bluuebunny/crossref_metadata_2025 huggingface dataset:
Sustaining a warm corona in active galactic nucleus accretion discs
Authors: Ballantyne D R , Xiang X
Published: June 2020

Warm coronae, thick (τT = 10–20, where τT is the Thomson depth) Comptonizing regions with temperatures of ∼1 keV, are proposed to exist at the surfaces of accretion discs in active galactic nuclei (AGNs). By combining with the reflection spectrum, warm coronae may be responsible for producing the smooth soft excess seen in AGN X-ray spectra. This paper studies how a warm corona must adjust in order to sustain the soft excess through large changes in the AGN flux. Spectra from one-dimensional constant density and hydrostatic warm corona models are calculated assuming that the illuminating hard X-ray power law, gas density, Thomson depth, and coronal heating strength vary in response to changes in the accretion rate. We identify models that produce warm coronae with temperatures between 0.3 and 1.1 keV, and measure the photon indices and emitted fluxes in the 0.5–2 and 2–10 keV bands. Correlations and anticorrelations between these quantities depend on the evolution and structure of the warm corona. Tracing the path that an AGN follows through these correlations will constrain how warm coronae are heated and connected to the accretion disc. Variations in the density structure and coronal heating strength of warm coronae will lead to a variety of soft excess strengths and shapes in AGNs. A larger accretion rate will, on average, lead to a warm corona that produces a stronger soft excess, consistent with observations of local Seyfert galaxies.
The ram pressure stripped radio tails of galaxies in the Coma cluster
Authors: Chen Hao , Sun Ming , Yagi Masafumi , Bravo-Alfaro Hector , Brinks Elias , Kenney Jeffrey , Combes Francoise , Sivanandam Suresh , Jachym Pavel , Fossati Matteo , Gavazzi Giuseppe , Boselli Alessandro , Nulsen Paul , Sarazin Craig , Ge Chong , Yoshida Michitoshi , Roediger Elke
Published: June 2020

Previous studies have revealed a population of galaxies in galaxy clusters with ram pressure stripped (RPS) tails of gas and embedded young stars. We observed 1.4 GHz continuum and H i emission with the Very Large Array in its B-configuration in two fields of the Coma cluster to study the radio properties of RPS galaxies. The best continuum sensitivities in the two fields are 6 and 8 µJy per 4 arcsec beam, respectively, which are 4 and 3 times deeper than those previously published. Radio continuum tails are found in 10 (8 are new) out of 20 RPS galaxies, unambiguously revealing the presence of relativistic electrons and magnetic fields in the stripped tails. Our results also hint that the tail has a steeper spectrum than the galaxy. The 1.4 GHz continuum in the tails is enhanced relative to their H α emission by a factor of ∼7 compared to the main bodies of the RPS galaxies. The 1.4 GHz continuum of the RPS galaxies is also enhanced relative to their infrared emission by a factor of ∼2 compared to star-forming galaxies. The enhancement is likely related to ram pressure and turbulence in the tail. We furthermore present H i detections in three RPS galaxies and upper limits for the other RPS galaxies. The cold gas in D100’s stripped tail is dominated by molecular gas, which is likely a consequence of the high ambient pressure. No evidence of radio emission associated with ultra-diffuse galaxies is found in our data.
Highly efficient ‘hit-and-run’ genome editing with unconcentrated lentivectors carrying Vpr.Prot.Cas9 protein produced from RRE-containing transcripts
Authors: Indikova Ivana , Indik Stanislav
Published: June 2020

The application of gene-editing technology is currently limited by the lack of safe and efficient methods to deliver RNA-guided endonucleases to target cells. We engineered lentivirus-based nanoparticles to co-package the U6-sgRNA template and the CRISPR-associated protein 9 (Cas9) fused with a virion-targeted protein Vpr (Vpr.Prot.Cas9), for simultaneous delivery to cells. Equal spatiotemporal control of the vpr.prot.cas9 and gag/pol gene expression (the presence of Rev responsive element, RRE) greatly enhanced the encapsidation of the fusion protein and resulted in the production of highly efficient lentivector nanoparticles. Transduction of the unconcentrated, Vpr.Prot.Cas9-containing vectors led to >98% disruption of the EGFP gene in reporter HEK293-EGFP cells with minimal cytotoxicity. Furthermore, we detected indels in the targeted endogenous loci at frequencies of up to 100% in cell lines derived from lymphocytes and monocytes and up to 15% in primary CD4+ T cells by high-throughput sequencing. This approach may provide a platform for the efficient, dose-controlled and tissue-specific delivery of genome editing enzymes to cells and it may be suitable for simultaneous endogenous gene disruption and a transgene delivery.
Balloon Guide Catheter is Not Superior to Conventional Guide Catheter when Stent Retriever and Contact Aspiration are Combined for Stroke Treatment
Authors: Bourcier Romain , Marnat Gaultier , Labreuche Julien , Desal Hubert , Maria Federico Di , Consoli Arturo , Eugène François , Gory Benjamin , Dargazanli Cyril , Blanc Raphaël , Lapergue Bertrand ,   on behalf of the ETIS investigators
Published: June 2020

BACKGROUND

The effectiveness of balloon guide catheter (BGC) use has not been prospectively studied and its added value for improving reperfusion in acute ischemic stroke (AIS) treatment has only been reported in studies in which no contact aspiration was combined with the stent retriever (CA + SR).

