Recent Advances in Complex Fluids Modeling

In this chapter, we present a brief description of existing viscoelastic models, starting with the classical differential and integral models, and then focusing our attention on new models that take advantage of the enhanced properties of the Mittag-Leffler function (a generalization of the exponential function). The generalized models considered in this work are the fractional Kaye-Bernstein, Kearsley, Zapas (K-BKZ) integral model and the differential generalized exponential Phan-Thien and Tanner (PTT) model recently proposed by our research group. The integral model makes use of the relaxation function obtained from a step-strain applied to the fractional Maxwell model, and the differential model generalizes the familiar exponential Phan-Thien and Tanner constitutive equation by substituting the exponential function of the trace of the stress tensor by the Mittag-Leffler function. Since the differential model is based on local operators, it reduces the computational time needed to predict the flow behavior, and, it also allows a simpler description of complex fluids. Therefore, we explore the rheometric properties of this model and its ability (or limitations) in describing complex flows

Population genomics of Bombus terrestris reveals high but unstructured genetic diversity in a potential glacial refugium

Ongoing climate change is expected to cause an increase in temperature and a reduction of precipitation levels in the Mediterranean region, which might cause changes in many species distributions. These effects negatively influence species gene pools, decreasing genetic variability and adaptive potential. Here, we use mitochondrial DNA and RADseq to analyse population genetic structure and genetic diversity of the bumblebee species Bombus terrestris (subspecies Bombus terrestris lusitanicus), in the Iberian Peninsula. Although this subspecies shows a panmictic pattern of population structure across Iberia and beyond, we found differentiation between subspecies B. t. lusitanicus and B. t. africanus, probably caused by the existence of barriers to gene flow between Iberia and North Africa. Furthermore, the results revealed that the Iberian Peninsula harbours a large fraction of B. terrestris intraspecific genetic variation, with the highest number of mitochondrial haplotypes found when compared with any other region in Europe studied so far, suggesting a potential role for the Iberian Peninsula as a glacial refugium. Our findings strengthen the idea that Iberia is a very important source of diversity for the global genetic pool of this species, because rare alleles might play a role in population resilience against human- or climate-mediated changes.info:eu-repo/semantics/publishedVersio

A tutorial

PM003/2016. Publisher Copyright: © 2022 The Author(s)The capabilities of bioanalytical mass spectrometry to (i) detect and differentiate viruses at the peptide level whilst maintaining high sample throughput and (ii) to provide diagnosis and prognosis for infected patients are presented as a tutorial in this work to aid analytical chemists and physicians to gain insights into the possibilities offered by current high-resolution mass spectrometry technology and bioinformatics. From (i) sampling to sample treatment; (ii) Matrix-Assisted Laser Desorption Ionization- to Electrospray Ionization -based mass spectrometry; and (iii) from clustering to peptide sequencing; a detailed step-by-step guide is provided and exemplified using SARS-CoV-2 Spike Y839 variant and the variant of concern SARS-CoV-2 Alpha (B.1.1.7 lineage), Influenza B, and Influenza A subtypes AH1N1pdm09 and AH3N2.publishersversionpublishe

Invasive fish disrupt host-pathogen dynamics leading to amphibian declines

Sudden disease outbreaks may not necessarily reflect a recent pathogen introduction but may instead arise from the disruption of a host-pathogen equilibrium. Together with invasive species, emerging pathogens pose significant threats to biodiversity. The dynamics of each stressor have been studied separately, yet rarely when interacting. Using a 40-year dataset, we tested the hypothesis that the introduction of an invasive fish leads to such a disruption, manifested by ranavirosis outbreaks on amphibian hosts. MCP sequencing revealed the historical presence of two major Ranavirus clades, with low prevalence. The introduction of fish was not followed by the emergence of new viruses, but rather by an increase in the prevalence of the strains already present, fitting the ‘endemic pathogen hypothesis’. Two decades after the first die-offs, one amphibian species persists in extremely low numbers, but Ranavirus prevalence is closer to the enzootic phase that preceded the outbreaks. Models show that host population collapse and lack of recovery are best explained by the concerted interaction of Ranavirus and invasive fish. We provide robust evidence that invasive species can impact naïve communities by disrupting the host-pathogen balance, exacerbating health threats. This study emphasizes the importance of exploring the historical interactions between multiple stressors to understand population declines.info:eu-repo/semantics/publishedVersio

