bluuebunny/crossref_metadata_2025 huggingface dataset:
Dark Soliton of Polariton Condensates under Nonresonant

PT

-Symmetric Pumping*
Authors: Jia Chun-Yu , Liang Zhao-Xin
Published: May 2020

A quantum system in complex potentials obeying parity-time (

P
T

) symmetry could exhibit all real spectra, starting out in non-Hermitian quantum mechanics. The key physics behind a

P
T

-symmetric system consists of the balanced gain and loss of the complex potential. We plan to include the nonequilibrium nature (i.e., the intrinsic kinds of gain and loss of a system) to a

P
T

-symmetric many-body quantum system, with an emphasis on the combined effects of non-Hermitian due to nonequilibrium nature and

P
T

symmetry in determining the properties of a system. To this end, we investigate the static and dynamical properties of a dark soliton of a polariton Bose–Einstein condensate under the

P
T

-symmetric non-resonant pumping by solving the driven-dissipative Gross–Pitaevskii equation both analytically and numerically. We derive the equation of motion for the center of mass of the dark soliton’s center analytically with the help of the Hamiltonian approach. The resulting equation captures how the combination of the open-dissipative character and

P
T

-symmetry affects the properties of the dark soliton; i.e., the soliton relaxes by blending with the background at a finite time. Further numerical solutions are in excellent agreement with the analytical results.
Influence of Hot-Carriers on the On-State Resistance in Si and GaAs Photoconductive Semiconductor Switches Working at Long Pulse Width*
Authors: Luan Chong-Biao , Li Hong-Tao
Published: May 2020

We demonstrate that the transport of hot carriers may result in the phenomenon where an oscillated output current appears at the waveforms in a high-power photoconductive semiconductor switch (PCSS) working at long pulse width when the laser disappears or the electric field changes. The variational laser and electric field will affect the scattering rates of hot carriers and crystal lattice in high-power PCSS, and the drift velocity of hot carriers and also the on-state resistance will be changed. The present result is important for reducing the on-state resistance and improving the output characteristics of high-power Si/GaAs PCSS.
Resonant Quantum Search with Monitor Qubits*
Authors: Wilczek Frank , Hu Hong-Ye , Wu Biao
Published: May 2020

We present an algorithm for the generalized search problem (searching k marked items among N items) based on a continuous Hamiltonian and exploiting resonance. This resonant algorithm has the same time complexity

O
(

N
/
k

)

as the Grover algorithm. A natural extension of the algorithm, incorporating auxiliary “monitor” qubits, can determine k precisely, if it is unknown. The time complexity of our counting algorithm is

O
(

N

)

, similar to the best quantum approximate counting algorithm, or better, given appropriate physical resources.
Imaginary Time Crystal of Thermal Quantum Matter*
Authors: Cai Zi , Huang Yizhen , Vincent Liu W.
Published: May 2020

Temperature is a fundamental thermodynamic variable for matter. Physical observables are often found to either increase or decrease with it, or show a non-monotonic dependence with peaks signaling underlying phase transitions or anomalies. Statistical field theory has established connection between temperature and time: a quantum ensemble with inverse temperature β is formally equivalent to a dynamic system evolving along an imaginary time from 0 to iβ in the space one dimension higher. Here we report that a gas of hard-core bosons interacting with a thermal bath manifests an unexpected temperature-periodic oscillation of its macroscopic observables, arising from the microscopic origin of space-time locked translational symmetry breaking and crystalline ordering. Such a temperature crystal, supported by quantum Monte Carlo simulation, generalizes the concept of purely spatial density-wave order to the imaginary time axis for Euclidean action.
Unusual Destruction and Enhancement of Superfluidity of Atomic Fermi Gases by Population Imbalance in a One-Dimensional Optical Lattice*
Authors: Chen Qijin , Wang Jibiao , Sun Lin , Yu Yi
Published: May 2020

We study the superfluid behavior of a population imbalanced ultracold atomic Fermi gases with a short range attractive interaction in a one-dimensional (1D) optical lattice, using a pairing fluctuation theory. We show that, besides widespread pseudogap phenomena and intermediate temperature superfluidity, the superfluid phase is readily destroyed except in a limited region of the parameter space. We find a new mechanism for pair hopping, assisted by the excessive majority fermions, in the presence of continuum-lattice mixing, which leads to an unusual constant Bose-Einstein condensate (BEC) asymptote for T
c that is independent of pairing strength. In result, on the BEC side of unitarity, superfluidity, when it exists, may be strongly enhanced by population imbalance.
Consistent Scaling Exponents at the Deconfined Quantum-Critical Point*
Authors: Sandvik Anders W. , Zhao Bowen
Published: May 2020

We report a quantum Monte Carlo study of the phase transition between antiferromagnetic and valence-bond solid ground states in the square-lattice S = 1/2 J–Q model. The critical correlation function of the Q terms gives a scaling dimension corresponding to the value ν = 0.455 ± 0.002 of the correlation-length exponent. This value agrees with previous (less precise) results from conventional methods, e.g., finite-size scaling of the near-critical order parameters. We also study the Q-derivatives of the Binder cumulants of the order parameters for L
2 lattices with L up to 448. The slope grows as L
1/ν
with a value of ν consistent with the scaling dimension of the Q term. There are no indications of runaway flow to a first-order phase transition. The mutually consistent estimates of ν provide compelling support for a continuous deconfined quantum-critical point.
Loss characteristics of superconducting pancake, solenoid and spiral coils for wireless power transfer
Authors: Machura Philip , Zhang Hongye , Kails Kevin , Li Quan
Published: May 2020

