cssi/SciSciGPT-SciSciNet huggingface dataset:
Nuclear Magnetic Resonance Spectroscopy

Nuclear magnetic resonance (NMR) has developed into an important tool for investigating the structure and dynamics of biomacromolecules in solution, associated with membranes and in solids. This chapter provides an introduction to the theory of NMR and a description of basic concepts (excitation of NMR transitions, spin populations and coherence, relaxation phenomena, signal detection and processing). Types of structural and dynamic information available from NMR experiments are noted. Standard experiments used for sequential assignment of resonances in biomolecules in solution and solid state are discussed, along with instrumentation and sample requirements. In particular, the need for selective and uniform isotope labeling is detailed. Software used to process NMR data and generate structural and dynamic information are noted, and data needed for structure determinations and dynamic analysis outlined.
Validating a novel algorithm to identify patients with autoimmune hepatitis in an administrative database

Purpose Population-level studies on the treatment practices and comparative effectiveness of therapies in autoimmune hepatitis (AIH) are lacking due to the absence of validated methods to identify patients with AIH in large databases, such as administrative claims or electronic health records. This study ascertained the performance of International Classification of Diseases (ICD) codes for AIH, and developed and validated a novel algorithm that reliably identifies patients with AIH in health administrative data and claims. Methods This was a cross-sectional study of patients with ≥1 inpatient or ≥2 outpatient ICD codes for AIH between 2008 and 2019 at a single health system. In a random sample of 250 patients, definite or probable AIH was determined using the Simplified AIH score, Revised AIH score or expert adjudication. The positive predictive value (PPV) was obtained. Variations of this base algorithm were evaluated using additional criteria to increase its performance. Results Of the 250 patients, 143 (57.2%) patients had sufficient records available for review. The PPV of the base algorithm was 77.6% (95% CI: 69.9-84.2%). Exclusion of patients with ≥1 ICD code for primary biliary cholangitis or primary sclerosing cholangitis yielded a PPV of 89.7% (95% CI: 82.8-94.6%). Further exclusion of patients with recent immune checkpoint inhibitor therapy increased the PPV to 92.9% (95% CI: 86.5-96.9%). Conclusions The use of ICD codes for AIH alone are insufficient to reliably identify patients with AIH in health administrative data and claims. Our proposed algorithm that includes additional diagnostic and medication-related coding criteria demonstrates excellent performance.
Effects of psychosocial support interventions on survival in inpatient and outpatient healthcare settings: A meta-analysis of 106 randomized controlled trials

Background Hospitals, clinics, and health organizations have provided psychosocial support interventions for medical patients to supplement curative care. Prior reviews of interventions augmenting psychosocial support in medical settings have reported mixed outcomes. This meta-analysis addresses the questions of how effective are psychosocial support interventions in improving patient survival and which potential moderating features are associated with greater effectiveness. Methods and findings We evaluated randomized controlled trials (RCTs) of psychosocial support interventions in inpatient and outpatient healthcare settings reporting survival data, including studies reporting disease-related or all-cause mortality. Literature searches included studies reported January 1980 through October 2020 accessed from Embase, Medline, Cochrane Library, CINAHL, Alt HealthWatch, PsycINFO, Social Work Abstracts, and Google Scholar databases. At least 2 reviewers screened studies, extracted data, and assessed study quality, with at least 2 independent reviewers also extracting data and assessing study quality. Odds ratio (OR) and hazard ratio (HR) data were analyzed separately using random effects weighted models. Of 42,054 studies searched, 106 RCTs including 40,280 patients met inclusion criteria. Patient average age was 57.2 years, with 52% females and 48% males; 42% had cardiovascular disease (CVD), 36% had cancer, and 22% had other conditions. Across 87 RCTs reporting data for discrete time periods, the average was OR = 1.20 (95% CI = 1.09 to 1.31, p Conclusions In this meta-analysis, OR data indicated that psychosocial behavioral support interventions promoting patient motivation/coping to engage in health behaviors improved patient survival, but interventions focusing primarily on patients' social or emotional outcomes did not prolong life. HR data indicated that psychosocial interventions, predominantly focused on social or emotional outcomes, improved survival but yielded similar effects to health information/classes and were less effective among patients with apparently greater disease severity. Risk of research bias remains a plausible threat to data interpretation.
Algae to angiosperms: Autofluorescence for rapid visualization of plant anatomy among diverse taxa.

Premise Fluorescence microscopy is an effective tool for viewing plant internal anatomy. However, using fluorescent antibodies or labels hinders throughput. We present a minimal protocol that takes advantage of inherent autofluorescence and aldehyde-induced fluorescence in plant cellular and subcellular structures to markedly increase throughput in cellular and ultrastructural visualization. Methods and Results Twelve species distributed across the plant phylogeny were each subjected to five fixative treatments: 1% paraformaldehyde and 2% glutaraldehyde, 2% paraformaldehyde, 2% glutaraldehyde, formalin-acid-alcohol (FAA), and 70% ethanol. Samples were prepared by embedding and mechanically sectioning or via whole mount. A confocal laser scanning system was used to collect micrographs. We evaluated and compared fixative influence on sample structural preservation and tissue autofluorescence. Conclusions Formaldehyde fixation of Viridiplantae taxa samples generates useful structural data while requiring no additional histological staining or clearing. In addition, a fluorescence-capable microscope is the only specialized equipment required for image acquisition. The minimal protocol developed in this experiment enables high-throughput sample processing by eliminating the need for multi-day preparations.
Nuclear Reprogramming: Biological and Technological Constraints

