cssi/SciSciGPT-SciSciNet huggingface dataset:
Single-Event Response of the SiGe HBT Operating in Inverse-Mode

The single-event effect sensitivity of inverse-mode biased SiGe HBTs in both bulk and SOI technology platforms are investigated, for the first time, using digital circuits and stand-alone device test structures. Comparisons of heavy-ion broad beam data of shift register circuits constructed with forward-mode and inverse-mode biased SiGe HBTs from a first-generation, complementary SOI SiGe BiCMOS process, reveal an improvement in SEU mitigation for the inverse-mode shift register architecture. Full 3D TCAD simulations highlight the differences in transient current origination between forward and inverse-mode biased devices, illustrating the impact of doping profiles on ion-induced shunt duration. To extend the analysis to a bulk platform, new fourth-generation npn , SiGe HBTs were biased in both the forward and inverse-mode and irradiated at NRL using the two photon absorption measurement system. These measurements support the analysis of transient origination using 3D TCAD simulations. Furthermore, the isolation of the output terminal from the sensitive subcollector-substrate junction is experimentally demonstrated for the inverse-mode bias. Fully coupled mixed-mode simulations predict a significant reduction in sensitive area for inverse-mode shift registers built in a bulk SiGe platform.
A distributive N-amendment game with endogenous agenda formation

In this paper I analyze a 3-person voting game in which players sequentially choose amendments to a bill and then vote sophisticatedly on the resulting agenda. This game differs from previous work on endogenous agenda formation in that the number of items on the agenda is not fixed. Players keep making proposals until they can do no better. I find that there is a nonempty set of minimax equilibrium outcomes to the game, and that this set contains the simple von Neumann–Morgenstern stable set.
Inelastic phonon interactions at solid–graphite interfaces

Abstract The presented model predicts thermal boundary conductance at interfaces where one material comprising the junction is characterized by high elastic anisotropy. In contrast to previous approaches, the current methodology accounts for contributions from inelastic scattering through consideration of multiple-phonon interactions. Inelastic contributions become significant as the temperature, as well as the degree of acoustic mismatch between the materials, increases. Inclusion of the inelastic interactions is necessary for a variety of interfacial systems including the metal–graphite boundary examined here. Improvement is shown over existing approaches that address only elastic scattering as both three- and four-phonon interactions significantly augment the transport.
On the Calculation of Antieigenvalues and Antieigenvectors

Abstract We provide a simple approach for computing antieigenvalues and antieigenvectors of a real symmetric positive definite matrix. Our approach closely follows that used for solving a statistical problem considered by Rao and Rao (1987). The approach is illustrated using certain examples.
High histologic grade and increased relative content of tryptophan in breast cancer using ratios from fingerprint fluorescence spectral peaks

Histologic grade is a very important, but underappreciated, parameter of breast cancer aggressiveness. Despite its importance, it has historically not been included as one of the criteria for staging of this cancer. In this study, spectral fluorescence profiles from patients with breast carcinoma were acquired. Ratios of emission peaks at 340 over 440,460 nm from biomolecules in malignant and normal samples were calculated. Cancerous over normal ratios (double ratio (DR) method) were evaluated with respect to tumor characteristics. Increased tryptophan content in breast cancer tissues correlates strongly with high grade, but not with lymph node metastases, estrogen receptor, progesterone receptor or Her-2-Neu receptor status.
Stability constant studies on some new thioether carboxylic acid chelating agents

Abstract The ionization constants of four recently prepared thioethercarboxylic acid chelating agents have been determined along with the stability constants of the complexes of these chelating agents with Hg2+, Zn2+, Ca2+, Ni2+, Mg2+, Cd2+, and Cu2+. The marked selectivity of these chelating agents for Hg2+ is quite striking. For ions with which a bond to a thioether sulfur is not strong, the stability constants are fairly low. A combination of pH measurements and pM measurements were used to determine the stability constants of the species MY and MHY. Because of the geometry of these chelating agents the proton in MHY is far removed from the metal bonding site and a consequence of this is the fact that the stability constants for MY and MHY may be quite close in some cases.
Diversity Combining for Frequency-Hop Spread-Spectrum Communications with Partial-Band Interference

Several diversity combining techniques are considered for frequency-hop communication systems with M-ary orthogonal signaling and noncoherent demodulation in the presence of uniform Gaussian noise and partial-band Gaussian noise. Some of the results apply to general (non-Gaussian) partial-band interference. Among the techniques described are square-law combining, linear combining, and linear combining of the outputs of the cascade of an envelope detector followed by a clipper. The primary goal is to find combining techniques which perform well in an unknown or changing interference environment.
A kinetic study of the initial oxidation of a Ta(110) surface using oxygen kα X-ray emission

