bluuebunny/crossref_metadata_2025_split huggingface dataset:
Finding the Good Stuff in Hrem Images
Authors: Fraundorf P. , Armbruster B. , Ebner J. 
Published: June 2020

Except in the most carefully designed installations, the commercial availability of TEM,s with point resolution near to or below 2Å has resulted in a class of instruments whose contrast transfer at Scherzer defocus is limited by instability damping, but not by zeros in the contrast transfer function. This means that in HREM images from these instruments there is often much lattice-scale information about periodicity phases at the exit surface of the specimen, along with the usual lattice information about spacings and interspot angles. Moreover, this information is not scrambled by zeros in the contrast transfer function. Because of the large amount (e.g. tens of megabytes) of data in individual HREM negatives, however, guidelines on finding as well as interpreting the useful phase information may be helpful.In work with micro-crystalline periodic structures (even those only a few unit cells across), our guidelines are the same as those used in setting up HREM zone axis images of single crystals: Look for regions of maximum symmetry in the intensity of lattice periodicities. The difference is that the search in HREM images is commonly done in direct space, whereas the search while tilting for a single crystal zone axis is commonly done in diffraction (i.e. reciprocal) space. We illustrate here with an example taken from a study of the complicated (and beam sensitive) family of PVO catalysts. Fig. 1 shows a region 2.3mm on a side from a 240kx negative of a fine-grained (VO)2P2O7 catalyst whose structure was not conclusively known, in part because of the difficulty of growing large crystals. The region, which represents only 7×10−4 of the negative area, was chosen as part of a promising crystal by inspection. The power spectrum of this image has a 7×7 array of spots which index nicely with the <010> projection of the candidate structure shown in Fig. 3a. A 2x closeup of Fig. 1 after Fourier window filtering of these periodicities is shown in Fig. 2. If the region with periodicities most nearly equal in strength is chosen again (here the lower left corner of Fig. 2), and the result is rotated to match the model orientation, Fig. 3b results. The correlation between image and model structure is striking. Some words of caution, of course, are in order. The periodicities observed are present in the specimen crystal, but the periodicity phases at best represent a map of exit surface electron properties. The rigorous connection between image and specimen atomic structure therefore requires knowledge of specimen thickness at least. Nonetheless, without an ability in direct space to recognize such regions of high symmetry, the correlation (rigorous or otherwise) would have remained hidden in a stack of TEM negatives.
Carbon Surfaces and Carbon Film Morphology Studied by Emission Electron Microscopy
Authors: Wang Congjun , Kordesch Martin E. 
Published: June 2020

Carbon is a pervasive contaminant on technologically important surfaces, and has long been of interest in surface science and microscopy. Recent advances in the production of high density carbon films and synthetic diamond films [1,2] have focused attention on the nucleation and growth of carbon on refractory metal substrates, semiconductors and other phases of carbon itself. Some of the issues involved are the role of carbides in promoting diamond nucleation and the specifics of graphite removal from the film through reactive sputtering or conversion to more dense phases (by as yet not understood processes).Emission microscopy, in particular photo- and thermal emission microscopy, is especially suited to the study of carbon film nucleation and growth. Carbides are easily observed. [3] Because several carbon phases have differing work functions, they may be selectively imaged by variation of the incident light wavelength, and thus the photoemission threshold, providing information on film composition in the image. Figures 1 and 2 show a Pt(100) surface covered with CO, atomic carbon and some graphitic areas, imaged with a microscope similar to the one in [3] using an HBO 100 lamp. [4] In figure 2 a 280 nm edge filter was placed in front of the lamp, so that only the graphitic areas (work function below 4.4 eV) are visible. Due to the image contrast in photoemission from differing materials, decoration of steps and defects by carbon is visible. In figure 3 step bunch edges on the Pt(100) surface have been decorated with carbon from the decomposition of ethylene; figure 4 shows another area of the surface where the terraces are carbon coated, and the step edges are “clean.” The slip trace features suggest that the dark lines are mono-atomic steps.[5]
Electron Channelling Contrast Imaging of Dislocations
Authors: Czernuszka J.T. , Long N.J. , Hirsch P.B. 
Published: June 2020

