RETRACTED: Anohova et al. The Dosidicus gigas Collagen for Scaffold Preparation and Cell Cultivation: Mechanical and Physicochemical Properties, Morphology, Composition and Cell Viability. Polymers 2023, 15, 1220.

The Polymers Editorial Office retracts the article, "The Dosidicus gigas Collagen for Scaffold Preparation and Cell Cultivation: Mechanical and Physicochemical Properties, Morphology, Composition and Cell Viability" [...].

The Dosidicus gigas Collagen for Scaffold Preparation and Cell Cultivation: Mechanical and Physicochemical Properties, Morphology, Composition and Cell Viability.

Directed formation of the structure of the culture of living cells is the most important task of tissue engineering. New materials for 3D scaffolds of living tissue are critical for the mass adoption of regenerative medicine protocols. In this manuscript, we demonstrate the results of the molecular structure study of collagen from Dosidicus gigas and reveal the possibility of obtaining a thin membrane material. The collagen membrane is characterized by high flexibility and plasticity as well as mechanical strength. The technology of obtaining collagen scaffolds, as well as the results of studies of its mechanical properties, surface morphology, protein composition, and the process of cell proliferation on its surface, are shown in the given manuscript. The investigation of living tissue culture grown on the surface of a collagen scaffold by X-ray tomography on a synchrotron source made it possible to remodel the structure of the extracellular matrix. It was found that the scaffolds obtained from squid collagen are characterized by a high degree of fibril ordering and high surface roughness and provide efficient directed growth of the cell culture. The resulting material provides the formation of the extracellular matrix and is characterized by a short time to living tissue sorption.

Polished diamond X-ray lenses.

High-quality bi-concave 2D focusing diamond X-ray lenses of apex-radius R = 100 µm produced via laser-ablation and improved via mechanical polishing are presented here. Both for polished and unpolished individual lenses and for stacks of ten lenses, the remaining figure errors determined using X-ray speckle tracking are shown and these results are compared with those of commercial R = 50 µm beryllium lenses that have similar focusing strength and physical aperture. For two stacks of ten diamond lenses (polished and unpolished) and a stack of eleven beryllium lenses, this paper presents measured 2D beam profiles out of focus and wire scans to obtain the beam size in the focal plane. These results are complemented with small-angle X-ray scattering (SAXS) measurements of a polished and an unpolished diamond lens. Again, this is compared with the SAXS of a beryllium lens. The polished X-ray lenses show similar figure errors to commercially available beryllium lenses. While the beam size in the focal plane is comparable to that of the beryllium lenses, the SAXS signal of the polished diamond lenses is considerably lower.

Green Synthesis of Co-Zn Spinel Ferrite Nanoparticles: Magnetic and Intrinsic Antimicrobial Properties.

Spinel ferrite magnetic nanoparticles have attracted considerable attention because of their high and flexible magnetic properties and biocompatibility. In this work, a set of magnetic nanoparticles of cobalt ferrite doped with zinc was synthesized via the eco-friendly sol-gel auto-combustion method. Obtained particles displayed a room-temperature ferromagnetic behavior with tuned by chemical composition values of saturation magnetization and coercivity. The maximal values of saturation magnetization ~74 Am2/kg were found in cobalt ferrite nanoparticles with a 15-35% molar fraction of cobalt replaced by zinc ions. At the same time, the coercivity exhibited a gradually diminishing trend from ~140 to ~5 mT whereas the concentration of zinc was increased from 0 to 100%. Consequently, nanoparticles produced by the proposed method possess highly adjustable magnetic properties to satisfy the requirement of a wide range of possible applications. Further prepared nanoparticles were tested with bacterial culture to display the influence of chemical composition and magnetic structure on nanoparticles-bacterial cell interaction.

High-dynamic-range transmission-mode detection of synchrotron radiation using X-ray excited optical luminescence in diamond.

Enhancement of X-ray excited optical luminescence in a 100 µm-thick diamond plate by introduction of defect states via electron beam irradiation and subsequent high-temperature annealing is demonstrated. The resulting X-ray transmission-mode scintillator features a linear response to incident photon flux in the range 7.6 × 108 to 1.26 × 1012 photons s-1 mm-2 for hard X-rays (15.9 keV) using exposure times from 0.01 to 5 s. These characteristics enable a real-time transmission-mode imaging of X-ray photon flux density without disruption of X-ray instrument operation.

Development of a Biocompatible PLGA Polymers Capable to Release Thrombolytic Enzyme Prourokinase.

