cssi/SciSciGPT-SciSciNet huggingface dataset:
High‐resolution X‐ray structure of UDP‐galactose 4‐epimerase complexed with UDP‐phenol

UDP-galactose 4-epimerase from Escherichia coli catalyzes the interconversion of UDP-glucose and UDP-galactose. In recent years, the enzyme has been the subject of intensive investigation due in part to its ability to facilitate nonstereospecific hydride transfer between beta-NADH and a 4-keto hexopyranose intermediate. The first molecular model of the epimerase from E. coli was solved to 2.5 A resolution with crystals grown in the presence of a substrate analogue, UDP-phenol (Bauer AJ, Rayment I, Frey PA, Holden HM, 1992, Proteins Struct Funct Genet 12:372-381). There were concerns at the time that the inhibitor did not adequately mimic the sugar moiety of a true substrate. Here we describe the high-resolution X-ray crystal structure of the ternary complex of UDP-galactose 4-epimerase with NADH and UDP-phenol. The model was refined to 1.8 A resolution with a final overall R-factor of 18.6%. This high-resolution structural analysis demonstrates that the original concerns were unfounded and that, in fact, UDP-phenol and UDP-glucose bind similarly. The carboxamide groups of the dinucleotides, in both subunits, are displaced significantly from the planes of the nicotinamide rings by hydrogen bonding interactions with Ser 124 and Tyr 149. UDP-galactose 4-epimerase belongs to a family of enzymes known as the short-chain dehydrogenases, which contain a characteristic Tyr-Lys couple thought to be important for catalysis. The epimerase/NADH/UDP-phenol model presented here represents a well-defined ternary complex for this family of proteins and, as such, provides important information regarding the possible role of the Tyr-Lys couple in the reaction mechanism.
Effects of cell shape and cell wall thickness variations on the elastic properties of two-dimensional cellular solids

Abstract The Voronoi tessellation technique and the finite element method are utilized to investigate the microstructure-property relations of two-dimensional cellular solids having irregular cell shapes and non-uniform cell wall thickness. Twenty finite element models are constructed for each type of honeycomb samples (specimens) to obtain the mean values and standard deviations of the effective elastic properties. Spatially periodic boundary conditions are applied to each specimen containing 360 complete cells. The simulation results indicate that the elastic moduli increase as cell shapes become more irregular, but decrease as cell wall thickness gets less uniform. The Poisson’s ratios are insignificantly affected by the presence of these two types of imperfections. The effect of the interaction between the co-existing cell shape and cell wall thickness imperfections on the elastic moduli is found to be weak. Bending remains as the dominant deformation mechanism in a loaded honeycomb having irregular cell shapes and/or non-uniform cell wall thickness. In addition, it is revealed that such imperfect honeycombs can be regarded as isotropic.
Kinetics of release of serotonin from isolated secretory granules. I. Amperometric detection of serotonin from electroporated granules.

We developed a method for measuring the efflux of 5-hydroxytryptamine (5-HT, serotonin) from isolated intact granules of the mast cell of the beige mouse. This method combines electroporation of the vesicle membrane with amperometric detection of 5-HT. A single secretory granule is placed between two platinum electrodes (distance approximately 100 microm) and positioned adjacent (
Emerging drugs for lysosomal storage diseases

Importance of the field: Because orphan drug regulations encouraged development of drugs for rare disorders by granting marketing exclusivity for many years and other commercial benefits, treatment has become achievable for a few lysosomal storage disorders also. The presently available therapies, however, are not able to address all aspects of these multisystemic disorders and do not cure the patient. Therefore, there is a need for producing new drugs that are based on known pathophysiological mechanisms, such as enzyme replacement or inhibition of substrate synthesis, or which use new approaches to prevent the build-up of storage material.Areas covered in this review: New compounds that are being designed by different pharmaceutical companies can be divided in two groups, enzyme targeted and substrate targeted drugs. Enzyme targeted drugs include substances that modify the enzyme to make it more accessible to organs such as the bone or the brain, enhance enzyme activity (chaperones) or activate enzyme s...
Toxicity of nystatin and its methyl ester toward parental and hybrid mammalian cells.

Nystatin methyl ester (NME), the methyl ester derivative of the polyene macrolide antibiotic nystatin, is known to be effective against fungi and is now found to be relatively less toxic than the parent antibiotic nystatin (NYS) to animal cells in culture as measured by51Cr release, cell survival at different posttreatment periods and cell growth. NYS and NME were tested on TK− mouse (B82) and hamster (B1) cells, HGPRT− mouse (RAG) cells, and on lysolecithin-fused cells selected in HAT medium and confirmed as B82-RAG an B1-RAG hybrids by chromosomal analysis plus polyacrylamide gel electrophoresis of lactate dehydrogenase. NME was less toxic and caused less immediate membrane damage than NYS when tested in all five cell systems. However, differences in innate polyene sensitivity were evident between the three parental cell types. B82 and B1 cells were more resistant than RAG cells to NYS and NME. B82-RAG hybrids reflected the higher level resistance of B82 parental cells, and B1-RAG hybrids reflected the higher level resistance of B1 cells. Where one parental cell type is relatively more polyene sensitive, the use of polyenes in the future may be applicable as selective agents in cell hybridization.
Computer control of a number of analyzing magnets at the Van de Graaff facility of the Los Alamos scientific laboratory

Abstract A system is described which can calculate, set up, and control the frequency of nuclear resonance fluxmeter using an on-line control computer. The magnetic field of an associated analyzing magnet is adjusted by the computer to produce and maintain a resonance signal. This can be accomplished for a number of magnets and particles accelerated by either one or two Van de Graaff accelerators.
Use of Portfolio Assessment with Students with Cognitive Disabilities/Mental Retardation.

