bluuebunny/crossref_metadata_2025 huggingface dataset:
Local Ties in the Social Networks of Older Adults
Authors: York Cornwell Erin , Goldman Alyssa W
Published: March 2020

Objectives

Family members and friends who live nearby may be especially well-positioned to provide social support and companionship for community-residing older adults, but prior research has not examined the distribution and characteristics of local ties in older adults’ networks. We hypothesize that local ties are newer, more frequently accessed, and more embedded in the network, and that social disadvantage and neighborhood conditions structure older adults’ access to local ties.

Methods

We use egocentric network data from 15,137 alters named by 3,735 older adults in Wave 3 of the National Social Life, Health, and Aging Project (NSHAP). We conduct dyadic analysis to compare characteristics of local and nonlocal ties. Logistic regression models estimate how personal and neighborhood characteristics are associated with naming local kin and local non-kin ties.

Results

Nearly half of the older adults named at least one local network tie, and about 60% of these local ties are non-kin. Local ties are newer, frequently accessed, and highly embedded in older adults’ networks. Local kin ties are most common among socially disadvantaged older adults. Local non-kin ties are most common among white older adults and those who live in areas with high levels of collective efficacy, although local non-kin ties are also associated with residence in high-poverty neighborhoods.

Discussion

Local ties may bring unique benefits for community-residing older adults, but their availability is likely structured by residential mobility, neighborhood context, disparities in resources, and support needs. Future research should consider their implications for health and well-being.
PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes
Authors: Zafeiropoulos Haris , Viet Ha Quoc , Vasileiadou Katerina , Potirakis Antonis , Arvanitidis Christos , Topalis Pantelis , Pavloudi Christina , Pafilis Evangelos
Published: March 2020

Background

Environmental DNA and metabarcoding allow the identification of a mixture of species and launch a new era in bio- and eco-assessment. Many steps are required to obtain taxonomically assigned matrices from raw data. For most of these, a plethora of tools are available; each tool's execution parameters need to be tailored to reflect each experiment's idiosyncrasy. Adding to this complexity, the computation capacity of high-performance computing systems is frequently required for such analyses. To address the difficulties, bioinformatic pipelines need to combine state-of-the art technologies and algorithms with an easy to get-set-use framework, allowing researchers to tune each study. Software containerization technologies ease the sharing and running of software packages across operating systems; thus, they strongly facilitate pipeline development and usage. Likewise programming languages specialized for big data pipelines incorporate features like roll-back checkpoints and on-demand partial pipeline execution.

Findings

PEMA is a containerized assembly of key metabarcoding analysis tools that requires low effort in setting up, running, and customizing to researchers' needs. Based on third-party tools, PEMA performs read pre-processing, (molecular) operational taxonomic unit clustering, amplicon sequence variant inference, and taxonomy assignment for 16S and 18S ribosomal RNA, as well as ITS and COI marker gene data. Owing to its simplified parameterization and checkpoint support, PEMA allows users to explore alternative algorithms for specific steps of the pipeline without the need of a complete re-execution. PEMA was evaluated against both mock communities and previously published datasets and achieved results of comparable quality.

Conclusions

A high-performance computing–based approach was used to develop PEMA; however, it can be used in personal computers as well. PEMA's time-efficient performance and good results will allow it to be used for accurate environmental DNA metabarcoding analysis, thus enhancing the applicability of next-generation biodiversity assessment studies.
Inflammation-like changes in the urothelium of Lifr-deficient mice and LIFR-haploinsufficient humans with urinary tract anomalies
Authors: Christians Anne , Weiss Anna-Carina , Martens Helge , Klopf Maximilian Georg , Hennies Imke , Haffner Dieter , Kispert Andreas , Weber Ruthild G
Published: March 2020

Congenital anomalies of the kidney and urinary tract (CAKUT) are the most common cause of end-stage kidney disease in children. While the genetic aberrations underlying CAKUT pathogenesis are increasingly being elucidated, their consequences on a cellular and molecular level commonly remain unclear. Recently, we reported rare heterozygous deleterious LIFR variants in 3.3% of CAKUT patients, including a novel de novo frameshift variant, identified by whole-exome sequencing, in a patient with severe bilateral CAKUT. We also demonstrated CAKUT phenotypes in Lifr−/− and Lifr+/− mice, including a narrowed ureteric lumen due to muscular hypertrophy and a thickened urothelium. Here, we show that both in the ureter and bladder of Lifr−/− and Lifr+/− embryos, differentiation of the three urothelial cell types (basal, intermediate and superficial cells) occurs normally but that the turnover of superficial cells is elevated due to increased proliferation, enhanced differentiation from their progenitor cells (intermediate cells) and, importantly, shedding into the ureteric lumen. Microarray-based analysis of genome-wide transcriptional changes in Lifr−/− versus Lifr+/+ ureters identified gene networks associated with an antimicrobial inflammatory response. Finally, in a reverse phenotyping effort, significantly more superficial cells were detected in the urine of CAKUT patients with versus without LIFR variants indicating conserved LIFR-dependent urinary tract changes in the murine and human context. Our data suggest that LIFR signaling is required in the epithelium of the urinary tract to suppress an antimicrobial response under homeostatic conditions and that genetically induced inflammation-like changes underlie CAKUT pathogenesis in Lifr deficiency and LIFR haploinsufficiency.
Challenges in interpretation of WGS and epidemiological data to investigate nosocomial transmission of vancomycin-resistant Enterococcus faecium in an endemic region: incorporation of patient movement network and admission screening
Authors: Eichel Vanessa , Klein Sabrina , Bootsveld Carolin , Frank Uwe , Heeg Klaus , Boutin Sébastien , Nurjadi Dennis
Published: March 2020

