cssi/SciSciGPT-SciSciNet huggingface dataset:
Deformation nanomechanics and dislocation quantification at the atomic scale in nanocrystalline magnesium

Abstract Classical molecular dynamics (MD) simulation method is employed to study the uniaxial tensile deformation of nanocrystalline magnesium (Mg) of varying grain size levels. The mean grain size of the sample is varied from 6.4 nm to 45 nm, with each sample containing about 43 million atoms in the modeling system. The deformation nanomechanics reveals two distinct deformation mechanisms. For larger grain-sized samples, dislocation dominated deformation is observed while, in smaller grain-sized samples, grain boundary-based mechanisms such as grain boundary sliding, grain boundary rotation are observed. The transition of normal and inverse Hall–Petch relation occurs at around 10 nm. Dislocation density quantification shows that the dislocation density in the sample drastically reduces with decreasing grain size. Elastic modulus of nanocrystalline Mg with mean grain size above 20 nm remains comparable to that of the coarse-grained polycrystalline bulk, followed by a rapid reduction below that grain size. The present work reveals the nanomechanics of nanocrystalline Mg, facilitating the design and development of Mg-based nanostructured alloys with superior mechanical properties.
A Slimy Business: the Future of Fish Skin Microbiome Studies

Fish skin contains a mucosal microbiome for the largest and oldest group of vertebrates, a location ideal for microbial community ecology and practical applications in agriculture and veterinary medicine. These selective microbiomes are dominated by Proteobacteria, with compositions different from the surrounding water. Core taxa are a small percentage of those present and are currently functionally uncharacterized. Methods for skin sampling, DNA extraction and amplification, and sequence data processing are highly varied across the field, and reanalysis of recent studies using a consistent pipeline revealed that some conclusions did change in statistical significance. Further, the 16S gene sequencing approaches lack quantitation of microbes and copy number adjustment. Thus, consistency in the field is a serious limitation in comparing across studies. The most significant area for future study, requiring metagenomic and metabolomics data, is the biochemical pathways and functions within the microbiome community, the interactions between members, and the resulting effects on fish host health being linked to specific nutrients and microbial species. Genes linked to skin colonization, such as those for attachment or mucin degradation, need to be uncovered and explored. Skin immunity factors need to be directly linked to microbiome composition and individual taxa. The basic foundation has been laid, and many exciting future discoveries remain.
Legal Writing for the Real World: A Practical Guide to Success

One of the most significant complaints among practicing attorneys is that newly admitted lawyers are not effective writers. Many young attorneys also express concern that their law school experience did not adequately prepare them to be good legal writers. This Article is designed to bridge the gap between the law school classroom and the law firm experience. In so doing, this Article is more practical rather than pedagogical, based on experience rather than theory, and founded upon “real-world” examples rather than abstract constructs.
H 2 RSPET: a 0.5 mm resolution high-sensitivity small-animal PET scanner, a simulation study

With the goal of developing a total-body small-animal PET system with a high spatial resolution of ~ 0.5 mm and a high sensitivity > 10% for mouse/rat studies, we simulated four scanners using the graphical processing unit (GPU)-based Monte Carlo simulation package (gPET) and compared their performance in terms of spatial resolution and sensitivity. We also investigated the effect of depth-of-interaction (DOI) resolution on the spatial resolution. All the scanners are built upon 128 DOI encoding dual-ended readout detectors with lutetium yttrium oxyorthosilicate (LYSO) arrays arranged in 8 detector rings. The solid angle coverage of the four scanners are all ~0.85 steradians. Each LYSO element has a cross-section of 0.44 × 0.44 mm2and the pitch size of the LYSO arrays are all 0.5 mm. The four scanners can be divided into two groups: (1) H2RS110-C10 and H2RS110-C20 with 40 × 40 LYSO arrays, a ring diameter of 110 mm and axial length of 167 mm, and (2) H2RS160-C10 and H2RS160-C20 with 60 × 60 LYSO arrays, a diameter of 160 mm and axial length of 254 mm. C10 and C20 denote the crystal thickness of 10 and 20 mm, respectively. The simulation results show that all scanners have a spatial resolution better than 0.5 mm at the center of the field-of-view (FOV). The radial resolution strongly depends on the DOI resolution and radial offset, but not the axial resolution and tangential resolution. Comparing the C10 and C20 designs, the former provides better resolution, especially at positions away from the center of the FOV, whereas the latter has 2x higher sensitivity (~10% vs. ~20%). This simulation study provides evidence that the 110 mm systems are a good choice for total-body mouse studies at a lower cost, whereas the 160 mm systems are suited for both total-body mouse and rat studies.
Word-Level Multi-Fix Rectifiability of Finite Field Arithmetic Circuits