Publisher Summary This chapter focuses on the nuclear reprogramming process and how both the technological parameters of the cloning process and the biological limitation of nuclear reprogramming might relate to the inefficiencies and phenotypes observed during the development of cloned animals. The four key parameters of nuclear transfer technology that influence the development of cloned embryos are the state and nature of the recipient cytoplast; the cell cycle status of the donor cell; the identity, differentiation state, and developmental potency of the donor cell; and the genetic influences on the successful development of cloned embryos. Although a G0 cell cycle state is clearly not necessary for the successful development of cloned embryos, the somatic nucleus has to be in a conformation compatible with nuclear envelope breakdown and chromosome condensation. The most interesting issue in cloning by nuclear transfer is epigenetic reprogramming. For clones to complete development, genes normally expressed during embryogenesis but silent in the somatic donor cell must be reactivated. Nuclei isolated from embryonic stem (ES) cells and embryonic blastomeres generate viable cloned animals with a significantly higher efficiency compared to any somatic donor cell type. During cloning, reprogramming has to occur in the short interval between transfer of the donor nucleus into the egg and the onset of cellular differentiation, a context that is dramatically different from normal fertilization. Because of cloning's inherent inefficiencies, the nuclear transfer experiments using lymphocytes and other terminally differentiated cells as nuclear donors must be carefully designed and carried out.
Chapter 12 Ontogeny and metabolism of brown adipose tissue in livestock species

Publisher Summary This chapter focuses on brown adipose tissue (BAT) in lambs and calves. Distinctive brown adipocytes do not appear to be present in porcine adipose tissue. Several aspects of BAT development and response to environmental stimuli are described in the chapter. The metabolism of BAT resembles from mature ruminant white adipose tissue, in that acetate is the primary precursor for lipogenesis. There is a precipitous decline in rates of de novo lipogenesis during the last trimester, indicating that the contribution of fatty acid biosynthesis to lipid filling is important earlier in fetal development. The mixture of brown and white adipocytes in subcutaneous adipose tissues from newborn calves suggests that brown adipocytes may involute into white adipocytes in this species. In rodent species, brown and white adipocytes differentiate and develop independently. Brown adipose tissue from sheep and cattle rapidly dedifferentiates and/or is lost through apoptosis early postnatally. In Wagyu × Angus crossbred calves; brown adipose tissue function is remarkably refractory to profound reductions in dietary protein intake in dams, indicating the high priority animals place in ensuring adequate thermogenic capacity in their newborn.
Cellular differentiation is required for cAMP but not Ca(2+)-dependent Cl- secretion in colonic epithelial cells expressing high levels of cystic fibrosis transmembrane conductance regulator.

Abstract The gene responsible for cystic fibrosis (CF) has recently been cloned and sequenced. When transfected into CF epithelial cells, normal transcripts of this gene correct the underlying defect in CF, i.e. cAMP-dependent Cl- secretion is restored. Thus, the protein encoded by this gene, designated "cystic fibrosis transmembrane conductance regulator" (CFTR), somehow participates in the Cl- secretory response. In this paper we have correlated CFTR gene expression with cAMP and Ca(2+)-dependent Cl- secretion in unpolarized (parental) and polarized (Cl.19A) clones of the human colonic adenocarcinoma cell line HT-29. These cell lines were found to express equally high levels of CFTR mRNA at 4 days post-passage. In addition, protein expression (determined by immunoprecipitation) was also identical. The cAMP-generating agonist forskolin had little effect on 125I efflux from the unpolarized cells. In contrast, this agonist increased 125I efflux 3-fold in polarized cells. The lack of response in the unpolarized cells was not due to the inability of forskolin to raise cAMP levels. Neurotensin, a Ca(2+)-mobilizing agonist, stimulated 125I efflux from both cell lines. In the polarized cells, the magnitude of this response was attenuated at 8 days post-seeding. At this time, the undifferentiated line attained some cAMP responsiveness. This latter effect was paralleled by the appearance of monolayers within areas of the multicell layer. Cell-attached patch-clamp recording from apical membrane patches of polarized cells revealed the presence of a forskolin-stimulated 8-pS Cl- channel; no channel activity was observed in forskolin-stimulated unpolarized cells. Ca(2+)-activated Cl- channels were found in both cell lines. In agreement with the 125I efflux data, the single-channel activation response to [Ca2+]i was smaller in the polarized cell line. From these studies, we can conclude that CFTR expression, measured both at the mRNA and protein level, does not correlate with the colonocyte's ability to secrete chloride ions in response to a cAMP-generating agonist. Cyclic AMP-dependent Cl- secretion requires cellular polarization; specifically, the delineation of an apical membrane. Differences in the cellular location of CFTR during differentiation are likely to explain our results. In contrast, Ca(2+)-stimulated Cl- secretion occurred independently of cellular polarization but was reduced when the cells formed tight junctions.
Nonlinear Structural Response

