bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting FIR lines from simulated galaxies
Authors: Lupi Alessandro , Pallottini Andrea , Ferrara Andrea , Bovino Stefano , Carniani Stefano , Vallini Livia 
Published: June 2020

ABSTRACT
Far-infrared (FIR) emission lines are a powerful tool to investigate the properties of the interstellar medium, especially in high-redshift galaxies, where ALMA observations have provided unprecedented information. Interpreting such data with state-of-the-art cosmological simulations post-processed with cloudy, has provided insights on the internal structure and gas dynamics of these systems. However, no detailed investigation of the consistency and uncertainties of this kind of analysis has been performed to date. Here, we compare different approaches to estimate FIR line emission from state-of-the-art cosmological simulations, either with cloudy or with on-the-fly non-equilibrium chemistry. We find that [C ii]158μ predictions are robust to the model variations we explored. [O i] emission lines, that typically trace colder and denser gas relative to [C ii]158μ, are instead model dependent, as these lines are strongly affected by the thermodynamic state of the gas and non-equilibrium photoionization effects. For the same reasons, [O i] lines represent an excellent tool to constrain emission models, hence future observations targeting these lines will be crucial.
Time lags of the type-B quasi-periodic oscillation in MAXI J1348−630
Authors: Belloni Tomaso M , Zhang Liang , Kylafis Nikolaos D , Reig Pablo , Altamirano Diego 
Published: June 2020

ABSTRACT
The fast variability observed in the X-ray emission from black hole binaries has a very complex phenomenology, but offers the possibility to investigate directly the properties of the inner accretion flow. In particular, type-B oscillations in the 2–8 Hz range, observed in the soft-intermediate state, have been associated with the emission from a relativistic jet. We present the results of the timing and spectral analysis of a set of observations of the bright transient MAXI J1348−630 made with the NICER (Neutron Star Interior Composition Explorer) telescope. The observations are in the brightest part of the outburst and all feature a strong type-B quasi-periodic oscillation (QPO) at ∼4.5 Hz. We compute the energy dependence of the fractional rms and the phase lags at the QPO frequency, obtaining high signal-to-noise data and sampling for the first time at energies below 2 keV. The fractional rms decreases from more than 10 per cent at 9 keV to 0.6 per cent at 1.5 keV, and is constant below that energy. Taking the 2–3 keV band as reference, photons at all energies show a hard lag, increasing with the distance from the reference band. The behaviour below 2 keV has never been observed before, due to the higher energy bandpass of previous timing instruments. The energy spectrum can be fitted with a standard model for this state, consisting of a thin disc component and a harder power law, plus an emission line between 6 and 7 keV. We discuss the results, concentrating on the phase lags, and show that they can be interpreted within a Comptonization model.
Properties of the circumgalactic medium in cosmic ray-dominated galaxy haloes
Authors: Ji Suoqing , Chan T K , Hummels Cameron B , Hopkins Philip F , Stern Jonathan , Kereš Dušan , Quataert Eliot , Faucher-Giguère Claude-André , Murray Norman 
Published: June 2020

ABSTRACT
We investigate the impact of cosmic rays (CRs) on the circumgalactic medium (CGM) in FIRE-2 simulations, for ultra-faint dwarf through Milky Way (MW)-mass haloes hosting star-forming (SF) galaxies. Our CR treatment includes injection by supernovae, anisotropic streaming and diffusion along magnetic field lines, and collisional and streaming losses, with constant parallel diffusivity $\kappa \sim 3\times 10^{29}\, \mathrm{cm^2\ s^{-1}}$ chosen to match γ-ray observations. With this, CRs become more important at larger halo masses and lower redshifts, and dominate the pressure in the CGM in MW-mass haloes at z ≲ 1–2. The gas in these ‘CR-dominated’ haloes differs significantly from runs without CRs: the gas is primarily cool (a few ${\sim}10^{4}\,$ K), and the cool phase is volume-filling and has a thermal pressure below that needed for virial or local thermal pressure balance. Ionization of the ‘low’ and ‘mid’ ions in this diffuse cool gas is dominated by photoionization, with O vi columns ${\gtrsim}10^{14.5}\, \mathrm{cm^{-2}}$ at distances ${\gtrsim}150\, \mathrm{kpc}$. CR and thermal gas pressure are locally anticorrelated, maintaining total pressure balance, and the CGM gas density profile is determined by the balance of CR pressure gradients and gravity. Neglecting CRs, the same haloes are primarily warm/hot ($T\gtrsim 10^{5}\,$K) with thermal pressure balancing gravity, collisional ionization dominates, O vi columns are lower and Ne viii higher, and the cool phase is confined to dense filaments in local thermal pressure equilibrium with the hot phase.
Constraints on the star formation histories of galaxies in the Local Cosmological Volume
Authors: Kroupa P , Haslbauer M , Banik I , Nagesh S T , Pflamm-Altenburg J 
Published: June 2020

