cssi/SciSciGPT-SciSciNet huggingface dataset:
Diversity among Tacaribe serocomplex viruses (Family Arenaviridae) associated with the southern plains woodrat (Neotoma micropus).

The southern plains woodrat (Neotoma micropus) is the principal host of Catarina virus in southern Texas and a natural host of other North American Tacaribe serocomplex viruses. The objectives of this study were to increase our knowledge of the genetic diversity among Tacaribe serocomplex viruses associated with N. micropus and to define better the natural host relationships of these viruses. Pairwise comparisons of complete glycoprotein precursor gene sequences and complete nucleocapsid protein gene sequences revealed a high level of genetic diversity among Tacaribe serocomplex viruses associated with N. micropus in western Oklahoma, southern New Mexico, and northern and southern Texas. Collectively, the results of Bayesian analyses of nucleotide sequences and pairwise comparisons of amino acid sequences confirmed that the arenaviruses associated with N. micropus in Oklahoma and New Mexico should be included in the Whitewater Arroyo species complex, and indicated that that the arenaviruses associated with N. micropus in northern Texas are strains of a novel arenaviral species – tentatively named “Middle Pease River virus”. Together, the results of assays for arenavirus and assays for anti-arenavirus antibody in 54 southern plains woodrats and 325 other rodents captured at 2 localities suggested that the southern plains woodrat is the principal host of Middle Pease River virus in northern Texas.
Casein kinase II activity and polyamine-stimulated protein phosphorylation of cytosolic and plasma membrane proteins in bovine sperm.

Abstract A highly purified preparation of sperm cytosolic protein kinase was obtained by repeated chromatography with phosphocellulose. The preferred substrate of the enzyme was casein and the activity was not stimulated by added Ca 2+ , calmodulin, or cAMP. With casein as substrate, both ATP and GTP served as phosphate donors and the activity was inhibited by low micromolar heparin and stimulated by low millimolar spermine and spermidine. These properties are characteristic of casein kinase II from other cells. Endogenous protein substrates of the enzyme in sperm cytosolic fractions and in plasma membranes were demonstrated by incubating the preparations with [γ- 32 P]GTP, under conditions unfavorable to other protein kinases, and analyzing the products by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and autoradiography. Spermine greatly enhanced the phosphorylation of three (55, 92, and 106 kDa) proteins in both cytosolic and plasma membrane preparations. Our results indicate that polyamines play a role in modulating the phosphorylation state of proteins in sperm and may further regulate sperm function through this mechanism.
Sickle cell disease: time for a closer look at treatment options?

Summary Tremendous progress has been made in the care of individuals with sickle cell over the past several decades. Major successes have been comprehensive infection prophylaxis, prediction and prevention of stroke, and better transfusion care, the latter including both prevention of alloimmunization and treatment of iron overload. However, definitive therapies remain limited to hydroxycarbamide (hydroxyurea) and stem cell transplantation, both of which have been in use for at least two decades. Despite knowing the progressive natural history of the disease with organ dysfunction, failure, and ultimately death at a young age, definitive therapies are considered for only a small proportion of individuals. Consequently, while life expectancy has improved dramatically from the last century, the ongoing pace of advancement has slowed or stalled. We believe that it is time to broaden the use of definitive therapy for those with asymptomatic disease, being cautiously more aggressive in our approach.
Save the World on Your Own Time: Or, What’s the Matter with Sociology?

This essay explores the question of why sociology departments, compared to other university departments, are often viewed negatively by higher-level administrators (deans, provosts, chancellors and presidents). We are asked to consider, as sociologists, how departments are ranked and evaluated by administrators. The characteristics of any good university department are identified (e.g., grants, support from alumni, publications, quality of teaching, national rankings, student enrollments); and, the characteristics of dynamic and healthy departments are outlined (e.g., student learning is primary; there is a commitment to the goals of the larger organization; leadership is provided by the unit to solve all-university problems; there is a focus on learning; faculty are productive; there are strong communication links across the organization). The question is posed and then systemically answered as to how sociology departments compare in terms of these standards. It is suggested that a major factor in terms of how and why sociology departments are negatively evaluated is the fact that sociology uses narratives of power and explanations of organizational behavior that are inherently oppositional, i.e., there is an “us” and “them” mentally that sometimes develops. Other reasons for organizational marginalization are identified such as the “canon wars” and their lingering effects, and the fact that the sociological enterprise has been diluted by the teaching of “sociology” in many other campus units, such as composition programs. Finally, questions are raised about how sociology, as an intellectual enterprise, differs from other disciplines in terms of pedagogy, the sequencing of courses, “grand” theory, and forms of apprenticeship. It is recommended that sociologists act positively to help the organizations within which they work to identify common problems and solve them. It is argued that sociology can and should “own” the area of civic engagement as a means of making a positive and distinctive contribution. Sociological “stories” grounded in the reality of everyday life are compelling. It is suggested that sociologists need to deepen connections with their communities and to offer real solutions to real problems.
Geochemical signatures of thermochemical sulfate reduction in controlled hydrous pyrolysis experiments