In discussing the dynamic behavior of single-degree-of-freedom systems, we assumed that in the model representing the structure, the restoring force was proportional to the displacement. We also assumed the dissipation of energy through a viscous damping mechanism in which the damping force was proportional to the velocity. In addition, the mass in the model was always considered to be unchanging with time. As a consequence of these assumptions, the equation of motion for such a system resulted in a linear, second order ordinary differential equation with constant coefficients, namely, $$m\ddot{u} + c\dot{u} + ku = F(t)$$ (6.1) In the previous chapters it was illustrated that for particular forcing functions such as harmonic functions, it was relatively simple to solve this equation (6.1) and that a general solution always existed in terms of Duhamel’s integral. Equation (6.1) thus represents the dynamic behavior of many structures modeled as a single-degree-of-freedom system. There are, however, physical situations for which this linear model does not adequately represent the dynamic characteristics of the structure. The analysis in such cases requires the introduction of a model in which the spring force or the damping force may not remain proportional, respectively, to the displacement or to the velocity. Consequently, the resulting equation of motion will no longer be linear and its mathematical solution, in general, will have a much greater complexity, often requiring a numerical procedure for its integration.
An in cockpit 'situation awareness' autostereoscopic avionics display

Studies have shown that pilot performance is improved by up to 44% in certain tasks when situational awareness information, on an electronic display, is presented in stereoscopic (3D) format. The United States Air Force has also indicated that LCDs are preferable to CRTs in the cockpit due to their smaller volume, power, and weight. With these efficiencies in mind, DTI has designed and built a prototype autostereoscopic cockpit situation awareness display that generates three dimensional images using an LCD. The pilot can see the 3D images without special glasses from anywhere within a wide viewing volume in front of the LCD. DTI's autostereoscopic displays are particularly well suited to presenting symbology in 3D space, and flight path information for low visibility, high speed, and low level flying. >
The Cell-Cell Adhesion Molecule Carcinoembryonic Antigen-Related Cellular Adhesion Molecule 1 Inhibits IL-2 Production and Proliferation in Human T Cells by Association with Src Homology Protein-1 and Down-Regulates IL-2 Receptor

The cell adhesion molecule, carcinoembryonic Ag-related cellular adhesion molecule 1, shown by others to both activate and inhibit T cell proliferation, exhibits a reciprocal relationship to IL-2R expression over the time course of activation of PBMCs, and upon Ab ligation, inhibits both the production of IL-2 and cell proliferation. Carcinoembryonic Ag-related cellular adhesion molecule 1 associates with CD3 and is found in lipid rafts of PBMCs, is phosphorylated on the immunoreceptor tyrosine-based inhibitory motifs (ITIMs) of the -4L isoform, and associates with Src homology protein-1, providing an explanation for its inhibitory activity. When the ITIM-containing -4L and non-ITIM-containing -4S isoforms are transfected into Jurkat cells that produce, but do not depend on IL-2 for growth, both IL-2 production and cell proliferation are differentially inhibited, demonstrating that the two isoforms signal via different pathways. When the two isoforms are transfected into Kit-225 cells that depend on IL-2 for growth, IL-2Rβ and γ, but not α subunits are down-regulated, and the -4L, but not the -4S isoform inhibits cell proliferation by 6-fold in an IL-2 dose-response study.
Heterogeneities of the instrumental seismicity catalog (1904-1980) for strong shallow earthquakes

We analyze the world-wide consistency of teleseismic reporting, completeness of the seismicity record, and homogeneity of magnitude determination for strong shallow earthquakes (magnitude, M ≧ 6; depth, h ≦ 70 km) in the period 1904 to 1980. For earthquakes with magnitude M ≦ 7, we used the catalog given by Abe (1981), which lists the surface-wave magnitude ( Ms ) of every reported large event that occurred between 1904 and 1980, according to the original formulation of Gutenberg (1945). Under the postulate that the rate of earthquake occurrence for the entire world as a whole is consistent on a time scale of decades, and that since the installation of the World-Wide Standardized Seismograph Network in the early 1960s the earthquake catalog for strong ( M ≧ 6) shocks is complete and the seismicity rates are typical of all periods in the century, we find that, for instrumental-related reasons, the Ms of large events prior to 1908 have been systemically overestimated by at least 0.5 magnitude unit, and the Ms of events in the period 1908 to 1948 have been consistently overestimated by 0.2 unit, relative to the Ms assigned to shocks occurring after 1948. When these corrections are taken into account, the catalog of events with Ms ≧ 7.0 is shown to be largely complete (i.e., nearly all the large shallow shocks which occurred in the earth are listed) for most of the world since early in the century. For earthquakes as the magnitude 6 level, we used the International Seismological Center (ISC) tape and Regional Catalogues of Earthquakes. This file compiles the earthquake data given by Gutenberg and Richter (1954) for the first half of the century, and data from various international agencies after ≈ 1945. We find a highly incomplete seismicity catalog at this magnitude level for the first half of the century, mainly due to numerous increases and decreased in the earthquake detection and reporting capabilities; a more complete but extremely inhomogeneous catalog for the period 1950 to 1963, due to the use of different formulations and criteria to calculate and report the parameter “magnitude” by the various seismological agencies; and a largely complete and homogeneous (in Ms ) record since 1964.
Land use and wetland drainage affect water levels and dynamics of remaining wetlands

