cssi/SciSciGPT-SciSciNet huggingface dataset:
Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data.

High-throughput “omics” technologies bring new opportunities for biological and biomedical researchers to ask complex questions and gain new scientific insights. However, the voluminous, complex, and context-dependent data being maintained in heterogeneous and distributed environments plus the lack of well-defined data standard and standardized nomenclature imposes a major challenge which requires advanced computational methods and bioinformatics infrastructures for integration, mining, visualization, and comparative analysis to facilitate data-driven hypothesis generation and biological knowledge discovery. In this paper, we present the challenges in high-throughput “omics” data integration and analysis, introduce a protein-centric approach for systems integration of large and heterogeneous high-throughput “omics” data including microarray, mass spectrometry, protein sequence, protein structure, and protein interaction data, and use scientific case study to illustrate how one can use varied “omics” data from different laboratories to make useful connections that could lead to new biological knowledge.
Appreciating and Mitigating Bleeding Risk

Excessive bleeding is a hazard that has been noted throughout history. As early as the 12th century, physicians identified males who died of uncontrollable bleeding and noted familial relationships. Although hemophilia was probably the source, over the past decade there has been a therapy-induced increase in hemorrhagic disorders. Until recently, treatment for obstructive cardiovascular disease has primarily focused on vessel patency and relief of the thrombosis. Although bleeding has been the accepted primary side effect of antithrombotics, the success and proliferation of novel antiplatelet and antithrombin therapies has tipped the hemorrhage-thrombosis scale. As has been appreciated in many recent clinical trials, the risk of bleeding has now limited efficacy for many of these therapies, leading to a reexamination of new and combinatorial therapeutic uses for antithrombotics. Although it seems evident that adding more powerful antithrombotic therapies would lead to greater bleeding, the increase in hemorrhage was not entirely anticipated. New antithrombotics typically have favorable bleeding/thrombotic profiles in preclinical models and are primarily evaluated singularly and, therefore, may or may not be directly applicable to clinical use.1 For example, warfarin treatment is associated with hematoma expansion after intracerebral hemorrhage, and it was hoped that direct thrombin inhibitors would mitigate this side effect. In the use of different animal models of intracerebral hemorrhage, warfarin-treated animals had enlarged cerebral hematomas and bleeding, but no difference was found between oral thrombin inhibitor–treated animals and controls.2 Although this is similar to clinical observations,3 other therapies have not had the same consistency in bleeding with preclinical trials.4 Potential inconsistencies between preclinical and clinical studies have made the development of …
Can varying concepts of susceptibility in risk assessment affect particulate matter standards

The Clean Air Act mandates that sensitive subpopulations be considered in setting standards to protect the public's health. The purposes of this paper are to point out different conceptualizations of susceptibility, examine how it is approached in risk-related processes, and recommend ways it may be more explicitly framed for risk assessment and management purposes. We studied the traditional risk assessment paradigm, the U.S. Environmental Protection Agency (EPA) guidelines and revised PM standard, discussions from recent interdisciplinary meetings, and peer-reviewed literature. Areas of controversy include what factors intrinsic and extrinsic to the host should be incorporated in susceptibility, what health endpoints are of concern, whether susceptibility is deterministic or stochastic, and whether it should be defined on an individual or population scale. Recent discussions about susceptibility applied to PM indicate that it needs to be more clearly defined and evaluated for scientific and policy purposes. We conclude that varying concepts of susceptibility can affect risk-related processes such as PM standard setting. We recommend that susceptibility be clearly defined in the problem statement of risk assessments and be addressed in a specific subsection of risk characterization, integrating all susceptibility findings from the prior three steps in the risk assessment paradigm.
Starter fertilizers for corn on soils testing high in phosphorus in the northeastern USA

Starter fertilizers with a high P analysis are commonly used in the northeastern USA for corn (Zea mays L.) production, despite many soils testing above optimum (>50 mg P kg -1 ). The objective of this study was to evaluate responses to high P starter fertilizers in a band 5 cm from the row compared to alternatives such as banded higher N or conventional and low-salt in-furrow fertilizers. Two studies were conducted during 2000 through 2003 in Pennsylvania. The first study was a 3-yr on-form study conducted to evaluate an untreated check, (NH 4 ) 2 SO 4 (AS), and 10-13-8.3 (N-P-K) as starters at 41 locations across Pennsylvania on high P testing soils. Early growth increased by 17% using 10-13-8.3 and 15% using AS compared to the check. Grain yields were 3.3% higher than the check for the AS treatment Yields from the 10-13-8.3 were not different than the check but averaged 2.0% higher. A second 3-yr study consisted of an untreated check, five banded granular starter fertilizer blends (10-13-8.3, 21-0-0-24, 16-3.5-6.7-16, 16-3.5-6.7, and 16-0-6.7-16) applied at 202 kg ha -1 , and three liquid in-furrow treatments applied at 35 kg ha -1 (7-9.1-5.8, 7-7.4-2.5 and 7-7.8-7.5). Early growth and grain yield were significantly increased in 1 of 3 yr with some higher N starters. Eliminating starters, using higher N or in-furrow starters on high P soils all appear to be possible management alternatives to high P starters.
Beyond the Technical and Bureaucratic Theories of Utilization: Some Thoughts on Synthesizing Reviews and the Knowledge Base of the Evaluation Profession