Wireless power transfer (WPT) is an emerging technology with widespread applications, such as wireless charging for electric vehicles (EVs), which has become a major point of interest. Conventionally, it is used for stationary charging, but also dynamic systems emerge. Key drawbacks of standard WPT systems are the limited transfer distance between the copper coils and the transfer efficiency. By employing high-temperature superconductors (HTS) as coil material these limitations can be alleviated. However, HTS coils have highly nonlinear ac loss characteristics, which will be studied. This paper investigates the transport current loss and the magnetisation loss of HTS coils individually and when combined in the high frequency range relevant to WPT for EVs. A multilayer 2D axisymmetric coil model based on
H
-formulation is proposed and validated by experimental results as the HTS film layer is inapplicable at such frequencies. Three of the most commonly employed coil configurations, namely: double pancake, solenoid and circular spiral are examined. While spiral coils experience the highest transport current loss, solenoid coils are subject to the highest magnetisation loss due to the overall distribution of the turns. Furthermore, a transition frequency is defined for each coil when losses in the copper layer exceed the HTS losses. It is much lower for coils due to the interactions between the different turns compared to single HTS tapes. At higher frequencies, the range of magnetic field densities, causing a shift where the highest losses occur, decreases until losses in the copper stabilisers always dominate. In addition, case studies investigating the suitability of HTS-WPT are proposed.
Toward heterogeneous information fusion: bipartite graph convolutional networks for in silico drug repurposing
Authors: Wang Zichen , Zhou Mu , Arnold Corey
Published: May 2020

Motivation

Mining drug–disease association and related interactions are essential for developing in silico drug repurposing (DR) methods and understanding underlying biological mechanisms. Recently, large-scale biological databases are increasingly available for pharmaceutical research, allowing for deep characterization for molecular informatics and drug discovery. However, DR is challenging due to the molecular heterogeneity of disease and diverse drug–disease associations. Importantly, the complexity of molecular target interactions, such as protein–protein interaction (PPI), remains to be elucidated. DR thus requires deep exploration of a multimodal biological network in an integrative context.

Results

In this study, we propose BiFusion, a bipartite graph convolution network model for DR through heterogeneous information fusion. Our approach combines insights of multiscale pharmaceutical information by constructing a multirelational graph of drug–protein, disease–protein and PPIs. Especially, our model introduces protein nodes as a bridge for message passing among diverse biological domains, which provides insights into utilizing PPI for improved DR assessment. Unlike conventional graph convolution networks always assuming the same node attributes in a global graph, our approach models interdomain information fusion with bipartite graph convolution operation. We offered an exploratory analysis for finding novel drug–disease associations. Extensive experiments showed that our approach achieved improved performance than multiple baselines for DR analysis.

Availability and implementation

Source code and preprocessed datasets are at: https://github.com/zcwang0702/BiFusion.
MetaSanity: an integrated microbial genome evaluation and annotation pipeline
Authors: Neely Christopher J , Graham Elaina D , Tully Benjamin J
Published: May 2020

As the importance of microbiome research continues to become more prevalent and essential to understanding a wide variety of ecosystems (e.g. marine, built, host associated, etc.), there is a need for researchers to be able to perform highly reproducible and quality analysis of microbial genomes. MetaSanity incorporates analyses from 11 existing and widely used genome evaluation and annotation suites into a single, distributable workflow, thereby decreasing the workload of microbiologists by allowing for a flexible, expansive data analysis pipeline. MetaSanity has been designed to provide separate, reproducible workflows that (i) can determine the overall quality of a microbial genome, while providing a putative phylogenetic assignment, and (ii) can assign structural and functional gene annotations with varying degrees of specificity to suit the needs of the researcher. The software suite combines the results from several tools to provide broad insights into overall metabolic function. Importantly, this software provides built-in optimization for ‘big data’ analysis by storing all relevant outputs in an SQL database, allowing users to query all the results for the elements that will most impact their research.

Availability and implementation

MetaSanity is provided under the GNU General Public License v.3.0 and is available for download at https://github.com/cjneely10/MetaSanity. This application is distributed as a Docker image. MetaSanity is implemented in Python3/Cython and C++. Instructions for its installation and use are available within the GitHub wiki page at https://github.com/cjneely10/MetaSanity/wiki, and additional instructions are available at https://cjneely10.github.io/year-archive/. MetaSanity is optimized for users with limited programing experience.

