cssi/SciSciGPT-SciSciNet huggingface dataset:
Optical Lithography Simulation with Focus Variation using Wavelet Transform

Printed image on silicon wafer differs from layout due to optical diffraction. Optical proximity correction (OPC) is a layout distortion technique to improve printed image. During manufacturing, parameters such as focus, dose and resist thickness may vary within tolerance margins. These factors contribute to additional distortion of expected printed shape, not addressed directly by OPC. To ensure a robust IC, a process window consideration is extremely important while running lithography simulations as we scale the technology even further, where the sensitivity of patterns printed on silicon to process variations is very high. Optical Lithography simulation has always been an important link in the chain for Design for manufacturability (DFM) and a lot of research has been put into making it faster and more accurate. However, being a compute intensive process, speeding up litho simulation without significant compromise in accuracy has always been tricky. In this paper we propose a new method to approximate litho simulation based on wavelet transform as opposed to the traditional method employed and we validate the speed and accuracy of our simulator by comparing our results with those of a popular commercial Lithography simulator considering focus variations. While our simulator suffers from an RMS error of 15X and (2) the ability to simulate very large circuit masks where the commercial software fails and direct incorporation of (3) manufacturing process variation. This allows litho simulation against multiple manufacturing process corners, which in turn helps in producing robust design.
Comparison of sister chromatid exchange frequency in peripheral lymphocytes in lung cancer cases and controls

Cytogenetic alterations have been associated with the occurrence of many cancers. However, limited data exist to address whether increased chromosomal changes in surrogate normal tissue are similarly associated with malignancy. As part of an ongoing case-control study of lung cancer, we have studied the factors that affect sister chromatid exchange (SCE) frequency in lymphocytes from lung cancer patients. Further, we sought to investigate whether the factors that affect SCE frequencies were comparable in lung cancer cases and controls. Cases had newly diagnosed, operable primary lung cancer. Controls were friends and spouses of cases. Detailed information on smoking, family history of cancer, medical history, and environmental and occupational exposures was obtained in an interviewer-administered questionnaire. Intake of antioxidants was also determined through the administration of a validated semiquantitative food frequency questionnaire. Metabolic traits studied included the polymorphic glutathione-S-transferase class mu (GST-mu) and variants of P450 isoenzymes CYP1A1 and CYP 2D6. Overall, 78 cases and 78 controls were included in the analysis. Although there was a small number of lung cancer patients who had never smoked in the study (9% of cases), these patients had higher SCE frequencies than current or former smokers. This suggests that factors associated with genomic instability may also play a role in the pathogenesis of lung cancer. The best fit model for SCE frequency, which had been previously generated from control data alone, included age, gender, smoking, GST-mu, and vitamin A intake. However, when this model was applied to lung cancer patients, smoking was not associated with an elevated SCE frequency. Thus, it is not clear that SCE frequency data in prevalent lung cancer cases and controls are comparable.
A Quasi-Optical Method for Measuring the Complex Permittivity of Materials

A quasi-optical method for measuring the complex permittivity of materials is described. The determination is derived from measurements of the transmission of a perpendicularly polarized wave through a dielectric slab at different angles of incidence. This relatively simple method is quite sensitive. Accurate estimates of the relative permittivity and the loss tangent can be obtained by accurately measuring the frequency of the signal and by the use of large, precisely machined Fabry-Perot plates. Estimates of the standard errors in the determinations are obtained by using a bootstrap resampling technique. The measurements here are made at a frequency of 93.788 GHz at ambient temperature.
Fields or subfields of knowledge: Rejection rates and agreement in peer review

The trend toward specialization in sociology continues as in other disciplines. This has led to a corresponding move of scholars from research problems on the field level to those contextualized in subfields. Data collected from 279 manuscripts were studied to examine the Zuckerman-Merton hypothesis suggesting that higher rejection rates may indicate higher agreement among referees. In this study, three measures of agreement are compared to demonstrate the association of agreement and rejection rates within specialties. In addition to agreement measures, mean ratings of contribution to the literature and writing style represented different aspects of the referees’ judgments. Referee agreement on recommendation to the editor is a good predictor of a manuscript’s final outcome. Thus, it correlates very highly to the rejection rate based on the editorial decision outcome. This confirms the findings of Hargens (1988) that rejection rates remain good indicators of referee agreement. According to our findings, they are even better indicators on the subfield level. The findings demonstrate peer review responds differently to subfields than fields. This level of analysis improved our ability to predict editorial decision outcomes for peer-reviewed manuscripts over a previous model.
Jumping in the Salamander Desmognathus ocoee

Unlike most terrestrial vertebrates, which use force generated from the hind limbs to jump, salamanders jump by laterally bending and then rapidly straightening the body, using momentum to carry the individual through the air. This movement is strikingly similar to both the terrestrial escape response of mudskippers and terrestrial blennies, and shares a general pattern of movement with the C-start escape response in several aquatic vertebrates. While the axial musculature appears to be responsible for this behavior, it remains to be seen what role the limbs and tail play. Across a two-fold range in body sizes, few kinematic parameters were correlated with size. The lack of strong scaling relationships suggests a spring mechanism that allows performance to be maintained despite a two-fold increase in size.
Pediatric cataract surgery with an intraocular lens implant

