cssi/SciSciGPT-SciSciNet huggingface dataset:
CERES: a cryo-EM re-refinement system for continuous improvement of deposited models

The field of electron cryomicroscopy (cryo-EM) has advanced quickly in recent years as the result of numerous technological and methodological developments. This has led to an increase in the number of atomic structures determined using this method. Recently, several tools for the analysis of cryo-EM data and models have been developed within the Phenix software package, such as phenix.real_space_refine for the refinement of atomic models against real-space maps. Also, new validation metrics have been developed for low-resolution cryo-EM models. To understand the quality of deposited cryo-EM structures and how they might be improved, models deposited in the Protein Data Bank that have map resolutions of better than 5 A were automatically re-refined using current versions of Phenix tools. The results are available on a publicly accessible web page (https://cci.lbl.gov/ceres). The implementation of a Cryo-EM Re-refinement System (CERES) for the improvement of models deposited in the wwPDB, and the results of the re-refinements, are described. Based on these results, contents are proposed for a `cryo-EM Table 1', which summarizes experimental details and validation metrics in a similar way to `Table 1' in crystallography. The consistent use of robust metrics for the evaluation of cryo-EM models and data should accompany every structure deposition and be reported in scientific publications.
Reflecting on Your Reflection: Examining the Effect of a Non-Reversing Mirror on Self-Perception.

BACKGROUND Photographic images can clash markedly with patients' self-perception. Individuals are more familiar with their mirror image, where their facial asymmetries are reversed. A non-reversing mirror (NRM) allows patients to see their dynamic non-reversed image and familiarize themselves with how they appear in photographs and to others. OBJECTIVES The aim of this study was to explore the effect that a NRM has on facial self-perception and investigate whether a NRM changes an individual's goals when considering cosmetic surgery. METHODS Individuals (n = 30) filled out portions of the FACE-Q questionnaire after inspecting their reflections in a NRM and in a standard mirror for 30 seconds each. After these two inspections had been completed, investigators asked qualitative questions comparing the 2 mirrors. Wilcoxon signed-rank test, Mann-Whitney U test, and Pearson's chi-squared test were used to analyze the differences. RESULTS Participants scored significantly better on the FACE-Q Age Appraisal and Appearance-Related Psychosocial Distress scales when looking in a standard mirror vs a NRM (P = 0.007 and 0.001, respectively). Qualitatively, most reported that their faces seemed less symmetric and less balanced (73% and 53%, respectively) in the NRM. Overall, 83.3% reported seeing a qualitative difference in their appearance, with 30% endorsing that looking in the NRM had changed their facial aesthetic goals. CONCLUSIONS A NRM can bridge between the familiarity of the patient's reversed reflection and their less-familiar, non-reversed true image. It may serve as a useful physician-patient communication tool when discussing goals and expectations for facial aesthetic procedures.
Enraged and Engaged? Emotions as Motives for Discussing Politics:

The 2016 presidential campaign made some feel angry, while others felt anxious, embarrassed, or enthusiastic. We explore how these emotions relate to patterns of political talk within informal conv...
Quantifying the feasibility of shortening clinical trial duration using surrogate markers.

The potential benefit of using a surrogate marker in place of a long-term primary outcome is very attractive in terms of the impact on study length and cost. Many available methods for quantifying the effectiveness of a surrogate endpoint either rely on strict parametric modeling assumptions or require that the primary outcome and surrogate marker are fully observed that is, not subject to censoring. Moreover, available methods for quantifying surrogacy typically provide a proportion of treatment effect explained (PTE) measure and do not directly address the important questions of whether and how the trial can be ended earlier using the surrogate marker. In this article, we specifically address these important questions by proposing a PTE measure to quantify the feasibility of ending trials early based on endpoint information collected at an earlier landmark point t0 in a time-to-event outcome setting. We provide a framework for deriving an optimally predicted outcome for individual patients at t0 based on a combination of surrogate marker and event time information in the presence of censoring. We propose a non-parametric estimator for the PTE measure and derive the asymptotic properties of our estimators. Finite sample performance of our estimators are illustrated via extensive simulation studies and a real data application examining the potential of hemoglobin A1c and fasting plasma glucose to predict treatment effects on long term diabetes risk based on the Diabetes Prevention Program study.
Epilogue: Meaningful Learning, Knowledge Restructuring and Conceptual Change: On Ways of Teaching Science for Understanding

Publisher Summary This chapter presents a model designed to help teachers reflect on and evaluate new ways of teaching science for understanding. The model is based on a convergence of evidence from a number of closely related disciplines and draws heavily on the findings of cognitive scientists, applied learning theorists, and epistemologists as well as historians and philosophers of science. The model emerges directly from our human constructivist perspective and focuses attention on the critical relationships among meaningful learning, knowledge restructuring, and conceptual change. The challenge for teachers is finding ways to devise questions, experiments, and demonstrations that require students to rethink their ideas without unnecessarily emphasizing that their current ideas are wrong. By the time children begin the formal study of animal diversity, most of them have had a wide range of intense, personal, and often emotionally laden experiences with living organisms. Selecting intervention strategies and sequencing teaching episodes are among the most important decisions science teachers make.
Generalized Boundary Conditions for Imperfect Interface between Two Solid Anisotropic Media

