bluuebunny/crossref_metadata_2025_split huggingface dataset:
A native conjugative plasmid confers potential selective advantages to plant growth-promoting Bacillus velezensis strain GH1-13
Authors: Choi Yunhee , Pham Ha , Nguyen Mai Phuong , Tran Le Viet Ha , Kim Jueun , Kim Songhwa , Lee Chul Won , Song Jaekyeong , Kim Yong-Hak 
Published: May 2021

AbstractThe conjugative plasmid (pBV71) possibly confers a selective advantage to Bacillus velezensis strain GH1-13, although a selective marker gene is yet to be identified. Here we show that few non-mucoid wild-type GH1-13 cells are spontaneously converted to mucoid variants with or without the loss of pBV71. Mucoid phenotypes, which contain or lack the plasmid, become sensitive to bacitracin, gramicidin, selenite, and tellurite. Using the differences in antibiotic resistance and phenotype, we isolated a reverse complement (COM) and a transconjugant of strain FZB42 with the native pBV71. Transformed COM and FZB42p cells were similar to the wild-type strain GH1-13 with high antibiotic resistance and slow growth rates on lactose compared to those of mucoid phenotypes. RT-PCR analysis revealed that the expression of plasmid-encoded orphan aspartate phosphatase (pRapD) was coordinated with a new quorum-sensing (QS) cassette of RapF2–PhrF2 present in the chromosome of strain GH1-13, but not in strain FZB42. Multi-omics analysis on wild-type and plasmid-cured cells of strain GH1-13 suggested that the conjugative plasmid expression has a crucial role in induction of early envelope stress response that promotes cell morphogenesis, biofilm formation, catabolite repression, and biosynthesis of extracellular-matrix components and antibiotics for protection of host cell during exponential phase.
Specification of oxytocinergic and vasopressinergic circuits in the developing mouse brain
Authors: Madrigal María Pilar , Jurado Sandra 
Published: May 2021

AbstractOxytocin (OXT) and arginine vasopressin (AVP) support a broad range of behaviors and homeostatic functions including sex-specific and context-appropriate social behaviors. Although the alterations of these systems have been linked with social-related disorders such as autism spectrum disorder, their formation and developmental dynamics remain largely unknown. Using novel brain clearing techniques and 3D imaging, we have reconstructed the specification of oxytocinergic and vasopressinergic circuits in the developing mouse brain with unprecedented cellular resolution. A systematic quantification indicates that OXT and AVP neurons in the hypothalamus display distinctive developmental dynamics and high cellular plasticity from embryonic to early postnatal stages. Our findings reveal new insights into the specification and consolidation of neuropeptidergic systems in the developing CNS.
PD-L2 suppresses T cell signaling via coinhibitory microcluster formation and SHP2 phosphatase recruitment
Authors: Takehara Tomohiro , Wakamatsu Ei , Machiyama Hiroaki , Nishi Wataru , Emoto Katsura , Azuma Miyuki , Soejima Kenzo , Fukunaga Koichi , Yokosuka Tadashi 
Published: May 2021

AbstractThe coinhibitory receptor, PD-1, is of major importance for the suppression of T cell activation in various types of immune responses. A high-resolution imaging study showed that PD-1 forms a coinhibitory signalosome, “PD-1 microcluster”, with the phosphatase, SHP2, to dephosphorylate the TCR/CD3 complex and its downstream signaling molecules. Such a consecutive reaction entirely depended on PD-1–PD-L1/2 binding. PD-L2 is expressed on professional antigen-presenting cells and also on some tumor cells, which possibly explains the discrepant efficacy of immune checkpoint therapy for PD-L1-negative tumors. Here, we performed precise imaging analysis of PD-L2 forming PD-1–PD-L2 clusters associating with SHP2. PD-L2 could compete with PD-L1 for binding to PD-1, occupying the same space at TCR microclusters. The PD-1 microcluster formation was inhibited by certain mAbs with functional consequences. Thus, PD-1 microcluster formation provides a visible index for the effectiveness of anti-PD-1- or anti-PD-L1/2-mediated T cell suppression. PD-L2 may exert immune suppressive responses cooperatively with PD-L1 on the microcluster scale.
Functionalized Au15 nanoclusters as luminescent probes for protein carbonylation detection
Authors: Combes Guillaume F. , Fakhouri Hussein , Moulin Christophe , Girod Marion , Bertorelle Franck , Basu Srestha , Ladouce Romain , Bakulić Martina Perić , Maršić Željka Sanader , Russier-Antoine Isabelle , Brevet Pierre-François , Dugourd Philippe , Krisko Anita , Trajković Katarina , Radman Miroslav , Bonačić-Koutecký Vlasta , Antoine Rodolphe 
Published: May 2021

