cssi/SciSciGPT-SciSciNet huggingface dataset:
Democracy, Dialectics, and Difference: Hegel, Marx, and 21st Century Social Movements

It has been nearly two centuries since Marx famously turned Hegel on his head in order to repurpose dialectics as a revolutionary way of thinking about the internal contradictions of our social relations. Despite critiques from post-structuralists, post-colonialists, and others, there has been a resurgence of dialectical thought among political theorists as of late. This resurgence has coincided with a rise in the mention of words like class warfare, socialism, and communism among the general public on the streets of Seattle in 1999, in Cairo’s Tahrir Square, in the actions of the Greek anarchists and the Spanish indignados, and in the rallying cry of "we are the 99%" of the Occupy Movement, and in academia. This book explores how it is that dialectical thought might respond to the critiques brought forth by those on the left who are critical of Marxism’s universalizing and authoritarian legacy. Brian C. Lovato singles out Ernesto Laclau and Chantal Mouffe as the key interlocutors in this ongoing conversation between Marxism and post-structuralism. Laclau and Mouffe argue that Marxist theory is inherently authoritarian, cannot escape a class-reductionist theory of revolutionary subjectivity, and is bound by a closed Hegelian ontology. Lovato argues the opposite by turning to two heterodox Marxist thinkers, Raya Dunayevskaya and C. L. R. James, in order to construct a radically democratic, dynamic, and open conceptualization of dialectical thought. In doing so, he advances a vision of Marxist theory that might serve as a resource to scholars and activists committed not only to combatting capitalism, but also to fighting against colonialism, patriarchy, white supremacy, and heteronormativity. The writings of Dunayevskaya and James allow for Marxism to become relevant again in these tumultuous early years of the 21st century.
A.I. Ethics in the City

Artificial Intelligence (A.I) is the science of making machines act in a way human beings might call intelligent. Ethics of A.I. seek to make A.I. behave responsibly. A recent surge in national and international initiatives in support of A.I and A.I ethics speaks to both the significance of as well as anxieties surrounding the project. This short text is only a sketch with more questions than answers. It points out two factors in the A.I. ethics debate that receive less attention than they should: the significance of situatedness and of decision mechanisms in A.I. The big city, I contend, will be the site where complex A.I ethics conflicts will emerge most prominently; in different ways in different parts of the world.
Pancreatic Cancer Detection in Whole Slide Images Using Noisy Label Annotations.

We propose an approach to accurately predict regions of pancreatic cancer in whole-slide images (WSIs) by leveraging a relatively large, but noisy, dataset. We employ a noisy label classification (NLC) method (called the NLC model) that utilizes a small set of clean training samples and assigns the appropriate weights to training samples to deal with sample noise. The weights are assigned online so that the network loss approximates the loss for the clean samples. This method results in a 9.7% performance improvement over the baseline non-NLC method (the Baseline-Noisy model). We use both methods in an ensemble setup to generate labels for a large training dataset to train a classifier. This classifier outperforms a classifier trained with manually annotated data by 2.94%–3.74% in terms of AUC for testing patches in WSIs.
G115(P) Parechovirus meningitis in infants – time for routine CSF viral screening?

Human parechovirus (HPeV) is a virus belonging to the picornaviridae family; certain subtypes of which have been found to cause meningitis, particularly in infants. We describe a series of 7 infants who were diagnosed to have parechovirus meningitis by CSF PCR testing. Mean age at presentation was 2.4 months with a gender distribution of M:F 1.2:1. Clinical features included fever and severe irritability (100%), rash (60%) and diarrhoea (30%). All infants were clinically diagnosed to have sepsis of unknown aetiology and underwent a complete sepsis screen. CSF analysis was completely normal in all the infants, with normal CSF white cell count, CSF protein and glucose levels. Blood tests showed normal total white blood cell and neutrophil counts in all infants and a CRP less than 10 in 90% of the infants. CSF and blood cultures showed no growth in all infants. All infants received intravenous antibiotics (Cefotaxime and Amoxycillin) and 45% of infants received intravenous antiviral treatment (Aciclovir) at presentation. Positive identification of HPeV by PCR led to cessation of intravenous antibiotics and antiviral therapy in all infants and facilitated early discharge. HPeV is increasingly recognised to cause of meningitis in young infants, without accompanying CSF pleocytosis or CSF biochemical abnormalities. Standard criteria for CSF viral screening including CSF pleocytosis and/or CSF biochemical abnormalities would result in a failure to diagnose the majority of HPeV meningitis in infants. Undertaking routine viral screening of CSF samples in infants who present with clinical features of sepsis enables confirmation of a definitive diagnosis, avoidance of unnecessary antimicrobial therapy and a reduction in length of hospital stay.
Using the 12-item short form health survey (SF-12) to assess self rated health of an engaged population impacted by hurricane Harvey, Houston, TX

