Proteome Based Approach Defines Candidates for Designing a Multitope Vaccine against the Nipah Virus

Nipah virus is one of the most harmful emerging viruses with deadly effects on both humans and animals. Because of the severe outbreaks, in 2018, the World Health Organization focused on the urgent need for the development of effective solutions against the virus. However, up to date, there is no effective vaccine against the Nipah virus in the market. In the current study, the complete proteome of the Nipah virus (nine proteins) was analyzed for the antigenicity score and the virulence role of each protein, where we came up with fusion glycoprotein (F), glycoprotein (G), protein (V), and protein (W) as the candidates for epitope prediction. Following that, the multitope vaccine was designed based on top-ranking CTL, HTL, and BCL epitopes from the selected proteins. We used suitable linkers, adjuvant, and PADRE peptides to finalize the constructed vaccine, which was analyzed for its physicochemical features, antigenicity, toxicity, allergenicity, and solubility. The designed vaccine passed these assessments through computational analysis and, as a final step, we ran a docking analysis between the designed vaccine and TLR-³ and validated the docked complex through molecular dynamics simulation, which estimated a strong binding and supported the nomination of the designed vaccine as a putative solution for Nipah virus. Here, we describe the computational approach for design and analysis of this vaccine.     

SuretyAssist: Fuzzy Expert System to Assist Surety Underwriters in Evaluating Construction Contractors for Bonding

In construction, many owners mitigate the risk of unforeseen contractor default by accepting only bonded contractors who must endure a rigorous evaluation process by surety brokers and surety underwriters. This evaluation process includes a financial analysis and a review of work on hand and past performance, all of which have reliable structured methods for their evaluation. Additionally, a number of subjective criteria are considered that are more difficult to capture and assess objectively but which can be modeled effectively using fuzzy logic. The purpose of this paper is to illustrate how fuzzy logic and expert systems can be combined to provide a structured approach to evaluating contractors for surety underwriting purposes. Fuzzy logic is used to model both the objective and subjective factors considered in contractor evaluation using linguistic terms, and expert rules are used to capture the surety experts’ reasoning process. A fuzzy expert system, SuretyAssist, is presented that can be used to provide an initial evaluation of general contractors as well as periodic reviews to determine whether or not to accept them as clients for bonding. SuretyAssist was validated using 31 actual cases of contractor evaluation and found to be accurate in 81% of the cases.     

Multivariate analysis of a biologically activated carbon (BAC) system and its efficiency for removing PAHs and aliphatic hydrocarbons from wastewater polluted with petroleum products

The efficiency of a biologically activated carbon system for treating wastewater polluted with petroleum products was examined and the effects of process parameters on its efficacy were evaluated. In each experiment 17 alkylated and 19 non-alkylated polycyclic aromatic hydrocarbons (PAHs) and total petroleum hydrocarbons (TPHs, C₁₀–C₄₀) were extracted using semipermeable membrane devices from wastewater before and after treatment. The acquired data during experiments were analyzed using principal component analysis (PCA). The treatment system robustly removed dissolved PAHs across the studied ranges of the process parameters, providing overall removal efficiencies of 96.9–99.7% for the sum of 36 PAHs. However, the major contributor to their removal was sorption rather than biodegradation, and despite the general efficiency of the process there was up to a 9-fold range in the sums of quantified PAHs in the effluents between experiments. Combinations of long process contact time (24 h) with high temperature (24 °C) and moderate oxygen concentration (6–7 mg O₂ L⁻¹) resulted in good removal of bioavailable PAHs. The removal of TPHs was more dependent on biological activities during the wastewater treatment, and consequently more dependent on the process parameters. In addition, small but significant proportions of PAHs were volatilized and released during the wastewater treatment.     

Tumor-Associated Macrophages and Inflammatory Microenvironment in Gastric Cancer: Novel Translational Implications

Gastric cancer (GC) represents the fifth most frequently diagnosed cancer worldwide, with a poor prognosis in patients with advanced disease despite many improvements in systemic treatments in the last decade. In fact, GC has shown resistance to several treatment options, and thus, notable efforts have been focused on the research and identification of novel therapeutic targets in this setting. The tumor microenvironment (TME) has emerged as a potential therapeutic target in several malignancies including GC, due to its pivotal role in cancer progression and drug resistance. Therefore, several agents and therapeutic strategies targeting the TME are currently under assessment in both preclinical and clinical studies. The present study provides an overview of available evidence of the inflammatory TME in GC, highlighting different types of tumor-associated cells and implications for future therapeutic strategies.     