Deciding whether a faulty circuit can be rectified at a given set of nets to match its intended specification constitutes a critical problem in post-verification debugging and rectification. Contemporary approaches which utilize Boolean SAT and Craig Interpolation techniques are infeasible in proving the rectifiability of arithmetic circuits. This paper presents a novel approach using symbolic computer algebra to prove the rectifiability of a faulty finite field arithmetic circuit at a given set of m nets. Our approach uses a word-level polynomial model and an application of a Grobner basis decision procedure. The finite fields corresponding to the datapath word-length (n) and the patch word-length (m) may not be compatible. We make new mathematical and algorithmic contributions which resolve this disparity by modeling the problem in an appropriate composite field. Experiments demonstrate the efficacy of our word-level approach to ascertain multi-fix rectifiability compared to contemporary approaches.
39 Using artificial intelligence to analyze horse gait parameters for genomics research in musculoskeletal traits

Arguably the most important factors considered when assessing elite performance horses, traits of “lameness susceptibility” and “gait quality” lack objective and quantitative measures. Popular qualitative approaches to determine lameness or gait quality do not provide accurate measures amenable to genetic study, nor can producers easily apply them. However, digital video analysis of gait utilizing recently developed artificial intelligence based approaches holds significant promise to meet these industry needs. It also provides quantitative endophenotypes, the comparison of behavior to phenotypes through genetic correlation, with sufficient precision for genome-wide association studies. Here we describe pilot work using consumer level digital video cameras to capture high-resolution and high speed videos of horses at the trot during mandatory veterinary inspection for Federation Equestre Internationale (FEI) level competitions. Twenty-three key skeletal landmarks, selected based on gait mobility, on each horse in 20 different frames of the video are labeled with DeepLabCut, a software package applying a deep neural network approach for object recognition in the frame image. Raw quantitative gait parameters such as stride length, stance time, and angular range of the fetlock joint were derived from the landmark tracking data by a robust data processing pipeline. The pipeline comprises many operations, including outlier removal due to occlusion, trajectory smoothing, model-fitting-based phase identification, and gait parameters calculation. The ease of video capture allowed for 1,597 samples of 945 horse and rider combinations from 5 FEI competitive levels within the same discipline of eventing to be captured from just 6 competitions around the southeast US, before closing of travel due to the pandemic. The current training run was applied to 1,280 frames from 64 videos with 23 landmark points plotted per frame. This training will be applied to our database of 1,533 additional videos allowing gait parameter analysis for horses exhibiting 3–5 trot strides in a single direction. Future work will incorporate additional trot strides, both directions of travel, and enlarging our sampling of horses. This database will be used in future applications in animal selection and lameness diagnosis, as well as in construction of quantitative performance traits suitable for genomics research.
Effects of Flashing Blue Lights Mounted on Paving Equipment on Vehicle Speed Behavior in Work Zones

AbstractVehicle speed in work zones is a significant concern to state transportation agencies and their construction partners. Prior research indicates that law enforcement vehicles within a work z...
Severe Guillain-Barré syndrome

Abstract Guillain-Barre syndrome (GBS) is currently the most common cause of acute flaccid paralysis. The disorder is a polyradiculoneuropathy involving mainly motor occasionally sensory and autonomic nerves presenting as acute, usually symmetrical, typically ascending paralysis. Rapidly progressive weakness is the main clinical feature of GBS. It may involve bulbar weakness, respiratory failure, and autonomic nervous system dysfunction. The acute progression of limb weakness, often with sensory and cranial nerve involvement 1–2 weeks after immune stimulation, proceeds to its peak clinical deficit in 2–4 weeks. GBS usually follows a preceding infection or rarely vaccination. Molecular mimicry between microbial and nerve antigens is clearly underlying pathophysiological mechanism behind the development of the disorder. In countries where Zika virus infection is common, an increase in GBS cases has been reported. Treatment of GBS comprises intravenous immunoglobulin (IVIG) or plasma exchange (PE). Approximately one-third of GBS patients are admitted to an intensive care unit, and many require mechanical ventilation. Despite the demonstrated efficacy of PE and IVIG, GBS however remains a disabling disease in a significant proportion of patients, and these treatments have not improved mortality.
Articular Surface Failure of a Hybrid Anatomic Glenoid Component: A Case Report.

CASE We present a case of a 71-year-old woman with history of left-sided shoulder arthritis who underwent standard total shoulder arthroplasty using a novel hybrid glenoid component. After 3 years, she sustained traumatic dissociation of the interface between the polyethylene face and central titanium post, a unique failure mechanism of the hybrid glenoid component. This was successfully corrected through conversation to reverse shoulder arthroplasty (RSA). Follow-up after 2 years demonstrated marked improvement in pain and function. CONCLUSION Hybrid glenoid components present a unique failure mechanism as compared to traditional glenoid loosening and can be effectively corrected with RSA.
Gatekeeper: A Reliable Reconfiguration Protocol for Real-Time Ethernet Systems

