cssi/SciSciGPT-SciSciNet huggingface dataset:
Carbon monoxide binding to cytochrome P450BM-3: evidence for a substrate-dependent conformational change.

Abstract The kinetics of carbon monoxide binding to cytochrome P450BM-3 in the presence and absence of substrate has been investigated using flash photolysis. The second order kinetics for CO association with the substrate-free form of the protein appear biphasic. Deconvolution into two exponentials yields fast and slow rate constants of 11.1 ± 0.6 × 106M−1s−1 and 3.5 ± 0.2 × 106M−1s−1, respectively with 52% of the signal being attributed to the fast phase. Interestingly, upon binding of a substrate such as laurate, the second order kinetics become monophasic, with a value of 3.5 × 106M−1s−1, which are similar to the slow rate found in the substrate-free from of the protein. We have also examined the geminate CO rebinding kinetics in the presence and absence of various substrates. In the substrate-free form the overall geminate yield is 30%, and addition of a substrate increases the geminate yield to roughly 50%. Both the substrate-free and substrate-bound forms exhibit complex geminate kinetics which cannot be described by a simple three-state kinetic model. Extension of this model to include four states is required. The addition of substrate causes an increase in the geminate rate constants resulting in a larger geminate amplitude when compared to the substrate-free form. There is also evidence for a correlation between the volume occupied by the substrate and the geminate rate constants. These results are discussed in terms of substrate-dependent conformational changes in cytochrome P450BM-3 and the overall energy landscape of the hemoprotein which couples to conformer equilibria.
Comparison of rRNA Cleavage by Complementary 1,10-Phenanthroline-Cu(II)- and EDTA-Fe(II)-Derivatized Oligonucleotides

The chemical nucleases 1,10-phenanthroline-Cu(II) and EDTA-Fe(II), have proven to be valuable tools for structural analysis of nucleic acids. Both have found applications in footprinting and directed proximity studies of DNA and RNA. Derivatives of each that provide for tethering to nucleic acid or protein are commercially available, allowing their widespread use for structural analysis of macromolecules. Although their applications are somewhat overlapping, differences in their cleavage mechanisms and chemical properties allow them to provide distinct and complementary structural information. The purpose of this study is to compare directly the cleavage patterns of tethered 1,10-phenanthroline-Cu(II) and EDTA-Fe(II) complexes within a similar experimental system. Here, the region surrounding nucleotide 1400 of 16S rRNA from Escherichia coli serves as a substrate for chemical cleavage directed by a derivatized complementary oligonucleotide. This region of rRNA is known to be involved in the decoding of mRNA during translation. The results of this study provide evidence in support of the mechanistic differences previously established for EDTA-Fe(II) and 1,10-phenathroline-Cu(II). The delocalized cleavage envelope produced by EDTA-Fe(II) cleavage suggests the involvement of a diffusible reactive species. On the other hand, rRNA cleavage induced by the tethered 1,10-phenanthroline-Cu(II) complex appears localized to the proximity of the chemical nuclease under normal conditions, although the production of an unknown diffusible species appears to occur during long reaction times.
Information from combined 1H and 31P NMR studies of cell extracts : differences in metabolism between drug-sensitive and drug-resistant MCF-7 human breast cancer cells

Combined analysis of both 1H and 31P NMR spectra of extracts of drug-sensitive and multidrug-resistant MCF-7 human breast cancer cells enabled quantitative comparisons between the concentrations of major metabolites, as well as of their precursors. In resistant cells high energy phosphorus compounds, phosphocreatine and ATP, and also their precursors, creatine and ADP, were elevated compared to the sensitive cells. In phospholipid metabolism, the sensitive cells showed higher phosphocholine and phosphoethanolamine concentrations than the resistant cells, but choline levels were similar. These results delineated the differences in control of metabolic pathways between drug-sensitive and drug-resistant cells.
Scattered radiation in chest radiography

Luminance scatter fractions were measured for patients and phantoms in various regions of the chest film. Scatter fractions were found to be highly variable, being quite high in the regions of the chest with a large equivalent tissue thickness (e.g. mediastinum, chest wall, and subdiaphragmatic areas). For example, approximately 90% of the radiation reaching the mediastinum region of the chest film was found to be scattered radiation when a grid was not used. Even with a 12:1 grid, less than 50% of the available primary beam contrast was being displayed in the mediastinum. In regions of the chest film with high scatter fractions, film latitude was also a problem, further reducing image contrast in these regions. Image contrast and scatter fractions in chest radiography were investigated for different scatter rejection techniques including air gaps, antiscatter grids, and slit radiography.
Pancreas microenvironment promotes VEGF expression and tumor growth: novel window models for pancreatic tumor angiogenesis and microcirculation.

