bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural Studies on the Eukaryotic Ribosome
Authors: Verschoor Adriana , Milligan Ronald , Srivastava Suman , Frank Joachim
Published: June 2020

We have studied the eukaryotic ribosome from two vertebrate species (rabbit reticulocyte and chick embryo ribosomes) in several different electron microscopic preparations (Fig. 1a-d), and we have applied image processing methods to two of the types of images. Reticulocyte ribosomes were examined in both negative stain (0.5% uranyl acetate, in a double-carbon preparation) and frozen hydrated preparation as single-particle specimens. In addition, chick embryo ribosomes in tetrameric and crystalline assemblies in frozen hydrated preparation have been examined. 2D averaging, multivariate statistical analysis, and classification methods have been applied to the negatively stained single-particle micrographs and the frozen hydrated tetramer micrographs to obtain statistically well defined projection images of the ribosome (Fig. 2a,c). 3D reconstruction methods, the random conical reconstruction scheme and weighted back projection, were applied to the negative-stain data, and several closely related reconstructions were obtained. The principal 3D reconstruction (Fig. 2b), which has a resolution of 3.7 nm according to the differential phase residual criterion, can be compared to the images of individual ribosomes in a 2D tetramer average (Fig. 2c) at a similar resolution, and a good agreement of the general morphology and of many of the characteristic features is seen.

Both data sets show the ribosome in roughly the same ’view’ or orientation, with respect to the adsorptive surface in the electron microscopic preparation, as judged by the agreement in both the projected form and the distribution of characteristic density features. The negative-stain reconstruction reveals details of the ribosome morphology; the 2D frozen-hydrated average provides projection information on the native mass-density distribution within the structure. The 40S subunit appears to have an elongate core of higher density, while the 60S subunit shows a more complex pattern of dense features, comprising a rather globular core, locally extending close to the particle surface.
High Resolution Scanning Electron Microscopy of Surfaces
Authors: Cowley J.M.
Published: June 2020

Electron beams of small diameter, generated with field emission guns may be used to investigate surfaces in many different ways. Images may be formed in the scanning mode by use of the elastically, or quasi-elastically scattered electrons or by the detection of secondary radiation including low energy secondary electrons, Auger electrons and X-rays. Except in the case of low-energy secondary electrons, high spatial resolution has not yet been achieved by detection of the secondary radiations so these imaging modes will not be discussed here.

The scanning modes used with the detection of elastic or quasi-elastic electrons in a dedicated STEM instrument are analogous to those used in conventional TEM instruments for surface studies, such as profile imaging and reflection electron microscopy. In each case, the practical limitations of current STEM systems tend to limit the quality of the imaging but the flexibility of the STEM detector system has provided several important advantages. In scanning reflection microscopy (SREM) the resolution attained is comparable with that for REM. The important advantage over REM is that microdiffraction patterns may be obtained from any surface features as small as the resolution limit for imaging. Also it is relatively easy to make use of the surface channelling conditions in order to enhance the contrast of surface steps or other surface features.
Comparison of Low-and High-Voltage SEM Images of Beryllium
Authors: Price C. W.
Published: June 2020

Beryllium has a low secondary electron (SE) coefficient that produces a low signal-to-noise ratio, and in the past, this deficiency caused many workers to routinely coat beryllium with a high-Z material such as Au/Pd and examine the specimens at high voltage (HV). In principle, beryllium should be an ideal candidate for improved imaging with low voltage (LV), because its low atomic number permits excessive electron-beam penetration during HVSEM imaging — the use of LVSEM to analyze beryllium films was demonstrated previously. Unfortunately, low SE emission can seriously compromise LVSEM images from uncoated beryllium specimens, even with the improved LVSEM imaging capability of a SEM equipped with a field-emission gun (FESEM). This work demonstrates that some beryllium structures yield improved results with LVSEM imaging in a FESEM, particularly at low magnifications, while structures that require high magnification often yield better results with HVSEM.

