Integrated and interactive 4D system for archaeological stratigraphy

The digitization of some of the processes carried out in an archaeological excavation is changing the way of working at the site. Today, new technologies coexist with traditional methodologies. The study of stratigraphy can combine drawings of profiles and plans, the Harris Matrix diagram, as well as digitized files that perform a complete record of the stratigraphic sequence. However, this information is usually unaggregated from the rest of the information system that makes up the archaeological record. In this paper, we present an integrated software tool and the associated methodology to record, store, visualize and analyze the 3D stratigraphy of a site. The implementation uses spatial databases to store information of a heterogeneous nature and game engines for the visualization and interaction with this information. During the excavation process, the strata are scanned using the Tof technology, which is available in many smartphones. The resulting 3D model of the stratum, once uploaded to the software system, allows us to visualize the sequence of strata incorporating the findings into their original arrangement. Some additional tools, such as the scrollbar, help to perform a temporal analysis of the site. The result is a 4D interactive stratigraphy tool, which together with the Harris Matrix, complements the archaeological record and facilitates the work to archaeologists. This methodology also allows to speed up the on-site work and the subsequent analysis, while improving the user experience with the 3D archaeological site replica.CRUE-CSICSpringer NatureSpanish GovernmentEuropean Commission TIN2017-84968-

Comparative study of transvaginal ultrasonography and CA 125 in the preoperative evaluation of myometrial invasion in endometrial carcinoma

To compare the ability of transvaginal sonography and serum CA 125 levels to predict myometrial invasion in patients with endometrial carcinoma. DESIGN AND METHODS: Prospective study in 50 consecutive patients (mean age 60 years, SD 10.5, range 29-77 years) diagnosed as having endometrial cancer and scheduled for surgical staging. All patients were evaluated by transvaginal ultrasonography. Endometrial thickness was measured in all cases and myometrial invasion was estimated as or = 50%. Serum CA 125 level was determined in each patient. A cut-off level of > or = 35 IU/ml was considered to predict myometrial invasion of > or = 50%. All patients underwent surgical staging, and definitive histopathological findings regarding myometrial invasion were used as the 'gold standard'. Sensitivity, specificity and positive predictive value (PPV) and negative predictive value (NPV) were calculated for transvaginal ultrasonography and CA 125 and compared. RESULTS: On histopathological analysis, myometrial invasion was found to be or = 50% in 15 cases (30%). Mean endometrial thickness in patients with superficial invasion was significantly lower than in those with deep invasion (13.4 mm (95% CI 11.2-15.7) vs. 18.7 mm (95% CI 15.0-22.3), respectively; p = 0.014). Median CA 125 was significantly higher in patients with deep invasion than in those with superficial invasion (30 IU/ml, interquartile range (IQR) 46.0 vs. 16.9 IU/ml, IQR 13.9, respectively; p = 0.002). The sensitivity, specificity, PPV and NPV for transvaginal ultrasonography were 86.7% (95% CI 59.5-98.3), 94.3% (95% CI 80.8-99.3), 86.7% (95% CI 59.5-98.3) and 94.3% (95% CI 80.8-99.3), respectively. The sensitivity, specificity, PPV and NPV for CA 125 were 40% (95% CI 16.3-67.7), 91.4% (95% CI 76.9-98.2), 66.7% (95% CI 29.9-92.5) and 78% (95% CI 63.4-89.5), respectively. The sensitivity of transvaginal ultrasonography was significantly higher than that of CA 125 (p = 0.008). No differences were found in terms of specificity, PPV or NPV. CONCLUSION: Our results indicate that transvaginal ultrasonography is more sensitive than CA 125 in predicting myometrial invasion in endometrial cancer

An out-of-core method for GPU image mapping on large 3D scenarios of the real world

[Abstract] Image mapping on 3D huge scenarios of the real world is one of the most fundamental and computational expensive processes for the integration of multi-source sensing data. Recent studies focused on the observation and characterization of Earth have been enhanced by the proliferation of Unmanned Aerial Vehicle (UAV) and sensors able to capture massive datasets with a high spatial resolution. Despite the advances in manufacturing new cameras and versatile platforms, only a few methods have been developed to characterize the study area by fusing heterogeneous data such as thermal, multispectral or hyperspectral images with high-resolution 3D models. The main reason for this lack of solutions is the challenge to integrate multi-scale datasets and high computational efforts required for image mapping on dense and complex geometric models. In this paper, we propose an efficient pipeline for multi-source image mapping on huge 3D scenarios. Our GPU-based solution significantly reduces the run time and allows us to generate enriched 3D models on-site. The proposed method is out-of-core and it uses available resources of the GPU’s machine to perform two main tasks: (i) image mapping and (ii) occlusion testing. We deploy highly-optimized GPU-kernels for image mapping and detection of self-hidden geometry in the 3D model, as well as a GPU-based parallelization to manage the 3D model considering several spatial partitions according to the GPU capabilities. Our method has been tested on 3D scenarios with different point cloud densities (66M, 271M, 542M) and two sets of multispectral images collected by two drone flights. We focus on launching the proposed method on three platforms: (i) System on a Chip (SoC), (ii) a user-grade laptop and (iii) a PC. The results demonstrate the method’s capabilities in terms of performance and versatility to be computed by commodity hardware. Thus, taking advantage of GPUs, this method opens the door for embedded and edge computing devices for 3D image mapping on large-scale scenarios in near real-time.This work has been partially supported through the research projects TIN2017-84968-R, PID2019-104184RB-I00 funded by MCIN/AEI/10.13039/501100011033 and ERDF funds “A way of doing Europe”, as well as by ED431C 2021/30, ED431F 2021/11 funded by Xunta de Galicia and 1381202 by Junta de AndalucíaXunta de Galicia; ED431C 2021/30Xunta de Galicia; ED431F 2021/11Junta de Andalucía; 138120

