bluuebunny/crossref_metadata_2025_split huggingface dataset:
Charged particles energization during magnetic reconnection in the Earth’s magnetosphere by double layers: an analytical approach
Authors: Shamir M , Khan Imran A , Murtaza G 
Published: November 2021

ABSTRACT
Charged particles energization at the magnetic reconnection sites in the Earth’s magnetosphere is a subject of active debate in space plasma, specifically in magnetopause and magnetotail regions. In the proximity of the reconnection region, Magnetospheric Multiscale (MMS) and other satellite missions have confirmed the existence of electron acceleration ranging from 100 keV to MeV. There is also evidence of cold ions acceleration in the separatrix region of the Earth’s magnetopause. An important candidate responsible for charged particles acceleration is believed to be the double layer (DL) structures, and which were first observed by the Cluster satellite in the separatrix region of the Earth’s magnetosphere. Moreover, the MMS mission also observed parallel electric field fluctuations up to 100 mV/m carried by DL at the magnetic reconnection site in the Earth’s magnetosphere. Motivated by the reported literature, we investigate the DL and its associated electric field at the magnetopause magnetic reconnection site by using a simple analytical model in which the DLs associated with kinetic Alfvén waves are studied in a low- $\beta$ electron-ion plasma with Tsallis distributed electrons and fluid ions using the Sagdeev potential technique. The non-extensive parameter (superthermality) of the Tsallis distribution has a pronounced effect on the DL’s strength (as defined by the potential drop) and its associated parallel electric field. Our results are consistent with the earlier studies on DLs in Earth’s magnetosphere. Additionally, we discuss the implications of our findings on charged particle energization in the separatrix region of the Earth’s magnetopause during magnetic reconnection.
Bottling the champagne: dynamics and radiation trapping of wind-driven bubbles around massive stars
Authors: Geen Sam , de Koter Alex 
Published: November 2021

ABSTRACT
In this paper, we make predictions for the behaviour of wind bubbles around young massive stars using analytic theory. We do this in order to determine why there is a discrepancy between theoretical models that predict that winds should play a secondary role to photoionization in the dynamics of H iiregions, and observations of young H iiregions that seem to suggest a driving role for winds. In particular, regions such as M42 in Orion have neutral hydrogen shells, suggesting that the ionizing radiation is trapped closer to the star. We first derive formulae for wind bubble evolution in non-uniform density fields, focusing on singular isothermal sphere density fields with a power-law index of -2. We find that a classical ‘Weaver’-like expansion velocity becomes constant in such a density distribution. We then calculate the structure of the photoionized shell around such wind bubbles, and determine at what point the mass in the shell cannot absorb all of the ionizing photons emitted by the star, causing an ‘overflow’ of ionizing radiation. We also estimate perturbations from cooling, gravity, magnetic fields and instabilities, all of which we argue are secondary effects for the conditions studied here. Our wind-driven model provides a consistent explanation for the behaviour of M42 to within the errors given by observational studies. We find that in relatively denser molecular cloud environments around single young stellar sources, champagne flows are unlikely until the wind shell breaks up due to turbulence or clumping in the cloud.
Period-change rates in Large Magellanic Cloud Cepheids revisited
Authors: Rodríguez-Segovia N , Hajdu G , Catelan M , Espinoza-Arancibia F , Boggiano G , Cenzano C , Garcés E H , Joachimi K , Muñoz-López C , Ordenes-Huanca C , Orquera-Rojas C , Torres P , Valenzuela-Navarro Á 
Published: November 2021