The interface between two solids has properties different from those of the bulk. The actual structure of such an interface depends on the particular type of solid contact: contact formed during solidification, metallurgical solid state bond, dry mechanical or lubricated contact et cetera. The classical boundary conditions which are satisfied for an infinitely thin perfect bond are not adequate to describe wave interaction with an imperfect interface.
The chemistry of uranium(IV)—III: Some new chelate complexes of uranium(IV)☆

Abstract Several new chelate complexes of uranium(IV) have been synthesized and characterized. Among these are included a very stable eight-co-ordinated complex in which two quadridentate ligands are bound to the same U(IV), U(ensal) 2 , and a complex believed to be the first example of U(IV) bound to a phosphine ligand, (UCl 4 ) 2 (diphos). All complexes reported are believed to contain eight-co-ordinated U(IV).
Limb Darkening Observations of Venus from 5 μ to 18 μ

Limb darkening measurements of the thermal radiation from Venus at 5, 9, 11, 13 and 18 μ are presented. This data, produced by deconvolving the observations with a measured instrumental response function, indicates a complex atmospheric structure which will require careful atmospheric modeling to fully interpret.
Gecas and the Ge/Honeywell Merger: A Response to Reynolds and Ordover

The European Commission blocked the proposed 2001 merger of General Electric and Honeywell in part because of fears about the past and future effect on competition of GE's aircraft leasing arm, GECAS. It argued that in the past GECAS had skewed aircraft engine sales toward GE in a way that harmed competition, and that a post-merger GECAS would have brought about an even greater foreclosure in Honeywell's aircraft systems markets. A recent article by Reynolds and Ordover (2002) articulates in more detail a theoretical and empirical basis for this prediction. It estimates GECAS's past engine impact, and details theoretical steps that lead to a GECAS-based rationale for blocking the merger. This paper shows that the Reynolds and Ordover empirical analysis of GECAS' past impact is flawed, and that a better estimate yields at most a shift of 1.5% of large commercial aircraft engine sales toward GE after GECAS' arrival. It argues that this small engine share shift does not translate into past or future anticompetitive effects in any market and that Reynolds and Ordover's model, which does predict such an outcome, rests on flawed assumptions.
SU-F-207-10: Simulation Study of Patient Off-Centering Effect On Organ Dose in Chest CT Scan

Purpose: To simulate off-center chest CT scans on adult phantoms and to determine the impact on organ dose. Methods: A GPU-based fast Monte Carlo code ARCHER was used for simulation of chest CT scan on RPI-adult female (RPI-AF) and RPI-adult male (RPI-AM) phantoms. A CT scanner model of GE LightSpeed Pro 16 previously developed was simulated with a fixed 200 mAs per rotation. The human phantom was placed in supine posture at the isocenter of CT model to generate organ doses for the “centered” case. Off-center table positions were simulated by moving the phantom towards and away from the 12 o’clock position on the CT model. A 5cm change in either direction of table height change was simulated in 1 cm increments. Organ doses were calculated at each table height, and compared to determine the effect of off-centering on dose. Results: Breast dose for female adult phantom changed the most with position by up to 25%, where lower position increased breast dose and higher position decreased it. The thymus shared the same trend as the breasts, with total dose change of 17% for male adult phantom. The adrenals, which were near the back surface of phantom, had a dose trend opposed to the breasts that decreased at lower position and increased at higher position. The lungs, which were large organs in chest cavity near body center, were only slightly affected by off-centering with 4% decrease in dose at most. Conclusion: Organs at or near body surface were affected most by off-centering. Lower table height increased dose to the breasts and thymus. Higher table height increased dose to the adrenals. This study confirmed the results found in physical phantom measurements. National Institutes of Health R01EB015478
Mission-aware time-dependent cyber asset criticality and resilience

Determining mission-aware criticality, dependency, and resilience of cyber assets is required to support mission assurance in cyber defense and continuous operation of networks. This paper addresses the characterization of mission-aware asset criticality and the real-time dependencies of assets, services, tasks, and missions using Time Petri Nets and impact dependency graphs. In order to assess whether a system is resilient enough to keep supporting mission assurance in the face of cyber attacks, this paper introduces a new approach to determining whether the required resources will be available at the required time intervals. This approach leads to a better assessment of whether missions can be accomplished in a given time window over a mission-oriented network.
The Effect of Oral Contraceptives on Total-Body Potassium

In an effort to delineate one facel of the effects of synthetic progestogens on basic intracellular and extracellular electrolyte and fluid distribution, total body potassium was calculated, after background counts, from the average of three two- minute counts of γ-emissions of naturally occurring; radioactive potassium (40K) by whole-body counting of two groups of women in the child- bearing age. Group 1 consisted of 42 women taking a constant dosage over a period of nine months to four years of several combinations of synthetic; steroids comprising antifertility agents commercially available. Group 2 had 39 women not taking these drugs. Results showed that total- body potassium was the same in each group. Studies have shown body potassium to correlate well with intracellular water. One can speculate from this study that intracellular water appears to be unaffected by antifertility agents.
Antigen-specific and nonspecific deletion of immature cortical thymocytes caused by antigen injection

