cssi/SciSciGPT-SciSciNet huggingface dataset:
S-glutathionyl quantification in the attomole range using glutaredoxin-3-catalyzed cysteine derivatization and capillary gel electrophoresis with laser-induced fluorescence detection

S-glutathionylation (Pr–SSG) is a specific post-translational modification of cysteine residues by the addition of glutathione. S-Glutathionylated proteins induced by oxidative or nitrosative stress play an essential role in understanding the pathogenesis of the aging and age-related disorder, such as Alzheimer’s disease (AD). The purpose of this research is to develop a novel and ultrasensitive method to accurately and rapidly quantify the Pr–SSG by using capillary gel electrophoresis with laser-induced fluorescence detection (CGE-LIF). The derivatization method is based on the specific reduction of protein-bound S-glutathionylation with glutaredoxin (Grx) and labeling with thiol-reactive fluorescent dye (Dylight 488 maleimide). The experiments were performed by coupling the derivatization method with CGE-LIF to study electrophoretic profiling in in vitro oxidative stress model–S-glutathionylated bovine serum albumin (BSA-SSG), oxidant-induced human colon adenocarcinoma (HT-29) cells, brain tissues, and whole blood samples from an AD transgenic (Tg) mouse model. The results showed almost an eightfold increase in S-glutathionyl abundance when subjecting HT-29 cells in an oxidant environment, resulting in Pr–SSG at 232 ± 10.64 (average ±SD; n = 3) nmol/mg. In the AD–Tg mouse model, an initial quantitative measurement demonstrated the extent of protein S-glutathionylation in three brain regions (hippocampus, cerebellum, and cerebrum), ranging from 1 to 10 nmol/mg. Additionally, we described our developed method to potentially serve as a highly desirable diagnostic tool for monitoring S-glutathionylated protein profile in minuscule amount of whole blood. The whole blood samples for S-glutathionyl expression of 5-month-old AD–Tg mice are quantified as 16.3 μmol/L (=7.2 nmol/mg protein). Altogether, this is a fast, easy, and accurate method, reaching the lowest limit of Pr–SSG detection at 1.8 attomole (amol) level, reported to date.
Mental representations of spatial and nonspatial relations.

Four experiments investigated the representation and integration in memory of spatial and nonspatial relations. Subjects learned two-dimensional spatial arrays in which critical pairs of object names were semantically related (Experiment 1), semantically and episodically related (Experiment 2), or just episodically related (Experiments 3a and 3b). Episodic relatedness was established in a paired-associate learning task that preceded array learning. After learning an array, subjects participated in two tasks: item recognition, in which the measure of interest was priming; and distance estimation. Priming in item recognition was sensitive to the Euclidean distance between object names and, for neighbouring locations, to nonspatial relations. Errors in distance estimations varied as a function of distance but were unaffected by nonspatial relations. These and other results indicated that nonspatial relations influenced the probability of encoding spatial relations between locations but did not lead to distor...
Basement thrust sheets in the Clearwater orogenic zone, central Idaho and western Montana

The Clearwater orogenic zone in central Idaho and western Montana contains at least two major northeast-directed Cordilleran thrust plates of Early Proterozoic metasedimentary and metaigneous rocks that overrode previously folded Middle Proterozoic rocks of the Belt basin in Cretaceous time. The northeastward migration of the resultant thickened wedge of crustal material combined with Cretaceous subduction along the western continental margin produced a younger northern Bitterroot lobe of the Idaho batholith relative to an older southern Atlanta lobe. Eocene extensional unroofing and erosion of the Bitterroot lobe has exposed the roots of the thick Cordilleran thrust sheets.
Biodegradability and microbial toxicity of aircraft fuel system icing inhibitors

In a pollution prevention and chemical substitution effort, the U.S. Air Force and Navy formed a joint initiative to find safer, more environmentally acceptable jet fuel system icing inhibitors (FSII) for military aircraft. Standard biochemical oxygen demand (BOD) analysis and variations of the BOD procedure were used as simple screening tools to evaluate the potential for aquatic biodegradation and microbial toxicity of proposed FSIIs. This laboratory evaluation of biological properties allows prediction of the biotreatability of the chemicals in wastewater treatment plants, and their potential application as biocides at higher concentrations. The current FSII, diethylene glycol monomethyl ether (DiEGME) was evaluated along with two new candidate compounds, dipropylene glycol and glycerol formal. At a low concentration (3.5 mg/L), DiEGME exerted a BOD5 of about 27% of theoretical oxygen demand. Test concentrations of ≥7 mg/L had decreasing oxygen consumption rate and extent, typical of a material with potential aquatic microbial toxicity. Dipropylene glycol began to moderately degrade only after more than 3 weeks exposure to microorganisms obtained from raw sewage. Glycerol formal showed no signs of biodegradation during a 5-week test period. In a simple microbial toxicity test DiEGME was most toxic, dipropylene glycol was moderately toxic, and glycerol formal showed little toxicity. At low concentrations (7 mg/L), none of the chemicals significantly inhibited microbial activity (P=0.34). ©1999 John Wiley & Sons, Inc. Environ Toxicol 14: 383–390, 1999
A dose–response study in animals to evaluate the anticoagulant effect of the stage 2 unfractionated heparin USP monograph change

