bluuebunny/crossref_metadata_2025_split huggingface dataset:
In situ transmission electron microscopy study of the formation and migration of vacancy defects in atomically thin black phosphorus
Authors: Yao Fenfa , Cai Yongqing , Xiao Zhangru , Zhang Gang , Xie Rong-Jun , Jin Chuanhong 
Published: November 2020

Abstract
Structural defects play an important role in the optimization of material structures and properties, especially in low-dimensional systems such as two-dimensional (2D) materials. In this work, we investigated the formation, aggregation, and diffusion of vacancy defects in atomically thin black phosphorus (BP) via in situ high-resolution transmission electron microscopy. Vacancy defects including di-vacancies (DVs), vacancy clusters (e.g. tetra-vacancy and TV), and vacancy lines were confirmed as the primary forms of structural defects in BP. DV and TV defects were found to be highly mobile. The defects preferentially diffused and migrated along the diagonal and in a zigzag pattern (rather than an armchair pattern). After prolonged thermal excitation and electron-beam irradiation, all these as-formed vacancies tended to aggregate and line up parallel to the zigzag pattern direction to form extended vacancy lines with a total length reaching hundreds of nanometers or even the micrometer scale. Ab initio calculations were conducted to reveal the vacancy migration pathway, energy landscape, and modifications to the electronic structure of the host BP monolayers (MLs). It was found that the migration of a 5-8-5 DV was accomplished via sequential structural transformations including several transitions and intermediate configurations, such as 5-7-7-5 DVs. The associated migration barriers were determined as 2.1 eV for diagonal migration and 2.6 eV along the zigzag path, respectively. Calculations further confirmed that the presence of vacancy defects induced considerable electronic structure modification of the host ML-BP; for example, the bandgap was reduced from 0.9 eV (for defect-free ML-BP) to 0.7 eV in the presence of vacancy lines with a concentration of 1.2 at.%. The present study expands the current understanding of the formation and dynamic behaviors of primary vacancy defects and illustrates methods available to alter the electronic structures of 2D BP materials. It can further serve as a guideline for the function-oriented design and fabrication of BP-based devices via precisely controlled defect engineering.
Acousto-optic systems for advanced microscopy
Authors: Duocastella Martí , Surdo Salvatore , Zunino Alessandro , Diaspro Alberto , Saggau Peter 
Published: November 2020

Abstract
Acoustic waves in an optical medium cause rapid periodic changes in the refraction index, leading to diffraction effects. Such acoustically controlled diffraction can be used to modulate, deflect, and focus light at microsecond timescales, paving the way for advanced optical microscopy designs that feature unprecedented spatiotemporal resolution. In this article, we review the operational principles, optical properties, and recent applications of acousto-optic (AO) systems for advanced microscopy, including random-access scanning, ultrafast confocal and multiphoton imaging, and fast inertia-free light-sheet microscopy. As AO technology is reaching maturity, designing new microscope architectures that utilize AO elements is more attractive than ever, providing new exciting opportunities in fields as impactful as optical metrology, neuroscience, embryogenesis, and high-content screening.
One-pot synthesis of highly magnetic and stable citrate coated superparamagnetic iron oxide nanoparticles by modified coprecipitation method
Authors: Noqta Osama Abu , Sodipo Bashiru Kayode , Aziz Azlan Abdul 
Published: November 2020

Abstract
Highly stable superparamagnetic iron oxide nanoparticles (SPION) prepared through a modified one-pot coprecipitation technique using citrate as a surfactant and capping agent. The result of the as-synthesized citrate–SPION via a one-pot technique is compared with peptized SPION synthesized via the coprecipitation method. Formation of citrate–SPION is characterized using transmission electron microscopy, x-ray diffractometer (XRD), Fourier transform infrared, zeta potential, and vibrating sample magnetometer. XRD result reveals that the citrate does not affect the crystalline structure and purity of the SPION. Zeta potential of the citrate–SPION and the peptized SPION is −44 mV and 38.4 mV, respectively. Similarly, the saturation magnetization values of citrate–SPION and peptized SPION are 53.9 emu g−1 and 43.8 emu g−1, respectively. The results show that the citrate–SPION prepared by modified a one pot technique has a higher saturation magnetization and is more stable than the peptized SPION.
An overview of laser-based multiple metallic material additive manufacturing: from macro- to micro-scales
Authors: Wei Chao , Zhang Zhizhou , Cheng Dongxu , Sun Zhe , Zhu Menghui , Li Lin 
Published: November 2020