Supplementary information

Supplementary data are available at Bioinformatics online.
Mixture and Concentration Effects on Odorant Receptor Response Patterns In Vivo
Authors: McClintock Timothy S , Wang Qiang , Sengoku Tomoko , Titlow William B , Breheny Patrick
Published: May 2020

Natural odors are mixtures of volatile chemicals (odorants). Odors are encoded as responses of distinct subsets of the hundreds of odorant receptors and trace amine-associated receptors expressed monogenically by olfactory sensory neurons. This is an elegantly simple mechanism for differentially encoding odors but it is susceptible to complex dose–response relationships and interactions between odorants at receptors, which may help explain olfactory phenomena, such as mixture suppression, synthetic versus elemental odor processing, and poorly predictable perceptual outcomes of new odor mixtures. In this study, in vivo tests in freely behaving mice confirm evidence of a characteristic receptor response pattern consisting of a few receptors with strong responses and a greater number of weakly responding receptors. Odorant receptors responsive to an odor are often unrelated and widely divergent in sequence, even when the odor consists of a single species of odorant. Odorant receptor response patterns to a citrus odor broaden with concentration. Some highly sensitive receptors respond only to a low concentration but others respond in proportion to concentration, a feature that may be critical for concentration-invariant perception. Other tests find evidence of interactions between odorants in vivo. All of the odorant receptor responses to a moderate concentration of the fecal malodor indole are suppressed by a high concentration of the floral odorant, α-ionone. Such suppressive effects are consistent with prior evidence that odorant interactions at individual odorant receptors are common.
Placental lncRNA expression associated with placental cadmium concentrations and birth weight
Authors: Hussey Michael R , Burt Amber , Deyssenroth Maya A , Jackson Brian P , Hao Ke , Peng Shouneng , Chen Jia , Marsit Carmen J , Everson Todd M
Published: May 2020

Heavy metal exposures, such as cadmium, can have negative effects on infant birth weight (BW)—among other developmental outcomes—with placental dysfunction potentially playing a role in these effects. In this study, we examined how differential placental expression of long non-coding RNAs (lncRNAs) may be associated with cadmium levels in placenta and whether differences in the expression of those lncRNAs were associated with fetal growth. In the Rhode Island Child Health Study, we used data from Illumina HiSeq whole transcriptome RNA sequencing (n = 199) to examine association between lncRNA expression and measures of infant BW as well as placental cadmium concentrations controlled for appropriate covariates. Of the 1191 lncRNAs sequenced, 46 demonstrated associations (q < 0.05) with BW in models controlling for infant sex, maternal age, BMI, maternal education, and smoking during pregnancy. Furthermore, four of these transcripts were associated with placental cadmium concentrations, with MIR22HG and ERVH48-1 demonstrating increases in expression associated with increasing cadmium exposure and elevated odds of small for gestational age birth, while AC114763.2 and LINC02595 demonstrated reduced expression associated with cadmium, but elevated odds of large for gestational age birth with increasing expression. We identified relationships between lncRNA expression with both placental cadmium concentrations and BW. This study provides evidence that disrupted placental expression of lncRNAs may be a part of cadmium’s mechanisms of reproductive toxicity.
Pre-procedural planning of transcatheter mitral valve replacement in mitral stenosis with multi-detector tomography-derived 3D modeling and printing: a case report
Authors: Ooms Joris , Minet Magali , Daemen Joost , Van Mieghem Nicolas
Published: May 2020

Background

Transcatheter mitral valve replacement (TMVR) may be a valuable treatment option for mitral annular calcification and severe mitral stenosis (MS) in patients at high operative risk. Pre-procedural virtual and printed simulations may aid in procedure planning, device sizing, and mitigate complications such as valve embolization or left ventricular outflow tract (LVOT) obstruction.

Case summary

We describe a case of TMVR in which multi-detector computed tomography (MDCT) derived, three-dimensional virtual planning and a 3D-printed model of the patients’ left heart provided enhanced understanding of an individual patient’s unique anatomy to determine feasibility, device sizing, and risk stratification. This resulted in deployment of an adequately sized valve. Post-TMVR LVOT obstruction was treated with LVOT balloon dilatation and percutaneous transluminal septal myocardial ablation.

Discussion

Advanced MDCT-derived planning techniques introduce consistent 3D modeling and printing to enhance understanding of intracardiac anatomical relationships and test device implantation. Still, static measurements do not feature haemodynamic factors, tissue, or device characteristics and do not predict device host interaction. Transcatheter mitral valve replacement is feasible in MS when adequately pre-procedurally planned. Multi-detector computed tomography-derived, 3D, virtual and printed models contribute to adequate planning in terms of determining patient eligibility, procedure feasibility, and device sizing. However, static 3D modeling cannot completely eliminate the risk of peri-procedural complications.
The Politics of Apology and the Prospects for ‘Post-conflict’ Reconciliation: The Case of the Provisional Irish Republican Movement
Authors: Hopkins Stephen
Published: May 2020

This article analyses the Irish Provisional Republican movement and the evolution of its approach to the politics of apology. The first section analyses recent scholarship regarding ‘political apologies’, and provides a challenge to the existing literature, which concentrates upon ‘official’ or state apologies, rather than examples involving non-state armed groups (paramilitary or ‘terrorist’ organisations). This section argues that it remains difficult to discern an adequate general model for establishing criteria for a ‘successful’ or ‘sincere’ political apology involving such groups. The second section considers a number of case studies, including the statements of the IRA in 2002, and after the Enniskillen bombing in 1987. It is argued that the Provisional movement’s apologies have not generally proven helpful to its declared aim of post-conflict reconciliation. This article argues that attempted apologies or quasi-apologies by non-state groups may not ameliorate the sense of grievance experienced by victims/survivors, and may also serve to revivify social and political ‘framing battles’ over the past.
A Generalized Framework for Moral Dilemmas Involving Autonomous Vehicles: A Commentary on Gill
Authors: Novak Thomas P
Published: May 2020

