cssi/SciSciGPT-SciSciNet huggingface dataset:
SIMA: Python software for analysis of dynamic fluorescence imaging data.

Fluorescence imaging is a powerful method for monitoring dynamic signals in the nervous system. However, analysis of dynamic ﬂuorescence imaging data remains burdensome, in part due to the shortage of available software tools. To address this need, we have developed SIMA, an open source Python package that facilitates common analysis tasks related to ﬂuorescence imaging. Functionality of this package includes correction of motion artifacts occurring during in vivo imaging with laser-scanning microscopy, segmentation of imaged ﬁelds into regions of interest (ROIs), and extraction of signals from the segmented ROIs. We have also developed a graphical user interface (GUI) for manual editing of the automatically segmented ROIs and automated registration of ROIs across multiple imaging datasets. This software has been designed with ﬂexibility in mind to allow for future extension with different analysis methods and potential integration with other packages. Software, documentation, and source code for the SIMA package and ROI Buddy GUI are freely available at http://www.losonczylab.org/sima/.
Effects of clay orientation and aspect ratio on mechanical behavior of nylon-6 nanocomposite

Abstract The mechanical properties of nylon-6/clay nanocomposites with variations in clay aspect ratio and orientation were studied. A large-scale simple shear process was utilized to alter the clay aspect ratio and orientation within the reference nanocomposite. It was found that the modulus, strength, and heat distortion temperature of the nanocomposites decreased as the clay aspect ratio and degree of orientation were reduced. Furthermore, the reduction of clay aspect ratio and orientation led to an increase in fracture toughness and ductility. The Halpin–Tsai and Mori–Tanaka micromechanics-based models were implemented to gain a better understanding with regard to the dependence of clay structural parameters, i.e. aspect ratio and orientation, on the reinforcement effect of the nanofillers. The micromechanical models can accurately describe the relationship between clay structural parameters and the corresponding moduli for exfoliated nanocomposites.
Seismic characteristics of gas hydrates at Hydrate Ridge, offshore Oregon

Gas hydrate is an ice-like substance that contains low molecular weight gases (mostly methane) in a lattice of water molecules (Sloan, 1998). Gas hydrates are widely present in permafrost and deep oceanic environments around the world. Hydrate Ridge, offshore Oregon, is one of the areas where hydrates are found in relatively high concentration. In marine environments, methane hydrates are usually stable at temperatures of 0–20° C, water depths greater than 500 m, and in sediments up to 300 m below the seafloor. Small amounts of free gas are often present below the gas-hydrate stability zone (GHSZ). The hydrate-to-free-gas contact gives a strong acoustic impedance contrast, which is evident on seismic sections as a bottom-simulating reflection (BSR). Offshore gas hydrate systems have received attention from the scientific community because of their potential to be:
Integration of End-of-Life Care Content in Undergraduate Nursing Curricula: Student Knowledge and Perceptions

Studies indicate that nurses spend more time with patients at the end of life than any other health care discipline (K. M. Foley & H. Gelband, 2003). So it is imperative that nurses be educated so they can provide this high-quality end-of-life care. The purpose of this project was to provide a current state of end-of-life nursing education in the literature and to report on end-of-life knowledge and experiences of two groups of nursing students in one small, liberal arts university. A total of 111 undergraduate students (61 sophomores and 50 seniors) were administered a 50-item, multiple-choice test to determine their baseline knowledge about end-of-life care. Sophomore scores ranged from 20% to 86% with a mean of 60.98 ( SD = 11.83). Senior pretest scores ranged from 70% to 96% with a mean of 83.26 ( SD = 6.6). An independent samples t test was conducted to determine if there was a difference in group mean knowledge between sophomore and senior students. Levene's test for equality of variance was significant ( F = 4.22, P t test with equal variance assumed revealed a significant difference between sophomore and senior group means ( t = −10.44, P
Molecular Events Mediating Sperm Activation

Fertilization is a unique event in the life of an organism and results from requisite and reciprocal cell-induced sperm and egg activation events mediated by unique cellular and environmental cues associated with either the gametes or the reproductive tract/environment. Sperm interaction with the female reproductive tract/environment and sperm-egg interaction both at a distance and in close proximity represent a series of integrated processes designed to deliver sperm with optimal fertilizing potential to the site of fertilization. The idea that sperm and eggs "communicate" prior to fertilization, and that these communicative processes are requisite for successful fertilization, has been proposed for nearly a century. Recent studies have revealed that many aspects of gamete activation prior and subsequent to fertilization have similarities to intercellular and intracellular signaling systems utilized by somatic cells. The nature of these signaling systems is now being elucidated at the molecular level in both vertebrate and nonvertebrate systems and has revealed some unique aspects of communication and transmembrane signaling between gametes. This review will consider the mechanisms by which eggs communicate with sperm to initiate sperm activation events that are essential for fertilization. It will focus particularly on some of the most recent work surrounding these issues, and new directions and questions that are relevant to this most highly specialized interaction between gametes will be discussed.
The replication of bacteriophage MS2. 1. Transfer of parental nucleic acid to progeny phage

