bluuebunny/crossref_metadata_2025_split huggingface dataset:
A physical model for [C ii] line emission from galaxies
Authors: Ferrara A , Vallini L , Pallottini A , Gallerani S , Carniani S , Kohandel M , Decataldo D , Behrens C 
Published: July 2019

ABSTRACT
A tight relation between the [C ii] 158 $\mu$m line luminosity and star formation rate is measured in local galaxies. At high redshift (z > 5), though, a much larger scatter is observed, with a considerable (15–20 per cent) fraction of the outliers being [C ii]-deficient. Moreover, the [C ii] surface brightness ($\Sigma_{\rm [C\, \small {II}]}$) of these sources is systematically lower than expected from the local relation. To clarify the origin of such [C ii]-deficiency, we have developed an analytical model that fits local [C ii] data and has been validated against radiative transfer simulations performed with cloudy. The model predicts an overall increase of $\Sigma_{\rm [C\, \small {II}]}$ with ΣSFR. However, for ΣSFR ${\gtrsim} 1 \, \mathrm{M}_\odot \,{\rm yr}^{-1}\,{\rm kpc}^{-2}$, $\Sigma_{\rm [C\, \small {II}]}$ saturates. We conclude that underluminous [C ii] systems can result from a combination of three factors: (a) large upward deviations from the Kennicutt–Schmidt relation (κs ≫ 1), parametrized by the ‘burstiness’ parameter κs; (b) low metallicity; (c) low gas density, at least for the most extreme sources (e.g. CR7). Observations of [C ii] emission alone cannot break the degeneracy among the above three parameters; this requires additional information coming from other emission lines (e.g. [O iii]88 $\mu$m, C iii]1909 Å, CO lines). Simple formulae are given to interpret available data for low- and high-z galaxies.
Fast radio burst dispersion measures and rotation measures and the origin of intergalactic magnetic fields
Authors: Hackstein S , Brüggen M , Vazza F , Gaensler B M , Heesen V 
Published: July 2019

ABSTRACT
We investigate the possibility of measuring intergalactic magnetic fields using the dispersion measures and rotation measures of fast radio bursts. With Bayesian methods, we produce probability density functions for values of these measures. We distinguish between contributions from the intergalactic medium, the host galaxy, and the local environment of the progenitor. To this end, we use constrained, magnetohydrodynamic simulations of the local Universe to compute lines-of-sight integrals from the position of the Milky Way. In particular, we differentiate between predominantly astrophysical and primordial origins of magnetic fields in the intergalactic medium. We test different possible types of host galaxies and probe different distribution functions of fast radio burst progenitor locations inside the host galaxy. Under the assumption that fast radio bursts are produced by magnetars, we use analytic predictions to account for the contribution of the local environment. We find that less than 100 fast radio bursts from magnetars in stellar-wind environments hosted by starburst dwarf galaxies at redshift z ≳ 0.5 suffice to discriminate between predominantly primordial and astrophysical origins of intergalactic magnetic fields. However, this requires the contribution of the Milky Way to be removed with a precision of ≈1 rad m−2. We show the potential existence of a subset of fast radio bursts whose rotation measures carry information on the strength of the intergalactic magnetic field and its origins.
Generation of a caged lentiviral vector through an unnatural amino acid for photo-switchable transduction
Authors: Wang Yan , Li Shuai , Tian Zhenyu , Sun Jiaqi , Liang Shuobin , Zhang Bo , Bai Lu , Zhang Yuanjie , Zhou Xueying , Xiao Sulong , Zhang Qiang , Zhang Lihe , Zhang Chuanling , Zhou Demin 
Published: July 2019

Abstract
Application of viral vectors in gene delivery is attracting widespread attention but is hampered by the absence of control over transduction, which may lead to non-selective transduction with adverse side effects. To overcome some of these limitations, we proposed an unnatural amino acid aided caging–uncaging strategy for controlling the transduction capability of a viral vector. In this proof-of-principle study, we first expanded the genetic code of the lentiviral vector to incorporate an azido-containing unnatural amino acid (Nϵ-2-azidoethyloxycarbonyl-l-lysine, NAEK) site specifically within a lentiviral envelope protein. Screening of the resultant vectors indicated that NAEK incorporation at Y77 and Y116 was capable of inactivating viral transduction upon click conjugation with a photo-cleavable chemical molecule (T1). Exposure of the chimeric viral vector (Y77-T1) to UVA light subsequently removed the photo-caging group and restored the transduction capability of lentiviral vector both in vitro and in vivo. Our results indicate that the use of the photo-uncage activation procedure can reverse deactivated lentiviral vectors and thus enable regulation of viral transduction in a switchable manner. The methods presented here may be a general approach for generating various switchable vectors that respond to different stimulations and adapt to different viral vectors.
Targeted short read sequencing and assembly of re-arrangements and candidate gene loci provide megabase diplotypes
Authors: Shin GiWon , Greer Stephanie U , Xia Li C , Lee HoJoon , Zhou Jun , Boles T Christian , Ji Hanlee P 
Published: July 2019

