cssi/SciSciGPT-SciSciNet huggingface dataset:
Isotope-edited FTIR of alkaline phosphatase resolves paradoxical ligand binding properties and suggests a role for ground-state destabilization.

Escherichia coli alkaline phosphatase (AP) can hydrolyze a variety of chemically diverse phosphate monoesters while making contacts solely to the transferred phosphoryl groupanditsincomingandoutgoingatoms.Stronginteractions between AP and the transferred phosphoryl group are not presentinthegroundstatedespitetheapparent similarityofthe phosphoryl group in the ground and transition states. Such modest ground-state affinity is required to curtail substrate saturationandproductinhibitionandtoallowefficientcatalysis. To investigate how AP achieves limited affinity for its ground state, we first compared binding affinities of several related AP ligands. This comparison revealed a paradox: AP has a much stronger affinity for inorganic phosphate (Pi) than for related compounds thatare similarto Pigeometricallyand in overall charge but lacka transferable proton.Wepostulated thatthe Piproton couldplay animportant role viatransfer tothe nearbyanion, the active siteserine nucleophile(Ser102),resulting inthe attenuation of electrostatic repulsion between bound Pi and the Ser102 oxyanion and the binding of Pi in its trianionic form adjacent to a now neutral Ser residue. To test this model, isotope-edited Fourier transform infrared (FTIR) spectroscopy was used to investigate the ionic structure of AP-bound Pi. The FTIR results indicate that the Pi trianion is bound and, in conjunction with previous studies of pH-dependent Pi binding and other results, suggest that Pi dianion transfers its proton to the Ser102 anion of AP. This internal proton-transfer results instronger Pibindingpresumably because the additional negative charge on the trianionic Piallows stronger electrostatic interactions within the AP active site and because the electrostatic repulsion between bound Pi and anionic Ser102 is eliminated when the transferred Pi proton neutralizes Ser102. Indeed, when Ser102 is neutralized the Pi trianion binds AP with a calculatedKdofe290fM.Theseresultssuggest thatelectrostaticrepulsionbetweenSer102andnegativelychargedphosphate ester substrates contributes to catalysis by the preferential destabilization of the reaction' sE 3 S ground state.
Resistance to cucumber mosaic virus in potato

Summary Reactions to two subgroup I isolates (Fny-CMV and Pf-CMV) and two subgroup II isolates (A9-CMV and LS-CMV) of cucumber mosaic virus (CMV) were studied in three non tuber-bearing wild potato species (Solanum spp.) of the series Etuberosa, and in two tuber-bearing interspecific potato hybrids and four potato cultivars using graft-inoculation. Three classes of phenotypic reactions (susceptible, hypersensitive, extreme resistance) were observed in the tuber-bearing genotypes. Susceptible genotypes developed mosaic or severe mosaic with leaf malformation and had high CMV titres. Hypersensitive genotypes developed either top necrosis or vein necrosis and/or necrotic spots on apical leaves, and had low CMV titres. Extremely resistant genotypes had no symptoms and no CMV was detected. The hybrid 87HW13.7 (S. tuberosum×S. multidissectum) developed top necrosis specific to infection with Fny-CMV. The hybrid ‘A6’ (S. demissum×S. tuberosum cv. Aquila) was hypersensitive to all CMV isolates tested. Extreme resistance was not functional against all CMV isolates. Neither hypersensitivity nor extreme resistance were related to the CMV subgroup.
Photofragmentation pathways and photodeposition of nanoparticles from a gas phase copper-containing precursor.

Pulsed laser excitation of bis(2,2,6,6-tetramethyl-3,5-heptanedionato)copper(II) (Cu(TMHD)2) in the gas phase produced neutral gaseous copper atoms and nanoparticulate copper deposits on substrates. Copper atoms were formed by the complete dissociation of the ligands from the metal. Time of flight mass spectrometry and resonance enhanced multiphoton ionization spectroscopy were used to study the details of this reaction and led to the discovery of other gaseous fragments that were produced by incomplete fragmentation of the ligands including monoligated species and coordinated ligand fragments. Laser-assisted chemical vapor deposition resulted in monodispersed nanoparticles under 100 nm in diameter. X-ray photoelectron spectroscopy and energy dispersive analysis of X-rays were used to determine the elemental composition of the deposit. The relationships between the photofragmentation pathways and the deposited particles are discussed.
Tracing metal defect relating to yield for VLSI manufacturing