The genetic information of the small bacteriophage MS2 is stored in a single-stranded RNA molecule. This thesis is an analysis of the mechanism whereby the MS2 genetic material is replicated. In Part I, the presence of phage-specific double-stranded RNA in MS2-infected cells is demonstrated. The kinetics of conversion of the input parental strand to a duplex form, and of the formation of progeny duplexes, is also described. In Part II, the replication of phage-specific RNA duplexes is studied by means of density, labeling and CsC1 equilibrium density sedimentation. Neither progeny nor parental duplexes are conserved, which is strong evidence that the duplex plays some role in replication. The above experiments were performed on material isolated after ribonuclease digestion of the nucleic acids from infected cells. In Part III, two other procedures are described which permit identification of phage-specific replicative intermediates (RI) without use of ribonuclease: the host cell RNA synthesis can be preferentially blocked by use of the antibiotic, Actinomycin D; or RI can be separated from the other infected cell components by a centrifugal method based on studies of RNA denaturation with the organic solvent DMSO. These procedures lead to the conclusion that the true RI is a heterogeneous, approximately 15S component which is only partially double-stranded. In Part IV, use is made of this partial double-stranded nature to purify and fractionate the RI on columns of benzoylated, naphthoylated DEAE cellulose, which seem to fractionate nucleic acids on the basis of secondary structure. From measurements of the ribonuclease-resistance and the buoyant densities of purified RI fractions it was concluded that the RI consists of a duplex of constant length to which is attached one single-stranded "tail" of length less than the viral RNA. The RI is only infective in the spheroplast assay when denatured. This structure for the RI is interpreted to mean that the nascent strand is still attached after purification of the RI. It was therefore possible to determine the mode of replication by determining whether the "tail" consisted of the nascent strand (conservative replication) or the displaced portion of the viral strand (semi-conservative replication). Appropriate labeling experiments indicated that the tail could arise from either origin, equally often. It was concluded that double-stranded RNA is involved in phage RNA replication and that replication is both conservative and semi-conservative, equally often
Microfluidic Protein Patterning on Silicon Nitride Using Solvent Extracted Poly(dimethylsiloxane) Channels

Biomolecular patterning is essential for the creation of sensing motifs that rely on receptor-ligand binding for selectivity. Microfluidic devices have the potential to aid in the development of simple, robust methods for biomolecular patterning and therefore contribute to the generation of protein, DNA, and cell microarrays. In microfluidic patterning, the choice of both substrate and microfluidic channel material is essential for control of both the receptor binding for maximal signal generation as well as non-specific adsorption that acts as chemical noise. In this study, polystyrene, glass, silicon nitride, and poly(dimethylsiloxane) (PDMS) were evaluated as substrates for protein patterning using two types of PDMS microchannels for patterning, native PDMS and solvent-extracted PDMS (E-PDMS). E-PDMS microfluidic channels resulted in better patterning characteristics than native PDMS channels as determined by a higher fluorescence intensity of immobilized protein on all substrate types tested. Microfluidic patterning was then applied to perform two- and four-layer immunoassays.
GestureQuery: a multitouch database query interface

Multitouch interfaces allow users to directly and interactively manipulate data. We propose bringing such interactive manipulation to the task of querying SQL databases. This paper describes an initial implementation of such an interface for multitouch tablet devices called GestureQuery that translates multitouch gestures into database queries. It provides database users with immediate constructive feedback on their queries, allowing rapid iteration and refinement of those queries. Based on preliminary user studies, Gesture-Query is easier to use, and lets users construct target queries quicker than console-based SQL and visual query builders while maintaining interactive performance.
Postshock Arrhythmogenesis in a Slice of the Canine Heart

Introduction: Recent evidence has demonstrated that defibrillation shocks terminate or reset reentrant activity in the myocardium through the generation of virtual electrode polarization (VEP). Previous research has revealed that the shock establishes phase singularities (PSs) in the tissue via the VEP mechanism. The aim of this study was to examine, as a function of shock strength and electrode configuration, the relationship between end-shock PSs and the reentrant circuits established after failed defibrillation attempts. Methods and Results: The study uses a complex three-dimensional finite-element bidomain model of a slice of the canine heart characterized by realistic geometry and fiber architecture and undergoing a single scroll wave. Defibrillation shocks of increasing strength are delivered through three different electrode configurations. The results demonstrated that >98% of all PSs have a lifetime of half a reentrant cycle or less. Stronger shocks result in a faster rate of annihilation of postshock PSs. For failed shocks, the surviving PSs underlie the activity of one or more scroll waves, which remain stationary in the slice. For all electrode configurations tested, the increase in shock strength leads to a rapid initial increase in the number of postshock reentries followed by a slower decrease; similar behavior is observed with regard to end-shock PSs. Conclusion: These results present new evidence regarding the mechanisms underlying failure of defibrillation shocks. (J Cardiovasc Electrophysiol, Vol. 14, pp. S249-S256, October 2003, Suppl.)
NSAID-induced apoptosis in Rous sarcoma virus-transformed chicken embryo fibroblasts is dependent on v-src and c-myc and is inhibited by bcl-2.