AbstractAdditive manufacturing (AM) is an emerging customized three-dimensional (3D) functional product fabrication technology. It provides a higher degree of design freedom, reduces manufacturing steps, cost and production cycles. However, existing metallic component 3D printing techniques are mainly for the manufacture of single material components. With the increasing commercial applications of AM technologies, the need for 3D printing of more than one type of dissimilar materials in a single component increases. Therefore, investigations on multi-material AM (MMAM) emerge over the past decade. Lasers are currently widely used for the AM of metallic components where high temperatures are involved. Here we report the progress and trend in laser-based macro- and micro-scale AM of multiple metallic components. The methods covered in this paper include laser powder bed fusion, laser powder directed energy deposition, and laser-induced forward transfer for MMAM applications. The principles and process/material characteristics are described. Potential applications and challenges are discussed. Finally, future research directions and prospects are proposed.
Low percolation density and charge noise with holes in germanium
Authors: Lodari Mario , Hendrickx Nico W , Lawrie William I L , Hsiao Tzu-Kan , Vandersypen Lieven M K , Sammak Amir , Veldhorst Menno , Scappucci Giordano 
Published: November 2020

Abstract
We engineer planar Ge/SiGe heterostructures for low disorder and quiet hole quantum dot operation by positioning the strained Ge channel 55 nm below the semiconductor/dielectric interface. In heterostructure field effect transistors, we measure a percolation density for two-dimensional hole transport of 2.1 × 1010 cm−2, indicative of a very low disorder potential landscape experienced by holes in the buried Ge channel. These Ge heterostructures support quiet operation of hole quantum dots and we measure an average charge noise level of

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. These results establish planar Ge as a promising platform for scaled two-dimensional spin qubit arrays.
Dynamic modelling of cold-hardiness in tea buds by imitating past temperature memory
Authors: Kimura Kensuke , Yasutake Daisuke , Oki Takahiro , Yoshida Koichiro , Kitano Masaharu 
Published: November 2020

AbstractBackground and AimsMost perennial plants memorize cold stress for a certain period and retrieve the memories for cold acclimation and deacclimation, which leads to seasonal changes in cold-hardiness. Therefore, a model for evaluating cold stress memories is required for predicting cold-hardiness and for future frost risk assessments under warming climates. In this study we develop a new dynamic model of cold-hardiness by introducing a function imitating past temperature memory in the processes of cold acclimation and deacclimation.MethodsWe formulated the past temperature memory for plants using thermal time weighted by a forgetting function, and thereby proposed a dynamic model of cold-hardiness. We used the buds of tea plants (Camellia sinensis) from two cultivars, ‘Yabukita’ and ‘Yutakamidori’, to calibrate and validate this model based on 10 years of observed cold-hardiness data.Key ResultsThe model captured more than 90 % of the observed variation in cold-hardiness and predicted accurate values for both cultivars, with root mean square errors of ~1.0 °C. The optimized forgetting function indicated that the tea buds memorized both short-term (recent days) and long-term (previous months) temperatures. The memories can drive short-term processes such as increasing/decreasing the content of carbohydrates, proteins and antioxidants in the buds, as well as long-term processes such as determining the bud phenological stage, both of which vary with cold-hardiness.ConclusionsThe use of a forgetting function is an effective means of understanding temperature memories in plants and will aid in developing reliable predictions of cold-hardiness for various plant species under global climate warming.
dittoSeq: universal user-friendly single-cell and bulk RNA sequencing visualization toolkit
Authors: Bunis Daniel G , Andrews Jared , Fragiadakis Gabriela K , Burt Trevor D , Sirota Marina 
Published: November 2020

Abstract

Summary
A visualization suite for major forms of bulk and single-cell RNAseq data in R. dittoSeq is color blindness-friendly by default, robustly documented to power ease-of-use and allows highly customizable generation of both daily-use and publication-quality figures.