Pancreatic cancer has a poor prognosis, and treatment strategies based on preclinical research have not succeeded in significantly extending patient survival. This failure likely stems from the general lack of information on pancreatic tumor physiology, attributable to the difficulties in developing relevant, orthotopic models that accurately reflect pancreatic cancer in the clinic. To overcome this limitation, we developed abdominal wall windows suitable for intravital microscopy that allowed us to monitor angiogenesis and microvascular function noninvasively during tumor growth in vivo. We used two complementary tumor models in mice: orthotopic (human ductal pancreatic adenocarcinoma, PANC-1, grown in the pancreas), and ectopic (PANC-1 grown in the abdominal wall). We found that orthotopic PANC-1 tumors grew faster than the ectopic tumors and exhibited metastatic spread in the late stage similar to advanced pancreatic cancer in the clinic. Orthotopic PANC-1 tumors expressed vascular endothelial growth factor (VEGF)121 and VEGF165, contained higher levels of tumor cell–derived VEGF protein, and maintained vascular density and hyperpermeability during exponential tumor growth. Orthotopic PANC-1 tumors showed lower leukocyte–endothelial interactions in the early stage of growth. In addition, both VEGF121 and VEGF165 promoted the growth of PANC-1 cells in vitro. Finally, Anti-VEGF neutralizing antibody inhibited angiogenesis and tumor growth of PANC-1 tumors in both sites. We conclude that the orthotopic pancreas microenvironment enhances VEGF expression, which stimulates growth of PANC-1 tumors (compared with ectopic tumors). The mechanism is autocrine and/or paracrine and also is involved in the maintenance of blood vessels. This comparative system of orthotopic and ectopic pancreatic cancer will provide the rigorous understanding of pancreatic tumor pathophysiology needed for development of novel therapeutic strategies.
Deployable reconnaissance from a VTOL UAS in urban environments

Reconnaissance collection in unknown or hostile environments can be a dangerous and life threatening task. To reduce this risk, the Unmanned Systems Group at Virginia Tech has produced a fully autonomous reconnaissance system able to provide live video reconnaissance from outside and inside unknown structures. This system consists of an autonomous helicopter which launches a small reconnaissance pod inside a building and an operator control unit (OCU) on a ground station. The helicopter is a modified Bergen Industrial Twin using a Rotomotion flight controller and can fly missions of up to one half hour. The mission planning OCU can control the helicopter remotely through teleoperation or fully autonomously by GPS waypoints. A forward facing camera and template matching aid in navigation by identifying the target building. Once the target structure is identified, vision algorithms will center the UAS adjacent to open windows or doorways. Tunable parameters in the vision algorithm account for varying launch distances and opening sizes. Launch of the reconnaissance pod may be initiated remotely through a human in the loop or autonomously. Compressed air propels the half pound stationary pod or the larger mobile pod into the open portals. Once inside the building, the reconnaissance pod will then transmit live video back to the helicopter. The helicopter acts as a repeater node for increased video range and simplification of communication back to the ground station.
Transformation of Cells in vitro by Viruses

The first paragraph of "Transformation of cells in vitro by viruses" by R. Dulbecco [Science 142, 932 (15 Nov. 1963)] is a repetition of paragraph 8. The article begins with paragraph 2.
Development and evaluation of an agent-based model of sexual partnership

The agent-based model presented here builds on existing models, allowing for multiple partnerships, including those overlapping in time, to examine sexual partnerships, with the goal of hypothesis testing and guiding data collection. Within each model run, agents are assigned characteristics (including quality, aspiration, courtship duration, and ideal number of lifetime partners) and then search for partners; existing couples choose whether they should break up, remain dating, or become sexual partners. Model behavior was tested across a wide range of parameters and compared with empirical data. The model produces numbers of lifetime sexual partners, and partners in the last year, rates of concurrency, and relationship durations similar to nationally representative data from the United States; it also generates correlations in partners' quality similar to those reported for marriage and dating partners. Model results highlight the importance of individual preferences, interactions between individuals, and contextual factors in sexual decision making.
Kinetics of cytokine production in experimental autoimmune anterior uveitis (EAAU)

PURPOSE. Experimental autoimmune anterior uveitis (EAAU) can be induced in Lewis rats with bovine melanin associated antigen (MAA) extracted from the iris/ciliary body (CB) and does not require adjuvant. The present investigation was undertaken to study the expression of various cytokines in EAAU. METHODS. Lewis rats were immunized with bovine MAA and sacrificed at various time points. The iris/CB and popliteal lymph nodes were harvested, and total RNA isolated. The reverse transcription polymerase chain reaction (RT-PCR) was utilized to determine the mRNA expression of IFN-?, TNF-a, IL-2, IL-4, IL-6 and IL-10. RESULTS. TNF-a mRNA levels in iris/CB paralleled the course of EAAU and increased dramatically at the peak of disease. However, mRNA levels of TNF-a demonstrated little change in the popliteal lymph node. IFN-? mRNA was barely detectable in the iris/CB and increased only slightly at the peak of disease. In contrast, IFN-? mRNA levels in the popliteal lymph node paralleled the course of disease and ...
Cysteamine Depletes Prolactin (PRL) but Does Not Alter the Structure of PRL-Containing Granules in the Anterior Pituitary