Abstract Mounting epidemiological and experimental evidence implicates nonsteroidal antiinflammatory drugs as anti-tumorigenic agents. Our previous work showed that nonsteroidal antiinflammatory drug treatment of src-transformed chicken embryo fibroblasts caused apoptosis -- a mechanism by which these drugs might exert their anti-tumorigenic effect. The present studies employ a sensitive technique for detecting single- and double-stranded DNA cleavage (the comet assay) to quantitate apoptosis. By this method pp60v-src, which antagonizes apoptosis in many cell systems, was found to induce apoptosis in 11–23% of serum-starved fibroblasts. However, treatment with diclofenac following pp60v-src activation produced a much stronger response beginning within 6 hours of treatment that resulted in 100% lethality. During cell death, cyclooxygenase-2 but not cyclooxygenase-1 mRNA was found to be uniformly increased by all apoptotic drugs tested. Examination of the expression of apoptosis-associated genes showed that c-rel and p53 (found in normal or v-src-transformed chicken embryo fibroblasts at moderate levels), and bcl-2 (present at an extremely low level) were largely unchanged by treatment with eight different nonsteroidal antiinflammatory drugs. However, over-expression of human bcl-2 inhibited diclofenac-mediated apoptosis by 90%, demonstrating directly that bcl-2 expression can regulate nonsteroidal antiinflammatory drug induction of cell death. The proto-oncogene c-myc is known to cause apoptosis in chicken embryo fibroblasts when artificially overexpressed in cells deprived of trophic factors. We found that nonsteroidal antiinflammatory drug treatment following pp60v-src activation persistently induced myc protein and mRNA by more than 20-fold above that evoked by pp60v-src activation alone. Moreover, transfection of antisense c-myc oligonucleotides reduced drug-induced myc expression by 80% and caused a concomitant 50% reduction in cell death. These findings suggest that nonsteroidal antiinflammatory drug-induced apoptosis proceeds through a src/myc dependent pathway which is negatively regulated by bcl-2.
Control of hot spots in plug flow reactors

This paper addresses the problem of suppressing the magnitude of hot spots in plug flow reactors by manipulating the jacket coolant temperature. A nonlinear control law is derived which guarantees that the hot spot temperature remains below a pre-specified bound for all times after an initial transient, under relatively mild assumptions on the inlet conditions. The performance and robustness of the derived control law are evaluated for the case of a first-order irreversible exothermic reaction.
A comparison of methods for the determination of the pyritic sulfur content of coal

Abstract The accurate determination of the concentration of inorganic sulfur in coal is of major environmental importance. With few exceptions, unless the coal is weathered, the inorganic sulfur present within the coal is iron disulfide minerals, chiefly pyrite and to a lesser extent, marcasite. The accuracy of the presently used ASTM procedure for the determination of iron disulfide sulfur can be questioned because various quantities of the mineral grains encapsulated by the coal matrix are not available to the acid-leaching reaction utilized in the procedure. The goal of this study was to test this hypothesis and to devise a procedure which would give analytical results in agreement with a matrix-independent analytical procedure, namely Mossbauer spectroscopy. The concentration of inorganic sulfur was determined for a suite of coal samples varying in sulfur abundance by the ASTM D2492 procedure on two particle sizes of coal, −60 mesh and −220 mesh. The coal samples were subjected to low-temperature ashing and the resultant ashes were leached with 0.5 N hydrochloric acid. The total weight loss from the ashing process was made up by adding sulfur-free spectrographic grade carbon and the sulfur content of the mixture was determined using a LECO 1R32 sulfur analyzer. The inorganic sulfur contents as determined by the three methods were then compared to the sulfur concentrations as calculated from the iron disulfide abundance as determined by Mossbauer spectroscopy. The data show that the sulfur analysis using ASTM D2492 and the −60 mesh coal sample is unsatisfactory. Acceptable sulfur data can, however, be determined using the ASTM method and −220 mesh coal. The best comparison of data was obtained with the sulfur content obtained by the LECO analysis of the acid-leached low-temperature ash. These results strongly suggest a significant error in inorganic sulfur analysis due to the encapsulation of iron disulfide grains within the organic matrix of the coal when a procedure is used based upon the leaching of the coal sample. The problem can be minimized by utilizing fine-grained coal (−325 mesh) and essentially eliminated by utilizing an hydrochloric acid-leached low-temperature ash.
Cholinergic nucleus basalis neurons may influence the cortex via the thalamus

The cholinergic neurons of the nucleus basalis of Meynert have been shown to provide the major cholinergic innervation of the cerebral cortex through which cholinergic transmission may modulate cortical activity. This study describes a projection from the cholinergic and non-cholinergic neurons of the nucleus basalis to the reticular nucleus of the thalamus, and a projection from the brainstem cholinergic neurons to the reticular nucleus as well as to other thalamic nuclei. The projection from the nucleus basalis to the reticular nucleus, which itself is synaptically interconnected with other thalamic nuclei, may provide an additional pathway for the modulation of cortical activity by the cholinergic basal forebrain and brainstem groups.
Simple pair-wise interactions for hybrid Monte Carlo?molecular dynamics simulations of titania/yttria-doped iron