Analysis of antigen-induced negative selection of thymocytes in T cell receptor (TCR)-transgenic mice is complicated by the presence of an antigen-responsive peripheral T cell compartment. Our experiments address the question of whether and how peripheral T cell activation can affect immature thymocytes. Following three daily injections of peptide antigen into mice expressing a peptide-specific transgenic TCR and deficient for TAP1, we and others have found profound deletion of the CD4+CD8+ (DP) thymocyte subset. However, our work shows that even though mature CD8+ T cells are inefficiently selected in TAP1-deficient mice, there was a striking degree of peripheral expansion and activation of CD8+ peripheral T cells. Furthermore, when cells from TCR-transgenic mice were adoptively transferred, we found that deletion of nontransgenic DP thymocytes occurred in Thy-1-congenic and even more efficiently in TAP1-deficient recipients after repeated peptide injection resulting in peripheral T cell activation. In the adoptive transfer experiments the degree of deletion of immature bystander thymocytes was decreased upon blocking of TNF. These data show that deletion of DP thymocytes can result from excessive peripheral T cell activation and identify TNF as an important effector molecule for this process. When steps are taken to avoid peripheral T cell activation, peptide antigen can induce TCR-mediated thymocyte deletion, presumably in the thymus cortex, since injection of TAP1-deficient TCR-transgenic mice resulted in deletion of immature DP thymocytes prior to detectable peripheral T cell expansion and activation. This effect was not blocked by inhibiting tumor necrosis factor activity. In addition, DP depletion was seen in the absence of peripheral T cell activation when antibody-mediated depletion of CD8+ T cells was performed. Our work clearly shows that two mechanisms for deletion of DP thymocytes exist: deletion induced by antigen presentation in the thymus and deletion as a consequence of repeated stimulation of mature peripheral T cells.
Utilization of SiC MOSFET Body Diode in Hard Switching Applications

This work discusses the possibility of using SiC MOSFET body diode in switching power conversion applications, focusing on performance and reliability aspects.
Geochemical constraints on chemolithoautotrophic reactions in hydrothermal systems

Thermodynamic calculations provide the means to quantify the chemical disequilibrium inherent in the mixing of reduced hydrothermal fluids with seawater. The chemical energy available for metabolic processes in these environments can be evaluated by taking into account the pressure and temperature dependence of the apparent standard Gibbs free energies of reactions in the S-H2-H2O system together with geochemical constraints on pH, activities of aqueous sulfur species and fugacities of H2 and/or O2. Using present-day mixing of hydrothermal fluids and seawater as a starting point, it is shown that each mole of H2S entering seawater from hydrothermal fluids represents about 200,000 calories of chemical energy for metabolic systems able to catalyze H2S oxidation. Extrapolating to the early Earth, which was likely to have had an atmosphere more reduced than at present, shows that this chemical energy may have been a factor of two or so less. Nevertheless, mixing of hydrothermal fluids with seawater would have been an abundant source of chemical energy, and an inevitable consequence of the presence of an ocean on an initially hot Earth. The amount of energy available was more than enough for organic synthesis from CO2 or CO, and/or polymer formation, indicating that the vicinity of hydrothermal systems at the sea floor was an ideal location for the emergence of the first chemolithoautotrophic metabolic systems.
The TWEAK is weak for alcohol screening among female Veterans Affairs outpatients.

Background: The optimal brief questionnaire for alcohol screening among female patients has not yet been identified. This study compared the performance of the TWEAK (tolerance, worried, eye-opener, amnesia, cutdown), the Alcohol Use Disorders Identification Test (AUDIT), and the AUDIT Consumption (AUDIT-C) as self-administered screening tests for hazardous drinking and/or active alcohol abuse or dependence among female Veterans Affairs (VA) outpatients. Methods: Women were included in the study if they received care at VA Puget Sound and completed both a self-administered survey containing the AUDIT and TWEAK screening questionnaires and subsequent in-person interviews with the Alcohol Use Disorders and Associated Disabilities Interview Schedule. Sensitivities, specificities, positive and negative likelihood ratios, and areas under Receiver Operating Characteristic curves were computed for each screening questionnaire compared with two interview-based comparison standards: (1) active DSM-IV alcohol abuse or dependence and (2) hazardous drinking and/or active DSM-IV alcohol abuse or dependence, the more appropriate target for primary care screening. Results: Of 393 women who completed screening questionnaires and interviews, 39 (9.9%) met diagnostic criteria for alcohol abuse or dependence, and 89 (22.7%) met criteria for hazardous drinking or alcohol abuse or dependence. The TWEAK had relatively low sensitivities (0.62 and 0.44) but adequate specificities (0.86 and 0.89) for both interview-based comparison standards, even at its lowest cut-point (≥1). The AUDIT and AUDIT-C were superior, with the following areas under the receiver operating characteristic curve for active alcohol abuse or dependence and hazardous drinking and/or active alcohol abuse or dependence, respectively: AUDIT, 0.90 [95% confidence interval (CI), 0.85–0.95] and 0.87 (95% CI, 0.84–0.91); AUDIT-C, 0.91 (95% CI, 0.88–0.95) and 0.91 (95% CI, 0.88–0.94); and TWEAK, 0.76 (95% CI, 0.66–0.86) and 0.67 (95% CI, 0.60–0.74). Conclusions: The TWEAK has low sensitivity as an alcohol-screening questionnaire among female VA outpatients and should be evaluated further before being used in other female primary care populations. The three-item AUDIT-C was the optimal brief alcohol-screening questionnaire in this study.
MO-D-AUD-01: A Comprehensive Study On the Heterogeneity Dose Calculation Accuracy in IMRT Using An Anthropomorphic Thorax Phantom

