bluuebunny/crossref_metadata_2025 huggingface dataset:
Undecidability, unit groups, and some totally imaginary infinite extensions of ℚ
Authors: Springer Caleb
Published: April 2020

We produce new examples of totally imaginary infinite extensions of

Q

\mathbb {Q}

which have undecidable first-order theory by generalizing the methods used by Martínez-Ranero, Utreras, and Videla for

Q

(
2
)

\mathbb {Q}^{(2)}

. In particular, we use parametrized families of polynomials whose roots are totally real units to apply methods originally developed to prove the undecidability of totally real fields. This proves the undecidability of

Q

a
b

(
d
)

\mathbb {Q}^{(d)}_{ab}

for all

d
≥
2

d \geq 2

.
Reading Climate Change in the Palimpsest: The Ecocritical Potential of Novel-to-Film Adaptation
Authors: Mahajan Nandita
Published: April 2020

This essay theorizes the manifestation of the theme of climate change in the reception of novels and their film adaptations. To this end, I draw from and adapt Amitav Ghosh’s conception of textual hybridity: asserting that the era of climate change perhaps requires a movement beyond language to the image, which he believes is better capable of representing physical form, Ghosh prophesies that literature will evolve to incorporate hybrid forms that entwine text and image, such as the graphic novel. Drawing from Gérard Genette, as well as from various adaptation theorists’ descriptions of the doubled perception of an adaptation by audiences acquainted with its source text, I suggest a shift from Ghosh’s idea of hybrid creation to that of hybrid reception. I argue that the reception of a film adaptation of a novel as an adaptation, rather than as a standalone cinematic text, involves a palimpsest-like superimposition of literature and cinema—text and image—in the spectator’s mind, constituting a rich, hybrid experience that can potentially enhance the recipient’s perception of environmental issues in both texts involved. I demonstrate this theory via close readings of Suzanne Collins’s The Hunger Games trilogy and its film adaptations, and Cormac McCarthy’s The Road and its film adaptation, illustrating the various kinds of intertextual relationships that arise out of what I call palimpsestuous reading, and ultimately indicating the value of adaptation in an age of environmental crisis.
Ageism and COVID-19: what does our society’s response say about us?
Authors: Fraser Sarah , Lagacé Martine , Bongué Bienvenu , Ndeye Ndatté , Guyot Jessica , Bechard Lauren , Garcia Linda , Taler Vanessa ,   CCNA Social Inclusion and Stigma Working Group, Andrew Melissa , Bayly Melanie , Bethell Jennifer , Chasteen Alison , Elliot Valerie , Herron Rachel , Itzhak Inbal , Kortzman August , Maxwell Colleen , McGilton Kathy , Middleton Laura , Morgan Debra , O’Connell Megan , O’Rourke Hannah , Phillips Natalie , Pichora-Fuller Margaret , Wallace Kayla , Wittich Walter , Adam Stéphane , Beaulieu Marie , Bergeron Caroline D , Boudjemadi Valérian , Desmette Donatienne , Donizzetti Anna Rosa , Éthier Sophie , Garon Suzanne , Gillis Margaret , Levasseur Mélanie , Lortie-lussier Monique , Marier Patrik , Robitaille Annie , Sawchuk Kim , Lafontaine Constance , Tougas Francine
Published: April 2020

The goal of this commentary is to highlight the ageism that has emerged during the COVID-19 pandemic. Over 20 international researchers in the field of ageing have contributed to this document. This commentary discusses how older people are misrepresented and undervalued in the current public discourse surrounding the pandemic. It points to issues in documenting the deaths of older adults, the lack of preparation for such a crisis in long-term care homes, how some ‘protective’ policies can be considered patronising and how the initial perception of the public was that the virus was really an older adult problem. This commentary also calls attention to important intergenerational solidarity that has occurred during this crisis to ensure support and social-inclusion of older adults, even at a distance. Our hope is that with this commentary we can contribute to the discourse on older adults during this pandemic and diminish the ageist attitudes that have circulated.
Alcohol, Alcoholic Beverages and Risk of Esophageal Cancer by Histological Type: A Dose–Response Meta-Analysis of Observational Studies
Authors: Yu Xiaohui , Chen Jiahao , Jiang Wenjie , Zhang Dongfeng
Published: April 2020

Aims

We conducted a dose–response meta-analysis to explore the association between alcohol and particular alcoholic beverages with risk of esophageal cancer (EC) by histological type [esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC)] and whether the association differs according to gender.

Methods

PubMed and Web of Science databases were searched for relevant articles published between January 1960 and December 2019. The pooled relative ratios (RRs) and 95% confidence interval (CI) were calculated with the fixed or random effect model. The dose–response relationship was assessed by restricted cubic spline.

Results

A total of 74 published articles involving 31,105 cases among 3,369,024 participants were included in this meta-analysis. The pooled RRs of the highest versus lowest alcohol intake were 3.67 (95% CI, 2.89,4.67) for EC, 5.11 (95% CI, 3.60,7.25) for ESCC and 0.96 (95% CI, 0.79,1.16) for EAC. The above-mentioned associations were observed in cohort design, for different alcoholic beverages (beer, wine and liquor/spirits) and gender. Evidence of a nonlinear dose–response relationship for EC risk with alcohol intake was found (Pnon-linearity < 0.001), and a linear relationship (Pnon-linearity = 0.216) suggested that the risk of ESCC increased by 33% for every 12.5 g/day increment of alcohol intake.