its contents are properly organized; both, however, have limitations. Data synthesis assumes scores of statistically comparable studies. Social problem study groups are not well-designed for making the knowledge frontiers they define generally accessible. This article suggests supplementing these approaches to building knowledge with an increased emphasis on synthesizing reviews. Even though such reviews currently enjoy modest status at bestthey serve to strengthen the profession and promote utilization. GR.ecent developments lend urgency to the well-established debate ~ ecent developments lend urgency to the well-established debate over the utilization of evaluation. Only a few years after thoughtful practitioners issued mixed predictions for the field (Freeman and Solomon, 1981: 19-21), it faces shortages in funding, changes in norms concerning the role of government in society, and uncertainty about which kinds of products will draw committed userships. The funding shortages pose a special threat because they reduce not only the material
Vulvar vestibulodynia: strategies to meet the challenge.

Vulvodynia is a condition that affects approximately 8% to 12% of women during their lifetimes. Vulvar vestibulodynia (VVD), the most common form of this condition, is characterized by pain with touch at the vulvar vestibule and resulting entryway dyspareunia. Studies suggest a multifactorial etiolo
A case study in clock synchronization for distributed camera systems

We studied several well-known timing synchronization algorithms in this paper, and applied them to our distributed real-time camera system. We proposed a peer-to-peer framework for distributed real-time gesture recognition, and this study serves as the keystone of the system. Cameras and microprocessors are now cheap enough that many smart camera nodes can be used in a single system. A smart camera node contains not only video capturing devices, but also processing elements to perform both capture and process in the same package. Sometimes, using multiple relatively inexpensive cameras with lower resolution might even provide better performance and be more cost efficient than using single high-end camera. In order to perform real-time video processing, distributed multiple cameras require distributed processing power, and the distributed nodes have to remain synchronized to ensure the correctness of distributed video processing. Though clock synchronization has already been well studied in decades, most previous work uses domain knowledge to achieve good synchronization result on a certain network structure. Precision in microseconds could be achieved in several previous approaches. However, for our distributed real-time video processing system, such precision is not required; only frame-precision is needed for our system, which is around tens of milliseconds. In our distributed camera system we assume no deterministic network structure for the camera nodes. Since there is no single time synchronization algorithm would suit every network structure, we would like to investigate the possibility to perform clock synchronization in application layer, where domain knowledge of underlying structure is not needed. We choose algorithms that achieve synchronization by exchanging messages between camera nodes to achieve synchronization on heterogeneous network structures. We investigate three well-known message-exchanging timing synchronization methods: Lamport’s; Lundelius’ and Halpern’s algorithms, and perform experiments on our distributed camera system. All these methods can tolerate up to one third of faulty camera nodes, and Halpern’s algorithm could even survive as long as the network is connected. Three different network configurations are used in our simulation, and each configuration can represent certain realistic camera distributions. Among all the algorithms we studied, Halpern’s algorithm is the simplest one in sense of computation complexity, and can achieve the most precise synchronization, regardless the huge variation in transmission delay. Halpern’s algorithm also uses less message exchanges, and can even be hidden within normal data packages, which is a better choice for our distributed real-time camera system.
An aptamer-functionalized chemomechanically modulated biomolecule catch-and-release system

The efficient extraction of (bio)molecules from fluid mixtures is vital for applications ranging from target characterization in (bio)chemistry to environmental analysis and biomedical diagnostics. Inspired by biological processes that seamlessly synchronize the capture, transport and release of biomolecules, we designed a robust chemomechanical sorting system capable of the concerted catch and release of target biomolecules from a solution mixture. The hybrid system is composed of target-specific, reversible binding sites attached to microscopic fins embedded in a responsive hydrogel that moves the cargo between two chemically distinct environments. To demonstrate the utility of the system, we focus on the effective separation of thrombin by synchronizing the pH-dependent binding strength of a thrombin-specific aptamer with volume changes of the pH-responsive hydrogel in a biphasic microfluidic regime, and show a non-destructive separation that has a quantitative sorting efficiency, as well as the system's stability and amenability to multiple solution recycling.
The Games Ecologists Play: The Contrarian

In today’s crowded market for life scientists, especially ecologists, it is hard to stand out or get ahead. Work poured into a dissertation or long-term project, no matter how excellent, may not help, if the research doesn’t pan out or the topic becomes unfashionable. Similarly, if one does get a job as a junior faculty member, the university and universe will conspire to restrict opportunities to do original research. Finally, we all would like to start a Kuhnian revolution (Kuhn 1996), overturning some major paradigm. However, science rarely has those Crick and Watson moments. Fortunately there are ways around these problems that can help your career.
What Aspect of Dependence Does the Fagerström Test for Nicotine Dependence Measure

