Browsing by Subject "SYSTEM"

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  • Andrienko, Gennady; Andrienko, Natalia; Boldrini, Chiara; Caldarelli, Guido; Cintia, Paolo; Cresci, Stefano; Facchini, Angelo; Giannotti, Fosca; Gionis, Aristides; Guidotti, Riccardo; Mathioudakis, Michael; Muntean, Cristina Ioana; Pappalardo, Luca; Pedreschi, Dino; Pournaras, Evangelos; Pratesi, Francesca; Tesconi, Maurizio; Trasarti, Roberto (2021)
    The exponential increase in the availability of large-scale mobility data has fueled the vision of smart cities that will transform our lives. The truth is that we have just scratched the surface of the research challenges that should be tackled in order to make this vision a reality. Consequently, there is an increasing interest among different research communities (ranging from civil engineering to computer science) and industrial stakeholders in building knowledge discovery pipelines over such data sources. At the same time, this widespread data availability also raises privacy issues that must be considered by both industrial and academic stakeholders. In this paper, we provide a wide perspective on the role that big data have in reshaping cities. The paper covers the main aspects of urban data analytics, focusing on privacy issues, algorithms, applications and services, and geo-referenced data from social media. In discussing these aspects, we leverage, as concrete examples and case studies of urban data science tools, the results obtained in the "City of Citizens" thematic area of the Horizon 2020 SoBigData initiative, which includes a virtual research environment with mobility datasets and urban analytics methods developed by several institutions around Europe. We conclude the paper outlining the main research challenges that urban data science has yet to address in order to help make the smart city vision a reality.
  • Kallio, Galina (2020)
    Questions of value are central to understanding alternative practices of food exchange. This study introduces a practice-based approach to value that challenges the dominant views, which capture value as either an input for or an outcome of practices of exchange (value as values, standards, or prices). Building on a longitudinal ethnographic study on food collectives, I show how value, rather than residing in something that people share, or in something that objects have, is an ideal target that continuously unfolds and evolves in action. I found that people organized their food collectives around pursuing three kinds of value-ideals, namely good food, good price and good community. These value-ideals became reproduced in food collectives through what I identified as valuing modes, by which people evaluated the goodness of food, prices and community. My analysis revealed that, while participating in food collectives in order to pursue their value-ideals, people were likely to have differing reasons for pursuing them and tended to attach different meanings to the same value-ideal. I argue that understanding how value as an ideal target is reproduced through assessing and assigning value (valuing modes) is essential in further explorations of the formation of value and in better understanding the dynamics of organizing alternative practices of food exchange.
  • Torlen, Klara; Kurland, Lisa; Castren, Maaret; Olanders, Knut; Bohm, Katarina (2017)
    Background: Emergency medical dispatching should be as accurate as possible in order to ensure patient safety and optimize the use of ambulance resources. This study aimed to compare the accuracy, measured as priority level, between two Swedish dispatch protocols - the three-graded priority protocol Medical Index and a newly developed prototype, the four-graded priority protocol, RETTS-A. Methods: A simulation study was carried out at the Emergency Medical Communication Centre (EMCC) in Stockholm, Sweden, between October and March 2016. Fifty-three voluntary telecommunicators working at SOS Alarm were recruited nationally. Each telecommunicator handled 26 emergency medical calls, simulated by experienced standard patients. Manuscripts for the scenarios were based on recorded real-life calls, representing the six most common complaints. A cross-over design with 13 + 13 calls was used. Priority level and medical condition for each scenario was set through expert consensus and used as gold standard in the study. Results: A total of 1293 calls were included in the analysis. For priority level, n = 349 (54.0%) of the calls were assessed correctly with Medical Index and n = 309 (48.0%) with RETTS-A (p = 0.012). Sensitivity for the highest priority level was 82.6% (95% confidence interval: 76.6-87.3%) in the Medical Index and 54.0% (44.3-63.4%) in RETTS-A. Overtriage was 37.9% (34.2-41.7%) in the Medical Index and 28.6% (25.2-32.2%) in RETTS-A. The corresponding proportion of undertriage was 6.3% (4.7-8.5%) and 23.4% (20.3-26.9%) respectively. Conclusion: In this simulation study we demonstrate that Medical Index had a higher accuracy for priority level and less undertriage than the new prototype RETTS-A. The overall accuracy of both protocols is to be considered as low. Overtriage challenges resource utilization while undertriage threatens patient safety. The results suggest that in order to improve patient safety both protocols need revisions in order to guarantee safe emergency medical dispatching.
