bluuebunny/crossref_metadata_2025 huggingface dataset:
A Comprehensive Multi-Analyte Method for Hair Analysis: Substance-Specific Quantification Ranges and Tool for Task-Oriented Data Evaluation
Authors: Scholz C , Cabalzar J , Kraemer T , Baumgartner M R
Published: September 2020

The aim of the present study was to quantify a large number of analytes including opioids, stimulants, benzodiazepines, z-drugs, antidepressants and neuroleptics within a single sample workup followed by a single analytical measurement. Expected drug concentrations in hair are strongly substance dependent. Therefore, three different calibration ranges were implemented: 0.5 to 600 pg/mg (group 1), 10 to 12,000 pg/mg (group 2) and 50 to 60,000 pg/mg (group 3). In order to avoid saturation effects, different strategies were applied for selected transitions including the use of parent mass ions containing one or two 13C-isotopes and detuning of the declustering potential and/or collision energy. Drugs were extracted from pulverized hair by a two-step extraction protocol and measured by liquid chromatrography--tandem mass spectrometry (LC--MS-MS) using Scheduled MRM™ Algorithm Pro. In total, 275 MRM transitions including 43 deuterated standards were measured. The method has been fully validated according to international guidelines. A MultiQuant™ software based tool for task-oriented data evaluation was established, which allows extracting selected information from the measured data sets. The matrix effects and recoveries were within the allowed ranges for the majority of the analytes. The lower limits of quantification (LLOQs) were for ∼72% of the analytes in the low-pg/mg range (0.5–5 pg/mg) and for ∼24% of the analytes between 10 and 50 pg/mg. These LLOQs considered cut-offs by the Society of Hair Testing (SoHT), if recommended. The herein established multi-analyte approach meets the specific requirements of forensic hair testing and can be used for the rapid and robust measurement of a wide range of psychoactive substances. The analyte-specific wide concentration ranges open up a wide field of applications.
COVID-19 and Canadian Gastroenterology Trainees
Authors: Khan Rishad , Tandon Parul , Scaffidi Michael A , Bishay Kirles , Pawlak Katarzyna M , Kral Jan , Amin Sunil , Bilal Mohammad , Lui Rashid N , Sandhu Dalbir S , Hashim Almoutaz , Bollipo Steven , Charabaty Aline , de-Madaria Enrique , Rodríguez-Parra Andrés F , Sánchez-Luna Sergio A , Żorniak Michał , Siau Keith , Walsh Catharine M , Grover Samir C
Published: September 2020

Background

The coronavirus disease 2019 (COVID-19) pandemic has impacted endoscopy services and education worldwide. This study aimed to characterize the impact of COVID-19 on gastroenterology trainees in Canada.

Methods

An analysis of Canadian respondents from the international EndoTrain survey, open from April 11 to May 2 2020 and distributed by program directors, trainees, and national and international gastroenterology societies’ representatives, was completed. The survey included questions on monthly endoscopy volume, personal protective equipment availability, trainee well-being and educational resources. The primary outcome was change in procedural volume during the COVID-19 pandemic. Secondary outcomes included trainee’s professional and personal concerns, anxiety and burnout.

Results

Thirty-four Canadian trainees completed the survey. Per month, participants completed a median of 30 esophagogastroduodenoscopies (interquartile range 16 to 50) prior to the pandemic compared to 2 (0 to 10) during the pandemic, 20 (8 to 30) compared to 2 (0 to 5) colonoscopies and 3 (1 to 10) compared to 0 (0 to 3) upper gastrointestinal bleeding procedures. There was a significant decrease in procedural volumes between the pre-COVID-19 and COVID-19 time periods for all procedures (P < 0.001). Thirty (88%) trainees were concerned about personal COVID-19 exposure, 32 (94%) were concerned about achieving and/or maintaining clinical competence and 24 (71%) were concerned about prolongation of training time due to the pandemic. Twenty-six (79%) respondents experienced some degree of anxiety, and 10 (31%) experienced some degree of burnout.

Conclusion

The COVID-19 pandemic has substantially impacted gastroenterology trainees in Canada. As the pandemic eases, it important for gastrointestinal programs to adapt to maximize resident learning, maintain effective clinical care and ensure development of endoscopic competence.
Numerical study on combined thermal radiation and magnetic field effects on entropy generation in unsteady fluid flow past an inclined cylinder
Authors: Mburu Zachariah Mbugua , Mondal Sabyasachi , Sibanda Precious
Published: September 2020

This study reports on combined thermal radiation, chemical reaction, and magnetic field effects on entropy generation in an unsteady nanofluid flow past an inclined cylinder using the Buongiorno model. We consider the impact of viscous dissipation, velocity slip conditions, thermal slip conditions, and the Brownian motion. The transport equations governing the flow are solved using an overlapping grid spectral collocation method. The results indicate that entropy generation is suppressed significantly by thermal radiation and chemical reaction parameters but enhanced with the magnetic field, viscous dissipation, the Brinkman number, and the Reynolds number. Also, fluid flow variables are affected by the thermophoresis parameter, the angle of cylinder inclination, and the Richardson number. We present the findings of the skin friction coefficient, the Nusselt number, and the Sherwood number. The model is applicable in fields such as the petroleum industry, building industries, and medicine.
Second primary cancers and recurrence in patients after resection of colorectal cancer: An integrated analysis of trials by Japan Clinical Oncology Group: JCOG1702A
Authors: Tanaka Kiyo , Ogawa Gakuto , Mizusawa Junki , Kadota Tomohiro , Nakamura Kenichi , Shimada Yasuhiro , Hamaguchi Tetsuya , Fujita Shin , Kitano Seigo , Inomata Masafumi , Kanemitsu Yukihide , Fukuda Haruhiko ,   Colorectal Cancer Study Group of Japan Clinical Oncology Group (JCOG)
Published: September 2020

Background

Improvements in early detection and treatment have resulted in an increasing number of long-term survivors of colorectal cancer (CRC). For the survivors, second primary cancer and recurrence are important issues; however, evidence for an appropriate surveillance strategy remains limited.