In the last decade there has been an increase in community-based organizations providing support and educational outreach to populations effected by hazards. Prior research has demonstrated various roles that community social capital can play in both the enhancement of disaster preparedness and the mitigation of physical and mental health impacts following a natural disaster. To assess self-reported health of residents of South Houston, Texas impacted by Hurricane Harvey, attendees of a community event completed a survey that included the 12 item short form health survey version 2 (SF-12v2). Although survey participants were older and more likely to be African-American than the overall population of Houston, they had higher mental health composite scores that the national average, with increases in mental wellbeing associated with a longer length of residence in their neighborhood. The City of Houston, with highly segregated, socially vulnerable populations at high risk from natural hazards, should consider ways to support community engagement around disaster preparedness, response, and recovery that may build community cohesion and improve post-disaster mental health.
Intra- and inter-rater reliability of ultrasound measures of the anterior cruciate ligament

Diagnostic ultrasound has accurately and reliably been utilized by clinicians to determine ACL morphology at the tibial insertion site, specifically measuring the entire ACL diameter, the anteromedial bundle (AM), and the posterolateral bundle. However, intra- and inter-rater reliability of these measures in a research setting is unknown. The purpose of this study was to determine intra- and inter-rater reliability of ultrasound measures of ACL diameter and AM diameter in researchers with low-to-moderate ultrasound experience. We hypothesized that intra- and inter-rater reliability of ACL and AM diameters would reach acceptable levels, a minimal intraclass correlation (ICC) of 0.6 and a desired ICC of 0.8 with an α of 0.05 and β of 0.20. Fourteen volunteers participated in this study. During the ACL ultrasound measures, participants were seated with their knee flexed to at least 90°. Each rater recorded two images of both the right and left ACL and AM bundles. Next, participants were re-examined by rater one for intra-rater reliability analyses. Two-way random ICCs were conducted for intra-rater (between sessions) and inter-rater reliability for both the full ACL and the AM bundle diameters. Standard errors between sessions for Rater 1’s AM bundle and ACL diameters were less than 0.03 cm. Intra-rater reliability was higher in AM bundles compared to full ACL, 0.76 versus 0.59, respectively. Standard errors between Rater 1 and Rater 2 were less than 0.03 cm. Inter-rater reliability was higher in AM bundles compared to full ACL, 0.71 versus 0.41, respectively. The results of the study indicate researchers with low-to-moderate training with ultrasound measures can locate and measure the ACL, but with greater reliability using the AM.
Designing Tunable Capacitive Pressure Sensors Based on Material Properties and Microstructure Geometry.

Rationally designed pressure sensors for target applications have been in increasing demand. Capacitive pressure sensors with microstructured dielectrics demonstrate a high capability of meeting th...
Infrastructure for teacher reflection and instructional change: An exploratory study

In the US, instruction reforms, especially those intended to help teachers move beyond typical teaching practices, have regularly fallen short of aspirations. An important reason for this state of affairs is that reforms, often fail to provide teachers sufficient infrastructure they need to overcome fundamental uncertainties of teaching. Progress has been made in recent years in developing conceptual frameworks that help explain why some professional learning experiences provided by infrastructure might be more effective than others. Despite the progress that has been made, however, these new ways of thinking have generally not made deep inroads into practice and there is a scarcity of research on what happens when new ideas about professional learning are put into practice. This study of 887 teachers in a large urban district attempts to address some of these gaps in the literature by investigating how teachers’ engagement in a range of different professional learning experiences provided through infrastructure are associated with two learning outcomes—reflective practice and changed literacy instructional practices. We found that teachers were more likely to reflect on their practice and change their literacy instruction when their learning experiences focused directly on classroom teaching. We also found that teachers who worked with coaches more often and who engaged in reflective practice more regularly were more likely to report changing their literacy teaching.
Potential Contribution of Pleiotropic Effects of Direct Anticoagulants to Clinical Benefits

Clinical Development Phases I-III Regulatory, Quality, Manufacturing Two recent large clinical trials that enrolled exclusively or predominantly patients with ST elevation myocardial infarction and tested direct acting anticoagulants (bivalirudin, rivaroxaban) demonstrated a reduction in mortality. While the anticoagulant properties of these agents likely contributed to the beneficial effects, this Commentary will focus on the nonanticoagulant effects and will consider the premise that pleiotropic effects may have contributed to the observed benefit. In these trials, hearts experienced ischemia/reperfusion and the myocardium was directly exposed to activated coagulation factors. Activation of proteinase-activated receptors (PARs) by thrombin and factor Xa would be predicted to increase inflammation and promote ventricular dilatation and fibrosis. Because direct acting anticoagulants effectively inhibit both free and clot-bound coagulation factors, the extent of exposure to activated coagulation factors would be expected to be reduced. The anticipated preservation of left ventricular function should contribute to a reduction in the subsequent risk of death.
Modeling of Hot Carrier Effects for LDD MOSFETs

