cssi/SciSciGPT-SciSciNet huggingface dataset:
Fine-Needle Aspiration Biopsy of Liver Lesions Yields Higher Tumor Fraction for Molecular Studies: A Direct Comparison With Concurrent Core Needle Biopsy.

Author(s): Goldhoff, Patricia Ellen; Vohra, Poonam; Kolli, Kanti Pallav; Ljung, Britt-Marie | Abstract: BackgroundThis retrospective study evaluated and compared the diagnostic accuracy and suitability of tissue specimens for advanced molecular diagnostic testing obtained via 2 different techniques for percutaneous biopsy of primary and metastatic liver tumors.Patients and methodsSamples from 137 patients with liver masses who underwent concurrent fine-needle aspiration biopsy with cell block (FNAB-CB) and core needle biopsy (CNB) at 2 hospitals were assessed for diagnostic accuracy, tumor fraction, and tumor cellularity. A subset of FNAB-CBs, that were deemed to have less or equal tumor cellularity compared with CNBs, had level sections performed and were reassessed for tumor cellularity.ResultsDiagnostic accuracy was 96% for FNAB and 93% for CNB (P=.267). In FNAB-CBs, tumor fraction was significantly higher than in CNB samples (67% vs 36%; Pl.0001), whereas nontumor components were significantly lower (stromal component, 7% vs 29%; Pl.0001; background benign hepatocytes, 25% vs 36%; P=.003). Additionally, in 44% of cases, FNAB-CB tumor cellularity was equal to or greater than that of the concurrent CNB.ConclusionsIn the current age of personalized medicine, a minimally invasive, safe approach to obtaining adequate tissue for myriad molecular testing is paramount. We have shown that FNAB sampling is diagnostically accurate and produces higher tumor fractions than CNB. Thus, FNAB should be strongly considered as an initial sampling modality, especially for patients in whom molecular tests will determine management.
Cardiac-Pericardial Disease

This chapter describes the spectrum of imaging appearances of enlargement of various cardiac chambers, mitral annulus, ventricular aneurysm, and pericardial calcification, pericardial effusion, and constrictive pericarditis.
Classifying the Orbits of the Generalized Symmetric Spaces for SL2(Fq)

In this paper we will discuss the orbits of the fixed-point group on the tori of the generalized symmetric spaces of SL2(k) where k is a finite field. Specifically, we will provide a characterizati...
Molecular docking of substituted pteridinones and pyrimidines to the ATP-binding site of the N-terminal domain of RSK2 and associated MM/GBSA and molecular field datasets.

Abstract The data have been obtained for a series of substituted pteridinones and pyrimidines that were developed based on BI-D1870 to establish a structure-activity relationship for RSK inhibition. The 19 compounds, 12 of these with R- and S-isomeric forms, were docked into the ATP-binding site of the N-terminal domain of the RSK2 kinase using Schrodinger Glide. The binding conformations of these molecules and their interactions with RSK2 may inform the development of further small molecule RSK inhibitors. The molecular mechanics energies combined with the generalized Born and surface area continuum solvation (MM-BGSA) method was used to estimate the free energy of binding of the small molecules with RSK2. The molecular field characteristics of the docked confirmations of the inhibitors was examined using Cresset Forge software. The synthesis and evaluation of these compounds was reported in the related research article: Substituted pteridinones as p90 ribosomal S6 protein kinase 2 (RSK2) inhibitors: a structure-activity study (Casalvieri et al., 2020).
HAWC Observation of Supernova Remnants and Pulsar Wind Nebulae

The majority of Galactic TeV gamma-ray sources are pulsar wind nebulae (PWNe) and supernova remnants (SNRs), and the most common association for unidentified sources is PWN. Many of these sources were discovered in TeV by imaging air Cherenkov telescopes using overlapping pointed observations over sections of the Galactic plane. The HAWC observatory is a survey type instrument in the Northern hemisphere with an energy range of 100 GeV to 100 TeV. Preliminary analysis of data recorded with the partially completed HAWC array taken since 2013 shows extended detections that are coincident with known TeV SNRs and PWNe. The full array became operational in early 2015 and has been steadily surveying the Northern sky since. I will discuss detections in HAWC data taken since 2013 associated with PWNe and SNRs.
A simple instrumented insole algorithm to estimate plantar flexion moments.

Abstract Background Plantar flexion is critical for ambulatory function but there are few wearable solutions to monitor loading. Research question The purpose of this study was to develop and validate a method to calculate plantar flexion moment using a commercially-available instrumented insole. Methods Seven healthy young adults completed a battery of functional activities to characterize a range of plantar flexion loading which included single leg heel raise, step down, and drop jump as well as walking and running at comfortable speeds. Lower extremity trajectories were captured using motion capture and ground reaction forces were recorded with embedded force plates as well as the instrumented insole. We compared plantar flexion moment calculated by the instrumented insole to ‘gold standard’ inverse dynamics. Results We found that estimating plantar flexion moment using our instrumented insole algorithm compared favorably to moments calculated using inverse dynamics across all activities. Errors in the maximum plantar flexion moments were less than 10 % for all activities, averaging 4.9 %. Root mean square errors across the entire activity were also small, averaging 1.0 % bodyweight * height. Additionally, the calculated wave forms were strongly correlated with inverse dynamics (Rxy > 0.964). Significance Our findings demonstrate the utility and fidelity of a simple method for estimating plantar flexion moment using a commercially available instrumented insole. By leveraging this simple methodology, it is now feasible to prospectively track and eventually prescribe plantar flexion loading outside of the clinic to improve patient outcomes.
Changes in surface water quality from small-scale gold mining operations in the Surinamean rainforest