Portfolio assessment has gained momentum as educators search for more authentic ways to document student performance. Many aspects of portfolio assessment are beneficial for students with cognitive...
WE-G-108-06: Evaluating Pre-Treatment IMRT & VMAT QA Techniques Quantitatively Using Receiver Operating Characteristic (ROC) Analysis

Purpose: Pre‐treatment IMRT and VMAT QA techniques are often commissioned without knowledge of their sensitivity to clinically relevant delivery errors. The purpose of this work is to develop a method to quantify the sensitivity and specificity of pre‐treatment IMRT and VMAT QA techniques to treatment delivery errors. Methods: To evaluate a QA technique, a population of treatment plans and a population of clinically relevant delivery errors are defined. For each delivery error, a threshold magnitude is determined that induces a substantial change in clinically relevant dosimetric indices. Errors at the threshold magnitude are introduced into the plans and QA is performed with and without intentionally introduced errors. The QA technique is treated as a binary classifier to predict error plans using Receiver Operator Characteristic (ROC) analysis. We applied this technique to evaluate portal imager and 2D ion chamber array based QA for VMAT treatment of brain lesions. Delivery errors included discrepancies in MLC positioning (single leaf and leaf bank); lag of MLC trajectory; and discrepancy in dose rate per control point or gantry angle. The threshold magnitude was determined by achieving a 5% change in target conformity index. Results: The area under the curve (AUC) for the ROC analysis was 0.592 and 0.509 for the ion chamber array and portal imager, respectively, using a gamma index of 3%, 3mm. The AUC increased to 0.632 and 0.777 when 2%, 2mm was used for the ion chamber array and portal imager, respectively. Comparison based on 3% dose agreement resulted in an AUC of 0.557 and 0.693, respectively. Conclusion: For both portal imager and ion chamber array based QA, stricter tolerance than 3%, 3mm is needed to detect clinically relevant delivery errors. This method can be used to quantitatively compare the sensitivity of various QA techniques to clinically relevant dosimetric errors.
Further discussion of a time-continuous Gaussian channel

The purpose of this note is to simplify the proof of the coding theorem given by the author ( Ash, 1963 ) for a time-continuous Gaussian channel, and to correct an error in the proof of the weak converse. In addition, further comment will be made concerning the difference between the channel model considered by the author (see also Fortet, 1961 and Bethoux, 1962 ) and the model which is implicit in the Shannon theory.
Search for solar-neutrino related M1 transitions in 6Li using 180° electron scattering

Abstract The 6Li analog of the 11.5 MeV, 0+ state in 6Be proposed to explain the low flux of high-energy solar neutrinos has been searched for and not observed. An upper limit of 3 eV is placed on the M1 ground-state width of any such narrow 0+ state.
Street and park trees of Boston: a comparison of urban forest structure

Abstract This paper evaluates the structure of street and park trees in Boston's neighborhoods of Roxbury and North Dorchester. The general hypothesis is that forest structures of two components of the public urban forest, street and park trees, are significantly different such that they may warrant different policy and management strategies. Data from an inventory of the neighborhoods in 1988–1989 include species, diameter at breast height, and condition of each tree. Descriptive variables calculated from the data include species diversity, size class diversity, percentage of the tress that are in good condition, and species importance lists. From the descriptive variables, size class diversity is greater for street than for park trees. Species diversity and percentage of trees in good condition are greater for park than for street trees. Results from chi-square analyses on tree condition, size class categories, and size class categories for Acer platanoides and Quercus rubra for Condition Class 3 all reject the null hypothesis that street and park tree populations are distributed similarly. A comparison of the importance lists that include the species that collectively make up 75% of all individuals and total basal area shows that there are only seven species required to reach that percentage for street trees, and 14 for park trees. At the 75% level, all species that make up at least 5% of all individuals and total basal area are included. Of the seven tree species on the importance list for street trees, only one is a member of the presettlement forest and all are tolerant of urban environmental stress. For park trees, over half of the 14 species on the importance list are members of the presettlement forest, and at least seven are tolerant of urban environmental stress. The results indicate that street and park trees are distinct populations within urban forests, and hence the processes acting to create these two components of the urban forest resource may also differ.
Treatment of proximal vertebral artery disease