  • Bagheri, Mehrdad; Mladenovic, Milos; Kosonen, Iisakki; Nurminen, Jukka K; Roncoli, Claudio; Ylä-Jääski, Antti (2020)
    Evaluating potential of shifting to low-carbon transport modes requires considering limited travel-time budget of travelers. Despite previous studies focusing on time-relevant modal shift, there is a lack of integrated and transferable computational frameworks, which would use emerging smartphone-based high-resolution longitudinal travel datasets. This research explains and illustrates a computational framework for this purpose. The proposed framework compares observed trips with computed alternative trips and estimates the extent to which alternatives could reduce carbon emission without a significant increase in travel time.. The framework estimates potential of substituting observed car and public-transport trips with lower-carbon modes, evaluating parameters per individual traveler as well as for the whole city, from a set of temporal and spatial viewpoints. The illustrated parameters include the size and distribution of modal shifts, emission savings, and increased active-travel growth, as clustered by target mode, departure time, trip distance, and spatial coverage throughout the city. Parameters are also evaluated based on the frequently repeated trips. We evaluate usefulness of the method by analyzing door-to-door trips of a few hundred travelers, collected from smartphone traces in the Helsinki metropolitan area, Finland, during several months. The experiment's preliminary results show that, for instance, on average, 20% of frequent car trips of each traveler have a low-carbon alternative, and if the preferred alternatives are chosen, about 8% of the carbon emissions could be saved. In addition, it is seen that the spatial potential of bike as an alternative is much more sporadic throughout the city compared to that of bus, which has relatively more trips from/to city center. With few changes, the method would be applicable to other cities, bringing possibly different quantitative results. In particular, having more thorough data from large number of participants could provide implications for transportation researchers and planners to identify groups or areas for promoting mode shift. Finally, we discuss the limitations and lessons learned, highlighting future research directions.
  • Murthy, Rashmi; Lin, Yi-Hsuan; Shin, Kwancheol; Mueller, Jennifer L. (2020)
    A direct reconstruction algorithm based on Calderon's linearization method for the reconstruction of isotropic conductivities is proposed for anisotropic conductivities in two-dimensions. To overcome the non-uniqueness of the anisotropic inverse conductivity problem, the entries of the unperturbed anisotropic tensors are assumed known a priori, and it remains to reconstruct the multiplicative scalar field. The quasi-conformal map in the plane facilitates the Calderon-based approach for anisotropic conductivities. The method is demonstrated on discontinuous radially symmetric conductivities of high and low contrast.
  • Purps, Josephine; Siegert, Sabine; Willuweit, Sascha; Nagy, Marion; Alves, Cintia; Salazar, Renato; Angustia, Sheila M. T.; Santos, Lorna H.; Anslinger, Katja; Bayer, Birgit; Ayub, Qasim; Wei, Wei; Xue, Yali; Tyler-Smith, Chris; Bafalluy, Miriam Baeta; Martinez-Jarreta, Begona; Egyed, Balazs; Balitzki, Beate; Tschumi, Sibylle; Ballard, David; Court, Denise Syndercombe; Barrantes, Xinia; Bassler, Gerhard; Wiest, Tina; Berger, Burkhard; Niederstaetter, Harald; Parson, Walther; Davis, Carey; Budowle, Bruce; Burri, Helen; Borer, Urs; Koller, Christoph; Carvalho, Elizeu F.; Domingues, Patricia M.; Chamoun, Wafaa Takash; Coble, Michael D.; Hill, Carolyn R.; Corach, Daniel; Caputo, Mariela; D'Amato, Maria E.; Davison, Sean; Decorte, Ronny; Larmuseau, Maarten H. D.; Ottoni, Claudio; Rickards, Olga; Lu, Di; Jiang, Chengtao; Dobosz, Tadeusz; Jonkisz, Anna; Frank, William E.; Furac, Ivana; Gehrig, Christian; Castella, Vincent; Grskovic, Branka; Haas, Cordula; Wobst, Jana; Hadzic, Gavrilo; Drobnic, Katja; Honda, Katsuya; Hou, Yiping; Zhou, Di; Li, Yan; Hu, Shengping; Chen, Shenglan; Immel, Uta-Dorothee; Lessig, Rudiger; Jakovski, Zlatko; Ilievska, Tanja; Klann, Anja E.; Garcia, Cristina Cano; de Knijff, Peter; Kraaijenbrink, Thirsa; Kondili, Aikaterini; Miniati, Penelope; Vouropoulou, Maria; Kovacevic, Lejla; Marjanovic, Damir; Lindner, Iris; Mansour, Issam; Al-Azem, Mouayyad; El