A generalized Monte Carlo loop algorithm for frustrated Ising models

We introduce a Generalized Loop Move (GLM) update for Monte Carlo simulations of frustrated Ising models on two-dimensional lattices with bond-sharing plaquettes. The GLM updates are designed to enhance Monte Carlo sampling efficiency when the system's low-energy states consist of an extensive number of degenerate or near-degenerate spin configurations, separated by large energy barriers to single spin flips. Through implementation on several frustrated Ising models, we demonstrate the effectiveness of the GLM updates in cases where both degenerate and near-degenerate sets of configurations are favored at low temperatures. The GLM update's potential to be straightforwardly extended to different lattices and spin interactions allow it to be readily adopted on many other frustrated Ising models of physical relevance.Comment: 14 pages, 12 figure

Archeological Survey Of The Proposed State Highway 288 Access Road Bridges, In Harris And Brazoria Counties, Texas

On February 22, 2005 a crew from Moore Archeological Consulting, Inc. performed a shovel test survey of the proposed State Highway 288 Access Road Bridges Project in Harris and Brazoria Counties, Texas. This was performed for S&B Infrastructure and the Texas Department of Transportation (TxDOT) under Antiquities Permit Number 3681. The results will be subject to review by TxDOT, S&B and the Texas Historical Commission. A total of 10 shovel tests were excavated in the Project Area which totaled approximately 2 acres. The Project Corridor was entirely within the existing, state-owned, right-of-way. No prehistoric or historic resources or features were found. The soils in all ten shovel tests were observed to contain disturbed and/or fill soils over truncated natural soils. All but one shovel test reached basal clay subsoils. No artifacts were observed or recovered. The recommendation of Moore Archeological Consulting is that this project should be allowed to proceed without further investigation

Competitive titration in living sea urchin embryos of regulatory factors required for expression of the CyIIIa actin gene

Previous studies have located some twenty distinct sites within the 2.3 kb 5' regulatory domain of the sea urchin CyIIIa cytoskeletal actin gene, where there occur in vitro high-specificity interactions with nuclear DNA-binding proteins of the embryo. This gene is activated in late cleavage, exclusively in cells of the aboral ectoderm cell lineages. In this study, we investigate the functional importance in vivo of these sites of DNA-protein interaction. Sea urchin eggs were coinjected with a fusion gene construct in which the bacterial chloramphenicol acetyltransferase (CAT) reporter gene is under the control of the entire CyIIIa regulatory domain, together with molar excesses of one of ten nonoverlapping competitor subfragments of this domain, each of which contains one or a few specific site(s) of interaction. The exogenous excess binding sites competitively titrate the available regulatory factors away from the respective sites associated with the CyIIIa.CAT reporter gene. This provides a method for detecting in vivo sites within the regulatory domain that are required for normal levels of expression, without disturbing the structure of the regulatory domain. We thus identify five nonoverlapping regions of the regulatory DNA that apparently function as binding sites for positively acting transcriptional regulatory factors. Competition with a subfragment bearing an octamer site results in embryonic lethality. We find that three other sites display no quantitative competitive interference with CyIIIa.CAT expression, though as shown in the accompanying paper, two of these sites are required for control of spatial expression. We conclude that the complex CyIIIa regulatory domain must assess the state of many distinct and individually necessary interactions in order to properly regulate CyIIIa transcriptional activity in development

Testing and Data Recovery Excavations at Prehistoric Occupation Site 41HR1114, Harris County, Texas

This report documents the National Register significance testing and data recovery investigations conducted from February 27-March 15, 2012 (testing), and June 11-25, 2012 (data recovery), at the site of 41HR1114 by Moore Archeological Consulting, Inc. The site is located just west of Lower Mayde Creek, in west Harris County, Texas. The site had been first located during a February, 2012 survey conducted by Moore Archeological Consulting, Inc. in preparation for a proposed extension of the Park Row Boulevard Right-of-Way (Moore and Driver 2012). The survey alignment was privately owned at the time of the survey, and therefore, neither the Antiquities Code of Texas nor Section 106 of the National Historic Preservation Act of 1966 mandated the survey. However, the survey was carried out as proactive due diligence as a key element of the future regulatory requirements for a private development project on an ambitious development schedule. The survey identified three sites, 41HR1114, 41HR1115, and 41HR1116. Significance testing excavations at 41HR1114 were conducted in February and March, 2012, and were also carried out as proactive due diligence. The test excavations consisted of hand excavation and backhoe trenching with a focus on geomorphological assessment of the site, including the depositional reconstruction and identification of the degree of intactness of the deposits. These investigations determined that the site possessed the potential for future research, and should be considered eligible for listing on the National Register of Historic Places (NRHP). At that point, the development project was subsumed within the Harris County Improvement District No. 4, DBA Energy Corridor Management District, and further investigations fell under the jurisdiction of the Texas Historic Commission (THC) permitting process. To facilitate planned development schedules, the proposed Park Row Boulevard Right-of-Way alignment was divided into smaller segments, with 41HR1114 located in the Phase 1 segment. This portion of the alignment measures approximately 850 m (2800 ft) in length, and the area of potential effect (APE) in the area of 41HR1114 is limited to a 36.5 m (120 ft) wide ROW (Figure 1). The data recovery investigations at 41HR1114 were conducted under Texas Antiquities Permit Number 6274. During the significance testing and data recovery field investigations at 41HR1114, a total of sixteen 1 x 1 m hand units (XU 1-16) were excavated. XUs 1-4 were conducted as distinct 1 x 1 m units (XUs 1, 2, and 4 were placed adjacent to backhoe trenches) during the testing phase, while the remainder of the hand excavations were conducted as two 2 x 3 m block excavations (subdivided into XUs 5-10 and 11-16) as part of the data recovery phase. Three backhoe trenches (BHTs 1-3) totaling 45 m in length were excavated, two during the testing phase and one during the data recovery operations. The excavations produced a total of 4431 artifacts. These materials were recovered from Levels 1-14 (0-150 cmbs), but with the highest concentrations of artifacts encountered in Levels 3-7. The chronologically diagnostic dart point types, in conjunction with the presence of ceramics and the lack of arrow points, indicate occupations at the site spanning the Middle Archaic to Early Ceramic periods. However, the vertical distribution of diagnostic artifacts and the geoarchaeological assessment of the site deposits indicate the presence of significant bioturbation-related disturbance of cultural materials located throughout the site. Consequently, the real, and quite significant contribution of this project is instead, the intensive geoarcheological analysis of the Late Pleistocene and Early Holocene alluvium and of the nature and appearance of soil formation within such deposits at the site, and by extension for the Houston area. The current investigation has considerably diminished the paucity of information on the deposits lain down by small streams in the region, as well as provided insight into the pedogenic processes associated with argillic horizons in the late Pleistocene and Holocene soils of Southeast Texas. We may conclude by reiterating that the Data Recovery excavations at 41HR1114 were successful in providing new information on the prehistory of the site and the broader Houston region. The contribution from the strictly archeological analysis of the cultural materials and contexts yielded by the site are modest. In contrast, the results of the intensive geoarcheological analysis of the site are quite novel and important, and have considerable broader application in the future analysis and evaluation of prehistoric sites within the Houston region. No further archeological work is recommended for 41HR1114. Once the current report is finalized, the artifacts recovered from 41HR1114 will be curated at TARL

