Cyclic Mixed-Radix Dense Gray Codes

A Gray code is a sequence of n binary integers in the range 0 to n-1 that has the Gray-code property: each integer in the sequence differs from the integer before it in a single digit. Gray codes have many applications, ranging from rotary encoders to Boolean circuit minimization. We refer to Gray codes where the first and lastcodewords in the sequence fulfill the Gray-code property as cyclic. Additionally, we refer to a Gray code as dense if the sequence of n numbers consists of a permutation of ⟨0, 1, . . . , n − 1⟩. This thesis focuses on generating mixed-radix Gray codes under a variety of starting conditions. Mixed radix is a base representation that uses any d-tuple of radices r = (r_d−1, r_d−2, . . . , r_0) where each digit position can have a different base. This thesis will address a method to create a dense, cyclic Gray code for mixed radices when r_d−1 = 2, there is at least one odd radix, and n is odd

Effects of Mycorrhizal Fungi on Vigna Radiata Growth in Soil Differing in Fertilizer Concentration

Mycorrhizal fungi form mutualistic relationships with the roots of some plants, allowing the plant access to nutrients and minerals while the fungi obtain food from the plant. Given that this relationship is beneficial to the plant, this paper investigates the nature of the impact of presence of mycorrhizal fungi on the growth of Vigna radiata (mung beans) in soil of differing chemical environments. Through comparing the stem lengths of plants seven days after germination, it is found that in soil with 0.0% fertilizer, the presence of locally collected, unclassified mycorrhizal fungi impacts the growth of Vigna radiata negatively; in intermediate fertilizer concentrations (1.0%, 1.1%, 1.2%) there is no significant effect; at higher fertilizer concentrations, the mycorrhizal fungi aid in the plants’ survival and growth. This paper concludes that in nutrient-deficient environments, the mycorrhizal fungi compete for nutrients with the plant, yet benefits the plant by stabilizing its growth when nutrients are available. Due to the unclassified nature of the mycorrhizal fungi used in this experiment, this investigation is very preliminary and opens itself to many more topics of research in the future

Slug-based epithelial-mesenchymal transition gene signature is associated with prolonged time to recurrence in glioblastoma

Background
We previously identified a precise stage-associated gene expression signature of coordinately expressed genes, including the transcription factor Slug (SNAI2) and other epithelial mesenchymal transition (EMT) markers, present in samples from publicly available gene expression datasets in multiple cancer types. The expression levels of the co-expressed genes vary in a continuous and coordinate manner across the samples, ranging from absence of expression to strong co-expression of all genes. These data suggest that tumor cells may pass through an EMT like process of mesenchymal transition to varying degrees. 

Findings
Here we show that this signature in glioblastoma multiforme (GBM) is associated with time to recurrence following initial treatment. By analyzing data from The Cancer Genome Atlas (TCGA), we found that GBM patients who responded to therapy and had long time to recurrence had low levels of the signature in their tumor samples (P = 3x10^-7^). We also found that the signature is strongly correlated in gliomas with the putative stem cell marker CD44, and is highly enriched among the differentially expressed genes in glioblastomas vs. lower grade gliomas. 

Conclusions 
Our results suggest that long delay before tumor recurrence is associated with absence of the mesenchymal transition signature, raising the possibility that inhibiting this transition might improve the durability of therapy in glioma patients

Epigenetic domains found in mouse embryonic stem cells via a hidden Markov model

<p>Abstract</p> <p>Background</p> <p>Epigenetics is an important layer of transcriptional control necessary for cell-type specific gene regulation. Recent studies have shown significant epigenetic patterns associated with developmental stages and diseases. However, previous studies have been mostly limited to focal epigenetic patterns, whereas methods for analyzing large-scale organizations are still lacking.</p> <p>Results</p> <p>We developed a hidden Markov model (HMM) approach for detecting the types and locations of epigenetic domains from multiple histone modifications. We used this method to analyze a published ChIP-seq dataset of five histone modification marks (H3K4me2, H3K4me3, H3K27me3, H3K9me3, and H3K36me3) in mouse embryonic stem (ES) cells. We identified three types of domains, corresponding to active, non-active, and null states. In total, our three-state HMM identified 258 domains in the mouse genome containing 9.6 genes on average. These domains were validated by a number of criteria. The largest domains correspond to olfactory receptor (OR) gene clusters. Each <it>Hox </it>gene cluster also forms a separate epigenetic domain. We found that each type of domain is associated with distinct biological functions and structural changes during early cell differentiation.</p> <p>Conclusions</p> <p>The HMM approach successfully detects domains of consistent epigenetic patterns from ChIP-seq data, providing new insights into the role of epigenetics in long-range gene regulation.</p

