cssi/SciSciGPT-SciSciNet huggingface dataset:
Whole-Genome DNA Microarray Analysis of a Hyperthermophile and an Archaeon: Pyrococcus furiosus Grown on Carbohydrates or Peptides

The first complete-genome DNA microarray was constructed for a hyperthermophile or a nonhalophilic archaeon by using the 2,065 open reading frames (ORFs) that have been annotated in the genome of Pyrococcus furiosus (optimal growth temperature, 100°C). This was used to determine relative transcript levels in cells grown at 95°C with either peptides or a carbohydrate (maltose) used as the primary carbon source. Approximately 20% (398 of 2065) of the ORFs did not appear to be significantly expressed under either growth condition. Of the remaining 1,667 ORFs, the expression of 125 of them (8%) differed by more than fivefold between the two cultures, and 82 of the 125 (65%) appear to be part of operons, indicating extensive coordinate regulation. Of the 27 operons that are regulated, 5 of them encode (conserved) hypothetical proteins. A total of 18 operons are up-regulated (greater than fivefold) in maltose-grown cells, including those responsible for maltose transport and for the biosynthesis of 12 amino acids, of ornithine, and of citric acid cycle intermediate products. A total of nine operons are up-regulated (greater than fivefold) in peptide-grown cells, including those encoding enzymes involved in the production of acyl and aryl acids and 2-ketoacids, which are used for energy conservation. Analyses of the spent growth media confirmed the production of branched-chain and aromatic acids during growth on peptides. In addition, six nonlinked enzymes in the pathways of sugar metabolism were regulated more than fivefold—three in maltose-grown cells that are unique to the unusual glycolytic pathway and three in peptide-grown cells that are unique to gluconeogenesis. The catalytic activities of 16 metabolic enzymes whose expression appeared to be highly regulated in the two cell types correlated very well with the microarray data. The degree of coordinate regulation revealed by the microarray data was unanticipated and shows that P. furiosus can readily adapt to a change in its primary carbon source.
Design and synthesis of a library of tetracyclic hydroazulenoisoindoles.

Forty-four tetracyclic hydroazulenoisoindoles were synthesized via a tandem cyclopropanation/Cope rearrangement, followed by a Diels−Alder sequence from easily available five-membered cyclic cross-conjugated trienones. These trienones were obtained from two different routes depending upon whether R1 and R2 are alkyl or amino acid derived functional groups, via a rhodium(I)-catalyzed cycloisomerization reaction. To increase diversity, four maleimides and two 1,2,4-triazoline-3,5-diones were used as dienophiles in the Diels−Alder step. Several Diels−Alder adducts were further reacted under palladium-catalyzed hydrogenation conditions, leading to a diastereoselective reduction of the trisubstituted double bond. This library has demonstrated rapid access to a variety of structurally complex natural product-like compounds via stereochemical diversity and building block diversity approaches.
The anomaly structure of (2,0) heterotic world-sheet supergravity with gauged R-invariance

We present a supereld approach to the theory of (2; 0) worldsheet supergravity. The (2; 0) structure group is enlarged to Lorentz U(1) and the anomaly structure of this extended theory is studied. We then modify the theory by adding the Lorentz Chern-Simons term and present a two dimensional Green-Schwarz mechanism. The resultant theory corresponds to superconformally invariant string theories outside the critical dimension.
Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system

NAMD (nanoscale molecular dynamics) is a production molecular dynamics (MD) application for biomolecular simulations that include assemblages of proteins, cell membranes, and water molecules. In a biomolecular simulation, the problem size is fixed and a large number of iterations must be executed in order to understand interesting biological phenomena. Hence, we need MD applications to scale to thousands of processors, even though the individual timestep on one processor is quite small. NAMD has demonstrated its performance on several parallel computer architectures. In this paper, we present various compiler optimization techniques that use single-instruction, multiple-data (SIMD) instructions to obtain good sequential performance with NAMD on the embedded IBM PowerPC® 440 processor core. We also present several techniques to scale the NAMD application to 20,480 nodes of the IBM Blue Gene/L™ (BG/L) system. These techniques include topology-specific optimizations to localize communication, new messaging protocols that are optimized for the BG/L torus, topology-aware load balancing, and overlap of computation and communication. We also present performance results of various molecular systems with sizes ranging from 5,570 to 327,506 atoms.
A 3D mortar method for solid mechanics

A version of the mortar method is developed for tying arbitrary dissimilar 3D meshes with a focus on issues related to large deformation solid mechanics. Issues regarding momentum conservation, large deformations, computational efficiency and bending are considered. In particular, a mortar method formulation that is invariant to rigid body rotations is introduced. A scheme is presented for the numerical integration of the mortar surface projection integrals applicable to arbitrary 3D curved dissimilar interfaces. Here, integration need only be performed at problem initialization such that coefficients can be stored and used throughout a quasi-static time stepping process even for large deformation problems. A degree of freedom reduction scheme exploiting the dual space interpolation method such that direct linear solution techniques can be applied without Lagrange multipliers is proposed. This provided a significant reduction in factorization times. Example problems which touch on the aforementioned solid mechanics related issues are presented. Published in 2003 by John Wiley & Sons, Ltd.
No pathophysiologic relationship of soluble biliary proteins to cholesterol crystallization in human bile.

