bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of efficient semipolar InGaN long wavelength light-emitting diodes and blue laser diodes grown on a high quality semipolar GaN/sapphire template
Authors: Li Hongjian , Zhang Haojun , Li Panpan , Wong Matthew S , Chow Yi Chao , Pinna Sergio , Klamkin Jonathan , DeMierry Philippe , Speck James S , Nakamura Shuji , DenBaars Steven P
Published: April 2020

Semipolar/nonpolar GaN-based optoelectronic devices become attractive due to several advantages such as alleviation of quantum-confinement Stark effect, high polarization ratio and optical gain. High performance semipolar/nonpolar InGaN light-emitting diodes (LEDs) and laser diodes (LDs) grown on semipolar/nonpolar bulk GaN substrate have been demonstrated. Owing to the limited size of such costly substrate, hetero-epitaxial growth of semipolar/nonpolar LEDs and LDs on foreign substrate causes lots of attentions. However, it is very challenging to realize efficient semipolar/nonpolar optoelectronic devices on foreign substrate due to the high dislocation density and possibly high basal plane stacking fault density. In this article, we review two growth methods to obtain high crystal quality semipolar (11-22) and (20-21) GaN layers on specially patterned sapphire substrate. The use of these substrates leads to the realization of efficient long wavelength InGaN semipolar LEDs and the first demonstration of semipolar blue LDs grown on foreign substrate shown in our previous reports. These results demonstrate significant progress in exploring the semipolar GaN materials quality and the devices efficiency grown on foreign substrate.
6. The future of solar physics
Authors: Judge Philip
Published: April 2020

Solar physics is a historically data-starved science, but about to becomes less so. ‘The future of solar physics’ looks at new facilities, either online or about to come online, such as the Daniel K. Inouye Solar Telescope on Maui. This aims to see, through measurements of coronal magnetic fields and plasma, how the Sun’s magnetic fields generate flares, coronal mass ejections, and the solar wind. Other major missions include NASA’s Parker Solar Probe and the European Solar Orbiter mission, spacecraft intended to orbit the Sun in new ways and from different viewpoints on Earth. Supported by increasingly powerful computers, these missions are ushering in a new era.
5. Economy
Authors: Reus-Smit Christian
Published: April 2020

‘Economy’ examines the relationship between economies and the organization of political authority, arguing that the two are mutually dependent. After considering three shifting conditions—changes in the global economy, revolutions in technology, and shifts in the global distribution of economic resources from the West to the East—it examines key developments in the organization of political authority, and how these have affected global economic relations. It concludes with a brief discussion of three major economic challenges facing the global organization of political authority: the rise of new economies and actors, inequality and social dislocation, and the accelerating global environmental crisis.
6. Rights
Authors: Reus-Smit Christian
Published: April 2020

‘Rights’ begins by explaining the centrality of rights to all configurations of political authority, the nature of individual rights (and in turn human rights), and the role individual rights play as ‘power-mediators’. The struggles for individual rights have reshaped the global organization of political authority in two crucial ways. First, over the course of five centuries, these struggles helped transform a world of empires into today’s global system of sovereign states. Second, in the latter phases of this process, struggles for human rights drove the codification of legally binding international human rights norms, effectively qualifying the rights—and thus political authority—of sovereign states.
7. Culture
Authors: Reus-Smit Christian
Published: April 2020

The rise of non-Western great powers, especially China, raises important questions about how culture affects the global organization of political authority. While some predict that the modern international order will collapse as Western cultural influence wanes, others counter that liberal international institutions can accommodate states and peoples of diverse cultural complexions, ‘Culture’ presents a different view. Historically, all large-scale configurations of political authority have evolved in heterogeneous not homogeneous cultural contexts, and the form they have taken—the institutions they develop, the hierarchies they create, and the rights they distribute—have been deeply affected by the imperative to govern or rule this diversity.
Prospective Study on Clinical Efficacy and Safety of a Single Session of Microfocused Ultrasound With Visualization for Collagen Regeneration
Authors: Araco Antonino
Published: April 2020

Background

Recent studies have shown that transcutaneous microfocused ultrasound with visualization is beneficial for noninvasive skin tightening, collagen regeneration, and lower face contour improvement.

Objectives

The primary study endpoint was the improvement of the laxity and ptosis face skin; the secondary endpoint was the improvement of wrinkles, texture, and hemoglobin content; and the third endpoint was the patient’s responses to a patient satisfaction questionnaire.

Methods

Patients with soft to moderate skin laxity and ptosis of the face and neck were enrolled and their sex, ethnicity, age, Fitzpatrick skin type, and smoking habit recorded. Patient assessment was made by digital macro-photographs, Vectra H2, and Antera 3D, and strict exclusion criteria were set up.

Results

From November 2017 to November 2018, 47 women and 3 men with a mean age of 52.8 ± 7.43 years and Araco’s Ptosis Scale System 2.7 ± 0.46, which fit the inclusion criteria, were enrolled in the study. All patients signed a consent form and received 1200 spot-lines (400 lines from each transducer) of microfocused ultrasound with visualization. No major side effects were reported during the study and all patients completed the follow-up after 6 months. Wrinkles, texture, Surgeon Assessment Scoring System scores, and patient satisfaction questionnaire scores improved significantly. Patients found the treatment tolerable according to the patient pain scale rate. No statistically significative differences were found among homogenous groups of smokers and nonsmokers.

