cssi/SciSciGPT-SciSciNet huggingface dataset:
Fast and anisotropic flexibility-rigidity index for protein flexibility and fluctuation analysis

Protein structural fluctuation, typically measured by Debye-Waller factors, or B-factors, is a manifestation of protein flexibility, which strongly correlates to protein function. The flexibility-rigidity index (FRI) is a newly proposed method for the construction of atomic rigidity functions required in the theory of continuum elasticity with atomic rigidity, which is a new multiscale formalism for describing excessively large biomolecular systems. The FRI method analyzes protein rigidity and flexibility and is capable of predicting protein B-factors without resorting to matrix diagonalization. A fundamental assumption used in the FRI is that protein structures are uniquely determined by various internal and external interactions, while the protein functions, such as stability and flexibility, are solely determined by the structure. As such, one can predict protein flexibility without resorting to the protein interaction Hamiltonian. Consequently, bypassing the matrix diagonalization, the original FRI has a computational complexity of O(N2). This work introduces a fast FRI (fFRI) algorithm for the flexibility analysis of large macromolecules. The proposed fFRI further reduces the computational complexity to O(N). Additionally, we propose anisotropic FRI (aFRI) algorithms for the analysis of protein collective dynamics. The aFRI algorithms permit adaptive Hessian matrices, from a completely global 3N × 3N matrix to completely local 3 × 3 matrices. These 3 × 3 matrices, despite being calculated locally, also contain non-local correlation information. Eigenvectors obtained from the proposed aFRI algorithms are able to demonstrate collective motions. Moreover, we investigate the performance of FRI by employing four families of radial basis correlation functions. Both parameter optimized and parameter-free FRI methods are explored. Furthermore, we compare the accuracy and efficiency of FRI with some established approaches to flexibility analysis, namely, normal mode analysis and Gaussian network model (GNM). The accuracy of the FRI method is tested using four sets of proteins, three sets of relatively small-, medium-, and large-sized structures and an extended set of 365 proteins. A fifth set of proteins is used to compare the efficiency of the FRI, fFRI, aFRI, and GNM methods. Intensive validation and comparison indicate that the FRI, particularly the fFRI, is orders of magnitude more efficient and about 10% more accurate overall than some of the most popular methods in the field. The proposed fFRI is able to predict B-factors for α-carbons of the HIV virus capsid (313 236 residues) in less than 30 seconds on a single processor using only one core. Finally, we demonstrate the application of FRI and aFRI to protein domain analysis.
Syringomyelia: An Expanding Problem

Syringomyelia, a central cavitation of the spinal cord, was once thought to be a rare disorder. Associated with congenital malformations as well as trauma and tumors, a syringomyelia can cause a variety of sensory complaints, including parasthesias, changes in temperature recognition, and pain. Other symptoms may range from gastrointestinal problems to shoulder arthropathy. Left unchecked, a syringomyelia can expand and lead to permanent disability. The nurse practitioner should be suspicious of the presence of a syrinx in patients who have otherwise unexplained sensory deficits that follow cervical or thoracic dermatomes.
Isolated Synthetic Jet in Crossflow: Experimental Protocols for a Validation Dataset

An overview of the data acquisition, reduction, and uncertainty estimates of experimental measurements made of the flowfield created by the interaction of an isolated synthetic jet and a turbulent boundary layer is presented. The experimental measurements were undertaken to serve as the second of three computational fluid dynamics validation databases for active flow control. The validation databases were first presented at the NASA Langley Research Center Workshop on CFD Validation of Synthetic Jets and Turbulent Separation Control (CFDVAL2004) in March 2004. Detailed measurements were made to document the boundary conditions for the flow and also for the phase-averaged flowfield itself. Three component laser-Doppler velocimetry, 2-D particle image velocimetry, and stereo particle image velocimetry were used to document the phase-averaged velocity field and the turbulent stresses.
Port-A-Cath insertions in acute leukaemia and childhood malignancies.

Objective This retrospective case series sought to determine the incidence and profile of catheter-related complications associated with Port-A-Cath insertions in paediatric cancer patients, as well as predictive factors for infection-related port removals. Methods Between January 2002 and December 2004, 175 consecutive Port-A-Cath insertions were followed for a total of 75,000 days (median, 407; range, 6–1,074). Incidence of catheter-related bloodstream infections (CRBSIs), other complications and CRBSI-related port removals were analysed for cases with acute leukaemia versus other malignancies. Results A total of 33 CRBSIs were encountered in 26 cases (18.9%), an infection rate of 0.44 episodes per 1,000 catheter days. While mean preoperative platelet count was 125.34 ×10 9 /L in children with acute leukaemia and 392.11× 10 9 /L in those with other malignancies ( p Staphylococcus epidermidis (23.1%) and Klebsiella spp. (19.2%) were most commonly isolated from infected ports. Median patient age and duration of implantation in CRBSI-related port removals was 1.5 years and 111 days respectively, and 10.0 years and 414 days respectively in CRBSIs without port removal. Conclusion Minimal complications are associated with Port-A-Cath insertions, even in thrombocy-topaenic leukaemic patients. The dominance of Gram-negative organisms in CRBSIs parallels the changing trend of nosocomial infectious agents involved in catheter-related infections.
Second harmonic studies of ions crossing liposome membranes in real time.

