Groundwater microflora of the Aptian-Cenomanian deposits at the Igolsko-Talovoe field in Tomsk Region

The authors have studied the microbiological composition of the groundwater of the Aptian-Cenomanian deposits in the territory of the Igolsko-Talovoe field in Tomsk Region. The detected diversity of the physiological groups of bacteria can be a corrosive component for waters used in the reservoir pressure maintenance system. The research findings have allowed making conclusions about the need to study the contribution of all microorganisms inhabiting the waters of the Aptian-Cenomanian deposits to corrosion

DNA self-assembly-driven positioning of molecular components on nanopatterned surfaces.

We present a method for the specific, spatially targeted attachment of DNA molecules to lithographically patterned gold surfaces-demonstrated by bridging DNA strands across nanogap electrode structures. An alkanethiol self-assembled monolayer was employed as a molecular resist, which could be selectively removed via electrochemical desorption, allowing the binding of thiolated DNA anchoring oligonucleotides to each electrode. After introducing a bridging DNA molecule with single-stranded ends complementary to the electrode-tethered anchoring oligonucleotides, the positioning of the DNA molecule across the electrode gap, driven by self-assembly, occurred autonomously. This demonstrates control of molecule positioning with resolution limited only by the underlying patterned structure, does not require any alignment, is carried out entirely under biologically compatible conditions, and is scalable

Tight--binding description of the quasiparticle dispersion of graphite and few--layer graphene

A universal set of third--nearest neighbour tight--binding (TB) parameters is presented for calculation of the quasiparticle (QP) dispersion of $N$ stacked $sp^2$ graphene layers ($N=1... \infty$) with $AB$ stacking sequence. The QP bands are strongly renormalized by electron--electron interactions which results in a 20% increase of the nearest neighbour in--plane and out--of--plane TB parameters when compared to band structure from density functional theory. With the new set of TB parameters we determine the Fermi surface and evaluate exciton energies, charge carrier plasmon frequencies and the conductivities which are relevant for recent angle--resolved photoemission, optical, electron energy loss and transport measurements. A comparision of these quantitities to experiments yields an excellent agreement. Furthermore we discuss the transition from few layer graphene to graphite and a semimetal to metal transition in a TB framework.Comment: Corresponding author: A. Gr\"uneis Tel.: +49 351 4659 519 e--mail: [email protected]

Raman imaging and electronic properties of graphene

Graphite is a well-studied material with known electronic and optical properties. Graphene, on the other hand, which is just one layer of carbon atoms arranged in a hexagonal lattice, has been studied theoretically for quite some time but has only recently become accessible for experiments. Here we demonstrate how single- and multi-layer graphene can be unambiguously identified using Raman scattering. Furthermore, we use a scanning Raman set-up to image few-layer graphene flakes of various heights. In transport experiments we measure weak localization and conductance fluctuations in a graphene flake of about 7 monolayer thickness. We obtain a phase-coherence length of about 2 $\mu$m at a temperature of 2 K. Furthermore we investigate the conductivity through single-layer graphene flakes and the tuning of electron and hole densities via a back gate

Blood manufacturing methods affect red blood cell product characteristics and immunomodulatory activity

Transfusion of red cell concentrates (RCCs) is associated with increased risk of adverse outcomes that may be affected by different blood manufacturing methods and the presence of extracellular vesicles (EVs). We investigated the effect of different manufacturing methods on hemolysis, residual cells, cell-derived EVs, and immunomodulatory effects on monocyte activity. Thirty-two RCC units produced using whole blood filtration (WBF), red cell filtration (RCF), apheresis-derived (AD), and whole blood-derived (WBD) methods were examined (n = 8 per method). Residual platelet and white blood cells (WBCs) and the concentration, cell of origin, and characterization of EVs in RCC supernatants were assessed in fresh and stored supernatants. Immunomodulatory activity of RCC supernatants was assessed by quantifying monocyte cytokine production capacity in an in vitro transfusion model. RCF units yielded the lowest number of platelet and WBC-derived EVs, whereas the highest number of platelet EVs was in AD (day 5) and in WBD (day 42). The number of small EVs (<200 nm) was greater than large EVs (≥200 nm) in all tested supernatants, and the highest level of small EVs were in AD units. Immunomodulatory activity was mixed, with evidence of both inflammatory and immunosuppressive effects. Monocytes produced more inflammatory interleukin-8 after exposure to fresh WBF or expired WBD supernatants. Exposure to supernatants from AD and WBD RCC suppressed monocyte lipopolysaccharide-induced cytokine production. Manufacturing methods significantly affect RCC unit EV characteristics and are associated with an immunomodulatory effect of RCC supernatants, which may affect the quality and safety of RCCs

Transport through open quantum dots: making semiclassics quantitative

We investigate electron transport through clean open quantum dots (quantum billiards). We present a semiclassical theory that allows to accurately reproduce quantum transport calculations. Quantitative agreement is reached for individual energy and magnetic field dependent elements of the scattering matrix. Two key ingredients are essential: (i) inclusion of pseudo-paths which have the topology of linked classical paths resulting from diffraction in addition to classical paths and (ii) a high-level approximation to diffractive scattering. Within this framework of the pseudo-path semiclassical approximation (PSCA), typical shortcomings of semiclassical theories such as violation of the anti-correlation between reflection and transmission and the overestimation of conductance fluctuations are overcome. Beyond its predictive capabilities the PSCA provides deeper insights into the quantum-to-classical crossover.Comment: 20 pages, 19 figure

Explainability of deep neural networks for MRI analysis of brain tumors

Purpose Artificial intelligence (AI), in particular deep neural networks, has achieved remarkable results for medical image analysis in several applications. Yet the lack of explainability of deep neural models is considered the principal restriction before applying these methods in clinical practice. Methods In this study, we propose a NeuroXAI framework for explainable AI of deep learning networks to increase the trust of medical experts. NeuroXAI implements seven state-of-the-art explanation methods providing visualization maps to help make deep learning models transparent. Results NeuroXAI has been applied to two applications of the most widely investigated problems in brain imaging analysis, i.e., image classification and segmentation using magnetic resonance (MR) modality. Visual attention maps of multiple XAI methods have been generated and compared for both applications. Another experiment demonstrated that NeuroXAI can provide information flow visualization on internal layers of a segmentation CNN. Conclusion Due to its open architecture, ease of implementation, and scalability to new XAI methods, NeuroXAI could be utilized to assist radiologists and medical professionals in the detection and diagnosis of brain tumors in the clinical routine of cancer patients. The code of NeuroXAI is publicly accessible at https://github.com/razeineldin/NeuroXAI

Conductance of Open Quantum Billiards and Classical Trajectories

We analyse the transport phenomena of 2D quantum billiards with convex boundary of different shape. The quantum mechanical analysis is performed by means of the poles of the S-matrix while the classical analysis is based on the motion of a free particle inside the cavity along trajectories with a different number of bounces at the boundary. The value of the conductance depends on the manner the leads are attached to the cavity. The Fourier transform of the transmission amplitudes is compared with the length of the classical paths. There is good agreement between classical and quantum mechanical results when the conductance is achieved mainly by special short-lived states such as whispering gallery modes (WGM) and bouncing ball modes (BBM). In these cases, also the localization of the wave functions agrees with the picture of the classical paths. The S-matrix is calculated classically and compared with the transmission coefficients of the quantum mechanical calculations for five modes in each lead. The number of modes coupled to the special states is effectively reduced.Comment: 19 pages, 6 figures (jpg), 2 table