Modeling biological gradient formation: combining partial differential equations and Petri nets

Both Petri nets and differential equations are important modeling tools for biological processes. In this paper we demonstrate how these two modeling techniques can be combined to describe biological gradient formation. Parameters derived from partial differential equation describing the process of gradient formation are incorporated in an abstract Petri net model. The quantitative aspects of the resulting model are validated through a case study of gradient formation in the fruit fly.     

A study on using data clustering for feature extraction to improve the quality of classification

There is a certain belief among data science researchers and enthusiasts alike that clustering can be used to improve classification quality. Insofar as this belief is fairly uncontroversial, it is also very general and therefore produces a lot of confusion around the subject. There are many ways of using clustering in classification and it obviously cannot always improve the quality of predictions, so a question arises, in which scenarios exactly does it help? Since we were unable to find a rigorous study addressing this question, in this paper, we try to shed some light on the concept of using clustering for classification. To do so, we first put forward a framework for incorporating clustering as a method of feature extraction for classification. The framework is generic w.r.t. similarity measures, clustering algorithms, classifiers, and datasets and serves as a platform to answer ten essential questions regarding the studied subject. Each answer is formulated based on a separate experiment on 16 publicly available datasets, followed by an appropriate statistical analysis. After performing the experiments and analyzing the results separately, we discuss them from a global perspective and form general conclusions regarding using clustering as feature extraction for classification.

     

Phenolic compounds isolated from bitter lupine seeds and their inhibitory effects on germination and seedling growth of lettuce

The phenolic acids, including 4-hydroxybenzoic and 4-hydroxycinnamic acids, and their derivatives, such as 6,7-dihydroxycoumarin and 1,2-dihydroxybenzene, were isolated from bitter lupine seeds and were identified using gas chromatography-mass spectrometry. These compounds inhibited lettuce seed germination in the first 24 hr after sowing, but after 72 hr germination was comparable with that of the control. However, very strong suppression of seedling growth, especially the roots, was observed for higher concentrations of the lupine seed fractions containing phenolic acids. Effects observed in the lettuce germination bioassays were compared with those produced by nine pure phenolic acids previously identified in the mixture. The ethyl acetate fraction from lupine seed extract inhibited seedling growth as effectively as pure 1,2-dihydroxybenzene, the strongest inhibitor of the pure phenolic compounds studied. The possible reason for this could be the synergistic effect created in the mixture of phenolic compounds isolated from the extract.     

Methods of eliminating pollutant emissions from the work environment in welding and related processes

Abstract

The welding and joining of dissimilar metals which have very different properties, such as aluminium and carbon steel, is considered to be a subject for research and development in the welding/joining sector continuing into the 21st century. There are also huge requirements and expectations for this sector.¹ Due to the aforementioned, the research and development of welding and joining of dissimilar materials have been carried out over many years; for instance, eutectic bonding of copper pipe and aluminium pipe was developed 30 years ago and this process is still applied for the heat pipes of refrigerators. Recently it has even progressed for applications in joining of wide plate materials of aluminium alloy and stainless steel by means of the vacuum rolling process² and also for weldments of aluminium alloy and carbon steel joined by means of friction welding and employed as automobile components.³ However, there are problems from aspects of cost and restrictions concerning the configurations for which joining is feasible using conventional welding and joining processes and these techniques have not yet reached the stage where they can be applied in a number of industrial sectors. Accordingly, an extensive programme of research and development has been deployed in recent years using fusion welding processes, such as electron beam and laser welding and brazing, diffusion bonding and also friction stir welding (FSW).⁴     

The Implication of Reticulons (RTNs) in Neurodegenerative Diseases: From Molecular Mechanisms to Potential Diagnostic and Therapeutic Approaches

Reticulons (RTNs) are crucial regulatory factors in the central nervous system (CNS) as well as immune system and play pleiotropic functions. In CNS, RTNs are transmembrane proteins mediating neuroanatomical plasticity and functional recovery after central nervous system injury or diseases. Moreover, RTNs, particularly RTN4 and RTN3, are involved in neurodegeneration and neuroinflammation processes. The crucial role of RTNs in the development of several neurodegenerative diseases, including Alzheimer’s disease (AD), multiple sclerosis (MS), amyotrophic lateral sclerosis (ALS), or other neurological conditions such as brain injury or spinal cord injury, has attracted scientific interest. Reticulons, particularly RTN-4A (Nogo-A), could provide both an understanding of early pathogenesis of neurodegenerative disorders and be potential therapeutic targets which may offer effective treatment or inhibit disease progression. This review focuses on the molecular mechanisms and functions of RTNs and their potential usefulness in clinical practice as a diagnostic tool or therapeutic strategy.     

