cssi/SciSciGPT-SciSciNet huggingface dataset:
Abstract 4174: An integrative genomic analysis for clinically relevant cancer genetic aberration and targeted therapeutic prediction

Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA While the genomic and genetic basis of many cancers has been partly elucidated, less is known about the identity of specific cancer genes that are associated with clinical parameters such as clinical stage, metastasis, and survival. To address this question, we compiled multiple genomic data types (mutations, copy number alterations, gene expression and methylation status) as well as clinical meta-data for twelve different cancers in the Cancer Genome Atlas Project. We used an elastic-net regularized regression method on the combined genomic data to identify genetic aberrations and their associated cancer genes that are indicators of clinical parameters in each cancer type. To facilitate the identification of clinically actionable genetic aberrations from this cancer genomic data, we utilized genomic and drug response data from the Cancer Cell Line Encyclopedia (CCLE). These expansive data sets of hundreds of cancer cell lines include three genomic data types (mutations, copy number alterations, gene expression) and drug response data. To demonstrate the performance and validity of this approach, we demonstrated that our bioinformatics pipeline successfully identified i) synthetic genes that have their CNVs perfectly associated with stages from a simulated data ii) mutations of TGFBR2, methylation of MLH1 and other driver genes that have genetic changes associated with colorectal cancer (CRC) that demonstrate microsatellite instability CRC from TCGA data, and iii) IDH1 that obtained mutations associated with survival according to glioblastoma (GBM) data. We identify the top ranked genes that delineate key clinical features such as survival analysis or clinical stages for 13 cancers. A fit of the elastic-net regularized regression to more than 200 samples/cancer type and integrative analysis of integrative genomic platforms identified the set of top gene predictors of clinical parameters (TCGA data) and drug response (CCLE data). There are several genes ranked top in multiple cancer types while most of them are unique to a cancer type. These results provide us with new insights into the underlying genetic similarities and differences among 13 cancers; namely, common genetic characteristics that have implications for clinical phenotype. Finally, we are identifying the core set of gene aberrations that are both clinically relevant and drug responsible. Citation Format: HoJoon Lee, Hanlee P. Ji. An integrative genomic analysis for clinically relevant cancer genetic aberration and targeted therapeutic prediction. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4174. doi:10.1158/1538-7445.AM2014-4174
Abstract 20330: Cerebral Artery Dysfunction in a Mouse Model of Greater Large Artery Stiffness

Advancing age, as well as diseases such as diabetes, are characterized by increased large artery stiffness and increased cerebrovascular disease risk. It has been hypothesized that cerebral artery dysfunction connects these events; however a cause-and-effect relation between large artery stiffening and altered cerebral artery dilation and constriction has not been established. We studied elastin heterozygous mice (Eln+/-) as a model of increased large artery stiffness without co-morbidity. Eln+/- mice had ~35% greater aortic stiffness (pulse wave velocity) compared with Eln+/+ (p=0.04), but stiffness of the middle cerebral artery (MCA, ex vivo passive response) was similar between groups (p>0.05). MCA endothelium-dependent dilation (EDD), assessed by the maximal dilation to acetylcholine, was ~40% lower in Eln+/- compared with Eln+/+ (p 0.05), indicating that reduced NO bioavailability mediated ...
Mannose receptor and phagocytosis

Publisher Summary This chapter discusses the role of mannose receptor in phagocytosis. The mannose receptor (MR) is a ≈175 kDa transmembrane receptor expressed on resident macrophage subpopulations, dendritic cells, and on subsets of endothelial cells. The mannose receptor mediates the uptake of ligands bearing appropriately configured carbohydrate residues. Its ligand binding profile confers on it a broad capacity to recognize non-self over self-molecules, in keeping with its designation as a pattern recognition receptor. Ligation of the receptor is followed by internalization of the bound ligand, and is coupled to a variety of cellular processes directed toward destruction of pathogens, participation in the inflammatory response, or stimulation of the immune system. While this receptor is capable of both endocytic and phagocytic uptake, the signaling pathways utilized remain to be determined.
Energy cost comparison between bicycles and cars for urban travel

The direct and indirect energy required for urban travel by both bicycles and motor cars were compared. USEPA published mileage estimates and the Urban Driving Cycle were used in the case of motor cars, while for bicycles, a series of test rides were performed. While riding a simulated urban trip, bicycle velocity and pedalling rate were indirectly monitored. When combined with knowledge of the power required for propulsion, these data allowed for the computation of the direct energy used during the bicycle ride. Results show that for urban travel, the bicycle offers an energy saving of more than 90% over that required by the motor car.
The Difficulty of Historical Work in the Nineteenth-Century Museum and the Thackeray Novel