Conclusions

The study proves that microfocused ultrasound with visualization in a single session of treatment in monotherapy is safe and effective for the treatment of face laxity and ptosis when a proper number of energy spot-lines is delivered in the correct tissue layer.

Level of Evidence: 4
Optimization of co-evolution analysis through phylogenetic profiling reveals pathway-specific signals
Authors: Bloch Idit , Sherill-Rofe Dana , Stupp Doron , Unterman Irene , Beer Hodaya , Sharon Elad , Tabach Yuval
Published: April 2020

The exponential growth in available genomic data is expected to reach full sequencing of a million genomes in the coming decade. Improving and developing methods to analyze these genomes and to reveal their utility is of major interest in a wide variety of fields, such as comparative and functional genomics, evolution and bioinformatics. Phylogenetic profiling is an established method for predicting functional interactions between proteins based on similarities in their evolutionary patterns across species. Proteins that function together (i.e. generate complexes, interact in the same pathways or improve adaptation to environmental niches) tend to show coordinated evolution across the tree of life. The normalized phylogenetic profiling (NPP) method takes into account minute changes in proteins across species to identify protein co-evolution. Despite the success of this method, it is still not clear what set of parameters is required for optimal use of co-evolution in predicting functional interactions. Moreover, it is not clear if pathway evolution or function should direct parameter choice. Here, we create a reliable and usable NPP construction pipeline. We explore the effect of parameter selection on functional interaction prediction using NPP from 1028 genomes, both separately and in various value combinations. We identify several parameter sets that optimize performance for pathways with certain biological annotation. This work reveals the importance of choosing the right parameters for optimized function prediction based on a biological context.

Availability and implementation

Source code and documentation are available on GitHub: https://github.com/iditam/CompareNPPs.

Contact

yuvaltab@ekmd.huji.ac.il

Supplementary information

Supplementary data are available at Bioinformatics online.
Impact of Revised Infectious Diseases Society of America and Society for Healthcare Epidemiology of America Clinical Practice Guidelines on the Treatment of Clostridium difficile Infections in the United States
Authors: Clancy Cornelius J , Buehrle Deanna , Vu Michelle , Wagener Marilyn M , Nguyen M Hong
Published: April 2020

Background

Our objective was to determine if oral vancomycin, fidaxomicin, and oral metronidazole use in the United States changed after publication of revised clinical practice guidelines for Clostridium difficile infection (CDI) in February 2018.

Methods

We obtained US antibiotic prescription data (IQVIA) from 2006–August 2019 and used guideline-recommended dosing regimens to estimate monthly numbers of 10-day treatment courses of vancomycin, fidaxomicin and metronidazole. Interrupted time-series analyses were performed, adjusted by month. We compared linear trends for monthly numbers of treatment courses in different time periods.

Results

Cumulative treatment courses of oral vancomycin and fidaxomicin increased by 54% (n = 226 166) and 48% (n = 18 518), respectively, in 18 months following guidelines compared with 18 months before; those of oral metronidazole decreased by 3% (n = 238 372). Monthly vancomycin and fidaxomicin use significantly increased throughout the period following revised guidelines (P < .0001 and P = .0002, respectively), whereas that of metronidazole decreased significantly (P < .0001). Monthly vancomycin use increased and metronidazole use decreased to a significantly greater extent after publication of revised guidelines than after publication of clinical trials establishing superiority of vancomycin over metronidazole (P < .0001).

Conclusions

Revised practice guidelines have had a significant impact on CDI treatment in the US. Clinical trial data used for the revised guidelines were available since 2007–2014 and 2011–2012 for oral vancomycin and fidaxomicin, respectively. Guidelines or guidance documents for treating CDI and other infections should be updated in more timely fashion.
Profile of Immunoglobulin G and IgM Antibodies Against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)
Authors: Qu Jiuxin , Wu Chi , Li Xiaoyong , Zhang Guobin , Jiang Zhaofang , Li Xiaohe , Zhu Qing , Liu Lei
Published: April 2020

We profiled the serological responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid (N) protein and spike (S) glycoprotein. The majority of the patients developed robust antibody responses between 17 and 23 days after illness onset. Delayed, but stronger, antibody responses were observed in critical patients.
BET bromodomain-containing epigenetic reader proteins regulate vascular smooth muscle cell proliferation and neointima formation
Authors: Dutzmann Jochen , Haertlé Marco , Daniel Jan-Marcus , Kloss Frederik , Musmann Robert-Jonathan , Kalies Katrin , Knöpp Kai , Pilowski Claudia , Sirisko Mirja , Sieweke Jan-Thorben , Bauersachs Johann , Sedding Daniel G , Gegel Simona
Published: April 2020

Aims

Recent studies revealed that the bromodomain and extra-terminal (BET) epigenetic reader proteins resemble key regulators in the underlying pathophysiology of cancer, diabetes, or cardiovascular disease. However, whether they also regulate vascular remodelling processes by direct effects on vascular cells is unknown. In this study, we investigated the effects of the BET proteins on human smooth muscle cell (SMC) function in vitro and neointima formation in response to vascular injury in vivo.