Variations of training load, monotony, and strain and dose-response relationships with maximal aerobic speed, maximal oxygen uptake, and isokinetic strength in professional soccer players

This study aimed to identify variations in weekly training load, training monotony, and training strain across a 10-week period (during both, pre- and in-season phases); and to analyze the dose-response relationships between training markers and maximal aerobic speed (MAS), maximal oxygen uptake, and isokinetic strength. Twenty-seven professional soccer players (24.9±3.5 years old) were monitored across the 10-week period using global positioning system units. Players were also tested for maximal aerobic speed, maximal oxygen uptake, and isokinetic strength before and after 10 weeks of training. Large positive correlations were found between sum of training load and extension peak torque in the right lower limb (r = 0.57, 90%CI[0.15;0.82]) and the ratio agonist/antagonist in the right lower limb (r = 0.51, [0.06;0.78]). It was observed that loading measures fluctuated across the period of the study and that the load was meaningfully associated with changes in the fitness status of players. However, those magnitudes of correlations were small-to-large, suggesting that variations in fitness level cannot be exclusively explained by the accumulated load and loading profile

Relatório técnico sobre o Programa de Monitorização dos Ecossistemas Terrestre e Estuarino na Envolvente à CTRSU de S. João da Talha

A monitorização ambiental desempenha um papel fundamental no contexto da avaliação de impacto ambiental, permitindo acompanhar a evolução dos ecossistemas e inventariar e descrever as possíveis alterações decorrentes da implementação do projecto. A monitorização biológica dos ecossistemas terrestre e estuarino da envolvente à CTRSU teve como objectivo, no seu primeiro ano de trabalho, a criação de uma situação de referência que permitisse a comparação com os dados a obter nos anos seguintes e já durante a fase de exploração do empreendimento. Neste contexto procurou-se estabelecer o programa de recolha de dados que melhor permitisse equacionar os efeitos sobre o ecossistema em vários descritores que vêm sendo avaliados desde 1998: flora epífita, flora vascular e aves (ambiente terrestre); fitoplâncton, zooplâncton, algas macrófitas, vegetação halófita, macroinvertebrados e ictiofauna (ambiente estuarino). No presente trabalho apenas serão apresentados os resultados de um número reduzido de componentes (flora epifítica, aves, fitoplâncton, zooplâncton, macroinvertebrados e ictiofauna).info:eu-repo/semantics/publishedVersio

Predictive and therapeutic implications of a novel PLCγ1/SHP2-driven mechanism of cetuximab resistance in metastatic colorectal cancer

© 2022 The Authors; Published by the American Association for Cancer Research. This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 International (CC BY-NC-ND)Purpose: Cetuximab is an EGFR-targeted therapy approved for the treatment of RAS wild-type (WT) metastatic colorectal cancer (mCRC). However, about 60% of these patients show innate resistance to cetuximab. To increase cetuximab efficacy, it is crucial to successfully identify responder patients, as well as to develop new therapeutic approaches to overcome cetuximab resistance. Experimental design: We evaluated the value of EGFR effector phospholipase C gamma 1 (PLCγ1) in predicting cetuximab responses, by analyzing progression-free survival (PFS) of a multicentric retrospective cohort of 94 treated patients with mCRC (log-rank test and Cox regression model). Furthermore, we used in vitro and zebrafish xenotransplant models to identify and target the mechanism behind PLCγ1-mediated resistance to cetuximab. Results: In this study, levels of PLCγ1 were found increased in RAS WT tumors and were able to predict cetuximab responses in clinical samples and in vitro and in vivo models. Mechanistically, PLCγ1 expression was found to bypass cetuximab-dependent EGFR inhibition by activating ERK and AKT pathways. This novel resistance mechanism involves a noncatalytic role of PLCγ1 SH2 tandem domains in the propagation of downstream signaling via SH2-containing protein tyrosine phosphatase 2 (SHP2). Accordingly, SHP2 inhibition sensitizes PLCγ1-resistant cells to cetuximab. Conclusions: Our discoveries reveal the potential of PLCγ1 as a predictive biomarker for cetuximab responses and suggest an alternative therapeutic approach to circumvent PLCγ1-mediated resistance to cetuximab in patients with RAS WT mCRC. In this way, this work contributes to the development of novel strategies in the medical management and treatment of patients with mCRC.M. Martins' research was supported by Liga Portuguesa Contra o Cancro (LPCC): Terry Fox Fundation; Investigador FCT- Fundação para a Ciência e Technologia (IF/00409/2014) and IMM Bridge grant; RC-D research was supported by Fundação para a Ciência e Technologia (SFRH/BD/139138/2018). A. Fernandes was supported by LPCC-IMM BIOBANK; R. Fior was supported by Champalimaud Foundation and L. Costa was supported by Merck Serono.info:eu-repo/semantics/publishedVersio

