Showing papers by "Jagiellonian University published in 2022"

Lithiophilic N-doped carbon bowls induced Li deposition in layered graphene film for advanced lithium metal batteries

Abstract: Lithium (Li) metal with high theoretical capacity and low electrochemical potential is the most ideal anode for next-generation high-energy batteries. However, the practical implementation of Li anode has been hindered by dendritic growth and volume expansion during cycling, which results in low Coulombic efficiency (CE), short lifespan, and safety hazards. Here, we report a highly stable and dendrite-free Li metal anode by utilizing N-doped hollow porous bowl-like hard carbon/reduced graphene nanosheets (CB@rGO) hybrids as three-dimensional (3D) conductive and lithiophilic scaffold host. The lithiophilic carbon bowl (CB) mainly works as excellent guides during the Li plating process, whereas the rGO layer with high conductivity and mechanical stability maintains the integrity of the composite by confining the volume change in long-range order during cycling. Moreover, the local current density can be reduced due to the 3D conductive framework. Therefore, CB@rGO presents a low lithium metal nucleation overpotential of 18 mV, high CE of 98%, and stable cycling without obvious voltage fluctuation for over 600 cycles at a current density of 1 mA·cm−2. Our study not only provides a good CB@rGO host and pre-Lithiated CB@rGO composite anode electrode, but also brings a new strategy of designing 3D electrodes for those active materials suffering from severe volume expansion.

Preclinical evaluation of a SARS-CoV-2 mRNA vaccine PTX-COVID19-B

Abstract: Safe and effective vaccines are needed to end the COVID-19 pandemic. Here, we report the preclinical development of a lipid nanoparticle–formulated SARS-CoV-2 mRNA vaccine, PTX-COVID19-B. PTX-COVID19-B was chosen among three candidates after the initial mouse vaccination results showed that it elicited the strongest neutralizing antibody response against SARS-CoV-2. Further tests in mice and hamsters indicated that PTX-COVID19-B induced robust humoral and cellular immune responses and completely protected the vaccinated animals from SARS-CoV-2 infection in the lung. Studies in hamsters also showed that PTX-COVID19-B protected the upper respiratory tract from SARS-CoV-2 infection. Mouse immune sera elicited by PTX-COVID19-B vaccination were able to neutralize SARS-CoV-2 variants of concern, including the Alpha, Beta, Gamma, and Delta lineages. No adverse effects were induced by PTX-COVID19-B in either mice or hamsters. Based on these results, PTX-COVID19-B was authorized by Health Canada to enter clinical trials in December 2020 with a phase 2 clinical trial ongoing.

Three-dimensional gas property geological modeling and simulation

Abstract: 3D visualization of geological and geophysical data has been continuously developed in recent decades for better prediction and simulation of subsurface systems. 3D modeling has gained attention from interpreters as well as decisions makers in the energy sector. The integration of 3D structural, facies, petrophysical, and geomechanical models can be used to obtain more reliable estimates of gas in place in the conventional and unconventional gas reservoirs. As well, 3D geomechanical model can be used to expose the root cause of drilling difficulties in gas reservoir and development of gas reservoirs. This chapter seeks to introduce the workflow and 3D modeling procedures in gas reservoirs. It provides a case study of 3D structural, facies, petrophysical, and geomechanical modeling in a gas reservoir from the southern central, Gulf of Suez, Egypt. Banner headline Three-dimensional modeling and visualization of subsurface gas reservoirs is a critical industry practice, and its significance originates from its theoretical and application value in exploration, development, and production. When modeling the subsurface system in both conventional and unconventional resources, it is critical to take into account a large number of datasets. The more data entered into the model, the better the model's accuracy. The heterogeneity of the data, the time required for data handling, numerical storage and accessibility, and the reliability of geological information assessments could all be sources of uncertainty that impact the 3D modeling process, posing modeling challenges. Such 3D modeling challenges can be overcome with more integrated data, precise calibration, and core measurements, resulting in more precise models.

