bluuebunny/crossref_metadata_2025 huggingface dataset:
Mobility restores the mechanism which supports cooperation in the voluntary prisoner’s dilemma game
Authors: Cardinot Marcos , O’Riordan Colm , Griffith Josephine , Szolnoki Attila
Published: July 2019

It is generally believed that in a situation where individual and collective interests are in conflict, the availability of optional participation is a key mechanism to maintain cooperation. Surprisingly, this effect is sensitive to the use of microscopic dynamics and can easily be broken when agents make a fully rational decision during their strategy updates. In the framework of the celebrated prisoner’s dilemma game, we show that this discrepancy can be fixed automatically if we leave the strict and frequently artifact condition of a fully occupied interaction graph, and allow agents to change not just their strategies but also their positions according to their success. In this way, a diluted graph where agents may move offers a natural and alternative way to handle artifacts arising from the application of specific and sometimes awkward microscopic rules.
Lagrangian dynamics of the coupled field-medium state of light
Authors: Partanen Mikko , Tulkki Jukka
Published: July 2019

In the recently introduced mass-polariton (MP) theory of light (Partanen et al 2017 Phys. Rev. A 95 063850), the optical force of light drives in a medium forward an atomic mass density wave. In this work, we present the Lagrangian formulation of the MP theory starting directly from the principle of least action and the well-known Lagrangian densities of the electromagnetic field and the medium within the special theory of relativity. The Lagrangian densities and the resulting Euler–Lagrange equations lead directly and without any further postulates to the unique expression of the optical Abraham force that dynamically couples the electromagnetic field and the medium in the MP theory of light. The field-medium coupling is symmetric and bi-directional and it fulfills the law of action and counteraction. The coupled dynamical equations also enable the exact description of the very small kinetic energy of the medium as a part of the total energy of the coupled state of light. Thus, the Lagrangian formulation of the present work is a complementary approach to Lorentz covariance properties of the MP theory discussed in our recent work (Partanen and Tulkki 2019 Phys. Rev. A 99 033852). We show how the coupled dynamical equations of the field and the medium can be solved analytically for a Gaussian light pulse. It is astonishing how the simple analytic results for the dynamical equations, the optical force, and the stress-energy-momentum tensor of the MP theory follow ab initio from the Lagrangian densities that have been well known for almost a century.
Microwave to optical conversion with atoms on a superconducting chip
Authors: Petrosyan David , Mølmer Klaus , Fortágh József , Saffman Mark
Published: July 2019

We describe a scheme to coherently convert a microwave photon of a superconducting co-planar waveguide resonator to an optical photon emitted into a well-defined temporal and spatial mode. The conversion is realized by a cold atomic ensemble trapped close the surface of the superconducting atom chip, near the antinode of the microwave cavity. The microwave photon couples to a strong Rydberg transition of the atoms that are also driven by a pair of laser fields with appropriate frequencies and wavevectors for an efficient wave-mixing process. With only several thousand atoms in an ensemble of moderate density, the microwave photon can be completely converted into an optical photon emitted with high probability into the phase matched direction and, e.g. fed into a fiber waveguide. This scheme operates in a free-space configuration, without requiring strong coupling of the atoms to a resonant optical cavity.
Review on process-microstructure-performance relationship in ALD-engineered SOFCs
Authors: Shin Jeong Woo , Go Dohyun , Kye Seung Hyeon , Lee Sungje , An Jihwan
Published: July 2019

Solid oxide fuel cells (SOFCs) are promising candidates for next-generation energy conversion devices, and much effort has been made to lower their operating temperature for wider applicability. Recently, atomic layer deposition (ALD), a novel variant of chemical vapor deposition, has demonstrated interesting research opportunities for SOFCs due to its unique features such as conformality and precise thickness/doping controllability. Individual components of SOFCs, namely the electrolyte, electrolyte–electrode interface, and electrode, can be effectively engineered by ALD nanostructures to yield higher performance and better stability. While the particulate or porous structures may benefit the electrode performance by maximizing the surface area, the dense film effectively blocks the chemical or physical shorting even at nanoscale thickness when applied to the electrolyte, which helps to increase the performance at low operating temperature. In this article, recent examples of the application of ALD-processed nanostructures to SOFCs are reviewed, and the quantitative relationship between ALD process, ALD nanostructure and the performance and stability of SOFCs is elucidated.
The Effects of Cardiovascular Risk Factors on Repeatable Battery for the Assessment of Neuropsychological Status (RBANS) Performance in Cognitively Healthy Older Adults
Authors: De Vito Alyssa N , Bernstein John P K , Weitzner Daniel , Calamia Matthew , Keller Jeffrey N
Published: July 2019

Objective

The current study investigated the differential impact cardiovascular risk factors (CVRFs) on Repeatable Battery for the Assessment of Neuropsychological Status (RBANS) performance in a large, cognitively healthy, older adult sample across 4 years.

Method

Participants were 486 individuals recruited through a longitudinal aging research study in the southeastern United States. Participants were 69.3% female, an average of 69.96 years old (SD = 6.58), 16.32 years of education (SD = 2.27), and Mini-Mental Status Exam score of 29.12 (SD = 1.16). Participants completed the RBANS at baseline and yearly thereafter, as well as the Uniform Data Set demographic and health questionnaires and the Geriatric Depression Scale.

Results

Multilevel modeling was conducted using standardized RBANS index scores. Overall, across indices, performance generally improved across time consistent with practice effects from repeated testing. Some CVRFs were associated with worse performance over time. For example, individuals with hypertension performed more poorly on immediate memory over time (t = −2.06, p < .05). Other CVRFs (e.g., BMI) were not associated with baseline performance or performance over time. (p > .05).

