Ribonanza: deep learning of RNA structure through dual crowdsourcing

Prediction of RNA structure from sequence remains an unsolved problem, and progress has been slowed by a paucity of experimental data. Here, we present Ribonanza, a dataset of chemical mapping measurements on two million diverse RNA sequences collected through Eterna and other crowdsourced initiatives. Ribonanza measurements enabled solicitation, training, and prospective evaluation of diverse deep neural networks through a Kaggle challenge, followed by distillation into a single, self-contained model called RibonanzaNet. When fine tuned on auxiliary datasets, RibonanzaNet achieves state-of-the-art performance in modeling experimental sequence dropout, RNA hydrolytic degradation, and RNA secondary structure, with implications for modeling RNA tertiary structure.

In vivo characterization of the novel ebolavirus Bombali virus suggests a low pathogenic potential for humans

Ebolaviruses cause outbreaks of haemorrhagic fever in Central and West Africa. Some members of this genus such as Ebola virus (EBOV) are highly pathogenic, with case fatality rates of up to 90%, whereas others such as Reston virus (RESTV) are apathogenic for humans. Bombali virus (BOMV) is a novel ebolavirus for which complete genome sequences were recently found in free-tailed bats, although no infectious virus could be isolated. Its pathogenic potential for humans is unknown. To address this question, we first determined whether proteins encoded by the available BOMV sequence found in Chaerephon pumilus were functional in in vitro assays. The correction of an apparent sequencing error in the glycoprotein based on these data then allowed us to generate infectious BOMV using reverse genetics and characterize its infection of human cells. Furthermore, we used HLA-A2-transgenic, NOD-scid-IL-2γ receptor-knockout (NSG-A2) mice reconstituted with human haematopoiesis as a model to evaluate the pathogenicity of BOMV in vivo in a human-like immune environment. These data demonstrate that not only does BOMV show a slower growth rate than EBOV in vitro, but it also shows low pathogenicity in humanized mice, comparable to previous studies using RESTV. Taken together, these findings suggest a low pathogenic potential of BOMV for humans.

Soft wetting with (a)symmetric Shuttleworth effect

The wetting of soft polymer substrates brings in multiple complexities when compared with the wetting on rigid substrates. The contact angle of the liquid is no longer governed by Young’s Law, but is affected by the substrate’s bulk and surface deformations. On top of that, elastic interfaces exhibit a surface energy that depends on how much they are stretched—a feature known as the Shuttleworth effect (or as surface-elasticity). Here, we present two models through which we explore the wetting of drops in the presence of a strong Shuttleworth effect. The first model is macroscopic in character and consistently accounts for large deformations via a neo-Hookean elasticity. The second model is based on a mesoscopic description of wetting, using a reduced description of the substrate’s elasticity. While the second model is more empirical in terms of the elasticity, it enables a gradient dynamics formulation for soft wetting dynamics. We provide a detailed comparison between the equilibrium states predicted by the two models, from which we deduce robust features of soft wetting in the presence of a strong Shuttleworth effect. Specifically, we show that the (a)symmetry of the Shuttleworth effect between the ‘dry’ and ‘wet’ states governs horizontal deformations in the substrate. Our results are discussed in the light of recent experiments on the wettability of stretched substrates.

Microbial diversity characterization of seawater in a pilot study using Oxford Nanopore Technologies long-read sequencing

OBJECTIVE

Currently the majority of non-culturable microbes in sea water are yet to be discovered, Nanopore offers a solution to overcome the challenging tasks to identify the genomes and complex composition of oceanic microbiomes. In this study we evaluate the utility of Oxford Nanopore Technologies (ONT) sequencing to characterize microbial diversity in seawater from multiple locations. We compared the microbial species diversity of retrieved environmental samples from two different locations and time points.

RESULTS

With only three ONT flow cells we were able to identify thousands of organisms, including bacteriophages, from which a large part at species level. It was possible to assemble genomes from environmental samples with Flye. In several cases this resulted in > 1 Mbp contigs and in the particular case of a Thioglobus singularis species it even produced a near complete genome. k-mer analysis reveals that a large part of the data represents species of which close relatives have not yet been deposited to the database. These results show that our approach is suitable for scalable genomic investigations such as monitoring oceanic biodiversity and provides a new platform for education in biodiversity.