Cysteamine causes a profound depletion of PRL in the anterior pituitary and in the systemic circulation, as measured by RIA and bioassay. However, electron microscopic study of PRL-containing cells in rat anterior pituitary does not reveal changes in secretory granule or cytoplasmic structure during the interval of depressed PRL content and of subsequent recovery to normal levels. In contrast to the results obtained by RIA, PRL-like immunoreactivity as detected by immunocyto-chemistry is present and similar to that of control preparations after cysteamine administration. We suggest that cysteamine alters PRL structure in secretory granules, probably by interacting with the disulfide bonds of PRL, thereby altering bioactivity and immunoreactivity. The presence of cysteamine-altered PRL in secretory granules does not seem to trigger degradation of granules by the lysosomal system.
A microchemical analysis of alkaline phosphatase in human malignant and benign breast tumours

A microchemical technique has been adapted to the evaluation of the membrane-bound enzyme alkaline phosphatase within human malignant and benign breast lesions. Frozen tissue sections were either stained or lyophilized in alternating sequence in order that samples for enzyme analysis could be chosen from well-defined regions of epithelial proliferation. Microgram quantities of human tumors could then be examined with multiple replications to elucidate patterns of overall enzyme activity, the activity of tissue fractions, and the isoenzyme form present within individual tumors. A significant difference (p<0.001) was found to exist between the specific activity of alkaline phosphatase from human infiltrating ductal carcinomas and human fibroadenomas. The activity value determined for the malignant group of tumors was 2.12±1.80, while that for benign tumors was 7.52±4.31 mmoles/min/kg dry weight at 37° C. The percentage of alkaline phosphatase activity found within 29,000 g pellets of malignant tumors was variable and constituted approximately 60% of the total activity found in all fractions, while that for benign tumors was more constant and amounted to approximately 90% of the total found. The malignant and benign tumor alkaline phosphatase of both supernatant and pellet fractions was shown to be 90% labile to incubation at 65° C for 5 min and to be 50% inhibited by 20 mM 1-phenylalanine. Polyacrylamide gel electrophoresis revealed a single enzyme band of identical Rf for each of these fractions from the two tumor types. When varying proportions of malignant and benign tissue samples were co-incubated, no influence of tumor type on the total activity or the percentage membrane-bound activity was found. However, a change in the proportion of enzyme activity pelleted at 29,000 g could be shown when the cellularity of the tissue sample was varied. While homogenization of the total sample or of the insoluble material could release some of this activity, greater enzyme activities were always found within insoluble, 480 g pellets and 29,000 g pellets taken from benign tumors. An entrapment of membrane proteins could account for these results and should be considered when tissues are analyzed in the manner described.
Spontaneous representations of small numbers of objects by rhesus macaques: Examinations of content and format

Abstract The project of comparative cognition benefits from common measures across species. We report here on five experiments using the violation of expectancy looking time measure with free-ranging rhesus macaques ( Macaca mulatta ), each designed to build on current knowledge concerning spontaneous representations of number. Each subject, tested in only one experimental condition, watched as eggplants were placed behind a screen one at a time, after which the screen was removed revealing an outcome that either matched or did not match the number placed there. Subjects looked longer at impossible than possible outcomes in 1+1=2 or 3, 1 small + 1 small=1 big or 2 small, 2+1=2 or 3, and 2+1=3 or 4 conditions. They failed in 2+1+1=4 or 3 or 5 and in 1+1+1=2 or 3 conditions. This pattern of results closely matches that observed across several previous studies of human infants. The data allow us to test among four different proposals concerning the format and content of the mental representations underlying looking in these experiments. Object file representations are favored over: (i) low-level perceptual representations, (ii) representations of continuous variables such as volume or surface area, and (iii) analog magnitude representations of number. We conclude by considering exactly how the object tracking system revealed in these and other related experiments does and does not represent number, and how it might be one evolutionary precursor of the human specific system of number representations.
Ultrastructural morphometry of membrane-bound intracytoplasmic collagen fibrils in tendon fibroblasts exposed to He : Ne laser beam

Collagen fibrils are not found in fibroblast cytoplasm except in certain pathological conditions or in the presence of drugs and other agents that accelerate collagen turnover. Because low energy laser photostimulation is both a non-pathogenic and non-chemical accelerator of collagen synthesis, its effects were studied on four groups of calcaneal tendons from 18 rabbits (1) to test the hypothesis that vacuolar fibrils are not produced exclusively by diseases and chemical agents, and (2) to compare the morphometry of matrical and vacuolar fibrils. The right calcaneal tendons of nine rabbits were surgically tenotomized and repaired; six of these were transcutaneously irradiated with He:Ne laser everyday. The right calcaneal tendon of six of the remaining nine rabbits were similarly irradiated with laser, but without prior tenotomy and repair. 21 days later, all tendons were fixed in situ and processed for electron microscopy. Fibril-bearing vacuoles were found only in fibroblasts of tenotomized laser-irradiated tendons. Similar vacuoles were not seen in non-tenotomized laser-irradiated tendons nor in non-irradiated tendons whether tenotomized or not. Mann-Whitney U tests revealed no statistically significant differences in the cross-sectional areas or diameters of matrical and vacuolar fibrils. These findings suggest (a) that matrical and vacuolar fibrils have a common origin, and (b) that vacuolar fibrils can be induced by a non-pathologic, non-chemical accelerator of collagen synthesis.
Attachment of Functionalized Poly(ethylene glycol) Films to Gold Surfaces