By using scenarios based on moral dilemmas, Gill (2020) found that when consumers are riding in an autonomous vehicle (AV), they are more willing to harm a pedestrian than when they, themselves, are driving a regular car. By taking a first-person perspective, in contrast to most prior research that has taken a third-person perspective, the problem is framed in a personal way that allows identification of a mechanism of responsibility attribution. In this commentary, a generalized framework is developed in which we can locate the work of Gill (2020), as well as prior research that uses moral dilemmas, to understand how consumers believe that AVs should respond when faced with competing life-and-death alternatives. The framework shows the distinct positions that research to date has adopted, points out gaps in research, and suggests a family of four research agendas that can be pursued going forward, driven in large part by the perspective taken to the moral dilemma. Research employing these different perspectives, including the unresearched problem of taking the perspective of the object, holds promise for using moral dilemmas for enabling our understanding of consumer experience and consumer–object relationships with AVs.
Electropenetrographic Comparison of Feeding Behavior of Dichelops furcatus (Hemiptera: Heteroptera: Pentatomidae) on Soybean and Spring Cereals
Authors: Lucini Tiago , Panizzi Antônio R
Published: May 2020

We used electropenetrography to quantify and compare counts and durations of selected waveforms, produced by adult females of the stink bug Dichelops furcatus (F.). Insects fed on immature soybean pods and immature seed heads of four spring cereals: wheat, black oat, barley, and rye. On all foods, bugs spent over 60% of their plant access time in non-probing activities. This total waveform duration was significantly longer on barley and rye compared to those on soybean and oat; wheat was intermediate. Considering only probing activities, bugs spent longer durations (ca. 2×), on soybean and oat compared to barley, rye, and wheat plants. Bugs produced significantly more pathway events on soybean and rye than on wheat and barley; with a significantly shorter duration per event on rye. The counts and durations of xylem ingestion did not differ among foods. Cell rupturing activities on seeds were longer on soybean (ca. 23%) and oat (ca. 21%), than on barley and rye (ca. 6%). The durations of ingestion events on seeds were significantly shorter on soybean (over 3×) compared to those on barley and wheat; oat and rye were intermediate. However, the ingestion duration per insect did not show significant difference among foods. Results demonstrated that D. furcatus spent more time overall in probing activities on soybean and oat; whereas, rye and barley presented the worst feeding behavior. This study provides important background information for further quantitative studies of stink bugs on different plants, such as development of resistant host plants.
The Effects of Temperature and Humidity on a Field Population of Bradysia odoriphaga (Diptera: Sciaridae)
Authors: Shi Cai-hua , Hu Jing-rong , Zhang You-jun
Published: May 2020

The production of Chinese chives is reduced throughout China due to a root-feeding dipteran pest Bradysia odoriphaga Yang et Zhang (Diptera: Sciaridae), therefore deciphering the conditions influencing its growth and development are important in developing ecological control strategies. A study was conducted from 2014 to 2017 to determine the relationship between the abundance of B. odoriphaga and temperature (atmospheric and soil), soil water content, and atmospheric humidity in a Chinese chive field in Beijing City, China. Numbers of adults peaked in March and October to November and were lowest in July to August and December to next February; numbers of larvae were highest in December to next February and lowest in July to August. From 2014 to 2017, the numbers of adults and larvae were significantly correlated with monthly mean atmospheric temperatures and soil temperatures, but were not significantly correlated with monthly mean atmospheric relative humidity and soil water content. However, for both adults and larvae, numbers were significantly greater with high soil water contents compared with drought treatment. The results of this study suggest that the very low soil water contents, high atmospheric temperatures, and high soil temperatures were critical for regulating field populations of B. odoriphaga.
Tomato Yellow Leaf Curl Virus Infection Alters Bemisia tabaci MED (Hemiptera: Aleyrodidae) Vulnerability to Flupyradifurone
Authors: Liu Baiming , Preisser Evan L , Jiao Xiaoguo , Zhang Youjun
Published: May 2020

The whitefly, Bemisia tabaci Gennadius, is a major phloem-feeding pest of agricultural crops that is also an important vector of many plant diseases. The B. tabaci Mediterranean (‘MED’) biotype is a particularly effective vector of Tomato yellow leaf curl virus (TYLCV), a devastating plant pathogen. Although insecticides play an important role in the control of MED and TYLCV, little is known about how TYLCV infection affects MED susceptibility to insecticides. We conducted research addressing how MED susceptibility to flupyradifurone, the first commercially available systemic control agent derived from the butenolide class of insecticides, was affected by TYLCV infection. We first conducted bioassays determining the LC15 and LC50 for control and viruliferous MED feeding on either water- or insecticide-treated plants. We next measured several demographic parameters of control and viruliferous MED exposed to either insecticide- or water-treated plants. TYLCV infection increased MED tolerance of flupyradifurone: the LC15 and LC50 of viruliferous MED were double that of uninfected MED. Viral infection also altered MED demographic responses to flupyradifurone, but in an inconsistent manner. Although the ability of TYLCV and other persistently transmitted viruses to benefit Bemisia via manipulation of host plant defense is well known, this appears to be the first example of virally mediated changes in vector susceptibility to an insecticide.
The Alzheimer Disease-Causing Presenilin-1 L435F Mutation Causes Increased Production of Soluble Aβ43 Species in Patient-Derived iPSC-Neurons, Closely Mimicking Matched Patient Brain Tissue
Authors: Oakley Derek H , Chung Mirra , Klickstein Naomi , Commins Caitlin , Hyman Bradley T , Frosch Matthew P
Published: May 2020

