GIM (Groundwater Integrated Modelling). The hydrogeological compiler

Complex problems in Earth Sciences demand the use of numerical models. To this end, a large number of codes have been developed during the last two decades. In spite of their power, as displayed in their many applications, these codes are sparse and, most often, used in the academic framework. To make things worse, they are aimed at solving a given set of physical phenomena (e.g. most codes solve groundwater flow and contaminant transport, but they do not take into account material defor- mation, others include deformation but not heat transfer, etc.) and most often they do not integrate stochastic techniques. GIM (Groundwater Integrated Modelling) is aimed at providing a platform to fill this gap. The objective is to integrate the existing codes in an overall fully-parallel object oriented FORTRAN 95 structure. Thus, the capabilities of GIM are numerous (differ- ent solvers of direct and inverse problem, of groundwater flow, contaminant (conservative or not) or heat transport, etc.) as it takes profit of those of the codes embedded in its structure. The use of GIM is illustrated with a simple example consisting of a Monte Carlo analysis of flow and transport problem: 1. Read data common to most of the existing \u201chost\u201d codes (finite elements or finite differences mesh, geostatistical model, state variable measurements, etc.) in an XML fashion. \u201cHost\u201d code particular variables (options, tolerances, convergence criteria, etc.) are supplied separately. 2. The data are used to pre-process the initial hydraulic conductivity fields on the basis of the geostatistical model. These fields will be calibrated in step 4.3. Write data in the appropriate format for the \u201chost\u201d code. 4. Execute \u201chost\u201d code(s). In this example, an inversion code is used. However, many codes can be used at step 4 (e.g. for solving the inherent direct problem, modeller can use a flow simulator to calculate the velocity field driving the con- taminant transport, which will be simulated using a \u201craw\u201d transport simulator). 5. Collect results (the calibrated fields). 6. Post-process the output (e.g. histogram of hydraulic conductivity). Including \u201chost\u201d codes in the overall structure of GIM is easy. One needs to add a routine for writing data at step 3 and a routine for reading the output at step 5. This confers versatility and an ample room for future developments

Trastuzumab and pertuzumab without chemotherapy in early-stage HER2+ breast cancer: a plain language summary of the PHERGain study

This is a summary of a publication about the PHERGain study, which was published in The Lancet Oncology in May 2021. The study includes 376 women with a type of breast cancer called HER2-positive breast cancer that can be removed by surgery. In the study, researchers wanted to learn if participants could be treated with two medicines called trastuzumab and pertuzumab without the need for chemotherapy. To identify HER2-positive tumors with more sensitivity to anti-HER2 therapies, the researchers used a type of imaging called a FDG-PET scan to check how well the treatments were working.Participants took a treatment before surgery, consisting of either chemotherapy (docetaxel and carboplatin) plus trastuzumab and pertuzumab (group A) or trastuzumab and pertuzumab alone (plus hormone therapy if the tumor was hormone receptor-positive; group B). After two cycles of treatment, participants underwent a FDG-PET scan. Participants assigned to group A completed 6 cycles of treatment regardless of 18F-FDG-PET results. Participants in group B continued the same treatment until surgery if their FDG-PET scan showed the treatment was working. While participants who did not show a response started treatment with chemotherapy in addition to trastuzumab and pertuzumab. All participants then had surgery.The results revealed that, of the participants in group B who showed a response using FDG-PET scan, 37.9% achieved a disappearance of all invasive cancer in the breast and axillary lymph nodes. This rate appears to be higher than those reported in previous studies evaluating the same treatment. These participants also had less side effects and improved overall quality of life compared with participants taking chemotherapy plus trastuzumab and pertuzumab.Early monitoring of how well participants respond to treatment by FDG-PET scan seems to identify participants with operable HER2-positive breast cancer who were more likely to benefit from trastuzumab and pertuzumab without the need to have chemotherapy. The PHERGain study is still ongoing and results on long-term survival are expected to be released in 2023. Clinical Trial Registration: NCT03161353 (ClinicalTrials.gov)