We present pair-wise, charge-neutral model potentials for an iron–titanium–yttrium–oxygen system. These simple models are designed to provide a tractable method of simulating nanostructured ferritic alloys (NFAs) using off-lattice Monte Carlo and molecular dynamics techniques without deviating significantly from the formalism employed in existing Monte Carlo simulations. The model is fitted to diamagnetic density functional theory (DFT) calculations of the various species over a range of densities and concentrations. The resulting model potentials provide reasonable and in some cases even excellent mechanical and thermodynamic properties for the pure metals. The model replicates the qualitative trends in formation energy predicted by DFT, though the energies of formation do not agree as well for dilute systems as they do for more concentrated systems. We find that on-lattice models will consistently favor tetrahedral oxygen interstitial sites over octahedral interstitial sites, while relaxed systems typically favor octahedral sites. This emphasizes the need for the off-lattice simulations for which this potential was designed.
Propagation of evidence in rule based systems

Abstract This paper extends Shafer's theory of evidence so that the concept of evidence/ignorance can be applied to inference in a rule-based framework. Evidences supporting the truth of the conditions (antecedents) of a rule are propagated together with the evidence supporting the truth of the rule to become the evidence supporting the hypothesis (consequent) of the rule. Propagation with respect to two groups of rules is discussed: algorithmic rules and conditional rules. The propagation procedure is analogous to Dempster's rule of evidence combination, and can be considered a generalization of Dempster's ideas. Ample examples are used to illustrate the procedure.
USE OF HAEMOPHILUS VACCINE IN CONNECTICUT

Although the vaccine against Haemophilus influenzae type b (Hib) is recommended for all children 24-60 months of age and high risk children 18-23 months of age, there is little information about the extent to which these recommendations have been implimented. To assess the use of the vaccine we randomly selected from the hospital logs 202 (2.5%) of the 8.026 children who were born at Yale-New Haven Hospital and were between 18 and 36 months of age on 2/28/86. Parents of the children were interviewed and their physicians were contacted to ascertain whether the child had received the vaccine. After children were excluded because of: inability to locate them (12%), refusal to participate (4%), having moved out of state (2%), death (2%), prior Hib disease (1%) and refusal of the physician to participate (1%), 157 children (78%) were enrolled in the study. Overall, 75 children (48%) had received the vaccine. The vaccine had been received by 2 of 28 children (7%) between 18 and 23 months of age and by 73 of 129 children (57%) between 24 and 36 months of age. Among children whose day care status was known, 17/33 (52%) who attended group day care and 35/77 (45%) who did not attend group day care had received the vaccine. Among children between 24 and 36 months of age, 55/87 (63%) who attended private physicians, 14/28 (50%) who attended prepaid health maintenance organizations, but only 4/14 (29%) who attended public clinics (P<0.05) had received the vaccine. Although widespread implimentation of recommendations for universal immunization had begun 10 months after licensure of the Hib vaccine, rates of immunization were lower among indigent patients who are at increased risk of disease.
Clinical trials report: low-dose oral desmopressin for nocturia.

Introduction: According to the International Continence Society, nocturia is the need to awaken to void one or more times at night [1]. Nocturnal polyuria (NP) is a subclassification of nocturia characterized by nocturnal urine volume that is over 33% of the 24-hour voided volume. Nocturia is a common manifestation of bladder outlet obstruction (BOO) due to prostatic enlargement and one of the most common reasons for interrupted sleep in the adult population [2, 3]. Interrupted sleep can lead to fatigue during waking hours and impairment in daily activities. The act of getting out of bed during the night to void has been linked to a greater risk of hip fractures in older patients [4]. Such a negative impact on quality of life (QOL) can be especially pronounced in elderly adults. The normal diurnal rhythm of decreased urine production at night is not uniformly preserved in the elderly. This phenomenon may be secondary to decreased secretion of antidiuretic hormone (ADH) during the night in this population. Desmopressin is a synthetic analogue of ADH that acts as an antidiuretic by increasing water absorption in the distal and collecting tubules of the kidney. Although a previous study demonstrated that desmopressin does not affect baseline levels of ADH, the administration of desmopressin may compensate for reduced ADH secretion and help restore a normal diurnal rhythm of urine production [5]. Several studies have demonstrated that desmopressin is effective for the treatment of nocturnal enuresis and central diabetes insipidus [6]. Desmopressin also has been shown to significantly reduce nocturia in elderly patients [7, 8]. The study by Wang and colleagues enhances the current literature supporting the use of desmopressin for nocturia with the addition of a welldesigned trial with focus on an elderly male population, longterm follow-up, and uniform use of low-dose desmopressin.
Drought and biodiversity in grasslands

The local species richness of four different grassland fields fell an average of 37% during a 1988 drought that decreased above-ground living plant mass by an average of 47%. Despite the return to more normal plant mass and precipitation during the next two years, there was no significant recovery in species richness in the 46 permanent plots, suggesting that local species richness became recruitment limited. The drought led to the loss of annual species independent of their abundance. For perennial grasses, perennial forbs, legumes and woody species, the probability of a species being lost from a plot was significantly negatively correlated with its predrought abundance. These results demonstrate that environmentally extreme conditions can limit species richness by causing the local extinction of rare species. Because droughts of this intensity occur about every 50 years in the prairie, periodic drought may have limited prairie diversity. Moreover, if the accumulation of greenhouse gases leads to a more variable or extreme climate, it could cause increased rates of species extinctions.
Renal tumor with associated venous tumor thrombus prolapsing through tricuspid valve during diastole

We describe the case of a 76-year-old man with a renal cell carcinoma thrombus extending into the right atrium, prolapsing across the tricuspid valve into the right ventricle during diastole, and producing sufficient portal venous pressure to result in intestinal venous thrombosis and necrosis of the upper gastrointestinal mucosa. The related published studies are reviewed and discussed.
The small splice variant of HPV16 E6, E6, reduces tumor formation in cervical carcinoma xenografts.

