bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational cytometer based on magnetically modulated coherent imaging and deep learning
Authors: Zhang Yibo , Ouyang Mengxing , Ray Aniruddha , Liu Tairan , Kong Janay , Bai Bijie , Kim Donghyuk , Guziak Alexander , Luo Yi , Feizi Alborz , Tsai Katherine , Duan Zhuoran , Liu Xuewei , Kim Danny , Cheung Chloe , Yalcin Sener , Ceylan Koydemir Hatice , Garner Omai B. , Di Carlo Dino , Ozcan Aydogan 
Published: October 2019

AbstractDetecting rare cells within blood has numerous applications in disease diagnostics. Existing rare cell detection techniques are typically hindered by their high cost and low throughput. Here, we present a computational cytometer based on magnetically modulated lensless speckle imaging, which introduces oscillatory motion to the magnetic-bead-conjugated rare cells of interest through a periodic magnetic force and uses lensless time-resolved holographic speckle imaging to rapidly detect the target cells in three dimensions (3D). In addition to using cell-specific antibodies to magnetically label target cells, detection specificity is further enhanced through a deep-learning-based classifier that is based on a densely connected pseudo-3D convolutional neural network (P3D CNN), which automatically detects rare cells of interest based on their spatio-temporal features under a controlled magnetic force. To demonstrate the performance of this technique, we built a high-throughput, compact and cost-effective prototype for detecting MCF7 cancer cells spiked in whole blood samples. Through serial dilution experiments, we quantified the limit of detection (LoD) as 10 cells per millilitre of whole blood, which could be further improved through multiplexing parallel imaging channels within the same instrument. This compact, cost-effective and high-throughput computational cytometer can potentially be used for rare cell detection and quantification in bodily fluids for a variety of biomedical applications.
Short- and long-term impact of hyperoxia on the blood and retinal cells’ transcriptome in a mouse model of oxygen-induced retinopathy
Authors: Zasada Magdalena , Madetko-Talowska Anna , Revhaug Cecilie , Rognlien Anne Gro W. , Baumbusch Lars O. , Książek Teofila , Szewczyk Katarzyna , Grabowska Agnieszka , Bik-Multanowski Miroslaw , Józef Pietrzyk Jacek , Kwinta Przemko , Saugstad Ola Didrik 
Published: October 2019

Abstract

Background
We aimed to identify global blood and retinal gene expression patterns in murine oxygen-induced retinopathy (OIR), a common model of retinopathy of prematurity, which may allow better understanding of the pathogenesis of this severe ocular prematurity complication and identification of potential blood biomarkers.

Methods
A total of 120 C57BL/6J mice were randomly divided into an OIR group, in which 7-day-old pups were maintained in 75% oxygen for 5 days, or a control group. RNA was extracted from the whole-blood mononuclear cells and retinal cells on days 12, 17, and 28. Gene expression in the RNA samples was evaluated with mouse gene expression microarrays.

Results
There were 38, 1370 and 111 genes, the expression of which differed between the OIR and control retinas on days 12, 17, and 28, respectively. Gene expression in the blood mononuclear cells was significantly altered only on day 17. Deptor and Nol4 genes showed reduced expression both in the blood and retinal cells on day 17.

Conclusion
There are sustained marked changes in the global pattern of gene expression in the OIR mice retinas. An altered expression of Deptor and Nol4 genes in the blood mononuclear cells requires further investigation as they may indicate retinal neovascularization.
Lytic bacteriophage have diverse indirect effects in a synthetic cross-feeding community
Authors: Fazzino Lisa , Anisman Jeremy , Chacón Jeremy M , Heineman Richard H , Harcombe William R 
Published: October 2019

