cssi/SciSciGPT-SciSciNet huggingface dataset:
Scaffold mining of kinase hinge binders in crystal structure database

Protein kinases are the second most prominent group of drug targets, after G-protein-coupled receptors. Despite their distinct inhibition mechanisms, the majority of kinase inhibitors engage the conserved hydrogen bond interactions with the backbone of hinge residues. We mined Pfizer internal crystal structure database (CSDb) comprising of several thousand of public as well as internal X-ray binary complexes to compile an inclusive list of hinge binding scaffolds. The minimum ring scaffolds with directly attached hetero-atoms and functional groups were extracted from the full compounds by applying a rule-based filtering procedure employing a comprehensive annotation of ATP-binding site of the human kinase complements. The results indicated large number of kinase inhibitors of diverse chemical structures are derived from a relatively small number of common scaffolds, which serve as the critical recognition elements for protein kinase interaction. Out of the nearly 4,000 kinase-inhibitor complexes in the CSDb we identified approximately 600 unique scaffolds. Hinge scaffolds are overwhelmingly flat with very little sp3 characteristics, and are less lipophilic than their corresponding parent compounds. Examples of the most common as well as the uncommon hinge scaffolds are presented. Although the most common scaffolds are found in complex with multiple kinase targets, a large number of them are uniquely bound to a specific kinase, suggesting certain scaffolds could be more promiscuous than the others. The compiled collection of hinge scaffolds along with their three-dimensional binding coordinates could serve as basis set for hinge hopping, a practice frequently employed to generate novel invention as well as to optimize existing leads in medicinal chemistry.
Measuring mandibular vertical bone resorption by radiographic cephalometry.

Abstract A radiographic cephalometric method was established to measure the vertical bone resorption of the residual ridges in edentulous patients. No attempt was made to correlate the results with the many variables interacting on the rate of resorption. The pattern of bone resorption was different in all patients and was not the same on both sides of the mandible in the same patient. The highest incidence of bone resorption occurred in the region of the retromolar pad behind the distal border of the lower denture. This problem needs further investigation to determine the exact effect of wearing dentures on bone resorption to help develop the best technique and materials for denture construction.
Transgenerational effects of the endocrine disruptor vinclozolin on the prostate transcriptome and adult onset disease.

PURPOSE The ability of an endocrine disruptor exposure during gonadal sex determination to promote a transgenerational prostate disease phenotype was investigated in the current study. METHODS Exposure of an F0 gestating female rat to the endocrine disruptor vinclozolin during F1 embryo gonadal sex determination promoted a transgenerational adult onset prostate disease phenotype. The prostate disease phenotype and physiological parameters were determined for males from F1 to F4 generations and the prostate transcriptome was assessed in the F3 generation. RESULTS Although the prostate in prepubertal animals develops normally, abnormalities involving epithelial cell atrophy, glandular dysgenesis, prostatitis, and hyperplasia of the ventral prostate develop in older animals. The ventral prostate phenotype was transmitted for four generations (F1–F4). Analysis of the ventral prostate transcriptome demonstrated 954 genes had significantly altered expression between control and vinclozolin F3 generation animals. Analysis of isolated ventral prostate epithelial cells identified 259 genes with significantly altered expression between control and vinclozolin F3 generation animals. Characterization of regulated genes demonstrated several cellular pathways were influenced, including calcium and WNT. A number of genes identified have been shown to be associated with prostate disease and cancer, including beta-microseminoprotein (Msp) and tumor necrosis factor receptor superfamily 6 (Fadd). CONCLUSIONS The ability of an endocrine disruptor to promote transgenerational prostate abnormalities appears to involve an epigenetic transgenerational alteration in the prostate transcriptome and male germ-line. Potential epigenetic transgenerational alteration of prostate gene expression by environmental compounds may be important to consider in the etiology of adult onset prostate disease. Prostate 68: 517–529, 2008. © 2008 Wiley-Liss, Inc.
Near-IR surface-enhanced Raman spectrum of lignin

Compacted powders of commercially available nano- and microparticles of silver were used to successfully induce the surface-enhanced Raman scattering (SERS) effect in spruce milled-wood lignin (MWL). For the two silver particle sizes used in this investigation, the spectra were mostly similar. Some general characteristics of the lignin SERS spectrum are described. The SERS technique was found to be sensitive for detecting lignin. Significant spectral changes were present between the SERS and normal Raman spectra of MWL. The SERS spectrum was assigned on the basis of literature-reported vibrational assignments of lignin and its models. Based on significant changes in Raman features, we propose that the lignin is strongly adsorbed on silver. To determine whether SERS of lignin can be obtained directly from wood without its isolation, Wiley-milled spruce wood (WMW) adsorbed on silver was studied. The results indicated that not only the surface-enhancement effect was successfully induced in the WMW, but that its spectrum was similar to MWL SERS. Moreover, for WMW, no signals from the carbohydrate components were observed, and therefore, lignin was detected selectively. This nano- and microparticle-based molecularly specific method is expected to make a significant contribution in identifying and investigating lignin in various lignin-containing materials. Published in 2009 by John Wiley & Sons, Ltd.
Limitations of Computerized Tomography in the Localization of intraocular Foreign Bodies