Abstract The application of reflection high-energy electron diffraction (RHEED) and electron excited X-ray emission to the study of the initial stages of oxidation of the Ta(110) surface is demonstrated. Oxidation in both dry oxygen and water vapour is investigated over a temperature range of 25–275°C and a pressure range of 10 −7 to 1 torr. In dry oxygen, the thickness ( y ) of the uniform amorphous oxide is a function of the oxygen exposure in langmuirs (L) and its growth can be described by the lograthmic relation y = k 1 log( L + L 0 ) + k 2 , where k 1 = 1.09 ± 0.07 × 10 −8 g/cm 2 , k 2 = 1.3 ± 0.3 × 10 −8 g/cm 2 and L 0 = 1 L. The growth of oxides up to 8 A was observed with dry oxygen exposures of about 10 9 L. Thicker films grow in the presence of water vapour and films formed after chemical polishing and short periods of atmospheric exposure were found to be 35 ± 5 A mean thickness. Problems associated with the preparation of the Ta(110) surface in a “clean” starting condition are discussed, particularly with reference to the formation of precipitated oxygen structures and the adsorption of background carbon monoxide on “oxygen-free” surfaces.
Female sexuality, social reproduction, and the politics of medical intervention in Niger: Kel Ewey Tuareg perspectives

This essay explores connections between political institutions, forms of power, and women's health care concerns from a cultural anthropological perspective. I focus on the roles of different medical establishments among the Kel Ewey Tuareg of Niger—Western-European sponsored, central state, traditional herbalism and Islamic scholarship—in creating, maintaining, and disputing these constructs, through the invention and elaboration of disease categories and through the selective application of medical and reproductive models and technology to women. I also explore women's attempts to manage these forces, as they draw upon a cultural inventory that is alternately supportive and in conflict with their interests.
Biaxial Creep Strains at Notch Roots—Measurement and Modeling

Biaxial strains were measured at the roots of single notches in zirconium alloy specimens under loading and creep conditions (up to 1200 hours) at 250°C. A laser-based interferometric technique was used; details of the measurement procedures are given in another paper. Here, the Bodner model is incorporated into the ABAQUS finite element code and used to predict the biaxial strains at the notch root during loading and for a creep duration of 100 hours. The strains during loading agree quite well with the measured ones while the predicted creep strains are smaller. This discrepancy is attributed to the lack of precision in determining the constants for the Bodner model from smooth-specimen tests. Both the measurement technique and the Bodner model are well-suited for studies of notch response.
Impulsive control and synchronization of nonlinear dynamical systems and application to secure communication

Impulsive control is a newly developed control theory which is based on the theory of impulsive differential equations. In this paper, we stabilize nonlinear dynamical systems using impulsive contr...
Lyotropic mesophases of cellulose in the ammonia/ammonium thiocyanate solvent system: Phase relationships

Mesophase formation of the cellulose/NH3/NH4SCN system has been studied as a function of system composition at 25°C. Compositions for incipience of mesophase formation and for wholly anisotropic phase formation have been determined and relevant phase diagrams constructed. The biphasic gap narrowed when the solvent composition approached 75.5 weight percent NH4SCN and as the cellulose concentration decreased. As solvent composition was changed, the minimum cellulose volume fraction for mesophase formation ranged between 0.02 to 0.045.
Benefit Assessment of the Precision Departure Release Capability Concept

A Precision Departure Release Capability concept is being evaluated by both the National Aeronautics and Space Administration and the Federal Aviation Administration as part of a larger goal of improving throughput, efficiency and capacity in integrated departure, arrival and surface operations. The concept is believed to have the potential of increasing flight efficiency and throughput by avoiding missing assigned slots and minimizing speed increase or path stretch to recover the slot. The main thrust of the paper is determining the impact of early and late departures from the departure runway when an aircraft has a slot assigned either at a meter fix or at the arrival airport. Results reported in the paper are for two scenarios. The first scenario considers flights out of Dallas/Fort Worth destined for Hartsfield-Jackson International Airport in Atlanta flying through the Meridian meter-fix in the Memphis Center with miles-in-trail constraints. The second scenario considers flights destined to George Bush Intercontinental/Houston Airport with specified airport arrival rate constraint. Results show that delay reduction can be achieved by allowing reasonable speed changes in scheduling. It was determined that the traffic volume between Dallas/Fort Worth and Atlanta via the Meridian fix is low and the departures times are spread enough that large departure schedule uncertainty can be tolerated. Flights can depart early or late within 90 minutes without accruing much more delay due to miles-in-trail constraint at the Meridian fix. In the Houston scenario, 808 arrivals from 174 airports were considered. Results show that delay experienced by the 16 Dallas/Fort Worth departures is higher if initial schedules of the remaining 792 flights are kept unaltered while they are rescheduled. Analysis shows that the probability of getting the initially assigned slot back after perturbation and rescheduling decreases with increasing standard deviation of the departure delay distributions. Results show that most Houston arrivals can be expected to be on time based on the assumed zero-mean Normal departure delay distributions achievable by Precision Departure Release Capability. In the current system, airport-departure delay, which is the sum of gate-departure delay and taxi-out delay, is observed at the airports. This delay acts as a bias, which can be reduced by Precision Departure Release Capability.
Gd HP-DO3A--experimental evaluation in brain and renal MR.