AbstractAtomically precise, ligand-protected gold nanoclusters (AuNCs) attract considerable attention as contrast agents in the biosensing field. However, the control of their optical properties and functionalization of surface ligands remain challenging. Here we report a strategy to tailor AuNCs for the precise detection of protein carbonylation—a causal biomarker of ageing. We produce Au15SG13 (SG for glutathione) with atomic precision and functionalize it with a thiolated aminooxy moiety to impart protein carbonyl-binding properties. Mass spectrometry and molecular modelling reveal the key structural features of Au15SG12-Aminooxy and its reactivity towards carbonyls. Finally, we demonstrate that Au15SG12-Aminooxy detects protein carbonylation in gel-based 1D electrophoresis by one- and two-photon excited fluorescence. Importantly, to our knowledge, this is the first application of an AuNC that detects a post-translational modification as a nonlinear optical probe. The significance of post-translational modifications in life sciences may open avenues for the use of Au15SG13 and other nanoclusters as contrast agents with tailored surface functionalization and optical properties.
1D charge density wave in the hidden order state of URu2Si2
Authors: Herrera Edwin , Barrena Víctor , Guillamón Isabel , Galvis José Augusto , Herrera William J. , Castilla José , Aoki Dai , Flouquet Jacques , Suderow Hermann 
Published: May 2021

AbstractSingle crystals of URu2Si2 show below 17.5 K a transition into an ordered state with a significantly reduced entropy. The low temperature phase is called the hidden order (HO) state, because its microscopic origin is still unknown—there are no charge, structural or magnetic transitions associated to HO. Here we report a one-dimensional (1D) charge modulation within the HO state of URu2Si2. We perform detailed Scanning Tunneling Microscopy (STM) experiments with high resolution on many atomically flat surfaces of URu2Si2 obtained by fracturing single crystals at cryogenic temperatures and find a 1D charge density wave with a large wavevector. We show that the 1D modulation is connected to the dynamical magnetic excitations of the HO through a moiré construction and appears as a consequence of excitations quenched through the interaction between the travelling fracture front and the dynamic modes of the crystal. The combination of fracture dynamics and the dynamics of the solid provides a method to create ground states and shows that charge interactions are among the most relevant features competing with HO in URu2Si2.
Chemical transport models often underestimate inorganic aerosol acidity in remote regions of the atmosphere
Authors: Nault Benjamin A. , Campuzano-Jost Pedro , Day Douglas A. , Jo Duseong S. , Schroder Jason C. , Allen Hannah M. , Bahreini Roya , Bian Huisheng , Blake Donald R. , Chin Mian , Clegg Simon L. , Colarco Peter R. , Crounse John D. , Cubison Michael J. , DeCarlo Peter F. , Dibb Jack E. , Diskin Glenn S. , Hodzic Alma , Hu Weiwei , Katich Joseph M. , Kim Michelle J. , Kodros John K. , Kupc Agnieszka , Lopez-Hilfiker Felipe D. , Marais Eloise A. , Middlebrook Ann M. , Andrew Neuman J. , Nowak John B. , Palm Brett B. , Paulot Fabien , Pierce Jeffrey R. , Schill Gregory P. , Scheuer Eric , Thornton Joel A. , Tsigaridis Kostas , Wennberg Paul O. , Williamson Christina J. , Jimenez Jose L. 
Published: May 2021