Intraocular lens (IOL) implantation has become the standard of care for the optical rehabilitation of children with cataract from the toddler age group and up. However, the use of IOLs in infants remains controversial. Management of congenital and childhood cataracts is more challenging than cataract management in adults. The surgical techniques for children have evolved because of collaboration between pediatric ophthalmologists and adult cataract surgeons. Although pediatric surgical technique has evolved, IOL power calculation has not kept pace. Selection of IOL power is one of the remaining challenges of management of cataract in children. We discuss the issues and possible solutions for IOL implantation in children.
Distribution of immunoreactive atrial natriuretic peptides in the central nervous system of the rat.

The distribution of immunoreactive (ir) atrial natriuretic peptides (ANPs) in 47 microdissected brain and spinal cord regions of the rat was determined by radioimmunoassay. The highest concentrations of ir-ANPs exist in the paraventricular nucleus and median preoptic nucleus (580.9 and 558.0 fmol/mg protein, respectively). High concentrations of ir-ANP (< 300 fmol/mg protein) are present in the interpeduncular nucleus, preoptic and hypothalamic periventricular nuclei, median eminence and organum vasculosum of the lamina terminalis. Moderate concentrations of ir-ANPs (between 100 and 300 fmol/mg protein) are found in 16 brain regions such as the bed nucleus of the stria terminalis, nucleus of the diagonal band, most of the hypothalamic nuclei, central gray, locus coeruleus and parabrachial nuclei. Low levels of ir-ANPs (< 100 fmol/mg protein) exist in 22 brain regions including cortical areas, amygdala, caudate nucleus, nucleus accumbens, hippocampus, supraoptic nucleus, subfornical organ, medial mammillary nucleus, substantia nigra, dorsal raphe nucleus, cerebellum, nucleus of the solitary tract and others. Cervical spinal cord and neurointermediate lobe of pituitary gland contain low levels of ir-ANPs.
Experimental models of amyotrophic lateral sclerosis.

Amyotrophic lateral sclerosis (ALS) is a chronic neurodegenerative disease characterized by the progressive loss of motor neurons, leading to profound weakness and eventual death of affected individuals. For the vast majority of patients with ALS, the etiology of the disorder is unknown, and although multiple clinical trials of various therapeutic agents have been undertaken, truly effective therapy is not currently available for the disease. The selection of treatments used in ALS clinical trials frequently has its basis in promising data obtained from experimental model systems in which the proposed agent has shown some effect in protecting motor neurons from a particular insult. The likelihood of a successful clinical outcome for a given treatment in ALS would therefore depend on two principal factors, including the similarity of the model to the disease and the biologic action of the potential therapeutic agent. Partly because early experimental models of ALS failed to replicate the disease process, treatment success in these models did not carry over into human trials. Recently, however, a variety of newer model systems have been developed and utilized to investigate motor neuron degeneration as related to ALS. For example, in this issue, Corse et al. use a rat spinal cord organotypic slice subjected to glutamate excitotoxicity as a model system to test the effectiveness of neurotrophic factors in preventing motor neuron degeneration. This review will assess the strengths and weaknesses of differing ALS model systems that have been used to preclinically test potential drug efficacy in ALS.
Gastrointestinal bleeding in the elderly patient

The elderly patient with acute gastrointestinal bleeding requires a management approach that attends to age-dependent demands, such as functional status, the independent impact of functional status on outcomes such as short term mortality, and the consent process. This review examines issues such as patient triage, resuscitation, diet and medications, anticoagulation, endoscopy and conscious sedation, informed consent in the impaired patient, and discharge planning in light of these age-dependent demands.
XSB as an efficient deductive database engine

This paper describes the XSB system, and its use as an in-memory deductive database engine. XSB began from a Prolog foundation, and traditional Prolog systems are known to have serious deficiencies when used as database systems. Accordingly, XSB has a fundamental bottom-up extension, introduced through tabling (or memoing)[4], which makes it appropriate as an underlying query engine for deductive database systems. Because it eliminates redundant computation, the tabling extension makes XSB able to compute all modularly stratified datalog programs finitely and with polynomial data complexity. For non-stratified programs, a meta-interpreter with the same properties is provided. In addition XSB significantly extends and improves the indexing capabilities over those of standard Prolog. Finally, its syntactic basis in HiLog [2], lends it flexibility for data modelling.The implementation of XSB derives from the WAM [25], the most common Prolog engine. XSB inherits the WAM's efficiency and can take advantage of extensive compiler technology developed for Prolog. As a result, performance comparisons indicate that XSB is significantly faster than other deductive database systems for a wide range of queries and stratified rule sets. XSB is under continuous development, and version 1.3 is available through anonymous ftp.
A computational study of the effect of fuel type on ignition time in homogenous charge compression ignition engines