Abstract GD HP-DO3A, a neutral (nonionic) IV MR contrast agent presently in clinical trials, was evaluated with respect to imaging characteristics in rats. Following administration of 0.25 mmol/kg I.V., 58 ± 19%, i.e. ( n = 6) enhancement was noted in a brain gliosarcoma model. Meningeal spread of neoplasia could be identified due to its enhancement (69 ± 26%) in nine animals. The time course of renal enhancement was quantitated at two dosages, 0.05 ( n = 4) and 0.25 mmol/kg ( n = 8). At the higher dose, enhancement of both cortex and medulla plateaued between 9 and 23 min postinjection. At the lower dose, enhancement of renal medulla was maximum at 2 min postinjection. These enhancement characteristics (both brain and kidney), at equivalent contrast dosages, are comparable to that previously published for Gd-DTPA. However, Gd HP-DO3A has the potential to be utilized clinically at higher doses than Gd-DTPA, with no reported adverse effects in initial trials employing up to 0.3 mmol/kg.
Dilemmas of Project-Based Media Work: Contexts and Choices

Media firms exist in dynamic business contexts which influence how they and their creative workers respond to a series of project-based work dilemmas. The paper reviews three forms of dilemmas or tensions within media-based businesses: identity dilemmas of individualization versus collective belonging, organizing dilemmas of creative autonomy versus corporate control, and learning dilemmas of creative exploration versus commercial exploitation. The paper conceptualizes how creative businesses and creative workers respond to these dilemmas in terms of separating, integrating and shifting response options. It then examines how contextual features of media industry technologies, markets, institutional practices, and user coproduction convergences impact how project businesses and their creative workers are likely to respond to the dilemmas.
The cracked lap shear specimen revisited—a closed form solution

This paper revisits the cracked lap shear specimen and reports a closed form solution to determine three fracture parameters, the energy release rate, the fracture mode mixity, and the fracture efficiency parameter. The solution is based on a beam-column approach pioneered by Goland and Reissner. Because of the geometrically nonlinear nature of this specimen, it is found that the fracture parameters are functions of five independent nondimensional parameters. The closed form solution reported in this paper provides a simple and useful tool to design the cracked lap shear specimen and to understand the behavior of this test geometry. The results in this paper suggest that to design a specimen with an energy release rate less dependent on the crack length, the adherend thickness should be small compared to the specimen length, and the thicker or stiffer adherend should be used as the strap. For a specimen of unequal adherend thickness, using the thicker adherend as the strap would significantly reduce the likelihood of yielding in the adherend. Compared with the finite element analyses found in the literature, the closed form solution shows good agreement in energy release rates, but less satisfactory agreement in fracture mode mixities. Finally, the closed form solution is used to give a reasonable explanation of anomalous debond behavior in a series of fatigue experiment using the cracked lap shear specimen.
A critique of finite Hilbert basis set calculations for the angular distribution of ionized electrons produced in p + H impact at 20 keV

We present a critique of a finite Hilbert basis set calculation of the angular distribution of ejected electrons in a p + H collision at 20 keV.
Postdocs: the power of unions.

![Figure][1] Speaking with one voice. Postdoc unions can negotiate better benefits for their members. CREDIT: ISTOCKPHOTO.COM As a postdoc at the University of California–Santa Cruz and President of UAW Local 5810, the union that represents over 6000 postdocs at the University of
Distribution and Observed Associations of Orthostatic Blood Pressure Changes in Elderly General Medicine Outpatients

Factors associated with orthostatic blood pressure change in elderly outpatients were determined by surveying 398 medical clinical outpatients aged 65 years and older. Blood pressure was measured with random-zero sphygmomanometers after patients were 5 minutes in a supine and 5 minutes in a standing position. Orthostatic blood pressure changes were at normally distributed levels with systolic and diastolic pressures dropping an average of 4 mm Hg (standard deviation [SD]=15 mm Hg) and 2 mm Hg (SD=11 mm Hg), respectively. Orthostatic blood pressure changes were unassociated with age, race, sex, body mass, time since eating, symptoms, or other factors. According to multiple linear regression analysis, supine systolic pressure, chronic obstructive pulmonary disease (COPD), and diabetes mellitus were associated with a decrease in systolic pressure on standing. Hypertension, antiarthritic drugs, and abnormal heartbeat were associated with an increase in systolic pressure on standing. For orthostatic diastolic pressure changes, supine diastolic pressure and COPD were associated with a decrease in diastolic pressure on standing. Congestive heart failure was associated with an increase in standing diastolic pressure. Using logistic regression analysis, only supine systolic pressure was associated with a greater than 20-mm Hg drop in systolic pressure (n=53, prevalence=13%). Supine diastolic pressure and COPD were the only variables associated with a greater than 20-mm Hg drop in diastolic pressure (n=16, prevalence=4%). These factors may help physicians in identifying older persons at risk for having orthostatic hypotension.
Tabacco‐induced primary‐position upbeat nystagmus