Real-time Ethernet systems are becoming increasingly popular for avionics and embedded applications. By regulating network traffic according to predefined configurations, these protocols enable highly deterministic communication, while still conforming to the Ethernet standard. However, the strengths of a statically configured system become weaknesses when the system requirements are changed. In the worst case, the entire network may need to be reloaded with new configurations, resulting in significant downtime. As a result, there is significant growing interest in reconfiguring real-time Ethernet networks online, without restarting the network. Several recent works focus on minimizing frame loss and configuration conflicts during online reconfiguration. Unfortunately, in doing so, they also sacrifice the system’s ability to tolerate faulty components.In this paper, we describe Gatekeeper, the first reconfiguration protocol for real-time Ethernet systems that minimizes downtime while still tolerating faults. Gatekeeper consists of two main sub-protocols: 1) a reliable distribution protocol that ensures consistent configurations are deployed on all non-faulty devices (i.e., switches and network cards), and 2) a dependable test-and-migrate reconfiguration protocol that allows the system to gain confidence that the configurations are correct as they are rolled out to an increasing number of devices. Our evaluation shows that Gatekeeper has modest overheads, and causes up to 2.5× shorter network disruptions than other solutions.
Minimum Norm Method for Linear and Planar Sparse Arrays

Coprime and nested arrays are sparse arrays with enhanced degrees of freedom, which can be exploited in direction of arrival estimation using algorithms such as product processing, min processing, and MUSIC. This paper applies the minimum norm method for direction of arrival estimation. Comparison of the root mean squared errors and probabilities of resolution of the minimum norm method with MUSIC for a given linear coprime or nested array demonstrates the superiority of the minimum norm method. Specifically, minimum norm method exhibits lower mean squared error, narrower peaks at the locations of the true sources, and a lower noise floor in the spatial spectral estimate. This work also formulates two different minimum norm methods for planar sparse arrays: direct and linear. Comparison of the linear minimum norm method with the linear MUSIC for planar arrays also demonstrates higher accuracy of the minimum norm method.
Using all gene families vastly expands data available for phylogenomic inference in primates

Abstract Traditionally, single-copy orthologs have been the gold standard in phylogenomics. Most phylogenomic studies identify putative single-copy orthologs by using clustering approaches and retaining families with a single sequence from each species. However, this approach can severely limit the amount of data available by excluding larger families. Recent methodological advances have suggested several ways to include data from larger families. For instance, tree-based decomposition methods facilitate the extraction of orthologs from large families. Additionally, several popular methods for species tree inference appear to be robust to the inclusion of paralogs, and hence could use all of the data from larger families. Here, we explore the effects of using all families for phylogenetic inference using genomes from 26 primate species. We compare single-copy families, orthologs extracted using tree-based decomposition approaches, and all families with all data (i.e., including orthologs and paralogs). We explore several species tree inference methods, finding that across all nodes of the tree except one, identical trees are returned across nearly all datasets and methods. As in previous studies, the relationships among Platyrrhini remain contentious; however, the tree inference methods matter more than the dataset used. We also assess the effects of each dataset on branch length estimates, measures of phylogenetic uncertainty and concordance, and in detecting introgression. Our results demonstrate that using data from larger gene families drastically increases the number of genes available for phylogenetic inference and leads to consistent estimates of branch lengths, nodal certainty and concordance, and inferences of introgression.
Undoing Somatic Repression through Kinesthetic and Kinetic Body Imagery

Most adults who are asked to imagine in what part of their bodies they locate most tension, the greatest feeling of vulnerability, the most attractive part of themselves or even significant others in their lives, seem to have little difficulty in assigning a body location to these diverse sensations, affects and attitudes (Fisher, 1970; Shorr, 1977). According to Fisher (1970), body feelings form a grid or system of coordinates upon which life impressions may be located. The reason that human beings can readily locate any experience in their bodies may lie in the fact that they use their bodies simultaneously to experience and to react to their environment. Furthermore, because their bodies act as repositories for all of their experiences, including preverbal ones, the recall and associative processes involved in relating affects to their appropriate or relevant social contexts, is facilitated when these affects are first located in their bodies (Fisher, 1973; Paivio, 1971).
The dynamics of hurricane balls

We examine the theory of the hurricane balls toy. This toy consists of two steel balls, welded together that are sent spinning on a horizontal surface somewhat like a top. Unlike a top, at high frequency the symmetry axis approaches a limiting inclination that is not perpendicular to the surface. We calculate (and experimentally verify) the limiting inclinations for three toy geometries. We find that at high frequencies, hurricane balls provide an easily realized and testable example of the Poinsot theory of freely rotating symmetrical bodies.
Serotonin activation of the ERK pathway in Hermissenda: contribution of calcium-dependent protein kinase C.

The mitogen-activated protein kinase (MAPK) cascade is an important contributor to synaptic plasticity and learning in both vertebrates and invertebrates. In the nudibranch mollusk Hermissenda, phosphorylation and activation of the extracellular signal-regulated protein kinase (ERK), a key member of a MAPK cascade, is produced by one-trial and multitrial Pavlovian conditioning. Several signal transduction pathways that are activated by 5-hydroxytryptamine (5-HT) and may contribute to conditioning have been identified in type B photoreceptors. However, the regulation of ERK activity by ‘upstream’ signaling molecules has not been previously investigated in Hermissenda. In the present study we examined the role of protein kinase C (PKC) in the serotonin (5-HT) activation of the ERK pathway. The phorbol ester TPA produced an increase in ERK phosphorylation that was blocked by the PKC inhibitors GF109203X or Go6976. TPA-dependent ERK phosphorylation was also blocked by the MEK1 inhibitors PD098059 or U0126. The increased phosphorylation of ERK by 5-HT was reduced but not blocked by pretreatment with the calcium chelator BAPTA-AM or pretreatment with Go6976 or GF109203X. These results indicate that Ca2+-dependent PKC activation contributes to ERK phosphorylation, although a PKC-independent pathway is also involved in 5-HT-dependent ERK phosphorylation and activation.
Estimating Radial Measures of Productivity Growth: Frontier vs Non-Frontier Approaches