Andari, Ansar; Marino, Miguel; Furfuro, Sandra; Locarno, Laura; Martin, Pablo; Luque, Gracia M.; Alonso, Antonio; Miranda, Luis Souto; Moreira, Helena; Mizuno, Natsuko; Iwashima, Yasuki; Moura Neto, Rodrigo S.; Nogueira, Tatiana L. S.; Silva, Rosane; Nastainczyk-Wulf, Marina; Edelmann, Jeanett; Kohl, Michael; Nie, Shengjie; Wang, Xianping; Cheng, Baowen; Nunez, Carolina; Martinez de Pancorbo, Marian; Olofsson, Jill K.; Morling, Niels; Onofri, Valerio; Tagliabracci, Adriano; Pamjav, Horolma; Volgyi, Antonia; Barany, Gusztav; Pawlowski, Ryszard; Maciejewska, Agnieszka; Pelotti, Susi; Pepinski, Witold; Abreu-Glowacka, Monica; Phillips, Christopher; Cardenas, Jorge; Rey-Gonzalez, Danel; Salas, Antonio; Brisighelli, Francesca; Capelli, Cristian; Toscanini, Ulises; Piccinini, Andrea; Piglionica, Marilidia; Baldassarra, Stefania L.; Ploski, Rafal; Konarzewska, Magdalena; Jastrzebska, Emila; Robino, Carlo; Sajantila, Antti; Palo, Jukka U.; Guevara, Evelyn; Salvador, Jazelyn; Corazon De Ungria, Maria; Russell Rodriguez, Jae Joseph; Schmidt, Ulrike; Schlauderer, Nicola; Saukko, Pekka; Schneider, Peter M.; Sirker, Miriam; Shin, Kyoung-Jin; Oh, Yu Na; Skitsa, Iulia; Ampati, Alexandra; Smith, Tobi-Gail; de Calvit, Lina Solis; Stenzl, Vlastimil; Capal, Thomas; Tillmar, Andreas; Nilsson, Helena; Turrina, Stefania; De Leo, Domenico; Verzeletti, Andrea; Cortellini, Venusia; Wetton, Jon H.; Gwynne, Gareth M.; Jobling, Mark A.; Whittle, Martin R.; Sumita, Denilce R.; Wolanska-Nowak, Paulina; Yong, Rita Y. Y.; Krawczak, Michael; Nothnagel, Michael; Roewer, Lutz (2014)
    In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent.
  • Manoilov, Kyrylo Yu; Verkhusha, Vladislav V.; Shcherbakova, Daria M. (2021)
    Genetically encoded tools for the regulation of endogenous molecules (RNA, DNA elements and protein) are needed to study and control biological processes with minimal interference caused by protein overexpression and overactivation of signaling pathways. Here we focus on light-controlled optogenetic tools (OTs) that allow spatiotemporally precise regulation of gene expression and protein function. To control endogenous molecules, OTs combine light-sensing modules from natural photoreceptors with specific protein or nucleic acid binders. We discuss OT designs and group OTs according to the principles of their regulation. We outline characteristics of OT performance, discuss considerations for their use in vivo and review available OTs and their applications in cells and in vivo. Finally, we provide a brief outlook on the development of OTs. This Review discusses optogenetic tools for manipulating endogenous targets such as genes and signaling pathways in a physiological range.
  • West, Gun; Turunen, Minttu; Aalto, Anna; Virtanen, Laura; Li, Song-Ping; Heliö, Tiina; Meinander, Annika; Taimen, Pekka (2022)
    Lamins A and C are nuclear intermediate filament proteins that form a proteinaceous meshwork called lamina beneath the inner nuclear membrane. Mutations in the LMNA gene encoding lamins A and C cause a heterogenous group of inherited degenerative diseases known as laminopathies. Previous studies have revealed altered cell signaling pathways in lamin-mutant patient cells, but little is known about the fate of mutant lamins A and C within the cells. Here, we analyzed the turnover of lamins A and C in cells derived from a dilated cardiomyopathy patient with a heterozygous p.S143P mutation in LMNA. We found that transcriptional activation and mRNA levels of LMNA are increased in the primary patient fibroblasts, but the protein levels of lamins A and C remain equal in control and patient cells because of a meticulous interplay between autophagy and the ubiquitin-proteasome system (UPS). Both endogenous and ectopic expression of p.S143P lamins A and C cause significantly reduced activity of UPS and an accumulation of K48-ubiquitin chains in the nucleus. Furthermore, K48-ubiquitinated lamins A and C are degraded by compensatory enhanced autophagy, as shown by increased autophagosome formation and binding of lamins A and C to microtubule-associated protein 1A/1B-light chain 3. Finally, chaperone 4-PBA augmented protein degradation by restoring UPS activity as well as autophagy in the patient cells. In summary, our results suggest that the p.S143P-mutant lamins A and C have overloading and deleterious effects on protein degradation machinery and pharmacological interventions with compounds enhancing protein degradation may be beneficial for cell homeostasis.