Hsp90 activity is necessary to acquire a proper neuronal polarization

Chaperones are critical for the folding and regulation of a wide array of cellular proteins. Heat Shock Proteins (Hsps) are the most representative group of chaperones. Hsp90 represents up to 1-2% of soluble protein. Although the Hsp90 role is being studied in neurodegenerative diseases, its role in neuronal differentiation remains mostly unknown. Since neuronal polarity mechanisms depend on local stability and degradation, we asked whether Hsp90 could be a regulator of axonal polarity and growth. Thus, we studied the role of Hsp90 activity in a well established model of cultured hippocampal neurons using an Hsp90 specific inhibitor, 17-AAG. Our present data shows that Hsp90 inhibition at different developmental stages disturbs neuronal polarity formation or axonal elongation. Hsp90 inhibition during the first 3. h in culture promotes multiple axon morphology, while this inhibition after 3. h slows down axonal elongation. Hsp90 inhibition was accompanied by decreased Akt and GSK3 expression, as well as, a reduced Akt activity. In parallel, we detected an alteration of kinesin-1 subcellular distribution. Moreover, these effects were seconded by changes in Hsp70/Hsc70 subcellular localization that seem to compensate the lack of Hsp90 activity. In conclusion, our data strongly suggests that Hsp90 activity is necessary to control the expression, activity or location of specific kinases and motor proteins during the axon specification and axon elongation processes. Even more, our data demonstrate the existence of a >time-window> for axon specification in this model of cultured neurons after which the inhibition of Hsp90 only affects axonal elongation mechanisms. © 2013 Elsevier B.V.Peer Reviewe

Integration of proteomics with transcriptomics and metallomics for the study of environmental issues

Comunicaciones a congreso

Surveillance of Influenza Viruses in Waterfowl Used As Decoys in Andalusia, Spain

A longitudinal study was carried out to determine the seroprevalence of avian influenza viruses (AIVs) in waterfowl used as decoys in Andalusia, southern Spain. A total of 2319 aquatic birds from 193 flocks were analyzed before and after the hunting season 2011–2012. In the first sampling, 403 out of 2319 (18.0%, CI95%: 15.8–19.0) decoys showed antibodies against AIVs by ELISA. The AI seroprevalence was significantly higher in geese (21.0%) than in ducks (11.7%) (P,0.001). Besides, the spatial distribution of AIVs was not homogeneous as significant differences among regions were observed. The prevalence of antibodies against AIVs subtypes H5 and H7 were 1.1% and 0.3%, respectively, using hemagglutination inhibition test (HI). The overall and H5 seroprevalences slightly increased after the hunting period (to 19.2% and 1.4%, respectively), while the H7 seroprevalence remained at the same level (0.3%). The proportion of flocks infected by AIVs was 65.3%, while 11.2% and 4.9% of flocks were positive for H5 and H7, respectively. Viral shedding was not detected in any of the 47 samples positive by both ELISA and HI, tested by RRT-PCR. The individual incidence after the hunting season was 3.4%. The fact that 57 animals seroconverted, 15 of which were confirmed by HI (12 H5 and 3 H7), was indication of contact with AIVs during the hunting period. The results indicate that waterfowl used as decoys are frequently exposed to AIVs and may be potentially useful as sentinels for AIVs monitoring. The seroprevalence detected and the seropositivity against AIVs H5 and H7, suggest that decoys can act as reservoirs of AIVs, which may be of animal and public health concer

Phyllobacterium catacumbae sp. nov., a member of the order 'Rhizobiales' isolated from Roman catacombs