In this paper, we propose an alternative econometric framework for estimating and decomposing productivity change that does not require a distribution for inefficiency or the uncorrelatedness between inefficiency and the regressors. We develop our methodology for the input-oriented radial measure of productivity change and establish that this equals the negative of the time change in the log cost function. Our econometric framework is based on a fixed-effects, multiple-output cost frontier, where we decompose productivity change into discrete shifts in the frontier and changes in firm efficiency levels relative to the frontier. We also show that the standard non-frontier specification is nested within our frontier model and thus can produce different estimates of productivity change. Using a panel of twelve US railroads from 1951 to 1975, our estimated cost frontier suggests average annual productivity growth of roughly 0.3 percent, with efficiency change rising then falling over the period. Specification tests reject the non-frontier model, which yields smaller gains in productivity.
“And since the Italians are always one step ahead of us, and of everyone…” Italian Thought Between Ontological Weakness and Governmentality

It is March 8th 1978, and Michel Foucault is entering the second half of his lesson on governmentality at the College de France. The room is packed as usual. And towards the end of the session, Foucault – half-joking – claims: Italians were the first to formalize the difference between law and police, because they are always one step ahead of anyone. In this essay, Lorenzo Fabbri takes at face value Foucault’s remark and shows how it is the discovery of life that in the 16th century propelled, and still propels today, Italian thought ahead of its times.
INTRAUTERINE TRANSFUSION OF FETUS FOR SEVERE ERYTHROBLASTOSIS FETALIS. A CASE REPORT.

I N R E c E N T years, the management of problems arising from Rh incompatibility in obstetrical patients has been greatly facilitated by spectrophotometric analysis of fluid obtained by amniocentesis. Accurate determination of the optimal time for delivery of infants with erythroblastosis fetalis has decreased both intrauterine and neonatal losses from this disease. In this manner physicians have been able to reduce the perinatal mortality from this condition by more than 50 per cent.* In spite of this remarkable advance, there remain certain pregnancies in which the fetal involvement becomes severe at a stage too early to permit extrauterine survival on the basis of prematurity alone. If the fetus is left in the uterus to gain valuable maturity, the outcome is usually an intrauterine death. It is in this situation that intrauterine transfusion enables the fetus to survive to viability. The amniocentesis is invaluable. to determine the cases in which the fetus is (deteriorating. In November, 1963, Liley’ reported the first successful intrauterine transfusion by injecting Rh-negative blood into the fetal
Neighborhood Disadvantage and the Nature of Violence

Although numerous studies have examined the influence of neighborhood socioeconomic disadvantage on the quantity of violence, little attention has been devoted to whether such conditions also shape the quality of violence. Drawing on Anderson's (1999) influential ethnography, we derive several hypotheses about how the nature of violence differs across neighborhoods with varying socioeconomic conditions. Using data on assaults and robberies from the area-identified National Crime Victimization Survey (NCVS), our analyses reveal support for Anderson's description of the nature of violence in different neighborhood contexts, but only mixed support for his argument that those differences are due to neighborhood effects.
Mechanisms of killing of spores of Bacillus subtilis by iodine, glutaraldehyde and nitrous acid

Treatment of wild-type spores of Bacillus subtilis with glutaraldehyde or an iodine-based disinfectant (Betadine) did not cause detectable mutagenesis, and spores (termed alpha-beta-) lacking the major DNA-protective alpha/beta-type, small, acid-soluble proteins (SASP) exhibited similar sensitivity to these agents. A recA mutation did not sensitize wild-type or alpha-beta- spores to Betadine or glutaraldehyde, nor did spore treatment with these agents result in significant expression of a recA-lacZ fusion when the treated spores germinated. Spore glutaraldehyde sensitivity was increased dramatically by removal of much spore coat protein, but this treatment had no effect on Betadine sensitivity. In contrast, nitrous acid treatment of wild-type and alpha-beta- spores caused significant mutagenesis, with alpha-beta- spores being much more sensitive to this agent. A recA mutation further sensitized both wild-type and alpha-beta- spores to nitrous acid, and there was significant expression of a recA-lacZ fusion when nitrous acid-treated spores germinated. These results indicate that: (a) nitrous acid kills B. subtilis spores at least in part by DNA damage, and alpha/beta-type SASP protect against this DNA damage; (b) killing of spores by glutaraldehyde or Betadine is not due to DNA damage; and (c) the spore coat protects spores against killing by glutaraldehyde but not Betadine. Further analysis also demonstrated that spores treated with nitrous acid still germinated normally, while those treated with glutaraldehyde or Betadine did not.
Regional-scale ground water quality monitoring via integer programming