The transport kinetics of the positively charged triphenylmethane dye, malachite green (MG+), across liposome bilayers effects the transport of monovalent inorganic cations when ionophores are pres...
History and evolution of Fresnel zone plate antennas for microwaves and millimeter waves

This paper summarizes some of the growth in technology for Fresnel zone plate antennas in the microwave and millimeter-wave regions. A description is given of the earliest developments of Fresnel zone plates at optical frequencies. Most of the material concerns previous results obtained for microwaves and millimeter-waves.
Hydroperoxoferric heme intermediate as a second electrophilic oxidant in cytochrome P450-catalyzed reactions

Experimental evidence supporting the catalytic activity of the peroxoferric and hydroperoxoferric cytochrome P450 intermediates as alternative oxidants to the compound I (ferryl) state in the oxygenation of organic substrates is reviewed. The peroxoferric P450 state is proposed to function as a nucleophile in the lyase step of the P450-aromatase reaction. Several systems are reviewed in which the hydroperoxoferric P450 intermediate likely functions as a second electrophilic oxidant, the “two-oxidants” model. These include alkene epoxidation, sulfoxidation, and hydroxylation of methyl groups on cyclopropane rings. The key use of the P450 mutants from different sources in which the conserved threonine in the distal substrate binding pocket is replaced with alanine, in order to minimize the formation of the compound I intermediate and unmask the reactivity of the hydroperoxoferric state, is emphasized. These data are discussed in the context of the “two-states” model, which proposes that the compound I P450 intermediate has both high- and low-spin states with different reactivities. A complicated reaction profile emerges for the wide range of P450 reactions involving up to three reactive intermediates, of which the most reactive, the compound I P450 state, has two spin states with different reactivities.
Atom transfer and electron exchange processes with cobalt complexes

The results of some investigations of several redox processes involving cobalt complexes are presented. For the first group of reactions below, oxidation appears to be accomplished in a single act by the direct addition of the oxidizing atom or group to the cobaltous complex: On the other hand, cases studied which appear to involve an electron transfer type of process include: (1) Co(CN)5−3+Fe(CN)6−3+H2O= [Co(CN)5(H2O)]−2+Fe(CN)6−4 (2) Co(C2O4)3−4+Ce(IV)=Co(C2O4)5−3+Ce(III) (3) CoV−2+Fe(CN)5−3=CoV−1+Fe(CN)6−4 (V=ethylene diaminetetracetate) (4) Co*(C2O4)3−4+Co(C2O4)3−3 = exchange (5) Co V−2+Co*V−1 = exchange Reactions of the first type are generally faster than those of the second, and possible explanations are discussed, along with some details of the kinetics of the reactions and a description of the several new complexes involved. In particular, an examination of the energy level diagrams predicted by Crystal Field Theory provides some explanation of the slowness of the electron transfer processes.
Reduction-based analysis of BGP systems with BGPVerif

Today's inter-domain routing protocol, the Border Gateway Protocol (BGP), is increasingly complicated and fragile due to policy misconfiguration by individual autonomous systems (ASes). Existing configuration analysis techniques are either manual and tedious, or do not scale beyond a small number of nodes due to the state explosion problem. To aid the diagnosis of misconfigurations in real-world large BGP systems, this paper presents BGPVerif , a reduction based analysis toolkit. The key idea is to reduce BGP system size prior to analysis while preserving crucial correctness properties. BGPVerif consists of two components, NetReducer that simplifies BGP configurations, and NetAnalyzer that automatically detects routing oscillation. BGPVerif accepts a wide range of BGP configuration inputs ranging from real-world traces (Rocketfuel network topologies), randomly generated BGP networks (GT-ITM), Cisco configuration guidelines, as well as arbitrary user-defined networks. BGPVerif illustrates the applicability, efficiency, and benefits of the reduction technique, it also introduces an infrastructure that enables networking researchers to interact with advanced formal method tool.
Start-up, short-circuit and dynamic characteristics of the full-load-range ZVS hybrid converter

A soft-switching hybrid converter achieving zero-voltage switching over the full load-range and significant reduction in the filter requirement was proposed by R. Ayyanar et al. (see IEEE Trans. Power Electron., vol.16, p.184-200, 2001). It uses a combination of a normally uncontrolled section and a controlled section using two transformers to achieve the improved soft-switching characteristics and reduction in the filter requirement. This paper discusses in detail the start-up, short-circuit and dynamic characteristics of the hybrid converter, which were previously considered inferior to those of the conventional full-bridge converters.
Water versus NaCl intake by rats administered certain dipsogens acutely.