Development and inter-laboratory validation of the VISAGE enhanced tool for age estimation from semen using quantitative DNA methylation analysis

Abstract: The analysis of DNA methylation has become an established method for chronological age estimation. This has triggered interest in the forensic community to develop new methods for age estimation from biological crime scene material. Various assays are available for age estimation from somatic tissues, the majority from blood. Age prediction from semen requires different DNA methylation markers and the only assays currently developed for forensic analysis are based on SNaPshot or pyrosequencing. Here, we describe a new assay using massively parallel sequencing to analyse 13 candidate CpG sites targeted in two multiplex PCRs. The assay has been validated by five consortium laboratories of the VISible Attributes through GEnomics (VISAGE) project within a collaborative exercise and was tested for reproducible quantification of DNA methylation levels and sensitivity with DNA methylation controls. Furthermore, DNA extracts and stains on Whatman FTA cards from two semen samples were used to evaluate concordance and mimic casework samples. Overall, the assay yielded high read depths (> 1000 reads) at all 13 marker positions. The methylation values obtained indicated robust quantification with an average standard deviation of 2.8% at the expected methylation level of 50% across the 13 markers and a good performance with 50 ng DNA input into bisulfite conversion. The absolute difference of quantifications from one participating laboratory to the mean quantifications of concordance and semen stains of remaining laboratories was approximately 1%. These results demonstrated the assay to be robust and suitable for age estimation from semen in forensic investigations. In addition to the 13-marker assay, a more streamlined protocol combining only five age markers in one multiplex PCR was developed. Preliminary results showed no substantial differences in DNA methylation quantification between the two assays, indicating its applicability with the VISAGE age model for semen developed with data from the complete 13-marker tool.

Gas adsorption and reserve estimation for conventional and unconventional gas resources

Abstract: This chapter describes the traditional approaches and recently developed models for in-place natural gas resource and reserve estimation calculations suitable for reservoir rocks displaying a wide range of permeability and porosity distributions. The inclusion of gas adsorption in these models is assessed and identified as being essential for unconventional gas reservoirs (tight zones, organic-rich shales, and coal bed methane). Volumetric, material balance equation (MBE), decline curve analysis (DCA), and other numerical models, including reservoir simulations, are used for in-place resource and reserve estimation. The many technical and commercial uncertainties involved in such estimations are identified and approaches for taking them into account are addressed over the reservoir life-cycle. Formulations for material balance calculations taking into account gas adsorption are provided and their performance assessed. Factors influencing gas adsorption and alternative gas isotherms suitable for shale gas and coal bed methane reservoirs are considered in detail. Whereas the Langmuir isotherm is widely used to estimate adsorbed gas contents for shale gas and coal bed methane reservoirs, its mono-layer adsorption assumptions are found to be inaccurate. Research has shown that the more realistic adsorption assumptions of the Freundlich and BET isotherms provide improved accuracy in resource and reserve estimates. Taking into account temperature, as well as pressure, further improves the prediction performance of the gas adsorption isotherms. Total organic carbon, temperature, porosity, pore size, thermal maturity, and clay content are some of the factors identified as influencing gas adsorption. Banner headline It is essential to consider gas adsorption when calculating the in-place resource and reserves associated with natural gas reservoirs, especially for the unconventional reservoirs including tight zones, organic-rich shales, and coal bed methane. Volumetric, material balance equations, decline curve analysis, and reservoir simulations are all used to provide resource and reserves estimates. Numerical methods applied to unconventional reservoirs use gas adsorption isotherms to distinguish the contribution to reserves made by adsorbed gas.

Programmable polymorphism of a virus-like particle

Abstract: Virus-like particles (VLPs) have significant potential as artificial vaccines and drug delivery systems. The ability to control their size has wide ranging utility but achieving such controlled polymorphism using a single protein subunit is challenging as it requires altering VLP geometry. Here we achieve size control of MS2 bacteriophage VLPs via insertion of amino acid sequences in an external loop to shift morphology to significantly larger forms. The resulting VLP size and geometry is controlled by altering the length and type of the insert. Cryo electron microscopy structures of the new VLPs, in combination with a kinetic model of their assembly, show that the abundance of wild type (T = 3), T = 4, D3 and D5 symmetrical VLPs can be biased in this way. We propose a mechanism whereby the insert leads to a change in the dynamic behavior of the capsid protein dimer, affecting the interconversion between the symmetric and asymmetric conformers and thus determining VLP size and morphology.

