bluuebunny/crossref_metadata_2025_split huggingface dataset:
A complete census of circumgalactic Mg ii at redshift z ≲ 0.5
Authors: Huang Yun-Hsin , Chen Hsiao-Wen , Shectman Stephen A , Johnson Sean D , Zahedy Fakhri S , Helsby Jennifer E , Gauthier Jean-René , Thompson Ian B 
Published: February 2021

ABSTRACT
This paper presents a survey of Mg ii absorbing gas in the vicinity of 380 random galaxies, using 156 background quasi-stellar objects (QSOs) as absorption-line probes. The sample comprises 211 isolated (73 quiescent and 138 star-forming galaxies) and 43 non-isolated galaxies with sensitive constraints for both Mg ii absorption and H α emission. The projected distances span a range from d = 9 to 497 kpc, redshifts of the galaxies range from z = 0.10 to 0.48, and rest-frame absolute B-band magnitudes range from MB = −16.7 to −22.8. Our analysis shows that the rest-frame equivalent width of Mg ii, Wr(2796), depends on halo radius (Rh), B-band luminosity(LB), and stellar mass (Mstar) of the host galaxies, and declines steeply with increasing d for isolated, star-forming galaxies. At the same time, Wr(2796) exhibits no clear trend for either isolated, quiescent galaxies or non-isolated galaxies. In addition, the covering fraction of Mg ii absorbing gas 〈κ〉 is high with 〈κ〉 ≳ 60 per cent at &lt;40 kpc for isolated galaxies and declines rapidly to 〈κ〉 ≈ 0 at d ≳ 100 kpc. Within the gaseous radius, the incidence of Mg ii gas depends sensitively on both Mstar and the specific star formation rate inferred from H α. Different from what is known for massive quiescent haloes, the observed velocity dispersion of Mg ii absorbing gas around star-forming galaxies is consistent with expectations from virial motion, which constrains individual clump mass to $m_{\rm cl} \gtrsim 10^5 \, \rm M_\odot$ and cool gas accretion rate of $\sim 0.7\!-\!2 \, \mathrm{ M}_\odot \, \rm yr^{-1}$. Finally, we find no strong azimuthal dependence of Mg ii absorption for either star-forming or quiescent galaxies. Our results demonstrate that multiple parameters affect the properties of gaseous haloes around galaxies and highlight the need of a homogeneous, absorption-blind sample for establishing a holistic description of chemically enriched gas in the circumgalactic space.
On the origin of nitrogen at low metallicity
Authors: Roy Arpita , Dopita Michael A , Krumholz Mark R , Kewley Lisa J , Sutherland Ralph S , Heger Alexander 
Published: February 2021

ABSTRACT
Understanding the evolution of the N/O ratio in the interstellar medium (ISM) of galaxies is essential if we are to complete our picture of the chemical evolution of galaxies at high redshift, since most observational calibrations of O/H implicitly depend upon the intrinsic N/O ratio. The observed N/O ratio, however, shows large scatter at low O/H, and is strongly dependent on galactic environment. We show that several heretofore unexplained features of the N/O distribution at low O/H can be explained by the N seen in metal-poor galaxies being mostly primary nitrogen that is returned to the ISM via pre-supernova winds from rapidly rotating massive stars (M ≳ 10 M⊙, v/vcrit ≳ 0.4). This mechanism naturally produces the observed N/O plateau at low O/H. We show that the large scatter in N/O at low O/H also arises naturally from variations in star-formation efficiency. By contrast, models in which the N and O come primarily from supernovae provide a very poor fit to the observed abundance distribution. We propose that the peculiar abundance patterns we observe at low O/H are a signature that dwarf galaxies retain little of their SN ejecta, leaving them with abundance patterns typical of winds.
Regulation, Diversity and Evolution of Boron Transporters in Plants
Authors: Onuh Amarachukwu Faith , Miwa Kyoko 
Published: February 2021

