoprotein of the cyanobacteriochrome-class photosensor RcaE. Yield of the photoactive holoprotein was improved by optimization of the expression conditions and cell disruption in the presence of Tween 20. Our method can be applied for the isotopic labeling of other PCB-binding proteins and for the commercial production of non-labeled PCB for food, cosmetic and medical applications.
A continuation method for building invisible obstacles in waveguides
Authors: Bera Antoine , Bonnet-Ben Dhia Anne-Sophie , Chesnel Lucas 
Published: December 2020

Summary
We consider the propagation of acoustic waves in a waveguide which is unbounded in one direction. We explain how to construct at a given wavenumber penetrable obstacles characterised by a physical coefficient $\rho$ which are invisible in various ways. In particular, we focus our attention on invisibility in reflection (the reflection matrix is zero), invisibility in reflection and transmission (the scattering matrix is the same as if there were no obstacle) and relative invisibility (two different obstacles have the same scattering matrix). To study these problems, we use a continuation method which requires to compute the scattering matrix $\mathbb{S}(\rho)$ as well as its differential with respect to the material index $d\mathbb{S}(\rho)$. The justification of the method also needs for the proof of abstract results of surjectivity of well-chosen functionals constructed from the terms of $d\mathbb{S}(\rho)$. We provide a complete proof of the results in monomode regime when the wavenumber is such that only one mode can propagate. And we give all the ingredients to implement the method in multimode regime. We end the article by presenting numerical results to illustrate the analysis.