Adaptive transfer functions: improved multiresolution visualization of medical models

The final publication is available at Springer via http://dx.doi.org/10.1007/s00371-016-1253-9Medical datasets are continuously increasing in size. Although larger models may be available for certain research purposes, in the common clinical practice the models are usually of up to 512x512x2000 voxels. These resolutions exceed the capabilities of conventional GPUs, the ones usually found in the medical doctors’ desktop PCs. Commercial solutions typically reduce the data by downsampling the dataset iteratively until it fits the available target specifications. The data loss reduces the visualization quality and this is not commonly compensated with other actions that might alleviate its effects. In this paper, we propose adaptive transfer functions, an algorithm that improves the transfer function in downsampled multiresolution models so that the quality of renderings is highly improved. The technique is simple and lightweight, and it is suitable, not only to visualize huge models that would not fit in a GPU, but also to render not-so-large models in mobile GPUs, which are less capable than their desktop counterparts. Moreover, it can also be used to accelerate rendering frame rates using lower levels of the multiresolution hierarchy while still maintaining high-quality results in a focus and context approach. We also show an evaluation of these results based on perceptual metrics.Peer ReviewedPostprint (author's final draft

Environmental drivers of large-scale movements of baleen whales in the mid-North Atlantic Ocean

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Perez-Jorge, S., Tobena, M., Prieto, R., Vandeperre, F., Calmettes, B., Lehodey, P., & Silva, M. A. Environmental drivers of large-scale movements of baleen whales in the mid-North Atlantic Ocean. Diversity and Distributions, 00, (2020): 1-16, doi:10.1111/ddi.13038.Aim Understanding the environmental drivers of movement and habitat use of highly migratory marine species is crucial to implement appropriate management and conservation measures. However, this requires quantitative information on their spatial and temporal presence, which is limited in the high seas. Here, we aimed to gain insights of the essential habitats of three baleen whale species around the mid‐North Atlantic (NA) region, linking their large‐scale movements with information on oceanographic and biological processes. Location Mid‐NA Ocean. Methods We present the first study combining data from 31 satellite tracks of baleen whales (15, 10 and 6 from fin, blue and sei whales, respectively) from March to July (2008–2016) with data on remotely sensed oceanography and mid‐ and lower trophic level biomass derived from the spatial ecosystem and population dynamics model (SEAPODYM). A Bayesian switching state‐space model was applied to obtain regular tracks and correct for location errors, and pseudo‐absences were created through simulated positions using a correlated random walk model. Based on the tracks and pseudo‐absences, we applied generalized additive mixed models (GAMMs) to determine the probability of occurrence and predict monthly distributions. Results This study provides the most detailed research on the spatio‐temporal distribution of baleen whales in the mid‐NA, showing how dynamic biophysical processes determine their habitat preference. Movement patterns were mainly influenced by the interaction of temperature and the lower trophic level biomass; however, this relationship differed substantially among species. Best‐fit models suggest that movements of whales migrating towards more productive areas in northern latitudes were constrained by depth and eddy kinetic energy. Main conclusions These novel insights highlight the importance of integrating telemetry data with spatially explicit prey models to understand which factors shape the movement patterns of highly migratory species across large geographical scales. In addition, our outcomes could contribute to inform management of anthropogenic threats to baleen whales in sparsely surveyed region.We are very grateful to Cláudia Oliveira, Irma Cascão, Maria João Cruz, Miriam Romagosa and many volunteers, skilled skippers, crew and spotters that participated in the tagging fieldwork. This work was supported by Fundação para a Ciência e Tecnologia (FCT), Azores 2020 Operational Programme and Fundo Regional da Ciência e Tecnologia (FRCT) through research projects FCT‐Exploratory project (IF/00943/2013/CP1199/CT0001), TRACE (PTDC/MAR/74071/2006) and MAPCET (M2.1.2/F/012/2011) co‐funded by FEDER, COMPETE, QREN, POPH, ESF, ERDF, Portuguese Ministry for Science and Education, and Proconvergencia Açores/EU Program. We also acknowledge funds provided by FCT to MARE, through the strategic project UID/MAR/04292/2013. SPJ was supported by a postdoctoral grant (REF.GREENUP/001‐2016), MT by a DRCT doctoral grant (M3.1.a/F/028/2015), MAS by an FCT‐Investigator contract (IF/00943/2013), FV by an FCT Investigator contract (CEECIND/03469/2017) and RP by an FCT postdoctoral grant (SFRH/BPD/108007/2015). LMTL modelling work has been supported by the CMEMS Service Evolution GREENUP project, funded by Mercator Ocean. We are grateful to Elliott Hazen for offering guidance and advice, and to two anonymous referees whose comments greatly improved this work