ABSTRACT
The period-change rate (PCR) of pulsating variable stars is a useful probe of changes in their interior structure, and thus of their evolutionary stages. So far, the PCRs of classical Cepheids in the Large Magellanic Cloud (LMC) have been explored in a limited sample of the total population of these variables. Here, we use a template-based method to build observed-minus-computed (O − C) period diagrams, from which we can derive PCRs for these stars by taking advantage of the long time baseline afforded by the Digital Access to a Sky Century @ Harvard light curves, combined with additional data from the Optical Gravitational Lensing Experiment, the MAssive Compact Halo Object project, Gaia’s Data Release 2, and in some cases the All-Sky Automated Survey. From an initial sample of 2315 sources, our method provides an unprecedented sample of 1303 LMC classical Cepheids with accurate PCRs, the largest for any single galaxy, including the Milky Way. The derived PCRs are largely compatible with theoretically expected values, as computed by our team using the Modules for Experiments in Stellar Astrophysics code, as well as with similar previous computations available in the literature. Additionally, five long-period ($P\,\gt\, 50\, \rm {d}$) sources display a cyclic behaviour in their O − C diagrams, which is clearly incompatible with evolutionary changes. Finally, on the basis of their large positive PCR values, two first-crossing Cepheid candidates are identified.
Inferring the morphology of AGN torus using X-ray spectra: a reliability study
Authors: Saha Tathagata , Markowitz Alex G , Buchner Johannes 
Published: November 2021

ABSTRACT
Numerous X-ray spectral models have been developed to model emission reprocessed by the torus of an active galactic nucleus (AGN), e.g. UXCLUMPY, CTORUS, and MYTORUS. They span a range of assumed torus geometries and morphologies – some posit smooth gas distributions, and others posit distributions of clouds. It is suspected that given the quality of currently available data, certain model parameters, such as coronal power-law photon index and parameters determining the morphology of the AGN torus, may be poorly constrained due to model degeneracies. In this work, we test the reliability of these models in terms of recovery of parameters and the ability to discern the morphology of the torus using XMM–Newton and NuSTAR spectral data. We perform extensive simulations of X-ray spectra of Compton-thick AGNs under six X-ray spectral models of the torus. We use Bayesian methods to investigate degeneracy between model parameters, distinguish models and determine the dependence of the parameter constraints on the instruments used. For typical exposure times and fluxes for nearby Compton-thick AGN, we find that several parameters across the models used here cannot be well constrained, e.g. the distribution of clouds, the number of clouds in the radial direction, even when the applied model is correct. We also find that Bayesian evidence values can robustly distinguish between a correct and a wrong model only if there is sufficient energy coverage and only if the intrinsic flux of the object is above a particular value determined by the instrument combination and the model considered.
Variation in Release Factor Abundance Is Not Needed to Explain Trends in Bacterial Stop Codon Usage
Authors: Ho Alexander T , Hurst Laurence D 
Published: November 2021

Abstract
In bacteria stop codons are recognized by one of two class I release factors (RF1) recognizing TAG, RF2 recognizing TGA, and TAA being recognized by both. Variation across bacteria in the relative abundance of RF1 and RF2 is thus hypothesized to select for different TGA/TAG usage. This has been supported by correlations between TAG:TGA ratios and RF1:RF2 ratios across multiple bacterial species, potentially also explaining why TAG usage is approximately constant despite extensive variation in GC content. It is, however, possible that stop codon trends are determined by other forces and that RF ratios adapt to stop codon usage, rather than vice versa. Here, we determine which direction of the causal arrow is the more parsimonious. Our results support the notion that RF1/RF2 ratios become adapted to stop codon usage as the same trends, notably the anomalous TAG behavior, are seen in contexts where RF1:RF2 ratios cannot be, or are unlikely to be, causative, that is, at 3′untranslated sites never used for translation termination, in intragenomic analyses, and across archaeal species (that possess only one RF1). We conclude that specifics of RF biology are unlikely to fully explain TGA/TAG relative usage. We discuss why the causal relationships for the evolution of synonymous stop codon usage might be different from those affecting synonymous sense codon usage, noting that transitions between TGA and TAG require two-point mutations one of which is likely to be deleterious.
RNA marker modifications reveal the necessity for rigorous preparation protocols to avoid artifacts in epitranscriptomic analysis
Authors: Richter Florian , Plehn Johanna E , Bessler Larissa , Hertler Jasmin , Jörg Marko , Cirzi Cansu , Tuorto Francesca , Friedland Kristina , Helm Mark 
Published: November 2021