OBJECTIVE

To compare the reperfusion results and clinical outcomes with and without BGC use when a combined CA + SR strategy is employed in first line to treat AIS.

METHODS

From January 2016 to April 2019, data from the ETIS registry (Endovascular Treatment in Ischemic Stroke) were reviewed. We included patients having undergone endovascular treatment with a combined CA + SR strategy and use or not of a BGC according to the operator's discretion. We compared BGC and nonBGC populations with matching and inverse probability of treatment weighting propensity scores. Primary outcome was the final near-complete/complete revascularization (mTICI2c/3) rate. Secondary outcomes included clinical outcomes and safety considerations.

RESULTS

Among 607 included patients, BGC was used in 32.9% (n = 200), and 190 matched pairs could be found. We found no significant difference in final mTICI2c/3 between patients with and without BGC (60.1% in BGC group compared to 62.7% in nonBGC group (matched RR, 0.92; 95%CI, 0.80 to 1.14)), first-pass mTICI2c/3 (35.1% vs 37.3%, matched RR, 0.94; 95%CI, 0.68 to 1.30), clinical outcome (matched RR of 1.12 (95%CI, 0.85 to 1.47) for favorable outcome.

CONCLUSION

The reperfusion and clinical results with and without BGC use are not significantly different when combined CA + SR are used as a first-line strategy for large vessel occlusion in the setting of AIS.
Support for Minimum Legal Sales Age Laws Set to Age 21 Across Australia, Canada, England, and United States: Findings From the 2018 ITC Four Country Smoking and Vaping Survey
Authors: Hawkins Summer Sherburne , Chung-Hall Janet , Craig Lorraine , Fong Geoffrey T , Borland Ron , Cummings K Michael , Levy David , Hitchman Sara C
Published: June 2020

Introduction

Although the United States has seen a rapid increase in tobacco minimum legal sales age (MLSA) laws set to age 21, there is wide variation across high-income countries and less is known about policy support outside of the United States. We examined the prevalence of support for tobacco MLSA 21 laws as well as associations by sociodemographic, smoking, and household characteristics among current and former adult smokers.

Methods

In this cross-sectional analysis, we used the 2018 International Tobacco Control Four Country Smoking and Vaping Survey to examine support for MLSA 21 laws among 12 904 respondents from Australia, Canada, England, and United States.

Results

Support for raising the legal age of purchasing cigarettes/tobacco to 21 ranged from 62.2% in the United States to 70.8% in Canada. Endorsement also varied by age, such that 40.6% of 18–20 years old supported the policy compared with 69.3% of those aged ≥60 years. In the adjusted regression model, there was also higher support among respondents who were female than male, non-white than white, those who did not allow smoking in the household than those that did, and those who had children in the household than those that did not. There were no differences by household income, education, or smoking status.

Conclusions

Most current and former smokers, including a sizable minority of those aged ≤20 years, support raising the legal age of purchasing cigarettes/tobacco to 21.

Implications

There was strong support for MLSA 21 laws among smokers and former smokers across Australia, Canada, England, and the United States, providing evidence for the increasing public support of the passage of these laws beyond the United States.
The Clinical and Radiological Manifestations in Coronavirus Disease 2019 With Negative Nucleic Acid Results
Authors: Lang Guanjing , Su Junwei , Wu Wenrui , Zhao Hong , Ying Shihong , Lou Haiyan , Shen Xiaomin , Yin Michael T , Xu Kaijin , Liu Jun , Ren Cheng , Sheng Jifang
Published: June 2020

Background

Coronavirus disease 2019 (COVID-19) was a new emerging disease with high infectiousness. Its diagnosis primarily depended on real-time polymerase chain reaction (RT-PCR) results. This study investigated epidemiological, clinical, and radiological characteristics of COVID-19 with negative RT-PCR results before confirmation.

Methods

Patients with COVID-19 were enrolled and divided into 2 groups: a negative group with negative RT-PCR results before confirmation and a positive group with positive results at the first detection. Epidemiological and clinical features were compared. Dynamic chest computerized tomography (CT) images of the negative group were evaluated.

Results

Ninety-nine laboratory-confirmed patients with COVID-19 including 8 patients (8%) with negative RT-PCR results were included. Patients from the negative group had similar epidemiological features: the average age (50.25 ± 13.27 years in the negative group and 53.70 ± 16.64 years in the positive group) and gender distribution (males made up 50% of the negative group and 62.6% of the positive group) were comparable. No significant differences were observed in clinical symptoms between the 2 groups. We found that fever was the most common symptom for both groups, followed by cough, expectoration, chest distress, fatigue, and gastroenterological symptoms. Moreover, ground-glass opacities and consolidations were the main manifestation in chest CT of patients with COVID-19 with or without confirmed RT-PCR results.

