The Comparative Toxicogenomics Database (CTD).

The Mount Desert Island Biological Laboratory in Salsbury Cove, Maine, USA, is developing the Comparative Toxicogenomics Database (CTD), a community-supported genomic resource devoted to genes and proteins of human toxicologic significance. CTD will be the first publicly available database to a) provide annotated associations among genes, proteins, references, and toxic agents, with a focus on annotating data from aquatic and mammalian organisms; b) include nucleotide and protein sequences from diverse species; c) offer a range of analysis tools for customized comparative studies; and d) provide information to investigators on available molecular reagents. This combination of features will facilitate cross-species comparisons of toxicologically significant genes and proteins. These comparisons will promote understanding of molecular evolution, the significance of conserved sequences, the genetic basis of variable sensitivity to environmental agents, and the complex interactions between the environment and human health. CTD is currently under development, and the planned scope and functions of the database are described herein. The intent of this report is to invite community participation in the development of CTD to ensure that it will be a valuable resource for environmental health, molecular biology, and toxicology research

Response to First Course of Intensified Immunosuppression in Genetically-Stratified Steroid Resistant Nephrotic Syndrome

BACKGROUND AND OBJECTIVES: Intensified immunosuppression in steroid-resistant nephrotic syndrome is broadly applied, with disparate outcomes. This review of patients from the United Kingdom National Study of Nephrotic Syndrome cohort aimed to improve disease stratification by determining, in comprehensively genetically screened patients with steroid-resistant nephrotic syndrome, if there is an association between response to initial intensified immunosuppression and disease progression and/or post-transplant recurrence. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS: Pediatric patients with steroid-resistant nephrotic syndrome were recruited via the UK National Registry of Rare Kidney Diseases. All patients were whole-genome sequenced, whole-exome sequenced, or steroid-resistant nephrotic syndrome gene-panel sequenced. Complete response or partial response within 6 months of starting intensified immunosuppression was ascertained using laboratory data. Response to intensified immunosuppression and outcomes were analyzed according to genetic testing results, pattern of steroid resistance, and first biopsy findings. RESULTS: Of 271 patients, 178 (92 males, median onset age 4.7 years) received intensified immunosuppression with response available. A total of 4% of patients with monogenic disease showed complete response, compared with 25% of genetic-testing-negative patients (P=0.02). None of the former recurred post-transplantation. In genetic-testing-negative patients, 97% with complete response to first intensified immunosuppression did not progress, whereas 44% of nonresponders developed kidney failure with 73% recurrence post-transplant. Secondary steroid resistance had a higher complete response rate than primary/presumed resistance (43% versus 23%; P=0.001). The highest complete response rate in secondary steroid resistance was to rituximab (64%). Biopsy results showed no correlation with intensified immunosuppression response or outcome. CONCLUSIONS: Patients with monogenic steroid-resistant nephrotic syndrome had a poor therapeutic response and no post-transplant recurrence. In genetic-testing-negative patients, there was an association between response to first intensified immunosuppression and long-term outcome. Patients with complete response rarely progressed to kidney failure, whereas nonresponders had poor kidney survival and a high post-transplant recurrence rate. Patients with secondary steroid resistance were more likely to respond, particularly to rituximab

CITRIC: A low-bandwidth wireless camera network platform

In this paper, we propose and demonstrate a novel wireless camera network system, called CITRIC. The core component of this system is a new hardware platform that integrates a camera, a frequency-scalable (up to 624 MHz) CPU, 16 MB FLASH, and 64 MB RAM onto a single device. The device then connects with a standard sensor network mote to form a camera mote. The design enables in-network processing of images to reduce communication requirements, which has traditionally been high in existing camera networks with centralized processing. We also propose a back-end client/server architecture to provide a user interface to the system and support further centralized processing for higher-level applications. Our camera mote enables a wider variety of distributed pattern recognition applications than traditional platforms because it provides more computing power and tighter integration of physical components while still consuming relatively little power. Furthermore, the mote easily integrates with existing low-bandwidth sensor networks because it can communicate over the IEEE 802.15.4 protocol with other sensor network platforms. We demonstrate our system on three applications: image compression, target tracking, and camera localization

Esrrb Is a Direct Nanog Target Gene that Can Substitute for Nanog Function in Pluripotent Cells

