bluuebunny/crossref_metadata_2025_split huggingface dataset:
The completed SDSS-IV extended Baryon Oscillation Spectroscopic Survey: measurement of the growth rate of structure from the small-scale clustering of the luminous red galaxy sample
Authors: Chapman Michael J , Mohammad Faizan G , Zhai Zhongxu , Percival Will J , Tinker Jeremy L , Bautista Julian E , Brownstein Joel R , Burtin Etienne , Dawson Kyle S , Gil-Marín Héctor , de la Macorra Axel , Ross Ashley J , Rossi Graziano , Schneider Donald P , Zhao Gong-Bo 
Published: July 2022

ABSTRACT
We measure the small-scale clustering of the Data Release 16 extended Baryon Oscillation Spectroscopic Survey Luminous Red Galaxy sample, corrected for fibre-collisions using Pairwise Inverse Probability weights, which give unbiased clustering measurements on all scales. We fit to the monopole and quadrupole moments and to the projected correlation function over the separation range $7-60\, h^{-1}{\rm Mpc}$ with a model based on the aemulus cosmological emulator to measure the growth rate of cosmic structure, parametrized by fσ8. We obtain a measurement of fσ8(z = 0.737) = 0.408 ± 0.038, which is 1.4σ lower than the value expected from 2018 Planck data for a flat ΛCDM model, and is more consistent with recent weak-lensing measurements. The level of precision achieved is 1.7 times better than more standard measurements made using only the large-scale modes of the same sample. We also fit to the data using the full range of scales $0.1\text{--}60\, h^{-1}{\rm Mpc}$ modelled by the aemulus cosmological emulator and find a 4.5σ tension in the amplitude of the halo velocity field with the Planck + ΛCDM model, driven by a mismatch on the non-linear scales. This may not be cosmological in origin, and could be due to a breakdown in the Halo Occupation Distribution model used in the emulator. Finally, we perform a robust analysis of possible sources of systematics, including the effects of redshift uncertainty and incompleteness due to target selection that were not included in previous analyses fitting to clustering measurements on small scales.
Fuzzy dark matter and the Dark Energy Survey Year 1 data
Authors: Dentler Mona , Marsh David J E , Hložek Renée , Laguë Alex , Rogers Keir K , Grin Daniel 
Published: July 2022

ABSTRACT
Gravitational weak lensing by dark matter haloes leads to a measurable imprint in the shear correlation function of galaxies. Fuzzy dark matter (FDM), composed of ultralight axion-like particles of mass m ∼ 10−22 eV, suppresses the matter power spectrum and shear correlation with respect to standard cold dark matter. We model the effect of FDM on cosmic shear using the optimized halo model HMCode, accounting for additional suppression of the mass function and halo concentration in FDM as observed in N-body simulations. We combine Dark Energy Survey Year 1 (DES-Y1) data with the Planck cosmic microwave background anisotropies to search for shear correlation suppression caused by FDM. We find no evidence of suppression compared to the preferred cold dark matter model, and thus set a new lower limit to the FDM particle mass. Using a log-flat prior and marginalizing over uncertainties related to the non-linear model of FDM, we find a new, independent 95 per cent C.L. lower limit log10m &gt; −23 combining Planck and DES-Y1 shear, an improvement of almost two orders of magnitude on the mass bound relative to CMB-only constraints. Our analysis is largely independent of baryonic modelling, and of previous limits to FDM covering this mass range. Our analysis highlights the most important aspects of the FDM non-linear model for future investigation. The limit to FDM from weak lensing could be improved by up to three orders of magnitude with $\mathcal {O}(0.1)$ arcmin cosmic shear angular resolution, if FDM and baryonic feedback can be simultaneously modelled to high precision in the halo model.
Correlations between X-ray spectral parameters of Mkn 421 using long-term Swift–XRT data
Authors: Khatoon Rukaiya , Shah Zahir , Hota Jyotishree , Misra Ranjeev , Gogoi Rupjyoti , Pradhan Ananta C 
Published: July 2022