ABSTRACT
The majority of galaxies with current star formation rates (SFRs), $\rm SFR_{\rm o} \ge 10^{-3} \, M_\odot\,yr^{-1}$, in the Local Cosmological Volume, where observations should be reliable, have the property that their observed SFRo is larger than their average SFR. This is in tension with the evolution of galaxies described by delayed-τ models, according to which the opposite would be expected. The tension is apparent in that local galaxies imply the star formation time-scale τ ≈ 6.7 Gyr, much longer than the 3.5–4.5 Gyr obtained using an empirically determined main sequence at several redshifts. Using models where the SFR is a power law in time of the form ∝(t − t1)η for t1 = 1.8 Gyr (with no stars forming prior to t1) implies that η = 0.18 ± 0.03. This suggested near-constancy of a galaxy’s SFR over time raises non-trivial problems for the evolution and formation time of galaxies, but is broadly consistent with the observed decreasing main sequence with increasing age of the Universe.
FETCH: A deep-learning based classifier for fast transient classification
Authors: Agarwal Devansh , Aggarwal Kshitij , Burke-Spolaor Sarah , Lorimer Duncan R , Garver-Daniels Nathaniel 
Published: June 2020

ABSTRACT
With the upcoming commensal surveys for Fast Radio Bursts (FRBs), and their high candidate rate, usage of machine learning algorithms for candidate classification is a necessity. Such algorithms will also play a pivotal role in sending real-time triggers for prompt follow-ups with other instruments. In this paper, we have used the technique of Transfer Learning to train the state-of-the-art deep neural networks for classification of FRB and Radio Frequency Interference (RFI) candidates. These are convolutional neural networks which work on radio frequency-time and dispersion measure-time images as the inputs. We trained these networks using simulated FRBs and real RFI candidates from telescopes at the Green Bank Observatory. We present 11 deep learning models, each with an accuracy and recall above 99.5 per cent on our test data set comprising of real RFI and pulsar candidates. As we demonstrate, these algorithms are telescope and frequency agnostic and are able to detect all FRBs with signal-to-noise ratios above 10 in ASKAP and Parkes data. We also provide an open-source python package fetch (Fast Extragalactic Transient Candidate Hunter) for classification of candidates, using our models. Using fetch, these models can be deployed along with any commensal search pipeline for real-time candidate classification.
A unified view of the sequence and functional organization of the human RNA polymerase II promoter
Authors: Luse Donal S , Parida Mrutyunjaya , Spector Benjamin M , Nilson Kyle A , Price David H 
Published: June 2020