Small-scale miners often engage in environmentally damaging activities, are subject to poor safety conditions, and utilize inefficient mineral extraction technologies. Here, we explore environmenta...
Electronic entropy contribution to the metal insulator transition in VO 2

${\mathrm{VO}}_{2}$ experiences a metal-insulator transition at 340 K. Discontinuities in electronic transport properties, such as the Seebeck coefficient and the electronic conductivity, suggest that there is a significant change in the electronic structure upon metallization. However, the thermodynamic nature of this transformation remains difficult to describe using conventional computational and experimental methods. This has led to disagreement over the relative importance of the change in electronic entropy with respect to the overall transition entropy. A method is presented that links measurable electronic transport properties to the change in electronic state entropy of conduction electrons. The change in electronic entropy is calculated to be $9.2\ifmmode\pm\else\textpm\fi{}0.7$ J/mol K which accounts for 62%--67% of the total transition entropy. This compares favorably with some estimates of the vibrational entropy.
Radiation-sensitization in the absence of Bax/Bak

4953 Abstract Bax and Bak act as a mitochondrial gateway for various apoptotic signals. However, cells lacking both Bax and Bak are resistant to apoptosis induced by various apoptotic stimuli. Instead, they undergo autophagic cell death. Resistance to apoptosis has been associated with radiation resistance, although little is known regarding the relationship between Bax/Bak -/- and irradiation-induced autophagy. In the present study, we investigated radiation-induced autophagy in the presence or absence of Bax and Bak. We found that mouse embryonic fibroblasts (MEFs) lacking both Bax and Bak are much more sensitive to radiation than the wild-type (WT) MEFs as demonstrated by clonogenic assay. Following radiation, increased levels of cleaved caspase 3 and higher apoptotic index were detected in the WT cells, but not in the Bax/Bak -/- double knockout (DKO) cells. Punctate fluorescence of GFP-LC3, characteristic of autophagy, was significantly increased in the irradiated DKO cells. Electron microscopy revealed that these cells had numerous autophagosomes and lysosomes. Inhibition of autophagy by 3-methyl adenine (3MA) increased the radiation resistance of Bax/Bak-/- MEF cells. In addition, expression of the pro-autophagic proteins APG5 and Beclin 1 was induced by radiation in the DKO cells. These results indicate that deficiency of Bax and Bak sensitized MEF cells to radiation and upregulated non-apoptotic cell death in response to radiation.
Physical model testing I for investigating the effects of managed ice-field characteristics on a dynamic positioning vessel

Abstract This paper presents details of an extensive physical model testing program for evaluating the performance of a dynamic positioning (DP) controlled vessel in different realistic managed ice environments. It describes the model vessel, the preparation of the ice-field, the procedure of the model tests, the methodologies of data analysis, and highlights of the measurements. A simplified generic drillship model at 1:40 scale was tested in multiple managed ice configurations. A total of 372 test runs were carried out in 17 ice sheets to evaluate the thruster forces and motion responses of the vessel in various ice conditions. The physical and mechanical characteristics of the ice-field were modelled by controlling ice concentration, thickness, floe size, flexural strength, and the ice drift speed and direction. The ice concentration ranged from a light condition (7/10th) to a heavy condition (9/10th+) with multiple ice floe sizes ranging between 25 m to 100 m. Also, multiple ice thicknesses ranging between 0.60 m to 2.0 m and multiple ice drift speeds (0.2 knots, 0.5 knots, and 1.2 knots) with various moderate to extreme ice drift angles were investigated. The thruster forces on the model vessel along the surge and sway directions and the yawing moment were measured. Besides, the vessel model's 6-DOF motions and accelerations were recorded. Multiple cameras were used to capture the global and local ice-structure interactions placed in different above-water locations. All reported values presented in the paper are in full-scale unless otherwise specified. The time series of thruster forces and yawing moments are presented along with the vessel's positioning capabilities in various managed ice conditions. Results and discussions on the effects of various managed ice-field parameters on the time-averaged thruster forces and moment are offered. Generally, the analysis reveals that each of the ice parameters under investigation had a moderate to strong effect on global thruster force in the surge direction. The measurements and the videos showed complex and highly stochastic ice-vessel-basin wall interactions and different ice failure modes. Overall, the DP system used in the testing demonstrated the vessel's capabilities in maintaining the station for the majority of test head-on test cases and the oblique ice tests not exceeding 10°. The program generated a large dataset and video recordings to evaluate and improve understanding of the dynamic ice-vessel interactions and provided sufficient information for developing novel ice force models for real-time applications.
Integrating SIMD into the undergraduate curriculum

Assembly language instruction today, in our view, should include instruction in the newly important area of single-instruction, multiple-data (SIMD) instructions. Such instructions are available on all major platforms, and they considerably speed up operations on arrays, particularly large arrays. This speedup is more pronounced with assembly language than with algebraic language programming, and thus provides another reason for undergraduate students to learn assembly language. We discuss the differences among approaches to SIMD on various platforms; then we describe our own experience with teaching this material.
Studies of the pharynx. II. Poliomyelitic disabilities of the lower pharynx.