Abstract High-risk types of human papillomavirus (HPV) cause nearly all cases of cervical cancer. The E6 oncoprotein is produced as a full-length variant (E6) as well as several shorter isoforms (E6 ⁎ ). E6 ⁎ inhibits certain oncogenic activities of E6, suggesting that it might play an anti-oncogenic role in vivo . To test this, we created E6 ⁎ -expressing SiHa (HPV + ) and C33A (HPV − ) cells, then examined the ability of both the parental and E6 ⁎ -expressing cells to form tumors in nude mice. We found that over-expression of E6 ⁎ indeed decreased the growth of tumors derived from both SiHa and C33A cells, with the reduction greatest in tumors derived from E6 ⁎ -expressing SiHa cells. These findings point to multiple anti-oncogenic characteristics of E6 ⁎ , some of which likely involve down-regulation of the full-length isoform, and others that are independent of HPV. These data represent the first demonstration of biologically-relevant E6 ⁎ activities distinct from those of the full-length isoform in vivo .
WE‐B‐BRA‐01: GPU‐Based Ultra Fast Direct Aperture Optimization in IMRT Treatment Planning

Purpose: To develop a graphics processing unit (GPU) based ultra fast direct aperture optimization (DAO) algorithm in intensity modulated radiation therapy(IMRT)treatment planning.Method and Materials: While DAO problems are well‐studied, most of them focus on heuristic search methods such as simulated annealing and the computational efficiency is often very low. In contrast, we formulate this problem as a large‐scale convex programming problem in terms of all multi‐leaf collimator(MLC) deliverable apertures and their associated intensities. An exact method called column generation method is used which iteratively adds high‐quality deliverable apertures while the treatment plan quality is improved. The efficiency of this approach has been ensured by exploiting fine‐grained parallelism to effectively utilize the computational recourses on GPU. Results: A clinical prostate IMRT case with various beamlet and voxel sizes is used to evaluate our implementation. High quality treatment plans are obtained at a high efficiency. In particular, for a 9‐field prostate case with 5×5 mm2 beamlet size and 2.5×2.5×2.5 mm3 voxel size, the implementation takes only 7.1 seconds to generate 50 MLC apertures on an NVIDIA Tesla C1060 GPU. Conclusion: This work solved a major problem in developing ultra fast (re‐)planning technologies for fast treatment planning in conventional IMRT and for real‐time re‐planning for online adaptive radiotherapy.
THE EFFECTS OF ASPECT RATIO AND SURFACE ROUGHNESS ON SATELLITE RETRIEVALS OF ICE-CLOUD PROPERTIES

Abstract This study investigates the effects of non-sphericity on satellite retrievals of ice-cloud properties including optical thickness and particle sizes. Ray-tracing technique is used to calculate single scattering phase function and single scattering albedo for both smooth and rough surfaces of hexagonal columns and plates at visible and near-infrared wavelengths. Two parameters, aspect ratio and distortion parameter, are used to simulate different, randomly oriented, ice crystal shapes and surface roughnesses in the ray-tracing process. A wide range of aspect ratio and distortion parameter is explored in the calculations. The resultant phase functions and single scattering albedos are used to compute bidirectional reflection functions by a radiative transfer model with adding–doubling technique. The results show that in a direct backscattering regima (Θ>150°), if no information of particle shape is available, the uncertainties in the retrieved optical thickness (a factor of more than ten) would make the retrieval meaningless. For images with viewing geometry outside of this region, the typical range of uncertainty of retrieved optical thickness is less than a factor of about two. Using averaged phase function will cut this uncertainty in half. That is, the uncertainty in the retrieved optical thickness is about 40%. Sensitivity tests show that aspect ratios are critical in reducing the uncertainties of the retrieved optical thickness using satellite data. The uncertainties in the retrieved ice particle sizes are also estimated in a similar way. It is found that using an averaged aspect ratio and roughness, the uncertainty of retrieved particle size is about 30% for small particles and 10% for large particles at λ=3.7 μ m. The corresponding uncertainties are about 70% for small particles and 35% for large particles if data at λ=1.6 or 2.2 μ m are used in the retrieval. However, at λ=1.6 and 2.2 μ m, retrieval of particle size may encounter even larger uncertainties for thin ice-clouds (τ
Estimator Conditioning Diagnostics for Covariance Structure Models