The attachment of linear poly(ethylene glycol) (PEG) molecules (MW = 2000−5000) to gold surfaces via orthopyridyl−disulfide (OPSS) terminal groups has been studied with X-ray photoelectron spectroscopy (XPS), time-of-flight secondary ion mass spectrometry (TOF−SIMS), and surface plasmon resonance (SPR). The molecules examined included a PEG molecule terminated with a methoxy group and derivatized with an OPSS group at the other end (M-PEG-OPSS), a PEG molecule derivatized with OPSS at both ends (PEG-(OPSS)2), and a PEG derivatized with an N-hydroxysuccinimide group at one end and an OPSS group at the other (NHS-PEG-OPSS). Exposure of gold to aqueous solutions of these resulted in immobilization via gold−thiolate bonds from the OPSS disulfide groups. The resulting mixed PEG−/OPS− thiolate monolayers were not always in 1:1 ratio. Most of the PEG-(OPSS)2 molecules formed gold−thiolate bonds at both ends, but some left a free, intact OPSS group. For biosensor applications, this or the free NHS groups in the N...
Latency-associated peptide prevents skin fibrosis in murine sclerodermatous graft-versus-host disease, a model for human scleroderma.

Murine sclerodermatous graft-versus-host disease (Scl GVHD), produced by transplanting B10.D2 bone marrow and spleen cells to lethally irradiated BALB/cJ mice, is a model for human scleroderma. Mice with Scl GVHD have skin thickening, lung fibrosis, cutaneous mononuclear cell infiltration, and upregulation of cutaneous transforming growth factor β1 (TGF-β1) and type I collagen mRNAs by day 21 after bone marrow transplantation. Elevated TGF-β1 appears to be the critical cytokine driving fibrosis in Scl GVHD, which can be prevented with antibodies to TGF-β administered early in disease. Here we demonstrate that we can also prevent skin thickening in mice with Scl GVHD with a naturally occurring antagonist to TGF-β1, human latency-associated peptide (LAP). By quantitative real-time PCR analysis and immunostaining, LAP treatment also abrogates the upregulation of cutaneous TGF-β1 and connective tissue growth factor mRNAs and type I collagen synthesis in Scl GVHD. In contrast to anti-TGF-β antibodies, LAP at 4 ng total per mouse has no significant suppressive effect on cutaneous influx of T cells and monocytes or immune cell activation. LAP may be a potential new therapy in scleroderma and other TGF-β-driven fibrosing disease that targets TGF-β more specifically, without affecting systemic critical roles of TGF-β on immune cell function.
Textural critical velocity of 3He-A in the limit of large magnetic fields

Abstract A path linking any uniform, current carrying state to the true equilibrium one is proposed, which becomes monotonically decreasing in energy if the superfluid velocity exceeds a critical value. This critical velocity as a function of the orientation is calculated.
Cationic Hydrogen Complexes of Rhenium. 2. Synthesis, Reactivity, and Competition Studies

Cationic rhenium dihydrogen complexes, [Re(H2)(PR3)2(CO)3]B(Ar‘)4 (PR3 = PCy3, PiPr3, PiPrPh2, PPh3; Ar‘ = 3,5-(CF3)2C6H3), have been prepared by the protonation of ReX(PR3)2(CO)3 (X = H, CH3) with [H(Et2O)2]B(Ar‘)4 under a hydrogen atmosphere. Deuterium is incorporated into the H2 ligand when placed under a D2 atmosphere and large JHD values (30−33 Hz) are consistent with a dihydrogen formulation. Relaxation data indicate very short T1min for these complexes. These complexes are susceptible to heterolytic cleavage of dihydrogen, and the reactivity with several bases has been investigated. Under vacuum or argon atmosphere the complexes readily lose hydrogen to form 16-electron complexes. In the solid state, [Re(PCy3)2(CO)3]B(Ar‘)4 exhibits an agostic interaction to a β C−H bond of the phosphine ligand. Variable-temperature 31P{1H} NMR spectra of [Re(PCy3)2(CO)3]B(Ar‘)4 indicate a dynamic process involving hindered rotation about the Re−P bond. Competition studies have been conducted, and the hydrogen bind...
Influence of Fe substitutions on the deformation behavior and fault energies of Ni3Ge–Fe3Ge L12 intermetallic alloys

Abstract Ni3Ge exhibits a yield strength anomaly, whereas the yield strength of Fe3Ge shows a normal decline with temperature, and there is a gradual transition from anomalous to normal behavior as Fe content increases. A dramatic strengthening for 77 K deformation has also been noted to occur in these alloys as a result of increasing Fe content. The combined use of transmission electron microscopy (TEM) and image simulations has facilitated identification of the operative deformation mechanisms and allowed for a quantitative measure of superdislocation dissociations. A transition from octahedral glide and Kear–Wilsdorf locking to cube glide of superdislocations has been observed to coincide with an increase in either deformation temperature or Fe content. The low-temperature strengthening has been correlated with enhanced cross-slip, which is aided by a significant lowering of the cube-plane antiphase boundary energy with increasing Fe content. It is proposed that the strengthening and the transition to cube glide are promoted by an increase in the complex stacking fault energy, which enhances both cross-slip and cube-plane mobility.
Computer-aided photo-identification system with an application to polar bears based on whisker spot patterns

