cssi/SciSciGPT-SciSciNet huggingface dataset:
Self-Induced Docking Site of a Deeply Embedded Peripheral Membrane Protein

As a first step toward understanding the principles of the targeting of C2 domains to membranes, we have carried out a molecular dynamics simulation of the C2 domain of cytosolic phospholipase A2 (cPLA2-C2) in a 1-palmitoyl-2-oleoyl-phosphatidylcholine bilayer at constant pressure and temperature (NPT, 300 K and 1 atm). Using the high-resolution crystal structure of cPLA2-C2 as a starting point, we embedded two copies of the C2 domain into a preequilibrated membrane at the depth and orientation previously defined by electron paramagnetic resonance (EPR). Noting that in the membrane-bound state the three calcium binding loops are complexed to two calcium ions, we initially restrained the calcium ions at the membrane depth determined by EPR. But the depth and orientation of the domains remained within EPR experimental errors when the restraints were later removed. We find that the thermally disordered, chemically heterogeneous interfacial zones of phosphatidylcholine bilayers allow local lipid remodeling to produce a nearly perfect match to the shape and polarity of the C2 domain, thereby enabling the C2 domain to assemble and optimize its own lipid docking site. The result is a cuplike docking site with a hydrophobic bottom and hydrophilic rim. Contrary to expectations, we did not find direct interactions between the protein-bound calcium ions and lipid headgroups, which were sterically excluded from the calcium binding cleft. Rather, the lipid phosphate groups provided outer-sphere calcium coordination through intervening water molecules. These results show that the combined use of high-resolution protein structures, EPR measurements, and molecular dynamics simulations provides a general approach for analyzing the molecular interactions between membrane-docked proteins and lipid bilayers.
On use of partial area under the ROC curve for evaluation of diagnostic performance

Evaluation of diagnostic performance is a necessary component of new developments in many fields including medical diagnostics and decision making. The methodology for statistical analysis of diagnostic performance continues to develop, offering new analytical tools for conventional inferences and solutions for novel and increasingly more practically relevant questions. In this paper, we focus on the partial area under the Receiver Operating Characteristic (ROC) curve or pAUC. This summary index is considered to be more practically relevant than the area under the entire ROC curve (AUC), but because of several perceived limitations, it is not used as often. To improve interpretation, results for pAUC analysis are frequently reported using a rescaled index such as the standardized partial AUC proposed by McClish (1989). We derive two important properties of the relationship between the 'standardized' pAUC and the defined range of interest, which could facilitate a wider and more appropriate use of this important summary index. First, we mathematically prove that the 'standardized' pAUC increases with increasing range of interest for practically common ROC curves. Second, using comprehensive numerical investigations, we demonstrate that, contrary to common belief, the uncertainty about the estimated standardized pAUC can either decrease or increase with an increasing range of interest. Our results indicate that the partial AUC could frequently offer advantages in terms of statistical uncertainty of the estimation. In addition, selection of a wider range of interest will likely lead to an increased estimate even for standardized pAUC.
Observed Equipment Damage and Analytically Estimated Car Decelerations in Selected Passenger Train Accidents

The Federal Railroad Administration has conducted a number of detailed investigations of passenger train accidents which result in fatal injuries and/or multiple serious injuries. The objective of these investigations is to reconstruct the sequence of events and to determine the causal mechanisms for injuries and fatalities.This paper presents a reconstruction of the sequence of events and the train collision dynamics results for three accidents:- the passenger train to freight train collision with a closing speed of 80 mph in Chatsworth, California on September 12, 2008;- the passenger train to freight train collision with a closing speed of 33 mph in Chicago, Illinois on November 30, 2007;- the passenger train to freight car collision with a closing speed of 23 mph in Canton, Massachusetts on March 25, 2008.The reconstructions are developed from information gathered during field investigations of occupant injury (via interview and reports), damage to the interior fixtures, structural damage to the equipment, and wayside damage. Engineering analyses are then conducted to integrate the data gathered during the field investigation, including train collision dynamics modeling which estimates the gross motions of each of the rail cars during the collision.To assure that the model reasonably captures the collision dynamics, model results are first compared with the post-accident equipment damage information gathered in the investigations. The model is then used to estimate the severity of the decelerations experienced by the occupants. The Secondary Impact Velocity (SIV) provides an indication of severity of the interior environment experienced by the passengers and crew during the accident. In a companion paper, the SIVs are correlated with the observed level of damage to the interior seats and fixtures.The selected accidents represent a range of collision conditions, with closing speeds from 23 to 80 mph, single- and multi-level passenger cars, and colliding freight equipment from a long train to a single car. The selected accidents are similar in that in all cases the passenger trains are locomotive-led. The differences in collision speed and mass of the colliding equipment resulted in substantial differences in the observed damage to the equipment as well as differences in the estimated SIVs. These differences are discussed in the paper.
Desire, ritual, and cuisine