A pattern-search-based inverse method

Uncertainty in model predictions is caused to a large extent by the uncertainty in model parameters, while the identification of model parameters is demanding because of the inherent heterogeneity of the aquifer. A variety of inverse methods has been proposed for parameter identification. In this paper we present a novel inverse method to constrain the model parameters (hydraulic conductivities) to the observed state data (hydraulic heads). In the method proposed we build a conditioning pattern consisting of simulated model parameters and observed flow data. The unknown parameter values are simulated by pattern searching through an ensemble of realizations rather than optimizing an objective function. The model parameters do not necessarily follow a multi-Gaussian distribution, and the nonlinear relationship between the parameter and the response is captured by the multipoint pattern matching. The algorithm is evaluated in two synthetic bimodal aquifers. The proposed method is able to reproduce the main structure of the reference fields, and the performance of the updated model in predicting flow and transport is improved compared with that of the prior model.The authors gratefully acknowledge the financial support from the Ministry of Science and Innovation, project CGL2011-23295. The first author also acknowledges the scholarship provided by the China Scholarship Council (CSC [2007] 3020). The authors would like to thank Gregoire Mariethoz (University of New South Wales) and Philippe Renard (University of Neuchatel) for their enthusiastic help in answering questions about the direct sampling algorithm. Gregoire Mariethoz and two anonymous reviewers are also thanked for their comments during the reviewing process, which helped improving the final paper.Zhou ., H.; Gómez-Hernández, JJ.; Li ., L. (2012). A pattern-search-based inverse method. Water Resources Research. 48(3):1-17. https://doi.org/10.1029/2011WR011195S117483Alcolea, A., & Renard, P. (2010). Blocking Moving Window algorithm: Conditioning multiple-point simulations to hydrogeological data. Water Resources Research, 46(8). doi:10.1029/2009wr007943Alcolea, A., Carrera, J., & Medina, A. (2006). Pilot points method incorporating prior information for solving the groundwater flow inverse problem. Advances in Water Resources, 29(11), 1678-1689. doi:10.1016/j.advwatres.2005.12.009Arpat, G. B., & Caers, J. (2007). Conditional Simulation with Patterns. Mathematical Geology, 39(2), 177-203. doi:10.1007/s11004-006-9075-3Caers , J. 2002 Geostatistical history matching under training-image based geological model constraintsCaers, J. (2003). Efficient gradual deformation using a streamline-based proxy method. Journal of Petroleum Science and Engineering, 39(1-2), 57-83. doi:10.1016/s0920-4105(03)00040-8Caers, J., & Hoffman, T. (2006). The Probability Perturbation Method: A New Look at Bayesian Inverse Modeling. Mathematical Geology, 38(1), 81-100. doi:10.1007/s11004-005-9005-9Capilla, J. E., & Llopis-Albert, C. (2009). Gradual conditioning of non-Gaussian transmissivity fields to flow and mass transport data: 1. Theory. Journal of Hydrology, 371(1-4), 66-74. doi:10.1016/j.jhydrol.2009.03.015Carrera, J., & Neuman, S. P. (1986). Estimation of Aquifer Parameters Under Transient and Steady State Conditions: 1. Maximum Likelihood Method Incorporating Prior Information. Water Resources Research, 22(2), 199-210. doi:10.1029/wr022i002p00199Chen, Y., & Zhang, D. (2006). Data assimilation for transient flow in geologic formations via ensemble Kalman filter. Advances in Water Resources, 29(8), 1107-1122. doi:10.1016/j.advwatres.2005.09.007Christiansen, L., Binning, P. J., Rosbjerg, D., Andersen, O. B., & Bauer-Gottwein, P. (2011). Using time-lapse gravity for groundwater model calibration: An application to alluvial aquifer storage. Water Resources Research, 47(6). doi:10.1029/2010wr009859De Marsily, G., Delay, F., Gonçalvès, J., Renard, P., Teles, V., & Violette, S. (2005). Dealing with spatial heterogeneity. Hydrogeology Journal, 13(1), 161-183. doi:10.1007/s10040-004-0432-3Deutsch, C. V., & Tran, T. T. (2002). FLUVSIM: a program for object-based stochastic modeling of fluvial depositional systems. Computers & Geosciences, 28(4), 525-535. doi:10.1016/s0098-3004(01)00075-9Dubuisson, M.