This study explores the pathophysiologic effects of soluble biliary glycoproteins in comparison to mucin gel and cholesterol content on microscopic crystal and liquid crystal detection times as well as crystallization sequences in lithogenic human biles incubated at 37 8 C. Gallbladder biles from 13 cholesterol gallstone patients were ultracentrifuged and microfiltered (samples I). Total biliary lipids were ex- tracted from portions of samples I, and reconstituted with 0.15 m NaCl (pH 7.0) (samples II). Portions of samples II were supplemented with purified concanavalin A-binding biliary glycoproteins (final concentration 5 1 mg/mL) (samples III), or mucin gel (samples IV), respectively, iso- lated from the same cholesterol gallstone biles. Samples V consisted of extracted biliary lipids from uncentrifuged and unfiltered bile samples reconstituted with 0.15 m NaCl (pH 7.0). Analytic lipid compositions of samples I through IV were identical for individual biles but, as anticipated, sam- ples V displayed significantly higher cholesterol saturation indexes. Detection times of cholesterol crystals and liquid crystals were accelerated in the rank order of samples: IV . V. I 5 II 5 III, indicating that total soluble biliary glyco- proteins in pathophysiologic concentration had no appre- ciable effect. Crystallization sequences ( D. Q-H. Wang and M. C. Carey. J. Lipid Res . 1996. 37: 606-630; and 2539-2549) were similar among samples I through V. Crystal detection times and numbers of solid cholesterol crystals were accel- erated in proportion to added mucin gel and the cholesterol saturation of bile only. For pathophysiologically relevant conditions, our results clarify that mucin gel and cholesterol content, but not soluble biliary glycoproteins, promote cho- lesterol crystallization in human gallbladder bile.— Wang, D. Q-H., D. E. Cohen, F. Lammert, and M. C. Carey. No pathophysiologic relationship of soluble biliary proteins to cholesterol crystallization in human bile. J. Lipid Res. 1999. 40: 415-425.
When one sample is not enough: improving text database selection using shrinkage

Database selection is an important step when searching over large numbers of distributed text databases. The database selection task relies on statistical summaries of the database contents, which are not typically exported by databases. Previous research has developed algorithms for constructing an approximate content summary of a text database from a small document sample extracted via querying. Unfortunately, Zipf's law practically guarantees that content summaries built this way for any relatively large database will fail to cover many low-frequency words. Incomplete content summaries might negatively affect the database selection process, especially for short queries with infrequent words. To improve the coverage of approximate content summaries, we build on the observation that topically similar databases tend to have related vocabularies. Therefore, the approximate content summaries of topically related databases can complement each other and increase their coverage. Specifically, we exploit a (given or derived) hierarchical categorization of the databases and adapt the notion of "shrinkage" -a form of smoothing that has been used successfully for document classification-to the content summary construction task. A thorough evaluation over 315 real web databases as well as over TREC data suggests that the shrinkage-based content summaries are substantially more complete than their "unshrunk" counterparts. We also describe how to modify existing database selection algorithms to adaptively decide -at run-time-whether to apply shrinkage for a query. Our experiments, which rely on TREC data sets, queries, and the associated "relevance judgments," show that our shrinkage-based approach significantly improves state-of-the-art database selection algorithms, and also outperforms a recently proposed hierarchical strategy that exploits database classification as well.
Passive constraint analysis of the knee

An anatomically based mathematical model of the passive constraints, including both surface contacts and ligaments and based on screw theory, is presented as a method of assessing the instantaneous total freedom of the knee. Screw theory address the full three-dimensional kinematics and allows consideration of motions that release or violate constraints. Models for the ligamentous and articular surface constraints are proposed and procedures for formulating and solving model equations are presented. >
Unsupervised Change Detection in High Resolution Satellite Imagery from Fusion of Spectral and Spatial Information

In this paper, we present an unsupervised change detection approach that combines pixel-based local Haar-like features, color information, vegetation index, and man-made structure features using fuzzy logic rules to provide multi-level change detection results. An illumination invariant descriptor for each pixel is introduced to describe a Haar-like feature in a local area. Hue is used as a color feature in our change detection method. For the purpose of enhancing the change area with man-made structures, we de-weight the level of detected change areas where there are no man-made objects. The comparison of all features is done separately and the decision results are then combined under seven fuzzy logic rules to provide multi-level change detection results. The performance of the change detection is evaluated qualitatively by visual inspection and quantitatively using ground truth. The quantitative test results show that more than 90% of changes are correctly detected.
Semiparametric nonlinear regression for detecting gene and environment interactions