Abstract Isotonic saline was ingested in a greater volume than water when any one of three dipsogenic agents [L-5-hydroxytryptophan (25 mg/kg, SC), isoproterenol (25 μg/kg, SC), and angiotensin II (100 μg/kg, SC)] was administered acutely to rats given either isotonic saline or water to drink. These results are consistent with, but not exclusive to, the hypothesis that feedback inhibition of ingested isotonic saline on further fluid intake is less than that of water. Additional studies showed that the dipsogenic response to angiotensin II (200 μg/kg, SC) decreased as the concentration of NaCl solution offered to drink increased beyond 0.15 M in rats given either water or NaCl solution to drink. This suggests the possibility that the intensity of taste of the NaCl solutions may be a factor in their intake ander these conditions, although the intake of these salt solutions by untreated controls did not reflect this. When the rats were allowed to choose between either 0.15 or 0.25 M NaCl solution and water, administration of angiotensin II (either 100 or 200 μg/kg, SC) increased water intake in preference to the NaCl solution. These results suggest that the rat, ander these conditions, has a preference for water over NaCl solution.
Ethanol Fuels: Energy Balance, Economics, and Environmental Impacts are Negative

Several studies suggest that the $1.4 billion in government subsidies are encouraging the ethanol program without substantial benefits to the U.S. economy. Large ethanol industries and a few U.S. government agencies, such as the USDA, support the production of ethanol. Corn-farmers receive minimal profits. In the U.S. ethanol system, considerably more energy, including high-grade fossil fuel, is required to produce ethanol than is available in the energy-ethanol output. Specifically about 29% more energy is used to produce a gallon of ethanol than the energy in a gallon of ethanol. Fossil energy powers corn production and the fermentation/distillation processes. Increasing subsidized ethanol production will take more feed from livestock production, and is estimated to currently cost consumers an additional $1 billion per year. Ethanol production increases environmental degradation. Corn production causes more total soil erosion than any other crop. Also, corn production uses more insecticides, herbicides, and nitrogen fertilizers than any other crop. All these factors degrade the agricultural and natural environment and contribute to water pollution and air pollution. Increasing the cost of food and diverting human food resources to the costly inefficient production of ethanol fuel raise major ethical questions. These occur at a time when more than half of the world's population is malnourished. The ethical priority for corn and other food crops should be for food and feed. Subsidized ethanol produced from U.S. corn is not a renewable energy source.
Landsat-7 ETM+ on-orbit reflective-band radiometric stability and absolute calibration

Launched in April 1999, the Landsat-7 Enhanced Thematic Mapper Plus (ETM+) instrument is in its sixth year of operation. The ETM+ instrument has been the most stable of any of the Landsat instruments. To date, the best onboard calibration source for the reflective bands has been the Full Aperture Solar Calibrator, a solar-diffuser-based system, which has indicated changes of between 1% to 2% per year in the ETM+ gain for bands 1-4 and 8 and less than 0.5%/year for bands 5 and 7. However, most of this change is believed to be caused by changes in the solar diffuser panel, as opposed to a change in the instrument's gain. This belief is based partially on vicarious calibrations and observations of "invariant sites", hyperarid sites of the Sahara and Arabia. Weighted average slopes determined from these datasets suggest changes of 0.0% to 0.4% per year for bands 1-4 and 8 and 0.4% to 0.5% per year for bands 5 and 7. Absolute calibration of the reflective bands of the ETM+ is consistent with vicarious observations and other sensors generally at the 5% level, though there appear to be some systematic differences.
On “best” interpolation☆

Abstract Recent interest in the problem of minimizing ∥ f (k) ∥ ∞ under the constraint that ft i ) = f 0 ( t i ), i = 1,…, n + k , for some given f 0 and given ( t i ) 1 n + k seems to make it worthwhile to explain how Favard solved this problem in the thirties, particularly since Favard's paper on the subject is rather sketchy in places. The explanation is given in terms of a dual problem, using a technique initiated by M. Krein. In addition, the analogous problem of minimizing ∥ f (k) ∥ p for 1 ⩽ p
Linking H3K79 trimethylation to Wnt signaling through a novel Dot1-containing complex (DotCom)

Epigenetic modifications of chromatin play an important role in the regulation of gene expression. KMT4/Dot1 is a conserved histone methyltransferase capable of methylating chromatin on Lys79 of histone H3 (H3K79). Here we report the identification of a multisubunit Dot1 complex (DotCom), which includes several of the mixed lineage leukemia (MLL) partners in leukemia such as ENL, AF9/MLLT3, AF17/MLLT6, and AF10/MLLT10, as well as the known Wnt pathway modifiers TRRAP, Skp1, and b-catenin. We demonstrated that the human DotCom is indeed capable of trimethylating H3K79 and, given the association of b-catenin, Skp1, and TRRAP, we investigated, and found, a role for Dot1 in Wnt/Wingless signaling in an in vivo model system. Knockdown of Dot1 in Drosophila results in decreased expression of a subset of Wingless target genes. Furthermore, the loss of expression for the Drosophila homologs of the Dot1-associated proteins involved in the regulation of H3K79 shows a similar reduction in expression of these Wingless targets. From yeast to human, specific trimethylation of H3K79 by Dot1 requires the monoubiquitination of histone H2B by the Rad6/Bre1 complex. Here, we demonstrate that depletion of Bre1, the E3 ligase required for H2B monoubiquitination, leads specifically to reduced bulk H3K79 trimethylation levels and a reduction in expression of many Wingless targets. Overall, our study describes for the first time the components of DotCom and links the specific regulation of H3K79 trimethylation by Dot1 and its associated factors to the Wnt/Wingless signaling pathway.
A Semantic Framework for Mode Change Protocols