Conclusions

CVRFs differentially affect RBANS performance over time. These results extend previous cross-sectional findings regarding the impact of different cardiovascular health risks to a large, cognitively healthy, longitudinal sample.
Noise-cancelling repeat finder: uncovering tandem repeats in error-prone long-read sequencing data
Authors: Harris Robert S , Cechova Monika , Makova Kateryna D
Published: July 2019

Tandem DNA repeats can be sequenced with long-read technologies, but cannot be accurately deciphered due to the lack of computational tools taking high error rates of these technologies into account. Here we introduce Noise-Cancelling Repeat Finder (NCRF) to uncover putative tandem repeats of specified motifs in noisy long reads produced by Pacific Biosciences and Oxford Nanopore sequencers. Using simulations, we validated the use of NCRF to locate tandem repeats with motifs of various lengths and demonstrated its superior performance as compared to two alternative tools. Using real human whole-genome sequencing data, NCRF identified long arrays of the (AATGG)n repeat involved in heat shock stress response.

Availability and implementation

NCRF is implemented in C, supported by several python scripts, and is available in bioconda and at https://github.com/makovalab-psu/NoiseCancellingRepeatFinder.

Supplementary information

Supplementary data are available at Bioinformatics online.
Osteosarcoma cell-derived exosomes affect tumor microenvironment by specific packaging of microRNAs
Authors: Raimondi Lavinia , De Luca Angela , Gallo Alessia , Costa Viviana , Russelli Giovanna , Cuscino Nicola , Manno Mauro , Raccosta Samuele , Carina Valeria , Bellavia Daniele , Conigliaro Alice , Alessandro Riccardo , Fini Milena , Conaldi Pier Giulio , Giavaresi Gianluca
Published: July 2019

Bone microenvironment provides growth and survival signals essential for osteosarcoma (OS) initiation and progression. OS cells regulate communications inside tumor microenvironment through different ways and, among all, tumor-derived exosomes support cancer progression and metastasis. To define the contribution of OS-derived exosomes inside the microenvironment, we investigated the effects induced in bone remodeling mechanism and tumor angiogenesis. We demonstrated that exosomes promoted osteoclasts differentiation and bone resorption activity. Furthermore, exosomes potentiated tube formation of endothelial cells and increased angiogenic markers expression. We therefore investigated the micro RNA (miRNA) cargo from exosomes and their parental cells by performing small RNA sequencing through NGS Illumina platform. Hierarchical clustering highlighted a unique molecular profile of exosomal miRNA; bioinformatic analysis by DIANA-mirPath revealed that miRNAs identified take part in various biological processes and carcinogenesis. Among these miRNAs, some were already known for their involvement in the tumor microenvironment establishment, as miR-148a and miR-21-5p. Enforced expression of miR-148a and miR-21-5p in Raw264.7 and hTert immortalized umbilical vein endothelial cells recapitulated the effects induced by exosomes. Overall, our study highlighted the importance of OS exosomes in tumor microenvironment also by a specific packaging of miRNAs.
Unique Features of Subcortical Circuits in a Macaque Model of Congenital Blindness
Authors: Magrou Loïc , Barone Pascal , Markov Nikola T , Scheeren Gwylan , Killackey Herbert P , Giroud Pascale , Berland Michel , Knoblauch Kenneth , Dehay Colette , Kennedy Henry
Published: July 2019

There is an extensive modification of the functional organization of the brain in the congenital blind human, although there is little understanding of the structural underpinnings of these changes. The visual system of macaque has been extensively characterized both anatomically and functionally. We have taken advantage of this to examine the influence of congenital blindness in a macaque model of developmental anophthalmia. Developmental anophthalmia in macaque effectively removes the normal influence of the thalamus on cortical development leading to an induced “hybrid cortex (HC)” combining features of primary visual and extrastriate cortex. Here we show that retrograde tracers injected in early visual areas, including HC, reveal a drastic reduction of cortical projections of the reduced lateral geniculate nucleus. In addition, there is an important expansion of projections from the pulvinar complex to the HC, compared to the controls. These findings show that the functional consequences of congenital blindness need to be considered in terms of both modifications of the interareal cortical network and the ascending visual pathways.
Efficacy of catheter ablation for paroxysmal atrial fibrillation in patients with atrial septal defect: a comparison with transcatheter closure alone
Authors: Nakagawa Koji , Akagi Teiji , Nagase Satoshi , Takaya Yoichi , Kijima Yasufumi , Toh Norihisa , Watanabe Atsuyuki , Nishii Nobuhiro , Nakamura Kazufumi , Morita Hiroshi , Kusano Kengo , Ito Hiroshi
Published: July 2019

Aims

There is no valid treatment strategy for addressing paroxysmal atrial fibrillation (AF) in patients with unclosed atrial septal defect (ASD). We aimed to assess the efficacy of catheter ablation (CA) compared with transcatheter ASD closure alone for treating pre-existing paroxysmal AF in patients with ASD.

Methods and results

Among 908 patients who underwent transcatheter ASD closure, we evaluated 50 consecutive patients (63 ± 12 years) with paroxysmal AF. We compared the AF outcomes of these patients after transcatheter ASD closure between those with and without CA prior to ASD closure. Thirty (60%) patients underwent CA. During the follow-up period after ASD closure (mean: 49 ± 23 months), recurrence of AF was observed in 6/30 (20%) patients with upfront CA and 12/20 (60%) patients with ASD closure alone. Kaplan–Meier analysis showed that the AF-free survival rate was significantly higher for patients with CA than for those with ASD closure alone (79% vs. 37% at 5 years, P = 0.002). Upfront CA and previous heart failure hospitalization were associated with recurrence of AF after ASD closure [hazard ratio (HR) 0.18, 95% confidence interval (CI) 0.06–0.53; P = 0.002 and HR 4.64, 95% CI 1.60–13.49; P = 0.005, respectively].

