abstract

Defining the bacterial communities associated with healthy status will permit rapid
detection of shifts associated with disease and foster effective probiotic intervention. This study
compares the PCR-RFLP of oral metagenomes and cultured bacterial community, as well as the
bacterial diversity profile of smokers, non-smokers and oral disease patients. The goal was to
evaluate the stability of bacteria associated with health and capture possible shifts potentially
diagnostic of smokers and oral disease.
Oral wash samples were obtained from 5 healthy and 5 smokers twice, 3 months apart. Samples
from 5 oral disease patients were also collected. Metagenomic and the genomic DNA of a
cultured subset were amplified using primer 1492R and 27F.The generated 16SrRNA gene
amplicons were used for arestriction digestion assay and bcloning with the Gene Hunter PCRTrap
vector and pCR 4- TOPO cloning kits. The restriction fingerprints were statistically tested
using Gel Compare II. The cloned 16S genes were sequenced using the ABI GeneAmp 9700
Thermal cycler. Sequences were analyzed by BLAST on the RDB II database and the HOMD.
Sau 3AI and Alu I produced the best distinctive markers of 300 bp in healthy nonsmokers and
500bp in smokers in plate wash communities. The 16S sequence data suggest the presence of a
core microbiota in all subjects mostly Streptococcus, Gamella, Candidatuse spp and confirmed
that the smokers harbored highly diverse and distinct community Neisseria pharynges, Rothia
mucilaginosa. Remarkably, there was a high stability of the fingerprints and diversity profile for
smokers and nonsmokers after 3 months.

Global sea-level rise SLR is projected to accelerate over the next century, with research
indicating that global mean sea level may rise 18–48 cm by 2050, and 50–140 cm by 2100.
Decision-makers, faced with the problem of adapting to SLR, utilize elevation data to identify
assets that are vulnerable to inundation. This paper reviews techniques and challenges stemming
from the use of Light Detection and Ranging LiDAR Digital Elevation Models DEMs in support
of SLR decision-making. A significant shortcoming in the methodology is the lack of
comprehensive standards for estimating LiDAR error, which causes inconsistent and sometimes
misleading calculations of uncertainty. Workers typically aim to reduce uncertainty by analyzing
the difference between LiDAR error and the target SLR chosen for decision-making. The
practice of mapping vulnerability to SLR is based on the assumption that LiDAR errors follow a
normal distribution with zero bias, which is intermittently violated. Approaches to correcting
discrepancies between vertical reference systems for land and tidal datums may incorporate tidal
benchmarks and a vertical datum transformation tool provided by the National Ocean Service
VDatum. Mapping a minimum statistically significant SLR increment of 32 cm is difficult to
achieve based on current LiDAR and VDatum errors. LiDAR DEMs derived from ‘ground’
returns are essential, yet LiDAR providers may fail to remove returns over vegetated areas
successfully. LiDAR DEMs integrated into a GIS can be used to identify areas that are
vulnerable to direct marine inundation and groundwater inundation reduced drainage coupled
with higher water tables. Spatial analysis can identify potentially vulnerable ecosystems as well
as developed assets. A standardized mapping uncertainty needs to be developed given that SLR
vulnerability mapping requires absolute precision for use as a decision-making tool.

The overuse and misuse of antibiotics in environmental and clinical settings have been a
driving force for the prevalence of bacterial resistance. In constant interaction with these
chemicals which can harm them, adaptively and inherently, bacteria have devised resistance
mechanisms to combat the deleterious effects posed. In the presence of a particular antibiotic, it
is expected there will be selection of resistant micro-organisms and their associated resistance
genes if present. In this study, a set of 10 samples were taken from recreational beaches in Ft.
Lauderdale, Miami and Hollywood and four different agricultural soils. These soils were
enriched after being collected aseptically with three commonly used antibiotics; Ciprofloxacin,
Tetracycline and Vancomycin to select for resistant organisms, which produced 29 total samples.
A metagenomic analysis was done with 16S rDNA amplification with primers 27F and 1492R
which produced 14 out of 29 amplicons producing the expected ~1400 bp fragment from the
conserved SSU 16S rDNA region using Agarose gel electrophoresis. From these 14 samples
amplified, a second PCR would be run from each enriched antibiotic sample with their respective
antibiotic resistance primers eg. vanA-D, tetO and qnrA to identify the resistance genes present
expecting that the antibiotic used for enrichment would select for the resistant organisms. Future
work includes the sequencing of the amplified resistance genes to help identify novel genetic
alterations indicative of new adaptive mechanisms.