This essay suggests that conservation debates occasioned by the democratization of the nineteenth-century museum had an important impact on William Makepeace Thackeray's reimagination of the historical novel. Both the museum and the historical novel had traditionally made it their mission to present the past to an ever-widening public, and thus necessarily to preserve it. But in the middle of the nineteenth century, the museum and the novel also shared the experience of seeming to endanger precisely what they sought to protect, and as they tried to choose how aggressive to be in their conservingmeasures, they had to deliberate about the costs and benefits of going after the full reconstruction (the novel) or restoration (the museum) of what once had been. The first part of this essay shows how people fretted about the relation of conservation, destruction, and national identity at the museum, in The Times and in special Parliamentary sessions alike; the second part of the essay traces how Thackeray drew on the resulting debates in novels including The Newcomes (1853-55) and The History of Henry Esmond (1852), as he looked for a way to revivify the historical novel after it had gone out of fashion. He invoked broken statues and badly restored pictures as he navigated his own worries that he might be doing history all wrong, and damaging its shape in the process.
The mechanical and clinical reliability of the kinetic communicator's gravity correction procedure

The purpose of this study was to determine the reliability of the Kinetic Communicator's (Kin-Com) gravity correction procedure. To determine mechanical reliability, gravity correction was performed at 11 different angles while weights (1.15, 2.30, 3.45 and 4.60 kg) were suspended from the lever arm. Intraclass correlation (ICC) between trials showed that the Kin-Com was able to gravity correct weights with high reliability (R = 0.961-0.999). Gravity correction values from the 11 angles were analyzed with a one-way analysis of variance with repeated measures to determine if differences existed between gravity correction values collected at different angles for each weight condition. Even though reliability was good for each angle, gravity correction values collected near the vertical position differed from the gravity correction values collected at the horizontal position (P < 05). Differences decreased as weight increased. To determine clinical reliability, 25 subjects (age = 21.0 years, height = 16.6 cm, weight = 59.8 kg) were also gravity corrected in both the seated and prone positions at six different angles on 2 separate days. Correlation analysis between days showed good reliability (R = 0.83) for both positions when subjects were corrected at the horizontal. Reliability decreased as the lever arm approached vertical. Differences between gravity correction values existed at every angle measured for both positions. Even though the gravity correction was shown to be reliable at positions other than the horizontal, gravity correction should be performed at the horizontal position each time subjects are assessed.
Entextualized Humor in the Formation of Scientist Identities among U.S. Undergraduates

Studies of the socialization of novices into scientific cultures typically emphasize official knowledge-making activities. However, scientific socialization is also accomplished informally through humor. As entextualized humor, formulaic jokes enable U.S. undergraduate students in science to claim scientist identities both through a displayed orientation to scientific knowledge and through the cultural practice of circulating humorous scientific texts. In response, recipients may align or disalign with these identities and thus position themselves in relation to science cultures. [humor, higher education, identity, science, stance]
Hide and show: using real compiler code for teaching

In this paper, we present a novel approach that enables students in graduate compiler courses to examine and experiment with a real compiler without becoming overwhelmed by complexity. The key to the idea is the use of a debugger directly on a compiler during the compilation process. By providing instructions on breakpoints and variables of interest, the student is only shown the relevant portions of the compiler; the rest is hidden. We describe our strategy of using exercise sessions targeted toward illustration of core compiler concepts such as lexical analysis, parsing and code generation.
Characterization of the bupropion cue in the rat: lack of evidence for a dopaminergic mechanism.

Using a two-lever operant task rats were trained to discriminate 40 mg/kg IP of bupropion from saline. Despite bupropion's established dopaminergic activity in vitro and in vivo, it was found that the bupropion cue was neither mimicked by the dopaminergic drugs l-DOPA and bromocriptine nor blocked by a variety of neuroleptics (haloperidol, thioridazine, and thiothixene). In addition, bupropion was active in attenuating the behavior-suppressing effects of haloperidol, unlike amphetamine and the atypical antidepressants, nomifensine and viloxazine. The bupropion cue was not mimicked or disrupted by adrenergic or serotonergic drugs, but it did generalize to some stimulants (amphetamine, cocaine and caffeine) as well as to nomifensine and viloxazine. The generalizations were blocked by neuroleptics. These data indicate that bupropion's cue properties may not be based on its ability to modulate dopaminergic receptor activity. The possible involvement of phenylethylamine in the bupropion cue is also discussed.
The reliability of chest roentgenography and its clinical implications.

