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Esthetic dermatology is a growing field, and different noninvasive therapies are gaining attention. The objective of this narrative review was to update current evidence-based knowledge about recombinant enzymes. The PubMed, SciELO, Cochrane Central, and Imbiomed databases were searched for meta-analyses, systematic reviews, randomized controlled clinical trials, observational registries, and preclinical data published in English, Spanish, and Portuguese. Effectivity, safety, and tolerability of recombinant hyaluronidases, lyases, collagenases, and lipases, including their combinations, were evaluated and confirmed in diverse indications. Further research could increase current knowledge on this constantly developing and promising therapeutic area.

The significant microbiota variability represents a key feature that makes the full comprehension of the functional interaction between microbiota and the host an ongoing challenge. To overcome this limitation, in this study, fish intestinal microbiota was analyzed through a meta-analysis, identifying the core microbiota and constructing stochastic Bayesian network (BN) models with SAMBA. We combined three experiments performed with gilthead sea bream juveniles of the same hatchery batch, reared at the same season/location, and fed with diets enriched on processed animal proteins (PAP) and other alternative ingredients (NOPAP-PP, NOPAP-SCP). Microbiota data analysis disclosed a high individual taxonomic variability, a high functional homogeneity within trials and highlighted the importance of the core microbiota, clustering PAP and NOPAP fish microbiota composition. For both NOPAP and PAP BNs, >99% of the microbiota population were modelled, with a significant proportion of bacteria (55–69%) directly connected with the diet variable. Functional enrichment identified 11 relevant pathways expressed by different taxa across the different BNs, confirming the high metabolic plasticity and taxonomic heterogeneity. Altogether, these results reinforce the comprehension of the functional bacteria–host interactions and in the near future, allow the use of microbiota as a species-specific growth and welfare benchmark of livestock animals, and farmed fish in particular.

In this work, we describe the implementation of an infrastructure of conversational chatbots by using natural language processing and training within the Rasa framework. We use this infrastructure to create a chatbot assistant for the users of a bioinformatics suite. This suite provides a customized interface solution for omic pipelines and workflows, and it is named GPRO. The infrastructure has also been used to build another chatbot for a Laboratory Information Management System (LIMS). The two chatbots (namely, Genie and Abu) have been built on an open framework that uses natural language understanding (NLU) and machine learning techniques to understand user queries and respond to them. Users can seamlessly interact with the chatbot to receive support on navigating the GPRO pipelines and workflows. The chatbot provides a bridge between users and the wealth of bioinformatics knowledge available online.

ABSTRACTThe epidemiology of sexually transmitted infections (STIs) is complex due to the coexistence of various pathogens, the variety of transmission modes derived from sexual orientations and behaviors at different ages and genders, and sexual contact hotspots resulting in network transmission. There is also a growing proportion of recreational drug users engaged in high-risk sexual activities, as well as pharmacological self-protection routines fostering non-condom practices. The frequency of asymptomatic patients makes it difficult to develop a comprehensive approach to STI epidemiology. Modeling approaches are required to deal with such complexity. Membrane computing is a natural computing methodology for the virtual reproduction of epidemics under the influence of deterministic and stochastic events with an unprecedented level of granularity. The application of the LOIMOS program to STI epidemiology illustrates the possibility of using it to shape appropriate interventions. Under the conditions of our basic landscape, including sexual hotspots of individuals with various risk behaviors, an increase in condom use reduces STIs in a larger proportion of heterosexuals than in same-gender sexual contacts and is much more efficient for reducing Neisseria gonorrhoeae than Chlamydia and lymphogranuloma venereum infections. Amelioration from diagnostic STI screening could be instrumental in reducing N. gonorrhoeae infections, particularly in men having sex with men (MSM), and Chlamydia trachomatis infections in the heterosexual population; however, screening was less effective in decreasing lymphogranuloma venereum infections in MSM. The influence of STI epidemiology of sexual contacts between different age groups (

Candida albicans is a clinically important polymorphic fungal pathogen that causes life-threatening invasive infections in immunocompromised patients. Antifungal therapy failure is a substantial clinical problem, due to the emergence of an increasing number of drug-resistant isolates. Caspofungin is a common antifungal drug, often used as first-line therapy that inhibits cell wall β-(1,3)-glucan synthesis. In this work, the cell surface of different echinocandin-resistant C. albicans clinical isolates was compared with sensitive isolates and their responses to echinocandin treatment analyzed. Proteomic analysis detected changes in the repertoire of proteins involved in cell wall organization and maintenance, in drug-resistant strains compared to susceptible isolates and after incubation with caspofungin. Moreover, an interaction network was created from the differential expression results. Our findings suggest drug resistance may involve not only a different cell wall architecture, but also a different response to drugs.