Abstract A network design approach developed in this paper identifies monitoring sites in multi-layered, regional ground water flow systems at risk of contamination from waste storage facilities. Candidate locations are assigned weights that quantify monitoring value in terms of the prospect of plume detection and exposure hazard criteria. Detection criteria are based on the location of a site with respect to the source of contamination and potential contaminant plumes. Exposure criteria are based on the size of the population that consumes water from a supply well and the distances between the supply well and probable zones of contamination. The weights are used in a binary integer mathematical programming problem which selects the monitoring locations. On a 100-point rating scale developed to quantify composite plume detection and characterization efficiency, the network design model scored 87, compared with a score of 76 for a pre-existing monitoring network. (The model and pre-existing schemes involve the same number of wells.) The model selects well sites that are close together near the source of contamination, facilitating early detection of a contaminant release, and further apart downgradient, resulting in areal coverage for plume characterization.
Angiographic occurrence and clinical correlates of intraluminal coronary artery thrombus: Role of unstable angina

The importance of intraluminal coronary artery thrombus in acute myocardial infarction is now recognized. Coronary thrombi, however, may be important in ischemic syndromes other than infarction. The coronary angiograms of 268 consecutive patients undergoing diagnostic angiography were prospectively examined for intracoronary thrombus and form the basis of this study. Of these patients, 29 (11%) (25 men and 4 women) met the criteria for coronary artery thrombus. Of the 29 patients with thrombus, 24 (83%) had unstable angina before angiography. The five remaining patients with thrombus had had a transmural myocardial infarction 3 to 18 months before cardiac catheterization. In 21 patients, the thrombus was distal to a significant stenosis; in 8 it was proximal to or at the site of a significant stenosis. Coronary artery thrombus was identified in 24 (35 %) of 67 patients with unstable angina compared with only 5 (2.5 %) of 201 patients with stable angina (p
Modeling, simulation, and optimization of five-axis milling processes

The five-axis milling is widely applied to complex surface machining. When cutting forces of milling processes increase, the consequent workpiece and tool deflections may result in poor machining quality and high processing cost. There are a lot of researches on three-axis milling processes simulation, but very few about five-axis milling. To solve these disadvantages, this paper presents an integrated system containing modeling, simulation, and optimization of five-axis milling processes. The system has three major applications: (1) simulation verification of milling processes, (2) cutting forces prediction, and (3) cutting parameters (feedrate) optimization. The material removal process simulation used for verifying the five-axis milling is based on the three-dexel (depth element) model, and the cutter-workpiece engagement regions are extracted from the geometric model. According to the extracted cutter-workpiece engagement regions, the instantaneous cutting forces could be predicted. The feedrate is off-line modified for balancing the given maximum or the reference cutting forces with the predicted cutting forces on different machining steps. The developed system is validated experimentally to show that the modeling, simulation, and optimization methods could improve the accuracy and efficiency of five-axis milling processes.
Neglecting the Question of Being: Heidegger's Argument Against Husserl

Abstract This paper claims that the argument Heidegger leveled at Husserl in his Marburg lecture courses trades on a confusion. Heidegger confused neglecting the question of being with presupposing an answer to the question of being. No reasons have been given for thinking that the former is objectionable, and the latter is only as objectionable as the thing presupposed. This paper does not, thereby, show Heideggerian phenomenology is inferior to Husserlian phenomenology; but it does show that Heidegger's so-called “immanent critique of Husserl” was anything but, and hence that Husserlian phenomenology was not (as Heidegger claimed) “unphenomenological”.
Warming of the Arctic Ocean by a strengthened Atlantic Inflow: Model results

An ice-ocean model is used to examine the behavior of the Arctic Ocean in response to recent changes in Arctic climate. The model shows that, starting about 1989, there has been a significant warming and salinification in the Arctic Ocean, in agreement with recent observations. The warming and salinification occur mainly in the upper ocean owing to a sustained increase of Atlantic inflow both at Fram Strait and, most significantly, via the Barents Sea. The increased incoming warm and salty Atlantic Water “flushes” out cold and fresh Arctic Water, thus increasing the temperature and salinity of the upper ocean and resulting in more oceanic heat flux to the mixed layer and ice cover. Concomitantly, the model shows a continuing decrease in ice volume beginning in 1987.
Jointly Optimizing Stream Allocation, Beamforming and Combining Weights for the MIMO Interference Channel

We propose an algorithm whose goal is to maximize the sum rate of a set of interfering multiple-input multiple-output (MIMO) links by jointly optimizing which subset of transmitters should transmit, the number of streams for each transmitter (if any), and the beamforming and combining weights that support those streams. We present numerical results to illustrate that our algorithm achieves a sum rate higher than previously reported algorithms at high interference, and that it achieves comparable performance to the top-performing algorithms at medium and low interference. In one high-interference example with many links, our algorithm achieves a 65% higher sum rate than previously reported algorithms.
Uncertainty in Light Scattering Measurements by TSI Nephelometer: Results from Laboratory Studies and Implications for Ambient Measurements