Conclusions

This meta-analysis suggests that alcohol intake might significantly increase the incidence of EC, especially for ESCC.
The extension of arbitration agreements to third parties through the lens of Egyptian courts
Authors: Shehata Ibrahim
Published: April 2020

Extending arbitration agreements to third parties has long been a recurring debate in the world of international commercial arbitration. There are various mechanisms by which an arbitration agreement might be extended to third parties. This includes the doctrines of group of companies, group of contracts, universal succession, and assignment of contracts. The fact that the Egyptian Arbitration Law—alike most arbitration laws—does not deal specifically with this issue leaves a gap to be filled by the courts. This article tries to analyse and synthesize the various decisions rendered by the Egyptian courts in an attempt to identify their stance in this area. In this regard, this article will first discuss the privity of contracts from an Egyptian legal perspective, then will delve into the various constructs and mechanisms that could be utilized under Egyptian law when it comes to the extension of arbitration agreements to third parties. Special attention will then be paid to a specific issue, namely the extension of arbitration agreements under a contract to the letters of guarantee issued in connection with the same contract.
Molecular Testing for Acute Respiratory Tract Infections: Clinical and Diagnostic Recommendations From the IDSA’s Diagnostics Committee
Authors: Hanson Kimberly E , Azar Marwan M , Banerjee Ritu , Chou Andrew , Colgrove Robert C , Ginocchio Christine C , Hayden Mary K , Holodiny Mark , Jain Seema , Koo Sophia , Levy Jaclyn , Timbrook Tristan T , Caliendo Angela M
Published: April 2020

The clinical signs and symptoms of acute respiratory tract infections (RTIs) are not pathogen specific. Highly sensitive and specific nucleic acid amplification tests have become the diagnostic reference standard for viruses, and translation of bacterial assays from basic research to routine clinical practice represents an exciting advance in respiratory medicine. Most recently, molecular diagnostics have played an essential role in the global health response to the novel coronavirus pandemic. How best to use newer molecular tests for RTI in combination with clinical judgment and traditional methods can be bewildering given the plethora of available assays and rapidly evolving technologies. Here, we summarize the current state of the art with respect to the diagnosis of viral and bacterial RTIs, provide a practical framework for diagnostic decision making using selected patient-centered vignettes, and make recommendations for future studies to advance the field.
Human Immunodeficiency Virus Infection Is Associated With Increased Meningococcal Carriage Acquisition Among First-year Students in 2 South African Universities
Authors: Meiring Susan , Cohen Cheryl , de Gouveia Linda , du Plessis Mignon , Ganesh Karistha , Kleynhans Jackie , Quan Vanessa , Tempia Stefano , von Gottberg Anne
Published: April 2020

Background

Invasive meningococcal disease clusters occur among university students and may reflect higher carriage prevalence among this population. We aimed to measure meningococcal carriage prevalence, acquisition, and risk factors among first-year university students in South Africa.

Methods

In summer–autumn 2017, after consenting to participate, we collected oropharyngeal swabs and questionnaires on carriage risk factors and tested students for HIV at 2 universities, during registration week (survey 1) and 6–8 weeks later (survey 2). Meningococci were detected by culture and polymerase chain reaction.

Results

We enrolled 2120 students at registration. Mean age was 18.5 years, 59% (1252/2120) were female and 0.8% (16/1984) had HIV. Seventy-eight percent of students returned for survey 2 (1655/2120). Among the cohort, carriage prevalence was 4.7% (77/1655) at registration, increasing to 7.9% (130/1655) at survey 2: 5.0% (83) acquired new carriage, 2.8% (47) had persistent carriage, 1.8% (30) cleared the initial carriage, and 90.3% (1495) remained carriage free. At both surveys, nongenogroupable meningococci predominated, followed by genogroups Y, B, W, and C. On multinomial analysis, risk factors for carriage acquisition included attending nightclubs (adjusted relative risk ratio [aRRR], 2.1; 95% CI, 1.1–4.0), having intimate kissing partners (aRRR, 1.8; 95% CI, 1.1–2.9) and HIV (aRRR, 5.0; 95% CI, 1.1–24.4).

Conclusions

Meningococcal carriage among first-year university students increased after 2 months. Sociobehavioral risk factors were associated with increased carriage for all analyses. HIV was associated with carriage acquisition. Until vaccination programs become mandatory in South African universities, data suggest that students with HIV could benefit most from meningococcal vaccination.
Bacterial and Fungal Coinfection in Individuals With Coronavirus: A Rapid Review To Support COVID-19 Antimicrobial Prescribing
Authors: Rawson Timothy M , Moore Luke S P , Zhu Nina , Ranganathan Nishanthy , Skolimowska Keira , Gilchrist Mark , Satta Giovanni , Cooke Graham , Holmes Alison
Published: April 2020

Background

To explore and describe the current literature surrounding bacterial/fungal coinfection in patients with coronavirus infection.

Methods

MEDLINE, EMBASE, and Web of Science were searched using broad-based search criteria relating to coronavirus and bacterial coinfection. Articles presenting clinical data for patients with coronavirus infection (defined as SARS-1, MERS, SARS-CoV-2, and other coronavirus) and bacterial/fungal coinfection reported in English, Mandarin, or Italian were included. Data describing bacterial/fungal coinfections, treatments, and outcomes were extracted. Secondary analysis of studies reporting antimicrobial prescribing in SARS-CoV-2 even in absence of coinfection was performed.