Depressional wetlands are productive and unique ecosystems found around the world. Their value is due, in part, to their dynamic nature, in which water levels fluctuate in response to climate, occasionally drying out. However, many wetlands have been altered by consolidation drainage, where multiple, smaller wetlands are drained into fewer, larger, wetlands causing higher water levels. We evaluated whether current (2003–2010) water surface areas were greater than historical (1937–1969) water surface areas of 141 randomly selected semipermanent and permanent wetlands across the Prairie Pothole Region of North Dakota, USA. We also evaluated whether differences between historical and current hydrology of these wetlands were attributable to consolidation drainage. For each of these wetlands, we digitized water surface areas from aerial photography during historical and current eras. Our results indicated that water surface areas are currently 86% greater in sample wetlands than they were historically and that differences can be attributed to consolidation drainage. Water surface areas of consolidated wetlands in extensively drained landscapes were 197% greater than those with no drainage and now require more extreme drought conditions to dry out. Wetlands in extensively drained catchments were larger, dry out less frequently, and have more surface-water connections to other wetlands via ditches. These factors make conditions more favorable for the presence of fish that decrease abundances of aquatic invertebrates and reduce the productivity and quality of these wetlands for many species. Our results support the idea that intact wetlands serve an important role in water storage and groundwater recharge and reduce down-stream runoff.
Experimental infection of pig-tailed macaques (Macaca nemestrina) with Campylobacter cinaedi and Campylobacter fennelliae.

Abstract Campylobacter cinaedi and C. fennelliae have been associated with proctocolitis, bacteremia, and asymptomatic rectal infection, primarily in homosexual men. To more directly assess the pathogenic role of these organisms, we studied their disease-producing potential in 12- to 25-day-old pig-tailed macaques (Macaca nemestrina). Four infant monkeys were challenged with 10(8) to 10(9) C. cinaedi, three were challenged with C. fennelliae, two were challenged with C. jejuni, and one received no microorganisms. Watery or loose stools without associated fever or fecal leukocytes developed 3 to 7 days postinoculation in all of the animals given C. cinaedi, C. fennelliae, and C. jejuni, but not in the control animal. Stool cultures were simultaneously positive and remained so in the animals challenged with C. cinaedi or C. fennelliae for 3 weeks after inoculation despite the resolution of clinical illness. All of the animals challenged with C. cinaedi and C. fennelliae became bacteremic, and three had clinical evidence of septicemia. Histopathologic evaluation of rectal biopsies (five animals) and necropsy (one animal) showed no evidence of mucosal disruption. Specific immunoglobulin M and immunoglobulin G antibody responses occurred in all of the animals challenged with C. cinaedi and C. fennelliae, as determined by enzyme-linked immunosorbent assay and immunoblotting. We conclude that C. cinaedi and C. fennelliae consistently produce a diarrheal illness accompanied by bacteremia and followed by prolonged gastrointestinal colonization in M. nemestrina.
Learning to Search and Searching to Learn: Income, Education, and Experience Online

Using data from the Pew Internet and American Life Project surveys, this article explores changing trends in reported sophistication and satisfaction with search skills and with search engines. We find that the proportion of Internet users searching online for answers to specific questions—as opposed to casual browsing—has grown significantly. Moreover, as users get more experience online, they increasingly become dependent on search engines, confident in their findings, and savvy about how search engines structure information, privilege paid results, and track users. When other factors are controlled, years of online experience is a strong predictor of the likelihood of a person doing specific searches on a daily basis, and experience can have an even stronger positive effect than education and income. We also find that years of online experience, frequency of use, and sophistication with multiple search engines can overcome socio-economic status in predicting how active a person is in searching across different topics.
A Web-Based Approach to Real-Time Machine Condition Monitoring and Control

The objective of this research is to develop a web-based approach to remote machine condition monitoring and control enabled by Java technologies and based on publish-subscribe design pattern. On top of a Wise-ShopFloor framework (W eb-based i ntegrated s ensor-driven e-ShopFloor ), this system can serve real-time data from bottom up and can function as a constituent component of e-manufacturing, particularly for web-based collaborative manufacturing. It is designed to use the popular client-server architecture, VCM (view-control-model) design pattern, and publish-subscribe design pattern for secure device control and efficient machine condition monitoring. This paper presents the basis of the developed technology for building a web-based monitoring and control system that can be easily integrated to the e-manufacturing paradigm. A case study of a tripod parallel kinematic machine is carried out to demonstrate the effectiveness and validate our approach to web-based real-time machine condition monitoring and remote control for collaborative manufacturing.Copyright © 2005 by ASME
Banking on red blood cells.