Conclusions

Regardless of initial RT-PCR results, patients with COVID-19 had similar epidemiological, clinical, and chest CT features. Our study suggests value from early chest CT scans in COVID-19 screening and dynamic significance of radiology in disease monitoring should guide clinical decisions.
Justice in Automated Administration
Authors: Tomlinson Joe
Published: June 2020

Abstract—

Public administration has, for some time now, been undergoing a digital transformation. Part of this change is the replacement of human public officials with automated decision-making systems. Beyond its immediate social and political significance, the EU Settlement Scheme—the mechanism established to allow EU citizens to remain resident in the UK after Brexit—represents the coming of age of a new template for automated administration. Understood in its context, this template raises foundational questions about the nature of administrative justice in the emerging digital state. This template, while it has various potential advantages, is essentially half-baked, contains significant risks without sufficient safeguards and requires revision before its suggested wider future application becomes a reality. Amendments to the template ought to be framed by reference to the precautionary principle, as this would continue to make for efficient implementation of policy while better protecting individuals in this experimental phase of automated administration.
ON A FORMULA FOR THE REGULARIZED DETERMINANT OF ZETA FUNCTIONS WITH APPLICATION TO SOME DIRICHLET SERIES
Authors: Hajli Mounir
Published: June 2020

In this paper, we study a large class of zeta functions. We evaluate explicitly the special values of these zeta functions and the associated derivatives at $0$. As an application, we recover several results on the zeta functions defined by two polynomials already obtained in the literature.
One Clonal Lineage of Calonectria pseudonaviculata Is Primarily Responsible for the Boxwood Blight Epidemic in the United States
Authors: Castroagudín Vanina L. , Weiland Jerry E. , Baysal-Gurel Fulya , Cubeta Marc A. , Daughtrey Margery L. , Gauthier Nicole Ward , LaMondia James , Luster Douglas G. , Hand Francesca Peduto , Shishkoff Nina , Williams-Woodward Jean , Yang Xiao , LeBlanc Nicholas , Crouch Jo Anne
Published: June 2020

Boxwood blight caused by Calonectria pseudonaviculata and C. henricotiae is destroying cultivated and native boxwood worldwide, with profound negative economic impacts on the horticulture industry. First documented in the United States in 2011, the disease has now occurred in 30 states. Previous research showed that global C. pseudonaviculata populations prior to 2014 had a clonal structure, and only the MAT1-2 idiomorph was observed. In this study, we examined C. pseudonaviculata genetic diversity and population structure in the United States after 2014, following the expansion of the disease across the country over the past 5 years. Two hundred eighteen isolates from 21 states were genotyped by sequencing 11 simple sequence repeat (SSR) loci and by MAT1 idiomorph typing. All isolates presented C. pseudonaviculata-specific alleles, indicating that C. henricotiae is still absent in the U.S. states sampled. The presence of only the MAT1-2 idiomorph and gametic linkage disequilibrium suggests the prevalence of asexual reproduction. The contemporary C. pseudonaviculata population is characterized by a clonal structure and composed of 13 multilocus genotypes (SSR-MLGs) unevenly distributed across the United States. These SSR-MLGs grouped into two clonal lineages (CLs). The predominant lineage CL2 (93% of isolates) is the primary contributor to U.S. disease expansion. The contemporary U.S. C. pseudonaviculata population is not geographically subdivided and not genetically differentiated from the U.S. population prior to 2014, but is significantly differentiated from the main European population, which is largely composed of CL1. Our findings provide insights into the boxwood blight epidemic that are critical for disease management and breeding of resistant boxwood cultivars.
Difficult Bag-Mask Ventilation in Critically Ill Children Is Independently Associated With Adverse Events*
Authors: Daigle Curran Hunter , Fiadjoe John E. , Laverriere Elizabeth K. , Bruins Benjamin B. , Lockman Justin L. , Shults Justine , Krawiec Conrad , Harwayne-Gidansky Ilana , Page-Goertz Christopher , Furlong-Dillard Jamie , Nadkarni Vinay M. , Nishisaki Akira
Published: June 2020

Objectives:

Bag-mask ventilation is commonly used prior to tracheal intubation; however, the epidemiology, risk factors, and clinical implications of difficult bag-mask ventilation among critically ill children are not well studied. This study aims to describe prevalence and risk factors for pediatric difficult bag-mask ventilation as well as its association with adverse tracheal intubation–associated events and oxygen desaturation in PICU patients.

Design:

A retrospective review of prospectively collected observational data from a multicenter tracheal intubation database (National Emergency Airway Registry for Children) from January 2013 to December 2018.

Setting:

Forty-six international PICUs.

Patients:

Children receiving bag-mask ventilation as a part of tracheal intubation in a PICU.

Interventions:

None.

Measurements and Main Results:

The primary outcome is the occurrence of either specific tracheal intubation–associated events (hemodynamic tracheal intubation–associated events, emesis with/without aspiration) and/or oxygen desaturation (< 80%). Factors associated with perceived difficult bag-mask ventilation were found using univariate analyses, and multivariable logistic regression identified an independent association between bag-mask ventilation difficulty and the primary outcome. Difficult bag-mask ventilation is reported in 9.5% (n = 1,501) of 15,810 patients undergoing tracheal intubation with bag-mask ventilation during the study period. Difficult bag-mask ventilation is more commonly reported with increasing age, those with a primary respiratory diagnosis/indication for tracheal intubation, presence of difficult airway features, more experienced provider level, and tracheal intubations without use of neuromuscular blockade (p < 0.001). Specific tracheal intubation–associated events or oxygen desaturation events occurred in 40.2% of patients with reported difficult bag-mask ventilation versus 19.8% in patients without perceived difficult bag-mask ventilation (p < 0.001). The presence of difficult bag-mask ventilation is independently associated with an increased risk of the primary outcome: odds ratio, 2.28 (95% CI, 2.03–2.57; p < 0.001).