Brain Waves Reflect Cognition-Emotion State as a Diagnostic Tool for Intervention in Dysfunctional States: A Real-World Evidence

Objective: This study aims to characterize electrical signals to establish a diagnosis of cognitive-emotional dysfunction and guide a successful therapeutic intervention. Therefore, the present study aimed to observe these frequency bands in a sample of dysfunctional neurological behaviors to establish a neural marker of neural dysfunction that helps diagnose and monitor treatment. Methods: A descriptive retrospective (extracted from the database) observational study design based on real-world historical data from routine clinical practice. According to DSM-5, low academic achievement (n =70), disruptive behavior (externalizing behavior problems) (n=70), and somatic syndrome disorder (n=70) were the subjects. The mean age of the sample was 14.13 (SD = 1.46; range 12-18), 31.5% women. The measuring instrument was the NeXus-10, which is suitable for acquiring a wide range of physiological signals. Brain electrical activity was recorded by using the quantitative electroencephalograph (qEEG) in accordance with the 10-20 International Electrode Placement System. In particular, the specific form of miniQ (mini-qEEG) was used. Results: A pattern record present in all cases were identified. The record refers to (a) activity along the midline, namely, Fz-Cz-Pz, (b) activity from the center (Cz) to back, namely, Pz-O1 and O2, (c) activity from the center (Cz) forward (Fz), and (d) comparison between hemispheres. The characteristics of theta, alpha, and beta waves define the characteristic pattern of neurological dysfunction. The reversal of the dysfunctional pattern coincided with the remission of the clinical symptoms after treatment, which occurred in 87,6% of the subjects. We define remission as not meeting DSM-5 criteria. Conclusion: This study suggests that miniQ register could be considered a simple and objective tool for studying neurological dysfunction. This dysfunction is explained according to current neurological knowledge of interactive cognition-emotion processing. MiniQ may be a cheap and reliable method and a promising tool for the investigation in the field

Dust in the reionization era: ALMA observations of a zz=8.38 Galaxy

We report on the detailed analysis of a gravitationally-lensed Y-band dropout, A2744_YD4, selected from deep Hubble Space Telescope imaging in the Frontier Field cluster Abell 2744. Band 7 observations with the Atacama Large Millimeter Array (ALMA) indicate the proximate detection of a significant 1mm continuum flux suggesting the presence of dust for a star-forming galaxy with a photometric redshift of $z\simeq8$. Deep X-SHOOTER spectra confirms the high redshift identity of A2744_YD4 via the detection of Lyman $\alpha$ emission at a redshift $z$=8.38. The association with the ALMA detection is confirmed by the presence of [OIII] 88$\mu$m emission at the same redshift. Although both emission features are only significant at the 4 $\sigma$ level, we argue their joint detection and the positional coincidence with a high redshift dropout in the HST images confirms the physical association. Analysis of the available photometric data and the modest gravitational magnification ($\mu\simeq2$) indicates A2744_YD4 has a stellar mass of $\sim$ 2$\times$10$^9$ M$_{\odot}$, a star formation rate of $\sim20$ M$_{\odot}$/yr and a dust mass of $\sim$6$\times$10$^{6}$ M$_{\odot}$. We discuss the implications of the formation of such a dust mass only $\simeq$200 Myr after the onset of cosmic reionisation.Comment: Accepted for publication in ApJ

Mapping of Functional Subdomains in the atALKBH9B m6A-Demethylase Required for Its Binding to the Viral RNA and to the Coat Protein of Alfalfa Mosaic Virus