Particles from four stages: prior to metal sputter, after metal sputter, metal photo (ADI) and metal etching (AEI) were detected with KLA inspection tool. Different type defect counts at four stages were discussed in detail. Correlation of die yield and visual defect are analyzed. Also a technical megasonic clean prior to metal sputter which expected to reduced particles during the metal process is discussed. Experimental result shows 53.78% of the visual defects were caused prior to metal sputter, 25% occurs at metal sputter, 13.64% occurs at metal photo and 7.58% occurs at metal etching, respectively. According to the yield sorting results, 40% of visual defect which occurs prior to metal sputter, 25% at metal sputter, 83% at metal photo and 80% at metal etching are considered killer defects, respectively. Megasonic clean before metal sputter cannot reduce particle, even cause yield 3 - 8% drop due to contact resistance rising. All the evidence point out the yield impact relating particle contributed by each stage cannot be ignored.
Electrophoresis of human serum albumin at pH 4.0. III. Interpretation of the electrophoretic behavior of different albumin preparations.

A series of human serum albumin preparations obtained by the fractionation procedures ofCohn were analyzed by free moving boundary electrophoresis at pH 4.0 in acetate buffer (I 0.1), paper electrophoresis at pH 8.6 and 4.0, ultracentrifugation and starch-gel electrophoresis. Most preparations exhibited similar patterns by any one of the three techniques. Albumins that exhibited an inverse ratio of the two moving boundaries fall into two sub-groups, those which could be made to appear as a single moving boundary on electrophoresis and did not reveal any changes on ultracentrifugation and starch-gel electrophoresis, and those which could not be stabilized so as to display a single boundary and exhibited significant changes on ultracentrifugation and starch-gel electrophoresis as compared with the corresponding properties of most albumin preparations. The different ratios of the area of the faster to the slower moving boundary of any human serum albumin preparations, observed on free electrophoresis at pH 4.0 in acetate (I 0.1), can be interpreted largely as the effect of stabilizers (nature and concentration) and of altered isomerization bonds upon the isomerization reaction of the albumin molecule.
Vancomycin dosing in morbidly obese patients.

Objectives and methods: Vancomycin hydrochloride dosing requirements in morbidly obese patients with normal renal function were computed to determine the dose of vancomycin necessary to achieve target steady-state peak and trough concentrations and compared with a normal weight population. Results: Morbidly obese patients [total body weight (TBW) 165 kg, ideal body weight (IBW) 63 kg] required 31.2 mg · kg−1 · d−1 TBW or 81.9 mg · kg−1 · d−1 IBW to achieve the target concentrations. Normal weight patients (TBW 68.6 kg) required 27.8 mg · kg−1 · d−1 to achieve the same concentrations. Because of altered kinetic parameters in the morbidly obese patients (obese: t1/2=3.3 h, V=52 l, CL =197 ml · min−1; normal: t1/2=7.2 h, V=46 l, CL=77 ml · min−1, 20 of 24 patients required q8h dosing (1938 mg q8h) compared with q12h dosing (954 mg q12h) in all normal weight patients in order to avoid trough concentrations that were too low for prolonged periods. There was a good correlation between TBW and CL, but only fair correlation between TBW and V. Conclusion: Doses required to achieve desired vancomycin concentrations are similar in morbidly obese and normal weight patients when TBW is used as a dosing weight for the obese (approximately 30 mg · kg−1 · d−1). Shorter dosage intervals may be needed when dosing morbidly obese patients so that steady-state trough concentrations remain above 5 μg · ml−1 in this population. Because of the large amount of variation in required doses, vancomycin serum concentrations should be obtained in morbidly obese patients to ensure that adequate doses are being administered. Dosage requirements for morbidly obese patients with renal dysfunction require further study.
Plagiarism and Academic Integrity Systems

The role of librarians has been neglected in the academic integrity literature. A probe of the plagiarism problem can illuminate potential roles for librarians beyond that of technical support of faculty. Librarians should assert the centrality of their roles in bridging tradition and adaptability as they provide robust platforms for guardianship of accumulated knowledge and the creation of new knowledge. Thinking strategically and organizationally will benefit both librarians and the academy more broadly.
SYNTHETIC MODIFICATION OF THE ESCHERICHIA COLI CHROMOSOME : ENHANCING THE BIOCATALYTIC CONVERSION OF GLUCOSE INTO AROMATIC CHEMICALS

The yield of l-phenylalanine, racemic phenyllactic acid, and prephenic acid synthesized from glucose has been doubled and contamination of these aromatic end products by biosynthetic intermediates drastically reduced. These improvements resulted from increasing the in vivo catalytic activity of specific enzymes in the common pathway of aromatic amino acid biosynthesis by chromosomal modification of Escherichia coli. The centerpiece of these changes was the synthesis of a multigene cassette carrying aroA (encoding EPSP synthase), aroC (encoding chorismate synthase), and aroB (encoding DHQ synthase). Chromosomal insertion of the synthesized multigene cassette into E. coli KAD29B, a strain having a mutation in the tyrR locus which relieves transcriptional repression of aroL (encoding shikimate kinase), resulted in biocatalysts KAD1D and KAD11D. Improved catalytic activities of individual common pathway enzymes have previously been accomplished with extrachromosomal plasmids encoding the appropriate loci. By ...
Discovery of native autoantigens via antigen surrogate technology: application to type 1 diabetes.