Specimens selected for this study include craters formed by a Cs+ ion beam in specimens that had been analyzed in an ion microanalyzer by secondary-ion mass spectroscopy (SIMS), machined surfaces, and fracture surfaces. SE images were obtained for this study with a Hitachi S-800 FESEM equipped with a cryogenic vacuum pumping system.

Surface structure in a sputtered SIMS crater is shown at 2.0 kV in Fig. 1a and at 20 kV in Fig. 1b. This specimen was from commercial grade beryllium sheet. Prominent microtwins are visible in several grains in Fig. 1, and because of the excessive beam penetration at HV, the microtwins are better defined at LV in Fig. 1a than they are at HV in Fig. 1b. In addition, a fine faceted microstructure was formed by the ion beam that could be observed at intermediate magnifications, and it also was better defined at LV than at HV. The dark contamination film that is visible around some of the particles in Fig. 1a also is significant; this film was not apparent at voltages of 5 kV and higher, as demonstrated in Fig. 1b. SIMS ion images revealed that this material contained particles of several different compositions including carbides; since beryllium carbide hydrolyzes when exposed to moist air, the films are suspected to have formed by the decomposition of carbides when the specimen was removed from the ion microanalyzer after the SIMS analysis. This example demonstrates the excellent sensitivity of LVSEM to detect thin films, and it also suggests that contamination and the thin oxide film that forms on beryllium may impair SE imaging.
Generalized C-Means Algorithms for Medical Image Analysis
Authors: Bezdek James C.
Published: June 2020

Diagnostic machine vision systems that attempt to interpret medical imagery almost always include (and depend upon) one or more pattern recognition algorithms (cluster analysis and classifier design) for low and intermediate level image data processing. This includes, of course, image data collected by electron microscopes. Approaches based on both statistical and fuzzy models are found in the texts by Bezdek, Duda and Hart, Dubes and Jain,and Pao. Our talk examines the c-means families as they relate to medical image processing. We discuss and exemplify applications in segmentation (MRI data); clustering (flow cytometry data); and boundary analysis.

The structure of partition spaces underlying clustering algorithms is described briefly. Let (c) be an integer, 1n and let X = {x1, x2, ..., xn} denote a set of (n) column vectors in Rs. X is numerical object data; the k-th object (some physical entity such as a medical patient, PAP smear image, color photograph, etc.) has xk as its numerical representation; xkj is the j-th characteristic (or feature) associated with object k.
Tomographic Reconstructions of 0.25 μm-Thick Serial Sections of a Mammalian Kinetochore
Authors: Liu Y. , McEwen B.F. , Rieder C.L. , Frank J.
Published: June 2020

The kinetochore has been the subject of considerable recent research prompted, in part, by recent results indicating that the molecular motors for chromosomes movement are located within the kinetochore. In sectioned material it appears as a trilaminar structure containing two densely stained plates separated by a lightly stained zone. In colcemid treated cells, only the outer two zones are visible and a dense fibrous corona is observed radiating out from the outer plate. We have previously used high-voltage EM (HVEM) and computer image processing to obtain three-dimensional (3D) information about a single kinetochore from colcemid treated PtKl cells. Since then we have computed 3D reconstructions of a sister pair from similar cells in 0.25 μm-thick serial sections. Each kinetochore was present in three sections and reconstructions were computed for kinetochores in the middle and one of the end sections. The tilt series collected from the middle section has a range from −64° to 64° with an angular interval of 2°, while the tilt series collected from the end section has a tilt range from −60° to 59° with the same angular interval. All micrographs were recorded in the HVEM at 1 MV (Fig. 1) and aligned as previously described. The 3D reconstructions were computed by weighted back-projection.
Industrial Applications and Future Directions
Authors: Labun P.A.
Published: June 2020

In recent years the industrial community has become increasingly aware that in order to understand complex materials they require both high resolution imaging (<.2nm) and high spatial resolution microanalysis (≤2.0nm). In working with the members of the Industrial Associates Program at Arizona State University, we have come to recognize and acknowledge these needs and to accept that such needs are on the increase. Each new project has involved complex and difficult analyses, pushing the limits of available technology. The following outlined examples highlight some of the work currently in progress.