In the past decade, what might be called a collective “lust for food” has permeated mainstream American culture. One need not look further than magazine racks, cable television shows, and the Internet to find a society in the grip of an obsession with food and its purveyors. As a departure from the 1950s meat and mashed potatoes mentality, we have evolved into an era in which the desire for creative and beautiful food seems insatiable. This lust for food in popular culture has also been reflected in academic culture: Food studies as a scholarly area of inquiry has seen an explosive growth, with the development of a number of scholarly associations, journals, classes, and conferences devoted to food and foodways (Cargill, 2005; Goldstein, 2002). This interdisciplinary area of study spans the humanities, social sciences, and natural sciences, and draws from anthropology, sociology, and history, among others. Psychology and psychoanalysis, however, are curiously underrepresented in this body of work, often because they are not viewed by other scholars as relevant. Given that the historical focus of psychoanalysis has been almost exclusively on pathological eating behaviors such as clinical eating disorders and childhood feeding disturbances (Crastnopol, 2001; A. Freud, 1946; Krueger, 1997; Petrucelli & Stuart, 2001; Shainess, 1979), this has served to reinforce the long-standing criticism from both within and outside of the discipline that psychology and psychoanalysis are overly focused on the individual and fail to adequately take social context into account (Ainslie & Brabeck, 2003; Cushman, 1996; Ingham, 1996; Schwartz, White, & Lutz, 1992). In order to more fully engage in the academic dialogue on the study of food and society, this paper advances an interdisci
A New Multiple High-Speed Air Circuit Breaker for Mercury-Arc-Rectifier Anode Circuits and Its Relation to the Arc-Back Problem

Mercury-arc power rectifiers have been used increasingly to supply power to d-c utilization systems in the United States since the early twenties. War requirements, because they have multiplied the demand for aluminum, magnesium, chlorine, zinc, and copper, all of which utilize d-c current in their reduction, have tremendously increased d-c power consumption. It is estimated that 12 1/2 per cent of the kilowatt-hours generated in 1941 were consumed in such electrochemical processes. Since the mercury-arc rectifier is now the almost universally accepted form of conversion apparatus for this purpose, the attention of many more engineers has recently been focused on it. Many advantages of the modern rectifier have led to its wide acceptance, but it is not within the scope of this paper to deal with these. One persistent factor in connection with the application of rectifiers which has claimed much attention is the phenomenon of arc-back. Various methods of attack have been employed successfully. High-speed anode switching appears to be the most satisfactory way to handle this problem. Such a solution is widely used in the aluminum industry.1 Part I of this paper includes an analysis of the arc-back problem and various means of protection from its effects. Reasons why high-speed anode switching is an improved type of arc-back protection are set forth. Part II of this paper describes this multi-pole high-speed air circuit breaker. The requirements which the breaker must meet are discussed, and the electrical and mechanical features described. Performance of the breaker was checked in field tests. Oscillographic data are presented and prove that the performance is acceptable.
Linking structure to function: Recent lessons from inositol 1,4,5-trisphosphate receptor mutagenesis

Great insight has been gained into the structure and function of the inositol 1,4,5 trisphosphate receptor (InsP(3)R) by studies employing mutagenesis of the cDNA encoding the receptor. Notably, early studies using this approach defined the key constituents required for InsP(3) binding in the N-terminus and the membrane spanning regions in the C-terminal domain responsible for channel formation, targeting and function. In this article we evaluate recent studies which have used a similar approach to investigate key residues underlying the in vivo modulation by select regulatory factors. In addition, we review studies defining the structural requirements in the channel domain which comprise the conduction pathway and are suggested to be involved in the gating of the channel.
Theory of Raman scattering by molecules adsorbed on electrode surfaces

In this work, we provide a simple classical model to explain the enormous intensity enhancement observed for Raman scattering from molecules adsorbed on electrode surfaces. It is proposed that the origin of the intensity enhancement arises from very large changes in the polarizability derivative with respect to a normal coordinate, by virtue of the image field at the admolecule. A qualitative discussion of the role of adsorbed counter ions is presented. We tentatively propose that the dependence of the intensity enhancement on counter ion concentration may be understood in terms of nearest neighbor dipole–dipole stabilization of surface clusters of counter ions with the adsorbate molecule. We also discuss some limitations of the classical model, and propose some further experiments that may lead to clarification of the ideas presented in this work.
A Bayesian technique for refining the uncertainty in global energy model forecasts

Abstract Global energy models have a large degree of uncertainty associated with them. This consists of uncertainty in the model structure as well as uncertainty in the exogenous input parameters. This paper combines Monte Carlo methods with Bayesian updating techniques to provide a method for refining the uncertainty in the Edmonds-Reilly global energy model. The Bayesian updating technique uses likelihood-based windows constructed from actual observations of the output variables to filter out the model simulations that do not conform with the observed output. The windows are based on outputs of energy consumption and carbon emissions. Two alternative model structures are examined: one with uncorrelated input parameters and the other with correlated input parameters. Statistical properties are calculated to measure the effects of windowing on the output distributions. The partial rank correlations between the inputs and outputs and between the inputs are also determined. The prior distributions and correlation structure of the inputs are then revised through the updating process. An application of the windowing process illustrates the effects of capping carbon emissions on the input structure.
Microfluidic Assembly of Cationic-β-Cyclodextrin:Hyaluronic Acid-Adamantane Host:Guest pDNA Nanoparticles.