Results

1007 abstracts were identified. Eighteen full texts reporting bacterial/fungal coinfection were included. Most studies did not identify or report bacterial/fungal coinfection (85/140; 61%). Nine of 18 (50%) studies reported on COVID-19, 5/18 (28%) on SARS-1, 1/18 (6%) on MERS, and 3/18 (17%) on other coronaviruses. For COVID-19, 62/806 (8%) patients were reported as experiencing bacterial/fungal coinfection during hospital admission. Secondary analysis demonstrated wide use of broad-spectrum antibacterials, despite a paucity of evidence for bacterial coinfection. On secondary analysis, 1450/2010 (72%) of patients reported received antimicrobial therapy. No antimicrobial stewardship interventions were described. For non–COVID-19 cases, bacterial/fungal coinfection was reported in 89/815 (11%) of patients. Broad-spectrum antibiotic use was reported.

Conclusions

Despite frequent prescription of broad-spectrum empirical antimicrobials in patients with coronavirus-associated respiratory infections, there is a paucity of data to support the association with respiratory bacterial/fungal coinfection. Generation of prospective evidence to support development of antimicrobial policy and appropriate stewardship interventions specific for the COVID-19 pandemic is urgently required.
Apathy and the Risk of Predementia Syndromes in Community-Dwelling Older Adults
Authors: Ceïde Mirnova E , Warhit Alana , Ayers Emmeline I , Kennedy Gary , Verghese Joe
Published: April 2020

Objectives

Apathy is a potential predictor of dementia in older adults, but this investigation has been limited to older adults with a preexisting neurological illness like mild cognitive impairment (MCI), stroke or Parkinson’s disease. The objective of this study was to investigate the association between apathy at baseline and incident predementia syndromes, including MCI and motoric cognitive risk syndrome (MCR), subjective cognitive complaints and slow gait, in community-dwelling older adults.

Method

We prospectively studied the association between apathy (using the 3-item subscale of the Geriatric Depression Scale [GDS3A]) and incident cognitive disorders in 542 community-dwelling older adults enrolled in the Central Control of Mobility in Aging study using Cox proportional hazard models. Associations were reported as hazard ratio (HR) with 95% confidence intervals (CIs), adjusting for age, education, baseline cognitive performance, and depressive symptoms.

Results

Apathy was associated with incident MCR (HR 2.39, 95% CI: 1.10–5.20), but not predementia syndromes overall nor MCI. In sensitivity analyses of MCI subtypes, apathy was associated with nonamnestic MCI (HR 2.44, 95% CI: 1.14–5.22), but not amnestic MCI. Our study was limited by a short follow-up time (median 13.6 months; interquartile range 29.8) and a brief subscale measurement of apathy, GDS3A.

Discussion

In our study, apathy predicted MCR but not MCI in community-dwelling older adults. These results and the current literature suggest that apathy is an early risk factor for dementia. Additionally, apathy may be a novel treatment target that could forestall the disability of dementia.
Ambient seismic noise imaging of the lowermost mantle beneath the North Atlantic Ocean
Authors: Retailleau Lise , Boué Pierre , Li Lei , Campillo Michel
Published: April 2020

Body waves can be extracted from correlation functions computed from seismic records even at teleseismic distances. Here we use P and PcP waves from the secondary microseism frequency band that are propagating between Europe and the Eastern United States to image the core–mantle boundary (CMB) and D” structure beneath the North Atlantic. This study presents the first 3-D image of the lower mantle obtained from ocean-generated microseism data. Robustness of our results is evaluated by comparing images produced by propagation in both directions. Our observations reveal complex patterns of lateral and vertical variations of P-wave reflectivity with a particularly strong anomaly extending upward in the lower mantle up to 2600 km deep. We compare these results with synthetic data and associate this anomaly to a Vp velocity increase above the CMB. Our image aims at promoting the study of the lower mantle with microseism noise excitations.
Common misconceptions about validation studies
Authors: Fox Matthew P , Lash Timothy L , Bodnar Lisa M
Published: April 2020

Information bias is common in epidemiology and can substantially diminish the validity of study results. Validation studies, in which an investigator compares the accuracy of a measure with a gold standard measure, are an important way to understand and mitigate this bias. More attention is being paid to the importance of validation studies in recent years, yet they remain rare in epidemiologic research and, in our experience, they remain poorly understood. Many epidemiologists have not had any experience with validations studies, either in the classroom or in their work. We present an example of misclassification of a dichotomous exposure to elucidate some important misunderstandings about how to conduct validation studies to generate valid information. We demonstrate that careful attention to the design of validation studies is central to determining how the bias parameters (e.g. sensitivity and specificity or positive and negative predictive values) can be used in quantitative bias analyses to appropriately correct for misclassification. Whether sampling is done based on the true gold standard measure, the misclassified measure or at random will determine which parameters are valid and the precision of those estimates. Whether or not the validation is done stratified by other key variables (e.g. by the exposure) will also determine the validity of those estimates. We also present sample questions that can be used to teach these concepts. Increasing the presence of validation studies in the classroom could have a positive impact on their use and improve the validity of estimates of effect in epidemiologic research.
On a Conjecture of Sharifi and Mazur’s Eisenstein Ideal
Authors: Lecouturier Emmanuel , Wang Jun
Published: April 2020