Abstract
Bacteriophage shape the composition and function of microbial communities. Yet it remains difficult to predict the effect of phage on microbial interactions. Specifically, little is known about how phage influence mutualisms in networks of cross-feeding bacteria. We mathematically modeled the impacts of phage in a synthetic microbial community in which Escherichia coli and Salmonella enterica exchange essential metabolites. In this model, independent phage attack of either species was sufficient to temporarily inhibit both members of the mutualism; however, the evolution of phage resistance facilitated yields similar to those observed in the absence of phage. In laboratory experiments, attack of S. enterica with P22vir phage followed these modeling expectations of delayed community growth with little change in the final yield of bacteria. In contrast, when E. coli was attacked with T7 phage, S. enterica, the nonhost species, reached higher yields compared with no-phage controls. T7 infection increased nonhost yield by releasing consumable cell debris, and by driving evolution of partially resistant E. coli that secreted more carbon. Our results demonstrate that phage can have extensive indirect effects in microbial communities, that the nature of these indirect effects depends on metabolic and evolutionary mechanisms, and that knowing the degree of evolved resistance leads to qualitatively different predictions of bacterial community dynamics in response to phage attack.
Correction: Defining lower limits of biodegradation: atrazine degradation regulated by mass transfer and maintenance demand in Arthrobacter aurescens TC1
Authors: Kundu Kankana , Marozava Sviatlana , Ehrl Benno , Merl-Pham Juliane , Griebler Christian , Elsner Martin 
Published: October 2019

Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Endogenous stimulus-powered antibiotic release from nanoreactors for a combination therapy of bacterial infections
Authors: Wu Yang , Song Zhiyong , Wang Huajuan , Han Heyou 
Published: October 2019

AbstractThe use of an endogenous stimulus instead of external trigger has an advantage for targeted and controlled release in drug delivery. Here, we report on cascade nanoreactors for bacterial toxin-triggered antibiotic release by wrapping calcium peroxide (CaO2) and antibiotic in a eutectic mixture of two fatty acids and a liposome coating. When encountering pathogenic bacteria in vivo these nanoreactors capture the toxins, without compromising their structural integrity, and the toxins form pores. Water enters the nanoreactors through the pores to react with CaO2 and produce hydrogen peroxide which decomposes to oxygen and drives antibiotic release. The bound toxins reduce the toxicity and also stimulate the body’s immune response. This works to improve the therapeutic effect in bacterially infected mice. This strategy provides a Domino Effect approach for treating infections caused by bacteria that secrete pore-forming toxins.
Pacific subduction control on Asian continental deformation including Tibetan extension and eastward extrusion tectonics
Authors: Schellart W. P. , Chen Z. , Strak V. , Duarte J. C. , Rosas F. M. 
Published: October 2019

AbstractThe India-Asia collision has formed the highest mountains on Earth and is thought to account for extensive intraplate deformation in Asia. The prevailing explanation considers the role of the Pacific and Sunda subduction zones as passive during deformation. Here we test the hypothesis that subduction played an active role and present geodynamic experiments of continental deformation that model Indian indentation and active subduction rollback. We show that the synchronous activity and interaction of the collision zone and subduction zones explain Asian deformation, and demonstrate that east-west extension in Tibet, eastward continental extrusion and Asian backarc basin formation are controlled by large-scale Pacific and Sunda slab rollback. The models require 1740 ± 300 km of Indian indentation such that backarc basins form and central East Asian extension conforms estimates. Indentation and rollback produce ~260–360 km of eastward extrusion and large-scale clockwise upper mantle circulation from Tibet towards East Asia and back to India.
Fast objective coupled planar illumination microscopy
Authors: Greer Cody J. , Holy Timothy E. 
Published: October 2019

AbstractAmong optical imaging techniques light sheet fluorescence microscopy is one of the most attractive for capturing high-speed biological dynamics unfolding in three dimensions. The technique is potentially millions of times faster than point-scanning techniques such as two-photon microscopy. However light sheet microscopes are limited by volume scanning rate and/or camera speed. We present speed-optimized Objective Coupled Planar Illumination (OCPI) microscopy, a fast light sheet technique that avoids compromising image quality or photon efficiency. Our fast scan system supports 40 Hz imaging of 700 μm-thick volumes if camera speed is sufficient. We also address the camera speed limitation by introducing Distributed Planar Imaging (DPI), a scaleable technique that parallelizes image acquisition across cameras. Finally, we demonstrate fast calcium imaging of the larval zebrafish brain and find a heartbeat-induced artifact, removable when the imaging rate exceeds 15 Hz. These advances extend the reach of fluorescence microscopy for monitoring fast processes in large volumes.
Principles for enhancing virus capsid capacity and stability from a thermophilic virus capsid structure
Authors: Stone Nicholas P. , Demo Gabriel , Agnello Emily , Kelch Brian A. 
Published: October 2019

