bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pectin methylesterase selectively softens the onion epidermal wall yet reduces acid-induced creep
Authors: Wang Xuan , Wilson Liza , Cosgrove Daniel J 
Published: January 2020

AbstractDe-esterification of homogalacturonan (HG) is thought to stiffen pectin gels and primary cell walls by increasing calcium cross-linking between HG chains. Contrary to this idea, recent studies found that HG de-esterification correlated with reduced stiffness of living tissues, measured by surface indentation. The physical basis of such apparent wall softening is unclear, but possibly involves complex biological responses to HG modification. To assess the direct physical consequences of HG de-esterification on wall mechanics without such complications, we treated isolated onion (Allium cepa) epidermal walls with pectin methylesterase (PME) and assessed wall biomechanics with indentation and tensile tests. In nanoindentation assays, PME action softened the wall (reduced the indentation modulus). In tensile force/extension assays, PME increased plasticity, but not elasticity. These softening effects are attributed, at least in part, to increased electrostatic repulsion and swelling of the wall after PME treatment. Despite softening and swelling upon HG de-esterification, PME treatment alone failed to induce cell wall creep. Instead, acid-induced creep, mediated by endogenous α-expansin, was reduced. We conclude that HG de-esterification physically softens the onion wall, yet reduces expansin-mediated wall extensibility.
Inhibition of jasmonate-mediated plant defences by the fungal metabolite higginsianin B
Authors: Dallery Jean-Félix , Zimmer Marlene , Halder Vivek , Suliman Mohamed , Pigné Sandrine , Le Goff Géraldine , Gianniou Despoina D , Trougakos Ioannis P , Ouazzani Jamal , Gasperini Debora , O’Connell Richard J 
Published: January 2020

Abstract
Infection of Arabidopsis thaliana by the ascomycete fungus Colletotrichum higginsianum is characterized by an early symptomless biotrophic phase followed by a destructive necrotrophic phase. The fungal genome contains 77 secondary metabolism-related biosynthetic gene clusters, whose expression during the infection process is tightly regulated. Deleting CclA, a chromatin regulator involved in the repression of some biosynthetic gene clusters through H3K4 trimethylation, allowed overproduction of three families of terpenoids and isolation of 12 different molecules. These natural products were tested in combination with methyl jasmonate, an elicitor of jasmonate responses, for their capacity to alter defence gene induction in Arabidopsis. Higginsianin B inhibited methyl jasmonate-triggered expression of the defence reporter VSP1p:GUS, suggesting it may block bioactive jasmonoyl isoleucine (JA-Ile) synthesis or signalling in planta. Using the JA-Ile sensor Jas9-VENUS, we found that higginsianin B, but not three other structurally related molecules, suppressed JA-Ile signalling by preventing the degradation of JAZ proteins, the repressors of jasmonate responses. Higginsianin B likely blocks the 26S proteasome-dependent degradation of JAZ proteins because it inhibited chymotrypsin- and caspase-like protease activities. The inhibition of target degradation by higginsianin B also extended to auxin signalling, as higginsianin B treatment reduced auxin-dependent expression of DR5p:GUS. Overall, our data indicate that specific fungal secondary metabolites can act similarly to protein effectors to subvert plant immune and developmental responses.
‘Turn it Over and Over’ (Avot 5:22): American Jewish Women’s Poetry on Lot’s Wife
Authors: Koplowitz-Breier Anat 
Published: January 2020

Abstract
Although mentioned only twice in Genesis (19:17, 26), Lot’s wife has been a topic of much discussion amongst both traditional and modern commentators and exegetes. However, as opposed to the androcentric traditional midrash, the Jewish American women poets, who write midrashic-poetry, re-read the biblical story with a feminine/feminist lens, making what Alicia Ostriker calls ‘revisionist mythmaking.’ In this article, I shall focus on seven poems written from the 1980s through to 2014. I shall endeavor to evince the way(s) in which they make use of the biblical text, dealing with themes raised in the traditional midrash or re-reading the latter. I will show how by adducing to her emotions, longings and memories and even fear of the future, the poets portray Lot’s wife first and foremost as a woman.
Unveiling Vela – variability of interstellar lines in the direction of the Vela supernova remnant – III. Na D and Ca ii K
Authors: Kameswara Rao N , Lambert David L , Reddy Arumalla B S , Gupta Ranjan , Muneer S , Varghese Baba , Singh Harinder P 
Published: January 2020