Familial Alzheimer disease-causing mutations in Presenilin 1 (PSEN1) are generally thought to shift the processing of APP toward longer, more amyloidogenic Aβ fragments. However, certain PSEN1 mutations cause severe reduction in gamma secretase function when expressed in the homozygous state, thus challenging the amyloid hypothesis. We sought to evaluate the effects of one such mutation, PSEN1 L435F, in more physiologic conditions and genetic contexts by using human induced pluripotent stem cell (iPSC)-derived neurons from an individual with familial AD (fAD) linked to the PSEN1 L435F mutation, and compared the biochemical phenotype of the iPS-derived neurons with brain tissue obtained at autopsy from the same patient. Our results demonstrate that in the endogenous heterozygous state, the PSEN1 L435F mutation causes a large increase in soluble Aβ43 but does not change the overall levels of soluble Aβ40 or Aβ42 when compared with control iPSC-neurons. Increased pathologically phosphorylated tau species were also observed in PSEN1-mutant iPSC-neurons. Concordant changes in Aβ species were present in autopsy brain tissue from the same patient. Finally, the feasibility of using Aβ43 immunohistochemistry of brain tissue to identify fAD cases was evaluated in a limited autopsy case series with the finding that strong Aβ43 staining occurred only in fAD cases.
Distribution of TDP-43 Pathology in Hippocampal Synaptic Relays Suggests Transsynaptic Propagation in Frontotemporal Lobar Degeneration
Authors: Jamshidi Pouya , Kim Garam , Shahidehpour Ryan K , Bolbolan Kabriya , Gefen Tamar , Bigio Eileen H , Mesulam Marek-Marsel , Geula Changiz
Published: May 2020

Hyperphosphorylation, nuclear depletion, and aggregation of TDP-43 in ubiquitinated inclusions is a hallmark of frontotemporal lobar degeneration (FTLD-TDP). Evidence of potential spread of TDP-43 along synaptic connections in the human is largely limited to qualitative and semiquantitative observations. We quantitatively investigated potential transsynaptic propagation of TDP-43 across the well-established chain of single synaptic connections of the hippocampus. Hippocampi from 5 participants with clinical diagnoses of primary progressive aphasia and 2 participants with behavioral variant frontotemporal dementia, all with postmortem diagnoses of FTLD-TDP, were examined. TDP-43-positive mature (darkly stained) and pre-inclusions (diffuse puncta or fibrillar staining) in the granule cell layer of dentate gyrus (DG) and pyramidal cell layers of Cornu Ammonis (CA)3, CA2, and CA1 were quantified using unbiased stereology. The density of mature TDP-43 inclusions was higher in the DG than in the CA fields (p < 0.05). There were no differences in inclusion densities across the CA fields. TDP-43 pre-inclusions densities were not different across the 4 subregions. There was significantly higher preinclusion density than mature inclusions in CA3, but not in other subregions. Analysis of normalized total counts in place of densities revealed virtually identical results. Our finding of greatest mature inclusion deposition in the DG, coupled with more preinclusions than mature inclusions at the next relay station (CA3), and reduced densities of both in CA2-CA1, provide evidence in support of a sequential transsynaptic propagation mechanism of TDP-43 aggregates.
Localized Hypertrophic Neuropathy as a Neoplastic Manifestation of KRAS-Mediated RASopathy
Authors: Vizcaino M Adelita , Belzberg Allan , Ahlawat Shivani , Belakhoua Sarra , Chen Liam , Staedtke Verena , Rodriguez Fausto J
Published: May 2020

Localized hypertrophic neuropathy is a rare Schwann cell proliferation that usually affects single nerves from the extremities, and it is of unclear etiology in its pure form. RASopathies are a defined group of genetic diseases with overlapping clinical features, usually secondary to germline mutations in genes encoding either components or regulators of the RAS/MAPK pathway. Herein, we report an 11-year-old boy presenting with café au lait spots and right leg length discrepancy. A fascicular nerve biopsy of the tibial nerve demonstrated a Schwann cell proliferation with prominent onion-bulb formation, satisfying criteria for localized hypertrophic neuropathy. Molecular genetic analysis demonstrated identical KRAS mutations (c38_40dupGCG) in the peripheral nerve lesion and melanocytes from café au lait spots, but not in blood, supporting a diagnosis of a KRAS-mediated rasopathy with mosaicism. Immunohistochemical staining in the peripheral nerve lesion demonstrated strong pERK staining consistent with downstream MAPK pathway activation. This report suggests that at least a subset of localized hypertrophic neuropathies are bonafide, well-differentiated Schwann cell neoplasms developing through oncogenic RAS signaling, which provides new insights into the controversial entity historically known as localized hypertrophic neuropathy.
Transposon insertions within alleles of BnaFLC.A10 and BnaFLC.A2 are associated with seasonal crop type in rapeseed
Authors: Yin Shuai , Wan Ming , Guo Chaocheng , Wang Bo , Li Haitao , Li Ge , Tian Yanyong , Ge Xianhong , King Graham J , Liu Kede , Li Zaiyun , Wang Jing
Published: May 2020