Abstract
To better understand human RNA polymerase II (Pol II) promoters in the context of promoter-proximal pausing and local chromatin organization, 5′ and 3′ ends of nascent capped transcripts and the locations of nearby nucleosomes were accurately identified through sequencing at exceptional depth. High-quality visualization tools revealed a preferred sequence that defines over 177 000 core promoters with strengths varying by &gt;10 000-fold. This sequence signature encompasses and better defines the binding site for TFIID and is surprisingly invariant over a wide range of promoter strength. We identified a sequence motif associated with promoter-proximal pausing and demonstrated that cap methylation only begins once transcripts are about 30 nt long. Mapping also revealed a ∼150 bp periodic downstream sequence element (PDE) following the typical pause location, strongly suggestive of a +1 nucleosome positioning element. A nuclear run-off assay utilizing the unique properties of the DNA fragmentation factor (DFF) coupled with sequencing of DFF protected fragments demonstrated that a +1 nucleosome is present downstream of paused Pol II. Our data more clearly define the human Pol II promoter: a TFIID binding site with built-in downstream information directing ubiquitous promoter-proximal pausing and downstream nucleosome location.
Bone marrow metastasis of glioblastoma multiforme mimicking acute myeloid leukemia
Authors: Nagata Akihito , Kanemasa Yusuke , Kikuchi Miyu , Otani Ryohei , Yamada Ryoji , Motoi Toru , Tamura Taichi , Nakamura Shohei , Funasaka Chikako , Kageyama Akihiko , Shimoyama Tatsu , Shinoura Nobusada , Hishima Tsunekazu , Omuro Yasushi 
Published: June 2020

Abstract
A 46-year-old female patient with glioblastoma multiforme (GBM), IDH wild type developed severe pancytopenia 5 months after postoperative chemoradiotherapy. Bone marrow aspirate showed normocellular marrow with 70.0% abnormal cells, which suggested the possibility of acute myeloid leukemia. Immunophenotypic analysis did not show any hematological lineage markers, except for cluster of differentiation 56. The results of immunohistochemical staining of glial fibrillary acidic protein and oligodendrocyte transcription Factor 2 were positive. Based on these findings, the patient was diagnosed with bone marrow metastasis from GBM. Bone marrow metastasis from GBM is rare and little is known about the morphological characteristics of bone marrow aspiration smear findings. We experienced a rare case with marrow metastasis from GBM mimicking acute myeloid leukemia.
Pterygo-Maxillary Fissure as a Landmark for Localization of Internal Maxillary Artery for Use in Extracranial-Intracranial Bypass
Authors: Peto Ivo , Nouri Mohsen , Agazzi Siviero , Langer David , Dehdashti Amir R 
Published: June 2020

Abstract

BACKGROUND
Internal maxillary artery (IMax) is a relatively new donor vessel used in the extracranial-intracranial bypass surgery. However, unfamiliarity and relatively elaborate techniques of its harvest precluded its widespread use.

OBJECTIVE
To present a simplified technique of IMax harvest based on constant anatomical landmarks without the need of extensive skull-base drilling while providing adequate space for proximal anastomosis.

METHODS
Cadaveric dissection on 4 cadaveric heads (8 sides) was performed. Zygomatic osteotomy was performed and temporal muscle was dissected off the zygomatic process of the frontal bone and the frontal process of the zygomatic bone and reflected inferiorly into the bony gap created by the zygomatic osteotomy. Posterior wall of the maxilla (PWoM) was palpated. Following PWoM inferiorly leads to pterygo-maxillary fissure (PMF), which is a constant landmark IMax passes through.

RESULTS
IMax was localized following this technique before its entrance into PMF in every specimen. Proximal dissection was carried on to the exposed adequate length of the vessel. Depending on the relationship with the lateral pterygoid muscle, this might need to be incised to allow for identification of the IMax. After its transection, proximal stump is mobilized superiorly into the surgical field. Clinical application of this technique was demonstrated on an aneurysm case.

CONCLUSION
Using the palpation of the PWoM as a landmark for localization of PMF facilitates harvesting of IMax without need for extensive skull-base drilling and shortens the time of the surgery.
Does geodemographic segmentation explain differences in route of cancer diagnosis above and beyond person-level sociodemographic variables?
Authors: Bright C J , Gildea C , Lai J , Elliss-Brookes L , Lyratzopoulos G 
Published: June 2020

ABSTRACT

Background
Emergency diagnosis of cancer is associated with poorer short-term survival and may reflect delayed help-seeking. Optimal targeting of interventions to raise awareness of cancer symptoms is therefore needed.