A fundamental goal in understanding the mechanisms of autoimmune disease is the characterization of autoantigens that are targeted by autoreactive antibodies and T cells. Unfortunately, the identification of autoantigens is a difficult problem. We have begun to explore a novel route to the discovery of autoantibody/autoantigen pairs that involves comparative screening of combinatorial libraries of unnatural, synthetic molecules for compounds that bind antibodies present at much higher levels in the serum of individuals with a given autoimmune disease than in the serum of control individuals. We have shown that this approach can yield “antigen surrogates” capable of capturing disease-specific autoantibodies from serum. In this report, we demonstrate that the synthetic antigen surrogates can be used to affinity purify the autoantibodies from serum and that these antibodies can then be used to identify their cognate autoantigen in an appropriate tissue lysate. Specifically, we report the discovery of a pepto...
Reexamination of evidence for a radiatively decaying neutrino

Large-aperture low-dispersion exposures obtained with the IUE short-wavelength camera have been reanalyzed to examine the possibility of using nonstandard electroweak models to explain the steplike signal of 5-sigma significance in the cosmic background claimed by Auriemma et al. (1985). The present results show that no evidence yet exists for the postulated cosmic UV radiation from neutrino decay. Error bars of the order of 20,000 photons/sq cm per s per A per sr are found for the brightnesses of Auriemma et al., and it is suggested that their steps may be due to fixed pattern noise in the detector rather than to a cosmic signal.
CAUSATIVE AGENT OF A SPONTANEOUSLY ORIGINATING VISCERAL TUMOUR IN THE NEWT, TRITURUS.

A SPONTANEOUS visceral tumour was found about ten years ago by one of us in the Japanese newt, Triturus pyrrhogaster1. The original animal showed a number of tumorous nodules in the liver and spleen ranging in size from tiny ones to the largest measuring 1.1 cm × 0.7 cm × 0.4 cm. The tumour was transplanted through many generations to other pyrrhogaster; and it was classified as a lymphosarcoma on the basis of its histogenesis after transmission2. It may be transmitted not only to pyrrhogaster but also to other species of newts and salamanders3 and, as we have found recently, to the adult anuran, Xenopus laevis (unpublished). Moreover, the supernatant of tumour homogenates retained the capacity to produce tumour even after the homogenates were frozen and thawed and dried in vacuo. Evidence presented here points to a bacterium as the likely agent.
Finite difference identification of noisy distributed systems using scanning measurements

Most of the present-day literature concerned with identification theory and techniques is directed toward lumped parameter systems, and many comprehensive surveys of the field are available, (see Refs. 1 and 2) for example(s)). Relatively little has appeared in the literature concerning distributed identification, and even more noticeable is the scarcity of papers dealing with systems described by the one-dimensional wave equation. Perdeauville and Goodson (Ref. 3) were perhaps the first researchers with a workable but time consuming method for the identification of coefficients of the wave equation. Fairman and Shen (Raf. 4) also considering the wave equation, used the technique of finite differencing to approximate spatial derivatives, and Poisson filter chains to approximate temporal derivatives.
Absorption kinetics of local anesthetics from rat subcutaneous tissue. II. Effects of vasodilators

The effects of acetylcholine at two concentrations (10−4g/ml, solution A, and 5.0×10−5g/ml, solution B) and methacholine (10−4g/ml) on the subcutaneous absorption kinetics of lidocaine, diethylaminoacetanilide (I), and 5-methyl-diethylaminoacetanilide (II) were investigated using the rat model of Ballard and Menczel (8) under uncontrolled pH conditions (isotonic saline). The absorption half-life measurements were made before and after the addition of each vasodilator solution to the subcutaneous absorption cell containing the three local anesthetics. Equivalent concentrations of acetylcholine (solution A) and methacholine significantly decreased the absorption half-lives of lidocaine, I, and II, whereas solution B of acetylcholine significantly decreased the absorption half-lives of lidocaine and I only. Lidocaine and I were affected to the same extent (percent decrease in absorption half-life) by each vasodilator solution. The percent decrease in absorption half-life of II was significantly lower than that of lidocaine and I in the case of all three vasodilator solutions. Solution A and solution B of acetylcholine did not produce a significantly different percent decrease in absorption half-life of either lidocaine, I, or II. Likewise, no significant difference in the effects of acetylcholine (solution A) and methacholine was observed. The role of blood flow at the absorption site is discussed.
Uptake and loss of chlorpyrifos and atrazine by Juncus effusus l. in a mesocosm study with a mixture of pesticides.

