bluuebunny/crossref_metadata_2025_split huggingface dataset:
LED Light Source: Major Advance in Fluorescence Microscopy
Authors: Hohman Becky 
Published: May 2018

Abstract
Fluorescence microscopy requires an intense light source at the specific wavelength that will excite fluorescent dyes and proteins. The traditional method employs a white light, typically from a Mercury or Xenon arc lamp. Although such broad-spectrum lamps can generate ample light at desired wavelengths, only a small percentage of the projected light is useful in any particular application. The other wavelengths need to be suppressed to avoid background noise that reduces image contrast and obscures the fluorescent light emissions.
This process of suppressing extraneous light is complex, expensive, and only partially effective: even after decades of refinements, the best filters are not 100% percent successful at blocking the bleed through of non-specific photons. Some mitigation techniques end up not only suppressing peripheral light, but also significantly diminishing the intensity of the desired wavelengths. To address the root cause of the problem – the presence of non-specific photons – a radically different approach is coming to light.
CellProfiler: Open-Source Software to Automatically Quantify Images
Authors: Vokes Martha S , Carpenter Anne E 
Published: May 2018

Abstract
Researchers often examine samples by eye on the microscope — qualitatively scoring each sample for a particular feature of interest. This approach, while suitable for many experiments, sacrifices quantitative results and a permanent record of the experiment. By contrast, if digital images are collected of each sample, software can be used to quantify features of interest. For small experiments, quantitative analysis is often done manually using interactive programs like Adobe Photoshop©. For the large number of images that can be easily collected with automated microscopes, this approach is tedious and time-consuming. NIH Image/ImageJ (http://rsb.info.nih.gov/ij) allows users comfortable writing in a macro language to automate quantitative image analysis. We have developed Cell- Profiler, a free, open-source software package, designed to enable scientists without prior programming experience to quantify relevant features of samples in large numbers of images automatically, in a modular system suitable for processing hundreds of thousands of images.
Imaging Multilayers of Ice with Scanning Tunneling Microscopy
Authors: Thürmer Konrad , Bartelt Norman C 
Published: May 2018

Abstract
Ice plays an important role in many naturally occurring phenomena. For example, most rainfall in temperate climates is triggered by the nucleation of ice around μm-sized particles in atmospheric clouds. Another reason to be interested in ice is that thin supported ice films provide excellent model systems for studying the interaction of water with solid surfaces. Despite the importance of water-solid interactions for catalysis, corrosion, water purification and fuel cells, even the basics of this interaction are poorly understood. In fact, the best theoretical models often fail to predict even the simplest phenomena. A fundamental question, for example, is whether water/ice wets a given substrate, i.e., whether the substrate is covered up by a uniformly thick water/ice film. (In the case of non-wetting an ice film would break up into separate three-dimensional (3D) crystallites of varying height, exposing the substrate.)
Application of the Gatan X-ray Ultramicroscope (XuM) to the Investigation of Material and Biological Samples
Authors: Mainwaring Paul 
Published: May 2018

Abstract
X-ray ultramicroscopy in the SEM is a relatively new application in the wider field of X-ray microscopy. This latter field includes synchrotron and cabinet-based systems that vary in their X-ray power, capability, sample size, spatial resolution, and convenience. One important capability of the SEM-hosted X-ray microscope is that the normal SEM imaging and analytical functions such as secondary and backscattered imaging and microanalysis by EDX or WDS are unimpeded. X-ray imaging then serves as a complement to the normal use of the SEM. The convenience of easy access in an SEM lab to an X-ray microscope with 3D tomographic capability makes this an important development.
Drainage from the Critical Zone: Lithologic Controls on the Persistence and Spatial Extent of Wetted Channels during the Summer Dry Season
Authors: Lovill S. M. , Hahm W. J. , Dietrich W.E. 
Published: May 2018