Treating Homeless Opioid Dependent Patients with Buprenorphine in an Office-Based Setting

CONTEXT Although office-based opioid treatment with buprenorphine (OBOT-B) has been successfully implemented in primary care settings in the US, its use has not been reported in homeless patients. OBJECTIVE To characterize the feasibility of OBOT-B in homeless relative to housed patients. DESIGN A retrospective record review examining treatment failure, drug use, utilization of substance abuse treatment services, and intensity of clinical support by a nurse care manager (NCM) among homeless and housed patients in an OBOT-B program between August 2003 and October 2004. Treatment failure was defined as elopement before completing medication induction, discharge after medication induction due to ongoing drug use with concurrent nonadherence with intensified treatment, or discharge due to disruptive behavior. RESULTS Of 44 homeless and 41 housed patients enrolled over 12 months, homeless patients were more likely to be older, nonwhite, unemployed, infected with HIV and hepatitis C, and report a psychiatric illness. Homeless patients had fewer social supports and more chronic substance abuse histories with a 3- to 6-fold greater number of years of drug use, number of detoxification attempts and percentage with a history of methadone maintenance treatment. The proportion of subjects with treatment failure for the homeless (21%) and housed (22%) did not differ (P=.94). At 12 months, both groups had similar proportions with illicit opioid use [Odds ratio (OR), 0.9 (95% CI, 0.5–1.7) P=.8], utilization of counseling (homeless, 46%; housed, 49%; P=.95), and participation in mutual-help groups (homeless, 25%; housed, 29%; P=.96). At 12 months, 36% of the homeless group was no longer homeless. During the first month of treatment, homeless patients required more clinical support from the NCM than housed patients. CONCLUSIONS Despite homeless opioid dependent patients' social instability, greater comorbidities, and more chronic drug use, office-based opioid treatment with buprenorphine was effectively implemented in this population comparable to outcomes in housed patients with respect to treatment failure, illicit opioid use, and utilization of substance abuse treatment

Ornamental marine species culture in the coral triangle: seahorse demonstration project in the Spermonde Islands, Sulawesi, Indonesia.

Ornamental marine species ('OMS') provide valuable income for developing nations in the Indo-Pacific Coral Triangle, from which most of the specimens are exported. OMS culture can help diversify livelihoods in the region, in support of management and conservation efforts to reduce destructive fishing and collection practices that threaten coral reef and seagrass ecosystems. Adoption of OMS culture depends on demonstrating its success as a livelihood, yet few studies of OMS culture exist in the region. We present a case study of a land-based culture project for an endangered seahorse (Hippocampus barbouri) in the Spermonde Islands, Sulawesi, Indonesia. The business model demonstrated that culturing can increase family income by seven times. A Strengths Weaknesses Opportunities Threats (SWOT) analysis indicated good collaboration among diverse stakeholders and opportunities for culturing non-endangered species and for offshoot projects, but complicated permitting was an issue as were threats of market flooding and production declines. The OMS international market is strong, Indonesian exporters expressed great interest in cultured product, and Indonesia is the largest exporting country for H. barbouri. Yet, a comparison of Indonesia ornamental marine fish exports to fish abundance in a single local market indicated that OMS culture cannot replace fishing livelihoods. Nevertheless, seahorse and other OMS culture can play a role in management and conservation by supplementing and diversifying the fishing and collecting livelihoods in the developing nations that provide the majority of the global OMS

A new approach to the chronology of caves 268/272/275 in the Dunhuang Mogao Grottoes: combining radiocarbon dates and archaeological information within a Bayesian statistical framework

The construction chronology of three of the earliest Dunhuang Mogao Grottoes (Caves 268, 272, and 275) has been the subject of ongoing debate for over half a century. This chronology is a crucial topic in terms of further understanding of the establishment of the Dunhuang Mogao Grottoes, early Buddhism in the Gansu corridor, and its relationship with Buddhism developed in the Central Plains. Building upon archaeological, art historical and radiocarbon (14C) dating studies, we integrate new 14C data with these previously published findings utilizing Bayesian statistical modeling to improve the chronological resolution of this issue. Thus, we determine that all three of these caves were constructed around AD 410–440, suggesting coeval rather than sequential construction