The bulk production of human red blood cells in culture is a first step toward an alternative source of transfusible blood.
The development and validation of a method using high-resolution mass spectrometry (HRMS) for the qualitative detection of antiretroviral agents in human blood

Background Antiretroviral drugs are used for the treatment and prevention of HIV infection. Non-adherence to antiretroviral drug regimens can compromise their clinical efficacy and lead to emergence of drug-resistant HIV. Clinical trials evaluating antiretroviral regimens for HIV treatment and prevention can also be compromised by poor adherence and non-disclosed off-study antiretroviral drug use. This report describes the development and validation of a high throughput, qualitative method for the identification of antiretroviral drugs using high-resolution mass spectrometry (HRMS) for the retrospective assessment of off-study antiretroviral drug use and the determination of potential antiretroviral therapy (ART) non-compliance.
A vanadium containing nitrogenase preparation: Implications for the role of molybdenum in nitrogen fixation

Abstract Cell free extracts containing significant amounts of non-dialyzable vanadium have been obtained by substitution of vanadium for molybdenum in the growth medium of nitrogen fixing Azotobacter vinelandii OP cells. These extracts exhibited much lower specific activity, total metal content, and binding affinity for acetylene than extracts obtained from cells grown on molybdenum. The results indicated that vanadium will replace molybdenum in nitrogenase and that molybdenum plays a role in the substrate binding and reduction site of the enzyme complex.
The structure of young oceanic crust near a very fast spreading ridge

We have modeled the structure of the young oceanic crust near the fastest spreading ridge ever to be profiled using seismic refraction techniques. The data were originally collected during the Capricorn expedition of the Scripps Institute of Oceanography in 1953. One of the split leg profiles from that expedition, C22, was conducted near the East Pacific Rise at 15°S, where the half spreading rate is over 80 mm/yr. By digitizing the data, and modeling the two splits of C22 using synthetic seismograms, we have found that the crust is normal in thickness (5 to 7 km) and in velocity structure. An upper crustal transition zone is present on both legs and would appear to be a regular feature of young oceanic crust. It is probably too deep (1.5 to 2 km beneath the seafloor) to be correlated with the boundary between pillow basalts and sheeted dikes. Instead, we attribute this transition zone to changes in crustal porosity and/or hydrous minerals in the oceanic crust. From the appearance of wide-angle moho reflections near the rise axis, we suggest that the very large crustal magma chamber that might be expected under this fast spreading ridge is not present. This presumably results from the cooling of the crust by pervasive hydrothermal circulation.
Molecular Response of the Bloom-Forming Cyanobacterium, Microcystis aeruginosa, to Phosphorus Limitation

Cyanobacteria blooms caused by species such as Microcystis have become commonplace in many freshwater ecosystems. Although phosphorus (P) typically limits the growth of freshwater phytoplankton populations, little is known regarding the molecular response of Microcystis to variation in P concentrations and sources. For this study, we examined genes involved in P acquisition in Microcystis including two high-affinity phosphate-binding proteins (pstS and sphX) and a putative alkaline phosphatase (phoX). Sequence analyses among ten clones of Microcystis aeruginosa and one clone of Microcystis wesenbergii indicates that these genes are present and conserved within the species, but perhaps not the genus, as phoX was not identified in M. wesenbergii. Experiments with clones of M. aeruginosa indicated that expression of these three genes was strongly upregulated (50- to 400-fold) under low inorganic P conditions and that the expression of phoX was correlated with alkaline phosphatase activity (p < 0.005). In contrast, cultures grown exclusively on high levels of organic phosphorus sources (adenosine 5′-monophosphate, β-glycerol phosphate, and d-glucose-6-phosphate) or under nitrogen-limited conditions displayed neither high levels of gene expression nor alkaline phosphatase activity. Since Microcystis dominates phytoplankton assemblages in summer when levels of inorganic P (Pi) are often low and/or dominate lakes with low Pi and high organic P, our findings suggest this cyanobacterium may rely on pstS, sphX, and phoX to efficiently transport Pi and exploit organic sources of P to form blooms.
A marginal-cost pricing model for gas distribution utilities

We develop a natural gas distribution utility pricing model that includes optimization of supply mix and capacity expansion, financial analysis of revenue requirements, and design of either average-cost-or marginal-cost-based rates, and apply it using data from the East Ohio Gas Company. The results clearly point to the superiority of marginal-cost over average-cost pricing policies in terms of lesser capital requirements, better capacity utilization and higher end-use economic efficiency.
CHARACTERISTIC X-RAY PRODUCTION IN THE Mv SHELL IN YTTERBIUM BY 30-100-kev PROTONS

Characteristic $M$-shell x rays produced when protons of 30-100-keV energy are stopped in a thick target of ytterbium were observed by proportional-counter detection. By use of an aluminum absorber, radiation originating from the filling of ${M}_{\mathrm{V}}$-subshell vacancies can be isolated. Thick-target yields of the ${M}_{\mathrm{V}}$-shell and $({M}_{\mathrm{I}}+{M}_{\mathrm{II}}+{M}_{\mathrm{III}}+{M}_{\mathrm{IV}})$-shell x rays were measured separately. With extrapolated values of the fluorescence yield (0.06), the mass absorption coefficient (1500 ${\mathrm{cm}}^{2}$/g) and the stopping power, estimates of the ionization cross section for the ${\mathrm{M}}_{\mathrm{v}}$ shell have been made (neglecting contributions from other subshells by Coster-Kroning transitions). These vary from 6\ifmmode\times\else\texttimes\fi{}${10}^{\ensuremath{-}26}$ ${\mathrm{cm}}^{2}$ at 30 keV to 2\ifmmode\times\else\texttimes\fi{}${10}^{\ensuremath{-}22}$ ${\mathrm{cm}}^{2}$ at 100 keV.
GaAs Nanowires: A New Place to Explore Polytype Physics