The United States Pharmacopeia (USP) monograph for unfractionated heparin (UFH) was revised in October 2009. This revision was anticipated, based upon in vitro tests, to reduce UFH potency by approximately 10%. To study the potential in vivo consequences of the monograph change, we evaluated activated partial thromboplastin time (aPTT) and activated clotting time (ACT) responses in animals. Female mini-pigs and monkeys (n=8/species) were administered intravenously 60, 54, 48, or 42 U/kg and 50, 45, 40, or 35 U/kg "old" (pre-USP revision) UFH, respectively, in a Williams 4×4 crossover design. Blood samples for aPTT and ACT were collected at 15 min after dosing. The same study design was then repeated using "new" (post-USP revision) UFH. Mean "new" UFH aPTT and ACT values were generally lower than those for "old" UFH although individual animal responses varied considerably. The aPTT and ACT response was generally dose-proportional for both "old" and "new" UFH. These studies indicate that the USP monograph alteration for UFH may result in a modest reduction in the anticoagulant response across a population, but the variability in animal responses underscores the importance of individualization of clinical UFH dosing and the importance of anticoagulant test monitoring.
Condensation of nitriles with amides promoted by coordinatively unsaturated bis-nickel(II)-hydroxy complex: a new route to alkyl- and aryl-imidoylamidines

A pentacoordinate bis(μ-hydroxy) nickel dimer promotes formation of alkyl- and aryl-imidoylamidines from nitriles and ureas or amides under mild conditions.
Efficacy of topical cyclosporin 0.05% in the treatment of posterior blepharitis.

We assessed the efficacy of topical cyclosporin 0.05% ophthalmic emulsion versus tobramycin 0.3%/dexamethasone 0.1% in patients with posterior blepharitis. Posterior blepharitis improved significantly from the initial study visit with both cyclosporin treatment and tobramycin/dexamethasone. Cyclosporin provided greater improvements in Schirmer's scores (P < 0.001) and tear break-up time (P =0.018) than tobramycin/dexamethasone after 12 weeks of treatment. Eyelid health also improved in both groups, but the mean improvement in meibomian gland secretion quality was significantly greater with cyclosporin than with tobramycin/dexamethasone (P = 0.015). Moreover, a higher percentage of patients in the cyclosporin treatment group had improvements in symptoms of blurred vision, burning, and itching and more cyclosporin-treated patients experienced resolution of lid telangiectasia. The findings in this prospective study suggest that posterior blepharitis can be more effectively treated with cyclosporin than with ...
Saving China through Science: The Science Society of China, Scientific Nationalism, and Civil Society in Republican China

The Science Society of China, the first comprehensive Chinese scientific association, was actually organized in 1914 by a group of Chinese students at Cornell University in the United States. Four years later, many members returned to China, where the association, until its dissolution by the Communists in the 1950s, played a crucial role in Chinese science and society, not the least by publishing the Kexue (Science) monthly. This paper presents a twofold thesis: first, the Science Society of China and the Kexue represent attempts by Chinese scientists to create a civil society and a public sphere in Republican China. Second, in contrast to the conventional Western model, the Science Society, even as it critiqued government actions in public, maintained intimate and complex connections with successive regimes in the Republican era. If professionalism drove the Science Society's rhetoric of autonomy, scientific nationalism, I argue, moderated the association's interactions with the state in practice.
Failure Analysis and Mechanical Performance Evaluation of a Cast Aluminum Hybrid-Iron Golf Club Hosel

This article details the failure analysis of a commercial golf club hybrid-iron that fractured through the hosel during normal use. The golf club hosel was manufactured from a cast aluminum alloy, and the optical analysis revealed casting pores up to 20% through the hosel thickness. Mechanical properties of the aluminum alloy were determined for material characterization and used to construct a finite element model to analyze the performance of the material under failure conditions. In addition, a full structural scale experiment was conducted to determine the failure strength.
Reptilian gastrointestinal diseases

Owners of reptiles are beginning to demand the same level of care for their companions as do our canine and feline clients. One of the more common presenting complaints of the reptilian patient is gastrointestinal (GI) disease. Signs associated with GI disease include: anorexia, polyphagia, pica, prolapse, regurgitation, diarrhea, constipation, lethargy, and weight loss. Diagnostic modalities commonly employed in domestic species can be employed in reptiles. Anemnesis, physical examination, imaging techniques, and fecal parasite analyses are most important in herpetological medicine, as the two most common causes of GI disease are parasites and obstructive phenomena. This article reviews reported causes of GI disease and is arranged in the same manner that many would generate a list of differential diagnoses using the DAMNIT (Degenerative, Anatomic, Metabolic, Neoplastic/Nutritional, Inflammatory/Infectious, Toxic/Traumatic) scheme.
Matched G k -constructions always yield C k -continuous isogeometric elements