Objectives

VRE are listed, by the WHO, among the leading resistant pathogens causing greatest public concern; hence the spread and transmission of VRE, especially in hospitalized patients, need to be monitored. Despite the advancements in typing methods since the implementation of WGS for outbreak investigations, data interpretation, especially for vancomycin-resistant Enterococcus faecium (VREfm) in an endemic setting, remains challenging. In this study we explored the potential added benefit of incorporating patient movement data and admission screening to accurately estimate the magnitude of an outbreak.

Methods

We sequenced 73 VREfm isolates from patients with bacteraemia (n = 43) and rectal colonization (n = 30/32). Genetic relatedness was determined by SNP distance (≤10) between isolates. Patient movements were visualized in a movement network, along with contact intensity and rectal colonization status prior to infection onset.

Results

ST117, ST80 and ST203 were the predominant STs in our study population. Forty-four percent (18/41) of VREfm bacteraemia cases were of endogenous origin. SNP analysis of infection and colonization isolates revealed nine clonal groups. Eighty-six percent (37/43) of the patients were visualized in a transmission network due to spatiotemporal overlap. Nineteen out of 43 (44%) belonged to five transmission clusters. Incorporation of prior colonization status revealed that transmission was very likely in only 63% (12/19) of patients in these transmission clusters.

Discussion

Although interpretation of WGS data is challenging, incorporation of patient movement data and colonization status by admission screening of high-risk patients may provide additional resolution when interpreting the magnitude of an outbreak in an endemic setting.
Rapid Determination of Listeria monocytogenes by Automated Enzyme-Linked Immunoassay and Nonradioactive DNA Probe
Authors: Kerdahi Khalil F , Istafanos Philip F
Published: March 2020

A rapid and reliable analytical method was developed to detect and confirm the presence of Listeria monocytogenes in raw and partially processed foods. Forty-nine food samples (25 mixed cut vegetable salad, 12 smoked salmon, and 12 sterile smoked salmon) were individually inoculated with high levels [10–100 colony forming units (cfu)/25 g sample] and low levels (1–10 cfu/25 g sample) of L. monocytogenes, and were screened using the Vitek Immuno Diagnostic Assay (VIDAS) Listeria monocytogenes (VIDAS LMO)]. Positive test results were confirmed as L. monocytogenes by nonradioactive DNA probe. All samples inoculated with high levels of L. monocytogenes were detected by VIDAS and 96% were confirmed as L. monocytogenes by DNA probe. VIDAS LMO detected 89% of samples inoculated with low levels of L. monocytogenes, and 87% of these were confirmed as positive by DNA probe. In addition, 12 other samples (4 from each of mixed cut vegetable salad, smoked salmon, and sterile smoked salmon) were inoculated with high levels of L. ivanovii, L. seeligeri, L. welshimeri, L. innocua, L. grayi, and L. murrayi. Samples were assayed by the same protocol and all gave negative results. Compared with the cultural method, the VIDAS LMO nonradioactive DNA probe combination is highly specific, discriminates between L. monocytogenes and all other Listeria species, and reduces analytical time.
Determination of Fumonisins B1 and B2 in Various Maize Products by a Combined SAX + C18 Column and Immunoaffinity Column
Authors: Möller Tord E , Gustavsson Håkan F
Published: March 2020

Fumonisins B1 and B2 were determined in 42 samples of different maize products from the Swedish market by 2 different methods based on cleanup steps using an immunoaffinity column and a combination of SAX + C18 columns, respectively. A simple “precipitation step” was included before the samples were added to the main column(s), giving less column clogging, fewer interfering peaks, and better recoveries for the different sample matrixes. Recovery, repeatability, and results from the survey showed comparable results with the methods. The limit of detection for both methods was 5 μg/kg for fumonisin B1 and 10 μg/kg for fumonisin B2. All 7 maize chips analyzed and 6 of 8 popcorn samples contained fumonisins (B1 + B2) with averages of 180 and 115 μg/kg, respectively. All other samples except a maize flour sample contained little or no fumonisins.
Development and Validation of a Method for Direct Analysis of Aflatoxins in Animal Feeds by Ultra-High-Performance Liquid Chromatography with Fluorescence Detection
Authors: Kumar Anup , Dhanshetty Manisha , Banerjee Kaushik
Published: March 2020

Background and Objective

Aflatoxin (AF) contamination is one of the major regulatory concerns for animal feed. As feed is a complex analytical matrix, validated methods on AFs in feed are scanty. The available methods involve a derivatization step before AF analysis by high-performance liquid chromatography (HPLC) with fluorescence detection (FLD). The aim of this study was thus to develop and validate a simple and rapid method for direct analysis of AFs (AFB1, AFB2, AFG1, AFG2) in a range of animal feed matrices.

Methods

Feed samples were extracted with 80% methanol, followed by dilution with water and immmunoaffinity column cleanup. AFs were estimated using an ultra-high performance liquid chromatography (UHPLC) instrument. Use of a large volume flow cell in FLD allowed direct analysis of all AFs with high sensitivity. The method was thoroughly validated in a range of feed matrices.