Abstract
The accurate definition of an epitranscriptome is endangered by artefacts resulting from RNA degradation after cell death, a ubiquitous yet little investigated process. By tracing RNA marker modifications through tissue preparation protocols, we identified a major blind spot from daily lab routine, that has massive impact on modification analysis in small RNAs. In particular, m6,6A and Am as co-varying rRNA marker modifications, appeared in small RNA fractions following rRNA degradation in vitro and in cellulo. Analysing mouse tissue at different time points post mortem, we tracked the progress of intracellular RNA degradation after cell death, and found it reflected in RNA modification patterns. Differences were dramatic between liver, where RNA degradation commenced immediately after death, and brain, yielding essentially undamaged RNA. RNA integrity correlated with low amounts of co-varying rRNA markers. Thus validated RNA preparations featured differentially modified tRNA populations whose information content allowed a distinction even among the related brain tissues cortex, cerebellum and hippocampus. Inversely, advanced cell death correlated with high rRNA marker content, and correspondingly little with the naïve state of living tissue. Therefore, unless RNA and tissue preparations are executed with utmost care, interpretation of modification patterns in tRNA and small RNA are prone to artefacts.
Voltage-dependent anion channel proteins associate with dynamicBamboo mosaic virus-induced complexes
Authors: Lee Hsiang-Chi , Huang Ying-Ping , Huang Ying-Wen , Hu Chung-Chi , Lee Chin-Wei , Chang Chih-Hao , Lin Na-Sheng , Hsu Yau-Heiu 
Published: November 2021

AbstractInfection cycles of viruses are highly dependent on membrane-associated host factors. To uncover the infection cycle of Bamboo mosaic virus (BaMV) in detail, we purified the membrane-associated viral complexes from infected Nicotiana benthamiana plants and analyzed the involved host factors. Four isoforms of voltage-dependent anion channel (VDAC) proteins on the outer membrane of mitochondria were identified due to their upregulated expression in the BaMV complex-enriched membranous fraction. Results from loss- and gain-of-function experiments indicated that NbVDAC2, -3, and -4 are essential for efficient BaMV accumulation. During BaMV infection, all NbVDACs concentrated into larger aggregates, which overlapped and trafficked with BaMV virions to the structure designated as the “dynamic BaMV-induced complex.” Besides the endoplasmic reticulum and mitochondria, BaMV replicase and double-stranded RNAs were also found in this complex, suggesting the dynamic BaMV-induced complex is a replication complex. Yeast two-hybrid and pull-down assays confirmed that BaMV triple gene block protein 1 (TGBp1) could interact with NbVDACs. Confocal microscopy revealed that TGBp1 is sufficient to induce NbVDAC aggregates, which suggests that TGBp1 may play a pivotal role in the NbVDAC–virion complex. Collectively, these findings indicate that NbVDACs may associate with the dynamic BaMV-induced complex via TGBp1 and NbVDAC2, -3, or -4 and can promote BaMV accumulation. This study reveals the involvement of mitochondrial proteins in a viral complex and virus infection.
DE-STRESS: a user-friendly web application for the evaluation of protein designs
Authors: Stam Michael J , Wood Christopher W 
Published: November 2021

Abstract
De novo protein design is a rapidly growing field, and there are now many interesting and useful examples of designed proteins in the literature. However, most designs could be classed as failures when characterised in the lab, usually as a result of low expression, misfolding, aggregation or lack of function. This high attrition rate makes protein design unreliable and costly. It is possible that some of these failures could be caught earlier in the design process if it were quick and easy to generate information and a set of high-quality metrics regarding designs, which could be used to make reproducible and data-driven decisions about which designs to characterise experimentally.
We present DE-STRESS (DEsigned STRucture Evaluation ServiceS), a web application for evaluating structural models of designed and engineered proteins. DE-STRESS has been designed to be simple, intuitive to use and responsive. It provides a wealth of information regarding designs, as well as tools to help contextualise the results and formally describe the properties that a design requires to be fit for purpose.
Making university and industry research collaboration: Evidence from co-inventions in Japan
Authors: Nishimura Junichi , Nagaoka Sadao , Akaike Shinichi , Hosono Mitsuaki 
Published: November 2021

