Data-driven reconstruction of chaotic dynamical equations: the H\'enon-Heiles type system

In this study, the classical two-dimensional potential $V_N=\frac{1}{2}\,m\,\omega^2\,r^2 + \frac{1}{N}\,r^N\,\sin(N\,\theta)$, $N \in {\mathbb Z}^+$, is considered. At $N=1,2$, the system is superintegrable and integrable, respectively, whereas for $N>2$ it exhibits a richer chaotic dynamics. For instance, at $N=3$ it coincides with the H\'enon-Heiles system. The periodic, quasi-periodic and chaotic motions are systematically characterized employing time series, Poincar\'e sections, symmetry lines and the largest Lyapunov exponent as a function of the energy $E$ and the parameter $N$. Concrete results for the lowest cases $N=3,4$ are presented in complete detail. This model is used as a benchmark system to estimate the accuracy of the Sparse Identification of Nonlinear Dynamical Systems (SINDy) method, a data-driven algorithm which reconstructs the underlying governing dynamical equations. We pay special attention at the transition from regular motion to chaos and how this influences the precision of the algorithm. In particular, it is shown that SINDy is a robust and stable tool possessing the ability to generate non-trivial approximate analytical expressions for periodic trajectories as well

Characterization of digestive proteases in the Senegal sole Solea senegalensis Kaup, 1858

The digestive proteases of Senegal sole Solea senegalensis Kaup, 1858 were studied. Acid proteases showed their peak of activity between pH:2.0 and pH:2.5. Optimum activity for intestinal proteases was found in the range of pH:9.5-10.0. The results of acid protease stability under different pH indicated that only pH 12.0 affect these enzymes. Alkaline proteases were highly sensitive to acidic pH. Temperature optimums were found at 37-40 °C. Thermal stability analysis showed that proteases kept up their activities until 50 °C. The use of specific proteases inhibitors showed the presence of aspartic proteases in stomach and serine proteases (trypsin and chymotrypsin-like) in the intestine. Zymograms confirm the existence of a single protease in stomach extract, and seven active fractions in the intestine extracts.Se caracterizan las proteasas digestivas de Solea senegalensis Kaup, 1858. El óptimo de actividad para el extracto estomacal se situó en valores de pH entre 2,0 y 2,5 y para los intestinales entre pH:9,5 y pH:10,0. El extracto de estómago se mostró muy estable a distintos valores de pH, excepto a pH:12,0. Los extractos intestinales mostraron ser inestables a pH ácido. Los óptimos de temperatura se localizaron entre 37 y 40 °C. Las proteasas fueron termolábiles por encima de 50 °C. El uso de sustratos e inhibidores específicos evidenció la presencia mayoritaria de pepsina en el estómago y de serina proteasas de tipo tripsina y quimotripsina en el intestino. Los zimogramas confirmaron la existencia de una sola proteasa en el extracto de estómago y de siete fracciones activas en el intestino.Instituto Español de Oceanografí

Antimicrobial resistance and associated risk factors in Escherichia coli isolated from Peruvian dogs: A focus on extended-spectrum β-lactamases and colistin

Background and Aim: Established antimicrobial resistance (AMR) surveillance in companion animals is lacking, particularly in low-middle-income countries. The aim of this study was to analyze AMR and its risk factors in Escherichia coli isolated from dogs at two veterinary centers in Lima (Peru). Materials and Methods: Ninety dogs were included in the study. Antimicrobial susceptibility was established by disk diffusion, whereas microdilution was used to determine colistin susceptibility. Mechanisms related to extended-spectrum β-lactamases (ESBL) and colistin resistance were determined by polymerase chain reaction. Clonal relationships of colistin-resistant isolates were assessed by XbaI-pulsed-field gel electrophoresis. Results: Thirty-five E. coli strains were isolated. High levels of resistance to ampicillin (57.1%), nalidixic acid (54.3%), tetracycline (48.6%), and azithromycin (25.7%) were detected. Cephalosporin resistance levels were ≥20% and those for colistin were 14.3%. Twelve (34.2%) isolates were ESBL producers; of these, six blaCTX-M-55 (50.0%), 2 (16.6%) blaCTX-M-15, and 2 (16.6%) blaCTX-M-8-like genes were found. The five colistin-resistant isolates were clonally unrelated, with four of them presenting amino acid codon substitutions in the mgrB gene (V8A) or mutations in the mgrB promoter (a12g, g98t, and c89t). Furthermore, dog age, <6 years (p = 0.027) and raw diet (p = 0.054) were associated with resistance to a greater number of antibiotic families. Conclusion: Despite small number of samples included, the study found that dogs studied were carriers of multidrug-resistant E. coli, including last-resort antimicrobials, representing a public health problem due to close contact between dogs and humans. This issue suggests the need for larger studies addressed to design strategies to prevent the spread of resistant micro-organisms in small animal clinics and domestic settings