Transfection complexes are typically formed by bulk mixing, producing particles with high polydispersity and limited control over vector size. Herein, we demonstrate the use of a commercial microreactor to assemble pDNA:cationic cyclodextrin:pendant polymer nanoparticles using a layer-by-layer approach. Our studies reveal that the particles formulated via microfluidic assembly have much smaller sizes, lower polydispersity, lower ζ-potentials, and comparable cell viability and transfection profiles in HeLa cells than bulk mixed particles. The complexes also show a flow rate-dependent stability, with particles formed at slower flow rates giving rise to more stable complexes as determined by heparin challenge experiments. Our findings suggest that microfluidic reactors offer an attractive method for assembling reproducible, size-controlled complexes from multi-component transfection complex assemblies.
Deuterium Isotope Effect in Enzymatic Transamination of L-Deuterio-phenylalanine to Deuterio-phenylpyruvic Acid

L-Deuterio-phenylalanine was isolated by gradient elution ion-exchange chromatography of the ionic fraction obtained from the cell wall hydrolysate of algae grown in culture medium containing 99.6% deuterium oxide. The enzyme system present in rat brain extract was used for determining the rate of transamination of L-deuterio-phenylalanine and its protio analog. The phenylpyruvate formed was determined spectrophotometrically at 300 nm. using the arsenate-catalyzed enol-borate assay procedure. Transamination rates were determined in media containing verying concentrations of amino acid and α-ketoglutarate. Kinetic determination of maximum velocity was conducted through graphical analysis of the data. The deuterium isotope effect, expressed as the VH/VD value, was 1.64.
Draft Genome Sequences for Three Mercury Methylating Sulfate-Reducing Bacteria

The genetic basis for bacterial mercury methylation has been described recently. For insights into the physiology of mercury-methylating bacteria, we present genome sequences for Desulfococcus multivorans strain DSM 2059, Desulfovibrio alkalitolerans strain DSM 16529, and Desulfovibrio species strain X2.
Spatial analysis of vector-borne disease: A four-species model

Disease can influence a host population's dynamics directly or indirectly through effects on the host's interactions with competitors and exploiters. We present a stochastic, spatially explicit model for the epidemiological landscape of a vector-borne disease. Two host species, of unequal competitive strength, are attacked by a selective parasite; the parasite serves as a vector for a pathogen. We emphasize the importance of the ecological stencil, i.e. the local area where ecological interactions govern a site's species composition. We demonstrate analytically that varying the size of the ecological stencil critically affects the dynamics of the host densities and the potential equilibrium configuration of the system. We point out how parallel computing can efficiently employ the geometry of the stencil's local transitions to predict large-scale spatio-temporal patterns of the model community.
Total-dose radiation-induced degradation of thin film ferroelectric capacitors

The radiation hardness of thin-film PbZr/sub y/Ti/sub 1-y/O/sub 3/ (PZT) ferroelectric capacitors is explored. Ferroelectric capacitors were irradiated using X-ray and Co-60 sources to dose levels up to 16 Mrad(Si). The capacitors were characterized for their memory properties both before and after irradiation. The radiation hardness was process dependent. Three out of four processes resulted in capacitors that showed less than 30% radiation-induced degradation in retained polarization charge and remnant polarization after irradiating to 16 Mrad(Si). On the other hand, one of the processes showed significant radiation-induced degradation in retained polarization charge and remanent polarization at dose levels above 1 Mrad(Si). A model for simulating the observed degradation is developed. The model indicates that the data are consistent with trapping of radiation-induced charge in the ferroelectric material. The radiation hardness levels indicate that ferroelectric devices can be fabricated that can survive radiation exposures well in excess of 10 Mrad(Si). >
A boundary element method for modeling viscoelastic flow in thermal oxidation

At temperatures encountered in thermal oxidation, silicon dioxide flows viscoelastically, A reduced-dimension, generalized boundary element method for modeling such a problem has been developed. A modified Kelvin's solution is used as the kernel; constant-velocity loading is chosen to operate with a wide range of stress relaxation times. Simulation results are reported for simple cases of focal oxidation. >
Nasal albumin in a population exposed for the first time to urban pollution.