Results

This sample preparation workflow minimized co-extractives, along with matrix interferences. In pigeon pea husk feed, the method provided a limit of quantification (LOQ) of 0.5 ng/g for each AF with recoveries of AF- B1, B2, G1, and G2 as 71.5, 75.6, 82.4, and 78.2%, respectively. The precision (relative standard deviation, RSD) was below 5%. A similar method performance was also recorded in other matrices, including wheat bran feed and poultry feed.

Conclusions

The optimized method is suitable for regulatory testing because it is simple, robust, cost-effective, and high throughput in nature, with high sensitivity and selectivity.

Highlights

Our workflow has provided a straightforward method for the analysis of AFs in a wide range of animal feed matrices with high sensitivity, selectivity, throughput, and cost-effectiveness. The method allowed a direct analysis of AFs by UHPLC-FLD without a step of derivatization.
Analyzing Molecular Basis of Heat-Induced Loss-of-Wheat Resistance to Hessian Fly (Diptera: Cecidomyiidae) Infestation Using RNA-Sequencing
Authors: Zhu Lieceng , Yuan Jiazheng (John) , O’Neal Jordan , Brown Daria , Chen Ming-Shun
Published: March 2020

Heat stress compromises wheat resistance to Hessian fly (HF, Mayetiola destructor (Say)) (Diptera: Cecidomyiidae) infestation. The objective of this research is to analyze the molecular basis of heat-induced loss of wheat resistance to HF infestation using RNA Sequencing (RNA-seq). To this end, two resistant wheat cultivars ‘Molly’ and ‘Caldwell’ containing the resistance genes H13 and H6, respectively, were infested with an avirulent HF biotype GP and treated with different temperatures to examine the impact of heat stress on their resistance phenotypes. Tissue samples collected from HF feeding sites in Molly plants were subjected to RNA-seq analysis to determine the effect of heat stress on transcript expression of genes in wheat plants. Our results indicate that resistance to HF infestation in Caldwell is more sensitive to heat stress than that in Molly, and that heat stress down-regulates most genes involved in primary metabolism and biosynthesis of lignin and cuticular wax, but up-regulate most or all genes involved in auxin and 12-oxo-phytodienoic acid (OPDA) signaling pathways. Our results and previous reports suggest that heat stress may impair the processes in wheat plants that produce and mobilize chemical resources needed for synthesizing defensive compounds, weaken cell wall and cuticle defense, decrease OPDA signaling, but increase auxin signaling, leading to the suppressed resistance and activation of susceptibility.
Severe Insect Pest Impacts on New Zealand Pasture: The Plight of an Ecological Outlier
Authors: Goldson Stephen L , Barker Gary M , Chapman Hazel M , Popay Alison J , Stewart Alan V , Caradus John R , Barratt Barbara I P
Published: March 2020

New Zealand’s intensive pastures, comprised almost entirely introduced Lolium L. and Trifolium L. species, are arguably the most productive grazing-lands in the world. However, these areas are vulnerable to destructive invasive pest species. Of these, three of the most damaging pests are weevils (Coleoptera: Curculionidae) that have relatively recently been controlled by three different introduced parasitoids, all belonging to the genus Microctonus Wesmael (Hymenoptera: Braconidae). Arguably that these introduced parasitoids have been highly effective is probably because they, like many of the exotic pest species, have benefited from enemy release. Parasitism has been so intense that, very unusually, one of the weevils has now evolved resistance to its parthenogenetic parasitoid. This review argues that New Zealand’s high exotic pasture pest burden is attributable to a lack of pasture plant and natural enemy diversity that presents little biotic resistance to invasive species. There is a native natural enemy fauna in New Zealand that has evolved over millions of years of geographical isolation. However, these species remain in their indigenous ecosystems and, therefore, play a minimal role in creating biotic resistance in the country’s exotic ecosystems. For clear ecological reasons relating to the nature of New Zealand pastures, importation biological control can work extremely well. Conversely, conservation biological control is less likely to be effective than elsewhere.
Otodectes cynotis (Sarcoptiformes: Psoroptidae): New Records on Wild Carnivores in Brazil With a Case Report
Authors: Huang-Bastos Matheus , Bassini-Silva Ricardo , Rolim Luna Scarpari , OConnor Barry , Ochoa Ronald , Barros-Battesti Darci Moraes , Jacinavicius Fernando de Castro
Published: March 2020

The genus Otodectes Canestrini 1894, comprises an unique species, Otodectes cynotis (Hering, 1838), that is responsible for the ‘ear mange’ in terrestrial carnivores worldwide. Here we report its occurrence in four Brazilian host species from the southeastern region, based on records from Carnivora in the Acari Collection of the Butantan Institute, São Paulo state (IBSP). We also register a case report of a crab-eating fox, Cerdocyon thous L. 1758 found parasitized by this mite species.
The positive impact of lockdown in Wuhan on containing the COVID-19 outbreak in China
Authors: Lau Hien , Khosrawipour Veria , Kocbach Piotr , Mikolajczyk Agata , Schubert Justyna , Bania Jacek , Khosrawipour Tanja
Published: March 2020

Background

With its epicenter in Wuhan, China, the COVID-19 outbreak was declared a Public Health Emergency of International Concern by the World Health Organization (WHO). Consequently, many countries have implemented flight restrictions to China. China itself has imposed a lockdown of the population of Wuhan as well as the entire Hubei province. However, whether these two enormous measures have led to significant changes in the spread of COVID-19 cases remains unclear.