Conclusion

In ASD patient with paroxysmal AF, transcatheter ASD closure alone demonstrated high AF recurrence rate after ASD closure. On the other hand, upfront CA prior to ASD closure substantially suppressed AF recurrence over the long term. A combination of CA and transcatheter ASD closure may be a feasible treatment strategy for paroxysmal AF in patients with ASD.
Integrated specialized atrial fibrillation clinics reduce all-cause mortality: post hoc analysis of a randomized clinical trial
Authors: Hendriks Jeroen M L , Tieleman Robert G , Vrijhoef Hubertus J M , Wijtvliet Petra , Gallagher Celine , Prins Martin H , Sanders Prashanthan , Crijns Harry J G M
Published: July 2019

Aims

An integrated chronic care programme in terms of a specialized outpatient clinic for patients with atrial fibrillation (AF), has demonstrated improved clinical outcomes. The aim of this study is to assess all-cause mortality in patients in whom AF management was delivered through a specialized outpatient clinic offering an integrated chronic care programme.

Methods and results

Post hoc analysis of a Prospective Randomized Open Blinded Endpoint Clinical trial to assess all-cause mortality in AF patients. The study included 712 patients with newly diagnosed AF, who were referred for AF management to the outpatient service of a University hospital. In the specialized outpatient clinic (AF-Clinic), comprehensive, multidisciplinary, and patient-centred AF care was provided, i.e. nurse-driven, physician supervised AF treatment guided by software based on the latest guidelines. The control group received usual care by a cardiologist in the regular outpatient setting.

After a mean follow-up of 22 months, all-cause mortality amounted 3.7% (13 patients) in the AF-Clinic arm and 8.1% (29 patients) in usual care [hazard ratio (HR) 0.44, 95% confidence interval (CI) 0.23–0.85; P = 0.014]. This included cardiovascular mortality in 4 AF-Clinic patients (1.1%) and 14 patients (3.9%) in usual care (HR 0.28; 95% CI 0.09–0.85; P = 0.025). Further, 9 patients (2.5%) died in the AF-Clinic arm due to a non-cardiovascular reason and 15 patients (4.2%) in the usual care arm (HR 0.59; 95% CI 0.26–1.34; P = 0.206).

Conclusion

An integrated specialized AF-Clinic reduces all-cause mortality compared with usual care. These findings provide compelling evidence that an integrated approach should be widely implemented in AF management.
A reduced stochastic model of core surface dynamics based on geodynamo simulations
Authors: Gillet N , Huder L , Aubert J
Published: July 2019

We make use of recent geodynamo simulations to propose a reduced stochastic model of the dynamics at the surface of Earth’s core. On decadal and longer periods, this model replicates the most energetic eigen directions of the geodynamo computation. Towards shorter timescales, it proposes a compensation for weaknesses of these simulations. This model furthermore accounts for the signature, in the geomagnetic secular variation, of errors of representativeness associated with unresolved processes. We incorporate the reduced stochastic model into a geomagnetic data assimilation algorithm—an augmented state ensemble Kalman filter—and apply it to re-analyse magnetic field changes over the period 1880–2015. Errors of representativeness appear to be responsible for an important fraction of the observed changes in the secular variation, as it is the case in the dynamo simulation.

Recovered core surface motions are primarily symmetric with respect to the equator. We observe the persistence of the eccentric westward gyre over the whole studied era and vortices that partly follow isocontours of the radial magnetic field at the core surface. Our flow models provide a good fit to decadal changes in the length-of-day and predict its interannual variations over the period 1940–2005. The largest core flow acceleration patterns are found in an equatorial belt below 10° in latitude and are associated with non-axisymmetric features. No systematic longitudinal drift of acceleration patterns is found, even over the past decades where satellite data are available. The acceleration of the high-latitude westward jet in the Pacific hemisphere is, during the satellite era, a factor 5 smaller than previously reported and its structure shows some evidence for equatorial asymmetry. The era of continuous satellite records provides enhanced contrast on the rapid core flow variations. The proposed assimilation algorithm offers the prospect of evaluating Earth-likeness of geodynamo simulations.
LMO2 gene deletions significantly worsen the prognosis of Wilms’ tumor development in patients with WAGR syndrome
Authors: Marakhonov Andrey V , Vasilyeva Tatyana A , Voskresenskaya Anna A , Sukhanova Natella V , Kadyshev Vitaly V , Kutsev Sergey I , Zinchenko Rena A
Published: July 2019

WAGR syndrome (OMIM #194072) is a rare genetic disorder that consists of development of Wilms’ tumor (nephroblastoma), aniridia, genitourinary anomalies and intellectual disability (mental retardation). It is associated with WAGR-region deletions in the 11p13 chromosome region. Our previous study of congenital aniridia patients revealed a noticeable number of aniridia patients with WAGR-region deletions but without Wilms’ tumor in their medical history. We assessed the involvement of other neighboring genes from affected chromosome regions in the patients with and without Wilms’ tumor. Reliable confidence was obtained for the LMO2 gene, which is significantly more often deleted in patients with nephroblastoma. Thus, our study presents genetic evidence that the development of Wilms tumors in WAGR syndrome patients should be attributed to the deletion of WT1 and LMO2 rather than WT1 only.
Reproduction, DNA methylation and biological age
Authors: Kresovich Jacob K , Harmon Quaker E , Xu Zongli , Nichols Hazel B , Sandler Dale P , Taylor Jack A
Published: July 2019

STUDY QUESTION

Are reproductive characteristics associated with genome-wide DNA methylation and epigenetic age?