Performance of the hypopharynx was observed clinically and roentgenographically during oropharyngeal inflation, phonation, and swallow in a group of 20 normal subjects and 27 patients recovered incompletely from bulbar-pharyngeal poliomyelitis. The varied disabilities of motor performance of the hypopharynx resulting from poliomyelitis have been classified, with indication of the particular muscular paralyses causing certain of these entities of disability. Recent contributions to physiologic and clinical understanding of the motor event of swallow are reviewed. The total failure of swallow in poliomyelitis is not completely explained by familiar paralytic phenomena and possible alternative explanations of contracture or sclerosis of the sphincter muscles, distortions of afferent elements of the swallow reflex, disability of a swallow center, or of functional impairment must be considered.
Protease inhibitors as potential antiviral agents for the treatment of picornaviral infections

The picornavirus family contains several human pathogens including human rhinovirus (HRV) and hepatitis A virus (HAV). In the case of HRVs, these small single-stranded positive-sense RNA viruses translate their genetic information into a polyprotein precursor which is further processed mainly by two viral proteases designated 2A and 3C. The 2A protease (2Apro) makes the first cleavage between the structural and non-structural proteins, while 3C protease (3Cpro) catalyzes most of the remaining internal cleavages. It has been shown that both 2Apro and 3Cpro are cysteine proteases but their overall protein folding is more like trypsin-type serine proteases. Due to their unique protein structure and essential roles in viral replication, 2Apro and 3Cpro have been viewed as excellent targets for antiviral intervention. In recent years, considerable efforts have been made in the development of antiviral compounds targeting these proteases. This article summarizes the recent approaches in the design of novel 2A and 3C protease inhibitors as potential antiviral agents for the treatment of picornaviral infections.
Substructural Surrogates for Learning Decomposable Classification Problems

This paper presents a learning methodology based on a substructural classification model to solve decomposable classification problems. The proposed method consists of three important components: (1) a structural model, which represents salient interactions between attributes for a given data, (2) a surrogate model, which provides a functional approximation of the output as a function of attributes, and (3) a classification model, which predicts the class for new inputs. The structural model is used to infer the functional form of the surrogate. Its coefficients are estimated using linear regression methods. The classification model uses a maximally-accurate, least-complex surrogate to predict the output for given inputs. The structural model that yields an optimal classification model is searched using an iterative greedy search heuristic. Results show that the proposed method successfully detects the interacting variables in hierarchical problems, groups them in linkages groups, and builds maximally accurate classification models. The initial results on non-trivial hierarchical test problems indicate that the proposed method holds promise and also shed light on several improvements to enhance the capabilities of the proposed method.
Teleology as Higher-Order Causation: A Situation-Theoretic Account

Situation theory, as developed by Barwise and his collaborators, is used to demonstrate the possibility of defining teleology (and related notions, like that of proper or biological function) in terms of higher order causation, along the lines suggested by Taylor and Wright. This definition avoids the excessive narrowness that results from trying to define teleology in terms of evolutionary history or the effects of natural selection. By legitimating the concept of teleology, this definition also provides promising new avenues for solving long standing problems in the philosophy of mind, such as the problems of intentionality and mental causation.
TGF-β1 enhances T-cell PD-1 expression through a Smad3-dependant increase in transcription. (IRM4P.499)

Programmed cell death-1 (PD-1) is an inhibitory receptor highly expressed on T cells specific for viral and tumor antigens. TGF-β1 affects the tumor microenvironment and high serum levels are associated with both malignancy and pathogenesis in some chronic viral infections. However, the effect of TGF-β1 on PD-1 expression is unknown. PD-1 expression requires nuclear factor of activated T cells (NFATc1) activation through T cell receptor (TCR) signaling. We found that TGF-β1 signaling increases NFATc1-induced pdcd-1 mRNA and PD-1 expression on human peripheral CD4+ and CD8+ T cells. Smad2 and Smad3 are phosphorylated following TGF-β Receptor I binding and ultimately mediate gene transcription. We found that inhibition of TGFβRI kinase activity or Smad3 phosphorylation blocked TGF-β1-dependent PD-1 enhancement on T cells. Similarly, when compared to TCR stimulation alone, TGF-β1 increased PD-1 expression on murine wild-type (WT) but not on Smad3 knock-out (KO) CD4+ T cells. In contrast, Smad2 KO CD4+ T cells maintain increased PD-1 expression in the presence of TGF-β1, demonstrating a specific role for Smad3. We show that Smad3 increases pdcd-1 transcription by directly binding to a proximal region of the human PD-1 promoter and stabilizing NFATc1 binding. In addition to TGF-β1’s previously known effects on T cell function, our findings suggest that TGF-β1 mediates suppression via PD-1 upregulation. Smad3 may represent an additional target in therapeutic modulation of PD-1.
Automated hedcut illustration using isophotes