Vertebral arterial disease (VAD) is a less commonly recognized and treated source of cerebrovascular ischemia compared with carotid artery disease. Patients are often referred for treatment after they have developed symptoms in the form of transient ischemic attacks or had a posterior hemispheric stroke. Traditional treatment of VAD has been surgical. More recently, endovascular treatment of VAD has been utilized. We performed a retrospective review of our institutional experience in treating VAD from 2001 to 2010. For treatment of proximal VAD, perioperative morbidity is lower for the endovascular group than for the surgical group, but six-week mortality was higher for the endovascular group. Complete resolution of symptoms occurred more frequently with surgery than with endovascular therapy. Therefore surgical reconstruction appears to be preferable to angioplasty and stenting for treatment of proximal vertebral artery occlusive disease.
Field evaluation of the temperature stability of a multispectral radiometer

Abstract Measurements of radiance from a calibrated barium sulfate painted reflectance panel, made during the course of routine field experiments, were used to evaluate the effect of detector temperature on the voltage output from silicon (Si) and lead sulfide (PbS) detectors of a multiband spectral radiometer. The four Si detectors were found to be nearly independent of temperature changes. However, the voltage output from the three PbS detectors decreased linearly with increasing detector temperature at a rate of 4–5%°C−1, which is considerably more than expected from manufacturer's specifications for the instrument. The error in reflectance values caused by a detector temperature change of 1°C was less than 0.25% of value for the Si detectors, but was about 2.5% of value for the PbS detectors. A correction factor was derived to adjust measured voltages to a reference temperature and to compute corrected reflectances. The correction factor can be derived from analysis of field measurements of radiance from a calibrated reflectance panel, if the detector temperature is known at the time of measurement.
A DEVELOPMENTAL ANALYSIS OF THE RELATION BETWEEN CELL SIZE AND FRUIT SIZE IN CUCURBITS

THE PROBLEM of the relation between cell size and organ or body size in plants has been extensively studied and forms the basis of a considerable literature, but the lack of any general agreement in the results obtained indicates that the question is not a simple one. Sachs ( 1893) and Amelung (1893) presented evidence that size differences in body and organ are due primarily to differences in the number rather than in the size of their constituent cells, and this conclusion has been frequently confirmed. Other workers, however, among them the present writer (1930), have found that in many cases differences in organ size are in part, at least, related to cell size. Almost all the evidence has been gathered from a study of organs and cells which had reached maturity. Both structures attain final size, however, as the result of growth from small beginnings; and a developmental analysis of the growing organ in terms of changes in the size. and in the number of its cells should yield important results. A study of the whole developmental process, with particular reference to the relative rates and durations of cell division and cell expansion, is evidently needed as a fundamental approach to the problem. Such studies have been made in only a few cases. Notable among these is the work of Houghtaling (1935) on tomatoes, in which she showed that early fruit growth is due chiefly to cell multiplication an-d later growth entirely to cell expansion and that the extent of both these processes was greater in the larger fruits than in the smaller ones. Similar results have been reported by MacArthur and Butler (1938). The present study was undertaken to determine the developmental relations between cell size, cell number, and ovary and fruit size in several genera of the Cucurbitaceae and particularly in various races of Cucurbita Pepo differing markedly in fruit size.
A Pneumatic Artificial Muscle Articulated Knee Prosthesis

This paper describes the mechanical design and control approach for an above-knee (AK) prosthesis actuated by pneumatic artificial muscle. Pneumatic artificial muscle (PAM) affords great potential in prosthetics, since this type of actuator features a high power density, and similar characteristics to human muscles. However, there is no application of PAM in AK prosthetics in existing literature to the best knowledge of the authors. In this paper, a design of the prosthesis is presented, which provides sufficient actuation torque for the knee joint in energy consuming locomotive functions such as fast walking and stair climbing. The corresponding control approach is developed to mimic the human motor control in locomotive functions, which includes a lower-level equilibrium-point hypothesis-inspired motion controller, and a higher-level joint-behavior-based motion planner.Copyright © 2010 by ASME
A case for tree evolution in QoS multicasting

The continuous growth of group communications and QoS-aware applications over the Internet have accelerated the development of multicasting technologies. The Core-Based Tree (CBT) multicasting approach provides a scalable solution for large groups and for large networks, such as the Internet. However, unlike in shortest-path trees, the quality (tree cost) of the CBT may eventually degrade over time due to group dynamics (join/leave). In order to counteract this degradation, the core may be migrated and a new tree constructed. The method of migrating group members from the old core to the new core has a profound impact on the quality of the tree and also on the service disruption experienced by group members. Thus, there exists a trade-off between tree cost and service disruption as higher rate of migration decreases the overall tree cost but results in more service disruption. In this paper, we develop a new paradigm for tree migration, namely tree evolution. The proposed tree evolution model (Split-based Tree Evolution Protocol) provides an elegant solution that strikes a balance between service disruption and tree cost for highly dynamic groups. We propose two forms of evolution, viz. QoS-based and timer-based. We provide an analysis to estimate the evolution timer which determines the number of cores present in the group, and also compare and contrast the merits of tree evolution versus tree migration through extensive simulation studies. We also provide a soft state implementation of the evolution protocol which is an extension of the CBT soft state approach. Our simulation studies show that the proposed evolution model demonstrates excellent tree cost and service disruption for highly dynamic groups.
Performance measures and data requirements for congestion management systems