-P., & Jain, A. K. (s. f.). A modified Hausdorff distance for object matching. Proceedings of 12th International Conference on Pattern Recognition. doi:10.1109/icpr.1994.576361Emsellem, Y., & De Marsily, G. (1971). An Automatic Solution for the Inverse Problem. Water Resources Research, 7(5), 1264-1283. doi:10.1029/wr007i005p01264Evensen, G. (2003). The Ensemble Kalman Filter: theoretical formulation and practical implementation. Ocean Dynamics, 53(4), 343-367. doi:10.1007/s10236-003-0036-9Falivene, O., Cabello, P., Arbués, P., Muñoz, J. A., & Cabrera, L. (2009). A geostatistical algorithm to reproduce lateral gradual facies transitions: Description and implementation. Computers & Geosciences, 35(8), 1642-1651. doi:10.1016/j.cageo.2008.12.003Fernàndez-Garcia, D., Illangasekare, T. H., & Rajaram, H. (2005). Differences in the scale dependence of dispersivity and retardation factors estimated from forced-gradient and uniform flow tracer tests in three-dimensional physically and chemically heterogeneous porous media. Water Resources Research, 41(3). doi:10.1029/2004wr003125Feyen, L., & Caers, J. (2006). Quantifying geological uncertainty for flow and transport modeling in multi-modal heterogeneous formations. Advances in Water Resources, 29(6), 912-929. doi:10.1016/j.advwatres.2005.08.002Fu, J., & Gómez-Hernández, J. J. (2008). A Blocking Markov Chain Monte Carlo Method for Inverse Stochastic Hydrogeological Modeling. Mathematical Geosciences, 41(2), 105-128. doi:10.1007/s11004-008-9206-0Jaime Gómez-Hernánez, J., Sahuquillo, A., & Capilla, J. (1997). Stochastic simulation of transmissivity fields conditional to both transmissivity and piezometric data—I. Theory. Journal of Hydrology, 203(1-4), 162-174. doi:10.1016/s0022-1694(97)00098-xGuardiano, F. B., & Srivastava, R. M. (1993). Multivariate Geostatistics: Beyond Bivariate Moments. Geostatistics Tróia ’92, 133-144. doi:10.1007/978-94-011-1739-5_12Harbaugh , A. W. E. R. Banta M. C. Hill M. G. McDonald 2000 MODFLOW-2000, the U.S. Geological Survey modular ground-water model-User guide to modularization concepts and the ground-water flow process Reston, Va.Hendricks Franssen, H. J., & Kinzelbach, W. (2008). Real-time groundwater flow modeling with the Ensemble Kalman Filter: Joint estimation of states and parameters and the filter inbreeding problem. Water Resources Research, 44(9). doi:10.1029/2007wr006505Franssen, H.-J. H., Gómez-Hernández, J., & Sahuquillo, A. (2003). Coupled inverse modelling of groundwater flow and mass transport and the worth of concentration data. Journal of Hydrology, 281(4), 281-295. doi:10.1016/s0022-1694(03)00191-4Henrion, V., Caumon, G., & Cherpeau, N. (2010). ODSIM: An Object-Distance Simulation Method for Conditioning Complex Natural Structures. Mathematical Geosciences, 42(8), 911-924. doi:10.1007/s11004-010-9299-0Hoeksema, R. J., & Kitanidis, P. K. (1984). An Application of the Geostatistical Approach to the Inverse Problem in Two-Dimensional Groundwater Modeling. Water Resources Research, 20(7), 1003-1020. doi:10.1029/wr020i007p01003Hoeksema, R. J., & Kitanidis, P. K. (1985). Analysis of the Spatial Structure of Properties of Selected Aquifers. Water Resources Research, 21(4), 563-572. doi:10.1029/wr021i004p00563Hu, L. Y. (2000). Mathematical Geology, 32(1), 87-108. doi:10.1023/a:1007506918588Hu, L. Y., & Chugunova, T. (2008). Multiple-point geostatistics for modeling subsurface heterogeneity: A comprehensive review. Water Resources Research, 44(11). doi:10.1029/2008wr006993Huysmans, M., & Dassargues, A. (2009). Application of multiple-point geostatistics on modelling groundwater flow and transport in a cross-bedded aquifer (Belgium). Hydrogeology Journal, 17(8), 1901-1911. doi:10.1007/s10040-009-0495-2Jafarpour, B., & Khodabakhshi, M. (2011). A Probability Conditioning Method (PCM) for Nonlinear Flow Data Integration into Multipoint Statistical Facies Simulation. Mathematical Geosciences, 43(2), 133-164. doi:10.1007/s11004-011-9316-yJournel, A., & Zhang, T. (2006). The Necessity of a Multiple-Point Prior Model. Mathematical Geology, 38(5), 591-610. doi:10.1007/s11004-006-9031-2Kerrou, J., Renard, P., Hendricks Franssen, H.