Computerized tomography (CT) scanning was used to evaluate nine patients with intraocular foreign bodies. We found that significant limitations of this method still exist, even with high resolution scanners, in the localization of extremely small, multiple or relatively radiolucent foreign bodies and those located near the ocular wall.
Polystyrene/wood composites and hydrophobic wood coatings from water-based hydrophilic-hydrophobic block copolymers

The combination of synthetic thermoplastic polymers and wood is normally problematic because wood surfaces are hydrophilic while typical thermoplastic polymers are hydrophobic. A possible solution is to use block copolymer coupling agents. In this work we show the use of a potentially useful synthetic method of producing hydrophilic-hydrophobic block copolymers as hydrophobic coatings and coupling agents in polystyrene/ wood flour composites. In particular, wood veneers are coated with water-based emulsions of hydrophilic-hydro- phobic block copolymers from styrene and methacrylic acid. Dried coated surfaces are shown to become hydro- phobic through dynamic contact angle measurements. When wood flour is coated with the hydrophilic-hydro- phobic block copolymer based on styrene and acrylic acid, significant improvement in the ultimate tensile properties of composites formed from coated wood flour/ polystyrene mixtures is realized. Since no volatile organic compounds (VOCs) are used in coating wood surfaces and subsequent composite production, improvement in mechanical properties of thermoplastic/wood flour composites are shown to occur in environmentally responsible formulations.
The Contribution of Executive Skills to Reading Comprehension

Although word recognition deficits (WRD) are a known cause of reading comprehension deficits (RCD), other contributions to RCD, including executive function (EF), have not been fully explored. We examined the contribution of EF (working memory and planning), along with attention, decoding, fluency, and vocabulary to reading comprehension in 60 children (including 16 WRD and 10 RCD), ages 9–15 years. After controlling for commonly accepted contributors to reading comprehension (i.e., attention, decoding skills, fluency, and vocabulary), EF continued to make a significant contribution to reading comprehension but not to word recognition skills. These findings highlight the need for consideration of the role of EF in RCD.
Perovskite stacking in the structures of the high temperature cuprate superconductors

Abstract Most of the known cuprate superconductors belong structurally to one family and are closely related to each other. Ignoring odd structural details and considering the idealized structures only, most of them adopt a Ruddlesden-Popper (R-P) or an oxygen-deficient R-P structure with or without intergrowth layers which are composed of either a rock-salt type atomic arrangement, chains, bare cations, or a mixture of them. The rock-salt layers found in R-P structures are simply the result of the stacking of perovskite unit cells. Sometimes a fluorite type structural unit can be found, but the structures containing fluorite blocks may also be considered to be of the R-P structure type with minor readjustment of anions in the rock-salt layers to stabilize the structure. A general formula can be used to describe the basic structures of all the cuprate superconductors, even those having fluorite units.
Catalytic removal of NO from post-flame gases in low pressure stagnation-point flames over platinum

Abstract Experimental NO profiles in H 2 /O 2 /NH 3 stagnation point flames over platinum substrates are obtained with laser-induced fluorescence for a range of flame equivalence ratios and substrate temperatures. This study generates baseline data against which comprehensive gas-phase and surface chemical models of NO destruction can be compared. The experimental profiles are compared with the predictions of a one-dimensional stagnation flow model that includes full gas-phase chemistry, multicomponent transport, and detailed surface chemistry. A baseline surface chemistry mechanism, assembled by using conventional H/O heterogeneous chemistry and NO adsorption and dissociation followed by N 2 desorption, provides good agreement with the experimental results for only a limited range of operating conditions. At low temperatures (425 K), the mechanism underpredicts NO removal, while at high temperatures (940 K) and fuel-lean conditions (Φ = 0.7) the mechanism overpredicts NO destruction. Addition of NH 2 and N 2 O production to the surface mechanism does not improve the level of agreement. However, consideration of the reconstruction of the platinum surface at high temperatures tends to shift the predicted profiles closer to those observed in the experiment for the high temperature cases.
A simple derivation of field-effect transistor characteristics

In the conventional treatment of the field effect transistor, the first step is the specification of an impurity profile that describes the nature of the gate-channel contact. Solutions for the static and small-signal characteristics are then valid only for the particular impurity profile chosen, and must be repeated from the beginning for different structures. The purpose of this communication is to present a simple, though approximate, development of the characteristics of an FET without specifying the detailed nature of the structure. The charge-control approach is used, and it is shown that in the pinch-off region the relation between the drain current and the gate-source voltage is approximately square law. The results are applicable to all gate-channel structures, including the insulated gate types.
Using Phase Effects to Understand Measurements of the Quantum Efficiency and Related Luminescent Coupling in a Multijunction Solar Cell