Supra-Molecular Assemblies of ORAI1 at Rest Precede Local Accumulation into Puncta after Activation

The Ca²⁺ selective channel ORAI1 and endoplasmic reticulum (ER)-resident STIM proteins form the core of the channel complex mediating store operated Ca²⁺ entry (SOCE). Using liquid phase electron microscopy (LPEM), the distribution of ORAI1 proteins was examined at rest and after SOCE-activation at nanoscale resolution. The analysis of over seven hundred thousand ORAI1 positions revealed a number of ORAI1 channels had formed STIM-independent distinct supra-molecular clusters. Upon SOCE activation and in the presence of STIM proteins, a fraction of ORAI1 assembled in micron-sized two-dimensional structures, such as the known puncta at the ER plasma membrane contact zones, but also in divergent structures such as strands, and ring-like shapes. Our results thus question the hypothesis that stochastically migrating single ORAI1 channels are trapped at regions containing activated STIM, and we propose instead that supra-molecular ORAI1 clusters fulfill an amplifying function for creating dense ORAI1 accumulations upon SOCE-activation.     

Application of 252Cf-PDMS to characterize airborne particles deposited in an Antarctic glacier

The aim of this study is to apply the (252)Cf-PDMS (plasma desorption mass spectrometry) technique to characterize particles deposited in ice samples. This technique allows identification of molecular ions, even large molecules, desorbed from the sample surface, in contrast with PIXE (particle induced X-ray emission) or EDS (energy dispersive spectrometry). Two shallow snow cores obtained from different glacial drainage basins on King George Island ice cap, South Shetland Islands (Antarctica), were analyzed by PDMS. The chemical compounds identified in the ice mass spectra show that the particle contents of both samples were statistically different, indicating a non-homogeneous spatial deposition distribution for the deposited particles. The analysis of the ice mass spectra suggests some possible sources for the airborne particles. The mass spectra of ice samples collected at a site exposed directly to air masses coming from the Drake Passage show a significant contribution of particles from crustal and anthropogenic sources. However, the mass spectra of ice samples taken from a site on a slope towards a local inlet point out a high influence of marine aerosol. Therefore, it was concluded that particles deposited onto the ice cap were attributable to different aerosol sources, besides long-range atmospheric transport. The (252)Cf-PDMS technique can be considered a powerful tool for studies of snow and ice samples, providing important information for understanding the global atmospheric transport and deposition of airborne particles.     

Life‐history traits of three Ambassid fishes (Chanda nama,Parambassis lala and Parambassis ranga) from the Mathabhanga River,southwestern Bangladesh

The present study provides the first indication of the life‐history traits, including, population structure, growth pattern, condition factor, form factor (a_3.0), size at first sexual maturity (L_m), natural mortality (M_W) and optimum catchable length (L_opt), of three Ambassid (Chanda nama, Parambassis lala and Parambassis ranga) fishes from the Mathabhanga River in southwest Bangladesh. A total of 370 individuals were occasionally collected from August 2017 to July 2018 with cast nets, gill nets, square lift nets, and conical‐ and box‐traps. The total length (TL) ranged from 2.4 to 7.5 cm for C. nama, 1.9–3.8 cm for P. lala and 1.8–6.5 cm for P. ranga. The length‐frequency distributions (LFDs) showed the 4.0–5.0 cm TL size group for C. nama and the 3.0–4.0 cm TL size group were numerically dominant for P. lala and P. ranga. The length–weight relationships (LWRs) indicated isometric growth for C. nama, and positive allometric growth for P. lala and P. ranga. All the LWR values were very significant (p < .001), with all r² values > .950. Based on the Spearman rank correlation test, body weight (BW) versus Fulton's‐condition factor (K_F) was extremely correlated (p < .001), indicating a better wellbeing for these species. The a_3.0 value was 0.0082, 0.0138 and 0.0104 for C. nama, P. lala and P. ranga, respectively. Based on the maximum length (L_max), the L_m was 4.4 cm TL for C. nama, 2.5 cm TL for P. lala, and 4.0 cm TL for P. ranga. Based on the asymptotic length (L_∞), the L_m was 4.88 cm TL for C. nama, 2.63 cm TL for P. lala, and 4.28 cm TL for P. ranga. The M_W value was 2.2, 3.3 and 2.7/year for C. nama, P. lala and P. ranga, respectively. The optimum catchable length (L_opt) was 5.36 cm TL for C. nama, 2.75 cm TL for P. lala and 4.65 cm TL for P. ranga. The findings of the present study should be very useful for effective and sustainable management of these fishes in the Mathabhanga River and the connecting ecosystems.