AbstractThe capsids of double-stranded DNA viruses protect the viral genome from the harsh extracellular environment, while maintaining stability against the high internal pressure of packaged DNA. To elucidate how capsids maintain stability in an extreme environment, we use cryoelectron microscopy to determine the capsid structure of thermostable phage P74-26 to 2.8-Å resolution. We find P74-26 capsids exhibit an overall architecture very similar to those of other tailed bacteriophages, allowing us to directly compare structures to derive the structural basis for enhanced stability. Our structure reveals lasso-like interactions that appear to function like catch bonds. This architecture allows the capsid to expand during genome packaging, yet maintain structural stability. The P74-26 capsid has T = 7 geometry despite being twice as large as mesophilic homologs. Capsid capacity is increased with a larger, flatter major capsid protein. Given these results, we predict decreased icosahedral complexity (i.e. T ≤ 7) leads to a more stable capsid assembly.
Complex DNA knots detected with a nanopore sensor
Authors: Kumar Sharma Rajesh , Agrawal Ishita , Dai Liang , Doyle Patrick S. , Garaj Slaven 
Published: October 2019

AbstractEquilibrium knots are common in biological polymers—their prevalence, size distribution, structure, and dynamics have been extensively studied, with implications to fundamental biological processes and DNA sequencing technologies. Nanopore microscopy is a high-throughput single-molecule technique capable of detecting the shape of biopolymers, including DNA knots. Here we demonstrate nanopore sensors that map the equilibrium structure of DNA knots, without spurious knot tightening and sliding. We show the occurrence of both tight and loose knots, reconciling previous contradictory results from different experimental techniques. We evidence the occurrence of two quantitatively different modes of knot translocation through the nanopores, involving very different tension forces. With large statistics, we explore the complex knots and, for the first time, reveal the existence of rare composite knots. We use parametrized complexity, in concert with simulations, to test the theoretical assumptions of the models, further asserting the relevance of nanopores in future investigation of knots.
Controlled growth of single-crystalline metal nanowires via thermomigration across a nanoscale junction
Authors: Xie De-Gang , Nie Zhi-Yu , Shinzato Shuhei , Yang Yue-Qing , Liu Feng-Xian , Ogata Shigenobu , Li Ju , Ma Evan , Shan Zhi-Wei 
Published: October 2019

AbstractMass transport driven by temperature gradient is commonly seen in fluids. However, here we demonstrate that when drawing a cold nano-tip off a hot solid substrate, thermomigration can be so rampant that it can be exploited for producing single-crystalline aluminum, copper, silver and tin nanowires. This demonstrates that in nanoscale objects, solids can mimic liquids in rapid morphological changes, by virtue of fast surface diffusion across short distances. During uniform growth, a thin neck-shaped ligament containing a grain boundary (GB) usually forms between the hot and the cold ends, sustaining an extremely high temperature gradient that should have driven even larger mass flux, if not counteracted by the relative sluggishness of plating into the GB and the resulting back stress. This GB-containing ligament is quite robust and can adapt to varying drawing directions and velocities, imparting good controllability to the nanowire growth in a manner akin to Czochralski crystal growth.
Deciphering photocarrier dynamics for tuneable high-performance perovskite-organic semiconductor heterojunction phototransistors
Authors: Lin Yen-Hung , Huang Wentao , Pattanasattayavong Pichaya , Lim Jongchul , Li Ruipeng , Sakai Nobuya , Panidi Julianna , Hong Min Ji , Ma Chun , Wei Nini , Wehbe Nimer , Fei Zhuping , Heeney Martin , Labram John G. , Anthopoulos Thomas D. , Snaith Henry J. 
Published: October 2019

