The Impact of Tides on the Capillary Transition Zone

The capillary transition zone, also known as the capillary fringe, is a zone where water saturations decrease with height above the water table/oil–water contact as a result of capillary action. In some oil reservoirs, this zone may contain a significant proportion of the oil in place. In groundwater assessments, the capillary fringe can profoundly affect contaminant transport. In this study, we investigated the influence of a tidally induced, semi-diurnal, change in water table depth on the water saturation distribution in the capillary fringe/transition zone. The investigation used a mixture of laboratory experiments, in which the change in saturation with depth was monitored over a period of 90 days, and numerical simulation. We show that tidal changes in water table depth can significantly alter the vertical water saturation profile from what would be predicted using capillary–gravity equilibrium and the drainage or imbibition capillary pressure curves.     

Beyond statistical methods: teaching critical thinking to first-year university students

We discuss a major change in the way we teach our first-year statistics course. We have redesigned this course with emphasis on teaching critical thinking. We recognized that most of the students take the course for general knowledge and support of other majors, and very few are planning to major in statistics. We identified the essential aspects of a first-year statistics course, given this student mix, focusing on a simple question, ‘Given this is the last chance you have to teach statistics, what are the essential skills students need?’ We have moved from thinking about statistics skills needed for a statistician to skills needed to participate in today's society. We have changed the way we deliver the course with less emphasis on lectures and more on alternative resources including on-line tutorials, Excel, computer-based skills testing, web-based learning materials and smaller group activities such as study groups and example classes. Feedback from students shows that they are very receptive and enthusiastic.     

Extension of the 2-p-opt and 1-shift algorithms to the heterogeneous probabilistic traveling salesman problem

The probabilistic traveling salesman problem is a well known problem that is quite challenging to solve. It involves finding the tour with the lowest expected cost for customers that will require a visit with a given probability. There are several proposed algorithms for the homogeneous version of the problem, where all customers have identical probability of being realized. From the literature, the most successful approaches involve local search procedures, with the most famous being the 2-p-opt and 1-shift procedures proposed by Bertsimas [D.J. Bertsimas, L. Howell, Further results on the probabilistic traveling salesman problem, European Journal of Operational Research 65 (1) (1993) 68–95]. Recently, however, evidence has emerged that indicates the equations offered for these procedures are not correct, and even when corrected, the translation to the heterogeneous version of the problem is not simple. In this paper we extend the analysis and correction to the heterogeneous case. We derive new expressions for computing the cost of 2-p-opt and 1-shift local search moves, and we show that the neighborhood of a solution may be explored in O(n²) time, the same as for the homogeneous case, instead of O(n³) as first reported in the literature.     

Toward the computer-aided discovery of FabH inhibitors. Do predictive QSAR models ensure high quality virtual screening performance?

Antibiotic resistance has increased over the past two decades. New approaches for the discovery of novel antibacterials are required and innovative strategies will be necessary to identify novel and effective candidates. Related to this problem, the exploration of bacterial targets that remain unexploited by the current antibiotics in clinical use is required. One of such targets is the \(\beta \) -ketoacyl-acyl carrier protein synthase III (FabH). Here, we report a ligand-based modeling methodology for the virtual-screening of large collections of chemical compounds in the search of potential FabH inhibitors. QSAR models are developed for a diverse dataset of 296 FabH inhibitors using an in-house modeling framework. All models showed high fitting, robustness, and generalization capabilities. We further investigated the performance of the developed models in a virtual screening scenario. To carry out this investigation, we implemented a desirability-based algorithm for decoys selection that was shown effective in the selection of high quality decoys sets. Once the QSAR models were validated in the context of a virtual screening experiment their limitations arise. For this reason, we explored the potential of ensemble modeling to overcome the limitations associated to the use of single classifiers. Through a detailed evaluation of the virtual screening performance of ensemble models it was evidenced, for the first time to our knowledge, the benefits of this approach in a virtual screening scenario. From all the obtained results, we could arrive to a significant main conclusion: at least for FabH inhibitors, virtual screening performance is not guaranteed by predictive QSAR models.     

Hydrophobic switching nature of methylcellulose ultra-thin films: thickness and annealing effects

We have studied the thermosensitive property of methylcellulose (MC) thin films supported on Si substrate by static sessile drop contact angle measurements, and their surface properties and thin film structure by x-ray reflectivity (XRR) and atomic force microscopy (AFM) techniques. From the static sessile drop contact angle measurements, the MC thin films showed the characteristic hydrophilic-to-hydrophobic transition at ～70?°C, which is the lower critical solution temperature of the bulk solution volume phase separation transition. For films with thickness d ≤ R(g), the onset of such a transition is affected by the film thickness while very thick films, d ? R(g), yielded higher contact angles. Annealing the MC thin films with thicknesses ～200 ? (near the radius of gyration, R(g), of the polymer) below the bulk glass transition temperature (T(g) ～ 195?° C) would not change the hydrophobic switch nature of the film but annealing 'at' and above the bulk T(g) would change its surface property. From surface topography images by AFM, there were no significant changes in either the roughness or the film texture before and after annealing. With XRR data, we were able to determine that such changes in the surface properties are highly correlated to the film thickness changes after the annealing process. This study, we believe, is the first to examine the thermal annealing affects on the thermal response function of a thermoresponsive polymer and is important for researching how to tailor the hydrophobic switching property of MC thin films for future sensing applications.     

Differentiation between intra-axial metastatic tumor progression and radiation injury following fractionated radiation therapy or stereotactic radiosurgery using MR spectroscopy, perfusion MR imaging or volume progression modeling

Objective

To determine the accuracy of magnetic resonance spectroscopy (MRS), perfusion MR imaging (MRP), or volume modeling in distinguishing tumor progression from radiation injury following radiotherapy for brain metastasis.

Methods

Twenty-six patients with 33 intra-axial metastatic lesions who underwent MRS (n=41) with or without MRP (n=32) after cranial irradiation were retrospectively studied. The final diagnosis was based on histopathology (n=4) or magnetic resonance imaging (MRI) follow-up with clinical correlation (n=29). Cho/Cr (choline/creatinine), Cho/NAA (choline/N-acetylaspartate), Cho/nCho (choline/contralateral normal brain choline) ratios were retrospectively calculated for the multi-voxel MRS. Relative cerebral blood volume (rCBV), relative peak height (rPH) and percentage of signal-intensity recovery (PSR) were also retrospectively derived for the MRPs. Tumor volumes were determined using manual segmentation method and analyzed using different volume progression modeling. Different ratios or models were tested and plotted on the receiver operating characteristic curve (ROC), with their performances quantified as area under the ROC curve (AUC). MRI follow-up time was calculated from the date of initial radiotherapy until the last MRI or the last MRI before surgical diagnosis.

Results

Median MRI follow-up was 16 months (range: 2-33). Thirty percent of lesions (n=10) were determined to be radiation injury; 70% (n=23) were determined to be tumor progression. For the MRS, Cho/nCho had the best performance (AUC of 0.612), and Cho/nCho >1.2 had 33% sensitivity and 100% specificity in predicting tumor progression. For the MRP, rCBV had the best performance (AUC of 0.802), and rCBV >2 had 56% sensitivity and 100% specificity. The best volume model was percent increase (AUC of 0.891); 65% tumor volume increase had 100% sensitivity and 80% specificity.

Conclusion

Cho/nCho of MRS, rCBV of MRP, and percent increase of MRI volume modeling provide the best discrimination of intra-axial metastatic tumor progression from radiation injury for their respective modalities. Cho/nCho and rCBV appear to have high specificities but low sensitivities. In contrast, percent volume increase of 65% can be a highly sensitive and moderately specific predictor for tumor progression after radiotherapy. Future incorporation of 65% volume increase as a pretest selection criterion may compensate for the low sensitivities of MRS and MRP.     

Atom-scale ptychographic electron diffractive imaging of boron nitride cones

Ptychographic coherent diffractive imaging (CDI) has been extensively applied using both x rays and electrons. The extension to atomic resolution has been elusive. This Letter demonstrates ptychographic electron diffractive imaging at atomic resolution, permitting identification of structure in a boron nitride helical cone at a resolution of order 1 ?, beyond that of comparative Z-contrast images. A scanning transmission electron microscope is used to create a diverging illumination in a defocused Fresnel CDI geometry, providing a robust strategy leading to a unique solution.