This article studies the utility of a general set of diagnostics for assessing conditioning problems in the covariance structure modeling framework. The diagnostics are based on extensions of the condition index and variance decomposition proportions advanced by Belsley and are based on using the covariance matrix of the estimates. A series of simulations with a variety of covariance structure models as well as a real data example show that these diagnostics are useful for gauging the sensitivity of parameter estimates to conditioning problems arising from collinearity in the raw data. The relationship between ill-conditioning and local identification as it pertains to the proposed diagnostics is also discussed. It is suggested that these diagnostics be implemented in existing covariance structure modeling software.
Taking Back Our Streets: A Clinical Model for Empowering Urban Youths Through Participation in Peace Promotion

A three-stage empowerment model is developed based on the experience of a psychotherapy group conducted with Black and Latino youth residents in an urban housing project with high rates of community violence. The model aims to not only ameliorate mental health symptoms related to exposure to community violence, but also enhance youths' ability to transform their sociocultural context through peace promotion. The three stages are (a) addressing chief complaints and symptom reduction, (b) exploring narratives, and (c) fostering empowerment and peace through community action. Conceptual and clinical strategies are described within each stage, using case illustrations from the psychotherapy group.
Temperature impacts on economic growth warrant stringent mitigation policy

Integrated assessment models estimate the impact of climate change on current economic output, but not on its rate of growth. This study modifies a standard integrated assessment model to allow climate change to directly affect gross GDP growth rates. Results show that climate change significantly slows down GDP growth in poor regions but not in rich countries, with implications for the level of near-term mitigation.
Correlation of corneal thickness and volume with intraoperative phacoemulsification parameters using Scheimpflug imaging and optical coherence tomography.

Purpose To evaluate post-phacoemulsification corneal edema using central corneal thickness (CCT) and central corneal volume (CCV) derived from Scheimpflug imaging, optical coherence tomography (OCT), and ultrasound (US) pachymetry and to correlate CCV with phacoemulsification parameters. Setting Department of Ophthalmology, Boston Medical Center, Boston, Massachusetts, USA. Design Prospective case study. Methods Scheimpflug imaging (Pentacam HR), OCT (Cirrus HD-OCT), and US pachymetry (Pachmate) were used to measure the CCT, CCV, and phacoemulsification parameters after uneventful phacoemulsification over a 1-month follow-up. Results In the 16 eyes assessed, the Scheimpflug CCT was less than the US CCT preoperatively ( P =.01) and 1 week postoperatively ( P =.02). The OCT CCT was less than the US CCT at 1 week and 1 month (both P P P =.09). However, the 7.0 mm CCV remained elevated at 1 month ( P r = 0.76) and phacoemulsification time ( r = 0.61). Conclusions Scheimpflug imaging and OCT underestimated the CCT in normal eyes compared with US pachymetry, with a trend toward thicker measurements in acutely edematous corneas. Although the CCV returned to preoperative values at 1 month, the peripheral cornea remained edematous, possibly because of a correlation with the estimated amount of fluid used and phacoemulsification time. Financial Disclosure No author has a financial or proprietary interest in any material or method mentioned.
Simultaneous determination of nitroglycerin and dinitrate metabolites in metabolism studies using liquid chromatography-mass spectrometry with electrospray ionization

We have developed a liquid chromatographic-mass spectrometric method for the simultaneous determination of nitroglycerin (NTG) and its active metabolites, glyceryl 1,2-dinitrate (1,2-GDN) and glyceryl 1,3-dinitrate (1,3-GDN), for metabolism studies in cell cultures. 1,2,4-Butanetriol-1,4-dinitrate was chosen as an internal standard. Using a linear gradient of water/methanol containing 0.025 mM NH(4)Cl, the compounds were eluted within 12.5 min on an Allure Aqueous C(18) column (100 mm x 2.1 mm). Detection and quantification was achieved with multiple reaction monitoring in the negative ion mode. Intra- and inter-day variabilities for simultaneous determination of the three nitrates were below 10 and 18%, respectively, over a range of NTG and GDN concentrations of 0.5-15 ng/ml. The lower limit of quantification was found to be about 0.01 ng on column. Application of this method was illustrated through in vitro metabolism studies of NTG in culture media bathing LLC-PK1 cells and human vascular smooth muscle cells (HA-VSMC) at 37 degrees C. The degradation half-life of NTG was found to be 4.5 +/- 0.4 h and 39.2 +/- 0.02 h, respectively, for LLC-PK1 cells versus HA-VSMC. At 5 h, the 1,2-GDN versus 1,3-GDN metabolite distribution ratio in the bathing medium was found to be 1.5 +/- 0.1 and 0.2 +/- 0.02 for LLC-PK1 and HA-VSMC cells, respectively. With this method, the degradation half-life of NTG in rat plasma at 37 degrees C was shown to be 26.8 +/- 1.8 min, consistent with previous values obtained using gas chromatography.
Scanning tunneling microscope observations of pulsed laser modification of the basal plane of graphite

Abstract Scanning tunneling microscopy has been used to investigate changes in the morphology of the basal plane of graphite after exposure to 7 ns, 1064 nm laser pulses in air. Damage appears first on step edges and consists of exfoliation of graphite layers. Results indicate that a process other than oxidation is responsible.
13C NMR assignments of the protonated carbons of [d(TAGCGCTA)]2 by two-dimensional proton-detected heteronuclear correlation.