Many metropolitan areas have started programs to monitor the performance of their transportation network and to develop systems to measure and manage congestion. This paper presents a review of issues, procedures, and examples of application of geographic information system (GIS) technology to the development of congestion management systems (CMSs). The paper examines transportation network performance measures and discusses the benefit of using travel time as a robust, easy to understand performance measure. The paper addresses data needs and examines the use of global positioning system (GPS) technology for the collection of travel time and speed data. The paper also describes GIS platforms and sample user interfaces to process the data collected in the field, data attribute requirements and database schemas, and examples of application of GIS technology for the production of maps and tabular reports.
Non-linear charge transport in polythiophene under high AC field

Complex impedance and conductivity were measured for regioregular poly(3-hexylthiophene) (P3HT) at alternating current (AC) voltages using a waveform technique. The waveforms were Fourier transformed from time domain to frequency domain and analyzed at fundamental and higher order harmonic frequencies. It was found that the impedance of the semi-conducting P3HT decreases with increasing electric field strength. The non-linear charge transport is dominated by a third harmonic response that originates from extended polarizability of π-type electronic states. The third order non-linear conductivity can be used to quantify the effect of an electric field on the conduction mechanism and to correlate the intrinsic charge carriers mobility with molecular structure.
Influence of oxygenation on endothelial modulation of coronary vasomotor function during hyperkalemic cardioplegia.

Background: The purpose of this study was to determine the influence of oxygenation of a hyperkalemic cardioplegic solution (K-CP) on endothelial modulation of vasomotor tone and to correlate these changes with the intracellular calcium concentration ([Ca++]i) in microvascular smooth muscle. Methods: Rat coronary arterioles were studied in a pressurized, no-flow normothermic state. Simultaneous monitoring of luminal diameter and [Ca++]i (fura-2) was performed with use of microscopic image analysis. Vessels were subjected to 60 minutes of oxygenated or hypoxic K-CP (K+ = 25.0 mmol/L) and were then reperfused with oxygenated Krebs–physiologic saline solution for 60 minutes. Results: In oxygenated K-CP, the K-CP–induced contraction and [Ca++]i accumulation were significantly increased in endothelium-denuded (ED) vessels compared with endothelium-intact vessels. The effect of ED in oxygenated K-CP was mimicked by administration of the nitric oxide synthase inhibitor NG-monomethyl-L -arginine. Conversely, in hypoxic K-CP the contraction was significantly attenuated in ED vessels compared with endothelium-intact vessels, although there was no significant difference in [Ca++]i. Indomethacin did not affect the endothelium-dependent contraction during hypoxic K-CP. Conclusions: Endothelium-derived nitric oxide modulates the vascular tone during K-CP by regulating the vascular smooth muscle [Ca++]i, whereas endothelium-derived contracting factor(s), which is not predominantly a product of cyclo-oxygenase, may play a prominent role under hypoxic K-CP by increasing vascular smooth muscle Ca++ sensitivity. (Surgery 1999;126:264-71.)
Functional amyloid formation by Streptococcus mutans

Dental caries is a common infectious disease associated with acidogenic and aciduric bacteria, including Streptococcus mutans. Organisms that cause cavities form recalcitrant biofilms, generate acids from dietary sugars and tolerate acid end products. It has recently been recognized that micro-organisms can produce functional amyloids that are integral to biofilm development. We now show that the S. mutans cell-surface-localized adhesin P1 (antigen I/II, PAc) is an amyloid-forming protein. This conclusion is based on the defining properties of amyloids, including binding by the amyloidophilic dyes Congo red (CR) and Thioflavin T (ThT), visualization of amyloid fibres by transmission electron microscopy and the green birefringent properties of CR-stained protein aggregates when viewed under cross-polarized light. We provide evidence that amyloid is present in human dental plaque and is produced by both laboratory strains and clinical isolates of S. mutans. We provide further evidence that amyloid formation is not limited to P1, since bacterial colonies without this adhesin demonstrate residual green birefringence. However, S. mutans lacking sortase, the transpeptidase enzyme that mediates the covalent linkage of its substrates to the cell-wall peptidoglycan, including P1 and five other proteins, is not birefringent when stained with CR and does not form biofilms. Biofilm formation is inhibited when S. mutans is cultured in the presence of known inhibitors of amyloid fibrillization, including CR, Thioflavin S and epigallocatechin-3-gallate, which also inhibited ThT uptake by S. mutans extracellular proteins. Taken together, these results indicate that S. mutans is an amyloid-forming organism and suggest that amyloidogenesis contributes to biofilm formation by this oral microbe.
The Melungeon Identity Movement and the Construction of Appalachian Whiteness