In Brassicaceae, the requirement for vernalization is conferred by high expression of FLOWERING LOCUS C (FLC). The expression of FLC is known to be repressed by prolonged exposure to cold. Rapeseed (Brassica napus L.) cultivars can be classified into spring, winter, and semi-winter crop types, depending on their respective vernalization requirements. In addition to two known distinct transposon insertion events, here we identified a 4.422 kb hAT and a 5.625 kb long interspersed nuclear element transposon insertion within BnaFLC.A10, and a 810 bp miniature inverted-repeat transposable element (MITE) in BnaFLC.A2. Quantitative PCR demonstrated that these insertions lead to distinct gene expression patterns and contribute differentially to the vernalization response. Transgenic and haplotype analysis indicated that the known 621 bp MITE in the promoter region of BnaFLC.A10 is a transcriptional enhancer that appears to be the main determinant of rapeseed vernalization, and has contributed to the adaptation of rapeseed in winter cultivation environments. In the absence of this transposon insertion, the functional allele of BnaFLC.A2 is a major determinant of vernalization demand. Thus, the combination of BnaFLC.A10 carrying the 621 bp MITE insertion and a functional BnaFLC.A2 appears necessary to establish the winter rapeseed crop phenotype.
Haunted Roadscapes in Jesmyn Ward’s Sing, Unburied, Sing
Authors: Dib Nicole
Published: May 2020

In this article, I argue that Jesmyn Ward deploys a road trip in her 2017 novel Sing, Unburied, Sing as a literary formula through which she demonstrates the immobilizing effects of racism and incarceration on contemporary black lives. The association of the American road-trip novel with freedom and free movement is strong in the American imaginary, and Ward manipulates this association to explore what happens when automobile travelers are precarious rather than privileged. The road trip in Ward's novel makes visible various forces of mobility and immobility that differentiate citizens by race. She conjures two dimensions of the African American experience that are immobilizing: the carceral system and the risk of “driving while black.” Sing, Unburied, Sing already critiques the traditional road trip in its plot and narrative structure; for Ward, it is the linkages of dimensions of African American immobilization around the road trip that are powerful. Ward's novel demonstrates that black automobility, or the unique experience of the road for racialized drivers, reveals the political and social dynamics that shape our conception of the road for all drivers. Furthermore, I analyze how the road trip within the novel “unburies” a story about the violence of incarceration. I explore how Ward finesses that iconic American narrative trope, the journey by car that ought to be freeing, to heighten her critique of racist, anti-black structures of oppression in the United States.
Differentiation, Entanglement, and Worth in Ruth Ozeki’s A Tale for the Time Being
Authors: Hogue Beverly
Published: May 2020

Ruth Ozeki's 2013 novel A Tale for the Time Being suggests that garbage provides the raw material for meaning-making, an emphasis evident in both the content and the structure of the novel. Constructed as an assemblage of curated texts discarded and washed up on shore, the novel follows characters who wonder whether their own identities and communities are collages of flotsam whose worth is dependent on arbitrary judgments and accidental encounters. This essay examines how Ozeki excavates literary landfills to recuperate trashed narratives and devalued people, proposing that the very stuff cultures reject as worthless provides compost for the growth of new meaning. The essay further explores how Ozeki deploys the Schrödinger's cat thought experiment to critique the process of assigning worth and posit the concept of entanglement as a foundation for construction of community.
Correlation between relativistic reflection fraction and photon index in NuSTAR sample of Seyfert 1 AGN
Authors: Ezhikode Savithri H , Dewangan Gulab C , Misra Ranjeev , Philip Ninan Sajeeth
Published: May 2020

The primary X-ray emission from active galactic nuclei (AGNs), described by a power-law, irradiates the accretion disc producing reflection features in the spectrum. The reflection features arising from the inner regions of the disc can be significantly modified by the relativistic effects near the black hole. We investigate the relationship between the relativistic reflection fraction Rf, defined as the ratio of the coronal intensity that illuminates the accretion disc to the coronal intensity observed directly, and the hard X-ray photon index Γ of a Nuclear Spectroscopic Telescope Array (NuSTAR) sample of Seyfert 1 galaxies. The X-ray spectra are modelled using relxill code that helps to directly obtain the reflection fraction of a relativistically smeared reflection component. The parameter Rf depends on the amount of Comptonized X-ray emission intercepted by the inner accretion disc. We found a positive correlation between Γ and Rf in our sample. Seed photons from a larger area of an accretion disc entering the corona will result in increased cooling of the coronal plasma, giving rise to steeper X-ray spectrum. The corona irradiating the larger area of the disc will result in higher reflection fraction. Thus, the observed Rf –Γ relation is most likely related to the variations in the disc–corona geometry of AGNs.
Microlensed radio emission from exoplanets
Authors: Shiohira Yuta , Terada Yuka , Mukuno Den , Fujii Yuka , Takahashi Keitaro
Published: May 2020