Abstract A series of gold tube hydrous pyrolysis experiments was conducted in order to investigate the effect of thermochemical sulfate reduction (TSR) on gas generation, residual saturated hydrocarbon compositional alteration, and solid pyrobitumen formation. The intensity of TSR significantly depends on the H2O/MgSO4 mole ratio, the smaller the ratio, the stronger the oxidizing conditions. Under highly oxidizing conditions (MgSO4/hydrocarbon wt/wt 20/1 and hydrocarbon/H2O wt/wt 1/1), large amounts of H2S and CO2 are generated indicating that hydrocarbon oxidation coupled with sulfate reduction is the dominant reaction. Starting with a mixture of C21–C35 n-alkanes, these hydrocarbons are consumed totally at temperatures below the onset of hydrocarbon thermal cracking in the absence of TSR (400 °C). Moreover, once the longer chain length hydrocarbons are oxidized, secondarily formed hydrocarbons, even methane, are oxidized to CO2. Using whole crude oils as the starting reactants, the TSR reaction dramatically lowers the stability of hydrocarbons leading to increases in gas dryness and gas/oil ratio. While their concentrations decrease, the relative distributions of n-alkanes do not change appreciably from the original composition, and consequently, are non-diagnostic for TSR. However, distinct molecular changes related to TSR are observed, Pr/n-C17 and Ph/n-C18 ratios decrease at a faster rate under TSR compared to thermal chemical alteration (TCA) alone. TSR promotes aromatization and the incorporation of sulfur and oxygen into hydrocarbons leading to a decrease in the saturate to aromatic ratio in the residual oil and in the generation of sulfur and oxygen rich pyrobitumen. These experimental findings could provide useful geochemical signatures to identify TSR in settings where TSR has occurred in natural systems.
Ambulation and Parkinson Disease

Parkinson disease is a progressive neurodegenerative disorder characterized by a variety of motor and nonmotor features. This article reviews the problems of postural instability and gait disturbance in persons with Parkinson disease through the discussion of (1) the neuropathology of parkinsonian motor deficits, (2) behavioral manifestations of gait and postural abnormalities observed in persons with Parkinson disease, and (3) pharmacologic, surgical, and physical therapy-based interventions to combat postural instability and gait disturbance. This article advances the treatment of postural instability and gait disturbance by condensing up-to-date knowledge and making it available to clinicians and rehabilitation professionals.
Land‐use effects on water quality of a first‐order stream in the Ozark Highlands, mid‐southern United States

Urban and agricultural land uses can alter the natural hydrologic conditions of streams and rivers and often degrade water quality. In the Ozark Highlands of the mid-southern United States, the climate, topography, soil properties, karst limestone geology, agricultural practices and rapid urbanization make water quality of particular concern due to the increased potential for water quality degradation by contaminant leaching to groundwater and runoff to surface waters. The objective of this study was to evaluate the effects of season (i.e. dry/cool and wet/warm) and riparian land use (i.e. urban, grazed pasture, ungrazed pasture, wetland, cultivated agriculture and grassland) on surface water quality in a first-order stream within a diverse agricultural watershed in the Ozark Highlands. Water samples were collected twice a month within each land use during base-flow conditions from October 2006 through October 2007. Samples were also collected periodically during storm-flow conditions from October 2006 through December 2007. The greatest in-stream pH was adjacent to the grazed pasture. In-stream NO3-N concentrations were greatest adjacent to the cultivated agriculture and grassland during the dry/cool season (i.e. October 2006 to March 2007) and averaged 2.67 mg L−1. In-stream soluble reactive P (SRP) concentrations were greatest adjacent to the grassland during the wet/warm season (i.e. April 2007 to October 2007) and averaged 0.81 mg L−1. Concentrations of SRP, K, Mg and Zn were greater during storm- than base-flow conditions and in-stream As concentrations frequently exceeded 0.01 mg L−1. Discharge and in-stream NH4-N concentrations were unaffected by land use or season and averaged 0.003 m3 s−1 and 0.10 mg L−1, respectively, across all land uses and seasons. Results of this study clearly demonstrate the significant effect of adjacent land use on in-stream water quality of a first-order stream in a diverse agricultural watershed and highlight the importance of managing upstream land use in order to regulate downstream water quality. Copyright © 2010 John Wiley & Sons, Ltd.
Frequentistic adverbs as measures of egocentric biases

Research by Messick et al. (1985) concerning the egocentric fairness bias was replicated using linguistic choices rather than rating scales. Subjects were asked to choose from among six frequency quantifiers to describe the estimated frequency of moral and immoral behaviours as performed by 'I' or 'Other people'. Results replicate the dual slope phenomenon found by previous researchers. Subjects chose quantifiers referring to higher frequencies when estimating frequencies for 'I'- moral behaviour than for 'Other people'- moral behaviour, and quantifiers referring to lower frequencies when estimating frequencies for 'I' - immoral behaviour than for 'Other people'- immoral behaviour. This 'I'-'Other' differentiation was greater for the immoral behaviours than the moral behaviours.
Decreased toxicity of liposomal amphotericin B due to association of amphotericin B with high‐density lipoproteins: Role of lipid transfer protein