The homogeneous charge, compression ignition (HCCI) engine has advantages in terms of efficiency and reduced emissions in comparison to conventional internal combustion engines. One of the distinguishing characteristics of an HCCI engine is that the ignition is controlled by the chemical kinetics, unlike the diesel or spark ignition engines, for which ignition time can be controlled externally by the fuel injection or spark time. As a consequence of being controlled by chemical kinetics, the HCCI ignition time can vary significantly with changes in the operating conditions, and this variation can limit the practical range of operation of the engine. Using a single-zone combustion model and established reaction rate mechanisms, the influences of the compression ratio, intake temperature, equivalence ratio, engine speed, and exhaust gas recirculation on the ignition time of two fuels, normal heptane and iso-octane, were studied. The model simulated the environment in the engine combustion chamber by assuming adiabatic compression and expansion. The sensitivity of the ignition time to changes in operating conditions was found to be dependent on the type of fuel. The results indicate that the use of fuels with a characteristics two-stage ignition (e.g., n -heptane) exacerbates the problem of ignition control compared with the use of fuels with a single-stage ignition (e.g., iso-octane).
Characterization of single-crystal SiC polytypes using X-ray and Auger photoelectron spectroscopy

Abstract Carbon core-valance-valence (KVV) Auger electron spectroscopy (AES) and core-level X-ray photoelectron spectroscopy (XPS) features are shown to be conspicuously different for cubic, hexagonal and rhombohedral phases of SiC. This was also observed for p- and n-type 6H–SiC epilayers. The origin and assignments of these features are discussed. Application of these results to the identification of post-growth SiC phases is presented.
Separation of Hydrogen-Lean Mixtures for a High-Purity Hydrogen by Vacuum Swing Adsorption

Abstract High-purity hydrogen is commercially produced by pressure swing adsorption from hydrogen-rich mixtures. In this work, a vacuum pressure swing adsorption cycle is used to produce high purity hydrogen from a hydrogen-lean binary mixture (20/80 H2/CO) using zeolite 5A as the sorbent. The effects of different process variables on separation performance have been studied. The purity of hydrogen product increases at low throughput, high feed pressure, high end pressure of cocurrent depressurization, low end pressure of countercurrent evacuation, and short cycle time. Also, it was found that for a H2-lean mixture, the separation is improved at higher ambient temperature. In addition, a new “vacuum purge” step was found to improve the separation and is therefore a promising step for commercial application.
Errors Are Aversive Defensive Motivation and the Error-Related Negativity

The error-related negativity (ERN) is a negative deflection in the event-related potential that is maximal approximately 50 ms after the commission of an error. The ERN is generated in the anterior cingulate cortex, a region of the medial prefrontal cortex implicated in both cognitive and emotional processing. Affective and motivational variables influence the magnitude of the ERN, which suggests that the ERN may relate to emotional or motivational aspects of error detection. In the present study, we evaluated the possibility that errors prime defensive motivational responses, and that the ERN may predict the magnitude of defensive reactivity after errors. We found that (a) the defensive startle response was larger following errors than following correct responses, and (b) the magnitude of the ERN predicted the degree of startle potentiation following errors. Thus, response errors prime defensive motivation—and the ERN predicts individual differences in the aversive response to errors.
Optimizing global health experiences in emergency medicine residency programs: a consensus statement from the Council of Emergency Medicine Residency Directors 2011 Academic Assembly global health specialty track

Background: An increasing number of emergency medicine (EM) residency training programs have residents interested in participating in clinical rotations in other countries. However, the policies that each individual training program applies to this process are different. To our knowledge, little has been done in the standardization of these experiences to help EM residency programs with the evaluation, administration and implementation of a successful global health clinical elective experience. The objective of this project was to assess the current status of EM global health electives at residency training programs and to establish recommendations from educators in EM on the best methodology to implement successful global health electives. Methods: During the 2011 Council of Emergency Medicine Residency Directors (CORD) Academic Assembly, participants met to address this issue in a mediated discussion session and working group. Session participants examined data previously obtained via the CORD online listserve, discussed best practices in global health applications, evaluations and partnerships, and explored possible solutions to some of the challenges. In addition a survey was sent to CORD members prior to the 2011 Academic Assembly to evaluate the resources and processes for EM residents’ global experiences. Results: Recommendations included creating a global health working group within the organization, optimizing a clearinghouse of elective opportunities for residents and standardizing elective application materials, site evaluations and resident assessment/feedback methods. The survey showed that 71.4% of respondents have global health partnerships and electives. However, only 36.7% of programs require pre-departure training, and only 20% have formal competency requirements for these global health electives. Conclusions: A large number of EM training programs have global health experiences available, but these electives and the trainees may benefit from additional institutional support and formalized structure.
Tracking the development of the petaloid fertile stamen in Canna indica: insights into the origin of androecial petaloidy in the Zingiberales