Methods

We analyzed the available data on the development of confirmed domestic and international COVID-19 cases before and after lockdown measures. We evaluated the correlation of domestic air traffic to the number of confirmed COVID-19 cases and determined the growth curves of COVID-19 cases within China before and after lockdown as well as after changes in COVID-19 diagnostic criteria.

Results

Our findings indicate a significant increase in doubling time from 2 days (95% CI: 1.9–2.6) to 4 days (95% CI: 3.5–4.3), after imposing lockdown. A further increase is detected after changing diagnostic and testing methodology to 19.3 (95% CI: 15.1–26.3), respectively. Moreover, the correlation between domestic air traffic and COVID-19 spread became weaker following lockdown (before lockdown: r = 0.98, P < 0.05 vs after lockdown: r = 0.91, P = NS).

Conclusions

A significantly decreased growth rate and increased doubling time of cases was observed, which is most likely due to Chinese lockdown measures. A more stringent confinement of people in high risk areas seems to have a potential to slow down the spread of COVID-19.
Pennycress, carbon wise: labeling experiments reveal how pennycress seeds efficiently incorporate carbon into biomass
Authors: Sedbrook John C , Durrett Timothy P
Published: March 2020

This article comments on:

Tsogtbaatar E, Cocuron J-C, Alonso AP. 2020. Non-conventional pathways enable pennycress (Thlaspi arvense L.) embryos to achieve high biosynthetic efficiency. Journal of Experimental Botany 71, 3037–3051.
Radio view of a broad-line Type Ic supernova ASASSN-16fp
Authors: A. J. Nayana , Chandra Poonam
Published: March 2020

We present extensive radio observations of a Type Ic supernova, ASASSN-16fp. Our data represent the lowest frequency observations of the supernova beyond 1000 d with a frequency range of 0.33–25 GHz and a temporal range of ∼8–1136 d post-explosion. The observations are best represented by a model of synchrotron emission from a shocked circumstellar shell initially suppressed by synchrotron self-absorption. Assuming equipartition of energy between relativistic particles and magnetic fields, we estimate the velocity and radius of the blast wave to be $v$ ∼ 0.15c and r ∼ 3.4 × 1015 cm, respectively, at t0 ∼ 8 d post-explosion. We infer the total internal energy of the radio-emitting material evolves as E ∼ 0.37 × 1047 (t/t0)0.65 erg. We determine the mass-loss rate of the progenitor star to be $\dot{M} \sim (0.4\!-\!3.2) \times 10^{-5}\, \mathrm{M}_{\odot }\, \rm yr^{-1}$ at various epochs post-explosion, consistent with the mass-loss rate of Galactic Wolf–Rayet stars. The radio light curves and spectra show a signature of density enhancement in the circumstellar medium at a radius of ∼1.10 × 1016 cm from the explosion centre.
Turbulence in stratified atmospheres: implications for the intracluster medium
Authors: Mohapatra Rajsekhar , Federrath Christoph , Sharma Prateek
Published: March 2020

The gas motions in the intracluster medium (ICM) are governed by turbulence. However, since the ICM has a radial profile with the centre being denser than the outskirts, ICM turbulence is stratified. Stratified turbulence is fundamentally different from Kolmogorov (isotropic, homogeneous) turbulence; kinetic energy not only cascades from large to small scales, but it is also converted into buoyancy potential energy. To understand the density and velocity fluctuations in the ICM, we conduct high-resolution (10242 × 1536 grid points) hydrodynamical simulations of subsonic turbulence (with rms Mach number $\mathcal {M}\approx 0.25$) and different levels of stratification, quantified by the Richardson number Ri, from Ri = 0 (no stratification) to Ri = 13 (strong stratification). We quantify the density, pressure, and velocity fields for varying stratification because observational studies often use surface brightness fluctuations to infer the turbulent gas velocities of the ICM. We find that the standard deviation of the logarithmic density fluctuations (σs), where s = ln (ρ/ < ρ($z$) >), increases with Ri. For weakly stratified subsonic turbulence (Ri ≲ 10, $\mathcal {M}\lt 1$), we derive a new σs–$\mathcal {M}$–Ri relation, $\sigma _\mathrm{ s}^2=\ln (1+b^2\mathcal {M}^4+0.09\mathcal {M}^2 \mathrm{Ri} H_\mathrm{ P}/H_\mathrm{ S})$, where b = 1/3–1 is the turbulence driving parameter, and HP and HS are the pressure and entropy scale heights, respectively. We further find that the power spectrum of density fluctuations, P(ρk/ < ρ >), increases in magnitude with increasing Ri. Its slope in k-space flattens with increasing Ri before steepening again for Ri ≳ 1. In contrast to the density spectrum, the velocity power spectrum is invariant to changes in the stratification. Thus, we find that the ratio between density and velocity power spectra strongly depends on Ri, with the total power in density and velocity fluctuations described by our σs–$\mathcal {M}$–Ri relation. Pressure fluctuations, on the other hand, are independent of stratification and only depend on $\mathcal {M}$.
Semi-analytic forecasts for JWST – III. Intrinsic production efficiency of Lyman-continuum radiation
Authors: Yung L Y Aaron , Somerville Rachel S , Popping Gergö , Finkelstein Steven L
Published: March 2020