Previously, we have shown that liposomal amphotericin B (L-AmpB) composed of dimyristoylphosphatidylcholine (DMPC) and dimyristoylphosphatidylglycerol (DMPG) was less nephrotoxic but equally as effective as Fungizone, which consists of amphotericin (AmpB) and deoxycholate. We have also observed that AmpB predominantly associates with high-density lipoproteins (HDL) in human serum and that the amount of AmpB associated with HDL increases when AmpB is incorporated into negatively charged liposomes. Furthermore, we observe that AmpB was less toxic in vitro to pig kidney cells when associated with HDL, but still toxic when associated with LDL. To further understand why HDL-associated AmpB causes reduced renal toxicity, we first examined LLC PK1 cells for the presence of LDL and HDL receptors and then the cytotoxic effects of HDL- and LDL-associated AmpB following trypsin treatment of LLC PK1 renal cells, which removed only the high-affinity LDL receptors. We found that LLC PK1 renal cells expressed high- and low-affinity LDL receptors but only low-affinity HDL receptors. Furthermore, when LLC PK1 cells were treated with trypsin, HDL- and LDL-associated AmpB were less toxic to the cells than was AmpB. The reduced renal cell toxicity of HDL-associated AmpB may be due to its lack of interaction with renal cells because of the absence of HDL receptors. Since AmpB interacts with cholesteryl esters (CE) whose transfer among lipoproteins is regulated by lipid transfer protein (LTP), the role of LTP on the distribution of AmpB to HDL and LDL was next investigated. We observed that LTP facilitated the transfer of AmpB, but not L-AmpB, from HDL to LDL.(ABSTRACT TRUNCATED AT 250 WORDS)
CO2 Sequestration at Material rates: Inherent limits and Engineering Solutions

Abstract The most important technical challenge now facing geologic carbon storage (GCS) involves rates of storage, not volumes. The factors governing well injectivity combine to make achieving material storage rates (of order 0.1 Gt CO2/y in a basin or region) difficult. One such factor is the correlation between injectivity and storage volume of structural traps, which restricts access to much space that is desirable for secure storage for centuries. This limitation is exacerbated by the reduction in fracture pressure when injected CO2 is cooler than the storage formation. Changing the storage paradigm, so that brine is extracted from the storage formation as CO2 is injected, is the only robust option for materiality. A solution to the resulting brine disposal problem is to dissolve CO2 into the brine, then reinject it into the storage formation. This and other alternatives to injection-only storage must be examined if GCS is to play a substantive role in mitigating CO2 emissions over the course of decades.
Cell type-dependent gene transcription profile in a three-dimensional human skin tissue model exposed to low doses of ionizing radiation: Implications for medical exposures

The concern over possible health risks from exposures to low doses of ionizing radiation has been driven largely by the increase in medical exposures, the routine implementation of X-ray backscatter devices for airport security screening, and, most recently, the nuclear incident in Japan. Because of a paucity of direct epidemiological data at very low doses, cancer risk must be estimated from high dose exposure scenarios. However, there is increasing evidence that low and high dose exposures result in different signaling events and may have different response mechanisms than higher doses. We have examined the radiation-induced temporal response after exposure to 10 cGy of an in vitro three dimensional (3D) human skin tissue model using microarray-based transcriptional profiling. Cell type-specific analysis showed significant changes in gene expression with the levels of >1,400 genes altered in the dermis and >400 genes regulated in the epidermis. The two cell layers rarely exhibited overlapping responses at the mRNA level. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) measurements validated the microarray data in both regulation direction and value. Key pathways identified relate to cell cycle regulation, immune responses, hypoxia, reactive oxygen signaling, and DNA damage repair. The proliferation status as well as the expression of PCNA was examined in histological samples. We discuss in particular the role of proliferation, emphasizing how the disregulation of cellular signaling in normal tissue may impact progression toward radiation-induced secondary diseases. Environ. Mol. Mutagen. 2012. © 2012 Wiley Periodicals, Inc.
Cyclic geomorphic patterns of washover on a barrier Island in southeastern North Carolina

A detailed analysis of historic aerial photographs provided the data for determining the magnitude and importance of oceanic overwash on Masonboro Island, southeastern North Carolina. Overwash, which is both temporally and spatially distributed, produces a suite of physiographic features on the subaerial portion of the island. Four physiographic types are recognized including: A) small coalescing loosely vegetated dunes, B) intact, well-vegetated dunes and terraces, C) individual, isolated washover fans, and D) washover terraces. Vegetation patterns, including shrub thickets and black needle rush marshes are related to old fan sites. Sites dominated by saltmeadow cordgrass and goldenrod are associated with recent overwashes. A process-response model, which synthesizes the physiographic types and vegetation patterns, provides input for a management program for the island. Five sections on Masonboro Island are delineated on the basis of washover history and potential for future washovers. The response of Masonboro Island to overwash is similar to that observed on Core Banks, North Carolina; however there are several differences, probably because of the rapidity with which dune ridges redevelop after washovers.
An attachment theory perspective on the proposed matrix model.