Abstract It is commonly accepted that gene and environment (G × E) interactions play a pivotal role in determining the risk of human diseases. In conventional parametric models such as linear models and generalized linear models which are applied frequently to study statistical interactions, effects of covariates are decomposed into main effects and interaction effects (products of two components). Such decomposition, however, may not reflect the true interaction effect of gene and environment. In this paper, we propose a semiparametric regression approach to capture possible nonlinear G × E interactions. A profile quasi-log-likelihood estimation method is applied with asymptotic consistency and normality established for the profile estimators. Moreover, we develop Rao-score-type test procedures based on the profile estimation for regression parameters and nonparametric coefficient functions, respectively. Our models and methods are illustrated by both simulation studies and analysis of a dataset application.
Combinatorial compound libraries for drug discovery: an ongoing challenge

Almost 20 years of combinatorial chemistry have emphasized the power of numbers, a key issue for drug discovery in the current genomic era, in which it has been estimated that there might be more than 10,000 potential targets for which it would be desirable to have small-molecule modulators. Combinatorial chemistry is best described as the industrialization of chemistry; the chemistry has not changed, just the way in which it is now carried out, which is principally by exploiting instrumentation and robotics coupled to the extensive use of computers to efficiently control the process and analyse the vast amounts of resulting data. Many researchers have contributed to the general concepts as well as to the technologies in present use. However, some interesting challenges still remain to be solved, and these are discussed here in the context of the application of combinatorial chemistry to drug discovery.
A History of Devices as an Alternative to Heart Transplantation

The rapid evolution of mechanical circulatory support (MCS) has extended survival and improved quality of life for patients suffering from the most advanced heart failure (HF). Survival at one year after placement of a left ventricular assist device exceeds 80%. MCS and transplant have developed in counterpoint to each other. Patients with HF now have a meaningful option for lifelong support even if they are not candidates for heart transplant. As the profiles of MCS recipients change and the next generation of devices emerges, new challenges and opportunities await physicians caring for patients with cardiac failure.
Warming trends in Asia amplified by brown cloud solar absorption

Atmospheric brown clouds are mostly the result of biomass burning and fossil fuel consumption. They consist of a mixture of light-absorbing and light-scattering aerosols and therefore contribute to atmospheric solar heating and surface cooling. The sum of the two climate forcing terms-the net aerosol forcing effect-is thought to be negative and may have masked as much as half of the global warming attributed to the recent rapid rise in greenhouse gases. There is, however, at least a fourfold uncertainty in the aerosol forcing effect. Atmospheric solar heating is a significant source of the uncertainty, because current estimates are largely derived from model studies. Here we use three lightweight unmanned aerial vehicles that were vertically stacked between 0.5 and 3 km over the polluted Indian Ocean. These unmanned aerial vehicles deployed miniaturized instruments measuring aerosol concentrations, soot amount and solar fluxes. During 18 flight missions the three unmanned aerial vehicles were flown with a horizontal separation of tens of metres or less and a temporal separation of less than ten seconds, which made it possible to measure the atmospheric solar heating rates directly. We found that atmospheric brown clouds enhanced lower atmospheric solar heating by about 50 per cent. Our general circulation model simulations, which take into account the recently observed widespread occurrence of vertically extended atmospheric brown clouds over the Indian Ocean and Asia, suggest that atmospheric brown clouds contribute as much as the recent increase in anthropogenic greenhouse gases to regional lower atmospheric warming trends. We propose that the combined warming trend of 0.25 K per decade may be sufficient to account for the observed retreat of the Himalayan glaciers.
Distributed locomotion algorithms for self-reconfigurable robots operating on rough terrain

In this paper, we describe a set of distributed algorithms for self-reconfiguring modular robots that allow them to explore an area in parallel. The algorithms are based on geometric rules that each module evaluates independently relative to its local neighborhood. This paper concentrates on developing algorithms within this framework to enable travel over the widest variety of terrain. In particular, we show how to perform straight-line motion, turning while on obstacles, climbing over tall obstacles, and tunneling under overhangs, all of which work for groups of arbitrary size. This last feature is important, as it also allows a large system of self-reconfiguring modules to divide up into several groups of various sizes, each of which is equally capable of motion and participation in the overall group task. We also discuss implementations and ways to improve efficiency and switching between tasks.
Climatology of Lake-Effect Snowstorms of the Great Salt Lake

Abstract Characteristics of lake-effect snowstorms associated with the Great Salt Lake are described. Using WSR-88D radar imagery, 16 well-defined and 18 marginal lake-effect events were identified from September 1994 through May 1998 (excluding June–August), with the former used for more detailed analysis. Precipitation during the well-defined events was frequently characterized by the irregular development of radar echoes over and downstream of the Great Salt Lake. The most commonly observed precipitation structures were solitary wind-parallel bands that developed along or near the major axis of the GSL and broad-area precipitation shields with embedded convective elements that formed near the southern shoreline. Regional-scale composite analyses and rawinsonde-derived statistics showed that the lake-effect events occurred in post frontal westerly to northerly 700-hPa flow following the passage of an upper-level trough and associated low-level cold front. The lake-effect environment was characterized by...
Sunitinib: From Rational Design to Clinical Efficacy