Purpose: To provide a comprehensive study on the accuracy of many commonly used Intensity Modulated Radiation Therapy(IMRT)treatment planning systems using the Radiological Physics Center's (RPC) anthropomorphic thorax phantom. Method and Materials:Treatment planning systems (TPSs) from Corvus, Eclipse, Pinnacle, and Tomotherapy were evaluated using the RPC anthropomorphic phantom. Treatment plans were designed using the same clinical constraints and prescriptions so that 96% of the planning target volume (PTV) was covered by the prescription dose. The phantom is equipped with TLD located in the tumor,heart, and spinal cord and radiochromic film located in three anatomical planes intersecting the tumor center and extending into the lung.IMRT QA was performed to adjust the calculated dose distributions in order to isolate the effects of heterogeneity. Comparisons were made between each TPS calculation and measurement. In two instances, re‐calculations of the original correction based pencil beam (PB) plans were performed using the superposition convolution (SC) method. Results: TPSs employing superposition convolution algorithms predicted dose within 3.6% of the target TLD, while TPSs using correction based pencil beam algorithms predicted dose within 5.0% of the target TLD. Both algorithm types showed variations (2% to 38% in the cord and heart) in predicting low dose to normal structures. The dose distributions within the PTV and penumbra lung regions showed good agreement when using an SC algorithm. However, TPSs using the PB type algorithm overestimated dose in the PTV and underestimated the extent of penumbra broadening corresponding to the surrounding lung.Conclusion: This work demonstrated that superposition convolution algorithms found in widely used IMRTtreatment planning systems are able to calculate the dose accurately to the PTV and penumbra regions when low density heterogeneities are involved. Conflict of Interest: This work supported by PHS CA010953 and CA081647 awarded by NCI, DHHS.
Effects of system parameters on the performance of CO2-selective WGS membrane reactor for fuel cells

Abstract Performing water gas shift (WGS) reaction efficiently is critical to hydrogen purification for fuel cells. In our earlier work, we proposed a CO2-selective WGS membrane reactor, developed a one-dimensional non-isothermal model to simulate the simultaneous reaction and transport process and verified the model experimentally under an isothermal condition. Further modeling investigations were made on the effects of several important system parameters, including inlet feed temperature, inlet sweep temperature, feed-side pressure, feed inlet CO concentration, and catalyst activity, on membrane reactor performance. The synthesis gases from both autothermal reforming and steam reforming were used as the feed gas. As the inlet feed temperature increased, the required membrane area reduced because of the higher WGS reaction rate. Increasing the inlet sweep temperature decreased the required membrane area more significantly, even though the required membrane area increased slightly when the inlet sweep temperature exceeded about 160 °C. Higher feed-side pressure decreased the required membrane area as a result of the higher permeation driving force and reaction rate. A potentially more active catalyst could make the membrane reactor more compact because of the enhanced reaction rate. The modeling results have shown that a CO concentration of less than 10 ppm is achievable from syngases containing up to 10% CO.
Adenosine 5′-triphosphate (ATP)-mediated stimulation and suppression of DNA synthesis in lymphoid cells. II. Suppressive effect of ATP on murine T-cell functions

The suppressive effects of ATP on murine T-cell functions were studied. The suppressive effects of ATP as well as adenosine on the DNA synthesis of spleen cells are due to the presence of mature T-cells, because ATP has no suppressive effect on athymic nu/nu spleen cells. Further characterization of the cells which are responsible for ATP-mediated suppression of DNA synthesis revealed that the cells are nylon wool-adherent T-cells and PHA-reactive T-cells. In addition, the suppressive effects of ATP on both spontaneous and mitogen-induced proliferative responses are stronger than that of adenosine, and T-cells are more sensitive to ATP than B-cells. The observation that both ATP and adenosine have unique effects on T-cells compared to B-cells may contribute toward explaining why patients with severe combined immunodeficiency (SCID) associated with adenosine deaminase (ADA) deficiency have greater T-cell than B-cell abnormalities.
Analytical modeling of vehicle-to-vehicle communication using spread of infection models