Although the Fagerstrom Test for Nicotine Dependence (FTND) and the Heaviness of Smoking Index (HSI) are widely used, there is a uncertainty regarding what is measured by these scales. We examined associations between these instruments and items assessing different aspects of dependence. Adult current smokers (n = 422, mean age 33.3 years, 61.9% female) completed a web-based survey comprised of items related to demographics and smoking behavior plus (1) the FTND and HSI; (2) the Autonomy over Tobacco Scale (AUTOS) with subscales measuring Withdrawal, Psychological Dependence, and Cue-Induced Cravings; (3) 6 questions tapping smokers' wanting, craving, or needing experiences in response to withdrawal and the latency to each experience during abstinence; (4) 3 items concerning how smokers prepare to cope with periods of abstinence. In regression analyses the Withdrawal subscale of the AUTOS was the strongest predictor of FTND and HSI scores, followed by taking precautions not to run out of cigarettes or smoking extra to prepare for abstinence. The FTND and its six items, including the HSI, consistently showed the strongest correlations with withdrawal, suggesting that the behaviors described by the items of the FTND are primarily indicative of a difficulty maintaining abstinence because of withdrawal symptoms.
Simulation of 14-MeV Neutron Damage to Potential CTR Materials

The reaction D(T, n)4 He occurs either as the primary-plasma reaction or as a side reaction in nearly all the controlled thermonuclear reactor (CTR) design schemes. Neutrons produced by this reaction possess an energy of 14.1 MeV and are capable of causing an enormous amount of damage, the extent and character of which is still mostly unknown.
4D Electron Tomography

Electron tomography provides three-dimensional (3D) imaging of noncrystalline and crystalline equilibrium structures, as well as elemental volume composition, of materials and biological specimens, including those of viruses and cells. We report the development of 4D electron tomography by integrating the fourth dimension (time resolution) with the 3D spatial resolution obtained from a complete tilt series of 2D projections of an object. The different time frames of tomograms constitute a movie of the object in motion, thus enabling studies of nonequilibrium structures and transient processes. The method was demonstrated using carbon nanotubes of a bracelet-like ring structure for which 4D tomograms display different modes of motion, such as breathing and wiggling, with resonance frequencies up to 30 megahertz. Applications can now make use of the full space-time range with the nanometer-femtosecond resolution of ultrafast electron tomography.
Radiation pattern reconfigurable planar Yagi-Uda antenna

A radiation pattern reconfigurable planar Yagi-Uda antenna is investigated. The beam peak direction of the patterns is reconfigured to opposite sides by activating or deactivating PIN diode switches. Achieved patterns are directional with good front-to-back (F/B) ratios.
Polybromo-1-bromodomains bind histone H3 at specific acetyl-lysine positions

Abstract The human polybromo-1 protein is thought to localize the Polybromo, BRG1-associated factors chromatin-remodeling complex to kinetochores during mitosis via direct interaction of its six tandem bromodomains with acetylated nucleosomes. Bromodomains are acetyl-lysine binding modules roughly 100 amino acids in length originally found in chromatin associated proteins. Previous studies verified acetyl-histone binding by each bromodomain, but site-specificity, a central tenet of the histone code hypothesis, was not examined. Here, the acetylation site-dependence of bromodomain–histone interactions was examined using steady-state fluorescence anisotropy. Results indicate that single bromodomains bind specific acetyl-lysine sites within the histone tail with sub-micromolar affinity. Identification of duplicate target sites suggests that native Pb1 interacts with both copies of histone H3 upon nucleosome assembly. Quantitative analysis of single bromodomain–histone interactions can be used to develop hypotheses regarding the histone acetylation pattern that acts as the binding target of the native polybromo-1 protein.
Linear Modular Sequential Circuits

Sequential circuits comprising 1) modulo- p ( p = prime) summers, 2) amplifiers whose gains are integers , and 3) unit delays are considered in this paper which constitutes an extension of earlier work by Huffman. Such circuits are characterized in terms of the modular field GF(p) and vectors and matrices defined thereover. A summary of the properties of GF(p) is given. A linear sequential circuit is defined in terms of \overrightarrow{y}(n) = C \overrightarrow{s}(n) + D \overrightarrow{x}(n) \overrightarrow{s}(n + 1) = A \overrightarrow{s}(n) + B \overrightarrow{x}(n) where A, B, C, and D are k \times k matrices defined over GF(p) . The latter equations constitute a canonical representation of any circuit comprising the above listed components. It is shown that circuits of this type meet the usual additivity criterion of linear systems. The behavior of the circuit is described in a finite state space of k dimensions and p^k states. The autonomous circuit (A, B, C, D = constant and \overrightarrow{x}(n) \equiv \overrightarrow{O} , all n ) is characterized by the matrix A . If A is nonsingular all initial states are either finite equilibrium points or lie in periodic sequences of length T_{\tau} \leq T_{\max} = p^{k} - 1 . If the minimum polynomial of A_{\tau} has distinct roots, T_{\tau} , divides r(p - 1) . If A is singular, there are some singular initial states to which the circuit cannot return in the absence of excitation. The use of Z transforms for linear modular sequential circuits is demonstrated. Inputs and outputs are represented by their "transforms" and the circuit by its "transfer function." The transform of the output is the product of the transfer function and the transform of the input. Several illustrative examples are included.
The use of AFFF in sprinkler systems

This paper reports the results of a series of fire tests to measure the effectiveness of a 1% aqueous film forming foam concentrate against flammable hydrocarbon fires when applied through conventional, automatic, wet-pipe sprinkler systems using closed sprinklers.
Age-related differences in care preferences, treatment decisions, and clinical outcomes of seriously ill hospitalized adults: Lessons from support

