Performing and Visualizing Temporal Analysis of Large Text Data Issued for Open Sources: Past and Future Methods

International audienceIn this paper we first propose a state of the art on the methods for the visualization and the interpretation of textual data, in particular of scientific data. We then shortly present our contributions to this field in the form of original methods for the automatic classification of documents and easy interpretation of their content through characteristic keywords and classes created by our algorithms. In a second step, we focus our analysis on the data evolving over time. We detail our di-achronic approach, especially suitable for the detection and visualization of topic changes. This allows us to conclude with Diachronic'Explorer, our upcoming tool for visual exploration of evolutionary data

Effects of Transmitters and Amyloid-Beta Peptide on Calcium Signals in Rat Cortical Astrocytes: Fura-2AM Measurements and Stochastic Model Simulations

BACKGROUND: To better understand the complex molecular level interactions seen in the pathogenesis of Alzheimer's disease, the results of the wet-lab and clinical studies can be complemented by mathematical models. Astrocytes are known to become reactive in Alzheimer's disease and their ionic equilibrium can be disturbed by interaction of the released and accumulated transmitters, such as serotonin, and peptides, including amyloid- peptides (A). We have here studied the effects of small amounts of A25-35 fragments on the transmitter-induced calcium signals in astrocytes by Fura-2AM fluorescence measurements and running simulations of the detected calcium signals. METHODOLOGY/PRINCIPAL FINDINGS: Intracellular calcium signals were measured in cultured rat cortical astrocytes following additions of serotonin and glutamate, or either of these transmitters together with A25-35. A25-35 increased the number of astrocytes responding to glutamate and exceedingly increased the magnitude of the serotonin-induced calcium signals. In addition to A25-35-induced effects, the contribution of intracellular calcium stores to calcium signaling was tested. When using higher stimulus frequency, the subsequent calcium peaks after the initial peak were of lower amplitude. This may indicate inadequate filling of the intracellular calcium stores between the stimuli. In order to reproduce the experimental findings, a stochastic computational model was introduced. The model takes into account the major mechanisms known to be involved in calcium signaling in astrocytes. Model simulations confirm the principal experimental findings and show the variability typical for experimental measurements. CONCLUSIONS/SIGNIFICANCE: Nanomolar A25-35 alone does not cause persistent change in the basal level of calcium in astrocytes. However, even small amounts of A25-35, together with transmitters, can have substantial synergistic effects on intracellular calcium signals. Computational modeling further helps in understanding the mechanisms associated with intracellular calcium oscillations. Modeling the mechanisms is important, as astrocytes have an essential role in regulating the neuronal microenvironment of the central nervous system

Evaluating Effects of Divided Hemispheric Processing on Word Recognition in Foveal and Extrafoveal Displays: The Evidence from Arabic

Background: Previous studies have claimed that a precise split at the vertical midline of each fovea causes all words to the left and right of fixation to project to the opposite, contralateral hemisphere, and this division in hemispheric processing has considerable consequences for foveal word recognition. However, research in this area is dominated by the use of stimuli from Latinate languages, which may induce specific effects on performance. Consequently, we report two experiments using stimuli from a fundamentally different, non-Latinate language (Arabic) that offers an alternative way of revealing effects of split-foveal processing, if they exist. Methods and Findings: Words (and pseudowords) were presented to the left or right of fixation, either close to fixation and entirely within foveal vision, or further from fixation and entirely within extrafoveal vision. Fixation location and stimulus presentations were carefully controlled using an eye-tracker linked to a fixation-contingent display. To assess word recognition, Experiment 1 used the Reicher-Wheeler task and Experiment 2 used the lexical decision task. Results: Performance in both experiments indicated a functional division in hemispheric processing for words in extrafoveal locations (in recognition accuracy in Experiment 1 and in reaction times and error rates in Experiment 2) but no such division for words in foveal locations. Conclusions: These findings from a non-Latinate language provide new evidence that although a functional division i

High proportion of cactus species threatened with extinction

This is the author accepted manuscript. The final version is available from Nature Publishing Group via the DOI in this record.Consejo Nacional de Ciencia y Tecnologí

From Late Miocene to Holocene: Processes of Differentiation within the Telestes Genus (Actinopterygii: Cyprinidae)

Investigating processes and timing of differentiation of organisms is critical in the understanding of the evolutionary mechanisms involved in microevolution, speciation, and macroevolution that generated the extant biodiversity. From this perspective, the Telestes genus is of special interest: the Telestes species have a wide distribution range across Europe (from the Danubian district to Mediterranean districts) and have not been prone to translocation. Molecular data (mtDNA: 1,232 bp including the entire Cyt b gene; nuclear genome: 11 microsatellites) were gathered from 34 populations of the Telestes genus, almost encompassing the entire geographic range. Using several phylogenetic and molecular dating methods interpreted in conjunction with paleoclimatic and geomorphologic evidence, we investigated the processes and timing of differentiation of the Telestes lineages. The observed genetic structure and diversity were largely congruent between mtDNA and microsatellites. The Messinian Salinity Crisis (Late Miocene) seems to have played a major role in the speciation processes of the genus. Focusing on T. souffia, a species occurring in the Danube and Rhone drainages, we were able to point out several specific events from the Pleistocene to the Holocene that have likely driven the differentiation and the historical demography of this taxon. This study provides support for an evolutionary history of dispersal and vicariance with unprecedented resolution for any freshwater fish in this region