Racial classification in the United States is ultimately binary, categorizing individuals as "white" or "nonwhite." How this binary system is discursively constituted depends upon the ways in which elements of a repertoire interconnect to distribute or consolidate power and privilege across discursive contexts. Circulation of the revitalized lexeme Melungeon as a valued "object" within Appalachian discourse reveals linguistic processes by which white racial privilege is constructed and expanded, mixed-race classification excluded, and nonwhite disenfranchisement reproduced.
A general form of ordinal association

A general form of ordinal association is defined in a prediction analysis framework. This definition provides a useful way of identifying and selecting prediction rules a priori. Various classes of association are considered and a general approach is provided for the selection and significance testing of optimal prediction rules (ex post). This methodology is also extended to the degree‐k, k ≥ 2, and multivariate cases. Nearly all of the common measures of ordinal association are special cases of the general type of association considered here.
Reaching those most in need: Participation in a Planned Parenthood smoking cessation program

We evaluated the representativeness of women approached and enrolled in a brief smoking cessation intervention conducted in Planned Parenthood clinics. In this effectiveness study, regular clinic staff were trained to identify, offer participation, and counsel willing smoking clients as part of their clinic visit. Chart audits were conducted to determine the percent of clients who had smoking status identified, as well as the percent and characteristics of potentially eligible clients who were not approached. Baseline and non-participant questionnaires were analyzed to determine participation rate and characteristics of those participating versus those not participating. Smoking status was documented in 99% of charts. Seventy percent of eligible smokers were approached about study participation and 74% of those approached participated. There were no significant differences between those approached and those not approached or between those who participated versus those who did not on a host of sociodemographic variables. This project was able to approach and attract a representative sample of young, lower income women to participate in a brief, clinic-based smoking cessation program.
Optimal Requantization-Based Rate Adaptation for H.264

Bit rate adaptation is one of the most important types of video transcoding. With H. 264 becoming the predominant video codec of choice in video coding and streaming, prudent rate-adaptation techniques should be developed. In this paper, we investigate certain critical points in the spectrum of rate shaping requests. We show that the selection of quantization step sizes may not have monotonic effects on rate-distortion characteristics in the transcoding sense. In other words, distortion in the regular sense can be different from the distortion in the context of transcoding in which a requantization process is carried out. We show in a generic form that careful selections of the step size can lead to much improved performance. Experiments based on both simulation and real transcoding show the effectiveness of the proposed solution.
Reduced Transaminase B (IlvE) Activity Caused by the Lack of yjgF Is Dependent on the Status of Threonine Deaminase (IlvA) in Salmonella enterica Serovar Typhimurium

The YjgF/YER057c/UK114 family is a highly conserved class of proteins that is represented in the three domains of life. Thus far, a biochemical function demonstrated for these proteins in vivo or in vitro has yet to be defined. In several organisms, strains lacking a YjgF homolog have a defect in branched-chain amino acid biosynthesis. This study probes the connection between yjgF and isoleucine biosynthesis in Salmonella enterica. In strains lacking yjgF the specific activity of transaminase B, catalyzing the last step in the synthesis of isoleucine, was reduced. In the absence of yjgF, transaminase B activity could be restored by inhibiting threonine deaminase, the first enzymatic step in isoleucine biosynthesis. Strains lacking yjgF showed an increased sensitivity to sulfometruron methyl, a potent inhibitor of acetolactate synthase. Based on work described here and structural reports in the literature, we suggest a working model in which YjgF has a role in protecting the cell from toxic effects of imbalanced ketoacid pools.
Upper mantle structure from long-period differential traveltimes and free oscillation data

SUMMARY We have performed an inversion to model upper mantle structure using SS-S differential traveltime residuals in conjunction with previously reported structure coefficient estimates obtained from free oscillation frequency and attenuation measurements. The model we obtain is consistent with both the differential traveltime and structure coefficient data sets and provides nearly the same level of fit as independent inversions of these data sets. We find that a relatively simple model parametrization appears to be adequate for the data used. Upper mantle velocity perturbations and lateral variations in the radii of boundaries at 400 and 670 km depth are parametrized with spherical harmonic expansions up to degree and order 8. The expansions are fixed at specific depth knots (separated by roughly 200 km) spanning the range 20-670 km. Radial variations in velocity are obtained by linear interpolation between these depth knots. Smoothness constraints were applied as part of the inversion procedure, as well as corrections for the thickness and velocity variations of the crust. The smoothness constraints were adjusted to require a smoother structure in the bottom portion (400 to 670 km depth) of the model, where the structure coefficients have the greatest sensitivity. The upper part of the model is primarily constrained by the differential traveltime data. The resulting misfit of the final model shows that, on average, the individual structure coefficients and SS-S measurements are fit to within approximately 1.5 standard deviations. We suggest that some of the misfit is due to lower mantle structure which is not included in the modelling. The power as a function of harmonic degree for the top portion of the model (20 to 220 km depth) does not fall off significantly at the higher harmonic degrees, suggesting that the differential traveltime data may require models which include structure for degrees greater than 8. Boundary perturbations at depths of 400 and 670 km trade off strongly with the velocity variations. Allowing variations of the order of f10 km in the radii of the discontinuities at 400 and 670 km provides a slight improvement to the data fit. Comparisons of several depths of our upper mantle velocity model to the geoid show the strongest correlation at degree 2 for structure near 670 km depth. The distribution of slab structures is highly correlated to the degree 2 components of the model for depths of 200 to 670 km. Examination of the model in the vicinity of hotspots shows no consistent hotspot related signal.
Numerical investigation of quenching for a nonlinear diffusion equation with a singular Neumann boundary condition