We present a unified framework for the specification and analysis of mode-change protocols used in multi-mode real-time systems. We propose a highly expressive formalism, called MCP, to model the system behavior during mode transitions, and show how various existing mode change protocols can be described as MCPs. The explicit representation of the MCP model provides a means to analyze the system state during a mode transition as well as during an intra-mode execution. We introduce the concept of feasibility with respect to the MCP model, and give a decidable method for checking the feasibility of a MCP for a given multi-mode system. The formalization of mode change behaviors using the MCP model allows a range of mode change protocols to be modeled, evaluated, and optimized to the specific operations and performance requirements of the system. Besides feasibility analysis, it is also possible to analyze other system behaviors (e.g., delay between modes, buffer backlog) using automata verification techniques. Our framework can also be used to describe mode change semantics of multi-mode systems whose modes/transitions have different criticality levels, or of systems composed of multiple multi-mode components that require different mode change protocols.
Regulation of Telomere Length and Telomerase in T and B Cells: A Mechanism for Maintaining Replicative Potential

Recent studies have established that telomere length is altered during differentiation of both T and B lymphocytes. There exists a clear and strong correlation of replicative capacity with telomere length in normal somatic cells. In human T cells, this correlation extends to differences in telomere length and replicative capacity in subsets such as naive and memory CD4 cells, or CD28−positive and negative CD8 T cells. In addition, telomerase, a unique reverse transcriptase that is capable of extending telomeric length, is highly regulated during development and activation of both T and B lymphocytes. Together, these findings have provided a basis for hypotheses linking telomere length regulation to a functional role in sustaining the capacity for extensive clonal expansion in antigen-specific lymphocytes. In addition to providing insights into basic immune function, manipulation of telomere length has potential therapeutic applications as well. For example, the ability to extend the replicative capacity of cells such as hematopoietic stem cells or mature lymphocytes through telomerase induction by transfection could be critical to therapeutic approaches to adoptive cell transfer or reconstitution. In assessing the feasibility of such approaches, it will be critical not only to measure extension of the capacity for cell division but also to consider other possible consequences such as enhanced susceptibility to malignant transformation through dysregulated telomerase activity. Conversely, the proposed use of telomerase inhibition as a modality for anticancer therapy should consider the possible impact of such intervention on any telomerase-dependent aspects of immune function. The rapid pace of gene discovery and genetic engineering, in combination with a richness of available systems for studying immune cell biology, should allow vigorous pursuit of these remaining questions.‡To whom correspondence should be addressed (e-mail: Richard_Hodes@nih.gov).
Licking Microstructure Reveals Rapid Attenuation of Neophobia

Many animals hesitate when initially consuming a novel food and increase their consumption of that food between the first and second sessions of access-a process termed attenuation of neophobia (AN). AN has received attention as a model of learning and memory; it has been suggested that plasticity resulting from an association of the novel tastant with "safe outcome" results in a change in the neural response to the tastant during the second session, such that consumption increases. Most studies have reported that AN emerges only an hour or more after the end of the first exposure to the tastant, consistent with what is known of learning-related plasticity. But these studies have typically measured consumption, rather than real-time behavior, and thus the possibility exists that a more rapidly developing AN remains to be discovered. Here, we tested this possibility, examining both consumption and individual lick times in a novel variant of a brief-access task (BAT). When quantified in terms of consumption, data from the BAT accorded well with the results of a classic one-bottle task-both revealed neophobia/AN specific to higher concentrations (for instance, 28mM) of saccharin. An analysis of licking microstructure, however, additionally revealed a real-time correlate of neophobia-an explicit tendency, similarly specific for 28-mM saccharin, to cut short the initial bout of licks in a single trial (compared with water). This relative hesitancy (i.e., the shortness of the first lick bout to 28-mM saccharin compared with water) that constitutes neophobia not only disappeared between sessions but also gradually declined in magnitude across session 1. These data demonstrate that the BAT accurately measures AN, and that aspects of AN-and the processes underlying familiarization-begin within minutes of the very first taste.
Rank Reversal in Indirect Comparisons

Objective: To describe rank reversal as a source of inconsistent interpretation intrinsic to indirect comparison (Bucher HC, Guyatt GH, Griffith LE, Walter SD. The results of direct and indirect treatment comparisons in meta-analysisofrandomizedcontrolledtrials.JClinEpi1997;50:683‐91)of treatments and to propose best practice. Methods: We prove our main points with intuition, examples, graphs, and mathematical proofs. We also provide software and discuss implications for research and policy. Results: When comparing treatments by indirect means and sorting them by effect size, three common measures of comparison (risk ratio, risk difference, and odds ratio) may lead to vastly different rankings. Conclusions: The choice of risk measure matters when making indirect comparisons of treatments. The choice should depend primarily on the study design and the conceptual framework for that study.
Facial analysis and synthesis using image-based models