The interpretation of chest roentgenograms, like any other human activIty, is subject to considerable variation. It has been demonstrated that competent and experienced physicians are likely to disagree with each other in a significant proportion of roentgenographic interpretations. These inconsistencies were found when single roentgenograms were interpreted for the presence or absence of abnormal shadows. Even greater discrepancies were demonstrated in attempts to classify single roentgenographic shadows according to character, extent, and probable “activity” of the lesion. The implications of these findings to mass case finding programs have been discussed in a number of publications.’-5 More recently inconsistencies of similar magnitude were found to exist in the Interpretation of serial roentgenograms. It was shown that in evaluating film pairs for evidence of progression, regression, or stability of disease, well qualified radiologists and phthisiologists disagreed significantly with each other. Moreover, a physician did not always agree with himself In two independent interpretations of a set of serial roentgenograms.6 These findings are of great importance in clinical phthisiology In view of the universal employment of the procedure as an aid in the clinical management of tuberculosis patients. It is no doubt superfluous to state that, in spite of these difficult problems of interpretation, serial roentgenograms are among the most valuable criteria for assessing the course of disease in a patient with pulmonary tuberculosis. The most reliable estimate of changes in the extent and character of a lesion is provided by roentgenography and is perceived by a comparison of serial chest films. The evidence provided by roentgenography, however, must be integrated with other clinical findings and results of other tests. For the proper evaluation of these, and for the derivation of the most probable diagnosis, it Is desirable to have knowledge of the limitations of each test. What is wanted Is a quantitative evaluation of the errors inherent in each. Unfortunately, our knowledge of the subjective error in clinical medicine and of the variations In the different diagnostic tests is meager. The quantitative data which have recently been accumulating on the evaluation of roentgenographlc interpretations are, it may be hoped, the forerunner of similar data which will be forthcoming In other fields of medicine. One of the advantages which results from the demonstration of the existence of observer errors is the stimulation which It provides for devising
Greenhouse Gas Emissions from the Construction, Manufacturing, Operation, and Maintenance of U.S. Distribution Infrastructure for Petroleum and Biofuels

AbstractTo meet greenhouse gas (GHG) emissions for the transportation sector, the United States is expected to expand infrastructure for producing and distributing lignocellulosic biofuels over the next decade. To compare the life-cycle GHG footprint of biofuels to the petroleum baseline, emissions associated with feedstock and fuel handling, storage, and transportation must be included. U.S.-specific life-cycle GHG emission factors were developed for each major distribution chain activity by applying a hybrid life-cycle assessment methodology to the construction, manufacturing, operation and maintenance of each component. A projection was then made for the fleet of infrastructure components necessary to distribute 21 billion gal. (79.5 billion L) of ethanol derived entirely from Miscanthus grass for comparison to the baseline petroleum system. Owing to geographic, physical, and chemical properties of biomass and alcohols, the distribution system for Miscanthus-based ethanol is more capital- and energy-in...
On the preparation of 80Br-biomolecules—III: The effect of various experimental parameters on radiochemical yields

Abstract The effect of several experimental parameters on the efficiency of the 80 Br incorporation via the “CF 3 80 m Br-KBrO 3 ” gas exposure resulting in carrier free radiobrominated compounds was investigated by using two model compounds, L -tyrosine and guanosine. The 80 Br labelling proceeds very rapidly in the case of the L -tyrosine and is fairly independent of “labelling time” and substrate concentration as long as a certain minimum amount of L -tyrosine is used. This is in contrast to the guanosine system where rapid secondary reactions reduce the initially high yields of 80 Br-8-bromoguanosine at extended “labelling times” and where larger amounts of substrate are needed to produce optimum yields.
Calibration of the Geostationary Imaging Fourier Transform Spectrometer (GIFTS)

The NASA New Millennium Program's Geostationary Imaging Fourier Transform Spectrometer (GIFTS) requires highly accurate radiometric and spectral calibration in order to carry out its mission to provide water vapor, wind, temperature, and trace gas profiling from geostationary orbit. A calibration concept has been developed for the GIFTS Phase A instrument design. The in-flight calibration is performed using views of two on-board blackbody sources along with cold space. A radiometric calibration uncertainty analysis has been developed and used to show that the expected performance for GIFTS exceeds its top level requirement to measure brightness temperature to better than 1 K. For the Phase A GIFTS design, the spectral calibration is established by the highly stable diode laser used as the reference for interferogram sampling, and verified with comparisons to atmospheric calculations.
Hybrid Dysfunction and Physiological Compensation in Gene Expression

The formation of new species is often a consequence of genetic incompatibilities accumulated between populations during allopatric divergence. When divergent taxa interbreed, these incompatibilities impact physiology and have a direct cost resulting in reduced hybrid fitness. Recent surveys of gene regulation in interspecific hybrids have revealed anomalous expression across large proportions of the genome, with 30-70% of all genes exhibiting transgressive expression (i.e., higher or lower levels compared with both parental taxa), and these were mostly in the direction of downregulation. However, as most of these studies have focused on pairs of species exhibiting high degrees of reproductive isolation, the association between regulatory disruption and reduced hybrid fitness prior to species formation remains unclear. Within the copepod species Tigriopus californicus, interpopulation hybrids at F2 or later generations show reduced fitness associated with mitochondrial dysfunction. Here we show that in contrast to studies of interspecific hybrids, only 1.2% of the transcriptome is transgressively expressed in F3+ interpopulation hybrids of T. californicus, and nearly 80% of these genes are overexpressed rather than underexpressed; remarkably, none of these genes are among those showing divergent expression between parentals, nor is magnitude of transgressive gene expression in hybrids dependent on levels of protein sequence divergence. Moreover, many genes with transgressive expression are components of functional pathways impacted by mitonuclear incompatibilities in hybrid T. californicus (e.g., oxidative phosphorylation and antioxidant response). Our results suggest that hybrid breakdown at early stages of speciation may result from initial incompatibilities amplified by the cost of compensatory physiological responses.
TIMELINESSound in computing: a short history