SummaryEmbryonic stem cell (ESC) self-renewal efficiency is determined by the level of Nanog expression. However, the mechanisms by which Nanog functions remain unclear, and in particular, direct Nanog target genes are uncharacterized. Here we investigate ESCs expressing different Nanog levels and Nanog−/− cells with distinct functionally inducible Nanog proteins to identify Nanog-responsive genes. Surprisingly, these constitute a minor fraction of genes that Nanog binds. Prominent among Nanog-reponsive genes is Estrogen-related receptor b (Esrrb). Nanog binds directly to Esrrb, enhances binding of RNAPolII, and stimulates Esrrb transcription. Overexpression of Esrrb in ESCs maintains cytokine-independent self-renewal and pluripotency. Remarkably, this activity is retained in Nanog−/− ESCs. Moreover, Esrrb can reprogram Nanog−/− EpiSCs and can rescue stalled reprogramming in Nanog−/− pre-iPSCs. Finally, Esrrb deletion abolishes the defining ability of Nanog to confer LIF-independent ESC self-renewal. These findings are consistent with the functional placement of Esrrb downstream of Nanog

High-pressure rheological analysis of CO2-induced melting point depression and viscosity reduction of poly(ε-caprolactone)

High-pressure rheology has been used to assess the effects of supercritical carbon dioxide (scCO2) on the melting point (Tm) and viscosity of poly (ε-caprolactone) (PCL) over a range of temperatures and pressures up to 300 bar over a wide range of shear rates. Plots of the storage and loss moduli against temperature show a significant shift of Tm to lower temperatures in the presence of CO2, indicating that the polymer crystals melt at temperatures much lower than the ambient pressure Tm. Furthermore, a significant decrease in the viscosity of two PCL grades with different molecular weight (Mn ~ 10 kDa and 80 kDa) was also detected upon increasing the CO2 pressure to 300 bar. Experimental viscosity data were fitted to the Carreau model to quantify the extent of the plasticising effects on the zero-shear viscosity and relaxation time under different conditions. Similar analyses were conducted under high-pressure nitrogen, to compare the effects obtained in the presence of a non-plasticising gas

Sustainable Food Systems At Urban Public Universities: A Survey Of U‐21 Universities

Urban communities are challenged by the conventional food system in diverse ways. To mitigate these challenges, a growing sustainable food system (SFS) movement mobilizes existing resources—including public institutions—to resolve disparities in access to healthy food, increase economic opportunities, conserve natural resources, and build a stronger, more local food system. Many public universities located in inner cities have adopted missions committing themselves to the improvement of their cities and regions. They also perform anchoring roles to revitalize their immediate neighborhoods, and, in a contemporary extension of their civic purposes, embrace sustainability as an institutional goal. Urban public universities therefore can play many SFS leadership roles, including through links to innovative scholarship, campus dining halls, other food retail such as farmers markets, and civic engagement activities such as community gardens. Through a study of 21 urban public universities, this paper investigates the presence and characteristics of SFS leadership, underlying rationales, and factors that support and oppose leadership.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/112274/1/juaf12149.pd

Identifying generalised segmental acceleration patterns that contribute to ground reaction force features across different running tasks

Objective: To support future developments of field-based biomechanical load monitoring tools, this study aimed to identify generalised segmental acceleration patterns and their contribution to ground reaction forces (GRFs) across different running tasks. Design: Exploratory experimental design. Methods: A multivariate principal component analysis (PCA) was applied to a combination of segmental acceleration data from all body segments for fifteen team-sport athletes performing accelerated, decelerated and constant low-, moderate- and high-speed running, and 90° cutting trials. Segmental acceleration profiles were then reconstructed from each principal component (PC) and used to calculate their specific GRF contributions. Results: The first PC explained 48.57% of the acceleration variability for all body segments and was primarily related to the between-task differences in the overall magnitude of the GRF impulse. Magnitude and timing of high-frequency acceleration and GRF features (i.e. impact related characteristics) were primarily explained by the second PC (12.43%) and also revealed important between-task differences. The most important GRF characteristics were explained by the first five PCs, while PCs beyond that primarily contained small contributions to the overall GRF impulse. Conclusions: These findings show that a multivariate PCA approach can reveal generalised acceleration patterns and specific segmental contributions to GRF features, but their relative importance for different running activities are task dependent. Using segmental acceleration to assess whole-body biomechanical loading generically across various movements may thus require task identification algorithms and/or advanced sensor or data fusion approaches