Aquatic organisms in agricultural regions typically are exposed to mixtures of agrochemicals, and effects are not adequately predicted from results of single pesticide exposure studies. Thus, a mesocosm study was designed to examine the fate and effects of varying mixtures of three pesticides (chlorpyrifos, atrazine, and monosodium methanearsonate) and mercury-contaminated sediment to the common freshwater macrophyte Juncus effusus L. Exposure doses of pesticides added to mesocosms represented those that might be encountered in a typical runoff or direct spray application. This study reports the uptake and loss of chlorpyrifos and atrazine in the leaves of J. effusus after a single and a repeated dose of the chemical mixture over 94 d. The measured chlorpyrifos levels in leaves were highest on day 1, but levels in both leaves and water dropped rapidly and were at background levels by day 32. Atrazine remained near nominal concentrations in the water through day 16 and reached maximum accumulation in the leaves on day 16. The chemical mixture affected uptake of chlorpyrifos more strongly than atrazine as measured by differences in uptake variability. After the second dose, J. effusus showed a similar uptake pattern for both compounds, although somewhat faster, to that observed after the first dose, with no diminished capacity for uptake of either compound. The greater volatility of chlorpyrifos, the higher solubility of atrazine, and the more efficient transport of atrazine to the root zone are characteristics that are consistent with the differences observed in their uptake and loss behavior.
The Gilbert Islands (Republic of Kiribati) earthquake swarm of 1981—1983

Abstract A major swarm of intraplate earthquakes at the southeastern end of the Gilbert Islands Chain (3.5°S, 177.5°E) commenced in December 1981 and lasted through March 1983. No seismicity had been reported in the historical record in this region prior to 1981, but during the swarm 217 events with mb ⩾ 4.0 were located by the NEIS, with 86 events having mb ⩾ 5.0. The source region is quite remote, and the uniform detection level for the NEIS is for mb ⩾ 4.8. A b-value of 1.35 is found for the swarm using the maximum likelihood method. Four events in the sequence were large enough (mb = 5.6−5.9) to determine focal mechanisms teleseismically using body- and surface-wave analysis. These events are found to have a range of mechanisms, from predominantly thrust with a significant oblique component, to purely strike-slip. The compression axes are consistent for all four events, with horizontal orientation trending NNE-SSW. This orientation is perpendicular to the direction of plate motion. The events are located at depths between 15 and 20 km placing them deep in the oceanic crust or in the upper mantle. No obvious bathymetric feature can be related to the fault plane orientations, though there is an offset in the island chain near the epicenters. While some characteristics of the swarm suggest a magmatic origin, the nature of the focal mechanisms, the location of the swarm, and the large accumulated moment release of the sequence favor a tectonic origin.
Renal Cell Carcinoma Genetic Analysis by Comparative Genomic Hybridization and Restriction Fragment Length Polymorphism Analysis

AbstractPurpose: To compare comparative genomic hybridization (CGH) with restriction fragment length polymorphism (RFLP) analysis in renal cell carcinoma (RCC).Materials and Methods: Fifteen RCC specimens were analyzed by both CGH and RFLP analysis at 18 loci.Results: Restriction fragment length polymorphism analysis was informative on 90 chromosomal arms. Allelic imbalance was identified on 27 chromosomal arms by RFLP and on 26 arms by CGH. Data from CGH and RFLP demonstrated a high degree of concordance (p less than 0.001). Comparative genomic hybridization identified previously documented areas of interest in RCC as well as potential new areas of interest including loss of genetic material on chromosome 2 and gains of genetic material on chromosome 16p.Conclusions: Comparative genomic hybridization can successfully be performed in RCC As it surveys the entire genome simultaneously, it may be more efficient than conventional cytogenetics or RFLP analysis in analyzing RCC.
Effect of task difficulty and interstimulus interval on blink parameters