Availability and implementation
dittoSeq is an R package available through Bioconductor via an open source MIT license.

Supplementary information
Supplementary data are available at Bioinformatics online.
Impact of lossy compression of nanopore raw signal data on basecalling and consensus accuracy
Authors: Chandak Shubham , Tatwawadi Kedar , Sridhar Srivatsan , Weissman Tsachy 
Published: November 2020

Abstract

Motivation
Nanopore sequencing provides a real-time and portable solution to genomic sequencing, enabling better assembly, structural variant discovery and modified base detection than second generation technologies. The sequencing process generates a huge amount of data in the form of raw signal contained in fast5 files, which must be compressed to enable efficient storage and transfer. Since the raw data is inherently noisy, lossy compression has potential to significantly reduce space requirements without adversely impacting performance of downstream applications.

Results
We explore the use of lossy compression for nanopore raw data using two state-of-the-art lossy time-series compressors, and evaluate the tradeoff between compressed size and basecalling/consensus accuracy. We test several basecallers and consensus tools on a variety of datasets at varying depths of coverage, and conclude that lossy compression can provide 35–50% further reduction in compressed size of raw data over the state-of-the-art lossless compressor with negligible impact on basecalling accuracy (≲0.2% reduction) and consensus accuracy (≲0.002% reduction). In addition, we evaluate the impact of lossy compression on methylation calling accuracy and observe that this impact is minimal for similar reductions in compressed size, although further evaluation with improved benchmark datasets is required for reaching a definite conclusion. The results suggest the possibility of using lossy compression, potentially on the nanopore sequencing device itself, to achieve significant reductions in storage and transmission costs while preserving the accuracy of downstream applications.

Availabilityand implementation
The code is available at https://github.com/shubhamchandak94/lossy_compression_evaluation.

Supplementary information
Supplementary data are available at Bioinformatics online.
Loss of ITGB3 in ovine conceptuses decreases conceptus expression of NOS3 and SPP1: implications for the developing placental vasculature†
Authors: Frank James W , Steinhauser Chelsie B , Wang Xiaoqiu , Burghardt Robert C , Bazer Fuller W , Johnson Greg A 
Published: November 2020

Abstract
During the peri-implantation period of pregnancy in sheep, there is an initial period of loose apposition of the elongating conceptuses (embryos and associated placental membranes) to the endometrial luminal epithelium (LE) that is followed by adhesion of the conceptus trophectoderm to the endometrial LE for implantation. Integrins and maternal extracellular matrix (ECM) molecules are major contributors to stable adhesion at implantation, and the β3 integrin subunit (ITGB3) is implicated in the adhesion cascade for implantation in several species including the sheep. We blocked mRNA translation for trophectoderm-expressed ITGB3 by infusing morpholino antisense oligonucleotides into the uterine lumen of pregnant ewes on Day 9 to assess effects on conceptus elongation, and on Day 16 to assess effects on early placental development in sheep. Results indicate that sheep conceptuses elongate and implant to the uterine wall in the absence of ITGB3 expression by the conceptuses; however, loss of ITGB3 in conceptuses decreased the growth of embryos to Day 24 of gestation, and decreased expression of secreted phosphoprotein 1 (SPP1) and nitric oxide synthase 3 (NOS3). Abundant SPP1 was localized around the blood vessels in the placental allantoic membrane in normal sheep pregnancies. We hypothesize that NOS3 and SPP1 positively influence the development of the vasculature within the allantois, and that decreased expression of NOS3 and SPP1, in response to knockdown of ITGB3 in conceptuses, alters development of the vasculature in the allantois required to transport nutrients from the endometrium to support growth and development of the embryo.
Predictors of volitional motor recovery with epidural stimulation in individuals with chronic spinal cord injury
Authors: Mesbah Samineh , Ball Tyler , Angeli Claudia , Rejc Enrico , Dietz Nicholas , Ugiliweneza Beatrice , Harkema Susan , Boakye Maxwell 
Published: November 2020