In this paper we describe image-based modeling techniques that make possible the creation of photo-realistic computer models of real human faces. The image-based model is built using example views of the face, bypassing the need for any three-dimensional computer graphics models. A learning network is trained to associate each of the example images with a set of pose and expression parameters. For a novel set of parameters, the network synthesizes a novel, intermediate view using a morphing approach. This image-based synthesis paradigm can adequately model both rigid and non-rigid facial movements. We also describe an analysis-by-synthesis algorithm, which is capable of extracting a set of high-level parameters from an image sequence involving facial movement using embedded image-based models. The parameters of the models are perturbed in a local and independent manner for each image until a correspondence-based error metric is minimized. A small sample of experimental results is presented.
Energy content of methyl radicals produced in the UV photodissociation of azomethane

Abstract A pulsed UV laser has been used to photolyze azomethane and effect state-selective ionization of neutral methyl photofragments. The resultant methyl ions, detected using time-of-flight mass spectrometry, have translational energies consistent with one of the two energetically distinct methyl photofragments observed in a study carried out by North et al. A recently developed barrier impulsive model provides a good qualitative prediction of the observed methyl photofragment kinetic energy. In addition, the partitioning of energy within the methyl photofragment observed in this study is consistent with its having originated from the second step in the overall dissociation process (CH3N2 → CH3′ + N2).
THE KITH AND KIN OF EDUCATIONAL MEASURERS1

This discussion is a plea for educational measurement specialists to broaden the repertoire of methodologies for data collection and analysis by borrowing from elsewhere than psychology and agronomy. It suggests that such disciplines as history, economics, and sociology have techniques highly appropriate to evaluation of educational endeavors.
Geographic distribution of stroke mortality in the United States 1939‐1941 to 1979‐1981

I used data from the National Center for Health Statistics to map the geographic distribution of age-adjusted, race- and gender-specific stroke mortality rates in the United States from 1939-1941 to 1979-1981. Over this interval, stroke mortality rates declined dramatically with convergence of age-adjusted, state-specific stroke rates both within and between the various race-gender groups. For each race-gender group, high age-adjusted stroke mortality rates were significantly clustered in the southeastern United States, particularly in the South Atlantic census division, with persistent extreme rates in Georgia and the Carolinas. For whites, low-rate states were concentrated in the Mountain census division and along the northern Atlantic coast. The nonrandom distribution of stroke mortality across the United States, the large magnitude of the difference between high- and low-rate areas, the persistence of the pattern over more than four decades, the similarity of the distribution for different race-gender groups, the lack of delimitation by administrative or political boundaries, and results of national cooperative studies completed in the late 1960s and early 1970s together suggest that the pattern of excess stroke mortality is not an artifact of different diagnostic and reporting practices. Some of the observed geographic variation may be due to both the effects of selective migration and variations in the distributions of stroke risk factors.
The transverse and oblique cylindrical equal-area projection of the ellipsoid.

To prepare an equal-area map of a region predominantly north to south in extent or along an oblique great circle route, the transverse or oblique cylindrical equal-area projection has long been available for the sphere. To minimize shape and scale distortion along and near the central line of a larger-scale map and to eliminate all area distortion, this projection should be based on the ellipsoid. The formulas for the ellipsoidal projection are derived for both forward and inverse computations and consist of modifying the formulas obtained by using the authalic sphere so that the scale along the central line of the projection is constant. Fourier series are used to eliminate recurring numerical integration and other lengthy trigonometric computations of coordinates.
Implementation of an interpreter for abstract equations

This paper summarizes a project whose goal is the implementation of a useful interpreter for abstract equations that is absolutely faithful to the logical semantics of equations. The interpreter was first distributed to Berkeley UNIX VAX sites in May 1983. The main novelties of the interpreter are strict adherence to semantics based on logical consequences, ‘lazy’ (outermost) evaluation applied uniformly, an implementation based on table-driven pattern matching, with no run-time penalty for large sets of equations, and strict separation of syntactic and semantic processing, so that different syntaxes may be used for different problems.
The Liberal Peace and Conflictive Interactions: The Onset of Militarized Interstate Disputes, 1950-78

Over the past few years, there has been an increasing focus on the connection at the dyadic level between democracy, interdependence, and international conflict. This has led to some contention, with scholars taking different positions on both substantive and methodological matters. This article seeks to advance this literature by building explicitly on the work of Oneal and Russett. It adds an additional facet to this literature: exploring the impact of conflictive interactions on the chances of a dyad experiencing conflict. A conflictive interaction is the presence of a conflict below the level at which military force is used. The question is whether the issue at stake in a conflictive interaction influences the chances of the dyad experiencing a militarized interstate dispute (MID). The scope of the research is all dyads from 1950 to 1978, with observations at the quarter-year. Results are generally consistent with Oneal and Russett. However, there are several differences. First, the effect of joint democracy, while negative, is not statistically significant (this may be an artifact of our research design). Second, the coefficient for the higher trade-to-GDP ratio, while positive as in their work, is statistically significant here. But trade does reduce conflict (as embodied in the lower trade-to-GDP ratio) even when including the 'peaceyears' correction for temporal dependence. As for the impact of issue area, conflictive interactions involving issues of 'high politics' increase the chances of a dispute. Thus, elements of both 'high politics' and the liberal peace have independent impacts on the chances of an MID outbreak.
Production and Characterization of Synthetic Carboxysome Shells with Incorporated Luminal Proteins