AbstractIn seasonally dry environments, critical zone drainage provides base flow that sustains river ecosystems. The extent of wetted channels and magnitude of base flow throughout the network, however, are rarely documented, and no general theory currently exists enabling the prediction of these key ecosystem properties. We conducted channel surveys in early and late summers of 2012, 2014, and 2015 in four headwater drainage networks (2.8–17.0 km2, in the Franciscan Formation of the Eel River (Northern California)), two of which are underlain by the Coastal Belt (argillite and inter‐bedded sandstone) and two of which are underlain by the Central Belt (sheared argillaceous‐matrix, meta‐sedimentary mélange). In all networks, stationary springs controlled the extent of flow. Though surveyed during a period of multiyear drought, the two adjacent Coastal Belt networks remained flowing throughout late‐summer months, sustained by drainage from groundwater stored in thick weathered bedrock above fresh, impermeable bedrock. Flow magnitudes, however, decreased and surface flows became increasingly discontinuous, largely due to infiltration into thick gravel deposits on the channel bed. Only 23 km away, in the Central Belt mélange, channel flow ceased early in the summer because the thin critical zone (typically <3 m) stored little water. All late‐summer flowing water initiated from deep‐rooted sandstone blocks and terminated a short distance downslope. Our findings suggest that lithology and critical zone development exert primary controls on wetted channel extent. Given similar annual precipitation, nearby watersheds can have dramatically different summer wetted channel networks that result in fundamentally different aquatic ecosystems.
Kinetic Dissipation Around a Dipolarization Front
Authors: Sitnov M. I. , Merkin V. G. , Roytershteyn V. , Swisdak M. 
Published: May 2018

AbstractKinetic aspects of energy conversion and dissipation near a dipolarization front (DF) in the magnetotail are considered using fully kinetic 3‐D particle‐in‐cell simulations. The energy conversion is described in terms of the pressure dilatation, as well as the double contraction of deviatoric pressure tensor and traceless strain rate tensor, also known as the Pi‐D parameter in turbulence studies. It is shown that in contrast to the fluid dissipation measure, the Joule heating rate, which cannot distinguish between ion and electron dissipation and reveals deep negative dips at the DF, the Pi‐D parameters, as kinetic analogs of the Joule heating rate, are largely positive and drastically different for ions and electrons. Further analysis of these parameters suggests that ions are heated at and ahead of the DF due to their reflection from the front, while electrons are heated at and behind the DF due to the long‐wavelength lower‐hybrid drift instability.
Spectroscopic stimulated Raman scattering imaging of highly dynamic specimens through matrix completion
Authors: Lin Haonan , Liao Chien-Sheng , Wang Pu , Kong Nan , Cheng Ji-Xin 
Published: May 2018

AbstractSpectroscopic stimulated Raman scattering (SRS) imaging generates chemical maps of intrinsic molecules, with no need for prior knowledge. Despite great advances in instrumentation, the acquisition speed for a spectroscopic SRS image stack is fundamentally bounded by the pixel integration time. In this work, we report three-dimensional sparsely sampled spectroscopic SRS imaging that measures ~20% of pixels throughout the stack. In conjunction with related work in low-rank matrix completion (e.g., the Netflix Prize), we develop a regularized non-negative matrix factorization algorithm to decompose the sub-sampled image stack into spectral signatures and concentration maps. This design enables an acquisition speed of 0.8 s per image stack, with 50 frames in the spectral domain and 40,000 pixels in the spatial domain, which is faster than the conventional raster laser-scanning scheme by one order of magnitude. Such speed allows real-time metabolic imaging of living fungi suspended in a growth medium while effectively maintaining the spatial and spectral resolutions. This work is expected to promote broad application of matrix completion in spectroscopic laser-scanning imaging.
A real-time detection and positioning method for small and weak targets using a 1D morphology-based approach in 2D images
Authors: Wei Min-Song , Xing Fei , You Zheng 
Published: May 2018

AbstractA small and weak target detection method is proposed in this work that outperforms all other methods in terms of real-time capability. It is the first time that two-dimensional (2D) images are processed using only one-dimensional1D structuring elements in a morphology-based approach, enabling the real-time hardware implementation of the whole image processing method. A parallel image readout and processing structure is introduced to achieve an ultra-low latency time on the order of nanoseconds, and a hyper-frame resolution in the time domain can be achieved by combining the row-by-row structure and the electrical rolling shutter technique. Experimental results suggest that the expected target can be successfully detected under various interferences with an accuracy of 0.1 pixels (1σ) under the worst sky night test condition and that a centroiding precision of better than 0.03 pixels (1σ) can be reached for static tests. The real-time detection method with high robustness and accuracy is attractive for application to all types of real-time small target detection systems, such as medical imaging, infrared surveillance, and target measurement and tracking, where an ultra-high processing speed is required.
Microfluidics-enabled phenotyping of a whole population of C. elegans worms over their embryonic and post-embryonic development at single-organism resolution
Authors: Letizia Maria Cristina , Cornaglia Matteo , Trouillon Raphaël , Sorrentino Vincenzo , Mouchiroud Laurent , Bou Sleiman Maroun S. , Auwerx Johan , Gijs Martin A. M. 
Published: May 2018