We performed a series of laboratory studies to assess uncertainties in aerosol optical property measurements. We used a pulsed cavity ring-down spectrometer (CRD) to measure the aerosol light extinction coefficient, a photo-acoustic absorption spectrometer (PAS) for light absorption, and a commercial integrating nephelometer (TSI, model 3563) for the scattering coefficient. The test aerosols generated for the study consisted of both non-absorbing and slightly-to-highly absorbing polydisperse submicron particles, delivered to the systems as pure compounds or mixtures. For aerosols with single scattering albedo (ω) > 0.7, we found that the ω values calculated by combining the three instruments agreed within expected uncertainty. For aerosols with ω < 0.7, the discrepancy was outside of the boundaries of existing uncertainties. Mie theory calculations of the nephelometer correction factors indicate that the current literature expressions for nephelometer truncation correction are not adequate at ω < 0.7 due ...
Construction and Characterization of Monomeric Tryptophan Repressor: A Model for an Early Intermediate in the Folding of a Dimeric Protein†

Tryptophan repressor (TR) from Escherichia coli is a homodimer whose highly helical subunits intertwine in a complex fashion. A monomeric version of Trp repressor has been constructed by introducing a pair of polar amino acids at the hydrophobic dimer interface. Analytical ultracentrifugation was used to show that the replacement of leucine at position 39 with glutamic acid results in a monomer/dimer equilibrium whose dissociation constant is 1.11 × 10-4 M at 25 °C and pH 7.6. Tryptophan fluorescence, both near- and far-UV circular dichroism, and NMR spectroscopies demonstrated that, at the micromolar concentrations where the monomer predominates, secondary and tertiary structure are present. Hydrophobic dye-binding experiments showed that nonpolar surface is accessible in the monomeric form. The urea-induced equilibrium unfolding of monomeric L39E TR was monitored by circular dichroism, fluorescence, and absorbance spectroscopies. Coincident transitions show that the urea denaturation process follows a s...
Gastric mucosa-associated lymphoid tissue in autoimmune thyroid diseases.

Background: There is increasing evidence for a link between Helicobacter pylori infection and the development of lymphoid follicles in the gastric mucosa. It is not known whether other factors may also play a role. The aim of this study was to investigate the role played by the host with peculiar immunogenic disorders, in the presence or absence of a known antigenic stimulus such as H. pylori For this, we studied patients with autoimmune thyroid diseases. Methods: Thirty patients with autoimmune thyroid diseases and 30 dyspeptic patients without a history of thyroid disorders (as control group) underwent upper endoscopy. Lymphoid follicles and H. pylori status were assessed by histopathologic and enzymatic analysis. Results: Organized mucosa-associated lymphoid tissue was found in 73.3% of the patients and in 33.3% of control group. Lymphoid follicles were found in 87.5% of the H. pylori-positive patients and in 57.1% of the H. pylori-negative patients (P = NS). In the control group these follicles were p...
Diel changeover in sandbank fish assemblages in a neotropical floodplain river

Fishes were collected over 7 months (February to June and November to December 1999) from seven sandbanks located on the main channel of the Cinaruco River, Venezuela. Significant shifts in assemblage structure and species richness were documented between diurnal and nocturnal samples. Seine samples standardized for effort yielded 41 604 individual fishes representing seven orders, 25 families, 80 genera and 134 species. Nocturnal samples yielded 68% of the total individuals, and 54% of species were collected exclusively at night. Nocturnal samples were significantly more species rich than their paired diurnal samples, even after rarefaction. Correspondence analysis revealed consistent differences in assemblage structure between diurnal and nocturnal samples probably due to species-specific habitat use and activity patterns. In spite of the magnitude of seasonal variation in hydrology and habitat availability in the Cinaruco River, species richness and abundance on sandbanks varied relatively little. The study of biological diversity and understanding of patterns of habitat use in a neotropical river were enhanced by nocturnal sampling.
The Interrelationship of Lens Anatomy and Optical Quality I. Non-primate Lenses

We have quantified the influence of lens sutural anatomy on optical quality (focal length variability, i.e. spherical aberration) in adult monkeys (Macaque nemestrina). Adult lenses (n = 6) were initially scanned by a low-power helium-neon laser beam that was passed at a series of acute angles to, and/or directly through, lens sutures. Optical analysis showed that while the 'star' sutures of primate lenses exerted a quantifiable negative effect on focal length variability, this detrimental effect was far less significant than that attributable to 'line' and 'Y' sutures in non-primate lenses. Correlative morphological and 3-D computer-assisted drawing (CAD) analysis of the laser-scanned lenses areas, as well as of variably aged lenses (n = 30), revealed that primates have a more complex lens architecture than non-primates. Non-primate lenses feature suture planes, aligned along the visual axis that are responsible for a significant quantifiable increase in spherical aberration. Primate lenses are characterized by an absence of continuous suture planes aligned along the visual axis. Rather, 3-D-CADs of primate lenses demonstrate that distinct generations of progressively more complex sutures are produced as a function of development, growth, and age. In succession, 'Y' sutures (three branches) are formed throughout embryonic development, 'simple star' sutures (three-six branches) evolve after birth and through infancy, 'star' sutures (six-nine branches) are made in young adult lenses and, finally, 'complex star' sutures (nine-15 branches) are laid down from middle through old age. In view of the fact that slit-lamp evaluation of cataractous lenses often reveals abnormally thin zones of discontinuity, it is significant to note that the temporal development of the zones of discontinuity in normal human lenses is essentially identical to the progressive iteration of offset monkey lens sutures. In conclusion, these studies describe a specific structural aspect of lenses that adversely influences optical quality, and relates it to the most commonly employed clinical technique to identify and monitor the progress of cataracts.
THE ROLE OF SUSPENSION STRUCTURE IN THE DYNAMIC RESPONSE OF ELECTRORHEOLOGICAL SUSPENSIONS

