Discovering genomic patterns in SARS-CoV-2 variants

SARS-CoV-2 is a novel severe acute respiratory syndrome-like coronavirus (SARS-CoV), which is responsible of the ongoing world pandemic of COVID-19 disease. Although many approaches are being investigated to address this issue, nowaday there are no vaccines available and there is little evidence supporting the efficiency of potential therapeutic agents. Moreover, the high mutation rate of this virus heavily affects the understanding of its evolution and diffusion mechanisms, and, in turn, the development of effective solutions. In this study, two novel algorithms are provided for finding out recurrent patterns of nucleotide subsequences of different SARS-CoV-2 genomes as a unique signature capable of identifying the most peculiar features of the pathogen. In particular, we provide several subsequence patterns related to the Spike glycoprotein, which is believed to be the main target for developing effective drugs and vaccines against the COVID-19 disease because of its role in the entrance of coronaviruses into host cells. The experimental results, obtained by analyzing 5000 genomes of SARS-CoV-2, have shown that the extracted patterns are able to recognize the Spyke protein in the 99.35% of the considered genomes. In addition, such patterns have proven to be highly discriminating with respect to other pathogenic genomes, such as SARS, Middle East respiratory syndrome, Nipah, and the streptococcus bacteria. We hope that the findings presented in this study can help specialists in speeding up the design of more accurate drugs or vaccines against SARS-CoV-2.     

A meta-analytic review of competency to stand trial research.

The present study is a meta-analysis of competency to stand trial research. One meta-analysis was previously conducted in this area, but the large number of empirical studies that have been conducted since and the introduction of new instruments and revision of old instruments warranted updating and expanding upon the previously conducted study via contemporary meta-analytic methods. We meta-analyzed 68 studies published between 1967 and 2008 that compared competent and incompetent defendants on a number of demographic, psychiatric, and criminological variables. Categorical and continuous variables commonly investigated in competency research were coded and aggregated to generate cumulative effect sizes in the form of odds ratios and Cohen's d statistics, and moderation was tested via meta-F and meta-regression analyses. The most robust findings were that defendants diagnosed with a Psychotic Disorder were approximately eight times more likely to be found incompetent than defendants without a Psychotic Disorder diagnosis and the likelihood of being found incompetent was approximately double for unemployed defendants as compared to employed defendants. The likelihood of being found incompetent was also double for defendants with a previous psychiatric hospitalization compared to those without a hospitalization history. Comparative data on 12 competency assessment instruments and three traditional instruments were also explored and the effect sizes associated with the competency measures were substantially larger (i.e., approximately one Cohen's d-point) than those for the traditional measures. Limitations of the primary research and the previous and present meta-analyses are presented and future directions in this area are outlined. (PsycINFO Database Record (c) 2011 APA, all rights reserved)     

Documentation of fatty acid profiles in lamb meat and lamb-based infant foods

Lamb meat, when used in the weaning diet of children, is presumed to have a lower allergenicity than other forms of red meat. In children with atopic dermatitis and multiple food hypersensitivities, consumption of lamb meat has also resulted in significant clinical improvements in the severity of the eczematous lesions. Lamb meat is also of special interest in infant nutrition because it provides a somewhat unique fatty acid (FA) profile that mirrors what is thought to be optimal for neonatal growth and development. However, very little is known about how the processing of fresh meat (FM) into prepared infant foods influences its FA composition. In this study, we compared the FA profile of FM from suckling lambs with those of homogenized (HO) and lyophilized (LIO) baby foods prepared primarily with lamb meat. The results show that the content of total omega-3 polyunsaturated FAs was the highest in FM (more than 3-fold) compared to commercial baby food, due to largely higher contents of α-linolenic acid (1.5-fold higher), eicosapentaenoic acid (6-fold higher), and docosahexaenoic acid (10-fold higher). Furthermore, arachidonic acid was more than 6-fold higher in FM compared to LIO and HO. Results from this study suggest the possibility of enhancing the FA profile of commercial baby food based on meat by using lamb meat, but care should be taken during processing so that important FAs are not lost. PRACTICAL APPLICATION: In this article, we have documented that meat from the suckling lamb is an interesting and potentially important source of omega-3-FAs, especially some of the long-chain polyunsaturated FAs (LC-PUFAs) that are essential for optimal neonatal growth and development. These results may have special implications to the infant food industry, in that products made using meat from suckling lambs may provide not only exceptional amounts of these FAs, but also other limiting essential nutrients such as iron. This may be especially important in regions of the world, such as Italy, where use of lamb meat as a weaning food is common during infancy.     

