Total allowable catch for managing squat lobster fishery using stochastic nonlinear programming

The authors’ work on lobster fishery in Chile is summarized in this paper. The paper presents the formulation and algorithmic resolution of a two-stage stochastic nonlinear programming model with recourse. The proposed model considers a long-term planning horizon and specifically allows an optimal total allowable catch quota to be obtained for the first planning period. This model takes into account biomass dynamics, the conditions guaranteeing sustained species management and uncertain parameters such as growth rate and species carrying capacity. These parameters are explicitly incorporated via a discrete random variable (scenarios). The proposed model is solved by Lagrangian decomposition using the algebraic modeling software AMPL, in combination with the solver MINOS to solve the nonlinear models resulting from the scenario decomposition. The article also presents the results obtained with this methodology and the conclusions drawn from the work.     

ONT-Based Alternative Assemblies Impact on the Annotations of Unique versus Repetitive Features in the Genome of a Romanian Strain of Drosophila melanogaster

To date, different strategies of whole-genome sequencing (WGS) have been developed in order to understand the genome structure and functions. However, the analysis of genomic sequences obtained from natural populations is challenging and the biological interpretation of sequencing data remains the main issue. The MinION device developed by Oxford Nanopore Technologies (ONT) is able to generate long reads with minimal costs and time requirements. These valuable assets qualify it as a suitable method for performing WGS, especially in small laboratories. The long reads resulted using this sequencing approach can cover large structural variants and repetitive sequences commonly present in the genomes of eukaryotes. Using MinION, we performed two WGS assessments of a Romanian local strain of Drosophila melanogaster, referred to as Horezu_LaPeri (Horezu). In total, 1,317,857 reads with a size of 8.9 gigabytes (Gb) were generated. Canu and Flye de novo assembly tools were employed to obtain four distinct assemblies with both unfiltered and filtered reads, achieving maximum reference genome coverages of 94.8% (Canu) and 91.4% (Flye). In order to test the quality of these assemblies, we performed a two-step evaluation. Firstly, we considered the BUSCO scores and inquired for a supplemental set of genes using BLAST. Subsequently, we appraised the total content of natural transposons (NTs) relative to the reference genome (ISO1 strain) and mapped the mdg1 retroelement as a resolution assayer. Our results reveal that filtered data provide only slightly enhanced results when considering genes identification, but the use of unfiltered data had a consistent positive impact on the global evaluation of the NTs content. Our comparative studies also revealed differences between Flye and Canu assemblies regarding the annotation of unique versus repetitive genomic features. In our hands, Flye proved to be moderately better for gene identification, while Canu clearly outperformed Flye for NTs analysis. Data concerning the NTs content were compared to those obtained with ONT for the D. melanogaster ISO1 strain, revealing that our strategy conducted to better results. Additionally, the parameters of our ONT reads and assemblies are similar to those reported for ONT experiments performed on various model organisms, revealing that our assembly data are appropriate for a proficient annotation of the Horezu genome.     

The PINK1 p.Asn521Thr Variant Is Associated with Earlier Disease Onset in GRN/C9orf72 Frontotemporal Lobar Degeneration

Genetic frontotemporal lobar degeneration (FTLD) is characterized by heterogeneous phenotypic expression, with a disease onset highly variable even in patients carrying the same mutation. Herein we investigated if variants in lysosomal genes modulate the age of onset both in FTLD due to GRN null mutations and C9orf72 expansion. In a total of 127 subjects (n = 74 GRN mutations and n = 53 C9orf72 expansion carriers), we performed targeted sequencing of the top 98 genes belonging to the lysosomal pathway, selected based on their high expression in multiple brain regions. We described an earlier disease onset in GRN/C9orf72 pedigrees in subjects carrying the p.Asn521Thr variant (rs1043424) in PTEN-induced kinase 1 (PINK1), a gene that is already known to be involved in neurodegenerative diseases. We found that: (i) the PINK1 rs1043424 C allele is significantly associated with the age of onset; (ii) every risk C allele increases hazard by 2.11%; (iii) the estimated median age of onset in homozygous risk allele carriers is 10–12 years earlier than heterozygous/wild type homozygous subjects. A replication study in GRN/C9orf72 negative FTLD patients confirmed that the rs1043424 C allele was associated with earlier disease onset (−5.5 years in CC versus A carriers). Understanding the potential mechanisms behind the observed modulating effect of the PINK1 gene in FTLD might prove critical for identifying biomarkers and/or designing drugs to modify the age of onset, especially in GRN/C9orf72-driven disease.     

