Calculation of model Hamiltonian parameters for LaMnO_3 using maximally localized Wannier functions

Maximally localized Wannier functions (MLWFs) based on Kohn-Sham band-structures provide a systematic way to construct realistic, materials specific tight-binding models for further theoretical analysis. Here, we construct MLWFs for the Mn e_g bands in LaMnO_3, and we monitor changes in the MLWF matrix elements induced by different magnetic configurations and structural distortions. From this we obtain values for the local Jahn-Teller and Hund's rule coupling strength, the hopping amplitudes between all nearest and further neighbors, and the corresponding reduction due to the GdFeO_3-type distortion. By comparing our results with commonly used model Hamiltonians for manganites, where electrons can hop between two "e_g-like" orbitals located on each Mn site, we find that the most crucial limitation of such models stems from neglecting changes in the underlying Mn(d)-O(p) hybridization.Comment: 15 pages, 11 figures, 3 table

Transcriptional and conformational changes of the tau molecule in Alzheimer's disease

Mutations in the tau gene cause frontotemporal dementia with parkinsonism, presumably by affecting the balance between tau isoforms (with either three or four microtubule-binding repeats) or by impairing tau-tubulin binding. Although to date no mutations have been found for Alzheimer's disease, it is plausible that tangle pathology in this disorder is also driven by similar molecular modifications. Investigations of Alzheimer brain tissue with new technologies such as laser capture microscopy, quantitative PCR and fluorescence lifetime imaging will shed light on whether transcriptional or conformational alterations play a role in Alzheimer pathogenesis

Final Report: Efficient Databases for MPC Microdata

The purpose of this grant was to develop the theory and practice of high-performance databases for massive streamed datasets. Over the last three years, we have developed fast indexing technology, that is, technology for rapidly ingesting data and storing that data so that it can be efficiently queried and analyzed. During this project we developed the technology so that high-bandwidth data streams can be indexed and queried efficiently. Our technology has been proven to work data sets composed of tens of billions of rows when the data streams arrives at over 40,000 rows per second. We achieved these numbers even on a single disk driven by two cores. Our work comprised (1) new write-optimized data structures with better asymptotic complexity than traditional structures, (2) implementation, and (3) benchmarking. We furthermore developed a prototype of TokuFS, a middleware layer that can handle microdata I/O packaged up in an MPI-IO abstraction

The Near-Infrared Broad Emission Line Region of Active Galactic Nuclei -- I. The Observations

We present high quality (high signal-to-noise ratio and moderate spectral resolution) near-infrared (near-IR) spectroscopic observations of 23 well-known broad-emission line active galactic nuclei (AGN). Additionally, we obtained simultaneous (within two months) optical spectroscopy of similar quality. The near-IR broad emission line spectrum of AGN is dominated by permitted transitions of hydrogen, helium, oxygen, and calcium, and by the rich spectrum of singly-ionized iron. In this paper we present the spectra, line identifications and measurements, and address briefly some of the important issues regarding the physics of AGN broad emission line regions. In particular, we investigate the excitation mechanism of neutral oxygen and confront for the first time theoretical predictions of the near-IR iron emission spectrum with observations.Comment: 45 pages, 17 figures, accepted by ApJ

Don't Thrash: How to Cache Your Hash on Flash

This paper presents new alternatives to the well-known Bloom filter data structure. The Bloom filter, a compact data structure supporting set insertion and membership queries, has found wide application in databases, storage systems, and networks. Because the Bloom filter performs frequent random reads and writes, it is used almost exclusively in RAM, limiting the size of the sets it can represent. This paper first describes the quotient filter, which supports the basic operations of the Bloom filter, achieving roughly comparable performance in terms of space and time, but with better data locality. Operations on the quotient filter require only a small number of contiguous accesses. The quotient filter has other advantages over the Bloom filter: it supports deletions, it can be dynamically resized, and two quotient filters can be efficiently merged. The paper then gives two data structures, the buffered quotient filter and the cascade filter, which exploit the quotient filter advantages and thus serve as SSD-optimized alternatives to the Bloom filter. The cascade filter has better asymptotic I/O performance than the buffered quotient filter, but the buffered quotient filter outperforms the cascade filter on small to medium data sets. Both data structures significantly outperform recently-proposed SSD-optimized Bloom filter variants, such as the elevator Bloom filter, buffered Bloom filter, and forest-structured Bloom filter. In experiments, the cascade filter and buffered quotient filter performed insertions 8.6-11 times faster than the fastest Bloom filter variant and performed lookups 0.94-2.56 times faster.Comment: VLDB201

Hyaluronan concentration and size distribution in human knee synovial fluid: variations with age and cartilage degeneration.