Conclusions:

Difficult bag-mask ventilation is reported in approximately one in 10 PICU patients undergoing tracheal intubation. Given its association with adverse procedure–related events and oxygen desaturation, future study is warranted to improve preprocedural planning and real-time management strategies.
Psychometric Evaluation of the Chinese Version of Hypertension Self-care Profile
Authors: Ma Yue , Cheng Ho Yu , Sit Janet W.H. , Chien Wai Tong
Published: June 2020

Background

Valid and reliable assessment of the multidimensional self-care of patients with hypertension is important to tailor individualized care. The Hypertension Self-care Profile (HBP SCP), which comprises behavior, motivation, and self-efficacy scales, has been widely tested in various settings.

Objective

The aims of this study were to translate the HBP SCP into a Chinese version (HBP SCP-C) and evaluate its psychometric properties among Chinese adults with hypertension.

Methods

The HBP SCP was translated to Chinese using Cha's combined translation technique, and its content validity was examined by a panel of 7 experts. The psychometric properties of HBP SCP-C were tested in 200 Chinese patients with hypertension. Reliability tests included internal consistency and test-retest reliability. Exploratory factor analysis was performed to explore the structure of HBP SCP-C. Discriminative validity was examined by the known-group approach.

Results

The HBP SCP-C demonstrated satisfactory content validity. The 2-factor structures of the behavior (“health promotion” and “habit modification”) and self-efficacy (“intake management” and “health maintenance”) scales and 1-factor structure of the motivation scale were determined. The behavior, motivation, and self-efficacy scales had Cronbach α coefficients of 0.86, 0.94, and 0.93, respectively, and test-retest reliabilities were 0.82 to 0.98, 0.90 to 0.98, and 0.81 to 0.95, respectively. Significant differences between patients with or without comorbidities in behavior (t = 2.55, P = .011), motivation (t = 3.25, P = .001), and self-efficacy (t = 3.02, P = .003) supported the discriminative validity of HBP SCP-C.

Conclusions

The HBP SCP-C could be a reliable and valid instrument for evaluating hypertension self-care in Chinese patients.
Prevalence of Seizures and Risk Factors for Mortality in a Continuous Cohort of Pediatric Extracorporeal Membrane Oxygenation Patients
Authors: Yuliati Asri , Federman Myke , Rao Lekha M , Chen Lucia , Sim Myung Shin , Matsumoto Joyce H.
Published: June 2020

Objectives:

To evaluate the risk factors for mortality in pediatric extracorporeal membrane oxygenation patients.

Design:

Retrospective, single-center study.

Setting:

PICU and Pediatric cardiothoracic ICU in an urban, quaternary care center.

Patients:

All neonatal and pediatric patients requiring extracorporeal membrane oxygenation at our institution between January 2014 and December 2018, who underwent a standardized continuous electroencephalogram neuromonitoring protocol during most of the duration of extracorporeal membrane oxygenation support. We excluded patients who had extracorporeal membrane oxygenation initiated at another institution.

Intervention:

None.

Measurements and Main Results:

Sixty-six children required extracorporeal membrane oxygenation support during this period. Four patients were excluded, three due to lack of electroencephalogram data, one with extracorporeal membrane oxygenation initiated at other institution. In the remaining 62, 11 patients (17%) had seizures, of which 5 (45%) had status epilepticus. Eight of 11 patients (72%) had exclusively electrographic seizures. A total of 33 patients (53.2%) died, of which 22 died during extracorporeal membrane oxygenation course, and one died 3 years after hospital discharge. Mean survival from extracorporeal membrane oxygenation initiation was 766.9 days (standard deviation, 691.7; median, 546.5; interquartile range 1–3, 97.7–1255.0). In multivariate analysis, increased risk of mortality was associated with the use of extracorporeal cardiopulmonary resuscitation (hazard ratio, 4.33; 95% CI, 1.75–10.72; p = 0.002), imaging findings of cerebral edema (hazard ratio, 14.31; 95% CI, 5.18–39.54; p < 0.001), high lactate level (> 100 mg/dL within 2 hr preextracorporeal membrane oxygenation) (hazard ratio, 1.22; 95% CI, 1.03–1.44; p = 0.022), and prolonged deep hypothermic circulatory arrest (hazard ratio, 3.43; 95% CI, 1.65–7.13; p < 0.001). Presence of seizures was associated with imaging findings of cerebral edema (hazard ratio, 4.16; 95% CI, 1.04–16.58; p = 0.04).

Conclusions:

Seizures are common in children requiring extracorporeal membrane oxygenation support, with a high rate of electrographic seizures and status epilepticus, as in prior studies. Presence of cerebral edema is both risk factor for mortality and seizures. Other risk factors for mortality include extracorporeal cardiopulmonary resuscitation, high lactate levels, and prolonged deep hypothermic circulatory arrest.
An unusual case of Scedosporium apiospermum fungaemia in an immunocompetent patient with a left ventricular assist device and an implantable cardiac device
Authors: Tan Shireen Yan Ling , Chung Shimin Jasmine , Tan Teing Ee , Teo Louis , Tan Ban Hock , Tan Yen Ee
Published: June 2020