Let $N$ and $p$ be prime numbers $\geq 5$ such that $p$ divides $N-1$. Let $I$ be Mazur’s Eisenstein ideal of level $N$ and $H_+$ be the plus part of $H_1(X_0(N), \mathbf Z_{p})$ for the complex conjugation. We give a conjectural explicit description of the group $I\cdot H_+/I^2\cdot H_+$ in terms of the 2nd $K$-group of the cyclotomic field $\mathbf Q(\zeta _N)$. We prove that this conjecture follows from a conjecture of Sharifi about some Eisenstein ideal of level $\Gamma _1(N)$. Following the work of Fukaya–Kato, we prove partial results on Sharifi’s conjecture. This allows us to prove partial results on our conjecture.
‘Worth the Effort’?
Authors: Orentlicher Diane
Published: April 2020

Every international and hybrid war crimes court has attracted a measure of controversy, but none more than the Extraordinary Chambers in the Courts of Cambodia (ECCC). While myriad aspects of the ECCC’s record are crucial to its legacy, this article explores one question of overarching importance: whether its performance has justified a key risk the UN assumed when it agreed to support the court — that case selection would be improperly influenced by the Cambodian government. More particularly, it assesses the ECCC’s performance in light of two questions: How well have safeguards against political interference worked? Are survivors of Khmer Rouge atrocities and other Cambodian citizens satisfied with ECCC justice? Along with their intrinsic importance, these benchmarks for assessment derive from the primacy of both considerations in deliberations leading to the Court’s creation.
Root anatomical traits contribute to deeper rooting of maize under compacted field conditions
Authors: Vanhees Dorien J , Loades Kenneth W , Bengough A Glyn , Mooney Sacha J , Lynch Jonathan P
Published: April 2020

To better understand the role of root anatomy in regulating plant adaptation to soil mechanical impedance, 12 maize lines were evaluated in two soils with and without compaction treatments under field conditions. Penetrometer resistance was 1–2 MPa greater in the surface 30 cm of the compacted plots at a water content of 17–20% (v/v). Root thickening in response to compaction varied among genotypes and was negatively associated with rooting depth at one field site under non-compacted plots. Thickening was not associated with rooting depth on compacted plots. Genotypic variation in root anatomy was related to rooting depth. Deeper-rooting plants were associated with reduced cortical cell file number in combination with greater mid cortical cell area for node 3 roots. For node 4, roots with increased aerenchyma were deeper roots. A greater influence of anatomy on rooting depth was observed for the thinner root classes. We found no evidence that root thickening is related to deeper rooting in compacted soil; however, anatomical traits are important, especially for thinner root classes.
Responses of mature symbiotic nodules to the whole-plant systemic nitrogen signaling
Authors: Lambert Ilana , Pervent Marjorie , Le Queré Antoine , Clément Gilles , Tauzin Marc , Severac Dany , Benezech Claire , Tillard Pascal , Martin-Magniette Marie-Laure , Colella Stefano , Lepetit Marc
Published: April 2020

In symbiotic root nodules of legumes, terminally differentiated rhizobia fix atmospheric N2 producing an NH4+ influx that is assimilated by the plant. The plant, in return, provides photosynthates that fuel the symbiotic nitrogen acquisition. Mechanisms responsible for the adjustment of the symbiotic capacity to the plant N demand remain poorly understood. We have investigated the role of systemic signaling of whole-plant N demand on the mature N2-fixing nodules of the model symbiotic association Medicago truncatula/Sinorhizobium using split-root systems. The whole-plant N-satiety signaling rapidly triggers reductions of both N2 fixation and allocation of sugars to the nodule. These responses are associated with the induction of nodule senescence and the activation of plant defenses against microbes, as well as variations in sugars transport and nodule metabolism. The whole-plant N-deficit responses mirror these changes: a rapid increase of sucrose allocation in response to N-deficit is associated with a stimulation of nodule functioning and development resulting in nodule expansion in the long term. Physiological, transcriptomic, and metabolomic data together provide evidence for strong integration of symbiotic nodules into whole-plant nitrogen demand by systemic signaling and suggest roles for sugar allocation and hormones in the signaling mechanisms.
Stimulation of surfactant exocytosis in primary alveolar type II cells by A. fumigatus
Authors: Schiefermeier-Mach Natalia , Perkhofer Susanne , Heinrich Lea , Haller Thomas
Published: April 2020

Aspergillus fumigatus is an opportunistic fungal pathogen with small airborne spores (conidia) that may escape clearance by upper airways and directly impact the alveolar epithelium. Consequently, innate alveolar defense mechanisms are being activated, including professional phagocytosis by alveolar macrophages, recruitment of circulating neutrophils and probably enhanced secretion of pulmonary surfactant by the alveolar type II (AT II) cells. However, no data are available in support of the latter hypothesis. We therefore used a coculture model of GFP-Aspergillus conidia with primary rat AT II cells and studied fungal growth, cellular Ca2+ homeostasis, and pulmonary surfactant exocytosis by live cell video microscopy. We observed all stages of fungal development, including reversible attachment, binding and internalization of conidia as well as conidial swelling, formation of germ tubes and outgrowth of hyphae. In contrast to resting conidia, which did not provoke immediate cellular effects, metabolically active conidia, fungal cellular extracts (CE) and fungal culture filtrates (CF) prepared from swollen conidia caused a Ca2+-independent exocytosis. Ca2+ signals of greatly varying delays, durations and amplitudes were observed by applying CE or CF obtained from hyphae of A. fumigatus, suggesting compounds secreted by filamentous A. fumigatus that severely interfere with AT II cell Ca2+ homeostasis. The mechanisms underlying the stimulatory effects, with respect to exocytosis and Ca2+ signaling, are unclear and need to be identified.
The appearance of a compact jet in the soft–intermediate state of 4U 1543−47
Authors: Russell D M , Casella P , Kalemci E , Vahdat Motlagh A , Saikia P , Pirbhoy S F , Maitra D
Published: April 2020