The dynamic response of electrorheological (ER) suspensions has received little attention relative to the effort devoted to the study of the steady shear response. We report on simulation and experimental investigations of the dynamic oscillatory response of ER suspensions, in particular focusing on the relationship between suspension structure and the rheological response. We consider the response of monodisperse and polydisperse suspensions under linear deformation, as well as the response in the nonlinear regime. Dimensional analysis of the equations of motion predict that the linear rheological response obeys a time-field strength superposition principle, which is confirmed by experiment. The response is found to exhibit a sharp dispersion that is only broadened slightly by polydispersity. Nonlinear deformation is found to significantly broaden the observed dispersion.
Analysis of PKR Dimerization by Resonance Energy Transfer

Protein kinase R (PKR) is a critical component of the interferon-induced innate immunity pathway. PKR is expressed in a latent inactive form and becomes activated upon binding dsRNA to undergo autophosphorylation. PKR contains a C-terminal kinase domain and two tandem dsRNA binding motifs. It is believed that dimerization plays a critical role in the mechanism of activation of PKR by dsRNA. Activation requires dsRNA long enough to accommodate at least two PKRs. In addition, the kinase domain has been crystalized as a dimer and the structure suggests a mechanism linking the dimer interface with the active site. However, there is no direct evidence for dimerization of PKR on dsRNA lattices and some RNAs that bind multiple PKRs fail to activate. Therefore, we have developed a fluorescence assay to quantitatively probe PKR dimerization upon binding to dsRNA. Using unnatural amino acid mutagenesis, p-azidophenylalanine was selectively incorporated into PKR at a site that lies near the kinase dimer interface. This residue was labeled with an Alexa Fluor 488 - alkyne conjugate using click chemistry. This fluorophore has a small Stokes shift and is capable of homo Forster Resonance Energy Transfer (homo-FRET). The fluorescence anisotropy of this probe decreases upon PKR binding to an activating 40 bp dsRNA due to depolarization induced by homo-FRET. The anisotropy increases upon further addition of the dsRNA due to dilution of the PKR monomers onto separate dsRNAs. Hetero-FRET between Alexa Fluor 488- and Cy3-labeled PKR confirms that depolarization is due to dimerization. PKR binding to non-activating dsRNAs does not induce a decrease in anisotropy, indicating the absence of kinase dimer formation.
Effects of exogenous corticosterone on locomotor activity in the red-eared slider turtle, Trachemys scripta elegans.

We investigated the effects of exogenous corticosterone on the locomotor activity of captive red-eared slider turtles, Trachemys scripta elegans. An increase in plasma corticosterone often increases locomotor activity in mammals and birds, but there are no reported findings for turtles. In this study turtles implanted with corticosterone-filled Silastic ® implants showed a sig- nificant increase in caged locomotor activity when compared to control animals with empty im- plants. Corticosterone-treated turtles also showed a significant increase in plasma corticosterone concentration when pre-trial plasma samples were compared to post-trial plasma samples, while control turtles exhibited no such increase, validating the effectiveness of our implants to deliver corticosterone. Although corticosterone remained high at the end of the activity trials, the in- crease in activity was ephemeral in nature, peaking within 48 hr after the implant was in place. This suggests that the effects of corticosterone on behavior may be context-dependent (i.e., whether the turtles can find food) and concentration-dependent, and that there are underlying physiologi- cal mechanisms, perhaps mediated at the receptor level in the brain, involved in locomotor activ- ity behavior in slider turtles. Environmental perturbations that cause a reduction in available food resources may cause the organism to increase its level of locomotor activity to increase food encounter rate but later reduce activity to conserve energy reserves. These data are important when considering behavioral and physiological mechanisms involved in a turtle's response to chang- ing conditions in habitat quality. J. Exp. Zool. 284:637-644, 1999. © 1999 Wiley-Liss, Inc.
Influence of chronic antigen exposure on the metabolism of PGH2 by microsomal preparations of airway and parenchymal tissues in the sheep