Flowers of the order Zingiberales demonstrate a remarkable trend of reduction in the number of fertile stamens; from five or six fertile, filamentous stamens bearing two thecae each in Musaceae and Strelitziaceae to just a single petaloid stamen bearing a single theca in Cannaceae and Marantaceae. As one progresses from ancestral to derived floral forms, 5–6 fertile stamens are replaced by 4–5 petaloid staminodes. In Cannaceae and Costaceae, all members of the androecial whorls exhibit petaloidy, including the fertile stamen. In Costaceae, a single fertile stamen develops two thecae embedded on a broad petaloid appendage, while in Cannaceae the single fertile stamen is further reduced to a single theca with a prominent, expanded petaloid appendage. Whether petaloidy of the fertile stamen is a synapomorphy of the entire ginger clade (including Cannaceae, Costaceae, Zingiberaceae and Marantaceae), or the result of independent convergent evolution in Cannaceae, Costaceae, and some Zingiberaceae, is unclear. We combine a developmental series of the formation of the petaloid fertile stamen in Canna indica with data on the expression of B- and C-class floral organ identity genes to elucidate the organogenetic identity of the petaloid stamen and staminodes. Our data indicate that the single fertile theca in C. indica and its petaloid appendage are derived from one-half of the primordium of a single stamen, with no contribution from the remaining part of the stamen (i.e. the second theca primordium) which aborts early in development. The petaloid appendage expands later, and develops from the position of the filament/connective of the developing theca. Floral identity gene expression shows that petal identity genes (i.e. B-class genes) are expressed in all floral organs studied while C-class gene AG-1 is expressed in an increasing gradient from sepals to gynoecium, and AG-2 is expressed in all floral organs except the petals. The canonical model for molecular specification of floral organ identity is not sufficient to explain petaloidy in the androecial whorl in Canna sp. Further studies understanding the regulation of gene networks are required.
Symbolism in the Early Palaeolithic: A Conceptual Odyssey

Archaeologists have been naive to expect that symbolic behaviour can be inferred more or less directly from the characteristics of an archaeological record. This article examines various construals of symbolism and its relationship to signs, indexes and style that are derived from more fully axiomatized theories of cognition in psychology, anthropology, linguistics and primatology. The authors' intent is to develop a more adequate operational definition of symbolism, and to determine whether our more stringent criteria for inferring symbolic behaviour can be met in ‘pre-modern’ contexts. A review of the archaeopalaeontological record suggests that the roots of symbolism can be traced to the Lower and Middle Palaeolithic, but that evidence for a robust pattern documenting its presence is not found until the Upper Palaeolithic. It is argued that symbolism had adaptive significance, but that it probably developed in contexts distinct from those in which it is manifest today.
The oasis image in two desert cities

(1986). The oasis image in two desert cities. Landscape Research: Vol. 11, No. 3, pp. 7-11.
The Importance of Non-LTE Effects to the Interpretation of Radio Recombination Lines

We review the ramifications of non-LTE effects on the determination of nebular properties made by interpreting radio recombination line observations. In particular we focus on the effect that departures from b = 1 and τc << 1 have on the determination of nebular temperatures, and we discuss the effect of impact broadening on the interpretation of radio recombination lines (hydrogen and helium) from inhomogeneous nebulae.
Scheduling Conditions for Real-Time Software Transactional Memory

Software transactional memory (STM) is a transactional mechanism of controlling access to shared resources in memory. Recently, variants of STM with real-time support have been presented. Due to its abort-restart nature, the execution semantics of STM are different from the classical preemptive or nonpreemptive model. In this letter, we formally derive utilization based necessary and sufficient scheduling condition for a STM system using lazy conflict detection.
MCP-1-deficient mice show reduced neuroinflammatory responses and increased peripheral inflammatory responses to peripheral endotoxin insult

Background An endotoxin insult mimics a severe peripheral infection and recent evidence suggests that a single exposure can cause long-term cognitive deficits. A peripheral injection of LPS results in production of pro-inflammatory cytokines, such as IL-1β and TNF-α, in the brain and periphery and these cytokines mediate many effects of the acute phase response including activation of the HPA axis. The chemokine MCP-1 is highly expressed during endotoxemia and although much is known about the importance of MCP-1 in peripheral inflammatory responses to LPS, information about MCP-1 and CNS responses to peripheral LPS is lacking.
A Novel Semi-Distributed Cooperative Localization Technique for MANET: Achieving High Performance

This paper introduces a semi-distributed cooperative localization technique realized via multi-node time-of-arrival (TOA) and direction-of-arrival (DOA) optimal fusion: Each base-node estimates the position of target-nodes by joint TOA- DOA evaluation, and then, the target-node position estimation error is minimized by TOA-DOA optimal fusion across multiple base-nodes. The performance of the proposed technique is studied and compared to two GPS-based positioning techniques, i.e., GPS-aided TOA fusion and GPS-aided DOA fusion. The circular error probability (CEP) is derived theoretically and verified via simulations. The results confirm the superiority of the proposed localization technique in moderate scale mobile ad- hoc networks (MANETs) compared to the two GPS-based fusion schemes. Thus, while the proposed technique is applicable to MANETs in GPS-denied environments, it is also suitable for GPS available environments. Finally, compared to the centralized scheme, the positioning updating rate of the semi-distributed technique is higher and its power consumption in the reference base node is considerably lower.
A novel technique for full-wave modeling of large-scale three-dimensional high-speed on/off-chip interconnect structures