SUMMARY ANSWER

Our data suggest that increasing parity is associated with differences in blood DNA methylation and small increases in epigenetic age.

WHAT IS KNOWN ALREADY

A study of 397 young Filipino women (ages 20–22) observed increasing epigenetic age with an increasing number of pregnancies.

STUDY DESIGN, SIZE, DURATION

We used data from 2356 non-Hispanic white women (ages 35–74) enrolled in the Sister Study cohort.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Data on reproductive history were ascertained via questionnaire. Of the 2356 women, 1897 (81%) reported at least one live birth. Among parous women, 487 (26%) women reported ever experiencing a pregnancy complication. Three epigenetic clocks (i.e. Hannum, Horvath and Levine) and genome-wide methylation were measured in DNA from whole blood using Illumina’s HumanMethylation450 BeadChip. We estimated association β-values and 95% CIs using linear regression.

MAIN RESULTS AND THE ROLE OF CHANCE

All three epigenetic clocks showed weak associations between number of births and epigenetic age (per live birth; Hannum: β = 0.16, 95% CI = 0.02, 0.29, P = 0.03; Horvath: β = 0.12, 95% CI = −0.04, 0.27, P = 0.14; Levine: β = 0.27, 95% CI = 0.08, 0.45, P = 0.01); however, additional adjustment for current BMI attenuated the associations. Among parous women, a history of abnormal glucose tolerance during pregnancy was associated with increased epigenetic age by the Hannum clock (β = 0.96; 95% CI = 0.10, 1.81; P = 0.03) and Levine clocks (β = 1.69; 95% CI = 0.54, 2.84; P < 0.01). In epigenome-wide analysis, increasing parity was associated with methylation differences at 17 CpG sites (Bonferroni corrected P≤ 1.0 × 10-7).

LIMITATIONS, REASONS FOR CAUTION

We relied on retrospective recall to ascertain reproductive history and pregnancy complications.

WIDER IMPLICATIONS OF THE FINDINGS

Our findings suggest that parity is associated with small increases in epigenetic age and with DNA methylation at multiple sites in the genome.

STUDY FUNDING/COMPETING INTEREST(S)

This research was supported by the Intramural Research program of the NIH, National Institute of Environmental Health Sciences (Z01-ES049033, Z01-ES049032 and Z01-ES044055). None of the authors have a conflict of interest.

TRIAL REGISTRATION NUMBER

Not applicable.
Patents and corporate credit risk
Authors: Frey Carl Benedikt , Neuhäusler Peter , Blind Knut
Published: July 2019

A vast literature documents a positive relationship between patents and companies stock market performance. Nevertheless, evidence on the influence of patents on companies’ debt capacity remains sparse. In this article, we examine the relationship between companies’ patent portfolios and their credit rating, providing relevant, albeit indirect, evidence on patents as a debt funding mechanism. Using a panel dataset on 155 U.S. firms, we find a positive relationship between companies’ credit rating and the size of their patent portfolio. Our indicators for valuable patents, however, provide a mixed picture. While there is a positive link between the average family size of a company’s patent portfolio and its credit ratings, we surprisingly find a significant negative relationship between patent forward citations and companies ratings. We hypothesize that this finding is the result of citations being associated with patent lawsuits, potentially incurring substantial losses on creditors.
Klebsiella pneumoniae and Klebsiella quasipneumoniae define the population structure of blaKPC-2Klebsiella: a 5 year retrospective genomic study in Singapore
Authors: Octavia Sophie , Kalisvar Marimuthu , Venkatachalam Indumathi , Ng Oon Tek , Xu Weizhen , Sridatta Prakki Sai Rama , Ong Yi Fa , Wang Liang De , Chua Amanda , Cheng Bernadette , Lin Raymond T P , Teo Jeanette W P
Published: July 2019

Objectives

To describe the population structure, molecular epidemiology and genetic context of blaKPC-2-bearing Klebsiella pneumoniae.

Methods

Isolates (n = 157) were retrospective, phenotypically carbapenem-resistant blaKPC-positive K. pneumoniae, collected from public hospitals. WGS was performed on the Illumina platform. Phylogenomic analysis, screening of resistance and virulence genes, and comparison of the genetic environment of blaKPC were carried out.

Results

Based on core-tree phylogeny, 67.5% of the isolates were K. pneumoniae and the remainder comprised Klebsiella quasipneumoniae. No Klebsiella variicola strains were observed. Only a single K. pneumoniae carbapenemase (KPC) variant type, blaKPC-2, was seen. MLSTs were diverse and did not comprise the ‘traditional’ KPC clonal group (CG) 258. blaKPC-2 was associated with a non-Tn4401 element (NTE) in >99% of genomes. Screening for four key virulence loci: yersiniabactin (ybt), aerobactin (iuc), salmochelin (iro) and colibactin (clb) as well as ICEKp (virulence-associated integrative conjugative element of K. pneumoniae), revealed the lack of virulence factors and ICEKp within K. quasipneumoniae. Amongst the K. pneumoniae, there were 32 ybt+ isolates (32/106, 30.2%) and, of these, 8 isolates were also clb+ (7.5%). K. pneumoniae serotypes K1 and K2, the majority of capsular serotype seen in patients with invasive liver abscess syndrome, were detected at 4.5% (7/157).