G k (geometrically continuous surface) constructions were developed to create surfaces that are smooth also at irregular points where, in a quad-mesh, three or more than four elements come together. Isogeometric?elements were developed to unify the representation of geometry and of engineering analysis. We show how matched G k constructions for geometry and analysis automatically yield C k isogeometric elements. This provides a formal framework for the existing and any future isogeometric elements based on geometric continuity. A construction principle for engineering analysis elements is formally verified.The principle yields isogeometric C k elements from G k -manifold constructions.The manifold representations can have irregular (extraordinary, star)points.The principle applies in any number of variables and any number of range dimensions.As a consequence, G k -constructions can directly be used to solve PDEs on manifolds
An Improved, Multiplier Adjustment Procedure for the Segregated Storage Problem

The segregated storage problem consists of determining an optimal distribution of products among existing storage compartments such that at most one product may be stored in a given compartment. The problem is solved using linear programming, Lagrangean relaxation and multiplier adjustment techniques. The procedures are easily adapted to obtain good heuristic solutions quickly. Computational results are given.
Lesion studies of human emotion and feeling.

The lesion method provides unique insight into how the human brain generates emotion and feeling. Recent work has explored a number of interesting topics including the dissociation of emotional experience from memory in patients with amnesia, the reliability of specific emotional deficits following focal brain damage (including fear and the amygdala), and the investigation of compensatory neural mechanisms in lesion patients. Several detailed case studies have challenged the necessary role of the insular cortex in both awareness and feeling by showing that even in rare instances of complete bilateral insula destruction, the patient remains fully sentient and capable of expressing and feeling emotion. These findings highlight the distributed nature of emotion processing in the human brain and emphasize the importance of utilizing the lesion method for elucidating brain–behavior relationships.
Standard errors in covariance structure models: asymptotics versus bootstrap

Commonly used formulae for standard error (SE) estimates in covariance structure analysis are derived under the assumption of a correctly specified model. In practice, a model is at best only an approximation to the real world. It is important to know whether the estimates of SEs as provided by standard software are consistent when a model is misspecified, and to understand why if not. Bootstrap procedures provide nonparametric estimates of SEs that automatically account for distribution violation. It is also necessary to know whether bootstrap estimates of SEs are consistent. This paper studies the relationship between the bootstrap estimates of SEs and those based on asymptotics. Examples are used to illustrate various versions of asymptotic variance-covariance matrices and their validity. Conditions for the consistency of the bootstrap estimates of SEs are identified and discussed. Numerical examples are provided to illustrate the relationship of different estimates of SEs and covariance matrices.
An application of Ryser's ( x,y )-theorem to a problem in statistics

Abstract A general combinatorial matrix theory result of Ryser is shown to imply the non-existence of a class of tight balanced statistical designs.
A mutation in human CMP-sialic acid hydroxylase occurred after the Homo-Pan divergence

Sialic acids are important cell-surface molecules of animals in the deuterostome lineage. Although humans do not express easily detectable amounts of N-glycolylneuraminic acid (Neu5Gc, a hydroxylated form of the common sialic acid N-acetylneuraminic acid, Neu5Ac), it is a major component in great ape tissues, except in the brain. This difference correlates with lack of the hydroxylase activity that converts CMP-Neu5Ac to CMP-Neu5Gc. Here we report cloning of human and chimpanzee hydroxylase cDNAs. Although this chimpanzee cDNA is similar to the murine homologue, the human cDNA contains a 92-bp deletion resulting in a frameshift mutation. The isolated human gene also shows evidence for this deletion. Genomic PCR analysis indicates that this deletion does not occur in any of the African great apes. The gene is localized to 6p22–p23 in both humans and great apes, which does not correspond to known chromosomal rearrangements that occurred during hominoid evolution. Thus, the lineage leading to modern humans suffered a mutation sometime after the common ancestor with the chimpanzee and bonobo, potentially affecting recognition by a variety of endogenous and exogenous sialic acid-binding lectins. Also, the expression of Neu5Gc previously reported in human fetuses and tumors as well as the traces detected in some normal adult humans must be mediated by an alternate pathway.
Leveraging Indigenous Knowledge for Sustainable Workplace Harmony: A Conflict Management Tool for International Managers

In the multinational enterprise (MNE), workplace conflict is generally managed within organisational systems adopted from the West. When MNEs operate in emerging economies, there is a potential disconnect between these systems and the conflict management preferences of local employees. We propose that international managers consider using indigenous knowledge to inform the conflict management systems in their subsidiaries in order to enhance and sustain cooperative workplace relations. Drawing on literature from management, anthropology, and international development, as well as the authors’ experience as participant observers in the industrial sector in Sri Lanka, we develop a conceptual model for ‘leveraging’ indigenous knowledge. The model is illustrated by a practical application in the Sri Lankan subsidiary of a European MNE. We conclude by suggesting that the leveraging of indigenous dispute resolution knowledge from the community into the organisation contributes to greater workplace harmony and global corporate citizenship.
DEMOGRAPHIC CORRELATES OF GROUP ACHIEVEMENT: CONTRASTING PATTERNS OF MEXICAN-AMERICANS AND JAPANESE-AMERICANS