Abstract The resonances of the protonated carbons of [d(TAGCGCTA)]2 have been assigned by the two-dimensional proton-detected double-quantum heteronuclear correlation experiment ([1H-l3C]-DQCOSY). 13C-coupled and l3C-decoupled versions of the experiment were used. The assignment method is discussed in detail. The deoxyribose cross peaks segregate into five well-resolved regions, and the base cross peaks have distinct features that are helpful for assignments. The cross peaks from the 1H-13C pairs at the Cyd5, Ado2 and ThdCH3 base positions fall in separate regions of the spectrum from each other; they also are resolved from the closely spaced Ado8, Guo8, Cyd6 and Thd6. Additional parameters for distinction of the base signals are their differing J-coupling values and long-range coupling patterns.
Characterization of quantum-confined CuCl microcrystals in a glassy matrix

Abstract Quantum confinement effects of semiconductor microcrystallites (CuC1) embedded in a glassy ( aluminoborosilicate) matrix are of current interest due to their exceptional nonlinear optical properties. Theprecipitation of microcrystals occurs upon heat-treatment of a glass in a supersaturated solution. The timeand/or temperature of heat-treatment and the degree of supersaturation of the solution determines the size ofthe microcrystals. This paper characterizes the microcrystals using TEM when the heat-treatment conditions arevaried. Room temperature ESR measurements were performed in order to determine the ratio of Cu2 to Cu'in the glass at various compositions before heat-treatment. Low temperature optical absorption data werejobtained to study the quantum confinement and the effect of varying the microcrystal size.I. IntroductionWithin the last ten years the optical properties of semiconductor microcrystals embedded in a glassy matrix have attracted considerable interest.19 Much is known about the large nonlinearities of thin film quantum-
Real time motion analysis toward semantic understanding of video content

Video motion analysis and its applications have been a classic research topic for decades. In this paper, we explore the problem of real time video semantics understanding based on motion information. The work can be divided into two segments: global / camera motion estimation and object motion analysis. The former involves optical flow analysis and semantic meaning parsing, and the latter involves object detection and tracking. Although each of these topics has been studied extensively in the literature, a thorough system combining all of them without human intervention, especially under a real time application scenario, is still worthy of further investigation. In this paper we develop our approach toward such a destination and propose an integral architecture. The usability and efficiency of the proposed system have been demonstrated through experiments. Results of this project have numerous applications in digital entertainment, such as video and image summarization, annotation, retrieval and editing.
Cell-free recombination of immunoglobulin switch-region DNA with nuclear extracts.

We have developed an in vitro recombination system employing cell-free nuclear extracts from human B lymphocytes capable of detecting the recombination between human mu switch (Smu) and Sepsilon sequences in a model plasmid. Nuclear extracts from CD40-stimulated B lymphocytes gave a higher frequency of recombination in the assay than the unstimulated B cells. Recombination between Smu and Sepsilon was mediated by the nuclear extracts as the recombinational products could be amplified prior to bacterial transformation. Characterization of the recombination products demonstrated that the recombination process had the characteristics of immunoglobulin (Ig) isotype switching, as it was (i) switch-region-sequence specific, (ii) nonhomologous recombination, and (iii) enhanced by CD40 stimulation. Transcription through the S region DNA was not required for recombination in the system. These results demonstrate that Ig switch-region DNA recombination can be accomplished in vitro by cell-free nuclear extracts. This in vitro system for Ig switch-region DNA recombination using cell-free nuclear extracts will permit the dissection of the events involved in IgE class switch recombination, a critical event in the development of allergic diseases.
Proportion of the HeLa cell genome complementary to transfer RNA and 5 s RNA

Abstract The proportion of the HeLa cell genome complementary to tRNA and to 5 s RNA has been investigated by using the technique of RNA-DNA hybridization. The specificity of hybrids formed between HeLa DNA and these highly purified RNA classes has been assessed by analysis of the size distribution and nucleotide composition of the RNA recovered from the ribonuclease-treated hybrids. The value of saturation of HeLa DNA by tRNA corresponds to a fraction of the DNA of about 1.1 × 10 −5 , i.e. to about 4900 sites for this RNA class per exponentially growing cell, or about 1310 tRNA sites per haploid genome. The data on the size distribution of the hybridized RNA chains suggest the possibility that there is some sequence variability among the multiple sites in DNA for the same tRNA species and that each tRNA is capable of hybridizing with different sites for the same tRNA species. The saturation value obtained for 5 s RNA corresponds to a fraction of the DNA of about 2.5 × 10 −5 , i.e. to about 7600 sites per exponentially growing cell or 2000 per haploid genome. The large difference in number between 45 s and 5 s sites in the HeLa cell genome suggests that most of the 5 s sites are not being transcribed at all, or are being transcribed at a reduced rate relative to the 45 s sites, or are being transcribed at a similar rate as the 45 s sites, but that much of the 5 s RNA is being degraded. The analysis of size distribution of the hybridized 5 s RNA supports the conclusion of previous structural studies that there exists a limited degree of heterogeneity among 5 s sites in the HeLa cell genome.
Remediation of hemorrhagic shock-induced intestinal barrier dysfunction by treatment with diphenyldihaloketones EF24 and CLEFMA.