ABSTRACT
High-resolution optical spectra were obtained in 2017–2019 with The Southern African Large Telescope of 15 stars in the direction of the Vela supernova remnant. Interstellar Ca ii H & K and Na i D lines are discussed in this paper. In particular, the line profiles are compared with profiles at a comparable spectral resolution obtained in 1993–1996 by Cha and Sembach. Ten of the lines of sight show changes to one or more of the components in that line of sight. Changes include small changes (1–2 km s−1) in radial velocity and/or increases/decreases in equivalent width over the two decades between the periods of observation. Changes are more obvious in the Ca K line than in the Na D lines. These changes are attributed to gas disturbed by interactions between the supernova ejecta and the surrounding interstellar medium. A representative time-scale may be 20–50 yr. Small-scale variations in line profiles across the face of the remnant suggest, as previously remarked, that a linear scale for interactions is a small fraction of the 40 pc size of the present remnant.
Do dense molecular cores with broad emission spectra at |l| ≈ 5.4°, |b| ≈ 0.4° trace the Galactic bar? A multimolecular line study from HOPS
Authors: Akhter Shaila , Cunningham Maria R , Harvey-Smith Lisa , Nawaz Mohammad Ali , Jones Paul A , Walsh Andrew , de Gouveia Dal Pino Elisabete M , Falceta-Gonçalves Diego 
Published: January 2020

ABSTRACT
We used NH$\rm _3$(1,1) data from the H$\rm _2$O Southern Galactic Plane Survey (HOPS) between −60° &lt; l &lt; −2.7° and 3.9° &lt; l &lt; 30° and |b| &lt; 0.5° to identify dense molecular regions/clumps of the Milky Way Galaxy that are likely to form high-mass stars. We identified ∼500 such clumps and in this paper we report on 14 of these clumps near the Central Molecular Zone that show broad emission spectral lines (with observed velocity widths between 19.8 and 47.6 km s−1 corresponding to intrinsic velocity widths between 7.1 and 25.2 km s−1). We find that these clumps are grouped into three clusters of dense molecular cores centred at l ≈ 5.4°, −5.4°, and −10°. We name them ‘Cluster-1’, ‘Cluster-2’ (also known as ‘Bania’s Clump 1’), and ‘Cluster-3’. We find that the same clumps exhibit broad emission spectra for other molecular lines – NH$\rm _3$(2,2), (3,3), and HC3N(3 − 2). The antisymmetry of Cluster-1 and Cluster-2 in the l − b plane, and the large velocity dispersion of each clump in these two clusters suggest that clusters 1 and 2 may be associated with the Galactic bar potential x−1 orbits. Our assessments show that the clumps of these three clusters host hot gases and their emission-line broadening are associated with shock heating. We find that Cluster-3 is likely to be undergoing high-mass star formation, as suggested by the presence of emission from H$\rm _2$O maser and radio recombination line (H69α) from HOPS.
Modelling the AGN broad-line region using single-epoch spectra − II. Nearby AGNs
Authors: Raimundo S I , Vestergaard M , Goad M R , Grier C J , Williams P R , Peterson B M , Treu T 
Published: January 2020

ABSTRACTThe structure of the broad-line region (BLR) is an essential ingredient in the determination of active galactic nucleus (AGN) virial black hole masses, which in turn are important to study the role of black holes in galaxy evolution. Constraints on the BLR geometry and dynamics can be obtained from velocity-resolved studies using reverberation mapping data (i.e. monitoring data). However, monitoring data are observationally expensive and only available for a limited sample of AGNs, mostly confined to the local Universe. Here, we explore a new version of a Bayesian inference, physical model of the BLR that uses an individual spectrum and prior information on the BLR size from the radius–luminosity relation, to model the AGN BLR geometry and dynamics. We apply our model to a sample of 11 AGNs, which have been previously modelled using monitoring data. Our single-epoch BLR model is able to constrain some of the BLR parameters with inferred parameter values that agree within the uncertainties with those determined from the modelling of monitoring data. We find that our model is able to derive stronger constraints on the BLR for AGNs with broad emission lines that qualitatively have more substructure and more asymmetry, presumably as they contain more information to constrain the physical model. The performance of this model makes it a practical and cost-effective tool to determine some of the BLR properties of a large sample of low- and high-redshift AGNs, for which monitoring data are not available.
Aging haloes: implications of the magnitude gap on conditional statistics of stellar and gas properties of massive haloes
Authors: Farahi Arya , Ho Matthew , Trac Hy 
Published: January 2020