Abstract Background High levels of albumin in some biological fluids are generally associated with abnormal process of permeation during an inflammatory response. In some cases, the nasal albumin levels can be used as an indirect molecular marker of epithelial damage. Methods We carried out an evaluation study of nasal albumin from a population (14 volunteers), exposed for 15 days to high urban pollution (O 3 10.644 ppm/h average 10.2 h/day) in Mexico City for the first time, and when they returned to their original non-polluted city (Veracruz, State of Veracruz, Mexico) 13 days later. The nasal albumin samples were fractionated by gel electrophoresis techniques, and albumin determination analyses were done by gel scanning. The densitometry values obtained from the albumin-stained bands were compared with an internal standard and the average values compared with other groups used as reference, under conditions of non-polluted and polluted cities. Results Our findings showed in the group exposed to pollution for the first time a significant increment 2 days after entering Mexico City urban pollution. They, subsequently, had a progressive recovery 4 days later up to day 13 in their original place of residence. The reference groups for comparison were from a non-polluted city (at sea level on the Pacific Ocean) Manzanillo, Colima, Mexico, and a very polluted urban metropolis (Mexico City). The group showed a significant difference of protein levels about 2.5 higher apparently at the expense of albumin. These populations were permanent residents of environmental conditions we wanted to evaluate. Our approach was to monitor quantitatively the time course of the change of a biochemical parameter in normal mucus from a population never exposed to Mexico City urban pollution. Conclusions Our conclusions from this study point out that pollution causes diverse mucosal damage that can be followed by biochemical monitoring.
Cell surface expression of the melanocortin-4 receptor is dependent on a C-terminal di-isoleucine sequence at codons 316/317.

Abstract Loss-of-function mutations in the human melanocortin-4 receptor (MC4R) are associated with obesity. Previous work has implicated a C-terminal di-isoleucine motif at residues 316/317 in MC4R cell surface targeting. It was therefore of interest to examine function and cell surface expression of an MC4R mutation found in an obese proband in which one of these isoleucines was substituted by threonine (I317T). Single mutant (I316T or I317T) and double mutant (I316T,I317T) forms of MC4R were constructed by oligonucleotide-directed mutagenesis and tested for function and cell surface expression in transfected cells. Function was assessed using assays for agonist, [Nle4-d-Phe7]α-melanocyte-stimulating hormone (NDP-α-MSH) or forskolin-stimulated cAMP accumulation. Cell surface expression was determined by whole-cell binding of [125I]NDP-α-MSH, fluorescence immunocytochemistry and fluorescence-activated cell sorting. Maximal cAMP generation of the single mutants was reduced by 40% of wild-type receptor; the double mutant further reduced function to 40% of control, effects that were mirrored by decreases in cell-surface expression. Quantitative RT-PCR showed that, relative to wild-type receptor, transcript levels for the mutated receptors were not reduced. The results further implicate the C-terminal di-isoleucines in cell surface expression of MC4R and suggest that mutations of residues 316 or 317 would predict MC4R hypofunction.
Contributions to the Theory of Single-Sample Uncertainty Analysis

Uncertainty Analysis is the prediction of the uncertainty interval which should be associated with an experimental result, based on observations of the scatter in the raw data used in calculating the result. In this paper, the process is discussed as it applies to single-sample experiments of the sort frequently conducted in research and development work. Single-sample uncertainty analysis has been in the engineering literature since Kline and McClintock's paper in 1953 [1] and has been widely, if sparsely, practiced since then. A few texts and references on engineering experimentation present the basic equations and discuss its importance in planning and evaluating experiments (see Schenck, for example [2]). Uncertainty analysis is frequently linked to the statistical treatment of the data, as in Holman [3], where it may be lost in the fog for many student engineers. More frequently, only the statistical aspects of data interpretation are taught, and uncertainty analysis is ignored. For whatever reasons, uncertainty analysis is not used as much as it should be in the planning, development, interpretation, and reporting of scientific experiments in heat transfer and fluid mechanics. There is a growing awareness of this deficiency among standards groups and funding agencies, and a growing determination to insist on a thorough description of experimental uncertainty in all technical work. Both the International Standards Organization [4] and the American Society of Mechanical Engineers [5] are developing standards for the description of uncertainties in fluid-flow measurements. The U. S. Air Force [6] and JANNAF [7] each have handbooks describing the appropriate procedures for their classes of problems. The International Committee on Weights and Measures (CIPM) is currently evaluating this issue [8]. The prior references, with the exception of Schenck and, to a lesser extent, Holman, treat uncertainty analysis mainly as a process for describing the uncertainty in an experiment, and end their discussion once that evaluation has been made. The present paper has a somewhat different goal: to show how uncertainty analysis can be used as an active tool in developing a good experiment, as well as reporting it. The concepts presented here were developed in connection with heat transfer and fluid mechanics research experiments of moderately large size (i.e., larger than a breadbox and smaller than a barn) and which may frequently require three
A study of logspline density estimation

A method of estimating an unknown density function @? based on sample data is studied. Our approach is to use maximum likelihood etimation to estimate log(@?) by a function s from a space of cubic splines that have a finite number of prespecified knots and are linear in the tails. The knots are placed at selected order statistics of the sample data. The number of knots can be determined either by a simple rule or by minimizing a variant of AIC. Examples using both simulated and real data show that the method works well both in obtaining smooth estimates and in picking up small details. The method is fully automatic and can easily be extended to yield estimates and confidence bounds for quantiles.
FISH INVASIONS IN CALIFORNIA WATERSHEDS: TESTING HYPOTHESES USING LANDSCAPE PATTERNS