Strategies to Target Tumor Immunosuppression

The tumor microenvironment is currently in the spotlight of cancer immunology research as a key factor impacting tumor development and progression. While antigen-specific immune responses play a crucial role in tumor rejection, the tumor hampers these immune responses by creating an immunosuppressive microenvironment. Recently, major progress has been achieved in the field of cancer immunotherapy, and several groundbreaking clinical trials demonstrated the potency of such therapeutic interventions in patients. Yet, the responses greatly vary among individuals. This calls for the rational design of more efficacious cancer immunotherapeutic interventions that take into consideration the “immune signature” of the tumor. Multimodality treatment regimens that aim to enhance intratumoral homing and activation of antigen-specific immune effector cells, while simultaneously targeting tumor immunosuppression, are pivotal for potent antitumor immunity

Plan de Acción en España para la erradicación de la poliomelitis: Vigilancia de la Parálisis Flácida Aguda y Vigilancia de Enterovirus en España. Informe 2020

Centro Nacional de Epidemiología y Centro Nacional de Microbiología. ISCIII. Plan de acción en España para la Erradicación de la Poliomielitis. Vigilancia de la Parálisis Flácida Aguda y Vigilancia de Enterovirus en España, Informe año 2020. Madrid, 5 de noviembre de 2021.[ES] En España la situación libre de polio se monitoriza con la vigilancia de Parálisis Flácida Aguda (PFA) en niños menores de 15 años, como recomienda la Organización Mundial de la Salud (OMS). La vigilancia la realizan los servicios de vigilancia autonómicos y la red de laboratorios de PFA y a nivel nacional se coordina en el Centro Nacional de Epidemiología (CNE, ISCIII) y en el Laboratorio de Poliovirus del Centro Nacional de Microbiología (CNM, ISCIII). En el año 2020 en España no hubo casos de poliomielitis. Se notificaron 0,17 casos de PFA por 100.000 niños menores de 15 años, por debajo del objetivo de sensibilidad establecido por la OMS de un caso de PFA al año por cada 100.000 menores de 15 años. Solamente se detectaron enterovirus no-polio (EVNP) en las muestras de dos casos (EV-D68 y EV-B, respectivamente). En España también se realiza la vigilancia de EVNP en otros síndromes neurológicos para complementar el sistema de vigilancia de PFA. En las muestras investigadas en 2020 no se identificó ningún poliovirus y los EVNP más frecuentemente identificados fueron E-18, CV-A6 y E-21. Mientras haya circulación de poliovirus en el mundo hay que mantener activos los sistemas de vigilancia para detectar a tiempo cualquier importación de poliovirus. [EN] Spain monitors its polio-free status by conducting surveillance for cases of acute flaccid paralysis (AFP) in children less than 15 years of age, as recommended by the World Health Organization (WHO). The AFP surveillance is performed by the 19 Regional Epidemiological Surveillance Units and the AFP Surveillance Laboratory Network, coordinated at national level by the National Centre for Epidemiology (CNE. ISCIII) and the National Poliovirus Laboratory at Nacional Center of Microbiology (CNM. ISCIII) respectively. In 2020, no cases of poliomyelitis were reported from clinical surveillance; Spain reported 0.17 non-polio AFP cases per 100,000 children, below the WHO's performance criterion for a sensitive surveillance system (1 non-polio AFP cases per 100,000 children). The non-polio enteroviruses EV-D68, EV-B were identified from clinical specimens collected from AFP cases. Spain also performs enterovirus surveillance to complement the clinical system In 2020, non poliovirus were identified; The non-polioviruses E-18, CV-A6 y E-21 were the most frequently identified serotypes. As long as poliovirus is circulating in the world, surveillance systems must remain active to detect any importation of poliovirus in a timely manner.1. Resumen. 2. Introducción. 3. Resultados de la vigilancia de Parálisis Flácida Aguda (PFA) en España, 2020. 4. Resultados de la vigilancia de enterovirus, España 2020. 5. Resultados de la vigilancia medioambiental de poliovirus. España, 2020. 6. Sistema de Información Microbiológica (SIM). Meningitis por enterovirus. Tendencia. 7. Conclusiones.N

Annual Epidemiological Report: Acute Flaccid Paralysis Surveillance and Enterovirus Surveillance, Spain, 2019