Breast cancer PAM50 signature: correlation and concordance between RNA-Seq and digital multiplexed gene expression technologies in a triple negative breast cancer series

[Background]: Full RNA-Seq is a fundamental research tool for whole transcriptome analysis. However, it is too costly and time consuming to be used in routine clinical practice. We evaluated the transcript quantification agreement between RNA-Seq and a digital multiplexed gene expression platform, and the subtype call after running the PAM50 assay in a series of breast cancer patients classified as triple negative by IHC/FISH. The goal of this study is to analyze the concordance between both expression platforms overall, and for calling PAM50 triple negative breast cancer intrinsic subtypes in particular.[Results]: The analyses were performed in paraffin-embedded tissues from 96 patients recruited in a multicenter, prospective, non-randomized neoadjuvant triple negative breast cancer trial (NCT01560663). Pre-treatment core biopsies were obtained following clinical practice guidelines and conserved as FFPE for further RNA extraction. PAM50 was performed on both digital multiplexed gene expression and RNA-Seq platforms. Subtype assignment was based on the nearest centroid classification following this procedure for both platforms and it was concordant on 96% of the cases (N = 96). In four cases, digital multiplexed gene expression analysis and RNA-Seq were discordant. The Spearman correlation to each of the centroids and the risk of recurrence were above 0.89 in both platforms while the agreement on Proliferation Score reached up to 0.97. In addition, 82% of the individual PAM50 genes showed a correlation coefficient > 0.80.[Conclusions]: In our analysis, the subtype calling in most of the samples was concordant in both platforms and the potential discordances had reduced clinical implications in terms of prognosis. If speed and cost are the main driving forces then the preferred technique is the digital multiplexed platform, while if whole genome patterns and subtype are the driving forces, then RNA-Seq is the preferred method.M.M was supported by two research grants from Ministry of Economy and Competitiveness ISCIII-FIS grants (PI 12/02684): “Predictores genómicos de respuesta a la quimioterapia neoadyuvante con docetaxel-carboplatino en pacientes con cáncer de mama triple negativo”/“Genomic predictors of response to neoadjuvant chemotherapy with docetaxel-carboplatin in patients with triple negative breast cancer”; and (PI 15/00117): “Cáncer de mama triple negative: Predicción de respuesta a docetaxel-carboplatino neoadyuvante mediante caracterización de TILs y firmas inmunes basadas en secuenciación masiva de RNA”/” Triple negative breast cancer: Prediction of response to neoadjuvant docetaxel-carboplatin by characterization of TILs and immune signatures based on massive RNA sequencing”. C.M.P was supported by funds from the NCI Breast SPORE program (P50-CA58223).Peer reviewe

PR-LncRNA Signature Regulates Glioma Cell Activity Through Expression of SOX Factors

Long non-coding RNAs (LncRNAs) have emerged as a relevant class of genome regulators involved in a broad range of biological processes and with important roles in tumor initiation and malignant progression. We have previously identified a p53-regulated tumor suppressor signature of LncRNAs (PR-LncRNAs) in colorectal cancer. Our aim was to identify the expression and function of this signature in gliomas. We found that the expression of the four PR-LncRNAs tested was high in human low-grade glioma samples and diminished with increasing grade of disease, being the lowest in glioblastoma samples. Functional assays demonstrated that PR-LncRNA silencing increased glioma cell proliferation and oncosphere formation. Mechanistically, we found an inverse correlation between PR-LncRNA expression and SOX1, SOX2 and SOX9 stem cell factors in human glioma biopsies and in glioma cells in vitro. Moreover, knock-down of SOX activity abolished the effect of PR-LncRNA silencing in glioma cell activity. In conclusion, our results demonstrate that the expression and function of PR-LncRNAs are significantly altered in gliomagenesis and that their activity is mediated by SOX factors. These results may provide important insights into the mechanisms responsible for glioblastoma pathogenesis.PA, JA-I and AS-A were recipients of a predoctoral fellowship from the Spanish Association Against Cancer (AECC Gipuzkoa), Basque Government and Instituto Salud Carlos III. This work was supported by grants from the Carlos III Institute of Health and the European Regional Development Fund (PI13/02277, CP16/00039, DTS16/084, and PI16/01580) and Industry and Health Departments of the Basque Country