Patterns of family size, family stability, and timing of family formation characteristic of Mexican-Americans are contrasted with those of Japanese-Americans, and consequences of their demographic differences for group achievement are explored. Mexican-Americans are found to have a demographic system marked by young ages at marriage, young ages at beginning of childbearing, high rates of reproduction, and high rates of marital instability. Japanese-Americans display just the opposite pattern of behavior on each of these variables. Using existing research on determinants of individual achievement, reasons are then suggested why the demographic environment encountered by Japanese-American youth is more conducive to educational and economic achievement than is that encountered by Mexican-American youth.
International evidence on misspecification of the standard money demand equation

Abstract This paper tests the proposition that the interest rate in the standard money demand equation acts as a proxy for the expected change in interest rates. If this is true, the interest elasticity in the standard equation will depend on the expectations process for interest rates. Using cross-country data, we find that there does exist a relationship between the observed interest elasticity in the standard equation and the predictability of future interest rates from current interest rates.
Long-Term Prognostic Value of Coronary Calcification Detected by Electron Beam Computed Tomography in Patients Undergoing Coronary Arteriography

To the Editor: The paper by Keelan et al1 addresses an important issue, namely how to define which patients with symptomatic coronary artery disease (CAD) are at risk for future events. They argue that coronary artery calcification (CAC) provides incremental prognostic value after clinical risk factors and coronary arteriography are included in the analysis, and indeed, only age and CAC were predictive in their model. Several issues need to be addressed before accepting this conclusion. The authors used several methods of quantifying CAC. Quartile analysis was done, but no data are provided on the number of patients at risk in each quartile, and apparently this analysis did not reach significance. Log transformation was used to analyze the data and was found significant in the Cox model. Lastly, a score of 100 formed the basis of their survival …
Structure evolution in polymer blending using microfabricated samples

Abstract The transient rheological behavior and morphology evolution of polymethyl methacrylate (PMMA)/polystyrene (PS) binary polymer blends with well-defined initial structure were measured in simple shear flow under isothermal conditions. The size and distribution of the dispersed phase and the composition of the blends were designed and fabricated by Computer Numerical Controlling (CNC) machining, photolithography, and micro-embossing. Compatibilizer can easily be placed at the interface of the two components during sample preparation. The effects of initial dispersed domain size, blend composition, and interfacial tension on rheological behavior and morphology evolution were investigated. It was found that the transient shear stress and first normal stress difference are very sensitive to these parameters. The transient rheological responses up to the breakup point are compared with those predicted by both Doi–Ohta and Vinckier–Moldenaers–Mewis models.
A Practical and Novel Method to Extract Genomic DNA from Blood Collection Kits for Plasma Protein Preservation

Laboratory tests can be done on the cellular or fluid portions of the blood. The use of different blood collection tubes determines the portion of the blood that can be analyzed (whole blood, plasma or serum). Laboratories involved in studying the genetic basis of human disorders rely on anticoagulated whole blood collected in EDTA-containing vacutainer as the source of DNA for genetic / genomic analysis. Because most clinical laboratories perform biochemical, serologic and viral testing as a first step in phenotypic outcome investigation, anticoagulated blood is also collected in heparin-containing tube (plasma tube). Therefore when DNA and plasma are needed for simultaneous and parallel analyses of both genomic and proteomic data, it is customary to collect blood in both EDTA and heparin tubes. If blood could be collected in a single tube and serve as a source for both plasma and DNA, that method would be considered an advancement to existing methods. The use of the compacted blood after plasma extraction represents an alternative source for genomic DNA, thus minimizing the amount of blood samples processed and reducing the number of samples required from each patient. This would ultimately save time and resources. The BD P100 blood collection system for plasma protein preservation were created as an improved method over previous plasma or serum collection tubes1, to stabilize the protein content of blood, enabling better protein biomarker discovery and proteomics experimentation from human blood. The BD P100 tubes contain 15.8 ml of spray-dried K2EDTA and a lyophilized proprietary broad spectrum cocktail of protease inhibitors to prevent coagulation and stabilize the plasma proteins. They also include a mechanical separator, which provides a physical barrier between plasma and cell pellets after centrifugation. Few methods have been devised to extract DNA from clotted blood samples collected in old plasma tubes2-4. Challenges from these methods were mainly associated with the type of separator inside the tubes (gel separator) and included difficulty in recovering the clotted blood, the inconvenience of fragmenting or dispersing the clot, and obstruction of the clot extraction by the separation gel. We present the first method that extracts and purifies genomic DNA from blood drawn in the new BD P100 tubes. We compare the quality of the DNA sample from P100 tubes to that from EDTA tubes. Our approach is simple and efficient. It involves four major steps as follows: 1) the use of a plasma BD P100 (BD Diagnostics, Sparks, MD, USA) tube with mechanical separator for blood collection, 2) the removal of the mechanical separator using a combination of sucrose and a sterile paperclip metallic hook, 3) the separation of the buffy coat layer containing the white cells and 4) the isolation of the genomic DNA from the buffy coat using a regular commercial DNA extraction kit or a similar standard protocol.
Disease tropism of c-erbB: effects of carboxyl-terminal tyrosine and internal mutations on tissue-specific transformation