Conclusions

Results suggest that dissemination of blaKPC-2 is driven by NTEKPC in non-ST258 isolates. The detection of blaKPC-2K. pneumoniae serotypes K1/K2 carrying virulence factors, albeit in low numbers, reflects the worrisome convergence of carbapenem resistance and hypervirulence in K. pneumoniae.
Phase III study of tri-modality combination therapy with induction docetaxel plus cisplatin and 5-fluorouracil versus definitive chemoradiotherapy for locally advanced unresectable squamous-cell carcinoma of the thoracic esophagus (JCOG1510: TRIANgLE)
Authors: Terada Mitsumi , Hara Hiroki , Daiko Hiroyuki , Mizusawa Junki , Kadota Tomohiro , Hori Keisuke , Ogawa Hirofumi , Ogata Takashi , Sakanaka Katsuyuki , Sakamoto Takeshi , Kato Ken , Kitagawa Yuko
Published: July 2019

A randomized phase III trial commenced in Japan in February 2018. Definitive chemoradiotherapy (CRT) with cisplatin plus 5-fluorouracil is the current standard treatment for locally advanced unresectable esophageal carcinoma. The purpose of this study is to confirm the superiority of induction chemotherapy with docetaxel plus cisplatin and 5-fluorouracil (DCF) followed by conversion surgery or definitive CRT over definitive CRT alone for overall survival (OS) in patients with locally advanced unresectable squamous-cell carcinoma of thoracic esophagus. A total of 230 patients will be accrued from 47 Japanese institutions over 4.5 years. The primary endpoint is OS, and the secondary endpoints are progression-free survival, complete response rate of CRT, response rate of DCF, adverse events of DCF and CRT, late adverse events and surgical complications. This trial has been registered at the Japan Registry of Clinical Trials as jRCTs031180181.
TRIM65 E3 ligase targets VCAM-1 degradation to limit LPS-induced lung inflammation
Authors: Li Yong , Huang Xuan , Guo Fang , Lei Tianhua , Li Shitao , Monaghan-Nichols Paula , Jiang Zhisheng , Xin Hong-Bo , Fu Mingui
Published: July 2019

Although the adhesion molecules-mediated leukocyte adherence and infiltration into tissues is an important step of inflammation, the post-translational regulation of these proteins on the endothelial cells is poorly understood. Here, we report that TRIM65, an ubiquitin E3 ligase of tripartite protein family, selectively targets vascular cell adhesion molecule 1 (VCAM-1) and promotes its ubiquitination and degradation, by which it critically controls the duration and magnitude of sepsis-induced pulmonary inflammation. TRIM65 is constitutively expressed in human vascular endothelial cells. During TNFα-induced endothelial activation, the protein levels of TRIM65 and VCAM-1 are inversely correlated. Expression of wild-type TRIM65, but not expression of a TRIM65 mutant that lacks E3 ubiquitin ligase function in endothelial cells, promotes VCAM-1 ubiquitination and degradation, whereas small interference RNA-mediated knockdown of TRIM65 attenuates VCAM-1 protein degradation. Further experiments show that TRIM65 directly interacts with VCAM-1 protein and directs its polyubiquitination, by which TRIM65 controls monocyte adherence and infiltration into tissues during inflammation. Importantly, TRIM65-deficient mice are more sensitive to lipopolysaccharide-induced death, due to sustained and severe pulmonary inflammation. Taken together, our studies suggest that TRIM65-mediated degradation of VCAM-1 represents a potential mechanism that controls the duration and magnitude of inflammation.
Insights into the function of NADPH thioredoxin reductase C (NTRC) based on identification of NTRC-interacting proteins in vivo
Authors: González Maricruz , Delgado-Requerey Víctor , Ferrández Julia , Serna Antonio , Cejudo Francisco Javier
Published: July 2019

Redox regulation in heterotrophic organisms relies on NADPH, thioredoxins (TRXs), and an NADPH-dependent TRX reductase (NTR). In contrast, chloroplasts harbor two redox systems, one that uses photoreduced ferredoxin (Fd), an Fd-dependent TRX reductase (FTR), and TRXs, which links redox regulation to light, and NTRC, which allows the use of NADPH for redox regulation. It has been shown that NTRC-dependent regulation of 2-Cys peroxiredoxin (PRX) is critical for optimal function of the photosynthetic apparatus. Thus, the objective of the present study was the analysis of the interaction of NTRC and 2-Cys PRX in vivo and the identification of proteins interacting with them with the aim of identifying chloroplast processes regulated by this redox system. To assess this objective, we generated Arabidopsis thaliana plants expressing either an NTRC–tandem affinity purification (TAP)-Tag or a green fluorescent protein (GFP)–TAP-Tag, which served as a negative control. The presence of 2-Cys PRX and NTRC in complexes isolated from NTRC–TAP-Tag-expressing plants confirmed the interaction of these proteins in vivo. The identification of proteins co-purified in these complexes by MS revealed the relevance of the NTRC–2-Cys PRX system in the redox regulation of multiple chloroplast processes. The interaction of NTRC with selected targets was confirmed in vivo by bimolecular fluorescence complementation (BiFC) assays.
Tissue-specific respiratory burst oxidase homolog-dependent H2O2 signaling to the plasma membrane H+-ATPase confers potassium uptake and salinity tolerance in Cucurbitaceae
Authors: Huang Yuan , Cao Haishun , Yang Li , Chen Chen , Shabala Lana , Xiong Mu , Niu Mengliang , Liu Juan , Zheng Zuhua , Zhou Lijian , Peng Zhaowen , Bie Zhilong , Shabala Sergey
Published: July 2019