This study aimed to investigate the frequency and timing of second primary cancer in patients after surgery for exploring an appropriate surveillance strategy by using an integrated analysis of three large-scale randomized controlled trials in Japan.

Methods

The eligibility criteria of three trials included histologically confirmed CRC and having received surgery. The timing, site and frequency of second primary cancers and recurrence were investigated. Risk factors associated with second primary cancers were also examined. The standardized incidence ratio (SIR) of second primary cancers compared with the national database of the Japan Cancer Registry was estimated.

Results

A total of 2824 patients were included in this study. The cumulative incidence of second primary cancer increased over time. The SIR of any second primary cancer was 1.07 (95% CI: 0.94–1.21). The SIR for second primary cancers of colon was 1.09 (95% CI: 0.79–1.47). The cumulative incidence of recurrence almost reached plateau at 3 years.

Conclusions

A common surveillance strategy for the general population can be applied even for curatively resected CRC patients, as the risk of second primary cancers was almost the same as that of the general population.
Fragmentation does not affect gene flow in forest populations of the dusky pipistrelle bat on the eastern seaboard of South Africa
Authors: Moir Monika , Richards Leigh R , Rambau Ramugondo V , Wannenburgh Andrew , Cherry Michael I
Published: September 2020

The Eastern Cape Province harbors almost half of the indigenous forest in South Africa, but these forests are threatened by large-scale agricultural and urban development planned for the coming decade. Additional anthropogenic development is likely to cause further fragmentation and degradation of forests inhabited by the dusky pipistrelle bat (Pipistrellus hesperidus). We used eight microsatellite markers to study the genetic diversity, population structure, and migration, of P. hesperidus (n = 120) across 14 sites in the Eastern Cape and KwaZulu-Natal provinces of South Africa. We examined the effect of contemporary land cover types on genetic differentiation to assess whether current levels of urbanization and agricultural development affect gene flow. High gene flow and low population structure were evident across sampled sites, apart from genetic discontinuities at the northern (Oribi Gorge Nature Reserve) and southern (Alexandria Forest) ends of the seaboard. Genetic discontinuity at Oribi Gorge may relate to anthropogenic modification of two rivers surrounding the forest, while the Alexandria-linked barrier is a climatic break known as the Bedford gap. Migration rates generally were low between sites except for one Scarp forest, Manubi State Forest, from which individuals dispersed to other sites. The Amatole Mistbelt forests supported high genetic diversity, and likely served as a refugium for P. hesperidus during the Last Glacial Maximum. The composition of land cover classes between sites was a poor predictor of genetic differentiation, although it seems likely that P. hesperidus uses riparian habitats and wetlands for dispersal. Lastly, urban and agricultural development did not have a significant effect on genetic differentiation, which may reflect the wide niche breadth and intermediate distribution range of the species. This study provides insights into genetic diversity and gene flow of P. hesperidus across the study region prior to agricultural intensification and large-scale urbanization.
Diphenylurea-derived cytokinin oxidase/dehydrogenase inhibitors for biotechnology and agriculture
Authors: Nisler Jaroslav , Kopečný David , Pěkná Zuzana , Končitíková Radka , Koprna Radoslav , Murvanidze Nino , Werbrouck Stefaan P O , Havlíček Libor , De Diego Nuria , Kopečná Martina , Wimmer Zdeněk , Briozzo Pierre , Moréra Solange , Zalabák David , Spíchal Lukáš , Strnad Miroslav
Published: September 2020

Increasing crop productivity is our major challenge if we are to meet global needs for food, fodder and fuel. Controlling the content of the plant hormone cytokinin is a method of improving plant productivity. Cytokinin oxidase/dehydrogenase (CKO/CKX) is a major target in this regard because it degrades cytokinins. Here, we describe the synthesis and biological activities of new CKX inhibitors derived mainly from diphenylurea. They were tested on four CKX isoforms from maize and Arabidopsis, where the best compounds showed IC50 values in the 10–8 M concentration range. The binding mode of the most efficient inhibitors was characterized from high-resolution crystal complexed structures. Although these compounds do not possess intrinsic cytokinin activity, we have demonstrated their tremendous potential for use in the plant tissue culture industry as well as in agriculture. We have identified a key substance, compound 19, which not only increases stress resistance and seed yield in Arabidopsis, but also improves the yield of wheat, barley and rapeseed grains under field conditions. Our findings reveal that modulation of cytokinin levels via CKX inhibition can positively affect plant growth, development and yield, and prove that CKX inhibitors can be an attractive target in plant biotechnology and agriculture.
‘Beauty is Truth, Truth Beauty’: A Novel Account of Beauty, Bildung, and Truth in Hegel and Thomas Mann
Authors: Casewell Deborah
Published: September 2020