Recently, polytypism has been observed in nanowires in materials, for which normally only one crystal structure is stable. For example, GaAs, nanowires can have wurtzite or mixed zincblende/wurtzite. Here we provide band structure parameters for wurzite and 4H GaAs and use them for modeling the nanowire electronic states. The band gap, crystal field splitting, and its strain dependence, as well as the effective mass parameters are calculated using the quasiparticle self-consistent GW method. The nanowire electronic states are obtained in the envelope function approximation within a simplified cylindrical model. The crystal field splitting of the wurtzite GaAs valence band is found to be 180 meV while in 4H-GaAs it is less than half 69 meV, suggesting a downward bowing as function of hexagonality. The conduction band minimum at Γ changes symmetry character under strain. We discuss the consequences for nanowires and determine the conditions under which a polarization reversal of photoluminescence can occur from mostly perpendicular to parallel to the wire.
Oxidative leaching of Cu atoms from PdCu particles in zeolite Y

Abstract NaY-supported PdCu samples of various Cu/Pd ratios were prepared by ion exchange with Pd(NH3)42+ and Cu(NH3)42+ precursors. Reduction of Cu is enhanced by Pd; however, after calcination at 500°C the bare ions have migrated into sodalite cages, and reduction is only enhanced for those Cu2+ ions which happen to share their cage with a Pd2+ ion. Reduction with HZ results in bimetallic PdCu particles and protons of high Bronsted acidity. At 280°C, and in an inert atmosphere, these protons selectively reoxidize surface Cu atoms to Cu+ ions, which are still attached to the surface of the bimetal particles; they can be reduced at 210°C. Complete oxidation of the Cu component takes place at 500°C; the Cu2+ ions leached from PdCu particles migrate to small zeolite cages, as indicated by EXAFS and a peak at 290°C in the profile of subsequent TPR. After complete leaching of Cu, the monometallic Pd particles are discerned from the original particles in PdCu/NaY and PdCu2/NaY by their propensity to form hydrides that are detectable by TPD. No hydride is formed with bimetal particles with Cu/Pd > 0.5; particles in Pd2Cu/NaY do form a hydride which is, however, distinguished from Pd hydride by its TPD peak position.
In-Situ Doped Multi-Layer Epitaxial Structures with Abrupt Doping Transitions by Ultra High Vacuum Rapid Thermal Chemical Vapor Deposition (UHV-RTCVD)

In this work, we have studied boron doped multi-layer epitaxial structures as active regions of deep submicron (< 0.25 gtm)metal oxide silicon field effect transistors (MOSFETs).The structures were formed by ultra high vacuum chemical vapor deposition (UHV-RTCVD) using Si2H6 and B2H6 as the source gases and H2 as the carrier gas at 750°C - 800°C and at a total pressure of 80 mTorr. With the high growth rates provided by Si2H6, thermal budgets were kept below the limit of boron diffusion in Si resulting in extremely abrupt doping transitions pushing the depth resolution limits of secondary ion mass spectroscopy. The structures consist of three epitaxial layers with thicknesses ranging from 100 A to 625 T. The top layer on which the gate oxide is formed is lightly doped (lxl016 cm-3) to minimize vertical electrical field and ionized impurity scattering for higher MOSFET channel mobility. The second layer is doped to lx1018 cm-3 for suppression of punchthrough short channel effects and finally the third layer is doped to lx 1017 cm-3 to decrease the parasitic source/drain junction capacitance that will result from the relatively high doping density of the intermediate layer. To minimize dopant diffusion in Si, low temperature (or low thermal budget) processes were employed for gate oxidation and polysilicon implant activation. A typical source/drain activation anneal was also included in sample preparation in order to simulate complete MOSFET fabrication assuming remaining steps could be carried out at lower temperatures with little contribution to dopant diffusion. Our results indicate that after all process steps a lightly doped region can still be obtained under the gate oxide with sufficient thickness to contain the MOSFET inversion layer. In these structures, the threshold voltage is determined by the doping density and thickness of the top two layers and can be easily tailored to the desired value by optimizing these parameters. With the range of parameters used in this study, our measurements show threshold voltages within the range desired for 0.1 µm MOSFETs.
Lattice Effects in Superconducting Cuprates

It is widely accepted that the remarkable properties of complex transition-metal oxides, such as colossal magnetoresistivity, are consequences of collaborative behaviors of many degrees of freedom, namely spin, charge, orbital moment and lattice. In stark contrast, most of the theories on the mechanism of the high-temperature superconductivity focus only on the spin degree of freedom. We suggest that the complex behaviors of the cuprates, including the electronic phase separation, involve charge as well as lattice degrees of freedom, and the interplay of the lattice and spin may be centrally important to the superconductivity of the cuprates. We speculate that an intermediate phase may appear when the Mott–Hubbard insulator is doped, and may support the two-component superconductivity involving spins and phonons.
The vitelline envelope, chorion, and micropyle of Fundulus heteroclitus eggs