For a nonlinear diffusion equation with a singular Neumann boundary condition, we devise a difference scheme which represents faithfully the properties of the original continuous boundary value problem. We use non-uniform mesh in order to adequately represent the spatial behavior of the quenching solution near the boundary. © 2002 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 18: 429–440, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/num.10013
Advance care planning: Beyond the living will

For a variety of reasons, the most commonly used advance directive documents (eg, the living will) may not be very useful in many situations that older adults encounter. The durable power of attorney for health care is a more versatile document. We advocate focusing less on "signing away" certain interventions and more on clarifying the goals of care in the ambulatory setting.
Dose-effect relationships of trauma to symptoms of depression and post-traumatic stress disorder among Cambodian survivors of mass violence.

BACKGROUND The dose-effect relationships of cumulative trauma to the psychiatric symptoms of major depression and post-traumatic stress disorder (PTSD) in a community study of Cambodian survivors of mass violence were evaluated. METHOD In 1990, a survey of 1000 households was conducted in a Thai refugee camp (Site 2) using a multi-stage random sampling design. Trauma history and psychiatric symptoms were assessed for two time periods. Analysis used linear dose-response regression modelling. RESULTS 993 Cambodian adults reported a mean of 14 Pol Pot era trauma events and 1.3 trauma events during the past year. Symptom categories of depression, PTSD, dissociative and culturally dependent symptoms exhibited strong dose-effect responses with the exception of avoidance. All symptom categories, except avoidant symptoms, were highly correlated. CONCLUSIONS Cumulative trauma continued to affect psychiatric symptom levels a decade after the original trauma events. The diagnostic validity of PTSD criteria, with the notable exception of avoidance, was supported. Inclusion of dissociative and culturally dependent symptoms increased the cultural sensitivity of PTSD.
Relation of Family History of Suicide to Suicide Attempts in Alcoholics

OBJECTIVE: This study was an examination of whether a family history of suicide is associated with attempts at suicide among alcoholics. METHOD: A consecutive series of 333 alcoholics were interviewed about whether or not they had ever attempted suicide and about their family history of suicide. RESULTS: Compared with alcoholics who had never attempted suicide, significantly more of the alcoholics who had attempted suicide reported that a first- or second-degree relative had committed suicide. CONCLUSIONS: A family history of suicide may indicate that an alcoholic has a higher risk of attempting suicide.
Conditionally replicating luciferase reporter phages : Improved sensitivity for rapid detection and assessment of drug susceptibility of Mycobacterium tuberculosis

TM4 is a lytic mycobacteriophage which infects mycobacteria of clinical importance. A luciferase reporter phage, phAE40, has been constructed from TM4 and was previously shown to be useful for the rapid detection and drug susceptibility testing of Mycobacterium tuberculosis. However, the lytic nature of the phage results in a loss of detectable light output and limits the sensitivity of detection. We describe several strategies aimed at improving the luciferase activity generated by TM4 luciferase phages, including (i) varying the position of the luciferase gene in the phage genome, (ii) isolating host-range mutants of the phage, and (iii) introducing temperature-sensitive mutations in the phage such that it will not replicate at the infecting temperature. Several new phages generated by these methods show increased intensity of luciferase production compared to the first-generation reporter phage phAE40, and one phage, phAE88, also demonstrates an enhanced duration of luciferase activity. This has allowed the detection of as few as 120 BCG cells and the determination of drug susceptibilities of M. tuberculosis in as little as 1 day.
Plasma Arginine and Ornithine Are the Main Citrulline Precursors in Mice Infused with Arginine-Free Diets