Both Thomas Mann and G.W.F. Hegel accord beauty a particular role in their work: that of revealing truth. However, both differ in its particular stature and effectiveness. For Hegel it is an essential part of Bildung, a step to fuller knowledge of the Absolute Idea, whereas for Mann it is revelatory of the failures of Bildung, of knowledge, and self-control, and doing so it unmasks an existential truth. Drawing on Nietzsche, Schopenhauer, Lukács, and Gadamer, this article explores the way in which Mann’s account of beauty, as detailed in Little Herr Friedemann and Death in Venice, challenges both Hegel’s philosophy and in doing so a particular ideal of Bildung, especially with regards to its relationship to truth.
The intrinsic reddening of the Magellanic Clouds as traced by background galaxies – II. The Small Magellanic Cloud
Authors: Bell Cameron P M , Cioni Maria-Rosa L , Wright A H , Rubele Stefano , Nidever David L , Tatton Ben L , van Loon Jacco Th , Zaritsky Dennis , Choi Yumi , Choudhury Samyaday , Clementini Gisella , de Grijs Richard , Ivanov Valentin D , Majewski Steven R , Marconi Marcella , Martínez-Delgado David , Massana Pol , Muñoz Ricardo R , Niederhofer Florian , Noël Noelia E D , Oliveira Joana M , Olsen Knut , Pennock Clara M , Ripepi V , Subramanian Smitha , Vivas A Katherina
Published: September 2020

We present a map of the total intrinsic reddening across ≃34 deg2 of the Small Magellanic Cloud (SMC) derived using optical (ugriz) and near-infrared (IR; YJKs) spectral energy distributions (SEDs) of background galaxies. The reddening map is created using a subsample of 29 274 galaxies with low levels of intrinsic reddening based on the lephare χ2 minimization SED-fitting routine. We find statistically significant enhanced levels of reddening associated with the main body of the SMC compared with regions in the outskirts [ΔE(B − V) ≃ 0.3 mag]. A comparison with literature reddening maps of the SMC shows that, after correcting for differences in the volume of the SMC sampled, there is good agreement between our results and maps created using young stars. In contrast, we find significant discrepancies between our results and maps created using old stars or based on longer wavelength far-IR dust emission that could stem from biased samples in the former and uncertainties in the far-IR emissivity and the optical properties of the dust grains in the latter. This study represents one of the first large-scale categorizations of extragalactic sources behind the SMC and as such we provide the lephare outputs for our full sample of ∼500 000 sources.
Dynamical modelling of globular clusters: challenges for the robust determination of IMBH candidates
Authors: Aros Francisco I , Sippel Anna C , Mastrobuono-Battisti Alessandra , Askar Abbas , Bianchini Paolo , van de Ven Glenn
Published: September 2020

The presence or absence of intermediate-mass black holes (IMBHs) at the centre of Milky Way globular clusters (GCs) is still an open question. This is due to either observational restrictions or limitations in the dynamical modelling method; in this work, we explore the latter. Using a sample of high-end Monte Carlo simulations of GCs, with and without a central IMBH, we study the limitations of spherically symmetric Jeans models assuming constant velocity anisotropy and mass-to-light ratio. This dynamical method is one of the most widely used modelling approaches to identify a central IMBH in observations.

With these models, we are able to robustly identify and recover the mass of the central IMBH in our simulation with a high-mass IMBH ($M_{\rm IMBH}/M_{\rm GC}\sim 4{{\ \rm per\ cent}}$). Simultaneously, we show that it is challenging to confirm the existence of a low-mass IMBH ($M_{\rm IMBH}/M_{\rm GC}\sim 0.3{{\ \rm per\ cent}}$), as both solutions with and without an IMBH are possible within our adopted error bars. For simulations without an IMBH, we do not find any certain false detection of an IMBH. However, we obtain upper limits that still allow for the presence of a central IMBH. We conclude that while our modelling approach is reliable for the high-mass IMBH and does not seem to lead towards a false detection of a central IMBH, it lacks the sensitivity to robustly identify a low-mass IMBH and to definitely rule out the presence of an IMBH when it is not there.
Non-parametric density reconstruction of the Galactic bulge area using red clump stars in the VVV survey
Authors: Paterson Dylan , Coleman Brenna , Gordon Chris
Published: September 2020

Studies of the red clump giant population in the inner Milky Way suggest the Galactic bulge/bar has a boxy/peanut/X-shaped structure as predicted by its formation via a disc buckling instability. We used a non-parametric method of estimating the Galactic bulge morphology that is based on maximum entropy regularization. This enabled us to extract the 3D distribution of the red giant stars in the bulge from deep photometric catalogues of the VISTA Variables in the Via Lactea survey. Our high-resolution reconstruction confirms the well-known boxy/peanut/X-shaped structure of the bulge. We also find spiral arm structures that extend to around 3 kpc in front of and behind the bulge and are on different sides of the bulge major axis. We show that the detection of these structures is robust to the uncertainties in the luminosity function.
Reproducing the CO-to-H2 conversion factor in cosmological simulations of Milky-Way-mass galaxies
Authors: Keating Laura C , Richings Alexander J , Murray Norman , Faucher-Giguère Claude-André , Hopkins Philip F , Wetzel Andrew , Kereš Dušan , Benincasa Samantha , Feldmann Robert , Loebman Sarah , Orr Matthew E
Published: September 2020