Analysis of the Human Protein Atlas Image Classification competition

Pinpointing subcellular protein localizations from microscopy images is easy to the trained eye, but challenging to automate. Based on the Human Protein Atlas image collection, we held a competition to identify deep learning solutions to solve this task. Challenges included training on highly imbalanced classes and predicting multiple labels per image. Over 3 months, 2,172 teams participated. Despite convergence on popular networks and training techniques, there was considerable variety among the solutions. Participants applied strategies for modifying neural networks and loss functions, augmenting data and using pretrained networks. The winning models far outperformed our previous effort at multi-label classification of protein localization patterns by ~20%. These models can be used as classifiers to annotate new images, feature extractors to measure pattern similarity or pretrained networks for a wide range of biological applications.

Failure of Local Thermal Equilibrium in Quantum Friction

Recent progress in manipulating atomic and condensed matter systems has instigated a surge of interest in nonequilibrium physics, including many-body dynamics of trapped ultracold atoms and ions, near-field radiative heat transfer, and quantum friction. Under most circumstances the complexity of such nonequilibrium systems requires a number of approximations to make theoretical descriptions tractable. In particular, it is often assumed that spatially separated components of a system thermalize with their immediate surroundings, although the global state of the system is out of equilibrium. This powerful assumption reduces the complexity of nonequilibrium systems to the local application of well-founded equilibrium concepts. While this technique appears to be consistent for the description of some phenomena, we show that it fails for quantum friction by underestimating by approximately 80% the magnitude of the drag force. Our results show that the correlations among the components of driven, but steady-state, quantum systems invalidate the assumption of local thermal equilibrium, calling for a critical reexamination of this approach for describing the physics of nonequilibrium systems.

Robust constraint on a drifting proton-to-electron mass ratio at z=0.89 from methanol observation at three radio telescopes

A limit on a possible cosmological variation of the proton-to-electron mass ratio μ is derived from methanol (CH3OH) absorption lines in the benchmark PKS1830-211 lensing galaxy at redshift z=0.89 observed with the Effelsberg 100-m radio telescope, the Institute de Radio Astronomie Millimétrique 30-m telescope, and the Atacama Large Millimeter/submillimeter Array. Ten different absorption lines of CH3OH covering a wide range of sensitivity coefficients K(μ) are used to derive a purely statistical 1σ constraint of Δμ/μ=(1.5±1.5)×10(-7) for a lookback time of 7.5 billion years. Systematic effects of chemical segregation, excitation temperature, frequency dependence, and time variability of the background source are quantified. A multidimensional linear regression analysis leads to a robust constraint of Δμ/μ=(-1.0±0.8(stat)±1.0(sys))×10(-7).

Schottky barrier SOI-MOSFETs with high-k La(2)O(3)/ZrO(2) gate dielectrics

Schottky barrier SOI-MOSFETs incorporating a La(2)O(3)/ZrO(2) high-k dielectric stack deposited by atomic layer deposition are investigated. As the La precursor tris(N,N'-diisopropylformamidinato) lanthanum is used. As a mid-gap metal gate electrode TiN capped with W is applied. Processing parameters are optimized to issue a minimal overall thermal budget and an improved device performance. As a result, the overall thermal load was kept as low as 350, 400 or 500 °C. Excellent drive current properties, low interface trap densities of 1.9 × 10(11) eV(-1) cm(-2), a low subthreshold slope of 70-80 mV/decade, and an I(ON)/I(OFF) current ratio greater than 2 × 10(6) are obtained.

Tuning the electrical performance of Ge nanowire MOSFETs by focused ion beam implantation

In this work, we demonstrate an approach to tune the electrical behavior of our Ω-gated germanium-nanowire (Ge-NW) MOSFETs by focused ion beam (FIB) implantation. For the MOSFETs, 35 nm thick Ge-NWs are covered by atomic layer deposition (ALD) of a high-κ gate dielectric. With the Ω-shaped metal gate acting as implantation mask, highly doped source/drain (S/D) contacts are formed in a self-aligned process by FIB implantation. Notably, without any dopant activation by annealing, the devices exhibit more than three orders of magnitude higher I(ON) currents, an improved I(ON)/I(OFF) ratio, a higher mobility and a reduced subthreshold slope of 140 mV/decade compared to identical Ge-NW MOSFETs without FIB implantation.