Sunitinib (SU011248) is an oral small molecular tyrosine kinase inhibitor that exhibits potent antiangiogenic and antitumor activity. Tyrosine kinase inhibitors such as SU6668 and SU5416 (semaxanib) demonstrated poor pharmacologic properties and limited efficacy; therefore, sunitinib was rationally designed and chosen for its high bioavailability and its nanomolar-range potency against the antiangiogenic receptor tyrosine kinases (RTKs)--vascular endothelial growth factor receptor (VEGFR) and platelet-derived growth factor receptor (PDGFR). Sunitinib inhibits other tyrosine kinases including, KIT, FLT3, colony-stimulating factor 1 (CSF-1), and RET, which are involved in a number of malignancies including small-cell lung cancer, GI stromal tumors (GISTs), breast cancer, acute myelogenous leukemia, multiple endocrine neoplasia types 2A and 2B, and familial medullary thyroid carcinoma. Sunitinib demonstrated robust antitumor activity in preclinical studies resulting not only in tumor growth inhibition, but tumor regression in models of colon cancer, non-small-cell lung cancer, melanoma, renal carcinoma, and squamous cell carcinoma, which were associated with inhibition of VEGFR and PDGFR phosphorylation. Clinical activity was demonstrated in neuroendocrine, colon, and breast cancers in phase II studies, whereas definitive efficacy has been demonstrated in advanced renal cell carcinoma and in imatinib-refractory GISTs, leading to US Food and Drug Administration approval of sunitinib for treatment of these two diseases. Studies investigating sunitinib alone in various tumor types and in combination with chemotherapy are ongoing. The clinical benchmarking of this small-molecule inhibitor of members of the split-kinase domain family of RTKs will lead to additional insights regarding the biology, potential biomarkers, and clinical utility of agents that target multiple signaling pathways in tumor, stromal, and endothelial compartments.
Neutrophil NADPH Oxidase Is Reduced at the Anaplasma phagocytophilum Phagosome

The intracellular organism Anaplasma phagocytophilum causes human granulocytic ehrlichiosis and specifically infects and multiplies in neutrophilic granulocytes. Previous reports have suggested that, for its survival, this bacterium suppresses the neutrophil respiratory burst. To investigate the mechanism of survival, we first assessed the kinetics of A. phagocytophilum entry into neutrophils by using double-labeling confocal microscopy. At 30, 60, 120, and 240 min of incubation, 25, 50, 55, and 70% of neutrophils contained bacteria, respectively. The neutrophil respiratory burst in the presence of A. phagocytophilum was assessed by a kinetic cytochrome c assay and by measurement of oxygen consumption. Neutrophils in the presence of A. phagocytophilum did not produce a significant respiratory burst, but A. phagocytophilum did not inhibit the neutrophil respiratory burst when phorbol myristate acetate was added. Immunoelectron microscopy of neutrophils infected with A. phagocytophilum or Escherichia coli revealed that NADPH oxidase subunits gp91phox and p22phox were significantly reduced at the A. phagocytophilum phagosome after 1 and 4 h of incubation. In neutrophils incubated simultaneously with A. phagocytophilum and E. coli for 30, 60, and 90 min, gp91phox was present on 20, 14, and 10% of the A. phagocytophilum phagosomes, whereas p22phox was present in 11, 5, and 4% of the phagosomes, respectively. Similarly, on E. coli phagosomes, gp91phox was present in 62, 64, and 65%, whereas p22phox was detected in 54, 48, and 48%. We conclude that A. phagocytophilum does not suppress a global respiratory burst and that, under identical conditions in the same cells, A. phagocytophilum, but not E. coli, significantly reduces gp91phox and p22phox from its phagosome membrane.
Strategies for pricing publicly provided health services

User fees are important in cofinancing health care but should not be the primary means of finance, and should not be applied uniformly - or the wealthy will benefit and the poor will suffer. Gertler and Hammer examine how governments finance and allocate public spending, with an eye to developing strategies for pricing publicly provided health services. They also examine the implications of current policy and the possibility for rationalizing competing government priorities. Because governments face budget constraints and cannot fully subsidize all programs and activities, Gertler and Hammer argue the following: Public spending on health can (1) improve health outcomes, (2) promote nonhealth aspects of well-being (for example, reducing individuals' risk of economic losses from random health crises), and (3) finance redistribution to the poor. Optimal subsidy and fee policy will depend on how much relative weight government places on those competing objectives. Subsidies need to be reallocated toward the poor and toward public health, but only a fraction of the resources needed to expand the health sector can be financed by increasing public subsidies. Prices for curative services (user fees) have two distinct roles. They can raise revenue, freeing public resources to be reallocated to public health activities and for limited cofinancing to improve the quality of curative care. More important, they can improve efficiency in the use of public facilities and the health care system as a whole. But those gains must be weighed against evidence that increased fees can compromise public health's three main goals. The literature has focused largely on how raising revenue affects the poor, but the more important effect is likely to be the guidance of resources. User fees are important in cofinancing health care but shouldn`t be the primary means of finance. Revenue generated from user fees is sometimes used to improve the quality of, and access to, curative medical care. There is some evidence that people are willing to pay some of the cost of improving health care (especially for drugs), but the wealthy are willing to pay a lot more than the poor. If governments charge the average willingness to pay, the wealthy will use the services more, the poor, less. Prepayment social insurance plans hold promise, but there is evidence that they may introduce inefficient inflation of medical care costs that lower- and middle-income countries cannot afford. This paper - a product of the Public Economics Division, Policy Research Department - is part of a larger effort in the department to analyze the impact of public expenditures. Jeffrey Hammer may be contacted at jhammer@worldbank.org.
RAIN FOREST FRAGMENTATION AND THE DYNAMICS OF AMAZONIAN TREE COMMUNITIES