Abstract Ecologists often rely on unique natural markings to identify individual free-ranging animals without disturbing them. We developed a computer-aided photo-identification system for identifying polar bears (Ursus maritimus) based on whisker spot pattern recognition. We automated our system so that the selection of 3 reference points on the input image is the only manual step required during image preprocessing. Our pattern-matching algorithm is unique in that the variability within spot patterns is considered fully rather than representing them as points and applying a point-pattern matching algorithm. We also measured the reliability of our method as probabilities of true positives and false positives using photographs of various qualities taken at different angles. When we excluded photographs of poor quality and angle the probability of true positives was >80% at a false positive probability of 10%. A new photograph could be preprocessed in <1 min and tested against a reference library of 100 in...
Cellular techniques for Ring Imaging Cherenkov detector image processing

Ring Imaging Cherenkov detectors (RICH) are a class of particle detectors used for particle identification whose principle involves a pattern recognition problem: identifying circles from a short number of their points. A real image hosts several circles which may eventually overlap. Actual techniques solving this problem are mainly non-local algorithms implemented on software requiring large computing time and resources. This point limits the use of RICH detectors in the trigger system of large experiments such as LHCb. An alternative solution, based on a cellular approach, is proposed. A list of possible templates from the standard library is established and considerations on the requirements for the hardware implementation in FPGAs are given. From the conceptual point of view, the cellular technique solution looks promising while the hardware implementation in FPGAs lays in the verge of the actual technical limitations if response times are to be in the order of the microsecond as required in the LHCb hardware trigger.
T-CELL MEDIATOR INDUCTION OF NON-T CELL CYTOTOXICITY

Publisher Summary This chapter focuses on the nonspecific lymphocyte cytotoxicity for allogeneic target cells, also termed spontaneous cytotoxicity or background cytotoxicity reported by several investigators studying graft rejection and tumor immunology phenomena. Experiments were performed to determine whether this activation was the result of removal of some suppressor population during separation procedures, but reconstitution of the non-E-RFC with either the E-RFC (T cell) population or with unseparated mononuclear cells failed to reverse the cytotoxic activity. The mechanism of the nonspecific cytotoxicity has been investigated and appears to be mediated by release of a lymphotoxin-like moiety from the ER Sup-activated non-T cells.
Absolute pair-production cross-section measurements in targets of Z = 26, 29, 50, 82, and 92 with 1. 119-MeV photons

Absolute cross sections for the production of electron-positron pairs by 1.119-MeV photons have been measured with targets of iron, copper, tin, lead, and uranium. An improved internal-source spectrometer was used which utilized two large intrinsic Ge detectors. The results are in excellent agreement with the exact numerical calculations of Tseng and Pratt for $Z=26, 29, \mathrm{and} 50$, and show a systematic departure of 13 and 19% above the theoretical values for $Z=82 \mathrm{and} 92$, respectively. The present cross section at $Z=92$ is lower than and slightly outside of the error limits from the results obtained with our older spectrometer. The present method has the definite advantage that the absolute activities of the radioactive sources need not be known. It also has the obvious advantages attributable to the high-energy resolution of the two intrinsic Ge detectors. A preliminary measurement in a lead target, using 1.0766-MeV $\ensuremath{\gamma}$ rays, clearly shows that this technique can be extended to lower photon energies with resulting errors comparable to those at 1.119 MeV.
The gravitational field of Phobos

The external gravitational field produced by a rigid body of uniform density but irregular shape is formulated in terms of spherical harmonics. The formalism is applied to the Martian satellite Phobos. Based on a three-dimensional shape model of Phobos by Duxbury (1989), the gravitational coefficients up to degree and order 4 for a homogeneous Phobos are computed. In particular, J2 is found to be 0.105. The in-plane libration amplitude of a homogeneous Phobos is predicted to be 0.97 deg, within the rather large uncertainty of the observed value of 0.78 + or - 0.4 deg.
WeBWorK for programming fundamentals

WeBWorK is a web-based assessment tool developed at the University of Rochester to generate, deliver, and automatically grade homework problems and distribute their solutions. Sharing the market with similar systems, WeBWorK differs in that it is free and open-source. It provides an advanced processing of mathematical formulae and a high-level of problem randomization. Although it was used initially used in mathematics and physics, we are working on extending and adapting WeBWorK for programming fundamentals and computer science.
Global tracking of the SO2 clouds from the June, 1991 Mount Pinatubo eruptions

The explosive June 1991 eruptions of Mount Pinatubo produced the largest sulfur dioxide cloud detected by the Total Ozone Mapping Spectrometer (TOMS) during its 13 years of operation: approximately 20 million tons of SO2, predominantly from the cataclysmic June 15th eruption. The SO2 cloud observed by the TOMS encircled the earth in about 22 days (about 21 m/s); however, during the first three days the leading edge of the SO2 cloud moved with a speed that averaged about 35 m/s. Compared to the 1982 El Chichon eruptions, Pinatubo outgassed nearly three times the amount of SO2 during its explosive phases. The main cloud straddled the equator within the first two weeks of eruption, whereas the El Chichon cloud remained primarily in the Northern Hemisphere. The measurements indicate that Mount Pinatubo has produced a much larger and perhaps longer-lasting SO2 cloud; thus, climatic responses to the Pinatubo eruption can exceed those of El Chichon.
New methods for the synthesis of oxindole alkaloids. Total syntheses of isopteropodine and pteropodine.