The novelty of the work lies in the creation and study of the physical and biological properties of biodegradable polymer coatings for stents based on poly(lactic-co-glycolic acid) (PLGA). Polymer coatings are capable of prolonged and directed release of molecules with a high molecular weight, in particular, protein molecules of prourokinase (m.w. 54 kDa). A technology has been developed to create coatings having a relative elongation of 40% to 165% and a tensile strength of 25-65 MPa. Coatings are biodegradable; the rate of degradation of the polymer in an isotonic solution varies in the range of 0.05%-1.0% per day. The created coatings are capable of controlled release of the protein of prourokinase, while about 90% of the molecules of prourokinase retain their enzymatic activity. The rate of release of prourokinase can vary from 0.01 to 0.08 mg/day/cm2. Coatings do not have a short-term toxic effect on mammalian cells. The mitotic index of cells growing on coatings is approximately 1.5%. When implanting the developed polymers in animals in the postoperative period, there are no complications. Histological examination did not reveal pathological processes. When implanting individual polymers 60 days after surgery, only traces of PLGA are detected. Thus, a biodegradable composite mechanically resistant polymer capable of prolonged release of the high molecular weight prourokinase enzyme has been developed.

Femtosecond Relativistic Electron Beam with Reduced Timing Jitter from THz Driven Beam Compression.

We propose and demonstrate a method to reduce the pulse width and timing jitter of a relativistic electron beam through THz driven beam compression. In this method the longitudinal phase space of a relativistic electron beam is manipulated by a linearly polarized THz pulse copropagating in a dielectric tube such that the bunch tail has a higher velocity than the bunch head, which allows simultaneous reduction of both pulse width and timing jitter after passing through a drift. In this experiment, the beam is compressed by more than a factor of 4 from 130 fs to 28 fs with the arrival time jitter also reduced from 97 fs to 36 fs, opening up new opportunities in using pulsed electron beams for studies of ultrafast dynamics. This technique provides an effective way to manipulate beam longitudinal phase space with a THz pulse and may have a strong impact in accelerator and ultrafast science facilities that require femtosecond electron beams with tight synchronization to external lasers.

Terahertz Oscilloscope for Recording Time Information of Ultrashort Electron Beams.

We propose and demonstrate a terahertz (THz) oscilloscope for recording time information of an ultrashort electron beam. By injecting a laser-driven THz pulse with circular polarization into a dielectric tube, the electron beam is swept helically such that the time information is uniformly encoded into the angular distribution that allows one to characterize both the temporal profile and timing jitter of an electron beam. The dynamic range of the measurement in such a configuration is significantly increased compared to deflection with a linearly polarized THz pulse. With this THz oscilloscope, nearly 50-fold longitudinal compression of a relativistic electron beam to about 15 fs (rms) is directly visualized with its arrival time determined with 3 fs accuracy. This technique bridges the gap between streaking of photoelectrons with optical lasers and deflection of relativistic electron beams with radio-frequency deflectors, and should have wide applications in many ultrashort electron-beam-based facilities.

Non-perturbing THz generation at the Tsinghua University Accelerator Laboratory 31 MeV electron beamline.

In recent experiments at Tsinghua University Accelerator Laboratory, the 31 MeV electron beam, which has been compressed to subpicosecond pulse durations, has been used to generate high peak power, narrow band Terahertz (THz) radiation by transit through different slow wave structures, specifically quartz capillaries metallized on the outside. Despite the high peak powers that have been produced, the THz pulse energy is negligible compared to the energy of the electron beam. Therefore, the THz generation process can be complementary to other beamline applications like plasma wakefield acceleration studies and Compton x-ray free electron lasers. This approach can be used at x-ray free electron laser beamlines, where THz radiation can be generated without disturbing the x-ray generation process. In the experiment reported here, a high peak current electron beam generated strong narrow band (∼1% bandwidth) THz signals in the form of a mixture of TM01 and TM02 modes. Each slow wave structure is completed with a mode converter at the end of the structure that allows for efficient (>90%) power extraction into free space. In the experiment, both modes in these two dielectric-loaded waveguides TM01 (0.3 THz/0.5 THz) and TM02 (0.9 THz/1.3 THz) were explicitly measured with an interferometer. The THz pulse energy was measured with a calibrated Golay cell at a few µJ.

The Oligomeric Form of the Escherichia coli Dps Protein Depends on the Availability of Iron Ions.