Two strains were isolated from tuff, a volcanic rock that forms the walls of the Roman Catacombs of Saint Callixtus in Rome, Italy. A polyphasic approach using nutritional and physiological tests, reactions to antibiotics, fatty acid profiles, DNA base ratios, DNA-DNA reassociation and 16S rRNA gene sequence comparisons showed that the two isolates belong to a novel species within the genus Phyllobacterium. The species Phyllobacterium catacumbae sp. nov. is proposed. The type strain is CSC19T (=CECT 5680T=LMG 22520T).V. J. and L. L. received fellowships from the Spanish Ministry of Education and Science (MEC), I3P programme and J. M. G. is supported by an MEC contract from the ‘Ramón y Cajal’ program. This study was supported by EC project EVK4-CT2000-00028 and MEC project BTE2002-04492-C02-01.Peer Reviewe

Reproducibility of the energy metabolism response to an oral glucose tolerance test: influence of a postcalorimetric correction procedure

Purpose Metabolic fexibility (MetF), which is a surrogate of metabolic health, can be assessed by the change in the respiratory exchange ratio (RER) in response to an oral glucose tolerance test (OGTT). We aimed to determine the day-to-day reproducibility of the energy expenditure (EE) and RER response to an OGTT, and whether a simulation-based postcalorimetric correction of metabolic cart readouts improves day-to-day reproducibility. Methods The EE was assessed (12 young adults, 6 women, 27±2 years old) using an Omnical metabolic cart (Maastricht Instruments, Maastricht, The Netherlands) after an overnight fast (12 h) and after a 75-g oral glucose dose on 2 separate days (48 h). On both days, we assessed EE in 7 periods (one 30-min baseline and six 15-min postprandial). The ICcE was performed immediately after each recording period, and capillary glucose concentration (using a digital glucometer) was determined. Results We observed a high day-to-day reproducibility for the assessed RER (coefcients of variation [CV]<4%) and EE (CVs<9%) in the 7 diferent periods. In contrast, the RER and EE areas under the curve showed a low day-to-day reproducibility (CV=22% and 56%, respectively). Contrary to our expectations, the postcalorimetric correction procedure did not infuence the day-to-day reproducibility of the energy metabolism response, possibly because the Omnical’s accuracy was~100%. Conclusion Our study demonstrates that the energy metabolism response to an OGTT is poorly reproducible (CVs>20%) even using a very accurate metabolic cart. Furthermore, the postcalorimetric correction procedure did not infuence the day-to-day reproducibility. Trial registration NCT04320433; March 25, 2020.Funding for open access charge: Universidad de Granada / CBUA. Supported by the Spanish Ministry of Economy and Competitiveness via Retos de la Sociedad grant DEP2016-79512-R (to JRR), and European Regional Development Funds (ERDF); Spanish Ministry of Education grant (FPU15/04059 to JMAA; and FPU19/01609 to LJ-F); the University of Granada Plan Propio de Investigación 2016-Excellence actions: Unit of Excellence on Exercise and Health (to JRR)—Plan Propio de Investigación 2018 and 2020 Programa Contratos-Puente and Programa Perfeccionamiento de Doctores (to GS-D, and to JMAA respectively); Junta de Andalucía, Consejería de Conocimiento, Investigación y Universidades grant SOMM17/6107/UGR (to JRR) via the ERDF; and the Fundación Alfonso Martín Escudero (to GS-D)

Three-dimensional power Doppler angiography in endometrial cancer: correlation with tumor characteristics

To assess the correlation between intratumoral vascularization using three-dimensional power Doppler angiography (3D-PDA) and several histological tumor characteristics in a series of patients with endometrial carcinoma. METHODS: Ninety-nine women (mean age, 61.7 (range, 31-84) years) diagnosed as having endometrial cancer were assessed by transvaginal 3D-PDA before surgical staging. Endometrial volume (EV) and 3D-PDA vascular indices (vascularization index (VI), flow index (FI) and vascularization flow index (VFI)) were calculated using the Virtual Organ Computer-aided AnaLysis (VOCAL) method. All patients were surgically staged. Individual tumor features such as histological type, tumor grade, myometrial infiltration depth, lymph-vascular space involvement, cervical involvement, lymph node metastases and tumor stage were considered for analysis. Multivariate logistic regression (MLR) analysis was used to determine which 3D-PDA parameters were independently associated with each histological characteristic. RESULTS: MLR analysis showed that only EV and VI were independently associated with myometrial infiltration (EV: odds ratio (OR), 1.119 (95% CI, 1.025-1.221), P = 0.012; VI: OR, 1.127 (95% CI, 1.063-1.195), P = 0.001) and tumor stage (EV: OR, 1.103 (95% CI, 1.012-1.202), P = 0.025; VI: OR, 1.120 (95% CI, 1.057-1.187), P = 0.001), only VI was independently associated with tumor grade (OR, 1.056 (95% CI, 1.023-1.091), P = 0.001) and only EV was independently associated with lymph node metastases (OR, 1.086 (95% CI, 1.017-1.161), P = 0.001). CONCLUSION: 3D-PDA analysis of tumor vascularization in endometrial cancer correlates with some prognostic histological characteristics