Recent advancements in the understanding of jet–disc coupling in black hole candidate X-ray binaries (BHXBs) have provided close links between radio jet emission and X-ray spectral and variability behaviour. In ‘soft’ X-ray states the jets are suppressed, but the current picture lacks an understanding of the X-ray features associated with the quenching or recovering of these jets. Here, we show that a brief, ∼4 d infrared (IR) brightening during a predominantly soft X-ray state of the BHXB 4U 1543−47 is contemporaneous with a strong X-ray type B quasi-periodic oscillation, a slight spectral hardening and an increase in the rms variability, indicating an excursion to the soft–intermediate state (SIMS). This IR ‘flare’ has a spectral index consistent with optically thin synchrotron emission and most likely originates from the steady, compact jet. This core jet emitting in the IR is usually only associated with the hard state, and its appearance during the SIMS places the ‘jet line’ between the SIMS and the soft state in the hardness–intensity diagram for this source. IR emission is produced in a small region of the jets close to where they are launched (∼0.1 light-seconds), and the time-scale of the IR flare in 4U 1543−47 is far too long to be caused by a single, discrete ejection. We also present a summary of the evolution of the jet and X-ray spectral/variability properties throughout the whole outburst, constraining the jet contribution to the X-ray flux during the decay.
Spectroscopic and geometrical evolution of the ejecta of the classical nova ASASSN-18fv
Authors: Pavana M , Raj A , Bohlsen T , Anupama G C , Gupta Ranjan , Selvakumar G
Published: April 2020

The optical spectroscopic observations of ASASSN-18fv observed from 2018 March 24 to 2019 January 26 are presented. The optical spectra are obtained from Mirranook, Vainu Bappu, and South African Astronomical observatories. The spectra are dominated by the hydrogen Balmer, Fe ii, and O i lines with P-Cygni profiles in the early phase, typical of an Fe ii class nova. The spectra show He i lines along with H i and O i emission lines in the decline phase placing the nova in the hybrid class of novae. The spectra show rapid development in high-ionization lines in this phase. Analysis of the light curve indicates t2 and t3 values of about 50 and 70 d, respectively, placing the nova in the category of moderately fast nova. The ejectum geometry, inclination, and position angle are estimated using morpho-kinematic analysis. The geometry of the ejecta is found to be an asymmetric bipolar structure with an inclination angle of about 53○. The ejected mass using photoionization analysis is found to be 6.07 × 10−4 M⊙.
Dynamical heating of the X-ray emitting intracluster medium: the roles of merger shocks and turbulence dissipation
Authors: Shi Xun , Nagai Daisuke , Aung Han , Wetzel Andrew
Published: April 2020

The diffuse plasma inside clusters of galaxies has X-ray emitting temperatures of a few keV. The physical mechanisms that heat this intracluster medium (ICM) to such temperatures include the accretion shock at the periphery of a galaxy cluster, the shocks driven by merger events, as well as a somewhat overlooked mechanism – the dissipation of intracluster turbulent motions. We study the relative role of these heating mechanisms using galaxy clusters in Lagrangian tracer particle re-simulations of the Omega500 cosmological simulation. We adopt a novel analysis method of decomposing the temperature increase at each time-step into the contribution from dissipative heating and that from adiabatic heating. In the high-resolution spatial–temporal map of these heating rates, merger tracks are clearly visible, demonstrating the dominant role of merger events in heating the ICM. The dissipative heating contributed by each merger event is extended in time and also occurs in the rarefaction regions, suggesting the importance of heating by the dissipation of merger-induced turbulence. Quantitative analysis shows that turbulence heating, rather than direct heating at merger shocks, dominates the temperature increase of the ICM especially at inner radii r < r500c. In addition, we find that many merger shocks can propagate with almost constant velocity to very large radii r ≫ r500c, some even reach and join with the accretion shock and becoming the outer boundary of the ICM. Altogether, these results suggest that the ICM is heated more in an ‘inside–out’ fashion rather than ‘outside–in’ as depicted in the classical smooth accretion picture.
A unified dinucleotide alphabet describing both RNA and DNA structures
Authors: Černý Jiří , Božíková Paulína , Svoboda Jakub , Schneider Bohdan
Published: April 2020