On Spatially Distributed Hydrological Ecosystem Services: Bridging the Quantitative Information Gap using Remote Sensing and Hydrological Models

One of the ways in which the CGIAR Research Program on Water, Land and Ecosystems (WLE) addresses the challenge of achieving sustainable growth is by improving our understanding of tradeoffs and synergies related to water, food, environment and energy. Essential to the success of these efforts is the availability of quantitative data on these tradeoffs and synergies, and how they vary across space and time. Specifically for the countries sharing the Mekong River, WLE Greater Mekong seeks to drive and inform research and dialogue around the rivers of the region. Hydrological EcoSystem Services (HESS) are heavily affected by intensive development across the region, such as the construction of hydropower dams and land use changes - in particular deforestation, urbanization and agricultural intensification. The full extent of such changes in the agro-ecological system is often unknown, and it is a challenge to account for tradeoffs in HESS in policy processes. As in many other areas of the world, improving governance and management of water resources and associated land and ecosystems in the Greater Mekong region is not only a matter of generating more data. Sharing of knowledge and practices is a key focus of WLE Greater Mekong, which we strive to promote by enhancing the accessibility of valuable information to a wide diversity of regional stakeholders, and promoting dialogue by facilitating the creation of communities of practice. This white paper demonstrates state-of-the-art methods for assessing different HESS and their tradeoffs under different development scenarios. It explores opportunities for spatial monitoring of HESS and predicting changes under different future scenarios, information that is essential for achieving a balanced and healthy agro-ecological system. By relying on tools in the public domain and leveraging the resulting HESS data through online information platforms, this white paper is an excellent example of current efforts supported by WLE Greater Mekong to stimulate uptake of ecosystem services assessments in decision-making processes

Evaluation of a novel magneto-optical method for the detection of malaria parasites

Improving the efficiency of malaria diagnosis is one of the main goals of current malaria research. We have recently developed a magneto-optical (MO) method which allows high-sensitivity detection of malaria pigment (hemozoin crystals) in blood via the magnetically induced rotational motion of the hemozoin crystals. Here, we evaluate this MO technique for the detection of Plasmodium falciparum in infected erythrocytes using in-vitro parasite cultures covering the entire intraerythrocytic life cycle. Our novel method detected parasite densities as low as approximately 40 parasites per microliter of blood (0.0008% parasitemia) at the ring stage and less than 10 parasites/microL (0.0002% parasitemia) in the case of the later stages. These limits of detection, corresponding to approximately 20 pg/microL of hemozoin produced by the parasites, exceed that of rapid diagnostic tests and compete with the threshold achievable by light microscopic observation of blood smears. The MO diagnosis requires no special training of the operator or specific reagents for parasite detection, except for an inexpensive lysis solution to release intracellular hemozoin. The devices can be designed to a portable format for clinical and in-field tests. Besides testing its diagnostic performance, we also applied the MO technique to investigate the change in hemozoin concentration during parasite maturation. Our preliminary data indicate that this method may offer an efficient tool to determine the amount of hemozoin produced by the different parasite stages in synchronized cultures. Hence, it could eventually be used for testing the susceptibility of parasites to antimalarial drugs

High genetic diversity of measles virus, World Health Organization European region, 2005-2006

During 2005-2006, nine measles virus (MV) genotypes were identified throughout the World Health Organization European Region. All major epidemics were associated with genotypes D4, D6, and B3. Other genotypes (B2, D5, D8, D9, G2, and H1) were only found in limited numbers of cases after importation from other continents. The genetic diversity of endemic D6 strains was low; genotypes C2 and D7, circulating in Europe until recent years, were no longer identified. The transmission chains of several indigenous MV strains may thus have been interrupted by enhanced vaccination. However, multiple importations from Africa and Asia and virus introduction into highly mobile and unvaccinated communities caused a massive spread of D4 and B3 strains throughout much of the region. Thus, despite the reduction of endemic MV circulation, importation of MV from other continents caused prolonged circulation and large outbreaks after their introduction into unvaccinated and highly mobile communities