In this study we propose a macroscopic analytical model for modeling the vehicle-to-vehicle (V2V) communication process. Real-time information propagation by V2V communication is part of the Vehicle Infrastructure Integration (VII) initiative, aimed at improving the traffic conditions on existing roadways. Vehicles communicate among themselves and pass information regarding congestion, unsafe pavement condition or accidents. This proposed information propagation model is based on the Susceptible-Infected-Removed (SIR) model that is used to model the spread of epidemics in a region. As an analogy, we call the vehicles that have received the signal as ‘infected vehicles’, and those instrumented vehicles that have not received the information are called ‘susceptible vehicles’. The proposed model predicts the number of infected vehicles present on the roadway at every instant of time. The model is developed for a variety of traffic conditions including different volumes, market share of instrumented vehicles, speed limits and number of lanes. Finally, it is validated using simulation results obtained from Paramics, traffic micro-simulation software.
Analytical study of the effluents from a high-temperature entrained flow gasifier

Effluents from a high temperature, high pressure, entrained flow gasifier were analysed for possible inorganic and organic pollutants. The effluents and product gases from this type of reactor are very clean compared to those produced in established commercial gasification processes. The only major potential pollutants are the particulate matter and NH4+ in the scrubber water, the bottom ash, and the H2S and HCN in the product and flash gases. All of the non-volatile organic compounds produced are quantitatively adsorbed by the particulate matter in the scrubber water. Increasing the pressure and decreasing the O2coal ratio tended to reduce pollutants in the effluents and increase coal conversion efficiency.
Parallel Software Abstractions for Structured Adaptive Mesh Methods

We describe and analyze parallelization techniques for the implementation of portable structured adaptive mesh applications on distributed memory parallel computers. Such methods are difficult to implement on parallel computers because they employ elaborate dynamic data structures to selectively capture localized irregular phenomena. Our infrastructure supports a set of layered abstractions that encapsulate low-level details of resource management, such as grid generation, interprocessor communication, and load balancing. Our layered design also provides the flexibility necessary to accommodate new applications and to fine-tune performance. This flexibility has enabled us to show that the uniformity restrictions imposed by a data parallel Fortran implementation (e.g., HPF) would significantly impact performance of structured adaptive mesh methods. We present computational results from eigenvalue computation arising in materials design.
Role of Commitments in the Decision to Stop a Theft

Summary A field experiment was conducted to test the relationship between previous commitments to a theft victim and a bystander's willingness to stop the thief. A pocket calculator was stolen in front of 30 bystanders under one of three experimental conditions. In one condition, the bystander was committed previously to watch the victim's calculator (First-Party Commitment). In a second treatment, the bystander made a commitment to the victim to watch the belongings of another student who earlier had been seated nearby (Second-Party Commitment). There was also a third, no-commitment group. Findings showed that direct, first-party commitments to the victim of the theft led to greater bystander intervention than no commitment or second-party commitments.
Hypokalemic periodic paralysis mutations: Confirmation of mutation and analysis of founder effect

Abstract In three families with hypokalemic periodic paralysis (HOPP) we have confirmed the presence of a missense mutation (arginine 528 to histidine) within the gene CACNLIA3 encoding the α 1 subunit of the L-type, voltage-sensitive calcium channel. Additionally, we have identified two novel polymorphisms within this gene located in close proximity to the mutation. Haplotype analysis using these and other polymorphisms indicates that these families do not share a common mutation due to a founder effect. Rather, an HOPP phenotype has arisen in these families from three separate but identical mutations.
The production of Mullerian inhibiting substance by the fetal, neonatal and adult rat.

The intensity and duration of Mullerian Inhibiting Substance (MIS) secretion by the fetal newborn and adult rat testes and the effect of the placenta and pituitary on the secretory pattern was studied in vivo and in vitro. A graded organ culture assay was used to determine the secretory pattern. Production of MIS was evident during the last trimester of pregnancy. MIS production continued during the 1st 3 weeks of neonatal life and then disappeared around the time of weaning. Hypophysectomy performed at 20 days of age failed to restore MIS activity in adult animals. Fragments of placenta in testis culture did not influence MIS activity in perinatal testes. MIS exhibited a regressive effect on Mullerian ducts placed at a distance from a testicular source.
Rye Cover Crop Effects on Soil Quality in No-Till Corn Silage–Soybean Cropping Systems

Corn (Zea mays L.) and soybean [Glycine max (L.) Merr.] farmers in the upper Midwest are showing increasing interest in winter cover crops. The effects of winter cover crops on soil quality in this region, however, have not been investigated extensively. The objective of this experiment was to determine the effects of a cereal rye (Secale cereale L.) winter cover crop after more than 9 yr in a corn silage–soybean rotation. Four cereal rye winter cover crop treatments were established in 2001: no cover crop, rye after soybean, rye after silage, and rye after both. Soil organic matter (SOM), particulate organ- ic matter (POM), and potentially mineralizable N (PMN) were measured in 2010 and 2011 for two depth layers (0–5 and 5–10 cm) in both the corn silage and soybean phases of the rotation. In the 0- to 5-cm depth layer, a rye cover crop grown after both main crops had 15% greater SOM, 44% greater POM, and 38% greater PMN than the treatment with no cover crops. In gen- eral, the treatments that had a rye cover crop after both crops or after corn silage had a positive effect on the soil quality indicators relative to treatments without a cover crop or a cover crop only after soybean. Apparently, a rye cover crop grown only after soybean did not add enough residues to the soil to cause measureable changes in SOM, POM, or PMN. In general, rye cover crop effects were most pronounced in the top 5 cm of soil.
Comparison of Promoters for the Murine and Human P-selectin Genes Suggests Species-specific and Conserved Mechanisms for Transcriptional Regulation in Endothelial Cells