The Dps protein of Escherichia coli, which combines ferroxidase activity and the ability to bind DNA, is effectively used by bacteria to protect their genomes from damage. Both activities depend on the integrity of this multi-subunit protein, which has an inner cavity for iron oxides; however, the diversity of its oligomeric forms has only been studied fragmentarily. Here, we show that iron ions stabilize the dodecameric form of Dps. This was found by electrophoretic fractionation and size exclusion chromatography, which revealed several oligomers in highly purified protein samples and demonstrated their conversion to dodecamers in the presence of 1 mM Mohr's salt. The transmission electron microscopy data contradicted the assumption that the stabilizing effect is given by the optimal core size formed in the inner cavity of Dps. The charge state of iron ions was evaluated using Mössbauer spectroscopy, which showed the presence of Fe3O4, rather than the expected Fe2O3, in the sample. Assuming that Fe2+ can form additional inter-subunit contacts, we modeled the interaction of FeO and Fe2O3 with Dps, but the binding sites with putative functionality were predicted only for Fe2O3. The question of how the dodecameric form can be stabilized by ferric oxides is discussed.

Validating and implementing modified Filinov phase filtration in semiclassical dynamics.

The Mixed Quantum-Classical Initial Value Representation (MQC-IVR) is a recently introduced approximate semiclassical (SC) method for the calculation of real-time quantum correlation functions. MQC-IVR employs a modified Filinov filtration (MFF) scheme to control the overall phase of the SC integrand, extending the applicability of SC methods to complex systems while retaining their ability to accurately describe quantum coherence effects. Here, we address questions regarding the effectiveness of the MFF scheme in combination with SC dynamics. Previous work showed that this filtering scheme is of limited utility in the context of semiclassical wavepacket propagation, but we find that the MFF is extraordinarily powerful in the context of correlation functions. By examining trajectory phase and amplitude contributions to the real-time SC correlation function in a model system, we clearly demonstrate that the MFF serves to reduce noise by damping amplitude only in regions of highly oscillatory phase leading to a reduction in computational effort while retaining accuracy. Further, we introduce a novel and efficient MQC-IVR formulation that allows for linear scaling in computational cost with the total simulation length, a significant improvement over the more-than quadratic scaling exhibited by the original method.

Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches.

Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quantum, semiclassical, and classical approaches to describe the ultrafast molecular dynamics, including the multiconfiguration time-dependent Hartree method, Bohmian dynamics, local control theory, semiclassical thawed Gaussian approximation, phase averaging, dephasing representation, molecular mechanics with proton transfer, and multipolar force fields. In addition to the general overview, some focus is given to the description of nuclear quantum effects and to the direct dynamics, in which the ab initio energies and forces acting on the nuclei are evaluated on the fly. Several practical applications, performed within the framework of the Swiss National Center of Competence in Research "Molecular Ultrafast Science and Technology," are presented: These include Bohmian dynamics description of the collision of H with H2, local control theory applied to the photoinduced ultrafast intramolecular proton transfer, semiclassical evaluation of vibrationally resolved electronic absorption, emission, photoelectron, and time-resolved stimulated emission spectra, infrared spectroscopy of H-bonding systems, and multipolar force fields applications in the condensed phase.

In Situ Observation of Dark Current Emission in a High Gradient rf Photocathode Gun.

Undesirable electron field emission (also known as dark current) in high gradient rf photocathode guns deteriorates the quality of the photoemission current and limits the operational gradient. To improve the understanding of dark current emission, a high-resolution (∼100 µm) dark current imaging experiment has been performed in an L-band photocathode gun operating at ∼100 MV/m of surface gradient. Scattered strong emission areas with high current have been observed on the cathode. The field enhancement factor ß of selected regions on the cathode has been measured. The postexaminations with scanning electron microscopy and white light interferometry reveal the origins of ∼75% strong emission areas overlap with the spots where rf breakdown has occurred.

Large-surface-area diamond (111) crystal plates for applications in high-heat-load wavefront-preserving X-ray crystal optics.

Fabrication and results of high-resolution X-ray topography characterization of diamond single-crystal plates with large surface area (10 mm × 10 mm) and (111) crystal surface orientation for applications in high-heat-load X-ray crystal optics are reported. The plates were fabricated by laser-cutting of the (111) facets of diamond crystals grown using high-pressure high-temperature methods. The intrinsic crystal quality of a selected 3 mm × 7 mm crystal region of one of the studied samples was found to be suitable for applications in wavefront-preserving high-heat-load crystal optics. Wavefront characterization was performed using sequential X-ray diffraction topography in the pseudo plane wave configuration and data analysis using rocking-curve topography. The variations of the rocking-curve width and peak position measured with a spatial resolution of 13 µm × 13 µm over the selected region were found to be less than 1 µrad.

Modes of Escherichia coli Dps Interaction with DNA as Revealed by Atomic Force Microscopy.