In the strive for faster and more complex integrated circuits, the device geometries and minimum feature size have been scaled down aggressively to achieve the desired circuit performance. The resulting high electric fields favor the generation and injection of hot carriers near the drain in MOS devices[1-3]. Both threshold voltage(Vt) shift and transconductance(gm) degradation have been reported by many researchers[4-8]. For LDD devices, only gm degradation was reported and was believed to be either caused by mobility degradation due to interface-state generation[6,7] or by localized charge [8]. One objective of our work is to show that for LDD devices in addition to gm degradation, Vt shift and variations for all short channel SPICE model parameters are observed. There are also good correlations between the variations of those short channel parameters. The other objective is to identify the degradation mechanisms by theoretical modeling, simulation, and experimental results. Our modeling results indicate that localized charge or mobility degradation alone can not explain the observed experimental results. A spatial charge distribution model was identified to predict the experimental results.
Atomistic study of the role of contact properties on nanotube conduction

Summary form only given. Transport through nanoelectronic systems is known to depend sensitively on the properties of their interfaces with bulk contacts. This becomes particularly important in the ballistic limit, where the contact resistance dominates conduction. Carbon nanotube field effect transistors, for example, are typically controlled by a Schottky-barrier at the contacts. There has been some progress in achieving low barrier heights to large diameter nanotubes, but producing good contacts is still something of an art. The theoretical understanding of the specific conditions required to generate ohmic or Schottky contacts, their dependence on the metal workfunctions or their wetting properties, is still limited. The challenge though in developing a rigorous simulation procedure is the need to do justice to the bonding geometry and surface chemistry of the metal-carbon bonds, the bulk bandstructures of the contact and the nanotube, the overall electrostatics, and the nonequilibrium quantum kinetics - all at the same time. We have developed a formalism that self-consistently combines electronic structure codes describing the nanotube Hamiltonian and the open-boundary contact self-energies with a non-equilibrium Green's function (NEGF)-based transport formalism. This formalism has been successfully used in the past to derive various first-principles properties of molecular conductors. We use extended Huckel theory parametrized to match ab-initio calculations to describe the bulk nanotube and metal bandstructures. The self-consistent potential describes both local charge transfers due to the interfacial bonding chemistry, as well as global transfers due to the differences in bulk electrochemical potentials of the contact and the nanotube. We are using this atomistic formalism to simulate transport through various metal-nanotube contacts. We discuss the formalism and its implementation, and present preliminary results that provide insights into the nature of metal contacts to nanotubes.
Studies on Modified Hemoglobins III. SPIN STATES OF FERRIC HEMOGLOBIN, SEMI-HEMOGLOBIN, AND ISOLATED SUBUNIT CHAINS

Abstract The pH dependencies of the spin state equilibria of ferric hemoglobin, of isolated α and β subunits, and of a semi-hemoglobin were investigated by measurements of paramagnetic susceptibilities at 293° K and 77° K, visible absorption spectra at 293° K and 77° K, and electron paramagnetic resonance spectra (EPR) at 77° K and 4.2° K. Similar results were obtained by all three methods. Acid ferric forms of hemoglobin, α chains, and semi-hemoglobin, which were in the high spin state at 293° K, were reversibly converted to a mixture of high spin and low spin compounds upon cooling to 77° K. Acid ferric β chains were a mixture of high spin and low spin compounds at 293° K and in an essentially low spin state at 77° K. The low spin compound formed in these preparations was not detected by EPR at 77° K but showed EPR signals at g1 = 2.75, g2 = 2.25, and g3 = 1.69 at 4.2° K. On the basis of its optical and EPR characteristics, the low spin compound was assigned a structure in which the 6th coordination position of the heme iron is occupied by a nitrogenous group, probably by the distal histidyl residue. It was proposed that the conformational constraint exerted by the loss of the α-β subunit contacts in the β chains and the steric hindrance caused by frozen media might be responsible for the proposed bonding of the distal group directly to the heme iron.
Shattering and Compressing Networks for Centrality Analysis

Who is more important in a network? Who controls the ow between the nodes or whose contribution is signicant for connections? Centrality metrics play an important role while answering these questions. The betweenness metric is useful for network analysis and implemented in various tools. Since it is one of the most computationally expensive kernels in graph mining, several techniques have been proposed for fast computation of betweenness centrality. In this work, we propose and investigate techniques which compress a network and shatter it into pieces so that the rest of the computation can be handled independently for each piece. Although we designed and tuned the shattering process for betweenness, it can be adapted for other centrality metrics in a straightforward manner. Experimental results show that the proposed techniques can be a great arsenal to reduce the centrality computation time for various types of networks.
Bis{2-hydr­oxy-N-[2-(2-pyrid­yl)eth­yl]benzamide}copper(I) tetra­fluoridoborate

The title complex, [Cu(C14H14N2O2)2]BF4, is a monomeric copper(I) species with linear two-coordinate geometry around the CuI atom. The asymmetric unit contains two half-cations that sit on crystallographic twofold rotation axes. The selected crystal was non-merohedrally twinned by a twofold rotation about an axis normal to the (100) family of planes. The ratio of the twin components refined to 0.4123 (6). Two 2-hydr­oxy-N-[2-(2-pyrid­yl)eth­yl]benzamide ligands coordinate to each CuI atom via the pyridyl N atom. Intra­molecular hydrogen bonding between the phenol OH groups and the amide O atoms imparts rigidity and planarity to the non-coordinating end of the ligand. The cationic complex is linked to the BF4− anions via hydrogen bonding between the amide NH groups in the cations and BF4− anions.
An experimental study of the interaction of internal cracks in PMMA