Methods and results

Selective inhibition of BETs by the small molecule (+)-JQ1 dose-dependently reduced proliferation and migration of SMCs without apoptotic or toxic effects. Flow cytometric analysis revealed a cell cycle arrest in the G0/G1 phase in the presence of (+)-JQ1. Microarray- and pathway analyses revealed a substantial transcriptional regulation of gene sets controlled by the Forkhead box O (FOXO1)1-transcription factor. Silencing of the most significantly regulated FOXO1-dependent gene, CDKN1A, abolished the antiproliferative effects. Immunohistochemical colocalization, co-immunoprecipitation, and promoter-binding ELISA assay data confirmed that the BET protein BRD4 directly binds to FOXO1 and regulates FOXO1 transactivational capacity. In vivo, local application of (+)-JQ1 significantly attenuated SMC proliferation and neointimal lesion formation following wire-induced injury of the femoral artery in C57BL/6 mice.

Conclusion

Inhibition of the BET-containing protein BRD4 after vascular injury by (+)-JQ1 restores FOXO1 transactivational activity, subsequent CDKN1A expression, cell cycle arrest and thus prevents SMC proliferation in vitro and neointima formation in vivo. Inhibition of BET epigenetic reader proteins might thus represent a promising therapeutic strategy to prevent adverse vascular remodelling.
Management of patients with combined arterial hypertension and aortic valve stenosis: a consensus document from the Council on Hypertension and Council on Valvular Heart Disease of the European Society of Cardiology, the European Association of Cardiovascular Imaging (EACVI), and the European Association of Percutaneous Cardiovascular Interventions (EAPCI)
Authors: Mancusi Costantino , de Simone Giovanni , Brguljan Hitij Jana , Sudano Isabella , Mahfoud Felix , Parati Gianfranco , Kahan Thomas , Barbato Emanuele , Pierard Luc A , Garbi Madalina , Flachskampf Frank A , Gerdts Eva
Published: April 2020

Aortic valve stenosis (AS) is the third most common cardiovascular disease. The prevalence of both AS and arterial hypertension increases with age, and the conditions therefore often co-exist. Co-existence of AS and arterial hypertension is associated with higher global left ventricular (LV) pressure overload, more abnormal LV geometry and function, and more adverse cardiovascular outcome. Arterial hypertension may also influence grading of AS, leading to underestimation of the true AS severity. Current guidelines suggest re-assessing patients once arterial hypertension is controlled. Management of arterial hypertension in AS has historically been associated with prudence and concerns, mainly related to potential adverse consequences of drug-induced peripheral vasodilatation combined with reduced stroke volume due to the fixed LV outflow obstruction. Current evidence suggests that patients should be treated with antihypertensive drugs blocking the renin–angiotensin–aldosterone system, adding further drug classes when required, to achieve similar target blood pressure (BP) values as in hypertensive patients without AS. The introduction of transcatheter aortic valve implantation has revolutionized the management of patients with AS, but requires proper BP management during and following valve replacement. The purpose of this document is to review the recent evidence and provide practical expert advice on management of hypertension in patients with AS.
The Justification of Privilege in International Investment Law: Preferential Treatment of Foreign Investors as a Problem of Legitimacy
Authors: Alvik Ivar
Published: April 2020

A fundamental feature of international investment law is that it only applies to foreign investment. This has historical reasons and is connected to deep-rooted principles of international law. It has also been a historical cause of controversy because it requires states to treat foreign investors better than they treat their own nationals. This article shows how the international minimum standard for treatment of foreigners nevertheless developed in a dialogue with such a concern for equality. The article argues that the way in which international investment law has developed in recent years into an effective remedial mechanism that can be invoked by individual foreign investors against host states ignores this historical lesson and now poses a particular challenge to its legitimacy. It privileges foreign investors as a select group worthy of more effective legal protection than ordinarily provided under municipal law, challenging the ideal of equality before the law as a basic constitutional value. The article discusses possible justifications of such privilege, arguing that only a more traditional international minimum standard rationale provides a convincing justification of special treatment of foreign investment. This has important implications for the reform of the current investment regime, suggesting that it should be redesigned to adopt a more supplementary role and deferential attitude to domestic law and courts – for example, through a requirement to exhaust local remedies.
Epigenetic Clock and Leukocyte Telomere Length Are Associated with Vitamin D Status but not with Functional Assessments and Frailty in the Berlin Aging Study II
Authors: Vetter Valentin Max , Spira Dominik , Banszerus Verena Laura , Demuth Ilja
Published: April 2020

DNA methylation (DNAm) age acceleration, a parameter derived via the epigenetic clock, has recently been suggested as a biomarker of aging. We hypothesized that accelerated biological aging, measured by both this new and the established biomarker of aging, relative leukocyte telomere length (rLTL), are associated with vitamin D deficiency. Moreover, we tested for an association between rLTL/DNAm age acceleration and different clinical assessments for functional capacity, including the Fried frailty score. Cross-sectional data of 1,649 participants of the Berlin Aging Study II was available (~50% female, age: 22–37 and 60–84 years). A seven cytosine-phosphate-guanine clock was estimated to calculate the DNAm age acceleration. rLTL was measured by quantitative real-time polymerase chain reaction (PCR). 25-hydroxyvitamin D (25(OH)D) serum levels <25 nmol/L was defined as vitamin D deficiency and <50 nmol/L as vitamin D insufficiency. Vitamin D-sufficient individuals had a 1.4 years lower mean DNAm age acceleration (p < .05, analysis of variance [ANOVA]) and a 0.11 longer rLTL (p < .001, ANOVA) than vitamin D-deficient participants. Likewise, vitamin D-sufficient participants had lower DNAm age acceleration (β = 1.060, p = .001) and longer rLTL (β = −0.070; p < .001) than vitamin D nonsufficient subjects in covariate-adjusted analysis. Neither DNAm age acceleration nor rLTL were significantly associated with the Fried frailty score or the functional assessments. Only the clock drawing test was associated with DNAm age acceleration (subgroup of older men: β = 1.898, p = .002). Whether the analyzed biomarkers of aging can be used to predict an individual’s functional capacity or will be associated with frailty in the advanced course of aging, will be clarified by future longitudinal analyses.
Bayesian trans-dimensional full waveform inversion: synthetic and field data application
Authors: Guo Peng , Visser Gerhard , Saygin Erdinc
Published: April 2020