Class imbalance is a frequent problem found in bioinformatics datasets. Unfortunately,
the minority class is usually also the class of interest. One of the methods to improve this
situation is data sampling. There are a number of different data sampling methods, each with
their own strengths and weaknesses, which makes choosing one a difficult prospect. In our work
we compare three data sampling techniques Random Undersampling, Random Oversampling,
and SMOTE on six bioinformatics datasets with varying levels of class imbalance. Additionally,
we apply two different classifiers to the problem 5-NN and SVM, and use feature selection to
reduce our datasets to 25 features prior to applying sampling. Our results show that there is very
little difference between the data sampling techniques, although Random Undersampling is the
most frequent top performing data sampling technique for both of our classifiers. We also
performed statistical analysis which confirms that there is no statistical difference between the
techniques. Therefore, our recommendation is to use Random Undersampling when choosing a
data sampling technique, because it is less computationally expensive to implement than
SMOTE and it also reduces the size of the dataset, which will improve subsequent computational
costs without sacrificing classification performance.

There are many available options today for treating small lesion cancer cells. Two of the
most used options are the planning systems BrainLab and Eclipse. The main difference between
the two is the algorithms that are used to calculate the dose distribution of external beam
radiation therapy. BrainLab offers a Monte Carlo based algorithm while Eclipse utilizes the
Anisotropic Analytical Algorithm. An investigative study on the quality of the planning system
is done for cases in lung, head and neck and prostate. In particular, lung cases are highly
heterogeneous which can lead to problems in the calculation. The ability to be able to plan on the
best system for individual cases can lead to better and more consistent treatments for cancer
patients.

Purpose: To explore offset values in dose optimization with pencil beam (PB) algorithm
to minimize dosimetric differences with plans calculated with Monte Carlo (MC) for lung cancer
treatment with Stereotactic Body Radiotherapy (SBRT). Methods: 20 cases of Non-Small Cell
Lung Cancer, treated with gated full motion range SBRT were selected. According to the
proximity of the Gross Tumor Volume (GTV) to the chest wall, two groups are defined.
Treatment plans were created on 4D average intensity projection (AIP) CT set with Brainlab
iPlanDose® 4.1.2 planning system. The D97 of PTV was normalized to 50Gy using the fast PB
and compared with MC. The optimized plan was then recomputed over each 4D respiratory
phase, and compared with MC. Results: The mean difference in the PB and MC D97 of the ITV
was 10.5% (±0.8%) of the prescription dose (50Gy). PB algorithm showed 2.3-2.4% less
overestimation to the D97 of the ITV, when comparing to MC, in the maximum exhalation phase
than in the maximal inhalation phase. Significantly smaller dose difference between PB and MC
is also shown in plans for peripheral lesions (7.7 ± 0.7%) versus for central lesions (12.7±0.8%)
(p< 0.01). Conclusions: The dosimetric differences between PB and MC can be reasonably
predicted depending on the location of lesion in the lung, and may be used as offset value in dose
optimization with PB. Caution is suggested when using the maximum inhalation phase for
treatment planning.

Purpose: This study was designed to define the antibiotic resistance index of the
cultivable oral microbiome to Amoxiacilin Clavulanic acid, Vancomycin, Ciprofloxacin,
Clarithomycin, Chlorotetracyclin, Bacitracin, Kanamycin and Tobramycin using a new method
adapted from the Kirby Bauer assay.
Method: Oral wash samples were collected from 2 current smokers and 2 nonsmokers. Bacterial
community were pelleted by centrifugation and used to create a lawn for the assay employing
standard disk diffusion assay. Zones of inhibition and number of colonies in the zone were
recorded. Mean values of inhibition zones were compared to established databases to draw
conclusions.
Result: The zones of inhibition of Bacitracin antibiotics shows that several bacteria from one of
the non smokers were resistant to Bacitracin, while the smokers showed marked susceptibility.
Conclusion: The new method developed in our lab yielded consistent set of data which serve as
criteria for determining resistance of the oral microbiome to antibiotics. Quite remarkably, it is
known that pathogenic beta Streptococci are susceptible to Bacitracin while non-pathogens are
not; confirming that healthy persons harbor the healthy strains of streptococci. However the
unanswered question is …. Could these normal biota pick up genes and become resistant too?
Only time and human habits will decide but we have developed a baseline and an easy method
for testing.