AbstractBoron (B) is an essential trace element in plants, and borate cross-linking of pectic polysaccharide rhamnogalacturonan-II (RG-II) in cell walls is required for normal cell growth. High concentrations of B are toxic to cells. Therefore, plants need to control B transport to respond to B conditions in the environment. Over the past two decades, genetic analyses of Arabidopsis thaliana have revealed that B transport is governed by two types of membrane transport molecules: NIPs (nodulin-26-like intrinsic proteins), which facilitate boric acid permeation, and BORs, which export borate from cells. In this article, we review recent findings on the (i) regulation at the cell level, (ii) diversity among plant species and (iii) evolution of these B transporters in plants. We first describe the systems regulating these B transporters at the cell level, focusing on the molecular mechanisms underlying the polar localization of proteins and B-dependent expression, as well as their physiological significance in A. thaliana. Then, we examine the presence of homologous genes and characterize the functions of NIPs and BORs in B homeostasis, in a wide range of plant species, including Brassica napus, Oryza sativa and Zea mays. Finally, we discuss the evolutionary aspects of NIPs and BORs as B transporters, and the possible relationship between the diversification of B transport and the occurrence of RG-II in plants. This review considers the sophisticated systems of B transport that are conserved among various plant species, which were established to meet mineral nutrient requirements.
Observational study of adult respiratory infections in primary care clinics in Myanmar: understanding the burden of melioidosis, tuberculosis and other infections not covered by empirical treatment regimes
Authors: Warrell Clare E , Phyo Aung Pyae , Win Mo Mo , McLean Alistair R D , Watthanaworawit Wanitda , Swe Myo Maung Maung , Soe Kyaw , Lin Htet Naing , Aung Yee Yee , Ko Chitmin Ko , Waing Cho Zin , Linn Kaung San , Aung Yadanar Phoo Wai , Aung Ne Myo , Tun Ni Ni , Dance David A B , Smithuis Frank M , Ashley Elizabeth A 
Published: February 2021

Abstract

Background
Lower respiratory infections constitute a major disease burden worldwide. Treatment is usually empiric and targeted towards typical bacterial pathogens. Understanding the prevalence of pathogens not covered by empirical treatment is important to improve diagnostic and treatment algorithms.

Methods
A prospective observational study in peri-urban communities of Yangon, Myanmar was conducted between July 2018 and April 2019. Sputum specimens of 299 adults presenting with fever and productive cough were tested for Mycobacterium tuberculosis (microscopy and GeneXpert MTB/RIF [Mycobacterium tuberculosis/resistance to rifampicin]) and Burkholderia pseudomallei (Active Melioidosis Detect Lateral Flow Assay and culture). Nasopharyngeal swabs underwent respiratory virus (influenza A, B, respiratory syncytial virus) polymerase chain reaction testing.

Results
Among 299 patients, 32% (95% confidence interval [CI] 26 to 37) were diagnosed with tuberculosis (TB), including 9 rifampicin-resistant cases. TB patients presented with a longer duration of fever (median 14 d) and productive cough (median 30 d) than non-TB patients (median fever duration 6 d, cough 7 d). One case of melioidosis pneumonia was detected by rapid test and confirmed by culture. Respiratory viruses were detected in 16% (95% CI 12 to 21) of patients.

Conclusions
TB was very common in this population, suggesting that microscopy and GeneXpert MTB/RIF on all sputum samples should be routinely included in diagnostic algorithms for fever and cough. Melioidosis was uncommon in this population.
Paraburkholderia acidiphila sp. nov., Paraburkholderia acidisoli sp. nov. and Burkholderia guangdongensis sp. nov., isolated from forest soil, and reclassification of Burkholderia ultramafica as Paraburkholderia ultramafica comb. nov.
Authors: Gao Zeng-hong , Zhang Qiu-mei , Lv Ying-ying , Wang You-qi , Zhao Bing-nan , Qiu Li-hong 
Published: February 2021

Three Gram-stain-negative, aerobic, motile and rod-shaped bacterial strains, 7Q-K02T, DHF22T and DHOM02T, were isolated from forest soil sampled at Dinghushan Biosphere Reserve, Guangdong Province, China. Strains 7Q-K02T, DHF22T and DHOM02T grew at 4–37, 4–42 and 12–37 °C, pH 3.0–8.5, 3.5–8.5 and 5.0–8.0, and in the presence of 0–3.0, 0–3.5 and 0–2.5 % (w/v) NaCl; with optima at 28–33, 28 and 28–33 °C, pH 3.5–6.5, 4.0–5.5 and 6.5–7.0, and 0–1.5, 0–1.5 and 0.5–1.5 % (w/v) NaCl, respectively. Strains 7Q-K02T and DHF22T have the highest 16S rRNA gene sequence similarities of 99.0 and 98.0 % to

Paraburkholderia sacchari

LMG 19450T and 97.7 % between themselves, while strain DHOM02T shares the highest similarity of 98.4 % to ‘Burkholderia rinojensis’ A396T followed by 98.3 % to

Burkholderia plantarii

ATCC 43733T. In the 16S rRNA gene sequence phylogram, strain 7Q-K02T formed a sister branch with