AbstractLooking beyond energy harvesting, metal-halide perovskites offer great opportunities to revolutionise large-area photodetection technologies due to their high absorption coefficients, long diffusion lengths, low trap densities and simple processability. However, successful extraction of photocarriers from perovskites and their conversion to electrical signals remain challenging due to the interdependency of photogain and dark current density. Here we report hybrid hetero-phototransistors by integrating perovskites with organic semiconductor transistor channels to form either “straddling-gap” type-I or “staggered-gap” type-II heterojunctions. Our results show that gradual transforming from type-II to type-I heterojunctions leads to increasing and tuneable photoresponsivity with high photogain. Importantly, with a preferential edge-on molecular orientation, the type-I heterostructure results in efficient photocarrier cycling through the channel. Additionally, we propose the use of a photo-inverter circuitry to assess the phototransistors’ functionality and amplification. Our study provides important insights into photocarrier dynamics and can help realise advanced device designs with “on-demand” optoelectronic properties.
Longitudinal associations between ability in arts activities, behavioural difficulties and self-esteem: analyses from the 1970 British Cohort Study
Authors: Mak Hei Wan , Fancourt Daisy 
Published: October 2019

AbstractArts engagement has been shown to have benefits for young people’s psychological and behavioural adjustment. However, it is unknown whether it is frequency of arts engagement or individual ability in arts activities that is associated with these benefits. This study therefore examines the link between arts ability and children’s behavioural difficulties and self-esteem independent of frequency of engagement. We analysed data from the 1970 British Cohort Study with an overall sample size of 7700 for the behavioural difficulties outcome, and of 4991 for the self-esteem outcome. Baseline measures were taken when the children were aged 10 and followed up at age 16. OLS regression analysis adjusted for identified confounders shows that ability in the arts at age 10 was associated with a lower level of behavioural difficulties at age 16 independent of baseline behaviours, identified confounders and frequency of arts engagement. An association between arts ability and self-esteem was only found amongst children who have higher educational ability. These result suggest that there may be a value to encouraging the cultivation of arts skills at the onset of adolescence as a way of helping to foster children’s positive behavioural development.
Palladium Nanoparticles/Graphitic Carbon Nitride Nanosheets-Carbon Nanotubes as a Catalytic Amplification Platform for the Selective Determination of 17α-ethinylestradiol in Feedstuffs
Authors: Zheng Zhi xiang , Wang Mei , Shi Xue zhao , Wang Chun ming 
Published: October 2019

AbstractA new kind of nanocomposite, graphitic carbon nitride (g-C3N4)-carbon nanotubes (CNTs), has been synthesized via solid grinding, and followed by thermal polymerization process of melamine and CNTs. Pd nanoparticles were loaded on the as-prepared nanocomposite by the self-assembly method. The Pd/g-C3N4-CNTs nanocomposite exhibited excellent electrocatalytic activity toward the oxidation of 17α-ethinylestradiol (EE2), and compared with other detection methods of EE2, such as HPLC, this detection platform does not need the samples for further purification processing. And this detection platform was compared with HPLC, there is no significant difference between two methods, and the accuracy and precision of the determination of EE2 in feedstuff sample by differential pulse voltammetry (DPV) to a satisfactory level. Thus, the Pd/g-C3N4-CNTs nanocomposite can be used as a signal amplification platform for the detection of EE2 in feedstuffs samples. Under the optimum condition, the current response increased linearly with EE2 concentration from 2.0 × 10−6 ~ 1.5 × 10−4M with a detection limit of 5.0 × 10−7M (S/N = 3) by DPV. The Pd/g-C3N4-CNTs showed good reproducibility and excellent anti-interference ability that the relative standard deviation was 3.3% (n = 5). This strategy may find widespread and promising applications in other sensing systems involving EE2.
Chemical proteomics reveals target selectivity of clinical Jak inhibitors in human primary cells
Authors: Eberl H. Christian , Werner Thilo , Reinhard Friedrich B. , Lehmann Stephanie , Thomson Douglas , Chen Peiling , Zhang Cunyu , Rau Christina , Muelbaier Marcel , Drewes Gerard , Drewry David , Bantscheff Marcus 
Published: October 2019