The objective of this work is to characterize the moisture transport in a unidirectional,
transversely isotropic carbon/vinylester composite. Diffusion occurs when the material is
immersed in sea water and the moisture is transported through the voids, and interface gaps. This
uptake of moisture can cause problems including matrix degradation and swelling, reduction of
fiber/matrix interface strength, etc. To characterize water transport, three diffusivities are
required, D1, D2, and D3. However, transversely isotropic material can be characterized by two
diffusivities, along and transverse to the fibers (D1=DL, and D2=D3=DT). Composite materials
may absorb moisture along the fiber/matrix interface, especially if the ends of the fibers are
exposed. This mechanism of moisture transport inside the composite is known as “wicking”,
which would increase the value of DL. Wicking is promoted by voids and unbonded regions
between the fiber and matrix.
Experiments will be conducted on specimens made from vinylester resin reinforced with
unidirectional carbon fibers. A range of specimens will be prepared and immersed in 40°C sea
water. The moisture content will be monitored until maximum saturation. Previous studies
indicate that the Fickian diffusion model is a reasonable descriptor of the moisture absorption
process. From the plots of moisture content versus time1/2, the apparent diffusivity will be
reduced for the different size panels. The longitudinal and transverse diffusivities will be
determined using a Matlab algorithm. The amount of moisture absorbed into the composite due
to wicking will be quantified from mass balance analysis and related to the longitudinal and
transverse diffusivities.

Iran’s long history of pottery making goes back ten thousand years, and it is as diverse as
the country’s geography and ethnic composition. Clay as a material connects contemporary
Iranian society to its ancient roots, and it permeates daily life in terms of the economy,
technology and even gender roles. This presentation focuses on the lives of three women potters
in northern and western Iran, one in the village of Jirdeh Central Gillan province, another in the
village of khomar Mahaleh East Gillan, and the third outside of the City of Marand West
Azerbaijan province. Each woman represents a particular genre of handmade pottery from
functional to sculptural work, and she establishes a unique identity in terms of production,
commercial distribution and her personal relationship to the social and geographic environment.
A selection of interviews, photographs and video clips taken during the summer of 2012
illustrate how these women work and thrive in their leadership, independence and creative
artistry. Key concepts include: 1 Land place, home, 2 Technique and work process, 3 Gender
roles, 4 Tradition and why their works are considered traditional, and 5 Authenticity and what
makes their works authentic. The solitude that separates and yet connects these women offers a
contrast to the nature of ceramics in the contemporary art world of Tehran and also opens a
dialog for gender and feminist issues that are relevant to study of art technology, design and the
roles of women in Iranian society today.

This thesis project will explore the role of visual design in the interaction of two different
cultures from two extremely different countries: Iran and the United States of America. Each has
a particular politic relation to each other in history. I want to explore design’s role comparatively
in illustrating and displaying the visual cultural subjects of both countries, their communication,
and how the two cultures impact each other. Some of the effects on culture are integrated with
technology and tradition too. Particularly tradition, which is part of the root of one’s culture,
slowly becomes obsolete due to turning into technology and becoming modern. So sometimes
we encounter with exchanging or replacing cultures. Moreover, since social culture and personal
culture play a crucial role in personal identity, assimilating with a different society brings about
various identities too. In my opinion immigrant people such as myself, as an international student
from Iran, are a good example to represent the clash and combination of two cultures and how
one adapts and work in accord these cultures. The overall intent of this project is to utilize
graphic design to design of series of seven to ten objects as a product packages or consumer
artifacts along with advertisement based on visualizing the communication and interaction of
these specific countries’ culture. It will demonstrate similarities and differences through visual
comparison, collation, and confronting of cultural and social elements through the visual
language and the tools of design.