A parallel direct solver for the self-adaptive hp Finite Element Method

In this paper we present a new parallel multi-frontal direct solver, dedicated for the hp Finite Element Method (hp-FEM). The self-adaptive hp-FEM generates in a fully automatic mode, a sequence of hp-meshes delivering exponential convergence of the error with respect to the number of degrees of freedom (d.o.f.) as well as the CPU time, by performing a sequence of hp refinements starting from an arbitrary initial mesh. The solver constructs an initial elimination tree for an arbitrary initial mesh, and expands the elimination tree each time the mesh is refined. This allows us to keep track of the order of elimination for the solver. The solver also minimizes the memory usage, by de-allocating partial LU factorizations computed during the elimination stage of the solver, and recomputes them for the backward substitution stage, by utilizing only about 10% of the computational time necessary for the original computations. The solver has been tested on 3D Direct Current (DC) borehole resistivity measurement simulations problems. We measure the execution time and memory usage of the solver over a large regular mesh with 1.5 million degrees of freedom as well as on the highly non-regular mesh, generated by the self-adaptive hp$hp$-FEM, with finite elements of various sizes and polynomial orders of approximation varying from p=1$p=1$ to p=9$p=9$. From the presented experiments it follows that the parallel solver scales well up to the maximum number of utilized processors. The limit for the solver scalability is the maximum sequential part of the algorithm: the computations of the partial LU factorizations over the longest path, coming from the root of the elimination tree down to the deepest leaf.     

Biological cardio-micro-pumps for microbioreactors and analytical micro-systems

Bio-hybrid microsystems actuated by living cells, as micro-bio-actuators and micro-bio-pumps have been developed recently. In these devices biological cells may be powered without external energy sources and the movement or the contraction of muscle cells trigger off the flow of fluid (i.e. culture medium or blood) through microchannels in micro-multi-bioreactor systems. Isolated and in vitro cultured cardiomyocytes (cardiac cells) are the most promising bio-material, which can be used to design a micro-bio-pump/actuator. These spontaneously contracting cells are autonomously powered with glucose as an energy source without any external power supply or stimulus, unlike conventional micro-actuators/micro-pumps. Cardio-micro-bio-pumps/actuators are using collective, synchronous contracting forces of cardiac cells or cardiac cell sheets to drive the flow of fluid. The feasibility of building such actuators was demonstrated in a few examples of bio-hybrid microsystems actuated by single or sheeted cardiomyocytes.     

First experiences with the Polish Optical Internet

The paper describes the new development programme of the Polish information infrastructure. The programme, called in Polish PIONIER: (English—PIONEER) Polish Optical Internet, Advanced Applications, Services and Technologies for the Information Society, has been proposed to the Polish State Committee for Scientific Research and has been accepted. The aim of the programme is to create an advanced infrastructure together with tools, services and applications available to the entire scientific community and eventually to government and local administrations as well as society in general. Services and applications are expected to appear as selected pilot realizations in order to verify deployed technologies. Some of the pilot realizations and testbeds are also presented in the paper.     

Verification of bounded Petri nets using integer programming

Model checking based on the causal partial order semantics of Petri nets is an approach widely applied to cope with the state space explosion problem. One of the ways to exploit such a semantics is to consider (finite prefixes of) net unfoldings—themselves a class of acyclic Petri nets—which contain enough information, albeit implicit, to reason about the reachable markings of the original Petri nets. In [19], a verification technique for net unfoldings was proposed, in which deadlock detection was reduced to a mixed integer linear programming problem. In this paper, we present a further development of this approach. The essence of the proposed modifications is to transfer the information about causality and conflicts between the events involved in an unfolding, into a relationship between the corresponding integer variables in the system of linear constraints. Moreover, we present some problem-specific optimisation rules, reducing the search space. To solve other verification problems, such as mutual exclusion or marking reachability and coverability, we adopt Contejean and Devie's algorithm for solving systems of linear constraints over the natural numbers domain and refine it, by taking advantage of the specific properties of systems of linear constraints to be solved. Another contribution of this paper is a method of re-formulating some problems specified in terms of Petri nets as problems defined for their unfoldings. Using this method, we obtain a memory efficient translation of a deadlock detection problem for a safe Petri net into an LP problem. We also propose an on-the-fly deadlock detection method. Experimental results demonstrate that the resulting algorithms can achieve significant speedups.