Abstract Avian leukosis virus induces erythroleukemia in chickens by proviral insertional mutation of the protooncogene c-erbB. The product of the insertionally activated c-erbB locus lacks the extracellular ligand-binding domain and is strictly leukemogenic. It has previously been demonstrated that the disease spectrum associated with aberrant c-erbB expression can be expanded by structural perturbation of the cytoplasmic domain of this protein. In this report, we use mutagenesis and retroviral vectors to identify specific mutations in the carboxyl-terminal domain of the insertionally activated c-erbB product that are sufficient to activate the sarcomagenic potential of this protein. Interestingly, a point mutation in the kinase domain appears to be sufficient for sarcomagenic activation. However, removal of the terminal tyrosine residue of the c-erbB product, implicated in modulating kinase activity, does not lead to a fully transforming phenotype. These studies suggest that there are multiple ways to activate the fibroblast-transforming potential of the insertionally activated c-erbB product. The conformation of this protein may play a more significant role in oncogenic activation than the phosphorylation status of the putative carboxyl-terminal autophosphorylation site.
Venous Dysfunction and the Change of Blood Viscosity During Head‐Up Tilt

The precise stimulus that induces vasovagal syncope is still unclear. We have previously demonstrated that the peripheral distribution of blood volume (venous pooling) is a strong predictor of tilt induced vasovagal reaction. We hypothesized that an increase in venous pooling during tilt accentuates the measured increase in blood viscosity. This hypothesis is based on the previously demonstrated increase in venous pressure and subsequent increase in transcapillary fluid transudation during tilt. The increased blood viscosity, in turn, increases vascular shear rate, which may alter the vasoconstrictive and other cardiovascular responses to decreased preload. We measured blood viscosity (supine and tilt) in 56 patients with a history of orthostatic intolerance (37 with venous pooling [VP] and 19 without venous pooling [non-VP]). VP and non-VP were separated into subgroups based on blood pressure and heart rate response to tilt. There was a positive correlation between blood viscosity and plasma aldosterone in the supine. In the group as a whole, neither supine blood viscosity nor its increase during tilt differed between VP and non-VP. However, the tilt induced increase of blood viscosity was significant only in patients with tilt provoked tachycardia plus normal blood pressure response in VP group. We suggest that the increase of blood viscosity in this group led to the normal blood pressure response. The positive correlation between supine blood viscosity and supine plasma aldosterone indicates that the normal blood pressure response in this group possibly was via stimulation of the renin-angiotensin-aldosterone system.
Order of intron removal during splicing of endogenous adenine phosphoribosyltransferase and dihydrofolate reductase pre-mRNA.

Abstract Using a strategy based on reverse transcription and the polymerase chain reaction, we have determined the order of splicing of the four introns of the endogenous adenine phosphoribosyltransferase (aprt) gene in Chinese hamster ovary cells. The method involves a pairwise comparison of molecules that retain one intron and have either retained or spliced another intron(s). A highly preferred order of removal was found: intron 3 > 2 > 4 = 1. This order did not represent a linear progression from one end of the transcript to the other, nor did it correlate with the conformity of the splice site sequences to the consensus sequences or to the calculated energy of duplex formation with U1 small nuclear RNA. By using actinomycin D to inhibit RNA synthesis, the in vivo rate of the first step in splicing was estimated for all four introns; a half-life of 6 min was found for introns 2, 3, and 4. Intron 1 was spliced more slowly, with a 12-min half-life. A substantial amount of RNA that retained intron 1 as the sole intron was exported to the cytoplasm. In the course of these experiments, we also determined that intron 3, but not intron 4, is spliced before 3'-end formation is complete, probably on nascent transcripts. This result is consistent with the idea that polyadenylation is required for splicing of the 3'-most intron. We applied a similar strategy to determine the last intron to be spliced in a very large transcript, that of the endogenous dihydrofolate reductase (dhfr) gene in Chinese hamster ovary cells (25 kb). Here again, intron 1 was the last intron to be spliced.
P-GaN/AlGaN/GaN high electron mobility transistors

Despite the considerable improvement in GaN-technology and material quality, RF-dispersion is still one of the main issues hampering device progress. RF-dispersion affects device output power and device power added efficiency (PAE) due to a reduction in saturation current and an increase in knee voltage at high frequencies and high biases. Surface passivation, using silicon nitride, has been found to mitigate RF-dispersion and microwave power degradation (B.M. Green et al, IEEE Electron Dev. Lett., vol. 21, pp. 268-270, 2000; S.C. Binari et al, IEEE Trans Electron. Dev., vol. 48, pp. 465-471, 2001; R. Vetury et al, ibid., vol. 48, pp. 560-566, 2001). This paper discusses a novel AlGaN/GaN high electron mobility transistor (HEMT) device structure which has been developed to reduce RF-dispersion prior to silicon nitride passivation. The device structure uses a p-doped GaN cap layer to screen surface potential changes (regardless of origin) from affecting the gate-drain access region resistance, reducing the amount of RF-dispersion in the device. The epilayers of AlGaN/GaN devices were grown by metal organic chemical vapor deposition (MOCVD) on a c-plane sapphire substrate. Sheet electron concentration and electron Hall mobility of the as-grown wafer were /spl sim/1.35/spl times/10/sup 13/ cm/sup 2/ and 1,475 cm/sup 2//V-s at room temperature.
Analysis of secure design patterns: a case study in e-commerce system