The effects of task difficulty and interstimulus interval (ISI) on blink rate, blink latency and blink duration, were studied in a modified Sternberg memory task in which either two or six characters were to be memorized. Stimuli were presented in ISI blocks at either 5.3 or 9.3 s (SOAs of 6 or 10 s). While blink rate and blink duration declined prior to each stimulus, the difficulty of the expected task (the length of the memory set) did not affect the rate of decline or the final prestimulus level. Concerning ISI, blink rate declined more rapidly during shorter ISIs but the final prestimulus level, as was the case with task difficulty, was unaffected by the ISI duration. Presentation of the 6-character memory set produced a marked immediate inhibition of blinking. The data suggest that the encoding of visual stimuli is more akin to processes invoked in preparation for input than to ensuing processing stages since both encoding as well as preparation are accompanied by inhibition of blinking.
USE OF URETEROSCOPY AND HOLMIUM:YAG LASER IN PATIENTS WITH BLEEDING DIATHESES

Abstract Objectives. To assess the safety and efficacy of ureteroscopy and holmium laser in patients with known bleeding diatheses and upper tract calculi or transitional cell carcinoma (TCC). Methods. Eight patients with stone disease and 1 patient with upper tract TCC were treated ureteroscopically with the holmium laser. The mean age was 58.3 years (range 42 to 74). Six patients were receiving Coumadin, with a mean international normalized ratio (INR) of 2.1 (normal INR less than 1.1). Two patients were thrombocytopenic, and 1 had von Willebrand’s disease. None of the bleeding diatheses were corrected before surgery. Semirigid or flexible ureteroscopes were used to access the ureter or intrarenal collecting system. The holmium laser was used to fragment calculi or ablate tumor. Results. Only 1 patient had a postoperative bleeding complication related to the procedure, involving an episode of oliguria secondary to a small ureteral clot. This cleared without surgical intervention. Another patient developed an episode of epistaxis after administration of ketorolac for pain. Six of 7 patients who underwent laser fragmentation for calculi were stone free on follow-up intravenous urogram at 1 month, and no tumor recurrence was noted in the patient with TCC (follow-up of 4 months). Conclusions. Ureteroscopy allowed excellent access to all regions of the upper tracts, and holmium laser fragmentation of calculi or ablation of tumor was effective in managing each particular problem. Use of the holmium laser with ureteroscopic access provides a safe and acceptable combination for treating upper tract pathology in patients with uncorrected bleeding diatheses. As a result, these patients can avoid added costs of extended hospital stay and risks associated with transfusions.
Model predictive control with signal temporal logic specifications

We present a mathematical programming-based method for model predictive control of discrete-time cyber-physical systems subject to signal temporal logic (STL) specifications. We describe the use of STL to specify a wide range of properties of these systems, including safety, response and bounded liveness. For synthesis, we encode STL specifications as mixed integer-linear constraints on the system variables in the optimization problem at each step of a model predictive control framework. We present experimental results for controller synthesis for building energy and climate control.
Sequence Discrimination by DNA-binding Domain of ETS Family Transcription Factor PU.1 Is Linked to Specific Hydration of Protein-DNA Interface

PU.1 is an essential transcription factor in normal hematopoietic lineage development. It recognizes a large number of promoter sites differing only in bases flanking a core consensus of 5′-GGAA-3′. DNA binding is mediated by its ETS domain, whose sequence selectivity directly corresponds to the transactivational activity and frequency of binding sites for full-length PU.1 in vivo. To better understand the basis of sequence discrimination, we characterized its binding properties to a high affinity and low affinity site. Despite sharing a homologous structural framework as confirmed by DNase I and hydroxyl radical footprinting, the two complexes exhibit striking heterogeneity in terms of hydration properties. High affinity binding is destabilized by osmotic stress, whereas low affinity binding is insensitive. Dimethyl sulfate footprinting showed that the major groove at the core consensus is protected in the high affinity complex but accessible in the low affinity one. Finally, destabilization of low affinity binding by salt is in quantitative agreement with the number of phosphate contacts but is substantially attenuated in high affinity binding. These observations support a mechanism of sequence discrimination wherein specifically bound water molecules couple flanking backbone contacts with base-specific interactions in a sequestered cavity at the core consensus. The implications of this model with respect to other ETS paralogs are discussed.
EXIT chart analysis of turbo-BLAST receivers in Rayleigh fading channels

Turbo-BLAST is an advanced space-time layered architecture developed to approach the capacity limit of multiple-input multiple-output (MIMO) systems. Various multiuser detection (MUD) techniques have been explored in conjunction with turbo-BLAST to combat cochannel interference (CCI) and improve significantly the performance of MIMO systems in a multicell structure (Dai, H. et al., IEEE Trans. Wireless Commun.. vol.3. p.442-53, 2004). We study the extrinsic information transfer (EXIT) functions of several such turbo-BLAST receivers. We show that the EXIT functions, which work primarily for AWGN channels, are not accurate in giving quantitative performance estimates in a fading environment. A method that copes with this problem and yields reasonably accurate estimates of convergence rate and bit-error-rate is proposed. The performance of different turbo-BLAST receivers is compared in both single-cell and multicell scenarios.
'Lighting tomorrow with today': towards a (strategic) sustainability revolution