In this work, we present an automated system for creating hedcut illustrations, portraits rendered using small image feature aligned dots (stipples). We utilize edge detection and shading cues from the input photograph to direct stipple placement within the image. Both image edges and isophotes are extracted as a means of describing the image feature and shading information. Edge features and isophotes are then assigned different priorities, with isophotes being assigned the highest priority to enhance the depth perception within the hedcut portrait. Priority assignment dictates the stipple alignment and spacing. Finally, stipple size is based on the number of points and intensity and the gradient magnitude of the input image.
Comparing consistency of clear corneal incisions using a traditional diamond keratome and a newly designed diamond keratome.

PURPOSE To compare the consistency of incision architecture utilizing a traditional diamond keratome and a newly designed diamond keratome. METHODS We used a traditional diamond keratome and newly designed diamond keratome to create clear corneal incisions in human cadaveric donor eyes. Three surgeons with varying levels of experience made 30 incisions with each keratome; and the wound architecture was measured including incision lengths, epithelial and endothelial widths, and the central epithelial incision's deviation from a straight line entrance. RESULTS The mean absolute difference in right and left incision lengths (traditional: 0.182 ± 0.158 mm and new 0.088±0.077 mm [P<0.003]), mean absolute difference in epithelial and endothelial incision width (traditional: 0.181±0.144 mm and new 0.080±0.092 mm [P<0.002]), endothelial incision central deviation from a straight line (traditional: 0.128±0.242 mm and new -0.046±0.124 mm [P<0.001]) were all significantly more consistent with the newly designed diamond keratome than with the traditional diamond keratome. CONCLUSION The newly designed diamond keratome creates a more consistent clear corneal incision than a traditional diamond keratome across a variety of surgical skill levels and does not require advanced levels of training to achieve this consistency.
Multi-component power and frequency estimation for a discrete TFD

In a previous article of Pielemeier and Wakefield (see Proc. of IEEE Symposium on Time-Frequency and Time-Scale Analysis, Oct. 4-6, p.421-424, 1992) a discrete time-frequency distribution (TFD) in Cohen's class was developed for multicomponent musical signals. This TFD's separable kernel employs low pass filtering in time to achieve limited superposition between components, and either constant-bandwidth or constant-Q smoothing in frequency. We develop instantaneous power and frequency estimators for the components analyzed by this TFD. In the literature, frequency estimators for discrete distributions often compute frequency based on discrete finite phase differences using periodic statistics. We instead start with the underlying continuous analog signal, and using linear statistics, show that estimates from the discrete distribution can be made arbitrarily accurate for the single component cast, while for the multicomponent case, the estimates are minimally biased by time smoothing. Results are demonstrated showing much less bias than common spectrogram estimators. Multicomponent examples include signals which are inharmonic and contain widely varying levels, and AM and FM signals. >
Guidelines for estimating repeatability

Summary 1. Researchers frequently take repeated measurements of individuals in a sample with the goal of quantifying the proportion of the total variation that can be attributed to variation among individuals vs. variation among measurements within individuals. The proportion of the variation attributed to variation among individuals is known as repeatability and is most frequently estimated as the intraclass correlation coefficient (ICC). The goal of our study is to provide guidelines for determining the sample size (number of individuals and number of measurements per individual) required to accurately estimate the ICC. 2. We report a range of ICCs from the literature and estimate 95% confidence intervals for these estimates. We introduce a predictive equation derived by Bonett (2002), and we test the assumptions of this equation through simulation. Finally, we create an R statistical package for the planning of experiments and estimation of ICCs. 3. Repeatability estimates were reported in 1·5% of the articles published in the journals surveyed. Repeatabilities tended to be highest when the ICC was used to estimate measurement error and lowest when it was used to estimate repeatability of behavioural and physiological traits. Few authors report confidence intervals, but our estimated 95% confidence intervals for published ICCs generally indicated a low level of precision associated with these estimates. This survey demonstrates the need for a protocol to estimate repeatability. 4. Analysis of the predictions from Bonett’s equation over a range of sample sizes, expected repeatabilities and desired confidence interval widths yields both analytical and intuitive guidelines for designing experiments to estimate repeatability. However, we find a tendency for the confidence interval to be underestimated by the equation when ICCs are high and overestimated when ICCs and the number of measurements per individual are low. 5. The sample size to use when estimating repeatability is a question pitting investigator effort against expected precision of the estimate. We offer guidelines that apply over a wide variety of ecological and evolutionary studies estimating repeatability, measurement error or heritability. Additionally, we provide the R package, icc, to facilitate analyses and determine the most economic use of resources when planning experiments to estimate repeatability.
Water Relations, Stomatal Behavior, and Root Conductivity of Red Osier Dogwood during Acclimation to Freezing Temperatures