Potassium (K+) is a critical determinant of salinity tolerance, and H2O2 has been recognized as an important signaling molecule that mediates many physiological responses. However, the details of how H2O2 signaling regulates K+ uptake in the root under salt stress remain elusive. In this study, salt-sensitive cucumber and salt-tolerant pumpkin which belong to the same family, Cucurbitaceae, were used to answer the above question. We show that higher salt tolerance in pumpkin was related to its superior ability for K+ uptake and higher H2O2 accumulation in the root apex. Transcriptome analysis showed that salinity induced 5816 (3005 up- and 2811 down-) and 4679 (3965 up- and 714 down-) differentially expressed genes (DEGs) in cucumber and pumpkin, respectively. DEGs encoding NADPH oxidase (respiratory burst oxidase homolog D; RBOHD), 14-3-3 protein (GRF12), plasma membrane H+-ATPase (AHA1), and potassium transporter (HAK5) showed higher expression in pumpkin than in cucumber under salinity stress. Treatment with the NADPH oxidase inhibitor diphenylene iodonium resulted in lower RBOHD, GRF12, AHA1, and HAK5 expression, reduced plasma membrane H+-ATPase activity, and lower K+ uptake, leading to a loss of the salinity tolerance trait in pumpkin. The opposite results were obtained when the plants were pre-treated with exogenous H2O2. Knocking out of RBOHD in pumpkin by CRISPR/Cas9 [clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9] editing of coding sequences resulted in lower root apex H2O2 and K+ content and GRF12, AHA1, and HAK5 expression, ultimately resulting in a salt-sensitive phenotype. However, ectopic expression of pumpkin RBOHD in Arabidopsis led to the opposite effect. Taken together, this study shows that RBOHD-dependent H2O2 signaling in the root apex is important for pumpkin salt tolerance and suggests a novel mechanism that confers this trait, namely RBOHD-mediated transcriptional and post-translational activation of plasma membrane H+-ATPase operating upstream of HAK5 K+ uptake transporters.
‘A Table, A Cup, A Meowing Cat’: Marie Howe’s Theopoetics of the Ordinary
Authors: Cunning Andrew
Published: July 2019

This article connects the work of contemporary poet, Marie Howe (1950–) to a lineage of American writing dedicated to and founded on ‘the ordinary’. Beginning with Emerson and the transcendentalists, the argument is made that a largely Protestant tradition of American poetry and theology runs from Emerson and Whitman, through Elizabeth Bishop and Wallace Stevens, to Marilynne Robinson. Having established a distinctly American and specifically Protestant tradition of writing sourced from the mundane and the particular, it is shown how Marie Howe’s poetry is in dialogue with this lineage, particularly in her overtly theological third collection, The Kingdom of Ordinary Time (2008). The article concludes with a close reading of Howe’s poem ‘The Teacher’ from Magdalene (2017) and demonstrates how Howe ultimately disrupts the Emersonian tradition through her metaphor-less poetry. Using the Lord’s Supper as a motif, it is shown how Howe’s poetry opts for a Catholic approach to symbol, metaphor and transcendence, diverging theologically from Emerson, Stevens and Robinson’s expectations of ‘the ordinary’.
Definitive Management of a Traumatic Airway: Case Report
Authors: Fabich Robert A , Franklin Benjamin T , Langan Nicholas
Published: July 2019

Maxillofacial and neck trauma from penetrating injuries present unique challenges for anesthesia providers and surgeons. In the austere conditions of a combat setting these challenges may be amplified due to limited resources and injury severity. Currently there is a lack of evidence and consensus on how to best manage a traumatized airway in this situation. The authors of this paper present the successful emergency management of a traumatized airway from a severe maxillofacial and neck-penetrating wound. A stepwise team approach using strong communication and a global mental model facilitated definitive airway management in this case allowing for safe transport to definitive care.
Realism Redux: Staging ‘Billy Budd’ in the Age of Television
Authors: Ward-Griffin Danielle
Published: July 2019

Although the term ‘realism’ is frequently deployed in discussing opera productions, its meanings are far from self-evident. Examining four stage and screen productions of Benjamin Britten’s Billy Budd (1951–66), this article traces how this mode was reworked through television in the mid-twentieth century. Linking theatrical and televisual developments in the UK and the USA, I demonstrate how television’s concerns for intimacy and immediacy guided both the 1951 premiere and the condensed 1952 NBC television version. I then show how challenges to the status quo, particularly the ‘angry young men’ of British theatre and the backlash against naturalism on television, spurred the development of a revamped ‘realistic’ style in the 1964 stage and 1966 BBC productions of Billy Budd. Beyond Billy Budd, this article explores how the meanings of realism changed during the 1950s and 1960s, and how they continue to influence our study of opera performance history.
The impact of baryonic physics and massive neutrinos on weak lensing peak statistics
Authors: Fong Matthew , Choi Miyoung , Catlett Victoria , Lee Brandyn , Peel Austin , Bowyer Rachel , King Lindsay J , McCarthy Ian G
Published: July 2019