Abstract This study combined crash reports, land use, real-time traffic, and weather data to form an integrated database to analyze the severity of crashes taking place on rural highways. As the traffic cameras are placed at fixed locations, there is a wide range of measured distances between crashes and the selected nearest camera for extracting traffic variables. This may change the significance of traffic variables. For the first time, spacing was introduced as the distance around the detectors in which traffic characteristics are inferred to crashes. Classification and Regression Tree (CART) was employed as an interpretable tool to explore how spacing affects model performance and the significance of traffic variables. Twelve spacing scenarios from 250 to 3000 m were evaluated. Except for short spacings suffering from the low sample size issue, each model has a good predictive performance based on overall accuracy and F2 score in the 1000–3000 m spacings. In this range, three dominant rules emerged: (1) high deviations of speed on the roads surrounded by wastelands are associated with severe crashes; (2) faded markings in residential zones increase the likelihood of severe outcomes; (3) installation of barriers decrease the probability of severe crashes. Comparing the Variable Importance Measure (VIM) reveals that the total importance of traffic variables reduces as the spacing increases. Also, results indicate that average speed is significant until 1750 m; but speed deviation, traffic flow, and percent of heavy vehicles are more stable variables for further spacings. In conclusion, for the first time, spacing scenarios were evaluated systematically and proved that they have a remarkable impact on the significance of variables. This novel research provides guidance not only on the spacing but also on which real-time traffic variables have a greater impact on crash severity, along with design, land use, and environmental variables.

Integrated land-use transport models are often accused of being too complex, too coarse or too slow. We tightly couple the microscopic land use model SILO (Simple Integrated Land Use Orchestrator) with the agent-based transport simulation model MATSim (Multi-Agent Transport Simulation). The integration of the two models is person-centric. It means, firstly, that travel demand is generated microscopically. Secondly, SILO agents can query individualized travel information to search for housing or jobs (and to choose among available modes). Consequently, travel time matrices (skim matrices) are not needed anymore. Travel time queries can be done for any time of the day (instead of for one or few time periods), any x/y coordinate (instead of a limited number of zones) and take into account properties of the individual. This way, we avoid aggregation issues (e.g., large zones that disguise local differences) and we can account for individual constraints (e.g., nighttime workers who cannot commute by public transport for lack of service). Therefore, the behavior of agents is represented realistically, which allows us to simulate their reaction to novel policies (e.g., emission-class-based vehicle restrictions) and to extract system-wide effects. The model is applied in two study areas: a toy scenario and the metropolitan region of Munich. We simulate various transport and land use policies to test the model capabilities, including public transport extensions, zones restricted for private cars and land use development regulations. The results demonstrate that the increase of the model resolution and model expressiveness facilitates the simulation of such policies and the interpretation of the results.

Abstract Background The paper presents a simulation model for freight. In the paper, this model is applied to understand the impacts of electric vans and cargo bikes for the last-mile delivery of parcels. Cargo bikes are electrically assisted vehicles that distribute parcels from micro depots located close to the final customers by means of short tours. The parcels are sent from the major distribution center to micro depots in vans (called feeders). Materials and methods An agent-based model is used for the purpose of the paper. The model is based on the disaggregation of commodity flows to represent trucks (for all commodities) and individual shipments (for parcel deliveries). The model represents microscopically every freight vehicle in the study area. Results The simulation of various scenarios with different shares of cargo bikes and electric vans assesses the impacts of electrification and cargo bikes. The use of cargo bikes to deliver parcels allows to reduce the number of motorized vehicles, although the presence of large parcels requires that at least half of deliveries by vans are still required. The shift to cargo bikes represents a slight increase in the total operating time to deliver the parcel demand. With low shares of cargo bikes, the total distance traveled increases, since the reduction of van tours cannot compensate the additional feeder trips from distribution centers to micro depots. The cargo bikes also do not reduce the number of vehicles for the served area, but modify the composition of vehicle types. Low noise, smaller, low emission vehicles increase, while delivery vans are reduced. Conclusion Both cargo bikes and electric vans are able to reduce CO2 emissions, even after accounting for the emissions related to electricity production.

Abstract Squamous cell carcinoma is the most frequent histologic type of anal carcinoma. The standard of care since the 1970s has been a combination of 5-fluorouracil, mitomycin C, and radiotherapy. This treatment is very effective in T1/T2 tumors (achieving complete regression in 80–90% of tumors). However, in T3/T4 tumors, the 3-year relapse free survival rate is only 50%. The VITAL trial aimed to assess the efficacy and safety of panitumumab in combination with this standard treatment. In this study, 27 paraffin-embedded samples from the VITAL trial and 18 samples from patients from daily clinical practice were analyzed by whole-exome sequencing and the influence of the presence of genetic variants in the response to panitumumab was studied. Having a moderate- or high-impact genetic variant in PIK3CA seemed to be related to the response to panitumumab. Furthermore, copy number variants in FGFR3, GRB2 and JAK1 were also related to the response to panitumumab. These genetic alterations have also been studied in the cohort of patients from daily clinical practice (not treated with panitumumab) and they did not have a predictive value. Therefore, in this study, a collection of genetic alterations related to the response with panitumumab was described. These results could be useful for patient stratification in new anti-EGFR clinical trials.