Therapeutic Efficacy and Outcomes of Remdesivir versus Remdesivir with Tocilizumab in Severe SARS-CoV-2 Infection

The infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) generated many challenges to find an effective drug combination for hospitalized patients with severe forms of coronavirus disease 2019 (COVID-19) pneumonia. We conducted a retrospective cohort study, including 182 patients with severe COVID-19 pneumonia hospitalized between March and October 2021 in a Pneumology Hospital from Cluj-Napoca, Romania. Among patients treated with standard of care, 100 patients received remdesivir (R group) and 82 patients received the combination of remdesivir plus tocilizumab (RT group). We compared the clinical outcomes, the inflammatory markers, superinfections, oxygen requirement, intensive care unit (ICU) admission and mortality rate before drug administration and 7 days after in R group and RT group. Borg score and oxygen support showed an improvement in the R group (p < 0.005). Neutrophiles, C-reactive protein (CRP) and serum ferritin levels decreased significantly in RT group but with a higher rate of superinfection in this group. ICU admission and death did not differ significantly between groups. The combination of remdesivir plus tocilizumab led to a significantly improvement in the inflammatory markers and a decrease in the oxygen requirement. Although the superinfection rate was higher in RT group than in R group, no significant difference was found in the ICU admission and mortality rate between the groups.     

Whole Body Vibration Improves Brain and Musculoskeletal Health by Modulating the Expression of Tissue-Specific Markers: FNDC5 as a Key Regulator of Vibration Adaptations

Whole body vibration (WBV) is well known to exert beneficial effects on multiple tissues, improving synaptic transmission, muscle mass, bone quality, and reducing anxiety and depressive behavior. However, the underlying molecular mechanisms are not yet fully understood, and organs and tissues may respond differently to the vibratory stimulus depending on multiple factors. Therefore, we investigated the WBV effects on the brain and musculoskeletal tissue of 4-month-old young mice, evaluating synaptic plasticity by electrophysiological recordings and tissue organization by histology and histomorphometric analysis. Specifically, WBV protocols were characterized by the same vibration frequency (45 Hz), but different in vibration exposure time (five series of 3 min for the B protocol and three series of 2 min and 30 s for the C protocol) and recovery time between two vibration sessions (1 min for the B protocol and 2 min and 30 s for the C protocol). In addition, immunohistochemistry was conducted to evaluate the expression of fibronectin type III domain-containing protein 5 (FNDC5), as well as that of tissue-specific markers, such as brain-derived neurotrophic factor (BDNF) in brain, myostatin in muscle and collagen I (COL-1) in bone. Our results suggest that the WBV effects depend closely on the type of protocol used and support the hypothesis that different organs or tissues have different susceptibility to vibration. Further studies will be needed to deepen our knowledge of physiological adaptations to vibration and develop customized WBV protocols to improve and preserve cognitive and motor functions.     

Adjusting Some Properties of Poly(methacrylic acid) (Nano)Composite Hydrogels by Means of Silicon-Containing Inorganic Fillers

The present work aims to show how the main properties of poly(methacrylic acid) (PMAA) hydrogels can be engineered by means of several silicon-based fillers (Laponite XLS/XLG, montmorillonite (Mt), pyrogenic silica (PS)) employed at 10 wt% concentration based on MAA. Various techniques (FT-IR, XRD, TGA, SEM, TEM, DLS, rheological measurements, UV-VIS) were used to comparatively study the effect of these fillers, in correlation with their characteristics, upon the structure and swelling, viscoelastic, and water decontamination properties of (nano)composite hydrogels. The experiments demonstrated that the nanocomposite hydrogel morphology was dictated by the way the filler particles dispersed in water. The equilibrium swelling degree (SDe) depended on both the pH of the environment and the filler nature. At pH 1.2, a slight crosslinking effect of the fillers was evidenced, increasing in the order Mt < Laponite < PS. At pH > pKa_MAA (pH 5.4; 7.4; 9.5), the Laponite/Mt-containing hydrogels displayed a higher SDe as compared to the neat one, while at pH 7.4/9.5 the PS-filled hydrogels surprisingly displayed the highest SDe. Rheological measurements on as-prepared hydrogels showed that the filler addition improved the mechanical properties. After equilibrium swelling at pH 5.4, G’ and G” depended on the filler, the Laponite-reinforced hydrogels proving to be the strongest. The (nano)composite hydrogels synthesized displayed filler-dependent absorption properties of two cationic dyes used as model water pollutants, Laponite XLS-reinforced hydrogel demonstrating both the highest absorption rate and absorption capacity. Besides wastewater purification, the (nano)composite hydrogels described here may also find applications in the pharmaceutical field as devices for the controlled release of drugs.     