Zeolites (molecular sieve materials): Of primary importance in utilizing these materials is structural determination of many of the new compounds that are being synthesized. In order to ascertain the complete structure, high-resolution images approaching .2nm are necessary. Considering the severe beam sensitivity of these materials, it is extremely difficult to acquire images that are close to optimum defocus, without drift and damage. Recently, however, with on-line image acquisition systems becoming available, an image can be captured in 1/30th of a second with very low beam doses and effectively no drift present. Contrast enhancement and band filtering (a ring filter cutting off low and high frequencies; the ring is the same in all directions) make it possible to greatly improve the image detail and thus improve the prospects of developing a crystal structure model, (see Fig. 1a,b).
High Resolution Cryo-Electron Microscopy Sheds A New Light Upon Biomembrane Architecture
Authors: Nahoaki Kume P. , Akiko Yuba D. , Akiyasu Yoshizawa C. , Satoshi Sato B. , Yoshinori Fujiyoshi
Published: June 2020

Cryo-electron microscopy, together with the rapid cryo-fixation technique, has made it possible to observe chemically unfixed unstained specimens under a transmission electron microscope. Aoki et al. constructed a new cryo-stage in order to reduce irradiation damage upon biological specimens further by cooling them with liquid helium. It was also designed to eliminate shaking of specimens as much as possible by the sophisticated mounting and the refined cooling mechanism of the stage. The stage has proved to achieve a higher contrast and higher resolution of images than a commonly-used cryo-stage cooled solely by liquid nitrogen does. This high resolution cryo-electron microscope (HiRCEM) was originally developed aiming at the improvement of resolution in structural analysis of proteins or nucleic acids, but it has turned out to be quite useful for detecting the architecture of biomembranes as well. This is due to the existence of phosphorus atoms of phospholipids which are heavier than C, H, O, N atoms abundant within biomembranes, and also due to the great optical depth of the membrane where it is aligned parallel to the electron beams.

We have examined several kinds of biomembranes as well as the synthesized liposomes under HiRCEM. Among them were the plasma membrane of human erythrocytes (ghosts), the nuclear membrane of chicken erythrocytes, the endoplasmic reticular membrane of rat nerve cells, the chromatophore membrane of a photosynthetic bacterium Chromatium vinosum , the thylakoid membrane of spinach chloroplasts and the envelope of influenza type A virus (PR8 & X31). Liposomes we employed were synthesized from the 2:1 mixture of phosphatidylcholine and cholesterol.
From Static Images To Dynamic Structures: The Use of Image Analysis and Video In Deriving Dynamical Information From Electron Microscopy
Authors: Egelman Edward H.
Published: June 2020

Advances in computer graphics and numerical processing, in video technology, and in image acquisition have enabled us to extend the power of the electron microscope in the analysis of macromolecular structures, particularly helical protein polymers. Three applications of this technology will be described:

1) There are frequently times where the static images acquired from fixed, stained or frozen specimens leads to a loss of information about the dynamical properties of the molecules or structures being studied. We have been using computed image analysis, graphics and animation to recover the dynamical information that can be obtained from electron microscopic images.