Red osier dogwood (Cornus stolonifera Michx.) was artificially acclimated by exposing plants to 8-hour short days (SD) and low (15/5 C) temperatures for 54 to 63 days. Several factors including transpiration rate, stomatal resistance, and root conductivity were correlated so that the rate of water loss in acclimating plants was higher during the first 30 to 40 days of the acclimation sequence. Six days after transferring plants to SD conditions, the stomatal resistance (r8) decreased significantly below the r8 of the 16-hour long day (LD) control plants at the same temperature. Transpiration rate increased by approximately 20 to 30% in the plants transferred to SD. After the initially higher transpiration rate and greater stomatal opening, the stomates closed tightly during the last 2 weeks of acclimation and the transpiration rate of the SD plants dropped to well below the LD control plants. By the end of the acclimation sequence, root conductivity to water uptake was two to three times lower in the SD plants. Leaf xylem water potentials were similar or slightly lower in the plants kept under SD conditions during the first 5 to 7 weeks of the acclimation sequence. During the last 10 to 15 days of acclimation when the stomates closed, SD leaf water potential rose significantly above the plants in the LD conditions. During acclimation, stem water content decreased by 40 to 50%. Changes in tissue hydration can be indirectly related to plant hardiness and may be affected by alteration of stomatal resistance, transpiration rate, and root conductivity during acclimation.
Catalytic reactions involving azomethines. XII. Transamination of 1-methyl-3-hydroxy-4-formylpyridinium chloride.

Abstract This paper reports the synthesis and investigation of the reactions of 1-methyl-3-hydroxy-4-formylpyridinium chloride (MPCHO 2 ) 4 with alanine, at 30 ° in aqueous solution, in the absence of metal ions. Rates of imine formation and transamination have been determined as well as the primary deuterium kinetic isotope effect on the transamination reaction. The reaction products have been determined by an isotopic dilution technique. The results of this study indicate that quaternization of the ring nitrogen in pyridoxal models increases the rate of transamination by alanine, by as much as 20-fold compared to the nonquaternized analogue.
Hypoxia increases the dependence of glioma cells on glutathione.

Glutathione (GSH) is an essential antioxidant responsible for the maintenance of intracellular redox homeostasis. As tumors outgrow their blood supply and become hypoxic, their redox homeostasis is challenged by the production of nitric oxide and reactive oxygen species (ROS). In gliomas, the sustained import of l-cystine via the l-cystine/l-glutamate exchanger, system xc−, is rate-limiting for the synthesis of GSH. We show that hypoxia causes a significant increase in NO and ROS but without affecting glioma cell growth. This is explained by a concomitant increase in the utilization of GSH, which is accompanied by an increase in the cell-surface expression of xCT, the catalytic subunit of system xc−, and l-cystine uptake. Growth was inhibited when GSH synthesis was blocked by buthionine sulfoximine (BSO), an inhibitor of the enzyme required for GSH synthesis, or when cells were deprived of l-cystine. These findings suggest that glioma cells show an increased requirement for GSH to maintain growth under hypoxic conditions. Therefore, approaches that limit GSH synthesis such as blocking system xc− may be considered as an adjuvant to radiation or chemotherapy.
Computational Semantics in Clinical Text

This special issue of Biomedical Informatics Insights presents the full paper proceedings of the first workshop on Computational Semantics in Clinical Text (CSCT), held in 2013. Along with Nigam Shah and Kevin Bretonnel Cohen, my co-organizers, I am grateful for BII’s willingness to produce this forward-looking publication.
Sentence memory: A constructive versus interpretive approach ☆ ☆☆

Abstract The present studies investigated the adequacy of an interpretive linguistic approach to the description of the knowledge communicated by sentences by asking whether sentence retention was primarily a function of memory for the semantically interpreted deep structural relations underlying the input sentences or a function of memory for the overall semantic situations that such sentences described. Results were shown to be primarily a function of memory for the semantic situations. A constructive approach to sentence memory was outlined that dealt with memory for individual sentences as well as memory for sets of semantically related sentences contributing to the same overall idea.
Cognitive radio-based geostationary satellite communications for Ka-band transmissions

This paper proposes an adaptive modulation scheme using rain fading predictions obtained via Kaiman filtering in order to mitigate the effects of rain on cognitive radio-based geostationary (GEO) satellites operating in the Ka-band. In the proposed scheme, the need for adaptation is identified prior to the rain attenuation event, allowing for enough time for the transmitter and receiver to reconfigure, which is a requirement when one of the communicating nodes are moving at a certain relative speed. We show that the bit error rate (BER) performance can be improved by two orders of magnitude for a system that accounts for the overall delay when adapting its modulation scheme based on the proposed predictor outputs.
Defining the Study Population for an Observational Study to Ensure Sufficient Overlap: A Tree Approach

The internal validity of an observational study is enhanced by only comparing sets of treated and control subjects which have sufficient overlap in their covariate distributions. Methods have been developed for defining the study population using propensity scores to ensure sufficient overlap. However, a study population defined by propensity scores is difficult for other investigators to understand. We develop a method of defining a study population in terms of a tree which is easy to understand and display, and that has similar internal validity as that of the study population defined by propensity scores.
A RESPONSE TO JEFFREY ALEXANDER'S THEORETICAL LOGIC IN SOCIOLOGY CONCERNING THE ALLEGED UNIDIMENSIONALITY OF MARXIAN THEORY