The effects of repeated antigen exposure on the synthesis of mediators by lung tissues are not well understood. To investigate the influence of antigen challenge on the synthesis of prostaglandins by central airway and peripheral lung tissues, fourteen sensitive sheep underwent biweekly exposure to aerosolized Ascaris suu antigen (7) or saline (7). Following the fifth exposure, microsomal and high speed supernatant fractions were prepared from trachealis muscle and lung parenchyma. Synthesis of thromboxane (TX) A2, prostaglandin (PG) D2 and PGI2 from the PG endoperoxide intermediate, PGH2, was assayed over a range of substrate concentrations from 3–200 uM. Synthesis of PGI2 by trachealis microsomes was approximately 5-fold greater than that of TXA2. PGI2 and TXA2 production was identical in tracheal preparations from Ascaris- and saline-exposed animals. In parenchymal tissues, where TXA2 production predominated over PGI2 by 9-fold, preparations from Ascaris- exposed animals synthesized 50% more TXA2 than controls at PGH2 concentrations of 25 uM and above, whereas synthesis of PGI2 and PGD2 were similar in preparations from both groups of animals. The density of pulmonary mast cells was decreased by 21% in the Ascaris group, whereas polymorphonuclear leukocyte density was unchanged. These results demonstrate the differential synthesis of TXA2 and PGI2 in central airways and peripheral lung regions of the sheep. They further indicate that repeated exposure of the airways to antigen selectively enhances TXA2 synthesis in the lung periphery of sensitized animals. The site of this increased enzymatic activity, whether in resident cells or newly-infiltrated cells, has not been determined.
Implicit and Explicit Goal-Directedness

In this paper, I develop and defend a theory of what I call ‘implicit goal-directedness’, which is a purely causal or dynamical notion, and can be separated from the notion of ‘explicit goal-directedness’, which implies the representation of a goal-state. I describe the problems that plagued earlier attempts at analyzing goal-directedness in causal/dynamical terms, and then present my own novel solution. I argue that implicit goal-directedness, in the sense presented, plays an important conceptual role in biology and cognitive science, and is distinct, not only from explicit goal-directedness, but also from the other major teleological notion familiar to philosophers of biology: evolutionary function. Indeed, an appreciation of this tripartite distinction is critical for understanding the structure of explanations of behavior in many scientific contexts.
Tornadogenesis by nonprecipitation induced wind shear lines

Abstract Five tornadoes occurred within a 40 min period on 18 May 1984 in eastern Colorado. The evolution of these tornadoes was documented by a single Doppler radar, research aircraft, mesonetwork and chase team. Three of these tornadoes were narrow (≈300 m), rotating dust columns extending from the surface to cloud base more than 5 km from the nearest precipitation. The Doppler-observed parent circulations were <2 km deep and <1 km in diameter. Tornadoes of this type do relatively minor damage and are frequently called gust front tornadoes or gustnadoes. It is believed this is the first Doppler radar documentation of this tornado type. In an operational environment, even at close radar range, it would be difficult to detect the parent circulation associated with these tornadoes. However, by closely monitoring wind shift boundaries and associated localized strong shear regions, preferred tornado areas can be identified. The other two tornadoes were associated with condensation funnels and occurred near p...
Frequency based satellite monitoring of small scale explosive activity at remote North Pacific volcanoes

Abstract Monitoring of volcanoes in the North Pacific can be an expensive and sometimes dangerous task, specifically for those located in Alaska (USA) and Kamchatka (Russia). An active frequency detection method previously used at Stromboli, Italy, uses the thermal- and mid-infrared wavelength bands from the Moderate Resolution Imaging Spectroradiometer (MODIS) satellite data to detect anomalies at a volcano. This method focuses on small scale explosive activity, often referred to as Strombolian activity which can produce small spatter fields near a volcano's active vent. In the North Pacific, there are a number of volcanoes which exhibit small scale explosive activity and three are the focus of this study: Chuginadak (Mt. Cleveland) and Shishaldin in Alaska, and Karymsky Volcano in Kamchatka. Satellite images from the Advanced Very High Resolution Radiometer (AVHRR) were used to monitor the frequency of thermal features as well as the occurrence of ash plumes at each volcano. This data was then used to produce a time series spanning 2005–2010 for all three volcanoes. During this time period, each volcano underwent a series of eruptive cycles including background levels of activity, heightened frequency of small explosions (identified as precursory activity), and heightened activity typified by ash plume-producing eruptions. Each location has a unique precursory signal, both in timing and magnitude. The use of a previously developed method on a new sample set of volcanoes has proved the validity of this method as a monitoring tool for volcanoes with small scale explosive activity. This method should be applied to a larger set of volcanoes to continue the development and database production for its use as a volcano monitoring tool.
Bold disciplinarianism, experimentation and failing spectacularly

When considering the disciplinary domains of child and youth research I surprise myself by advocating, as a first encounter, a stance of bold disciplinarianism. In 2000 I went for the first time to...
A Prototype Framework for Knowledge-Based Analog Circuit Synthesis

An organization for a knowledge-based analog circuit synthesis tool is described. Analog circuit topologies are represented as a hierarchy of functional blocks; a planning mechanism is introduced to translate performance specifications between levels in this circuit hierarchy. A prototype implementation, OASYS, synthesizes sized transistor schematics for simple CMOS operational amplifiers from performance specifications and process parameters, and demonstrates the workability of the approach.