Few studies have assessed effects of habitat fragmentation on tropical forest dynamics. We describe results from an 18-yr experimental study of the effects of rain forest fragmentation on tree-community dynamics in central Amazonia. Tree communities were assessed in 39 permanent, 1-ha plots in forest fragments of 1, 10, or 100 ha in area, and in 27 plots in nearby continuous forest. Repeated censuses of >56000 marked trees (≥10 cm diameter at breast height) were used to generate annualized estimates of tree mortality, damage, and turnover in fragmented and continuous forest. On average, forest fragments exhibited markedly elevated dynamics, apparently as a result of increased windthrow and microclimatic changes near forest edges. Mean mortality, damage, and turnover rates were much higher within 60 m of edges (4.01, 4.10, and 3.16%, respectively) and moderately higher within 60–100 m of edges (2.40, 1.96, and 2.05%) than in forest interiors (1.27, 1.48, and 1.15%). Less-pronounced changes in mortality and turnover rates were apparently detectable up to ∼300 m from forest edges. Edge aspect had no significant effect on forest dynamics. Tree mortality and damage rates did not vary significantly with fragment age, suggesting that increased dynamics are not merely transitory effects that occur immediately after fragmentation, while turnover rates increased with age in most (8/9) fragments. These findings reveal that fragmentation causes important changes in the dynamics of Amazonian forests, especially within ∼100 m of habitat edges. A mathematical “core-area model” incorporating these data predicted that edge effects will increase rapidly in importance once fragments fall below ∼100–400 ha in area, depending on fragment shape. Accelerated dynamics in fragments will alter forest structure, floristic composition, biomass, and microclimate and are likely to exacerbate effects of fragmentation on disturbance-sensitive species.
What is the significance of The Origin of Concepts for philosophers' and psychologists' theories of concepts?

Carey holds that the study of conceptual development bears on the theories of concepts developed by philosophers and psychologists. In this commentary, I scrutinize her claims about the significance of the study of conceptual development. Psychologists will probably come to view The Origin of Concepts (Carey 2009) as a landmark in the history of psychology, as important as Piaget's (1954) The Construction of Reality in the Child . Among other virtues, it illustrates how extraordinarily suc- cessful the nativist research program in developmental psychol- ogy has been since the 1970s.
A Curvature Smooth Lofting Scheme for Singular Point Treatments

This paper presents a new end condition scheme for lofting through singular points, one that is easily specified and can generate shapes that are appropriate for lofting to the noses of subsonic/transonic aerodynamic and some hydrodynamic crafts. A degeneracy in the tensor product parameterization is typical in representations of spheres and ellipsoids, or topological equivalents. In that case a grid of data typically sets a whole row to a single value, so it becomes difficult and cumbersome to specify shape characteristics in different directions emanating from that point. Some standardly used end conditions result in shapes that are \(C^0\) at the singular point, an undesirable outcome in nose regions of subsonic aircraft, so the straightforward nose-to-tail lofts are intractable for these vehicles. The proposed method overcomes this problem (See Figs. 1 and 2 for examples).
A multidimensional screening method for the selection of two-photon enhanced fluorescent proteins

Two-photon excitation of fluorescent proteins (FPs) is widely used in imaging whole organisms or living tissues. Many different FPs are now available but these proteins have only been optimized for their one-photon properties. We have developed a technique for screening entire libraries of E. coli colonies expressing FPs that utilizes multiple wavelengths of linear excitation as well as two-photon excitation. Single mutations in a particular protein that affect one or twophoton properties are easily identified, providing new views of structure/function relationships. An amplified femtosecond Ti:sapphire laser and a spectrally filtered lamp source are used to acquire the fluorescence signals of up to ~1000 E. coli colonies on a standard Petri dish. Automation of the analysis and acquisition of the fluorescent signals makes it feasible to rapidly screen tens of thousands of colonies. In a proof of principle experiment with the commonly used EGFP, we used two rounds of error prone PCR and selection to evolve new proteins with shifted absorption and increased two-photon cross sections at 790nm. This method of screening, coupled with careful measurements of photo bleaching dynamics and two-photon cross sections, should make it possible to optimize a wide variety of fluorescent proteins and biosensors for use in two-photon microscopes.
Development and serial cellfree passage of a highly potent strain of mouse leukemia virus.