-J., & Lunati, I. (2008). Issues in characterizing heterogeneity and connectivity in non-multiGaussian media. Advances in Water Resources, 31(1), 147-159. doi:10.1016/j.advwatres.2007.07.002Kwa, Franz, M. O., & Scholkopf, B. (2005). Iterative kernel principal component analysis for image modeling. IEEE Transactions on Pattern Analysis and Machine Intelligence, 27(9), 1351-1366. doi:10.1109/tpami.2005.181Kitanidis, P. K. (2007). On stochastic inverse modeling. Geophysical Monograph Series, 19-30. doi:10.1029/171gm04Kitanidis, P. K., & Vomvoris, E. G. (1983). A geostatistical approach to the inverse problem in groundwater modeling (steady state) and one-dimensional simulations. Water Resources Research, 19(3), 677-690. doi:10.1029/wr019i003p00677Li, L., Zhou, H., Hendricks Franssen, H. J., & Gómez-Hernández, J. J. (2011). Groundwater flow inverse modeling in non-MultiGaussian media: performance assessment of the normal-score Ensemble Kalman Filter. Hydrology and Earth System Sciences Discussions, 8(4), 6749-6788. doi:10.5194/hessd-8-6749-2011Li, L., Zhou, H., & Gómez-Hernández, J. J. (2011). Transport upscaling using multi-rate mass transfer in three-dimensional highly heterogeneous porous media. Advances in Water Resources, 34(4), 478-489. doi:10.1016/j.advwatres.2011.01.001Li, L., Zhou, H., & Gómez-Hernández, J. J. (2011). A comparative study of three-dimensional hydraulic conductivity upscaling at the macro-dispersion experiment (MADE) site, Columbus Air Force Base, Mississippi (USA). Journal of Hydrology, 404(3-4), 278-293. doi:10.1016/j.jhydrol.2011.05.001Mariethoz, G., Renard, P., & Straubhaar, J. (2010). The Direct Sampling method to perform multiple-point geostatistical simulations. Water Resources Research, 46(11). doi:10.1029/2008wr007621Mariethoz, G., Renard, P., & Caers, J. (2010). Bayesian inverse problem and optimization with iterative spatial resampling. Water Resources Research, 46(11). doi:10.1029/2010wr009274Neuman, S. P. (1973). Calibration of distributed parameter groundwater flow models viewed as a multiple-objective decision process under uncertainty. Water Resources Research, 9(4), 1006-1021. doi:10.1029/wr009i004p01006Oliver, D. S., Cunha, L. B., & Reynolds, A. C. (1997). Markov chain Monte Carlo methods for conditioning a permeability field to pressure data. Mathematical Geology, 29(1), 61-91. doi:10.1007/bf02769620RamaRao, B. S., LaVenue, A. M., De Marsily, G., & Marietta, M. G. (1995). Pilot Point Methodology for Automated Calibration of an Ensemble of conditionally Simulated Transmissivity Fields: 1. Theory and Computational Experiments. Water Resources Research, 31(3), 475-493. doi:10.1029/94wr02258Rubin, Y., Chen, X., Murakami, H., & Hahn, M. (2010). A Bayesian approach for inverse modeling, data assimilation, and conditional simulation of spatial random fields. Water Resources Research, 46(10). doi:10.1029/2009wr008799Strebelle, S. (2002). Mathematical Geology, 34(1), 1-21. doi:10.1023/a:1014009426274Suzuki, S., & Caers, J. (2008). A Distance-based Prior Model Parameterization for Constraining Solutions of Spatial Inverse Problems. Mathematical Geosciences, 40(4), 445-469. doi:10.1007/s11004-008-9154-8Wen, X. H., Capilla, J. E., Deutsch, C. V., Gómez-Hernández, J. J., & Cullick, A. S. (1999). A program to create permeability fields that honor single-phase flow rate and pressure data. Computers & Geosciences, 25(3), 217-230. doi:10.1016/s0098-3004(98)00126-5Zhang, T., Switzer, P., & Journel, A. (2006). Filter-Based Classification of Training Image Patterns for Spatial Simulation. Mathematical Geology, 38(1), 63-80. doi:10.1007/s11004-005-9004-xZhou, H., Gómez-Hernández, J. J., Hendricks Franssen, H.-J., & Li, L. (2011). An approach to handling non-Gaussianity of parameters and state variables in ensemble Kalman filtering. Advances in Water Resources, 34(7), 844-864. doi:10.1016/j.advwatres.2011.04.014Zhou, H., Li, L., Hendricks Franssen, H.-J., & Gómez-Hernández, J. J. (2011). Pattern Recognition in a Bimodal Aquifer Using the Normal-Score Ensemble Kalman Filter. Mathematical Geosciences, 44(2), 169-185. doi:10.1007/s11004-011-9372-