Intelligent product search with soft-boundary preference relaxation

This paper proposes a novel method for preference relaxation in online product search, which enables consumers to make quality choices without suffering from the commonly experienced information overload. In online shopping scenarios that involve multi-attribute choice tasks, it can be difficult for consumers to process the vast amounts of information available and to make satisfactory buying decisions. In such situations consumers are likely to eliminate potentially good choices early on, using hard-constraint filtering tools. Our approach uses edge sets to identify the alternatives on the soft boundary and the principle of alternative domination to suppress the alternatives on this boundary that are irrelevant. We demonstrate how our approach outperforms existing methods for product search in a set of simulations using two sets of 2650 car advertisements and 1813 digital cameras gathered from a popular online store.     

Polyphenol-Enriched Composite Bone Regeneration Materials: A Systematic Review of In Vitro Studies

One of the possible alternatives for creating materials for the regeneration of bone tissue supporting comprehensive reconstruction is the incorporation of active substances whose controlled release will improve this process. This systematic review aimed to identify and synthesize in vitro studies that assess the suitability of polyphenolics as additives to polymer-ceramic composite bone regeneration materials. Data on experimental studies in terms of the difference in mechanical, wettability, cytocompatibility, antioxidant and anti-inflammatory properties of materials were synthesized. The obtained numerical data were compiled and analyzed in search of percentage changes of these parameters. The results of the systematic review were based on data from forty-six studies presented in nineteen articles. The addition of polyphenolic compounds to composite materials for bone regeneration improved the cytocompatibility and increased the activity of early markers of osteoblast differentiation, indicating a high osteoinductive potential of the materials. Polyphenolic compounds incorporated into the materials presumably give them high antioxidant properties and reduce the production of reactive oxygen species in macrophage cells, implying anti-inflammatory activity. The evidence was limited by the number of missing data and the heterogeneity of the data.     

Biomarkers for the Diagnosis of Alzheimer’s Disease in Clinical Practice: The Role of CSF Biomarkers during the Evolution of Diagnostic Criteria

Alzheimer’s disease (AD) is a progressive condition and the most common cause of dementia worldwide. The neuropathological changes characteristic of the disorder can be successfully detected before the development of full-blown AD. Early diagnosis of the disease constitutes a formidable challenge for clinicians. CSF biomarkers are the in vivo evidence of neuropathological changes developing in the brain of dementia patients. Therefore, measurement of their concentrations allows for improved accuracy of clinical diagnosis. Moreover, AD biomarkers may provide an indication of disease stage. Importantly, the CSF biomarkers of AD play a pivotal role in the new diagnostic criteria for the disease, and in the recent biological definition of AD by the National Institute on Aging, NIH and Alzheimer’s Association. Due to the necessity of collecting CSF by lumbar puncture, the procedure seems to be an important issue not only from a medical, but also a legal, viewpoint. Furthermore, recent technological advances may contribute to the automation of AD biomarkers measurement and may result in the establishment of unified cut-off values and reference limits. Moreover, a group of international experts in the field of AD biomarkers have developed a consensus and guidelines on the interpretation of CSF biomarkers in the context of AD diagnosis. Thus, technological advancement and expert recommendations may contribute to a more widespread use of these diagnostic tests in clinical practice to support a diagnosis of mild cognitive impairment (MCI) or dementia due to AD. This review article presents up-to-date data regarding the usefulness of CSF biomarkers in routine clinical practice and in biomarkers research.     