Doñana, diversidad y ciencia

144 páginasLa biodiversidad es más que la suma de los elementos que componen el mundo vivo; también son biodiversidad las relaciones entre esos elementos, los procesos ecológicos que hacen posible su existencia y los procesos evolutivos que los han originado. […] Los seres humanos necesitamos a la biodiversidad más que ella a nosotros, ya que es la responsable de que la Tierra funcione de una manera satisfactoria. […] El entramado de la vida se ocupa de regular la composición de la atmósfera (y con ella, el clima), de depurar el aire y el agua, de hacer fértil al suelo, de evitar riadas y avalanchas, de polinizar las cosechas, de reducir las plagas, etc. Por todo ello es indispensable conservar la biodiversidad, hoy amenazada.” (Miguel Delibes) Doñana, diversidad y ciencia es un paseo conceptual por el espacio natural más emblemático de Europa. La esencia de un mito a través de decenas de fotografías… Un acercamiento respetuoso a la diversidad de sus conceptos, un paseo por la esencia de su historia y una curiosa aproximación a la ciencia que genera hoy en día. En este recorrido descubriremos el carácter distintivo de algunos de los parajes de la reserva, sus matices más interesantes, las texturas y las formas más sorprendentes de la naturaleza, sus colores y conjuntos, sus transformaciones en las últimas décadas y la influencia de la presencia humana en el privilegiado ecosistema de la Reserva Biológica de Doñana

Surrounded by sound: noise, rights and environments

Noise was probably the first environmental pollutant (apart from human waste) in the Ancient world. Yet today, by comparison with other environmental matters, noise and protection from its effects are often overlooked, except in specialist fields such as architecture or planning. One major reason for this may be that noise does not possess the same ability to spread that is characteristic of other forms of pollution. Noise is also an unusual form of environmental pollution in having a physical impact – it is ‘heard’ and can be ‘felt’ – but is predominantly interpreted subjectively. The impact and consequences of anthropogenic noise for humans and biodiversity in general, are currently under-investigated in criminology and are under-addressed in both public and private international environmental law. Here we question why noise has not (so far) been explored within green criminology and only tentatively explored within cultural criminology. The objectives are to provide an overview of noise as a topic, connecting media, culture, anti- and pro-social behaviour, and to unearth interconnections between the matter of noise and its implications for the environment

Cholangiocarcinoma progression depends on the uptake and metabolization of extracellular lipids