By analyzing almost 120 000 dinucleotides in over 2000 nonredundant nucleic acid crystal structures, we define 96+1 diNucleotide Conformers, NtCs, which describe the geometry of RNA and DNA dinucleotides. NtC classes are grouped into 15 codes of the structural alphabet CANA (Conformational Alphabet of Nucleic Acids) to simplify symbolic annotation of the prominent structural features of NAs and their intuitive graphical display. The search for nontrivial patterns of NtCs resulted in the identification of several types of RNA loops, some of them observed for the first time. Over 30% of the nearly six million dinucleotides in the PDB cannot be assigned to any NtC class but we demonstrate that up to a half of them can be re-refined with the help of proper refinement targets. A statistical analysis of the preferences of NtCs and CANA codes for the 16 dinucleotide sequences showed that neither the NtC class AA00, which forms the scaffold of RNA structures, nor BB00, the DNA most populated class, are sequence neutral but their distributions are significantly biased. The reported automated assignment of the NtC classes and CANA codes available at dnatco.org provides a powerful tool for unbiased analysis of nucleic acid structures by structural and molecular biologists.
mRNALoc: a novel machine-learning based in-silico tool to predict mRNA subcellular localization
Authors: Garg Anjali , Singhal Neelja , Kumar Ravindra , Kumar Manish
Published: April 2020

Recent evidences suggest that the localization of mRNAs near the subcellular compartment of the translated proteins is a more robust cellular tool, which optimizes protein expression, post-transcriptionally. Retention of mRNA in the nucleus can regulate the amount of protein translated from each mRNA, thus allowing a tight temporal regulation of translation or buffering of protein levels from bursty transcription. Besides, mRNA localization performs a variety of additional roles like long-distance signaling, facilitating assembly of protein complexes and coordination of developmental processes. Here, we describe a novel machine-learning based tool, mRNALoc, to predict five sub-cellular locations of eukaryotic mRNAs using cDNA/mRNA sequences. During five fold cross-validations, the maximum overall accuracy was 65.19, 75.36, 67.10, 99.70 and 73.59% for the extracellular region, endoplasmic reticulum, cytoplasm, mitochondria, and nucleus, respectively. Assessment on independent datasets revealed the prediction accuracies of 58.10, 69.23, 64.55, 96.88 and 69.35% for extracellular region, endoplasmic reticulum, cytoplasm, mitochondria, and nucleus, respectively. The corresponding values of AUC were 0.76, 0.75, 0.70, 0.98 and 0.74 for the extracellular region, endoplasmic reticulum, cytoplasm, mitochondria, and nucleus, respectively. The mRNALoc standalone software and web-server are freely available for academic use under GNU GPL at http://proteininformatics.org/mkumar/mrnaloc.
Tobacco Use and Orofacial Pain: A Meta-analysis
Authors: Alamir Abdulwahab H , Quadri Mir Faeq Ali
Published: April 2020

Introduction

The relationship between smoking and general body ache has been shown to be bidirectional. The specific association between tobacco consumption and orofacial pain remains unclear, however.

Aim and Methods

The aim of this systematic review was to explore the association between pain related to diseases of the oral cavity and use of tobacco. A systematic search of PubMed, Embase, Web of Science, and Cochrane databases was carried out in September 2019. Tobacco exposure was included irrespective of the method of consumption (smokeless and smoked tobacco), and frequency of the habit. The outcome was defined as clinically diagnosed or self-reported pain in the orofacial region, with no limitation in the duration of the condition or the site of the pain.

Results

Altogether, eight studies were selected, with three of them demonstrating good methodology and none of them being of poor quality. Meta-analysis of six studies showed that orofacial pain was significantly worse in tobacco (smoked and smokeless) users (odds ratio [OR] = 3.55, 95% confidence interval [CI]: 1.92, 6.58) in comparison to nonusers. Subgroup analysis showed that the odds of orofacial pain was three times (OR = 3.13, 95% CI: 1.16, 8.46) higher among smokers, but was not associated with smokeless tobacco.

Conclusions

The odds of experiencing orofacial pain among patients with oral diseases increase for patients who are also smokers. The findings could help dentists and other health specialists more effectively manage patients with orofacial pain who are tobacco consumers.

Implications

This study shows that the odds of orofacial pain among patients with oral diseases increase for patients who are smokers. The results are a significant contribution to the literature because, while the relationship between smoking and general body ache has been shown to be bidirectional, the specific association between tobacco use and orofacial pain warranted further study. The findings could help dentists and other specialists more effectively manage patients with orofacial pain who are also tobacco consumers.
Using functional genomics to advance the understanding of psoriatic arthritis
Authors: Shi Chenfu , Rattray Magnus , Barton Anne , Bowes John , Orozco Gisela
Published: April 2020

Psoriatic arthritis (PsA) is a complex disease where susceptibility is determined by genetic and environmental risk factors. Clinically, PsA involves inflammation of the joints and the skin, and, if left untreated, results in irreversible joint damage. There is currently no cure and the few treatments available to alleviate symptoms do not work in all patients. Over the past decade, genome-wide association studies (GWAS) have uncovered a large number of disease-associated loci but translating these findings into functional mechanisms and novel targets for therapeutic use is not straightforward. Most variants have been predicted to affect primarily long-range regulatory regions such as enhancers. There is now compelling evidence to support the use of chromatin conformation analysis methods to discover novel genes that can be affected by disease-associated variants. Here, we will review the studies published in the field that have given us a novel understanding of gene regulation in the context of functional genomics and how this relates to the study of PsA and its underlying disease mechanism.
Papillomaviruses infecting cetaceans exhibit signs of genome adaptation following a recombination event
Authors: Borvető Fanni , Bravo Ignacio G , Willemsen Anouk
Published: April 2020