AbstractKinobeads are a set of promiscuous kinase inhibitors immobilized on sepharose beads for the comprehensive enrichment of endogenously expressed protein kinases from cell lines and tissues. These beads enable chemoproteomics profiling of kinase inhibitors of interest in dose-dependent competition studies in combination with quantitative mass spectrometry. We present improved bead matrices that capture more than 350 protein kinases and 15 lipid kinases from human cell lysates, respectively. A multiplexing strategy is suggested that enables determination of apparent dissociation constants in a single mass spectrometry experiment. Miniaturization of the procedure enabled determining the target selectivity of the clinical BCR-ABL inhibitor dasatinib in peripheral blood mononuclear cell (PBMC) lysates from individual donors. Profiling of a set of Jak kinase inhibitors revealed kinase off-targets from nearly all kinase families underpinning the need to profile kinase inhibitors against the kinome. Potently bound off-targets of clinical inhibitors suggest polypharmacology, e.g. through MRCK alpha and beta, which bind to decernotinib with nanomolar affinity.
Experimental demonstration of coherent superpositions in an ultrasonic pseudospin
Authors: Calderin Lazaro , Hasan M. Arif , Jenkins Neil G. , Lata Trevor , Lucas Pierre , Runge Keith , Deymier Pierre A. 
Published: October 2019

AbstractWe experimentally demonstrate the existence and control of coherent superpositions of elastic states in the direction of propagation of an ultrasonic pseudospin i.e., a φ-bit. The experimental realization of this mechanical pseudospin consists of an elastic aluminum rod serving as a waveguide sandwiched between two heavy steel plates. The Hertzian contact between the rod and the plates leads to restoring forces which couple the directions of propagation (forward and backward). This coupling generates the coherence of the superposition of elastic states. We also demonstrate φ-bit gate operations on the coherent superposition analogous to those used in quantum computing. In the case of a φ-bit, the coherent superposition of states in the direction of propagation are immune to wave function collapse upon measurement as they result from classical waves.
Effects of mulching on soil CO2 fluxes, hay yield and nutritional yield in a forage maize field in Northwest China
Authors: Fan Ming , Li Qiang , Zhang Enhe , Liu Qinglin , Wang Qi 
Published: October 2019

AbstractIn arid areas of China, water shortage and heavy carbon emissions have been threatening agricultural sustainability and which has become a vital issue. A field experiment was conducted to explore how different mulching affects soil moisture and temperature, CO2 fluxes, forage-maize hay yield and nutritional value during 2 consecutive years: 2014 and 2015. The field experiment showed that mulching materials had distinct effects on soil moisture and temperature and CO2 fluxes. The soil temperature and CO2 fluxes were in order of common plastic film mulching (PFM) > bio-degradable mulch mulching (BMM) > no mulching (CK) > straw mulching (SM), while the soil moisture was in order of PFM > BMM > SM > CK over these two years. Compared with CK, hay yield respectively increased by 23.25%, 22.51% and 5.27% for PFM, BMM and SM, WUE increased by 35.60%, 32.34% and 10.88%, and the total nutrient yields increased by 17.75%, 21.35% and 6.95%, respectively. To sum up, in combination with ecology and environmental protection, bio-degradable mulch could replace common plastic film and bio-degradable mulch should be popular in future. As bio-degradable mulch is green non-pollution, it is conducive to the sustainable development of agricultural ecosystem.
Influence of the distribution of fibrosis within an area of myocardial infarction on wave propagation in ventricular tissue
Authors: Liang Cuiping , Wang Kuanquan , Li Qince , Bai Jieyun , Zhang Henggui 
Published: October 2019

AbstractThe presence of fibrosis in heart tissue is strongly correlated with an incidence of arrhythmia, which is a leading cause of sudden cardiac death (SCD). However, it remains incompletely understood how different distributions, sizes and positions of fibrotic tissues contribute to arrhythmogenesis. In this study, we designed 4 different ventricular models mimicking wave propagation in cardiac tissues under normal, myocardial infarction (MI), MI with random fibrosis and MI with gradient fibrosis conditions. Simulation results of ideal square tissues indicate that vulnerable windows (VWs) of random and gradient fibrosis distributions are similar with low levels of fibrosis. However, with a high level of fibrosis, the VWs significantly increase in random fibrosis tissue but not in gradient fibrosis tissue. In addition, we systematically analyzed the effects of the size and position of fibrosis tissues on VWs. Simulation results show that it is more likely for a reentry wave to appear when the length of the infarcted area is greater than 25% of the perimeter of the ventricle, when the width is approximately half that of the ventricular wall, or when the infarcted area is attached to the inside or outside of the ventricular wall.