Left ventricular assist device (LVAD)-related infections are a leading cause of morbidity and mortality, with fungal infections being particularly difficult to manage. We report a case of an immunocompetent 39-year-old male with an LVAD and an implantable cardiac device (ICD) who developed fatal Scedosporium apiospermum fungaemia. To the best of our knowledge, this is the first reported case of LVAD-related S. apiospermum fungaemia.
Genomic profiling reveals heterogeneous populations of ductal carcinoma in situ of the breast
Authors: Nagasawa Satoi , Kuze Yuta , Maeda Ichiro , Kojima Yasuyuki , Motoyoshi Ai , Onishi Tatsuya , Iwatani Tsuguo , Yokoe Takamichi , Koike Junki , Chosokabe Motohiro , Kubota Manabu , Seino Hibiki , Suzuki Ayako , Seki Masahide , Tsuchihara Katsuya , Inoue Eisuke , Tsugawa Koichiro , Ohta Tomohiko , Suzuki Yutaka
Published: June 2020

A substantial number of cases of ductal carcinoma in situ (DCIS) of the breast will never progress to invasive ductal carcinoma (IDC), indicating they are overtreated under the current criteria. Although various candidate markers are available, the relevant markers for delineating the risk categories have not been established. In this study, we analyzed of the integrated clinical features of 431 cases of DCIS followed by deep sequence analyses in a 21-case discovery cohort and a 72-case validation cohort. We identified the five most critical markers of the aggressiveness of DCIS: age <45 years,HER2amplification,GATA3mutation positivity,PIK3CAmutation negativity, and PgR protein negativity. Spatial transcriptome and single-cell DNA sequencing further revealed thatGATA3dysfunction, but notPIK3CAmutation, upregulates EMT, invasion, and angiogenic pathways followed by PgR downregulation. These results reveal the existence of heterogeneous populations of DCIS and provide predictive markers for classifying DCIS and optimizing treatment.
Centromere-specific antibody-mediated karyotyping of OkinawanOikopleura dioicasuggests the presence of three chromosomes
Authors: Liu Andrew W. , Tan Yongkai , Masunaga Aki , Plessy Charles , Luscombe Nicholas M.
Published: June 2020

Oikopleura dioicais a ubiquitous marine tunicate of biological interest due to features that include dioecious reproduction, short life cycle, and vertebrate-like dorsal notochord while possessing a relatively compact genome. The use of tunicates as model organisms, particularly with these characteristics, offers the advantage of facilitating studies in evolutionary development and furthering understanding of enduring attributes found in the more complex vertebrates. At present, we are undertaking an initiative to sequence the genomes ofOikopleuraindividuals in populations found among the seas surrounding the Ryukyu Islands in southern Japan. To facilitate and validate genome assemblies, karyotyping was employed to count individual animals’ chromosomesin situusing centromere-specific antibodies directed against H3S28P, a prophase-metaphase cell cycle-specific marker of histone H3. New imaging data of embryos and oocytes stained with two different antibodies were obtained; interpretation of these data lead us to conclude that the OkinawanOikopleura dioicahas three pairs of chromosomes, akin to previous results from genomic assemblies in Atlantic populations. The imaging data have been deposited to the open-access EBI BioImage Archive for reuse while additionally providing representative images of two commercially available anti-H3S28P antibodies’ staining properties for use in epifluorescent and confocal based fluorescent microscopy.
Organization and control of the ascorbate biosynthesis pathway in plants
Authors: Fenech Mario , Amorim-Silva Vítor , del Valle Alicia Esteban , Arnaud Dominique , Castillo Araceli G. , Smirnoff Nicholas , Botella Miguel A.
Published: June 2020

The enzymatic steps involved inl-ascorbate biosynthesis in photosynthetic organisms (the Smirnoff-Wheeler, SW pathway) has been well established and here we comprehensively analyze the subcellular localization, potential physical interactions of SW pathway enzymes and assess their role in control of ascorbate synthesis. Transient expression of GFP-fusions inNicotiana benthamianaand Arabidopsis (Arabidopsis thaliana) mutants complemented with genomic constructs showed that while GME is cytosolic, VTC1, VTC2, VTC4, andl-GalDH have cytosolic and nuclear localization. While transgenic lines GME-GFP, VTC4-GFP andl-GalDH-GFP driven by their endogenous promoters accumulated the fusion proteins, the functional VTC2-GFP protein is detected at low level using immunoblot in a complementedvtc2null mutant. This low amount of VTC2 protein and the extensive analyses using multiple combinations of SW enzymes inN. benthamianasupported the roleof VTC2as the main control point of the pathway on ascorbate biosynthesis. Interaction analysis of SW enzymes using yeast two hybrid did not detect the formation of heterodimers, although VTC1, GME and VTC4 formed homodimers. Further coimmunoprecipitation (CoIP) analysis indicted that consecutive SW enzymes, as well as the first and last enzymes (VTC1 andl-GalDH), associate thereby adding a new layer of complexity to ascorbate biosynthesis. Finally, metabolic control analysis incorporating known kinetic characteristics, showed that previously reported feedback repression at the VTC2 step confers a high flux control coefficient and rationalizes why manipulation of other enzymes has little effect on ascorbate concentration.

One sentence summary

Metabolic engineering, genetic analysis and functional mutant complementation identify GDP-l-galactose phosphorylase as the main control point in ascorbate biosynthesis in green tissues.
The Olivary Pretectal Nucleus Receives Visual Input of High Spatial Resolution
Authors: Levine Jared N. , Schwartz Gregory W.
Published: June 2020

In the mouse, retinal output is computed by over 40 distinct types of retinal ganglion cells (RGCs) (Baden et al., 2016). Determining which of these many RGC types project to a retinorecipient region is a key step in elucidating the role that region plays in visually-mediated behaviors. Combining retrograde viral tracing and single-cell electrophysiology, we identify the RGC types which project to the olivary pretectal nucleus (OPN), a major visual structure. We find that retinal input to the OPN consists of a variety of intrinsically-photosensitive and conventional RGC types, the latter a diverse set of mostly ON RGCs. Surprisingly, while the OPN is most associated with the pupillary light reflex (PLR) pathway, requiring information about absolute luminance, we show that the majority of the retinal input to the OPN is from single cell type which transmits information unrelated to luminance. This ON-transient RGC accounts for two-thirds of the input to the OPN, and responds to small objects across a wide range of speeds. This finding suggests a role for the OPN in visually-mediated behaviors beyond the PLR.