We analyze the quantum efficiency measurement of a series-connected multijunction solar cell by modeling the cell as an ac resistive-capacitive circuit and studying the complex current as a function of the light biasing. The photocurrent induced by directly absorbed photons is modeled as an independent current source, whereas the luminescent coupling current from higher bandgap to lower bandgap subcells is modeled as a dependent current source in the bottom subcell. We derive expressions for the equivalent impedance and the complex current in measurements of the top and bottom subcells of a two-junction device. High light biasing of the nonlimiting cell drives the magnitude and phase shift of the current toward well-defined limits, but insufficient light biasing yields a composite response that is not fully characteristic of either subcell. We recommend that the experimenter always monitor the phase shift of the signal for signs of insufficient light biasing, and to help identify genuine luminescent coupling effects.
Availability of Phosphorus to Sugar Cane in Hawaii as Influenced by Various Phosphorus Fertilizers and Methods of Application

An experiment was carried out in the glasshouse to determine the availability of P, and utilization of added phosphate fertilizers from three fertilizer materials, applied by two different methods to sugar cane grown in four diverse soil systems. Phosphorus was applied at the equivalent rate of 175 pounds P (400 pounds P 2 O 5 ) per acre. A larger response from added P in terms of plant yields was obtained from an aluminous ferruginous latosol and least from dark magnesium clay. Differences in yields of sugar cane were evidently associated with differences in P content in the cane plants and, in certain cases, with a reduction in Al content in plant tops, and the less soluble superphosphate increased yields more than the highly soluble NH 4 H 2 PO 4 . Phosphate fertilizers applied as foliar spray greatly increased the P content in the plants, and plants contained twenty times more P when sprayed with NH 4 H 2 PO 4 than when the same fertilizer was applied to the soil. However, increased P content in the plants did not necessarily indicate that the P was translocated within the plants or that the added P participated in metabolic processes. The evidence indicated that in soils where the ‘A’ value was high the P status of the sugar cane tops was not correspondingly high.
Photobacterium damselae subsp. piscicida Is Capable of Replicating in Hybrid Striped Bass Macrophages

Abstract The purpose of this study was to use an in vitro assay to evaluate the ability of Photobacterium damselae subsp. piscicida to survive and replicate within macrophages obtained from hybrid striped bass (striped bass Morone saxatilis × white bass M. chrysops). The results indicated that the number of bacteria recovered from macrophages after 3, 6, 12, and 18 h of incubation increased significantly from time 0 (105, 510, 1,091 and 1,385%, respectively). Replication of the intracellular bacteria was observed at a very low multiplicity of infection (1 bacterium to 100 macrophages). In contrast, the number of Escherichia coli recovered from macrophages declined 47, 80, 91, and 96%, respectively. Light and electron microscopy confirmed the internalization, uptake, and multiplication of bacteria within spacious, clear vacuoles in the macrophages. Using acid phosphatase as a lysosomal marker, we provide evidence that P. damselae subsp. piscicida inhibits phagolysosomal fusion. This study demonstrates that...
Dual probe use for the remote measurement of an antenna under test

This paper explores an alternative to the previous remote impedance measurement of antennas to improve the dynamic range of the needed data for the measurements. Previous work evaluated the refection coefficient of a source antenna as a function of the termination on the antenna under test (AUT). The loads used in the measurement are the classic open-short-load, with measured data used for the actual termination impedances. The impedance of the AUT is determined by a standard calibration approach. For current vector network analyzers, the dynamic range of the analog-to-digital converter limits the impedance estimate, particularly if the distance between the source and AUT is increased to reduce interaction affecting the impedance of the AUT. The new approach separates the transmit and receive functions to allow the use of a LNA to improve the receive signal strength and offer the opportunity to overcome some of the limitations of the reflection approach.
Antibacterial factors in the sipunculid worms Golfingia gouldii and Dendrostomum pyroides.

Abstract The coelomic fluid of Golfingia gouldii (an east coast sipunculid worm) exhibited in vitro antibacterial activity against several marine bacteria. This activity is heat labile and is lost after trypsinization. It is resistant to treatment with pepsin, lipase, or toluene extraction and appears to be unaffected by freezing and thawing. Dialysis against seawater also causes the loss of antibacterial activity. Dendrostomum pyroides (a west coast sipunculid) exhibits a similar type of in vitro antibacterial activity in its coelomic fluid, suggesting that nonspecific antimicrobial substances may be common in this phylum.
Nuclear magnetic resonance relaxation of water adsorbed on bacterial cell walls.

Abstract The nuclear magnetic resonance (nmr) relaxation of water adsorbed on the isolated walls of a representative bacterium, Bacillus megaterium, has been investigated. Pulsed nmr methods were applied to walls containing 33% water over a temperature range of 160°–330°K. The results are in accord with the accepted model of nmr relaxation according to which relaxation is due to the relative motion of nuclear dipoles with respect to one another, and for which a log-normal distribution of molecular jump times is assumed. The interpretation is that at 0°C the median jump time of a water molecule in the cell wall at low hydration is lower by almost two orders of magnitude than in bulk water, yet higher by almost four orders of magnitude than in ice. The width at half height of the distribution of jump times is about four orders of magnitude. From the standpoint of mobility, the water in the cell walls, even at this low hydration, is more nearly “liquid-like” than “icelike.”
Fumonisin B1 does not prevent apoptosis in A431 human epidermoid carcinoma cells after photosensitization with a silicon phthalocyanine.