The effects of tobacco smoking on the eye movements of normal human subjects were studied using direct current electrooculography and the magnetic search coil technique. Tobacco induced a transient primary-position upbeat nystagmus in the dark, which was suppressed by visual fixation. It obeyed Alexander's law and was associated with oblique upward fast phases that alternated from side to side. Tobacco-induced nystagmus exhibited a latency of onset at 40 to 90 seconds, a duration of 10 to 20 minutes, and maximum slow-phase velocities at 2 to 3 minutes. We suggest that tobacco induces primary-position upbeat nystagmus through the excitatory effects of nicotine on the central vestibular pathways.
An example of information management in biology: Qualitative data economizing theory applied to the Human Genome Project databases

Ironically, although much work has been done on elucidating algorithms for enabling scientists to efficiently retrieve relevant information from the glut of data derived from the efforts of the Human Genome Project and other similar projects, little has been performed on optimizing the levels of data economy across databases. One technique to qualify the degree of data economization is that constructed by Boisot. Boisot's Information Space (I-Space) takes into account the degree to which data are written (codification), the degree to which the data can be understood (abstraction), and the degree to which the data are effectively communicated to an audience (diffusion). A data system is said to be more data economical if it is relatively high in these dimensions. Application of the approach to entries in two popular, publicly available biological data repositories, the Protein DataBank (PDB) and GenBank, leads to the recommendation that PDB increases its level of abstraction through establishing a larger set of detailed keywords, diffusion through constructing hyperlinks to other databases, and codification through constructing additional subsections. With these recommendations in place, PDB would achieve the greater data economies currently enjoyed by GenBank. A discussion of the limitations of the approach is presented. © 2006 Wiley Periodicals, Inc.
Onset of Water Hammer Phenomenon Following Flow Surge Characteristics in Tube-Type Condensing Flows

Two-Phase region, in condensing flow undergoing complete condensation inside a tube, acts as an amplifier of any small internal or external disturbances. A small, externally imposed change in the inlet vapor flow rate, or heat flux, leads to substantial surges in the outlet liquid flow rate, including the possibility of flow reversals. Also, if the conditions are right, slight internal disturbances as a result of vapor/liquid interaction, can lead to sustained oscillations of large amplitude, such as in the outlet liquid flow rate. Such surging characteristics coupled with rapid bubble collapse may lead to water hammer phenomenon. This paper will summarize both experimental observations and theoretical models as a result of externally imposed, or internally induced, flow changes in condensing flows. The physics of the processes, including liquid/vapor density ratio, vapor compressibility, bubble collapse, and liquid inertia will be highlighted. The condensing flow stability criterion will be used to provide a possible physical and an analytical basis for the catastrophic piping failure due to a condensation induced water hammer.Copyright © 2003 by ASME
Globalization and Brazilian biosafety: the politics of scale over biotechnology governance

Abstract Monsanto’s request to commercialize its genetically-modified (GM) herbicide-resistant soybean technology in Brazil sparked heated debate and protest. This paper explores the conflict and illustrates how biosafety politics and policy outcomes are highly contested and situated, rather than controlled by external forces within the ever-expanding global economy. This paper argues that GM crops are not inherently artifacts of economic globalization and trade liberalization. What makes GM crops ‘global’ and part of a new iterative and uneven globalization process are the new and unanticipated sites of contradiction and contestation and the multi-scaled conflict over biotechnology governance. Political strategies taken by the state government in Rio Grande do Sul, Brazilian consumer protection activists, and Greenpeace exploit the new ‘nature’ of GM crops as a means to expand the debate, change the rules governing the genetic commons, and consequently, rescale biotechnology governance.
Intermittent encephalopathy, reversible nerve conduction slowing, and mri evidence of cerebral white matter disease in methylene– tetrahydrofolate reductase deficiency

We describe a patient with methylenetetrahydrofolate reductase (MTHFR) deficiency in whom clinical and electrophysiologic fluctuations paralleled exacerbations of hyperhomocyst(e)inemia. MRI demonstrated abnormalities characteristic of a leukodystrophy.
Constipation, diarrhea, and symptomatic hemorrhoids during pregnancy

Constipation, diarrhea, and symptomatic hemorrhoids are disorders common in the general population, particularly in women. These conditions, if mild, often are self-treated with various home remedies or nonprescription preparations. Few of these patients, moreover, are referred to gastroenterologists, as primary care providers generally are confident managing these conditions, unless they are severe, refractory to conventional management, or require additional diagnostic studies.
SUMO modification regulates the transcriptional activity of XBP1

The UPR (unfolded protein response), a cellular defence mechanism against misfolded protein accumulation in the ER (endoplasmic reticulum), is associated with many human diseases such as aging, cancer and diabetes. XBP1 (X-box-binding protein 1), a key transcription factor of the UPR, is critical in maintaining ER homoeostasis. Nevertheless, the mechanism by which XBP1 transcriptional activity is regulated remains unexplored. In the present study we show that XBP1s, the active spliced form of XBP1 protein, is SUMOylated, mainly by PIAS2 [protein inhibitor of activated STAT (signal transducer and activator of transcription) 2] at two lysine residues located in the C-terminal transactivation domain. Ablation of these SUMOylation events significantly enhances the transcriptional activity of XBP1s towards UPR target genes. Thus our results reveal an unexpected role for SUMO (small ubiquitin-related modifier) in the regulation of UPR activation and ER homoeostasis.
A Therapeutic Opportunity in Melanoma: ErbB4 Makes a Mark on Skin