This account of ways in which computers have interacted with us via our ears is a welcome first, an over-the-transom, unsolicited Timelines contribution.---Jonathan Grudin
Optimal range and Doppler centroid estimation for a ScanSAR system

This paper presents a new range and Doppler centroid estimation algorithm for a ScanSAR system. This algorithm is based on processing the image data in the overlapped region of two bursts of the same beam or adjacent beams. It leads to highly accurate radar pointing angles that are paramount to achieving good radiometric performance in ScanSAR imagery. The achievable accuracy is derived theoretically and verified by tests performed using SIR-C ScanSAR data and ERS data. This algorithm is computationally efficient and easy to implement. The proposed Doppler centroid estimation algorithm is also an excellent candidate for a strip mode SAR system.
Structure of the Universal Stress Protein of Haemophilus influenzae

Abstract Background: The universal stress protein UspA is a small cytoplasmic bacterial protein whose expression is enhanced several-fold when cellular viability is challenged with heat shock, nutrient starvation, stress agents which arrest cell growth, or DNA-damaging agents. UspA enhances the rate of cell survival during prolonged exposure to such conditions, suggesting that it asserts a general "stress endurance" activity. However, neither the structure of UspA nor the biochemical mechanism by which it protects cells from the broad spectrum of stress agents is known. Results: The crystal structure of Haemophilus influenzae UspA reveals an asymmetric dimer with a tertiary α/β fold similar to that of the Methanococcus jannaschi MJ0577 protein, a protein whose crystal structure revealed a novel ATP binding motif. UspA differs significantly from the MJ0577 structure in several details, including the triphosphate binding loop of the ATP binding motif; UspA shows no ATP binding activity. Conclusions: Within the universal stress protein family that is delineated by sequence similarity, UspA is the only member which has been correlated with a cellular activity, and MJ0577 is the only member which has been assigned a biochemical activity, i.e., ATP binding. UspA has a similar fold to the MJ0577 protein but does not bind ATP. This suggests that members of this protein family will segregate into two groups, based on whether or not they bind ATP. By implication, one subset of the universal stress proteins presumably has an ATP-dependent function, while another subset functions in ATP-independent activities.
Application of artificial intelligence and computer-based methods to predicting chemical toxicity

The toxicity prediction problem lies squarely at the interface of biology, chemistry and computational domains and will require the integrated application of knowledge and approaches from each domain for its solution. It is not a single modeling problem, but rather multiple levels of modeling compartments derived from the goals of toxicity risk assessment. These compartments include different categories and characteristics of toxicity (e.g., cancer vs. non-cancer, acute vs. delayed) and, therein, different levels of biofunctional organization and multiple mechanisms of toxicity extending to the level of individual chemical structures. A toxicity prediction model should strive to resolve the global toxicity prediction problem to local modeling compartments that reflect coherent biofunctional mechanisms and common modes of action while retaining some level of useful generalizations. This paper attempts to use these general concepts to frame the challenges and opportunities for application of Artificial Intelligence (AI) and computer-based methods to the goal of chemical toxicity prediction.
Attendance at a survivorship clinic: impact on knowledge and psychosocial adjustment

Purpose Due to their heightened risk of developing late-occurring adverse outcomes, pediatric cancer survivors are advised to receive follow-up care in specialized Survivor Clinics. However, little is known about the impact of attending such clinics on psychosocial adjustment, knowledge, and morbidity. This study assesses the differences between those who attended a Survivorship Clinic and those who did not on knowledge, perception of risk, and psychosocial adjustment.
Large Piezoelectric Effect Induced by Direct Current Bias in PMN:PT Relaxor Ferroelectric Ceramics

The longitudinal piezoelectric effect induced by a direct current bias field was investigated in PMN:PT family of relaxor ferroelectric ceramics in the frequency range from 0. 1 Hz to 50 kHz. The piezoelectric d33 coefficient was studied by measuring the strain induced by the applied electric field. Under the 10 kHz driving field, the large piezoelectric strain coefficient, d33, of 800 pC/N is obtained. The piezoelectric strain coefficient related dielectric and electrostrictive parameters were also studied under direct current bias and the d33 coefficient was calculated by the equation d33=2Q11P3e33. The results are in good agreement with the directly measured ones. The dispersion of the piezoelectric effect is mainly due to the dielectric dispersion.
Highly cross-linked self-assembled monolayer stationary phases: an approach to greatly enhancing the low pH stability of silica-based stationary phases.