Retrofitting security requirement into an existing system tends to result in less wanted qualities. So, it is a preferred practice to design with security in mind right from the beginning of the development process. An NFR framework has been established to incorporate non-functional requirements (NFRs) (L. Chung et al., 2000) that are crucial to secure system design into the development process. In this paper, we propose a methodology that utilizes the NFR framework to come up with secure design by selecting security design patterns for the domain specific application such as e-commerce system.
Calibrating a Riparian Vegetation Model for Sacramento River Studies

A one-dimensional flow and sediment transport model (Sedimentation and River Hydraulics- one dimensional, SRH-1D), was expanded to incorporate and assess riparian vegetation in the flood plain. The combined flow, sediment transport, and vegetation model SRH-1DV includes a ground water and vegetation module linking ground water fluctuations (in response to river flow) and the growth and removal of vegetation to geomorphic processes of river hydraulics and sediment transport. The various components of SRH-1DV were calibrated to measured data on the Sacramento River. Modeled flow was calibrated to the water surface elevation between gaging stations, and ground water was calibrated to well data. Sediment transport was calibrated to gravel bedload measurements at the Hamilton Bridge gaging station on the Sacramento River, but ultimately sediment transport computations were not used in the simulations. Cottonwood germination, growth, and removal were simulated for the Sacramento River from RM 300 to RM 150, including Red Bluff to Colusa. Data from two field studies (2005 and 2006) of cottonwood growth on sand bars at three sites were used to calibrate the cottonwood model and improve cottonwood desiccation methods. In a second round of simulations, the Sacramento SRH-1DV model was expanded to multiple vegetation types. Cottonwood vegetation was validated using repeat vegetation mapping from 1999 and 2007, and four additional vegetation types: mixed forest, Gooding’s black willow, narrow leaf willow, and the invasive plant, arundo, were calibrated with the 1999 and 2007 vegetation mapping of the Red Bluff to Colusa Reach (RM 250 to RM 143). Based on results, the arundo vegetation type was eliminated. Narrow leaf willow and Gooding’s black willow proved to be successful indicators of riparian lands in model simulations. Model simulations of cottonwood forest and mixed forests also compared well with mapped results when combined.
WAVELET ANALYSIS OF PROTEIN MOTION

As high-throughput molecular dynamics simulations of proteins become more common and the databases housing the results become larger and more prevalent, more sophisticated methods to quickly and accurately mine large numbers of trajectories for relevant information will have to be developed. One such method, which is only recently gaining popularity in molecular biology, is the continuous wavelet transform, which is especially well-suited for time course data such as molecular dynamics simulations. We describe techniques for the calculation and analysis of wavelet transforms of molecular dynamics trajectories in detail and present examples of how these techniques can be useful in data mining. We demonstrate that wavelets are sensitive to structural rearrangements in proteins and that they can be used to quickly detect physically relevant events. Finally, as an example of the use of this approach, we show how wavelet data mining has led to a novel hypothesis related to the mechanism of the protein γδ resolvase.
Fast filtering for RNA homology search

Motivation: Homology search for RNAs can use secondary structure information to increase power by modeling base pairs, as in covariance models, but the resulting computational costs are high. Typical acceleration strategies rely on at least one filtering stage using sequence-only search. Results: Here we present the multi-segment CYK (MSCYK) filter, which implements a heuristic of ungapped structural alignment for RNA homology search. Compared to gapped alignment, this approximation has lower computation time requirements (O(N4) reduced to O(N3)), and space requirements (O(N3) reduced to O(N2)). A vector-parallel implementation of this method gives up to 100-fold speed-up; vector-parallel implementations of standard gapped alignment at two levels of precision give 3-and 6-fold speed-ups. These approaches are combined to create a filtering pipeline that scores RNA secondary structure at all stages, with results that are synergistic with existing methods. Availability: http://selab.janelia.org/publications.html#KolbeEddy11 Contact: eddys@janelia.hhmi.org
A comparison of dung beetle (Coleoptera: Scarabaeidae) attraction to native and exotic mammal dung