Malignant melanomas are aggressive tumors that are largely refractory to conventional drug therapies. A recent study reported in Nature Genetics identified mutationally activated ErbB4 alleles in 20% of cases. These tumor cells exhibit ErbB4 dependency, suggesting that ErbB4 kinase inhibition may constitute an effective therapeutic strategy in this setting.
Solid-Phase Synthesis of Substituted Imidazoline-Tethered 2,3-Diketopiperazines, Cyclic Ureas, and Cyclic Thioureas

Efficient methods for the solid-phase synthesis of imidazoline-tethered 2,3-diketopiperazines, cyclic ureas, and cyclic thioureas are described. Following the exhaustive reduction of resin-bound dipeptides derived from orthogonally protected diamino acids, the primary amine of the resulting tetraamines was selectively protected with Dde. The compounds were then selectively cyclized via their secondary amines with three different diimidazole derivatives ((COIm)2, COIm2, CSIm2). Upon Dde removal, the compounds were selectively N-acylated and dehydratively cyclized with POCl3 to afford the imidazoline-tethered analogues in moderate yield and high purity. These procedures have been extended to prepare mixture-based combinatorial libraries. Details of the selection of building blocks for preparation of the positional scanning libraries based on the “libraries from libraries” approach are discussed.
Effects of Chronic Excess Salt Feeding: Demonstration of Normal Thyroid Function in Salt-Fed Dogs with Hypercholesterolemia

SummaryThe hypercholesterolemia associated with chronic excess salt feeding is not due to hypothyroidism. As shown by thyroidal 131I uptake, by plasma protein-bound iodine concentrations, and by hi...
PREPARATIVE SEPARATION OF CURCUMINOIDS FROM CRUDE CURCUMIN AND TURMERIC POWDER BY pH-ZONE-REFINING COUNTERCURRENT CHROMATOGRAPHY

Turmeric powder and its main component, curcumin, have a wide range of medicinal and culinary uses. The purpose of this study was to separate and purify curcumin from demethoxycurcumin and bis-demethoxycurcumin which are present in both turmeric powder, and commercial crude curcumin. The separation and purification of curcumin was accomplished through standard high-speed countercurrent chromatography (CCC) as well as pH-zone-refining CCC. The pH-zone-refining CCC technique was able to separate multi-gram quantities of curcumin and other curcuminoids from crude curcumin and turmeric powder, while maintaining a high level of purity.
Shoulder arthroplasty in patients with prior mastectomy for breast cancer.

Twenty women, all of whom had undergone mastectomy for breast cancer and 11 of whom had undergone radiation therapy, underwent shoulder arthroplasty. Two of these patients subsequently underwent resection arthroplasty for delayed infection and uncontrollable instability. Seventeen patients were available for follow-up, which averaged 4.6 years (range, 23 months to 13 years). There was significant improvement in pain (P < .0001), with no pain in 8, slight pain in 7, occasional moderate pain in 1, and moderate pain in 1 of the patients. A significant improvement in active motion occurred only in external rotation. Active elevation increased 7 degrees, from 92 degrees to 99 degrees; external rotation increased 17 degrees, from 25 degrees to 42 degrees; and internal rotation increased 1 level, to L3. All patients were pleased with their results. Complications were frequent. Apart from the 2 patients who underwent reoperation, 5 patients with preoperative lymphedema experienced exacerbation of their edema and 2 others developed new lymphedema. The edema returned to prearthroplasty levels or resolved in all patients by 5 months. In addition, antecubital vein thrombosis occurred in 1 patient, delayed long head of biceps rupture in 2 patients, and late rotator cuff tearing in 3 patients. In carefully selected patients, shoulder arthroplasty can be effective in pain reduction, but little increase in range of motion should be expected. Complications (often involving soft tissues) are frequent. New or increased arm edema can occur; however, edema resolved or returned to prearthroplasty levels in our patients.
CSAR Benchmark Exercise of 2010: Combined Evaluation Across All Submitted Scoring Functions

As part of the Community Structure-Activity Resource (CSAR) center, a set of 343 high-quality, protein–ligand crystal structures were assembled with experimentally determined Kd or Ki information from the literature. We encouraged the community to score the crystallographic poses of the complexes by any method of their choice. The goal of the exercise was to (1) evaluate the current ability of the field to predict activity from structure and (2) investigate the properties of the complexes and methods that appear to hinder scoring. A total of 19 different methods were submitted with numerous parameter variations for a total of 64 sets of scores from 16 participating groups. Linear regression and nonparametric tests were used to correlate scores to the experimental values. Correlation to experiment for the various methods ranged R2 = 0.58–0.12, Spearman ρ = 0.74–0.37, Kendall τ = 0.55–0.25, and median unsigned error = 1.00–1.68 pKd units. All types of scoring functions—force field based, knowledge based, an...
Accurate 3′ End Processing and Adenylation of Human Signal Recognition Particle RNA and Alu RNA in Vitro