OBJECTIVES: To review previously published findings about how patient age influenced patterns of care for seriously ill patients enrolled in the Study to Understand Prognoses and Preferences for Outcomes and Risks of Treatments (SUPPORT). DESIGN: An observational prospective study. SETTING: Five acute care hospitals. PARTICIPANTS: A total of 9105 seriously ill patients enrolled in SUPPORT. MEASUREMENTS: The outcomes examined included patients' preferences for aggressive care, decision making regarding cardiopulmonary resuscitation and use of other life-sustaining treatments, hospital costs, intensity of resource use, and survival. RESULTS: Although older patients preferred less aggressive care than younger patients, many older patients wanted cardiopulmonary resuscitation and care focused on life extension. Patients' families and healthcare providers underestimated older patients' desire for aggressive care. After adjustment for illness severity, comorbidity, baseline function, and patients' preferences for aggressive care, older age was associated with lower hospital costs and resource intensity and higher rates of decisions to withhold life-sustaining treatments. In adjusted analyses, older age was associated with a slight survival disadvantage. This survival disadvantage persisted, even after adjustment for aggressiveness of care, suggesting that the relation between age and survival is not accounted for by less aggressive treatment of older patients. CONCLUSIONS: Even after adjustment for patients' prognoses and care preferences, seriously ill hospitalized older patients were treated less aggressively than younger patients. SUPPORT cannot fully identify whether the relationship between older age and less aggressive treatment is better explained by the withholding of potentially beneficial treatments from older patients, or by the excessive provision of ineffective treatment to younger patients. However, the latter explanation is favored by the SUPPORT finding that less aggressive treatment for older patients does not contribute to the modest survival disadvantage associated with older age.
The basis for surgical resection of pulmonary metastases

INTRODUCTION In the past relatively little attention has been focused on the control of metastatic disease because of the ominous effect on prognosis that its presence usually signifies and the common supposition that any remote foci of disease indicates widespread dissemination. The rationale for surgical resection of pulmonary metastases derives from observations at autopsy which demonstrate that metastatic disease is confined to the lungs in U-25% of cancer patients who die with pulmonary metastasis.’ The potential of these patients for survival has been reported in the literature since 1939 when Barney and Churchill documented the first long term survival following resection for puhnonary metastases.’ In several series reported in the literature since 1970583*‘4.*s303’ overall survival rates for highly selected groups of patients having surgical resection as the primary treatment of their pulmonary metastases ranged from 25 to 40%. There were 173 five year survivors in a total of 589 patients collected from these series, for a collective crude survival rate of 29.3%. Innumerable factors influence the growth and spread of cancer; although certain growth features portend metastasis it is difficult to determine in what stage of growth secondary spread will take place. It occurs at inconsistent times.6 Careful study of the patients selected for curative resection of pulmonary metastases may yield valuable information as to how spread of cancer can be controlled and the tumor ultimately destroyed. SELECTION OF PATIENTS A greater percentage of failure may be reported as efforts are made to extend the application of surgical resection in the treatment of pulmonary metastases, even though this may result in the salvage and palliation of more patients. Therefore, success with this therapeutic approach depends almost entirely on the selection of patients. Three basic questions must be answered to fulfill the criteria for initial selection of cases. First, can the patient tolerate the contemplated surgery; second, has the primary site of the tumor been definitely and successfully treated without evidence of recurrent disease; and third, can all known metastatic disease be encompassed by the projected pulmonary resection? If these basic criteria can be fulfilled, surgical resection is recommended. In general the factors which favorably affect prognosis are absence of metastatic tumor in regional or mediastinal nodes, slow growth rate of the pulmonary metastasis and a long interval of time from primary treatment to appearance of metastasis. Controversy exists regarding the prognostic implications of this time interval. Indications are that the survival rate increases as the interval between the treatment of the primary tumor and discovery of the metastasis becomes longer. This may be logical since, during the disease free interval, the host resistance to the tumor is strong enough to prevent growth into gross metastases and may be strong enough to further contain the disease.6 However, our studies do not confirm
An elliptical polarization synthesizer

An electronic instrument is described which automatically determines the resultant polarization of two superimposed elliptically polarized waves when the polarization of the individual components is known. In addition, a study of the effect of ground pulse contamination on polarization data obtained by sounding the ionosphere is presented. The study serves to demonstrate the usefulness of the instrument.
Rainfall or Rainmaking? Lawyers, Courts, and the Price of Mold Insurance in Texas

AbstractIn well-functioning property-liability insurance markets, the price of coverage reects theimpact of the legal environment on the frequency and severity of claims. This paper presentsa case study of the Texas mold insurance crisis of 2001-02. We provide a narrative of the con-troversy in Texas over insurance coverage for household mold and use county-level data from asingle Texas insurer to assess the determinants of post-crisis prices for supplemental mold, slab,and extended water loss coverages. We nd that more attorneys per capita and more heavilyDemocratic courts were both associated with higher prices for mold and slab coverage.JEL Codes:G22 - Insurance; Insurance CompaniesK41 { Litigation Process For helpful comments, the authors thank two anonymous referees, Michael Makowsky, Allen Seward, HampSkelton, and Robert Woody. We thank Malcolm Gold for research assistance. All mistakes are solely those of theauthors.y Associate Professor of Economics at Baylor University z Designated Contact Author, Frank S. Groner Memorial Chair in Finance and Professor of Finance and Insuranceat Baylor University,James Garven@baylor.edu.
Baryon Spectral-Function Sum Rules