The architecture and transformation of the vitelline envelope of the developing oocyte into the chorion of the mature egg of Fundulus heteroclitus have been examined by scanning and transmission electron microscopy. The mature vitelline envelope is structurally complex and consists of about nine strata. The envelope is penetrated by pore canals that contain microvilli arising from the oocyte and macrovilli from follicle cells. During the envelope's transformation into the chorion, the pore canals are lost and the envelope becomes more fibrous and compact and its stratified nature less apparent. The micropyle, or pore, through which the sperm gains access to the enclosed egg is located at the bottom of a small funnel-shaped depression in the envelope. Internally, the micropyle opens on the apex of a cone-like elevation of the chorion. During the development of the envelope, structured chorionic fibrils, the components of which are presumed to be synthesized by the follicle cells, become attached to its surface. These chorionic fibrils are thought to aid in the attachment of the egg to the substratum and perhaps to help prevent water loss during low tides when the egg may be exposed.
Comparative Evaluation of Heating Techniques for Room Temperature Startup of a PEMFC

We study the use of different external heating techniques for startup of a PEM fuel cell initially at room temperature. If a hot liquid is used to heat the fuel cell, the startup time depends on the Reynolds number of the hot liquid flow and also on the convective heat transfer coefficient at the liquid channel/bipolar plate interface. Therefore, apart from the energy required to heat the liquid, additional power is required for the external hot liquid pump. Fuel cell can also be directly heated by using electric heaters. Thin flexible heaters were found to be most suitable for the purpose as they allow the use of thin bipolar plates and reduce the thermal contact resistance at the heater/bipolar plate interface. The thermal mass of the bipolar plates was found to be an important factor affecting the startup time. Hence using materials with lower heat capacities reduces startup time. Embedding a heating element in the GDL reduces the startup time as the thermal mass of the GDLs and MEA is much smaller than the bipolar plate. GDLs with low through-plane thermal conductivities and high in-plane thermal conductivities are able to further reduce the startup time when used in conjunction with a heating element in the GDL.Copyright © 2008 by ASME
Incorporating systematic uncertainties into an upper limit

Abstract We discuss the problem of incorporating the uncertainty in the experimental sensitivity into the calculation of an upper confidence limit on a branching ratio or similar quantity. If the number of events is small or zero but without background, the correction to the usual result is given by a simple, easily applied formula. The case of an accurately known background also has a simple solution.
On the strength of oceanic fracture zones and their influence on the intraplate stress field

We use the locations and source mechanisms of oceanic intraplate earthquakes to test the hypothesis that the strength of oceanic fracture zones is less than that of normal oceanic lithosphere. The 77 earthquakes selected for the study have well-determined focal mechanisms and epicenters in regions where fracture zones are well mapped. We have search for dependence of faulting style, fault orientation, or principal stress direction on the distance from the nearest fracture zone. If fracture zones were generally weaker than the surrounding lithosphere, one of the principal horizontal stresses would be oriented nearly perpendicular to the fracture zone; we find no evidence that principal stresses near fracture zones are oriented preferentially in this manner. There is a slight tendency for earthquakes to occur near fracture zones, and patterns of fault orientation and sense of slip support the view that differential cooling and horizontal contraction on fracture zones may contribute seismogenic stress.
A Comparison of Internal, External, and Successive Unfolding Based on Occupational Judgments

Successive unfolding is a recently developed tech nique that appears to have advantages over traditional unfolding techniques. To assess its usefulness, succes sive, internal, and a type of external unfolding were compared with regard to the stimulus configurations recovered, the fit of the models as a whole, the fit of individual subjects, and each model's stability in a cross-validation sample. The data were obtained from judgments of similarity of and preference for occupa tional titles. Internal unfolding yielded degenerate so lutions and was dropped from subsequent analyses. External and successive unfolding yielded interpretable dimensions, but the nature of the dimensions uncov ered differed somewhat from one type of unfolding to the other. Both types of unfolding fit the data ade quately for the stimulus configuration, though succes sive unfolding appeared to fit better. The first two di mensions of both models were well reproduced in cross-validation samples. Dimensions beyond the sec ond were mo...
Natural rolling responses of a delta wing in transonic and subsonic flows

The unsteady, three-dimensional, full Navier-Stokes (NS) equations and the Euler equations of rigid-body dynamics are sequentially solved to simulate the natural rolling response of slender delta wings of zero thickness at moderate to high angles of attack, to transonic and subsonic flows. The governing equations of fluid flow and dynamics of the present multi-disciplinary problem are solved using the time-accurate solution of the NS equations with the implicit, upwind, Roe flux-difference splitting, finite-volume scheme and a four-stage Runge-Kutta scheme, respectively. The main focus is to analyze the effect of Mach number and angle of attack on the leading edge vortices and their breakdown, the resultant rolling motion, and overall aerodynamic response of the wing. Three cases demonstrate the natural response of a 65 deg swept, cropped delta wing in a transonic flow with breakdown of the leading edge vortices and an 80 deg swept delta wing in a subsonic flow undergoing either damped or self-excited limit-cycle rolling oscillations as a function of angle of attack. Comparisons with an experimental investigation completes this study, validating the analysis and illustrating the complex details afforded by computational investigations.
Fixation of C14O2 in amino acids by Brucella abortus