This paper presents a novel, rigorous, and fast method for full-wave modeling of high-speed interconnect structures. In this method, the original wave propagation problem is represented into a generalized eigenvalue problem. The resulting eigenvalue representation can comprehend conductor and dielectric losses, arbitrary dielectric and conductor configurations, and arbitrary materials such as dispersive, and anisotropic media. The edge basis function is employed to accurately represent the unknown field, and the triangular element is adopted to flexibly model arbitrary geometry. A mode-matching technique applicable to lossy system is developed to solve large-scale 3D problems by using 2D-like CPU time and memory. A circuit-based extraction technique is developed to obtain S-parameters from the unknown fields. The proposed technique can generate S-parameters, full-wave RLGC, propagation constants, characteristic impedances, voltage, current, and field distributions, and hence yield a comprehensive representation of interconnect structures. Experimental and numerical results demonstrate its accuracy and efficiency.
Tools for advancing research into social networks and cognitive function in older adults.

People are good for your brain. Decades of research have shown that individuals who have a larger number of people in their social network or higher quality ties with individuals within their network have lower rates of morbidity and mortality across a wide range of health outcomes. Among these outcomes, cognitive function, especially in the context of brain aging, has been one area of particular interest with regard to social engagement, or more broadly, socially integrated lifestyles. Many studies have observed an association between the size of a person’s social network or levels of social engagement and the risk for cognitive decline or dementia (e.g. see review by Fratiglioni et al., 2004). The dementia risk reduction associated with a larger social network or social engagement shown by some epidemiological studies is fairly large. The population effect size of increasing social engagement on delaying dementia disease progression could exceed that of current FDA approved medications for Alzheimer’s disease. The positive effects of social interactions and engagement on cognitive function have been demonstrated even at the level of biomarkers. For example, recent MRI studies found associations between the size and complexity of real-world social networks and the density of gray matter (Kanai et al., 2012) and amygdala volume (Bickart et al., 2011). Possible modifiable effects of larger social networks on symptomatic outcomes of Alzheimer’s disease pathologies have also been shown (Bennett et al., 2006). Human epidemiological studies are not free from possible reverse causations such as lower levels of social engagement being the result of presymptomatic dementia, not the cause of dementia. However, non-human research suggests that social network size could actually contribute to changes both in brain structure and function, providing further support for causal links (Sallet et al., 2011).
Appropriateness of commercially available and partially customized medication dosing alerts among pediatric patients

Objectives To evaluate dosing alert appropriateness, categorize orders with alerts, and compare the appropriateness of alerts due to customized and non-customized dose ranges at a pediatric hospital. Methods This was a retrospective analysis of medication orders causing dosing alerts. Orders for outpatient prescriptions, patients ≥18 years of age, and research protocols were excluded. Patient medical records were reviewed and ordered doses compared with a widely used pediatric reference (Lexi-Comp) and institutional recommendations. The alerted orders were categorized and the occurrence of appropriate alerts was compared. Results There were 47 181 inpatient orders during the studied period; 1935 orders caused 3774 dosing alerts for 369 medications in 573 patients (median age 6.1 years). All alerted orders had an alert overridden by the prescriber. The majority (86.2%) of alerted orders inappropriately caused alerts; 58.0% were justifiable doses and 28.2% were within Lexi-Comp. However, 13.8% of alerted orders appropriately caused alerts; 8.0% were incorrect doses and 5.8% had no dosing recommendations available. Appropriately alerted orders occurred in 19.7% of alerted orders due to customized ranges compared to 12.8% due to non-customized ranges (p=0.002). Preterm and term neonates, infants, and children (2–5 years) had higher proportions of inappropriate alerts compared to appropriate alerts (all p<0.01). Conclusions The vast majority of dosing alerts were presented to practitioners inappropriately, potentially contributing to alert fatigue. Appropriate alerts occurred more often when alerts were due to customized ranges. Advances in dosing alerts should aim to provide accurate and clinically relevant alerts that minimize excessive inappropriate alerting. Medications requiring dosing adjustments based on clinical parameters must be taken into account when designing and evaluating dosing alerts.
Enhanced TheraJoy technology for use in upper-extremity stroke rehabilitation