We present models of CO(1–0) emission from Milky-Way-mass galaxies at redshift zero in the FIRE-2 cosmological zoom-in simulations. We calculate the molecular abundances by post-processing the simulations with an equilibrium chemistry solver while accounting for the effects of local sources, and determine the emergent CO(1–0) emission using a line radiative transfer code. We find that the results depend strongly on the shielding length assumed, which, in our models, sets the attenuation of the incident UV radiation field. At the resolution of these simulations, commonly used choices for the shielding length, such as the Jeans length, result in CO abundances that are too high at a given H2 abundance. We find that a model with a distribution of shielding lengths, which has a median shielding length of ∼3 pc in cold gas (T < 300 K) for both CO and H2, is able to reproduce both the observed CO(1–0) luminosity and inferred CO-to-H2 conversion factor at a given star formation rate compared with observations. We suggest that this short shielding length can be thought of as a subgrid model, which controls the amount of radiation that penetrates giant molecular clouds.
Fast algorithms to approximate the position-dependent point spread function responses in radio interferometric wide-field imaging
Authors: Atemkeng M , Smirnov O , Tasse C , Foster G , Makhathini S
Published: September 2020

The desire for wide field of view, large fractional bandwidth, high sensitivity, high spectral and temporal resolution has driven radio interferometry to the point of big data revolution where the data are represented in at least three dimensions with an axis for spectral windows, baselines, sources, etc., where each axis has its own set of subdimensions. The cost associated with storing and handling these data is very large, and therefore several techniques to compress interferometric data and/or speed up processing have been investigated. Unfortunately, averaging-based methods for visibility data compression are detrimental to the data fidelity, since the point spread function (PSF) is position-dependent, that is, distorted and attenuated as a function of distance from the phase centre. The position dependence of the PSF becomes more severe, requiring more PSF computations for wide-field imaging. Deconvolution algorithms must take the distortion into account in the major and minor cycles to properly subtract the PSF and recover the fidelity of the image. This approach is expensive in computation since at each deconvolution iteration a distorted PSF must be computed. We present two algorithms that approximate these position-dependent PSFs with fewer computations. The first algorithm approximates the position-dependent PSFs in the uv-plane and the second algorithm approximates the position-dependent PSFs in the image plane. The proposed algorithms are validated using simulated data from the MeerKAT telescope.
Three- and two-point spatial correlations of IGM at z ∼ 2: cloud-based analysis using simulations
Authors: Maitra Soumak , Srianand Raghunathan , Gaikwad Prakash , Choudhury Tirthankar Roy , Paranjape Aseem , Petitjean Patrick
Published: September 2020

Ly α forest absorption spectra decomposed into multiple Voigt profile components (clouds) allow us to study clustering of intergalactic medium (IGM) as a function of H i column density ($N_{\rm H\, \small{I}}$). Here, we explore the transverse three-point correlation (ζ) of Ly α clouds using mock triplet spectra from simulations at z ∼ 2 on scales of 1–5 h−1 cMpc. We find ζ to depend strongly on $N_{\rm H\, \small{I}}$ and scale and weakly on angle of the triplet configuration. We show that the ‘hierarchical ansatz’ is applicable for scales $\ge ~ 3\, h^{-1}$ cMpc, and obtain a median reduced three-point correlation (Q) in the range 0.2–0.7. We show, ζ is influenced strongly by the thermal and ionization state of the gas. As in the case of galaxies, the influence of physical parameters on Q is weaker compared to that on ζ. We show difference in ζ and Q between different simulations are minimized if we use appropriate $N_{\rm H\, \small{I}}$ cut-offs corresponding to a given baryon overdensity (Δ) using the $N_{\rm H\, \small{I}}~versus~\Delta$ relationship obtained from simulations. We study the effect of pressure broadening on ζ using a model with artificially boosted heating rates. However, for models with realistic thermal and ionization histories the effect of pressure broadening on ζ is subdominant compared to other local effects. We find the strong redshift evolution shown by ζ, mainly originating from the redshift evolution of thermal and ionization state of the IGM. We discuss the observational requirements for the detection of three-point correlation, specifically, in small intervals of configuration parameters and redshift.
High-resolution simulations of dark matter subhalo disruption in a Milky-Way-like tidal field
Authors: Webb Jeremy J , Bovy Jo
Published: September 2020

We compare the results of high-resolution simulations of individual dark matter subhaloes evolving in external tidal fields with and without baryonic bulge and disc components, where the average dark matter particle mass is three orders of magnitude smaller than cosmological zoom-in simulations of galaxy formation. The Via Lactea II simulation is used to setup our initial conditions and provides a basis for our simulations of subhaloes in a dark-matter-only tidal field, while an observationally motivated model for the Milky-Way is used for the tidal field that is comprised of a dark matter halo, a stellar disc, and a stellar bulge. Our simulations indicate that including stellar components in the tidal field results in the number of subhaloes in Milky-Way-like galaxies being only $65{{\ \rm per\ cent}}$ of what is predicted by Λ cold dark matter (ΛCDM). For subhaloes with small pericentres (rp ≲ 25 kpc), the subhalo abundance is reduced further to $40{{\ \rm per\ cent}}$, with the surviving subhaloes being less dense and having a tangentially anisotropic orbital distribution. Conversely, subhaloes with larger pericentres are minimally affected by the inclusion of a stellar component in the tidal field, with the total number of outer subhaloes $\approx 75{{\ \rm per\ cent}}$ of the ΛCDM prediction. The densities of outer subhaloes are comparable to predictions from ΛCDM, with the subhaloes having an isotropic distribution of orbits. These ratios are higher than those found in previous studies that include the effects baryonic matter, which are affected by spurious disruption caused by low resolution.
Recovery of 21-cm intensity maps with sparse component separation
Authors: Carucci Isabella P , Irfan Melis O , Bobin Jérôme
Published: September 2020