Abstract
The human genome is composed of two haplotypes, otherwise called diplotypes, which denote phased polymorphisms and structural variations (SVs) that are derived from both parents. Diplotypes place genetic variants in the context of cis-related variants from a diploid genome. As a result, they provide valuable information about hereditary transmission, context of SV, regulation of gene expression and other features which are informative for understanding human genetics. Successful diplotyping with short read whole genome sequencing generally requires either a large population or parent-child trio samples. To overcome these limitations, we developed a targeted sequencing method for generating megabase (Mb)-scale haplotypes with short reads. One selects specific 0.1–0.2 Mb high molecular weight DNA targets with custom-designed Cas9–guide RNA complexes followed by sequencing with barcoded linked reads. To test this approach, we designed three assays, targeting the BRCA1 gene, the entire 4-Mb major histocompatibility complex locus and 18 well-characterized SVs, respectively. Using an integrated alignment- and assembly-based approach, we generated comprehensive variant diplotypes spanning the entirety of the targeted loci and characterized SVs with exact breakpoints. Our results were comparable in quality to long read sequencing.
Malaria.tools—comparative genomic and transcriptomic database for Plasmodium species
Authors: Tan Qiao Wen , Mutwil Marek 
Published: July 2019

AbstractMalaria is a tropical parasitic disease caused by the Plasmodium genus, which resulted in an estimated 219 million cases of malaria and 435 000 malaria-related deaths in 2017. Despite the availability of the Plasmodium falciparum genome since 2002, 74% of the genes remain uncharacterized. To remedy this paucity of functional information, we used transcriptomic data to build gene co-expression networks for two Plasmodium species (P. falciparum and P. berghei), and included genomic data of four other Plasmodium species, P. yoelii, P. knowlesi, P. vivax and P. cynomolgi, as well as two non-Plasmodium species from the Apicomplexa, Toxoplasma gondii and Theileria parva. The genomic and transcriptomic data were incorporated into the resulting database, malaria.tools, which is preloaded with tools that allow the identification and cross-species comparison of co-expressed gene neighbourhoods, clusters and life stage-specific expression, thus providing sophisticated tools to predict gene function. Moreover, we exemplify how the tools can be used to easily identify genes relevant for pathogenicity and various life stages of the malaria parasite. The database is freely available at www.malaria.tools.
Engineering DNA recognition and allosteric response properties of TetR family proteins by using a module-swapping strategy
Authors: Dimas Rey P , Jordan Benjamin R , Jiang Xian-Li , Martini Catherine , Glavy Joseph S , Patterson Dustin P , Morcos Faruck , Chan Clement T Y 
Published: July 2019

Abstract
The development of synthetic biological systems requires modular biomolecular components to flexibly alter response pathways. In previous studies, we have established a module-swapping design principle to engineer allosteric response and DNA recognition properties among regulators in the LacI family, in which the engineered regulators served as effective components for implementing new cellular behavior. Here we introduced this protein engineering strategy to two regulators in the TetR family: TetR (UniProt Accession ID: P04483) and MphR (Q9EVJ6). The TetR DNA-binding module and the MphR ligand-binding module were used to create the TetR-MphR. This resulting hybrid regulator possesses DNA-binding properties of TetR and ligand response properties of MphR, which is able to control gene expression in response to a molecular signal in cells. Furthermore, we studied molecular interactions between the TetR DNA-binding module and MphR ligand-binding module by using mutant analysis. Together, we demonstrated that TetR family regulators contain discrete and functional modules that can be used to build biological components with novel properties. This work highlights the utility of rational design as a means of creating modular parts for cell engineering and introduces new possibilities in rewiring cellular response pathways.
Determinants of change in arterial stiffness over 5 years in early chronic kidney disease
Authors: McIntyre Natasha J , Shardlow Adam , Fluck Richard J , McIntyre Christopher W , Taal Maarten W 
Published: July 2019

Abstract

Background
Arterial stiffness (AS) is an established and potentially modifiable risk factor for cardiovascular disease associated with chronic kidney disease (CKD). There have been few studies to evaluate the progression of AS over time or factors that contribute to this, particularly in early CKD. We therefore investigated AS over 5 years in an elderly population with CKD Stage 3 cared for in primary care.