In the 1970s there was considerable interest in the development of the electron channelling contrast imaging (ECCI) technique for imaging near surface defects in bulk (electron opaque) specimens. The predictions of the theories were realised experimentally by Morin et al., who used a field emission gun (FEG) operating at 40-50kV and an energy filter such that only electrons which had lost no more than a few 100V were detected. This paper presents the results of a set of preliminary experiments which show that an energy filter system is unneccessary to image and characterise the Burgers vectors of dislocations in bulk specimens. The examples in the paper indicatethe general versatility of the technique.A VG HB501 STEM with a FEG was operated at 100kV. A single tilt cartridge was used in the reflection position of the microscope. A retractable back-scattered electron detector was fitted into the secondary electron port and positioned to within a few millimetres of the specimen. The image was acquired using a Synoptics Synergy framestore and digital scan generator and subsequently processed using Semper 6. The beam divergence with the specimen in this position was 2.5 mrads with a spot size of approximately 4nm. Electron channelling patterns were used to orientate the sample.
High-Resolution electron crystallography of the light-harvesting chlorophyll-a/b protein complex from chloroplast membranes
Authors: Kühlbrandt Werner , Wang Da Neng , Downing K.H. 
Published: June 2020

The light-harvesting chlorophyll-a/b protein complex (LHC-II) is the most abundant membrane protein in the chloroplasts of green plants where it functions as a molecular antenna of solar energy for photosynthesis. We have grown two-dimensional (2d) crystals of the purified, detergent-solubilized LHC-II . The crystals which measured 5 to 10 μm in diameter were stabilized for electron microscopy by washing with a 0.5% solution of tannin. Electron diffraction patterns of untilted 2d crystals cooled to 130 K showed sharp spots to 3.1 Å resolution. Spot-scan images of 2d crystals were recorded at 160 K with the Berkeley microscope . Images of untilted crystals were processed, using the unbending procedure by Henderson et al . A projection map of the complex at 3.7Å resolution was generated from electron diffraction amplitudes and high-resolution phases obtained by image processing .A difference Fourier analysis with the same image phases and electron diffraction amplitudes recorded of frozen, hydrated specimens showed no significant differences in the 3.7Å projection map. Our tannin treatment therefore does not affect the structural integrity of the complex.
The COVID-19 pandemic: a new challenge for syndromic surveillance
Authors: Elliot Alex J. , Harcourt Sally E. , Hughes Helen E. , Loveridge Paul , Morbey Roger A. , Smith Sue , Soriano Ana , Bains Amardeep , Smith Gillian E. , Edeghere Obaghe , Oliver Isabel 
Published: June 2020

Abstract
The COVID-19 pandemic is exerting major pressures on society, health and social care services and science. Understanding the progression and current impact of the pandemic is fundamental to planning, management and mitigation of future impact on the population. Surveillance is the core function of any public health system, and a multi-component surveillance system for COVID-19 is essential to understand the burden across the different strata of any health system and the population. Many countries and public health bodies utilise ‘syndromic surveillance’ (using real-time, often non-specific symptom/preliminary diagnosis information collected during routine healthcare provision) to supplement public health surveillance programmes. The current COVID-19 pandemic has revealed a series of unprecedented challenges to syndromic surveillance including: the impact of media reporting during early stages of the pandemic; changes in healthcare-seeking behaviour resulting from government guidance on social distancing and accessing healthcare services; and changes in clinical coding and patient management systems. These have impacted on the presentation of syndromic outputs, with changes in denominators creating challenges for the interpretation of surveillance data. Monitoring changes in healthcare utilisation is key to interpreting COVID-19 surveillance data, which can then be used to better understand the impact of the pandemic on the population. Syndromic surveillance systems have had to adapt to encompass these changes, whilst also innovating by taking opportunities to work with data providers to establish new data feeds and develop new COVID-19 indicators. These developments are supporting the current public health response to COVID-19, and will also be instrumental in the continued and future fight against the disease.
Growth and longevity of the Antarctic scallopAdamussium colbeckiunder annual and multiannual sea ice
Authors: Cronin Kelly E. , Walker Sally E. , Mann Roger , Chute Antonie S. , Long M. Chase , Bowser Samuel S. 
Published: June 2020