Abstract Background The argasid tick Ornithodoros erraticus is the main vector of tick-borne human relapsing fever (TBRF) and African swine fever (ASF) in the Mediterranean Basin. Tick salivary proteins secreted to the host at the feeding interface play critical roles for tick feeding and may contribute to host infection by tick-borne pathogens; accordingly, these proteins represent interesting antigen targets for the development of vaccines aimed at the control and prevention of tick infestations and tick-borne diseases. Methods To identify these proteins, the transcriptome of the salivary glands of O. erraticus was de novo assembled and the salivary gene expression dynamics assessed throughout the trophogonic cycle using Illumina sequencing. The genes differentially upregulated after feeding were selected and discussed as potential antigen candidates for tick vaccines. Results Transcriptome assembly resulted in 22,007 transcripts and 18,961 annotated transcripts, which represent 86.15% of annotation success. Most salivary gene expression took place during the first 7 days after feeding (2088 upregulated transcripts), while only a few genes (122 upregulated transcripts) were differentially expressed from day 7 post-feeding onwards. The protein families more abundantly overrepresented after feeding were lipocalins, acid and basic tail proteins, proteases (particularly metalloproteases), protease inhibitors, secreted phospholipases A2, 5′-nucleotidases/apyrases and heme-binding vitellogenin-like proteins. All of them are functionally related to blood ingestion and regulation of host defensive responses, so they can be interesting candidate protective antigens for vaccines. Conclusions The O. erraticus sialotranscriptome contains thousands of protein coding sequences—many of them belonging to large conserved multigene protein families—and shows a complexity and functional redundancy similar to those observed in the sialomes of other argasid and ixodid tick species. This high functional redundancy emphasises the need for developing multiantigenic tick vaccines to reach full protection. This research provides a set of promising candidate antigens for the development of vaccines for the control of O. erraticus infestations and prevention of tick-borne diseases of public and veterinary health relevance, such as TBRF and ASF. Additionally, this transcriptome constitutes a valuable reference database for proteomics studies of the saliva and salivary glands of O. erraticus.

Replication of SARS-CoV-2 in the human population is defined by distributions of mutants that are present at different frequencies within the infected host and can be detected by ultra-deep sequencing techniques. In this study, we examined the SARS-CoV-2 mutant spectra of amplicons from the spike-coding (S-coding) region of 5 nasopharyngeal isolates derived from patients with vaccine breakthrough. Interestingly, all patients became infected with the Alpha variant, but amino acid substitutions that correspond to the Delta Plus, Iota, and Omicron variants were present in the mutant spectra of the resident virus. Deep sequencing analysis of SARS-CoV-2 from patients with vaccine breakthrough revealed a rich reservoir of mutant types and may also identify tolerated substitutions that can be represented in epidemiologically dominant variants.

El presente estudio realiza un análisis bibliométrico del Anuario de Psicología Jurídica entre 1991-2019. Los datos se recogieron en una base de datos que permite analizar autores, instituciones, países, género, temáticas e impacto. Los resultados señalan diferencia de género en el número de autores, con una mayor presencia de mujeres (50.2%), y el número de firmas (53.7% hombres). Con los años se observa un aumento del número de autores y de firmas, de trabajos en coautoría, una mayor presencia de firmas internacionales representando el 23.5% de las firmas entre 2011 y 2019. Se identifican tres grupos de colaboración, dos procedentes de España y uno de Colombia. Son las categorías de Psicología Jurídica y Forense y Evaluación Psicológica y Testimonio las más representadas en los trabajos publicados. Se puede concluir que el Anuario de Psicología Jurídica es un referente en su área principalmente para autores y profesionales de países latinoamericanos.

ABSTRACT Mutant spectra of RNA viruses are important to understand viral pathogenesis and response to selective pressures. There is a need to characterize the complexity of mutant spectra in coronaviruses sampled from infected patients. In particular, the possible relationship between SARS-CoV-2 mutant spectrum complexity and disease associations has not been established. In the present study, we report an ultradeep sequencing (UDS) analysis of the mutant spectrum of amplicons from the nsp12 (polymerase)- and spike (S)-coding regions of 30 nasopharyngeal isolates (diagnostic samples) of SARS-CoV-2 of the first COVID-19 pandemic wave (Madrid, Spain, April 2020) classified according to the severity of ensuing COVID-19. Low-frequency mutations and deletions, counted relative to the consensus sequence of the corresponding isolate, were overwhelmingly abundant. We show that the average number of different point mutations, mutations per haplotype, and several diversity indices was significantly higher in SARS-CoV-2 isolated from patients who developed mild disease than in those associated with moderate or severe disease (exitus). No such bias was observed with RNA deletions. Location of amino acid substitutions in the three-dimensional structures of nsp12 (polymerase) and S suggest significant structural or functional effects. Thus, patients who develop mild symptoms may be a richer source of genetic variants of SARS-CoV-2 than patients with moderate or severe COVID-19. IMPORTANCE The study shows that mutant spectra of SARS-CoV-2 from diagnostic samples differ in point mutation abundance and complexity and that significantly larger values were observed in virus from patients who developed mild COVID-19 symptoms. Mutant spectrum complexity is not a uniform trait among isolates. The nature and location of low-frequency amino acid substitutions present in mutant spectra anticipate great potential for phenotypic diversification of SARS-CoV-2.

Combination antiretroviral therapy (cART) effectively blocks HIV replication but cannot completely eliminate HIV from the body mainly due to establishment of a viral reservoir. To date, clinical strategies designed to replace cART for life and alternatively to eliminate the HIV reservoir have failed. The reduced expression of viral antigens in the latently infected cells is one of the main reasons behind the failure of the strategies to purge the HIV reservoir. This situation has forced the scientific community to search alternative therapeutic strategies to control HIV infection. In this regard, recent findings have pointed out extracellular vesicles as therapeutic agents with enormous potential to control HIV infection. This review focuses on their role as pro-viral and anti-viral factors, as well as their potential therapeutic applications.