An important goal of invasion biology is to identify physical and environ- mental characteristics that may make a region particularly receptive to invasions. The inland waters of California (USA) are highly invaded, particularly by fishes, although there is wide variation in numbers of nonnative fishes across the state's watersheds. Here we examine patterns of fish invasions in California watersheds and their associations with natural en- vironmental characteristics, native fish diversity, and various measures of human habitat disturbance. Our analysis is based on an extensive data set on the distribution of freshwater fishes across California's watersheds and on GIS land-use coverages for the entire state. We used canonical correspondence analysis to examine associations between environmental characteristics and the distributions of both native and nonnative fish species. We then employed an information-theoretic model-selection approach to rank hypothesized models derived from the fish invasion literature with regard to how well they predicted numbers of nonnative fishes in California watersheds. Our results indicate that pervasive, anthro- pogenic, landscape-level changes (particularly the extent of urban development, small-scale water diversions, aqueducts, and agriculture) influenced spatial patterns of invasion. In addition, we find that deliberately stocked fishes have different habitat associations, in- cluding a strong association with the presence of dams, than other introduced fishes. In our analysis, watersheds with the most native species also contain the most nonnative species. We find no evidence that existing watershed protection helps to prevent fish invasions in California, but we suggest that restoration of natural hydrologic processes may reduce invasion impacts.
Maintenance Dose of Warfarin in Sheep and Effect of Diet: A Preliminary Report

Sheep models are widely used to evaluate the feasibility of various cardiac assist devices. Anticoagulation therapy postoperatively, however, is seldomly reported on. Continuous heparin infusion is often used, but is cumbersome due to long-term line management with the risk of infection and dislodgement. We contemplated using warfarin instead and started a pilot dose-finding study. Three sheep were given oral warfarin between 0.1 and 0.3 mg/kg/day. Prothrombin time was monitored and INR was calculated daily. If the INR did not reach a target of 2.5-3.5, warfarin dose was doubled. We found that sheep required a dose of warfarin between 1.6 and 2.4 mg/kg/day to raise the INR to the target zone. In a subsequent study to evaluate the effect of diet on INR in sheep, three sheep were fed alfalfa hay or alfalfa pellets in a crossover design. All the animals were given warfarin at the dose of 1.6 mg/kg. The diet was switched when the INR reached the target zone of 2.5-3.5. Hay-fed animals reached the target INR on days 6 and 7. On the other hand, pellet-fed animals did not reach the target value by day 7 with the initial dose and required 2.4 mg/kg of warfarin to achieve the goal. Hay raised the INR faster and higher than pellets with the same warfarin dose. Hay may be advantageous when using oral warfarin therapy in sheep.
Neoplasia in the ileoanal pouch following colectomy in patients with ulcerative colitis and primary sclerosing cholangitis.

Abstract Background & Aims Primary sclerosing cholangitis (PSC) is typically associated with inflammatory bowel disease (IBD), particularly ulcerative colitis (UC). PSC–IBD patients are at an increased risk for colorectal neoplasia. The ileal pouch-anal anastomosis (IPAA) is a treatment option for patients with medically refractory UC or neoplasia. However, little is known about the development of pouch neoplasia in PSC–UC patients following an IPAA. We aim to describe the incidence of pouch neoplasia in PSC–UC patients after an IPAA. Methods We conducted a retrospective chart review of patients with a confirmed diagnosis of PSC and IBD who underwent colectomy with IPAA followed by pouch surveillance between 1995 and 2012. Results Sixty-five patients were included in the cohort and were followed up from the time of colectomy/IPAA for a median of 6years. The most common indications for surgery were low-grade dysplasia (LGD) and refractory colitis. Only 3 patients developed evidence of neoplasia (LGD n=1, high-grade dysplasia n=1, adenocarcinoma n=1). The cumulative 5-year incidence of pouch neoplasia was 5.6% (95% confidence intervals [CI], 1.8%–16.1%). Conclusion Based on our short-term follow-up, surveying the pouch frequently appears to be an unnecessary practice in PSC–IBD patients. Longer follow-up will be needed to develop an optimal surveillance strategy for the development of dysplasia and cancer in such patients.
On formal verification of Toyota's electronic throttle controller

This practice paper examines Toyota's electronic throttle controller (ETC) problem. ETC for passenger cars is a safety-critical, embedded control system and it must meet very high reliability and safety requirements. ETC systems continue to increase in complexity, making formal specification and verification processes an essential component of the development of safer systems. There are two ways to represent the real-time system. Firstly, we can describe the system's structure and function by detailing its electrical, mechanical, and other components. Secondly, the real-time system's behavior as it responds to actions and events can be described. Then we can compare the system's specification to the safety assertion to show that the system meets the safety properties. This paper describes two research threads. In the first, we present the specification of Toyota's electronic throttle control (ETC) system including the timing constraints. The second thread, which will be explored in a longer version of this paper, evaluates the use of conventional design versus electronic engine control by applying classical control theory.1
Fractured hydrothermal dolomite reservoirs in the Devonian Dundee Formation of the central Michigan Basin