Multifunctional protein Dps plays an important role in iron assimilation and a crucial role in bacterial genome packaging. Its monomers form dodecameric spherical particles accumulating ~400 molecules of oxidized iron ions within the protein cavity and applying a flexible N-terminal ends of each subunit for interaction with DNA. Deposition of iron is a well-studied process by which cells remove toxic Fe2+ ions from the genetic material and store them in an easily accessible form. However, the mode of interaction with linear DNA remained mysterious and binary complexes with Dps have not been characterized so far. It is widely believed that Dps binds DNA without any sequence or structural preferences but several lines of evidence have demonstrated its ability to differentiate gene expression, which assumes certain specificity. Here we show that Dps has a different affinity for the two DNA fragments taken from the dps gene regulatory region. We found by atomic force microscopy that Dps predominantly occupies thermodynamically unstable ends of linear double-stranded DNA fragments and has high affinity to the central part of the branched DNA molecule self-assembled from three single-stranded oligonucleotides. It was proposed that Dps prefers binding to those regions in DNA that provide more contact pads for the triad of its DNA-binding bundle associated with one vertex of the protein globule. To our knowledge, this is the first study revealed the nucleoid protein with an affinity to branched DNA typical for genomic regions with direct and inverted repeats. As a ubiquitous feature of bacterial and eukaryotic genomes, such structural elements should be of particular care, but the protein system evolutionarily adapted for this function is not yet known, and we suggest Dps as a putative component of this system.

Dynamically consistent method for mixed quantum-classical simulations: A semiclassical approach.

We introduce a new semiclassical (SC) framework, the Mixed Quantum-Classical Initial Value Representation (MQC-IVR), that can be tuned to reproduce existing quantum-limit and classical-limit SC approximations to quantum real-time correlation functions. Applying a modified Filinov transformation to a quantum-limit SC formulation leads to the association of a Filinov parameter with each degree of freedom in the system; varying this parameter from zero to infinity controls the extent of quantization of the corresponding mode. The resulting MQC-IVR expression provides a consistent dynamic framework for mixed quantum-classical simulations and we demonstrate its numerical accuracy in the calculation of real-time correlation functions for a model 1D system and a model 2D system over the full range of quantum- to classical-limit behaviors.

Observation of Field-Emission Dependence on Stored Energy.

Field emission from a solid metal surface has been continuously studied for a century over macroscopic to atomic scales. It is general knowledge that, other than the surface properties, the emitted current is governed solely by the applied electric field. A pin cathode has been used to study the dependence of field emission on stored energy in an L-band rf gun. The stored energy was changed by adjusting the axial position (distance between the cathode base and the gun back surface) of the cathode while the applied electric field on the cathode tip is kept constant. A very strong correlation of the field-emission current with the stored energy has been observed. While eliminating all possible interfering sources, an enhancement of the current by a factor of 5 was obtained as the stored energy was increased by a factor of 3. It implies that under certain circumstances a localized field emission may be significantly altered by the global parameters in a system.

Promoter islands as a platform for interaction with nucleoid proteins and transcription factors.

Seventy-eight promoter islands with an extraordinarily high density of potential promoters have been recently found in the genome of Escherichia coli. It has been shown that RNA polymerase binds internal promoters of these islands and produces short oligonucleotides, while the synthesis of normal mRNAs is suppressed. This quenching may be biologically relevant, as most islands are associated with foreign genes, which expression may deplete cellular resources. However, a molecular mechanism of silencing with the participation of these promoter-rich regions remains obscure. It has been demonstrated that all islands interact with histone-like protein H-NS--a specific sentinel of foreign genes. In this study, we demonstrated the inhibitory effect of H-NS using Δhns mutant of Escherichia coli and showed that deletion of dps, encoding another protein of bacterial nucleoid, tended to decrease rather than increase the amount of island-specific transcripts. This observation precluded consideration of promoter islands as sites for targeted heterochromatization only and a computer search for the binding sites of 53 transcription factors (TFs) revealed six proteins, which may specifically regulate their transcriptional output.

Formation of the SiP radical through radiative association.

Formation of the SiP radical through radiative association of Si((3)P) and P((4)S) atoms is studied using classical and quantum dynamics. Rate coefficients for formation in the two lowest doublet states and the two lowest quartet states are calculated for T = 10-20,000 K. Breit-Wigner theory is used to properly account for contribution from quantum mechanical resonances.

High power terahertz radiation source based on electron beam wakefields.

A table top device for producing high peak power (tens of megawatts to a gigawatt) T-ray beams is described. An electron beam with a rectangular longitudinal profile is produced out of a photoinjector via stacking of the laser pulses. The beam is also run off-crest of the photoinjector rf to develop an energy chirp. After passing through a dielectric loaded waveguide, the beam's energy becomes modulated by its self-wake. In a chicane beamline following the dielectric energy-bunching section this energy modulation is converted to a density modulation-a bunch train. The density modulated beam can be sent through a power extraction section, like a dielectric loaded accelerating structure, or simply can intercept a foil target, producing THz radiation of various bandwidths and power levels.