Abstract
This paper examines the making of university and industry research collaboration from the perspective of matching theory. Our analysis, based on an original survey in Japan, aims at identifying the mechanism of matching. The major findings are as follows. There is significant evidence for positive assortative matching at the project level: a researcher with better seeds or better needs gives a higher value to the partner’s research capability and the goodness-of-fit between the project and the partner’s capability in selecting its partner. The projects with the partners selected for research capability and goodness-of-fit are associated with high university and industry research collaboration performance. Furthermore, own contact is most used for positive assortative matching. These results indicate the importance of deep field knowledge and tacit knowledge of the researcher in the search process. These findings suggest that technology transfer policy would need to pay significant attention to the contribution of the decentralized matching process.
The Impact of Unplanned Return to the Operating Room on Health-related Quality of Life at the End of Growth-friendly Surgical Treatment for Early-onset Scoliosis
Authors: Roye Benjamin D. , Fano Adam N. , Matsumoto Hiroko , Fields Michael W. , Emans John B. , Sponseller Paul , Smith John T. , Thompson George H. , White Klane K. , Vitale Michael G. 
Published: November 2021

Background:
Limiting complications, especially unplanned return to the operating room (UPROR), is a major focus in the surgical management of early-onset scoliosis (EOS). Although UPROR remains common in this population, its effect on long-term health-related quality of life (HRQoL) remains unclear. The purpose of this study was to investigate the association between UPROR and end-of-treatment HRQoL in EOS patients treated with growth-friendly instrumentation.

Methods:
Patients with EOS who underwent growth-friendly instrumentation at age less than 10 years from 1993 to 2018, and completed treatment, were identified in a multicenter EOS registry. UPROR events were recorded, and end-of-treatment (defined as skeletal maturity and/or definitive spinal fusion) HRQoL was assessed via the 24-item Early-Onset Scoliosis Questionnaire (EOSQ-24).

Results:
A total of 825 patients were identified, and 325 patients (age at surgery: 6.4 y, follow-up: 8.1 y) had end-of-treatment HRQoL data necessary for our investigation. Overall, 129/325 (39.7%) patients experienced 264 UPROR events; the majority (54.2%) were implant-related. Aside from age and etiology, no other variables were determined to be confounders or effect modifiers. Congenital patients with UPROR had worse pain/discomfort by 10.4 points (P=0.057) and worse pulmonary function by 7.8 points (P=0.102) compared with non-UPROR patients adjusting for age. Neuromuscular patients with UPROR had worse pulmonary function by 10.1 points compared with non-UPROR patients adjusting for age (P=0.037). Idiopathic and syndromic patients with UPROR reported consistently worse domain scores than their non-UPROR counterparts, but smaller (<5-point) differences were seen.

Conclusions:
UPROR during growth-friendly surgical treatment for EOS is associated with worse HRQoL in all patients, but particularly in those with neuromuscular or congenital etiologies. Ongoing efforts to avoid UPROR are critical.

Level of Evidence:
Level II. This is a multicenter retrospective cohort study investigating the effect of UPROR on HRQoL (prognostic study).
The Associations Between Child-Care Services During the Preschool Years and High School Graduation: A 20-Year Longitudinal Population-Based Study
Authors: Losier Talia , Orri Massimiliano , Boivin Michel , Larose Simon , Japel Christa , Tremblay Richard E. , Côté Sylvana M. 
Published: November 2021

ABSTRACT:

Objective:
Together with family factors, early care and education (ECE) services were shown to improve school readiness in kindergarten. However, it is not clear whether better school readiness at age 6 years translates into higher rates of high school graduation years later. Our objective was therefore to investigate the long-term associations between the use of ECE and high school graduation while considering the sex of the child and the socioeconomic status of the parents as moderators.

Methods:
Participants were children from the Quebec Longitudinal Study on Child Development (QLSCD) born in 1997 to 1998 (N = 2001). Intensity and type of ECE exposure were measured from age 5 months to 5 years. Administrative records were used to determine whether students had obtained a high school diploma by age 20 years. Factors explaining differences in the profiles of ECE users were controlled using propensity score weights.