In the second volume of his Theoretical Logic in Sociology (1982b), Jeffrey Alexander argues that Marxian theory is predicated on a unidimensional model of human action. That means that Marxian theory overlooks the normative dimension of action, thereby portraying human action as entirely egoistic and deterministic. This article argues that Alexander's criticisms of Marxian theory are unfounded, and, more fundamentally, that Alexander's unfounded criticisms reveal that his whole neo-Parsonian project is based on an underlying conception of human action that is seriously mistaken. A major objective of this article is to present a more tenable conception of action.
Modulation of Oxygen Tensions via Microfabricated Devices

Oxygen is a key modulator of many cellular pathways and plays an important role in a number of cellular behaviors. The hypoxic inducible factor 1α (HIF-1α) is often considered the master regulator of the cellular response to oxygen tension (1). HIF-1α is a transcription factor involved in angiogenesis, glucose transport and glycolysis, apoptosis, migration, and differentiation, among many other functions (2). Unfortunately devices permitting in vitro oxygen modulation fail to meet the needs of biomedical research due to the inability to effectively mimic conditions found in vivo. The gold standard for hypoxia work is the hypoxic chamber, but the tool requires hours for equilibration and is not effective at generating very low oxygen levels (3). As an example demonstrating this disadvantage, cancer tumor oxygenation can change in the span of minutes (4). Intermittent hypoxia, or the changing of oxygen over time, has been shown to be important in heart attack, stroke, and sleep apnea as well. Other microfluidic approaches, although offering more oxygen control, are often difficult to disseminate to other labs due to the requirement of specialized methods and equipment for their operation. In this work, a microfabricated technology has been developed to grant precise control the temporal and spatial oxygen concentration exposed to both cell monolayers in the multiwell plate as well as with 3-D cell-seeded constructs. The concept is adaptable to both pre-established and novel experiments depending on the needs of the researcher. The devices are simple to use and require minimal additional equipment beyond what is available to a standard cell culture lab.Copyright © 2011 by ASME
Specialized CFD Grid Generation Methods for Near-Field Sonic Boom Prediction

Ongoing interest in analysis and design of low sonic boom supersonic transports re- quires accurate and ecient Computational Fluid Dynamics (CFD) tools. Specialized grid generation techniques are employed to predict near- eld acoustic signatures of these con- gurations. A fundamental examination of grid properties is performed including grid alignment with ow characteristics and element type. The issues a ecting the robustness of cylindrical surface extrusion are illustrated. This study will compare three methods in the extrusion family of grid generation methods that produce grids aligned with the freestream Mach angle. These methods are applied to con gurations from the First AIAA Sonic Boom Prediction Workshop.
Gag (Mycteroperca microlepis) vitellogenin: purification, characterization and use for enzyme-linked immunosorbent assay (ELISA) of female maturity in three species of grouper

Circulating levels of the egg yolk precursor protein, vitellogenin (VTG), can be used as a biochemical indicator of maturation in female fish. Here we report on purification and partial characterization of VTG from a temperate marine serranid, the gag(Mycteroperca microlepis). Development of a competitive, enzyme-linked immunosorbent assay (ELISA) for gag VTG (gVTG) is also described. The gVTG was purified by DEAE-agarose anion exchange chromatography from a pooled plasma sample collected from several juvenile gag after they were injected with 17βestradiol. The protein appeared as a major band of Mr≅183 000 after SDS-PAGE ± Western blotting using either a specific rabbit antiserum to gVTG or a universal monoclonal antibody for vertebrate VTGs. Amino acid composition analysis and N-terminal peptide sequencing verified that gVTG is similar in primary structure to VTG from several other teleost species. The purified gVTG and its specific antiserum were used to develop a sensitive, competitive, antibody-capture ELISA for quantifying the protein in blood plasma from maturing females. VTG levels in maturing female gag were highly correlated with oocyte growth and circulating testosterone and 17β-estradiol levels, whereas VTG was non-detectable in juveniles, immature females or males. Two size-based maturity schedules for female gag were constructed, one utilizing detection of VTG in their circulation as a marker of maturity and the other relying on histological evidence that their ovaries were in vitellogenic or later stages of maturation. The two schedules were virtually identical. The gVTG ELISA was also used to detect VTG in blood plasma from mature Nassau grouper (Epinephelus striatus) and red hind (E. guttatus). As with gag, the assay was completely reliable for discriminating between reproductively mature females versus males from these two grouper species.
Cardiac Output Determination in Infants and Small Children After Open Intracardiac Operations

Abstract Simple postoperative clinical observations of infants and small children are not truly objective or reliable. Direct measurement of cardiac output by means of a thermodilution catheter inserted at the time of operation has been used in conjunction with a computer in infants and small children. The technique is simple and can be done rapidly and repeatedly. The effects of various modes of cardiac stimulation can be assessed and the optimal method of treatment employed.
Genetic and physical map of the chromosome of Hemophilus influenzae.