Abstract Photodynamic therapy with the phthalocyanine photosensitizer Pc 4 (Pc 4-PDT), an apoptosis inducer, is associated with accumulation of ceramide in various cell lines. The role of ceramide in Pc 4-PDT-induced apoptosis was investigated in A431 cells. Caspase-3 (casp-3) was activated and TUNEL positive cells began to appear 30 and 60 min post-Pc 4-PDT, respectively. A rapid increase (10 min) in cellular ceramide levels was observed after Pc 4-PDT. Induced ceramide accumulation was maintained over 60 min. Acid sphingomyelinase, a ceramide-generating enzyme, was inhibited after photosensitization with Pc 4, suggesting that the enzyme was not required for stimulated ceramide accumulation. Co-treatment of A431 cells with fumonisin B1, a ceramide synthase inhibitor, and Pc 4-PDT led to a decrease in ceramide levels without any effect on induced casp-3 activity or apoptosis. In the presence of zVAD, a pan-caspase inhibitor, apoptosis was abolished, while ceramide levels remained elevated after Pc 4-PDT. Exposure of A431 cells to exogenous C6-ceramide for 22 h, led to induction of apoptosis, and the process was abrogated by zVAD. In conclusion, C6-ceramide-, like Pc 4-PDT-induced apoptosis, is zVAD-sensitive. Furthermore, Pc 4 photosensitization can lead to apoptosis without FB-sensitive elevation in ceramide levels upstream of caspases.
Two qubit entanglement when the RWA is violated

We investigate the entanglement dynamics of two quasi-degenerate qubits interacting with a quantized oscillator in a parameter regime where the rotating wave approximation breaks down. Analytical formulas for collapse and revival of entanglement are derived.
Immobilization of ethylene bis-indenyl ligands on functionalized silica gel

Abstract Four ethylene bis-indenyl ligands containing tethers of various lengths were successfully immobilized on the surface of functionalized silica gel. The strategy of immobilization was based on catalytic thiol–ene coupling of terminal alkene groups in the tethers with surface thiol groups. Obtained materials have high BET surface area and pore volume. The method developed can be used for immobilization of catalytically active bis-indenyl metallocene complexes, thus preventing their dimerization and deactivation.
501 SOMATOMEDIN (Sm-C) in FETAL GROWTH

In the postnatal rat, suboptimal nutrition leads to a decrease in Sm-C which may account for the resultant decrease in growth. To study the effect of fetal malnutrition on serum and tissue Sm-C concentrations, intrauterine growth retardation(IUGR) was induced by uterine artery ligation on day 17 of gestation in 15 pregnant rats. Fetuses of the non-ligated horns served as appropriately grown(AGA) controls. After surgery the animals were allowed ad libitum feeding. On day 21 fetal blood and organs were obtained and analyzed for Sm-C and insulin by radioimmunoassay and glucose by glucose oxidase. Data are presented in relation to uterine position with 1 denoting the fetus nearest the ovarian artery. At each position, IUGR fetuses had decreased weight, serum and liver Sm-C, glucose, and insulin concentrations. (x±sem, *p<.05) Fetal weight was significantly related to glucose (r=.730), liver Sm-C (r=.682) and serum Sm-C (r=.452). Stepwise linear regression demonstrated that these three factors in combination correlated highly with fetal weight (r=.836). A weaker correlation existed for insulin (r=.378) and lung Sm-C (r=.209). These data indicate that, in the fetus, Sm-C is influenced by nutrition and may have a mediating role in the control of growth.
Fluorine-18 fluorodeoxyglucose positron emission tomographic maximal standardized uptake value predicts survival independent of clinical but not pathologic TNM staging of resected non–small cell lung cancer

Objectives Positron emission tomographic maximal standardized uptake value has been shown to predict survival after resection of non–small cell lung cancer. The relative prognostic benefit of maximal standardized uptake value with respect to other clinical/pathologic variables has not been defined. Methods We reviewed patients who had positron emission tomographic imaging and an R0 resection for non–small cell lung cancer between January 1, 2000, and December 31, 2004, without induction or adjuvant therapy. The associations between overall survival, histology, pathologic TNM stage, pathologic tumor diameter, and standardized uptake value were tested. Results Four hundred eighty-seven patients met the study criteria. Median follow-up was 25.8 months. By using the median values for tumor size (2.5 cm) and standardized uptake value (5.3), standardized uptake value was an independent predictor of survival ( P = .03), adjusting for tumor size ( P = .02) and histology ( P P = .03) after adjusting for clinical TNM stage. Standardized uptake value was not an independent predictor of survival ( P = .09), adjusting for pathologic TNM stage (stage IA vs IB vs stage II–IV, P Conclusions Standardized uptake value does not add to the prognostic significance of pathologic TNM stage. Standardized uptake value was an independent prognostic factor from clinical TNM stage.
Harnessing systems biology approaches to engineer functional microvascular networks.