Methods
A total of 1741 persons with an estimated glomerular filtration rate of 30–59 mL/min/1.73 m2 underwent detailed clinical and biochemical assessment at baseline and Years 1 and 5. Carotid to femoral pulse wave velocity (PWV) was measured to assess AS using a Vicorder device.

Results
970 participants had PWV assessments at baseline and 5 years. PWV increased significantly by a mean of 1.1 m/s (from 9.7 ± 1.9 to 10.8 ± 2.1 m/s). Multivariable linear regression analysis identified the following independent determinants of ΔPWV at Year 5: baseline age, diabetes status, baseline systolic blood pressure (SBP) and diastolic blood pressure, baseline PWV, ΔPWV at 1 year, ΔSBP over 5 years and Δserum bicarbonate over 5 years (R2 = 0.38 for the equation).

Conclusions
We observed a clinically significant increase in PWV over 5 years in a cohort with early CKD despite reasonably well-controlled hypertension. Measures of BP were identified as the most important modifiable determinant of ΔPWV, suggesting that interventions to prevent arterial disease should focus on improved control of BP, particularly in those who evidence an early increase in PWV. These hypotheses should now be tested in prospective trials.
Changes in China’s lakes: climate and human impacts
Authors: Tao Shengli , Fang Jingyun , Ma Suhui , Cai Qiong , Xiong Xinyu , Tian Di , Zhao Xia , Fang Leqi , Zhang Heng , Zhu Jiangling , Zhao Shuqing 
Published: July 2019

Abstract
Lakes have played a critical role in providing water and ecosystem services for people and other organisms in China for millennia. However, accelerating climate change and economic boom have resulted in unprecedented changes in these valuable lakes. Using Landsat images covering the entity of the country, we explored the changes in China’s lakes and the associated driving forces over the last 30 years (i.e. mid-1980s to 2015). We discovered that China’s lakes have changed with divergent regional trends: in the sparsely populated Tibetan Plateau, lakes are abundant and the lake area has increased dramatically from 38 596 to 46 831 km2 (i.e. increased by 8235 km2, or 21.3%), whereas, in the densely populated northern and eastern regions, lakes are relatively scarce and the lake area has decreased from 36 659 to 33 657 km2 (i.e. decreased by 3002 km2, or 8.2%). In particular, severe lake decreases occurred in the Mongolia-Xinjiang Plateau and the Eastern Plain (−2151 km2). Statistical analyses indicated that climate was the most important factor controlling lake changes in the Tibetan Plateau, the Yun-Gui Plateau and the Northeast Plain. However, the strength of climatic control on lake changes was low in the Eastern Plain and the Mongolia-Xinjiang Plateau, where human activities, e.g. impoldering, irrigation and mining, have caused serious impacts on lakes. Further lake changes will exacerbate regional imbalances between lake resources and population distribution, and thus may increase the risk of water-resource crises in China.
Effects of oats on gastrointestinal health as assessed by in vitro, animal, and human studies
Authors: Korczak Renee , Kocher Megan , Swanson Kelly S 
Published: July 2019