AbstractThe organism Caenorhabditis elegans is a performant model system for studying human biological processes and diseases, but until now all phenome data are produced as population-averaged read-outs. Monitoring of individual responses to drug treatments would however be more informative. Here, a new strategy to track different phenotypic traits of individual C. elegans nematodes throughout their full life-cycle—i.e., embryonic and post-embryonic development, until adulthood onset, differently from life-span—is presented. In an automated fashion, single worms were synchronized, isolated, and cultured from egg to adulthood in a microfluidic device, where their identity was preserved during their whole development. Several phenotypes were monitored and quantified for each animal, resulting in high-content phenome data. Specifically, the method was validated by analyzing the response of C. elegans to doxycycline, an antibiotic fairly well-known to prolong the development and activate mitochondrial stress-response pathways in different species. Interestingly, the obtained extensive single-worm phenome not only confirmed the dramatic doxycycline effect on the worm developmental delay, but more importantly revealed subtle yet severe treatment-dependent phenotypes that are representative of minority subgroups and would have otherwise stayed hidden in an averaged dataset. Such heterogeneous response started during the embryonic development, which makes essential having a dedicated chip that allows including this early developmental stage in the drug assay. Our approach would therefore allow elucidating pharmaceutical or therapeutic responses that so far were still being overlooked.
CRISPR-LbCpf1 prevents choroidal neovascularization in a mouse model of age-related macular degeneration
Authors: Koo Taeyoung , Park Sung Wook , Jo Dong Hyun , Kim Daesik , Kim Jin Hyoung , Cho Hee-Yeon , Kim Jeungeun , Kim Jeong Hun , Kim Jin-Soo 
Published: May 2018

AbstractLbCpf1, derived from Lachnospiraceae bacterium ND2006, is a CRISPR RNA-guided endonuclease and holds promise for therapeutic applications. Here we show that LbCpf1 can be used for therapeutic gene editing in a mouse model of age-related macular degeneration (AMD). The intravitreal delivery of LbCpf1, targeted to two angiogenesis-associated genes encoding vascular endothelial growth factor A (Vegfa) and hypoxia inducing factor 1a (Hif1a), using adeno-associated virus, led to efficient gene disruption with no apparent off-target effects in the retina and retinal pigment epithelium (RPE) cells. Importantly, LbCpf1 targeted to Vegfa or Hif1a in RPE cells reduced the area of laser-induced choroidal neovascularization as efficiently as aflibercept, an anti-VEGF drug currently used in the clinic, without inducing cone dysfunction. Unlike aflibercept, LbCpf1 targeted to Vegfa or Hif1a achieved a long-term therapeutic effect on CNV, potentially avoiding repetitive injections. Taken together, these results indicate that LbCpf1-mediated in vivo genome editing to ablate pathologic angiogenesis provides an effective strategy for the treatment of AMD and other neovascularization-associated diseases.
Single molecule fate of HIV-1 envelope reveals late-stage viral lattice incorporation
Authors: Buttler Carmen A. , Pezeshkian Nairi , Fernandez Melissa V. , Aaron Jesse , Norman Sofya , Freed Eric O. , van Engelenburg Schuyler B. 
Published: May 2018

