Modeling vapor transfer in soil water and heat simulations: A modularized, partially-coupled approach

Coupled water and heat transfer models are widely used to analyze soil water content and temperature dynamics, evaluate agricultural management systems, and support crop growth modelling. In relatively dry soils, vapor transfer, rather than liquid water flux, becomes the main pathway for water redistribution. However, in some modularized soil simulators, e.g., 2DSOIL (Timlin et al., 1996), vapor transfer is not included, which may induce errors in soil water and heat modelling. Directly embedding vapor transfer into existing water and heat transfer modules may violate the modularized architecture of those simulators. Therefore, the objectives of this study are to design a vapor transfer model, evaluate its performance, and implement it as a separate module in a coupled soil water and heat simulator, e.g., 2DSOIL. The efficacy of the vapor transfer model is evaluated by comparing the simulated soil water content and temperature before and after including the new vapor transfer model, and the soil water content and temperature simulated with the standard Philip and de Vries (1957) model. By implementing vapor transfer as a separate module in 2DSOIL, modifications to existing water and heat transfer modules can be minimized and the modularized model architecture can be maintained. Numerical examples of 2DSOIL with the new vapor transfer model are presented to illustrate the effects of vapor flux on soil water and temperature redistributions. In conclusion, the new vapor transfer model provides an effective and easy-to-use method to account for the effects of vapor transfer on coupled soil water and heat simulations

Deep Learning versus Classical Regression for Brain Tumor Patient Survival Prediction

Deep learning for regression tasks on medical imaging data has shown promising results. However, compared to other approaches, their power is strongly linked to the dataset size. In this study, we evaluate 3D-convolutional neural networks (CNNs) and classical regression methods with hand-crafted features for survival time regression of patients with high grade brain tumors. The tested CNNs for regression showed promising but unstable results. The best performing deep learning approach reached an accuracy of 51.5% on held-out samples of the training set. All tested deep learning experiments were outperformed by a Support Vector Classifier (SVC) using 30 radiomic features. The investigated features included intensity, shape, location and deep features. The submitted method to the BraTS 2018 survival prediction challenge is an ensemble of SVCs, which reached a cross-validated accuracy of 72.2% on the BraTS 2018 training set, 57.1% on the validation set, and 42.9% on the testing set. The results suggest that more training data is necessary for a stable performance of a CNN model for direct regression from magnetic resonance images, and that non-imaging clinical patient information is crucial along with imaging information.Comment: Contribution to The International Multimodal Brain Tumor Segmentation (BraTS) Challenge 2018, survival prediction tas

Residual Enhancing Disease after Surgery for Glioblastoma: Evaluation of Practice in the United Kingdom

Background A growing body of clinical data highlights the prognostic importance of achieving gross total resection (GTR) in patients with glioblastoma. The aim of this study was to determine nationwide practice and attitudes towards achieving GTR and dealing with residual enhancing disease. Methods The study was in 2 parts: an electronic questionnaire sent to United Kingdom neuro-oncology surgeons to assess surgical practice followed by a 3-month prospective, multicenter observational study of current neurosurgical oncology practice. Results Twenty-seven surgeons representing 22 neurosurgical units completed the questionnaire. Prospective data were collected for 113 patients from 15 neurosurgical units. GTR was deemed to be achieved at time of surgery in 82% (91/111) of cases, but in only 45% (36/80) on postoperative MRI. Residual enhancing disease was deemed operable in 16.3% (13/80) of cases, however, no patient underwent early repeat surgery for residual enhancing disease. The most commonly cited reason (38.5%, 5/13) was perceived lack of clinical benefit. Conclusion There is a subset of patients for whom GTR is thought possible, but not achieved at surgery. For these patients, early repeat resection may improve overall survival. Further prospective surgical research is required to better define the prognostic implications of GTR for residual enhancing disease and examine the potential benefit of this early re-intervention

A piecewise analysis model for electrical conductivity calculation from time domain reflectometry waveforms