ABSTRACT
Cold dark matter model predicts that the large-scale structure grows hierarchically. Small dark matter haloes form first. Then, they grow gradually via continuous merger and accretion. These haloes host the majority of baryonic matter in the Universe in the form of hot gas and cold stellar phase. Determining how baryons are partitioned into these phases requires detailed modelling of galaxy formation and their assembly history. It is speculated that formation time of the same mass haloes might be correlated with their baryonic content. To evaluate this hypothesis, we employ haloes of mass above $10^{14}\, \mathrm{M}_{\odot }$ realized by TNG300 solution of the IllustrisTNG project. Formation time is not directly observable. Hence, we rely on the magnitude gap between the brightest and the fourth brightest halo galaxy member, which is shown that traces formation time of the host halo. We compute the conditional statistics of the stellar and gas content of haloes conditioned on their total mass and magnitude gap. We find a strong correlation between magnitude gap and gas mass, BCG stellar mass, and satellite galaxies stellar mass, but not the total stellar mass of halo. Conditioning on the magnitude gap can reduce the scatter about halo property–halo mass relation and has a significant impact on the conditional covariance. Reduction in the scatter can be as significant as 30 per cent, which implies more accurate halo mass prediction. Incorporating the magnitude gap has a potential to improve cosmological constraints using halo abundance and allows us to gain insight into the baryon evolution within these systems.
An analysis of galaxy cluster mis-centring using cosmological hydrodynamic simulations
Authors: Yan Z , Raza N , Van Waerbeke L , Mead A J , McCarthy I G , Tröster T , Hinshaw G 
Published: January 2020

ABSTRACT
The location of a galaxy cluster’s centroid is typically derived from observations of the galactic and/or gas component of the cluster, but these typically deviate from the true centre. This can produce bias when observations are combined to study average cluster properties. Using data from the BAryons and HAloes of MAssive Systems (BAHAMAS) cosmological hydrodynamic simulations, we study this bias in both two and three dimensions for 2000 clusters over the 1013–1015 M⊙ mass range. We quantify and model the offset distributions between observationally motivated centres and the ‘true’ centre of the cluster, which is taken to be the most gravitationally bound particle measured in the simulation. We fit the cumulative distribution function of offsets with an exponential distribution and a Gamma distribution fit well with most of the centroid definitions. The galaxy-based centres can be seen to be divided into a mis-centred group and a well-centred group, with the well-centred group making up about $60{{\ \rm per\ cent}}$ of all the clusters. Gas-based centres are overall less scattered than galaxy-based centres. We also find a cluster-mass dependence of the offset distribution of gas-based centres, with generally larger offsets for smaller mass clusters. We then measure cluster density profiles centred at each choice of the centres and fit them with empirical models. Stacked, mis-centred density profiles fit to the Navarro–Frenk–White dark matter profile and Komatsu–Seljak gas profile show that recovered shape and size parameters can significantly deviate from the true values. For the galaxy-based centres, this can lead to cluster masses being underestimated by up to $10{{\ \rm per\ cent}}$.
CellCoal: Coalescent Simulation of Single-Cell Sequencing Samples
Authors: Posada David 
Published: January 2020