Scalable approach for vertical device integration of epitaxial nanowires

In this letter, we demonstrate the simultaneous vertical integration of self-contacting and highly oriented nanowires (NWs) into airbridge structures, which have been developed into surround gated metal oxide semiconductor field effect transistors (MOSFETs). With the use of conventional photolithography, reactive ion etching (RIE), and low pressure chemical vapor deposition, a suspended vertical NW architecture is formed on a silicon on insulator (SOI) substrate where the nanodevice will later be fabricated on. The vapor-liquid-solid (VLS) grown Si-NWs are contacted to prepatterned airbridges by a self-aligned process, and there is no need for postgrowth NW assembly or alignment. Such vertical NW architecture can be easily integrated into existing ICs processes opening the path to a new generation of nonconventional nano devices. To demonstrate the potential of this method, surround gated vertical MOSFETs have been fabricated with a highly simplified integration scheme combining top-down and bottom-up approaches, but in the same way, one can think about the realization of integrated nano sensors on the industrial scale.

MMP-9-hemopexin domain hampers adhesion and migration of colorectal cancer cells

Matrix metalloproteinases (MMPs), in particular MMP-2 and MMP-9, are involved in colon cancer progression and metastasis due to their ability to degrade extracellular matrix (ECM) components. In previous studies we described the MMP-9 hemopexin like domain (MMP-9-PEX) as an MMP-9 antagonist. In the present study it was examined whether recombinant MMP-9-PEX has an inhibitory effect on migration and adhesion of colorectal carcinoma cells. Furthermore, we searched for MMP-9 substrate binding sites within the MMP-9-PEX by surface plasmon resonance. Migration of SW620 and LS174 cells was investigated in a modified Boyden chamber assay. In the presence of 0.2 microg/ml MMP-9-PEX migration of SW620 was decreased by 34%, while addition of 0.4 microg/ml diminished migration by 56%. Migration of LS174 cells was not affected by MMP-9-PEX. Adhesion studies were performed on 96-well plates coated with gelatin, collagen type I, and laminin, respectively. In the presence of MMP-9-PEX, adhesion of SW620 cells to these coating substrates was significantly inhibited. Surface plasmon resonance studies revealed binding of collagen type I and IV, elastin, and fibrinogen to proMMP-9 as well as to MMP-9-PEX. However, equilibrium constants (Kd) indicated a higher affinity of proMMP-9 to the matrix proteins. This could indicate that there is more than one binding site for matrix components within the entire proMMP-9 molecule. Since migration and adhesion of metastatic colorectal carcinoma cells were reduced by MMP-9-PEX, this recombinant MMP-9 antagonist might be of therapeutical interest.

Optical microscopy via spectral modifications of a nanoantenna

The existing optical microscopes form an image by collecting photons emitted from an object. Here we report on the experimental realization of microscopy without the need for direct optical communication with the sample. To achieve this, we have scanned a single gold nanoparticle acting as a nanoantenna in the near field of a sample and have studied the modification of its intrinsic radiative properties by monitoring its plasmon spectrum.

Identification of fibrosis-relevant proteins using DIGE (difference in gel electrophoresis) in different models of hepatic fibrosis

Proteomics became a more and more important technique for the large-scale analysis of proteins during the last years. Two-dimensional (2D) electrophoresis as a major tool of proteomics is a powerful method to compare two different biological stages (e. g. healthy and diseased tissue) and to find differences in their protein pattern. One major problem in proteomics is the gel to gel variation of two-dimensional gel electrophoresis, which could cause artefacts in the detection of expression differences. The "difference in gel electrophoresis" (DIGE) technique allows the separation of two proteomes in the same gel. The protein pools were labelled with different fluorescent dyes and equal amounts of protein were separated in the same gel. Another advantage of DIGE is the possibility to separate an internal standard labelled with a third dye in the same gel to allow quantitative expression analysis. We compared proteomes of three different fibrosis models with the appropriate control (tissue inhibitor of metalloproteinases-1 (TIMP-1) overexpressing HepG2 cells in comparison to a HepG2 control, freshly isolated HSC in comparison to activated HSC and healthy mouse liver in comparison to fibrotic mouse liver). Among the differentially expressed proteins several were already found to be relevant for fibrosis but we also detected some proteins like the selenium binding protein 2 which might be relevant for hepatic fibrosis.