ABSTRACT
We have performed a detailed analysis of the X-ray spectra of the blazar Mkn 421 using Swift–XRT observations taken between 2005 and 2020, to quantify the correlations between spectral parameters for different models. In an earlier work, it has been shown that such spectral parameter correlations obtained from a single short flare of duration ∼5 d of Mkn 421, can be used to distinguish spectrally degenerate models and provide estimates of physical quantities. In this work, we show that the results from the long-term spectral parameter correlations are consistent with those obtained from the single flare. In particular, that the observed spectral curvature is due to maximum cut-off energy in the particle distribution is ruled out. Instead, models where the curvature is due to the energy dependence of escape or acceleration time-scale of the particles are favoured. The estimated values of the physical parameters for these models are similar to the ones obtained from the single flare analysis and are somewhat incompatible with the physical assumption of the models, suggesting that more complex physical models are required. The consistency of the results obtained from the long- and short-term evolution of the source, underlines the reliability of the technique to use spectral parameter correlations to distinguish physical models.
Comparison of the active galactic nuclei Baldwin effect with the modified Baldwin effect of the ultraviolet-optical emission lines in a single sample
Authors: Wang Yongjiang , Liu Wanqing , Shang Zhaohui , Brotherton Michael S 
Published: July 2022

ABSTRACT
The inverse relationship between equivalent width (EW) of broad emission lines and the underlying continuum luminosity, known as the Baldwin effect (BE), is an important and well-studied correlation in active galactic nuclei (AGNs). However, the EW is also considered to be anticorrelated with the Eddington ratio, referred to as the modified Baldwin effect (MBE). Investigating whether the BE or MBE is the stronger correlation is important for studying the ionization mechanism and the broad-line region of AGN. Based on a sample of 85 bright quasars with quasi-simultaneous ultraviolet (UV)-optical spectra and a redshift range of 0.03–1.404 from Shang et al., we first present line fitting and measurements of the O vi line that were not previously available and the Si iv + O iv] line. We then investigate and compare the BE and MBE of multiple UV and optical emission lines from this single sample. We find that the BE of most of the broad emission lines is stronger than the MBE. Furthermore, we confirm the previous result that the slope of the BE steepens with the ionization energy of the line, and also find that the MBE slope shows a similar trend. In addition, compared with the C iv line, the O vi shows a broader line width and a larger peak velocity blueshift with respect to the systemic redshift. These results are also in agreement with previous studies and imply that, compared to the C iv gas, the O vi line-emitting gas is closer to the accretion disc and is more strongly influenced by the accretion disc wind.
SEQ2MGS: an effective tool for generating realistic artificial metagenomes from the existing sequencing data
Authors: Van Camp Pieter-Jan , Porollo Aleksey 
Published: July 2022

AbstractAssessment of bioinformatics tools for the metagenomics analysis from the whole genome sequencing data requires realistic benchmark sets. We developed an effective and simple generator of artificial metagenomes from real sequencing experiments. The tool (SEQ2MGS) analyzes the input FASTQ files, precomputes genomic content, and blends shotgun reads from different sequenced isolates, or spike isolate(s) in real metagenome, in desired proportions. SEQ2MGS eliminates the need for simulation of sequencing platform variations, reads distributions, presence of plasmids, viruses, and contamination. The tool is especially useful for a quick generation of multiple complex samples that include new or understudied organisms, even without assembled genomes. For illustration, we first demonstrated the ease of SEQ2MGS use for the simulation of altered Schaedler flora (ASF) in comparison with de novo metagenomics generators Grinder and CAMISIM. Next, we emulated the emergence of a pathogen in the human gut microbiome and observed that Kraken, Centrifuge, and MetaPhlAn, while correctly identified Klebsiella pneumoniae, produced inconsistent results for the rest of real metagenome. Finally, using the MG-RAST platform, we affirmed that SEQ2MGS properly transfers genomic information from an isolate into the simulated metagenome by the correct identification of antimicrobial resistance genes anticipated to appear compared to the original metagenome.
Changing Diagnostic Testing Practices for Foodborne Pathogens, Foodborne Diseases Active Surveillance Network, 2012–2019
Authors: Ray Logan C , Griffin Patricia M , Wymore Katie , Wilson Elisha , Hurd Sharon , LaClair Bethany , Wozny Sophia , Eikmeier Dana , Nicholson Cyndy , Burzlaff Kari , Hatch Julie , Fankhauser Melissa , Kubota Kristy , Huang Jennifer Y , Geissler Aimee , Payne Daniel C , Tack Danielle M 
Published: July 2022

Abstract

Background
Pathogen detection has changed with increased use of culture-independent diagnostic tests (CIDTs). CIDTs do not yield isolates, which are necessary to detect outbreaks using whole-genome sequencing. The Foodborne Diseases Active Surveillance Network (FoodNet) monitors clinical laboratory testing practices to improve interpretation of surveillance data and assess availability of isolates. We describe changes in practices over 8 years.