Internal cracks in polymethyl methacrylate (PMMA) specimens were generated by pulsed laser light. The interactions of coplanar cracks, parallel cracks, and cracks in T and H configurations were investigated. The tensile strength of specimens with a single internal crack decreased with increasing crack size, and the strength correlated well with the initial crack and unstable crack size in the Griffith relationship. For specimens with coplanar and parallel cracks, the strength increased and decreased with the crack distance, respectively. For the T and H crack configurations, the presence of delamination cracks decreased the strength, and the reduction in strength became more significant when the crack distance was small. All fracture surfaces showed similar fracture morphology in the sequence of laser-generated crack, smooth fracture mirror, mist with hyperbolic markings, and rough hackle region with rib markings. Examination of the fracture surfaces revealed crack arrest by the delamination cracks in both T and H configurations, and crack bowing between delamination cracks in the H configuration. The propagating crack was eventually able to circumvent the delamination cracks. The experimental results are compared with the available theoretical analyses, and the relevance of the present study to the toughening of brittle materials is discussed.
Iron pyrite and iron marcasite thin films prepared by low pressure chemical vapor deposition

Abstract Thin films of iron pyrite and iron marcasite have been successfully prepared by low pressure chemical vapor deposition (LPCVD) from iron pentacarbonyl (Fe(CO)5) and tert-butyl disulfide (TBDS) over a wide temperature range from 200 to 500°C. A series of thin film deposition reactions were studied using Fe(CO)5 and different sulfur sources (H2S, tert-butyl sulfide, or tert-butyl disulfide). It was found that thin film iron marcasite could be prepared from Fe(CO)5 and tert-butyl disulfide (TBDS) at a deposition temperature of 200°C. Thin film growth rates greater than 10μ/h could be obtained over surfaces of more than 600 cm2. Thin film iron pyrite could be prepared at deposition temperatures of 480°C or higher. Thin film growth rates greater than 3 μm/h could be obtained over surfaces of 300 cm2. By modifying the growth temperatures, various phases of thin film FeS2 (pyrite, marcasite, and a mixture of pyrite and marcasite) were successfully prepared.
Cisplatin and DNA repair in cancer chemotherapy

Cisplatin, a DNA-damaging agent, is one of the most widely used anticancer drugs. As with all members of this class of chemotherapeutic compounds, the clinical success of cisplatin is compromised if tumor cells become resistant by various mechanisms, including enhanced DNA repair. In addition to its role in resistance, DNA repair has been linked to the cytotoxic mechanism of cisplatin. DNA damaged by the drug has proved to be a valuable tool for exploring the details of the nucleotide excision repair pathway.
Is treatment with 6-mercaptopurine for colitis associated with the development of colorectal cancer?

Background Patients with ulcerative colitis and Crohn's colitis have an increased risk of colon cancer influenced by the duration, extent, and severity of disease. Surveillance colonoscopy serves to detect cancer and precancerous dysplasia at the earliest possible time. Reduction of inflammation should theoretically reduce the development of cancer. Immunosuppressives should do so, but there is a fear that indeed the risk of cancer might be increased with their use. Our study was conducted to determine whether a relationship exists between receiving treatment with 6-MP for ulcerative and Crohn's colitis and increasing or decreasing the incidence of colorectal cancer (CRC). Methods We conducted a single-center, retrospective cohort study of patients with long standing colitis (ulcerative and Crohn's) using the database of the senior investigator (B.I.K.). Two groups were matched based on their propensity to receive treatment with 6-MP; one group received 6-MP treatment, the other did not. Both groups were compared on the incidence of colon cancer. Results No significant differences existed between the two cohorts with regard to type of disease, duration, extent, age, and sex. Six out of 27 patients not on 6-MP and seven out of 27 patients on 6-MP developed CRC (P= 1). Conclusions We conclude that there is neither sufficient evidence currently to state that 6-MP is associated with an increased development of CRC, nor that it has a chemopreventive effect.
Phase randomness in the one-dimensional Anderson model

The probability distribution $P(\ensuremath{\nu})$ of the phase $\ensuremath{\nu}$ which determines the scaling properties of the dimensionless resistance $\frac{R}{T}$ is analyzed for the one-dimensional Anderson model with diagonal disorder. For weak disorder ($\frac{W}{V}\ensuremath{\ll}1$) and $E\ensuremath{\ne}0$ we find that $P(\ensuremath{\nu})$ is initially sharply peaked for short chains but becomes uniform over $2\ensuremath{\pi}$ as $N$ increases. Moreover, the length at which $P(\ensuremath{\nu})$ becomes uniform is found to be independent of $\frac{W}{V}$ (as long as $\frac{W}{V}\ensuremath{\ll}1$); instead it appears to depend only on the distance in energy from band center, i.e., on the extent to which the electron's wavelength is incommensurate with the lattice. Thus, unlike the disordered Kronig-Penny model, there is a phase randomness length, shorter than the localization length but longer than the lattice spacing. $P(\ensuremath{\nu})$ is also studied in the limit of large disorder and analytic expressions for the mean and variance of the inverse localization length are derived for weak and strong disorder. Our results suggest that uniform phase randomness is indeed a property of most disordered 10 systems in the limit of weak disorder.
Spectral domain-optical coherence tomography to detect localized retinal nerve fiber layer defects in glaucomatous eyes.