The Middle Devonian Dundee Formation is the most prolific oil-producing unit in the Michigan Basin, with more than 375 million bbl of oil produced to date. Reservoir types in the Dundee Formation can be fracture controlled or facies controlled, and each type may have been diagenetically modified. Although fracture-controlled reservoirs produce more oil than facies-controlled reservoirs, little is known about the process by which they were formed and diagenetically modified. In parts of the Dundee, preexisting sedimentary fabrics have been strongly overprinted by medium- to coarse-grained dolomite. Dolomitized intervals contain planar and saddle dolomite, with minor calcite, anhydrite, pyrite, and uncommon fluorite. Fluid-inclusion analyses of two-phase aqueous inclusions in dolomite and calcite suggest that some water-rock interaction in these rocks occurred at temperatures as high as 120–150C in the presence of dense Na-Ca-Mg-Cl brines. These data, in conjunction with published organic maturity data and burial reconstructions, are not easily explained by a long-term burial model and have important implications for the thermal history of the Michigan Basin. The data are best explained by a model involving short-duration transport of fluids and heat from deeper parts of the basin along major fault and fracture zones connected to structures in the Precambrian basement. These data give new insight into the hydrothermal processes responsible for the formation of these reservoirs.
Apparent sialadenopathy of the sublingual glands after general anesthesia with placement of laryngeal mask airway.

Sialadenopathy, inflammation of the salivary glands, is a rare anesthetic complication. This case conference describes a patient who developed sialadenopathy of the sublingual glands after placement of a laryngeal mask airway during a brief surgical procedure. The patient's history is detailed, the surgical and anesthetic procedures are described, and a discussion follows, which describes the different causes of this inflammatory process. In the comment, the physiology of the salivary glands is described in detail.
Phase 1 study of 28-day, low-dose temozolomide and BCNU in the treatment of malignant gliomas after radiation therapy.

We conducted a study to determine the dose-limiting toxicity of an extended dosing schedule of temozolomide (TMZ) when used with a fixed dose of BCNU, or 1,3-bis(2-chloroethyl)-1-nitrosourea (carmustine), taking advantage of TMZ’s ability to deplete O6-alkylguanine-DNA-alkyltransferase and the synergistic activity of these two agents. Patients with malignant gliomas who had undergone radiation therapy were eligible. Patients were treated with TMZ for 28 days, followed by a 28-day rest (1 cycle). The TMZ was started at 50 mg/m2 and increased in 10-mg/m2 increments; a fixed dose of BCNU (150 mg/m2) was given within 72 h of starting TMZ. A standard phase 1 dose-escalation scheme was used with 3 patients per cohort. Fourteen glioblastoma patients and 10 anaplastic astrocytoma patients were treated. The dose-limiting toxicity was myelosuppression at 90 mg/m2 of TMZ. The total number of cycles given was 73 (median number was 2). Six patients (25%) required a dose reduction in BCNU, and six were removed from study for hematologic toxicity after cycle 1; three patients overlapped. The median time to progression and overall survival were, respectively, 82 and 132 weeks for anaplastic astrocytomas and 14 and 69 weeks for glioblastomas. We conclude that the combination of BCNU and the extended dosing schedule of TMZ is feasible and that the maximal tolerated dose of a 28-day course of TMZ is 80 mg/m2 when combined with a fixed dose of BCNU at 150 mg/m2. This is the recommended dose for phase 2, but myelosuppression after cycle 1 suggests that long-term treatment may be difficult
An Outbreak of Bloodstream Infections Arising from Hemodialysis Equipment

An outbreak of 29 cases of bloodstream infection by 16 pathogens occurred during 8 months at two chronic hemodialysis centers. Consequences included 21 hospital admissions and removal of 23 dialysis catheters. An epidemiologic investigation comparing case-patients with uninfected controls showed that risk was significantly (P < .05) associated with having a catheter for vascular access; receiving treatment on a Monday, Wednesday, Friday schedule; and receiving treatment on one heavily contaminated dialysis machine. Culture studies and mock trials showed that bloodstream pathogens were present in a recently installed, commercially marketed attachment for disposal of spent priming saline and could enter blood line tubing directly or indirectly during dialyzer priming and tubing assembly. The outbreak was halted by measures directed at the attachment. Investigation of this problem demonstrated that microbial overgrowth in the attachment caused bloodstream infections and underscores the importance of microbiologic considerations in the design and use of hemodialysis equipment.
Parallelization and performance characterization of protein 3D structure prediction of Rosetta

The prediction of protein 3D structure has become a hot research area in the post-genome era, through which people can understand a protein's function in health and disease, explore ways to control its actions and assist drug design. Many protein structure prediction approaches have been proposed in past decades. Among them, Rosetta is one of the best systems. However, the huge time complexity of Rosetta, e.g. a few days to predict a protein, limits its wide use in practice. To accelerate the prediction of protein 3D structure in Rosetta, this paper presents three different approaches, i.e., non-interactive, periodic interactive and asynchronous dynamic interactive scheme, to parallelize Rosetta. The asynchronous interactive scheme, with the adaptation of dynamic solution interaction, outperforms the other two, delivering much faster convergence speed and better solution quality. Detailed measurements and performance analysis also indicate that parallel Rosetta with asynchronous dynamic interactive scheme scales well.
Environment-dependent admixture dynamics in a tiger salamander hybrid zone.