Significance statement

The olivary pretectal nucleus is a midbrain structure which receives direct input from retinal ganglion cells (RGC), and modulates pupil diameter in response to changing absolute light level. In the present study, we combine viral tracing and electrophysiology to identify the RGC types which project to the OPN. Surprisingly, the majority of its input comes from a single type which does not encode absolute luminance, but instead responds to small objects across a wide range of speeds. These findings are consistent with a role for the OPN apart from pupil control and suggest future experiments to elucidate its full role in visually-mediated behavior.
Elucidation of regulatory modes for five two-component systems inEscherichia colireveals novel relationships
Authors: Choudhary Kumari Sonal , Kleinmanns Julia A. , Decker Katherine , Sastry Anand V , Gao Ye , Szubin Richard , Seif Yara , Palsson Bernhard O.
Published: June 2020

Escherichia coliuses two-component systems (TCSs) to respond to environmental signals. TCSs affect gene expression and are parts ofE. coli’s global transcriptional regulatory network (TRN). Here, we identified the regulons of five TCSs inE. coliMG1655: BaeSR and CpxAR, which were stimulated by ethanol stress; KdpDE and PhoRB, induced by limiting potassium and phosphate, respectively; and ZraSR, stimulated by zinc. We analyzed RNA-seq data using independent component analysis (ICA). ChIP-exo data was used to validate condition-specific target gene binding sites. Based on this data we (1) identify the target genes for each TCS; (2) show how the target genes are transcribed in response to stimulus; and (3) reveal novel relationships between TCSs, which indicate non-cognate inducers for various response regulators, such as BaeR to iron starvation, CpxR to phosphate limitation, and PhoB and ZraR to cell envelope stress. Our understanding of the TRN inE. coliis thus notably expanded.

Importance

E. coliis a common commensal microbe found in human gut microenvironment; however, some strains cause diseases like diarrhea, urinary tract infections and meningitis.E. coli’stwo-component system (TCS) modulates target gene expression, specially related to virulence, pathogenesis and anti-microbial peptides, in response to environmental stimuli. Thus, it is of utmost importance to understand the transcriptional regulation of the TCSs to infer its environmental adaptation and disease pathogenicity. Utilizing a combinatorial approach integrating RNAseq, independent component analysis, ChIP-exo and data mining, we show that TCSs have five different modes of transcriptional regulation. Our data further highlights non-cognate inducers of TCSs emphasizing cross-regulatory nature of TCSs inE. coliand suggests that TCSs may have a role beyond their cognate functionalities. In summary, these results when further incorporated with genome scale metabolic models can lead to understanding of metabolic capabilities of bacteria and correctly predict complex phenotype under diverse conditions.
Benchtop micro-mashing: high-throughput, robust, experimental beer brewing
Authors: Kerr Edward D. , Caboche Christopher H. , Josh Peter , Schulz Benjamin L.
Published: June 2020

Brewing science is undergoing a renaissance with the use of modern analytical chemistry and microbiology techniques. However, these modern analytical tools and techniques are not necessarily aligned with the scale and scope of brewing science. In particular, brewing processes can be time consuming, ingredient intensive, and require specialised technical equipment. These drawbacks compound with the need for appropriate numbers of replicates for adequately powered experimental design. Here, we describe a micro-scale mash method that can be performed using a common laboratory benchtop shaker/incubator, allowing for high throughput mashing and easy sample replication for statistical analysis. Proteomic profiles at both the protein and peptide levels were consistent between the 1 mL micro-mash and a 23 L Braumeister mash, and both mash scales produced wort with equivalent fermentable sugar and free amino acid profiles. The experimental flexibility offered by our micro-mash method allowed us to investigate the effects of altered mash parameters on the beer brewing proteome.
Deep learning model for ultrafast quantification of blood flow in diffuse correlation spectroscopy
Authors: Poon Chien-Sing , Long Feixiao , Sunar Ulas
Published: June 2020

Diffuse correlation spectroscopy (DCS) is increasingly used in the optical imaging field to assess blood flow in humans due to its non-invasive, real-time characteristics and its ability to provide label-free, bedside monitoring of blood flow changes. Previous DCS studies have utilized a traditional curve fitting of the analytical or Monte Carlo models to extract the blood flow changes, which are computationally demanding and less accurate when the signal to noise ratio decreases. Here, we present a deep learning model that eliminates this bottleneck by solving the inverse problem more than 2300% faster, with equivalent or improved accuracy compared to the nonlinear fitting with an analytical method. The proposed deep learning inverse model will enable real-time and accurate tissue blood flow quantification with the DCS technique.
Isolation by Distance in Populations with Power-law Dispersal
Authors: Smith Tyler B. , Weissman Daniel B.
Published: June 2020