Microvascular remodeling is a complex process that includes many cell types and molecular signals. Despite a continued growth in the understanding of signaling pathways involved in the formation and maturation of new blood vessels, approximately half of all compounds entering clinical trials will fail, resulting in the loss of much time, money, and resources. Most pro-angiogenic clinical trials to date have focused on increasing neovascularization via the delivery of a single growth factor or gene. Alternatively, a focus on the concerted regulation of whole networks of genes may lead to greater insight into the underlying physiology since the coordinated response is greater than the sum of its parts. Systems biology offers a comprehensive network view of the processes of angiogenesis and arteriogenesis that might enable the prediction of drug targets and whether or not activation of the targets elicits the desired outcome. Systems biology integrates complex biological data from a variety of experimental s...
POPBAM: Tools for Evolutionary Analysis of Short Read Sequence Alignments.

Background: While many bioinformatics tools currently exist for assembling and discovering variants from next-generation sequence data, there are very few tools available for performing evolutionary analyses from these data. Evolutionary and population genomics studies hold great promise for providing valuable insights into natural selection, the effect of mutations on phenotypes, and the origin of species. Thus, there is a need for an extensible and flexible computational tool that can function into a growing number of evolutionary bioinformatics pipelines. Results: This paper describes the POPBAM software, which is a comprehensive set of computational tools for evolutionary analysis of whole-genome alignments consisting of multiple individuals, from multiple populations or species. POPBAM works directly from BAM-formatted assembly files, calls variant sites, and calculates a variety of commonly used evolutionary sequence statistics. POPBAM is designed primarily to perform analyses in sliding windows across chromosomes or scaffolds. POPBAM accurately measures nucleotide diversity, population divergence, linkage disequilibrium, and the frequency spectrum of mutations from two or more populations. POPBAM can also produce phylogenetic trees of all samples in a BAM file. Finally, I demonstrate that the implementation of POPBAM is both fast and memory-efficient, and also can feasibly scale to the analysis of large BAM files with many individuals and populations. Software: The POPBAM program is written in C/C++ and is available from http://dgarriga.github.io/POPBAM. The program has few dependencies and can be built on a variety of Linux platforms. The program is open-source and users are encouraged to participate in the development of this resource.
Left Definite Theory for Second Order Differential Operators with Mixed Boundary Conditions

Abstract Left definite theory of regular self-adjoint operators in a Sobolev space was developed a few years ago when the boundary conditions were separated, the separation being necessary in order to properly define the Sobolev inner product. We show how this may be extended when the boundary conditions are not separated, but when evaluations at both ends are mixed together. There are essentially three cases which arise: First when a coefficient matrix is nonsingular, second when it is singular but not 0, third when it is 0. The middle case does not arise under separated conditions.
Forced Response of Translating Media With Variable Length and Tension and a Mass-Spring Termination

The lateral response of vertically translating media with variable length and tension and a mass-spring termination is determined for general initial conditions and external excitation. The translating media are modeled as a taut string and tensioned beams with pinned and fixed boundary at the upper end. In each case a spring-mass sub-system is attached at the lower end of the translating medium. The rates of change of the energies in each case are analyzed and interpreted from the control volume and system viewpoints. The models are used to predict the forced response of cable-car systems in high-speed elevators due to building sway, pulley eccentricity, and guide-rail irregularity. The optimal design of the suspension stiffness of the car is investigated. A resonance condition y(x,t) that leads to dramatically increasing vibratory energy of the cable-car system is identified.Copyright © 2005 by ASME
Effects of prior contect on lexical access during sentence comprehension: A replication and reinterpretation

In a phoneme monitoring task, prior biasing context eliminates the effect of lexical ambiguity, replicating and extending the results of Swinney and Hakes (1976). It is argued, however, that the conclusions drawn by Swinney and Hakes are not justified by the data and that a different model of the effects of context on lexical processing is more theoretically plausible than theirs.
Bioactive fatty acids: role in bone biology and bone cell function

Bone is a unique tissue providing support, movement, and mineral balance for the body. Bone growth is achieved in the young by a process called modeling, and maintained during adulthood by a process termed remodeling. Three types of cells are responsible for the formation of cartilage and bone; the chondrocyte, osteoblast, and osteoclast. These cells are under the influence of a plethora of regulatory molecules, which govern their action to provide an individual optimal bone mass. Interruption of this homeostatic machinery, especially in the elderly, often results in a loss of bone mass (osteoporosis) or cartilage damage (rheumatoid arthritis). Many pharmacological agents have been made available in an effort to prevent or alleviate these pathologies, however, one vector often overlooked is the diet. This review focuses on the relationship between dietary polyunsaturated fatty acids and bone biology, both in vivo and in vitro.
Hardware-efficient systolic architectures for inversion in GF(2/sup 2/)