Results:
Twenty-two percent of students did not have a high school diploma by age 20 years. Compared with children never exposed to center-based care, those exposed early (i.e., before toddlerhood) had better odds of graduating from high school (odds ratio = 1.49) after controlling for confounding factors. Late exposure to center-based care was not related to high school graduation rates.

Conclusion:
Exposure to regulated and center-based ECE on a regular basis from toddlerhood to school entry was associated with higher rates of high school graduation. Regulated center-based ECE at the population level may improve rates of high school graduation.
Application of the “Monitoring Child Development in Integrated Management of Childhood Illnesses Context” in Indian Infants and Toddlers
Authors: Mukherjee Sharmila Banerjee , Jain Abhishek , Annadurai Aswini , Sharma Suvasini 
Published: November 2021

Abstract:

Objective:
The objective of this study was to determine the diagnostic accuracy of “Monitoring Child Development in the Integrated Management of Childhood Illnesses Context” (MCDIC) for developmental screening of Indian children younger than 3 years.

Method:
A hospital-based study of diagnostic accuracy was conducted over 17 months after obtaining institutional ethics committee approval. Children younger than 3 years were included in this study. Children with acute illnesses and who presented without their primary caregiver were excluded from this study. The calculated sample size was 272. Eligible children were enrolled after informed consent and stratified by age. MCDIC (index tool) was administrated to primary caregivers by trained interviewers to identify “suspected/probable developmental delay (SDD/PDD).” The reference tools included Developmental Profile, Third Edition, which assessed developmental status based on General Developmental Score (GDS), and Vineland Adaptive Behavior Scale, Second Edition, which evaluated adaptive function based on Adaptive Behavior Composite (ABC). Parameters of diagnostic accuracy were computed according to the number of children with “SDD/PDD” and “developmental delay” (GDS and ABC < −2 SDs).

Results:
The number of eligible children was 312. The sensitivity of MCDIC was 88.0% (95% confidence interval [CI] 68.8–97.5), specificity 85.7 (95% CI 81.1–89.6), positive predictive value 34.9 (95% CI 28.0–42.5), and negative predictive value 98.8 (95% CI 96.6–99.6).

Conclusion:
MCDIC had a high sensitivity and specificity that were above 70% and 80%, respectively, and a high negative predictive value, making it a suitable tool for screening and surveillance of Indian children younger than 3 years.
Subjective Responses to Various Filling Solutions in the Posterior Fluid Reservoir of Miniscleral Lenses at Application
Authors: Tan Jacqueline , Peguda Rajini , Siddireddy Jaya Sowjanya , Briggs Nancy , Stapleton Fiona 
Published: November 2021

Purpose:
To compare the effect of the use of different lubrication eye drops and nonpreserved saline for the application of miniscleral contact lenses (CLs) on subjective experience during 6 hr of lens wear.

Methods:
Experienced soft CL wearers aged 18 to 45 years (inclusive) were enrolled in this prospective, randomized, double-masked, three arm comparison cross-over study. Subjects were custom fitted with KATT 16.5 mm diameter miniscleral lenses, ordered to their prescription. Subjects attended visits on three separate days and were randomized to receive instillation of an HP-guar/nanoemulsion drop or an HP-guar/sodium hyaluronate (HA) eye drop into the miniscleral lens before filling with saline or filling with saline alone (control). Subjective responses were collected up to 6 hr postapplication. Generalized linear mixed models with multinomial distribution and cumulative logit link were used to compare the rate at which responses improved post-CL application for the different treatments.

Results:
Twenty-four participants completed the study. Dryness symptoms were more likely to improve at a slower rate postlens application with saline alone compared with the addition of HP-guar/nanoemulsion (P=0.005) or HP-guar/HA (P=0.049) before lens application. Furthermore, the addition of HP-guar/nanoemulsion was more effective than saline alone in improving symptoms of fluctuating vision (P=0.011), grittiness/burning/stinging (P=0.001), and foreign body sensation (P=0.006) more quickly.

Conclusions:
The use of postlens lubrication may be useful in enhancing adaptation to miniscleral lenses.