Every sector needs to minimize GHG emissions to limit climate change. Emissions from transport, however, have remained mostly unchanged over the past thirty years. In particular, air travel for short-haul flights is a significant contributor to transport emissions. This article identifies factors that influence the demand for domestic air travel. An agent-based model was implemented for domestic travel in Germany to test policies that could be implemented to reduce air travel and CO2 emissions. The agent-based long-distance travel demand model is composed of trip generation, destination choice, mode choice and CO2 emission modules. The travel demand model was estimated and calibrated with the German Household Travel Survey, including socio-demographic characteristics and area type. Long-distance trips were differentiated by trip type (daytrip, overnight trip), trip purpose (business, leisure, private) and mode (auto, air, long-distance rail and long-distance bus). Emission factors by mode were used to calculate CO2 emissions. Potential strategies and policies to reduce air travel demand and its CO2 emissions are tested using this model. An increase in airfares reduced the number of air trips and reduced transport emissions. Even stronger effects were found with a policy that restricts air travel to trips that are longer than a certain threshold distance. While such policies might be difficult to implement politically, restricting air travel has the potential to reduce total CO2 emissions from transport by 7.5%.

Non-alcoholic fatty liver disease (NAFLD) is the most common liver disease with no therapeutic consensus. Oxidation and inflammation are hallmarks in the progression of this complex disease, which also involves interactions between the genetic background and the environment. Mastiha is a natural nutritional supplement known to possess antioxidant and anti-inflammatory properties. This study investigated how a 6-month Mastiha supplementation (2.1 g/day) could impact the antioxidant and inflammatory status of patients with NAFLD, and whether genetic variants significantly mediate these effects. We recruited 98 patients with obesity (BMI ≥ 30 kg/m2) and NAFLD and randomly allocated them to either the Mastiha or the placebo group for 6 months. The anti-oxidative and inflammatory status was assessed at baseline and post-treatment. Genome-wide genetic data was also obtained from all participants, to investigate gene-by-Mastiha interactions. NAFLD patients with severe obesity (BMI > 35kg/m2) taking the Mastiha had significantly higher total antioxidant status (TAS) compared to the corresponding placebo group (P value=0.008). We did not observe any other significant change in the investigated biomarkers as a result of Mastiha supplementation alone. We identified several novel gene-by-Mastiha interaction associations with levels of cytokines and antioxidant biomarkers. Some of the identified genetic loci are implicated in the pathological pathways of NAFLD, including the lanosterol synthase gene (LSS) associated with glutathione peroxidase activity (Gpx) levels, the mitochondrial pyruvate carrier-1 gene (MPC1) and the sphingolipid transporter-1 gene (SPNS1) associated with hemoglobin levels, the transforming growth factor‐beta‐induced gene (TGFBI) and the micro-RNA 129-1 (MIR129-1) associated with IL-6 and the granzyme B gene (GZMB) associated with IL-10 levels. Within the MAST4HEALTH randomized clinical trial (NCT03135873, www.clinicaltrials.gov) Mastiha supplementation improved the TAS levels among NAFLD patients with severe obesity. We identified several novel genome-wide significant nutrigenetic interactions, influencing the antioxidant and inflammatory status in NAFLD.Clinical Trial RegistrationClinicalTrials.gov, identifier NCT03135873.

The argasid tick Ornithodoros moubata is the main vector of human relapsing fever (HRF) and African swine fever (ASF) in Africa. Salivary proteins are part of the host-tick interface and play vital roles in the tick feeding process and the host infection by tick-borne pathogens; they represent interesting targets for immune interventions aimed at tick control. The present work describes the transcriptome profile of salivary glands of O. moubata and assesses the gene expression dynamics along the trophogonic cycle using Illumina sequencing. De novo transcriptome assembling resulted in 71,194 transcript clusters and 41,011 annotated transcripts, which represent 57.6% of the annotation success. Most salivary gene expression takes place during the first 7 days after feeding (6,287 upregulated transcripts), while a minority of genes (203 upregulated transcripts) are differentially expressed between 7 and 14 days after feeding. The functional protein groups more abundantly overrepresented after blood feeding were lipocalins, proteases (especially metalloproteases), protease inhibitors including the Kunitz/BPTI-family, proteins with phospholipase A2 activity, acid tail proteins, basic tail proteins, vitellogenins, the 7DB family and proteins involved in tick immunity and defence. The complexity and functional redundancy observed in the sialotranscriptome of O. moubata are comparable to those of the sialomes of other argasid and ixodid ticks. This transcriptome provides a valuable reference database for ongoing proteomics studies of the salivary glands and saliva of O. moubata aimed at confirming and expanding previous data on the O. moubata sialoproteome.

Populations of RNA viruses are composed of complex and dynamic mixtures of variant genomes that are termed mutant spectra or mutant clouds. This applies also to SARS-CoV-2, and mutations that are detected at low frequency in an infected individual can be dominant (represented in the consensus sequence) in subsequent variants of interest or variants of concern. Here we briefly review the main conclusions of our work on mutant spectrum characterization of hepatitis C virus (HCV) and SARS-CoV-2 at the nucleotide and amino acid levels and address the following two new questions derived from previous results: (i) how is the SARS-CoV-2 mutant and deletion spectrum composition in diagnostic samples, when examined at progressively lower cut-off mutant frequency values in ultra-deep sequencing; (ii) how the frequency distribution of minority amino acid substitutions in SARS-CoV-2 compares with that of HCV sampled also from infected patients. The main conclusions are the following: (i) the number of different mutations found at low frequency in SARS-CoV-2 mutant spectra increases dramatically (50- to 100-fold) as the cut-off frequency for mutation detection is lowered from 0.5% to 0.1%, and (ii) that, contrary to HCV, SARS-CoV-2 mutant spectra exhibit a deficit of intermediate frequency amino acid substitutions. The possible origin and implications of mutant spectrum differences among RNA viruses are discussed.