After an estimated five million years of independent evolution, the barred tiger salamander (Ambystoma tigrinum mavortium) was introduced by bait dealers into the native range of the California tiger salamander (A. californiense). Hybridization and backcrossing have been occurring in central California for 50-60 years, or an estimated 15-30 generations. We studied genetic and ecological factors influencing admixture of these two divergent gene pools by analyzing frequencies of hybrid genotypes in three kinds of breeding habitats: natural vernal pools, ephemeral man-made cattle ponds, and perennial man-made ponds. Perennial ponds tended to have higher frequencies of nonnative alleles than either type of seasonal pond, even in cases where perennial and seasonal ponds are within a few hundred meters. Thus, the hybrid zone has a mosaic structure that depends on pond hydrology or ecology. The presence of some broadly acting constraints on admixture is suggested by linkage disequilibria between physically unlinked molecular markers within ponds. In addition, we found several marker-specific deviations from Hardy- Weinberg equilibrium. One marker showed a consistent deficit of heterozygotes across pond types. Another showed heterozygote deficits only in vernal pools. A third was more likely to have heterozygote excess in ephemeral cattle ponds. These patterns indicate that admixture is influenced by complex genotype-by-environment interactions.
Tunneling effects in electromagnetic wave scattering by nonspherical particles: A comparison of the Debye series and physical-geometric optics approximations

Abstract The accuracy of the physical-geometric optics (PG-O) approximation is examined for the simulation of electromagnetic scattering by nonspherical dielectric particles. This study seeks a better understanding of the tunneling effect on the phase matrix by employing the invariant imbedding method to rigorously compute the zeroth-order Debye series, from which the tunneling efficiency and the phase matrix corresponding to the diffraction and external reflection are obtained. The tunneling efficiency is shown to be a factor quantifying the relative importance of the tunneling effect over the Fraunhofer diffraction near the forward scattering direction. Due to the tunneling effect, different geometries with the same projected cross section might have different diffraction patterns, which are traditionally assumed to be identical according to the Babinet principle. For particles with a fixed orientation, the PG-O approximation yields the external reflection pattern with reasonable accuracy, but ordinarily fails to predict the locations of peaks and minima in the diffraction pattern. The larger the tunneling efficiency, the worse the PG-O accuracy is at scattering angles less than 90°. If the particles are assumed to be randomly oriented, the PG-O approximation yields the phase matrix close to the rigorous counterpart, primarily due to error cancellations in the orientation-average process. Furthermore, the PG-O approximation based on an electric field volume-integral equation is shown to usually be much more accurate than the Kirchhoff surface integral equation at side-scattering angles, particularly when the modulus of the complex refractive index is close to unity. Finally, tunneling efficiencies are tabulated for representative faceted particles.
Antimicrobial Activity of Hop Resins.

The antimicrobial activity of hop resins against Streptococcus salivarius , Staphylococcus aureus (two strains), Bacillus megaterium , Escherichia coli B, and Bacillus subtilis was investigated. However, resistance development was carried out on Streptococcus salivarius , Staphylococcus aureus (two strains), and Bacillus megaterium . The two hop resins used were iso-alpha resin and beta resin. Prior to resistance development, S. salivarius , S. aureus , and B. megaterium were all inhibited by the iso-alpha-hop resin in the 0.01 to 0.03% range. The beta-hop resin which, according to the literature, is more active than the iso-alpha resin initially inhibited these organisms at the 0.003 to 0.01% concentrations. The ease of resistance development varied between the different microbes, B. megaterium being the least prone to develop resistance.
[18F]FIMX is a promising tracer to quantify metabotropic glutamate receptor 1 (mGluR1) in human brain

359 Objectives The metabotropic glutamate receptor 1 (mGluR1) may play a role in several neuropsychiatric disorders. Therefore a radioligand for mGluR1 would be useful to study the potential pathophysiological role of this receptor and may also facilitate therapeutic drug development aimed at this target. We recently reported that the novel radioligand [18F]FIMX provides excellent imaging of mGluR1 in monkey brain, showing high uptake, appropriate regional distribution (i.e., especially high in cerebellum), fast washout, and high receptor-specific signal. We present here preliminary PET imaging results in humans Methods To date, three healthy volunteers have been injected with [18F]FIMX. The first was imaged for two hours from head to mid-thigh to estimate the biodistribution of the radioligand. The other two had a two-hour dynamic brain PET scan with arterial input function to perform kinetic modeling Results All subjects had regional radioactivity distributions in brain reflecting that expected for mGluR1. The cerebellum had highest uptake (3 SUV at 15 min, decreasing to 1.8 at 120 min), whereas the uptake in other cortical regions with low density of mGluR1 ranged from 0.3 to 1 SUV at 120 min. Initial kinetic modeling with arterial input function suggests the data are well fit with a two-compartment model. VT (mL/cm3) in cerebellum was ~ 5, whereas that in caudate was ~ 1.3. Plasma free fraction was about 0.7%. The whole body images showed a high and accumulating activity in bowel and bladder, suggesting substantial fecal and urinary excretion routes. Uptake of radioactivity in skull appears absent. Conclusions As in monkey, [18F]FIMX shows promising characteristics for quantify mGluR1 in humans, based on initial results from three subjects
A Model Study of an Error-Free Magnetization Reversal Through Dipolar Coupling in a Two-Magnet System