Galbreath (2009), recognising the need for firms to more consciously link sustainability to core strategy, developed a sustainability-strategic issues framework. This article reinforces this framework by making assessment and feedback integral to the sustainable strategy process. Additional opportunities for sustainable competitive advantage through sustainability and beyond Galbreath are offered here. They are rooted in the core competencies of the firm and are made integral to the strategic management process. Galbreath is tentative as to whether the sustainability movement is like the industrial revolution in scope. This article seeks to reinforce that a revolution of just such a magnitude is at hand.
Pricing Communication Services with Delay Guarantee

Although pricing communication services has received attention, there has been little work where quality-of-service (QoS) guarantees are incorporated into ex ante pricing of communication links. In recent years, however, data networks providing services with QoS guarantees have become quite popular. We study optimal pricing for communication links provided over packet-switching networks with explicit QoS guarantees in terms of an expected per-packet delay. We first develop a pricing scheme for multiple classes of service when the delay guarantees are fixed and exogenously determined and analyze this scheme with one and two classes. Subsequently, we extend this analysis to the case where a provider can choose her own QoS parameters. We also examine long-run pricing and capacity planning for one and two classes of service. Finally, we consider other QoS guarantees such as jitter, packet-loss ratio and maximum delay.
Dynamic Sensor Management for Multisensor Multitarget Tracking

We study the problem of sensor scheduling for multisensor multitarget tracking?to determine which sensors to activate over time to trade off tracking error with sensor usage costs. Formulating this problem as a Partially Observable Markov Decision Process (POMDP) gives rise to a non-myopic sensor-scheduling scheme. Our method combines sequential multisensor Joint Probabilistic Data Association (MS-JPDA) and particle filtering for belief-state estimation, and uses simulation-based Q-value approximation method for ?lookahead.? The example of focus in this paper involves the activation of multiple sensors simultaneously for tracking multiple targets, illustrating the effectiveness of our approach.
Diffeomorphism parameters as coordinates in string field theory

Abstract Those modes ƒ a of the two-dimensional world-sheet metric g ab = ƒ ∗ ( exp (2σ)δ ab ) which represent reparametrizations o f the boundaries do not decouple in the path integral for off-shell Green's functionals. Instead, they can be used to fix the string field theory gauge. They can also be used as new coordinates in string field theory and are shown here to be equivalent to the new coordinates of Baulieu, Siegel, and Zwiebach.
Paraffin surfaces for culture-based detection of mycobacteria in environmental samples

In this paper, we describe the development of paraffin surfaces for culture-based detection of mycobacteria in environmental samples. The surfaces use the well-described paraffinophilic nature of mycobacteria to rapidly and selectively differentiate them from non-target microorganisms. New methods of depositing and patterning paraffin were developed, including using butanol or a heat gun to generate molten paraffin that was subsequently deposited by spin coating and patterned by wet and dry etching techniques. Using these techniques, 18 mm glass wafers with paraffin films of 10–70 µm were fabricated and subsequently etched to form different patterns. Prototype paraffin surfaces were experimentally tested to demonstrate the concept of rapid and selective detection of mycobacteria in environmental samples collected from a municipal sewage treatment plant. Our successful demonstration of the culture-based detection on paraffin substrates presents an alternative approach for tracking microorganisms in complex environmental samples.
The higher risk of bleeding in lung transplant recipients from bronchoscopy is independent of traditional bleeding risks: results of a prospective cohort study.

Study objective To determine whether recipients of lung transplants have a higher risk of bleeding from fiberoptic bronchoscopy (FOB) than other patients who undergo the procedure. Design Prospective cohort study. Setting Bronchoscopy services of Johns Hopkins Hospital, a tertiary referral center and Johns Hopkins Bayview Medical Center, a community hospital. Patients All adult patients (18 years) who underwent FOB between July 1, 1996 and June 30, 1997 by the full-time pulmonary medicine staff were included. A total of 720 procedures were performed, including 38 in lung transplant recipients. Measurements Bleeding was assessed by reviewing physician reports of bloody drainage after the procedure and whether the procedure was terminated early for bleeding. Patient reports of hemoptysis were assessed using questionnaires administered pre- and post-FOB. Predictor variables included patient demographics, bleeding parameters (platelets, prothrombin time, and activated partial thromboplastin time), immunosuppressive medications, aspirin use, use of transbronchial biopsy, and the time length of the procedure. Results Lung transplant recipients were significantly more likely to have used aspirin prior to FOB (18.4 vs 7.2%, p 25 mL of blood loss (44.5 vs 17.5%, p Conclusions Lung transplant recipients are at higher risk of bleeding from bronchoscopy than are other patients. This propensity to bleed is independent of coagulation parameters, platelet count, immunosuppressive medication use, aspirin use, or performance of transbronchial biopsy. The higher risk of bleeding should be considered when assessing the risks and benefits of bronchoscopy in lung transplant recipients.
Structural basis of the induction of unscheduled DNA synthesis in rat hepatocytes