We study the impact of baryonic processes and massive neutrinos on weak lensing peak statistics that can be used to constrain cosmological parameters. We use the BAHAMAS suite of cosmological simulations, which self-consistently include baryonic processes and the effect of massive neutrino free-streaming on the evolution of structure formation. We construct synthetic weak lensing catalogues by ray tracing through light-cones, and use the aperture mass statistic for the analysis. The peaks detected on the maps reflect the cumulative signal from massive bound objects and general large-scale structure. We present the first study of weak lensing peaks in simulations that include both baryonic physics and massive neutrinos (summed neutrino mass Mν = 0.06, 0.12, 0.24, and 0.48 eV assuming normal hierarchy), so that the uncertainty due to physics beyond the gravity of dark matter can be factored into constraints on cosmological models. Assuming a fiducial model of baryonic physics, we also investigate the correlation between peaks and massive haloes, over a range of summed neutrino mass values. As higher neutrino mass tends to suppress the formation of massive structures in the Universe, the halo mass function and lensing peak counts are therefore modified as a function of Mν. Over most of the S/N range, the impact of fiducial baryonic physics is greater (less) than neutrinos for 0.06 and 0.12 (0.24 and 0.48) eV models. Both baryonic physics and massive neutrinos should be accounted for when deriving cosmological parameters from weak lensing observations.
Proper motions of the satellites of M31
Authors: Hodkinson Ben , Scholtz Jakub
Published: July 2019

We predict the range of proper motions of 19 satellite galaxies of M31 that would rotationally stabilize the M31 plane of satellites consisting of 15–20 members as identified by Ibata et al. Our prediction is based purely on the current positions and line-of-sight velocities of these satellites and the assumption that the plane is not a transient feature. These predictions are therefore independent of the current debate about the formation history of this plane. We further comment on the feasibility of measuring these proper motions with future observations by the THEIA satellite mission as well as the currently planned observations by HST and JWST.
Nuisance hardened data compression for fast likelihood-free inference
Authors: Alsing Justin , Wandelt Benjamin
Published: July 2019

We show how nuisance parameter marginalized posteriors can be inferred directly from simulations in a likelihood-free setting, without having to jointly infer the higher dimensional interesting and nuisance parameter posterior first and marginalize a posteriori. The result is that for an inference task with a given number of interesting parameters, the number of simulations required to perform likelihood-free inference can be kept (roughly) the same irrespective of the number of additional nuisances to be marginalized over. To achieve this, we introduce two extensions to the standard likelihood-free inference set-up. First, we show how nuisance parameters can be recast as latent variables and hence automatically marginalized over in the likelihood-free framework. Secondly, we derive an asymptotically optimal compression from N data to n summaries – one per interesting parameter - such that the Fisher information is (asymptotically) preserved, but the summaries are insensitive to the nuisance parameters. This means that the nuisance marginalized inference task involves learning n interesting parameters from n ‘nuisance hardened’ data summaries, regardless of the presence or number of additional nuisance parameters to be marginalized over. We validate our approach on two examples from cosmology: supernovae and weak-lensing data analyses with nuisance parametrized systematics. For the supernova problem, high-fidelity posterior inference of Ωm and w0 (marginalized over systematics) can be obtained from just a few hundred data simulations. For the weak-lensing problem, six cosmological parameters can be inferred from just $\mathcal {O}(10^3)$ simulations, irrespective of whether 10 additional nuisance parameters are included in the problem or not.
Rice FLUORESCENT1 Is Involved in the Regulation of Chlorophyll
Authors: Li Zhiyun , Mo Weiping , Jia Liqiang , Xu Yong-Chao , Tang Weijiang , Yang Wenqiang , Guo Ya-Long , Lin Rongcheng
Published: July 2019

Chlorophyll biosynthesis plays essential roles in photosynthesis and plant growth in response to environmental conditions. The accumulation of excess chlorophyll biosynthesis intermediates under light results in the production of reactive oxygen species and oxidative stress. In this study, we identified a rice (Oryza sativa) mutant, oxidation under photoperiod (oxp), that displayed photobleached lesions on its leaves, reduced growth and decreased chlorophyll content during light/dark cycles or following a dark-to-light transition. The oxp mutant accumulated more chlorophyll precursors (5-aminolevulinic acid and protochlorophyllide) than the wild type in the dark, and more singlet oxygen following light exposure. Several singlet-oxygen-responsive genes were greatly upregulated in oxp, whereas the expression patterns of OsPORA and OsPORB, two genes encoding the chlorophyll biosynthesis enzyme NADPH:protochlorop hyllide oxidoreductase, were altered in de-etiolated oxp seedlings. Molecular and complementation studies revealed that oxp is a loss-of-function mutant in LOC_Os01g32730, a homolog of FLUORESCENT (FLU) in Arabidopsis thaliana. Rice PHYTOCHROME-INTERACTING FACTOR-LIKE14 (OsPIL14) transcription factor directly bound to the OsFLU1 promoter and activated its expression. Dark-grown transgenic rice seedlings overexpressing OsPIL14 accumulated more chlorophyll and turned green faster than the wild type upon light illumination. Thus, OsFLU1 is an important regulator of chlorophyll biosynthesis in rice.
Molecular Functions of Rice Cytosol-Localized RING Finger Protein 1 in Response to Salt and Drought and Comparative Analysis of Its Grass Orthologs
Authors: Park Yong Chan , Choi Seung Young , Kim Jong Ho , Jang Cheol Seong
Published: July 2019