Abstract Human signal recognition particle (SRP) RNA is transcribed by RNA polymerase III and terminates with -GUCUCUUUUOH on its 3′ end. Our previous studies showed that the three terminal uridylic acid residues of human SRP RNA are post-transcriptionally removed and a single adenylic acid residue is added, resulting in a 3′ end sequence of -GUCUCUAOH(Sinha, K. M., Gu, J., Chen, Y., and Reddy, R. (1998)J. Biol. Chem. 273, 6853–6859). In this study we show that the Alu RNA, corresponding to the 5′ and 3′ ends of SRP RNA, is also accurately processed and adenylated in vitro. Alu RNAs containing 7 or 11 additional nucleotides on the 3′ end were accurately processed and then adenylated. Deletion analysis showed that an 87-nucleotide-long motif comprising of the 5′ and 3′ ends, including stem IV of the Alu RNA, is sufficient and necessary for the 3′ end processing and adenylation. A 73-nucleotide-long construct with deletion of stem IV, required for the binding of SRP 9/14-kDa proteins, was neither processed nor adenylated. The adenylated Alu RNA as well as adenylated SRP RNA were bound to the SRP 9/14-kDa heterodimer and were immunoprecipitated by specific antibodies. A significant fraction of SRP RNA in the nucleoli was found to be processed and adenylated. These data are consistent with nascent SRP and/or Alu RNAs first binding to SRP 9/14-kDa protein heterodimer, followed by the removal of extra sequence on the 3′ end and then the addition of one adenylic acid residue in the nucleus, before transport into the cytoplasm.
Molecular and Thermodynamic Insights into the Conformational Transitions of Hsp90

Hsp90, the most abundant cellular protein, has been implicated in numerous physiological and pathological processes. It controls protein folding and prevents aggregation, but it also plays a role in cancer and neurological disorders, making it an attractive drug target. Experimental efforts have demonstrated its remarkable structural flexibility and conformational complexity, which enable it to accommodate a variety of clients, but have not been able to provide a detailed molecular description of the conformational transitions. In our molecular dynamics simulations, Hsp90 underwent dramatic structural rearrangements into energetically favorable stretched and compact states. The transitions were guided by key electrostatic interactions between specific residues of opposite subunits. Nucleotide-bound structures showed the same conformational flexibility, although ADP and ATP seemed to potentiate these interactions by stabilizing two different closed conformations. Our observations may explain the difference in dynamic behavior observed among Hsp90 homologs, and the atomic resolution of the conformational transitions helps elucidate the complex chaperone machinery.
Roles of P67/MetAP2 as a tumor suppressor.

Abstract A precise balance between growth promoting signals and growth inhibitory signals plays important roles in the maintenance of healthy mammalian cells. Any deregulation of this critical balance converts normal cells into abnormal or cancerous cells. Several macromolecules are being identified and characterized that are involved in the regulation of cell signaling pathways that connect to the cell cycle and thus they play roles as tumor promoters or tumor suppressors. In situ tumor formation needs active angiogenesis, a process that generates new blood vessels from existing ones either by splitting or sprouting. Several small molecule inhibitors and proteins have been identified as inhibitors of angiogenesis. One such protein, p67/MetAP2 also known as methionine aminopeptidase 2 (MetAP2), has been shown to bind covalently to fumagillin and its derivatives that have anti-angiogenic activity. In addition to fumagillin or its derivatives, several other small molecule inhibitors of p67/MetAP2 have been recently identified and some of these drugs are in phase III trials for cancer therapy. Although molecular details of actions toward tumor suppression by these drugs are largely unknown, a significant progress has been made to understand the structure–function relationship of p67/MetAP2 and its roles in the maintenance of the levels of phosphorylation of the ∝-subunit of eukaryotic initiation factor 2 (eIF2∝) and extracellular signal-regulated kinases 1 and 2 (ERK1/2). In this article, roles of p67/MetAP2 in the suppression of cancer development are also discussed.
P2Y Purinoceptors Are Responsible for Oscillatory Fluid Flow-induced Intracellular Calcium Mobilization in Osteoblastic Cells