We propose in-place systolic bit-serial, bit-parallel, and folded bit-parallel architectures for inversion in GF(2m). Our bit-serial architectures have the highest throughput 1/m of the three types but use more hardware than the other two types. Our bit-parallel architectures have throughput of 1/(2m − 1) with interleaved inputs and 1/(4m − 2) without interleaving. The new bit-serial and bit-parallel architectures proposed have the same throughput and latency but smaller hardware cost and shorter critical path delay than the best comparable architectures proposed previously. We also propose novel folded versions of our bit-parallel architectures which achieve 1/(4m − 2) non-interleaved throughput with even less hardware than our bit-parallel architectures. To the best of our knowledge, no comparable scheme has been proposed previously. The circuitry in each cell of our bit-serial architectures and the (folded and unfolded) bit-parallel architectures with distributed ring counters is the same for all values of m. Since there are no global control or data signals either, these architectures have excellent scalability properties and are very suitable for applications where m is large or variable. Implementation details using the TSMC Avanti 0.18 µm CMOS standard cell library are provided.
Structures of Self-Assembled Nonmetal Borates Derived from α,ω-Diaminoalkanes

A series of crystalline nonmetal borate compounds was prepared by reactions of linear α,ω-diaminoalkanes, H2N(CH2)nNH2 (n = 5−12), with excess boric acid in aqueous solution. These simple reagents ...
Calcium Dependency of Glucagon Secretion from the in Vitro Perfused Rat Pancreas

The present experiments were undertaken to investigate the effect of alterations in extracellular Ca++ concentration on glucagon release from the isolated perfusedrat pancreas.In control studies using perfusate containing 5.0 mEq/1 Ca++,arginine (19.2 HIM) alone or withglucose (100 mg/100 ml) caused biphasic glucagon release. Insulin responses to arginine alone were monophasic whereas arginine plus glucose caused biphasic insulin release. During perfusion with Ca++-free medium, glucagon releasewas inhibited > 90% and insulin release was inhibited about 75%. Subsequent introduction of 5.0 mEq/1 Ca++ to medium during stimulation of previously Ca++-depleted pancreases promptly restored glucagon and insulin responses toward control levels. Thus, like other endocrine tissue, the pancreatic alpha-cell requires calcium for normal secretory function. (Endocrinology 94: 1381, 1974)
Subjects' expectations and the search for alternatives to deception in social psychology

Two studies were performed, the first investigating subjects' attitudes towards participation in experimental research, the second testing a non-deceptive, non-role playing methodology. In Study 1, we asked a sample of 225 college students who might comprise a typical experimental sample for their attitudes towards deception. We found that those who had been previously deceived at least once were more likely to expect future deception than those who had not been deceived. To demonstrate that deception is not always essential, in Study 2 we used a simple non-deceptive parallel to a classic social influence experiment and successfully replicated its findings. These two studies give new empirical weight to the challenge to experimental deception in social psychology.
Perceptions of drinking and related findings from the Nationwide Campuses Study.

Abstract Proponents of social norms approaches maintain that correcting misperceptions of alcohol use among college students may reduce drinking and its consequences. The author used aggregate campus-level data from the Nationwide Campuses Study to test this hypothesis. He defined the misperceptions ratio as the ratio of the frequency of the “average student's” perceived alcohol use to the frequency of self-use at each campus. Each of the 57 colleges reported misperceptions ratios greater than unity. At campuses where students had more accurate perceptions of alcohol use, students were more likely to desire alcohol availability at campus events and to drink on more days throughout the year than at campuses where students had greater misperceptions of alcohol use. The author found no data to support the preferential use of social norms programming on campuses with high levels of self-reported alcohol use or binge drinking. These findings raise questions about potentially unexpected and unintended effects o...
W. E. B. Du Bois's THE SOULS OF BLACK FOLK, Chapter 11

“Of the Passing of the First-Born” is one of the most poignant chapters in The Souls of Black Folk (1903), as it situates the implications of W. E. B. Du Bois's most intense familial experience wit...
Presynaptic Modulation of Ia Afferents in Young and Old Adults When Performing Force and Position Control

The present work investigated presynaptic modulation of Ia afferents in the extensor carpi radialis (ECR) when young and old adults exerted a wrist extension force either to support an inertial loa...
DBXML - Connecting XML with Relational Databases

In this paper, we introduce a software system, called DBXML that provides a transformation utility to connect XML with relational databases. The transformation utility can convert data both ways -from XML-schema to relational database schema and from relational database schema to XML-schema. In the meantime it performs conversions between the data in the XML documents and the relational database. XML-schema as defined by the World Wide Web Consortium is used to enforce data type constraints and primary/foreign key relationships in the generated XML document. Most similar systems support conversion between relational databases and the document type definitions (DTD). The XML-schema is preferred over DTD for several reasons, such as customizable data types, stricter XML structures, and ability to enforce referential constraints. The system has a simple GUI (graphical user interface) that currently works on all versions of Windows. It can be extended to support other platforms, operating systems, and RDBMS
A Nearest Neighbors Analysis of Student Academic Performance in Computer Science (Abstract Only)