In higher plants, the post-translational modification of target proteins via the attachment of molecules such as ubiquitin (Ub) mediates a variety of cellular functions via the Ub/26S proteasome system. Here, a really interesting new gene (RING)-H2 type E3 ligase, which regulates target proteins via the Ub/26S proteasome system, was isolated from a rice plant, and its other grass orthologs were examined to determine the evolution of its molecular function during speciation. The gene encoding Oryza sativa cytoplasmic-localized RING finger protein 1 (OsCLR1) was highly expressed under salt and drought stresses. By contrast, the three grass orthologs, SbCLR1 from Sorghum bicolor, ZmCLR1 from Zea mays and TaCLR1 from Triticum aestivum, showed different responses to these stresses. Despite these differences, all four orthologs exhibited E3 ligase activity with cytosol-targeted localization, demonstrating conserved molecular functions. Although OsCLR1-overexpressing plants showed higher survival rates under both salt and drought stresses than that of the wild type (WT) plants, this pattern was not observed in the other orthologs. In addition, OsCLR1-overexpressing plants exhibited lower germination rates in ABA than that of WT plants, whereas the three ortholog CLR1-overexpressing plants showed rates similar to the WT plants. These results indicate the positive regulation of OsCLR1 in response to salt and drought in an ABA-dependent manner. Despite the molecular functions of the three CLR1 orthologs remaining largely unknown, our results provide an insight into the evolutionary fate of CLR1 grass orthologs during speciation after the divergence from a common ancestor.
Evolution of a Conduit System at the Marathon PGE–Cu Deposit: Insights from Silicate Mineral Textures and Chemistry
Authors: Shahabi Far Maryam , Samson Iain M , Gagnon Joel E , Good David J , Linnen Robert L , Ames Doreen
Published: July 2019

The Marathon platinum group element (PGE)–Cu deposit is hosted by the Two Duck Lake Gabbro of the Mesoproterozoic Coldwell Complex, Canada, and comprises three zones of mineralization, which have different textural, mineralogical and geochemical characteristics. The Footwall Zone occurs at the base of the Two Duck Lake Gabbro, at the contact with the Archean country rocks. The Main Zone occurs within the Two Duck Lake Gabbro, above the Footwall Zone. The W Horizon is an extraordinarily PGE-enriched zone that is characterized by very low Cu/Pd values, less pyrrhotite, and appreciably more bornite than the Footwall and Main zones. It occurs above Main Zone-equivalent mineralization in the southern half of the Two Duck Lake intrusion. Silicate mineral textures and chemistry reveal that the Marathon deposit formed in a dynamic magma conduit system with a complex magma evolution history. The deposit developed into three zones as a result of the multiple pulses of compositionally different magmas. Plagioclase commonly shows resorption surfaces with overgrowths and the anorthite content and concentrations of trace elements such as Fe, Sr, Ba, and rare earth elements in plagioclase change significantly across these surfaces. In rocks that contain sulfide minerals, plagioclase crystals have been partly resorbed and the resorbed rims are Ca-enriched and intergrown with sulfide mineral inclusions. These rims contain higher base-metal and sulfur contents and are light rare earth element-enriched compared with the primary plagioclase. These characteristics indicate input of a separate sulfide-enriched melt with a different composition compared with that from which the primary plagioclase crystallized. Additional evidence for the involvement of slightly different magmas during evolution of the three mineralized zones is derived from variations in pyroxene chemistry (e.g. higher Fe, lower Mg, V, and Sc) between the Footwall Zone and the other two zones and the absence of inverted pigeonite from the W Horizon. The PGE enrichment occurred at depth prior to intrusion and late-stage PGE-rich sulfide-bearing magmas intruded and formed the W Horizon. Therefore, the W Horizon is a zone of mineralization that formed late in the evolution of the Two Duck Lake Gabbro.
For the Sake of the Arguments: Reading the Headnotes to The Faerie Queene
Authors: Osorio Whewell Esther
Published: July 2019

This essay proposes taking a serious poetic and literary-historical interest in the ballad-stanza ‘Arguments’ which precede and summarize every Canto in Spenser’s Faerie Queene. Short, simple, and economical, the four-line Arguments seem at first a very different poetical space from the Spenserian stanza—but on closer reading, they demand an investment in the dimensions of printed language and the spaces and syntax of its storytelling which fits persuasively with the wider poetics of The Faerie Queene and with its narrative structures. The first section establishes the Arguments in a context of analogous early modern paratexts—in the Geneva Bible, Thomas Speght’s 1598 collected Chaucer, printed plays, and the Sternhold-Hopkins psalter. The second reads them closely as a ‘didactic technology’ which might, as well as helping us to read The Faerie Queene, help teach us how to.
Gut microbiota alterations associated with reduced bone mineral density in older adults
Authors: Das Mrinmoy , Cronin Owen , Keohane David M , Cormac Edel M , Nugent Helena , Nugent Michelle , Molloy Catherine , O’Toole Paul W , Shanahan Fergus , Molloy Michael G , Jeffery Ian B
Published: July 2019

Objective

To investigate compositional differences in the gut microbiota associated with bone homeostasis and fractures in a cohort of older adults.

Methods

Faecal microbiota profiles were determined from 181 individuals with osteopenia (n = 61) or osteoporosis (n = 60), and an age- and gender-matched group with normal BMD (n = 60). Analysis of the 16S (V3-V4 region) amplicon dataset classified to the genus level was used to identify significantly differentially abundant taxa. Adjustments were made for potential confounding variables identified from the literature using several statistical models.

Results

We identified six genera that were significantly altered in abundance in the osteoporosis or osteopenic groups compared with age- and gender-matched controls. A detailed study of microbiota associations with meta-data variables that included BMI, health status, diet and medication revealed that these meta-data explained 15–17% of the variance within the microbiota dataset. BMD measurements were significantly associated with alterations in the microbiota. After controlling for known biological confounders, five of the six taxa remained significant. Overall microbiota alpha diversity did not correlate to BMD in this study.

Conclusion

Reduced BMD in osteopenia and osteoporosis is associated with an altered microbiota. These alterations may be useful as biomarkers or therapeutic targets in individuals at high risk of reductions in BMD. These observations will lead to a better understanding of the relationship between the microbiota and bone homeostasis.