Abstract A genetic map of a large region of the chromosome of Hemophilus influenzae has been defined by transformation with high molecular weight DNA. In addition, a physical map was developed by the transfer of linked markers with specific sized pieces of donor DNA. The different sizes were determined by shearing the high molecular weight DNA and sedimenting it in sucrose density gradients. The molecular weight of the region of the chromosome which has been mapped is of the order of 5 × 10 8 daltons.
Xenopus flotillin1, a novel gene highly expressed in the dorsal nervous system

The two paralogues of the Xenopus flotillin1 gene (flotillin1A and flotillin1B), which encodes a putative membrane-associated protein, were cloned from egg, cleavage, and tadpole cDNA libraries. Both mRNAs are present during oogenesis and cleavage stages. After the onset of zygotic transcription, flotillin1 transcripts are first expressed throughout the embryonic ectoderm and become enhanced in the presumptive neural ectoderm as the neural plate forms. As the neural tube forms and differentiates, flotillin1 transcripts become enriched in the dorsal half, with particularly high expression in dorsal primary neurons. At early tail bud stages, there is additional expression in the paraxial mesoderm. At late tail bud stages, flotillin1A is expressed in branchial arch mesenchyme, the overlying branchial ectoderm and in dorsal somitic mesoderm, whereas flotillin1B expression is more restricted in the dorsal neural tube and head sensory structures. This report is the first comprehensive developmental description in any animal of the expression pattern of this gene, whose protein product in several systems plays important roles in signal transduction events.
A novel method for the small scale synthesis of N-acetoxy-2-acetylaminofluorene and its adducts.

The carcinogen N-acetoxy-2-acetylaminofluorene (N-acetoxy-AAF) can be synthesized effectively in milligram amounts by reacting N-hydroxy-2-acetylaminofluorene (N-hydroxy-AAF) with acetic anhydride in a continuously mixed, closed 2-phase system consisting of ethyl ether/petroleum ether (2 : 1 v/v) and dilute sodium bicarbonate. The organic phase containing N-acetoxy-AAF can be added directly to 10 mm sodium citrate/20% ethanol to synthesize nucleoside or nucleotide adducts without the need to crystallize or resuspend N-acetoxy-AAF in a polar solvent. The advantage of the method is that it makes possible the synthesis of nucleic acid derivatives of N-acetoxy-AAF with high specific activity in small quantities.
Cloning and Characterization of a Novel Serine/Threonine Protein Kinase Expressed in Early Xenopus Embryos

We have cloned from a Xenopus ovary cDNA library a novel protein kinase gene whose expression peaks in the oocyte and unfertilized egg, begins to decrease gradually after fertilization, and disappears during the gastrulation stage of embryogenesis. The cloned gene, termed XEEK1 (for Xenopus egg and embryo kinase), encodes a protein with a predicted molecular mass of 49 kDa. Bacterially expressed XEEK1 migrates at 57 kDa upon polyacrylamide gel electrophoresis analysis, and a XEEK1-specific antibody recognizes a protein of 57 kDa in Xenopus oocyte and egg extracts. The XEEK1 kinase domain shares 35% identity (approximately 65% similarity) with the yeast SNF1 kinase and related kinases. However, expression of XEEK1 does not complement a snf1 deletion mutation in yeast, which suggests that it is probably not a Xenopus homolog of SNF1. Recombinant XEEK1 protein autophosphorylates on threonine residues in vitro in a reaction that prefers Mn2+ to Mg2+ ions. Site-directed mutagenesis of the conserved lysine residue (Lys-81) within the kinase domain to isoleucine totally abolishes kinase activity, and threonine 192 has been identified as the autophosphorylation site. This site is distinct from the conserved threonine (Thr-215 in XEEK1) present in the protein kinase activation loop that is the site of autophosphorylation for many protein kinases. XEEK1 is a substrate for the cyclic AMP-dependent protein kinase both in vitro and in vivo, suggesting a possible mode of regulation of XEEK1. An immunoprecipitate of oocyte/egg extracts with anti-XEEK1 serum contains a protein of approximately 155 kDa that may be a substrate and/or a regulatory component of the kinase.
Two-dimensional registration of magnetic resonance brain images.

A fully automated two‐dimensional image registration technique based on cross correlation is presented. This technique is evaluated using magnetic resonance images of human brain. Results indicate that this algorithm is capable of accurately estimating both linear and angular offsets.
Real-time In Vivo Molecular Detection of Primary Tumors and Metastases with Ratiometric Activatable Cell-Penetrating Peptides

