bluuebunny/crossref_metadata_2025_split huggingface dataset:
On a Conjecture of Sharifi and Mazur’s Eisenstein Ideal
Authors: Lecouturier Emmanuel , Wang Jun 
Published: April 2020

Abstract
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

Abstract
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

AbstractTo 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

Abstract
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

Abstract
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

ABSTRACT
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

ABSTRACT
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

ABSTRACT
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 &lt; 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

AbstractBy 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

Abstract
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

Abstract

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

AbstractPsoriatic 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

Abstract
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

AbstractThe 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