The James Webb Space Telescope is expected to enable transformational progress in studying galaxy populations in the very early Universe, during the epoch of reionization. A critical parameter for understanding the sources that reionized the Universe is the Lyman-continuum production efficiency, ξion, defined as the rate of production of ionizing photons divided by the intrinsic UV luminosity. In this work, we combine self-consistent star formation and chemical enrichment histories predicted by semi-analytic models of galaxy formation with stellar population synthesis (SPS) models to predict the expected dependence of ξion on galaxy properties and cosmic epoch from z = 4–10. We then explore the sensitivity of the production rate of ionizing photons, $\dot{N}_\text{ion}$, to the choice of SPS model and the treatment of stellar feedback in our galaxy formation model. We compare our results to those of other simulations, constraints from empirical models, and observations. We find that adopting SPS models that include binary stars predict about a factor of 2 more ionizing radiation than models that only assume single stellar populations. We find that UV-faint, low-mass galaxies have values of ξion about 0.25 dex higher than those of more massive galaxies, but find weak evolution with cosmic time, about 0.2 dex from z ∼ 12–4 at fixed rest-UV luminosity. We provide predictions of $\dot{N}_\text{ion}$ as a function of Mh and a number of other galaxy properties. All results presented in this work are available at https://www.simonsfoundation.org/semi-analytic-forecasts-for-jwst/.
Testing tidal alignment models for anisotropic correlations of halo ellipticities with N-body simulations
Authors: Okumura Teppei , Taruya Atsushi , Nishimichi Takahiro
Published: March 2020

There is a growing interest of using the intrinsic alignment (IA) of galaxy images as a tool to extract cosmological information complimentary to galaxy clustering analysis. Recently, Okumura & Taruya derived useful formulas for the intrinsic ellipticity–ellipticity correlation, the gravitational shear–intrinsic ellipticity correlation, and the velocity–intrinsic ellipticity correlation functions based on the linear alignment (LA) model. In this paper, using large-volume N-body simulations, we measure these alignment statistics for dark-matter haloes in real and redshift space and compare them to the LA and non-linear alignment model predictions. We find that anisotropic features of baryon acoustic oscillations in the IA statistics can be accurately predicted by our models. The anisotropy due to redshift-space distortions (RSDs) is also well described in the large-scale limit. Our results indicate that one can extract the cosmological information encoded in the IA through the Alcock–Paczynski and RSD effects.
Realistic gravitational focusing of meteoroid streams
Authors: Moorhead Althea V , Clements Tiffany D , Vida Denis
Published: March 2020

The number density and flux of a meteoroid stream is enhanced near a massive body due to the phenomenon known as gravitational focusing. The greatest enhancement occurs directly opposite the massive body from the stream radiant: as an observer approaches this location, the degree of focusing is unbound for a perfectly collimated stream. However, real meteoroid streams exhibit some dispersion in radiant and speed that will act to eliminate this singularity. In this paper, we derive an analytic approximation for this smoothing that can be used in meteoroid environment models and is based on real measurements of meteor shower radiant dispersion.
Relaxation of NO+ by collision with para-H2 (j = 0)
Authors: Cabrera-González L D , Páez-Hernández D , Denis-Alpizar O
Published: March 2020

The first tentative detection of the nitrosylium ion (NO+) in the interstellar medium (ISM) was reported just a few years ago. The application of non-local thermal equilibrium models requires the knowledge of the collisional rate coefficients with the most common colliders in the ISM (e.g. He, H, H2, and e). The main goals of this paper are to study the collision of the NO+ molecule with para-H2 (j = 0) and report the rate coefficients for the lower rotational states of NO+. A large set of ab initio energies was computed at the CCSD(T)/aug-cc-pV5Z level of theory. A new potential energy surface averaged over the H2 orientations was then fitted using a reproducing kernel Hilbert space procedure. The state-to-state cross-sections of NO++para-H2 (j = 0) for the first 18 rotational levels were computed using the close-coupling method. The rotational rate coefficients of this system were compared with those for NO++He, and a different propensity rule was found. Furthermore, the hyperfine rate coefficients were also calculated using the infinite-order-sudden scaling procedure.
Atmospheric compositions and observability of nitrogen-dominated ultra-short-period super-Earths
Authors: Zilinskas Mantas , Miguel Yamila , Mollière Paul , Tsai Shang-Min
Published: March 2020

We explore the chemistry and observability of nitrogen-dominated atmospheres for ultra-short-period super-Earths. We base the assumption that super-Earths could have nitrogen-filled atmospheres on observations of 55 Cancri e that favour a scenario with a high-mean-molecular-weight atmosphere. We take Titan’s elemental budget as our starting point and using chemical kinetics compute a large range of possible compositions for a hot super-Earth. We use analytical temperature profiles and explore a parameter space spanning orders of magnitude in C/O and N/O ratios, while always keeping nitrogen the dominant component. We generate synthetic transmission and emission spectra and assess their potential observability with the future James Webb Space Telescope (JWST) and ARIEL. Our results suggest that HCN is a strong indicator of a high C/O ratio, which is similar to what is found for H-dominated atmospheres. We find that these worlds are likely to possess C/O > 1.0, and that HCN, CN, and CO should be the primary molecules to be searched for in thermal emission. For lower temperatures (T < 1500 K), we additionally find NH3 in high N/O ratio cases, and C2H4 and CH4 in low N/O ratio cases to be strong absorbers. Depletion of hydrogen in such atmospheres would make CN, CO, and NO exceptionally prominent molecules to look for in the 0.6–5.0 $\rm{\mu m}$ range. Our models show that the upcoming JWST and ARIEL missions will be able to distinguish atmospheric compositions of ultra-short-period super-Earths with unprecedented confidence.
Rampant Misexpression in a Mimulus (Monkeyflower) Introgression Line Caused by Hybrid Sterility, Not Regulatory Divergence
Authors: Kerwin Rachel E , Sweigart Andrea L
Published: March 2020