Paraburkholderia sacchari

,

Paraburkholderia oxyphila

and

Paraburkholderia paradisi

, and strain DHF22T was separated from all other species within the genus

Paraburkholderia

, while strain DHOM02T formed a separated clade with members of the genus

Burkholderia

. The DNA G+C contents of strains 7Q-K02T, DHF22T and DHOM02T wwe 64.3, 65.4 and 66.6 %, respectively. Digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values of strains 7Q-K02T, DHF22T and closely related

Paraburkholderia

strains were in the ranges of 25.5–43.7 % and 81.5–91.3 %, respectively. While dDDH and ANI values between strain DHOM02T and

Burkholderia

strains with genome sequence data were in the ranges of 22.4–31.0 % and 78.2–86.1 %, respectively. These three strains have the same major respiratory quinone: ubiquinone-8. Strains 7Q-K02T, DHF22T and DHOM02T have C16 : 0, C17 : 0 cyclo, C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1
ω7c/C18 : 1
ω6c) as their major fatty acid compositions. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. On the basis of phenotypic, phylogenetic, genomic analyses and chemotaxonomic data, strains 7Q-K02T and DHF22T represent two novel species of the genus

Paraburkholderia

, for which the names Paraburkholderia acidiphila sp. nov. (type strain 7Q-K02T=CGMCC 1.15433T=KCTC 62472T=LMG 29209T) and Paraburkholderia acidisoli sp. nov. (type strain DHF22T=GDMCC 1.1448T=LMG 30262T) are proposed, while strain DHOM02T represents a novel species in the genus

Burkholderia

, for which the name Burkholderia guangdongensis sp. nov. (type strain DHOM02T=KCTC 42625T=LMG 28843T) is proposed. We also propose to transfer

Burkholderia ultramafica

to the genus

Paraburkholderia

as Paraburkholderia ultramafica comb. nov. based mainly on the results of phylogenomic analysis.
The effect of respiratory activity, ventilatory therapy and facemasks on total aerosol emissions
Authors: Wilson Nick M. , Marks Guy B. , Eckhardt Andrew , Clarke Alyssa , Young Francis , Garden Frances L. , Stewart Warren , Cook Tim M. , Tovey Euan R. 
Published: February 2021

AbstractBackgroundExhaled respirable aerosols (<5 µm diameter) present a high risk of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) transmission. Many guidelines recommend using aerosol precautions during ‘aerosol generating procedures’ (AGPs) and droplet (>5 µm) precautions at other times. However, there is emerging evidence that respiratory activities such as cough and not AGPs are the important source of aerosols.MethodsWe used a novel chamber with an optical particle counter sampling at 100 L/min to count and size-fractionate all exhaled particles (0.5-25 µm). We compared emissions from ten healthy subjects during respiratory ‘activities’ (quiet breathing, talking, shouting, forced expiratory maneuvers, exercise and coughing) with respiratory ‘therapies’ designated as AGPs: high flow nasal oxygen (HFNO) and single or dual circuit non-invasive positive pressure ventilation, NIPPV-S and NIPPV-D, respectively. Activities were repeated wearing facemasks.ResultsCompared to quiet breathing, respiratory activities increased particle counts between 34.6-fold (95% confidence interval [CI], 15.2 to 79.1) during talking, to 370.8-fold (95% CI, 162.3 to 847.1) during coughing (p<0.001). During quiet breathing, HFNO at 60 L/min increased counts 2.3-fold (95% CI, 1.2 to 4.4) (p=0.03) and NIPPV-S and NIPPV-D at 25/10 cm H2O increased counts by 2.6-fold (95% CI, 1.7 to 4.1) and 7.8-fold (95% CI, 4.4 to 13.6) respectively (p<0.001). During activities, respiratory therapies and facemasks reduced emissions compared to activities alone.ConclusionTalking, exertional breathing and coughing generate substantially more aerosols than the respiratory therapies HFNO and NIPPV which can reduce total emissions. The risk of aerosol exposure is underappreciated and warrants widespread targeted interventions.
Extracellular vesicles induce aggressive phenotype of luminal breast cancer cells by PKM2 phosphorylation
Authors: Kang Seo Young , Lee Eun Ji , Byun Jung Woo , Han Dohyun , Choi Yoori , Hwang Do Won , Lee Dong Soo 
Published: February 2021