Management of metastatic disease is integral to cancer treatment. Evaluation of metastases often requires surgical removal of all anatomically susceptible lymph nodes for ex vivo pathologic examination. We report a family of novel ratiometric activatable cell-penetrating peptides, which contain Cy5 as far red fluorescent donor and Cy7 as near-infrared fluorescent acceptor. Cy5 is quenched in favor of Cy7 re-emission until the intervening linker is cut by tumor-associated matrix metalloproteinases-2 and 9 (MMP2,9) or elastases. Such cleavage increases the Cy5:Cy7 emission ratio 40-fold and triggers tissue retention of the Cy5-containing fragment. This ratiometric increase provides an accelerated and quantifiable metric to identify primary tumors and metastases to liver and lymph nodes with increased sensitivity and specificity. This technique represents a significant advance over existing nonratiometric protease sensors and sentinel lymph node detection methods, which give no information about cancer invasion.
The G-rich auxiliary downstream element has distinct sequence and position requirements and mediates efficient 3′ end pre-mRNA processing through a trans-acting factor

Abstract A downstream G-rich sequence (GRS), GGGGGAGGUGUGGG, has been previously shown to influence the efficiency of 3' end processing of the SV40 late polyadenylation signal. We have now defined several important parameters for GRS-mediated polyadenylation. The ability of the GRS to influence 3' end processing efficiency was sensitive to individual and multiple point mutations within the element, as well as the position of the element in the downstream region. Competition analysis indicated that the GRS functioned through a titratable trans-acting factor. The GRS-specific DSEF-1 protein was found to be bound to the same population of RNAs as the 64 kDa protein of the general polyadenylation factor CstF, indicating that DSEF-1 is associated with RNA substrates undergoing 3' end processing. Furthermore, an association was obtained between the relative strength of DSEF-1 protein binding to GRS variants and the relative ability of the GRS variants to mediate efficient cleavage in vitro. Finally, mutations in the GRS affected the efficiency of cross-linking of the 64 kDa protein of CstF. These data define a novel class of auxiliary downstream element and suggest an important role for DSEF-1 in 3' end processing.
An efficient, chromatic clustering-based background model for embedded vision platforms

People naturally identify rapidly moving foreground and ignore persistent background. Identifying background pixels belonging to stable, chromatically clustered objects is important for efficient scene processing. This paper presents a technique that exploits this facet of human perception to improve performance and efficiency of background modeling on embedded vision platforms. Previous work on the Multimodal Mean (MMean) approach achieves high quality foreground extraction (comparable to Mixture of Gaussians (MoG)) using fast integer computation and a compact memory representation. This paper introduces a more efficient hybrid technique that combines MMean with palette-based background matching based on the chromatic distribution in the scene. This hybrid technique suppresses computationally expensive model update and adaptation, providing a 45% execution time speedup over MMean. It reduces model storage requirements by 58% over a MMean-only implementation. This background analysis enables higher frame rate, lower cost embedded vision systems.
Left Ventricular Wall Motion Assessed by Using Fixed External Reference Systems

Of two methods utilized to assess ventricular wall motion, one (method A) assumes the left ventricular wall moves symmetrically during contraction toward the approximate geometric center of the left ventricle. The other (method B) assumes the left ventricular wall moves symmetrically toward the base of the heart. Clearly, both methods cannot be correct in all patients. We are presenting a method (R) which utilizes two external markers and the diaphragm as an internal marker to evaluate left ventricular contraction pattern. Of 44 patients studied, the diaphragm moved in four and ventricular wall motion could not be assessed. Fifteen patients had valvular heart disease; six were normal. Findings in method R corresponded to those determined by method B in five of eight patients (63%) with left ventricular hypertrophy and by method A in eight of 13 patients (62%) without left ventricular hypertrophy. This difference was significant ( P
Identification of chemicals triggering cercarial penetration responses of Schistosoma mansoni.

I HAVE carried out experiments to show that chemicals present on mammalian skin cause cercariae of S. mansoni to initiate penetration responses, and discharge the contents of the penetration glands.
Micro-angiography for neuro-vascular imaging. II. Cascade model analysis.

A micro-angiographic detector was designed and its performance was previously tested to evaluate its feasibility as an improvement over current x-ray detectors for neuro-interventional imaging. The detector was shown to have a modulation transfer function value of about 2% at the Nyquist frequency of 10 cycles/mm and a zero frequency detectivequantum efficiency [DQE(0)] value of about 55%. An assessment of the system was required to evaluate whether the current system was performing at its full potential and to determine if any of its components could be optimized to further improve the output. For the purpose, in this study, the parallel cascade theory was used to analyze the performance of the detector under neuro-angiographic conditions by studying the output at the various stages in the imaging chain. A simple model for the spread of light in the CsI(Tl) entrance phosphor was developed and the resolution degradation due to K -fluorescence absorption was calculated. The total gain of the system was found to result in 21 e − (rms) detected at the charge coupled device per absorbed x-ray photon. The gain and the spread of quanta in the imaging chain were used to calculate theoretically the DQE using the parallel cascade model. The results of the model-based calculations matched fairly well with the experimental data previously obtained. This model was then used to optimize the phosphor thickness for the detector. The results showed that the area under the DQE curve had a maximum value at 150 μm of CsI(Tl), though when weighted by the squared signal in frequency space of a 100-μm-diam iodinated vessel, the integral DQE reached a maximum at 250 μm of CsI(Tl). Further, possible locations for gain increase in the imaging chain were determined, and the output of the improved system was simulated. Thus a theoretical analysis for the micro-angiographic detector was performed to better assess its potential.