  • Amer Joint Comm Canc Ophthalmic On; Tomar, Ankit Singh; Finger, Paul T.; Gallie, Brenda; Kivela, Tero T.; Correa-Llano, Genoveva (2020)
    Purpose: To evaluate the ability of the 8th edition of the American Joint Committee on Cancer (AJCC) Cancer Staging Manual to estimate metastatic and mortality rates for children with retinoblastoma (RB). Design: International, multicenter, registry-based retrospective case series. Participants: A total of 2190 patients from 18 ophthalmic oncology centers from 13 countries over 6 continents. Methods: Patient-specific data fields for RB were designed and selected by subcommittee. All patients with RB with adequate records to allow tumor staging by the AJCC criteria and follow-up for metastatic disease were studied. Main Outcome Measures: Metastasis-related 5- and 10-year survival data after initial tumor staging were estimated with the KaplaneMeier method depending on AJCC clinical (cTNM) and pathological (pTNM) tumor, node, metastasis category and age, tumor laterality, and presence of heritable trait. Results: Of 2190 patients, the records of 2085 patients (95.2%) with 2905 eyes were complete. The median age at diagnosis was 17.0 months. A total of 1260 patients (65.4%) had unilateral RB. Among the 2085 patients, tumor categories were cT1a in 55 (2.6%), cT1b in 168 (8.1%), cT2a in 197 (9.4%), cT2b in 812 (38.9%), cT3 in 835 (40.0%), and cT4 in 18 (0.9%). Of these, 1397 eyes in 1353 patients (48.1%) were treated with enucleation. A total of 109 patients (5.2%) developed metastases and died. The median time (n = 92) from diagnosis to metastasis was 9.50 months. The 5-year KaplaneMeier cumulative survival estimates by clinical tumor categories were 100% for category cT1a, 98% (95% confidence interval [CI], 97-99) for cT1b and cT2a, 96% (95% CI, 95-97) for cT2b, 89% (95% CI, 88-90) for cT3 tumors, and 45% (95% CI, 31-59) for cT4 tumors. Risk of metastasis increased with increasing cT (and pT) category (P <0.001). Cox proportional hazards regression analysis confirmed a higher risk of metastasis in category cT3 (hazard rate [HR], 8.09; 95% CI, 2.55-25.70; P <0.001) and cT4 (HR, 48.55; 95% CI, 12.86-183.27; P <0.001) compared with category cT1. Age, tumor laterality, and presence of heritable traits did not influence the incidence of metastatic disease. Conclusions: Multicenter, international, internet-based data sharing facilitated analysis of the 8th edition AJCC RB Staging System for metastasis-related mortality and offered a proof of concept yielding quantitative, predictive estimates per category in a large, real-life, heterogeneous patient population with RB. (C) 2020 by the American Academy of Ophthalmology. This is an open access article under the CC BY-NC-ND license
  • Lång, M.; Skrifvars, M. B.; Siironen, J.; Tanskanen, P.; Ala-Peijari, M.; Koivisto, T.; Djafarzadeh, S.; Bendel, S. (2018)
    BackgroundNormobaric hyperoxia is used to alleviate secondary brain ischaemia in patients with traumatic brain injury (TBI), but clinical evidence is limited and hyperoxia may cause adverse events. MethodsAn open label, randomised controlled pilot study comparing blood concentrations of reactive oxygen species (ROS), interleukin 6 (IL-6) and neuron-specific enolase (NSE) between two different fractions of inspired oxygen in severe TBI patients on mechanical ventilation. ResultsWe enrolled 27 patients in the Fi O-2 0.40 group and 38 in the Fi O-2 0.70 group; 19 and 23 patients, respectively, completed biochemical analyses. In baseline, there were no differences between Fi O-2 0.40 and Fi O-2 0.70 