Features of changes in the nanostructure and colorizing of copper during scanning with a femtosecond laser beam

We have studied the nanostructuring and colorizing of the copper surface by scanning with a femtosecond laser beam with a near-Gaussian beam profile. The experimental studies were conducted using a femtosecond laser comprising a Ti:Sapphire oscillator and a multi-pass amplifier with the maximum pulse energy of 0.7 mJ, pulse frequency of 1 kHz, and pulse duration <30 fs. It is shown that the use of a short-pulsed femtosecond laser leads to the formation of wavelength scale periodic surface structures and eventually increases the brightness of the color of the copper surface. It is revealed that via reciprocally scanning the copper surface by multiple ultrashort laser pulses with a weakly asymmetric spatial energy density distribution and an energy density below the material ablation threshold, it is possible to create a combined nanostructure composed of low-spatial-frequency laser-induced periodic surface structures coated with nanoscale roughness. It is shown that relatively minor changes in the nanostructures obtained by scanning the copper surface by multiple ultrashort laser pulses can lead to a significant change in the color during surface colorizing

Effects of Pooling Samples on the Performance of Classification Algorithms: A Comparative Study

A pooling design can be used as a powerful strategy to compensate for limited amounts of samples or high biological variation. In this paper, we perform a comparative study to model and quantify the effects of virtual pooling on the performance of the widely applied classifiers, support vector machines (SVMs), random forest (RF), k-nearest neighbors (k-NN), penalized logistic regression (PLR), and prediction analysis for microarrays (PAMs). We evaluate a variety of experimental designs using mock omics datasets with varying levels of pool sizes and considering effects from feature selection. Our results show that feature selection significantly improves classifier performance for non-pooled and pooled data. All investigated classifiers yield lower misclassification rates with smaller pool sizes. RF mainly outperforms other investigated algorithms, while accuracy levels are comparable among all the remaining ones. Guidelines are derived to identify an optimal pooling scheme for obtaining adequate predictive power and, hence, to motivate a study design that meets best experimental objectives and budgetary conditions, including time constraints

Double- to Single-Strand Transition Induces Forces and Motion in DNA Origami Nanostructures

The design of dynamic, reconfigurable devices is crucial for the bottom-up construction of artificial biological systems. DNA can be used as an engineering material for the de-novo design of such dynamic devices. A self-assembled DNA origami switch is presented that uses the transition from double- to single-stranded DNA and vice versa to create and annihilate an entropic force that drives a reversible conformational change inside the switch. It is distinctively demonstrated that a DNA single-strand that is extended with 0.34 nm per nucleotide - the extension this very strand has in the double-stranded configuration - exerts a contractive force on its ends leading to large-scale motion. The operation of this type of switch is demonstrated via transmission electron microscopy, DNA-PAINT super-resolution microscopy and darkfield microscopy. The work illustrates the intricate and sometimes counter-intuitive forces that act in nanoscale physical systems that operate in fluids

Nanoscale FasL Organization on DNA Origami to Decipher Apoptosis Signal Activation in Cells

Cell signaling is initiated by characteristic protein patterns in the plasma membrane, but tools to decipher their molecular organization and activation are hitherto lacking. Among the well-known signaling pattern is the death inducing signaling complex with a predicted hexagonal receptor architecture. To probe this architecture, DNA origami-based nanoagents with nanometer precise arrangements of the death receptor ligand FasL are introduced and presented to cells. Mimicking different receptor geometries, these nanoagents act as signaling platforms inducing fastest time-to-death kinetics for hexagonal FasL arrangements with 10 nm inter-molecular spacing. Compared to naturally occurring soluble FasL, this trigger is faster and 100x more efficient. Nanoagents with different spacing, lower FasL number or higher coupling flexibility impede signaling. The results present DNA origami as versatile signaling scaffolds exhibiting unprecedented control over molecular number and geometry. They define molecular benchmarks in apoptosis signal initiation and constitute a new strategy to drive particular cell responses

Timing molecular motion and production with a synthetic transcriptional clock

The realization of artificial biochemical reaction networks with unique functionality is one of the main challenges for the development of synthetic biology. Due to the reduced number of components, biochemical circuits constructed in vitro promise to be more amenable to systematic design and quantitative assessment than circuits embedded within living organisms. To make good on that promise, effective methods for composing subsystems into larger systems are needed. Here we used an artificial biochemical oscillator based on in vitro transcription and RNA degradation reactions to drive a variety of “load” processes such as the operation of a DNA-based nanomechanical device (“DNA tweezers”) or the production of a functional RNA molecule (an aptamer for malachite green). We implemented several mechanisms for coupling the load processes to the oscillator circuit and compared them based on how much the load affected the frequency and amplitude of the core oscillator, and how much of the load was effectively driven. Based on heuristic insights and computational modeling, an “insulator circuit” was developed, which strongly reduced the detrimental influence of the load on the oscillator circuit. Understanding how to design effective insulation between biochemical subsystems will be critical for the synthesis of larger and more complex systems

Replacement of the Cobalt Center of Vitamin B 12 by Nickel: Nibalamin and Nibyric Acid Prepared from Metal‐Free B 12 Ligands Hydrogenobalamin and Hydrogenobyric Acid