AbstractOur capacity to study individual cells has enabled a new level of resolution for understanding complex biological systems such as multicellular organisms or microbial communities. Not surprisingly, several methods have been developed in recent years with a formidable potential to investigate the somatic evolution of single cells in both healthy and pathological tissues. However, single-cell sequencing data can be quite noisy due to different technical biases, so inferences resulting from these new methods need to be carefully contrasted. Here, I introduce CellCoal, a software tool for the coalescent simulation of single-cell sequencing genotypes. CellCoal simulates the history of single-cell samples obtained from somatic cell populations with different demographic histories and produces single-nucleotide variants under a variety of mutation models, sequencing read counts, and genotype likelihoods, considering allelic imbalance, allelic dropout, amplification, and sequencing errors, typical of this type of data. CellCoal is a flexible tool that can be used to understand the implications of different somatic evolutionary processes at the single-cell level, and to benchmark dedicated bioinformatic tools for the analysis of single-cell sequencing data. CellCoal is available at https://github.com/dapogon/cellcoal.
A Systematic Literature Review of Peripheral Nerve Stimulation Therapies for the Treatment of Pain
Authors: Deer Timothy R , Esposito Michael F , McRoberts W Porter , Grider Jay S , Sayed Dawood , Verrills Paul , Lamer Tim J , Hunter Corey W , Slavin Konstantin V , Shah Jay M , Hagedorn Jonathan M , Simopoulos Tom , Gonzalez David Abejon , Amirdelfan Kasra , Jain Sameer , Yang Ajax , Aiyer Rohit , Antony Ajay , Azeem Nomen , Levy Robert M , Mekhail Nagy 
Published: January 2020

AbstractObjectiveTo conduct a systematic literature review of peripheral nerve stimulation (PNS) for pain.DesignGrade the evidence for PNS.MethodsAn international interdisciplinary work group conducted a literature search for PNS. Abstracts were reviewed to select studies for grading. Inclusion/exclusion criteria included prospective randomized controlled trials (RCTs) with meaningful clinical outcomes that were not part of a larger or previously reported group. Excluded studies were retrospective, had less than two months of follow-up, or existed only as abstracts. Full studies were graded by two independent reviewers using the modified Interventional Pain Management Techniques–Quality Appraisal of Reliability and Risk of Bias Assessment, the Cochrane Collaborations Risk of Bias assessment, and the US Preventative Services Task Force level-of-evidence criteria.ResultsPeripheral nerve stimulation was studied in 14 RCTs for a variety of painful conditions (headache, shoulder, pelvic, back, extremity, and trunk pain). Moderate to strong evidence supported the use of PNS to treat pain.ConclusionPeripheral nerve stimulation has moderate/strong evidence. Additional prospective trials could further refine appropriate populations and pain diagnoses.
Unemployment Fluctuations, Match Quality, and the Wage Cyclicality of New Hires
Authors: Gertler Mark , Huckfeldt Christopher , Trigari Antonella 
Published: January 2020

Abstract
We revisit the issue of the high cyclicality of wages of new hires. We show that after controlling for composition effects likely involving procyclical upgrading of job match quality, the wages of new hires are no more cyclical than those of existing workers. The key implication is that the sluggish behaviour of wages for existing workers is a better guide to the cyclicality of the marginal cost of labour than is the high measured cyclicality of new hires wages unadjusted for composition effects. Key to our identification is distinguishing between new hires from unemployment versus those who are job changers. We argue that to a reasonable approximation, the wages of the former provide a composition-free estimate of the wage flexibility, while the same is not true for the latter. We then develop a quantitative general equilibrium model with sticky wages via staggered contracting, on-the-job search, and heterogeneous match quality, and show that it can account for both the panel data evidence and aggregate evidence on labour market volatility.
APPLICATION OF THE MCNP6.1 CODE TO ESTIMATE THE DIRECTIONAL DEPENDENCE OF RADIATION PROTECTION FACTOR VALUES FOR A SIMPLE SURROGATE VEHICLE
Authors: McHale Stephen R , Decker Andrew W , Huff Blake K 
Published: January 2020

Abstract
Radiation protection factor (RPF) values are relevant to various US defense and civil support organizations. An equation was developed to quantify the angular-dependent protection of a shielding configuration in the presence of a mono-energetic radiation field. Values of ambient dose equivalent, H*(10), were computed with version 6.1 of the Monte Carlo N-Particle Code (MCNP6.1) for more than 70 distinct, mono-energetic, planar photon and neutron fields using both the kerma approximation and energy deposition from primary and secondary radiations. The two computational approaches were compared, and the MCNP6.1 models were then modified to simulate the same radiation fields and compute values of directional dose equivalent, H′(10,α), in a tissue sphere centered inside a surrogate vehicle for 13 angles of incidence. Values of H*(10) and H′(10,α) were recast as energy- and angular-dependent RPF values for the incident field–shielding geometries and tabulated. Examples of implementation are provided, and limitations are discussed.
Age and time-of-day differences in the hypothalamo–pituitary–testicular, and adrenal, response to total overnight sleep deprivation
Authors: Liu Peter Y , Takahashi Paul Y , Yang Rebecca J , Iranmanesh Ali , Veldhuis Johannes D 
Published: January 2020