RFID: A Communication System Perspective

Thesis (Ph.D.)--University of Washington, 2014Backscatter modulation is the keystone behind the technical and commercial success of Radio Frequency IDentification (RFID) in applications that require fast, efficient, and automatic identification of tagged objects. Owing to RFID's ultra low cost and low power attributes, wireless sensor networks (WSNs) and other biological/physiological sensing applications now use backscatter modulation as a communication link. These systems build upon existing RFID industry protocols such as ISO 18000-6C (or EPC Gen2). RFID tags do not use an active RF transceiver architecture, but instead operate on a principle similar to RADAR. A nearby RFID reader transmits a continuous wave that the tag's antenna partially scatters back to the reader's antenna array. By switching its antenna impedance loading between different values, the tag modulates the antenna scattering observed by the reader. Therefore reverse engineering RFID at the systems level will provide new insights and design recommendations. This dissertation focuses on three key areas relating to backscatter modulation and RFID systems: 1) analyze the co-design of backscatter modulation and error correction coding, 2) characterize space-time coding and MIMO performance limits of the dyadic backscatter channel, and 3) hybrid-ARQ (HARQ) and random access improvements to the Gen2 protocol. Passive and semi-passive RFID tags depend on scavenged energy to power their IC. While backscatter modulation itself consumes a negligible amount of energy, the modulator creates an impedance mismatch between the tag's antenna and power harvester, thereby decreasing the antenna to the tag power transfer efficiency. This required impedance mismatch couples the link performance to the power harvester's performance, so to quantify this tradeoff, we introduce a new metric: backscatter power efficiency loss per bit. Higher order constellations improve the link's spectral efficiency, but have lower power efficiency as compared to binary modulation schemes. We propose new coded modulation schemes based on unequal error protection, which improves both the spectral efficiency and the backscatter power efficiency loss metric. MIMO processing is a canonical technique to improve wireless link capacity and reliability, which will require future tags and readers to have multiple antennas. The dyadic backscatter channel (DBC) models the behavior of small-scale fading in RFID MIMO systems, however, its statistics differ from those of the classic Rayleigh fading MIMO channel. We analytical characterize the performance of space-time trellis codes and orthogonal space-time block codes, derive an upper bound to the pairwise error probability (PEP), and derive the maximum diversity order of the DBC. Unlike Rayleigh fading, the diversity order only depends on the number of tag antennas but not the number of reader receive antennas. In fading channels, MIMO techniques offer two opposing performance gains: diversity (reliability against outage events) or multiplexing gain (spectral efficiency). The diversity multiplexing tradeoff (DMT) is an asymptotic measure that quantifies the achievable diversity for a given multiplexing gain. Starting from the definition of the DBC and the DMT of the double scattering channel, the corresponding DMT of the DBC is derived. The statistics of the DBC limit the amount diversity when compared to the Rayleigh MIMO channel, although the available multiplexing gain is unchanged. Increasing the number of receive antennas improves both diversity and multiplexing gain until the receive antenna count equals the number of tag antennas, otherwise additional receive antennas offer no gains with respect to the DMT. The current EPC Gen2 standard does not use any form of error correction and does not allow for fast link adaption between reading separate tags. We consider a protocol that uses HARQ algorithms without requiring major changes to the Gen2 protocol. In addition, we develop theoretical models that capture EPC Gen2's baseline performance and capacity in terms SNR and tag read rate. Existing HARQ algorithms, such as Chase combining (CC) and incremental redundancy (IR), are studied via simulations and the performance quantified in terms of tag read rate. The simulation results show that CC allows for graceful system degradation and IR achieves read rates close to EPC Gen2's capacity limit. Random access plays a critical role in RFID tag singulation. EPC Gen2 uses frame slotted ALOHA (FSA) to arbitrate channel resources between tags, but FSA has low efficiency due to empty slots and collisions. To aid in tag collision resolution, we consider multiuser detection (MUD) and incremental redundancy enhancements to the FSA protocol. The theoretical performance of the MUD receiver is analyzed from a compressive sensing viewpoint. As an example of a practical code construction, we evaluate the performance of punctured second order Reed Muller codes. These enhancements improve FSA's throughput and its response to high system loads

Attitudes about homelessness

This study looks at attitudes about homelessness. An online survey was administered gathering information about feelings and thoughts about homeless people, and the agencies that serve them

The Comparative Toxicogenomics Database: A Cross-Species Resource for Building Chemical-Gene Interaction Networks

Chemicals in the environment play a critical role in the etiology of many human diseases. Despite their prevalence, the molecular mechanisms of action and the effects of chemicals on susceptibility to disease are not well understood. To promote understanding of these mechanisms, the Comparative Toxicogenomics Database (CTD