[EN] N-6-methyladenosine (m(6)A) modification is a dynamically regulated RNA modification that impacts many cellular processes and pathways. This epitranscriptomic methylation relies on the participation of RNA methyltransferases (referred to as "writers") and demethylases (referred to as "erasers"), respectively. We previously demonstrated that the Arabidopsis thaliana protein atALKBH9B showed m(6)A-demethylase activity and interacted with the coat protein (CP) of alfalfa mosaic virus (AMV), causing a profound impact on the viral infection cycle. To dissect the functional activity of atALKBH9B in AMV infection, we performed a protein-mapping analysis to identify the putative domains required for regulating this process. In this context, the mutational analysis of the protein revealed that the residues between 427 and 467 positions are critical for in vitro binding to the AMV RNA. The atALKBH9B amino acid sequence showed intrinsically disordered regions (IDRs) located at the N-terminal part delimiting the internal AlkB-like domain and at the C-terminal part. We identified an RNA binding domain containing an RGxxxRGG motif that overlaps with the C-terminal IDR. Moreover, bimolecular fluorescent experiments allowed us to determine that residues located between 387 and 427 are critical for the interaction with the AMV CP, which should be critical for modulating the viral infection process. Finally, we observed that atALKBH9B deletions of either N-terminal 20 residues or the C-terminal's last 40 amino acids impede their accumulation in siRNA bodies. The involvement of the regions responsible for RNA and viral CP binding and those required for its localization in stress granules in the viral cycle is discussed.This work was funded by grant PID2020-115571RB-I00 from the Spanish Agencia Estatal de Investigacion (AEI) and Fondo Europeo de Desarrollo Regional (FEDER). LA-M is the recipient of a Ph.D. fellowship from the Ministerio de Ciencia, Tecnologia y Telecomunicaciones (MICITT) from Costa Rica.Alvarado-Marchena, L.; Marquez-Molins, J.; Martínez-Pérez, M.; Aparicio Herrero, F.; Pallás Benet, V. (2021). Mapping of Functional Subdomains in the atALKBH9B m6A-Demethylase Required for Its Binding to the Viral RNA and to the Coat Protein of Alfalfa Mosaic Virus. Frontiers in Plant Science. 12:1-12. https://doi.org/10.3389/fpls.2021.701683S1121

Measuring the functional impact of cognitive impairment in Huntington's disease

Acord transformatiu CRUE-CSICBackground: Patients with Huntington's disease (HD) exhibit a variable predominance of cognitive, behavioral and motor symptoms. A specific instrument focusing on the impact of cognitive impairment in HD over functional capacity is lacking. Objective: To address the need for a brief and specifically developed HD questionnaire able to capture functional aspects suspected to be sensitive to cognitive impairment. Methods: We developed and validated the "Huntington's Disease-Cognitive Functional Rating Scale" (HD-CFRS) in 78 symptomatic carriers of the Huntington's disease mutation. We also administered the HD-CFRS to a knowledgeable informant to measure the level of agreement. To explore the association between HD-CFRS scores and participants' cognitive status, we administered objective measures of cognition. Participants were classified as cognitively preserved (HD-NC), as having mild cognitive impairment (HD-MCI), or as having dementia (HD-Dem). Results: The HD-CFRS showed concurrent validity and internal consistency in the three groups. HD carriers and informants in the HD-NC group obtained similar HD-CFRS scores. However, in patients with mild cognitive impairment and dementia, informers reported greater functional impairment than HD participants. The HD-CFRS total score showed strong correlations with measures assessing cognition. Conclusions: These findings support the utility of the HD-CFRS as a brief and reliable instrument to measure functional defects associated with cognitive impairment in HD. We believe this questionnaire could be a useful tool both for clinical practice and research