This study examines the ability of RTVue, Cirrus and Spectralis OCT Spectral domain-optical coherence tomographs (SD-OCT) to detect localized retinal nerve fiber layer defects in glaucomatous eyes. In this observational case series, four glaucoma patients (8 eyes) were selected from the University of California, San Diego Shiley Eye Center and the Diagnostic Innovations in Glaucoma Study (DIGS) based on the presence of documented localized RNFL defects in at least one eye confirmed by masked stereophotograph assessment. One RTVue 3D Disc scan, one RTVue NHM4 scan, one Cirrus Optic Disk Cube 200×200 scan and one Spectralis scan centered on the optic disc (15×15 scan angle, 768 A-scans x 73 B-scans) were obtained on all undilated eyes within a single session. Results were compared with those obtained from stereophotographs. In 6 eyes the presence of localized RNFL defects was detected by stereophotography. In general, by qualitatively evaluating the retinal thickness maps generated, all SD-OCT instruments examined were able to confirm the presence of localized glaucomatous structural damage seen on stereophotographs. This study confirms SD-OCT is a promising technology for glaucoma detection as it may assist clinicians identify the presence of localized glaucomatous structural damage.
THE DEVELOPMENT OF MORAL JUDGMENTS CONCERNING CAPITAL PUNISHMENT

Data from a 20-year longitudinal study of the development of moral judgment in American males indicate that the most mature stages evince moral condemnation of the death penalty. The authors conclude that American moral standards are evolving towards a view of execution as unjust punishment. They contend that a theory of punishment based on the highest stage of moral reasoning is more valid than lower-stage justifications for capital punishment, and that it provides a rational basis for asserting the immorality--and unconstitutionality--of capital punishment, irrespective of uncertainties as to the deterrent efficacy of the death penalty.
Compact Hybrid Si Microring Lasers

In this paper we review the recent progress in developing compact microring lasers on the hybrid silicon platform. A simplified self-aligned process is used to fabricate devices as small as 15 μm in diameter. The optically-pumped, continuous wave (cw) devices show low threshold carrier density, comparable to the carrier density to reach material transparency. In the electrically-pumped lasers, the short cavity length leads to the minimum laser threshold less than 5 mA in cw operation. The maximum cw lasing temperature is up to 65 °C. Detailed studies in threshold as a function of coupling coefficient and bus waveguide width are presented. Surface recombination at the dry-etched exposed interface is investigated qualitatively by studying the current-voltage characteristics. Ring resonator-based figures of merits including good spectral purity and large side-mode suppression ratio are demonstrated. Thermal impedance data is extracted from temperature-dependent spectral measurement, and buried oxide layer in silicon-on-insulator wafer is identified as the major thermal barrier to cause high thermal impedance for small-size devices. The demonstrated compact hybrid ring lasers have low power consumption, small footprint and dynamic performance. They are promising for Si-based optical interconnects and flip-flop applications.
Networks of Corporate Interlocking: 1962—1995

This paper documents the changing patterns of corporate interlocking among approximately 250 corporations across four time periods—1962, 1973, 1983, and 1995. By utilizing network analyses, we describe several attributes of the overall set of interlocking corporate directors in a period of increasing corporate concentration, economic globalization, and changing regulatory environments. Measures of network density are based on all corporations and are broken-down by the ties formed by single versus multiple interlocking directorates. Three measures of network centralization are based on complete sociomatricies in which all ties between corporations are non-directional and have been recorded as either present or absent. Finally, we report the number of cliques formed by minimum size across time. Measures of network density, centralization and the number of cliques all underscore that the network of corporate ties in 1995 is less dense, less concentrated, and contain few subgroups. Our analyses at the corpor...
A powers theory of modality: or, how I learned to stop worrying and reject possible worlds

Possible worlds, concrete or abstract as you like, are irrelevant to the truthmakers for modality—or so I shall argue in this paper. First, I present the neo-Humean picture of modality, and explain why those who accept it deny a common sense view of modality. Second, I present what I take to be the most pressing objection to the neo-Humean account, one that, I argue, applies equally well to any theory that grounds modality in possible worlds. Third, I present an alternative, properties-based theory of modality and explore several specific ways to flesh the general proposal out, including my favored version, the powers theory. And, fourth, I offer a powers semantics for counterfactuals that each version of the properties-based theory of modality can accept, mutatis mutandis. Together with a definition of possibility and necessity in terms of counterfactuals, the powers semantics of counterfactuals generates a semantics for modality that appeals to causal powers and not possible worlds.
CLN3 defines a novel antiapoptotic pathway operative in neurodegeneration and mediated by ceramide.