Necessary and sufficient conditions for baryon spectral-function sum rules are obtained under the assumptions that (1) the equal-time commutator of the axial charges ${{Q}_{5}}^{a}({x}_{0})$ ($a=1, 2, 3$) and the nucleon field $\overline{\ensuremath{\psi}}(y)$ is given by $[{{Q}_{5}}^{a}({y}_{0}), \overline{\ensuremath{\psi}}(y)]=\ensuremath{-}{r}_{A}\overline{\ensuremath{\psi}}(y){\ensuremath{\gamma}}_{5}{\ensuremath{\tau}}^{a}+(\ensuremath{\Delta}I=\frac{3}{2} \mathrm{terms})$ and that (2) the axial-vector current ${{A}_{\ensuremath{\mu}}}^{a}(x)$ is conserved. For each of these sum rules (enumerated by $n=1, 2, 3\dots{}$), the equivalence to $\ensuremath{\int}{d}^{3}z{〈{[{{Q}_{5}}^{a}({y}_{0}), {[{(\frac{\ensuremath{\partial}}{\ensuremath{\partial}{y}_{0}})}^{2n\ensuremath{-}1}\ensuremath{\psi}(y), \overline{\ensuremath{\psi}}(z)]}_{+}]|}_{{y}_{0}={z}_{0}}〉}_{0}=0$ is actually shown under weaker conditions: assumption (1) and, instead of (2), ${{\ensuremath{\Sigma}}_{j=0}}^{2n\ensuremath{-}2}{〈{{[{{(\frac{\ensuremath{\partial}}{\ensuremath{\partial}{y}_{0}})}^{j}[\ensuremath{\int}{d}^{3}x{\ensuremath{\partial}}^{\ensuremath{\mu}}{{A}_{\ensuremath{\mu}}}^{a}({y}_{0}\mathrm{x}), {(\frac{\ensuremath{\partial}}{\ensuremath{\partial}{y}_{0}})}^{2n\ensuremath{-}2\ensuremath{-}j}\ensuremath{\psi}(y)]}, \ensuremath{\psi}(z)]}_{+}|}_{{y}_{0}={z}_{0}}〉}_{0}=0$. Further equivalences are given. The sum rules connect the ($I=\frac{1}{2}$, $J={\frac{1}{2}}^{+}$) and ($I=\frac{1}{2}$, $J={\frac{1}{2}}^{\ensuremath{-}}$) baryon spectrum and include (for $n=1$) a sum rule, obtained independently by Rothleitner and (in the one-particle approximation) by Sugawara. In our derivation we make no assumptions on high-energy behavior and we use an identity of the Jacobi type. Assuming the first two sum rules to be valid, the model then predicts a ${P}_{11}(mg1470 \mathrm{MeV})$ resonance [which may be identified as the observed ${P}_{11}(1750)$] from the existence of the four nucleon resonances ${P}_{11}(940)$, ${P}_{11}(1470)$, ${S}_{11}(1550)$, and ${S}_{11}(1710)$.
A contribution to the structure theory of operators in the class A

Soit #7B-H un espace de Hilbert separable, et soit T une contraction agissant sur #7B-H. On suppose que T est absolument continu. Soit #7B-A T l'etoile-fermee algebre faible engendree par T. Si T∈A on dit que T appartient a la classe A 1 si pour chaque fonctionnelle etoile-continue faible φ sur #7B-A T , il existe des vecteurs n,y∈#7B-H satisfaisant φ(A)= , A∈#7B-A T . On montre que chaque operateur T tel que T∈A et soit T n →0 soit T* n →O avec 1/n appartient a A 1
Ordination of deep river invertebrate communities in relation to environmental variables

A deep Main river was examined to determine the effects of selected environmental variables on benthic invertebrate community structure. Thirty-three sites were sampled by divers using artificial substrates. The Bray-Curtis ordination was used to establish community types based upon combinations of current velocity, siltation, and organic detritus. While some invertebrates were tightly clustered within particular communities, most taxa tended to concentrate in one community type but were not excluded from others. The results tended to support the individualistic hypothesis of species distribution.
Online learning in a chemical perceptron

Autonomous learning implemented purely by means of a synthetic chemical system has not been previously realized. Learning promotes reusability and minimizes the system design to simple input-output specification. In this article we introduce a chemical perceptron, the first full-featured implementation of a perceptron in an artificial simulated chemistry. A perceptron is the simplest system capable of learning, inspired by the functioning of a biological neuron. Our artificial chemistry is deterministic and discrete-time, and follows Michaelis-Menten kinetics. We present two models, the weight-loop perceptron and the weight-race perceptron, which represent two possible strategies for a chemical implementation of linear integration and threshold. Both chemical perceptrons can successfully identify all 14 linearly separable two-input logic functions and maintain high robustness against rate-constant perturbations. We suggest that DNA strand displacement could, in principle, provide an implementation substrate for our model, allowing the chemical perceptron to perform reusable, programmable, and adaptable wet biochemical computing.
Optimum error nonlinearities for long adaptive filters