A systematic study on the feasibility of an error-free switching of two nanomagnets coupled via their dipolar fields by applying a spin current to one of them is presented. It is demonstrated that the dynamic nature of dipolar interaction between the nanomagnets may cause the magnetization of the second magnet to precess back to its original state despite having crossed the free-axis equatorial plane during the transient phase. This non-reversal is very different than the purely successful or unsuccessful switchings noted in other reversal analyses presented in the literature and, in this paper, is referred to as a dipolar switching glitch. The dynamic dipolar coupling between nanomagnets creates temporary titled precessional trajectories pushing the magnetization of the nanomagnet into high-energy states. Relaxation from these high-energy positions leads to fast, but quasi-random switching behavior. The maximum separation between the magnets for perfect coupling has been quantified as a function of the magnet planar dimensions. It is also shown that the simpler models that do not consider the mutual coupling between the two magnets underestimate the maximum allowed separation between the two magnets and, as such, are too conservative.
A Convex Alternative to IBM Model 2

The IBM translation models have been hugely influential in statistical machine translation; they are the basis of the alignment models used in modern translation systems. Excluding IBM Model 1, the IBM translation models, and practically all variants proposed in the literature, have relied on the optimization of likelihood functions or similar functions that are non-convex, and hence have multiple local optima. In this paper we introduce a convex relaxation of IBM Model 2, and describe an optimization algorithm for the relaxation based on a subgradient method combined with exponentiated-gradient updates. Our approach gives the same level of alignment accuracy as IBM Model 2.
Southern Internal Medicine Conference: Whipple’s Disease

ABSTRACT Whipple’s disease is a systemic bacterial infection that once was uniformly fatal and now is treatable with several different antibiotics in most cases. The exact nature of the Whipple’s bacillus is unknown, since the organism cannot consistently be cultured. There is also controversy concerning the role of immunologic dysfunction in patients with Whipple’s disease. In addition to the small intestine, Whipple’s disease can involve the remainder of the gastrointestinal tract, as well as the lymph nodes, joints, nervous system, heart, eyes, hematopoietic system, lungs, liver, and other organs. The clinical manifestations, diagnosis, and treatment of this rare but fascinating disease will be reviewed in this article.
WebNav: A New Large-Scale Task for Natural Language based Sequential Decision Making.

We propose a goal-driven web navigation as a benchmark task for evaluating an agent with abilities to understand natural language and plan on partially observed environments. In this challenging task, an agent navigates through a web site, which is represented as a graph consisting of web pages as nodes and hyperlinks as directed edges, to find a web page in which a query appears. The agent is required to have sophisticated high-level reasoning based on natural languages and efficient sequential decision making capability to succeed. We release a software tool, called WebNav, that automatically transforms a website into this goal-driven web navigation task, and as an example, we make WikiNav, a dataset constructed from the English Wikipedia containing approximately 5 million articles and more than 12 million queries for training. We evaluate two different agents based on neural networks on the WikiNav and provide the human performance. Our results show the difficulty of the task for both humans and machines. With this benchmark, we expect faster progress in developing artificial agents with natural language understanding and planning skills.
‘Grey Dawn’ in the British Pacific: Race, Security and Colonial Sovereignty on the Eve of World War I

This article examines the way a group of colonies on the far reaches of British power – Australia, New Zealand, Canada, and India, dealt with the imperatives of their own security in the early twentieth century. Each of these evolved into Dominion status and then to sovereign statehood (India lastly and most thoroughly) over the first half of the twentieth century, and their sovereignties evolved amidst a number of related and often countervailing problems of self-defence and cooperative security strategy within the British Empire. The article examines how security – the abstracted political goods of military force – worked alongside race in the greater Pacific to build colonial sovereignties before the First World War. Its first section examines the internal-domestic dimension of sovereignty and its need to secure territory through the issue of imperial naval subsidies. A number of colonies paid subsidies to Britain to support the Royal Navy and thus to contribute in financial terms to their strategic de...
On the composition of the critical nucleus in phase separating glasses

Consideration is given to the composition of the critical nucleus in phase separating glasses. Using very weak assumptions it is shown that this composition always falls outside the phase diagram (binodal). This result is quite general and is independent of the free energy solution model employed.