The structural basis of the induction of unscheduled DNA synthesis (UDS) in isolated rat hepatocytes was studied with CASE, an expert system. The analysis identified a number of structural determinants associated with the induction of UDS. These structures accounted for 97.3% of the activity of the chemicals in the database. Further analyses indicated that the concordance between prediction and experimentally determined UDS of molecules not in the learning set is > 82%. A comparison of predictions of UDS and mutagenicity in Salmonella indicated that there is a dichotomy between these activities. The basis of this lack of coincidence remains to be elucidated.
Learning Sequential Structure in Simple Recurrent Networks

We explore a network architecture introduced by Elman (1988) for predicting successive elements of a sequence. The network uses the pattern of activation over a set of hidden units from time-step t-1, together with element t, to predict element t+1. When the network is trained with strings from a particular finite-state grammar, it can learn to be a perfect finite-state recognizer for the grammar. Cluster analyses of the hidden-layer patterns of activation showed that they encode prediction-relevant information about the entire path traversed through the network. We illustrate the phases of learning with cluster analyses performed at different points during training.
Targeting Aldehyde Dehydrogenase: a Potential Approach for Cell labeling

Abstract Introduction To advance the science and clinical application of stem cell therapy, the availability of a highly sensitive, quantitative and translational method for tracking stem cells would be invaluable. Because hematopoetic stem cells express high levels of the cytosolic enzyme aldehyde dehydrogenase-1A1 (ALDH1), we sought to develop an agent that is specific to ALDH1 and thus to cells expressing the enzyme. Such an agent might be also helpful in identifying tumors that are resistant to cyclophosphomide chemotherapy because ALDH1 is known to be responsible for this resistance. Methods We developed schemes for the synthesis of two radioiodinated aldehdyes — N -formylmethyl-5-[*I]iodopyridine-3-carboxamide ([*I]FMIC) and 4-diethylamino-3-[*I]iodobenzaldehyde ([*I]DEIBA)—at no-carrier-added levels from their respective tin precursors. These agents were evaluated using pure ALDH1 and tumor cells that expressed the enzyme. Results The average radiochemical yields for the synthesis of [ 125 I]FMIC and [ 125 I]DEIBA were 70±5% and 47±14%, respectively. ALDH1 converted both compounds to respective acids suggesting their suitability as ALDH1 imaging agents. Although ability of ALDH1 within the cells to oxidize one of these substrates was shown, specific uptake in ALDH-expressing tumor cells could not be demonstrated. Conclusion To pursue this approach for ALDH1 imaging, radiolabeled aldehydes need to be designed such that, in addition to being good substrates for ALDH1, the cognate products should be sufficiently polar so as to be retained within the cells.
Low-loss CPW on low-resistivity Si substrates with a micromachined polyimide interface layer for RFIC interconnects

The measured and calculated propagation constant of coplanar waveguide (CPW) on low-resistivity silicon (1 /spl Omega//spl middot/cm) with a micromachined polyimide interface layer is presented in this paper. With this new structure, the attenuation (decibels per centimeter) of narrow CPW lines on low-resistivity silicon is comparable to the attenuation of narrow CPW lines on high-resistivity silicon. To achieve these results, a 20-/spl mu/m-thick polyimide interface layer is used between the CPW and the Si substrate with the polyimide etched from the CPW slots. Only a single thin-film metal layer is used in this paper, but the technology supports multiple thick metal layers that will further lower the attenuation. These new micromachined CPW lines have a measured effective permittivity of 1.3. Design rules are presented from measured characteristics and finite-element method analysis to estimate the required polyimide thickness for a given CPW geometry.
Paper versus Electronic: Challenges Associated with Physicians - Usage of Electronic Medical Records