Improving scientific application execution on android mobile devices via code refactorings

The increasing number of mobile devices with ever‐growing capabilities makes them useful for running scientific applications. However, these applications have high computational demands, whereas mobile devices have limited capabilities when compared with non‐mobile devices. More importantly, mobile devices rely on batteries for their power supply. We initially measure the battery consumption of different versions of known micro‐benchmarks representing common programming primitives found in scientific applications. Then, we analyze the performance of such micro‐benchmarks in CPU‐intensive mobile applications. We apply good programming practices and code refactorings to reduce battery consumption of scientific mobile applications. Our results show the reduction in energy usage from applying these refactorings to three scientific applications, and we consequently propose guidelines for high‐performance computing applications. Our focus is on Android, the dominant mobile operating system. As a long‐term contribution, our results represent one more step in the progress towards hybrid distributed infrastructures comprising fixed and mobile nodes, that is, the so‐called mobile grids. Copyright © 2016 John Wiley & Sons, Ltd.     

Random 3-SAT: The Plot Thickens

This paper presents an experimental investigation of the following questions: how does the average-case complexity of random 3-SAT, understood as a function of the order (number of variables) for fixed density (ratio of number of clauses to order) instances, depend on the density? Is there a phase transition in which the complexity shifts from polynomial to exponential in the order? Is the transition dependent or independent of the solver? Our experiment design uses three complete SAT solvers embodying different algorithms: GRASP, CPLEX, and CUDD. We observe new phase transitions for all three solvers, where the median running time shifts from polynomial in the order to exponential. The location of the phase transition appears to be solver-dependent. GRASP shifts from polynomial to exponential complexity near the density of 3.8, CPLEX shifts near density 3, while CUDD exhibits this transition between densities of 0.1 and 0.5. This experimental result underscores the dependence between the solver and the complexity phase transition, and challenges the widely held belief that random 3-SAT exhibits a phase transition in computational complexity very close to the crossover point.     

Detection and identification of tyrDC + enterococcal strains from pasteurized commercial cheeses

The aim of this study was to isolate and identify strains of Enterococcus from commercial cheeses and then analyze their abilities to produce biogenic amines. The genotypic variability, studied by randomly amplified polymorphic DNA (RAPD)-PCR, showed a high degree of homogeneity among enterococcal strains. Afterward, genotypic analysis indicated that all strains contain genes encoding a tyrosine decarboxylase. Our results indicate that a potential health risk exists if the enterococcal strains are able to survive the pasteurization of milk or appear as post-pasteurization contaminants. These results highlight the importance of the hazard analysis and critical control point (HACCP) to minimize the risk of hazards associated with post-contamination during cheese elaboration     

Diminution of quinolizidine alkaloids,oligosaccharides and phenolic compounds from two species of Lupinus and soybean seeds by the effect of Rhizopus oligosporus

Lupinus, like Glycine max (soybean), is an ancient leguminous plant. It has been used as a food by people living around the Mediterranean Sea and in the Andean Highlands. This legume contains quinolizidine alkaloids (Qas), oligosaccharides (OGS) and phenolic compounds (PC). The objective of this study was to evaluate the effect of the growth of Rhizopus oligosporus on the levels of Qas, OGS and PC from L. mutabilis, L. campestris and G. max through tempeh elaboration. The results showed that the soaking and cooking processes of legume seeds diminished the Qas content of L. mutabilis and L. campestris by 50%, and after 48 h of fermentation these compounds decreased by more than 90% in total. OGS diminished by more than 90% in the lupin seeds. The PC content of the three seed species subjected to these processes increased their absorbance value, probably due to the enzymatic action of a fungal tannase. These results suggested that the L. mutabilis, L. campestris and G. max fermentation with R. oligosporus is an efficient method for diminishing antinutritional factors and for obtaining a product with optimal nutritional value. Copyright © 2007 Society of Chemical Industry