Summary1. A strain of a filterable mouse leukemia agent has been developed from a spontaneous Ak leukemia through several successive cell-free inoculations of newborn C3H mice. 2. This agent induced acute, generalized leukemia within 2 1/2 to 3 1/2 months in 40 to 100% of the inoculated newborn C3H mice (Bittner substrain). 3. Newborn mice had to be inoculated; adult C3H mice were with few exceptions resistant to inoculation of the cell-free agent. 4. The leukemic agent could be preserved at −70°C from 46 days to 5 1/2 months, with no apparent loss of infectivity.
Gas Sensing System Based on Correlation Spectroscopy and Differential Technology

Based on correlation spectroscopy and differential technology,a novel optical fiber gas sensing system was designed to realize high-sensitive,high-precision and real-time online detection of the trace gas. The theoretical basic of the system was analyzed in detail,and then appropriate devices for the sensing system were selected. Based on this,an optical fiber gas sensing system was constructed to measure the volume fraction of acetylene gas. The proposed system could not only eliminate the disturbances of light-intensity fluctuation and the contaminating gas in the measuring gas,but also avoid the influence of noise and ambient light in the surrounding environment. The experimental results showed that the system resolution could reach 0. 5‰, the measurement sensitivity was 6. 62 μV,the maximum absolue error was 0. 15‰,the relative error was 7. 5%,the system stability was 2. 27%,and the system repeatability error was 0. 817%.
Playing Our Absence

We are at the Old Vic on an evening in April 1967. As the stage-lights go up, two men dressed as Elizabethan courtiers are tossing coins. The one in a red coat — dark-haired and rather lanky - sits by a nearly empty money bag and spins them high in the air. His partner in a blue coat — blonder and stockier — walks about retrieving them and putting them into a nearly full bag. It is ‘heads’ every time. Soon the one in red says to nobody in particular, ‘There is an art to the building of suspense’. A comment on their game, or on this new play? A bit later he gets up, examines the stage while spinning coins over his shoulder, and speculates that the law of averages ‘means that if six monkeys were thrown up in the air for long enough they would land on their tails about as often as they would land on their —’‘Heads,’ says his partner, picking up a coin. By the time their run of ‘heads’ has exceeded eighty-five, the increasingly agitated courtier in red has begun also to spin fantastic syllogisms and hypotheses to account for what is happening.
Bone Mineral Density Testing Disparities Among Patients With Breast Cancer Prescribed Aromatase Inhibitors

Objectives: Aromatase inhibitors (AIs) are standard adjuvant therapy for postmenopausal women with early-stage, estrogen receptor–positive breast cancer. We designed our study to determine whether women initiating adjuvant therapy with an AI underwent baseline bone mineral density testing, as well as what factors predicted adherence with testing guidelines. Methods: Medicare Parts A, B, and D claims were used to identify a cohort of women aged 67 years and older with incident breast cancer in 2006 and 2007 who started AI therapy. Medicare claims provided information about bone density testing, as well as demographic and other treatment data through 2012. We also ascertained which patients were treated with bisphosphonates and studied the relationship of bisphosphonate therapy with bone density testing. Results: Approximately two-thirds of patients had baseline bone density testing. Older age, comorbidity, low income, and black race were associated with lower rates of baseline bone density testing. Testing rates decreased substantially with increasing age from 73% for women aged 67 to 70 years to 51% for those 85 years of age and older (adjusted odds ratio for not being tested, 2.48 [Cl, 2.17–2.82]). The proportion of women who had neither bone density testing nor bisphosphonate therapy increased with age as well. Conclusions: Despite the importance of age as a risk factor for fractures, older women starting treatment with AIs for treatment of breast cancer are less likely to undergo recommended bone density assessment.
Procedural Polarization in America

Almost everyone knows that political polarization has beset many American institutions. Some claim that the U.S. Congress can't get anything done. Some even say that many members of Congress regard frustrating the President's initiatives as one of their main objectives. Important observers regard the current Supreme Court as more polarized than in the past, though the question whether this should be regarded as "political" polarization may be debated. It seems that few can escape this escalation of polarization. One activity that might escape it is the process of making procedure rules. In the U.S. federal courts, that process has been somewhat insulated from political pressures, and that insulation has largely been respected in recent decades. Indeed, some have described the American arrangements as reflecting a "treaty" between Congress and the rule-makers. More generally, even though procedural changes occasionally seemed to have major impacts, they have largely been off the radar screen of political actors and the general public in the U.S. It is possible that this American reality is changing. American procedural changes in the mid-20th century spurred the development of American procedural "exceptionalism." But that development did not attract much attention until the last third of the last century. During that time, however, concern about the level and significance of litigation in the U.S. grew, and what could be called an effort to push back the most aggressive forms of American procedure emerged. As the 21st century dawned, the effort to preserve the exceptional mid -century features of American procedure and the effort to restrain them both gained in vehemence, and also began to attract broader political attention to procedural matters. This paper reports on these developments in the context of the most recent (and ongoing) set of proposed procedural reforms for the U.S. federal courts. It begins by introducing the seeming mid-century consensus on procedure in the U.S., and then presents the reaction that began in the 1970s to some features of American procedure. Against that background, it sketches prior episodes of procedural reform to introduce the most recent efforts. It then reports on the experience so far of the current reform effort, which has attracted unprecedented attention, including attention from political actors. It concludes with uncertainty. Not only is it uncertain whether the current reform proposals will ultimately go into effect, it is also unclear where procedural reform in the U.S. will go in the future.
Renewable energy carriers derived from concentrating solar power and nonstoichiometric oxides