Dietary arginine is the main dietary precursor for citrulline synthesis, but it is not known if other precursors can compensate when arginine is absent in the diet. To address this question, the contributions of plasma and dietary precursors were determined by using multitracer protocols in conscious mice infused i.g. either an arginine-sufficient diet [Arg(+)] or an arginine-free diet [Arg(-)]. The plasma entry rate of citrulline and arginine did not differ between the 2 diet groups (156 +/- 6 and 564 +/- 30 micromol kg(-1) h(-1), respectively); however, the entry rate of ornithine was greater in the mice fed the Arg(+) than the Arg(-) diet (332 +/- 33 vs. 180 +/- 16 micromol kg(-1) h(-1)). There was a greater utilization of plasma ornithine for the synthesis of citrulline (49 +/- 4 vs. 36 +/- 3 micromol kg(-1) h(-1), 30 +/- 3% vs. 24 +/- 2% of citrulline entry rate) in the mice fed the Arg(-) diet than the Arg(+) diet. The utilization of plasma arginine did not differ between the 2 diet groups for citrulline synthesis, either through plasma ornithine (approximately 29 +/- 3 micromol kg(-1) h(-1)) or at the site of citrulline synthesis (approximately 12 +/- 3 micromol kg(-1) h(-1)). The contribution of dietary proline to the synthesis of citrulline was mainly at the site of citrulline production (17 +/- 1 micromol kg(-1) h(-1)), rather than through plasma ornithine (5 +/- 0.4 micromol kg(-1) h(-1)). Dietary glutamine was utilized only at the site of citrulline synthesis (4 +/- 0.2 micromol kg(-1) h(-1)). Dietary glutamine and proline made a greater contribution to the synthesis of citrulline in mice fed the Arg(-) diet but remained minor sources for citrulline production. Plasma arginine and ornithine are able to support citrulline synthesis during arginine-free feeding.
Hemorrhagic Cystitis after Allogeneic Bone Marrow Transplantation in Children: Clinical Characteristics and Outcome

Abstract Hemorrhagic cystitis (HC) is a well-documented adverse event experienced by patients undergoing hematopoietic stem cell transplantation. When severe, HC causes significant morbidity, leads to renal complications, prolongs hospitalization, increases health-care costs, and occasionally contributes to death. We retrospectively studied the medical records of 245 children undergoing an initial allogeneic bone marrow transplantation for malignant disease at St. Jude Children's Research Hospital between 1992 and 1999 to describe the clinical course of HC in all patients and to identify the risk factors for HC in this cohort. Conditioning regimens included cyclophosphamide, cytarabine, and total body irradiation. Grafts from unrelated or mismatched related donors were depleted of T lymphocytes, whereas matched sibling grafts were unmanipulated. All patients received cyclosporine as prophylaxis for graft-versus-host disease. Recipients of grafts from matched siblings also received pentoxifylline or short-course methotrexate. Severe HC developed in 27 patients (11.0%). The median duration of HC was 73 days (range, 5–619 days); 12 patients had ongoing HC at the time of death. In univariate analyses, patients were at increased risk of severe HC if they were male (P = .021) or had received T cell-depleted grafts (P = .017), grafts from unrelated donors (P = .021), a lower total nucleated cell dose (P = .032), or antithymocyte globulin (P = .0446). Multiple regression analysis revealed male sex (β = .97; P = .027) and unrelated donor graft recipients (β = .83; P = .039) to be significant factors.
Fuc-TVII is required for T helper 1 and T cytotoxic 1 lymphocyte selectin ligand expression and recruitment in inflammation, and together with Fuc-TIV regulates naive T cell trafficking to lymph nodes.

To determine how the α(1,3)fucosyltransferases Fuc-TIV and Fuc-TVII, and the selectin ligands they control may contribute to the adaptive immune response, contact hypersensitivity (CHS) was characterized in mice deficient in either or both enzymes. We find a substantial CHS deficiency in Fuc-TVII−/− mice, and a complete deficiency in Fuc-TIV−/−/Fuc-TVII−/− mice. These defects are not accounted for by alterations in the number or function of epidermal Langerhans cells required for cutaneous antigen processing and presentation. By contrast, defective CHS in Fuc-TVII−/− mice or Fuc-TIV−/−/Fuc-TVII−/− mice is attributed in part to prominent, or nearly complete deficiencies, respectively, in the complement of naive T lymphocytes available in lymph nodes for antigen-dependent activation, expansion, differentiation, and dissemination. Fuc-TVII deficiency also deletes expression of E- and P-selectin ligands by Th1 and T cytotoxic 1 (Tc1) lymphocytes, annuls T cell trafficking to inflamed cutaneous sites in vivo, and thereby controls an essential component of the efferent phase of the cutaneous immune response. These observations indicate that collaborative contributions of Fuc-TIV and Fuc-TVII to L-selectin ligand synthesis, and to lymphocyte recruitment, are requisite components of the primary cellular immune response, and assign an essential role to Fuc-TVII in control of E- and P-selectin ligand expression by Th1 and Tc1 lymphocytes.
A consistent boundary condition for vorticity-streamfunction simulation of wall-bounded vortex flow

This paper was motivated by a computational effort to model the aircraft wake vortex hazard near airports. Those flows can usually be approximated as a pair of two-dimensional, incompressible vortices interacting with an infinite solid wall. The present numerical model uses a vorticity–streamfunction formulation to simulate the two-dimensional problem. Since vorticity generation near the wall alters the evolution of the secondary and tertiary vortices directly, accurate modeling of the wall region is critical. A local relationship between vorticity and streamfunction for a wall boundary condition has been established from a new point of view, by specifying the streamfunction at the boundary grid lifted away from the solid wall. The new method has utilized Taylor series expansions near the wall boundary. Although the resulting expressions are only first order accurate, the critical importance of physical and mathematical consistency has been achieved. Numerical test cases are discussed in the paper.
How The Genome Got a Life Span.

