3D Reconstruction of Plant Roots from MRI Images to Advance Root-Soil Systems Modelling

Background and Motivation: Roots are of particular interest for the efficient use of nutrients and water by plants. Therefore, the optimization of root system architecture (RSA) offers large potential in finding more sustainable agricultural practices. Magnetic resonance imaging (MRI) is one of the few phenotyping methods that allows us to observe the 3D RSA in opaque soil. Such volumetric data are essential to investigate favorable RSA traits with functional-structural root architecture models (FSRMs). However, the processing of MRI images and their integration into FSRMs is challenging and limits the use of the data to this day. In this work, we investigated how MRI images of plant roots and related experimental data can be processed more efficiently, and how their meaningful use in FSRMs can be optimized.Material and Methods: To alleviate the bottleneck in MRI image processing, we deployed a novel approach for automated root system reconstruction. The approach combines a semantic segmentation of raw MRI images into roots and soil with a root reconstruction algorithm. We evaluated the results by comparing them with state-of-the-art manual expert reconstructions. In the next step, we investigated if the current soil process descriptions in FSRMs are adequate to derive realistic root water uptake (RWU) predictions for RSAs derived from MRI images. We performed a soil grid convergence study of our default modelling approach in CPlantBox and implemented an alternative approach for RWU calculation. The results were evaluated by comparing them to a numerical reference solution. Finally, we explored new methods for the virtual replication of MRI experiments in FSRMs. We devised a novel parameterization method for mimicking root growth based on MRI time series. By combining the measured root growth with additional experimental data, we performed a virtual repetition of an MRI experiment.Results: We observed that the U-Net segmentation improved reconstruction performance in manual and automated workflows of root system reconstruction and allowed us to process MRI images more efficiently. Furthermore, the segmentation enabled the application of the automated reconstruction algorithm for MRI images with a low contrast-to-noise ratio. The soil grid convergency study highlighted that root system scale models are not able to spatially resolve the steep soil water potential gradients near plant roots during water uptake. This resulted in large errors in simulated RWU for dry soil conditions. The implemented alternative approach for RWU calculation showed the best agreement with the reference solution, while the computational cost was kept low. Mimicking root growth based on MRI time-series data with the novel parameterization method allowed us to derive time-dependent root system metrics and to create a functional representation of growing root systems. By combining this functional representation of growing root systems with additional experimental data, we have created a parameterization framework that allows a data-driven replication of the observed RWU in CPlantBox.Conclusions: We were able to improve several aspects of the 3D reconstruction of plant roots from MRI images and their integration into root-soil-system models. The improvements to manual and automated workflows for RSA reconstruction will facilitate the parameterization of RSA submodels with MRI data. In addition, the ability to derive RSAs from low CNR images broadens the general scope of MRI experiments. The grid convergence study raised awareness for errors related to current RWU modelling paradigms under drought conditions. Using the alternative approach for RWU calculation makes it possible to bring the level of detail of FSRMs closer to that of MRI-based RSAs. The novel parameterization method for virtual replication of MRI experiments facilitates the parameterization of RSA submodels based on time-dependent root system metrics. Furthermore, the parameterization method refines our ability to validate the mechanisms and assumptions underlying RWU in FSRMs

Molecular Level in Silico Studies for Oncology. Direct Models Review

The combination of therapy and diagnostics in one process "theranostics" is a trend in a modern medicine, especially in oncology. Such an approach requires development and usage of multifunctional hybrid nanoparticles with a hierarchical structure. Numerical methods and mathematical models play a significant role in the design of the hierarchical nanoparticles and allow looking inside the nanoscale mechanisms of agent-cell interactions. The current position of in silico approach in biomedicine and oncology is discussed. The review of the molecular level in silico studies in oncology, which are using the direct models, is presented

Case report of successful peginterferon, ribavirin, and daclatasvir therapy for recurrent cholestatic hepatitis C after liver retransplantation

A recurrent hepatitis C virus (HCV) infection after liver transplantation (LT) can lead to accelerated allograft injury and fibrosis. The aim of this article is to report the first ever use of daclatasvir (DCV; also known as BMS‐790052), a potent orally administered nonstructural 5A replication complex inhibitor, in combination with peginterferon α (PEG‐IFNα) and ribavirin in an LT recipient. A 49‐year‐old female developed a severe recurrent HCV genotype 1b infection 4 months after transplantation with severe cholestasis on biopsy, an HCV RNA level of 10,000,000 IU/mL, an alkaline phosphatase level of 1525 IU/mL, and a total bilirubin level of 8.4 mg/dL. Despite partial virological suppression with PEG‐IFNα and ribavirin, progressive allograft failure ensued and culminated in retransplantation at 9 months. Three months after the second transplant, DCV (20 mg/day), PEG‐IFNα2a (180 μg/week), and ribavirin (800 mg/day) were prescribed for early recurrent cholestatic HCV. Serum HCV RNA became undetectable at week 3 of treatment and remained undetectable during 24 weeks of triple therapy and during the posttreatment follow‐up. DCV was well tolerated, and the trough drug levels were within the targeted range throughout the treatment. The cyclosporine trough levels were also stable during and after therapy. In conclusion, the lack of anticipated drug‐drug interactions between DCV and calcineurin inhibitors and the potent antiviral efficacy of DCV make this agent (in combination with PEG‐IFN and ribavirin) an attractive antiviral regimen worthy of further study in LT recipients with recurrent HCV. Liver Transpl, 2012. © 2012 AASLD.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/93517/1/23482_ftp.pd