groups, respectively, in ROS (64.8 nM [22.6-102.1] vs. 64.9 nM [26.8-96.3], P = 0.80), IL-6 (group 92.4 pg/ml [52.9-171.6] vs. 94.3 pg/ml [54.8-133.1], P = 0.52) or NSE (21.04 ug/l [14.0-30.7] vs. 17.8 ug/l [14.1-23.9], P = 0.35). ROS levels did not differ at Day 1 (24.2 nM [20.6-33.5] vs. 29.2 nM [22.7-69.2], P = 0.10) or at Day 2 (25.4 nM [21.7-37.4] vs. 47.3 nM [34.4-126.1], P = 0.95). IL-6 concentrations did not differ at Day 1 (112.7 pg/ml [65.9-168.9) vs. 83.9 pg/ml [51.8-144.3], P = 0.41) or at Day 3 (55.0 pg/ml [34.2-115.6] vs. 49.3 pg/ml [34.4-126.1], P = 0.95). NSE levels did not differ at Day 1 (15.9 ug/l [9.0-24.3] vs. 15.3 ug/l [12.2-26.3], P = 0.62). There were no differences between groups in the incidence of pulmonary complications. ConclusionHigher fraction of inspired oxygen did not increase blood concentrations of markers of oxidative stress, inflammation or neurological injury or the incidence of pulmonary complications in severe TBI patients on mechanical ventilation.
  • Sippola, Suvi; Grönroos, Juha; Sallinen, Ville; Rautio, Tero; Nordström, Pia; Rantanen, Tuomo; Hurme, Saija; Leppäniemi, Ari; Meriläinen, Sanna; Laukkarinen, Johanna; Savolainen, Heini; Virtanen, Johanna; Salminen, Paulina (2018)
    Introduction Recent studies show that antibiotic therapy is safe and feasible for CT-confirmed uncomplicated acute appendicitis. Spontaneous resolution of acute appendicitis has already been observed over a hundred years ago. In CT-confirmed uncomplicated acute diverticulitis (left-sided appendicitis), studies have shown no benefit from antibiotics compared with symptomatic treatment, but this shift from antibiotics to symptomatic treatment has not yet been widely implemented in clinical practice. Recently, symptomatic treatment of uncomplicated acute appendicitis has been demonstrated in a Korean open-label study. However, a double-blinded placebo-controlled study to illustrate the role of antibiotics and spontaneous resolution of uncomplicated acute appendicitis is still lacking. Methods and analysis The APPAC III (APPendicitis ACuta III) trial is a multicentre, double-blind, placebo-controlled, superiority randomised study comparing antibiotic therapy with placebo in the treatment CT scan-confirmed uncomplicated acute appendicitis aiming to evaluate the role of antibiotics in the resolution of uncomplicated acute appendicitis. Adult patients (18-60 years) with CT scan-confirmed uncomplicated acute appendicitis (the absence of appendicolith, abscess, perforation and tumour) will be enrolled in five Finnish university hospitals. Primary endpoint is success of the randomised treatment, defined as resolution of acute appendicitis resulting in discharge from the hospital without surgical intervention within 10 days after initiating randomised treatment (treatment efficacy). Secondary endpoints include postintervention complications, recurrent symptoms after treatment up to 1year, late recurrence of acute appendicitis after 1year, duration of hospital stay, sick leave, treatment costs and quality of life. A decrease of 15 percentage points in success rate is considered clinically important difference. The superiority of antibiotic treatment compared with placebo will be analysed using Fisher's one-sided test and CI will be calculated for proportion difference. Ethics and dissemination This protocol has been approved by the Ethics Committee of Turku University Hospital and the Finnish Medicines Agency (FIMEA). The findings will be disseminated in peer-reviewed academic journals. Trial registration number NCT03234296; Pre-results.