Divergence in gene expression regulation is common between closely related species and may give rise to incompatibilities in their hybrid progeny. In this study, we investigated the relationship between regulatory evolution within species and reproductive isolation between species. We focused on a well-studied case of hybrid sterility between two closely related yellow monkeyflower species, Mimulus guttatus and Mimulus nasutus, that is caused by two epistatic loci, hybrid male sterility 1 (hms1) and hybrid male sterility 2 (hms2). We compared genome-wide transcript abundance across male and female reproductive tissues (i.e., stamens and carpels) from four genotypes: M. guttatus, M. nasutus, and sterile and fertile progeny from an advanced M. nasutus–M. guttatus introgression line carrying the hms1–hms2 incompatibility. We observed substantial variation in transcript abundance between M. guttatus and M. nasutus, including distinct but overlapping patterns of tissue-biased expression, providing evidence for regulatory divergence between these species. We also found rampant genome-wide misexpression, but only in the affected tissues (i.e., stamens) of sterile introgression hybrids carrying incompatible alleles at hms1 and hms2. Examining patterns of allele-specific expression in sterile and fertile introgression hybrids, we found evidence for interspecific divergence in cis- and trans-regulation, including compensatory cis–trans mutations likely to be driven by stabilizing selection. Nevertheless, species divergence in gene regulatory networks cannot explain the vast majority of the gene misexpression we observe in Mimulus introgression hybrids, which instead likely manifests as a downstream consequence of sterility itself.
Distortion of double-stranded DNA structure by the binding of the restriction DNA glycosylase R.PabI
Authors: Miyazono Ken-ichi , Wang Delong , Ito Tomoko , Tanokura Masaru
Published: March 2020

R.PabI is a restriction DNA glycosylase that recognizes the sequence 5′-GTAC-3′ and hydrolyses the N-glycosidic bond of adenine in the recognition sequence. R.PabI drastically bends and unwinds the recognition sequence of double-stranded DNA (dsDNA) and flips the adenine and guanine bases in the recognition sequence into the catalytic and recognition sites on the protein surface. In this study, we determined the crystal structure of the R.PabI-dsDNA complex in which the dsDNA is drastically bent by the binding of R.PabI but the base pairs are not unwound. This structure is predicted to be important for the indirect readout of the recognition sequence by R.PabI. In the complex structure, wedge loops of the R.PabI dimer are inserted into the minor groove of dsDNA to stabilize the deformed dsDNA structure. A base stacking is distorted between the two wedge-inserted regions. R.PabI is predicted to utilize the distorted base stacking for the detection of the recognition sequence.
Hyaluronidase-Facilitated High-Dose Subcutaneous IgG Effectively Controls Parvovirus B19 Infection in a Pediatric Cardiac Transplant Patient With Severe T-Cell Lymphopenia
Authors: Cruz Rachel J , Dasso Joseph F , Duff Carla , Krasnopero Diane , Long Zsofia , Ellison Maryssa , Nieves Daime , Sriaroon Panida , Asante-Korang Alfred , Walter Jolan E
Published: March 2020

We treated three pediatric cardiac transplant patients with chronic parvovirus viremia with high-dose intravenous immunoglobulin (HD-IVIG). One patient with severe T-cell lymphopenia suffered recurrent viremia and aseptic meningitis, which resolved remarkably when he was switched to high-dose hyaluronidase-facilitated subcutaneous immunoglobulin (HD-SCIG-Hy). We discuss the advantages of HD-SCIG-Hy vs HD-IVIG treatment for similar cases.
Species-specific content of thiamin (vitamin B1) in phytoplankton and the transfer to copepods
Authors: Fridolfsson Emil , Lindehoff Elin , Legrand Catherine , Hylander Samuel
Published: March 2020

Thiamin (vitamin B1) is primarily produced by bacteria and phytoplankton in aquatic food webs and transferred by ingestion to higher trophic levels. However, much remains unknown regarding production, content and transfer of this water-soluble, essential micronutrient. Hence, the thiamin content of six phytoplankton species from different taxa was investigated, along with the effect of thiamin amendment on thiamin content. Furthermore, thiamin transfer to copepods was estimated in feeding experiments. Prey type, not phytoplankton thiamin content per se, was the most important factor for the transfer of thiamin, as it was lowest from filamentous Cyanophyceae and highest from more easily ingested prey like Dunaliella tertiolecta and Rhodomonas salina. Cyanophyceae had the highest thiamin content of the investigated species, eightfold higher than the lowest. Phytoplankton varied in thiamin content related to the supply of thiamin, where thiamin addition enabled higher thiamin content in some species, while copepod thiamin content was less variable. In all, thiamin transfer is not only dependent on the prey thiamin content, but also the edibility and/or digestibility is of importance. Thiamin is essential for all organisms, and this study constitutes an important building block to understanding the dynamics and transfer of thiamin in the aquatic food web.
Capsaicin-Induced Changes in Electrical Pain Perception Threshold Can Be Used to Assess the Magnitude of Secondary Hyperalgesia in Humans
Authors: Hughes Sam W , Basra Meirvaan , Chan Calvin , Parr Callum , Wong Felyx , Gomes Sofia , Strutton Paul H
Published: March 2020