Using the RecA protein of E. coli , we have been able to capture different biochemical states as a function of time through the use of a slowly hydrolyzable ATP analog, ATP-γ-S. Threedimensional reconstruction of these helical structures, combined with computer-generated animation between different structures, have enabled us to directly visualize the motions within the protein polymer associated with the hydrolysis of the nucleotide analog. Modifications of the RecA protein, achieved through either proteolysis or mutation, have allowed us to use the same techniques to visualize domain-domain movements within the RecA filament which occur over a range of 5-10Å. The methods of analysis, graphics and animation which have been used will be discussed. The general applicability of these procedures to other systems will also be addressed.
Processing Video Images of Chemical Reactions
Authors: LeRoy Eyring , de Ruijter W.J.
Published: June 2020

The high-resolution transmission electron microscope is unique in its capacity to provide direct images of bulk matter at the atomic level. This suggests the electron microscope as a nanochemical laboratory in which elementary reaction mechanisms can be observed and deciphered. The nature, disposition, and evolution of defects, the agents of chemical change, must be studied intimately if the fundamentals of chemical reactivity in solids are to be understood fully. Chemical change during microscopical observation is inevitable since alterations in the electronic associations of the atoms are produced by the electron beam. For a chemist this presents an extraordinary opportunity for investigating the atomic-level mechanism of a chemical reaction.

Chemical reactions observed at near atomic resolution can be recorded on videotape at the rate of 30 images per second. Since the onset, extent and rapidity of a reaction varies over many orders of magnitude and is not predictable it is sometimes necessary to record for hours. The videotape provides a convenient storage medium for this immense quantity of information. The tapes can then be edited for those stretches bearing pertinent information and can be processed as needed. The purpose may simply be clear communication of scientific information to peers or more extensive processing may be desired for pedagogical use.
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

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

Ecosystem 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.
ENHANCED FINITE TRIANGULATED CATEGORIES
Authors: Muro Fernando
Published: June 2020

We give a necessary and sufficient condition for the existence of an enhancement of a finite triangulated category. Moreover, we show that enhancements are unique when they exist, up to Morita equivalence.
Digitalisierung an Pflegeschulen
Authors: Siebert Jeanette
Published: June 2020

Zusammenfassung. E-Learning und digital gestütztes Simulationslernen werden in deutschen Pflegeschulen eher ungern eingesetzt. Der Grund hierfür kann der mediale Habitus der Lehrenden sein, die digitale Kommunikation und das digitale Lehren und Lernen im Hinblick auf die Erreichung der Lehr- und Lernziele ablehnen. Um Lehrende bei der Implementierung von digitalen Medien zu unterstützen, bedarf es eines pädagogischen Konzeptes, welches auf die Anbahnung von medialen und digitalen Kompetenzen bei den Lehrenden abzielt.
Nudging: Ein „sanfter Weg“ zu gesundheitsbewusstem Verhalten?
Authors: Staudacher Diana
Published: June 2020

Zusammenfassung. Menschen ohne Zwang dazu bewegen, „gute Entscheidungen“ zu treffen – das ist das Ziel von „Nudging“. Diese Strategie der Verhaltensökonomie kommt auch im Gesundheitswesen verstärkt zum Einsatz. „Nudging“ gibt zwar vor, die menschliche Freiheit zu achten. Die Grenze zur Manipulation ist jedoch fließend. Was sollten Pflegefachpersonen über Nudging wissen? Wie wirksam sind Nudging-Strategien und welche ethischen Fragen werfen sie auf?
Europe Launches Biodiversity Strategy for the Coming Decade
Authors: Dacey James
Published: June 2020

Amid the coronavirus uncertainty, the European Union is standing by its Green Deal pledges.
Dissimilarity–Overlap analysis of replicate enrichment communities
Authors: Vila Jean C C , Liu Yang-Yu , Sanchez Alvaro
Published: June 2020

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

Posttraumatic 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

Long 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

In 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

Dimethylsulfoniopropionate (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

Cold-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

Forty 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.
The influence of hypoxia and energy depletion on the response of endothelial cells to the vascular disrupting agent combretastatin A-4-phosphate
Authors: Holmes Toby , Brown Andrew W. , Suggitt Marie , Shaw Lucy A. , Simpson Lucy , Harrity Joseph P. A. , Tozer Gillian M. , Kanthou Chryso
Published: June 2020