  • Mandelblum, Jorge; Fischer, Naomi; Achiron, Asaf; Goldberg, Mordechai; Tuuminen, Raimo; Zunz, Eran; Spierer, Oriel (2020)
    Background: The aim of this study was to evaluate whether a simplified pre-operative nuclear classification score (SPONCS) was valid, both for clinical trials and real-world settings. Methods: Cataract classification was based on posterior nuclear color: 0 (clear), 1 (subcapsular/posterior cataract with clear nucleus), 2 (mild "green nucleus" with plus sign for yellow reflection of the posterior cortex), 3 (medium "yellow nucleus" with plus sign for brown/red posterior cortex reflection), 4 (advanced with 4 being "red/brown nucleus" and 4+ white nucleus), and 5 (hypermature/Morgagnian nucleus). Inter- and intra-observer validity was assessed by 30 Ophthalmologists for 15 cataract cases. The reliability of the cataract grading score in a surgical setting was evaluated. Correlation of nuclear scores was compared with phacoemulsification cumulative dissipated energy (CDE) in 596 patients. Results: Analysis of mean intra-observer Cohen kappa agreement was 0.55 with an inter-observer score of 0.54 for the first assessment and 0.49 for the repeat assessment one week later. When evaluating results by nuclear color alone, there was a substantial agreement for both the intra-observer (0.70) and inter-observer parameters: 0.70 for the first test, and 0.66 on repetition with randomization of the cases after a week. CDE levels were found to be significantly different between all SPONCS score groups (p <0.001), with a lower CDE related to a lower SPONCS score. A strong correlation was found between the SPONCS score and CDE (Spearman ' s rho = 0.8, p <0.001). Conclusion: This method of grading cataract hardness is both simple and repeatable. This system can be easily incorporated in randomized controlled trials to lower bias and confounding effects regarding nuclear density along with application in the clinical setting.
  • Sanz-Garcia, Andres; Sodupe-Ortega, Enrique; Pernia-Espinoza, Alpha; Shimizu, Tatsuya; Escobedo-Lucea, Carmen (2020)
    Three-dimensional (3D) bioprinting promises to be essential in tissue engineering for solving the rising demand for organs and tissues. Some bioprinters are commercially available, but their impact on the field of Tissue engineering (TE) is still limited due to their cost or difficulty to tune. Herein, we present a low-cost easy-to-build printhead for microextrusion-based bioprinting (MEBB) that can be installed in many desktop 3D printers to transform them into 3D bioprinters. We can extrude bioinks with precise control of print temperature between 2-60 degrees C. We validated the versatility of the printhead, by assembling it in three low-cost open-source desktop 3D printers. Multiple units of the printhead can also be easily put together in a single printer carriage for building a multi-material 3D bioprinter. Print resolution was evaluated by creating representative calibration models at different temperatures using natural hydrogels such as gelatin and alginate, and synthetic ones like poloxamer. Using one of the three modified low-cost 3D printers, we successfully printed cell-laden lattice constructs with cell viabilities higher than 90% after 24-h post printing. Controlling temperature and pressure according to the rheological properties of the bioinks was essential in achieving optimal printability and great cell viability. The cost per unit of our device, which can be used with syringes of different volume, is less expensive than any other commercially available product. These data demonstrate an affordable open-source printhead with the potential to become a reliable alternative to commercial bioprinters for any laboratory.
  • Richardson, Dominique; Itkonen, Jaakko; Nievas, Julia; Urtti, Arto; Casteleijn, Marco G. (2018)
    The use of living cells for the synthesis of pharmaceutical proteins, though state-of-the-art, is hindered by its lengthy process comprising of many steps that may affect the protein’s stability and activity. We aimed to integrate protein expression, purification, and bioconjugation in small volumes coupled with cell free protein synthesis for the target protein, ciliary neurotrophic factor. Split-intein mediated capture by use of capture peptides onto a solid surface was efficient at 89–93%. Proof-of-principle of light triggered release was compared to affinity chromatography (His6 fusion tag coupled with Ni-NTA). The latter was more efficient, but more time consuming. Light triggered release was clearly demonstrated. Moreover, we transferred biotin from the capture peptide to the target protein without further purification steps. Finally, the target protein was released in a buffer-volume and composition of our choice, omitting the need for protein concentration or changing the buffer. Split-intein mediated capture, protein trans splicing followed by light triggered release, and bioconjugation for proteins synthesized in cell free systems might be performed in an integrated workflow resulting in the fast production of the target protein.