[Background and Aims] Cholangiocarcinoma (CCA) includes a heterogeneous group of biliary cancers with a dismal prognosis. We investigated if lipid metabolism is disrupted in CCA and its role in tumor proliferation.[Approach and Results] The in vitro and in vivo tumorigenic capacity of five human CCA cell lines was analyzed. Proteome, lipid content, and metabolic fluxes were evaluated in CCA cells and compared with normal human cholangiocytes (NHC). The Akt1/NOTCH1 intracellular cytoplasmic domain (Nicd1)-driven CCA mouse model was also evaluated. The proteome of CCA cells was enriched in pathways involved in lipid and lipoprotein metabolism. The EGI1 CCA cell line presented the highest tumorigenic capacity. Metabolic studies in high (EGI1) versus low (HUCCT1) proliferative CCA cells in vitro showed that both EGI1 and HUCCT1 incorporated more fatty acids (FA) than NHC, leading to increased triglyceride storage, also observed in Akt1/Nicd1-driven CCA mouse model. The highly proliferative EGI1 CCA cells showed greater uptake of very-low-density and HDLs than NHC and HUCCT1 CCA cells and increased cholesteryl ester content. The FA oxidation (FAO) and related proteome enrichment were specifically up-regulated in EGI1, and consequently, pharmacological blockade of FAO induced more pronounced inhibition of their tumorigenic capacity compared with HUCCT1. The expression of acyl-CoA dehydrogenase ACADM, the first enzyme involved in FAO, was increased in human CCA tissues and correlated with the proliferation marker PCNA.[Conclusions] Highly proliferative human CCA cells rely on lipid and lipoprotein uptake to fuel FA catabolism, suggesting that inhibition of FAO and/or lipid uptake could represent a therapeutic strategy for this CCA subclass.This work was supported by “Ayudas para apoyar grupos de investigación del sistema Universitario Vasco” (IT971‐16 to PA), MCIU/AEI/FEDER, UE (2018‐095134‐B‐100 to PA and by the University of Basque Country COLAB20/01 to PA; Spanish Carlos III Health Institute (ISCIII) (FIS PI15/01132, PI18/01075, PI21/00922, and Miguel Servet Program CON14/00129 and CPII19/00008 to JMB; FIS PI14/00399, PI17/00022 and PI20/00186 to MJP; Sara Borrell [CD19/00254 to PMR]) cofinanced by “Fondo Europeo de Desarrollo Regional” (FEDER); CIBERehd (ISCIII) to JMB, MJP, PMR, PA and LB); “Diputación Foral Gipuzkoa” (DFG15/010, DFG16/004 to JMB and 2020‐CIEN‐000067‐01 to PMR), Department of Health of the Basque Country (2019111024 to MJP, 2017111010 to JMB, and 2020111077 to JMB and PA), “Euskadi RIS3” (2016222001, 2017222014, 2018222029, 2019222054, 2020333010 to JMB), BIOEF (Basque Foundation for Innovation and Health Research: EiTB Maratoia BIO15/CA/016/BD to JMB) and Department of Industry of the Basque Country (Elkartek: KK‐2020/00008 to JMB); La Caixa Scientific Foundation (HR17‐00601 to JMB). “Fundación Científica de la Asociación Española Contra el Cáncer” (AECC Scientific Foundation, to JMB). AMMF‐The Cholangiocarcinoma Charity (EU/2019/AMMFt/001, to JMB and PMR). MRDG was funded by “Fundación Científica de la Asociación Española Contra el Cáncer” (AECC de Bizkaia), MJP was funded by the Spanish Ministry of Economy and Competitiveness (MINECO: “Ramón y Cajal” Program RYC‐2015‐17755), IL, AL and FG‐R by the Basque Government (PRE_2016_1_0152, PRE_2018_2_0195 and PRE 2020 2 02500, respectively), AN‐Z and BG‐S by the UPV/EHU, AB‐V by “Programa de especialización de Personal Investigador Doctor” at the UPV/EHU (2019‐2020) and MA by the MCIU/AEI/FEDER

Definition of a temporal distribution index for high temporal resolution precipitation data over Peninsular Spain and the Balearic Islands: the fractal dimension; and its synoptic implications

Precipitation on the Spanish mainland and in the Balearic archipelago exhibits a high degree of spatial and temporal variability, regardless of the temporal resolution of the data considered. The fractal dimension indicates the property of self-similarity, and in the case of this study, wherein it is applied to the temporal behaviour of rainfall at a fine (10-min) resolution from a total of 48 observatories, it provides insights into its more or less convective nature. The methodology of Jenkinson & Collison which automatically classifies synoptic situations at the surface, as well as an adaptation of this methodology at 500 hPa, was applied in order to gain insights into the synoptic implications of extreme values of the fractal dimension. The highest fractal dimension values in the study area were observed in places with precipitation that has a more random behaviour over time with generally high totals. Four different regions in which the atmospheric mechanisms giving rise to precipitation at the surface differ from the corresponding above-ground mechanisms have been identified in the study area based on the fractal dimension. In the north of the Iberian Peninsula, high fractal dimension values are linked to a lower frequency of anticyclonic situations, whereas the opposite occurs in the central region. In the Mediterranean, higher fractal dimension values are associated with a higher frequency of the anticyclonic type and a lower frequency of the advective type from the east. In the south, lower fractal dimension values indicate higher frequency with respect to the anticyclonic type from the east and lower frequency with respect to the cyclonic type