Anal squamous cell carcinoma (ASCC) is a rare neoplasm. Chemoradiotherapy is the standard of care, with no therapeutic advances achieved over the past three decades. Thus, a deeper molecular characterization of this disease is still necessary. We analyzed 46 paraffin-embedded tumor samples from patients diagnosed with primary ASCC by exome sequencing. A bioinformatics approach focused in the identification of high-impact genetic variants, which may act as drivers of oncogenesis, was performed. The relation between genetics variants and prognosis was also studied. The list of high-impact genetic variants was unique for each patient. However, the pathways in which these genes are involved are well-known hallmarks of cancer, such as angiogenesis or immune pathways. Additionally, we determined that genetic variants in BRCA2, ZNF750, FAM208B, ZNF599, and ZC3H13 genes are related with poor disease-free survival in ASCC. This may help to stratify the patient's prognosis and open new avenues for potential therapeutic intervention. In conclusion, sequencing of ASCC clinical samples appears an encouraging tool for the molecular portrait of this disease.

The U.S. Highway Capacity Manual (HCM 2010) methodology is used in Spain to evaluate traffic operation and quality of service. In two-lane undivided highways, the effect of limiting where drivers could pass slower vehicles, or passing restrictions, is considered through the percentage of no-passing zones. This measure does not account for how passing opportunities are distributed along the road. The objective of this research was to evaluate the effect percentage of no-passing zones and average passing zone length on a two-lane highway and, if significant, incorporate them in the analysis methodology,. The TWOPAS microsimulation program was calibrated and validated to the Spanish conditions. Passing restrictions had little effect on average traffic speed (ATS), with differences lower than 6 km/h between a road segment with no passing restrictions and a road segment with a passing restriction on 100% of its length. Conversely, passing restrictions can increase the percent time spent following (PTSF) up to 30%. Increasing the passing zone length beyond 2,000 m does not improve PTSF. The new models could be used to better estimate traffic operation on Spanish two-lane highways.

Abstract Exosome production from cancer-associated fibroblasts seems to be an important driver of tumor progression. We report the first in-depth biotype characterization of ncRNAs, analyzed by Next Generation Sequencing and Bioinformatics, expressed in established primary human normal and cancer-associated fibroblasts (CAFs) from cancer and normal mucosa tissues from 9 colorectal cancer patients, and/or packaged in their derived exosomes. Differential representation and enrichment analyses based on these ncRNAs revealed a significant number of differences between the ncRNA content of exosomes and the expression patterns of the normal and cancer-associated fibroblast cells. ncRNA regulatory elements are specifically packaged in CAF-derived exosomes, supporting a specific cross-talk between CAFs and colon cancer cells and/or other stromal cells, mediated by exosomes. These sncRNAs are potential biomarkers present in cancer-associated fibroblast-derived exosomes, which should thereby contribute to developing new non-invasive diagnostic, prognostic and predictive methods for clinical applications in management of cancer patients.

The most common travel demand model type is the trip-based model, despite major shortcomings due to its aggregate nature. Activity-based models overcome many of the limitations of the trip-based model, but implementing and calibrating an activity-based model is labor-intensive and running an activity-based model often takes long runtimes. This paper proposes a hybrid called MITO (Microsimulation Transport Orchestrator) that overcomes some of the limitations of trip-based models, yet is easier to implement than an activity-based model. MITO uses microsimulation to simulate each household and person individually. After trip generation, the travel time budget in minutes is calculated for every household. This budget influences destination choice; i.e., people who spent a lot of time commuting are less likely to do much other travel, while people who telecommute might compensate by additional discretionary travel. Mode choice uses a nested logit model, and time-of-day choice schedules trips in 1-minute intervals. Three case studies demonstrate how individuals may be traced through the entire model system from trip generation to the assignment.

Gilthead sea bream is an economically important fish species that is remarkably well-adapted to farming and changing environments. Understanding the genomic basis of this plasticity will serve to orientate domestication and selective breeding toward more robust and efficient fish. To address this goal, a draft genome assembly was reconstructed combining short- and long-read high-throughput sequencing with genetic linkage maps. The assembled unmasked genome spans 1.24 Gb of an expected 1.59 Gb genome size with 932 scaffolds (∼732 Mb) anchored to 24 chromosomes that are available as a karyotype browser at www.nutrigroup-iats.org/seabreamdb. Homology-based functional annotation, supported by RNA-seq transcripts, identified 55,423 actively transcribed genes corresponding to 21,275 unique descriptions with more than 55% of duplicated genes. The mobilome accounts for the 75% of the full genome size and it is mostly constituted by introns (599 Mb), whereas the rest is represented by low complexity repeats, RNA retrotransposons, DNA transposons, and non-coding RNAs. This mobilome also contains a large number of chimeric/composite genes (i.e., loci presenting fragments or exons mostly surrounded by LINEs and Tc1/mariner DNA transposons), whose analysis revealed an enrichment in immune-related functions and processes. Analysis of synteny and gene phylogenies uncovered a high rate of species-specific duplications, resulting from recent independent duplications rather than from genome polyploidization (2.024 duplications per gene; 0.385 excluding gene expansions). These species-specific duplications were enriched in gene families functionally related to genome transposition, immune response, and sensory responses. Additionally, transcriptional analysis of liver, skeletal muscle, intestine, gills, and spleen supported a high number of functionally specialized paralogs under tissue-exclusive regulation. Altogether, these findings suggest a role of recent large-scale gene duplications coupled to tissue expression diversification in the evolution of gilthead sea bream genome during its successful adaptation to a changing and pathogen-rich environment. This issue also underscores a role of evolutionary routes for rapid increase of the gene repertoire in teleost fish that are independent of polyploidization. Since gilthead sea bream has a well-recognized plasticity, the current study will advance our understanding of fish biology and how organisms of this taxon interact with the environment.