The matrix model (C.R. Snyder & T.R. Elliott, this issue) advocates an increased grounding of clinical psychology graduate students in theory. The matrix model is theory-based in the ways that it advances this goal. Accordingly, evaluating the matrix model from an extant theoretical perspective should shed light on its applicability and utility as an educational framework. The present attachment theory perspective on the matrix model demonstrates that it meets its stated goals in that it possesses adequate (a) breadth in incorporating theory from across subdisciplines in psychology, and (b) depth in how it facilitates conceptualizing clients and research participants at the intrapersonal, interpersonal, and societal levels. The benefits for incorporating the matrix model in clinical psychology graduate programs are discussed. © 2005 Wiley Periodicals, Inc. J Clin Psychol.
Enhanced Superoxide Activity Modulates Renal Function in NO-Deficient Hypertensive Rats

An enhancement of superoxide (O2-) activity was shown to contribute to the development of hypertension induced by NO deficiency. To better understand the mechanistic role of O2- in this NO-deficient hypertension, we evaluated the renal responses to acute intraarterial administration of an O2- scavenger, tempol (50 microg/min per 100 g of body weight) in anesthetized male Sprague-Dawley rats treated with NO synthase inhibitor nitro-L-arginine methyl ester (15 mg/kg per day in drinking water, n=7) for 4 weeks, which caused increases in mean arterial pressure (146+/-3 versus 124+/-2 mm Hg) compared with normotensive control rats (n=6). Hypertensive rats had higher renal vascular resistance (29+/-2 versus 20+/-1 mm Hg/mL per minute per gram), as well as lower renal blood flow (5.2+/-0.3 versus 6.3+/-0.2 mL/min per gram; cortical blood flow, 153+/-13 versus 191+/-8 perfusion units; medullary blood flow, 43+/-2 versus 51+/-3 perfusion units) and glomerular filtration rate (0.69+/-0.04 versus 0.90+/-0.05 mL/min per gram) without a significant difference in urinary sodium excretion (0.81+/-0.07 versus 0.86+/-0.12 micromol/min per gram) compared with normotensive rats. Urinary 8-isoprostane excretion rate (6.8+/-0.7 versus 4.5+/-0.3 pg/min per gram) was higher in hypertensive than normotensive rats. Intraarterial infusion of tempol did not alter renal function in normotensive rats. However, tempol significantly decreased renal vascular resistance by 12+/-2% and urinary 8-isoprostane excretion rate by 24+/-4% and increased renal blood flow by 10+/-2%, cortical blood flow by 9+/-2%, medullary blood flow by 15+/-6%, glomerular filtration rate by 11+/-3%, and urinary sodium excretion by 19+/-5% in hypertensive rats. These data indicate that enhanced O2- activity modulates renal hemodynamics and excretory function during reduced NO production and, thus, contributes to the pathophysiology of the NO-deficient form of hypertension.
Genetic and Environmental Portions of the Variation among Herds in Butterfat Production

Summary The genetic part of the variation between herds has been estimated. In Method A the intra-sire regression of heifer production on herd average is used; whereas, in Method B, the variance components for herd differences between related and between unrelated cows in different herds are compared. Both methods imply that the genetic part of the differences between herd averages is caused entirely by additive gene effects. Evidence from the literature, though scanty, indicates that this is a good approximation. Method A was applied to records of 1,072 Jersey HIR cows and of 880 Holstein DHIA cows. The results indicated that 14 and 10%, respectively, of the differences between herd averages in the two populations are heritable. Prediction equations which utilize both individual performance and herd average are developed. Selection according to these indexes should be 1.19 and 1.35 times as effective as selection based on individual performance alone, without reference to herd averages, in the Jersey and the Holstein population, respectively. Method B was used on records of 2,903 artificially sired Holstein DHIA heifers and of 735 of their dams. When the variance components were derived from an analysis within years, the heritability of herd differences was 6.5%, both for milk and butterfat production. When the analysis was within year-seasons, the resulting heritability estimates were much higher (28 and 24%). It is suspected that the large size of the latter estimates results from sampling variation and, therefore, that the latter values are too large.
Observed frustration in confined block copolymers.

Symmetric diblock copolymers confined between two solid surfaces were studied by neutron reflectivity. A multilayered morphology with an integral number of layers oriented parallel to the solid interfaces was found in all cases. The period of the confined multilayers deviated from the bulk period in a cyclic manner as a function of the confined film thickness. A first-order transition occurred between the expanded and contracted states of the copolymer chains. The data suggest that the deviation of the period from the bulk value decreases with increasing separation distance.
Electronic and vibrational spectra of defects in neutron-irradiated silicon

Silicon irradiated with fast neutrons exhibits a variety of infrared absorption, photoconductivity [1] and photoluminescence spectra [2] in the infrared. They have been attributed to photo-excitation and photoionization of carriers bound to vacancies, divacancies, and impurity-defect complexes. Local modes of impurity-defect complexes have been observed [3]. One-phonon density of states of the host crystal manifests itself in the first-order infrared absorption as well as the Raman effect, a consequence of the absence of the strict translational symmetry in the irradiated crystal [4,5]. Microscopic models are available for many of the defect centres. If silicon is subjected to slow-neutron irradiation, 30Si naturally present in 3.05% abundance, transmutes to 31P via the 30Si(n,Y)31 Si → 31P+β− reaction. After eliminating the radiation damage produced during this neutron transmutation doping, homogeneously doped Si(P) is obtained. The electronic excitation spectrum of the phosphorus donors observed as a function of annealing is highly instructive in the context of the charged defects produced during the neutron transmutation process [6].
Quasiclassical approach to transport in the vortex state and the Hall effect