21-cm intensity mapping has emerged as a promising technique to map the large-scale structure of the Universe. However, the presence of foregrounds with amplitudes orders of magnitude larger than the cosmological signal constitutes a critical challenge. Here, we test the sparsity-based algorithm generalized morphological component analysis (GMCA) as a blind component separation technique for this class of experiments. We test the GMCA performance against realistic full-sky mock temperature maps that include, besides astrophysical foregrounds, also a fraction of the polarized part of the signal leaked into the unpolarized one, a very troublesome foreground to subtract, usually referred to as polarization leakage. To our knowledge, this is the first time the removal of such component is performed with no prior assumption. We assess the success of the cleaning by comparing the true and recovered power spectra, in the angular and radial directions. In the best scenario looked at, GMCA is able to recover the input angular (radial) power spectrum with an average bias of ${\sim} 5{{\ \rm per\ cent}}$ for ℓ > 25 ($20\!-\!30 {{\ \rm per\ cent}}$ for $k_{\parallel } \gtrsim 0.02 \, h^{-1}$ Mpc), in the presence of polarization leakage. Our results are robust also when up to $40{{\ \rm per\ cent}}$ of channels are missing, mimicking a radio-frequency interference (RFI) flagging of the data. Having quantified the notable effect of polarization leakage on our results, in perspective we advocate the use of more realistic simulations when testing 21-cm intensity mapping capabilities.
Radiolysis of NH3:CO ice mixtures – implications for Solar system and interstellar ices
Authors: de Barros A L F , Bergantini A , Domaracka A , Rothard H , Boduch P , da Silveira E F
Published: September 2020

Experimental results on the processing of NH3:CO ice mixtures of astrophysical relevance by energetic (538 MeV 64Ni24+) projectiles are presented. NH3 and CO are two molecules relatively common in interstellar medium and Solar system; they may be precursors of amino acids. 64Ni ions may be considered as representative of heavy cosmic ray analogues. Laboratory data were collected using mid-infrared Fourier transform spectroscopy and revealed the formation of ammonium cation (NH$_4^+$), cyanate (OCN−), molecular nitrogen (N2), and CO2. Tentative assignments of carbamic acid (NH2COOH), formate ion (HCOO−), zwitterionic glycine (NH$_3^+$CH2COO−), and ammonium carbamate (NH$_4^+$NH2COO−) are proposed. Despite the confirmation on the synthesis of several complex species bearing C, H, O, and N atoms, no N–O-bearing species was detected. Moreover, parameters relevant for computational astrophysics, such as destruction and formation cross-sections, are determined for the precursor and the main detected species. Those values scale with the electronic stopping power (Se) roughly as σ ∼ a S$_\mathrm{ e}^n$, where n ∼ 3/2. The power law is helpful for predicting the CO and NH3 dissociation and CO2 formation cross-sections for other ions and energies; these predictions allow estimating the effects of the entire cosmic ray radiation field.
Power spectrum response of large-scale structure in 1D and in 3D: tests of prescriptions for post-collapse dynamics
Authors: Halle Anaëlle , Nishimichi Takahiro , Taruya Atsushi , Colombi Stéphane , Bernardeau Francis
Published: September 2020

The power spectrum response function of the large-scale structure of the Universe describes how the evolved power spectrum is modified by a small change in initial power through non-linear mode coupling of gravitational evolution. It was previously found that the response function for the coupling from small to large scales is strongly suppressed in amplitude, especially at late times, compared to predictions from perturbation theory (PT) based on the single-stream approximation. One obvious explanation for this is that PT fails to describe the dynamics beyond shell crossing. We test this idea by comparing measurements in N-body simulations to prescriptions based on PT but augmented with adaptive smoothing to account for the formation of non-linear structures of various sizes in the multistream regime. We first start with one-dimensional (1D) cosmology, where the Zel’dovich approximation provides the exact solution in the single-stream regime. Similarly to the three-dimensional (3D) case, the response function of the large-scale modes exhibits a strong suppression in amplitude at small scales that cannot be explained by the Zel’dovich solution alone. However, by performing adaptive smoothing of initial conditions to identify haloes of different sizes and solving approximately post-collapse dynamics in the three-stream regime, agreement between theory and simulations drastically improves. We extend our analyses to the 3D case using the pinocchio algorithm, in which similar adaptive smoothing is implemented on the Lagrangian PT fields to identify haloes and is combined with a spherical halo prescription to account for post-collapse dynamics. Again, a suppression is found in the coupling between small- and large-scale modes and the agreement with simulations is improved.
MAMMOTH: confirmation of two massive galaxy overdensities at z = 2.24 with Hα emitters
Authors: Zheng Xian Zhong , Cai Zheng , An Fang Xia , Fan Xiaohui , Shi Dong Dong
Published: September 2020