AbstractThe aerobic glycolysis is a hallmark of cancer glucose metabolism. Several studies have suggested that cancer-derived extracellular vesicles (EVs) can modulate glucose metabolism in adjacent cells and promote disease progression. Here we suggest that EVs originated from cancer cell with highly glycolytic activity can modulate glucose metabolism in the recipient cancer cells with relative low glycolytic activity, and further induce cell proliferation. Two types of breast cancer cell lines with different levels of glycolytic activity, MDA-MB-231 of a claudin low-type breast cancer cell and MCF7 of luminal type breast cancer cell, were selected and co-cultured using indirect co-culture system such as transwell system or microfluidic system. Glucose uptake of the recipient MCF7 cells was markedly increased after co-culture with MDA-MB-231 cells. MCF7 cells after co-culture with MDA-MB-231-tdTomato cells represented multiple tdTomato signal inside the cell, which proved that EVs originated from MDA-MB-231-tdTomato were transferred to MCF7 cell. In addition, serine phosphorylation of PKM2 necessary for tumorigenesis was highly activated, and tyrosine phosphorylation of PKM2 suggesting activated aerobic glycolysis was also increased in the co-cultured MCF7 cells. Proteomic profiling of the co-cultured MCF7 cells revealed the proliferation and dedifferentiation of MCF7 cells, and further confirmed epithelial-mesenchymal transition (EMT), which is a key phenomenon for cancer metastasis. In the transcriptomic analysis, glycolysis increased in co-cultured MCF7 cells, and the component analysis of genes associated with glycolysis revealed that the next major component after cytoplasm was extracellular exosome. Proteomic analysis of EVs revealed that there were important proteins in the EV such as EGFR, ERBB2 and MAPK for phosphorylating PKM2. This phenomenon suggests the potential for aggressive cancer cells to affect other cancer cells through EV mediators.
Avoiding Data Loss: Synthetic MRIs Generated from Diffusion Imaging Can Replace Corrupted Structural Acquisitions For Freesurfer-Seeded Tractography
Authors: Beaumont Jeremy , Gambarota Giulio , Prior Marita , Fripp Jurgen , Reid Lee B. 
Published: February 2021

1AbstractMagnetic Resonance Imaging (MRI) motion artefacts frequently complicate structural and diffusion MRI analyses. While diffusion imaging is easily ‘scrubbed’ of motion affected volumes, the same is not true for structural images. Structural images are critical to most diffusion-imaging pipelines thus their corruption can lead to disproportionate data loss. To enable diffusion-image processing when structural images have been corrupted, we propose a means by which synthetic structural images can be generated from diffusion MRI. This technique combines multi-tissue constrained spherical deconvolution, which is central to many existing diffusion analyses, with the Bloch equations which allow simulation of MRI intensities given scanner parameters and magnetic resonance (MR) tissue properties. We applied this technique to 32 scans, including those acquired on different scanners, with different protocols and with pathology present. The resulting synthetic T1w and T2w images were visually convincing and exhibited similar tissue contrast to acquired structural images. These were also of sufficient quality to drive a Freesurfer-based tractographic analysis. In this analysis, probabilistic tractography connecting the thalamus to the primary sensorimotor cortex was delineated with Freesurfer, using either real or synthetic structural images. Tractography for real and synthetic conditions was largely identical in terms of both voxels encountered (Dice 0.88 – 0.95) and mean fractional anisotropy (intrasubject absolute difference 0.00 – 0.02). We provide executables for the proposed technique in the hope that these may aid the community in analysing datasets where structural image corruption is common, such as studies of children or cognitively impaired persons.HighlightsWe propose a simple means of synthesizing T1w and T2w images from diffusion dataThe proposed method worked well for a variety of acquisitionsSynthetic images showed tissue contrast akin to acquired imagesSynthetic images were high enough quality to be used for Freesurfer seeded diffusion tractographyThis method enables analysis of datasets where motion has corrupted acquired structural MRIs
Mitochondriomics reveals the underlying neuoprotective mechanism of TrkB receptor agonist R13 in the 5×FAD mice
Authors: Li Xiao , Li Ting , Yu Hao , Li Shupeng , Zhang Zaijun , Xie Yongmei , Song Xiangrong , Liu Jianjun , Yang Xifei , Liu Gongping 
Published: February 2021

AbstractDecreased energy metabolism and mitochondrial biogenesis defects are implicated in the pathogenesis of Alzheimer’s disease (AD). In present study, mitochondriomics analysis revealed significant effects of R13, a prodrug of 7,8-dihydroxyflavone, on mitochondrial protein expression profile, including the proteins related to the biological processes: fatty acid beta-oxidation, fatty acid metabolic process, mitochondrial electron transport, and mitochondrial respiratory chain. Cluster analysis of mitochondriomics demonstrated that R13 promoted mitochondrial oxidative phosphorylation (OXPHOS). The functional analysis showed that R13 increased ATP levels and enhanced OXPHOS including complex I, complex II, complex III and complex IV. R13 treatment increased mitochondrial biogenesis by regulating the levels of p-AMPKα, p-CREB, PGC-1α, NRF1 and TFAM as a consequence of activation of TrkB receptor in the 5×FAD mice. Finally, R13 significantly reduced the levels of tau phosphorylation and Aβ plaque. Our data suggest that R13 may be used for treating AD via enhancing mitochondrial biogenesis and metabolism.
Visualizing endogenous RhoA activity with an improved localization-based, genetically encoded biosensor
Authors: Mahlandt Eike K. , Arts Janine J. G. , van der Meer Werner J. , van der Linden Franka H. , Tol Simon , van Buul Jaap D. , Gadella Theodorus W. J. , Goedhart Joachim 
Published: February 2021