AbstractHuman immunodeficiency virus type 1 (HIV-1) assembly occurs on the inner leaflet of the host cell plasma membrane, incorporating the essential viral envelope glycoprotein (Env) within a budding lattice of HIV-1 Gag structural proteins. The mechanism by which Env incorporates into viral particles remains poorly understood. To determine the mechanism of recruitment of Env to assembly sites, we interrogate the subviral angular distribution of Env on cell-associated virus using multicolor, three-dimensional (3D) superresolution microscopy. We demonstrate that, in a manner dependent on cell type and on the long cytoplasmic tail of Env, the distribution of Env is biased toward the necks of cell-associated particles. We postulate that this neck-biased distribution is regulated by vesicular retention and steric complementarity of Env during independent Gag lattice formation.
Determination of hot carrier energy distributions from inversion of ultrafast pump-probe reflectivity measurements
Authors: Heilpern Tal , Manjare Manoj , Govorov Alexander O. , Wiederrecht Gary P. , Gray Stephen K. , Harutyunyan Hayk 
Published: May 2018

AbstractDeveloping a fundamental understanding of ultrafast non-thermal processes in metallic nanosystems will lead to applications in photodetection, photochemistry and photonic circuitry. Typically, non-thermal and thermal carrier populations in plasmonic systems are inferred either by making assumptions about the functional form of the initial energy distribution or using indirect sensors like localized plasmon frequency shifts. Here we directly determine non-thermal and thermal distributions and dynamics in thin films by applying a double inversion procedure to optical pump-probe data that relates the reflectivity changes around Fermi energy to the changes in the dielectric function and in the single-electron energy band occupancies. When applied to normal incidence measurements our method uncovers the ultrafast excitation of a non-Fermi-Dirac distribution and its subsequent thermalization dynamics. Furthermore, when applied to the Kretschmann configuration, we show that the excitation of propagating plasmons leads to a broader energy distribution of electrons due to the enhanced Landau damping.
L-proline mixed with sodium benzoate as sustainable inhibitor for mild steel corrosion in 1M HCl: An experimental and theoretical approach
Authors: Parveen Mosarrat , Mobin Mohammad , Zehra Saman , Aslam Ruby 
Published: May 2018

AbstractFollowing standard experimental (gravimetric measurements, potentiodynamic polarization measurements, electrochemical impedance measurements, spectroscopic measurements, scanning electron microscopy technique) and theoretical (DFT) approach, inhibition effect of L-proline (LPr) and LPr mixed with sodium benzoate (LPr + NaBenz) for mild steel (MS) corrosion in 1M HCl was studied at 30, 40, 50 and 60 °C. The concentration of LPr was varied between 100–600 ppm, whereas that of NaBenz was fixed at 10 ppm. LPr lowered the corrosion rates of MS to a considerable extent. Corrosion mitigating efficacy of LPr is synergistically enhanced on adding NaBenz at all concentrations. Evaluation of polarization parameters suggested that both LPr and LPr + NaBenz act as mixed type inhibitor with more control on cathodic reaction whereas impedance parameters suggested inhibition of metal corrosion by adsorption at the MS/solution interface. Surface microscopic examination of corroded and uncorroded MS coupons supported the protective effect of adsorbed inhibitor layer at the MS surface. Spectroscopic studies are suggestive of the complex formation between inhibitor molecules and the metal. When LPr is combined with NaBenz, the corrosion inhibition rate was improved greatly. Corrosion mitigating efficacy of LPr or LPr mixed with NaBenz obtained by different techniques are in good agreement and correlate well with theoretical quantum chemical descriptors.
Revealing the nature of morphological changes in carbon nanotube-polymer saturable absorber under high-power laser irradiation
Authors: Chernysheva Maria , Araimi Mohammed Al , Rance Graham A. , Weston Nicola J. , Shi Baogui , Saied Sayah , Sullivan John L. , Marsh Nicholas , Rozhin Aleksey 
Published: May 2018