Seismic full waveform inversion (FWI) is a state-of-the-art technique for estimating subsurface physical models from recorded seismic waveform, but its application requires care because of high non-linearity and non-uniqueness. The final outcome of global convergence from conventional FWI using local gradient information relies on an informative starting model. Bayesian inference using Markov chain Monte Carlo (MCMC) sampling is able to remove such dependence, by a direct extensive search of the model space. We use a Bayesian trans-dimensional MCMC seismic FWI method with a parsimonious dipping layer parametrization, to invert for subsurface velocity models from pre-stack seismic shot gathers that contain mainly reflections. For the synthetic study, we use a simple four-layer model and a modified Marmousi model. A recently collected multichannel off-shore seismic reflection data set, from the Lord Howe Rise (LHR) in the east of Australia, is used for the field data test. The trans-dimensional FWI method is able to provide model ensembles for describing posterior distribution, when the dipping-layer model assumption satisfies the observed data. The model assumption requires narrow models, thus only near-offset data to be used. We use model stitching with lateral and depth constraints to create larger 2-D models from many adjacent overlapping submodel inversions. The inverted 2-D velocity model from the Bayesian inference can then be used as a starting model for the gradient-based FWI, from which we are able to obtain high-resolution subsurface velocity models, as demonstrated using the synthetic data. However, lacking far-offset data limits the constraints for the low-wavenumber part of the velocity model, making the inversion highly non-unique. We found it challenging to apply the dipping-layer based Bayesian FWI to the field data. The approximations in the source wavelet and forward modelling physics increase the multimodality of the posterior distribution; the sampled velocity models clearly show the trade-off between interface depth and velocity. Numerical examples using the synthetic and field data indicate that trans-dimensional FWI has the potential for inverting earth models from reflection waveform. However, a sparse model parametrization and far offset constraints are required, especially for field application.
Ocean acidification induces carry-over effects on the larval settlement of the New Zealand abalone,Haliotis iris
Authors: Espinel-Velasco Nadjejda , Lamare Miles , Kluibenschedl Anna , Moss Graeme , Cummings Vonda
Published: April 2020

Larval settlement is a key process in the lifecycle of benthic marine organisms; however, little is known on how it could change in reduced seawater pH and carbonate saturation states under future ocean acidification (OA). This is important, as settlement ensures species occur in optimal environments and, for commercially important species such as abalone, reduced settlement could decrease future population success. We investigated how OA could affect settlement success in the New Zealand abalone Haliotis iris by examining: (1) direct effects of seawater at ambient (pHT 8.05) and reduced pHT (7.65) at the time of settlement, (2) indirect effects of settlement substrates (crustose coralline algae, CCA) preconditioned at ambient and reduced pHT for 171 days, and (3) carry-over effects, by examining settlement in larvae reared to competency at ambient and reduced pHT (7.80). We found no effects of seawater pH or CCA incubation on larval settlement success. OA-induced carry-over effects were evident, with lower settlement in larvae reared at reduced pH. Understanding the mechanisms behind these responses is key to fully comprehend the extent to which OA will affect marine organisms and the industries that rely on them.
Phenotypic and genotypic quinolone resistance in Escherichia coli underlining GyrA83/87 mutations as a target to detect ciprofloxacin resistance
Authors: Muggeo Anaëlle , Cambau Emmanuelle , Amara Marlène , Micaëlo Maïté , Pangon Béatrice , Bajolet Odile , Benmansour Hanaa , de Champs Christophe , Guillard Thomas
Published: April 2020

Background

Quinolone resistance (QR) is one component of the MDR emerging in Escherichia coli and is of particular concern given the widespread use of fluoroquinolones.

Objectives

To characterize the QR phenotypes and genotypes in E. coli responsible for bloodstream infections and to propose molecular determinants that could be targeted to predict ciprofloxacin resistance.

Methods

E. coli isolates from blood cultures in three French hospitals were studied for quinolone MICs and characterization of genotypic QR determinants (QRg).

Results

Among 507 isolates tested for MICs, 148 (29.2%) were resistant to quinolones based on EUCAST breakpoints and 143 (28.2%) harboured at least one QRg. QRg were mainly mutations in the QRDR (138 isolates, 27.2%), with 55.8% of these isolates carrying at least three QRDR mutations. gyrA mutations predominated (92.8%) followed by parC (61.6%), parE (32.6%) and gyrB (1.4%) mutations. Only 4.7% of the isolates harboured a plasmid-mediated quinolone resistance (PMQR) gene: aac(6′)-Ib-cr (60.0%) or qnr (qnrS, qnrB) (32.0%). For the first time in France, we reported the qepA4 allele of the plasmid-encoded efflux pump QepA. Only five isolates carried PMQR without a QRDR mutation. The positive predictive value (PPV) for ciprofloxacin resistance was 100% for any QRg and 99.2% for gyrA mutations specifically.