Trends in biomedical analysis of red blood cells – Raman spectroscopy against other spectroscopic, microscopic and classical techniques

Abstract: Application of modern and innovative spectroscopic and microscopic approaches to biomedical analysis opens new horizons and sheds new light on many unexplored scientific territories. In this review, we critically summarize up-to-date Raman-based methodologies for red blood cells (RBCs) analysis used in biology and medicine, and compare them with both classical, as well as other spectroscopic and microscopic approaches. The main emphasis is put on advantages, disadvantages and capabilities of each technique for detection of RBC deteriorations and RBC-related diseases. Although currently used classical techniques of medical analytsis serve as a gold standard for clinicians in diagnosis of erythropathies, they provide insufficient insight into RBC alterations at the molecular level. In addition, there is a demand for non-destructive and label-free analytical techniques for rapid detection and diagnosis of erythropathies. Their recognition often requires multimodal methodology comprising application of methods including sophisticated spectroscopy-based techniques, where Raman-based approaches play an important role.

Multiwavelength Variability Power Spectrum Analysis of the Blazars 3C 279 and PKS 1510–089 on Multiple Timescales

Abstract: Abstract We present the results of variability power spectral density (PSD) analysis using multiwavelength radio to GeV γ -ray light curves covering timescales of decades/years to days/minutes for the blazars 3C 279 and PKS 1510−089. The PSDs are modeled as single power laws, and the best-fit spectral shape is derived using the “power spectral response” method. With more than 10 yr of data obtained with weekly/daily sampling intervals, most of the PSDs cover ∼2–4 decades in temporal frequency; moreover, in the optical band, the PSDs cover ∼6 decades for 3C 279 due to the availability of intranight light curves. Our main results are the following: (1) on timescales ranging from decades to days, the synchrotron and the inverse-Compton spectral components, in general, exhibit red-noise (slope ∼2) and flicker-noise (slope ∼1) type variability, respectively; (2) the slopes of γ -ray variability PSDs obtained using a 3 hr integration bin and 3 weeks total duration exhibit a range between ∼1.4 and ∼2.0 (mean slope = 1.60 ± 0.70), consistent within errors with the slope on longer timescales; (3) comparisons of fractional variability indicate more power on timescales ≤100 days at γ -ray frequencies compared to longer wavelengths, in general (except between the γ -ray and optical wavelengths for PKS 1510−089); (4) the normalization of intranight optical PSDs for 3C 279 appears to be a simple extrapolation from longer timescales, indicating a continuous (single) process driving the variability at optical wavelengths; and (5) the emission at optical/infrared wavelengths may involve a combination of disk and jet processes for PKS 1510−089.

Cell cycle dynamics controls fluidity of the developing mouse neuroepithelium

Abstract: Abstract As organs are remodelled by morphogenetic changes and pattern formation during development, their material properties may change. To address whether and how this occurs in the mouse neural tube, we combined highly resolved mosaic analysis, biophysical modelling and perturbation experiments. We found that at early developmental stages the neuroepithelium surprisingly maintains both high junctional tension and high fluidity. This is achieved via a previously unrecognized mechanism in which interkinetic nuclear movements generate cell area dynamics that drive extensive cell rearrangements. Over time, the proliferation rate declines, effectively solidifying the tissue. Thus, unlike well-studied jamming transitions, the solidification we uncovered resembles a glass transition that depends on the dynamics of stresses generated by proliferation and differentiation. This new link between epithelial fluidity, interkinetic movements and cell cycle dynamics has implications for the precision of pattern formation and could be relevant to multiple developing tissues.

Wave–particle complementarity: detecting violation of local realism with photon-number resolving weak-field homodyne measurements

Abstract: Non-existence of a local hidden variables (LHV) model for a phenomenon benchmarks its use in device-independent quantum protocols. Nowadays photon-number resolving weak-field homodyne measurements allow realization of emblematic gedanken experiments. Alas, claims that we can have no LHV models for such experiments on (a) excitation of a pair of spatial modes by a single photon, and (b) two spatial modes in a weakly squeezed vacuum state, involving constant local oscillator strengths, are unfounded. For (a) an exact LHV model resolves the dispute on the "non-locality of a single photon" in its original formulation. It is measurements with local oscillators on or off that do not have LHV models.