A new type of silica-based stationary phase with dramatically improved acid stability compared to any currently available silica-based stationary phase has been developed. Superior low pH stability is achieved by first self-assembling a densely bonded monolayer of (chloromethyl)-phenylethyltrichlorosilane (CMPES). The self-assembly step is followed by a Friedel−Crafts cross-linking of the reactive moieties with their neighbors, by addition of secondary, cross-linkable aromatic reagents, or by both. This phase is not endcapped. Elemental analysis data shows that an aluminum chloride catalyst is very effective at bonding aromatic cross-linking reagents, such as styrene heptamer and triphenylmethane, to the reactive CMPES monolayer. The stability of the retention factor of decylbenzene on the cross-linked self-assembled CMPES phases is compared to a sterically protected C18 phase to illustrate its superior resistance to acid-catalyzed-phase loss. Inverse size exclusion chromatography and flow-curve compariso...
A priori rate constants for kinetic modeling

The advent of computer-aided methods for constructing detailed kinetic models of multicomponent reacting systems provides fresh motivation for the development of efficient and accurate methods for estimating rate constants. There is now the real likelihood that a priori rate estimates, formerly of primarily academic interest, could directly impact major public policy and business decisions. This opportunity brings many challenges. The process of building a computer model for a real-world system can require hundreds of thousands of rate estimates, making most existing rate calculation techniques impractical. Also, the demands for tight error bars on model predictions used to make major decisions often imply levels of accuracy unachievable with existing rate calculation techniques. Past and recent progress towards developing fast and accurate rate estimates is selectively reviewed, and our methodology is outlined. New rate estimates for several types of reactions involving O and HO2 are presented. Several technical issues requiring further work by the theoretical chemistry community are highlighted. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00214-002-0368-4.
Biorefinery: Ensuring biomass as a sustainable renewable source of chemicals, materials, and energy

The Second International Biorefinery Conference was held in Syracuse, New York, October 6–7, 2009. Biorefinery and its potentials are discussed in this editorial, along with an introduction of the three guest editors.
Risk factors for toxic nephropathies.

The best definition of risk factors for renal injury, irrespective of the aetiological agent, comes from observations in patients with acute renal failure. From such observations, two subdivisions have evolved, i.e., acute insults and host risk factors. Acute renal insults include: hypertension, sepsis, use of nephrotoxic drugs (e.g., aminoglycoside antibiotics and contrast media), haemoglobinuria or myoglobinuria, liver disease and extracellular volume depletion. Host risk factors include: advanced age, hypertension, gout and hyperuricaemia, diabetes mellitus, chronic renal failure and use of diuretics. Furthermore, the mechanism of acute renal injury can be correlated with different risk factors: for a tubular toxic agent, acting either directly on the cells or haemodynamically, a dose-dependency is characteristic; while for immunologically mediated injury, genetic predisposition is more important. The identification of risk factors for chronic toxic injury is confounded by the possibilities of multiple episodes of subclinical renal injury, the distinct possibility that a major component of the ageing process may be a loss of renal reserve, and a progressive body burden, of, e.g., cadmium, which may deplete intrinsic protective mechanisms. However, clinically relevant risk factors can alert the clinician to exercise additional caution when prescribing medications that are potentially nephrotoxic. Such factors include dehydration, pre-existing renal disease, age, co-existing diseases that cause renal ischaemia, gender, concomitantly administered drugs, and electrolyte abnormalities.
Group processes in computer-mediated communication☆

Abstract Three experiments explored the effects of computer-mediated communication on communication efficiency, participation, interpersonal behavior, and group choice. Groups of three members were asked to reach consensus on career choice problems; they communicated face-to-face and in simultaneous computer-mediated discussions or through computer mail. When groups were linked by computer, group members made fewer remarks than they did face-to-face and took longer to make their group decisions. Social equalization was higher in computer-mediated groups in that group members participated more equally in discussions. Computer-mediated groups also exhibited more uninhibited behavior—using strong and inflammatory expressions in interpersonal interactions. Decisions of computer-mediated groups shifted further away from the members' initial individual choices than group decisions which followed face-to-face discussions. We discuss the implications of these findings for extension of theories about group interaction and for analyses of the effects of Computers in organizations.
The evolution of surnames: an analysis of their distribution and extinction.