In this paper, we investigate the detectability of radio emission from exoplanets, especially hot Jupiters, which are magnified by gravitational microlensing. Because hot Jupiters have orbital periods much shorter than the characteristic time-scale of microlensing, the magnification curve has a unique wavy feature depending on the orbital parameters. This feature is useful to identify radio emission from exoplanets and, in addition to magnification, makes it easier to detect exoplanets directly. We also estimate the expected event rate red of the detectable level of microlensed planetary radio emissions, assuming the Low Frequency Array and the first phase of the Square Kilometre Array.
Improved gravitational radiation time-scales: significance for LISA and LIGO-Virgo sources
Authors: Zwick Lorenz , Capelo Pedro R , Bortolas Elisa , Mayer Lucio , Amaro-Seoane Pau
Published: May 2020

We present a revised version of Peters’ time-scale for the gravitational wave (GW)-induced decay of two point masses. The new formula includes the effects of the first-order post-Newtonian perturbation and additionally provides a simple fit to account for the Newtonian self-consistent evolution of the eccentricity. The revised time-scale is found by multiplying Peters’ estimate by two factors, $R(e_0)= 8^{1-\sqrt{1-e_0}}$ and Qf(p0) = exp (2.5(rS/p0)), where e0 and p0 are the initial eccentricity and periapsis, respectively, and rS the Schwarzschild radius of the system. Their use can correct errors of a factor of 1–10 that arise from using the original Peters’ formula. We apply the revised time-scales to a set of typical sources for existing ground-based laser interferometers and for the future Laser Interferometer Space Antenna (LISA), at the onset of their GW-driven decay. We argue that our more accurate model for the orbital evolution will affect current event- and detection-rate estimates for mergers of compact object binaries, with stronger deviations for eccentric LISA sources, such as extreme and intermediate mass-ratio inspirals. We propose the correction factors R and Qf as a simple prescription to quantify decay time-scales more accurately in future population synthesis models. We also suggest that the corrected time-scale may be used as a computationally efficient alternative to numerical integration in other applications that include the modelling of radiation reaction for eccentric sources.
The Evolution of Human Cancer Gene Duplications across Mammals
Authors: Tollis Marc , Schneider-Utaka Aika K , Maley Carlo C
Published: May 2020

Cancer is caused by genetic alterations that affect cellular fitness, and multicellular organisms have evolved mechanisms to suppress cancer such as cell cycle checkpoints and apoptosis. These pathways may be enhanced by the addition of tumor suppressor gene paralogs or deletion of oncogenes. To provide insights to the evolution of cancer suppression across the mammalian radiation, we estimated copy numbers for 548 human tumor suppressor gene and oncogene homologs in 63 mammalian genome assemblies. The naked mole rat contained the most cancer gene copies, consistent with the extremely low rates of cancer found in this species. We found a positive correlation between a species’ cancer gene copy number and its longevity, but not body size, contrary to predictions from Peto’s Paradox. Extremely long-lived mammals also contained more copies of caretaker genes in their genomes, suggesting that the maintenance of genome integrity is an essential form of cancer prevention in long-lived species. We found the strongest association between longevity and copy numbers of genes that are both germline and somatic tumor suppressor genes, suggesting that selection has acted to suppress both hereditary and sporadic cancers. We also found a strong relationship between the number of tumor suppressor genes and the number of oncogenes in mammalian genomes, suggesting that complex regulatory networks mediate the balance between cell proliferation and checks on tumor progression. This study is the first to investigate cancer gene expansions across the mammalian radiation and provides a springboard for potential human therapies based on evolutionary medicine.
Patient- and parent proxy-reported outcome measures for life participation in children with chronic kidney disease: a systematic review
Authors: Kerklaan Jasmijn , Hannan Elyssa , Baumgart Amanda , Manera Karine E , Ju Angela , McCulloch Mignon , Admani Bashir , Dominello Amanda , Esezobor Christopher , Foster Bethany , Hamilton Alexander , Jankauskiene Augustina , Johnson Rebecca J , Liu Isaac , Marks Stephen D , Neu Alicia , Schaefer Franz , Sutton Shanna , Wolfenden Sebastian , Craig Jonathan C , Groothoff Jaap , Howell Martin , Tong Allison
Published: May 2020

Background

The burden of chronic kidney disease (CKD) and its treatment may severely limit the ability of children with CKD to do daily tasks and participate in family, school, sporting and recreational activities. Life participation is critically important to affected children and their families; however, the appropriateness and validity of available measures used to assess this outcome are uncertain. The aim of this study was to identify the characteristics, content and psychometric properties of existing measures for life participation used in children with CKD.

Methods

We searched MEDLINE, Embase, PsychINFO, Cumulative Index to Nursing and Allied Health Literature and the Cochrane Kidney and Transplant register to August 2019 for all studies that used a measure to report life participation in children with CKD. For each measure, we extracted and analyzed the characteristics, dimensions of life participation and psychometric properties.