The Catalytic Machinery of a Key Enzyme in Amino Acid Biosynthesis

The aspartate pathway of amino acid biosynthesis is essential for all microbial life but is absent in mammals. Characterizing the enzyme-catalyzed reactions in this pathway can identify new protein targets for the development of antibiotics with unique modes of action. The enzyme aspartate β-semialdehyde dehydrogenase (ASADH) catalyzes an early branch point reaction in the aspartate pathway. Kinetic, mutagenic, and structural studies of ASADH from various microbial species have been used to elucidate mechanistic details and to identify essential amino acids involved in substrate binding, catalysis, and enzyme regulation. Important structural and functional differences have been found between ASADHs isolated from these bacterial and fungal organisms, opening the possibility for developing species-specific antimicrobial agents that target this family of enzymes

Loss of the melanocortin-4 receptor in mice causes dilated cardiomyopathy.

Haploinsufficiency of the melanocortin-4 receptor, the most common monogenetic obesity syndrome in humans, is associated with a reduction in autonomic tone, bradycardia, and incidence of obesity-associated hypertension. Thus, it has been assumed that melanocortin obesity syndrome may be protective with respect to obesity-associated cardiovascular disease. We show here that absence of the melanocortin-4 receptor (MC4R) in mice causes dilated cardiomyopathy, characterized by reduced contractility and increased left ventricular diameter. This cardiomyopathy is independent of obesity as weight matched diet induced obese mice do not display systolic dysfunction. Mc4r cardiomyopathy is characterized by ultrastructural changes in mitochondrial morphology and cardiomyocyte disorganization. Remarkably, testing of myocardial tissue from Mc4r-/- mice exhibited increased ADP stimulated respiratory capacity. However, this increase in respiration correlates with increased reactive oxygen species production - a canonical mediator of tissue damage. Together this study identifies MC4R deletion as a novel and potentially clinically important cause of heart failure

Publishing and sharing multi-dimensional image data with OMERO

Imaging data are used in the life and biomedical sciences to measure the molecular and structural composition and dynamics of cells, tissues, and organisms. Datasets range in size from megabytes to terabytes and usually contain a combination of binary pixel data and metadata that describe the acquisition process and any derived results. The OMERO image data management platform allows users to securely share image datasets according to specific permissions levels: data can be held privately, shared with a set of colleagues, or made available via a public URL. Users control access by assigning data to specific Groups with defined membership and access rights. OMERO’s Permission system supports simple data sharing in a lab, collaborative data analysis, and even teaching environments. OMERO software is open source and released by the OME Consortium at www.openmicroscopy.org

The population pharmacokinetics of theophylline in neonates and young infants

The population pharmacokinetics of theophylline were evaluated using 391 theophylline serum concentration measurements from 108 neonates and young infants (postnatal age 0–26 weeks), who received theophylline for the treatment of neonatal apnea. A one-compartment pharmacokinetic model with first-order elimination was used, with intravenous aminophylline and oral theophylline administration modeled as zero-order infusions. The effect of a variety of developmental and demographic factors on clearance (CL) and volume (V) were investigated. Hypothesis testing to evaluate potentially significant factors produced a final model in which clearance was based on weight (kg) raised to an exponential power and postnatal age (weeks), with CL (ml/hr)=17.5 (weight) 1.28 + 1.17 (postnatal age). Clearance was reduced by 12% for patients receiving parenteral nutrition. Volume of distribution in this population was adequately described using only weight, with V (L)=0.858 L/kg. Bioavailability of orally administered drug was not significantly less than unity. Interindividual variability in clearance was modest, with a coefficient of variation for clearance of 16%. An estimate of interindividual variability in volume could not be obtained. As a measure of residual variability in theophylline serum concentrations, the coefficients of variation for theophylline serum concentrations of 5.0, 10.0, and 13.0 mg/L were found to be approximately, 25, 12, and 9%, respectively. The identification of influential patient factors and the quantification of their influence on theophylline disposition allow for a priori estimates of theophylline pharmacokinetic parameters in these patients.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/45039/1/10928_2005_Article_BF01059087.pd