Massive galaxy overdensities at the peak epoch of cosmic star formation provide ideal testbeds for the formation theories of galaxies and large-scale structure. We report the confirmation of two massive galaxy overdensities at z = 2.24, BOSS1244 and BOSS1542, selected from the Mapping the Most Massive Overdensities Through Hydrogen (MAMMOTH) project using Lyα absorption from the intergalactic medium over the scales of 15−30 h−1 Mpc imprinted on the quasar spectra. We use Hα emitters (HAEs) as the density tracer and identify them using deep narrow-band H2S(1) and broad-band Ks imaging data obtained with the wide-field infrared camera (WIRCam) at the Canada–France–Hawaii Telescope. In total, 244 and 223 line emitters are detected in these two fields, and 196 ± 2 and 175 ± 2 are expected to be HAEs with an Hα flux of >2.5 × 10−17 erg s−1 cm−2 (corresponding to a star formation rate of >5 M⊙ yr−1). The detection rate of HAE candidates suggests an overdensity factor of δgal = 5.6 ± 0.3 and 4.9 ± 0.3 over the volume of 54 × 32 × 32 co-moving Mpc3. The overdensity factor increases two to three times when focusing on the high-density regions of scales 10–15  co-moving Mpc. Interestingly, the HAE density maps reveal that BOSS1244 contains a dominant structure, while BOSS1542 manifests as a giant filamentary structure. We measure the Hα luminosity functions (HLFs), finding that BOSS1244’s HLF is nearly identical to that of the general field at the same epoch, while BOSS1542 shows an excess of HAEs with high Hα luminosity, indicating the presence of enhanced star formation or active galactic nuclei activity. We conclude that the two massive MAMMOTH overdensities are undergoing a rapid galaxy mass assembly.
Two-dimensional multifibre spectral image correction based on machine learning techniques
Authors: Xu Jiali , Yin Qian , Guo Ping , Zheng Xin
Published: September 2020

Owing to the limited size and imperfections of the optical components in a spectrometer, aberrations inevitably make their way into 2D multifibre spectral images in the Large Sky Area Multi-Object Fiber Spectroscopy Telescope (LAMOST), which leads to obvious spatial variation of the point spread functions (PSFs). However, if spatially variant PSFs are estimated directly, the large storage and intensive computational requirements result in the deconvolution spectrum extraction method becoming intractable. In this paper, we propose a novel method to solve the problem of spatial variation of the PSFs through image aberration correction. When CCD image aberrations are corrected, the convolution kernel can be approximated by only one spatially invariant PSF. Specifically, a novel method based on machine learning is proposed to calibrate the distorted spectral images. The method includes many techniques, such as total least squares (TLS) algorithm, self-supervised learning and multilayer feed-forward neural networksnetworks, and it makes use of a special training set sampling scheme combining 2D distortion features in a flat-field spectrum and calibration lamp spectrum. The calibration experiments on the LAMOST CCD images show that the proposed method is feasible. Furthermore, the spectrum extraction results before and after calibration are compared, and the experimental results show that the characteristics of the extracted 1D waveform are closer to those of an ideal optics system after image correction, and that the PSF of the corrected object spectrum estimated by the blind deconvolution method is nearly centrosymmetric, which indicates that our proposed method can significantly reduce the complexity of spectrum extraction and improve extraction accuracy.
LSD1 prevents aberrant heterochromatin formation in Neurospora crassa
Authors: Storck William K , Bicocca Vincent T , Rountree Michael R , Honda Shinji , Ormsby Tereza , Selker Eric U
Published: September 2020

Heterochromatin is a specialized form of chromatin that restricts access to DNA and inhibits genetic processes, including transcription and recombination. In Neurospora crassa, constitutive heterochromatin is characterized by trimethylation of lysine 9 on histone H3, hypoacetylation of histones, and DNA methylation. We explored whether the conserved histone demethylase, lysine-specific demethylase 1 (LSD1), regulates heterochromatin in Neurospora, and if so, how. Though LSD1 is implicated in heterochromatin regulation, its function is inconsistent across different systems; orthologs of LSD1 have been shown to either promote or antagonize heterochromatin expansion by removing H3K4me or H3K9me respectively. We identify three members of the Neurospora LSD complex (LSDC): LSD1, PHF1, and BDP-1. Strains deficient for any of these proteins exhibit variable spreading of heterochromatin and establishment of new heterochromatin domains throughout the genome. Although establishment of H3K9me3 is typically independent of DNA methylation in Neurospora, instances of DNA methylation-dependent H3K9me3 have been found outside regions of canonical heterochromatin. Consistent with this, the hyper-H3K9me3 phenotype of Δlsd1 strains is dependent on the presence of DNA methylation, as well as HCHC-mediated histone deacetylation, suggesting that spreading is dependent on some feedback mechanism. Altogether, our results suggest LSD1 works in opposition to HCHC to maintain proper heterochromatin boundaries.
Stabilization of G-quadruplex DNA structures in Schizosaccharomyces pombe causes single-strand DNA lesions and impedes DNA replication
Authors: Obi Ikenna , Rentoft Matilda , Singh Vandana , Jamroskovic Jan , Chand Karam , Chorell Erik , Westerlund Fredrik , Sabouri Nasim
Published: September 2020