Due to rising costs of health care and decreasing length of conventional therapy, it has become imperative to develop affordable, motivating devices that can be used in the home for upper-extremity stroke rehabilitation. In the TheraJoy project, a commercial joystick has been modified to enlarge the range of arm movement used during therapeutic movement tasks, and to support the application of light passive and actuated forces. The enhanced version presented here allows for motion in both the horizontal and vertical planes, uses a dynamic linkage model to map joystick-hand position and force data, uses motivating gaming technology, and can be used in both therapy and in home settings. This study compares performance and benefits of motion in the horizontal to vertical plane, evaluates user performance during assessment and therapy tasks, and documents user opinions of potential uses of this technology for stroke rehabilitation.
Improving the reliability of mobile software systems through continuous analysis and proactive reconfiguration

Most of the current software reliability analysis approaches are geared to traditional desktop software systems, which are relatively stable and static throughout their execution. In this paper, we present a framework targeted at mobile computing domain that addresses the uncertainties associated with the reliability analysis in this setting. Moreover, the framework's architecture-centric reliability estimates are leveraged to improve the runtime reliability of the system through dynamic architectural reconfiguration.
Developing a New Interdisciplinary Lab Course for Undergraduate and Graduate Students: Plant Cells and Proteins*

Studies of protein function increasingly use multifaceted approaches that span disciplines including recombinant DNA technology, cell biology, and analytical biochemistry. These studies rely on sophisticated equipment and methodologies including confocal fluorescence microscopy, mass spectrometry, and X-ray crystallography that are beyond the scope of traditional laboratory courses. To equip the advanced undergraduate and beginning graduate students with an enabling base of knowledge and initial experience with advanced protein research methodologies, a laboratory course entitled Plant Cells and Proteins was developed in a partnership between Washington University and the Donald Danforth Plant Science Center in St. Louis. In this one semester course, 10–12 students obtain hands-on experience with plant tissue culture, gene transformation, subcellular localization of fluorescent recombinant proteins using confocal microscopy, purification of affinity-tagged recombinant proteins, isolation of total protein extracts, enzymatic assays, one- and two-dimensional gel electrophoresis, MALDI-TOF and ESI-Q-TOF mass spectrometry, protein crystallization, and X-ray diffraction. The course is taught as a series of modules, each led by an expert researcher. Students are evaluated based on a series of graded written reports and tests of their mastery of key concepts, interpretations, and the limitations of the experimental methods.
Effects of antiplatelet agents alone or in combinations on platelet aggregation and on liver metastases from a human pancreatic adenocarcinoma in the nude mouse

There is ample evidence to suggest that hematogenous metastasis may be related to the ability of tumor cells to promote aggregation of host platelets. Arachidonic acid metabolism in platelets and vessel walls may also contribute to the metastatic process. Several preliminary trials of platelet inhibitory agents have been performed. Ketoconazole (inhibitor of lipoxygenase and thromboxane synthetase), verapamil (calcium antagonist), forskolin (stimulator of platelet adenylate cyclase), and indomethacin (inhibitor of cyclooxygenase) were examined, alone and in combination, to investigate their effects on platelet aggregation and on hepatic metastases from human pancreatic tumor cells (RWP-2) in nude mice. The tumor cells were injected intrasplenically, and the animals were divided into control, single-drug and combination treatment groups. The agents were administered intraperitoneally 1 hr before and every 24 hr after the tumor cell injections for 6 days. Statistically significant differences were observed between the control and single-treatment groups on the reduction of liver tumor nodules (range P less than 0.001-0.032) and in the liver surface areas occupied by tumor (range P less than 0.001-0.013). Furthermore, when these agents were combined, similar reductions in liver tumor nodules were noted (range P less than 0.001-0.008), while even greater inhibitory effects were seen in the liver surface areas occupied by tumor (P less than 0.001) compared with the single-treatment groups. Also, the combination studies strongly inhibited RWP-2-induced platelet aggregation in human platelet-rich plasma.
Strategies and Tactics in Multiscale Modeling of Cell-to-Organ Systems

Modeling is essential to integrating knowledge of human physiology. Comprehensive self-consistent descriptions expressed in quantitative mathematical form define working hypotheses in testable and reproducible form, and though such models are always "wrong" in the sense of being incomplete or partly incorrect, they provide a means of understanding a system and improving that understanding. Physiological systems, and models of them, encompass different levels of complexity. The lowest levels concern gene signaling and the regulation of transcription and translation, then biophysical and biochemical events at the protein level, and extend through the levels of cells, tissues and organs all the way to descriptions of integrated systems behavior. The highest levels of organization represent the dynamically varying interactions of billions of cells. Models of such systems are necessarily simplified to minimize computation and to emphasize the key factors defining system behavior; different model forms are thus often used to represent a system in different ways. Each simplification of lower level complicated function reduces the range of accurate operability at the higher level model, reducing robustness, the ability to respond correctly to dynamic changes in conditions. When conditions change so that the complexity reduction has resulted in the solution departing from the range of validity,detecting the deviation is critical, and requires special methods to enforce adapting the model formulation to alternative reduced-form modules or decomposing the reduced-form aggregates to the more detailed lower level modules to maintain appropriate behavior. The processes of error recognition, and of mapping between different levels of model complexity and shifting the levels of complexity of models in response to changing conditions, are essential for adaptive modeling and computer simulation of large-scale systems in reasonable time.
Comparing apples and oranges through partial orders: An empirical approach