Conclusions

QR observed in E. coli isolates involved in bloodstream infections is still mainly due to QRDR mutations, especially at codons GyrA83/87, which could be used as a molecular target to rapidly detect resistance.
Assessing New Tools for Management of the Pepper Weevil (Coleoptera: Curculionidae) in Greenhouse and Field Pepper Crops
Authors: Labbé Roselyne M , Gagnier Dana , Rizzato Rebecca , Tracey Amanda , McCreary Cara
Published: April 2020

The pepper weevil, Anthonomus eugenii Cano, is an economically important pest of field and greenhouse pepper crops in North America. In this study, a series of insecticides covering a broad-spectrum of insecticidal modes of action were assessed for their potential in managing the pepper weevil under laboratory and greenhouse conditions. To accomplish this, laboratory mini-spray tower and greenhouse cage trials were conducted that evaluated the efficacy of 16 conventional, reduced-risk, and microbial insecticides. In laboratory trials, adult weevils were sprayed with insecticides, placed on treated leaves within a cup cage, and were monitored for their survival over 10 d. Of the 16 insecticides tested, 8 provided greater than 60% weevil control, a threshold considered necessary for including products in further greenhouse testing. In greenhouse trials, adult weevil mortality, bud and foliar damage, bud and fruit abortion, and subsequent weevil offspring emergence were measured following each of three weekly insecticide applications. The most efficacious insecticides included kaolin clay and mineral oil, which performed as well as the thiamethoxam-positive control, and incurred 70 and 55% of adult weevil mortality, respectively. Additionally, kaolin clay and mineral oil reduced offspring weevil emergence by 59 and 54%, respectively, compared with untreated controls. Despite the clear challenge that controlling this pest represents, this study has identified useful new tools for the integrated management of the pepper weevil, which may accelerate the rate at which these become available for use in greenhouse and field pepper production.
A phase I/II trial of intraoperative breast radiotherapy in an Asian population: 10-year results with critical evaluation
Authors: Kawamura Mariko , Itoh Yoshiyuki , Kamomae Takeshi , Sawaki Masataka , Kikumori Toyone , Tsunoda Nobuyuki , Ito Junji , Shimoyama Yoshie , Satake Hiroko , Naganawa Shinji
Published: April 2020

Although phase III trials have been published comparing whole breast irradiation (WBI) with accelerated partial breast irradiation (APBI) using intraoperative radiotherapy (IORT), long-term follow-up results are lacking. We report the 10-year follow-up results of a prospective phase I/II clinical trial of IORT. The inclusion criteria were as follows: (i) tumor size <2.5 cm, (ii) desire for breast-conserving surgery, (iii) age >50 years, (iv) negative margins after resection and (v) sentinel lymph node-negative disease. A single dose of IORT (19–21 Gy) was delivered to the tumor bed in the operation room just after wide local excision of the primary breast cancer using a 6–12 MeV electron beam. Local recurrence was defined as recurrence or new disease within the treated breast and was evaluated annually using mammography and ultrasonography. A total of 32 patients were eligible for evaluation. The median patient age was 65 years and the median follow-up time was 10 years. Two patients experienced local recurrence just under the nipple, out of the irradiated field, after 8 years of follow-up. Three patients had contralateral breast cancer and one patient experienced bone metastasis after 10 years of follow-up. No patient experienced in-field recurrence nor breast cancer death. Eight patients had hypertrophic scarring at the last follow-up. There were no lung or heart adverse effects. This is the first report of 10-year follow-up results of IORT as APBI. The findings suggest that breast cancer with extended intraductal components should be treated with great caution.
Flavonoids are indispensable for complete male fertility in rice
Authors: Wang Lanxiang , Ying Lam Lydia Pui , Lui Andy C W , Zhu Fu-Yuan , Chen Mo-Xian , Liu Hongjia , Zhang Jianhua , Lo Clive
Published: April 2020

Flavonoids are essential for male fertility in some but not all plant species. In rice (Oryza sativa), the chalcone synthase mutant oschs1 produces flavonoid-depleted pollen and is male sterile. The mutant pollen grains are viable with normal structure, but they display reduced germination rate and pollen-tube length. Analysis of oschs1/+ heterozygous lines shows that pollen flavonoid deposition is a paternal effect and fertility is independent of the haploid genotypes (OsCHS1 or oschs1). To understand which classes of flavonoids are involved in male fertility, we conducted detailed analysis of rice mutants for branch-point enzymes of the downstream flavonoid pathways, including flavanone 3-hydroxylase (OsF3H; flavonol pathway entry enzyme), flavone synthase II (CYP93G1; flavone pathway entry enzyme), and flavanone 2-hydroxylase (CYP93G2; flavone C-glycoside pathway entry enzyme). Rice osf3h and cyp93g1 cyp93g2 CRISPR/Cas9 mutants, and cyp93g1 and cyp93g2 T-DNA insertion mutants showed altered flavonoid profiles in anthers, but only the osf3h and cyp93g1 cyp93g2 mutants displayed reduction in seed yield. Our findings indicate that flavonoids are essential for complete male fertility in rice and a combination of different classes (flavanones, flavonols, flavones, and flavone C-glycosides) appears to be important, as opposed to the essential role played primarily by flavonols that has been previously reported in several plant species.
Numerical simulations of colliding jets in an external wind: application to 3C 75
Authors: Musoke G , Young A J , Molnar S M , Birkinshaw M
Published: April 2020