Students increasingly decide to go to college in order to get better jobs and make more money. However, these advantages are typically thwarted if a student fails to graduate. Although much research has been aimed at predicting college performance using data collected before entering college, this preliminary work focuses on how college-level data could be used to inform student decision making. This work acquired historical class grades, test scores, and degree information for all students who have taken any computer science classes at Appalachian State University. This poster presents a web application that allows users to explore these data by selecting a target activity such as a class, and filtering students based on test scores, degrees, or how they have performed in other classes. The application displays overlaid histograms comparing how students in the subset perform relative to the class as a whole. For example, when a student considers retaking a course they may find it useful to know how other students with similar grades have performed in the major. For example, among the 29 attempts by 22 students with a 'C' in discrete math and CS 1, only 10 earned the required 'C' in CS 2 (35%) and 12 failed the course (41%). Three of these students went on to graduate with a degree in computer science (14%) and six in computer information systems (27%) while five did not graduate from Appalachian (23%).
Should women receiving tamoxifen be screened for endometrial cancer? An argument for screening.

(2000). Should Women Receiving Tamoxifen Be Screened for Endometrial Cancer? An Argument for Screening. Cancer Investigation: Vol. 18, No. 8, pp. 793-795.
A negative element involved in vimentin gene expression.

Vimentin is one member of the intermediate filament multigene family which exhibits both tissue- and developmental stage-specific expression. In vivo, vimentin is expressed in cells of mesenchymal origin. Previously, we identified both enhancer and promoter elements in the chicken vimentin gene which regulate gene expression in a positive manner. In this report, we have identified a 40-base-pair region at -568 base pairs between the proximal and distal enhancer elements which represses transcriptional activity. This silencer region can also repress the heterologous herpes simplex virus thymidine kinase promoter, which is comparable to the vimentin promoter. In addition, the element is able to function in a position- and orientation-independent manner, and the amount of repression is increased by multiple copies. Here we show by gel retardation assays and DNase I footprinting that this region binds a protein in nuclear extracts from HeLa cells. Southwestern (DNA-protein) blot analysis indicates this protein is approximately 95 kilodaltons in size. Moreover, protein distribution and activity mimic the expression pattern of vimentin during myogenesis, i.e., protein binding increases as vimentin gene expression decreases. The silencer region shares strong sequence similarity with 5'-flanking sequences found in both the human and hamster vimentin genes and with other characterized silencer elements, including the human immunodeficiency virus long terminal repeat, rat growth hormone, chicken lysozyme, and rat insulin genes. Thus, a negative element appears to bind a 95-kilodalton protein involved in regulating the tissue-specific expression of the chicken vimentin gene.
Are musical instrument gender associations changing

The researcher sought to examine gender associations across three decades to determine if changes in the sex stereotyping of musical instruments has occurred. First, the study examined the paired c...
Use of expanded polytetrafluoroethylene pericardial substitute with ventricular assist devices

Expanded polytetrafluoroethylene membrane was used to reconstruct the pericardium after ventricular assist device insertion in 7 consecutive patients. One patient remains on support with the membrane in place and 6 have had the membrane removed. The expanded polytetrafluoroethylene membrane protected the device cannulas during repeat sternotomy and expedited the dissection of the heart and great vessels at the time of device removal. Reconstruction of the pericardium with expanded polytetrafluoroethylene membrane is recommended at the time of ventricular assist device insertion.
A high-performance online assay interpreter for digital microfluidic biochips

We introduce an online interpreter to execute biochemical assays on droplet-based digital microfluidic biochips (DMFBs). Online interpretation enables adaptivity, e.g., response to faults during assay execution, variable-latency assay operations, and concurrent workloads whose composition is not known statically. Our online method routes droplets dynamically, making decisions in milliseconds while running on a low-cost Intel Atom" processor.
How to Combine Fast Heuristic Markov Chain Monte Carlo with Slow Exact Sampling

Given a probability law $\pi$ on a set $S$ and a function $g : S \rightarrow R$, suppose one wants to estimate the mean $\bar{g} = \int g d\pi$. The Markov Chain Monte Carlo method consists of inventing and simulating a Markov chain with stationary distribution $\pi$. Typically one has no a priori bounds on the chain's mixing time, so even if simulations suggest rapid mixing one cannot infer rigorous confidence intervals for $\bar{g}$. But suppose there is also a separate method which (slowly) gives samples exactly from $\pi$. Using $n$ exact samples, one could immediately get a confidence interval of length $O(n^{-1/2})$. But one can do better. Use each exact sample as the initial state of a Markov chain, and run each of these $n$ chains for $m$ steps. We show how to construct confidence intervals which are always valid, and which, if the (unknown) relaxation time of the chain is sufficiently small relative to $m/n$, have length $O(n^{-1} \log n)$ with high probability.
PKCalpha activation downregulates ATM and radio-sensitizes androgen-sensitive human prostate cancer cells in vitro and in vivo.

