MC-Net: a method for the construction of phylogenetic networks based on the Monte-Carlo method

Background  

A phylogenetic network is a generalization of phylogenetic trees that allows the representation of conflicting signals or alternative evolutionary histories in a single diagram. There are several methods for constructing these networks. Some of these methods are based on distances among taxa. In practice, the methods which are based on distance perform faster in comparison with other methods. The Neighbor-Net (N-Net) is a distance-based method. The N-Net produces a circular ordering from a distance matrix, then constructs a collection of weighted splits using circular ordering. The SplitsTree which is a program using these weighted splits makes a phylogenetic network. In general, finding an optimal circular ordering is an NP-hard problem. The N-Net is a heuristic algorithm to find the optimal circular ordering which is based on neighbor-joining algorithm.     

Bioaerosol emissions arising during application of municipal solid-waste compost

Although application of composted municipal waste has its benefits, there are also concerns about a range of adverse effects. Bioaerosol emissions are one cause of concern because of related health problems. To assess the concentration of bioaerosols emitted during application of compost, fungi and bacteria were collected using an Andersen biosampler. Temperature and relative humidity were also recorded at each location. Total bacterial concentrations averaged 2,887 cfu/m³ for background samples and 6,727 cfu/m³ for compost-application samples, which constitutes a significant difference. The mean concentration of fungi during application of compost was three times greater than the background, but the difference was not significant. Concentrations of total bacteria in compost-application samples decreased significantly with increasing humidity. These results indicated that bioaerosol emissions as a result of application of compost could increase levels of exposure to bacteria and pose a potential health risk for exposed individuals.     

Encapsulation of soybean meal with fats enriched in palmitic and stearic acids: effects on rumen-undegraded protein and in vitro intestinal digestibility

Fat coating of soybean meal (SBM) can reduce its protein degradability in the rumen, but the encapsulation of SBM with palmitic (PA) and stearic acids (SA) has not yet been investigated, despite both fatty acids are common energy sources in dairy cow diets. This study aimed to evaluate the effects of applying a novel method, using either 400 or 500 g fat/kg (treatments FL40 and FL50, respectively), which was enriched in PA and SA at different ratios (100:0, 75:25, 50:50, 25:75 and 0:100), on physical and chemical characteristics, ruminal degradability, solubility and in vitro intestinal protein digestibility (IVIPD) of the obtained products. Encapsulation of SBM in fat resulted in greater mean particle size and lower bulk density and protein solubility than unprotected SBM (USBM). Treatment FL50 resulted in increased (p < 0.01) rumen-undegraded protein (RUP) compared to USBM. There were no differences in RUP of SBM when different PA: SA ratios were used. The mean RUP content of treatments FL40 and FL50 (306 and 349 g/kg, respectively) was greater compared to USBM (262 g/kg, p < 0.05), but lower than that for a standard heat-treated SBM (431 g/kg). Values of IVIPD did not differ among SBM, heat-treated SBM and FL40 and FL50 samples, all being greater than 97.8%. In conclusion, encapsulation of SBM with fats enriched in PA and SA proved to be effective in reducing protein solubility and increasing RUP without depressing protein digestibility in the intestine. For validation of the method, in vivo research to investigate the effects of these products on the production of dairy cows is warranted.     

Predicting doxorubicin drug delivery by single-walled carbon nanotube through cell membrane in the absence and presence of nicotine molecules: a molecular dynamics simulation study

Abstract

In order to study the interaction of the anticancer agent Doxorubicin with the single-walled carbon nanotubes with different diameters as drug delivery systems, the molecular dynamics (MD) simulations have been used. Also, for design and development of intracellular Doxorubicin drug delivery systems, a series of steered MD simulations are applied to explore the possibility of encapsulated Doxorubicin–carbon nanotube penetration through a lipid bilayer in presence and absence of Nicotine molecules at different pulling rates. Our simulation results showed that in spite of the adsorption of drug molecules on the outer sidewall of the nanotubes, the spontaneous localization of one Doxorubicin molecule into the cavity of the nanovectors with larger diameters is observed. It is found that the presence of Nicotine molecules in extracellular medium increases the required force for pulling nanotube-encapsulated drug as well as the required time for penetration process, especially at higher velocity. Also, the entering process of the Nicotine molecules into the carbon nanotube causes that the encapsulated drug molecule is fully released in the hydrophobic phase of the lipid bilayer.

Communicated by Ramaswamy H. Sarma     

Vaccine development and therapeutic design for 2019-nCoV/SARS-CoV-2: Challenges and chances

The ongoing outbreak of the recently emerged 2019 novel coronavirus (nCoV), which has seriously threatened global health security, is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with high morbidity and mortality. Despite the burden of the disease worldwide, still, no licensed vaccine or any specific drug against 2019-nCoV is available. Data from several countries show that few repurposed drugs using existing antiviral drugs have not (so far) been satisfactory and more recently were proven to be even highly toxic. These findings underline an urgent need for preventative and therapeutic interventions designed to target specific aspects of 2019-nCoV. Again the major factor in this urgency is that the process of data acquisition by physical experiment is time-consuming and expensive to obtain. Scientific simulations and more in-depth data analysis permit to validate or refute drug repurposing opportunities predicted via target similarity profiling to speed up the development of a new more effective anti-2019-nCoV therapy especially where in vitro and/or in vivo data are not yet available. In addition, several research programs are being developed, aiming at the exploration of vaccines to prevent and treat the 2019-nCoV. Computational-based technology has given us the tools to explore and identify potentially effective drug and/or vaccine candidates which can effectively shorten the time and reduce the operating cost. The aim of the present review is to address the available information on molecular determinants in disease pathobiology modules and define the computational approaches employed in systematic drug repositioning and vaccine development settings for SARS-CoV-2.     

Sensory retraining improves light touch threshold of the paretic hand in chronic stroke survivors: a single-subject A-B design

Abstract

Background: Light touch, one of the primary and basic sensations, is often neglected in sensory retraining programmes for stroke survivors.

Objective: This study aimed to investigate the effects of sensory retraining on the light touch threshold of the hand, dexterity and upper limb motor function of chronic stroke survivors.

Methods: Five chronic stroke survivors with sensory impairment participated in this single-subject A-B design study. In baseline (A) phase, they only received standard rehabilitation. In the treatment (B) phase, they received a 6-week sensory retraining intervention in addition to standard rehabilitation. In both phases, they were evaluated every 3 days. Light touch threshold, manual dexterity and upper limb motor function were assessed using Semmes-Weinstein Monofilaments, Box-Block Test and Fugl-Meyer Assessment, respectively. Visual analysis, nonparametric Mann-Whitney U test and, c-statistic were used for assessing the changes between phases.

Results: All participants indicated changes in trend or slope of the total score of light touch or both between the two phases. The results of the c-statistic also showed the statistical difference in the total score of light touch between baseline and treatment in all participants (p?<?0.001). Also, the results of the c-statistic and Mann-Whitney U test supported the difference of manual dexterity and motor function of the upper limb between baseline and treatment in all participants (p?<?0.001).

Conclusion: Current findings showed that sensory retraining may be an effective adjunctive intervention for improving the light touch threshold of the hand, dexterity and upper limb motor function in chronic stroke survivors.     

Enhanced production of cichoric acid in cell suspension culture of Echinacea purpurea by silver nanoparticle elicitation

Plant Cell, Tissue and Organ Culture (PCTOC) - This study was conducted to optimize callus induction, cell suspension culture, and enhance cichoric acid production in Echinacea purpurea. For this...