Limited dispersal of individuals between generations results in isolation by distance, in which individuals further apart in space tend to be less related. Classic models of isolation by distance assume that dispersal distances are drawn from a thin-tailed distribution and predict that the proportion of the genome that is identical by descent between a pair of individuals should decrease exponentially with the spatial separation between them. However, in many natural populations, individuals occasionally disperse over very long distances. In this work, we use mathematical analysis and coalescent simulations to study the effect of long-range (power-law) dispersal on patterns of isolation by distance. We find that it leads to power-law decay of identity-by-descent at large distances with the same exponent as dispersal. We also find that broad power-law dispersal produces another, shallow power-law decay of identity-by-descent at short distances. These results suggest that the distribution of long-range dispersal events could be estimated from sequencing large population samples taken from a wide range of spatial scales.
Control of Cucumber green mottle mosaic virus in commercial greenhouse production with agricultural disinfectants and resistant cucumber varieties
Authors: Ellouze W. , Mishra V. , Howard R. J. , Ling K.-S. , Zhang W.
Published: June 2020

Cucumber green mottle mosaic virus (CGMMV) is a re-emerging threat to greenhouse cucumber and otherCucurbitaceaecrop productions worldwide. This seed-borne virus can easily spread from a contaminated seed to seedlings and to adjacent plants through mechanical contact of the foliage of diseased and healthy plants causing extensive yield losses. Additionally, infection may not be limited to the current crop but may also affect subsequent crops due to the long-term persistence of the virus on contaminated crop residues, greenhouse hard surfaces and soil or soil-less greenhouse substrates. In the present work, three greenhouse trials were conducted to develop an integrated pest management strategy towards controlling CGMMV in commercial cucumber greenhouses, by implementing an effective sanitization program and using resistant and grafted cucumber varieties. Results of sanitization trial highlighted that pressure washing and cleansing with an alkaline foam cleanser has eliminated CGMMV on some of the most heavily infested areas. However, three successive applications of cleanser and disinfectants were essential to completely eliminate CGMMV on porous and uneven surfaces, such as cement alleyway, tray gutter and floor mats. The varietal trial revealed that out of 15 cucumber varieties evaluated, two Mini (‘Katrina’ and ‘Khassib’) and three Long English (‘Sepire’, ‘Bomber’ and ‘LC13900’) had reduced or delayed CGMMV infection spread in the greenhouse but were intermediate in yield. The varieties ‘Sunniwell’ and ‘Bonbon’ were the most tolerant to CGMMV. They showed a high CGMMV infection level without compromising yield. These results proved the need for new productive cucumber varieties with CGMMV resistance. Grafting experiment showed only yield increase in case of grafted ‘Picowell’ over ‘Bonbon’ and not marked CGMMV resistance, which is a much desirable result when the grafting experiments are evaluated for their economic potential. In all, the current experimental trials unfold unique methodologies on CGMMV management in commercial greenhouses that are recommended to the growers to be followed for reducing crop losses and get benefitted on revenue compromise.
A robust and self-sustained peripheral circadian oscillator reveals differences in temperature compensation properties with central brain clocks
Authors: Versteven Marijke , Ernst Karla-Marlen , Stanewsky Ralf
Published: June 2020

Circadian clocks temporally organize physiology and behavior of organisms exposed to the daily changes of light and temperature on our planet, thereby contributing to fitness and health. Circadian clocks and the biological rhythms they control are characterized by three properties. (1) The rhythms are self-sustained in constant conditions with a period of ~ 24 hr, (2), they can be synchronized to the environmental cycles of light and temperature, and (3), they are temperature compensated, meaning they run with the same speed at different temperatures within the physiological range of the organism. Apart from the central clocks located in or near the brain, which regulate the daily activity rhythms of animals, the so-called peripheral clocks are dispersed throughout the body of insects and vertebrates. Based on the three defining properties, it has been difficult to determine if these peripheral clocks are true circadian clocks. We used a set of clock gene – luciferase reporter genes to address this question inDrosophilacircadian clocks. We show that self-sustained fly peripheral oscillators over compensate temperature changes, i.e., they slow down with increasing temperature. This over-compensation is not observed in central clock neurons in the fly brain, both in intact flies and in cultured brains, suggesting that neural network properties contribute to temperature compensation. However, an important neuropeptide for synchronizing the circadian neuronal network, the Pigment Dispersing Factor (PDF), is not required for self-sustained and temperature-compensated oscillations in subsets of the central clock neurons. Our findings reveal a fundamental difference between central and peripheral clocks, which likely also applies for vertebrate clocks.
Lung expression of genes encoding SARS-CoV-2 cell entry molecules and antiviral restriction factors: interindividual differences are associated with age and germline variants
Authors: Cotroneo Chiara E. , Mangano Nunzia , Dragani Tommaso A. , Colombo Francesca
Published: June 2020

Germline variants in genes involved in SARS-CoV-2 cell entry (i.e.ACE2andTMPRSS2) may influence the susceptibility to infection, as may polymorphisms in genes involved in the innate host response to viruses (e.g. APOBEC3 family). We searched for polymorphisms acting, in lung tissue, as expression quantitative trait loci (eQTLs) for 15 candidate COVID-19 susceptibility genes, selected for their roles in virus cell entry and host antiviral responses. No significant eQTLs were identified forACE2andTMPRSS2genes, whose expression levels did not associate with either sex or age of the 408 patients whose non-diseased lung tissue was analyzed. Instead, we identified sevencis-eQTLs (FDR<0.05) forAPOBEC3DandAPOBEC3G(rs139296, rs9611092, rs139331, rs8177832, rs17537581, rs61362448, and rs738469). The genetic control of the expression of APOBEC3 genes, which encode enzymes that interfere with virus replication, may explain interindividual differences in risk or severity of viral infections. Future studies should investigate the role of host genetics in COVID-19 patients using a genome-wide approach, to identify other genes whose expression levels are associated with susceptibility to SARS-CoV-2 infection or COVID-19 severity.