AbstractEcosystem engineers such as the Antarctic scallop (Adamussium colbecki) shape marine communities. Thus, changes to their lifespan and growth could have far-reaching effects on other organisms. Sea ice is critical to polar marine ecosystem function, attenuating light and thereby affecting nutrient availability. Sea ice could therefore impact longevity and growth in polar bivalves unless temperature is the overriding factor. Here, we compare the longevity and growth ofA. colbeckifrom two Antarctic sites: Explorers Cove and Bay of Sails, which differ by sea-ice cover, but share similar seawater temperatures, the coldest on Earth (-1.97°C). We hypothesize that scallops from the multiannual sea-ice site will have slower growth and greater longevity. We found maximum ages to be similar at both sites (18–19 years). Growth was slower, with higher inter-individual variability, under multiannual sea ice than under annual sea ice, which we attribute to patchier nutrient availability under multiannual sea ice. Contrary to expectations,A. colbeckigrowth, but not longevity, is affected by sea-ice duration when temperatures are comparable. Recent dramatic reductions in Antarctic sea ice and predicted temperature increases may irrevocably alter the life histories of this ecosystem engineer and other polar organisms.
Dissimilarity–Overlap analysis of replicate enrichment communities
Authors: Vila Jean C C , Liu Yang-Yu , Sanchez Alvaro 
Published: June 2020

Abstract
The taxonomic composition of microbial communities can vary substantially across habitats and within the same habitat over time. Efforts to build quantitative and predictive models of microbial population dynamics are underway, but fundamental questions remain. How different are population dynamics in different environments? Do communities that share the same taxa also exhibit identical dynamics? In vitro communities can help establish baseline expectations that are critical towards resolving these questions in natural communities. Here, we applied a recently developed tool, Dissimilarity–Overlap Analysis (DOA), to a set of experimental in vitro communities that differed in nutrient composition. The Dissimilarity and Overlap of these communities are negatively correlated in replicate habitats, as one would expect if microbial population dynamics were on average strongly convergent (or “universal”) across these replicate habitats. However, the existence of such a negative correlation does not necessarily imply that population dynamics are always universal in all communities. Even in replicate, identical habitats, two different communities may contain the same set of taxa at different abundances in equilibrium. The formation of alternative states in community assembly is strongly associated with the presence of specific taxa in the communities. Our results benchmark DOA, providing support for some of its core assumptions, and suggest that communities sharing the same taxa and external abiotic factors generally (but not necessarily) have a negative correlation between Dissimilarity and Overlap.
Mapping PTSD symptoms to brain networks: a machine learning study
Authors: Zandvakili Amin , Barredo Jennifer , Swearingen Hannah R. , Aiken Emily M. , Berlow Yosef A. , Greenberg Benjamin D. , Carpenter Linda L. , Philip Noah S. 
Published: June 2020