The (formal) replacement of Co in cobalamin (Cbl) by NiII generates nibalamin (Nibl), a new transition‐metal analogue of vitamin B12. Described here is Nibl, synthesized by incorporation of a NiII ion into the metal‐free B12 ligand hydrogenobalamin (Hbl), itself prepared from hydrogenobyric acid (Hby). The related NiII corrin nibyric acid (Niby) was similarly synthesized from Hby, the metal‐free cobyric acid ligand. The solution structures of Hbl, and Niby and Nibl, were characterized by spectroscopic studies. Hbl features two inner protons bound at N2 and N4 of the corrin ligand, as discovered in Hby. X‐ray analysis of Niby shows the structural adaptation of the corrin ligand to NiII ions and the coordination behavior of NiII. The diamagnetic Niby and Nibl, and corresponding isoelectronic CoI corrins, were deduced to be isostructural. Nibl is a structural mimic of four‐coordinate base‐off Cbls, as verified by its ability to act as a strong inhibitor of bacterial adenosyltransferase

Micro-endoscopy of the human vas deferens: a feasibility study of a novel device in several ex vivo models

The aim of this study was to show limitation as well as potential of micro-endoscopy techniques as an innovative diagnostic and therapeutic approach in andrology. Two kinds of custom-made micro-endoscopes (ME) were tested in ex vivo vas deferens specimen and in post-mortem whole body. The semi-rigid ME included a micro-optic (0.9mm outer diameter [OD], 10.000 pixels, 120 degrees vision angle [VE], 3-20mm field depth [FD]) and an integrated fibre-optic light source. The flexible ME was composed of a micro-optic (OD=0.6mm, 6.000 pixels, 120 degrees VE, 3-20mm FD). The ex vivo study included retrograde investigation of the vas deferens (surgical specimen n=9, radical prostatectomy n=3). The post-mortem investigation (n=4) included the inspection of the vas deferens via both approaches. The results showed that antegrade and retrograde rigid endoscopy of the vas deferens were achieved as a diagnostic tool. The working channel enabled therapeutic use including biopsies or baskets. Using the flexible ME, the orifices of the ejaculatory ducts were identified. In vivo cadaveric retrograde cannulation of the orifices was successful. Post-mortem changes of verumontanum hindered the examinations beyond. Orifices were identified shaded behind a thin transparent membrane. Antegrade vasoscopy using flexible ME was possible up to the internal inguinal ring. Further advancement was impossible because of anatomical angle and lack adequate vision guidance. The vas deferens interior was clearly visible and was documented by pictures and movies. Altogether, the described ME techniques were feasible and effective, offering the potential of innovative diagnostic and therapeutic approaches for use in the genital tract. Several innovative indications could be expected

Mixed cation halide perovskite under environmental and physical stress

Despite the ideal performance demonstrated by mixed perovskite materials when used as active layers in photovoltaic devices, the factor which still hampers their use in real life remains the poor stability of their physico-chemical and functional properties when submitted to prolonged permanence in atmosphere, exposure to light and/or to moderately high temperature. We used high resolution photoelectron spectroscopy to compare the chemical state of triple cation, double halide Cs-x(FA(0.83)MA(0.17))(()Pb-1-(x))(I0.83Br0.17)(3) perovskite thin films being freshly deposited or kept for one month in the dark or in the light in environmental conditions. Important deviations from the nominal composition were found in the samples aged in the dark, which, however, did not show evident signs of oxidation and basically preserved their own electronic structures. Ageing in the light determined a dramatic material deterioration with heavily perturbed chemical composition also due to reactions of the perovskite components with surface contaminants, promoted by the exposure to visible radiation. We also investigated the implications that 2D MXene flakes, recently identified as effective perovskite additive to improve solar cell efficiency, might have on the labile resilience of the material to external agents. Our results exclude any deleterious MXene influence on the perovskite stability and, actually, might evidence a mild stabilizing effect for the fresh samples, which, if doped, exhibited a lower deviation from the expected stoichiometry with respect to the undoped sample. The evolution of the undoped perovskites under thermal stress was studied by heating the samples in UHV while monitoring in real time, simultaneously, the behaviour of four representative material elements. Moreover, we could reveal the occurrence of fast changes induced in the fresh material by the photon beam as well as the enhanced decomposition triggered by the concurrent X-ray irradiation and thermal heating

Precursors for cytochrome P450 profiling breath tests from an in silico screening approach

The family of cytochrome P450 enzymes (CYPs) is a major player in the metabolism of drugs and xenobiotics. Genetic polymorphisms and transcriptional regulation give a complex patient-individual CYP activity profile for each human being. Therefore, personalized medicine demands easy and non-invasive measurement of the CYP phenotype. Breath tests detect volatile organic compounds (VOCs) in the patients’ exhaled air after administration of a precursor molecule. CYP breath tests established for individual CYP isoforms are based on the detection of 13CO2 or 14CO2 originating from CYP-catalyzed oxidative degradation reactions of isotopically labeled precursors. We present an in silico work-flow aiming at the identification of novel precursor molecules, likely to result in VOCs other than CO2 upon oxidative degradation as we aim at label-free precursor molecules. The ligand-based work-flow comprises five parts: (1) CYP profiling was encoded as a decision tree based on 2D molecular descriptors derived from established models in the literature and validated against publicly available data extracted from the DrugBank. (2) Likely sites of metabolism were identified by reactivity and accessibility estimation for abstractable hydrogen radical. (3) Oxidative degradation reactions (O- and N-dealkylations) were found to be most promising in the release of VOCs. Thus, the CYP-catalyzed oxidative degradation reaction was encoded as SMIRKS (a programming language style to implement reactions based on the SMARTS description) to enumerate possible reaction products. (4) A quantitative structure property relation (QSPR) model aiming to predict the Henry constant H was derived from data for 488 organic compounds and identifies potentially VOCs amongst CYP reaction products. (5) A blacklist of naturally occurring breath components was implemented to identify marker molecules allowing straightforward detection within the exhaled air.peer-reviewe