AbstractThe inorganic fraction of fine particles affects numerous physicochemical processes in the atmosphere. However, there is large uncertainty in its burden and composition due to limited global measurements. Here, we present observations from eleven different aircraft campaigns from around the globe and investigate how aerosol pH and ammonium balance change from polluted to remote regions, such as over the oceans. Both parameters show increasing acidity with remoteness, at all altitudes, with pH decreasing from about 3 to about −1 and ammonium balance decreasing from almost 1 to nearly 0. We compare these observations against nine widely used chemical transport models and find that the simulations show more scatter (generally R2 < 0.50) and typically predict less acidic aerosol in the most remote regions. These differences in observations and predictions are likely to result in underestimating the model-predicted direct radiative cooling effect for sulfate, nitrate, and ammonium aerosol by 15–39%.
Early Observation of Red Flags in 12-Month-Old Infant Siblings Later Diagnosed With Autism Spectrum Disorder
Authors: Pileggi Moira L. , Brane Natalie , Bradshaw Jessica , Delehanty Abigail , Day Taylor , McCracken Courtney , Stapel-Wax Jennifer , Wetherby Amy M. 
Published: May 2021

PurposeValid and reliable screening tools are needed to improve early detection and optimize developmental outcomes for toddlers at risk for autism spectrum disorder (ASD). The current study aimed to evaluate the utility of the Systematic Observation of Red Flags (SORF) for ASD at 12 months of age in a sample of high-risk infant siblings of children with ASD.MethodAs part of a prospective, longitudinal study, we examined the sensitivity and specificity of the SORF at 12 months for predicting a diagnosis of ASD at 24 months in a sample of 122 infants, 31 of whom were diagnosed with ASD.ResultsThe optimal SORF Composite cutoff score of 18 correctly identified 24 of the 31 twelve-month-olds who were diagnosed with ASD, yielding a sensitivity of .77 and a specificity of .76. The optimal SORF Red Flags cutoff score of 7 correctly identified 20 of the 31 infants, yielding a sensitivity of .65 and a specificity of .75.ConclusionThis preliminary study demonstrates the potential of the SORF as an effective observational screening measure for 12-month-olds at risk for ASD with good discrimination, sensitivity, and specificity.
How to Assess Proximal Femoral Shortening after Nailing of Proximal Femoral Fractures? A Short Review
Authors: Khalifa Ahmed A. , Khaled Mohammed , El-Hawary Ahmed S. , Ahmed Ahmed M. 
Published: May 2021

AbstractProximal femoral fractures (PFFs) are considered one of the most frequent situations faced by orthopaedic surgeons. Many lines of management had been described. Although management of PFFs with cephalomedullary nails (CMNs) is now considered the gold standard with many mechanical and biological advantages, this technique may have some disadvantages such as residual peritrochanteric pain, limping, limited walking distance, and difficulty with stairs. These complications may be attributed to fracture malreduction with shortening, which may result in either malunion or nonunion and ultimately implant failure. The resultant proximal femoral shortening (PFS) with alteration of the proximal femoral mechanics may affect both the hip abductor function and the daily patient activities. The purpose of this short review is to discuss the assessment and secondary effects of PFS after treating femoral fractures with CMNs.
Public attitudes towards algorithmic personalization and use of personal data online: evidence from Germany, Great Britain, and the United States
Authors: Kozyreva Anastasia , Lorenz-Spreen Philipp , Hertwig Ralph , Lewandowsky Stephan , Herzog Stefan M. 
Published: May 2021

AbstractPeople rely on data-driven AI technologies nearly every time they go online, whether they are shopping, scrolling through news feeds, or looking for entertainment. Yet despite their ubiquity, personalization algorithms and the associated large-scale collection of personal data have largely escaped public scrutiny. Policy makers who wish to introduce regulations that respect people’s attitudes towards privacy and algorithmic personalization on the Internet would greatly benefit from knowing how people perceive personalization and personal data collection. To contribute to an empirical foundation for this knowledge, we surveyed public attitudes towards key aspects of algorithmic personalization and people’s data privacy concerns and behavior using representative online samples in Germany (N = 1065), Great Britain (N = 1092), and the United States (N = 1059). Our findings show that people object to the collection and use of sensitive personal information and to the personalization of political campaigning and, in Germany and Great Britain, to the personalization of news sources. Encouragingly, attitudes are independent of political preferences: People across the political spectrum share the same concerns about their data privacy and show similar levels of acceptance regarding personalized digital services and the use of private data for personalization. We also found an acceptability gap: People are more accepting of personalized services than of the collection of personal data and information required for these services. A large majority of respondents rated, on average, personalized services as more acceptable than the collection of personal information or data. The acceptability gap can be observed at both the aggregate and the individual level. Across countries, between 64% and 75% of respondents showed an acceptability gap. Our findings suggest a need for transparent algorithmic personalization that minimizes use of personal data, respects people’s preferences on personalization, is easy to adjust, and does not extend to political advertising.
Isolating and enhancing single-photon emitters for 1550 nm quantum light sources using double nanohole optical tweezers
Authors: Sharifi Zohreh , Dobinson Michael , Hajisalem Ghazal , Shariatdoust Mirali Seyed , Frencken Adriaan L. , van Veggel Frank C. J. M. , Gordon Reuven 
Published: May 2021