AbstractRho GTPases are regulatory proteins, which orchestrate cell features such as morphology, polarity and movement. Therefore, probing Rho GTPase activity is key to understanding processes such as development, cell migration and wound healing. Localization-based reporters for active Rho GTPases are attractive probes to study Rho GTPase-mediated processes, in real time with subcellular resolution in living cells and tissue. Until now, relocation RhoA biosensors seem to only be useful in certain organisms and have not been characterized well. In this paper, we systematically examined the contribution of the fluorescent protein and RhoA binding peptides, on the performance of localization-based sensors. To test the performance, we compared relocation efficiency and specificity in cell-based assays. We identified several improved localization-based, genetically encoded, fluorescent biosensors for detecting endogenous RhoA activity. This enables a broader application of RhoA relocation biosensors, which was demonstrated by using the improved biosensor to visualize RhoA activity, during cell division, during random migration, at the Golgi membrane and induced by G protein-coupled receptor signaling. Due to the improved avidity of the new biosensors for RhoA activity, cellular processes regulated by RhoA can be better understood.Abstract Figure
Expanded Genomic Sampling of the Desulfobulbales Reveals Distribution and Evolution of Sulfur Metabolisms
Authors: Ward Lewis M. , Bertran Emma , Johnston David T. 
Published: February 2021

AbstractThe reconstruction of modern and paleo-sulfur cycling relies on understanding the long-term relative contribution of its main actors; these include microbial sulfate reduction (MSR) and microbial sulfur disproportionation (MSD). However, a unifying theory is lacking for how MSR and MSD, with the same enzyme machinery and intimately linked evolutionary histories, perform two drastically different metabolisms. Here, we aim at shedding some light on the distribution, diversity, and evolutionary histories of MSR and MSD, with a focus on the Desulfobulbales as a test case. The Desulfobulbales is a diverse and widespread order of bacteria in the Desulfobacterota (formerly Deltaproteobacteria) phylum primarily composed of sulfate reducing bacteria. Recent culture- and sequence-based approaches have revealed an expanded diversity of organisms and metabolisms within this clade, including the presence of obligate and facultative sulfur disproportionators. Here, we present draft genomes of previously unsequenced species of Desulfobulbales, substantially expanding the available genomic diversity of this clade. We leverage this expanded genomic sampling to perform phylogenetic analyses, revealing an evolutionary history defined by vertical inheritance of sulfur metabolism genes with numerous convergent instances of transition from sulfate reduction to sulfur disproportionation.
Modeling and algorithm for resource-constrained multi-project scheduling problem based on detection and rework
Authors: Zhu Hongwei , Lu Zhiqiang , Lu Chenyao , Ren Yifei 
Published: February 2021

Purpose
To meet the requirement of establishing an effective schedule for the assembly process with overall detection and rework, this paper aims to address a new problem named resource-constrained multi-project scheduling problem based on detection and rework (RCMPSP-DR).

Design/methodology/approach
First, to satisfy both online and offline scheduling, a mixed integer programming model is established with a weighted bi-objective minimizing the expected makespan and the solution robustness. Second, an algorithm that combines a tabu search framework with a critical chain-based baseline generation scheme is designed. The tabu search framework focuses on searching for a reasonable resource flow representing the execution sequence of activities, while the critical chain-based baseline generation scheme establishes a buffered baseline schedule by estimating the tradeoff between two aspects of bi-objective.

Findings
The proposed algorithm can get solutions with gaps from −4.45% to 2.33% when compared with those obtained by the commercial MIP solver CPLEX. Moreover, the algorithm outperforms four other algorithms in terms of both objective performance and stability over instances with different weighting parameters, which reveals its effectiveness.

Originality/value
The represented RCMPSP-DR considering the overall detection and rework is an extension of the scheduling problem for large-scale equipment. An effective algorithm is proposed to establish the baseline schedule and determine the execution sequence of activities for the assembly process, which is significant for practical engineering applications.