Centro Nacional de Epidemiología y Centro Nacional de Microbiología. ISCIII. Plan de acción en España para la Erradicación de la Poliomielitis. Vigilancia de la Parálisis Flácida Aguda y Vigilancia de Enterovirus en España, año 2019. Madrid, 1 julio 2020.[ES]Los resultados de la vigilancia de parálisis flácida aguda (PFA) y de la vigilancia de enterovirus (EV) muestran que en España en el año 2019 no hubo casos de poliomielitis ni circulación de poliovirus. La sensibilidad del sistema está por debajo del objetivo establecido por la OMS–Europa de 1 caso de PFA al año por cada 100.000 menores de 15 años, al situarse en 0,55/104 hab (0,58/104 <15años en 2018 ). Sin embargo, su estudio una vez detectados es adecuado. El índice de vigilancia, que sintetiza la sensibilidad del sistema de vigilancia y su estudio en laboratorio, fue de 0,28, similar a otros años. Gracias a la vigilancia de EV se detectó un PV derivado de vacuna (PVDV) en un paciente excretor inmunodeprimido; además se hallaron diferentes EV-no polio, los serotipos identificados fundamentalmente fueron E-7, E-30, E-11, CV-A6 y E-13. En 2019 la OMS declaró la eliminación del PV salvaje tipo 3(PVS3) a nivel mundial, aunque resulta preocupante el aumento en la detección de PVS1 y PVDVc 2 tanto en muestras humanas como medioambientales. La Evaluación de la Comisión Regional de Certificación clasifica a España en 2018 como de riesgo bajo de transmisión de poliovirus. En Europa hay tres países con riesgo alto, debido fundamentalmente a la baja inmunidad de su población. Hay que mantener los sistemas ya establecidos de vigilancia de la circulación de EV -polio y no polio- (vigilancia de PFA, meningitis víricas y EV), de manera que permitan detectar a tiempo la circulación inesperada de un poliovirus o de otro tipo de EV clínicamente relevante. [EN]The results of acute flaccid paralysis (AFP) and enterovirus (EV) surveillance show that there were no cases of polio or poliovirus circulation in Spain in 2019. The sensitivity of the system is below the target set by WHO-Europe of 1 case of AFP per year per 100,000 children under 15 years, at 0.55/104 inhab (0.58/104 <15 years in 2018 ). However, their study once detected is adequate. The surveillance index, which synthesizes the sensitivity of the surveillance system and its laboratory study, was 0.28, similar to other years. Thanks to the surveillance of EV, a vaccine derived PV (PVDV) was detected in an immunosuppressed excretory patient; in addition, different non-polio-EV were found. The serotypes identified were mainly E-7, E-30, E-11, CV-A6 and E-13. In 2019 the WHO declared the elimination of wild PV type 3 (PVS3) worldwide, although the increase in detection of PVS1 and cVP2 in both human and environmental samples is of concern. The evaluation of the Regional Certification Commission classifies Spain in 2019 as having a low risk of poliovirus transmission. In Europe there are three countries at high risk, mainly due to the low immunity of their population. The already established systems for surveillance of the circulation of EV-polio and non-polio- (surveillance of AFP, viral meningitis and EV) must be maintained, so that the unexpected circulation of a poliovirus or other clinically relevant EV can be detected in time.N

Precision measurement of CP\it{CP} violation in the penguin-mediated decay Bs0→ϕϕB_s^{0}\rightarrow\phi\phi

A flavor-tagged time-dependent angular analysis of the decay $B_s^{0}\rightarrow\phi\phi$ is performed using $pp$ collision data collected by the LHCb experiment at % at $\sqrt{s}=13$ TeV, the center-of-mass energy of 13 TeV, corresponding to an integrated luminosity of 6 fb^{-1}. The $\it{CP}$-violating phase and direct $\it{CP}$-violation parameter are measured to be $\phi_{s\bar{s}s} = -0.042 \pm 0.075 \pm 0.009$ rad and $|\lambda|=1.004\pm 0.030 \pm 0.009$, respectively, assuming the same values for all polarization states of the $\phi\phi$ system. In these results, the first uncertainties are statistical and the second systematic. These parameters are also determined separately for each polarization state, showing no evidence for polarization dependence. The results are combined with previous LHCb measurements using $pp$ collisions at center-of-mass energies of 7 and 8 TeV, yielding $\phi_{s\bar{s}s} = -0.074 \pm 0.069$ rad and $|lambda|=1.009 \pm 0.030$. This is the most precise study of time-dependent $\it{CP}$ violation in a penguin-dominated $B$ meson decay. The results are consistent with $\it{CP}$ symmetry and with the Standard Model predictions.Comment: All figures and tables, along with any supplementary material and additional information, are available at https://cern.ch/lhcbproject/Publications/p/LHCb-PAPER-2023-001.html (LHCb public pages