We derive generalized quasiclassical transport equations that include the terms responsible for the Hall effect in the vortex state of a clean type-II superconductor, and calculate the conductivity tensor for an $s$-wave superconductor in the high-field regime. We find that below the superconducting transition the contribution to the transverse conductivity due to dynamical fluctuations of the order parameter is compensated by the modification of the quasiparticle contribution. In this regime the nonlinear behavior of the Hall angle is governed by the change in the effective quasiparticle scattering rate due to the reduction in the density of states at the Fermi level. The connection with experimental results is discussed.
Point mutations at the thymidine kinase locus in L5178Y mouse lymphoma cells. II. Test validation and interpretation

The L5178Y Mouse Lymphoma TK assay was studied extensively to determine if this mammalian cell assay for gene mutations at the thymidine kinase (TK) locus could provide valid, interpretable determinations of mutagenic potential, and whether this information is of value in the safety evaluation of chemicals. We first determined that test-derived TFTR mutants were phenotypically stable, possessing little or no thymidine kinase activity as measured by labeled thymidine uptake, but demonstrating 100% cross resistance to bromodeoxyuridine. Common solvent vehicles such as acetone, dimethylsulfoxide and ethanol were shown to produce little cytotoxicity and no mutagenic activity when present at 1% levels. Out of a total of 10 noncarcinogens tested, all were negative when results were analyzed by a 2-sample loge t test on control and treated mutant count means. Of the 13 putative animal carcinogens tested, 10 were positive, 2 were negative (auramine O and sodium phenobarbital), and 1 showed sporadic activity (hydrazine sulfate) in the TK assay on the basis of test-derived t statistics. 2 compounds, 1,2-epoxybutane and ICR 191, which have been described as Ames positive non-carcinogens, were also positive in the TK assay. Although this sampling of a total of 29 compounds is insufficient for precise estimations of expected false-positive or false-negative frequencies, these data indicate the TK assay can be expected to detect a majority of carcinogens as mutagens including some missed by more established point-mutation assays.
The economics of temperature regulation in neutropical bats

Abstract 1. 1. The level and effectiveness of thermoregulation in bats is determined by the interaction of weight, basal rate of metabolism and thermal conductance. 2. 2. Conductances in tropical bats are greater than expected from weight. 3. 3. Basal rates of metabolism are higher than expected by weight in nectar-, fruit- and meat-eating bats, lower than expected in insectivorous species and intermediate in vampires, this correlation depending upon the seasonal stability of food resources in the environment. 4. 4. Therefore, nectar-, fruit- and meat-eating bats are effective thermoregulators, vampires are marginal regulators and insectivorous species readily enter torpor. 5. 5. Torpor evolved in the tropics in response to the high cost of thermoregulation at a small weight.
A Geometric Condition Implying an Energy Equality for Solutions of the 3D Navier–Stokes Equation

We prove that every weak solution u to the 3D Navier–Stokes equation that belongs to the class L3L9/2 and ∇u belongs to L3L9/5 locally away from a 1/2-Holder continuous curve in time satisfies the generalized energy equality. In particular every such solution is suitable.
ePet: when cellular phone learns to recognize its owner

In this paper an adaptive solution to secure the authentication process of cellular phones has been proposed. Gait and location tracks of the owner are used as the metrics for authentication. The cellular phone is envisioned to become as adaptive as a pet animal of the owner. The cellular phone learns various intrinsic attributes of the owner like his voice, face, hand and fingerprint geometry and interesting patterns in the owner's daily life and remembers those to continually check against any anomalous behavior that may occur due to the stealing of the phone. The checking is done level wise. Higher level of authentication is more stringent. Only when the cellular phone recognizes significant anomaly in a lower level, it goes one level up in the security hierarchy. The iPhone's accelerometer and A-GPS module have been utilized to record gait and location signatures. A fast and memory efficient variation of Dynamic Time Warping (DTW) algorithm called FastDTW has been used to compute the similarity score between gait samples.
Using invariants to optimize formal specifications before code synthesis

Formal specifications of required system behavior can be analyzed, verified, and validated, giving high confidence that the specification captures the desired behavior Transferring this confidence to the system implementation depends on a formal link between requirements and implementation. The automatic generation of probably correct code provides just such a link. While optimization is usually performed on code to achieve efficiency, we propose to optimize the formal specification before generating code, thus providing optimization independent of the particular code generation method. This paper investigates the use of invariants in optimizing code generated from formal specifications in the software cost reduction (SCR) tabular notation. We show that invariants (1) provide the basis for simplifying expressions that otherwise cannot be improved using traditional compiler optimization techniques, and (2) allow detection and elimination of parts of the specification that would lead to unreachable code.
It's not junk!: the search for functional elements in noncoding DNA