Gut is very sensitive to hypoperfusion and hypoxia, and deranged gastrointestinal barrier is implicated in systemic failure of various organs. We recently demonstrated that diphenyldihaloketone EF24 [3,5-bis(2-fluorobenzylidene)piperidin-4-one] improves survival in a rat model of hemorrhagic shock. In this study, we tested EF24 and its other analog CLEFMA (4-[3,5-bis(2-chlorobenzylidene)-4-oxo-piperidine-1-yl]-4-oxo-2-butenoic acid) for their effect on intestinal barrier dysfunction in hypovolemic shock. Hypovolemia was induced in rats by withdrawing 50% of blood. EF24 or CLEFMA (0.4 mg/kg i.p.) treatment was provided, without volume resuscitation, after 1 hour of hemorrhage. Ileum was collected 5 hours after the treatment to investigate the expression of tight junction proteins (zonula occludens, claudin, and occludin) and epithelial injury markers [myeloperoxidase, ileal lipid-binding protein (ILBP), CD163, and plasma citrulline]. The ileal permeability for dextran-fluoroisothiocyanate and Evan’s blue dye was determined. EF24 and CLEFMA reduced the hypovolemia-induced plasma citrulline levels and the ileal expression of myeloperoxidase, ILBP, and CD163. The drugs also restored the basal expression levels of zonula occludens, claudin, and occludin, which were substantially deranged by hypovolemia. In ischemic ileum, the expression of phospho(tyrosine)-zonula occludens-1 was reduced, which was reinstated by EF24 and CLEFMA. In contrast, the drug treatments maintained the hypovolemia-induced expression of phospho(threonine)-occludin, but reduced that of phospho(tyrosine)-occludin. Both EF24 and CLEFMA treatments reduced the intestinal permeability enhanced by hypovolemia. EF24 and CLEFMA attenuate hypovolemic gut pathology and protect barrier function by restoring the status of tight junction proteins. These effects were observed in unresuscitated shock, implying the benefit of EF24 and CLEFMA in prehospital care of shock.
Heterogeneity of heparan sulfate proteoglycans synthesized by PYS-2 cells

Antibodies to the basement membrane proteoglycan produced by the EHS tumor were used to immunoprecipitate [35S]sulfate-labeled protoglycans produced by PYS-2 cells. The immunoprecipitated proteoglycans were subsequently fractionated by CsCl density gradient centrifugation and Sepharose CL-4B chromatography. The culture medium contained a low-density proteoglycan eluting from Sepharose CL-4B at Kav = 0.18, containing heparan sulfate side chains of Mr = 35-40,000. The medium also contained a high-density proteoglycan eluting from Sepharose CL-4B at Kav = 0.23, containing heparan sulfate side chains of Mr = 30,000. The corresponding proteoglycans of the cell layer were all smaller than those in the medium. Since the antibodies used to precipitate those proteoglycans were directed against the protein core, this suggests that these proteoglycans share common antigenic features, and may be derived from a common precursor which undergoes modification by the removal of protein segments and a portion of each heparan sulfate chain.
L-Shaped Resonant Microring (LRM) filter with integrated thermal tuner

A new filter, an L-Shaped Resonant Microring (LRM), is introduced in the application of a highly efficient (3.3-μW/GHz) thermal tuner that enables electrical contact while maintaining single-mode operation and a large 4-THz spur-free FSR.
Interaction efficiencies in kronecker block designs

Abstract It is proved that in a multi-factor Kronecker design, the efficiency factor of the interaction involving m factors is at least as large as the efficiency factors of the main effects of those m factors.
Measurement of Orientation and Distribution of Cellular Alignment and Cytoskeletal Organization

Endothelial cells elongate and align with the direction of applied fluid shear stress. Previously, automated methods for analysis of cell orientation distribution have used Fourier- or fractal-based methods. We used intensity gradients in images of control and sheared endothelial cells to measure orientation distributions. Automated measurements of mean orientation and angular deviation compared favorably with manual measurements. There was a significantly greater angular deviation in images of control cells compared with sheared cells. Automated methods were also used to quantify organization of cytoskeletal fibers using the local angular deviation and a measure of the local coalignment of fibers called the coalignment ratio. The local angular deviation of microtubules and microfilaments was significantly smaller in sheared cells compared with control. The coalignment of cytoskeletal fibers was significantly greater in sheared cells. We conclude that image intensity gradients can be used rapidly, accurately, and objectively to measure cell orientation distributions and cytoskeletal filament organization. © 1999 Biomedical Engineering Society. PAC99: 8716Ka, 8717-d, 8719Rr, 8764Rr, 0705Pj
Diagnostic tests for pertussis: Culture vs. DFA vs. PCR

The “gold standard” for the laboratory diagnosis of Bordetella pertussis infections has always been culture, but for physicians and epidemiologists, that gold standard has always fallen short. With the advent of PCR, many argue that culture should be replaced by PCR. This article will review the three major laboratory methods used to diagnose pertussis and compare their advantages and disadvantages.