Abstract
Spinal cord epidural stimulation (scES) has enabled volitional lower extremity movements in individuals with chronic and clinically motor complete spinal cord injury and no clinically detectable brain influence. The aim of this study was to understand whether the individuals’ neuroanatomical characteristics or positioning of the scES electrode were important factors influencing the extent of initial recovery of lower limb voluntary movements in those with clinically motor complete paralysis. We hypothesized that there would be significant correlations between the number of joints moved during attempts with scES prior to any training interventions and the amount of cervical cord atrophy above the injury, length of post-traumatic myelomalacia and the amount of volume coverage of lumbosacral enlargement by the stimulation electrode array. The clinical and imaging records of 20 individuals with chronic and clinically motor complete spinal cord injury who underwent scES implantation were reviewed and analysed using MRI and X-ray integration, image segmentation and spinal cord volumetric reconstruction techniques. All individuals that participated in the scES study (n = 20) achieved, to some extent, lower extremity voluntary movements post scES implant and prior to any locomotor, voluntary movement or cardiovascular training. The correlation results showed that neither the cross-section area of spinal cord at C3 (n = 19, r = 0.33, P = 0.16) nor the length of severe myelomalacia (n = 18, r = −0.02, P = 0.93) correlated significantly with volitional lower limb movement ability. However, there was a significant, moderate correlation (n = 20, r = 0.59, P = 0.006) between the estimated percentage of the lumbosacral enlargement coverage by the paddle electrode as well as the position of the paddle relative to the maximal lumbosacral enlargement and the conus tip (n = 20, r = 0.50, P = 0.026) with the number of joints moved volitionally. These results suggest that greater coverage of the lumbosacral enlargement by scES may improve motor recovery prior to any training, possibly because of direct modulatory effects on the spinal networks that control lower extremity movements indicating the significant role of motor control at the level of the spinal cord.
Effect of ultraviolet radiation on the metabolomic profiles of potentially toxic cyanobacteria
Authors: Jacinavicius Fernanda Rios , Geraldes Vanessa , Crnkovic Camila M , Delbaje Endrews , Fiore Marli F , Pinto Ernani 
Published: November 2020

ABSTRACTInteractions between climate change and ultraviolet radiation (UVR) have a substantial impact on aquatic ecosystems, especially on photosynthetic organisms. To counteract the damaging effects of UVR, cyanobacteria developed adaptive strategies such as the biosynthesis of secondary metabolites. This study aimed to evaluate the effects of UVR on the metabolomic profiles of potentially toxic cyanobacteria. Twelve strains were irradiated with ultraviolet A and ultraviolet B radiation and parabolic aluminized reflector lamps for 3 days, followed by liquid chromatography–tandem mass spectometry (LC-MS/MS) analysis to assess changes in metabolomic profiles. Matrices were used to generate principal component analysis biplots, and molecular networks were obtained using the Global Natural Products platform. Most strains showed significant changes in their metabolomic profiles after UVR exposure. On average, 7% of MS features were shown to be exclusive to metabolomic profiles before UVR exposure, while 9% were unique to metabolomic profiles after UVR exposure. The identified compounds included aeruginosins, spumigins, cyanopeptolins, microginins, namalides, pseudospumigins, anabaenopeptins, mycosporine-like amino acids, nodularins and microcystins. Data showed that cyanobacteria display broad metabolic plasticity upon UVR exposure, including the synthesis and differential expression of a variety of secondary metabolites. This could result in a competitive advantage, supporting cyanobacterial blooms under various UVR light exposures.
Fear and loathing of the deep ocean: why don't people care about the deep sea?
Authors: Jamieson Alan J , Singleman Glenn , Linley Thomas D , Casey Susan 
Published: November 2020