Abstract

Study Objectives
In young men, sleep restriction decreases testosterone (Te) and increases afternoon cortisol (F), leading to anabolic–catabolic imbalance, insulin resistance, and other andrological health consequences. Age-related differences in the hypothalamo–pituitary–testicular/adrenal response to sleep restriction could expose older individuals to greater or lesser risk. We aimed to evaluate and compare the 24-h and time-of-day effect of sleep restriction on F, luteinizing hormone (LH), and Te in young and older men.

Methods
Thirty-five healthy men, aged 18–30 (n = 17) and 60–80 (n =18) years, underwent overnight sleep deprivation (complete nighttime wakefulness) or nighttime sleep (10 pm to 6 am) with concurrent 10-min blood sampling in a prospectively randomized crossover study. F, LH, and Te secretion were calculated by deconvolution analysis.

Results
Sleep deprivation had multiple effects on 24-h Te secretion with significant reductions in mean concentrations, basal, total and pulsatile secretion, and pulse frequency (each p &lt; 0.05), in the absence of detectable changes in LH. These effects were most apparent in older men and differed according to age for some parameters: pulsatile Te secretion (p = 0.03) and Te pulse frequency (p = 0.02). Time-of-day analyses revealed that sleep restriction significantly reduced Te in the morning and afternoon, reduced LH in the morning in both age groups, and increased F in the afternoon in older men.

Conclusions
These data suggest a time-of-day dependent uncoupling of the regulatory control of the testicular axis and of F secretion. Future studies will need to directly verify these regulatory possibilities specifically and separately in young and older men.

Clinical Trial
Not applicable.
Narcolepsy Severity Scale: a reliable tool assessing symptom severity and consequences
Authors: Dauvilliers Yves , Barateau Lucie , Lopez Regis , Rassu Anna Laura , Chenini Sofiene , Beziat Severine , Jaussent Isabelle 
Published: January 2020

Abstract

Study Objectives
To define clinically relevant Narcolepsy Severity Scale (NSS) score ranges, confirm its main performances and sensitivity to medications, and determine whether items need to be weighted.

Methods
One hundred and forty-three consecutive untreated and 238 treated adults with narcolepsy type 1 (NT1) completed the NSS, a 15-item self-administered questionnaire (score: 0–57) that assesses the severity and consequences of the five major narcolepsy symptoms such as daytime sleepiness, cataplexy, hallucinations, sleep paralysis, and disturbed nighttime sleep (DNS). They also completed the Epworth Sleepiness scale (ESS; daytime sleepiness), Beck Depression Inventory (BDI; depressive symptoms), and EQ5D (quality of life).

Results
The mean symptom number (4.3 vs 3.5), NSS total score (33.3 ± 9.4 vs 24.3 ± 10.2), and number of narcolepsy symptoms (five symptoms: 53.1% vs 24.8%; four symptoms: 26.6% vs 22.7%; three symptoms: 15.4% vs 32.4%; two symptoms: 4.9% vs 20.2%) were significantly different between untreated and treated patients (p &lt; 0.0001). DNS was often the third symptom (95.5 per cent). The symptom number was associated with diagnosis delay, age at onset, and ESS and BDI scores. Comparisons with ESS, BDI and EQ5D showed that NSS item weighting was not necessary to highlight between-group differences. Four NSS severity levels were defined (mild, moderate, severe, and very severe) with between-group differences related to treatment. The probability of having ESS ≥ 16, BDI ≥ 20, and EQ-5D &lt; 60 increased with the severity level.

Conclusion
NSS is valid, reliable, and responsive to treatment in patients with NT1, with four clinically relevant severity score ranges provided. NSS has adequate clinimetric properties for broadening its use for both clinic and research.