P-selectin, an adhesion receptor for leukocytes, is constitutively expressed in megakaryocytes and endothelial cells. Tumor necrosis factor-α (TNF-α) or lipopolysaccharide (LPS) increases synthesis of P-selectin in murine but not in human endothelial cells. To identify potential species-specific and conserved mechanisms for regulation of expression of P-selectin, we cloned the 5′-flanking region of the murine P-selectin gene and compared its features with those previously reported for the human gene. The murine and human genes shared conserved Stat-like, Hox, Ets, GATA, and GT-IIC elements. In the murine gene, a conserved GATA element bound to GATA-2 and functioned as a positive regulatory element, whereas a conserved Ets element bound to GA-binding protein and functioned as a negative regulatory element. Significantly, the murine P-selectin gene had several features not found in the human gene. These included an insertion from −987 to −649 that contained tandem GATA and tandem AP1-like sequences, which resembled enhancers in β-globin locus control regions. Both tandem elements bound specifically to nuclear proteins. The murine gene lacked the unique κB site specific for p50 or p52 homodimers found in the human gene. Instead, it contained two tandem κB elements and a variant activating transcription factor/cAMP response element site, which closely resembled sites in the E-selectin gene that are required for TNF-α- or LPS-inducible expression. TNF-α or LPS augmented expression of a reporter gene driven by the murine, but not the human, P-selectin promoter in transfected endothelial cells. Deletional analysis of the murine 5′-flanking region revealed several sequences that were required for either constitutive or inducible expression. These data suggest that both species-specific and conserved mechanisms regulate transcription of the human and murine P-selectin genes.
A simple technique for isolating pure cell populations from mixed primary cultures

We describe a simple method for isolating designated cell colonies from mixed primary cultures. Circles surrounding the chosen colonies are drawn on the underside of a 60-mm tissue culture dish. The medium in the dish is drained except for about 0.5 ml. The dish is tilted and the area surrounding a marked colony to a distance of about 5 mm is scraped with a sharpened rubber policeman. The low fluid level in the dish facilitates accurate scraping, while the dish is frequently reverted to a horizontal position to spread the retained medium and prevent inadvertent drying. When scraping is completed, the surface of the dish outside the marked areas is dried to destroy cells that escaped scraping and to prevent trypsin from spreading outside the marked areas. Then, either medium can be replenished to allow further growth of the colonies in the same dish, or each cell colony can be individually trypsinized or scraped off the dish for transferral to another dish for subsequent passaging.
Residual Ca2+ and short-term synaptic plasticity

At many synapses, the amount of transmitter released by action potentials increases progressively during a train of spikes. This enhancement of evoked transmitter release grows during tetanic stimulation with several time constants, each bearing a different name (facilitation: tens to hundreds of milliseconds; augmentation: several seconds; potentiation: several minutes), and the enhancement of release to test spikes after a tetanus decays with similar time constants. All these processes depend on presynaptic Ca2+ influx during the conditioning tetanus. It has often been proposed that these forms of synaptic plasticity are due to residual Ca2+ present in nerve terminals following conditioning activity. We tested this idea directly by using photolabile Ca2+ chelators to reduce residual Ca2+ following conditioning stimulation or to generate an artificial elevation in Ca2+ concentration, and observed the effects on synaptic transmission at crayfish neuromuscular junctions. We found that facilitation, augmentation and potentiation are caused by the continuing action of residual Ca2+. Augmentation and potentiation seem to arise from Ca2+ acting at a separate site from facilitation, and these sites are different from the molecular target triggering neurosecretion.
The role of stochasticity and priority effects in floodplain restoration.