The radio galaxy 3C 75 is remarkable because it contains a pair of radio-loud active galaxies, each of which produces a two-sided jet, with the jet beams appearing to collide and merge to the west of the galaxies. Motivated by 3C 75, we have conducted three-dimensional hydrodynamic simulations of jet collisions. We have extended previous studies by modelling the physical properties of the cluster atmosphere, including an external wind, and using realistic jet powers obtained from observational data. We are able to produce a morphology similar to that of 3C 75. The simulations imply that direct contact between the bulk jet flows on the west of the source is required to produce a morphology consistent with 3C 75. We quantify how the merging jets decelerate, how the wind deflects the jets and cocoons, the entrainment of intra-cluster material into the cocoons, the cocoon energetics, and how the jet interactions generate enstrophy. By comparing simulations of pairs of two-sided jets with those of single two-sided sources, we determine how the interaction between two bipolar jets changes their evolution. The unprecedented sensitivity and angular resolution of upcoming observatories will lead to the detection of many more complex sources at high redshift, where interacting jets are expected to be more numerous. The morphology of these complex sources can provide significant insight into the conditions in their environments.
Less noticeable shallow decay phase in early X-ray afterglows of GeV/TeV-detected gamma-ray bursts
Authors: Yamazaki Ryo , Sato Yuri , Sakamoto Takanori , Serino Motoko
Published: April 2020

The nature of the shallow decay phase in the X-ray afterglow of the gamma-ray burst (GRB) is not yet clarified. We analyse the data of early X-ray afterglows of 26 GRBs triggered by Burst Alert Telescope onboard Neil Gehrels Swift Observatory and subsequently detected by Fermi Large Area Telescope (LAT) and/or Imaging Atmospheric Cherenkov Telescopes. It is found that nine events (including two out of three very-high-energy gamma-ray events) have no shallow decay phase and that their X-ray afterglow light curves are well described by single power-law model except for the jet break at later epoch. The rest are fitted by double power-law model and have a break in the early epoch (around ks), however, eight events (including a very-high-energy gamma-ray event) have the pre-break decay index larger than 0.7. We also analyse the data of well-sampled X-ray afterglows of GRBs without LAT detection and compare their decay properties with those of high-energy and very-high-energy gamma-ray events. It is found that for the GeV/TeV bursts, the fraction of events whose X-ray afterglows are described by single power law is significantly larger than those for non-GeV/TeV GRBs. Even if the GeV/TeV GRBs have shallow decay phase, their decay slope tends to be steeper than non-GeV/TeV bursts, that is, they have less noticeable shallow decay phase in the early X-ray afterglow. A possible interpretation along with the energy injection model is briefly discussed.
Analysis of the galaxy size versus stellar mass relation
Authors: Almeida J Sánchez
Published: April 2020

The scatter in the galaxy size versus stellar mass (M⋆) relation gets largely reduced when, rather than the half-mass radius Re, the size at a fixed surface density is used. Here we address why this happens. We show how a reduction is to be expected because any two galaxies with the same M⋆ have at least one radius with identical surface density, where the galaxies have identical size. However, the reason why the scatter is reduced to the observed level is not trivial, and we pin it down to the galaxy surface density profiles approximately following Sersic profiles with their Re and Sersic index (n) anti-correlated (i.e., given M⋆, n increases when Re decreases). Our analytical results describe very well the behavior of the observed galaxies as portrayed in the NASA Sloan Atlas (NSA), which contains more than half a million local objects with 7 < log (M⋆/M⊙) < 11.5. The comparison with NSA galaxies also allows us to find the optimal values for the mass surface density ($2.4_{-0.9}^{+1.3}\, M_\odot \, {\rm pc}^{-2}$) and surface brightness (r-band 24.7 ± 0.5 mag arcsec−2) that minimize the scatter, although the actual values depend somehow on the subset of NSA galaxies used for optimization. The physical reason for the existence of optimal values is unknown but, as Trujillo et al. (2020) point out, they are close to the gas surface density threshold to form stars and thus may trace the physical end of a galaxy. Our NSA-based size–mass relation agrees with theirs on the slope as well as on the magnitude of the scatter. As a by-product of the narrowness of the size–mass relation (only 0.06 dex), we propose to use the size of a galaxy to measure its stellar mass. In terms of observing time, it is not more demanding than the usual photometric techniques and may present practical advantages in particular cases.
A non-linear mathematical model for the X-ray variability classes of the microquasar GRS 1915+105 – I. Quiescent, spiking states, and quasi-periodic oscillations
Authors: Massaro E , Capitanio F , Feroci M , Mineo T , Ardito A , Ricciardi P
Published: April 2020