A review of the international early recommendations for departments organization and cancer management priorities during the global COVID-19 pandemic: applicability in low- and middle-income countries.

Coronavirus disease 2019 (COVID-19) is an infectious disease caused by a new virus that has never been identified in humans before. COVID-19 caused at the time of writing of this article, 2.5 million cases of infections in 193 countries with 165,000 deaths, including two-third in Europe. In this context, Oncology Departments of the affected countries had to adapt quickly their health system care and establish new organizations and priorities. Thus, numerous recommendations and therapeutic options have been reported to optimize therapy delivery to patients with chronic disease and cancer. Obviously, while these cancer care recommendations are immediately applicable in Europe, they may not be applicable in certain emerging and low- and middle-income countries (LMICs). In this review, we aimed to summarize these international guidelines in accordance with cancer types, making a synthesis for daily practice to protect patients, staff and tailor anti-cancer therapy delivery taking into account patients/tumour criteria and tools availability. Thus, we will discuss their applicability in the LMICs with different organizations, limited means and different constraints

Inverse Methods in Hydrogeology: Evolution and Recent Trends

[EN] Parameter identification is an essential step in constructing a groundwater model. The process of recognizing model parameter values by conditioning on observed data of the state variable is referred to as the inverse problem. A series of inverse methods has been proposed to solve the inverse problem, ranging from trial-and-error manual calibration to the current complex automatic data assimilation algorithms. This paper does not attempt to be another overview paper on inverse models, but rather to analyze and track the evolution of the inverse methods over the last decades, mostly within the realm of hydrogeology, revealing their transformation, motivation and recent trends. Issues confronted by the inverse problem, such as dealing with multiGaussianity and whether or not to preserve the prior statistics are discussed. (C) 2013 Elsevier Ltd. All rights reserved.The authors gratefully acknowledge the financial support by the Spanish Ministry of Science and Innovation through project CGL2011-23295. We would like to thank Dr. Alberto Guadagnini (Politecnico di Milano, Italy) for his comments during the reviewing process, which helped improving the final paper.Zhou, H.; Gómez-Hernández, JJ.; Li, L. (2014). Inverse Methods in Hydrogeology: Evolution and Recent Trends. Advances in Water Resources. 63:22-37. https://doi.org/10.1016/j.advwatres.2013.10.014S22376