G-quadruplex (G4) structures are stable non-canonical DNA structures that are implicated in the regulation of many cellular pathways. We show here that the G4-stabilizing compound PhenDC3 causes growth defects in Schizosaccharomyces pombe cells, especially during S-phase in synchronized cultures. By visualizing individual DNA molecules, we observed shorter DNA fragments of newly replicated DNA in the PhenDC3-treated cells, suggesting that PhenDC3 impedes replication fork progression. Furthermore, a novel single DNA molecule damage assay revealed increased single-strand DNA lesions in the PhenDC3-treated cells. Moreover, chromatin immunoprecipitation showed enrichment of the leading-strand DNA polymerase at sites of predicted G4 structures, suggesting that these structures impede DNA replication. We tested a subset of these sites and showed that they form G4 structures, that they stall DNA synthesis in vitro and that they can be resolved by the breast cancer-associated Pif1 family helicases. Our results thus suggest that G4 structures occur in S. pombe and that stabilized/unresolved G4 structures are obstacles for the replication machinery. The increased levels of DNA damage might further highlight the association of the human Pif1 helicase with familial breast cancer and the onset of other human diseases connected to unresolved G4 structures.
Interactions of replication initiator RctB with single- and double-stranded DNA in origin opening of Vibrio cholerae chromosome 2
Authors: Chatterjee Soniya , Jha Jyoti K , Ciaccia Peter , Venkova Tatiana , Chattoraj Dhruba K
Published: September 2020

Studies of bacterial chromosomes and plasmids indicate that their replication initiator proteins bind to origins of replication at many double-stranded sites and also at AT-rich regions where single-stranded DNA is exposed during origin opening. Single-strand binding apparently promotes origin opening by stabilizing an open structure, but how the initiator participates in this process and the contributions of the several binding sites remain unclear. Here, we show that the initiator protein of Vibrio cholerae specific to chromosome 2 (Chr2) also has single-strand binding activity in the AT-rich region of its origin. Binding is strand specific, depends on repeats of the sequence 5′ATCA and is greatly stabilized in vitro by specific double-stranded sites of the origin. The stability derives from the formation of ternary complexes of the initiator with the single- and double-stranded sites. An IHF site lies between these two kinds of sites in the Chr2 origin and an IHF-induced looping out of the intervening DNA mediates their interaction. Simultaneous binding to two kinds of sites in the origin appears to be a common mechanism by which bacterial replication initiators stabilize an open origin.
tRFtarget: a database for transfer RNA-derived fragment targets
Authors: Li Ningshan , Shan Nayang , Lu Lingeng , Wang Zuoheng
Published: September 2020

Transfer RNA-derived fragments (tRFs) are a new class of small non-coding RNAs and play important roles in biological and physiological processes. Prediction of tRF target genes and binding sites is crucial in understanding the biological functions of tRFs in the molecular mechanisms of human diseases. We developed a publicly accessible web-based database, tRFtarget (http://trftarget.net), for tRF target prediction. It contains the computationally predicted interactions between tRFs and mRNA transcripts using the two state-of-the-art prediction tools RNAhybrid and IntaRNA, including location of the binding sites on the target, the binding region, and free energy of the binding stability with graphic illustration. tRFtarget covers 936 tRFs and 135 thousand predicted targets in eight species. It allows researchers to search either target genes by tRF IDs or tRFs by gene symbols/transcript names. We also integrated the manually curated experimental evidence of the predicted interactions into the database. Furthermore, we provided a convenient link to the DAVID® web server to perform downstream functional pathway analysis and gene ontology annotation on the predicted target genes. This database provides useful information for the scientific community to experimentally validate tRF target genes and facilitate the investigation of the molecular functions and mechanisms of tRFs.
Translation reprogramming by eIF3 linked to glioblastoma resistance
Authors: Bertorello Juliette , Sesen Julie , Gilhodes Julia , Evrard Solène , Courtade-Saïdi Monique , Augustus Meera , Uro-Coste Emmanuelle , Toulas Christine , Moyal Elizabeth Cohen-Jonathan , Seva Catherine , Dassi Erik , Cammas Anne , Skuli Nicolas , Millevoi Stefania
Published: September 2020

Intrinsic resistance to current therapies, leading to dismal clinical outcomes, is a hallmark of glioblastoma multiforme (GBM), the most common and aggressive brain tumor. Understanding the underlying mechanisms of such malignancy is, therefore, an urgent medical need. Deregulation of the protein translation machinery has been shown to contribute to cancer initiation and progression, in part by driving selective translational control of specific mRNA transcripts involved in distinct cancer cell behaviors. Here, we focus on eIF3, a multimeric complex with a known role in the initiation of translation and that is frequently deregulated in cancer. Our results show that the deregulated expression of eIF3e, the e subunit of eIF3, in specific GBM regions could impinge on selective protein synthesis impacting the GBM outcome. In particular, eIF3e restricts the expression of proteins involved in the response to cellular stress and increases the expression of key functional regulators of cell stemness. Such a translation program can therefore serve as a double-edged sword promoting GBM tumor growth and resistance to radiation.
A direct measurement method of quantum relaxation time
Authors: Zhang Peng , Tang Haoqi , Gu Chuanchuan , Wang Hong , Luo Guangfu , Lu Yalin , Xiang X-D
Published: September 2020