ABSTRACT Membrane computing is a bio-inspired computing paradigm whose devices are the so-called membrane systems or P systems. The P system designed in this work reproduces complex biological landscapes in the computer world. It uses nested “membrane-surrounded entities” able to divide, propagate, and die; to be transferred into other membranes; to exchange informative material according to flexible rules; and to mutate and be selected by external agents. This allows the exploration of hierarchical interactive dynamics resulting from the probabilistic interaction of genes (phenotypes), clones, species, hosts, environments, and antibiotic challenges. Our model facilitates analysis of several aspects of the rules that govern the multilevel evolutionary biology of antibiotic resistance. We examined a number of selected landscapes where we predict the effects of different rates of patient flow from hospital to the community and vice versa, the cross-transmission rates between patients with bacterial propagules of different sizes, the proportion of patients treated with antibiotics, and the antibiotics and dosing found in the opening spaces in the microbiota where resistant phenotypes multiply. We also evaluated the selective strengths of some drugs and the influence of the time 0 resistance composition of the species and bacterial clones in the evolution of resistance phenotypes. In summary, we provide case studies analyzing the hierarchical dynamics of antibiotic resistance using a novel computing model with reciprocity within and between levels of biological organization, a type of approach that may be expanded in the multilevel analysis of complex microbial landscapes. IMPORTANCE The work that we present here represents the culmination of many years of investigation in looking for a suitable methodology to simulate the multihierarchical processes involved in antibiotic resistance. Everything started with our early appreciation of the different independent but embedded biological units that shape the biology, ecology, and evolution of antibiotic-resistant microorganisms. Genes, plasmids carrying these genes, cells hosting plasmids, populations of cells, microbial communities, and host's populations constitute a complex system where changes in one component might influence the other ones. How would it be possible to simulate such a complexity of antibiotic resistance as it occurs in the real world? Can the process be predicted, at least at the local level? A few years ago, and because of their structural resemblance to biological systems, we realized that membrane computing procedures could provide a suitable frame to approach these questions. Our manuscript describes the first application of this modeling methodology to the field of antibiotic resistance and offers a bunch of examples—just a limited number of them in comparison with the possible ones to illustrate its unprecedented explanatory power.

L3 larvae of anisakid nematodes are an important problem for the fisheries industry and pose a potential risk for human health by acting as infectious agents causing allergies and as potential vectors of pathogens and microrganisms. In spite of the close bacteria–nematode relationship very little is known of the anisakids microbiota. Fresh fish could be contaminated by bacteria vectored in the cuticle or in the intestine of anisakids when the L3 larvae migrate through the muscles. As a consequence, the bacterial inoculum will be spread, with potential effects on the quality of the fish, and possible clinical effects cannot be discarded. A total of 2,689,113 16S rRNA gene sequences from a total of 113 L3 individuals obtained from fish captured along the FAO 27 fishing area were studied. Bacteria were taxonomically characterized through 1803 representative operational taxonomic units (OTUs) sequences. Fourteen phyla, 31 classes, 52 orders, 129 families and 187 genera were unambiguously identified. We have found as part of microbiome an average of 123 OTUs per L3 individual. Diversity indices (Shannon and Simpson) indicate an extraordinary diversity of bacteria at an OTU level. There are clusters of anisakids individuals (samples) defined by the associated bacteria which, however, are not significantly related to fish hosts or anisakid taxa. This suggests that association or relationship among bacteria in anisakids, exists without the influence of fishes or nematodes. The lack of relationships with hosts of anisakids taxa has to be expressed by the association among bacterial OTUs or other taxonomical levels which range from OTUs to the phylum level. There are significant biological structural associations of microbiota in anisakid nematodes which manifest in clusters of bacteria ranging from phylum to genus level, which could also be an indicator of fish contamination or the geographic zone of fish capture. Actinobacteria, Aquificae, Firmicutes, and Proteobacteria are the phyla whose abundance value discriminate for defining such structures.

Integrated land-use/transport models have five decades of history of both widely recognized successful implementations and implementations that remained far behind their originally stated goals. This paper summarizes the state of the art of integrated land-use/transport modeling and reports on findings from the Symposium for the Integration of Land-Use and Transport Models in Raitenhaslach, which is near Munich, in 2016. From these sources, the paper identifies major challenges in integrated land-use/transport modeling and proposes paths that support successful implementations. Particular attention is given to the coordination of short- and long-term decisions, the technical integration of models, microscopic versus macroscopic frameworks and appropriate levels of model complexity. The paper concludes with five themes that require further research to ensure that integrated land-use/transport models will keep up with modeling needs in the future.

