Miracle-dz/UniFAR-FTUs huggingface dataset:
Radiopaque Polymeric Nanoparticles for X‐Ray Medical Imaging

In this chapter we describe the synthesis of iodinated homopolymeric radiopaque nanoparticles of 28.9 ± 6.3 nm diameter prepared by emulsion polymerization of 2-methacryloyloxyethyl(2,3,5-triiodobenzoate) (MAOETIB). These nanoparticles dispersed in aqueous continuous phase tend to agglomerate in concentration above 0.3%. The agglomeration rate increases as the concentration of the nanoparticles in the aqueous phase rises, and prevents thereby the in vivo use as contrast agent for medical X-ray imaging. This limitation was solved by synthesis of copolymeric iodinated nanoparticles of 25.5 ± 4.2 nm diameter, via emulsion copolymerization of MAOETIB in the presence of a low concentration of glycidyl methacrylate (GMA). The surface of the resulting copolymeric nanoparticles is far more hydrophilic than that of the polyMAOETIB (PMAOETIB) nanoparticles. Therefore, P(MAOETIB-GMA) nanoparticles are significantly more stable against agglomeration in aqueous continuous phase. After intravenous injection of the P(MAOETIB-GMA) nanoparticles dispersed in 5% dextrose aqueous solution into rats and mice (including those with a liver cancer model) CT-imaging revealed a significant enhanced visibility of the blood pool for 30 min after injection. Later, lymph nodes, liver and spleen strongly enhanced due to nanoparticles uptake by the reticuloendothelial system. This favorably enabled the differentiation of cancerous from healthy liver tissue and suggests our particles for tumor imaging in liver and lymph nodes. Keywords: iodinated particles; contrast agents; core–shell nanoparticles; microparticles; computed tomography; X-ray
Psychosocial Stress and the Duration of Cocaine Use in Non‐treatment Seeking Individuals with Cocaine Dependence

The aim of this study was to explore a potential link between psychosocial stress and cocaine dependence among 36 non–treatment‐seeking individuals enrolled in a brain imaging protocol. Stress was assessed using computerized multidimensional instruments, including the Profile of Mood States (POMS) and Speilberger State‐Trait Anxiety Inventory (STAI). Additional clinical assessments employed were the Addiction Severity Index and the Hamilton Rating Scale for Depression (HRSD). Based on the median POMS' tension‐anxiety scale score the entire sample was divided into two groups, those with high and low levels of stress. The two groups (n = 16 and 20) were similar in terms of age, gender distribution, and severity of addiction. Compared with the low stress group, high‐stress individuals displayed significantly longer duration of cocaine use, greater POMS, STAI‐state, STAI‐Trait, and HRSD scores. Our results replicate those of prior reports implicating stress in the course of cocaine dependence and extend these prior findings by 1) including a new subject population of non–treatment‐seekers and 2) by suggesting that the stress‐cocaine link may be generalizable to psychosocial stress and negative affective states defined by POMS, STAI, and HRSD scores.
Evaluating policies and mechanisms to support distributed real‐time applications with CORBA

To be an effective platform for performance‐sensitive real‐time systems, commodity‐off‐the‐shelf (COTS) distributed object computing (DOC) middleware must support application quality of service (QoS) requirements end‐to‐end. However, conventional COTS DOC middleware does not provide this support, which makes it unsuited for applications with stringent latency, determinism, and priority preservation requirements. It is essential, therefore, to develop standards‐based, COTS DOC middleware that permits the specification, allocation, and enforcement of application QoS requirements end‐to‐end.
Behavioral/systems/cognitive Functional Imaging, Spatial Reconstruction, and Biophysical Analysis of a Respiratory Motor Circuit Isolated in Vitro