Objectives

Areas of secondary hyperalgesia can be assessed using quantitative sensory testing (QST). Delivering noxious electrocutaneous stimulation could provide added benefit by allowing multiple measurements of the magnitude of hyperalgesia. We aimed to characterize the use of electrical pain perception (EPP) thresholds alongside QST as a means by which to measure changes in pain thresholds within an area of secondary mechanical hyperalgesia.

Methods

EPP and heat pain thresholds (HPTs) were measured at five distinct points at baseline and following 1% capsaicin cream application, one within a central zone and four within a secondary zone. Areas of secondary mechanical hyperalgesia were mapped using QST. In a further 14 participants, capsaicin-induced reduction in EPP thresholds was mapped using a radial lines approach across 24 points.

Results

There was a reduction in EPP threshold measured at the four points within the secondary zone, which was within the mapped area of mechanical secondary hyperalgesia. The magnitude of secondary hyperalgesia could be split into a mild (∼4% reduction) and severe (∼21% reduction) area within an individual subject. There was no reduction in HPT within the secondary zone, but there was a reduction in both HPT and EPP threshold within the primary zone. EPP mapping revealed differences in the magnitude and spread of hyperalgesia across all subjects.

Conclusions

Measuring capsaicin-induced reduction in EPP thresholds can be used to map hyperalgesic areas in humans. This semi-automated approach allows rapid assessment of the magnitude of hyperalgesia, both within an individual subject and across a study population.
Stringy excited baryons in holographic quantum chromodynamics
Authors: Hayashi Yasuhiro , Ogino Takahiro , Sakai Tadakatsu , Sugimoto Shigeki
Published: March 2020

We analyze excited baryon states using a holographic dual of quantum chromodynamics that is defined on the basis of an intersecting D4/D8-brane system. Studies of baryons in this model have been made by regarding them as a topological soliton of a gauge theory on a five-dimensional curved spacetime. However, this allows one to obtain only a certain class of baryons. We attempt to present a framework such that a whole set of excited baryons can be treated in a systematic way. This is achieved by employing the original idea of Witten, which states that a baryon is described by a system composed of $N_c$ open strings emanating from a baryon vertex. We argue that this system can be formulated by an Atiyah–Drinfeld–Hitchin–Manin-type matrix model of Hashimoto–Iizuka–Yi together with an infinite tower of the open string massive modes. Using this setup, we work out the spectra of excited baryons and compare them with the experimental data. In particular, we derive a formula for the nucleon Regge trajectory assuming that the excited nucleons lying on the trajectory are characterized by the excitation of a single open string attached on the baryon vertex.
Production Networks and Stock Returns: The Role of Vertical Creative Destruction
Authors: Gofman Michael , Segal Gill , Wu Youchang
Published: March 2020

We examine empirically and theoretically the relation between firms’ risk and distance to consumers in a production network. We document two novel facts: firms farther away from consumers have higher risk premiums and higher exposure to aggregate productivity. We quantitatively explain these findings using a general equilibrium model featuring a multilayer production process. The economic force is “vertical creative destruction,” that is, positive productivity shocks to suppliers devalue customers’ assets-in-place, thereby lowering the cyclicality of downstream firms’ values. We show that vertical creative destruction varies with competition and firm characteristics and generates sizable cross-sectional differences in risk premiums.
An interferon-gamma release assay as a novel biomarker in systemic lupus erythematosus
Authors: Thomason Jenna L , Obih Uchechukwu M , Koelle David M , Lood Christian , Hughes and Grant
Published: March 2020

Objective

The mycobacterium tuberculosis (TB) IFN-γ release assay (TB-IGRA) assesses peripheral blood cell release of IFN-γ upon ex vivo exposure to mitogen (IGRA-MT), TB antigen or a negative/nil control (IGRA-NL); IGRA-NL is a measure of spontaneous IFN-γ release (SIR). Here, we investigate the diagnostic associations of elevated SIR and the potential use of IGRA-NL as a novel biomarker in SLE.

Methods

We analysed diagnostic code frequencies among 11 823 individuals undergoing TB-IGRA testing between 2010 and 2015 in a large urban US health-care system. To study the relationship between IGRA-NL and SLE, we identified 99 individuals with SLE and TB-IGRA test results then assessed correlations between IGRA-NL, normalized IGRA-NL (the quotient of IGRA-NL/IGRA-MT), disease manifestations and disease activity.

Results

We identified a discovery cohort of 108 individuals with elevated SIR (>5 S.d. above median) that was significantly enriched for a limited set of diagnoses, including SLE, TB infection, haemophagocytic lymphohistiocytosis and HIV infection. In SLE patients undergoing TB-IGRA testing, normalized IGRA-NL correlated better with disease activity than did anti-dsDNA or complement levels. This relationship appeared to reflect interactions between normalized IGRA-NL and the presence of acute skin disease, hypocomplementemia, fever and thrombocytopenia.