Vibrio vulnificus (Vv) is a multi-host pathogenic species currently subdivided into three biotypes (Bts). The three Bts are human-pathogens, but only Bt2 is also a fish-pathogen, an ability that is conferred by a transferable virulence-plasmid (pVvbt2). Here we present a phylogenomic analysis from the core genome of 80 Vv strains belonging to the three Bts recovered from a wide range of geographical and ecological sources. We have identified five well-supported phylogenetic groups or lineages (L). L1 comprises a mixture of clinical and environmental Bt1 strains, most of them involved in human clinical cases related to raw seafood ingestion. L2 is formed by a mixture of Bt1 and Bt2 strains from various sources, including diseased fish, and is related to the aquaculture industry. L3 is also linked to the aquaculture industry and includes Bt3 strains exclusively, mostly related to wound infections or secondary septicemia after farmed-fish handling. Lastly, L4 and L5 include a few strains of Bt1 associated with specific geographical areas. The phylogenetic trees for ChrI and II are not congruent to one another, which suggests that inter- and/or intra-chromosomal rearrangements have been produced along Vv evolution. Further, the phylogenetic trees for each chromosome and the virulence plasmid were also not congruent, which also suggests that pVvbt2 has been acquired independently by different clones, probably in fish farms. From all these clones, the one with zoonotic capabilities (Bt2-Serovar E) has successfully spread worldwide. Based on these results, we propose a new updated classification of the species based on phylogenetic lineages rather than on Bts, as well as the inclusion of all Bt2 strains in a pathovar with the particular ability to cause fish vibriosis, for which we suggest the name “piscis.”

Intermediate modes of transport, such as shared vehicles or ride sharing, are starting to increase their market share at the expense of traditional modes of car, public transport, and taxi. In the advent of autonomous vehicles, single occupancy shared vehicles are expected to substitute at least in part private conventional vehicle trips. The objective of this paper is to estimate the impact of shared autonomous vehicles on average trip duration and vehicle-km traveled in a large metropolitan area. A stated preference online survey was designed to gather data on the willingness to use shared autonomous vehicles. Then, commute trips and home-based other trips were generated microscopically for a synthetic population in the greater Munich metropolitan area. Individuals who traveled by auto were selected to switch from a conventional vehicle to a shared autonomous vehicle subject to their willingness to use them. The effect of shared autonomous vehicles on urban mobility was assessed through traffic simulations in MATSim with a varying autonomous taxi fleet size. The results indicated that the total traveled distance increased by up to 8% after autonomous fleets were introduced. Current travel demand can still be satisfied with an acceptable waiting time when 10 conventional vehicles are replaced with 4 shared autonomous vehicles.

Tras un meditado y sereno debate, se ha aprobado la ley del contrato de transporte terrestre de mercancías, que sustituye oportunamente, y con vocación de permanencia, a la caduca y desorganizada regulación vigente en esta materia en el Derecho español. La ley moderniza, con una buena técnica y siguiendo modelos contrastados, las reglas básicas regidoras de este tipo de contrato, por lo que merece un juicio positivo, si bien no exento de crítica en algunos aspectos en los que hubiese sido deseable una mayor decisión por parte del legislador, particularmente en lo que respecta a la regulación de los intermediarios del transporte y de la subcontratación. Aunque algunos de los aspectos contemplados por la ley resultarán ya familiares para los operadores del sector, y particularmente para quienes actúan en el ámbito del transporte internacional de mercancías por carretera, es recomendable, no obstante, iniciar una inmediata labor de divulgación sobre esta nueva legislación, tarea a la que se desea contribuir con este artículo en que se señalan sus claves más relevantes.Publicación en línea: 01 octubre 2012

The EU transport policy is trying to promote short sea shipping (SSS) in order to bring it up to a modern shape and as an alternative to the carriage of goods by road under certain circumstances. It is neither a short-term task nor an easy one and, additionally, it brings about some legal uncertainties which derive from the structural complexity of the transport operations which include SSS (contract overlapping), as well as from the divergent legal regimes applicable in each case to those operations. In order to overcome those uncertainties, transport operators dealing with SSS should, on the one hand, get acquainted with rules such as the one contained in article 2 CMR, which covers an special kind of roadsea combined transport (ro-ro) that fits ideally in regular operations with SSS. And, on the other hand, they should get a better knowledge of the similarities and differences between the road and sea liability regimes. With this article we will try both to describe the basic meaning of article 2 CMR and to compare those two liability regimes.

Freight forwarders are key players in the global and multimodal market of services for the transport of goods. Contrary to our neighbouring countries, Spain lacks regulation of the contract between the freight forwarder and its principal. Additionally, both articles 275 and 379 Code of Commerce, usually applicable to freight forwarders, are of seldom use here. The first one, because it is not contemplating freight forwarding activities. The second one because it addresses a different issue: the role of contracting carriers. The legal confusion among us has been increased simultaneously by a misleading and late scientific approach to the role of freight forwarders. It is about time, then, to remind we are in debt with this figure and, should the interested parties agree, to propose a debate based on the need to revise our legal system in this field.