Abstract The 2-oxindole alkaloids isopteropodine (11) and pteropodine (12) were conveniently synthesised from the known pentacycle (9) via a new and general protocol for oxidation and rearrangement of carboline lactams into 3,3-disubstituted-2-oxindoles.
Statistical and Kinetic Studies of the Changes in Soybean Quality during Storage as Related to Soymilk and Tofu Making

The objective of this study was to develop statistical equations and kinetic models to describe the changes of soybean quality during storage. Significant correlations (P < 0.0001) were found among most of quality attributes including color parameters (Hunter L, a, b, and DeltaE), solid extractability (as expressed by soymilk solids content), soymilk pH and protein content, tofu yield, hardness, and protein content. Regressed linear equations were developed between color indices (L/L(0), DeltaE) and soymilk/tofu making properties. Empirical equations were developed to relate soybean color indices (L/L(0), DeltaE) and storage conditions including variables of initial moisture content (MC), relative humidity (RH), temperature (T), and duration (t). Kinetics of the changes in soybean color and extractability during storage at 70% RH and 22 to 40 degrees C were investigated. The kinetics was well described by zero-order kinetics. The Arrhenius equation adequately described the temperature dependence of the reaction rate constants for all parameters, from which the activation energies and rate constant were obtained. The equations developed in this study provided simple methods to monitor soybean quality and predict quality changes of soybeans during storage at various conditions.
Calibration and implementation of a sand plasticity plane-strain model for earthquake engineering applications

Abstract The calibration and implementation of a sand plasticity plane-strain model for geotechnical earthquake engineering applications are presented. The constitutive model, as described by Boulanger and Ziotopoulou [1] in a companion paper, was formulated to improve its ability to approximate the stress–strain responses important to geotechnical earthquake engineering applications. A generalized calibration of the constitutive model is presented which attempts to produce drained and undrained, monotonic and cyclic responses under a broad range of stress conditions that are reasonably consistent with the behaviors expected based on engineering correlations to commonly available in-situ test data (i.e., SPT, CPT and V s data). Simulated single element responses are compared to various design correlations to illustrate and evaluate the model's performance. The calibrated model has three primary parameters that require input by the user: a shear modulus coefficient that is determined from in-situ shear wave velocity data, an apparent relative density which is estimated from SPT or CPT penetration resistances, and a contraction rate parameter that the user adjusts to fit the cyclic resistance ratio determined from a design liquefaction triggering correlation. The remaining parameters are assigned default values based on the calibration process presented herein. The constitutive model is shown to be relatively easy to calibrate and provide reasonable responses for key liquefaction behaviors. The numerical implementation as a user defined material for use in a two-dimensional explicit finite difference program is described.
On the hydrodynamic amplification of field separations

Abstract A new colloidal separation procedure is proposed which employs the distributed velocity profile in laminar flow to amplify the results of field-induced separations. A preliminary theoretical development is presented. Results calculated from the theory are used to identify a suitable range of operating parameters for achieving good separations. The results demonstrate the rapidity and effectiveness of the proposed technique, and illustrate an application to protein separations. Field-flow-fractionation (FFF) is another technique that combines field effects with distributed velocity profiles for achieving colloid separations; the differences between FFF and the proposed procedure are discussed in detail.
Conormality, cusps and non-linear interaction

In this note we consider the problem of associating to a given geometry, in the form of a C ∞ variety containing possibly singular submanifolds, spaces of finitely regular conormal functions. For non-linear problems it is highly desirable that the bounded elements in these spaces form algebras and that they have appropriate solvability properties for certain linear differential operators. This leads to the general approach discussed here, mixing microlocalization and blow-up techniques.
Understanding link-layer behavior in highly congested IEEE 802.11b wireless networks

The growing deployment and concomitant rise in wireless network usage necessitates the comprehensive understanding of its behavior. More importantly, as networks grow in size and number of users, congestion in the wireless portion of the network is likely to increase. We believe there is a strong need to understand the intricacies of the wireless portion of a congested network by interpreting information collected from the network. Congestion in a wireless network can be best analyzed by studying the transmission of frames at the link layer. To this end, we use vicinity sniffing techniques to analyze the link layer in an operational IEEE 802.11b wireless network. In this paper, we discuss how congestion in a network can be estimated using point-to-point link reliability. We then show how link reliability is correlated with the behavior of link-layer properties such as frame retransmissions, frame sizes, and data rates. Based on the results from these correlations, our hypothesis is that the performance of the link layer in congested networks can be improved by (1) sending smaller frames, and/or (2) using higher data rates with a fewer number of frames sent.
Mixed Bundling of Two Independently Valued Goods