The human genome is approximately 3 billion basepairs long. An estimated 2--3% of DNA codes for genes; the remaining 97--98% is noncoding DNA [11]. Although the noncoding regions in DNA were once called "junk DNA" (with the assumption that these regions were not serving a purpose) it is now understood that within noncoding DNA are functional regions that affect the expression of genes [34]. However, we are still far from understanding the breadth of function in the noncoding regions, and identification of functional elements is a complex problem, difficult to study in vitro because of the enormous number of possibilities. In this project, we are searching in silico for candidate functional elements in noncoding DNA. These candidates will then be studied at the bench to assess function. Our guiding principle is that regions of noncoding DNA that have been conserved across evolutionary time are good candidates as functional elements; we use a genetic algorithms approach to search for these candidate elements, called motifs. Our system is thus called GAMI, Genetic Algorithms for Motif Inference. GAMI has been demonstrated to be a successful approach to this task, as will be described below.
Longitudinal health-related quality of life assessment: implications for prognosis in ovarian cancer

There is no information in the literature on the impact of changes in quality of life (QoL) scores on prognosis in ovarian cancer. We investigated whether changes in QoL during treatment could predict survival in ovarian cancer patients. We evaluated 137 ovarian cancer patients treated at our institution between Jan 2001 and Dec 2009 who were available for a minimum follow-up of 3 months. QoL was evaluated at baseline and after 3 months of treatment using EORTC-QLQ-C30. Cox regression evaluated the prognostic significance of baseline and changes in QoL scores after adjusting for clinical and demographic variables. Associations between changes in QoL and survival were observed for global function, appetite loss and constipation. Every 10-point increase (improvement) in global function from baseline to 3 months was associated with a 10% decreased risk of death (HR=0.90; 95% CI: 0.81 to 0.99, p=0.03). The corresponding HRs for 10-point increase (deterioration) in appetite loss and constipation scales were 1.20 (95% CI: 1.06 to 1.35; p=0.005) and 1.13 (95% CI: 1.02 to 1.24; p=0.02) respectively. This exploratory study provides evidence that an improvement in appetite, constipation and global health scores during the first 3 months of treatment is significantly associated with improved survival time in ovarian cancer. These findings justify serial, systematic assessment of global health, appetite and constipation in ovarian cancer patients being treated, and suggest that modalities designed to improve these functions may be beneficial clinically.
A 25,000-year record of earthquakes on the Owens Valley fault near Lone Pine, California: Implications for recurrence intervals, slip rates, and segmentation models

Seven trenches in eastern California across the Owens Valley fault near Lone Pine expose two episodes of faulting since early Holocene time in the form of ∼1 m throw in lacustrine beds with liquefaction that were buried and then faulted again ∼1 m by the M 7.5 to 7.75 A.D. 1872 Owens Valley earthquake. Geomorphic maps, applications of sequence stratigraphy, and analyses of radiocarbon from charcoal and tufa deposits indicate that the paleoearthquake, the penultimate event here, occurred between 10,200 ± 200 and 8800 ± 200 cal yr B.P. The cumulative vertical displacement from these last two earthquakes in three trenches averages 2.4 ± 0.3 m (2σ), and the penultimate event has slightly larger displacements. A synthesis of available data indicates that the antepenultimate event was probably as large and occurred between ca. 24,000 and 14,000 cal yr B.P. (2σ). Thus, the two interseismic intervals between the last three surface-faulting earthquakes on the southern Owens Valley fault are each ∼10,000 yr. This ∼25,000-year record indicates that the “two-event” normal-oblique slip rate on the Owens Valley fault near Lone Pine is 1.0 ± 0.5 m/k.y. This result is similar to that of several previous geological studies here, yet it is still slower than slip rates on the northern Owens Valley fault and several factors slower than contemporary geodetic measurements. This study attempts to account for different dating methods and interpretational uncertainties, to acknowledge how little is known about the slip history of the Owens Valley fault and adjacent faults, and to consider the role of segmentation, as well as splay and distributed faulting, in comparisons of displacement data among different sites along the entire ∼100 ± 10 km length of the Owens Valley fault.
Rapidly Learned Identification of Epileptic Seizures from Sonified EEG

Sonification refers to a process by which data are converted into sound, providing an auditory alternative to visual display. Currently, the prevalent method for diagnosing seizures in epilepsy is by visually reading a patient’s electroencephalogram (EEG). However, sonification of the EEG data provides certain advantages due to the nature of human auditory perception. We hypothesized that human listeners will be able to identify seizures from EEGs using the auditory modality alone, and that accuracy of seizure identification will increase after a short training session. Here we describe an algorithm we have used to sonify EEGs of both seizure and non-seizure activity, followed by a training study in which subjects listened to short clips of sonified EEGs and determine whether each clip was of seizure or normal activity, both before and after a short training session. Results show that before training subjects performed at chance level in differentiating seizures vs. non-seizures, but there was a significant improvement of accuracy after the training session. After training, subjects successfully distinguished seizures from non-seizures using the auditory modality alone. Further analyses using signal detection theory demonstrated improvement in sensitivity and reduction in response bias as a result of training. This study demonstrates the potential of sonified EEGs to be used for the detection of seizures. Future studies will attempt to increase accuracy using novel training and sonification modifications, with the goals of managing, predicting, and ultimately controlling seizures using sonification as a possible biofeedback-based intervention for epilepsy.
Cognitive impairment in Coffin-Lowry syndrome correlates with reduced RSK2 activation