Spatial segregation of metabolism, such as cellular-localized CO2 fixation in C4 plants or in the cyanobacterial carboxysome, enhances the activity of inefficient enzymes by selectively concentrating them with their substrates. The carboxysome and other bacterial microcompartments (BMCs) have drawn particular attention for bioengineering of nanoreactors because they are self-assembling proteinaceous organelles. All BMCs share an architecturally similar, selectively permeable shell that encapsulates enzymes. Fundamental to engineering carboxysomes and other BMCs for applications in plant synthetic biology and metabolic engineering is understanding the structural determinants of cargo packaging and shell permeability. Here we describe the expression of a synthetic operon in Escherichia coli that produces carboxysome shells. Protein domains native to the carboxysome core were used to encapsulate foreign cargo into the synthetic shells. These synthetic shells can be purified to homogeneity with or without luminal proteins. Our results not only further the understanding of protein-protein interactions governing carboxysome assembly, but also establish a platform to study shell permeability and the structural basis of the function of intact BMC shells both in vivo and in vitro. This system will be especially useful for developing synthetic carboxysomes for plant engineering.
Clonidine Evokes Vasodepressor Responses via α2-Adrenergic Receptors in Gigantocellular Reticular Formation

The gigantocellular depressor area (GiDA) is a functionally defined subdivision of the medullary gigantocellular reticular formation where vasodepressor responses are evoked by glutamate nanoinjections. The GiDA also contains reticulospinal neurons that contain the alpha2A-adrenergic receptor (alpha2A-AR). In the present study, we sought to determine whether nanoinjections of the alpha2-AR agonist clonidine into the GiDA evoke cardiovascular responses and whether these responses can be attributed to the alpha2-AR. We found that nanoinjections of clonidine into the GiDA evoke dose-dependent decreases in arterial pressure and heart rate. These responses were equivalent in magnitude to responses produced by clonidine nanoinjections into the sympathoexcitatory region of the rostral ventrolateral medulla. Furthermore, the vasodepressor and bradycardic responses produced by clonidine injections into the GiDA were blocked in a dose-dependent fashion by the highly selective alpha2-AR antagonist 2-methoxyidazoxan, but not by prazosin, which is an antagonist at both the alpha1-AR and the 2B subtype of the alpha-AR. The antagonism by 2-methoxyidazoxan was site specific because injections of the antagonist into the rostral ventrolateral medulla failed to block the responses evoked by clonidine injections into the GiDA. These findings support the notion that clonidine produces sympathoinhibition through multiple sites within the medullary reticular formation, which is consistent with the wide distribution of the alpha2A-AR in reticulospinal neurons. These data also suggest that clonidine may have multiple mechanisms of action because it evokes a cardiovascular depressive response from regions containing neurons that have been determined to be both sympathoinhibitory and sympathoexcitatory.
Learning About Sickle Cell: The Patient in Early Sickle Cell Disease Case Reports, 1910–1933

Case reports of sickle cell disease (SCD) from its discovery in 1910 to 1933 provide glimpses into the disease's impact on patients and families. Attending physicians, trying to understand the pathophysiology of and treatments for this newly recognized disease, reported also on the effect of SCD on patients' ability to attend school, play, and work, the kinds and severity of the pain patients endured, the late onset of puberty and slowed development of secondary sex characteristics, and the ways families dealt with loved ones who had the disease. These anonymous patients and families helped "teach" physicians about SCD in the early years after its discovery. The current study uses information gleaned from the third published article in 1915 to 1933.
Phase II trial of preoperative bevacizumab (Bev), irinotecan (I), cisplatin (C), and radiation (RT) in esophageal adenocarcinoma: Preliminary safety analysis

4573 Background: Preo chemoRT with weekly I/C and 5040 cGy followed by surgery is well tolerated [JCO 24: Abstract 4032; 2006]. ECOG trial E1201recently reported a median survival of 34 months with this preop regimen [JCO 26: Abstract 4532; 2008]. Bev + chemo improves response rate (RR) and time to progression (TTP) when added to weekly I/C in advanced esophagogastric cancer but does not increase chemo toxicity [JCO 24: 5201; 2006]. We are now combining in a Phase II trial Bev/I/C with concurrent radiotherapy (RT) in esophageal adenocarcinoma (EA) with the primary endpoint of safety. Methods: Patients (pts) with resectable Siewert's I or II EA were staged by EUS, PET, and CT. Induction chemo consisted of I-50–65 mg/m2 and C-30 mg/m2 weeks 1,2,4,5, Bev-7.5 mg/kg weeks 1 and 4; and, during RT (180 cGy daily to 5040 cGy), I/C was given weeks 7,8,10,11 and Bev weeks 7,10. Esophagectomy was 6–8 weeks after RT. A planned toxicity analysis was made in 10–15 pts completing chemoRT, and in 10 pts undergoing surger...
Tsars, Task Forces and Standards: The New “IRS”?