This paper develops analytical results and insights for the mixed bundling problem of pricing a product line consisting of two component goods (with valuations distributed uniformly and independently in [0, a1] and [0, a2], respectively, with a1 ≤ a2) and a bundle of the two goods. This setting has previously been considered analytically intractable. By deriving component good prices as exact algebraic functions of the optimal bundle price, I reduce the multiproduct pricing problem to a univariate nonlinear optimization problem in the bundle price. When the two component goods are sufficiently asymmetric in valuations, the optimal solution is partial mixed bundling (one component good is not sold separately), for which I derive exact conditions and optimal prices. An exact analytical solution is also given for mixed bundling of two information goods (component goods with zero marginal costs). For the general case, I derive a closed-form approximation of the optimal bundle price: pB = 0.5724w1 + 0.5695w2 +...
Analysis of env Sequence Evolution in Human Immunodeficiency Virus-Infected Patients Receiving Therapy with Nonnucleoside Reverse-Transcriptase Inhibitors

Nonnucleoside reverse-transcriptase inhibitors (NNRTIs) can rapidly select for drug-resistant human immunodeficiency virus type 1 (HIV-1) variants, although their effect on HIV-1 quasi-species diversity is unknown. To determine if changes in env gene diversification occur with NNRTI therapy, we used the heteroduplex tracking assay (HTA) to study HIV-1 env sequence diversity in 2 groups of patients: those who were on no therapy or were on chronic antiretroviral therapy and those who had just initiated NNRTIs. Forty-nine paired samples from 46 patients were analyzed. Fourteen of 32 paired samples from the NNRTI group and 9 of 17 paired samples from the control group had HTA changes (P>.10). There was no correlation between HTA change and sampling time interval, baseline virus load, change in virus load, or development of NNRTI resistance. Thus, we found no significant correlation of NNRTI therapy with changes in env HTA patterns, suggesting that these treatments had little short-term impact on HIV-1 quasi-species diversity.
Categorization using chains of examples

People can infer unknown features of a stimulus by retrieving memories of similar examples. It is proposed that we can reason from chains of examples. For example, stimulus A may remind us of B, which reminds us of C. Information about C may then affect reasoning about A. A mathematical model for categorization (extended from the context model of Medin & Schaffer, 1978), using multiple-step chains of reasoning and memory for examples, is presented. In five experiments, subjects memorized feature descriptions of fictional people, then made predictions from incomplete descriptions. Various predictions could be made using one-, two-, or three-step chains of reasoning. These experiments varied in terms of stimulus structure, complexity of test questions, and response method (probability estimate or forced choice). The multiple-step context model, with the assumption that people performed one- and two-step chains of inference, successfully accounted for the results of all five experiments.
The Puzzle of Petitionary Prayer

The fact that our asking God to do something can make a difference to what he does underwrites the point of petitionary prayer. Here, however, a puzzle arises: Either doing what we ask is the best God can do or it is not. If it is, then our asking won’t make any difference to whether he does it. If it is not, then our asking won’t make any difference to whether he does it. So, our asking won’t make any difference to whether God does it. Our asking is therefore pointless. In this paper, we try to solve this puzzle without denying either that God must do the best he can or that petitioning God can make a difference to what he does.
Psychological sense of community: Suggestions for future research

The research on psychological sense of community leads to few firm conclusions. Among these are the idea that psychological sense of community is context specific, must be understood as involving more than individual behaviors, and should be researched at a community level. It is suggested that research on psychological sense of community could best be accomplished using a multidisciplinary approach and that the assumption that psychological sense of community is on the decline in modern American society should be empirically examined. Finally, it is suggested that in order to have a complete understanding of psychological sense of community, we need to begin to research its related construct, a sense of transcendence. © 1996 John Wiley & Sons, Inc.
Models of signalling networks - what cell biologists can gain from them and give to them

Computational models of cell signalling are perceived by many biologists to be prohibitively complicated. Why do math when you can simply do another experiment? Here, we explain how conceptual models, which have been formulated mathematically, have provided insights that directly advance experimental cell biology. In the past several years, models have influenced the way we talk about signalling networks, how we monitor them, and what we conclude when we perturb them. These insights required wet-lab experiments but would not have arisen without explicit computational modelling and quantitative analysis. Today, the best modellers are cross-trained investigators in experimental biology who work closely with collaborators but also undertake experimental work in their own laboratories. Biologists would benefit by becoming conversant in core principles of modelling in order to identify when a computational model could be a useful complement to their experiments. Although the mathematical foundations of a model are useful to appreciate its strengths and weaknesses, they are not required to test or generate a worthwhile biological hypothesis computationally.
Specialized Transduction Designed for Precise High-Throughput Unmarked Deletions in Mycobacterium tuberculosis