  • Simola, U.; Bonfanti, A.; Dumusque, X.; Cisewski-Kehe, J.; Kaski, S.; Corander, J. (2022)
    Context. Active regions on the photosphere of a star have been the major obstacle for detecting Earth-like exoplanets using the radial velocity (RV) method. A commonly employed solution for addressing stellar activity is to assume a linear relationship between the RV observations and the activity indicators along the entire time series, and then remove the estimated contribution of activity from the variation in RV data (overall correction method). However, since active regions evolve on the photosphere over time, correlations between the RV observations and the activity indicators will correspondingly be anisotropic. Aims. We present an approach that recognizes the RV locations where the correlations between the RV and the activity indicators significantly change in order to better account for variations in RV caused by stellar activity. Methods. The proposed approach uses a general family of statistical breakpoint methods, often referred to as change point detection (CPD) algorithms; several implementations of which are available in R and python. A thorough comparison is made between the breakpoint-based approach and the overall correction method. To ensure wide representativity, we use measurements from real stars that have different levels of stellar activity and whose spectra have different signal-to-noise ratios. Results. When the corrections for stellar activity are applied separately to each temporal segment identified by the breakpoint method, the corresponding residuals in the RV time series are typically much smaller than those obtained by the overall correction method. Consequently, the generalized Lomb-Scargle periodogram contains a smaller number of peaks caused by active regions. The CPD algorithm is particularly effective when focusing on active stars with long time series, such as alpha Cen B. In that case, we demonstrate that the breakpoint method improves the detection limit of exoplanets by 74% on average with respect to the overall correction method. Conclusions. CPD algorithms provide a useful statistical framework for estimating the presence of change points in a time series. Since the process underlying the RV measurements generates anisotropic data by its intrinsic properties, it is natural to use CPD to obtain cleaner signals from RV data. We anticipate that the improved exoplanet detection limit may lead to a widespread adoption of such an approach. Our test on the HD 192310 planetary system is encouraging, as we confirm the presence of the two hosted exoplanets and we determine orbital parameters consistent with the literature, also providing much more precise estimates for HD 192310 c.
  • Sodupe-Ortega, Enrique; Sanz-Garcia, Andres; Pernia-Espinoza, Alpha; Escobedo-Lucea, Carmen (2018)
    Most of the studies in three-dimensional (3D) bioprinting have been traditionally based on printing a single bioink. Addressing the complexity of organ and tissue engineering, however, will require combining multiple building and sacrificial biomaterials and several cells types in a single biofabrication session. This is a significant challenge, and, to tackle that, we must focus on the complex relationships between the printing parameters and the print resolution. In this paper, we study the influence of the main parameters driven multi-material 3D bioprinting and we present a method to calibrate these systems and control the print resolution accurately. Firstly, poloxamer hydrogels were extruded using a desktop 3D printer modified to incorporate four microextrusion-based bioprinting (MEBB) printheads. The printed hydrogels provided us the particular range of printing parameters (mainly printing pressure, deposition speed, and nozzle z-offset) to assure the correct calibration of the multi-material 3D bioprinter. Using the printheads, we demonstrated the excellent performance of the calibrated system extruding different fluorescent bioinks. Representative multi-material structures were printed in both poloxamer and cell-laden gelatin-alginate bioinks in a single session corroborating the capabilities of our system and the calibration method. Cell viability was not significantly affected by any of the changes proposed. We conclude that our proposal has enormous potential to help with advancing in the creation of complex 3D constructs and vascular networks for tissue engineering.
  • Nousiainen, Jalo; Rajani, Chang; Kasper, Markus; Helin, Tapio (2021)
    Reinforcement learning (RL) presents a new approach for controlling adaptive optics (AO) systems for Astronomy. It promises to effectively cope with some aspects often hampering AO performance such as temporal delay or calibration errors. We formulate the AO control loop as a model-based RL problem (MBRL) and apply it in numerical simulations to a simple Shack-Hartmann Sensor (SHS) based AO system with 24 resolution elements across the aperture. The simulations show that MBRL controlled AO predicts the temporal evolution of turbulence and adjusts to mis-registration between deformable mirror and SHS which is a typical calibration issue in AO. The method learns continuously on timescales of some seconds and is therefore capable of automatically adjusting to changing conditions. (C) 2021 Optical Society of America under the terms of the OSA Open Access Publishing Agreement