The microquasar GRS 1915+105 is known to exhibit a very variable X-ray emission on different time-scales and patterns. We propose a system of two ordinary differential equations, adapted from the Hindmarsh–Rose model, with two dynamical variables x(t), y(t), and an input constant parameter J0, to which we added a random white noise, whose solutions for the x(t) variable reproduce consistently the X-ray light curves of several variability classes as well as the development of low-frequency quasi-periodic oscillations (QPO). We show that changing only the value of J0, the system moves from stable to unstable solutions and the resulting light curves reproduce those of the quiescent classes like ϕ and χ, the δ class and the spiking ρ class. Moreover, we found that increasing the values of J0 the system induces high-frequency oscillations that evolve into QPO when it moves into another stable region. This system of differential equations gives then a unified view of the variability of GRS 1915+105 in term of transitions between stable and unstable states driven by a single input function J0. We also present the results of a stability analysis of the equilibrium points and some considerations on the existence of periodic solutions.
A tale of two sites – I. Inferring the properties of minihalo-hosted galaxies from current observations
Authors: Qin Yuxiang , Mesinger Andrei , Park Jaehong , Greig Bradley , Muñoz Julian B
Published: April 2020

The very first galaxies that started the cosmic dawn likely resided in so-called ‘minihaloes’, with masses of ∼105–$10^8{\, {\rm M}_\odot }$, accreting their gas from the intergalactic medium through H2 cooling. Such molecularly cooled galaxies (MCGs) mostly formed in pristine environments, hosted massive, metal-free stars, and were eventually sterilized by the build-up of a disassociating (Lyman–Werner; LW) background. Therefore, their properties might be very different from the galaxies we see in the later Universe. Although MCGs are probably too faint to be observed directly, we could nevertheless infer their properties from the imprint they leave in the cosmic 21-cm signal. Here we quantify this imprint by extending the public simulation code 21cmFAST to allow for a distinct population of MCGs. We allow MCGs to have different properties from other galaxies, including unique scaling relations for their stellar-to-halo mass ratios, ionizing escape fractions, and spectral energy distributions. We track inhomogeneous recombinations, disassociative LW feedback, and photoheating from reionization. After demonstrating how MCGs can shape the 21-cm signal, we explore to what extent current observations can already place constraints on their properties. The cosmic microwave background optical depth from Planck sets an upper limit on the product of the ionizing escape fraction and the stellar mass in MCGs. When including also the timing of the putative EDGES absorption signal, we find an additional strong degeneracy between the stellar mass and the X-ray luminosity of MCGs. If proven to be of cosmic origin, the timing of the EDGES signal would have been set by MCGs.
Mapping the relativistic electron gas temperature across the sky
Authors: Remazeilles Mathieu , Chluba Jens
Published: April 2020

With increasing sensitivity, angular resolution, and frequency coverage, future cosmic microwave background (CMB) experiments like PICO will allow us to access new information about galaxy clusters through the relativistic thermal Sunyaev–Zeldovich (SZ) effect. We will be able to map the temperature of relativistic electrons across the entire sky, going well beyond a simple detection of the relativistic SZ effect by cluster stacking methods that currently define the state-of-the-art. Here, we propose a new map-based approach utilizing SZ-temperature moment expansion and constrained-ILC methods to extract electron gas temperature maps from foreground-obscured CMB data. This delivers a new independent map-based observable, the electron temperature power spectrum $T_{\rm e}^{yy}(\ell)$, which can be used to constrain cosmology in addition to the Compton-y power spectrum $C_\ell ^{yy}(\ell)$ . We find that PICO has the required sensitivity, resolution, and frequency coverage to accurately map the electron gas temperature of galaxy clusters across the full sky, covering a broad range of angular scales. Frequency coverage at $\nu \gtrsim 300\, {\rm GHz}$ plays an important role for extracting the relativistic SZ effect in the presence of foregrounds. For Coma, PICO will allow us to directly reconstruct the electron temperature profile using the relativistic SZ effect. Coma’s average electron temperature will be measured to 10σ significance after foreground removal using PICO. Low angular resolution CMB experiment like LiteBIRD could achieve 2σ to 3σ measurement of the electron temperature of this largest cluster. Our analysis highlights a new spectroscopic window into the thermodynamic properties of galaxy clusters and the diffuse electron gas at large angular scales.
Do nuclear rings in barred galaxies form at the shear minimum of the rotation curve?
Authors: Sormani Mattia C , Li Zhi
Published: April 2020

It has been recently suggested that (i) nuclear rings in barred galaxies (including our own Milky Way) form at the radius where the shear parameter of the rotation curve reaches a minimum; and (ii) the acoustic instability of Montenegro et al. is responsible for driving the turbulence and angular momentum transport in the central regions of barred galaxies. Here, we test these suggestions by running simple hydrodynamical simulations in a logarithmic barred potential. Since the rotation curve of this potential is scale free, the shear minimum theory predicts that no ring should form. We find that in contrast to this prediction, a ring does form in the simulation, with morphology consistent with that of nuclear rings in real barred galaxies. This proves that the presence of a shear-minimum is not a necessary condition for the formation of a ring. We also find that perturbations that are predicted to be acoustically unstable wind up and eventually propagate off to infinity, so that the system is actually stable. We conclude that (i) the shear-minimum theory is an unlikely mechanism for the formation of nuclear rings in barred galaxies; and (ii) the acoustic instability is a spurious result and may not be able to drive turbulence in the interstellar medium, at least for the case without self-gravity. The question of the role of turbulent viscosity remains open.
Use of a human embryonic stem cell model to discover GABRP, WFDC2, VTCN1 and ACTC1 as markers of early first trimester human trophoblast
Authors: Karvas Rowan M , McInturf Samuel , Zhou Jie , Ezashi Toshihiko , Schust Danny J , Roberts R Michael , Schulz Laura C
Published: April 2020