Institutional processes for regulating government-nonprofit relations in the U.S. are experiencing substantial growth, particularly at the state level. First, cabinet-level nonprofit “tsars” are being appointed by state governments as point persons for communication and coordination with nonprofits. Second, high-level cross-sector task forces are being established to examine the current relations between the sectors and to recommend reforms in regulatory and oversight processes. Third, nonprofit industry associations are developing statements of operating standards that seek to promote greater discipline in operations. These processes are potentially harbingers of the creation of new institutionalized relationship systems (IRS). This paper examines the emergence of these new institutional arrangements, analyzes their short-term impacts and speculates about their durability.
Effect of fluorides and other solutions on solubility of powdered enamel in acid.

SummaryThe solubility of powdered human tooth enamel was measured after treatment with stannous fluoride, sodium fluoride, sodium N-palmitoyl sarcosinate, sodium de-hydroacetate, or sodium oxalate by a method which measures the amount of phosphorus dissolved from the treated enamel by acetic acid. The data indicate that stannous fluoride is markedly superior to sodium fluoride and that the sarcosinate is of only questionable value in its ability to reduce powdered enamel solubility. Sodium dehydroacetate and sodium oxalate were without effect in decreasing the solubility of powdered enamel.The author wishes to acknowledge the technical assistance of Mrs. Dorothy McKinney throughout this study.
Supramolecular photochemistry in solution and on surfaces: Encapsulation and dynamics of guest molecules and communication between encapsulated and free molecules

Supramolecular assemblies that help to preorganize reactant molecules have played an important role in the development of concepts related to the control of excited-state processes. This has led to a persistent search for newer supramolecular systems (hosts), and this review briefly presents our work with octa acid (OA) to a host to control excited-state processes of organic molecules. Octa acid, a water-soluble host, forms 1:1, 2:1, and 2:2 (host–guest) complexes with various organic molecules. A majority of the guest molecules are enclosed within a capsule made up of two molecules of OA whereas OA by itself remains as a monomer or aggregates. Luminescence and 1H NMR spectroscopy help to characterize the structure and dynamics of these host–guest complexes. The guest molecule as well as the host–guest complex as a whole undergoes various types of motion, suggesting that the guests possess freedom inside the confined space of the octa acid capsule. In addition, the confined guests are not isolated but are...
Anticonvulsant effect of nialamide and diphenylhydantoin.

Summary1. Nialamide increased the maximal electroshock seizure threshold in mice and rats. This effect was independent of the elevation of brain 5-HT and NE elicited by nialamide. 2. Diphenylhydantoin in doses from 6 to 55 mg/kg, which was almost 9 times the anticonvulsive dose, did not significantly alter the content of 5-HT or NE in the brain of mice. 3. Nialamide potentiated and reserpine decreased the anticonvulsant effect of diphenylhydantoin. No correlation could be found between these effects and brain amine levels.
Treating malnutrition in AIDS: comparison of dietitians' practices and nutrition care guidelines.

The acquired immunodeficiency syndrome (AIDS) is a complex disease; its manifestations include many opportunistic infections that lead to conditions causing severe malnutrition. Overcoming malnutrition can help AIDS patients increase their weight, improve their self-image, and enhance the quality of their lives Thirty-eight dietitians who work with AIDS patients in New York City were surveyed to determine whether their facilities followed 40 suggested guidelines for the assessment and treatment of malnutrition in AIDS. Thirty dietitians (80%) reported that their facilities followed more than half of the suggested guidelines. Many guidelines were “always” followed by a majority of facilities. Those not followed might provide a focus for dialogue among practitioners with regard to nutrition care procedures. Thirty-two (84%) dietitians reported receiving AIDS education, including in-service programs (n = 18), professional meetings (n = 27), and formal education (n 3). AIDS education in both undergraduate and graduate curriculums and additional continuing education programs are needed. Persons with AIDS are at high risk tor nutrition-related disorders. Practitioners need to know and apply nutrition care guidelines suggested in the literature to improve the quality of care for this growing population.
From Books to Bots: Using Medical Literature to Create a Chat Bot

The American Medical Association Family Medical Guide is a comprehensive medical reference book for non-medical professionals. The book uses a series of flow charts to help users diagnose their symptoms by answering yes and no questions. The idea presented in this paper is to leverage the information in the book to make a chat bot for a mobile phone user. We develop a tool for crowd workers to train the chat bot using the information in the book. We present a framework for the crowd worker. Information is classified as symptom, diagnosis, or care. The chat bot makes the information accessible to people that primarily use a mobile phone and are not medical professionals. By having the data on the phone, we are able to make the data actionable by integrating it with the computational capabilities and sensors of the phone.
Energetic Contributions of Aromatic Residues in HV1 Block by 2-Guanidinoimidazoles and in HV1 Voltage-Dependent Activation