  • Flamant, Cyrille; Deroubaix, Adrien; Chazette, Patrick; Brito, Joel; Gaetani, Marco; Knippertz, Peter; Fink, Andreas H.; de Coetlogon, Gaelle; Menut, Laurent; Colomb, Aurelie; Denjean, Cyrielle; Meynadier, Remi; Rosenberg, Philip; Dupuy, Regis; Dominutti, Pamela; Duplissy, Jonathan; Bourrianne, Thierry; Schwarzenboeck, Alfons; Ramonet, Michel; Totems, Julien (2018)
    The complex vertical distribution of aerosols over coastal southernWest Africa (SWA) is investigated using airborne observations and numerical simulations. Observations were gathered on 2 July 2016 offshore of Ghana and Togo, during the field phase of the Dynamics-Aerosol-Chemistry-Cloud Interactions in West Africa project. This was the only flight conducted over the ocean during which a downward-looking lidar was operational. The aerosol loading in the lower troposphere includes emissions from coastal cities (Accra, Lome, Cotonou, and Lagos) as well as biomass burning aerosol and dust associated with long-range transport from central Africa and the Sahara, respectively. Our results indicate that the aerosol distribution on this day is impacted by subsidence associated with zonal and meridional regional-scale overturning circulations associated with the land-sea surface temperature contrast and orography over Ghana and Togo, as typically observed on hot, cloud-free summer days such as 2 July 2016. Furthermore, we show that the zonal circulation evidenced on 2 July is a persistent feature over the Gulf of Guinea during July 2016. Numerical tracer re-lease experiments highlight the dominance of aged emissions from Accra on the observed pollution plume loadings over the ocean, in the area of aircraft operation. The contribution of aged emission from Lome and Cotonou is also evident above the marine boundary layer. Given the general direction of the monsoon flow, the tracer experiments indicate no contribution from Lagos emissions to the atmospheric composition of the area west of Cotonou, where our airborne observations were gathered. The tracer plume does not extend very far south over the ocean (i.e. less than 100 km from Accra), mostly because emissions are transported northeastward near the surface over land and westward above the marine atmospheric boundary layer. The latter is possible due to interactions between the monsoon flow, complex terrain, and land-sea breeze systems, which support the vertical mixing of the urban pollution. This work sheds light on the complex - and to date undocumented - mechanisms by which coastal shallow circulations can distribute atmospheric pollutants over the densely populated SWA region.
  • Price, D.; Tyler, L. K.; Henriques, R. Neto; Campbell, K. L.; Williams, N.; Treder, M. S.; Taylor, J. R.; Henson, R. N. A.; Cam-CAN (2017)
    Slowing is a common feature of ageing, yet a direct relationship between neural slowing and brain atrophy is yet to be established in healthy humans. We combine magnetoencephalo-graphic (MEG) measures of neural processing speed with magnetic resonance imaging (MRI) measures of white and grey matter in a large population-derived cohort to investigate the relationship between age-related structural differences and visual evoked field (VEF) and auditory evoked field (AEF) delay across two different tasks. Here we use a novel technique to show that VEFs exhibit a constant delay, whereas AEFs exhibit delay that accumulates over time. White-matter (WM) microstructure in the optic radiation partially mediates visual delay, suggesting increased transmission time, whereas grey matter (GM) in auditory cortex partially mediates auditory delay, suggesting less efficient local processing. Our results demonstrate that age has dissociable effects on neural processing speed, and that these effects relate to different types of brain atrophy.
  • Luyten, Walter; Antal, Peter; Braeckman, Bart P.; Bundy, Jake; Cirulli, Francesca; Fang-Yen, Christopher; Fuellen, Georg; Leroi, Armand; Liu, Qingfei; Martorell, Patricia; Metspalu, Andres; Perola, Markus; Ristow, Michael; Saul, Nadine; Schoofs, Liliane; Siems, Karsten; Temmerman, Liesbet; Smets, Tina; Wolk, Alicja; Rattan, Suresh I. S. (2016)
    Human longevity continues to increase world-wide, often accompanied by decreasing birth rates. As a larger fraction of the population thus gets older, the number of people suffering from disease or disability increases dramatically, presenting a major societal challenge. Healthy ageing has therefore been selected by EU policy makers as an important priority ; it benefits not only the elderly but also their direct environment and broader society, as well as the economy. The theme of healthy ageing figures prominently in the Horizon 2020 programme , which has launched several research and innovation actions (RIA), like "Understanding health, ageing and disease: determinants, risk factors and pathways" in the work programme on "Personalising healthcare". Here we present our research proposal entitled "ageing with elegans" (AwE), funded by this RIA, which aims for better understanding of the factors causing health and disease in ageing, and to develop evidence-based prevention, diagnostic, therapeutic and other strategies. The aim of this article, authored by the principal investigators of the 17 collaborating teams, is to describe briefly the rationale, aims, strategies and work packages of AwE for the purposes of sharing our ideas and plans with the biogerontological community in order to invite scientific feedback, suggestions, and criticism.