Amino acid classes and the protein folding problem

We present and implement a distance-based clustering of amino acids within the framework of a statistically derived interaction matrix and show that the resulting groups faithfully reproduce, for well-designed sequences, thermodynamic stability in and kinetic accessibility to the native state. A simple interpretation of the groups is obtained by eigenanalysis of the interaction matrix.Comment: REVTeX, 11 pages, 4 figures, To appear in J. Chem. Phy

SENSING AND INTERPRETATION TECHNIQUES

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72948/1/j.1749-6632.1966.tb50961.x.pd

POLLUTION SURVEILLANCE AND DATA ACQUISITION USING MULTISPECTRAL REMOTE SENSING 1

Large scale water resource investigations and effective pollution surveillance programs require the development of additional instrumentation and techniques to supplement existing methods of data acquisition. As a result, interest is growing in the concept of remote sensing. Described in this paper is the multispectral sensor concept and its application in water resource studies.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73841/1/j.1752-1688.1970.tb01651.x.pd

Procolipase gene : no association with early-onset obesity or fat intake

Copyright 2009 S. Karger AG, Basel.Peer reviewedPublisher PD

Macro material flow modeling for analyzing solid waste management options

A Macro Material Flow Modeling (MMFM) concept and approach are being adopted to develop a predictive modeling capability. This capability is intended to provide part of the basis for evaluating potential impacts from various solid waste management system configurations and operating scenarios, as well as evaluating the impacts of various policies on solid waste quantities and compositions. The MMFM capability, as part of a broader Solid Waste Initiative at Pacific Northwest Laboratory, is intended to provide an increased understanding of solid waste as a disposal, energy, and resource problem on a national and global scale, particularly over the long term. This model is a macro-level simulation of the flows of the various materials through the solid waste management system, and also through the associated materials production and use system. Inclusion of materials production and use within the modeling context allows a systems approach to be used, providing a much more complete understanding of the origins of the solid waste materials and also of possible options for materials recovery and reuse than if a more traditional end-of-pipe'' view of solid waste is adopted. The MMFM is expected to be useful in evaluating longer-term, broader-ranging solid waste impacts than are traditionally evaluated by decision-makers involved in implementing solutions to local or regional solid waste management problems. This paper discusses the types of questions of interest in evaluating long-term, broad-range impacts from solid waste. It then identifies the basic needs for predictive modeling capabilities like the MMFM, and provides a basic description of the conceptual framework for the model and the associated data. Status of the MMFM implementation is also discussed

Building financial management capacity for community ownership of development initiatives in rural Zambia

Background: Building financial management capacity is increasingly important in low- and middle-income countries to help communities take ownership of development activities. Yet, many community members lack financial knowledge and skills. Methods: As part of a larger health intervention, we designed and conducted financial management training for 83 members from 10 community groups in rural Zambia. Change scores between pre- and post-tests on financial knowledge were calculated and multivariate linear regression models run. Qualitative feedback was elicited. Results: The training significantly improved knowledge of financial concepts. Participants with some or more than some secondary education had greater improvements in knowledge (by 1.8 and 2.9 points out of 10 respectively; p=0.003 and p\u3c0.001). Participants appreciated exercises to contextualize financial concepts within daily life, and liked opportunities to learn from peers in small groups. Language barriers were a particular challenge. Conclusion: Financial management training may contribute to the sustainability of community-managed interventions but needs to be tailored to the background and education level of the participants. Training should relate financial concept to more tangible applications and provide time for active learning. This training approach could be used in similar settings to improve community oversight of resources intended to strengthen developmental initiatives

Application of Commercial Non-Dispersive Infrared Spectroscopy Sensors for Sub-Ambient Carbon Dioxide Detection

Monitoring carbon dioxide (CO2) concentration within a spacecraft or spacesuit is critically important to ensuring the safety of the crew. Carbon dioxide uniquely absorbs light at wavelengths of 3.95 micrometers and 4.26 micrometers. As a result, non-dispersive infrared (NDIR) spectroscopy can be employed as a reliable and inexpensive method for the quantification of CO2 within the atmosphere. A multitude of commercial-off-the-shelf (COTS) NDIR sensors exist for CO2 quantification. The COTS sensors provide reasonable accuracy so long as the measurements are attained under conditions close to the calibration conditions of the sensor (typically 21.1 C and 1 atm). However, as pressure deviates from atmospheric to the pressures associated with a spacecraft (8.0-10.2 PSIA) or spacesuit (4.1-8.0 PSIA), the error in the measurement grows increasingly large. In addition to pressure and temperature dependencies, the infrared transmissivity through a volume of gas also depends on the composition of the gas. As the composition is not known a priori, accurate sub-ambient detection must rely on iterative sensor compensation techniques. This manuscript describes the development of recursive compensation algorithms for sub-ambient detection of CO2 with COTS NDIR sensors. In addition, the basis of the exponential loss in accuracy is developed theoretically considering thermal, Doppler, and Lorentz broadening effects which arise as a result of the temperature, pressure, and composition of the gas mixture under analysis. As a result, this manuscript provides an approach to employing COTS sensors at sub-ambient conditions and may also lend insight into designing future NDIR sensors for aerospace application