In this paper, we consider the class of adaptive filters with error nonlinearities. In particular, we derive an expression for the optimum nonlinearity that minimizes the steady-state error and attains the limit mandated by the Cramer-Rae bound of the underlying estimation process.
Thermal oxidation of lipids in monolayers II. Unsaturated fatty acid esters

To investigate whether oxidation of lipids in the ordered state differs from that in the bulk phase upon heating, ethyl oleate, ethyl linoleate and ethyl linolenate adsorbed as monolayers on silica were used as model systems. For both bulk and monolayer samples, the major decomposition products found were those typical of classical decomposition of hydroperoxides. However, quantitative and qualitative differences were observed after heating. The decomposition patterns in monolayers were much simpler than those of the bulk samples.
From Mario to FIFA: what qualitative case study research suggests about games-based learning in a US classroom

This article explores the impact of using commercial-off-the-shelf (COTS) videogames in a high school curriculum when developed through a connected learning frame by examining the influence that COTS videogames have on transforming students’ literacy learning in-school. However, it must be noted that transforming literacy in school is about more than bridging in- and out-of-school literacies; it concerns developing a deeper understanding of the meaning of literacy in today’s multimediated world, and the ways that these experiences are connected not only to media, but to traditional texts, peers, and guiding teachers, so that we can better grasp how to harness new learning styles and new ways of making meaning in contemporary classroom spaces. To understand how to capture in and out-of-school practices, we conducted a qualitative case study of two high school students enrolled in a reading intervention class that incorporated a COTS videogames curriculum. Data were analyzed via a constant comparison analys...
Infinite‐dilution viscoelastic properties of sodium poly(styrene sulfonate)

The storage and loss shear moduli G′ and G″ of dilute solutions of two samples of sodium poly(styrene sulfonate) with molecular weights (M) of 3.28 × 105 have been measured. The Birnboim–Schrag multiple-lumped resonator technique was used in the frequency range 100–8000 Hz, and the intrinsic moduli were obtained by extrapolation to infinite dilution. Measurements were performed over the temperature range from 1.0 to 25.0°C in aqueous solvents containing from 0 to 60% by weight glycerol and from 0.001 to 0.005M added salt. The large intrinsic viscosities indicated high extension of the polymer, and the frequency dependences of G′ and G″ were matched well by hybrid relaxation spectra combining rodlike and coil-like behavior. In a solvent containing 0.001M sodium ion and no glycerol, the end-over-end rotational relaxation times for the two molecular weights corresponded to proportionality to the 1.7 power of M. With increasing molecular weight, ionic strength, and/or glycerol concentration, the polyelectrolyte appeared to become less extended, and its behavior more nearly coil-like.
The Role of Philosophy in the Contemporary Abortion Debate

Inspired by Patrick Lee's "A Christian Philosopher's View of Recent Directions in the Abortion Debate," this essay raises the question of how effective philosophical arguments can be in determining the moral status of legalized abortion. On one hand, Christian philosophers have been successful in explaining both the humanity and the personhood of the unborn child, as well as exposing the incoherence of those who would deny the unborn child's humanity or personhood. Nevertheless, in order to confront the pro-abortion position in its most radical form, a much more complex philosophical argument must be given. Following thinkers such as Alasdaire MacIntyre, Christian philosophers must articulate and promote a philosophical position according to which morality is conceived in richer terms than the mere respecting of individual rights. The social dimension of human nature must be rediscovered in order that the happiness and welfare of others becomes a desirable goal in and of itself. According to a morality where individual rights is the bottom line (for example, that of Judith Jarvis Thompson), women very well may have the right to "extricate" themselves from their pregnancy even when doing so will result in the death of their child. What must be explained, therefore, is the more profound insight that social morality is equally concerned with obligations to others, including those who are most helpless and unable to speak for themselves.
Malignant tumors of Stensen’s duct

A rare case of squamous cell carcinoma arising in Stensen's duct is reported. The literature concerning malignant neoplasia originating in this site is reviewed, with attention given to the histopathologic diversity of neoplasms occurring in the duct, criteria for determination of origin in the duct, and outcomes of therapy.
Value of peritoneoscopy for nonfunctioning continuous ambulatory peritoneal dialysis catheters

We examined our results in restoring continuous ambulatory peritoneal dialysis (CAPD) catheter function via peritoneoscopy in 10 procedures performed on nine patients. Malfunction was caused by the catheter being encased in adhesions, being buried in small bowel, or being wrapped and occluded in omentum. In five of these cases we were successful in restoring catheter patency, thereby allowing immediate reinstitutton of dialysis. Neither previous abdominal surgeries nor the length of time the catheter had been in place prior to malfunction appeared to be predictive for the cause of malfunction or the success of peritoneoscopic manipulation. We found outpatient peritoneoscopy to be safe and cost effective. We recommend it as the initial procedure to restore patency to malfunctioning CAPD catheters after conservative therapy has failed.
Parents’ perceptions of pharmacological and cognitive-behavioral treatments for childhood anxiety disorders