Abstract Surname distribution and evolution can be analyzed by a theory put forward for neutral mutation by Karlin and McGregor. This theory allows us to predict the distribution of surnames, and to predict immigration on the basis of knowledge of population size, and of the total number of different surnames or, in lieu of the latter, a quantity known as random isonymy. Another approach allows us to predict probabilities of extinction after any number of generations and various sets of conditions. The predictions of these theories have been tested successfully on a number of empirical data from the Upper Parma Valley.
The biometric technologies business case: a systematic approach

Purpose – This paper aims to assist readers to develop a compelling business case, including quantifiable and non‐quantifiable costs and benefits, for the deployment of biometric technologies in information systems to enhance corporate security for access control, identification and verification applications.Design/methodology/approach – The paper reviews the strengths and weaknesses of leading biometric technologies, while commenting on their practical applicability in real world implementations. In addition, the paper develops a process for ensuring that the best biometric applications are chosen, considering both the technology and related business issues.Findings – The paper suggests that biometrics must be carefully selected to achieve a good fit to the security problem, giving examples of how a good fit might be evaluated by the user. The one‐time and recurring charges associated with the typical biometric implementation are evaluated, arguing that these costs must be offset by a formal risk evaluat...
Renal Vascular Disease: Pathology of Large Blood Vessel Disease

Lesions of the extrarenal arteries which are associated with hypertension are described. Included are descriptions of the development, stages, and complications of atherosclerotic plaques; intimal fibroplasia and the medial fibromuscular dysplasias; Takayasu's aortitis; radiation injury; and a newly described arterial disease, medial agenesis. Also described is the development of atherosclerosis in saphenous vein bypass grafts and the effects of transluminal angioplasty.
Production and oxidation of indole by Haemophilus influenzae.

During growth in high concentrations of iron nitrate, H. influenzae produces compounds reactive in biochemical assays for hydroxamates. Mixing experiments established that nitrate was responsible for inducing these compounds. Analysis by 1H and 13C NMR and high resolution mass spectrometry identified the active species as 2,2-bis(3′-indolyl)indoxyl. Bacterial production of the latter compound has been previously observed only in Pseudomonas aureofaciens. A mutant defective in the production of 2,2-bis(3′-indolyl)indoxyl was constructed by marker insertion. The formation of indole and 2,2-bis(3′-indolyl)indoxyl was quantitated by reverse-phase high pressure liquid chromatography during growth in high concentrations of nitrate. The mutant produced high concentrations of indole, but only minimal amounts of 2,2-bis(3′-indolyl)indoxyl, and also proved to be defective in nitrate reduction. These data suggest that indole may function as an electron donor for nitrate reductase in H. influenzae.
Design and model demonstration of a camera that removes the infrared OH background from two-dimensional images

Very deep images in the near IR could be recorded from ground based telescopes, if the strong night sky emission lines of OH were blocked and the continuum transmitted. For example, in the H band, of width 330 nm, 87 line groups contribute nearly all the emission. If 1 to 3 nm bandwidth sections of spectrum were removed at each group, the total background--lines plus continuum--would be reduced by 95 to 99.8%, depending on the continuum strength, while the light from the object under observation would be reduced by only approximately 40%. This would greatly enhance sensitivity to faint diffuse objects, such as distant redshifted galaxies. Our camera passes the 2D dimensional image through a large Littrow spectrograph. A long spectrum is formed, such that the full image width projects to a spectral resolution (lambda) /(Delta) (lambda) equals 1500. After reflection at a mirrored `staircase' along the focused spectrum, the light retraces its path through the spectrograph to form a high resolution white image at the original entrance. By placing a comb-like mask along the dispersed spectrum, the OH lines are removed from the rebuilt image, while an optical arrangement involving a polarized beam-splitter efficiently separates the original and rebuilt images. A small scale demonstration in the laboratory with a 10 cm grating proves the method. The source was a resolution chart 6 x 8 mm at f/15. Working in the optical with 10% bandwidth, the spectral resolution was up to 50,000 for individual image resolution elements, 370 for the full rebuilt image. A CCD image of the result image shows 100 x 130 spatial resolution elements. A design optimized for use with a 2 m telescope has a grating size 50 cm x 66 cm and 20% bandwidth. It gives a nominal field of 3 by 5 arcmin and is limited by seeing rather than aberrations. The 2.5 m paraboloidal reflector needed for such an instrument could be built inexpensively as a spinning liquid mirror.© (1994) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
Deletion of Thymidine Kinase Gene Attenuates Channel Catfish Herpesvirus While Maintaining Infectivity