AbstractPosttraumatic Stress Disorder (PTSD) is a prevalent and debilitating condition with complex and variable presentation. While PTSD symptom domains (intrusion, avoidance, cognition/mood, and arousal/reactivity) correlate highly, the relative importance of these symptom subsets often differs across patients. In this study, we used machine learning to derive how PTSD symptom subsets differ based upon brain functional connectivity. We acquired resting-state magnetic resonance imaging in a sample (N = 50) of PTSD patients and characterized clinical features using the PTSD Checklist for DSM-5 (PCL-5). We compared connectivity among 100 cortical and subcortical regions within the default mode, salience, executive, and affective networks. We then used principal component analysis and least-angle regression (LARS) to identify relationships between symptom domain severity and brain networks. We found connectivity predicted PTSD symptom profiles. The goodness of fit (R2) for total PCL-5 score was 0.29 and theR2for intrusion, avoidance, cognition/mood, and arousal/reactivity symptoms was 0.33, 0.23, −0.01, and 0.06, respectively. The model performed significantly better than chance in predicting total PCL-5 score (p = 0.030) as well as intrusion and avoidance scores (p = 0.002 andp = 0.034). It was not able to predict cognition and arousal scores (p = 0.412 andp = 0.164). While this work requires replication, these findings demonstrate that this computational approach can directly link PTSD symptom domains with neural network connectivity patterns. This line of research provides an important step toward data-driven diagnostic assessments in PTSD, and the use of computational methods to identify individual patterns of network pathology that can be leveraged toward individualized treatment.
Long noncoding RNA DLEU2 predicts a poor prognosis and enhances malignant properties in laryngeal squamous cell carcinoma through the miR-30c-5p/PIK3CD/Akt axis
Authors: Li Xiaoming , Xu Fenglei , Meng Qiu , Gong Ningyue , Teng Zhenxiao , Xu Runtong , Zhao Miaoqing , Xia Ming 
Published: June 2020

AbstractLong noncoding RNAs (lncRNAs) have been identified as potential prognostic tools and therapeutic biomarkers for a variety of human cancers. However, the functional roles and underlying mechanisms of key lncRNAs affecting laryngeal squamous cell carcinomas (LSCCs) are largely unknown. Here, we adopted a novel subpathway strategy based on the lncRNA-mRNA profiles from the Cancer Genome Atlas (TCGA) database and identified the lncRNA deleted in lymphocytic leukemia 2 (DLEU2) as an oncogene in the pathogenesis of LSCCs. We found that DLEU2 was significantly upregulated and predicted poor clinical outcomes in LSCC patients. In addition, ectopic overexpression of DLEU2 promoted the proliferation and migration of LSCC cells both in vivo and in vitro. Mechanistically, DLEU2 served as a competing endogenous RNA to regulate PIK3CD expression by sponging miR-30c-5p and subsequently activated the Akt signaling pathway. As a target gene of DLEU2, PIK3CD was also upregulated and could predict a poor prognosis in LSCC patients. In conclusion, we found that the novel LSCC-related gene DLEU2 enhances the malignant properties of LSCCs via the miR-30c-5p/PIK3CD/Akt axis. DLEU2 and its targeted miR-30c-5p/PIK3CD/Akt axis may represent valuable prognostic biomarkers and therapeutic targets for LSCCs.
An operator-theoretical study of the specific heat and the critical magnetic field in the BCS-Bogoliubov model of superconductivity
Authors: Watanabe Shuji 
Published: June 2020

AbstractIn the preceding paper, introducing a cutoff, the present author gave a proof of the statement that the transition to a superconducting state is a second-order phase transition in the BCS-Bogoliubov model of superconductivity on the basis of fixed-point theorems, and solved the long-standing problem of the second-order phase transition from the viewpoint of operator theory. In this paper we study the temperature dependence of the specific heat and the critical magnetic field in the model from the viewpoint of operator theory. We first show some properties of the solution to the BCS-Bogoliubov gap equation with respect to the temperature, and give the exact and explicit expression for the gap in the specific heat divided by the specific heat. We then show that it does not depend on superconductors and is a universal constant. Moreover, we show that the critical magnetic field is smooth with respect to the temperature, and point out the behavior of both the critical magnetic field and its derivative. Mathematics Subject Classification 2010. 45G10, 47H10, 47N50, 82D55.
Dimethylsulfoniopropionate concentration in coral reef invertebrates varies according to species assemblages
Authors: Guibert Isis , Bourdreux Flavien , Bonnard Isabelle , Pochon Xavier , Dubousquet Vaimiti , Raharivelomanana Phila , Berteaux-Lecellier Véronique , Lecellier Gael 
Published: June 2020