Inferences of evolutionary relationships from a population survey of LTR-retrotransposons and telomeric-associated sequences in the Saccharomyces sensu stricto complex

The Saccharomyces sensu stricto complex consists of six closely related species and one natural hybrid. Intra- and inter- species variability in repetitive elements can help elucidate the population structure and evolution of these close relatives. The chromosome positions of several telomeric associated sequences (TASs) and LTR-retrotransposons have been determined, using PFGE, in 112 isolates. Most of the repetitive elements studied are found in multiple copies in each strain, although in some subpopulations these elements are present in low copy number or are absent. Hybridization patterns and copy numbers of the repetitive elements correlate with geographic distribution. These patterns may yield interesting clues as to the origins and evolution of some TASs and retrotransposons, e.g. we can infer that Y' originated on the left end of chromosome XIV. There is strong evidence for horizontal transfer of Ty2 between S. cerevisiae and S. mikatae. Ty1 and Ty5 are either lost easily or frequently horizontally transferred. We have also found some gross chromosomal rearrangements in isolates within species and a few new natural hybrids between species, indicating that these processes occur in the wild and are not limited to conditions of human influence. DNA sequences have been deposited with the EMBL/GenBank database under Accession Nos AJ632279-AJ632293.     

Multi-mycotoxins Analysis in Dried Fruit by LC/MS/MS and a Modified QuEChERS Procedure

A sensitive and reliable multi-mycotoxin method was developed for the simultaneous determination of 16 toxicological important mycotoxins, such as aflatoxins B₁, B₂, G₁, and G₂; enniatins A, A₁, B, and B₁; beauvericin; ochratoxin A; fumonisin B₁, B₂, and B₃; diacetoxyscirprenol; HT-2; and T-2 toxin in dried fruits using liquid chromatography combined with electrospray ionization-triple quadrupole tandem-mass spectrometry. Mycotoxins have been extracted from the samples using a modified quick, easy, cheap, effective, rugged, and safe procedure. The method was based on a single extraction with acidified acetonitrile, followed by partitioning with salts, avoiding any further clean-up step. Limits of detections ranged from 0.08 to 15 μg kg^?1 and limits of quantification ranged from 0.2 to 45 μg kg^?1, which were below the legal limit set by the European Union for the legislated mycotoxines. The recoveries in spiked samples ranged from 60 to 135 % except for beauvericin using matrix-matched calibration curves for quantification, with good inter- and intraday repeatability (respective relative standard deviation ≤20 and 9 %). The developed method was applied to 15 commercial dried fruits: raisins, figs, apricots, plums, and dates purchased in local markets from Spain. Among the mycotoxins studied, enniantins and aflatoxins were the most predominant mycotoxins.     

Relative populations and toxin production by Aspergillus flavus and Fusarium verticillioides in artificially inoculated corn at various stages of development under field conditions

The presence, development and production of mycotoxins by Aspergillus flavus and Fusarium verticillioides were studied in corn ears under field conditions after artificial contamination of corn silks. The planted area was divided into five treatments: T1, inoculated with A. flavus solution containing 1 × 10⁸ spores, ears covered; T2, inoculated with F. verticillioides solution containing 1 × 10⁸ spores, ears covered; T3, inoculated with F. verticillioides plus A. flavus solution containing 1 × 10⁸ spores of each, ears covered; T4, sprayed with sterile phosphate‐buffered saline, ears covered; T5, non‐sprayed silks, uncovered ears. Soil and air samples were also collected and analysed for the occurrence of fungi. Water activity, relative air humidity, rainfall and temperature were determined to assess the correlation between abiotic factors and the presence of fungi in the samples. Contamination with the inoculated fungus predominated in T1 and T2. In the other treatments, F. verticillioides was the most frequently isolated contaminant irrespective of treatment. Considering the production of mycotoxins, a positive relation between the production of fumonisins B₁ and B₂ and the frequency of F. verticillioides was statistically verified in all treatments. Copyright © 2007 Society of Chemical Industry     

