Specific protein-protein binding in many-component mixtures of proteins

Proteins must bind to specific other proteins in vivo in order to function. The proteins must bind only to one or a few other proteins of the of order a thousand proteins typically present in vivo. Using a simple model of a protein, specific binding in many component mixtures is studied. It is found to be a demanding function in the sense that it demands that the binding sites of the proteins be encoded by long sequences of bits, and the requirement for specific binding then strongly constrains these sequences. This is quantified by the capacity of proteins of a given size (sequence length), which is the maximum number of specific-binding interactions possible in a mixture. This calculation of the maximum number possible is in the same spirit as the work of Shannon and others on the maximum rate of communication through noisy channels.Comment: 13 pages, 3 figures (changes for v2 mainly notational - to be more in line with notation in information theory literature

Concreteness and word production

Two experiments are reported that investigated the effect of concreteness on the ability to generate words to fit sentence contexts. When participants attempted to retrieve words from dictionary definitions in Experiment 1, abstract words were associated with more omissions and more alternates than were concrete words. These findings are consistent with the view that the semantic-lexical weights in the word production system are weaker for abstract than for concrete words. We found no evidence that greater competition from semantic neighbors was an additional reason why abstract words were harder to produce. Participants also reported more positive tip-of-the-tongue states (TOTs) when attempting to produce abstract words from their definitions, consistent with more phonological retrieval problems for abstract than for concrete words. In Experiment 2, participants attempted to generate words to fit into a sentence that described a specific event. The difference between the numbers of abstract and concrete words recalled was significantly smaller in the event condition than in the definition condition, and evidence no longer emerged of greater phonological retrieval failure for abstract words. Overall, the results are consistent with the view that the semantic-lexical weights, but not the lexical-phonological weights, are weaker for abstract than for concrete words in the word production system. © 2012 Psychonomic Society, Inc

Fiscal Year 2006

The status of groundwater level monitoring at Los Alamos National Laboratory in Fiscal Year 2006 is provided in this report. The Groundwater Level Monitoring Project was instituted in 2005 for providing a framework for the collection and processing of quality controlled groundwater level data. This report summarizes groundwater level data for 158 monitoring wells, including 43 regional aquifer wells, 23 intermediate wells, and 92 alluvial wells. Pressure transducers were installed in 132 monitoring wells for continuous monitoring of groundwater levels. Time-series hydrographs of groundwater level data are presented along with pertinent construction and location information for each well

Groundwater Level Status Report for Fiscal Year 2007 - Los Alamos National Laboratory

The status of groundwater level monitoring at Los Alamos National Laboratory in Fiscal Year 2007 is provided in this report. The Groundwater Level Monitoring Project was instituted in 2005 to provide a framework for the collection and processing of quality controlled groundwater level data. This report summarizes groundwater level data for 166 monitoring wells, including 45 regional aquifer wells, 25 intermediate wells, and 96 alluvial wells, and 11 water supply wells. Pressure transducers were installed in 133 monitoring wells for continuous monitoring of groundwater levels. Time-series hydrographs of groundwater level data are presented along with pertinent construction and location information for each well

Schumacher's quantum data compression as a quantum computation

An explicit algorithm for performing Schumacher's noiseless compression of quantum bits is given. This algorithm is based on a combinatorial expression for a particular bijection among binary strings. The algorithm, which adheres to the rules of reversible programming, is expressed in a high-level pseudocode language. It is implemented using $O(n^3)$ two- and three-bit primitive reversible operations, where $n$ is the length of the qubit strings to be compressed. Also, the algorithm makes use of $O(n)$ auxiliary qubits; however, space-saving techniques based on those proposed by Bennett are developed which reduce this workspace to $O(\sqrt{n})$ while increasing the running time by less than a factor of two.Comment: 37 pages, no figure

Relationship of Objectively-Measured Habitual Physical Activity to Chronic Inflammation and Fatigue in Middle-Aged and Older Adults

Habitual (non-exercise) physical activity (PA) declines with age, and aging-related increases in inflammation and fatigue may be important contributors to variability in PA

Revision of Madagascar's Dwarf Lemurs (Cheirogaleidae:Cheirogaleus): Designation of Species, Candidate Species Status and Geographic Boundaries Based on Molecular and Morphological Data

The genus Cheirogaleus, the dwarf lemurs, is a radiation of strepsirrhine primates endemic to the island of Madagascar. The dwarf lemurs are taxonomically grouped in the family Cheirogaleidae (Infraorder: Lemuriformes) along with the genera Microcebus, Mirza, Allocebus, and Phaner. The taxonomic history of the genus Cheirogaleus has been controversial since its inception due to a paucity of evidence in support of some proposed species. In this study, we addressed this issue by expanding the geographic breadth of samples by 91 individuals and built upon existing mitochondrial (cytb and COII) and nuclear (FIBA and vWF) DNA datasets to better resolve the phylogeny of Cheirogaleus. The mitochondrial gene fragments D-loop and PAST as well as the CFTR-PAIRB nuclear loci were also sequenced. In agreement with previous genetic studies, numerous deep divergences were resolved in the C. major, C. minor and C. medius lineages. Four of these lineages were segregated as new species, seven were identified as confirmed candidate species, and four were designated as unconfirmed candidate species based on comparative mitochondrial DNA sequence data gleaned from the literature or this study. Additionally, C. thomasi was resurrected. Given the widespread distribution of the genus Cheirogaleus throughout Madagascar, the methodology employed in this study combined all available lines of evidence to standardize investigative procedures in a genus with limited access to type material and a lack of comprehensive sampling across its total distribution. Our results highlighted lineages that likely represent new species and identified localities that may harbor an as-yet undescribed cryptic species diversity pending further field and laboratory work.We are most grateful to the Ahmanson Foundation, the Theodore F. and Claire M. Hubbard Family Foundation, the Primate Action Fund / Conservation International, the Margot Marsh Biodiversity Foundation, and the National Geographic Society, for financial assistance

PPAR γ

The resolution of inflammation is an active and dynamic process, mediated in large part by the innate immune system. Resolution represents not only an increase in anti-inflammatory actions, but also a paradigm shift in immune cell function to restore homeostasis. PPARγ, a ligand activated transcription factor, has long been studied for its anti-inflammatory actions, but an emerging body of literature is investigating the role of PPARγ and its ligands (including thiazolidinediones, prostaglandins, and oleanolic acids) in all phases of resolution. PPARγ can shift production from pro- to anti-inflammatory mediators by neutrophils, platelets, and macrophages. PPARγ and its ligands further modulate platelet and neutrophil function, decreasing trafficking, promoting neutrophil apoptosis, and preventing platelet-leukocyte interactions. PPARγ alters macrophage trafficking, increases efferocytosis and phagocytosis, and promotes alternative M2 macrophage activation. There are also roles for this receptor in the adaptive immune response, particularly regarding B cells. These effects contribute towards the attenuation of multiple disease states, including COPD, colitis, Alzheimer’s disease, and obesity in animal models. Finally, novel specialized proresolving mediators—eicosanoids with critical roles in resolution—may act through PPARγ modulation to promote resolution, providing another exciting area of therapeutic potential for this receptor