A Liquid Biopsy-Based Approach for Monitoring Treatment Response in Post-Operative Colorectal Cancer Patients

Monitoring the therapeutic response of colorectal cancer (CRC) patients is crucial to determine treatment strategies; therefore, we constructed a liquid biopsy-based approach for tracking tumor dynamics in non-metastatic (nmCRC) and metastatic (mCRC) patients (n = 55). Serial blood collections were performed during chemotherapy for measuring the amount and the global methylation pattern of cell-free DNA (cfDNA), the promoter methylation of SFRP2 and SDC2 genes, and the plasma homocysteine level. The average cfDNA amount was higher (p < 0.05) in nmCRC patients with recurrent cancer (30.4 ± 17.6 ng) and mCRC patients with progressive disease (PD) (44.3 ± 34.5 ng) compared to individuals with remission (13.2 ± 10.0 ng) or stable disease (12.5 ± 3.4 ng). More than 10% elevation of cfDNA from first to last sample collection was detected in all recurrent cases and 92% of PD patients, while a decrease was observed in most patients with remission. Global methylation level changes indicated a decline (75.5 ± 3.4% vs. 68.2 ± 8.4%), while the promoter methylation of SFRP2 and SDC2 and homocysteine level (10.9 ± 3.4 µmol/L vs. 13.7 ± 4.3 µmol/L) presented an increase in PD patients. In contrast, we found exact opposite changes in remission cases. Our study offers a more precise blood-based approach to monitor the treatment response to different chemotherapies than the currently used markers.     

Automating regression testing using web-based application similarities

Web-based applications are one of the most widely used types of software, and have become the backbone of many e-commerce and communications businesses. These applications are often mission-critical for many organizations, motivating their precise validation. Although regression testing has been widely used to gain confidence in the reliability of software by providing information about the quality of an application, it has suffered limited use in this domain due to the frequent nature of updates to websites and the difficulty of automatically comparing test case output. We present techniques to address these challenges in regression testing web-based applications. Without precise comparators, test cases that fail due to benign program evolutions must be manually inspected. Our approach harnesses the inherent similarities between unrelated web-based applications to provide fully automated solutions to reduce the number of such false positives, while simultaneously returning true faults. By applying a model derived from regression testing other programs, our approach can predict which test cases merit human inspection. Our method is 2.5 to 50 times as accurate as current industrial practice, but requires no user annotations.     

Poly(ε-caprolactone)-based membranes with tunable physicochemical,bioactive and osteoinductive properties

In contrast to currently used materials, membranes for the treatment of bone defects should actively promote regeneration of bone tissue beyond their physical barrier function. What is more, both material properties and biological features of membranes should be easily adaptable to meet the needs of particular therapeutic applications. Therefore, the role of preparation methods (non-solvent-induced phase separation and thermal-induced phase separation) of poly(ε-caprolactone)-based membranes and their modification with gel-derived bioactive glass (BG) particles of two different sizes (<45 and <3 μm) in modulating material morphology, polymer matrix crystallinity, surface wettability, kinetics of in vitro bioactivity and also osteoblast response was investigated. Both surfaces of membranes were characterised in terms of their properties. Our results indicated a possibility to modulate microstructure (pore size ranging from submicron to hundreds of micrometres), wettability (from hydrophobic to fully wettable surface) and polymer crystallinity (from 19 to 60%) in a wide range by the use of various preparation methods and different BG particle sizes. Obtained composite membranes showed excellent in vitro hydroxyapatite forming ability after incubation in simulated body fluid. Here we demonstrated that bioactive layer formation on the surface of membranes occurred through ACP–OCP–CDHA–HCA transformation, that mimic in vivo bone biomineralization process. Composite membranes supported human osteoblast proliferation, stimulated cell differentiation and matrix mineralization. We proved that kinetics of bioactivity process and also osteoinductive properties of membranes can be easily modulated with the use of proposed variables. This brings new opportunities to obtain multifunctional membranes for bone regeneration with tunable physicochemical and biological properties.     

Lithography‐Free Fabrication of Silica Nanocylinders with Suspended Gold Nanorings for LSPR‐Based Sensing

Tunable plasmonic platforms are important for a variety of applications such as photovoltaics, LED's, optoelectronics, medical research, and biosensors. In particular, development of label‐free plasmonic biosensors is one of the key research areas that utilizes plasmonic nanostructures for detection of biologically relevant molecules at low concentrations. The authors have developed a cost‐effective, fast, and lithography‐free method to fabricate transparent fused silica nanocylinders. The technique allows tuning of nanocylinder height, diameter, and density and can be scaled to large surface areas, such as 8 in. wafers. The authors demonstrate that gold coated nanocylinders support localized surface plasmon resonances (LSPR) from visible to near infrared wavelengths. The plasmonic platform can be characterized as suspended gold nanorings and exhibits a sensitivity of 658 nm RIU^–1 with a figure‐of‐merit of 10, comparable to other state‐of‐the‐art LSPR sensing platforms that utilize more complex nanofabrication pathways. It was observed that the LSPR peak positions can be controlled by varying the geometry of the nanocylinders. The authors illustrate surface functionalization, biosensing, and surface regeneration properties of the platform using thiols and detection of bovine serum albumin (BSA). The observed LSPR shifts for 11‐mercaptoundecanoic acid and BSA was 12 and 26 nm, respectively.     