Benefits of blood cell transplant cryopreservation with oxypolygelatine (Gelifundol) plasma substitute

In two groups of 11 patients with poor prognosis malignancies undergoing high-dose sequential chemotherapy, we have evaluated the cryopreservation of blood cell transplants with oxypolygelatine-containing (55% oxypolygelatine, 6% hydroxyethylstarch, 5% dimethyl sulfoxide) vs standard human serum-containing (55% human serum, 6% hydroxyethylstarch, 5% dimethyl sulfoxide) cryoprotectant mixtures. Evidence is presented demonstrating that substitution of human serum proteins with oxypolygelatine has no detrimental effect either in vitro on the post-thawing recovery of hematopoietic progenitors or in vivo on the capacity of marrow reconstituting function in patients treated with myeloablative cancer therapy and autologous blood cell transplant. Oxypolygelatine is commercially available for clinical use as a plasma expander, is 30-fold less expensive than human serum albumin, is certified free of foreign serum proteins and antibodies as well as free of pyrogen, viral, mycoplasmal and bovine spongiform encephalopathy contaminants. Because of these characteristics, oxypolygelatine permits avoidance of: (1) the use of expensive serum albumin; (2) the fastidious preparation of autologous plasma or serum, and (3) the risk of infection associated with the infusion of allogeneic serum. Because of these practical advantages, we recommend the clinical use of oxypolygelatine as a substitute for human serum proteins for the routine cryopreservation of blood cell transplants.     

Disposition of Cremophor EL in humans limits the potential for modulation of the multidrug resistance phenotype in vivo

The purpose of the present study was to characterize the distribution and elimination kinetics of the paclitaxel vehicle Cremophor EL (CrEL), a polyoxyethylated castor oil that can modulate P-glycoprotein-mediated multidrug resistance in vitro. The pharmacokinetics of CrEL were studied using noncompartmental models in 23 patients with histological proof of malignant solid tumors, receiving paclitaxel as a 3-h i.v. infusion at dose levels ranging from 100-225 mg/m2 (corresponding to CrEL doses of 8.33-18.8 ml/m2). Serial plasma samples were obtained before and up to 72 h after drug administration, and were analyzed for the presence of CrEL by a novel colorimetric dye-binding microassay. The area under the plasma concentration versus time curves and the peak plasma levels of CrEL increased from 253+/-36.8 (mean+/-SD) to 680+/- 180 microl.h/ml, and from 3.40+/-0.10 to 6.58+/-0.52 microl/ml, respectively, consistent with linear pharmacokinetics. Disappearance of CrEL from the central plasma compartment was characterized by a terminal elimination half-life of 84.1+/-20.4 h, resulting in extended persistence of substantial levels even at 1 week after paclitaxel treatment. The observed volume of distribution was extremely low and averaged 3.70+/-0.49 liters/m2, implying that the tumor delivery of CrEL is insignificant. Our results indicate that CrEL is a relatively slow clearance compound and that its distribution is limited to the central plasma compartment. Hence, CrEL is not likely to play a role in reversing P-glycoprotein-mediated multidrug resistance to paclitaxel in vivo.     

New Wines in New Bottles: The “Renaissance” of the Italian Wine Industry

Unexpected events such as crises challenge organizations and actors who must search for solutions and alternatives. Severe crises can be fatal, especially when they affect entire industries. The ability to identify a viable course to address contingencies brought about by a crisis is critical to determining outcomes. In this paper, we examine the systemic response to a crisis at different levels within an industry in order to obtain a better understanding of industry responses to crises. Through a historical case study of the Italian wine industry renaissance, we show how a sudden and devastating crisis was circumvented to spur a renewed industry imbued with better practices and knowledge. Our findings also show the key role of preconditions in sustaining the renaissance.