The Hv1 protein consists of four transmembrane segments folded into a voltage-sensing domain (VSD) and linked to a cytoplasmic coiled-coil domain. The channel is made of two VSD subunits, each containing a gated proton pore. 2-Guanidinobenzimidazole (2GBI) and its analogues inhibit Hv1 by acting as blockers of the channel's VSD in the open conformation. The phenylalanine at position 150 plays an important role in 2GBI binding. In particular, the aromatic ring of F150 was previously shown to interact with the condensed phenyl ring of the positively charged inhibitor. However, the physical nature of this interaction has remained elusive. F150 is also part of the gating-charge transfer center and its mutation strongly influences channel gating. Here, we used electrophysiological recordings and site-specific incorporation of unnatural amino acids via nonsense suppression methodology to investigate the energetic contributions of F150 and other aromatic residues to 2GBI binding and channel gating. We found that an encoded phenylalanine introduced at position 150 via this approach produced channels indistinguishable from wild type, while phenylalanines with one, two, or three electron-withdrawing fluorine substituents produced channels with altered 2GBI binding, gating curves, and voltage-dependent activation and deactivation kinetics. However, these alterations were inconsistent with a cation-pi interaction with endogenous residues. We also found that, under specific conditions, Hv1 aromatic residue F182 can be recruited to increase binding affinity. We discuss how our results can shed light on the involvement of cation-pi and steric interactions in the process of Hv1 inhibition by 2GBI, and in channel gating.
Parents’ Narratives in an Online PHPV Forum Toward a Typology of Caregiver Illness Narratives

The authors analyzed messages from an online support group for parents of children with Persistent Hyperplastic Primary Vitreous. This eye disorder, while not life-threatening, affects children’s eyesight and can impinge on the lives of parents and caretakers. The literature review examines Frank’s typology of illness narratives, prompting the question of whether Frank’s work is applicable to the narrative accounts of people who do not experience illness firsthand. Analysis of support group discourse not only confirms prior studies of illness narratives but also suggests that current typologies do not fully address the accounts of those who witness and are affected by the illness of another.
Green tea extract treatment reduces NFκB activation in mice with diet-induced nonalcoholic steatohepatitis by lowering TNFR1 and TLR4 expression and ligand availability

NFκB-mediated inflammation contributes to liver injury during nonalcoholic steatohepatitis (NASH). We hypothesized that antiinflammatory activities of green tea extract (GTE) during NASH would lower tumor necrosis factor receptor-1 (TNFR1)- and Toll-like receptor-4 (TLR4)-mediated NFκB activation. Male C57BL6/J mice (6 weeks old) were fed a low-fat (LF) or high-fat (HF) diet for 12 weeks to induce NASH. They were then randomized to continue on these diets supplemented with 0 or 2% GTE (n=10/group) for an additional 8 weeks prior to evaluating NASH, NFκB inflammation and TNFR1 and TLR4 receptor complexes and their respective ligands, TNFα and endotoxin. HF feeding increased (P .05) on liver histology or inflammatory responses. However, GTE in HF mice decreased biochemical and histological parameters of NASH and lowered hepatic p65 phosphorylation in association with decreased serum TNFα, mRNA expression of TNFR1 and TLR4 and MyD88 protein. GTE in HF-fed mice also lowered serum endotoxin and up-regulated mRNA expression of duodenal occludin and zonula occluden-1 and ileal occludin and claudin-1 that were otherwise lowered in expression by HF feeding. These data suggest that dietary GTE treatment reduces hepatic inflammation in NASH by decreasing proinflammatory signaling through TNFR1 and TLR4 that otherwise increases NFκB activation and liver injury.
Improved Scheduling Algorithms for Single-Path Multiple Bandwidth Reservation Requests

Colossal amounts of data are being generated in extreme-scale e-Sciences with the advent of new computation tools and experimental infrastructures. Such extremely large and complex data sets normally need to be transferred remotely for data storage and analysis. Reserving bandwidth as needed along selected paths in high-performance networks (HPNs) has proved to be an effective way to satisfy the high-demanding requirements of such data transfer. The most common data transfer requirement from users is the data transfer deadline. However, users oftentimes want to achieve other data transfer performance parameters, such as the earliest completion time (ECT) and the shortest duration (SD). For the bandwidth reservation service provider, all bandwidth reservation requests (BRRs) in one batch should be scheduled for high scheduling efficiency and system throughput. In this paper, we study the problem of scheduling all BRRs in one batch while achieving their best average transfer performance on one reservation path in an HPN. Two data transfer performance parameters, ECT and SD, are specifically considered. Because of the limited bandwidth resources of the reservation path, the problems of scheduling all BRRs in one batch on one reservation path while achieving their best average ECT and SD are converted into the problems of scheduling as many BRRs as possible while achieving the average ECT and SD of scheduled BRRs, respectively. We prove these two converted problems as NP-complete problems, and improve two existing heuristic algorithms proposed previously for similar problems. Extensive simulation experiments show the superior scheduling performance of these improved algorithms in terms of several performance metrics.