Abstract A recombinant thymidine kinase (TK) gene deletion mutant of channel catfish herpesvirus (CCV) was constructed and compared to the parent virus for replicative ability in cell culture, for the ability to infect, replicate, and cause lethal disease in the channel catfish host, and for the ability to induce protective immunity in channel catfish fingerlings. There was no difference between parent CCV and the TK-negative mutant (CCVTK - ) in vital production in cell culture. However, in immersion challenge trials, 100-fold more CCVTK - than parent CCV was required to kill similar numbers of channel catfish fingerlings. The attenuation was confirmed as a TK-associated characteristic in marker rescue; the revertant regained the pathogenic characteristic of the parent virus. When catfish were immersion challenged with equal amounts of CCVTK - or CCV, the levels of virus isolated from the posterior kidney were similar through the peak production period which occurred 4 days postinfection. Subsequently, CCVTK - levels decreased dramatically when compared to CCV levels. Exposure to CCVTK - induced protective immunity against challenge with a lethal dose of wild-type CCV. The degree of protection provided by CCVTK - was related to of dose of CCVTK - given. This study demonstrates that the genetically distant CCV retains recombination properties and TK-associated attenuation properties of herpesviruses of higher vertebrates. Additionally, the unique characteristic of CCV containing two copies of the TK gene did act prevent the use of this gene as a selectable site of homologous recombination.
Hemospermia and expressed tumor in the urethra: an unusual presentation of ductal carcinoma of the prostate.

A 49-year-old white man presented with a 3-year history of hemospermia. Digital rectal examination was unremarkable and prostate specific antigen was 0.9 ng./ml. A prostatic massage yielded tissue per the urethra. Histological examination revealed moderate to poorly differentiated adenocarcinoma. Transrectal ultrasound demonstrated a 23 gm. prostate, and biopsies showed fibromuscular and glandular hyperplasia. Excretory urography, abdominal and pelvic computerized tomography, and bone scans were unremarkable. A second transrectal ultrasound with prostatic biopsies showed focal basal and nodular hyperplasia. Flexible cystoscopy and bladder wash cytology were negative. Two months later a third transrectal ultrasound revealed an egg-shaped hypoechoic area at the prostatic base. Biopsies demonstrated prostatic adenocarcinoma in 5 of 16 cores. Papillary areas suggested a ductal variant. The patient underwent radical prostatectomy. Final pathological evaluation indicated a Gleason score 9 (4 1 5) ductal prostatic carcinoma. The tumor appeared to arise from a prostatic duct superior to the verumontanum on the posterior urethra (figs. 1 and 2). The left seminal vesicle lumen contained tumor fragments. However, its wall was spared. Surgical margins were negative. DISCUSSION
Classical Music on CD's: Creating and Controlling the Collection

Developing a collection of compact disc sound recordings is beginning to emerge as a goal for many libraries, yet the commitment of resources and energy involved in this effort is not to be taken lightly. In addition to the inevitable practical problems to be solved, there is the rare responsibility of constructing a collection from the ground up, an enterprise particularly challenging with a new medium. Satisfying both patron needs and staff requirements is seldom easy; the task of choosing CD's therefore requires careful thought, planning, and monitoring.
Tobacco and the Escalating Global Cancer Burden

The global burden of cancer is escalating as a result of dramatic increases in the use of tobacco in the developing world. The use of tobacco is linked to the development of a broad variety of cancers, mainly lung cancer, the single most common cancer in the world. Tobacco smoking-attributable deaths extends beyond cancer and include stroke, heart attack and COPD. Widening disparities in cancer-related mortality have shifted towards a more dramatic burden in the developing world. Appropriate interventions must be implemented to reduce tobacco use and prevent global mortality that has escalated to epidemic levels. Tobacco control policies, including public health advertisement campaigns, warning labels, adoption of smoke-free laws, comprehensive bans and tax policies are highly effective measures to control tobacco use. Clinicians and academic institutions have to be actively committed to support tobacco control initiatives. The reduction in cancer related morbidity and mortality should be viewed as a global crisis and definitive results will depend on a multilevel effort to effectively reduce the burden of cancer, particularly in underprivileged regions of the world.
Modification of the palatal lift speech aid

Abstract A modification in the construction of a speech aid restoration, and the incorporation of the palatal lift design into the cleft palate prosthesis were described. The palatal lift restoration reduces hypernasal speech by elevating the soft palate in an upward and backward direction, approximately into a position which the velum would attain during normal speech. In patients whose soft palates are insufficient in length, the lift portion of the restoration is extended, and the pharyngeal part is modified in order to effect velopharyngeal closure. The various steps in the construction of a speech aid restoration, and the use of cephalometric roentgenography to demonstrate elevation of the soft palate and velopharyngeal closure were described.
Value of a Life: What Difference Does It Make?'