Human placental development during early pregnancy is poorly understood. Many conceptuses are lost at this stage. It is thought that preeclampsia, intrauterine growth restriction and other placental syndromes that manifest later in pregnancy may originate early in placentation. Thus, there is a need for models of early human placental development. Treating human embryonic stem cells (hESCs) with BMP4 (bone morphogenic protein 4) plus A83-01 (ACTIVIN/NODAL signaling inhibitor) and PD173074 (fibroblast growth factor 2 or FGF2 signaling inhibitor) (BAP conditions) induces differentiation to the trophoblast lineage (hESCBAP), but it is not clear which stage of trophoblast differentiation these cells resemble. Here, comparison of the hESCBAP transcriptome to those of trophoblasts from human blastocysts, trophoblast stem cells and placentas collected in the first–third trimester of pregnancy by principal component analysis suggests that hESC after 8 days BAP treatment most resemble first trimester syncytiotrophoblasts. To further test this hypothesis, transcripts were identified that are expressed in hESCBAP but not in cultures of trophoblasts isolated from term placentas. Proteins encoded by four genes, GABRP (gamma-aminobutyric acid type A receptor subunit Pi), WFDC2 (WAP four-disulfide core domain 2), VTCN1 (V-set domain containing T-cell activation inhibitor 1) and ACTC1 (actin alpha cardiac muscle 1), immunolocalized to placentas at 4–9 weeks gestation, and their expression declined with gestational age (R2 = 0.61–0.83). None are present at term. Expression was largely localized to syncytiotrophoblast of both hESCBAP cells and placental material from early pregnancy. WFDC2, VTCN1 and ACTC1 have not previously been described in placenta. These results support the hypothesis that hESCBAP represent human trophoblast analogous to that of early first trimester and are a tool for discovery of factors important to this stage of placentation.
DIS3L2 and LSm proteins are involved in the surveillance of Sm ring-deficient snRNAs
Authors: Roithová Adriana , Feketová Zuzana , Vaňáčová Štěpánka , Staněk David
Published: April 2020

Spliceosomal small nuclear ribonucleoprotein particles (snRNPs) undergo a complex maturation pathway containing multiple steps in the nucleus and in the cytoplasm. snRNP biogenesis is strictly proofread and several quality control checkpoints are placed along the pathway. Here, we analyzed the fate of small nuclear RNAs (snRNAs) that are unable to acquire a ring of Sm proteins. We showed that snRNAs lacking the Sm ring are unstable and accumulate in P-bodies in an LSm1-dependent manner. We further provide evidence that defective snRNAs without the Sm binding site are uridylated at the 3′ end and associate with DIS3L2 3′→5′ exoribonuclease and LSm proteins. Finally, inhibition of 5′→3′ exoribonuclease XRN1 increases association of ΔSm snRNAs with DIS3L2, which indicates competition and compensation between these two degradation enzymes. Together, we provide evidence that defective snRNAs without the Sm ring are uridylated and degraded by alternative pathways involving either DIS3L2 or LSm proteins and XRN1.
GSK-3 is an RNA polymerase II phospho-CTD kinase
Authors: Nieto Moreno Nicolás , Villafañez Florencia , Giono Luciana E , Cuenca Carmen , Soria Gastón , Muñoz Manuel J , Kornblihtt Alberto R
Published: April 2020

We have previously found that UV-induced DNA damage causes hyperphosphorylation of the carboxy terminal domain (CTD) of RNA polymerase II (RNAPII), inhibition of transcriptional elongation and changes in alternative splicing (AS) due to kinetic coupling between transcription and splicing. In an unbiased search for protein kinases involved in the AS response to DNA damage, we have identified glycogen synthase kinase 3 (GSK-3) as an unforeseen participant. Unlike Cdk9 inhibition, GSK-3 inhibition only prevents CTD hyperphosphorylation triggered by UV but not basal phosphorylation. This effect is not due to differential degradation of the phospho-CTD isoforms and can be reproduced, at the AS level, by overexpression of a kinase-dead GSK-3 dominant negative mutant. GSK-3 inhibition abrogates both the reduction in RNAPII elongation and changes in AS elicited by UV. We show that GSK-3 phosphorylates the CTD in vitro, but preferentially when the substrate is previously phosphorylated, consistently with the requirement of a priming phosphorylation reported for GSK-3 efficacy. In line with a role for GSK-3 in the response to DNA damage, GSK-3 inhibition prevents UV-induced apoptosis. In summary, we uncover a novel role for a widely studied kinase in key steps of eukaryotic transcription and pre-mRNA processing.
Metabolic reprogramming in cancer: the bridge that connects intracellular stresses and cancer behaviors
Authors: Zhou Yi , Sun Huiyan , Xu Ying
Published: April 2020

Extensive changes in cellular metabolisms have been observed in cancer. They are probably induced by the same intracellular stressor, persistent off-balance in intracellular pH across possibly all adult cancers. It is these altered metabolisms that gives rise to a variety of cancerous behaviors such as continuous cell division, metastasis and drug resistance.