Electrical conductivity (EC) represents a material’s ability to conduct electric current. Soil EC has been used as a soil quality attribute related to soil pH, nutrient availability, crop suitability and soil microbial activity. Time domain reflectometry (TDR) estimates soil water content and EC based on the propagation/reflection and energy attenuation of voltage signals along a waveguide. To maximize the data use efficiency, waveform interpretations for simultaneous water content and EC determination are needed. A tangent line/bounded mean oscillation (TL-BMO) model is available to estimate soil water content from TDR waveforms, but an associated EC model is not yet available. The objectives of this study are (1) to introduce a piecewise analysis method for TDR waveform interpretation, and (2) to develop a model for EC computation along a TDR waveguide under homogeneous water content. The proposed model sequentially fits a TDR waveform for the coaxial cable, the connection, and the waveguide according to the transmission line equation. A TDR waveguide can be discretized into multiple successive pieces for the determination of EC variations along the waveguide. Simplifications of the fitting procedures via (1) existing models, e.g., TL-BMO and Topp et al. (1988) models, and (2) analysis of waveforms obtained from controlled conditions, e.g., in distilled water under room temperature (~20 °C) and air pressure (~101 kPa), are also applied. Accuracy and stability of the proposed model are tested via observed TDR waveforms obtained under uniform EC conditions but perturbated with a range of noise levels. EC values computed with only one discretized piece (i.e., no discretization along the waveguide) are consistent with the theoretical EC values, and the results are robust for all of the tested noise levels. As the number of discretized pieces and the noise levels increase, numerical oscillations in the results increase. The maximum relative errors are \u3c20%, occurring when the mean power of noise is as large as the mean power of waveforms (0 dB noise). Flexibility of the proposed model is tested using waveforms simulated under spatially varying EC, and the EC variations along a TDR waveguide can be detected by the proposed model. In summary, the proposed model provides reliable EC estimations, and it can evaluate uniform or varying EC distributions along a TDR waveguide under uniform moisture conditions. This model can be imbedded into the TL-BMO model for integrated water content and EC determination for commonly measured (251-scanning point) TDR waveforms

DNA strand break repair and neurodegeneration.

A number of DNA repair disorders are known to cause neurological problems. These disorders can be broadly characterised into early developmental, mid-to-late developmental or progressive. The exact developmental processes that are affected can influence disease pathology, with symptoms ranging from early embryonic lethality to late-onset ataxia. The category these diseases belong to depends on the frequency of lesions arising in the brain, the role of the defective repair pathway, and the nature of the mutation within the patient. Using observations from patients and transgenic mice, we discuss the importance of double strand break repair during neuroprogenitor proliferation and brain development and the repair of single stranded lesions in neuronal function and maintenance

Co-Deletion of Chromosome 1p/19q and IDH1/2 Mutation in Glioma Subsets of Brain Tumors in Chinese Patients

OBJECTIVE: To characterize co-deletion of chromosome 1p/19q and IDH1/2 mutation in Chinese brain tumor patients and to assess their associations with clinical features. METHODS: In a series of 528 patients with gliomas, pathological and radiological materials were reviewed. Pathological constituents of tumor subsets, incidences of 1p/19q co-deletion and IDH1/2 mutation in gliomas by regions and sides in the brain were analyzed. RESULTS: Overall, 1p and 19q was detected in 339 patients by FISH method while the sequence of IDH1/2 was determined in 280 patients. Gliomas of frontal, temporal and insular origin had significantly different pathological constituents of tumor subsets (P<0.001). Gliomas of frontal origin had significantly higher incidence of 1p/19q co-deletion (50.4%) and IDH1/2 mutation (73.5%) than those of non-frontal origin (27.0% and 48.5%, respectively) (P<0.001), while gliomas of temporal origin had significantly lower incidence of 1p/19q co-deletion (23.9%) and IDH1/2 mutation (41.7%) than those of non-temporal origin (39.9% and 63.2%, respectively) (P = 0.013 and P = 0.003, respectively). Subgroup analysis confirmed these findings in oligoastrocytic and oligodendroglial tumors, respectively. Although the difference of 1p/19q co-deletion was not statistically significant in temporal oligodendroglial tumors, the trend was marginally significant (P = 0.082). However, gliomas from different sides of the brain did not show significant different pathological constituents, incidences of 1p/19q co-deletion or IDH1/2 mutation. CONCLUSION: Preferential distribution of pathological subsets, 1p/19q co-deletion and IDH1/2 mutation were confirmed in some brain regions in Chinese glioma patients, implying their distinctive tumor genesis and predictive value for prognosis

Role of SDF1/CXCR4 Interaction in Experimental Hemiplegic Models with Neural Cell Transplantation

Much attention has been focused on neural cell transplantation because of its promising clinical applications. We have reported that embryonic stem (ES) cell derived neural stem/progenitor cell transplantation significantly improved motor functions in a hemiplegic mouse model. It is important to understand the molecular mechanisms governing neural regeneration of the damaged motor cortex after the transplantation. Recent investigations disclosed that chemokines participated in the regulation of migration and maturation of neural cell grafts. In this review, we summarize the involvement of inflammatory chemokines including stromal cell derived factor 1 (SDF1) in neural regeneration after ES cell derived neural stem/progenitor cell transplantation in mouse stroke models