Methods
We examined the risk of emergency presentation of lung and colorectal cancer (diagnosed in 2016 in England). By cancer site, we used logistic regression (outcome emergency/non-emergency presentation) adjusting for patient-level variables (age, sex, deprivation and ethnicity) with/without adjustment for geodemographic segmentation (Mosaic) group.

Results
Analysis included 36 194 and 32 984 patients with lung and colorectal cancer. Greater levels of deprivation were strongly associated with greater odds of emergency presentation, even after adjustment for Mosaic group, which nonetheless attenuated associations (odds ratio [OR] most/least deprived group = 1.67 adjusted [model excluding Mosaic], 1.28 adjusted [model including Mosaic], P &lt; 0.001 for both, for colorectal; respective OR values of 1.42 and 1.18 for lung, P &lt; 0.001 for both). Similar findings were observed for increasing age. There was large variation in risk of emergency presentation between Mosaic groups (crude OR for highest/lowest risk group = 2.30, adjusted OR = 1.89, for colorectal; respective values of 1.59 and1.66 for lung).

Conclusion
Variation in risk of emergency presentation in cancer patients can be explained by geodemography, additional to deprivation group and age. The findings support proof of concept for public health interventions targeting all the examined attributes, including geodemography.
Latent Clinical-Anatomical Dimensions of Schizophrenia
Authors: Kirschner Matthias , Shafiei Golia , Markello Ross D , Makowski Carolina , Talpalaru Alexandra , Hodzic-Santor Benazir , Devenyi Gabriel A , Paquola Casey , Bernhardt Boris C , Lepage Martin , Chakravarty M Mallar , Dagher Alain , Mišić Bratislav 
Published: June 2020

Abstract
Widespread structural brain abnormalities have been consistently reported in schizophrenia, but their relation to the heterogeneous clinical manifestations remains unknown. In particular, it is unclear whether anatomical abnormalities in discrete regions give rise to discrete symptoms or whether distributed abnormalities give rise to the broad clinical profile associated with schizophrenia. Here, we apply a multivariate data-driven approach to investigate covariance patterns between multiple-symptom domains and distributed brain abnormalities in schizophrenia. Structural magnetic resonance imaging and clinical data were derived from one discovery sample (133 patients and 113 controls) and one independent validation sample (108 patients and 69 controls). Disease-related voxel-wise brain abnormalities were estimated using deformation-based morphometry. Partial least-squares analysis was used to comprehensively map clinical, neuropsychological, and demographic data onto distributed deformation in a single multivariate model. The analysis identified 3 latent clinical-anatomical dimensions that collectively accounted for 55% of the covariance between clinical data and brain deformation. The first latent clinical-anatomical dimension was replicated in an independent sample, encompassing cognitive impairments, negative symptom severity, and brain abnormalities within the default mode and visual networks. This cognitive-negative dimension was associated with low socioeconomic status and was represented across multiple races. Altogether, we identified a continuous cognitive-negative dimension of schizophrenia, centered on 2 intrinsic networks. By simultaneously taking into account both clinical manifestations and neuroanatomical abnormalities, the present results open new avenues for multi-omic stratification and biotyping of individuals with schizophrenia.
Long-term efficacy and tolerability of lemborexant compared with placebo in adults with insomnia disorder: results from the phase 3 randomized clinical trial SUNRISE 2
Authors: Kärppä Mikko , Yardley Jane , Pinner Kate , Filippov Gleb , Zammit Gary , Moline Margaret , Perdomo Carlos , Inoue Yuichi , Ishikawa Kohei , Kubota Naoki 
Published: June 2020

Abstract

Study Objectives
To assess long-term efficacy and safety of lemborexant (LEM), a novel dual orexin receptor antagonist, versus placebo in adults with insomnia disorder.

Methods
This was a 12-month, global, multicenter, randomized, double-blind, parallel-group phase 3 study comprising a 6-month placebo-controlled period (reported here) followed by a 6-month active-treatment-only period (reported separately). A total of 949 participants with insomnia (age ≥18 years) were randomized, received treatment with an oral dose of placebo or LEM (5 mg [LEM5] or 10 mg [LEM10]) and were analyzed. Sleep onset and sleep maintenance endpoints were analyzed from daily electronic sleep diary data. Treatment-emergent adverse events (TEAEs) were monitored throughout the study.