AbstractComposites of single-walled carbon nanotubes (SWNTs) and water-soluble polymers (WSP) are the focus of significant worldwide research due to a number of applications in biotechnology and photonics, particularly for ultrashort pulse generation. Despite the unique possibility of constructing non-linear optical SWNT-WSP composites with controlled optical properties, their thermal degradation threshold and limit of operational power remain unexplored. In this study, we discover the nature of the SWNT-polyvinyl alcohol (PVA) film thermal degradation and evaluate the modification of the composite properties under continuous high-power ultrashort pulse laser operation. Using high-precision optical microscopy and micro-Raman spectroscopy, we have examined SWNT-PVA films before and after continuous laser radiation exposure (up to 40 hours) with a maximum optical fluence of 2.3 mJ·cm−2. We demonstrate that high-intensity laser radiation results in measurable changes in the composition and morphology of the SWNT-PVA film due to efficient heat transfer from SWNTs to the polymer matrix. The saturable absorber modification does not affect the laser operational performance. We anticipate our work to be a starting point for more sophisticated research aimed at the enhancement of SWNT-PVA films fabrication for their operation as reliable saturable absorbers in high-power ultrafast lasers.
Genomic features of renal cell carcinoma with venous tumor thrombus
Authors: Warsow Gregor , Hübschmann Daniel , Kleinheinz Kortine , Nientiedt Cathleen , Heller Martina , Van Coile Laura , Tolstov Yanis , Trennheuser Lukas , Wieczorek Kathrin , Pecqueux Carine , Gasch Claudia , Kuru Timur , Nyarangi-Dix Joanne , Hatiboglu Gencay , Teber Dogu , Perner Sven , Stenzinger Albrecht , Roth Wilfried , Hadaschik Boris , Pahernik Sascha , Jäger Dirk , Grüllich Carsten , Duensing Anette , Eils Roland , Schlesner Matthias , Sültmann Holger , Hohenfellner Markus , Duensing Stefan 
Published: May 2018

AbstractA venous tumor thrombus (VTT) is a potentially lethal complication of renal cell carcinoma (RCC) but virtually nothing is known about the underlying natural history. Based on our observation that venous thrombi contain significant numbers of viable tumor cells, we applied multiregion whole exome sequencing to a total of 37 primary tumor and VTT samples including normal tissue specimens from five consecutive patients. Our findings demonstrate mutational heterogeneity between primary tumor and VTT with 106 of 483 genes (22%) harboring functional SNVs and/or indels altered in either primary tumor or thrombus. Reconstruction of the clonal phylogeny showed clustering of tumor samples and VTT samples, respectively, in the majority of tumors. However, no new subclones were detected suggesting that pre-existing subclones of the primary tumor drive VTT formation. Importantly, we found several lines of evidence for “BRCAness” in a subset of tumors. These included mutations in genes that confer “BRCAness”, a mutational signature and an increase of small indels. Re-analysis of SNV calls from the TCGA KIRC-US cohort confirmed a high frequency of the “BRCAness” mutational signature AC3 in clear cell RCC. Our findings warrant further pre-clinical experiments and may lead to novel personalized therapies for RCC patients.
Live-cell imaging of nuclear–chromosomal dynamics in bovine in vitro fertilised embryos
Authors: Yao Tatsuma , Suzuki Rie , Furuta Natsuki , Suzuki Yuka , Kabe Kyoko , Tokoro Mikiko , Sugawara Atsushi , Yajima Akira , Nagasawa Tomohiro , Matoba Satoko , Yamagata Kazuo , Sugimura Satoshi 
Published: May 2018

AbstractNuclear/chromosomal integrity is an important prerequisite for the assessment of embryo quality in artificial reproductive technology. However, lipid-rich dark cytoplasm in bovine embryos prevents its observation by visible light microscopy. We performed live-cell imaging using confocal laser microscopy that allowed long-term imaging of nuclear/chromosomal dynamics in bovine in vitro fertilised (IVF) embryos. We analysed the relationship between nuclear/chromosomal aberrations and in vitro embryonic development and morphological blastocyst quality. Three-dimensional live-cell imaging of 369 embryos injected with mRNA encoding histone H2B-mCherry and enhanced green fluorescent protein (EGFP)-α-tubulin was performed from single-cell to blastocyst stage for eight days; 17.9% reached the blastocyst stage. Abnormalities in the number of pronuclei (PN), chromosomal segregation, cytokinesis, and blastomere number at first cleavage were observed at frequencies of 48.0%, 30.6%, 8.1%, and 22.2%, respectively, and 13.0%, 6.2%, 3.3%, and 13.4%, respectively, for abnormal embryos developed into blastocysts. A multivariate analysis showed that abnormal chromosome segregation (ACS) and multiple PN correlated with delayed timing and abnormal blastomere number at first cleavage, respectively. In morphologically transferrable blastocysts, 30–40% of embryos underwent ACS and had abnormal PN. Live-cell imaging may be useful for analysing the association between nuclear/chromosomal dynamics and embryonic development in bovine embryos.