BackgroundOne potential mechanism for early superficial cartilage wear in normal joints is alteration of the lubricant content and quality of synovial fluid. The purpose of this study was to determine if the concentration and quality of the lubricant, hyaluronan, in synovial fluid: (1) was similar in left and right knees; (2) exhibited similar age-associated trends, whether collected postmortem or antemortem; and (3) varied with age and grade of joint degeneration.MethodsHuman synovial fluid of donors (23-91 years) without osteoarthritis was analyzed for the concentrations of protein, hyaluronan, and hyaluronan in the molecular weight ranges of 2.5-7 MDa, 1-2.5 MDa, 0.5-1 MDa, and 0.03-0.5 MDa. Similarity of data between left and right knees was assessed by reduced major axis regression, paired t-test, and Bland-Altman analysis. The effect of antemortem versus postmortem collection on biochemical properties was assessed for age-matched samples by unpaired t-test. The relationships between age, joint grade, and each biochemical component were assessed by regression analysis.ResultsJoint grade and the concentrations of protein, hyaluronan, and hyaluronan in the molecular weight ranges of 2.5-7 MDa, 1-2.5 MDa, and 0.5-1 MDa in human synovial fluid showed good agreement between left and right knees and were similar between age-matched patient and cadaver knee joints. There was an age-associated decrease in overall joint grade (-15 %/decade) and concentrations of hyaluronan (-10.5 %/decade), and hyaluronan in the molecular weight ranges of 2.5-7 MDa (-9.4 %/decade), 1-2.5 MDa (-11.3 %/decade), 0.5-1 MDa (-12.5 %/decade), and 0.03-0.5 MDa (-13.0 %/decade). Hyaluronan concentration and quality was more strongly associated with age than with joint grade.ConclusionsThe age-related increase in cartilage wear in non-osteoarthritic joints may be related to the altered hyaluronan content and quality of synovial fluid

Selective incorporation of proteinaceous over nonproteinaceous cationic amino acids in model prebiotic oligomerization reactions.

Numerous long-standing questions in origins-of-life research center on the history of biopolymers. For example, how and why did nature select the polypeptide backbone and proteinaceous side chains? Depsipeptides, containing both ester and amide linkages, have been proposed as ancestors of polypeptides. In this paper, we investigate cationic depsipeptides that form under mild dry-down reactions. We compare the oligomerization of various cationic amino acids, including the cationic proteinaceous amino acids (lysine, Lys; arginine, Arg; and histidine, His), along with nonproteinaceous analogs of Lys harboring fewer methylene groups in their side chains. These analogs, which have been discussed as potential prebiotic alternatives to Lys, are ornithine, 2,4-diaminobutyric acid, and 2,3-diaminopropionic acid (Orn, Dab, and Dpr). We observe that the proteinaceous amino acids condense more extensively than these nonproteinaceous amino acids. Orn and Dab readily cyclize into lactams, while Dab and Dpr condense less efficiently. Furthermore, the proteinaceous amino acids exhibit more selective oligomerization through their α-amines relative to their side-chain groups. This selectivity results in predominantly linear depsipeptides in which the amino acids are α-amine-linked, analogous to today's proteins. These results suggest a chemical basis for the selection of Lys, Arg, and His over other cationic amino acids for incorporation into proto-proteins on the early Earth. Given that electrostatics are key elements of protein-RNA and protein-DNA interactions in extant life, we hypothesize that cationic side chains incorporated into proto-peptides, as reported in this study, served in a variety of functions with ancestral nucleic acid polymers in the early stages of life

Validity of Electronic Prescription Claims Records: A Comparison of Commercial Insurance Claims with Pharmacy Provider Derived Records

Objectives: To determine if and to what extent records obtained from PBM pharmacy claims differ from source documents obtained directly from pharmacy providers. This study also sought to explore possible associations between patient, pharmacy benefits, and pharmacy provider characteristics and the likelihood a patient would have missing prescription claims. Methods: This study used a cross-sectional design which included a sample of 1,484 patients residing in a single state with a common pharmacy benefit. Profiles describing all prescriptions filled in a pharmacy between January 1, 2002 through June 30, 2002 of these patients were requested directly from their pharmacy providers. Logistic regression was used to explore the factors associated with a person receiving a prescription that did not appear on the PBM claims. Results: Of the 1,484 eligible recipients sampled, profiles were obtained for 323 (22%) persons and there were analyzable profiles for 315 (21%) persons. There were a total of 2,977 prescriptions filled for the 315 subjects. Of those 2,977 prescriptions, 207 (7.0%) were missing from the claims files indicating that 93% were captured. Only prescription volume consistently influenced the likelihood a patient would have a missing prescription from the PBM claims (OR =1.08; 95%CI:1.05-1.12). Conclusion: Claims obtained from pharmacy benefit companies capture approximately 93% of prescription records when verified with records obtained from pharmacy providers. The rate of missing records from PBM claims does not appear to be meaningfully influenced by most finance based pharmacy benefit design features. However, certain classes of drugs such as iron products, digoxins, diuretics, sulfonylureas, and antigout may have incomplete claims records compared to other classes of drugs. Higher prescription utilizers are more likely to have prescription records filled that are not captured by PBMs. These conclusions should be interpreted in light of the modest usable response rate from pharmacy providers of 22% and the unknown generalizability of these patients utilizing one particular PBM from 2002 in the state of Georgia

A Search for Scalar Chameleons with ADMX

Scalar fields with a "chameleon" property, in which the effective particle mass is a function of its local environment, are common to many theories beyond the standard model and could be responsible for dark energy. If these fields couple weakly to the photon, they could be detectable through the "afterglow" effect of photon-chameleon-photon transitions. The ADMX experiment was used in the first chameleon search with a microwave cavity to set a new limit on scalar chameleon-photon coupling excluding values between 2*10^9 and 5*10^14 for effective chameleon masses between 1.9510 and 1.9525 micro-eV.Comment: 4 pages, 3 figure