We previously found that oscillatory fluid flow activated MC3T3-E1 osteoblastic cell Ca(2+)(i) mobilization via the inositol 1,4,5-trisphosphate pathway in the presence of 2% fetal bovine serum (FBS). However, the molecular mechanism of fluid flow-induced Ca(2+)(i) mobilization is unknown. In this study, we first demonstrated that oscillatory fluid flow in the absence of FBS failed to increase [Ca(2+)](i) in MC3T3-E1 cells. Apyrase (10 units/ml), which rapidly hydrolyzes 5' nucleotide triphosphates to monosphophates, prevented the fluid flow induced increases in [Ca(2+)](i) in the presence of FBS. Adding ATP or UTP to flow medium without FBS restored the ability of fluid flow to increase [Ca(2+)](i), suggesting that ATP or UTP may mediate the effect of fluid flow on [Ca(2+)](i). Furthermore, adenosine, ADP, UDP, or adenosine 5'-O-(3-thiotriphosphate) did not induce Ca(2+)(i) mobilization under oscillatory fluid flow without FBS. Pyridoxal phosphate 6-azophenyl-2,4'-disulfonic acid, an antagonist of P2X purinoceptors, did not alter the effect of fluid flow on the Ca(2+)(i) response, whereas pertussis toxin, a G(i/o)-protein inhibitor, inhibited fluid flow-induced increases in [Ca(2+)](i) in the presence of 2% FBS. Thus, by the process of elimination, our data suggest that P2Y purinoceptors (P2Y2 or P2Y4) are involved in the Ca(2+)(i) response to fluid flow. Finally, a decreased percentage of MC3T3-E1 osteoblastic cells treated with P2Y2 antisense oligodeoxynucleotides responded to fluid flow with an increase in [Ca(2+)](i), and an increased percentage of ROS 17/2.8 cells, which do not normally express P2Y2 purinoceptors, transfected with P2Y2 purinoceptors responded to fluid flow in the presence of 2% FBS, confirming that P2Y2 purinoceptors are responsible for oscillatory fluid flow-induced Ca(2+)(i) mobilization. Our findings shed new light of the molecular mechanisms responsible for oscillatory fluid flow-induced Ca(2+)(i) mobilization in osteoblastic cells.
Automated lipid identification and quantification by multidimensional mass spectrometry-based shotgun lipidomics.

This article presents the strategies underlying the automated identification and quantification of individual lipid molecular species through array analysis of multidimensional mass spectrometry-based shotgun lipidomics (MDMS-SL) data, which are acquired directly from lipid extracts after direct infusion and intrasource separation. The automated analyses of individual lipid molecular species in the program employ a strategy in which MDMS-SL data from building block analyses using precursor ion scans, neutral loss scans, or both are used to identify individual molecular species, followed by quantitation. Through this strategy, the program screens and identifies species in a high-throughput fashion from a built-in database of over 36 000 potential lipid molecular species constructed employing known building blocks. The program then uses a two-step procedure for quantitation of the identified species possessing a linear dynamic range over 3 orders of magnitude and reverifies the results when necessary throug...
Logic as an integrated modeling framework

There is a growing interest in the application of Artificial Intelligence (AI) tools and techniques to management science problems. A rich variety of commercial AI software products is now emerging to facilitate this. However, there has been little integration between AI and Management Science (MS) at a theoretical level. This paper proposes the use of formal logic as the basis for this conceptual bridge, and the use of logic programming as a modeling language for management science applications. The framework is illustrated by a logic-based representation, called PM, for specifying production, distribution and inventory problems.
Rapid delineation of subsurface petroleum contamination using the site characterization and analysis penetrometer system

The Site Characterization and Analysis Penetrometer System (SCAPS) was used to investigate subsurface petroleum contamination at Aberdeen Proving Ground, Maryland. The SCAPS is a rapid site-screening tool developed by the Tri-Services (U.S. Army, Navy, and Air Force) to reduce the cost of installation restoration activities. The system, consisting of a geophysical cone penetrometer fitted with a laser-induced fluorescence petroleum sensor, is capable of simultaneous, real-time delineation of subsurface stratigraphy and petroleum contamination. Onsite processing of the SCAPS data allows three-dimensional visualization of both subsurface stratigraphy and petroleum contaminant distribution. The site investigation described herein successfully identified three distinct areas of subsurface petroleum contamination caused by leaking underground storage tanks containing No. 2 healing oil. The SCAPS petroleum sensor response was verified by obtaining 20 soil samples and performing onsite and conventional laboratory analyses for petroleum contaminants. Verification sample results indicate a strong correlation between the SCAPS fluorescence data and conventional measures of petroleum contamination. This investigation illustrates the capabilities of the SCAPS for rapid site characterization.
Limitations of the approximation capabilities of neural networks with one hidden layer

Lets≥1 be an integer andW be the class of all functions having integrable partial derivatives on [0, 1] s . We are interested in the minimum number of neurons in a neural network with a single hidden layer required in order to provide a mean approximation order of a preassignede>0 to each function inW. We prove that this number cannot be $$\mathcal{O}( \in ^{ - s} log(1/ \in ))$$ if a spline-like localization is required. This cannot be improved even if one allows different neurons to evaluate different activation functions, even depending upon the target function. Nevertheless, for anyδ>0, a network with $$\mathcal{O}( \in ^{ - s - \delta } )$$ neurons can be constructed to provide this order of approximation, with localization. Analogous results are also valid for otherL p norms.
Printed dipoles electromagnetically coupled to coplanar waveguide for linear or circular polarisation