Single-photon sources are required for quantum technologies and can be created from individual atoms and atom-like defects. Erbium ions produce single photons at low-loss fiber optic wavelengths, but they have low emission rates, making them challenging to isolate reliably. Here, we tune the size of gold double nanoholes (DNHs) to enhance the emission of single erbium emitters, achieving 50× enhancement over rectangular apertures previously demonstrated. This produces enough enhancement to show emission from single nanocrystals at wavelengths not seen in our previous work, i.e., 400 and 1550 nm. We observe discrete levels of emission for nanocrystals with low numbers of emitters and demonstrate isolating single emitters. We describe how the trapping time is proportional to the enhancement factor for a given DNH structure, giving us an independent way to measure the enhancement. This shows a promising path to achieving single emitter sources at 1550 nm.
Fully redundant auxiliary system for gyrotron-based terahertz sources in long-term operation
Authors: Wang Zhenglei , Zhang Jingwen , Sun Xianfeng , Wang Pengbo , Xiao Houxiu , Ding Tonghai , Xie Jianfeng , Han Xiaotao 
Published: May 2021

The Wuhan National High Magnetic Field Center is incorporating the flat-top pulsed magnetic field (FTPMF) into pulse gyrotrons. It will be the first chance to make a pulse-magnet gyrotron available for generating a long-pulse radiation of 100 ms or above without affecting its high operating frequency and high radiation power. However, unlike continuous wave gyrotrons, pulse gyrotrons in long-term operation have their own challenges, namely, misalignment caused by concussions, much stronger low-frequency electromagnetic interference from the pulse magnet, and inevitable explosion. This article will focus on the difficulties faced by pulse gyrotrons in years of operation, discuss the protection and restoration from failures, and, consequently, propose a fully redundant, explosion-proof, and quickly recoverable auxiliary system for long-term operation of pulse gyrotrons. This system integrates the control unit of traditional pulsed magnets and superconducting magnets so that it can be compatible with any form of gyrotron facilities. Therefore, once the FTPMF or the superconducting magnet is available, the long-pulse radiation will be obtained. Several experimental results, including the most recent explosion, show the reliability of the proposed system.
100-My history of bornavirus infections hidden in vertebrate genomes
Authors: Kawasaki Junna , Kojima Shohei , Mukai Yahiro , Tomonaga Keizo , Horie Masayuki 
Published: May 2021

Significance
Many viral diseases have emerged in recent decades, but prehistoric viral infections remain poorly understood. In some cases, nucleotide sequences of ancient viruses, which infected ancestral animals, have been integrated into their genomes during evolution. Such “molecular fossil records” of viruses help researchers trace past viral infections. Here, we reconstructed the infection history of an RNA virus, the bornavirus, for approximately 100 My in vertebrate evolution, using molecular fossils of ancient bornaviruses. Our analyses using ancient bornaviral sequences from over 100 vertebrate species genomes indicated that bornaviruses infected a broader range of host lineages during their long-term evolution than expected from extant bornaviral host ranges. Our findings highlighted the hidden history of this RNA viral infection over geological timescales.
Echinochloa pyramidalis.
Authors: Parker Chris 
Published: May 2021