We combined real-time calcium-based neural activity imaging with whole-cell patch-clamp recording techniques to map the spatial organization and analyze electrophysiological properties of respiratory neurons forming the circuit transmitting rhythmic drive from the pre-Bötzinger complex (pre-BötC) through premotoneurons to hypoglossal (XII) motoneurons. Inspiratory pre-BötC neurons, XII premotoneurons (preMNs), and XII motoneurons (MNs) were retrogradely labeled with Ca 2ϩ-sensitive dye in neonatal rat in vitro brainstem slices. PreMN cell bodies were arrayed dorsomedially to pre-BötC neurons with little spatial overlap; axonal projections to MNs were ipsilateral. Inspiratory MNs were distributed in dorsal and ventral subnuclei of XII. Voltage-clamp recordings revealed that two currents, persistent sodium current (NaP) and K ϩ-dominated leak current (Leak), primarily contribute to preMN/MN subthreshold current–voltage relationships. NaP or Leak conductance densities in preMNs and MNs were not significantly different. We quantified preMN and MN action potential time course and spike frequency– current (f–I) relationships and found no significant differences in repetitive spiking dynamics, steady-state f–I gains, and afterpolarizing potentials. Rhythmic synaptic drive current densities were similar in preMNs and MNs. Our results indicate that, despite topographic and morphological differences, preMNs and MNs have some common intrinsic membrane, synaptic integration, and spiking properties that we postulate ensure fidelity of inspiratory drive transmission and conversion of synaptic drive into (pre)motor output. There also appears to be a common architectonic organization for some respiratory drive transmission circuits whereby many preMNs are spatially segregated from pre-BötC rhythm-generating neurons, which we hypothesize may facilitate downstream integration of convergent inputs for premotor pattern formation.
DNA Algorithms for Petri Net Modeling

A defining moment for DNA computing was Adleman’s (1) fundamental contribution in which he demonstrated the potential of this novel computing paradigm by solving an instance of the Hamiltonian Path Problem in theoretical as well as practical terms. Since then, DNA computing has been proposed and tested in numerous areas including, finite automata (14), machine learning (12), relational database modeling (13), and, of course, solving computationally expensive problems (e.g., (6), (2), and (3)). This paper investigates Petri nets as a novel DNA computing application area. The paper provides brief introductions to Petri nets and DNA computing and demonstrates via an example algorithm how the DNA computing paradigm can be successfully applied for Petri net modeling. It is necessary to mention that the the paper does not include simulations of the work on a silicon computer or practical, experimental work involving real-life DNA material. Rather, the paper is of theoretical value only and largely neglects aspects of practical realizations of the proposed work (e.g., error rates). In a sense, the algorithm presented in this work is a high-level description for a program. The program/algorithm describes a sequence of biochemical events and these events are meant to execute/run in a biochemical environment—a DNA computer. Once this sequence of events is executed correctly, which is not a trivial bioengineering task, the result is available as/in the form of DNA strings. In order to extract the outcome of the algorithm, it is necessary to readout these strings and decode their information, but this is similar to reading out a sequence in a human genome (e.g., identifying a proteinencoding gene). Perhaps, one could think of the following analogy. It is possible to add and subtract two numbers with an electronic calculator, but the same thing can be done with an abacus (the abacus made of wood). Both procedures produce the same result but use entirely different machines and very different algorithms. Similarly, a DNA computer operates in a biochemical environment, executes real biochemical events, and uses real (usually synthetically modified) DNA. In the remainder, Section 2 provides a brief introduction to Petri nets, their design, and working. Section 3 starts with a summary on DNA computing and then describes a DNA algorithm for a Petri net example the paper uses as a run-through vehicle to explain the presented work. Section 4 provides a discussion and Section 5 ends the paper with a summary.
The Software-Cache Connection

This paper describes an adaptation of standard Fourier analysis techniques to the study of software-cache interactions. The cache is viewed as a "black box" boolean signal generator, where "ones" correspond to cache misses and "zeros" correspond to cache hits. The spectrum of this time sequence is used to study the dynamic characteristics of complex systems and workloads with minimal a priori knowledge of their internal organization. Line spectra identify tight loops accessing regular data structures, while the overall spectral density reveals the general structure of instruction localities.
Dislocation-drag contribution to high-rate plastic deformation in shock-loaded tantalum