Background: Gene expression and protein synthesis, mediated by the transcription factor CREB (cAMP response element binding protein), play an important role in learning and memory in several species, including Drosophila , snails, and mice. Patients with the X-linked disorder Coffin–Lowry syndrome (CLS) have cognitive disabilities, distinctive features, and bony abnormalities as well as mutations in RSK2 (ribosomal S6 kinase-2), a protein kinase that activates CREB by phosphorylation at serine 133. In fibroblasts from a single patient with CLS, epidermal growth factor (EGF)–stimulated CREB phosphorylation was reduced. Methods: The authors assessed endogenous CREB phosphorylation in a CLS fibroblast line by Western blotting and found impaired CREB phosphorylation in response to stimulation by EGF and the protein kinase C (PKC) agonist phorbol 12-myristate 13-acetate (PMA). They studied RSK2 immunoprecipitated from fibroblasts and lymphoblasts from seven patients with CLS and found a wide range in RSK2’s capacity to phosphorylate the synthetic CREB-like peptide, CREBtide, after cell stimulation by PMA. Results: In lymphoblasts from patients with CLS, PMA-stimulated CREBtide phosphorylation was increased 1.2- to 2.7-fold over baseline, compared to an average fourfold increase in controls. Regression analysis suggested a linear relationship between the magnitude of in vitro RSK2-mediated CREBtide phosphorylation and CLS patient intelligence level ( p Conclusions: This report suggests a correlation between human cognitive performance and cellular capacity to activate RSK2. It provides additional evidence that the CREB kinase, RSK2, and CREB phosphorylation may play important roles in human learning and memory, as they do in lower animals.
Estimating Sources of Soil Organic Matter in Natural and Transplanted Estuarine Marshes using Stable Isotopes of Carbon and Nitrogen

Abstract Stable isotopes of carbon (δ 13 C) a and nitrogen (δ 15 N) a were used to determine the origin of soil organic matter in irregularly flooded natural and transplanted estuarine marshes. a x = [R( sample )−R( standard )] R( standard )×1000 where X is δ 13 C or δ 15 N and R is 13 C 12 C or 15 N 14 N of the sample and the international standards Pee Dee Belemnite (CO 2 ) and atmospheric nitrogen (N 2 ).} Emergent and aquatic plants, soils, detritus and adjacent forest vegetation were collected from one natural and two transplanted marshes and the δ 13 C and δ 15 N values were measured. The isotopic composition of natural and transplanted marsh soils was similar to emergent vegetation. The δ 15 N of marsh soils fell within the range of emergent macrophytes (+ 1 to + 4%.), while soil δ 13 C ranged from −18 to −26%.. The δ 13 C of natural marsh soils (−20 to −24%.) reflected mixing between C 3 ( Juncus ) and C 4 ( Spartina, Distichlis ) marsh plants while the soil δ 13 C (−24 to −26%.) of one transplanted marsh was attributed to top soil applied prior to establishment of the marsh. The δ 13 C (−25%.) and δ 15 N (+ 5%.) of estuarine detritus suggested mixing between terrestrial material and phytoplankton. Marsh emergent vegetation appears to be the principal source of organic matter in soils of both natural and transplanted marshes. However, the young transplanted marsh soils also reflect external inputs of C (terrestrial material) contributed during marsh establishment.
A connection between fuzzy quantifiers and the classical modalities

The classical modalities, "necessity" and "possibility," are intuitively connected to probability theory by: proposition P is necessarily true if the probability of P's being true is I, and P possibly true if the probability of P's being true is greater than O. A prior work by the author introduced the logic QUAL, for reasoning symbolically with terms expressing fuzzy quantification, usuality, and likelihood. Within QUAL one can formalize syllogisms of the form "Most birds can fly; Tweety is a bird; therefore, it is likely that Tweety can By" and of the form "Usually, if something is a bird, it can fly; Tweety is a bird; therefore, it is likely that Tweety can fly," as well as other formulas and inference rules expressing the interrelationships between these three concepts. The present work shows how QUAL can be extended to include the above versions of possibility and necessity. The extent to which aspects of the well-known modal logics K, S.4, and S.5 can be encoded in this system are also explored. >
Stochastic Dominance Without Transitive Preferences

Traditional definitions of stochastic dominance assume that the decision agent's preference-or-indifference relation on outcomes of risky decisions is transitive. This paper proposes a stochastic dominance relation for the comparison of risky decisions that is applicable to any complete and reflexive preference-or-indifference relation, or to any asymmetric preference relation. The new dominance relation possesses a number of intuitively desirable properties and is equivalent to the usual stochastic dominance relation when preferences are transitive.
Minimax and L_{1} curve fitting in non-Gaussian MAP estimation