Results

From 128 studies, we identified 63 different measures used to assess life participation in children with CKD. Twenty-five (40%) of the measures were patient reported, 7 (11%) were parent proxy reported and 31 (49%) had both self and parent proxy reports available. Twenty-two were used in one study only. The Pediatric Quality of Life Inventory version 4.0 generic module was used most frequently in 62 (48%) studies. Seven (11%) were designed to assess ability to participate in life, with 56 (89%) designed to assess other constructs (e.g. quality of life) with a subscale or selected questions on life participation. Across all measures, the three most frequent activities specified were social activities with friends and/or family, leisure activities and self-care activities. Validation data in the pediatric CKD population were available for only 19 (30%) measures.

Conclusions

Life participation is inconsistently measured in children with CKD and the measures used vary in their characteristics, content and validity. Validation data supporting these measures in this population are often incomplete and are sparse. A meaningful and validated measure for life participation in children with CKD is needed.
Mineralogy of the deep lower mantle in the presence of H2O
Authors: Hu Qingyang , Liu Jin , Chen Jiuhua , Yan Bingmin , Meng Yue , Prakapenka Vitali B , Mao Wendy L , Mao Ho-Kwang
Published: May 2020

Understanding the mineralogy of the Earth's interior is a prerequisite for unravelling the evolution and dynamics of our planet. Here, we conducted high pressure-temperature experiments mimicking the conditions of the deep lower mantle (DLM, 1800–2890 km in depth) and observed surprising mineralogical transformations in the presence of water. Ferropericlase, (Mg, Fe)O, which is the most abundant oxide mineral in Earth, reacts with H2O to form a previously unknown (Mg, Fe)O2Hx (x ≤ 1) phase. The (Mg, Fe)O2Hx has a pyrite structure and it coexists with the dominant silicate phases, bridgmanite and post-perovskite. Depending on Mg content and geotherm temperatures, the transformation may occur at 1800 km for (Mg0.6Fe0.4)O or beyond 2300 km for (Mg0.7Fe0.3)O. The (Mg, Fe)O2Hx is an oxygen excess phase that stores an excessive amount of oxygen beyond the charge balance of maximum cation valences (Mg2+, Fe3+ and H+). This important phase has a number of far-reaching implications including extreme redox inhomogeneity, deep-oxygen reservoirs in the DLM and an internal source for modulating oxygen in the atmosphere.
Are Referendums Directly Democratic?
Authors: Trueblood Leah
Published: May 2020

Referendums are regularly defined as being directly democratic. Indeed, the term ‘direct democracy’ is often used synonymously with referendums. The label ‘direct democracy’ is used to make two different types of claims about referendums: (i) descriptive claims about what referendums are; and (ii) normative claims about how their use is justified. This article challenges the treatment of referendums as devices of direct democracy both in theory and in practice. I argue instead that referendums should be theoretically and practically understood as processes that provide direction to representatives. Indeed, one consequence of my argument is the broader claim that the term ‘direct democracy’ is generally misleading. In a contemporary context, all democratic processes are—at least in part—representative.
Dynamic Crystallization of a Haplogranitic Melt: Application to Pegmatites
Authors: Devineau Karine , Champallier Rémi , Pichavant Michel
Published: May 2020

Both equilibrium and dynamic crystallization experiments have been performed on a hydrous haplogranitic melt at 200 MPa to model nucleation and growth mechanisms and simulate pegmatite textures. The equilibrium results provide a reference frame (phase assemblages and compositions, liquidus and solidus temperatures and dependence with the melt H2O concentration) to parametrize the kinetic experiments. The seven H2O-saturated dynamic crystallization experiments followed a specific time-temperature path. After a pre-conditioning step at 800°C, charges were cooled between 3·5 and 7°C/min to 700, 660 and 600°C corresponding to ΔT of 20, 60 and 120°C. Dwell times ranged from 42 up to 1440h. Variable mineral assemblages and textures, and two types of polymineralic assemblages were obtained depending on ΔT and t. For ΔT = 120°C, crystallization is sequential and includes graphic quartz–alkali-feldspar intergrowths characteristic of pegmatite textures. The crystallization sequence reflects nucleation and growth of kinetically-favoured metastable phases and solid solution compositions from the supercooled melt. Early alkali-feldspars are more K-rich than expected at equilibrium and late albites more Na-rich. The K-rich graphic texture progressively evolves to a Na-rich intergrowth texture. Melts also follow a progressive though limited sodic evolution with time. At the interface of growing alkali-feldspars, melts are enriched in SiO2 and depleted in Al2O3, Na2O and, to a lesser extent, K2O. H2O accumulates at the interface reaching concentration levels higher (by 1–2 wt %) than the saturation. Rejection of SiO2 and H2O at the interface controls the effective undercooling in the local melt and promotes rapid textural changes toward larger grain sizes at the front of graphic zones. Textural ripening takes place contemporaneously to sequential crystallization. Growth rates for quartz and alkali-feldspar are tightly grouped, between 7·3 x 10-11 and 1·6 x 10-12 m s-1. Textures from the dynamic crystallization experiments closely resemble natural pegmatites, but layered aplite units have not been reproduced. Our results confirm and strengthen the importance of liquidus undercooling to generate pegmatite textures.