Time‐resolved plastic waves in plate‐impact experiments give information on the relationship between applied shear stress and plastic strain rate at low plastic strain. This information is essentially different from that obtained at intermediate strain rates using Hopkins on bar techniques, because in the former case the material deformation state is driven briefly into the regime dominated by dislocation drag rather than thermal activation. Two VISAR records of the particle velocity at the tantalum/sapphire (window) interface are obtained for symmetric impact producing peak in situ longitudinal stresses of approximately 75 kbar and 111 kbar. The risetimes of the plastic waves are about 100 ns and 60 ns, respectively, with peak strain rates of about 2×105/s and 1×106/s, respectively, as determined by weak‐shock analysis [Wallace, Phys. Rev. B 22, 1487 (1980), and Tonks, Los Alamos DataShoP Report LA‐12068‐MS (1991)]. These data show a much stronger dependence of plastic strain rate on applied shear stress.
Hierarchical Parallel Matrix Multiplication on Large-Scale Distributed Memory Platforms

Matrix multiplication is a very important computation kernel both in its own right as a building block of many scientific applications and as a popular representative for other scientific applications. Cannon's algorithm which dates back to 1969 was the first efficient algorithm for parallel matrix multiplication providing theoretically optimal communication cost. However this algorithm requires a square number of processors. In the mid-1990s, the SUMMA algorithm was introduced. SUMMA overcomes the shortcomings of Cannon's algorithm as it can be used on a nonsquare number of processors as well. Since then the number of processors in HPC platforms has increased by two orders of magnitude making the contribution of communication in the overall execution time more significant. Therefore, the state of the art parallel matrix multiplication algorithms should be revisited to reduce the communication cost further. This paper introduces a new parallel matrix multiplication algorithm, Hierarchical SUMMA (HSUMMA), which is a redesign of SUMMA. Our algorithm reduces the communication cost of SUMMA by introducing a two-level virtual hierarchy into the two-dimensional arrangement of processors. Experiments on an IBM Blue Gene/P demonstrate the reduction of communication cost up to 2.08 times on 2048 cores and up to 5.89 times on 16384 cores.
Northern Peatlands: Role in the Carbon Cycle and Probable Responses to Climatic Warming.

Boreal and subarctic peatlands comprise a carbon pool of 455 Pg that has accumulated during the postglacial period at an average net rate of 0.096 Pg/yr (1 Pg = 1015 g). Using Clymo's (1984) model, the current rate is estimated at 0.076 Pg/yr. Longterm drainage of these peatlands is estimated to be causing the oxidation to CO2 of a little more than 0.0085 Pg/yr, with conbustion of fuel peat adding °0.026 Pg/yr. Emissions of CH4 are estimated to release ° 0.046 Pg of carbon annually. Uncertainties beset estimates of both stocks and fluxes, particularly with regard to Soviet peatlands. The influence of water table alterations upon fluxes of both CO2 and CH4 is in great need of investigation over a wide range of peatland environments, especially in regions where permafrost melting, thermokarst erosion, and the development of thaw lakes are likely results of climatic warming. The role of fire in the carbon cycle of peatlands also deserves increased attention. Finally, satellite-monitoring of the abundance of open water in the peatlands of the West Siberian Plain and the Hudson/James Bay Lowland is suggested as a likely method of detecting early effects of climatic warming upon boreal and subarctic peatlands.
A sequence of generalized coordinate systems based on Voronoi diagrams and its application to interpolation