ABSTRACT Specialized transduction has proven to be useful for generating deletion mutants in most mycobacteria, including virulent Mycobacterium tuberculosis. We have improved this system by developing (i) a single-step strategy for the construction of allelic exchange substrates (AES), (ii) a temperature-sensitive shuttle phasmid with a greater cloning capacity than phAE87, and (iii) bacteriophage-mediated transient expression of site-specific recombinase to precisely excise antibiotic markers. The methods ameliorate rate-limiting steps in strain construction in these difficult-to-manipulate bacteria. The new methods for strain construction were demonstrated to generalize to all classes of genes and chromosomal loci by generating more than 100 targeted single- or multiple-deletion substitutions. These improved methods pave the way for the generation of a complete ordered library of M. tuberculosis null strains, where each strain is deleted for a single defined open reading frame in M. tuberculosis. IMPORTANCE This work reports major advances in the methods of genetics applicable to all mycobacteria, including but not limited to virulent M. tuberculosis, which would facilitate comparative genomics to identify drug targets, genetic validation of proposed pathways, and development of an effective vaccine. This study presents all the new methods developed and the improvements to existing methods in an integrated way. The work presented in this study could increase the pace of mycobacterial genetics significantly and will immediately be of wide use. These new methods are transformative and allow for the undertaking of construction of what has been one of the most fruitful resources in model systems: a comprehensive, ordered library set of the strains, each of which is deleted for a single defined open reading frame.
Valence Bond Theory of Partly-Filled Conductors

The presently known1,2 π-molecular conductors share important common features. They all contain segregated stacks... A-γA-γA-γ... of anion radicals and/or... D+γD+γD+γ... of cation radicals, as illustrated by A = TCNQ, (tetracyanoquinodimethane) and D = TTF (tetrathiofulvalene). They all crystallize with a single molecule per unit cell along the stack, or high conductivity, axis. They all have partial charge transfer, or γ < 1, in contrast2 to the semiconducting simple salts based on D+ or A- stacks. They are narrow-band systems, with 4t ~ 0.5 eV and π-electron overlaps along the stack of 3.1 – 3.5 A, or just shorter than the van der Waals separation. These common features, rather than differences in low-temperature phases, must guide the development of theoretical models.
Links among inflammation, sexual activity and ovulation Evolutionary trade-offs and clinical implications

Background and objectives: We examined a mechanism that may coordinate trade-offs between reproduction and immune response in healthy women, namely, changes in inflammation across the ovarian cycle. Methodology: We investigated C-reactive protein (CRP), an inflammation marker, across two consecutive ovarian cycles in 61 Bolivian women. Participants provided saliva samples every other day, and dried blood spots on 5–6 days spread across weeks 2–3 of each cycle. Cycles were characterized as ovulatory/anovulatory based on profiles of reproductive hormones. Participants also reported whether they were sexually partnered with a male or sexually abstinent during the study. Results: High early-cycle, but not late-cycle, CRP was associated with anovulation. High inflammation at the end of one cycle was not associated with anovulation in the subsequent cycle. Among ovulatory cycles, women with sexual partners had significantly lower CRP at midcycle, and higher CRP at follicular and luteal phases; in contrast, sexually abstinent women had little cycle-related change in CRP. In anovulatory cycles, partnership had no effect on CRP. CRP varied significantly with socioeconomic status (higher in better-off than in poorer women). Conclusions and implications: These findings suggest that the cycle-specific effect of inflammation on ovarian function may be a flexible, adaptive mechanism for managing trade-offs between reproduction and immunity. Sociosexual behavior may moderate changes in inflammation across the ovarian cycle, suggesting that these shifts represent evolved mechanisms to manage the trade-offs between reproduction and immunity. Clinically, these findings support considering both menstrual cycle phase and sexual activity in evaluations of pre-menopausal women’s CRP concentrations.
Safety of donor milk: a brief report

To review the standard processing and testing of human donors and donor milk and to report the frequency of detected markers of potential harm. This was a retrospective analysis of the data gathered by a donor and human milk screening and monitoring process over a period of 3 years. Screening results from 2011 to the end of 2015 demonstrated that careful history taking resulted in rejection or hold of 29.7% of willing donor candidates. Individual infection screening tests rejected an additional 0.3–2.9 per 1000 donations. DNA fingerprinting of donations eliminated 2 out of 13 491. Drug testing rejected 42 out of 12 408 and dilution or adulteration eliminated 73 out of 4935 donations. Only the dilution rejection rate was significantly higher in the remunerated donors. The details of these results are presented. There are significant risks involved in the collection, processing and distribution of donor milk-based products. The behaviors of the donors, biochemical and genetic screening and milk processing are critical to mitigation of these recognized risks. Testing at this level of rigor appears to be justified.
Involvement of Poly(ADP-Ribosylation) Reactions in Liver Carcinogenesis of Diethylnitrosamine in Rats

Our investigations of the possible involvement of poly(ADP-ribosylation) reaction in liver carcinogenesis were initiated by the evidence indicating that poly(ADP-ribose) participates in DNA damage and repair [1,2] since induction of DNA lesions by carcinogens and their repair have been considered to be closely related to carcinogenesis [3–6]. Previously, we reported enhancement of diethylnitrosamine (DEN) initiation of liver carcinogenesis by inhibitors of NAD+ ADP-ribosyl transferase in rats [7–9]. However, evidence for the direct involvement of the poly(ADP-ribosylation) reaction in the induction of liver carcinomas was lacking. In this paper, we describe a disturbance in NAD ADP-ribosyl transferase-dependent formation of homopolymers of repeating ADP-ribose units from NAD and possible inhibition of repair of DEN damaged DNA by ABA. The foci initiated by DEN and ABA were found to be capable of development into hepatocellular carcinomas without promotion by phenobarbital (PB).