Grateloupia imbricata is an intertidal marine seaweed and candidate model organism for both industry and academic research, owing to its ability to produce raw materials such as carrageenan. Here we report on the transcriptome of G. imbricata with the aim of providing new insights into the metabolic pathways and other functional pathways related to the reproduction of Grateloupia species. Next-generation sequencing was carried out with subsequent de novo assembly and annotation using state-of-the-art bioinformatic protocols. The results show the presence of transcripts required for the uptake of glycerol, which is a specific carbon source for in vitro culture of G. imbricata and nucleotide sequences that are involved in polyamine-based biosynthesis, polyamine degradation, and metabolism of jasmonates and ethylene. Polyamines, ethylene and methyl jasmonate are plant growth regulators that elicit the development and maturation of cystocarps and the release of spores from seaweeds. Our results will inform studies of the mechanisms that control polysaccharide accumulation, cystocarp formation and spore release. Moreover, our transcriptome information clarifies aspects of red seaweed carposporogenesis with potential benefits for enhancing reproduction.

Cryptocercus punctulatus and Parasphaeria boleiriana are two distantly related xylophagous and subsocial cockroaches. Cryptocercus is related to termites. Xylophagous cockroaches and termites are excellent model organisms for studying the symbiotic relationship between the insect and their microbiota. In this study, high-throughput 454 pyrosequencing of 16S rRNA was used to investigate the diversity of metagenomic gut communities of C. punctulatus and P. boleiriana, and thereby to identify possible shifts in symbiont allegiances during cockroaches evolution. Our results revealed that the hindgut prokaryotic communities of both xylophagous cockroaches are dominated by members of four Bacteria phyla: Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria. Other identified phyla were Spirochaetes, Planctomycetes, candidatus Saccharibacteria (formerly TM7), and Acidobacteria, each of which represented 1-2% of the total population detected. Community similarity based on phylogenetic relatedness by unweighted UniFrac analyses indicated that the composition of the bacterial community in the two species was significantly different (P < 0.05). Phylogenetic analysis based on the characterized clusters of Bacteroidetes, Spirochaetes, and Deltaproteobacteria showed that many OTUs present in both cockroach species clustered with sequences previously described in termites and other cockroaches, but not with those from other animals or environments. These results suggest that, during their evolution, those cockroaches conserved several bacterial communities from the microbiota of a common ancestor. The ecological stability of those microbial communities may imply the important functional role for the survival of the host of providing nutrients in appropriate quantities and balance.

A dedicated outdoor air system (DOAS) can be designed to supply 100% of the outside air and meet the latent load of the room with dry air. The objectives of this study were to develop a model of a DOAS equipped with a desiccant wheel and a vapor-compression refrigeration system, build a prototype, validate the model with experimental data, and gain knowledge about the system operation. The test facility was designed with the desiccant wheel downstream of the cooling coil to take advantage of the operating principles of cooling coils and desiccants. A model of the DOAS was developed in the TRNSYS environment. The root mean standard error (RMSE) was used for model validation by comparing the measured air and refrigerant properties with the corresponding calculated values. The results obtained with the developed model showed that the DOAS was able to maintain an indoor humidity ratio depending on outdoor conditions. Laboratory tests were also used to investigate the effect of changes in the regeneration air temperature and the process airflow rate on the process air humidity ratio at the outlet of the wheel. The results are consistent with the technical literature.

Viral M-dsRNAs encoding yeast killer toxins share similar genomic organization, but no overall sequence identity. The dsRNA full-length sequences of several known M-viruses either have yet to be completed, or they were shorter than estimated by agarose gel electrophoresis. High-throughput sequencing was used to analyze some M-dsRNAs previously sequenced by traditional techniques, and new dsRNAs from atypical killer strains of Saccharomyces cerevisiae and Torulaspora delbrueckii. All dsRNAs expected to be present in a given yeast strain were reliably detected and sequenced, and the previously-known sequences were confirmed. The few discrepancies between viral variants were mostly located around the central poly(A) region. A continuous sequence of the ScV-M2 genome was obtained for the first time. M1 virus was found for the first time in wine yeasts, coexisting with Mbarr-1 virus in T. delbrueckii. Extra 5′- and 3′-sequences were found in all M-genomes. The presence of repeated short sequences in the non-coding 3′-region of most M-genomes indicates that they have a common phylogenetic origin. High identity between amino acid sequences of killer toxins and some unclassified proteins of yeast, bacteria, and wine grapes suggests that killer viruses recruited some sequences from the genome of these organisms, or vice versa, during evolution.

Fusarium avenaceum is a fungus commonly isolated from soil and associated with a wide range of host plants. We present here three genome sequences of F. avenaceum, one isolated from barley in Finland and two from spring and winter wheat in Canada. The sizes of the three genomes range from 41.6-43.1 MB, with 13217-13445 predicted protein-coding genes. Whole-genome analysis showed that the three genomes are highly syntenic, and share>95% gene orthologs. Comparative analysis to other sequenced Fusaria shows that F. avenaceum has a very large potential for producing secondary metabolites, with between 75 and 80 key enzymes belonging to the polyketide, non-ribosomal peptide, terpene, alkaloid and indole-diterpene synthase classes. In addition to known metabolites from F. avenaceum, fuscofusarin and JM-47 were detected for the first time in this species. Many protein families are expanded in F. avenaceum, such as transcription factors, and proteins involved in redox reactions and signal transduction, suggesting evolutionary adaptation to a diverse and cosmopolitan ecology. We found that 20% of all predicted proteins were considered to be secreted, supporting a life in the extracellular space during interaction with plant hosts.