In this paper, we try to understand what people mean when they say that two objects are “similar.” This is an important question in the area of human-robot interactions, where robots must interpret human movements in order to act in a “similar” manner. Specifically, we assume that we are given a collection of empirically generated pairwise comparisons between a subset of so-called alternatives (members of a given set), which produces a partial order over the set of alternatives. Based on this partial order, an inverse optimization problem is solved, producing a cost associated with each alternative that is consistent with the partial order. This cost is, moreover, assumed to be generative in that it can be used to select the globally best alternative. An experimental study involving the comparison of apples and oranges is presented to highlight the operation of the proposed approach.
Population Dynamics and Recovery of Endangered Crested Ibis (Nipponia nippon ) in Central China

Abstract The Crested Ibis (Nipponia nippon) is one of the most endangered avian species in the world. In 1981, seven ibis were discovered in the Qinling Mountain, central China. The ibis population responded positively to 20 years of intensive conservation growing to more than 500 birds. Population growth of the Crested Ibis exhibited a nonlinear response to increased population size along an altitudinal gradient (600-1,400 m). Prior to 1993, the ibis population was constrained to high mountains with elevations greater than 1,000 m and exhibited density dependent growth in spite of small population size (less than 20 birds). Limited availability of habitats at high elevations might result in competition for food and other resources among the ibis. The ibis returned to traditional nesting habitats at low elevations (<1,000 m) and has grown exponentially since 1992. Fledging success of the ibis did not differ between low- and high-elevation habitats. Rapid population growth of the ibis in low-elevation habi...
Short-Term Effects of Intramuscular and Transdermal Testosterone on Bone Turnover, Prostate Symptoms, Cholesterol, and Hematocrit in Men Over Age 70 with Low Testosterone Levels

The objective of the study was to determine whether short-term testosterone administration to older men with low bioavailable testosterone would have any immediate adverse effects, especially on the symptoms of benign prostate hyperplasia, preliminary to embarking on a long-term study of testosterone treatment. Transdermal and intramuscular testosterone were compared to determine whether there were any rapid changes in markers of bone formation or resorption with either testosterone administration. We undertook a non-randomized trial of 9 weeks intervention with either intramuscular testosterone, transdermal testosterone or neither followed by a 9-week observation period. Twenty-seven men over age 70 years with no medical conditions known to affect bone turnover and total testosterone levels below 350 ng/dl (normal range 350-1230 ng/dl) or bioavailable testosterone levels below 128 ng/dl (normal range 128-430 ng/dl) received either testosterone via transdermal patch (TP; two 2.5 mg patches/d), intramuscular testosterone enanthate (IM; 200 mg every 3 weeks) or no testosterone for 9 weeks of treatment followed by a 9 week observation period. Nine men were enrolled in each group. The mean age of the men was 74 +/- 3 years (range 70-83 years). While all men receiving testosterone treatment increased levels above their own baseline, only 6 of 9 men receiving transdermal testosterone achieved bioavailable testosterone levels in the normal range for young men. Neither treatment group demonstrated changes in estradiol levels. No side effects were reported using the intramuscular testosterone while 5/9 men using transdermal testosterone developed a rash. There were no significant changes in markers of bone resorption or formation in either testosterone treatment group. There were no ill effects on prostate size, symptoms or prostate specific antigen level. PSA levels of 1.5 +/- 0.7 ng/dl and 1.6 +/- 0.7 ng/dl in the TP and IM groups, respectively. were 2.0 +/- 1.0 ng/dl and 1.8 +/- 0.9 ng/dl following treatment. Cholesterol profiles were also not affected by either transdermal or intramuscular testosterone. Similarly hemoglobin and hematocrit remained unchanged in men receiving either testosterone preparation.
Influence of Ischemia-Reperfusion Injury on Cardiac Metabolism

Abstract Ischemia is a condition of reduced or abolished blood flow that drives energy metabolism toward anaerobic glycolysis to adapt to the loss of oxygen delivery at the expense of using the energy-rich substrate: fatty acids, leading to significant changes in the metabolic program of the heart. Ischemia alters the redox status of the cell, ion channel regulation, and calcium homeostasis in addition to glycolysis to further affect the metabolic profile of the heart. Reperfusion is necessary to resolve ischemic injury or ultimately cell death will occur. However, the re-establishment of perfusion incurs further pathology, particularly in the acute phase. A number of pharmacologic interventions have been evaluated with mixed results and more recently metabolic modulators have been recognized as potentially attractive therapies in the ischemic heart.
Carbon-Free Electrocatalyst for Oxygen Reduction and Oxygen Evolution Reactions