A class of non-Gaussian estimation problems is equivalent to minimax and L 1 curve fitting. The curve fit is shown to be algebraically dual to optimization of a positive semidefinite quadratic form with linear inequalities, which is solved by a fast quadratic program based on Graves' simplex algorithm. An example compares the performance of this estimator with the (suboptimal) minimum mean-squared error (MMSE) estimations generated by quadratic curve fitting.
XRCC1 Genotype and Breast Cancer: Functional Studies and Epidemiologic Data Show Interactions between XRCC1 Codon 280 His and Smoking

Tobacco smoke produces oxidative and alkylative DNA damage that necessitates repair by base excision repair coordinated by X-ray cross-complementing gene 1 (XRCC1). We investigated whether polymorphisms in XRCC1 alter DNA repair capacity and modify breast cancer risk associated with smoking. To show the functionality of the 280His variant, we evaluated single-strand break (SSB) repair capacity of isogenic Chinese hamster ovary cells expressing human forms of XRCC1 after exposure to hydrogen peroxide (H(2)O(2)), methyl methanesulfonate (MMS), or camptothecin by monitoring NAD(P)H. We used data from the Carolina Breast Cancer Study (CBCS), a population-based, case-control study that included 2,077 cases (786 African Americans and 1,281 Whites) and 1,818 controls (681 African Americans and 1,137 Whites), to examine associations among XRCC1 codon 194, 280, and 399 genotypes, breast cancer, and smoking. Odds ratios and 95% confidence intervals (95% CI) were calculated by unconditional logistic regression. Only cells expressing the 280His protein accumulated SSB, indicated by NAD(P)H depletion, from both H(2)O(2) and MMS exposures. In the CBCS, positive associations were observed between breast cancer and smoking dose for participants with XRCC1 codon 194 Arg/Arg (P(trend) = 0.046), 399 Arg/Arg (P(trend) = 0.012), and 280 His/His or His/Arg (P(trend) = 0.047) genotypes. The 280His allele was in strong linkage disequilibrium with 194Arg (Lewontin's D' = 1.0) and 399Arg (D' = 1.0). These data suggest that less common, functional polymorphisms may lie within common haplotypes and drive gene-environment interactions.
Case report: cleft palate closure in 18-month-old female with epidermolysis bullosa.

Abstract Objective: In a patient with epidermolysis bullosa and cleft palate, perioperative guidelines and surgical management can be unclear. This case report illustrates the occurrence of a skin anomaly often associated with potentially significant morbidity and a cleft palate. Perioperative guidelines to successfully manage the cleft palate closure in these patients are presented.
THE ACTION OF GLUCAGON-INSULIN MIXTURES IN DIABETIC PATIENTS*

Studies on the action of glucagon-insulin mixtures in 30 unselected hospitalized diabetic patients are presented. The findings indicate that glucagon and insulin combined increase glucose uptake in the forearm significantly more than does insulin alone. This effect appears to be independent of the severity of the diabetes but is more pronounced when the fasting arterial glucose concentration is greater than 120 mg. per 100 ml. Analysis of the response of arterial glucose levels to the glucagon-insulin mixtures revealed that fasting blood glucose levels and the ratio of glucagon to insulin in the mixture are important factors in this response. Arterial glucose levels were consistently stabilized when the fasting level was greater than 170 mg. per 100 ml. and the ratio of glucagon to insulin in the mixture was 0.26 to 0.90. Possible applications of these findings to the treatment of diabetic patients are suggested.
Compiler-directed data partitioning for muiticluster processors

Multicluster architectures overcome the scaling problem of centralized resources by distributing the datapath, register file, and memory subsystem across multiple clusters connected by a communication network. Traditional compiler partitioning algorithms focus solely on distributing operations across the clusters to maximize instruction-level parallelism. The distribution of data objects is generally ignored. In this work, we examine explicit partitioning of data objects and its affects on operation partitioning. The partitioning of data objects must consider several factors: object size, access frequency/pattern, and dependence patterns between operations that manipulate the objects. This work proposes a compiler-directed approach to synergistically partition both data objects and computation across multiple clusters. First, a global view of the application determines the interaction between data memory objects and their associated computation. Next, data objects are partitioned across multiple clusters with knowledge of the associated computation required by the application. Finally, the resulting distribution of the data objects is relayed to a region-level computation partitioner, which carefully places computation operations in a performance-centric manner.
New method for conversion of gas sonic velocities to density second virial coefficients

A new, numerical method was developed to calculate density second virial coefficients B(T) from sonic velocity measurements in gases at low pressures. Unlike existing methods, this procedure requires no model assumption as to the form of the temperature variation of B(T). Rather, it differences the measured accoustic second virial coefficient according to a new mathematical identity. While two higher-ordered terms in the identity must be ignored to initiate the numerical calculations, the magnitude of these terms can later be found from the initial determination of B(T). This article describes new equations developed, numerical procedures, calculations with Redlich-Kwong and Peng-Robinson gases and, with a Lennard-Jones model gas, to show the accuracy of the method and the magnitude of the two error terms, and the method applied to existing sets of sonic velocity data.