Peripheral blood marker of residual acute leukemia after hematopoietic cell transplantation using multi-plex digital droplet PCR

BACKGROUND Relapse remains the primary cause of death after hematopoietic cell transplantation (HCT) for acute leukemia. The ability to identify minimal/measurable residual disease (MRD) via the blood could identify patients earlier when immunologic interventions may be more successful. We evaluated a new test that could quantify blood tumor mRNA as leukemia MRD surveillance using droplet digital PCR (ddPCR). METHODS The multiplex ddPCR assay was developed using tumor cell lines positive for the tumor associated antigens (TAA: WT1, PRAME, BIRC5), with homeostatic ABL1. On IRB-approved protocols, RNA was isolated from mononuclear cells from acute leukemia patients after HCT (n = 31 subjects; n = 91 specimens) and healthy donors (n = 20). ddPCR simultaneously quantitated mRNA expression of WT1, PRAME, BIRC5, and ABL1 and the TAA/ABL1 blood ratio was measured in patients with and without active leukemia after HCT. RESULTS Tumor cell lines confirmed quantitation of TAAs. In patients with active acute leukemia after HCT (MRD+ or relapse; n=19), the blood levels of WT1/ABL1, PRAME/ABL1, and BIRC5/ABL1 exceeded healthy donors (p<0.0001, p=0.0286, and p=0.0064 respectively). Active disease status was associated with TAA positivity (1+ TAA vs 0 TAA) with an odds ratio=10.67, (p=0.0070, 95% confidence interval 1.91 - 59.62). The area under the curve is 0.7544. Changes in ddPCR correlated with disease response captured on standard of care tests, accurately denoting positive or negative disease burden in 15/16 (95%). Of patients with MRD+ or relapsed leukemia after HCT, 84% were positive for at least one TAA/ABL1 in the peripheral blood. In summary, we have developed a new method for blood MRD monitoring of leukemia after HCT and present preliminary data that the TAA/ABL1 ratio may may serve as a novel surrogate biomarker for relapse of acute leukemia after HCT

Weak pairwise correlations imply strongly correlated network states in a neural population

Biological networks have so many possible states that exhaustive sampling is impossible. Successful analysis thus depends on simplifying hypotheses, but experiments on many systems hint that complicated, higher order interactions among large groups of elements play an important role. In the vertebrate retina, we show that weak correlations between pairs of neurons coexist with strongly collective behavior in the responses of ten or more neurons. Surprisingly, we find that this collective behavior is described quantitatively by models that capture the observed pairwise correlations but assume no higher order interactions. These maximum entropy models are equivalent to Ising models, and predict that larger networks are completely dominated by correlation effects. This suggests that the neural code has associative or error-correcting properties, and we provide preliminary evidence for such behavior. As a first test for the generality of these ideas, we show that similar results are obtained from networks of cultured cortical neurons.Comment: Full account of work presented at the conference on Computational and Systems Neuroscience (COSYNE), 17-20 March 2005, in Salt Lake City, Utah (http://cosyne.org

Disorder-to-order transition in the magnetic and electronic properties of URh_2Ge_2

We present a study of annealing effects on the physical properties of tetragonal single--crystalline URh_2Ge_2. This system, which in as-grown form was recently established as the first metallic 3D random-bond heavy-fermion spin glass, is transformed by an annealing treatment into a long-range antiferromagnetically (AFM) ordered heavy-fermion compound. The transport properties, which in the as-grown material were dominated by the structural disorder, exhibit in the annealed material signs of typical metallic behavior along the crystallographic a axis. From our study URh_2Ge_2 emerges as exemplary material highlighting the role and relevance of structural disorder for the properties of strongly correlated electron systems. We discuss the link between the magnetic and electronic behavior and how they are affected by the structural disorder.Comment: Phys. Rev. B, in print (scheduled 1 Mar 2000