Abstract
A recurring question within deep-sea science and conservation is why don't people care about the deep sea? How does the deep-sea science community convince non-scientific audiences to support, engage, and care more for the largest habitat on Earth? Here, we examine various aspects of an apparent dichotomy of perspectives between the scientific and non-scientific communities by discussing the problematic roots from within human neuropsychology, and how knowledge of the deep sea is delivered to, perceived by, and ultimately valued by non-scientific audiences. The answers are complex, covering issues such as conscious and subconscious thalassophobia, perspectivism, aesthetics, phenomenology, abstract interpretation, epistemology and media-driven enigmatization, self-deprecation by the science community, and perceived value-driven ethics. This discussion focusses on the nexus of scientific and non-scientific perceptions to catalyze meaningful societal engagement with the deep sea and to try and understand “Why don't people care about the deep sea?”
Protective low-avidity anti-tumour CD8+ T cells are selectively attenuated by regulatory T cells
Authors: Sugiyarto Gessa , Prossor David , Dadas Osman , Arcia-Anaya E David , Elliott Tim , James Edward 
Published: November 2020

Summary

Objectives
Regulatory T cells (Treg) play a major role in the suppression of protective anti-tumour T cell responses. In the CT26 BALB/c murine model of colorectal carcinoma, Tregs differentially suppress responses to two characterised CD8+ T epitopes, AH1 and GSW11, which results in an absence of detectable IFN-γ-producing GSW11-specific T cells in the spleen and lymph nodes of tumour challenged mice. Activation of GSW11-specific T cells correlates with protection against tumour progression. We wanted to examine the presence of non-functional GSW11-specific T cells in Treg replete and depleted mice, assess their phenotype and their affinity compared to AH1-specific T cells.

Methods
We used peptide-specific tetramers to identify tumour-specific CD8+ T cells and assessed the cell surface expression of markers associated with exhaustion (PD-1, Tim3 and Lag-3) and their function by IFN-g production using flow cytometry. We also assessed the T cell receptor (TcR) clonality of tumour-specific T cells. Tetramer competition assays were performed to determine the relative affinity of identified TcR.

Results
Here, we show that GSW11-specific T cells are in fact induced in Treg-replete, CT26-bearing mice, where they make up the majority of tumour-infiltrating CD8+ lymphocytes, but exhibit an ‘exhausted’ phenotype. This dysfunctional phenotype is induced early in the anti-tumour response in tumours. Depletion of Tregs prior to tumour challenge correlates with an altered T cell receptor (TcR) repertoire. Moreover, the avidity of GSW11-specific TcRs that expanded in the absence of Tregs was significantly lower compared with TcRs of CD8+populations that were diminished in protective anti-tumour responses.

Conclusion
Our results indicate that Tregs suppress the induction of protective anti-tumour T cell responses and may signify that low-avidity T cells play an important role in this protection.
CAR-T cells leave the comfort zone: current and future applications beyond cancer
Authors: Mazzi Mariana Torres , Hajdu Karina Lôbo , Ribeiro Priscila Rafaela , Bonamino Martín Hernán 
Published: November 2020

SummaryChimeric antigen receptor (CAR)-T cell therapy represents a breakthrough in the immunotherapy field and has achieved great success following its approval in 2017 for the treatment of B cell malignancies. While CAR-T cells are mostly applied as anti-tumor therapy in the present, their initial concept was aimed at a more general purpose of targeting membrane antigens, thus translating in many potential applications. Since then, several studies have assessed the use of CAR-T cells toward non-malignant pathologies such as autoimmune diseases, infectious diseases and, more recently, cardiac fibrosis, and cellular senescence. In this review, we present the main findings and implications of CAR-based therapies for non-malignant conditions.