AbstractDimethylsulfoniopropionate (DMSP) is a key compound in the marine sulfur cycle, and is produced in large quantities in coral reefs. In addition to Symbiodiniaceae, corals and associated bacteria have recently been shown to play a role in DMSP metabolism. Numerous ecological studies have focused on DMSP concentrations in corals, which led to the hypothesis that increases in DMSP levels might be a general response to stress. Here we used multiple species assemblages of three common Indo-Pacific holobionts, the scleractinian corals Pocillopora damicornis and Acropora cytherea, and the giant clam Tridacna maxima and examined the DMSP concentrations associated with each species within different assemblages and thermal conditions. Results showed that the concentration of DMSP in A. cytherea and T. maxima is modulated according to the complexity of species assemblages. To determine the potential importance of symbiotic dinoflagellates in DMSP production, we then explored the relative abundance of Symbiodiniaceae clades in relation to DMSP levels using metabarcoding, and found no significant correlation between these factors. Finally, this study also revealed the existence of homologs involved in DMSP production in giant clams, suggesting for the first time that, like corals, they may also contribute to DMSP production. Taken together, our results demonstrated that corals and giant clams play important roles in the sulfur cycle. Because DMSP production varies in response to specific species-environment interactions, this study offers new perspectives for future global sulfur cycling research.
Recycling pathways in cold-water coral reefs: Use of dissolved organic matter and bacteria by key suspension feeding taxa
Authors: Maier Sandra R. , Kutti Tina , Bannister Raymond J. , Fang James Kar-Hei , van Breugel Peter , van Rijswijk Pieter , van Oevelen Dick 
Published: June 2020

AbstractCold-water coral (CWC) reefs are one of the most diverse and productive ecosystems in the deep sea. Especially in periods of seasonally-reduced phytodetritus food supply, their high productivity may depend on the recycling of resources produced on the reef, such as dissolved organic matter (DOM) and bacteria. Here, we demonstrate that abundant suspension feeders Geodia barretti (high-microbial-abundance sponge), Mycale lingua (low-microbial-abundance sponge) and Acesta excavata (bivalve) are able to utilize 13C-enriched (diatom-derived) DOM and bacteria for tissue growth and respiration. While DOM was an important potential resource for all taxa, utilization of bacteria was higher for the sponges as compared to the bivalve, indicating a particle-size differentiation among the investigated suspension feeders. Interestingly, all taxa released 13C-enriched particulate organic carbon, which in turn may feed the detritus pathway on the reef. Especially A. excavata produced abundant (pseudo-)fecal droppings. A second stable-isotope tracer experiment revealed that detritivorous ophiuroids utilized these droppings. The high resource flexibility of dominant reef suspension feeders, and the efficient recycling of their waste products by the detritivore community, may provide important pathways to maintain the high productivity on cold-water coral reefs, especially in periods of low external food supply.
Quantifying the immediate computational effects of preceding outcomes on subsequent risky choices
Authors: Brooks Hayley R. , Sokol-Hessner Peter 
Published: June 2020

AbstractForty years ago, prospect theory introduced the notion that risky options are evaluated relative to their recent context, causing a significant shift in the study of risky monetary decision-making in psychology, economics, and neuroscience. Despite the central role of past experiences, it remains unclear whether, how, and how much past experiences quantitatively influence risky monetary choices moment-to-moment in a nominally learning-free setting. We analyzed a large dataset of risky monetary choices with trial-by-trial feedback to quantify how past experiences, or recent events, influence risky choice behavior and the underlying processes. We found larger recent outcomes both negatively influence subsequent risk-taking and positively influence the weight put on potential losses. Using a hierarchical Bayesian framework to fit a modified version of prospect theory, we demonstrated that the same risks will be evaluated differently given different past experiences. The computations underlying risky decision-making are fundamentally dynamic, even if the environment is not.