In the space of little more than a decade, ideas of the human genome have shifted significantly, with the emergence of the notion that the genome of an individual changes with development, age, disease, environmental inputs, and time. This paper examines the emergence of the genome with a life span, one that experiences drift, instability, and mutability, and a host of other temporal changes. We argue that developments in chromatin biology have provided the basis for this genomic embodiment of experience and exposure. We analyze how time has come to matter for the genome through chromatin, providing analysis of examples in which the human life course is being explored as a set of material changes to chromatin. A genome with a life span aligns the molecular and the experiential in new ways, shifting ideas of life stages, their interrelation, and the temporality of health and disease.
First‐degree Atrioventricular Block in Alprazolam Overdose Reversed by Flumazenil

This report describes a case of alprazolam overdose associated with marked first-degree atrioventricular block reversed by flumazenil. Animal and human evidence suggests activity of certain benzodiazepines at peripheral benzodiazepine receptors in the myocardium and elsewhere. Myocardial benzodiazepine receptor ligands appear to affect calcium-channel activity, which may explain the clinical findings. Benzodiazepines may behave like weak calcium-channel blockers. This case raises the possibility of a potential role for flumazenil as an adjunct in the management of calcium-channel blocker toxicity.
Indications, clinical course, and postoperative outcomes of urgent adenotonsillectomy in children.

Importance Children undergoing urgent adenotonsillectomy have been poorly described in literature. Objective To characterize the clinical course and outcomes of patients who underwent urgent adenotonsillectomy. Design, Setting, and Participants A 7-year retrospective medical record review of patients undergoing urgent adenotonsillectomy (study group) at a tertiary care pediatric hospital was undertaken. Comparisons were made between the study group and the control group consisting of children undergoing adenotonsillectomy following diagnostic polysomnography. Interventions Retrospective medical record review with no study interventions. Main Outcomes and Measures Demographics, hospital course, and clinical outcomes. Results A total of 35 patients (21 boys [60%] and 14 girls [40%]; mean age, 3.8 years) were identified as having undergone urgent adenotonsillectomy defined as severe obstructive sleep apnea with associated hypoxemia unresponsive to oxygen. The control group included 301 patients who received a diagnostic polysomnogram prior to nonurgent adenotonsillectomy. Patients undergoing urgent adenotonsillectomy patients were more likely to be younger than 3 years (54%) than nonurgent patients ( P Conclusions and Relevance Patients requiring urgent adenotonsillectomy are marked by younger age, elevated obstructive apnea-hypopnea indices, and persistent desaturations below 80% unresponsive to supplemental oxygen. Following surgery, some children have a dramatic improvement in gas exchange and will no longer require supplemental oxygen.
Neuroimaging study designs, computational analyses and data provenance using the LONI pipeline.

Modern computational neuroscience employs diverse software tools and multidisciplinary expertise to analyze heterogeneous brain data. The classical problems of gathering meaningful data, fitting specific models, and discovering appropriate analysis and visualization tools give way to a new class of computational challenges—management of large and incongruous data, integration and interoperability of computational resources, and data provenance. We designed, implemented and validated a new paradigm for addressing these challenges in the neuroimaging field. Our solution is based on the LONI Pipeline environment [3], [4], a graphical workflow environment for constructing and executing complex data processing protocols. We developed study-design, database and visual language programming functionalities within the LONI Pipeline that enable the construction of complete, elaborate and robust graphical workflows for analyzing neuroimaging and other data. These workflows facilitate open sharing and communication of data and metadata, concrete processing protocols, result validation, and study replication among different investigators and research groups. The LONI Pipeline features include distributed grid-enabled infrastructure, virtualized execution environment, efficient integration, data provenance, validation and distribution of new computational tools, automated data format conversion, and an intuitive graphical user interface. We demonstrate the new LONI Pipeline features using large scale neuroimaging studies based on data from the International Consortium for Brain Mapping [5] and the Alzheimer's Disease Neuroimaging Initiative [6]. User guides, forums, instructions and downloads of the LONI Pipeline environment are available at http://pipeline.loni.ucla.edu.
Are Teach For America Corps Members Highly Qualified to Teach English Learners?: An Analysis of Teacher Preparation for Culturally and Linguistically Diverse Populations

Teach For America (TFA) places novice teachers, referred to as corps members, in several regions across the United States that have among the highest English learner populations in the nation. In light of this fact, we offer an examination of federal policy and recommend programmatic strategies to better prepare TFA corps members to serve English learners. First, we describe the current Elementary and Secondary Education Act amendment that allows TFA corps members to be considered highly qualified without adequate training to work with culturally and linguistically diverse students. Next, we analyze the organizational curriculum and teacher preparation approach specific to English learners. We then compare TFA’s approach to those used in emerging residency models and community-based programs that prepare teachers for specific local contexts and student populations. We conclude with recommendations for TFA to improve its teaching corps for English learners and other culturally and linguistically diverse students.