Results
Decreases from baseline in patient-reported (subjective) sleep onset latency and subjective wake after sleep onset, and increases from baseline in subjective sleep efficiency, were significantly greater with LEM5 and LEM10 versus placebo. Significant benefits over placebo were observed at the end of month 6, and at most time points assessed over the 6-month period, indicating long-term sustained efficacy of LEM. A significantly greater percentage of sleep onset responders and sleep maintenance responders were observed with LEM treatment versus placebo. Participants treated with LEM reported a significant improvement in quality of sleep after 6 months versus placebo. The majority of TEAEs were mild or moderate. There was a low rate of serious TEAEs and no deaths.

Conclusions
LEM5 and LEM10 provided significant benefit on sleep onset and sleep maintenance in individuals with insomnia disorder versus placebo, and was well tolerated.

Clinical trial registration
ClinicalTrials.gov, NCT02952820; ClinicalTrialsRegister.eu, EudraCT Number 2015-001463-39
The Cumulative Indel Model: Fast and Accurate Statistical Evolutionary Alignment
Authors: De Maio Nicola 
Published: June 2020

AbstractSequence alignment is essential for phylogenetic and molecular evolution inference, as well as in many other areas of bioinformatics and evolutionary biology. Inaccurate alignments can lead to severe biases in most downstream statistical analyses. Statistical alignment based on probabilistic models of sequence evolution addresses these issues by replacing heuristic score functions with evolutionary model-based probabilities. However, score-based aligners and fixed-alignment phylogenetic approaches are still more prevalent than methods based on evolutionary indel models, mostly due to computational convenience. Here, I present new techniques for improving the accuracy and speed of statistical evolutionary alignment. The “cumulative indel model” approximates realistic evolutionary indel dynamics using differential equations. “Adaptive banding” reduces the computational demand of most alignment algorithms without requiring prior knowledge of divergence levels or pseudo-optimal alignments. Using simulations, I show that these methods lead to fast and accurate pairwise alignment inference. Also, I show that it is possible, with these methods, to align and infer evolutionary parameters from a single long synteny block ($\approx$530 kbp) between the human and chimp genomes. The cumulative indel model and adaptive banding can therefore improve the performance of alignment and phylogenetic methods. [Evolutionary alignment; pairHMM; sequence evolution; statistical alignment; statistical genetics.]
Defining Species When There is Gene Flow
Authors: Jiao Xiyun , Yang Ziheng 
Published: June 2020

AbstractWhatever one’s definition of species, it is generally expected that individuals of the same species should be genetically more similar to each other than they are to individuals of another species. Here, we show that in the presence of cross-species gene flow, this expectation may be incorrect. We use the multispecies coalescent model with continuous-time migration or episodic introgression to study the impact of gene flow on genetic differences within and between species and highlight a surprising but plausible scenario in which different population sizes and asymmetrical migration rates cause a genetic sequence to be on average more closely related to a sequence from another species than to a sequence from the same species. Our results highlight the extraordinary impact that even a small amount of gene flow may have on the genetic history of the species. We suggest that contrasting long-term migration rate and short-term hybridization rate, both of which can be estimated using genetic data, may be a powerful approach to detecting the presence of reproductive barriers and to define species boundaries.[Gene flow; introgression; migration; multispecies coalescent; species concept; species delimitation.]
Equitable compensation and Brickenden: fiduciary loyalty and causation
Authors: Lee Jonathan T H 
Published: June 2020

Abstract
This article reconsiders the causation rules of equitable compensation for breaches of non-custodial fiduciary duties. It argues that these rules should correspond with and reflect the nature of fiduciary duties. Being a compensatory remedy, correct identification of the breach and the relevant counterfactual are therefore crucial. The failure to do so has led to much unwarranted criticism of the Privy Council’s decision in Brickenden. It also argues that a fiduciary is precluded by principle and policy from relying on the ‘escape route’ argument that the loss would have been suffered by his principal anyway.