A nanoporous Ag-embedded SnO2 thin film was fabricated by anodic treatment of electrodeposited Ag–Sn alloy layers. The ordered nanoporous structure formed by anodization played a key role in enhancing the electrocatalytic performance of the Ag-embedded SnO2 layer in several ways: (1) the roughness factor of the thin film is greatly increased from 23 in the compact layer to 145 in the nanoporous layer, creating additional active sites that are involved in oxygen electrochemical reactions; (2) a trace amount of Ag (∼1.7 at %, corresponding to a Ag loading of ∼3.8 μg cm–2) embedded in the self-organized SnO2 nanoporous matrix avoids the agglomeration of nanoparticles, which is a common problem leading to the electrocatalyst deactivation; (3) the fabricated nanoporous thin film is active without additional additives or porous carbon that is usually necessary to support and stabilize the electrocatalyst. More importantly, the Ag-embedded SnO2 nanoporous thin film shows outstanding bifunctional oxygen electroch...
Impacts of chronic N input on the carbon and nitrogen storage of a postfire Mediterranean-type shrubland.

Mediterranean-type shrublands are subject to periodic fire and high levels of nitrogen (N) deposition, but little is known how chronic N deposition affects carbon (C) and N storage during succession. We conducted a long-term experiment in Californian chaparral to test the hypothesis that chronic N enrichment would increase postfire C and N accumulation. The experimental layout consisted of a randomized design where four 10 × 10 m plots received 5 g N m−2 annually since 2003 and four 10 × 10 m plots served as controls. Aboveground and belowground C and N pools and fluxes were measured seasonally (every 3 months) for a period of 10 years. Added N rapidly increased soil extractable N pools and decreased soil pH; however, total soil C and N storage were not affected. Added N plots initially had significantly lower C and N storage than control plots, presumably because of nutrient losses from leaching and/or higher belowground C allocation. However, rates of aboveground N and C storage became significantly higher in added N plots after 4–5 years of exposure, thus increasing fuel buildup, which has implications for future fire intensity. This recovering chaparral stand is not yet “N saturated” after 10 years of chronic N input. However, N leaching continues to be higher in added N plots, indicating that postfire chaparral stands in high-N deposition areas can be important sources of N to groundwater/aquatic systems even if productivity is stimulated by N input.
Exercise augments the nocturnal prolactin rise in exercise-trained men.

Objective:The objective of this study was to profile over a 24 h period the prolactin responses of exercise-trained men on a day involving rest with no exercise in comparison to a day involving exercise training sessions.Methods:This is a quasi-experimental design study using repeated measures determination of 24 h prolactin responses in exercise-trained men (n = 16; age = 27.3± 3.3 years (mean ± standard deviation)). Blood samples were taken hourly over a 24 h period on a day involving two intensive exercise training sessions (ED), and on a separate control day (CD) with no exercise activity. The order of the ED and CD was randomized. Physical activity and diet were controlled and replicated for the ED and CD. Blood specimens were handled, prepared and analyzed utilizing appropriate standard clinical practices. The data were analyzed with the Friedman analysis of variance and Nemenyi post hoc statistical procedure for repeated measures.Results:On the CD, prolactin displayed a typical circadian rhythm wit...
Rotatory laxity of the human knee joint.

A method was developed for measuring the rotatory laxity of fresh knee-joint specimens by automatic cyclic rotation. Twenty-seven cadaver specimens were studied at an angle of 25 degrees of flexion. Primary laxity was defined as the rotation for a low torque of ± S kilograms force-centimeter Secondary laxity was the additional rotation at the extremes of motion at the maximum torque applied. There was a wide variation in laxity among different knees, with no discernible correlation with age, sex, race, or body build The menisci played a part in controlling laxity, particularly in the primary laxity phase at high torque. The collateral ligaments were twice as effective as the cruciate ligaments in controlling rotatory laxity. Axial load on the knee greatly reduced rotatory laxity. A 100-kilogram load reduced rotation to 20 per cent of that at zero axial load.
The Effects of Humidity, Temperature and Carbon Dioxide on Sporulation of Choanephora Cucurbitarum

Under the usual laboratory conditions in test tubes, flasks or tightly closed Petri dishes, the high humidity and poor ventilation create abnormal conditions which may permit growth of the mycelium, but often greatly reduce sporulation of many fungi. This may be due to unfavorable humidity, insufficient oxygen or to an accumulation of carbon dioxide or other gases resulting from the metabolism of the fungus. Comparatively few studies of the effects of the conditions of the atmosphere in the culture vessels have been made, but it is known that these factors are important for some fungi. Henry and Andersen (1948) have shown that an accumulation of ammonia reduces sporula? tion of Piricularia oryzae, and Bright et al (1949) reported that an increase in carbon dioxide reduced sporulation of Saccharomyces cerevisiae.
Discretion of the Food and Drug Administration to enforce compounding rules.

Like all regulatory agencies, the Food and Drug Administration (FDA) has discretion to decide when to take enforcement action against a potential violator of the federal Food, Drug, and Cosmetic Act (FDCA).[1][1] Companies and individuals who engage in the manufacture and distribution of