AbstractOats are uniquely nutritious, owing to their composition of bioactive compounds, lipids, and β-glucan. Scientific research has established that oats can improve diet quality, reduce cholesterol, regulate satiety, and protect against carcinogenesis in the colon; however, determining the effects of oats on gastrointestinal health and the gut microbiome is a newer, evolving area of research. To better understand the effects of oats on gastrointestinal health in humans, a literature review with predefined search criteria was conducted using the PubMed database and keywords for common gastrointestinal health outcomes. Moreover, to examine the gastrointestinal effects of oats across the scientific spectrum, a similar search strategy was executed to identify animal studies. In vitro studies were identified from the reference lists of human and animal studies. A total of 8 human studies, 19 animal studies, and 5 in vitro studies met the inclusion criteria for this review. The evidence in humans shows beneficial effects of oats on gastrointestinal health, with supportive evidence provided by in vitro and animal studies. The effective dose of oats varies by type, although an amount providing 2.5 to 2.9 g of β-glucan per day was shown to decrease fecal pH and alter fecal bacteria. For oat bran, 40 to 100 g/d was shown to increase fecal bacterial mass and short-chain fatty acids in humans. Differences in study design, methodology, and type of oats tested make valid comparisons difficult. The identification of best practices for the design of oat studies should be a priority in future research, as the findings will be useful for determining how oats influence specific indices of gastrointestinal health, including the composition of the human gut microbiome.
KOOLS–IFU: Kyoto Okayama Optical Low-dispersion Spectrograph with optical-fiber Integral Field Unit
Authors: Matsubayashi Kazuya , Ohta Kouji , Iwamuro Fumihide , Iwata Ikuru , Kambe Eiji , Tsutsui Hironori , Izumiura Hideyuki , Yoshida Michitoshi , Hattori Takashi 
Published: July 2019

Abstract
Observations of transient objects, such as short gamma-ray bursts and electromagnetic counterparts of gravitational wave sources, require prompt spectroscopy. To carry out prompt spectroscopy, we have developed an optical-fiber integral field unit (IFU) and connected it with an existing optical spectrograph, KOOLS. KOOLS–IFU was mounted on the Okayama Astrophysical Observatory 188 cm telescope. The fiber core and cladding diameters of the fiber bundle are 100 μm and 125 μm, respectively, and 127 fibers are hexagonally close-packed in the sleeve of the two-dimensional fiber array. We conducted test observations to measure the KOOLS–IFU performance and obtained the following conclusions: (1) the spatial sampling is ${2{^{\prime\prime}_{.}}34}$$\, \pm \,$${0{^{\prime\prime}_{.}}05}$ per fiber, and the total field of view is ${30{^{\prime\prime}_{.}}4}$$\, \pm \,$${0{^{\prime\prime}_{.}}65}$ with 127 fibers; (2) the observable wavelength and the spectral resolving power of the grisms of KOOLS are 4030–7310 Å and 400–600, 5020–8830 Å and 600–900, 4160–6000 Å and 1000–1200, and 6150–7930 Å and 1800–2400, respectively; and (3) the estimated limiting magnitude is 18.2–18.7 AB mag during 30 min exposure under optimal conditions.
Chloroplast-Localized Protoporphyrinogen IX Oxidase1 Is Involved in the Mitotic Cell Cycle in Arabidopsis
Authors: Li Jialong , Zhang Fan , Li Yuhong , Yang Weicai , Lin Rongcheng 
Published: July 2019

AbstractProtoporphyrinogen IX oxidase1 (PPO1) catalyzes the oxidation of protoporphyrinogen IX to form protoporphyrin IX in the plastid tetrapyrrole biosynthesis pathway and is also essential for plastid RNA editing in Arabidopsis thaliana. The Arabidopsis ppo1-1 mutation was previously shown to be seedling lethal; however, in this study, we showed that the heterozygous ppo1-1/+ mutant exhibited reproductive growth defects characterized by reduced silique length and seed set, as well as aborted pollen development. In this mutant, the second mitotic division was blocked during male gametogenesis, whereas female gametogenesis was impaired at the one-nucleate stage. Before perishing at the seedling stage, the homozygous ppo1-1 mutant displayed reduced hypocotyl and root length, increased levels of reactive oxygen species accumulation and elevated cell death, especially under light conditions. Wild-type seedlings treated with acifluorfen, a PPO1 inhibitor, showed similar phenotypes to the ppo1-1 mutants, and both plants possessed a high proportion of 2C nuclei and a low proportion of 8C nuclei compared with the untreated wild type. Genome-wide RNA-seq analysis showed that a number of genes, including cell cycle-related genes, were differentially regulated by PPO1. Consistently, PPO1 was highly expressed in the pollen, anther, pistil and root apical meristem cells actively undergoing cell division. Our study reveals a role for PPO1 involved in the mitotic cell cycle during gametogenesis and seedling development.
CYP712K4 Catalyzes the C-29 Oxidation of Friedelin in the Maytenus ilicifolia Quinone Methide Triterpenoid Biosynthesis Pathway
Authors: Bicalho Keylla U , Santoni Mariana M , Arendt Philipp , Zanelli Cleslei F , Furlan Maysa , Goossens Alain , Pollier Jacob 
Published: July 2019