Methods
During 2012–2019, 10 FoodNet sites collected standardized data about practices in clinical laboratories (range, 664–723 laboratories) for select enteric pathogens. We assessed changes in practices.

Results
During 2012–2019, the percentage of laboratories that used only culture methods decreased, with the largest declines for Vibrio (99%–57%) and Yersinia (99%–60%). During 2019, the percentage of laboratories using only CIDTs was highest for Shiga toxin–producing Escherichia coli (43%), Campylobacter (34%), and Vibrio (34%). From 2015 to 2019, the percentage of laboratories that performed reflex culture after a positive CIDT decreased, with the largest declines for Shigella (75%–42%) and Salmonella (70%–38%). The percentage of laboratories that routinely submitted isolates to a public health laboratory decreased for all bacterial pathogens examined from 2015 to 2019.

Conclusions
By increasing use of CIDTs and decreasing reflex culture, clinical laboratories have transferred the burden of isolate recovery to public health laboratories. Until technologies allow for molecular subtyping directly from a patient specimen, state public health laboratories should consider updating enteric disease reporting requirements to include submission of isolates or specimens. Public health laboratories need resources for isolate recovery.
Prevalence of Histoplasmosis and Molecular Characterization of Histoplasma species in Patients with Presumptive Pulmonary Tuberculosis in Calabar, Nigeria
Authors: Ekeng Bassey E , Oladele Rita O , Emanghe Ubleni E , Ochang Ernest A , Mirabeau Tatfeng Y 
Published: July 2022

Abstract

Background
Several case reports abound in literature about cases of histoplasmosis misdiagnosed as tuberculosis (TB). Nigeria is one of the highest TB-burdened countries, but data on histoplasmosis in Nigeria are sparse in the literature. The aim of this research was to investigate patients with presumptive pulmonary TB in Calabar, Nigeria, for histoplasmosis.

Methods
This was a descriptive cross-sectional study of 213 participants with presumptive diagnosis of pulmonary TB between April 2020 and March 2021. Urine samples were collected from selected patients for Histoplasma antigen test using enzyme immunoassay kits, while sputum samples were collected for GeneXpert test for confirmed diagnosis of TB and conventional polymerase chain reaction (PCR) for the diagnosis of histoplasmosis.

Results
Of the 213 participants enrolled into the study, 94 subjects (44.1%) were confirmed TB patients, 75 (35.2%) were human immunodeficiency virus (HIV) positive, 41 (19.2%) had advanced HIV disease (AHD), and 138 (64.8%) were HIV negative. Twenty-seven of the 213 participants were Histoplasma positive by antigen test and/or PCR, giving an overall prevalence rate of 12.7%. The prevalence of histoplasmosis among confirmed TB patients (7.4% [7/94]) was significantly lower than in unconfirmed TB patients (16.8% [20/119]) (P = .04). Participants on anti-TB therapy also had a significantly lower rate of histoplasmosis compared to those not on anti-TB drugs (P = .00006). The internal transcribed spacer (ITS) sequencing of the Histoplasma revealed a closely relatedness to Histoplasma capsulatum.

Conclusions
Histoplasmosis is not uncommon among presumptive TB patients. There should be proper microbiological investigation of patients presenting with symptoms suggestive of TB to exclude cases of histoplasmosis.
Outcomes of Fungemia in Patients Receiving Extracorporeal Membrane Oxygenation
Authors: Rosas Melissa M , Sobieszczyk Michal J , Warren Whittney , Mason Phillip , Walter Robert J , Marcus Joseph E 
Published: July 2022