Gene Variants Related to Cardiovascular and Pulmonary Diseases May Correlate with Severe Outcome of COVID-19

Background: Severe outcomes of COVID-19 account for up to 15% of all cases. The study aims to check if any gene variants related to cardiovascular (CVD) and pulmonary diseases (PD) are correlated with a severe outcome of COVID-19 in a Polish cohort of COVID-19 patients. Methods: In this study, a subset of 747 samples from unrelated individuals collected across Poland in 2020 and 2021 was used and whole-genome sequencing was performed. Results: The GWAS analysis of SNPs and short indels located in genes related to CVD identified one variant significant in COVID-19 severe outcome in the HADHA gene, while for the PD gene panel, we found two significant variants in the DRC1 gene. In this study, both potentially protective and risk variants were identified, of which variants in the HADHA gene deserve the most attention. Conclusions: This is the first study reporting the association between the HADHA and DRC1 genetic variants and COVID-19 severe outcome based on the cohort WGS analysis. Although all the identified variants are localised in introns, they may be correlated and therefore inherited along with other risk variants, potentially causative to severe outcome of COVID-19 but not discovered yet.     

Fully polarimetric bistatic radar scattering behavior of forestedhills

The bistatic radar scattering measurements of forested hills were performed at grazing incidence and at azimuth scattering angles from 28° to 66° from the forward scatter plane. Using pulse-to-pulse switching between orthogonal transmitted polarizations, the radar simultaneously measures two orthogonally polarized components of the scattered wave to obtain full polarimetric information about the scattering process. These are the first fully polarimetric terrain clutter measurements to be conducted at large bistatic angles. The complete Stokes matrix, computed by averaging successive realizations of the polarization scattering matrix, is used to examine the polarization sensitivity of the bistatic clutter. It is found that the polarization state of the EM wave scattered out of the plane of incidence strongly depends on the polarization orientation of the incident electric field. Unlike the monostatic case, these two incident wave polarization states are found to produce substantially different scattered wave behavior when trees are viewed at large bistatic angles. Scattered fields resulting from vertically oriented incident fields are found to be highly polarized and to produce bistatic clutter power levels that are strongly dependent on the polarization of the receiving antenna. In contrast, horizontally oriented incident fields are found to produce weakly polarized scattered waves with bistatic clutter power levels that are insensitive to the polarization of the receiving antenna     

Mitochondrial Dysfunction in Spinocerebellar Ataxia Type 3 Is Linked to VDAC1 Deubiquitination

Dysfunctional mitochondria are linked to several neurodegenerative diseases. Metabolic defects, a symptom which can result from dysfunctional mitochondria, are also present in spinocerebellar ataxia type 3 (SCA3), also known as Machado–Joseph disease, the most frequent, dominantly inherited neurodegenerative ataxia worldwide. Mitochondrial dysfunction has been reported for several neurodegenerative disorders and ataxin-3 is known to deubiquitinylate parkin, a key protein required for canonical mitophagy. In this study, we analyzed mitochondrial function and mitophagy in a patient-derived SCA3 cell model. Human fibroblast lines isolated from SCA3 patients were immortalized and characterized. SCA3 patient fibroblasts revealed circular, ring-shaped mitochondria and featured reduced OXPHOS complexes, ATP production and cell viability. We show that wildtype ataxin-3 deubiquitinates VDAC1 (voltage-dependent anion channel 1), a member of the mitochondrial permeability transition pore and a parkin substrate. In SCA3 patients, VDAC1 deubiquitination and parkin recruitment to the depolarized mitochondria is inhibited. Increased p62-linked mitophagy, autophagosome formation and autophagy is observed under disease conditions, which is in line with mitochondrial fission. SCA3 fibroblast lines demonstrated a mitochondrial phenotype and dysregulation of parkin-VDAC1-mediated mitophagy, thereby promoting mitochondrial quality control via alternative pathways.