This paper is a test of two widely held assumptions in the practice of riparian restoration: (1) if physical processes are restored, plant communities will naturally reassemble themselves, and (2) restored communities will resemble reference sites. Seasonal flooding was restored to two interconnected floodplains in the Central Valley of California (USA), and plant community establishment was studied for six years at 300 permanent vegetation plots. If these two assumptions are valid, then the two floodplains should end up with similar plant assemblages, and they should both have followed a similar trajectory. Then, once the relevant physical processes are restored, (1) plots with similar environmental conditions should have increasingly similar species compositions, (2) plant communities should become more stable and cohesive, (3) both species distributions and plant communities should respond to changes in environmental conditions, (4) plot diversity should decrease, and (5) perennial species should replace annuals. The plots were classified into communities using TWINSPAN, and these communities differed significantly with respect to the main environmental gradient (inundation). Bray- Curtis similarities were calculated for each pair of plots. Patterns in similarity were used to test the strength of communities and the relative importance of proximity and inundation. On the northern floodplain, there was a trend of increasing similarity for plots with similar environmental conditions over the course of the study; plant communities became more stable and clearly responded to changes in environmental conditions. Plot diversity decreased, and the proportion of perennial species increased. On the southern floodplain, however, plots with similar environmental conditions became less similar, while plots that were close together became more similar; plant communities did not become more stable though they did shift in response to changes in environmental conditions. Taken together, this evidence suggests that assembly of communities is more stochastic than deterministic.
Electroluminescence from a polyester containing oligothiophenes in the main chain, enhanced by a diimide electron transport agent

Abstract Photoluminescence spectra in solution and thin films were measured for a polyester with isolated dimethoxyquaterthiophene units in the main chain. Light-emitting diodes were fabricated using indium—tin oxide (ITO)/polyester/AI sandwiches. N,N -dilauryl naphthalene tetracarboxylic acid diimide, added as an electron transport agent, gave improved performance. The emitted light was orange and had λ max 595 nm. Devices constructed with a 240 nm thick polymer film had an emission threshold of about 15 V and 4 mA cm −2 .
Burdened Societies and Transitional Justice

Following John Rawls, nonideal theory is typically divided into: (1) “partial-compliance theory” and (2) “transitional theory." The former is concerned with those circumstances in which individuals and political regimes do not fully comply with the requirements of justice, such as when people break the law or some individuals do not do their fair share within a distributive scheme. The latter is concerned with circumstances in which background institutions may be unjust or may not exist at all. This paper focuses on issues arising in transitional theory. In particular, I am concerned with what Rawls’ has called “burdened societies," that is, those societies that find themselves in unfavorable conditions, such that their historical, social or economic circumstances make it difficult to establish just institutions. The paper investigates exactly how such burdened societies should proceed towards a more just condition in an acceptable fashion. Rawls himself tells us very little, except to suggest that societies in this condition should look for policies and courses of action that are morally permissible, politically possible and likely to be effective. In this paper I first try to anticipate what a Rawlsian might say about the best way for burdened societies to handle transitional problems and so move towards the ideal of justice. Next, I construct a model of transitional justice for burdened societies. Ultimately, I argue for a model of transitional justice that makes use of a nonideal version of Rawls’ notion of the worst-off representative person.
Mitogen receptor redistribution defects and concomitant absence of blastogenesis in ataxia-telangiectasia T lymphocytes

Abstract The ultrastructural distribution of PHA receptors on lymphocytes from two patients with ataxia-telangiectasia was visualized using transmission electron microscopy and ferritin covalently linked to PHA. Lymphocytes from these two patients failed to undergo PHA-induced blastogenesis. The initial time course and ultrastructure of membrane adherence, endocytosis of PHA-Fe-receptor complexes, and formation of multivesicular bodies were the same as for control lymphocytes. The subsequent development of blastogenesis did not occur. At 48–72 hr, when blastogenesis was maximal in control cells, the lymphocytes from these patients failed to exhibit nuclear enlargement, remained heterochromatic and did not develop prominent nucleoli. There was also a marked delay in exocytosis of the multivesicular bodies as compared to control cells. It is concluded that receptor attachment to PHA occurs normally and that an intracellular rather than membrane defect is responsible for absent blastogenesis in these patients. Ferritin-labeled PHA and electron microscopy will be useful in examining lymphocyte activation in other immunodeficiency diseases.
Indentation of an Anisotropic Half-Space by a Heated Flat Punch

The two-dimensional thermoelastic contact problem of an anisotropic half-space indented by a heated rigid flat punch is studied using the extended version of Stroh's formalism. Two cases, where the contact interface is nonslip and frictionless, have been considered. In the first case, the contact is perfect throughout the punch face. In the second case, separation is assumed to occur at the edges of the punch.
Field validation of a habitat suitability index model for the American oyster

A habitat suitability index (HSI) model, developed for the American oyster,Crassostrea virginica, along the Gulf of Mexico, was field tested on 38 0.1-ha reef and nonreef sites in Galveston Bay, Texas. The HSI depends upon six (HSI1) or, optionally, eight (HSI2) variables. The six variables are percent of bottom covered with suitable cultch (V1), mean summer water salinity (V2), mean abundance of living oysters (V3) (a gregarious settling factor), historic mean water salinity (V4), frequency of killing floods (V5), and substrate firmness (V6). The optional variables are the abundance of the southern oyster drillThais haemostoma (V7), and the intensity of the oyster pathogenPerkinsus marinus (V8). The HSI values were lowest at high and low salinity sites and highest at intermediate-salinity sites. To validate the model, the hypothesis that the output of the HSI model was correlated with oyster density was therefore tested. A significant correlation was found between HSI1 and oyster density (Kendall Tau Beta correlation coefficient, τ=0.674, p<0.001, n=38); however, a statistical independence problem exists with the above test, that is, oyster density is both the independent standard for the test and a variable in the model. A regression model was constructed to test the relationship between log-transformed oyster density values (dependent variable) and the other variables of the model (independent variables). Most variation (r2=0.72, r=0.85) in the log-transformed density values were explained by a regression model that contained V2, V4, V5, V6, V7, and V8 as independent variables. The regression model was useful in constructing a modified HSI model (MHSI). A significant correlation (τ=0.674, p<0.05, n=10) was found between MHSI1 values and oyster densities from reefs closed to harvesting. The MHSI improves upon the original model by (i) simplifying the model structure, (ii) removing the requirement to measure V3, (iii) accounting better for the negative effects of high salinity, disease, and parasitism upon oysters, and (iv) eliminating the statistical independence problem by dropping V3 from the model. The MHSI should be tested against a new, independently-collected data set.
Chemical regulation of tall fescue reproductive development and quality with amidochlor