Papillomaviruses (PVs) have evolved through a complex evolutionary scenario where virus–host co-evolution alone is not enough to explain the phenotypic and genotypic PV diversity observed today. Other evolutionary processes, such as host switch and recombination, also appear to play an important role in PV evolution. In this study, we have examined the genomic impact of a recombination event between distantly related PVs infecting Cetartiodactyla (even-toed ungulates and cetaceans). Our phylogenetic analyses suggest that one single recombination was responsible for the generation of extant ‘chimeric’ PV genomes infecting cetaceans. By correlating the phylogenetic relationships to the genomic content, we observed important differences between the recombinant and non-recombinant cetartiodactyle PV genomes. Notably, recombinant PVs contain a unique set of conserved motifs in the upstream regulatory region (URR). We interpret these regulatory changes as an adaptive response to drastic changes in the PV genome. In terms of codon usage preferences (CUPrefs), we did not detect any particular differences between orthologous open reading frames in recombinant and non-recombinant PVs. Instead, our results are in line with previous observations suggesting that CUPrefs in PVs are rather linked to gene expression patterns as well as to gene function. We show that the non-coding URR of PVs infecting cetaceans, the central regulatory element in these viruses, exhibits signs of adaptation following a recombination event. Our results suggest that also in PVs, the evolution of gene regulation can play an important role in speciation and adaptation to novel environments.
Demand-Driven Youth Training Programs: Experimental Evidence from Mongolia
Authors: Alzúa Maria Laura , Batbekh Soyolmaa , Batchuluun Altantsetseg , Dalkhjav Bayarmaa , Galdo José
Published: April 2020

The effectiveness of a demand-driven vocational-training program for disadvantaged youth in Ulaanbaatar, the capital city of Mongolia is assessed through a randomized controlled trial. Mongolia, a transitional country whose economic structure shifted from a Communist, centrally planned economy to a free-market economy over a relatively short period, offers a new setting in which to test the effectiveness of market-based active-labor-market policies. Results show short-term positive impacts on self-employment and skills match, while positive but uncertain effects emerge for employment and earnings. Substantial heterogeneity emerges as relatively older, richer, and better-educated individuals drive these positive effects. A second intervention, in which participants were randomly assigned to receive newsletters with information on market returns to vocational training, shows statistically meaningful effects on the length of exposure to the program (i.e., number of training days attended). These positive impacts, however, do not lead to higher employment or greater earnings.
Sprengel Deformity
Authors: Öner Ali , Aşansu Mustafa Akif , Akman Yunus Emre
Published: April 2020

Study Design.

A retrospective, case series.

Objective.

The aim of this study is to evaluate the concomitant anomalies in patients with Sprengel deformity (SD).

Summary of Background Data.

SD is the most common congenital anomaly of the shoulder. One or more associated anomalies may coexist in SD patients, similar to congenital scoliosis (CS); however, these anomalies and their relationship have not been studied in detail previously.

Methods.

SD patients who have applied to our institution between 2005 and 2019 were retrospectively reviewed. The patients were evaluated clinically and radiologically. The patients were divided in two groups as SD patients with CS and without CS, to analyze if these anomalies are present due to CS or SD. Physical examination findings, MRI, CT, and USG reports were analysed for accompanying pathologies. Patients with missing data were excluded. Student-t and Fisher's exact tests were used to compare the groups. Significance value was set as p = 0.05.

Results.

Ninety patients met inclusion criteria. The most common spinal anomaly was omovertebra, followed by spina bifida and Klippel-Feil. Tethered cord and diastematomiyelia were associated with CS (P = 0.0026 and P = 0.0057, respectively). The most common extra-skeletal anomaly was rib anomalies, followed by urinary and cardiac system anomalies. Rib anomalies were associated with CS (P = 0.00001).

Conclusion.

Concomitant anomalies may accompany SD. The prognosis of SD may be affected by these anomalies. Therefore, patients should be evaluated for possible coexistent congenital anomalies.

Level of Evidence: 4
The Severity of Cervical Disc Degeneration Does Not Impact 2-year Postoperative Outcomes in Patients With Cervical Spondylotic Myelopathy Who Underwent Laminoplasty
Authors: Habibi Hasibullah , Suzuki Akinobu , Tamai Koji , Ohyama Shoichiro , Hori Yusuke , Yabu Akito , Terai Hidetomi , Hoshino Masatoshi , Toyoda Hiromitsu , Takahashi Shinji , Ahmadi Sayed Abdullah , Nakamura Hiroaki
Published: April 2020

Study Design.

Retrospective cohort study.

Objective.

The aim of this study was to evaluate the impact of cervical disc degeneration (CDD) severity on 2-year postoperative outcomes following laminoplasty.

Summary of Background Data.

The impact of CDD on postoperative outcomes of cervical laminoplasty has not been well established.

Methods.

A total of 144 patients who underwent open-door laminoplasty for cervical spondylotic myelopathy (CSM) were enrolled. Six cervical discs were independently analyzed for degeneration severity using a previously reported grading system (grade 0: none, grade 3: severest). The relationship between the segmental range of motion (ROM) and the severity of CDD was evaluated. Subsequently, after dividing overall patients into mild and severe CDD groups by the average of CDD scores, the mixed-effect model was applied to assess 2-year postoperative outcomes, including physician-assessed myelopathy scores, patient-reported outcomes, and preoperative radiographic parameters. Finally, as additional analysis, the severe CDD group was further divided into two groups: group 1 included patients with a grade 3 CDD change in their most stenotic level and group 2 included the others. The 2-year postoperative myelopathy score was compared between groups 1 and 2.