Liver transplantation in the critically ill: a multicenter Canadian retrospective cohort study

Introduction: Critically ill cirrhosis patients awaiting liver transplantation (LT) often receive prioritization for organ allocation. Identification of patients most likely to benefit is essential. The purpose of this study was to examine whether the Sequential Organ Failure Assessment (SOFA) score can predict 90-day mortality in critically ill recipients of LT and whether it can predict receipt of LT among critically ill cirrhosis listed awaiting LT. Methods: We performed a multicenter retrospective cohort study consisting of two datasets: (a) all critically-ill cirrhosis patients requiring intensive care unit (ICU) admission before LT at five transplant centers in Canada from 2000 through 2009 (one site, 1990 through 2009), and (b) critically ill cirrhosis patients receiving LT from ICU (n = 115) and those listed but not receiving LT before death (n = 106) from two centers where complete data were available. Results: In the first dataset, 198 critically ill cirrhosis patients receiving LT (mean (SD) age 53 (10) years, 66% male, median (IQR) model for end-stage liver disease (MELD) 34 (26-39)) were included. Mean (SD) SOFA scores at ICU admission, at 48 hours, and at LT were 12.5 (4), 13.0 (5), and 14.0 (4). Survival at 90 days was 84% (n = 166). In multivariable analysis, only older age was independently associated with reduced 90-day survival (odds ratio (OR), 1.07; 95% CI, 1.01 to 1.14; P = 0.013). SOFA score did not predict 90-day mortality at any time. In the second dataset, 47.9% (n = 106) of cirrhosis patients listed for LT died in the ICU waiting for LT. In multivariable analysis, higher SOFA at 48 hours after admission was independently associated with lower probability of receiving LT (OR, 0.89; 95% CI, 0.82 to 0.97; P = 0.006). When including serum lactate and SOFA at 48 hours in the final model, elevated lactate (at 48 hours) was also significantly associated with lower likelihood of receiving LT (0.32; 0.17 to 0.61; P = 0.001). Conclusions: SOFA appears poor at predicting 90-day survival in critically ill cirrhosis patients after LT, but higher SOFA score and elevated lactate 48 hours after ICU admission are associated with a lower probability receiving LT. Older critically ill cirrhosis patients (older than 60) receiving LT have worse 90-day survival and should be considered for LT with caution

Subnormothermic and Normothermic Ex Vivo Liver Perfusion as a Novel Preservation Technique

Due to the worldwide organ shortage, interest in the use of marginal liver allografts has increased. More widespread use of marginal grafts is limited by graft injury from cold storage and the risk of poor outcomes after transplantation. Warm (subnormothermic and normothermic) ex vivo liver perfusion has emerged as a novel preservation strategy to recover marginal organs and potentially increase the organ pool. Over the last decade, advances in the field have taken warm ex vivo liver perfusion from the laboratory to clinical trials. While most investigation thus far has focused on the rescue of marginal grafts for expansion of the donor pool, warm perfusion (WP) preservation also has great potential to facilitate novel graft interventions prior to transplantation

Liver transplantation is a preferable alternative to palliative therapy for selected patients with advanced hepatocellular carcinoma

Background: Patients with hepatocellular carcinoma (HCC) beyond the traditional criteria (advanced HCC) are typically offered palliation, which is associated with a 3-year survival rate lower than 30%. This study aimed to describe the outcomes for a subset of patients with advanced HCC who satisfied the Extended Toronto Criteria (ETC) and were listed for liver transplantation (LT). Materials & Methods: All patients listed in the Toronto liver transplant program with HCC beyond both the Milan and University of California, San Francisco criteria were included in this study. Data were extracted from the prospectively collected electronic database. All radiological images were reviewed by two independent radiologists. The primary endpoint was patient survival. Results: Between January 1999 and August 2014, 96 patients with advanced HCC were listed for LT, and 62 (65%) of these patients received bridging therapy while on the waiting list. Bridging therapy led to a significant reduction in tumor progression (p=0.02) and tumor burden (p <0.001). The majority of those listed underwent LT (n=69, 72%). Both tumor progression on waiting list (HR 4.973 [1.599 – 15.464], p=0.006) and peak AFP ≥400ng/ml (HR 4.604 [1.660 – 12.768], p=0.003) were independently associated with waiting list dropout. Post-LT HCC recurrence occurred in 35% (n=24). Among those with HCC recurrence, survival was significantly better for those who received curative treatment (p=0.004). The overall actuarial survival rates from the listing were 76% at 1 year, 56% at 3 years, and 47% at 5 years, and the corresponding rates from LT were 93%, 71%, and 66%. Conclusion: LT provides significantly better survival rates than palliation for patients with selected advanced HCC