Cognitive-behavioral therapy (CBT) and pharmacotherapy are the most well-established treatments for childhood anxiety disorders. This study examined how parents (N=71) seeking treatment for their child's anxiety disorder perceive the acceptability, believability, and effectiveness of these treatments. While both treatments were perceived favorably, CBT was rated as more acceptable, believable, and effective in the short- and long-term. Children's treatment history influenced parents' perceptions of pharmacotherapy, with parents of children with no treatment history perceiving medication treatment as less acceptable and believable than parents of children with a history of medication alone or in combination with behavior therapy. No effect of treatment history was found for perceptions of CBT. Significant positive correlations emerged between parents' perceived acceptance and believability for pharmacotherapy and child age and level of dysfunction due to their child's anxiety, respectively. The level of the child's anxiety was not significantly correlated with parents' perceptions of either CBT or pharmacotherapy. Our results suggest that parents of anxious children prefer CBT to medication for the treatment of their child's anxiety disorder. Directions for future research are discussed.
The sensitivity of high-resolution CT in detecting idiopathic pulmonary fibrosis proved by open lung biopsy: A prospective study

Objectives: To assess the sensitivity of high-resolution chest computed tomography (HRCT) in detecting idiopathic pulmonary fibrosis proved by biopsy specimen. To determine the degree of physiologic and pathologic abnormalities in patients with idiopathic pulmonary fibrosis who have a false-negative HRCT. Design: Prospective 2-year study. Setting: Tertiary care university hospital. Patients: All patients with dyspnea and suspected interstitial lung disease referred to the University of Michigan for enrollment in the Idiopathic Pulmonary Fibrosis Specialized Center of Research (SCOR) protocol were included; 25 underwent open lung biopsy and formed the final study group. Measurements: All patients underwent physiologic (pulmonary function, gas exchange, and exercise testing), radiologic (chest x-ray film and HRCT), and pathologic assessments (bronchoscopic and open lung biopsy). The results of HRCT were prospectively compared with results of standard pulmonary function tests, cardiopulmonary exercise testing, and open lung biopsy. Results: Of 25 patients who had both HRCT and open lung biopsy, 3 patients (12%) had HRCTs that demonstrated no evidence of interstitial lung disease. These three patients had less severe disease based on clinical, radiographic, and physiologic (CRP) scores, gas exchange abnormalities, and pathologic scoring of open lung biopsy specimens, compared with those with an abnormal HRCT. Conclusion: We conclude that in the evaluation of patients with dyspnea and abnormal results of pulmonary function studies, a normal HRCT does not exclude early and clinically significant interstitial lung disease. In our patient population, physiologic testing was more sensitive than HRCT in detecting mild abnormalities in patients with idiopathic pulmonary fibrosis proved by biopsy specimen.
Abstract LB-12: Estrogen-induced redox signaling via NRF-1 is involved in the development of breast cancer

The purpose of this study was to determine the role of estrogen-induced reactive oxygen species (ROS) signaling pathways in the development of breast cancer. Here we tested the postulate that activation of a redox sensitive transcription factor, nuclear respiratory factor-1 (NRF-1) signaling is essential for 4-hydroxyestradiol (4-OH-E2)-induced tumorigenesis. We observed that (i) 4-OH-E2 treatment of MCF-10A or MCF-7 cells increased the formation of ROS, (ii) Estrogen-induced ROS activated redox sensitive transcription factor NRF-1, (iii) 4-OH-E2 through activating a redox sensitive serine-threonine kinase AKT phosphorylated NRF-1, (iv) Overexpression of catalase and MnSOD, as well as silencing of NRF-1 prevented 4-OH-E2-induced anchorage-independent growth of MCF-10A and MCF-7 cells and xenograft tumor formation, and (v) 4-OH-E2-induced ROS through stimulating AKT kinase and histone acetyltransferase of CREB binding protein-associated factor (P/CAF), respectively, controlled phosphorylation and acetylation of NRF-1. The results also showed that 4-OH-E2-induced post-translational changes lead to NRF-1 activation, and silencing of NRF-1 and overexpression of MnSOD or catalase prevented 4-OH-E2-induced tumor formation. Taken together, these findings suggest a new paradigm for estrogen-induced breast carcinogenesis that deregulation of phosphorylation and aceytylation of NRF-1 may represent a major mechanism of 4-OH-E2-induced neoplastic transformation and tumorigenesis. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-12. doi:10.1158/1538-7445.AM2011-LB-12
High Throughput WAN Data Transfer with Hadoop-based Storage

Hadoop distributed file system (HDFS) is becoming more popular in recent years as a key building block of integrated grid storage solution in the field of scientific computing. Wide Area Network (WAN) data transfer is one of the important data operations for large high energy physics experiments to manage, share and process datasets of PetaBytes scale in a highly distributed grid computing environment. In this paper, we present the experience of high throughput WAN data transfer with HDFS-based Storage Element. Two protocols, GridFTP and fast data transfer (FDT), are used to characterize the network performance of WAN data transfer.
Parathyroidectomy outcomes according to operative approach.