Results.

The cervical segments with grade 3 CDD showed significantly smaller ROM compared with those with grade 0, 1, or 2 CDD (P < 0.01). There were no significant differences in postoperative improvements in myelopathy, pain, patient-reported physical and mental status, and radiographic parameters, except for quality of life (QOL) scores between CDD groups. A significant (P = 0.02) postoperative improvement in QOL scores was noted in the severe CDD group. In an additional analysis, myelopathy score at 2 years postoperatively was significantly higher in group 1 than group 2 (P = 0.041).

Conclusion.

The severity of CDD did not negatively impact 2-year postoperative laminoplasty outcomes. The postulated reason is that the decreased segmental instability in the level with severe CDD may affect surgical outcomes positively.

Level of Evidence: 3
Mechanical Ventilation and Predictors of In-Hospital Mortality in Fibrotic Interstitial Lung Disease With Acute Respiratory Failure: A Cohort Analysis Through the Paradigm of Acute Respiratory Distress Syndrome
Authors: Martin Max J. , Moua Teng
Published: April 2020

Objectives:

Prior studies report significant mortality in fibrotic interstitial lung disease patients undergoing mechanical ventilation. Little is known about baseline characteristics or ventilator strategies that might improve outcomes. We analyzed the ventilator characteristics of a large cohort of fibrotic interstitial lung disease patients from the perspective of an acute respiratory distress syndrome paradigm to see if any specific mechanical ventilation strategies might improve in-hospital mortality.

Design:

Retrospective cohort study.

Setting:

Single-center, multihospital medical ICUs.

Patients:

Consecutive fibrotic interstitial lung disease patients who experienced mechanical ventilation for acute respiratory failure.

Interventions:

Interstitial lung disease characteristics, demographics, and ventilator variables were analyzed for univariable and multivariable predictors of in-hospital mortality, adjusted for confounding with an a priori causation model.

Measurements and Main Results:

A total of 111 patients accounted for 114 admissions. Idiopathic pulmonary fibrosis comprised 34% with idiopathic acute exacerbation (65%) being the most common admission type. Ninety-five percent were initiated on mandatory volume-control ventilation with only 50% achieving a low tidal volume strategy (plateau pressure ≤ 30 cm H2O) within 3 hours of intubation. Unadjusted clinical predictors of in-hospital mortality included age (unit odds ratio, 1.05; 1.01–1.10; p = 0.015), time from admission to intubation (hr) (unit odds ratio, 1.01; 1.01–1.03; p = 0.017), and use of paralytics (relative risk, 1.54; 1.26–1.90, p < 0.001). Adjusted mechanical ventilation-related predictors of in-hospital mortality included achieving early targeted plateau pressures (odds ratio, 0.23; 0.07–0.76; p = 0.016), Pao
2/Fio
2 ratio at 3 (unit odds ratio, 0.98; 0.96–0.99, p = 0.002) and 48 hours (unit odds ratio, 0.98; 0.97–0.99, p = 0.018), initial mean airway pressure (unit odds ratio, 1.13; 1.02–1.28, p = 0.019), and total net fluid status (mL) (unit odds ratio, 1.01; 1.001–1.02, p = 0.0001).

Conclusions:

Several factors predict in-hospital mortality in fibrotic interstitial lung disease-associated mechanical ventilation when viewed through an acute respiratory distress syndrome model. Further research is needed to refine strategies that may perhaps improve survival if mechanical ventilation is pursued in this set of patients.
Effects of Exercise-Based Interventions on Fall Risk and Balance in Patients With Chronic Obstructive Pulmonary Disease
Authors: Delbressine Jeannet M. , Vaes Anouk W. , Goërtz Yvonne M. , Sillen Maurice J. , Kawagoshi Atsuyoshi , Meijer Kenneth , Janssen Daisy J. A. , Spruit Martijn A.
Published: April 2020

Purpose:

Chronic obstructive pulmonary disease (COPD) is a highly prevalent disease characterized by airflow limitation and is associated with decreased balance and increased fall risk. Since falls are related to increased mortality, interventions targeting balance and fall risk could reduce morbidity and mortality. The objective of this review was to systematically assess the effects of exercise-based interventions on fall risk and balance in patients with COPD.

Methods:

PubMed, Web of Science, EMBASE, and CINAHL were screened for randomized controlled trails and within-group studies evaluating effects of exercise-based interventions on fall risk or balance in patients with COPD. Data were presented in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement.

Results:

Fifteen studies were identified, 6 randomized controlled trails and 9 within-group studies. All interventions reported positive effects on balance outcomes. No studies reported fall risk. Taking current recommendations of balance outcome measures in patients with COPD into account, pulmonary rehabilitation combined with balance training had the highest effect size. Nine papers had concerns regarding bias, mostly due to the lack of blinding outcome assessors.

Conclusions:

Exercise-based interventions have a positive effect on balance in patients with COPD. Pulmonary rehabilitation with balance training seems to have the most beneficial effect on balance. The effects on fall risk, as well as the long-term intervention effects remain unclear. A standardized balance assessment and research on long-term effects and fall risk are recommended.