Conclusion

Elevated SIR appears to be associated with a limited number of disease processes, including SLE. The diagnostic utility of SIR remains to be determined. IFN-γ activation, as measured by the TB-IGRA test, may offer a readily available tool for assessing disease activity in patients with SLE.
Transporters and ascorbate–glutathione metabolism for differential cadmium accumulation and tolerance in two contrasting willow genotypes
Authors: Han Xiaojiao , Zhang Yunxing , Yu Miao , Zhang Jin , Xu Dong , Lu Zhuchou , Qiao Guirong , Qiu Wenmin , Zhuo Renying
Published: March 2020

Salix matsudana Koidz is a low cadmium (Cd)-accumulating willow, whereas its cultivated variety, Salix matsudana var. matsudana f. umbraculifera Rehd., is a high Cd-accumulating and tolerant willow (HCW). The physiological and molecular mechanisms underlying differential Cd accumulation and tolerance in the two Salix species are poorly understood. Here, we confirmed that the differential Cd translocation capacity from roots to the shoots leads to the differential Cd accumulation in their aboveground parts between these two willow genotypes. Cadmium accumulation happens preferentially in the transport pathway, and Cd is mainly located in the vacuolar, cell wall and intercellular space in HCW bark by cadmium location analysis at tissue and subcellular levels. Comparative transcriptome analysis revealed that higher expressions of several metal transporter genes (ATP-binding cassette transporters, K+ transporters/channels, yellow stripe-like proteins, zinc-regulated transporter/iron-regulated transporter-like proteins, etc.) are involved in root uptake and translocation capacity in HCW; meanwhile, ascorbate–glutathione metabolic pathways play essential roles in Cd detoxification and higher tolerance of the Cd-accumulator HCW. These results lay the foundation for further understanding the molecular mechanisms of Cd accumulation in woody plants and provide new insights into molecular-assisted-screening woody plant varieties for phytoremediation.
Structural abnormalities in the temporalis musculo-aponeurotic complex in chronic muscular temporomandibular disorders
Authors: Moayedi Massieh , Krishnamoorthy Gaurav , He Pei-Yuan (Tony) , Agur Anne , Weissman-Fogel Irit , Tenenbaum Howard C. , Lam Ernest W.N. , Davis Karen D. , Henderson Luke , Cioffi Iacopo
Published: March 2020

Some forms of chronic pain are thought to be driven and maintained by nociceptive input, which can drive plasticity within nociceptive pathways. We have previously identified abnormalities along the entire nociceptive pathway in chronic myalgic temporomandibular disorders (mTMD), including the trigeminal nerves, brainstem pathways, and in the thalamus and somatosensory cortex. These data suggest that there is a peripheral nociceptive drive in mTMD, but the source of this nociceptive activity remains unknown. Here, our aim was to determine whether structural abnormalities exist in the muscles of mastication of patients with chronic mTMD. Specifically, we tested whether the volume of the temporalis muscle and its tendon–aponeurosis complex (TAC, a structure that dissipates forces in a muscle) in mTMD patients differ compared to age- and sex-matched controls. To do so, we segmented these structures on T1-weighted structural magnetic resonance images. We found that muscle volumes in mTMD were not different to controls. However, the mTMD group had significantly smaller volumes of the bilateral temporalis TAC, and thus a smaller TAC-to-muscle volume ratio. These findings were consistent across 2 independent cohorts of 17 mTMD patients, compared to 17 age- and sex-matched controls. We propose a model where reduced TAC-to-muscle ratio could result in a predisposition to muscle tissue injury. In sum, abnormalities of the temporalis muscles in mTMD supports our hypothesis that chronic mTMD pathophysiology may be related to peripheral nociceptive barrage originating from the muscles of mastication.
Evaluation of Hospitalizations Preventable with Idealized Outpatient Care and Continuity of Care
Authors: Li Shawn X. , del Carmen Marcela G. , Thompson Ryan W. , Cafiero-Fonseca Elizabeth T. , Rockett Helaine , Ferris Timothy G. , Terry Dellara F. , Warner Ana Sofia , Yu Amy , Wasfy Jason H.
Published: March 2020

Background:

Unnecessary hospitalizations may pose the risk of iatrogenic complications, suboptimal patient experience, and increased cost. Administrative data lack granularity to understand the proportion and causes of hospitalizations preventable through optimizing care continuum (HPOCC). We aim to identify the incidence and causes of HPOCC through clinician-adjudicated chart review.

Methods:

A retrospective review was performed for inpatient admissions from the emergency department (ED) over 1 week. Each admission was reviewed by a clinician to determine whether it is an HPOCC defined as not requiring inpatient care with the assumption of idealized outpatient care and social support.

Results:

Of the 515 patients admitted from the ED, 31 (6.0%) patients were judged to have had an HPOCC. Causes of HPOCC include urgent diagnostics (9, 29.0%), unnecessary transfer from a long-term facility (7, 23.0%), needing IV therapy (5, 16.0%), benign incidental finding (5, 16.0%), diagnostic uncertainty in complex chronic illness (3, 10.0%), and lack of access to care for disposition (2, 6.0%).

Conclusion:

Hospitalizations preventable through optimizing care continuum account for about 1 in every 15 hospitalizations in an urban academic medical center. The need for urgent diagnostics accounts for a plurality of HPOCC and could be an important target for quality improvement.