We previously demonstrated that treatment of human androgen-responsive prostate cancer cell lines LNCaP and CWR22-Rv1 with 12-O-tetradecanoylphorbol 13-acetate (TPA), a known protein kinase C (PKC) activator, decreases ATM protein levels, thus de-repressing the enzyme ceramide synthase (CS) and promoting apoptosis as well as radio-sensitizing these cells.1 Here we show that PKCα mediates the TPA effect on ATM expression, since ATM suppression and apoptosis induced by either TPA or diacylglycerol-lactone (DAG-lactone), both inducing PKCα activation,2 are abrogated in LNCaP cells following transfection of a kinase-dead PKCα mutant (KD-PKCα). Similarly, KD-PKCα blocks the apoptotic response elicited by combination of TPA and radiation, whereas expression of constitutively active PKCα is sufficient to sensitize cells to radiation alone, without a need to pre-treat the cells with TPA. These findings identify CS activation as a downstream event of PKCα activity in LNCaP cells. Similar results were obtained in CWR22-Rv1 cells with DAG-lactone treatment. Using the LNCaP orthotopic prostate model it is shown that treatment with TPA or DAG-lactone induces significant reduction in tumor ATM levels coupled with tumor growth delay. Furthermore, while fractionated radiation alone produces significant tumor growth delay, pretreatment with TPA or DAG-lactone significantly potentiates tumor cure. These findings support a model in which activation of PKCα downregulates ATM, thus relieving CS repression by ATM and enhancing apoptosis via ceramide generation. This model may provide a basis for the design of new therapies in prostate cancer.
Polarization Diversity Using Mutual Information

An information-theoretic criterion is introduced for waveform polarization type selection in a synthetic aperture radar (SAR) configuration. The criterion is based on the concept of mutual information (MI). Specifically, the MI criterion (MIC) minimizes the MI between the radar return signal at two distinct instants of time: one is the just-received return due to the last-transmitted pulse with known polarization type, and the other is the to-be-received return due to the pulse to be transmitted next with to-be-determined polarization type. In that manner, the polarization type selected for the pulse transmitted next will result in the collection of the largest amount of new information, as measured by a formal criterion. The MIC involves the radar system model and the probabilistic definition of the clutter, interference, and noise processes. In particular, when all these processes are proper Gaussian processes, the MIC attains a simple analytic form. The formulation and simulation-based results are presented in the context of a first-order radar system model, for simplicity, but the MIC can be extended to cover more complex models in a straightforward manner. In addition, the MIC is applicable to other radar modes and sensor types. The results presented show that the MIC is an effective method for polarization type selection in a SAR.
Operations Analysis of Locating High-Speed Runway Exits

The purpose of high-speed runway exits is to increase the capacity of a runway. This can be accomplished if the exits are properly located along the runway and other operational conditions are met. These conditions are discussed and runway operation is described. A probabilistic model describing the landing of aircraft is developed and used to locate the exits optimally. Benefits from the use of high-speed exits are presented in terms of increased landing capacity, decreased service time, and decreased delay.
Human T-Cell Leukemia Virus Type 1 Tax Enhances Serum Response Factor DNA Binding and Alters Site Selection

Human T-cell leukemia virus type I (HTLV-1) is the etiological agent of adult T-cell leukemia. The viral transforming protein Tax regulates the transcription of viral and cellular genes by interacting with cellular transcription factors and coactivators. The effects of Tax on cellular gene expression have an important impact on HTLV-1-mediated cellular transformation. Expression of the c-fos cellular oncogene is regulated by serum response factor (SRF), and Tax is known to induce c-fos gene expression by activating SRF-responsive transcription. SRF activates cellular gene expression by binding to a consensus DNA sequence (CArG box) located within a serum response element (SRE). Since SRF activates transcription of many growth regulatory genes, this pathway is likely to have a significant impact on Tax-mediated transformation. Here we demonstrate that Tax interacts with SRF and enhances the binding of SRF to SREs located in the c-fos, Nur77, and viral promoters. Also, we establish that in the presence of Tax, SRF selects more divergent CArG box sequences than in the absence of Tax, revealing a novel mechanism for regulating SRF-responsive gene expression. Finally, increased association of SRF with chromatin and specific promoters was observed in Tax-expressing cells, correlating with increased c-fos and Nur77 mRNA levels in Tax-expressing cells. These results suggest that Tax activates SRF-responsive transcription by enhancing its binding affinity to multiple different SRE sequences.
Universal equation of state for engineering application: algorithm and application to non-polar and polar fluids

Engineering equations of state (EOS) deal with the majority of fluids of interest in process and equipment design in the chemical industries. Accuracy and universality are two desirable features the engineering EOS require, however, both of them cannot be simultaneously obtained without some degree of compromise. Therefore a simultaneous optimization algorithm is proposed to develop an accurate but compact engineering EOS for wide range of fluids with one single functional form. The algorithm is based on a simulated annealing method, and operates on different fluids at the same time to achieve the best average results. A 14-term EOS is developed based on this algorithm that has good accuracy for selected non-polar and polar fluids. The resulting equation is compared with two different 12-term EOS developed by Span and Wagner, one for polar fluids, the other for non-polar fluids. The new 14-term EOS also gives good predictions for some associating fluids such as alcohols and water.