Abstract
There are limited data on the treatment of fungal infections complicating extracorporeal membrane oxygenation (ECMO). In 14 patients who developed fungal bloodstream infections on ECMO, 8 (57%) survived to discharge. Of the 5 patients completing treatment prior to decannulation, 2 (40%) developed recurrent fungal infections.
Understanding emergency placements for Nova Scotian children in foster care
Authors: Cameron Hannah , Holland Alyson , Wong Tania 
Published: July 2022

Abstract
To cope with a critical lack of foster families, Nova Scotia’s Department of Community Services uses rented private facilities staffed by subcontracted companies, known as “places of safety”. Similar models are used across the country, with places of safety intended to be used for emergency placements only. The mean length of stay in a place of safety was 255 nights in 2020. Male children are far overrepresented, as are Indigenous children. Despite the increasing use of places of safety, little is known about the impacts of these short-term and unhomelike environments. Previous research on placement disruption shows that placement change and multiple placements impact children’s health, mental health, and attachment behaviour. This paper presents data on the use of places of safety in Nova Scotia and synthesizes existing research on placement disruption to present advocacy priorities and directions for further research.
Transcription factor CmbHLH16 regulates petal anthocyanin homeostasis under different lights in Chrysanthemum
Authors: Zhou Li-Jie , Wang Yuxi , Wang Yiguang , Song Aiping , Jiang Jiafu , Chen Sumei , Ding Baoqing , Guan Zhiyong , Chen Fadi 
Published: July 2022

Abstract
Light is essential to plant survival and elicits a wide range of plant developmental and physiological responses under different light conditions. A low red-to-far red (R/FR) light ratio induces shade-avoidance responses, including decreased anthocyanin accumulation, whereas a high R/FR light ratio promotes anthocyanin biosynthesis. However, the detailed molecular mechanism underpinning how different R/FR light ratios regulate anthocyanin homeostasis remains elusive, especially in non-model species. Here, we demonstrate that a low R/FR light ratio induced the expression of CmMYB4, which suppressed the anthocyanin activator complex CmMYB6-CmbHLH2, leading to the reduction of anthocyanin accumulation in Chrysanthemum (Chrysanthemum morifolium) petals. Specifically, CmMYB4 recruited the corepressor CmTPL (TOPLESS) to directly bind the CmbHLH2 promoter and suppressed its transcription by impairing histone H3 acetylation. Moreover, the low R/FR light ratio inhibited the PHYTOCHROME INTERACTING FACTOR family transcription factor CmbHLH16, which can competitively bind to CmMYB4 and destabilize the CmMYB4–CmTPL protein complex. Under the high R/FR light ratio, CmbHLH16 was upregulated, which impeded the formation of the CmMYB4-CmTPL complex and released the suppression of CmbHLH2, thus promoting anthocyanin accumulation in Chrysanthemum petals. Our findings reveal a mechanism by which different R/FR light ratios fine-tune anthocyanin homeostasis in flower petals.
Cryocampsis: a biophysical freeze-bending response of shrubs and trees under snow loads
Authors: Ray Peter M , Bret-Harte M Syndonia 
Published: July 2022

Abstract
We report a biophysical mechanism, termed cryocampsis (Greek cryo-, cold, + campsis, bending), that helps northern shrubs bend downward under a snow load. Subfreezing temperatures substantially increase the downward bending of cantilever-loaded branches of these shrubs, while allowing them to recover their summer elevation after thawing and becoming unloaded. This is counterintuitive, because biological materials (including branches that show cryocampsis) generally become stiffer when frozen, so should flex less, rather than more, under a given bending load. Cryocampsis involves straining of the cell walls of a branch’s xylem (wood), and depends upon the branch being hydrated. Among woody species tested, cryocampsis occurs in almost all Arctic, some boreal, only a few temperate and Mediterranean, and no tropical woody species that we have tested. It helps cold-winter climate shrubs reversibly get, and stay, below the snow surface, sheltering them from winter weather and predation hazards. This should be advantageous, because Arctic shrub bud winter mortality significantly increases if their shoots are forcibly kept above the snow surface. Our observations reveal a physically surprising behavior of biological materials at subfreezing temperatures, and a previously unrecognized mechanism of woody plant adaptation to cold-winter climates. We suggest that cryocampsis’ mechanism involves the movement of water between cell wall matrix polymers and cell lumens during freezing, analogous to that of frost-heave in soils or rocks.
Toward tensor renormalization group study of three-dimensional non-Abelian gauge theory
Authors: Kuwahara Takaaki , Tsuchiya Asato 
Published: July 2022