In this paper, we offer a perspective on the current state of material research in a part of the solar fuels community that exploits process heat derived from concentrated solar energy to power simple thermochemical gas-splitting cycles. The working fluid in this process is a nonstoichiometric oxide subject to extreme conditions that repeatedly distorts the lattice by forcing oxygen atoms to move in and out of the crystal. This technology is currently challenged by a need to discover optimal materials and derive robust processes to increase cycle efficiency. In the realm of emerging technologies for converting solar insulation to portable and storable energy carriers, this approach has already proven to be scalable with demonstrations that approach 100 kW. Innovations in materials and methods are required to increase solar utilization and process efficiency in order to achieve commercial viability.
ENZYMATIC RECOGNITION OF DNA DAMAGES INDUCED BY IONIZING RADIATION

ABSTRACT Both alkali-labile and alkali-stable damages in x-irradiated PM2 DNA are recognized by purified fractions of the Escherichia coli x-ray endonculease. An activity, partially purified from Saccharomyces cerevisiae using an x-irradiated PM2 DNA substrate, appears only to recognize alkali-labile lesions.
Outsourcing in bioanalysis: a CRO perspective

Steve Lowes from Q2 Solutions speaks to Sankeetha Nadarajah, Managing Commissioning Editor: about outsourcing strategy implementation. Steve started his industrial career at VG Biotech in the UK that became the LC–MS instrument entity of Waters Corporation. Since joining the CRO group that became Advion and then Q2 Solutions, his career has focused on regulated bioanalysis with particular emphasis on LC–MS. He is a founding member of the Global Bioanalysis Consortium and a past-chair of the AAPS Bioanalytical Focus Group. At Q2 Solutions, Steve leads the scientific disciplines around LC–MS bioanalysis for both small molecule and biomolecule applications including biomarker assays. Steve has over 40 peer-reviewed publications on bioanalysis and is a frequent speaker at national and international conferences.
Scaling Information Extraction to Large Document Collections.

Information extraction and text mining applications are just beginning to tap the immense amounts of valuable textual information available online. In order to extract information from millions, and in some cases, billions of documents, different solutions to scalability emerged. We review key approaches for scaling up information extraction, including using general-purpose search engines as well as indexing techniques specialized for information extraction applications. Scalable information extraction is an active area of research, and we highlight some of the opportunities and challenges in this area that are relevant to the database community.
Procedures and complications in late-nineteenth-century experimental neuroanatomical research exemplified by articles of Henry Herbert Donaldson (1857–1938)

Henry Herbert Donaldson (1857-1938) was a leader in neurological research in the United States for several decades, beginning about 1890. A detailed account of three of his earliest publications shows the neuroanatomical procedures involved in the study of the relation of brain and intelligence during the late-nineteenth-century in America. Two of the articles, published in September 1890 and December 1891, were titled, "Anatomical Observations on the Brain and Several Sense-Organs of the Blind Deaf-Mute, Laura Dewy Bridgman (1829-1889)"; the third, published in August 1892, used the information from the first two to delimit the extent of the visual processing area of the human cortex. Donaldson's procedures included brain cuttings and measures of macroscopic brain structures, histology of cellular structures, attempts to relate macroscopic brain structures with brain functions, data corrections, estimations, comparisons, and statistics. These procedures provide a view of the relative thoroughness, accuracy, and comparability of the various neuroanatomical techniques in use at that time and of Donaldson's implementation of the techniques. Donaldson's brain cutting techniques were much more comparable than his measurement techniques. The latter could be quite precise, but they were fraught with lack of standardized procedures that made corrections and estimations necessary when making data comparisons across studies. Donaldson emphasized these incompatibilities, implying a need for standardization. Statistical procedures were the least thorough and effective. His, and the field's, total complement of statistical techniques consisted of mean and range, which severely limited his ability to make complicated assessments. This limitation was not necessarily supplemented by stringent control group comparisons.
A Secure Alignment Algorithm for Mapping Short Reads to Human Genome