Background: Parathyroidectomy for primary sporadic hyperparathyroidism (psHPT) has evolved with advances in preoperative gland localization and intraoperative parathyroid hormone (ioPTH) monitoring to minimally invasive approaches (MIPS). Methods: Two hundred twenty patients underwent parathyroidectomy for psHPT. Forty-nine patients underwent bilateral neck exploration (BNE) (group 1), 60 patients underwent BNE with ioPTH monitoring (group 2), and 111 patients underwent MIPS with ioPTH monitoring (group 3). Results: At 3 months postoperatively, mean serum calcium and intact parathyroid hormone (PTH) levels were similar between groups, and eucalcemia rates were 100%, 100%, and 99%. The ultimate rates of persistent disease and recurrence were also similar. Operative time was shorter in group 3 compared to group 2 (P <.001) but not group 1. Frozen sections and patient charges were significantly lower in group 3 compared to groups 1 and 2 (P <.005). Conclusion: Parathyroidectomy for psHPT is highly successful with these techniques. When a MIPS approach can be done, it is potentially quicker and associated with lower patient charges.
Notes on permanents of doubly stochastic matrices

Using a simple probabilistic interpretation of the permanents of doubly stochastic matrices, we obtain in this paper some results which extend the work in [1]. An upper bound is obtained for the permanent on the doubly stochastic matrices A=(aij) with all of whose entries satisfying the condition . It is proved that for doubly stochastic matrices in the complement of a sufficiently large neighborhood of Jn , a conjecture of E. T. H. Wang holds, which asserts that per be the set of all n×n doubly stochastic matrices with at least one entry equal a. A necessary and sufficient condition on a is given such that the permanent function restricted to Ωn(a) achieves a local minimum at the matrices which are closest to Jn in Euclidean norm in Ωn(a).
Companion animals as reservoirs of eaeA+ Escherichia coli

22. Zanoni RG, Cordano P, Nauta IM, Peterhans E: 1996, Die PCR faur den Nachweis von Lentiviren der kleinen Wiederkuer [PCR for the detection of lentiviruses from small ruminants]. Schwiez Arch Tierheilkd 138:93–98. 23. Zimmerman JJ, Yoon KJ, Stevenson G, Dee SA: 1998, In: The 1998 porcine reproductive and respiratory syndrome compendium, pp. 13–15. National Pork Producers Council and National Pork Board, Des Moines, IA. 24. Zimmerman JJ, Yoon KJ, Stevenson G, Dee SA: 1998, In: The 1998 porcine reproductive and respiratory syndrome compendium, pp. 73–84. National Pork Producers Council and National Pork Board, Des Moines, IA.
The Algal Flora of Acadia National Park, Maine

Abstract The inland algal flora of Acadia National Park was studied based on over 200 samples from 119 localities. A total of 160 algal genera were found, representing 12 algal phyla. Among these were 140 new generic records for the Park. The most frequently encountered taxa were desmids and diatoms, and the genera and species in these groups were acidophilous, reflecting the low pH of the ponds, lakes, and streams of the Park. Ponds and streams were the most heavily sampled habitats in the Park, and coincidentally had the highest diversity (103 and 91 genera, respectively). Based on other similar studies, we estimate that the Park likely contains as many as 1000 algal species within its boundaries, indicating that the diversity is exceptionally high for an area of this size.
Design and performance of a monolithically integrated widely tunable all-optical wavelength converter with independent phase control

We report on a new widely tunable all-optical wavelength converter consisting of a sampled-grating distributed Bragg reflector (SGDBR) laser monolithically integrated with a Mach-Zehnder interferometer semiconductor optical amplifier (MZI-SOA)-based wavelength converter. The new design incorporates independent phase control of the interferometer and SOAs for amplification of the SGDBR output. For the first time, error-free operation for data rates of up to 10 Gb/s is reported for 35-nm output tuning range. The high-speed operation is enabled by high photon density in the SOA due to large power transfer from the on-board tunable laser and amplifiers. We also report on device sensitivity of -10 dBm at 2.5 Gb/s and -5 dBm at 10 Gb/s, with an average output power of 0 dBm.
Engagement and Games for Learning: Expanding Definitions and Methodologies

Aim. In this article, we argue for an expanded definition and treatment of engagement when studying games for learning. Background. It is common for researchers in the field to collapse behavioral, cognitive, and affective engagement into one shared category. We assert that educators and games for learning researchers should examine all types of engagement using multiple methodologies as a means to better understand precisely what students are learning from game play. Method. We present findings from a small (N = 58) qualitative study that highlights the importance of accounting for behavioral, cognitive, and affective engagement when evaluating learning from games. We also discuss methodologies that are successful for this type of evaluation. Results. Finally, we discuss the implications of our findings for those creating games for learning and for measuring learning gains.
Chlamydia pneumoniae infection accelerates hyperlipidemia induced atherosclerotic lesion development in C57BL/6J mice.

Abstract Considerable evidence of an association between Chlamydia pneumoniae infections and cardiovascular disease has emerged. Animal models using genetically altered mice and hypercholesterolemic rabbits have shown a pathogenic role of C. pneumoniae in accelerating atherosclerotic plaque development. In the present study, we evaluated the effect of chronic C. pneumoniae infection on atherosclerosis in C57BL/6J mice, fed either a regular chow diet or a high fat, high cholesterol diet. Infected animals on an atherogenic diet developed significantly larger lesion areas compared with control mice at 18 weeks (2.5-fold increase; 4177±777 vs. 1650±808 μm 2 ; P 2 ; P C. pneumoniae infection accelerates atherosclerotic lesion development in diet induced hypercholesterolemic mice, indicating that C. pneumoniae is a co-risk factor of hyperlipidemia in atherogenesis.