Combretastatin A-4 phosphate (CA4P) is a microtubule-disrupting tumour-selective vascular disrupting agent (VDA). CA4P activates the actin-regulating RhoA-GTPase/ ROCK pathway, which is required for full vascular disruption. While hypoxia renders tumours resistant to many conventional therapies, little is known about its influence on VDA activity. Here, we found that active RhoA and ROCK effector phospho-myosin light chain (pMLC) were downregulated in endothelial cells by severe hypoxia. CA4P failed to activate RhoA/ROCK/pMLC but its activity was restored upon reoxygenation. Hypoxia also inhibited CA4P-mediated actinomyosin contractility, VE-cadherin junction disruption and permeability rise. Glucose withdrawal downregulated pMLC, and coupled with hypoxia, reduced pMLC faster and more profoundly than hypoxia alone. Concurrent inhibition of glycolysis (2-deoxy-D-glucose, 2DG) and mitochondrial respiration (rotenone) caused profound actin filament loss, blocked RhoA/ROCK signalling and rendered microtubules  CA4P-resistant. Withdrawal of the metabolism inhibitors restored the cytoskeleton and CA4P activity. The AMP-activated kinase AMPK was investigated as a potential mediator of pMLC downregulation. Pharmacological AMPK activators that generate AMP, unlike allosteric activators, downregulated pMLC but only when combined with 2DG and/or rotenone. Altogether, our results suggest that Rho/ROCK and actinomyosin contractility are regulated by AMP/ATP levels independently of AMPK, and point to hypoxia/energy depletion as potential modifiers of CA4P response.
Wolf habitat selection when sympatric or allopatric with brown bears in Scandinavia
Authors: Ordiz Andrés , Uzal Antonio , Milleret Cyril , Sanz-Pérez Ana , Zimmermann Barbara , Wikenros Camilla , Wabakken Petter , Kindberg Jonas , Swenson Jon E. , Sand Håkan
Published: June 2020

Habitat selection of animals depends on factors such as food availability, landscape features, and intra- and interspecific interactions. Individuals can show several behavioral responses to reduce competition for habitat, yet the mechanisms that drive them are poorly understood. This is particularly true for large carnivores, whose fine-scale monitoring is logistically complex and expensive. In Scandinavia, the home-range establishment and kill rates of gray wolves (Canis lupus) are affected by the coexistence with brown bears (Ursus arctos). Here, we applied resource selection functions and a multivariate approach to compare wolf habitat selection within home ranges of wolves that were either sympatric or allopatric with bears. Wolves selected for lower altitudes in winter, particularly in the area where bears and wolves are sympatric, where altitude is generally higher than where they are allopatric. Wolves may follow the winter migration of their staple prey, moose (Alces alces), to lower altitudes. Otherwise, we did not find any effect of bear presence on wolf habitat selection, in contrast with our previous studies. Our new results indicate that the manifestation of a specific driver of habitat selection, namely interspecific competition, can vary at different spatial-temporal scales. This is important to understand the structure of ecological communities and the varying mechanisms underlying interspecific interactions.
Sex differences in the genetic architecture of depression
Authors: Kang Hee-Ju , Park Yoomi , Yoo Kyung-Hun , Kim Ki-Tae , Kim Eun-Song , Kim Ju-Wan , Kim Sung-Wan , Shin Il-Seon , Yoon Jin-Sang , Kim Ju Han , Kim Jae-Min
Published: June 2020