This paper presents a general framework for constructing a variety of multi-dimensional interpolants based on Voronoi diagrams. This framework includes previously known methods such as Sibson's interpolant and Laplace's interpolant; moreover it contains infinitely many new interpolants. Computational experiments suggest that the smoothness can be improved by the proposed generalization. In addition, this framework also includes the piecewise linear interpolant over the Delaunay triangulation, which is a finite-element interpolant. This fact suggests that already established techniques in the finite element method might be brought into the research of the Voronoi-based approach. Hence this framework gives a new and promising direction of research on interpolation based on Voronoi diagrams.
Embryonic Stem Cell Differentiation to Cardiomyocytes on Nanostructured Scaffolds for Myocardial Tissue Regeneration

With recent advances in developmental and stem cell biology, the application of stem cells in tissue engineering has received great attention and designing of suitable scaffolds to support cell growth, differentiation, and functional tissue organization are advancing toward effective tissue regeneration. Regeneration of the infarct myocardium after myocardial infarction (MI), which is caused by the abrupt occlusion of one or more of the coronary arteries in the heart is one of the most demanding aspects in tissue engineering. Embryonic stem cells (ESCs) can differentiate into many cell types and has been considered as a cell source for cardiac regeneration. In this regard, nanofibrous scaffolds received great attention in tissue engineering field due to their similarity in morphology to native extracellular matrix (ECM) and various scaffolds have been studied as cardiac patches over the previous years. In this study poly (ε-caprolactone) (PCL)/gelatin nanofibrous scaffolds were fabricated by electrospinning and embroyonic bodies (EBs) were formed using ESCs seeded on the nanofibrous scaffolds. SEM images revealed cell outgrowth from EBs and the spreading of cells over the nanofibrous scaffolds were observed. Immunocytochemistry results showed the cellular expression of cardiac proteins, namely α-actinin and connexin 43 on the nanofibrous scaffolds indicating the differentiation of EBs to cardiomyocytes. Results of our study showed that PCL/gelatin nanofibrous scaffolds can act as a promising substrate for differentiation of EBs to cardiomyocytes and could be applied for cardiac tissue engineering.
Laboratory Performance of Pervious Concrete Subjected to Deicing Salts and Freeze-Thaw

Significant research and development have occurred for pervious concrete, but its acceptance in cold climates is still limited. Vulnerability to freeze-thaw and salt exposure has led to uncertainty about its long-term performance. Additionally, the current standardized freeze-thaw testing procedure is not recommended for pervious concrete, as it is not representative of field conditions. This study employed testing processes that are more representative of field conditions to determine the effects of the inclusion of sand as a fine aggregate; fly ash, slag and silica fume as cementitious alternatives, and construction practices on freeze-thaw durability and deicing salts exposure of pervious concrete. The use of pervious concrete itself is considered a best management practice in stormwater management; possibility of substituting cement with a waste product such as fly ash, slag and silica fume promotes sustainability even further.
Modeling of mechanical dysfunction in regional stunned myocardium of the left ventricle

Reversible mechanical dysfunction of the myocardium after a single or multiple episode(s) of coronary artery occlusion has been observed in previous studies and is termed myocardial stunning. The hypothesis that stunning could be represented by a decrease in maximum available muscle force in the stunned region was examined by means of a mathematical model that incorporates series viscoelastic elements. A canine experimental model was also employed to demonstrate depressed contractility and a consistent delay of shortening in the stunned region. The mechanical model of the left ventricle was designed to include a normal and stunned region, for which the stunned region was allowed to have variable size. Each region consisted of a volume and time dependent force generator in parallel with a passive elastic force element. The passive elastic element was placed in series with a constant viscosity component and a series elastic component. The model was solved by means of a computer. Passive and active properties of each region could be altered independently. The typical regional measures of muscle performance such as percent shortening, percent bulge, percent thickening, delay of shortening, percent increase in end-diastolic length and other hemodynamic measures were computed. These results were similar to those observed in animal models of stunning. In addition, a nearly linear relationship with end-diastolic length and delay of shortening was predicted by the model. It was concluded that a decrease in the peak isovolumic elastance and augmentation of viscosity effect of creep during stunning can explain mechanical abnormalities of stunned myocardium.
Host Heterogeneity in Susceptibility and Disease Dynamics: Tests of a Mathematical Model