Abstract
The native Brazilian plant Maytenus ilicifolia accumulates a set of quinone methide triterpenoids with important pharmacological properties, of which maytenin, pristimerin and celastrol accumulate exclusively in the root bark of this medicinal plant. The first committed step in the quinone methide triterpenoid biosynthesis is the cyclization of 2,3-oxidosqualene to friedelin, catalyzed by the oxidosqualene cyclase friedelin synthase (FRS). In this study, we produced heterologous friedelin by the expression of M. ilicifolia FRS in Nicotiana benthamiana leaves and in a Saccharomyces cerevisiae strain engineered using CRISPR/Cas9. Furthermore, friedelin-producing N. benthamiana leaves and S. cerevisiae cells were used for the characterization of CYP712K4, a cytochrome P450 from M. ilicifolia that catalyzes the oxidation of friedelin at the C-29 position, leading to maytenoic acid, an intermediate of the quinone methide triterpenoid biosynthesis pathway. Maytenoic acid produced in N. benthamiana leaves was purified and its structure was confirmed using high-resolution mass spectrometry and nuclear magnetic resonance analysis. The three-step oxidation of friedelin to maytenoic acid by CYP712K4 can be considered as the second step of the quinone methide triterpenoid biosynthesis pathway, and may form the basis for further discovery of the pathway and heterologous production of friedelanes and ultimately quinone methide triterpenoids.
CFM9, a Mitochondrial CRM Protein, Is Crucial for Mitochondrial Intron Splicing, Mitochondria Function and Arabidopsis Growth and Stress Responses
Authors: Lee Kwanuk , Park Su Jung , Park Youn-Il , Kang Hunseung 
Published: July 2019

Abstract
Although the importance of chloroplast RNA splicing and ribosome maturation (CRM) domain-containing proteins has been established for chloroplast RNA metabolism and plant development, the functional role of CRM proteins in mitochondria remains largely unknown. Here, we investigated the role of a mitochondria-targeted CRM protein (At3g27550), named CFM9, in Arabidopsis thaliana. Confocal analysis revealed that CFM9 is localized in mitochondria. The cfm9 mutant exhibited delayed seed germination, retarded growth and shorter height compared with the wild type under normal conditions. The growth-defect phenotypes were more manifested upon high salinity, dehydration or ABA application. Complementation lines expressing CFM9 in the mutant background fully recovered the wild-type phenotypes. Notably, the mutant had abnormal mitochondria, increased hydrogen peroxide and reduced respiration activity, implying that CFM9 is indispensable for normal mitochondrial function. More important, the splicing of many intron-containing genes in mitochondria was defective in the mutant, suggesting that CFM9 plays a crucial role in the splicing of mitochondrial introns. Collectively, our results provide clear evidence emphasizing that CFM9 is an essential factor in the splicing of mitochondrial introns, which is crucial for mitochondrial biogenesis and function and the growth and development of Arabidopsis.
Response Regulators 9 and 10 Negatively Regulate Salinity Tolerance in Rice
Authors: Wang Wei-Chen , Lin Te-Che , Kieber Joseph , Tsai Yu-Chang 
Published: July 2019

Abstract
Cytokinins are involved in the regulation of many plant growth and development processes, and function in response to abiotic stress. Cytokinin signaling is similar to the prokaryotic two-component signaling systems and includes the transcriptional upregulation of type-A response regulators (RRs), which in turn act to inhibit cytokinin signal response via negative feedback. Cytokinin signaling consists of several gene families and only a handful full of genes is studied. In this study, we demonstrated the function of two highly identical type-A RR genes from rice, OsRR9 and OsRR10, which are induced by cytokinin and only OsRR10 repressed by salinity stress in rice. Loss-of-function mutations give rise to mutant genes, osrr9/osrr10, which have higher salinity tolerance than wild type rice seedlings. The transcriptomic analysis uncovered several ion transporter genes, which were upregulated in response to salt stress in the osrr9/osrr10 mutants relative to the wild type seedlings. These include high-affinity potassium transporters, such as OsHKT1;1, OsHKT1;3 and OsHKT2;1, which play an important role in sodium and potassium homeostasis. In addition, disruption of the genes OsRR9 and OsRR10 also affects the expression of multiple genes related to photosynthesis, transcription and phytohormone signaling. Taken together, these results suggest that the genes OsRR9 and OsRR10 function as negative regulators in response to salinity in rice.