Hubble Space Telescope and Very Large Array Observations of the H2O Gigamaser Galaxy TXS 2226-184

We present Hubble Space Telescope/Wide-Field and Planetary Camera 2 images in Halpha + [N ii] lambdalambda6548, 6583 lines and continuum radiation and a VLA map at 8 GHz of the H2O gigamaser galaxy TXS 2226-184. This galaxy has the most luminous H2O maser emission known to date. Our red continuum images reveal a highly elongated galaxy with a dust lane crossing the nucleus. The surface brightness profile is best fitted by a bulge plus exponential disk model, favoring classification as a highly inclined spiral galaxy (i=70&j0;). The color map confirms that the dust lane is aligned with the galaxy major axis and is crossing the putative nucleus. The Halpha + [N ii] map exhibits a gaseous, jetlike structure perpendicular to the nuclear dust lane and the galaxy major axis. The radio map shows compact, steep spectrum emission that is elongated in the same direction as the Halpha + [N ii] emission. By analogy with Seyfert galaxies, we therefore suspect that this alignment reflects an interaction between the radio jet and the interstellar medium. The axes of the nuclear dust disk, the radio emission, and the optical line emission apparently define the axis of the active galactic nucleus. The observations suggest that in this galaxy the nuclear accretion disk, obscuring torus, and large-scale molecular gas layer are roughly coplanar. Our classification of the host galaxy strengthens the trend for megamasers to be found preferentially in highly inclined spiral galaxies.

Specular versus diffuse reflection of atoms from an evanescent-wave mirror

We tested the specularity of the ref lection of slow atoms from an evanescent-wave mirror at normal incidence. In two of the three prisms that we tested the atoms were ref lected diffusely. This nonspecular ref lection appears to be correlated with the rms roughness of the surface supporting the evanescent wave. Only the highest quality surface (rms roughness of the order of 0.1 nm) leads to specular ref lection. This discovery imposes stringent limits on the use of these mirrors in atomic-optics experiments.

A water-vapour giga-maser in the active galaxy TXFS2226-184

Active galactic nuclei are thought to be powered by gas falling into a massive black hole; the different types of active galaxy may arise because we view them through a thick torus of molecular gas at varying angles of inclination. One way to determine whether the black hole is surrounded by a torus, which would obscure the accretion disk around the black hole along certain lines of sight, is to search for water masers, as these exist only in regions with plentiful molecular gas. Since the first detection of an extra-galactic water maser in 1979, they have come to be associated primarily with active galaxies, and have even been used to probe the mass of the central engine. Here we report the detection of a water giga-maser in the radio galaxy TXFS2226-184. The strength of the emission supports a recently proposed theory of maser pumping that allows for even more powerful masers, which might be detectable at cosmological distances. Water masers may accordingly provide a way to determine distances to galaxies outside the usual distance ladder, providing an independent calibration of the Hubble constant.

[Diagnostic and therapeutic aspects of subarachnoidal hemorrhage from the viewpoint of emergency medicine]

The subarchnoidal haemorrhage is an acute disease which has a high lethality and, therefore, in every case presents an indication for admission into an intensive-therapeutic department. It often occurs in younger age groups and appears more frequently than is assumed in general. Despite impressive clinical symptoms (suddenly beginning stabbing headache, vomiting and disturbances of consciousness of various degree of severity) the picture of the disease is not exactly diagnosed almost in every case. From 1970 to 1974 we treated 105 patients with subarachnoidal haemorrhages. In this paper is referred to the most important clinical and paraclinical parameters. Diagnostic and therapeutic possibilities are discussed.

[Poisoning with nitrosifying gas]

Nitrosifying gases are nitrogen-oxygen mixtures which are used in many branches of industry or which develop as a sideproduct. They are toxic already in a relatively slight concentration. It is reported on 12 patients who on account of an accident in a Berlin metal factory fell ill with an acute intoxication by nitrosifying gas. Symptoms, clinical and paraclinical findings are compiled and compared with the cases described in literature. Therapeutic orders are discussed.