Two configurations are proposed for feeding printed dipoles with coplanar waveguide transmission lines. The coplanar waveguide feed is printed on a ground plane sandwiched between a high-permittivity substrate and a low-permittivity substrate which supports the antenna. Both linear and circular polarisation can be achieved. Measured results are presented.
Thermal reactions of kerogen with added water, heavy water and pure organic substances

Abstract Finely divided samples of the Messel shale that had first been extracted with organic solvents were subjected to pyrolysis at 330°C for 3 days in the presence of excess water or heavy water and also with added pure organic substances. About 8% of the organic carbon was converted into an assemblage of saturated hydrocarbons that closely resembled petroleum hydrocarbons. No olefins were observed in the products. When the reaction was performed in heavy water, extensive deuteration occurred. The extent of substitution and the position of heavy hydrogen in a variety of hydrocarbon structural types were measured by mass spectrometry. A control experiment in which a saturated hydrocarbon was added showed that this deuterium substitution was not due to simple homogeneous exchange. A mechanism for the production of polydeuterated hydrocarbons is advanced, based on a model wherein the molecular fossils that are chemically bonded into kerogen matrix are released as free radicals. During the subsequent chain reactions, migration of olefinic bonds in intermediates and attack by deuterium free radicals result in multiple deuteration with retention of the carbon skeleton of the molecular fossil.
Cytopathology of thymic epithelial neoplasms

A cytologic diagnosis of thymoma is extremely challenging. In part, this is because the tumor is uncommon and aspirates are infrequently encountered, a technically proficient interventional radiologist is needed, epithelial cells may be difficult to recognize in lymphoid rich aspirate smears, and there is inherent sampling error in a tumor that frequently displays heterogeneous histopathology. Critical to the cytologic diagnosis of most WHO Type B thymomas is the recognition of a distinct population of epithelial cells mixed with lymphocytes. This is more easily accomplished using Papanicolaou or H&E stains, and often requires a cytokeratin stain for verification (in the correct clinical-radiologic context) because these cells are cytologically bland and have a varying amount of cohesiveness. WHO Type A thymoma may contain only epithelial cells and thus mimic a spindle cell neoplasm, or mesothelial cell clusters. Limitations of the cytologic method include an unproven ability to definitively separate thymoma into specific WHO subtypes using cytology alone, and to determine capsular invasion. Non-neuroendocrine thymic carcinomas mimic their extra-thymic counterparts in cytologic aspirates, and their malignant nature is usually readily recognizable. Thymic neuroendocrine carcinomas (NEC) are also cytologically identical to their more common pulmonary sites of origin, but identification of moderately-differentiated NEC is generally not possible.
Topology-function conservation in protein–protein interaction networks

Motivation: Proteins underlay the functioning of a cell and the wiring of proteins in protein–protein interaction network (PIN) relates to their biological functions. Proteins with similar wiring in the PIN (topology around them) have been shown to have similar functions. This property has been successfully exploited for predicting protein functions. Topological similarity is also used to guide network alignment algorithms that find similarly wired proteins between PINs of different species; these similarities are used to transfer annotation across PINs, e.g. from model organisms to human. To refine these functional predictions and annotation transfers, we need to gain insight into the variability of the topology-function relationships. For example, a function may be significantly associated with specific topologies, while another function may be weakly associated with several different topologies. Also, the topology-function relationships may differ between different species. Results: To improve our understanding of topology-function relationships and of their conservation among species, we develop a statistical framework that is built upon canonical correlation analysis. Using the graphlet degrees to represent the wiring around proteins in PINs and gene ontology (GO) annotations to describe their functions, our framework: (i) characterizes statistically significant topology-function relationships in a given species, and (ii) uncovers the functions that have conserved topology in PINs of different species, which we term topologically orthologous functions. We apply our framework to PINs of yeast and human, identifying seven biological process and two cellular component GO terms to be topologically orthologous for the two organisms. Availability and implementation: http://bio-nets.doc.ic.ac.uk/goCCA.zip Contact: ku.ca.lairepmi@ahsatan Supplementary information: Supplementary data are available at Bioinformatics online.
Minimizing electronic line terminals for automatic ring protection in general WDM optical networks

Automatic ring protection provides simple and rapid fault protection and restoration in telecommunication networks. To implement the automatic ring protection in general wavelength-division multiplexing (WDM) optical networks, the lightpaths are partitioned into groups each of which can be carried in a simple cycle of the underlying network. As the electronic line terminals are the dominant cost factor in the deployment of WDM optical networks, we study how to generate these partitions with minimum electronic line terminals. This optimization problem is NP-hard. We develop two polynomial-time approximation algorithms, with performance guarantees between 1.5 and 1.6 and between 1.5 and 1.5 + /spl epsi/, respectively. The second algorithm can be adapted, with the same performance guarantees, to the problem in which lightpaths are not prespecified and only the endpoints of each connection are given. Both algorithms can be easily adapted, with the same performance guarantees, to the problem in which only link protection is desired, and each group must be carried in a closed trail. The first algorithm matches and the second algorithm improves the approximation ratio obtained independently by Eilam et al. (see 14th Int. Symp. Distributed Computing, 2000).