Although the preference of dung beetles (Coleoptera: Scarabaeidae) for specific types and conditions of dung has been given substantial attention, little has been done to investigate the potential effects of exotic mammal introduction for game farms or rewilding projects. We used pitfall traps baited with various native and exotic herbivore, carnivore, and omnivore dung to evaluate dung beetle preference in the Great Plains of North America. Additionally, we analyzed of the nutrient quality of each dung type. In total, 9,089 dung beetles from 15 species were captured in 2 yr of sampling. We found significant differences (P < 0.05) in mean dung beetle capture among omnivore, herbivore, and carnivore dung, as well as differences in individual species preference for dung type. Omnivore dung was the most attractive with chimpanzee and human dung having the highest mean capture (291.1 ± 27.6 and 287.5 ± 28.5 respectively). Carrion also was highly attractive with a mean of 231.9 ± 20.6 beetles per trap (N = 8). Our results suggest definitive local preference of carrion in Phanaeus vindex Macleay and Onthophagus hecate (Panzer), while the congener, O. pennsylvanicus (Harold), was rarely captured in carrion and highly preferred omnivore dung. Preference for a specific bait type does not appear to be correlated with dung quality, mammalian diet, or origin of mammal. Results suggest niche segregation by dung type among dung beetle species.
The unity of the whole and freedom of parts: Facultativeness principle in the hereditary system

Facultativeness in the genome structure and function reflects the general principle of life organi� zation and evolution: the unity of the whole and the freedom of parts. The genome, or cell hereditary system code, maintains and transfers hereditary information both structurally and dynamically. The generalized genome concept presents a genome as an ensemble of both obligate and facultative elements. Template pro� cesses (Replication, Transcription and Translation) and Basic genetic processes (Repair, Recombination and Segregation) are capable of functional facultativeness and dynamic (epigenetic) modifications. It is reason� able to discriminate among three kinds of heritable changes: mutations, variations and epigenetic modifica� tions. Structural genome facultativeness is expressed as a subdivision of cell DNA and RNA elements into two subsystems: Obligate genetic elements (OGEs) and Facultative genetic elements (FGEs). FGEs include var� ious kinds of repeated sequences, mobile elements, amplicons, inserted viral and foreign DNA, Bchromo� somes, plasmids and cytobionts. The abundance and intracellular topography of FGEs are different in differ� ent cells, tissues and individuals. Changes in the structure or order of OGEs correspond to classical muta� tions. For diverse changes in the number or cell/tissue topography of FGEs the term variations seems appropriate. Mutations and variations significantly differ in the pattern of their occurrence. Variations may occur simultaneously in many cells/individuals and are induced by nonmutagenic factors. Spontaneous hereditary changes in nature usually occur in the system ENVIRONMENT—FGEs—OGEs via a twostep pathway. FGEs are first to respond to both internal and external environmental challenges. Then their acti� vation induces gene/chromosomal mutations. Both variations and epigenetic changes (epivariations and epimutations) may have nonMendelian features, some times reminding the phenomenon of inheritance of acquired characteristics.
Neuroprotective Actions of Brain Aromatase

The steroidal regulation of vertebrate neuroanatomy and neurophysiology includes a seemingly unending list of brain areas, cellular structures and behaviors modulated by these hormones. Estrogens, in particular have emerged as potent neuromodulators, exerting a range of effects including neuroprotection and perhaps neural repair. In songbirds and mammals, the brain itself appears to be the site of injury-induced estrogen synthesis via the rapid transcription and translation of aromatase (estrogen synthase) in astroglia. This induction seems to occur regardless of the nature and location of primary brain damage. The induced expression of aromatase apparently elevates local estrogen levels enough to interfere with apoptotic pathways, thereby decreasing secondary degeneration and ultimately lessening the extent of damage. There is even evidence suggesting that aromatization may affect injury-induced cytogenesis. Thus, aromatization in the brain appears to confer neuroprotection by an array of mechanisms that involve the deceleration and acceleration of degeneration and repair, respectively. We are only beginning to understand the factors responsible for the injury-induced transcription of aromatase in astroglia. In contrast, much of the manner in which local and circulating estrogens may achieve their neuroprotective effects has been elucidated. However, gaps in our knowledge include issues about the cell-specific regulation of aromatase expression, steroidal influences of aromatization distinct from estrogen formation, and questions about the role of constitutive aromatase in neuroprotection. Here we describe the considerable consensus and some interesting differences in knowledge gained from studies conducted on diverse animal models, experimental paradigms and preparations towards understanding the neuroprotective actions of brain aromatase.
What is Relevance? Defining Intersectional Praxis in Uruguay:

This article examines intersectional praxis via a focus on what constitutes relevant axes of difference. The author argues that a discussion of relevance should focus on two important issues: (1) which categories are of analytic importance and (2) those categories that activists consider relevant. This approach allows for activist debates over the most important social divisions in society while establishing some minimal number of axes that must be included to qualify activism as intersectional. In the Uruguayan case, gender and class constitute minimally important axes of difference; however, race and, less centrally, sexuality and ability constitute central points of debate.
First Impressions, Ingratiation, and the Learning Disabled Child

Two experiments were conducted concerning college students' immediate impressions of male learning disabled and nondisabled children. In both experiments, one half of the stimulus children within each group had been instructed to ingratiate an interviewer; the remaining youngsters had been instructed to act naturally. Interviews centered around the children's descriptions of their favorite television programs and movies. College students in the experiments viewed either 10- or 25-seconds of videotape of the interactions of each child. After each 10-or 25-second sequence the college students rated the child as to his degree of social adaptability and social hostility. Experiment I demonstrated that while LD children were judged more negatively under the “act naturally” instructions. thesechildren were judged as positively as nondisabled children when prompted to ingratiate. In Experiment II, judges based their ratings solely on the nonverbal behaviors of the target children. Again, a group by instruction i...
Identification and characterization of a novel tight junction-associated family of proteins that interacts with a WW domain of MAGI-1.