Abstract 1. 1. The major products of C14O2 fixation by growing cultures of B. abortus are glycine and alanine. C14O2 is fixed in alanine only if the culture is grown in a synthetic medium containing no preformed amino acids. 2. 2. Resting cells of B. abortus incorporate C14O2 into the carboxyl groups of both glycine and alanine. The rate of incorporation of C14O2 into alanine is much lower than the incorporation into glycine. 3. 3. Apparently glycine is not deaminated before exchanging with C14O2.
A pure S=3/2 [Fe4S4]+ cluster in the A33Y variant of Pyrococcus furiosus ferredoxin

The properties of the [4Fe-4S]2+/+ cluster in wild-type and the A33Y variant of Pyrococcus furiosus ferredoxin have been investigated by the combination of EPR, variable-temperature magnetic circular dichroism (VTMCD) and resonance Raman (RR) spectroscopies. The A33Y variant involves the replacement of an alanine whose α-C is less than 4 A from one of the cluster iron atoms by a tyrosine residue. Although the spectroscopic results give no indication of tyrosyl cluster ligation, the presence of a tyrosine residue in close proximity to the cluster results in a 38-mV decrease in the midpoint potential of the [4Fe-4S]2+,+ couple and has a marked effect on the ground state properties of the reduced cluster. The mixed spin [4Fe-4S]+ cluster in the wild-type protein, 80% S=3/2 (E/D=0.22, D=+3.3 cm−1) and 20% S=1/2 (g=2.10, 1.87, 1.80), is converted into a homogeneous S=3/2 (E/D=0.30, D=−0.7 cm−1) form in the A33Y variant. As the first example of a pure S=3/2 [4Fe-4S]+ cluster in a ferredoxin, this variant affords the opportunity for detailed characterization of the excited electronic properties via VTMCD studies and demonstrates that the protein environment can play a crucial role in determining the ground state properties of [4Fe-4S]+ clusters.
TU-EE-A3-04: Massive Training Artificial Neural Network (MTANN) to Reduce False Positives Due to Rectal Tubes in Computer-Aided Polyp Detection

Purpose: One limitation of current computer‐aided detection (CAD) of polyps in CT colonography is a relatively large number of false positives. Rectal tubes are a common source of false positives and may distract the reader from less common polyps in the rectum. Our purpose was to develop a three‐dimensional massive‐training artificial neural network (3D MTANN) for reduction of false positives due to rectal tubes generated by a CAD scheme. Material and Methods: Our database consisted of CT colonography of 73 patients, scanned in both supine and prone positions. Fifteen patients had 28 polyps (15 polyps: 5–9 mm; 13 polyps: 10–25 mm). These cases were subjected to our previously reported CAD scheme that included shape‐based detection of polyps and reduction of false positives with a Bayesian neural network. With this scheme, 96.4% (27/28) by‐polyp sensitivity with 3.1 (224/73) false positives per patient was achieved. To eliminate false‐positive rectal tubes, we developed a 3D MTANN that was trained to enhance polyps and suppress rectal tubes. Results: In the output volumes of the trained 3D MTANN, various polyps were represented by distributions of bright voxels, whereas rectal tubes appeared as darker voxels. The 3D MTANN removed all 20 false‐positive rectal tubes produced by our original CAD scheme without removing any true positives. To evaluate the overall performance, we applied the 3D MTANN to the entire database containing 27 polyps (true positives) and 224 non‐polyps (false positives). The 3D MTANN eliminated 33% (73/224) of non‐polyps without removal of any true positives in an independent test. Conclusion: The 3D MTANN was able to improve the false‐positive rate of our original CAD scheme from 3.1 to 2.1 false positives per patient, while an original by‐polyp sensitivity of 96.4% was maintained. Conflict of Interest: HY, SGA: shareholders, R2 Technology, Inc.
Inhibitory effect of beraprost sodium on formation of lipid peroxides in ischemia and recirculation-induced cerebral injury.

Abstract A cerebral injury was induced by the bilateral common carotid artery occlusion and recirculation in spontaneously hypertensive rats (SHRs). Employing this ischemia-recirculation rat model, the effects of beraprost sodium (beraprost) on (1) lipid peroxide formation, (2) the increase in the brain water content and (3) neurological signs were examined. In a dosage of 25 μg kg -1 or higher, beraprost, administered orally, significantly inhibited the formation of lipid peroxides in the brain and serum induced by cerebral ischemia and subsequent recirculation in a dose-dependent manner. Beraprost also alleviated ptosis and markedly inhibited abnormal running behaviour caused by the ischemia and subsequent recirculation. In addition, although administration of beraprost did not cause marked inhibition of the increase in the brain water content (used as an index of cerebral oedema) during the first 3 h after recirculation, it restored the normal brain water content within 24 h after recirculation. Therefore, this effect was observed evidently later than the effect of inhibition of lipid peroxide formation. Moreover, administration of beraprost resulted in improvement in the symptoms accompanying the ischemic treatment. These results suggest that beraprost is potentially useful for prevention or treatment of the pathological state accompanying cerebral infarction.
Selective reduction of 1-chloro-2-iodoperfluorocycloalkenes with sodium trimethoxyborohydride

Abstract In contrast to other chemical reducing agents, it has been found that sodium trimethoxyborohydride will selectively reduce 1-chloro-2-iodoperfluorocycloalkenes to give good yields of 1-hydro-2-chloroperfluorocycloalkenes. The selective displacement of iodine by hydrogen is discussed in terms of HSAB principles.