The quantum relaxation time of electrons in condensed matters is an important physical property, but its direct measurement has been elusive for a century. Here, we report a breakthrough that allows direct determination of quantum relaxation time at zero and non-zero frequencies using optical measurement. Through dielectric loss function, we connect bound electron effects to the physical parameters of plasma resonance and find an extra term of quantum relaxation time from inelastic scattering between bound electrons and conduction electrons at non-zero frequencies. We demonstrate here that the frequency-dependent inelastic polarization effect of bound electrons is the dominant contribution to quantum relaxation time of conduction electrons at optical frequencies, and the elastic polarization effect of bound electrons also dramatically changes the plasma resonance frequency through effective screening to charge carriers.
The Paradox of the Low Prevalence of Current Smokers Among COVID-19 Patients Hospitalized in Nonintensive Care Wards: Results From an Italian Multicenter Case–Control Study
Authors: Meini Simone , Fortini Alberto , Andreini Roberto , Sechi Leonardo Alberto , Tascini Carlo
Published: September 2020

Introduction

COVID-19, a respiratory illness due to SARS-CoV-2 coronavirus, was first described in December 2019 in Wuhan, rapidly evolving into a pandemic. Smoking increases the risk of respiratory infections; thus, cessation represents a huge opportunity for public health. However, there is scarce evidence about if and how smoking affects the risk of SARS-CoV-2 infection.

Methods

We performed an observational case–control study, assessing the single-day point prevalence of smoking among 218 COVID-19 adult patients hospitalized in seven Italian nonintensive care wards and in a control group of 243 patients admitted for other conditions to seven COVID-19-free general wards. We compared proportions for categorical variables by using the χ 2 test and performed univariate and multivariate logistic regression analyses to identify the variables associated with the risk of hospitalization for COVID-19.

Results

The percentages of current smokers (4.1% vs 16%, p = .00003) and never smokers (71.6% vs 56.8%, p = .0014) were significantly different between COVID-19 and non-COVID 19 patients. COVID-19 patients had lower mean age (69.5 vs 74.2 years, p = .00085) and were more frequently males (59.2% vs 44%, p = .0011). In the logistic regression analysis, current smokers were significantly less likely to be hospitalized for COVID-19 compared with nonsmokers (odds ratio = 0.23; 95% confidence interval, 0.11–0.48, p < .001), even after adjusting for age and gender (odds ratio = 0.14; 95% confidence interval, 0.06–0.31, p < .001).

Conclusions

We reported an unexpectedly low prevalence of current smokers among COVID-19 patients hospitalized in nonintensive care wards. The meaning of these preliminary findings, which are in line with those currently emerging in literature, is unclear; they need to be confirmed by larger studies.

Implications

An unexpectedly low prevalence of current smokers among patients hospitalized for COVID-19 in some Italian nonintensive care wards is reported. This finding could be a stimulus for the generation of novel hypotheses on individual predisposition and possible strategies for reducing the risk of infection from SARS-CoV-2 and needs to be confirmed by further larger studies designed with adequate methodology.
Trends in Economic Inequality and News Mediascape
Authors: Theine Hendrik , Grabner Daniel
Published: September 2020

Chapter 2 engages with two major background themes: a review of inequality trends and how these are addressed by researchers in the economics field, and, secondly, the contours of change in the news media landscape. The first section reviews a key set of recent contributions in the field of economics on economic inequality. The next section turns to an overview of wealth and income inequality in the four countries that are at the centre of the empirical part of this volume (UK, Germany, Austria, and Ireland). The next two sections are concerned with academic responses to Piketty’s (2014) book and the subsequent academic debate on shifts in policies and institutional settings which can contribute to the reduction of inequality. The latter part of the chapter turn to the analysis of communicative resources, in particular changes in the news media sectors. It examines forms of inequality in ownership structures and concentration trends unfolding within the daily newspaper markets. Chapter 2 also wraps up with some concluding comments.
Inequality, Mediatization, and Critical Takes on Making the News
Authors: Preston Paschal
Published: September 2020

Chapter 3 continues the initial review of existing research literature related to the changing role and forms of the media and economic affairs, and the issues of economic inequality in particular. It aims to identify some high-level ideas and concepts drawn from the fields of socioeconomics and political economy, as well as certain sub-sets of the communication and journalism studies fields, which shed light on the meaning of economic inequality and the key influences on the selection or making of news culture and journalistic practices. The chapter considers the shifting forms and meanings of economic equality in the modern social sciences, indicating the diversity of prior studies, engagement with, or neglect of inequality matters. It then moves on to address the notion of mediatization and select aspects of the evolving role and scope of the media in relation to economic and other societal processes, including those related to economic inequality. Next, some of the major approaches and prevailing perspectives on ‘making the news’ are identified. This outlines a typology of the prior research literature, noting a number of distinct schools in explaining the key influences on newsmaking and shaping journalism discourses. The authors focus on certain macro- and meso-level factors which influence news media and journalistic discourse (rather than individual-level characteristics or failings of journalists). The chapter ends with an outline of the authors’ transdisciplinary approach towards ‘making the news’, combining conceptual elements from both the critical cultural studies and political economy approaches. A final section considers conclusions and implications.