Niche-Independent Symmetrical Self-Renewal of a Mammalian Tissue Stem Cell

Pluripotent mouse embryonic stem (ES) cells multiply in simple monoculture by symmetrical divisions. In vivo, however, stem cells are generally thought to depend on specialised cellular microenvironments and to undergo predominantly asymmetric divisions. Ex vivo expansion of pure populations of tissue stem cells has proven elusive. Neural progenitor cells are propagated in combination with differentiating progeny in floating clusters called neurospheres. The proportion of stem cells in neurospheres is low, however, and they cannot be directly observed or interrogated. Here we demonstrate that the complex neurosphere environment is dispensable for stem cell maintenance, and that the combination of fibroblast growth factor 2 (FGF-2) and epidermal growth factor (EGF) is sufficient for derivation and continuous expansion by symmetrical division of pure cultures of neural stem (NS) cells. NS cells were derived first from mouse ES cells. Neural lineage induction was followed by growth factor addition in basal culture media. In the presence of only EGF and FGF-2, resulting NS cells proliferate continuously, are diploid, and clonogenic. After prolonged expansion, they remain able to differentiate efficiently into neurons and astrocytes in vitro and upon transplantation into the adult brain. Colonies generated from single NS cells all produce neurons upon growth factor withdrawal. NS cells uniformly express morphological, cell biological, and molecular features of radial glia, developmental precursors of neurons and glia. Consistent with this profile, adherent NS cell lines can readily be established from foetal mouse brain. Similar NS cells can be generated from human ES cells and human foetal brain. The extrinsic factors EGF plus FGF-2 are sufficient to sustain pure symmetrical self-renewing divisions of NS cells. The resultant cultures constitute the first known example of tissue-specific stem cells that can be propagated without accompanying differentiation. These homogenous cultures will enable delineation of molecular mechanisms that define a tissue-specific stem cell and allow direct comparison with pluripotent ES cells

Glioma stem cells are more aggressive in recurrent tumors with malignant progression than in the primary tumor, and both can be maintained long-term in vitro

<p>Abstract</p> <p>Background</p> <p>Despite the advances made during decades of research, the mechanisms by which glioma is initiated and established remain elusive. The discovery of glioma stem cells (GSCs) may help to elucidate the processes of gliomagenesis with respect to their phenotype, differentiation and tumorigenic capacity during initiation and progression. Research on GSCs is still in its infancy, so no definitive conclusions about their role can yet be drawn. To understand the biology of GSCs fully, it is highly desirable to establish permanent and biologically stable GSC lines.</p> <p>Methods</p> <p>In the current study, GSCs were isolated from surgical specimens of primary and recurrent glioma in a patient whose malignancy had progressed during the previous six months. The GSCs were cryopreserved and resuscitated periodically during long-term maintenance to establish glioma stem/progenitor cell (GSPC) lines, which were characterized by immunofluorescence, flow cytometry and transmission electronic microscopy. The primary and recurrent GSPC lines were also compared in terms of in vivo tumorigenicity and invasiveness. Molecular genetic differences between the two lines were identified by array-based comparative genomic hybridization and further validated by real-time PCR.</p> <p>Results</p> <p>Two GSPC lines, SU-1 (primary) and SU-2 (recurrent), were maintained <it>in vitro</it> for more than 44 months and 38 months respectively. Generally, the potentials for proliferation, self-renewal and multi-differentiation remained relatively stable even after a prolonged series of alternating episodes of cryopreservation and resuscitation. Intracranial transplantation of SU-1 cells produced relatively less invasive tumor mass in athymic nude mice, while SU-2 cells led to much more diffuse and aggressive lesions strikingly recapitulated their original tumors. Neither SU-1 nor SU-2 cells reached the terminal differentiation stage under conditions that would induce terminal differentiation in neural stem cells. The differentiation of most of the tumor cells seemed to be blocked at the progenitor cell phase: most of them expressed nestin but only a few co-expressed differentiation markers. Transmission electron microscopy showed that GSCs were at a primitive stage of differentiation with low autophagic activity. Array-based comparative genomic hybridization revealed genetic alterations common to both SU-1 and SU-2, including amplification of the oncogene <it>EGFR </it>and deletion of the tumor suppressor <it>PTEN</it>, while some genetic alterations such as amplification of <it>MTA1 </it>(metastasis associated gene 1) only occurred in SU-2.</p> <p>Conclusion</p> <p>The GSPC lines SU-1 and SU-2 faithfully retained the characteristics of their original tumors and provide a reliable resource for investigating the mechanisms of formation and recurrence of human gliomas with progressive malignancy. Such investigations may eventually have major impacts on the understanding and treatment of gliomas.</p