(...) Unimproved tall fescue pastures which were located on an Alford silt loam (fine-silty, mixed, mesic Typic Hapludalf) soil at the Dixon Springs Agricultural Research Center, near Simpson, IL, received amidochlor at 0, 0.56, and 1.12 kg a.i. ha −1 . Initial growth was harvested at 0, 14, 28, and 42 d after boot stage and regrowth harvested at 6 wk after initial cutting. (...)
Views of US drivers about driving safety.

Abstract Problem: To assess how drivers view dangers on the highway, what motivates them to drive safely, how they say they reduce their crash and injury risk, and how they rate their own driving skills. Results: Most drivers rated their skills as better than average. The biggest motivating factor for safe driving was concern for safety of others in their vehicle, followed by negative outcomes such as being in a crash, increased insurance costs, and fines. The greatest threats to their safety were thought to be other drivers' actions that increase crash risk such as alcohol impairment or running red lights. In terms of reducing crashes and injuries, drivers tended to focus on actions they could take such as driving defensively or using seat belts. There was less recognition of the role of vehicles and vehicle features in crash or injury prevention. Impact on research, practice, and policy: Knowing how drivers view themselves and others, their concerns, and their motivations and techniques for staying out of trouble on the roads provides insight into the difficulty of changing driving practices.
Effect of Physiological Parameters on the Temperature Distribution of a Layered Head Model

Brain temperature control is important in clinical therapy, because moderate temperature reduction of brain temperature increases the survival rate after head trauma. A factor that affects the brain temperature distribution is the cerebral blood flow, which is controlled by autoregulatory mechanisms. To improve the existing thermal models of brain, we incorporate the effect of the temperature over the metabolic heat generation, and the regulatory processes that control the cerebral blood perfusion and depend on physiological parameters like, the mean arterial blood pressure, the partial pressure of oxygen, the partial pressure of carbon dioxide, and the cerebral metabolic rate of oxygen consumption. The introduction of these parameters in a thermal model gives information about how specific conditions, such as brain edema, hypoxia, hypercapnia, or hypotension, affect the temperature distribution within the brain. Existing biological thermal models of the human brain, assume constant blood perfusion, and neglect metabolic heat generation or consider it constant, which is a valid assumption for healthy tissue. But during sickness, trauma or under the effect of drugs like anesthetics, the metabolic activity and organ blood flow vary considerably, and such variations must be accounted for in order to achieve accurate thermal modeling. Our work, on a layered head model, shows that variations of the physiological parameters have profound effect on the temperature gradients within the head.© 2002 ASME
Effect of norepinephrine, serotonin and tryptophan on the firing rate of sympathetic nerves

Abstract The firing rate of sympathetic nerves innervating interscapular brown adipose tissue (IBAT) has been recorded following microinjection of monoamines into the ventromedial (VMN) and paraventricular nuclei (PVN). Microinjection of norepinephrine (10 nmol) into the paraventricular nucleus produced a biphasic pattern in the firing rate of the sympathetic efferent nerves to IBAT. There was an initial dose-related 20% inhibition of firing rate followed 2 min later by 10% increase above control. When 10 times as much norepinephrine was injected into the ventromedial hypothalamus, there was a small 5% decrease in firing rate and a later significant dose-related increase in firing rate. These effects of norepinephrine were blocked by phentolamine, an α-adrenergic blocking drug, but not by propranolol, a s-adrenergic blocking drug. Injection of serotonin into the paraventricular nucleus produced a short-lived but significant increase in firing rate of sympathetic nerves to brown adipose tissue. Comparable amounts of serotonin injected into the ventromedial nucleus produced a similar magnitude of increase in firing rate which lasted longer. There was a clear dose-response effect of serotonin injected into the PVN, but a much less impressive response when serotonin was injected into the VMN. The response to injections of tryptophan in both the VMN and PVN was similar to those seen with serotonin. When serotonin or tryptophan were injected into the PVN and VMN simultaneously, there was a synergistic increase in sympathetic firing rate. These data are consistent with the hypothesis that both norepinephrine and serotonin can modulate sympathetic firing rate through interaction with neurons in either the VMN or PVN.