Juvenile neuronal ceroid lipofuscinosis or Batten disease (JNCL) is a neurodegenerative disorder characterized by blindness, seizures, cognitive decline and early death. Brain atrophy and retinitis pigmentosa ensue because of neuronal and photoreceptor apoptosis. The CLN3 gene defective in JNCL encodes a novel 438 amino acid protein. Most affected genes harbor a deletion resulting in a truncated protein. CLN3 overexpression in NT2 cells enhances growth, reverses growth inhibition induced by serum starvation and protects from apoptosis induced by vincristine, staurosporine, and etoposide but not from death caused by ceramide. CLN3 modulates endogenous and vincristine-activated ceramide, and therefore suppresses apoptosis by impacting generation of ceramide.
Material Spiraling in Stream Corridors: A Telescoping Ecosystem Model

Stream ecosystems consist of several subsystems that are spatially distributed concentrically, analogous to the elements of a simple telescope. Subsystems include the central surface stream, vertically and laterally arrayed saturated sediments (hyporheic and parafluvial zones), and the most distal element, the riparian zone. These zones are hydrologically connected; thus water and its dissolved and suspended load move through all of these subsystems as it flows downstream. In any given subsystem, chemical transformations result in a change in the quantity of materials in transport. Processing length is the length of subsystem required to “process” an amount of substrate equal to advective input. Long processing lengths reflect low rates of material cycling. Processing length provides the length dimension of each cylindrical element of the telescope and is specific to subsystem (for example, the surface stream), substrate (for instance, nitrate), and process (denitrification, for example). Disturbance causes processing length to increase. Processing length decreases during succession following disturbance. The whole stream-corridor ecosystem consists of several nested cylindrical elements that extend and retract, much as would a telescope, in response to disturbance regime. This telescoping ecosystem model (TEM) can improve understanding of material retention in running water systems; that is, their “nutrient filtration” capacity. We hypothesize that disturbance by flooding alters this capacity in proportion to both intensity of disturbance and to the relative effect of disturbance on each subsystem. We would expect more distal subsystems (for example, the riparian zone) to show the highest resistance to floods. In contrast, we predict that postflood recovery of functions such as material processing (that is, resilience) will be highest in central elements and decrease laterally. Resistance and resilience of subsystems are thus both inversely correlated and spatially separated. We further hypothesize that cross-linkages between adjacent subsystems will enhance resilience of the system as a whole. Whole-ecosystem retention, transformation, and transport are thus viewed as a function of subsystem extent, lateral and vertical linkage, and disturbance regime.
A view on future directions for macromolecular science

Polymer science has in recent years become one of the most dynamic components of materials science [1, 2, 3], which in turn is a powerful bridge between basic science and advanced technology. The National Science Foundation (NSF) has periodically reviewed the status of polymer science and engineering to ensure that this important field continues to develop in an appropriate fashion. Thus, the NSF asked the U.S. National Academy of Sciences on two previous occasions, in 1981 and again in 1994, to assess progress in polymer science and engineering and to make recommendations for the future. The resulting reports [4, 5] received wide circulation in many countries and helped to focus attention on the changing nature of the polymer field. A clear trend that was identified in these reports is the greater commonality with other materials-related disciplines [1-3] and with the biological sciences [1-5]. Increasingly, these changes are being reflected in the programs of government agencies funding polymer research which are tending to be broader and more interdisciplinary than in the past.
Hydrostatic versus Nonhydrostatic Euler-Equation Modeling of Nonlinear Internal Waves

Basin-scale internal waves are inherently nonhydrostatic; however, they are frequently resolved features in three-dimensional hydrostatic lake and coastal ocean models. Comparison of hydrostatic and nonhydrostatic formulations of the Centre for Water Research Estuary and Lake Computer Model provides insight into the similarities and differences between these representations of internal waves. Comparisons to prior laboratory experiments are used to demonstrate the expected wave evolution. The hydrostatic model cannot replicate basin-scale wave degeneration into a solitary wave train, whereas a nonhydrostatic model does represent the downscaling of energy. However, the hydrostatic model produces a nonlinear traveling borelike feature that has similarities to the mean evolution of the nonhydrostatic wave.
FUNCTIONAL PEARL Pickler combinators

The tedium of writing pickling and unpickling functions by hand is relieved using a combinator library similar in spirit to the well-known parser combinators. Picklers for primitive types are combined to support tupling, alternation, recursion, and structure sharing. Code is presented in Haskell; an alternative implementation in ML is discussed.
Development of antisickling compounds that chemically modify hemoglobin S specifically within the 2,3-diphosphoglycerate binding site.