Characteristics of liver transplant candidates delisted following recompensation and predictors of such delisting in alcohol-related liver disease: a case-control study

Whether and when recovery beyond the need for transplant may occur in patients listed for decompensation remains unclear. This study aimed to investigate the characteristics of patients delisted following recompensation. Seventy-seven patients who were listed between 2005 and 2015 for decompensation, but later delisted following recompensation were included. Alcohol-related liver disease (ALD) was the underlying etiology in the majority (n=47, 61%). Listing characteristics of these patients were compared with those of decompensated ALD patients who either underwent deceased donor liver transplantation or died on the waiting list. The model for end-stage liver disease (MELD) score <20 and serum albumin ≥32g/l at listing were the only independent predictors of recompensation/delisting in ALD. The probability of recompensation was 70% when both factors were present at listing. Interestingly, about a tenth of decompensated ALD patients who died on the waiting list (median duration on waiting list 11 months) and a quarter of decompensated ALD patients who underwent living donor liver transplantation (median duration on waiting list 2 months) also had both factors at listing. In conclusion, ALD seems to be the most favorable etiology for recompensation beyond the need for transplantation. Both MELD and serum albumin at listing independently predict recompensation/delisting in ALD. It seems advisable to implement a period of observation for ALD patients with both favorable factors, before embarking on living donor liver transplantation

Woman as Peacemaker or the Ambivalent Politics of Myth

Certains arguments féministes en faveur d’une participation accrue des femmes à la sphère politique ont mobilisé le thème de la capacité supposément supérieure des femmes à prendre en compte la dimension relationnelle des rapports humains, acquise dans le cadre privé de la vie familiale et parfois considérée comme une disposition innée. Dans ce cadre, le mythe de la femme pacificatrice a gagné une certaine visibilité et a pu fonctionner comme un contre-mythe dans le contexte des luttes féministes des deux derniers siècles. Cette contribution examine les traductions et les usages politiques de ce mythe depuis Aristophane jusqu’aux débats autour de la parité et de l’éthique de la sollicitude, en passant par le mouvement suffragiste du début du siècle dernier, ainsi que les critiques qui lui ont été adressées.Feminist arguments in favor of an increased participation of women in the public and the political spheres have sometimes resorted to the thesis of an alleged superior ability of women to take into account the relational dimension of human life, whether acquired in the private experience of family life or considered to be an innate feminine disposition. In this context, the myth of woman as a peacemaker has gained visibility and indeed has sometimes functioned as a countermyth in feminist politics. This paper examines the occurrences and uses of this myth from Aristophanes to the debates surrounding the ethics of care, through the suffragist movement, as well as the critiques that have been addressed to it

Addressing Limitations of Patent Research Using Machine-Learning: A Research Agenda Based on Automatic F-term Classification and Technology Spanning Vector Data

Patent classifications play a vital role in Information Systems (IS) research due to their structured but rich technological information. However, the hierarchical structure of patent classifications presents three significant limitations: restricted horizontal comparability, the creation of technological silos and inconsistencies in global classifications. In this paper, we address these limitations by introducing a machine learning (ML) classifier for automatic F-term classification of patents. Our model classifies 378,165 unique F-terms, enabling granular comparison of patents and consistent cross-national comparability. Additionally, we provide vector representations of F-terms, facilitating cross-domain technology analyses and improved technology similarity measurements. Based on this, we propose a future research agenda in five directions to refine patent classification-based metrics, enhance firm and competitor analysis, and develop analyses for cross-domain technologies. This paper sets a foundation for ongoing advancements in patent-based analyses thereby enriching IS research

The treatment response of chronically hepatitis C virus-infected patients depends on interferon concentration but not on interferon gene expression in peripheral blood mononuclear cells.

International audienceThe current treatment of chronic hepatitis C is based on pegylated alpha interferon (PEG-IFN-α) and ribavirin. The aim of this study was to identify biological and clinical variables related to IFN therapy that could predict patient outcome. The study enrolled 47 patients treated with PEG-IFN and ribavirin combined therapy. The interferon concentration was measured in serum by a bioassay. The expression of 93 interferon-regulated genes in peripheral blood mononuclear cells was quantified by real-time quantitative reverse transcription-PCR (RT-PCR) before and after 1 month of treatment. The interferon concentration in the serum was significantly lower in nonresponders than in sustained virological responders. Moreover, a significant correlation was identified between interferon concentration and interferon exposition as well as body weight. The analysis of interferon-inducible genes in peripheral blood mononuclear cells among the genes tested did not permit the prediction of treatment outcome. In conclusion, the better option seems to be to treat patients with weight-adjusted PEG-IFN doses, particularly for patients with high weight who are treated with PEG-IFN-α2a. Although the peripheral blood mononuclear cell samples are the easiest to obtain, the measurement of interferon-inducible genes seems not be the best strategy to predict treatment outcome