The prevalence and clinical characteristics of depressive disorders differ between women and men; however, the genetic contribution to sex differences in depressive disorders has not been elucidated. To evaluate sex-specific differences in the genetic architecture of depression, whole exome sequencing of samples from 1000 patients (70.7% female) with depressive disorder was conducted. Control data from healthy individuals with no psychiatric disorder (n = 72, 26.4% female) and East-Asian subpopulation 1000 Genome Project data (n = 207, 50.7% female) were included. The genetic variation between men and women was directly compared using both qualitative and quantitative research designs. Qualitative analysis identified five genetic markers potentially associated with increased risk of depressive disorder in females, including three variants (rs201432982 within PDE4A, and rs62640397 and rs79442975 within FDX1L) mapping to chromosome 19p13.2 and two novel variants (rs820182 and rs820148) within MYO15B at the chromosome 17p25.1 locus. Depressed patients homozygous for these variants showed more severe depressive symptoms and higher suicidality than those who were not homozygotes (i.e., heterozygotes and homozygotes for the non-associated allele). Quantitative analysis demonstrated that the genetic burden of protein-truncating and deleterious variants was higher in males than females, even after permutation testing. Our study provides novel genetic evidence that the higher prevalence of depressive disorders in women may be attributable to inherited variants.
Streptococcus agalactiae in childbearing age immigrant women in Comunitat Valenciana (Spain)
Authors: Sahuquillo-Arce José Miguel , Hernández-Cabezas Alicia , Castaño-Aroca María Jesús , Chouman-Arcas Rabab , Díaz-Aguirre Estefanía , Acosta-Boga Beatriz , López-Hontangas José Luis
Published: June 2020

Streptococcus agalactiae (GBS) remains the leading cause of meningitis and neonatal sepsis in the world, and causes disease in pregnant and puerperal women. This is a retrospective study of GBS infections on women of childbearing age living in Comunitat Valenciana, Spain (years 2009–2014) and GBS colonization rate on pregnant women attending Hospital La Fe (years 2013–2015) according to their origin. An aggregated total of 6,641,960 women exposed during the study period had an average GBS isolation rate of 5.19‰ (5.14–5.25‰), geographical group rates being: Western Europe (2.2‰), North America (2.1‰), Australia (3.7‰), Spain (4.6‰), Latin America II (4.5‰), Eastern Europe (5.3‰), Asia (6.7‰), Latin America I (7.7‰), Middle East (7.9‰), Indian Subcontinent (17.2‰), North Africa (17.8‰), Sub-Saharan Africa (22.7‰). The 4532 pregnant women studied had an average GBS colonization rate of 12.47% (11.51–13.43) and geographical group rates varied similar to geographical isolation rates. Low GDP and high temperatures of the birth country were associated with higher colonization rates. Thus, differences in GBS colonization depend on the country of origin; Africa and the Indian subcontinent presented the highest, while Western Europe and North America had the lowest. This variability portrays a geographical pattern influenced by temperature and GDP.
The bovine cumulus proteome is influenced by maturation condition and maturational competence of the oocyte
Authors: Walter J. , Monthoux C. , Fortes C. , Grossmann J. , Roschitzki B. , Meili T. , Riond B. , Hofmann-Lehmann R. , Naegeli H. , Bleul U.
Published: June 2020

In vitro maturation (IVM) of oocytes has still a negative impact on the developmental competence of oocytes. Therefore, this study analysed the cumulus proteome of individual cumulus-oocyte complexes (COCs) with and without maturational competence, matured under in vivo or in vitro conditions (n = 5 per group). A novel, ultrasensitive mass spectrometry (MS) based protein profiling approach, using label-free quantification, was applied. The detected cumulus proteome included 2226 quantifiable proteins and was highly influenced by the maturation condition (479 differentially expressed proteins) as well as maturational competence of the corresponding oocyte (424 differentially expressed proteins). Enrichment analysis showed an overrepresentation of the complement and coagulation cascades (CCC), ECM-receptor interaction and steroid biosynthesis in cumulus of COCs that matured successfully under in vivo conditions. Verification of the origin of CCC proteins was achieved through detection of C3 secretion into the maturation medium, with significantly increasing concentrations from 12 (48.4 ng/ml) to 24 hours (68 ng/ml: p < 0.001). In relation, concentrations in follicular fluid, reflecting the in vivo situation, were >100x higher. In summary, this study identified important pathways that are impaired in IVM cumulus, as well as potential markers of the maturational competence of oocytes.