The Effect of Platelet-Rich Plasma on the Intra-Articular Microenvironment in Knee Osteoarthritis

Knee osteoarthritis (KOA) represents a clinical challenge due to poor potential for spontaneous healing of cartilage lesions. Several treatment options are available for KOA, including oral nonsteroidal anti-inflammatory drugs, physical therapy, braces, activity modification, and finally operative treatment. Intra-articular (IA) injections are usually used when the non-operative treatment is not effective, and when the surgery is not yet indicated. More and more studies suggesting that IA injections are as or even more efficient and safe than NSAIDs. Recently, research to improve intra-articular homeostasis has focused on biologic adjuncts, such as platelet-rich plasma (PRP). The catabolic and inflammatory intra-articular processes that exists in knee osteoarthritis (KOA) may be influenced by the administration of PRP and its derivatives. PRP can induce a regenerative response and lead to the improvement of metabolic functions of damaged structures. However, the positive effect on chondrogenesis and proliferation of mesenchymal stem cells (MSC) is still highly controversial. Recommendations from in vitro and animal research often lead to different clinical outcomes because it is difficult to translate non-clinical study outcomes and methodology recommendations to human clinical treatment protocols. In recent years, significant progress has been made in understanding the mechanism of PRP action. In this review, we will discuss mechanisms related to inflammation and chondrogenesis in cartilage repair and regenerative processes after PRP administration in in vitro and animal studies. Furthermore, we review clinical trials of PRP efficiency in changing the OA biomarkers in knee joint.     

Fabrication of Paper Sheets Coatings Based on Chitosan/Bacterial Nanocellulose/ZnO with Enhanced Antibacterial and Mechanical Properties

Here, we designed paper sheets coated with chitosan, bacterial cellulose (nanofibers), and ZnO with boosted antibacterial and mechanical activity. We investigated the compositions, with ZnO exhibiting two different sizes/shapes: (1) rods and (2) irregular sphere-like particles. The proposed processing of bacterial cellulose resulted in the formation of nanofibers. Antimicrobial behavior was tested using E. coli ATCC^® 25922™ following the ASTM E2149-13a standard. The mechanical properties of the paper sheets were measured by comparing tearing resistance, tensile strength, and bursting strength according to the ISO 5270 standard. The results showed an increased antibacterial response (assigned to the combination of chitosan and ZnO, independent of its shape and size) and boosted mechanical properties. Therefore, the proposed composition is an interesting multifunctional mixture for coatings in food packaging applications.     

Temozolomide Induces the Acquisition of Invasive Phenotype by O6-Methylguanine-DNA Methyltransferase (MGMT)+ Glioblastoma Cells in a Snail-1/Cx43-Dependent Manner

Glioblastoma multiforme (GBM) recurrences after temozolomide (TMZ) treatment result from the expansion of drug-resistant and potentially invasive GBM cells. This process is facilitated by O6-Methylguanine-DNA Methyltransferase (MGMT), which counteracts alkylating TMZ activity. We traced the expansion of invasive cell lineages under persistent chemotherapeutic stress in MGMT^low (U87) and MGMT^high (T98G) GBM populations to look into the mechanisms of TMZ-induced microevolution of GBM invasiveness. TMZ treatment induced short-term, pro-invasive phenotypic shifts of U87 cells, in the absence of Snail-1 activation. They were illustrated by a transient induction of their motility and followed by the hypertrophy and the signs of senescence in scarce U87 sub-populations that survived long-term TMZ stress. In turn, MGMT^high T98G cells reacted to the long-term TMZ treatment with the permanent induction of invasiveness. Ectopic Snail-1 down-regulation attenuated this effect, whereas its up-regulation augmented T98G invasiveness. MGMT^low and MGMT^high cells both reacted to the long-term TMZ stress with the induction of Cx43 expression. However, only in MGMT^high T98G populations, Cx43 was directly involved in the induction of invasiveness, as manifested by the induction of T98G invasiveness after ectopic Cx43 up-regulation and by the opposite effect after Cx43 down-regulation. Collectively, Snail-1/Cx43-dependent signaling participates in the long-term TMZ-induced microevolution of the invasive GBM front. High MGMT activity remains a prerequisite for this process, even though MGMT-related GBM chemoresistance is not necessary for its initiation.     

The G-Protein-Coupled Membrane Estrogen Receptor Is Present in Horse Cryptorchid Testes and Mediates Downstream Pathways

Cryptorchidism in horses is a commonly occurring malformation. The molecular basis of this pathology is not fully known. In addition, the origins of high intratesticular estrogen levels in horses remain obscure. In order to investigate the role of the G-protein-coupled membrane estrogen receptor (GPER) and establish histological and biochemical cryptorchid testis status, healthy and cryptorchid horse testes were subjected to scanning electron microscopy analysis, histochemical staining for total protein (with naphthol blue black; NBB), acid content (with toluidine blue O; TBO), and polysaccharide content (with periodic acid–Schiff; PAS). The expression of GPER was analyzed by immunohistochemistry and Western blot. GPER-mediated intracellular cAMP and calcium (Ca2+) signaling were measured immunoenzymatically or colorimetrically. Our data revealed changes in the distribution of polysaccharide content but not the protein and acid content in the cryptorchid testis. Polysaccharides seemed to be partially translocated from the interstitial compartment to the seminiferous tubule compartment. Moreover, the markedly decreased expression of GPER and GPER downstream molecules, cAMP and Ca2+, suggests their potential role in testis pathology. Increased estrogen levels in cryptorchid conditions may be linked to disturbed GPER signaling. We postulate that GPER is a prominent key player in testis development and function and may be used as a new biomarker of horse testis in health and disease.