Abstract

E. pyramidalis, a perennial grass, has decidedly invasive characteristics with its vigorous shoot and rhizome growth and abundant seed production. As an aquatic, it also has the potential to be very damaging to sensitive aquatic habitats. Holm et al. (1979) record it as a major weed in its native area in Nigeria, Swaziland, Sudan and Madagascar. In Guyana, after being introduced and cultivated for some years, it was noticed as a weed in sugar cane in 1982 and increased rapidly to become one of the most troublesome weeds in the aquatic system of the Guyana Sugar Corporation (Bishundial et al., 1997). In Mexico, again after introduction as a fodder grass, it has become widely invasive in wetlands, tending to reduce native wetland species (López Rosas et al., 2010). Apart from its competitive growth, Wells et al. (1986) note its tendency to obstruct water flow. For the USA it is highly ranked as a potential invasive weed of the future (Parker et al., 2007) and it has been identified as a species 'not authorized (for introduction) pending pest risk analysis' (NAPPRA) (USDA-APHIS, 2012).
Structure of disordered materials under ambient to extreme conditions revealed by synchrotron x-ray diffraction techniques at SPring-8—recent instrumentation and synergic collaboration with modelling and topological analyses
Authors: Ohara Koji , Onodera Yohei , Murakami Motohiko , Kohara Shinji 
Published: May 2021

Abstract
The structure of disordered materials is still not well understood because of insufficient experimental data. Indeed, diffraction patterns from disordered materials are very broad and can be described only in pairwise correlations because of the absence of translational symmetry. Brilliant hard x-rays from third-generation synchrotron radiation sources enable us to obtain high-quality diffraction data for disordered materials from ambient to high temperature and high pressure, which has significantly improved our grasp of the nature of order in disordered materials. Here, we introduce the progress in the instrumentation for hard x-ray beamlines at SPring-8 over the last 20 years with associated results and advanced data analysis techniques to understand the topology in disordered materials.
A generative adversarial network (GAN)-based technique for synthesizing realistic respiratory motion in the extended cardiac-torso (XCAT) phantoms
Authors: Chang Yushi , Jiang Zhuoran , Segars William Paul , Zhang Zeyu , Lafata Kyle , Cai Jing , Yin Fang-Fang , Ren Lei 
Published: May 2021

Abstract

Objective. Synthesize realistic and controllable respiratory motions in the extended cardiac-torso (XCAT) phantoms by developing a generative adversarial network (GAN)-based deep learning technique. Methods. A motion generation model was developed using bicycle-GAN with a novel 4D generator. Input with the end-of-inhale (EOI) phase images and a Gaussian perturbation, the model generates inter-phase deformable-vector-fields (DVFs), which were composed and applied to the input to generate 4D images. The model was trained and validated using 71 4D-CT images from lung cancer patients and then applied to the XCAT EOI images to generate 4D-XCAT with realistic respiratory motions. A separate respiratory motion amplitude control model was built using decision tree regression to predict the input perturbation needed for a specific motion amplitude, and this model was developed using 300 4D-XCAT generated from 6 XCAT phantom sizes with 50 different perturbations for each size. In both patient and phantom studies, Dice coefficients for lungs and lung volume variation during respiration were compared between the simulated images and reference images. The generated DVF was evaluated by deformation energy. DVFs and ventilation maps of the simulated 4D-CT were compared with the reference 4D-CTs using cross correlation and Spearman’s correlation. Comparison of DVFs and ventilation maps among the original 4D-XCAT, the generated 4D-XCAT, and reference patient 4D-CTs were made to show the improvement of motion realism by the model. The amplitude control error was calculated. Results. Comparing the simulated and reference 4D-CTs, the maximum deviation of lung volume during respiration was 5.8%, and the Dice coefficient reached at least 0.95 for lungs. The generated DVFs presented comparable deformation energy levels. The cross correlation of DVFs achieved 0.89 ± 0.10/0.86 ± 0.12/0.95 ± 0.04 along the x/y/z direction in the testing group. The cross correlation of ventilation maps derived achieved 0.80 ± 0.05/0.67 ± 0.09/0.68 ± 0.13, and the Spearman’s correlation achieved 0.70 ± 0.05/0, 60 ± 0.09/0.53 ± 0.01, respectively, in the training/validation/testing groups. The generated 4D-XCAT phantoms presented similar deformation energy as patient data while maintained the lung volumes of the original XCAT phantom (Dice = 0.95, maximum lung volume variation = 4%). The motion amplitude control models controlled the motion amplitude control error to be less than 0.5 mm. Conclusions. The results demonstrated the feasibility of synthesizing realistic controllable respiratory motion in the XCAT phantom using the proposed method. This crucial development enhances the value of XCAT phantoms for various 4D imaging and therapy studies.