HIV and Proteomics: What We Have Learned from High Throughput Studies

The accelerated development of technology over the last three decades has driven biological sciences to high-throughput profiling experiments, now broadly referred to as systems biology. The unprecedented improvement of analytical instrumentation has opened new avenues for more complex experimental designs and expands the knowledge in genomics, proteomics, and other omics fields. Despite the collective efforts of hundreds of researchers, gleaning all the expected information from omics experiments is still quite far. This paper summarizes what has been learned from high-throughput proteomics studies thus far, and what is believed should be done to reveal even more valuable information from such studies. It is drawn from the background in using proteomics to study human immunodeficiency virus 1 infection of macrophages and/or T cells, but it is believed that some conclusions will be more broadly applicable.     

Oxidative Properties of Polystyrene Nanoparticles with Different Diameters in Human Peripheral Blood Mononuclear Cells (In Vitro Study)

With the ongoing commercialization, human exposure to plastic nanoparticles will dramatically increase, and evaluation of their potential toxicity is essential. There is an ongoing discussion on the human health effects induced by plastic particles. For this reason, in our work, we assessed the effect of polystyrene nanoparticles (PS-NPs) of various diameters (29, 44 and 72 nm) on selected parameters of oxidative stress and the viability of human peripheral blood mononuclear cells (PBMCs) in the in vitro system. Cells were incubated with PS-NPs for 24 h in the concentration range of 0.001 to 100 µg/mL and then labeled: formation of reactive oxygen species (ROS) (including hydroxyl radical), protein and lipid oxidation and cell viability. We showed that PS-NPs disturbed the redox balance in PBMCs. They increased ROS levels and induced lipid and protein oxidation, and, finally, the tested nanoparticles induced a decrease in PBMCs viability. The earliest changes in the PBMCs were observed in cells incubated with the smallest PS-NPs, at a concentration of 0.01 μg/mL. A comparison of the action of the studied nanoparticles showed that PS-NPs (29 nm) exhibited a stronger oxidative potential in PBMCs. We concluded that the toxicity and oxidative properties of the PS-NPs examined depended to significant degree on their diameter.     

Structures of Alcohol Dehydrogenases from Ralstonia and Sphingobium spp. Reveal the Molecular Basis for Their Recognition of ‘Bulky–Bulky’ Ketones

Alcohol dehydrogenases (ADHs) are applied in industrial synthetic chemistry for the production of optically active secondary alcohols. However, the substrate spectrum of many ADHs is narrow, and few, for example, are suitable for the reduction of prochiral ketones in which the carbonyl group is bounded by two bulky and/or hydrophobic groups; so-called ‘bulky–bulky’ ketones. Recently two ADHs, RasADH from Ralstonia sp. DSM 6428, and SyADH from Sphingobium yanoikuyae DSM 6900, have been described, which are distinguished by their ability to accept bulky–bulky ketones as substrates. In order to examine the molecular basis of the recognition of these substrates the structures of the native and NADPH complex of RasADH, and the NADPH complex of SyADH have been determined and refined to resolutions of 1.5, 2.9 and 2.5 Å, respectively. The structures reveal hydrophobic active site tunnels near the surface of the enzymes that are well-suited to the recognition of large hydrophobic substrates, as determined by modelling of the bulky–bulky substrate n-pentyl phenyl ketone. The structures also reveal the bases for NADPH specificity and (S)-stereoselectivity in each of the biocatalysts for n-pentyl phenyl ketone and related substrates.     

Nitrogen Oxides Ozonation as a Method for NOx Emission Abatement

Attempts to develop new technologies of reduction of NO_x emission are still carried out all around the world. However, most of them as literature survey suggests is focused on NO_x emission control from power plants and mobile vehicles. Fewer investigations are conducted on the NO_x emission abatement from the chemical industry. One of the relatively new approaches is the application of ozone injection into exhaust gas stream followed by an absorption process. Ozone is used to transform NO_x to higher nitrogen oxides that are more soluble in water, and therefore the higher yield of nitric acid is expected. The main objective of this article is to present results of our studies in which the effectiveness of the ozonation process, as well as the dependence of the conversion rate and the selectivities of NO ozonation into NO₂, N₂O₅ and HNO₃ on the residence time of reagents in the reactor space were studied. Results of laboratory investigations were confirmed during ozonation experiments with real exhaust gases from a nitric acid pilot plant in Fertilizers Research Institute in Pulawy, Poland.