Abstract In this paper we describe a class of affinity reagents that react specifically with hemoglobin S at the 2,3-diphosphoglycerate binding site and effectively disrupt the sickling process. The prototype of these compounds is the bifunctional acylating agent bis(3,5-dibromosalicyl) fumarate. Previously it was shown that this compound reacts selectively with oxyhemoglobin to cross-link the β chains of the tetramer ( Walder et al. , 1979 a ). The site of cross-linking has now been established by X-ray crystallographic studies to be from Lys82 β 1 to Lys82 β 2 , spanning the DPG ‡ binding site. The oxygen binding properties of the cross-linked hemoglobin are very similar to those of native hemoglobin A in the absence of DPG. However, in the presence of DPG, the oxygen affinity of the cross-linked hemoglobin is increased due to the blockade of the DPG site by the interchain bridge. This effect may indirectly interfere with the sickling process in vivo . More importantly the cross-link modification directly inhibits the polymerization of deoxyhemoglobin S. The solubility of the cross-linked derivative is increased by approximately 35% relative to that of native deoxyhemoglobin S. The X-ray crystallographic studies reveal that the cross-link strongly perturbs the acceptor site for Val6β in the lateral contact between molecules of deoxyhemoglobin S within the double strand of the sickle cell fiber. Our current hypothesis is that this structural perturbation weakens the lateral contact and is responsible for the observed increase in solubility. Due to the hydrophobic properties of the halogen substituents bis(3,5-dibromosalicyl) fumarate is able to traverse the red-cell membrane and, therefore, may be active in vivo . These studies provide the basis for further design and development of affinity reagents directed to the DPG binding site that may prove useful in the clinical management of sickle cell disease.
Breaking the virtual barrier: real-time interactions with spiking neural models.

The unrivaled complexity of the human brain has driven many researchers towards larger and more detailed models of neural processing. Often run on remote high-performance computing architectures, these simulations can be difficult to access at significant levels of detail. In general, after simulations are completed, the results are analyzed off-line. This paradigm can make development of large models exploring complex and time-consuming simulations, such as learning or persistent neural activity, very difficult. Presented here is a toolkit, dubbed NCSTools, used for real-time interactions with large-scale neural simulations run on the NeoCortical Simulator (NCS). NCSTools is a remote monitoring package that provides a number of options for input, output, and modification of a running simulation. Input stimuli can be voltage, current, or probabilities of firing. For output there are several options for both collection and visualization. Information can be compiled as cell voltages, currents, synaptic efficacy, or spike-events within a population. The model information flow can be altered dynamically by NCSTools, as can model parameters such as spike timing dependent plasticity, long-term potentiation, and long-term depression. Additionally, NCSTools includes a simple network server interface that supports multiple connections from different client programs. These programs can be used for control of defined NCSTools actions, monitoring specific neural information, or synchronization with the simulation. This allows dynamic construction of distributed neural processing systems. Recently, NCSTools was utilized for real-time interactions between a Hebbian-STDP enabled neural simulation, a virtual robotic interface, and a human participant. Presented in Figure ​Figure11 is a diagrammatic view of the learning scenario. Processed visual information, in this case the color of a card, was sent to NCSTools. The information was then converted and sent to the neural simulation running on a remote computing cluster. As the simulation proceeded, the competing neural areas of visual and motor processing were monitored by NCSTools. The resulting activity was correlated with a pointing action to one of two colored balls that matched the color presented. After the robot completed pointing, NCSTools would provide the human interacting with the simulation an interface to reward the robot if it pointed to the correct ball. The reward, analogous to a dopaminergic increase, resulted in an STDP dependent increase in synaptic efficacy. Figure 1 Diagram of a Virtual Neuro-Robotic Interface constructed around NCSTools. The ability to monitor and modify simulations in real-time can be incredibly useful in large-scale spiking-network research. More importantly, this demonstrates another step towards multi-scale visualization of neural simulations in a virtual environment.
Self-Diffusivity Estimation by Molecular Dynamics

Reference fluid simulations are combined with a mean field correction for attractive effects to achieve a correlation for diffusivity of unentangled species over a wide range of density, temperature, and molecular weight. Reference fluids are composed of hard united atom descriptions including branching, rings, bond angles, and chain length. The molecular model is consistent with the one studied previously by thermodynamic perturbation theory. Molecular simulations of methane through triacontane provide the basis for a diffusivity correlation of reference n-alkanes from zero density to the glass transition. The low density limit is shown to exhibit Rouse scaling, contradicting typical hard sphere models. Experimental data for n-alkanes ranging from methane to hexadecane are used to correlate the correction for attractive forces and for the softness of the potential function. The average deviation is 8.6% for 657 data points. Reference simulations of nonalkanes show that the reference simulations can be in...
Catalytic reaction and fouling effects on intraparticle diffusion