Abstract
We propose a method to represent the path integral over gauge fields as a tensor network. We introduce a trial action with variational parameters and generate gauge field configurations with the weight defined by the trial action. We construct initial tensors with indices labelling these gauge field configurations. We perform the tensor renormalization group (TRG) with the initial tensors and optimize the variational parameters. As a first step to the TRG study of non-Abelian gauge theory in more than two dimensions, we apply this method to three-dimensional pure SU(2) gauge theory. Our result for the free energy agrees with the analytical results in the weak and strong coupling regimes.
CRYSTAL CONFIGURATION DEPENDENCE OF CSI(TL) SCINTILLATION DETECTORS ON ENVIRONMENTAL DOSE RATE MEASUREMENT
Authors: Tsuda S , Saito K 
Published: July 2022

Abstract
The crystal configuration dependence of thallium-doped caesium iodide (CsI(Tl)) scintillation detectors was analysed on an ambient dose equivalent (H*(10)). H*(10) were systematically calculated in various crystal conditions for aspect ratios and sizes in a virtual environment contaminated by radionuclides to investigate directional characteristics by comparing the H*(10)s with the typical irradiation geometries in anterior–posterior (AP), lateral (LAT), rotational (ROT) and isotropic (ISO). The simulation revealed that H*(10) obviously changes according to the crystal configuration and cuboidal CsI(Tl) scintillation detectors with specific aspect ratios could be applied to environmental dose rate measurement without further changes in the calibration procedure.
14Psychoanalysis
Authors: Vashisht Jivitesh 
Published: July 2022

Abstract
This chapter discusses four major works of scholarship—three monographs and an edited volume—from 2021 that stage fresh and highly topical encounters between psychoanalysis, politics, and aesthetics, with transformative consequences for each. It is organized into four sections: 1. Introduction: Psychoanalysis On and Off the Couch; 2. Reframing the Clinic (I): A Travelling Psychoanalysis for the Urban Poor, on Ankhi Mukherjee’s Unseen City: The Psychic Lives of the Urban Poor; 3. Reframing the Clinic (II): Cultural Objects and/as Psychic Objects, on Noreen Giffney’s The Culture-Breast in Psychoanalysis: Cultural Experiences and the Clinic; and finally, 4. Literature and Psychoanalysis: Whither Now?, on Naomi Wynter-Vincent’s Wilfred Bion and Literary Criticism and Vera J. Camden’s edited volume, The Cambridge Companion to Literature and Psychoanalysis.
Evaluation of Protein Extraction Methods for Metaproteomic Analyses of Root-Associated Microbes
Authors: Salvato Fernanda , Vintila Simina , Finkel Omri M. , Dangl Jeffery L. , Kleiner Manuel 
Published: July 2022

Metaproteomics is a powerful tool for the characterization of metabolism, physiology, and functional interactions in microbial communities, including plant-associated microbiota. However, the metaproteomic methods that have been used to study plant-associated microbiota are very laborious and require large amounts of plant tissue, hindering wider application of these methods. We optimized and evaluated different protein extraction methods for metaproteomics of plant-associated microbiota in two different plant species ( Arabidopsis and maize). Our main goal was to identify a method that would work with low amounts of input material (40 to 70 mg) and that would maximize the number of identified microbial proteins. We tested eight protocols, each comprising a different combination of physical lysis method, extraction buffer, and cell-enrichment method on roots from plants grown with synthetic microbial communities. We assessed the performance of the extraction protocols by liquid chromatography-tandem mass spectrometry–based metaproteomics and found that the optimal extraction method differed between the two species. For Arabidopsis roots, protein extraction by beating whole roots with small beads provided the greatest number of identified microbial proteins and improved the identification of proteins from gram-positive bacteria. For maize, vortexing root pieces in the presence of large glass beads yielded the greatest number of microbial proteins identified. Based on these data, we recommend the use of these two methods for metaproteomics with Arabidopsis and maize. Furthermore, detailed descriptions of the eight tested protocols will enable future optimization of protein extraction for metaproteomics in other dicot and monocot plants. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .