A fractal fragmentation model for rockfalls

The final publication is available at Springer via http://dx.doi.org/10.1007/s10346-016-0773-8The impact-induced rock mass fragmentation in a rockfall is analyzed by comparing the in situ block size distribution (IBSD) of the rock mass detached from the cliff face and the resultant rockfall block size distribution (RBSD) of the rockfall fragments on the slope. The analysis of several inventoried rockfall events suggests that the volumes of the rockfall fragments can be characterized by a power law distribution. We propose the application of a three-parameter rockfall fractal fragmentation model (RFFM) for the transformation of the IBSD into the RBSD. A discrete fracture network model is used to simulate the discontinuity pattern of the detached rock mass and to generate the IBSD. Each block of the IBSD of the detached rock mass is an initiator. A survival rate is included to express the proportion of the unbroken blocks after the impact on the ground surface. The model was calibrated using the volume distribution of a rockfall event in Vilanova de Banat in the Cadí Sierra, Eastern Pyrenees, Spain. The RBSD was obtained directly in the field, by measuring the rock block fragments deposited on the slope. The IBSD and the RBSD were fitted by exponential and power law functions, respectively. The results show that the proposed fractal model can successfully generate the RBSD from the IBSD and indicate the model parameter values for the case study.Peer ReviewedPostprint (author's final draft

Spreadsheet data processing in Python

University of Illinois at Urbana-Champaign. Graduate College. Focal Point InitiativeOpe

Magnitude and frequency relations: are there geological constraints to the rockfall size?

The final publication is available at Springer via http://dx.doi.org/10.1007%2Fs10346-017-0910-zThere exists a transition between rockfalls, large rock mass failures, and rock avalanches. The magnitude and frequency relations (M/F) of the slope failure are increasingly used to assess the hazard level. The management of the rockfall risk requires the knowledge of the frequency of the events but also defining the worst case scenario, which is the one associated to the maximum expected (credible) rockfall event. The analysis of the volume distribution of the historical rockfall events in the slopes of the Solà d’Andorra during the last 50 years shows that they can be fitted to a power law. We argue that the extrapolation of the F-M relations far beyond the historical data is not appropriate in this case. Neither geomorphological evidences of past events nor the size of the potentially unstable rock masses identified in the slope support the occurrence of the large rockfall/rock avalanche volumes predicted by the power law. We have observed that the stability of the slope at the Solà is controlled by the presence of two sets of unfavorably dipping joints (F3, F5) that act as basal sliding planes of the detachable rock masses. The area of the basal sliding planes outcropping at the rockfall scars was measured with a terrestrial laser scanner. The distribution of the areas of the basal planes may be also fitted to a power law that shows a truncation for values bigger than 50 m2 and a maximum exposed surface of 200 m2. The analysis of the geological structure of the rock mass at the Solà d’Andorra makes us conclude that the size of the failures is controlled by the fracture pattern and that the maximum size of the failure is constrained. Two sets of steeply dipping faults (F1 and F7) interrupt the other joint sets and prevent the formation of continuous failure surfaces (F3 and F5). We conclude that due to the structural control, large slope failures in Andorra are not randomly distributed thus confirming the findings in other mountain ranges.Peer ReviewedPostprint (author's final draft

When Does Size Matter? An Empirical Study of Consumer Demographics and Product Package Choices

From the Washington University Senior Honors Thesis Abstracts (WUSHTA), 2017. Published by the Office of Undergraduate Research. Joy Zalis Kiefer, Director of Undergraduate Research and Associate Dean in the College of Arts & Sciences; Lindsey Paunovich, Editor; Helen Human, Programs Manager and Assistant Dean in the College of Arts and Sciences Mentor: Tat Cha

A New Rice Sowing Technology: Informing Small-Scale Farmers about Improved Methods of Planting

The Nakhon Sawan Rice Seed Center hopes to introduce a new rice sowing technology to small-scale farmers in an attempt to reduce labor and costs. Our team evaluated the current rice planting practices and obtained information from the small-scale farmers, the rice sowing machine inventor and Rice Seed Center representatives in order to form recommendations regarding improvements that could be made to the current machine and suggest ways to initiate the adoption and diffusion process

CarD stabilizes mycobacterial open complexes via a two-tiered kinetic mechanism

CarD is an essential and global transcriptional regulator in mycobacteria. While its biological role is unclear, CarD functions by interacting directly with RNA polymerase (RNAP) holoenzyme promoter complexes. Here, using a fluorescent reporter of open complex, we quantitate RP(o) formation in real time and show that Mycobacterium tuberculosis CarD has a dramatic effect on the energetics of RNAP bound complexes on the M. tuberculosis rrnAP3 ribosomal RNA promoter. The data reveal that Mycobacterium bovis RNAP exhibits an unstable RP(o) that is stabilized by CarD and suggest that CarD uses a two-tiered, concentration-dependent mechanism by associating with open and closed complexes with different affinities. Specifically, the kinetics of open-complex formation can be explained by a model where, at saturating concentrations of CarD, the rate of bubble collapse is slowed and the rate of opening is accelerated. The kinetics and open-complex stabilities of CarD mutants further clarify the roles played by the key residues W85, K90 and R25 previously shown to affect CarD-dependent gene regulation in vivo. In contrast to M. bovis RNAP, Escherichia coli RNAP efficiently forms RP(o) on rrnAP3, suggesting an important difference between the polymerases themselves and highlighting how transcriptional machinery can vary across bacterial genera

Integrating transcriptomics and metabonomics to unravel modes-of-action of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in HepG2 cells

<p>Abstract</p> <p>Background</p> <p>The integration of different 'omics' technologies has already been shown in several <it>in vivo </it>studies to offer a complementary insight into cellular responses to toxic challenges. Being interested in developing <it>in vitro </it>cellular models as alternative to animal-based toxicity assays, we hypothesize that combining transcriptomics and metabonomics data improves the understanding of molecular mechanisms underlying the effects caused by a toxic compound also <it>in vitro </it>in human cells. To test this hypothesis, and with the focus on non-genotoxic carcinogenesis as an endpoint of toxicity, in the present study, the human hepatocarcinoma cell line HepG2 was exposed to the well-known environmental carcinogen 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD).</p> <p>Results</p> <p>Transcriptomics as well as metabonomics analyses demonstrated changes in TCDD-exposed HepG2 in common metabolic processes, e.g. amino acid metabolism, of which some of the changes only being confirmed if both 'omics' were integrated. In particular, this integrated analysis identified unique pathway maps involved in receptor-mediated mechanisms, such as the G-protein coupled receptor protein (GPCR) signaling pathway maps, in which the significantly up-regulated gene son of sevenless 1 (SOS1) seems to play an important role. SOS1 is an activator of several members of the RAS superfamily, a group of small GTPases known for their role in carcinogenesis.</p> <p>Conclusions</p> <p>The results presented here were not only comparable with other <it>in vitro </it>studies but also with <it>in vivo </it>studies. Moreover, new insights on the molecular responses caused by TCDD exposure were gained by the cross-omics analysis.</p

Effects of increasing the affinity of CarD for RNA polymerase on Mycobacterium tuberculosis growth, rRNA transcription, and virulence

CarD is an essential RNA polymerase (RNAP) interacting protein in Mycobacterium tuberculosis that stimulates formation of RNAP-promoter open complexes. CarD plays a complex role in M. tuberculosis growth and virulence that is not fully understood. Therefore, to gain further insight into the role of CarD in M. tuberculosis growth and virulence, we determined the effect of increasing the affinity of CarD for RNAP. Using site-directed mutagenesis guided by crystal structures of CarD bound to RNAP, we identified amino acid substitutions that increase the affinity of CarD for RNAP. Using these substitutions, we show that increasing the affinity of CarD for RNAP increases the stability of the CarD protein in M. tuberculosis. In addition, we show that increasing the affinity of CarD for RNAP increases the growth rate in M. tuberculosis without affecting 16S rRNA levels. We further show that increasing the affinity of CarD for RNAP reduces M. tuberculosis virulence in a mouse model of infection despite the improved growth rate in vitro. Our findings suggest that the CarD-RNAP interaction protects CarD from proteolytic degradation in M. tuberculosis, establish that growth rate and rRNA levels can be uncoupled in M. tuberculosis and demonstrate that the strength of the CarD-RNAP interaction has been finely tuned to optimize virulence. IMPORTANCE Mycobacterium tuberculosis, the causative agent of tuberculosis, remains a major global health problem. In order to develop new strategies to battle this pathogen, we must gain a better understanding of the molecular processes involved in its survival and pathogenesis. We have previously identified CarD as an essential transcriptional regulator in mycobacteria. In this study, we detail the effects of increasing the affinity of CarD for RNAP on transcriptional regulation, CarD protein stability, and virulence. These studies expand our understanding of the global transcription regulator CarD, provide insight into how CarD activity is regulated, and broaden our understanding of prokaryotic transcription

Molecular dissection of RbpA-mediated regulation of fidaxomicin sensitivity in mycobacteria

RNA polymerase (RNAP) binding protein A (RbpA) is essential for mycobacterial viability and regulates transcription initiation by increasing the stability of the RNAP-promoter open complex (R

Population Density and Reproductive Seasonality of Tryonia cheatumi (Gastropoda: Cochliopidae), the Phantom Tryonia

We studied population density, population size, and reproductive seasonality of the Phantom Tryonia, Tryonia cheatumi (Pilsbry, 1935). This endangered freshwater snail is found only in the San Solomon Spring system, a cienega, or karst-based, arid-land freshwater spring system, in western Texas, USA. We sampled populations at seven locations in the system seasonally over a 2-yr period. San Solomon Spring, the system\u27s largest spring and modified into a swimming pool, had the largest population of T. cheatumi, with an estimated 49 million individuals and a mean density as high as 23,626 ± 39,030 (individuals/m2 ± SD). There were seasonal differences in mean density (up to 25-fold) and median snail size at all sites, but consistent seasonal patterns of mean density or size were not observed. Median snail size among samples was not related to water temperature, and juveniles were present in most samples in all seasons. These results support continuous, aseasonal reproduction, as expected in thermally stable habitats, but differences in median size and mean density among seasons and sites suggest that other factors affect reproduction and seasonal variation in population size of T. cheatumi