A comparison of the costs and benefits of 57 lifesaving programs reveals striking disparities across agencies and programs in cost/life saved and even greater disparities in cost/life-year saved. Within a broad range the monetary value assigned to the benefits of averting a death usually does not alter the policy implications of the analyses. The findings suggest that despite the substantial disagreements and uncertainties in the theory and practice of valuing lives, careful quantitative analysis can be helpful in setting health, safety, and environmental priorities.
Oxygen, pHi and arrest of biosynthesis in brine shrimp embryos

Embryos of the brine shrimp Artemia franciscana are able to withstand bouts of environmental anoxia for several years by entering a quiescent state, during which time metabolism is greatly depressed. Within minutes of oxygen removal, intracellular pH (pHi) drops at least 1.0 unit. This acidification has been strongly implicated in the arrest of both catabolic and anabolic processes in the cytoplasm. A global arrest of cytoplasmic translation accompanies the transition into anoxia or into aerobic acidosis (artificial quiescence imposed by intracellular acidification with CO2 in the presence of oxygen). Similarly, protein synthesis in isolated mitochondria from these embryos is also reduced markedly in response to acidic pH (80% reduction) or anoxia (79% reduction). The constancy of mRNA levels during quiescence indicates that protein synthesis is likely to be controlled at the translational level. Mitochondrial matrix pH is 8.2 during protein synthesis assays performed at the extramitochondrial pH optimum of 7.5. When this proton gradient is abolished with the K+/H+ ionophore nigericin, the extramitochondrial pH optimum for protein synthesis displays an alkaline shift of approximately 0.7 pH unit. These data suggest the presence of proton-sensitive translational components within the mitochondrion. The oxygen dependency of mitochondrial protein synthesis is not explained simply by blockage of the electron transport chain or by the increased redox state. Whereas oxygen deprivation substantially depresses protein synthesis by 77% after 1 h, normoxic incubations with saturating concentrations of cyanide or antimycin A have only a modest effect (36% reduction, cyanide; 20%, antimycin A). This cyanide- and antimycin-insensitive, but hypoxia-sensitive, inhibitory signature for the arrest of protein synthesis suggests the presence of a molecular oxygen sensor within the mitochondrion.
High-Resolution Solid-State NMR of Anisotropically Mobile Molecules Under Very Low Power 1H Decoupling and Moderate Magic-Angle Spinning

Abstract We show that for observing high-resolution heteronuclear NMR spectra of anisotropically mobile systems with order parameters less than 0.25, moderate magic-angle spinning (MAS) rates of ∼11 kHz combined with 1 H decoupling at 1–2 kHz are sufficient. Broadband decoupling at this low 1 H nutation frequency is achieved by composite pulse sequences such as WALTZ-16. We demonstrate this moderate MAS low-power decoupling technique on hydrated POPC lipid membranes, and show that 1 kHz 1 H decoupling yields spectra with the same resolution and sensitivity as spectra measured under 50 kHz 1 H decoupling when the same acquisition times (∼50 ms) are used, but the low-power decoupled spectra give higher resolution and sensitivity when longer acquisition times (>150 ms) are used, which are not possible with high-power decoupling. The limits of validity of this approach are explored for a range of spinning rates and molecular mobilities using more rigid membrane systems such as POPC/cholesterol mixed bilayers. Finally, we show 15 N and 13 C spectra of a uniaxially diffusing membrane peptide assembly, the influenza A M2 transmembrane domain, under 11 kHz MAS and 2 kHz 1 H decoupling. The peptide 15 N and 13 C intensities at low-power decoupling are 70–80% of the high-power decoupled intensities. Therefore, it is possible to study anisotropically mobile lipids and membrane peptides using liquid-state NMR equipment, relatively large rotors, and moderate MAS frequencies.
Contemporary presentation and evolution of management of neck paragangliomas

Background The aim of the present study was to review the contemporary presentation and evolution of management of neck paragangliomas. Methods Forty-one neck paragangliomas operated on in 36 patients over a 44 year period were included in the current report. The study period was divided into two parts, the first three decades (1964-1989), during which the current management techniques were evolved, and the last two decades (1990-2008). Results Patients presented with a palpable neck mass (n = 17), cranial nerve (CN) palsy (n = 3) or both (n = 6), or the lesion was an incidental finding (n = 14). The use of cross-section imaging modalities (n = 24) increased from 35% during the first part of the study to 95% during the second part of the study (P Conclusions In the modern era, neck paragangliomas can be managed with a low incidence of long-term sequelae. Smaller, asymptomatic, and incidentally detected tumors are currently the most common presentation pattern.
Quantum mechanics with extended probabilities

The quantum mechanics of closed systems such as the universe is formulated using an extension of familiar probability theory that incorporates negative probabilities. Probabilities must be positive for sets of alternative histories that are the basis of fair settleable bets. However, in quantum mechanics there are sets of alternative histories that can be described but which cannot be the basis for fair settleable bets. Members of such sets can be assigned extended probabilities that are sometimes negative. A prescription for extended probabilities is introduced that assigns extended probabilities to all histories that can be described, fine grained or coarse grained, members of decoherent sets or not. All probability sum rules are satisfied exactly. Sets of histories that are recorded to sufficient precision are the basis of settleable bets. This formulation is compared with the decoherent (consistent) histories formulation of quantum theory. Prospects are discussed for using this formulation to provide testable alternatives to quantum theory or further generalizations of it.