A pellet of gamma alumina with a unimodal pore structure and a mean pore radius of 47 A was exposed to cycles involving counterdiffusing butenes and helium, counterdiffusing nitrogen and helium, and varying catalyst treatments. When butenes were present and the catalyst was active, the isomerization of 1-butene to cis- and trans-2-butene occurred. In the nonreacting nitrogen-helium system, the helium diffusion rate was about 11% less through an air-fouled catalyst than through the catalyst immediately after activation; it was about 13% less through the catalyst when butene-fouled than through the freshly activated catalyst. In the reacting butenes-helium system, the helium diffusion rate was about 17% less through the air-fouled catalyst than through the freshly activated catalyst; it was about 32% less through the butene-fouled catalyst than through the freshly activated catalyst. Only in the freshly activated catalyst was the helium diffusion rate in the reacting system predictable from the helium diffusion rate in the nonreacting system. It is proposed that the diffusion behavior differences between the reacting and nonreacting systems result from differences in adsorption characteristics of the fouled and active surfaces. The differences in adsorption characteristics in turn may cause different degrees of pore blockage. The experimental temperature was 154 °C, and the pressure range was 1–2.5 atm for the butenes-helium system, and 1–13 atm for the nitrogen-helium system.
Protein Phase Behavior in Aqueous Solutions: Crystallization, Liquid-Liquid Phase Separation, Gels, and Aggregates☆

The aggregates and gels commonly observed during protein crystallization have generally been considered disordered phases without further characterization. Here their physical nature is addressed by investigating protein salting-out in ammonium sulfate and sodium chloride for six proteins (ovalbumin, ribonuclease A, soybean trypsin inhibitor, lysozyme, and β-lactoglobulin A and B) at 4°C, 23°C, and 37°C. When interpreted within the framework of a theoretical phase diagram obtained for colloidal particles displaying short-range attractive interactions, the results show that the formation of aggregates can be interpreted theoretically in terms of a gas-liquid phase separation for aggregates that are amorphous or gel-like. A notable additional feature is the existence of a second aggregation line observed for both ovalbumin and ribonuclease A in ammonium sulfate, interpreted theoretically as the spinodal. Further investigation of ovalbumin and lysozyme reveals that the formation of aggregates can be interpreted, in light of theoretical results from mode-coupling theory, as a kinetically trapped state or a gel phase that occurs through the intermediate of a gas-liquid phase separation. Despite the limitations of simple theoretical models of short-range attractive interactions, such as their inability to reproduce the effect of temperature, they provide a framework useful to describe the main features of protein phase behavior.
Heat Shock Inhibits Activation of NF-κB in the Absence of Heat Shock Factor-1

Abstract The heat shock response is known to inhibit NF-κB activation and NF-κB-dependent gene expression. Herein we determined if cells lacking heat shock factor-1 (HSF-1), the major transcription factor regulating heat shock protein gene expression, have an altered ability to modulate NF-κB activation. Embryonic fibroblasts from HSF-1-null mutant mice (HSF-1−/− cells) had a drastically reduced ability to express heat shock protein-70 in response to heat shock, compared to embryonic fibroblasts from wild-type mice (HSF+/+ cells). There was no difference, however, in the ability of heat shock to inhibit TNFα-mediated NF-κB activation, IκBα degradation, IκB kinase activation, and macrophage chemotactic protein-1 expression in the HSF-1−/− cells compared to the HSF-1+/+ cells. These data demonstrate that heat shock inhibits activation of the NF-κB/IκBα pathway and NF-κB-dependent gene expression in the absence of an intact heat shock response.
Mechanisms of carbon nanotube aggregation and the reversion of carbon nanotube aggregates in aqueous medium.

Single-walled carbon nanotubes (SWCNTs) dispersed in aqueous medium have many potential applications in chemistry, biology, and medicine. Reversible aggregation of SWCNTs dispersed in water has been frequently reported, but the mechanisms behind are not well understood. Here we show that SWCNTs dispersed into aqueous medium assisted by various charged molecules can be reversibly aggregated by a variety of electrolytes with two distinct mechanisms. Direct binding of counterions to SWCNTs leads to aggregation when the surface charge is neutralized from 74 to 86%. This aggregation is driven by electrostatic instead of van der Waals interactions, thus showing similarity to that of DNA condensation induced by multivalent cations. Sequestration of counterions by chelating reagents leads to the redispersion of SWCNT aggregates. In contrast to various metal ions, polyelectrolytes have the unique ability to induce SWCNT aggregation by bridging between individual SWCNTs. Aggregation through the latter mechanism can...
Offline preemptive scheduling of power demands to minimize peak power in smart grids

We consider the scheduling of flexible electric loads in a smart grid so as to minimize peak power demand. Specifically, we focus on the case when the loads are preemptable, their power requirement and duration are known in advance, and they have the same earliest start time and the same deadline. Our main results are (a) when power requests are scheduled preemptively, the peak power demand can be reduced by up to 50% relative to when these requests are scheduled non-preemptively, (b) preemptive scheduling to minimize peak power demand is NP-hard, (c) schedules with minimum peak power demand may be constructed using integer linear programming, and (d) the next-fit decreasing height heuristic may be used to quickly obtain schedules whose peak power demand is at most two times that of the optimal schedule when all jobs are preemptable and at most three times the optimal when only some jobs are preemptable. Experimental results for the integer linear program and the heuristic are also presented. Our experiments indicate a significant reduction in peak power when preemption is exploited. For example, on our data sets recharging collections of electric and plug-in hybrid vehicles without preemption required up to 26% more peak power than when this was done preemptively.