The membrane-associated guanylate kinase protein, MAGI-1, has been shown to be a component of epithelial tight junctions in both Madin–Darby canine kidney cells and in intestinal epithelium. Because we have previously observed MAGI-1 expression in glomerular visceral epithelial cells (podocytes) of the kidney, we screened a glomerular cDNA library to identify the potential binding partners of MAGI1 and isolated a partial cDNA encoding a novel protein. The partial cDNA exhibited a high degree of identity to an uncharacterized human cDNA clone, KIAA0989, which encodes a protein of 780 amino acids and contains a predicted coiled-coil domain in the middle of the protein. In vitro binding assays using the partial cDNA as a GST fusion protein confirm the binding to full-length MAGI-1 expressed in HEK293 cells, as well as endogenous MAGI-1, and also identified the first WW domain of MAGI-1 as the domain responsible for binding to this novel protein. Although a conventional PPxY binding motif for WW domains was not present in the partial cDNA clone, a variant WW binding motif was identified, LPxY, and found to be necessary for interacting with MAGI-1. When expressed in Madin–Darby canine kidney cells, the full-length novel protein was found to colocalize with MAGI-1 at the tight junction of these cells and the coiled-coil domain was found to be necessary for this localization. Because of its interaction with MAGI-1 and its localization to cell–cell junctions, this novel protein has been given the name MAGI-1-associated coiled-coil tight junction protein (MASCOT). D 2005 Elsevier B.V. All rights reserved.
Gender differences in risk/protection profiles for low academic performance.

The majority of research examining why children and adolescents do not achieve up to their potential in educational settings focuses on variable-centered research as opposed to person-centered research (Bauer, & Shanahan, 2007; Block, 1971). Variable-centered research methods have examined a number of important significant relationships between risk factors such as child maltreatment (Eckenrode, Laird, & Doris, 1993; Jimerson, Egeland, Sroufe, & Carlson, 2000; Kinard, 1999), intimate partner violence (Dawud-Noursi, Lamb, & Sternberg, 1998), and low socioeconomic status levels (Bradley & Corwyn, 2002; D'Angiulli, Siegel, & Hertzman, 2004; Greenberg, Lengua, Coie, & Pinderhughes, 1999; Silva, McGee, Thomas, & Williams, 1982) and low academic performance. However, it is important to supplement this understanding of the possible predictors of low academic achievement with methods that focus on the individual’s experience of various combinations of risk and protective factors (Bergman, Magnusson, & El-Khouri, 2003; Magnusson, 1988; Magnusson & Casaer, 1993). This study uses the holistic-interactionistic theory to guide a conception of individuals experiencing both risk and protective factors for low academic performance simultaneously throughout their lives. The simultaneous nature of risk and protective factors are examined using a person-centered cluster technique, latent profile analysis, for both males and females. The classes from this analysis are used to predict low academic performance in an attempt to illustrate how risk and protective factors might best be conceived as a unified whole.
A General Pressure Gradient Formulation for Ocean Models. Part I: Scheme Design and Diagnostic Analysis

Abstract A Jacobian formulation of the pressure gradient force for use in models with topography-following coordinates is proposed. It can be used in conjunction with any vertical coordinate system and is easily implemented. Vertical variations in the pressure gradient are expressed in terms of a vertical integral of the Jacobian of density and depth with respect to the vertical computational coordinate. Finite difference approximations are made on the density field, consistent with piecewise linear and continuous fields, and accurate pressure gradients are obtained by vertically integrating the discrete Jacobian from sea surface. Two discrete schemes are derived and examined in detail: the first using standard centered differencing in the generalized vertical coordinate and the second using a vertical weighting such that the finite differences are centered with respect to the Cartesian z coordinate. Both schemes achieve second-order accuracy for any vertical coordinate system and are significantly more a...
Dynamic intramyocardial blood volume: evaluation with a radiological opaque marker method

In this study the change of intramyocardial blood volume within one cardiac cycle was deduced from the time sequence of the volume delineated by radiopaque markers attached to the left ventricular wall. These data were compared with the change in the volume of the same region of myocardium estimated from the change in angiographic opacification of the heart wall. Five dogs were anesthetized, and four pairs of 2-mm-diameter lead beads were attached to the epicardial and endocardial regions. Two scans using the dynamic spatial reconstructor (a high-speed computed tomographic scanner) were performed during aortograms, one under control conditions and the other during adenosine infusion. The results have shown that the increases of myocardial volume defined by the beads (delta Vbead, % of volume at control) were comparable to the increase of intramyocardial blood volumes estimated by the increase in wall opacity (delta Vblood, % of muscle); delta Vblood = 0.93 delta Vbead + 1.54%; r = 0.987.