The elastic and inexpensive computing resources such as clouds have been recognized as a useful solution to analyzing massive human genomic data (e.g., acquired by using next-generation sequencers) in biomedical researches. However, outsourcing human genome computation to public or commercial clouds was hindered due to privacy concerns: even a small number of human genome sequences contain sufficient information for identifying the donor of the genomic data. This issue cannot be directly addressed by existing security and cryptographic techniques (such as homomorphic encryption), because they are too heavyweight to carry out practical genome computation tasks on massive data. In this article, we present a secure algorithm to accomplish the read mapping, one of the most basic tasks in human genomic data analysis based on a hybrid cloud computing model. Comparing with the existing approaches, our algorithm delegates most computation to the public cloud, while only performing encryption and decryption on the private cloud, and thus makes the maximum use of the computing resource of the public cloud. Furthermore, our algorithm reports similar results as the nonsecure read mapping algorithms, including the alignment between reads and the reference genome, which can be directly used in the downstream analysis such as the inference of genomic variations. We implemented the algorithm in C++ and Python on a hybrid cloud system, in which the public cloud uses an Apache Spark system.
Use of Positron Emission Tomography to Study Patterns of Brain Metabolism in Relation to Age and Disease: A Correlation Matrix Approach

Region-by-region comparisons of mean rCMRg1c data have proven uninformative for understanding behavior and cognition in patients with Down syndrome and childhood onset autism, and in the healthy elderly. Such comparisons ignore an important dimension of brain metabolism, namely patterns of regional cerebral metabolic rates. This paper shows that a correlation matrix approach can be used to determine these patterns, and to relate them to underlying functional neuroanatomy in health and disease.
Propagation of Elastic Waves in Equiaxed Iron Polycrystals with Aligned [001] Axes

A polycrystalline material is composed of numerous discrete grains, each having a regular, crystalline atomic structure. The elastic properties of the grains are anisotropic and their crystallographic axes are differently oriented. Thus the anisotropic nature of elastic wave propagation in a number of structural materials, such as austenitic stainless steel welds and castings, used in nuclear power plants stems from the details of their grain structures. Columnar grain structure is seen in the austenitic stainless steel welds while the microstructure of cast stainless could vary from randomly oriented equiaxed grains to highly oriented columnar grains. An acoustic wave travelling through such a microscopically inhomogeneous medium suffers scattering and consequently has frequency dependent attenuation and phase velocity that depend on the grain structure. This paper is motivated by the desire to better understand these effects.
Late Effects of Radiation Prime the Brain Microenvironment for Accelerated Tumor Growth.

Purpose Glioblastoma (GBM) remains incurable, despite state-of-the-art treatment involving surgical resection, chemotherapy, and radiation. GBM invariably recurs as a highly invasive and aggressive phenotype, with the majority of recurrences within the radiation therapy treatment field. Although a large body of literature reporting on primary GBM exists, comprehensive studies of how prior irradiation alters recurrent tumor growth are lacking. An animal model that replicates the delayed effects of radiation therapy on the brain microenvironment, and its impact on the development of recurrent GBM, would be a significant advance. Methods and Materials Cohorts of mice received a single fraction of 0, 20, 30, or 40 Gy Gamma Knife irradiation. Naive, nonirradiated mouse GBM tumor cells were implanted into the ipsilateral hemisphere 6 weeks postirradiation. Tumor growth was measured by magnetic resonance imaging, and animal survival was assessed by monitoring weight loss. Magnetic resonance imaging results were supported by hemotoxylin and eosin histology. Results Tumorous lesions generated from orthotopic implantation of nonirradiated mouse GBM tumor cells into irradiated mouse brain grew far more aggressively and invasively than implantation of these same cells into nonirradiated brain. Lesions in irradiated brain tissue were significantly larger, more necrotic, and more vascular than those in control animals with increased invasiveness of tumor cells in the periphery, consistent with the histologic features commonly observed in recurrent high-grade tumors in patients. Conclusions Irradiation of normal brain primes the targeted cellular microenvironment for aggressive tumor growth when naive (not previously irradiated) cancer cells are subsequently introduced. The resultant growth pattern is similar to the highly aggressive pattern of tumor regrowth observed clinically after therapeutic radiation therapy. The mouse model offers an avenue for determining the cellular and molecular basis for the aggressiveness of recurrent GBM.
Impact of electronic decision support and targeted educational intervention to increase adherence with ASCO Choosing Wisely breast cancer staging guideline.

e18826Background: ASCO Choosing Wisely recommends against ordering PET, CT, or bone scan as part of the initial staging workup for patients with early stage breast cancer. We implemented a two-step...
Subsurface nucleation of supercooled acetaminophen

The crystallization of supercooled amorphous materials limits their successful applications. The spatial origin of crystallization, nucleation, is one of the most debated topics. We show that homogeneous crystallization may be initiated from tens of micrometers beneath the surface of a supercooled acetaminophen liquid.
Simulating Negotiation in Protracted Conflicts

Protracted conflict presents students with an unfamiliar and often puzzling context. Why do negotiations sometimes succeed, while at other points, actors are unable to reach agreement on key issues...