Structural brain correlates of dementia in Huntington's disease

Altres ajuts: The present study was partially funded by the "Human Biology Project Grant" of the Huntington's Disease Society of America (USA).Huntington's disease (HD) is a fatal genetic neurodegenerative disorder with no effective treatment currently available. Progressive basal ganglia and whole-brain atrophy and concurrent cognitive deterioration are prototypical aspects of HD. However, the specific patterns of brain atrophy underlying cognitive impairment of different severity in HD are poorly understood. The aim of this study was to investigate the specific structural brain correlates of major cognitive deficits in HD and to explore its association with neuropsychological indicators. Thirty-five symptomatic early-to-mild HD patients and 15 healthy controls (HC) with available T1-MRI imaging were included in this study. In this cross-sectional study, HD patients were classified as patients with (HD-Dem) and without (HD-ND) major cognitive impairment in the range of dementia. This classification was based on previously validated PD-CRS cutoff scores for HD. Differences in brain atrophy across groups were studied by means of grey-matter volume voxel-based morphometry (GMV-VBM) and cortical thickness (Cth). Voxelwise and vertexwise general linear models were used to assess the group comparisons, controlling for the effects of age, sex, education, CAG repeat length and severity of motor symptoms. Clusters surviving p < 0.05 and family-wise error (FWE) correction were considered statistically significant. In order to characterize the impact on cognitive performance of the observed brain differences across groups, GMV and Cth values in the set of significant regions were computed and correlated with specific neuropsychological tests. All groups had similar sociodemographic profiles, and the HD groups did not significantly differ in terms of CAG repeat length. Compared to HC, both HD groups exhibited significant atrophy in multiple subcortical and parietal brain regions. However, compared to HC and HD-ND groups, HD-Dem patients showed a more prominent pattern of reduced GMV and cortical thinning. Importantly, this thinning was restricted to regions of the parietal-temporal and occipital cortices. Furthermore, these brain alterations were further associated with poorer cognitive performance in tasks assessing frontal-executive and attention domains as well as memory, language and constructional abilities. Major cognitive impairment in the range of dementia in HD is associated with brain and cognitive alterations exceeding the prototypical frontal-executive deficits commonly recognized in HD. The observed posterior-cortical damage identified by MRI and its association with memory, language, and visuoconstructive dysfunction suggest a strong involvement of extra-striatal atrophy in the onset of severe cognitive dysfunction in HD patients. Critically, major cognitive impairment in this sample was not associated with CAG repeat length, age or education. This finding could support a possible involvement of additional neuropathological mechanisms aggravating cognitive deterioration in HD

Financing future-proof local bioenergy: lessons learnt from mentoring of SME pilot projects. WP5 Final report

This deliverable D5.3 is the final report of the activities within WP5 led by UPC, from September 2016 to July 2018.The European bioenergy sector requires a wide promotion for strong investments in regional sustainable supply chain solutions. SMEs are central in the value chain in local bioenergy markets, as they are operating throughout all the stages of bioenergy mobilisation, from forestry management to energy plants or even energy commercialisation to final consumers. One of the major barriers that SMEs face when assessing potential bioenergy operations is the difficulty to access adequate financing; WP5 within project SECURECHAIN aims to analyse such difficulties and contribute to overcome them. The specific objectives of WP5 are: • O5.1 Carry out targeted market feasibility surveys, pre-checks and develop a risk assessment tool to support the implementation of priority SSCM pilot projects • O5.2 Mentor companies’ capital call strategies tailored to investor types and upgrade corporate finance disclosing in accordance with International Financial Reporting Standards (IFRS) • O5.3 Foster lobbying actions and dialogue between financial players and bioenergy market actors to promote the portfolio of investment proposals This deliverable D5.3 is the final report of the activities within WP5, mainly about period 2 from September 2016 to July 2018. The market pre-check (T5.1) was carried out in phase 1 and reported in deliverable D5.1. The risk assessment analysis (T5.2) performed, the continuous financial mentoring (T5.3) being worked out with the SME business projects, and the roadshows (T5.4) that have been attended, as well as planning activities that were performed during the final year of the project, are documented in this report.Preprin

Frequency-tuning dual-comb spectroscopy using silicon Mach-Zehnder modulators

[EN] Dual-comb spectroscopy using a silicon Mach-Zehnder modulator is reported for the first time. First, the properties of frequency combs generated by silicon modulators are assessed in terms of tunability, coherence, and number of lines. Then, taking advantage of the frequency agility of electro-optical frequency combs, a new technique for fine resolution absorption spectroscopy is proposed, named frequency-tuning dual-comb spectroscopy, which combines dual-comb spectroscopy and frequency spacing tunability to measure optical spectra with detection at a unique RF frequency. As a proof of concept, a 24 GHz optical bandwidth is scanned with a 1 GHz resolution.Agence Nationale de la Recherche (ANR-17-CE09-0041, ANR-18-CE39-0009).Deniel, L.; Weckenmann, E.; Pérez-Galacho, D.; Alonso-Ramos, C.; Boeuf, F.; Vivien, L.; Marris-Morini, D. (2020). Frequency-tuning dual-comb spectroscopy using silicon Mach-Zehnder modulators. Optics Express. 28(8):10888-10898. https://doi.org/10.1364/OE.390041S108881089828