Author summary

Identification of expression quantitative trait loci (eQTLs) has become commonplace in functional studies on the role of individual genetic variants in susceptibility to diseases. In COVID-19, it has been proposed that individual variants in SARS-CoV-2 cell entry and innate host response genes may influence the susceptibility to infection. We searched for polymorphisms acting, in non-diseased lung tissue of 408 patients, as eQTLs for 15 candidate COVID-19 susceptibility genes, selected for their roles in virus cell entry and host antiviral responses. Sevencis-eQTLs were detected forAPOBEC3DandAPOBEC3Ggenes, which encode enzymes that interfere with virus replication. No significant eQTLs were identified forACE2andTMPRSS2genes. Therefore, the identified eQTLs may represent candidate loci modulating interindividual differences in risk or severity of SARS-CoV-2 virus infection.
The native structure of the full-length, assembled influenza A virus matrix protein, M1
Authors: Peukes Julia , Xiong Xiaoli , Erlendsson Simon , Qu Kun , Wan William , Calder Leslie J. , Schraidt Oliver , Kummer Susann , Freund Stefan M. V. , Kräusslich Hans-Georg , Briggs John A. G.
Published: June 2020

Influenza A virus causes millions of severe illnesses during annual epidemics. The most abundant protein in influenza virions is the matrix protein M1 that mediates virus assembly by forming an endoskeleton beneath the virus membrane. The structure of full-length M1, and how it oligomerizes to mediate assembly of virions, is unknown. Here we have determined the complete structure of assembled M1 within intact virus particles, as well as the structure of M1 oligomers reconstituted in vitro. We found that the C-terminal domain of M1 is disordered in solution, but can fold and bind in trans to the N-terminal domain of another M1 monomer, thus polymerising M1 into linear strands which coat the interior surface of the assembling virion membrane. In the M1 polymer, five histidine residues, contributed by three different M1 monomers, form a cluster that can serve as the pH-sensitive disassembly switch after entry into a target cell. These structures therefore provide mechanisms for influenza virus assembly and disassembly.
Defining the signalling determinants of a posterior ventral spinal cord identity in human neuromesodermal progenitor derivatives
Authors: Wind Matthew , Gogolou Antigoni , Manipur Ichcha , Granata Ilaria , Butler Larissa , Andrews Peter W. , Barbaric Ivana , Ning Ke , Guarracino Mario R. , Placzek Marysia , Tsakiridis Anestis
Published: June 2020

The anteroposterior axial identity of motor neurons (MNs) determines their functionality and vulnerability to neurodegeneration. Thus it is a critical parameter in the design of strategies aiming to produce MNs from human pluripotent stem cells (hPSCs) for regenerative medicine and disease modelling applications. However, thein vitrogeneration of posterior spinal cord MNs has been challenging. Although the induction of cells resembling neuromesodermal progenitors (NMPs), thebona fideprecursors of the mammalian spinal cord, offers a promising solution, the progressive specification of posterior MNs from these cells is not well-defined. Here we determine the signals guiding the transition of human NMP-like cells toward posterior ventral spinal cord neurectoderm. We show that combined WNT-FGF activities drive a posterior dorsal early neural state while suppression of TGFβ-BMP signalling pathways, combined with SHH stimulation, promotes a ventral identity. Based on these results, we define an optimised protocol for the generation of posterior MNs that can efficiently integrate within the neural tube of chick embryos. We expect that our findings will facilitate the functional comparison of hPSC-derived spinal cord cells of distinct axial identities.
Targeted over-expression of PPARγ in pig skeletal muscle improves oxidative fiber formation and intramuscular fat deposition
Authors: Gu Hao , Zhou Ying , Yang Jinzeng , Li Jianan , Peng Yaxin , Zhang Xia , Miao Yiliang , Jiang Wei , Bu Guowei , Hou Liming , Li Ting , Zhang Lin , Xia Xiaoliang , Ma Zhiyuan , Xiong Yuanzhu , Zuo Bo
Published: June 2020

PPARγ is a master regulator of adipogenesis and lipogenesis. To understand its roles in fat deposition and fiber formation in skeletal muscle, we successfully generated muscle-specific overexpression of PPARγ by pig cloning procedures. The content of intramuscular fat was significantly increased in PPARγ transgenic pigs while the muscle mass as lean percentage of body weight was not changed. The proteomics analysis demonstrated oxidative metabolism of fatty acids and respiratory chain were increased in PPARγ pigs. Furthermore, expressions of oxidative muscle fiber-related genes such as MyHC1 and TNNT1 were enhanced. CAMK2, MEF2 and PGC1α were also significantly increased in skeletal muscle of PPARγ pigs, indicating that Ca2+-sensitive phosphatases and kinases may play an important role in the switch of muscle fiber types when PPARγ activity is elevated in skeletal muscle. The results support skeletal muscle-specific overexpression of PPARγ can promote oxidative fiber formation and intramuscular fat deposition in pigs.