Most mathematical models of disease assume that transmission is linearly dependent on the densities of host and pathogen. Recent data for animal diseases, however, have cast doubt on this assumption, without assessing the usefulness of alternative models. In this article, we use a combination of laboratory dose‐response experiments, field transmission experiments, and observations of naturally occurring populations to show that virus transmission in gypsy moths is a nonlinear function of virus density, apparently because of heterogeneity among individual gypsy moth larvae in their susceptibility to the virus. Dose‐response experiments showed that larvae from a laboratory colony of gypsy moths are substantially less heterogeneous in their susceptibility to the virus than are larvae from feral populations, and field experiments showed that there is a more strongly nonlinear relationship between transmission and virus density for feral larvae than for lab larvae. This nonlinearity in transmission changes the dynamics of the virus in natural populations so that a model incorporating host heterogeneity in susceptibility to the virus gives a much better fit to data on virus dynamics from large‐scale field plots than does a classical model that ignores host heterogeneity. Our results suggest that heterogeneity among individuals has important effects on the dynamics of disease in insects at several spatial and temporal scales and that heterogeneity in susceptibility may be of general importance in the ecology of disease.
Cocaine increases serotonergic activity in the hippocampus and nucleus accumbens in vivo: 5‐HT1a‐receptor antagonism blocks behavioral but potentiates serotonergic activation

The hippocampus is an important mediator of learning and reinforcement, but its role in cocaine effects has received little attention. Neuronal activity in the hippocampus and the nucleus accumbens (Nac) depend on serotonergic (5‐HT) transmission. Here we describe for the first time a cocaine‐induced increase in 5‐HT concentration in the hippocampus and the Nac parallel to behavioral activation. In addition, pretreatment with the 5‐HT1A‐receptor antagonist WAY 100635 blocked the behavioral activation after cocaine while potentiating the 5‐HT increase in the hippocampus and the Nac. In vivo microdialysis was used in behaving rats to measure extracellular concentration of 5‐HT in the hippocampus and the Nac. Four groups of animals received one of the following drug combinations: WAY 100635 (0.4 mg/kg) and cocaine (10 mg/kg), saline and cocaine (10 mg/kg), WAY 100635 (0.4 mg/kg) and saline, or saline and saline. The injections were administered i.p. and spaced 30 min apart. It was found that 1. ) cocaine, at a dose that activates behavior, increases 5‐HT levels in the hippocampus and in the Nac, and 2. ) 5‐HT1A‐receptor antagonism can cause a dissociation of the hippocampal and Nac 5‐HT activity from behavioral activation after cocaine. These results are discussed within the framework of the hippocampal‐accumbens projection and its contribution to behavioral activity. They suggest that the hippocampus may have a role in mediating the behavioral and neurochemical effects of cocaine. Synapse 45:67–77, 2002. © 2002 Wiley‐Liss, Inc.
Catching heuristics are optimal control policies

Two seemingly contradictory theories attempt to explain how humans move to intercept an airborne ball. One theory posits that humans predict the ball trajectory to optimally plan future actions; the other claims that, instead of performing such complicated computations, humans employ heuristics to reactively choose appropriate actions based on immediate visual feedback. In this paper, we show that interception strategies appearing to be heuristics can be understood as computational solutions to the optimal control problem faced by a ball-catching agent acting under uncertainty. Modeling catching as a continuous partially observable Markov decision process and employing stochastic optimal control theory, we discover that the four main heuristics described in the literature are optimal solutions if the catcher has sufficient time to continuously visually track the ball. Specifically, by varying model parameters such as noise, time to ground contact, and perceptual latency, we show that different strategies arise under different circumstances. The catcher's policy switches between generating reactive and predictive behavior based on the ratio of system to observation noise and the ratio between reaction time and task duration. Thus, we provide a rational account of human ball-catching behavior and a unifying explanation for seemingly contradictory theories of target interception on the basis of stochastic optimal control.