This study builds on the theory of planned behavior, institutional and diffusion theories to investigate physicians? attitudes and usage behaviors of electronic medical records (EMR). Interviews with seventeen physician-residents enrolled in a Family Practice residency program and eight attending physicians in the same clinic showed that most physicians held rather negative attitudes regarding the EMR system. EMR was often times seen as an intrusion in the patient-physician interaction. Other findings relate to the impacts EMR had on physicians? time, expertise, physicians? learning, the length (and sometimes the accuracy) of the clinical notes. Challenges associated with behavioral control issues such as availability of computers and the physical positioning of computers are shown to be very important in the context of this case. Physician-residents have to use EMR because of its mandatory nature, however, if they had a choice or the power, the majority of physicians would use the paper chart.
Separation and identification of some chemical warfare degradation products using electrospray high resolution ion mobility spectrometry with mass selected detection

High resolution electrospray ion mobility spectrometry (IMS) was used to analyze chemical warfare degradation products from liquid samples. For each degradation product analytical figures of merit for the technique were determined and each response ion was identified by mass spectrometry. From these data, reduced mobility constants ( K0) for a number of compounds were calculated for the first time. The detection limits for most of the compounds were less than 1 ppm in the positive mode. The more electronegative compounds such as the phosphonic acids were found to be more sensitive in the negative mode with detection limits in the low ppb range. This work represents the first published data of negative ion high resolution ion mobility spectrometry and is only the second publication in which negative ions have been produced and detected using atmospheric pressure electrospray ion mobility spectrometry. Linear response ranges were generally about two orders of magnitude and dynamic response ranges were approximately four orders of magnitude. Four degradation products from the G-type nerve agent differing only by a methyl group were separated with baseline resolution in less than 15 ms by IMS. This same mixture of components was separated and detected from a spiked Palouse river water sample demonstrating the potential of the technique to analyze chemical warfare degradation products from complex matrices. This represents the first quantitative study ever published for high resolution atmospheric pressure electrospray ion mobility spectrometry/mass spectrometry. ©2000 Elsevier Science B.V. All rights reserved.
Who wants to have a career in science or math? Exploring adolescents' future aspirations by gender and race/ethnicity.

Our study utilizes data from a national cohort of eighth-grade students to consider how different gender and racial/ethnic subgroups compare to White males in their likelihood to aspire toward a science or math occupation and examine the roles that self-concept, enjoyment, and achievement may play in shaping disparities at this early point in occupational trajectories. We find that the importance of enjoyment, self-concept, and achievement in explaining disparities in science career aspirations relative to White males varies according to the female subgroup considered, such that no singular story applies to females across different racial/ethnic backgrounds. For math, White and Hispanic females remain approximately half as likely as White males to aspire to a math occupation regardless of all indicators we consider. Finally, Black and Hispanic adolescent boys have generally comparable aspirations toward future careers in science and math as their White male peers, despite notably large differences in achievement. We discuss implications of our results for future research on equity. © 2010 Wiley Periodicals, Inc. Sci Ed95: 458–476, 2011
Unraveling the mysteries of dog evolution

The increased battery of molecular markers, derived from comparative genomics, is aiding our understanding of the genetics of domestication. The recent BMC Biology article pertaining to the evolution of small size in dogs is an example of how such methods can be used to study the origin and diversification of the domestic dog. We are still challenged, however, to appreciate the genetic mechanisms responsible for the phenotypic diversity seen in 'our best friend'.
Neogene Planktonic Events and Radiometric Scale, California: ABSTRACT

More than seven significant events are recorded by planktonic microfossils of the Neogene for the eastern Pacific and the Pacific Coast of North America, correlated with provincial microfaunal stages and a radiometric scale based on available K-Ar dates. (1) There was a significant evolution from Globigerina concinna to Globigerina bulloides about 17 m. y. ago marking the approximate Relizian-Luisian boundary of California. (2) The youngest known dextral specimens of Globoquadrina altispira occur about 12 m. y. ago correlating with part of the upper lower Mohnian. (3) The youngest known sinistral specimens of Globorotalia maveri occur about 12 m. y. ago, correlating with part of the lower Mohnian. (4) The radiolarian, Prunopyle titan, spans the interval of about 15-10 m. . B.P., becoming extinct before the end of the Miocene (Delmontian). (5) The transition from Sphaeroidinellopsis to Sphaeroidinella, the SPHAEROIDINELLA DEHISCENS DATUM, and the introduction of Globorotalia inflata marks the Miocene-Pliocene boundary (approximate Delmontian-Repetto boundary) and is about 9 m. y. B.P. (6) Globorotalia (Truncorotalia) truncatulinoides ranges from basal Pliocene to Recent; however, it is most characteristic End_Page 453------------------------------ of the 5-3 m. y.-interval or upper Pliocene of southern California. (7) Coiling preferences of Globigerina pachyderma are predominantly dextral during the past 11,000 years, mostly sinistral from this point back to 3 m. y. B.P. (Pleistocene), dextral although somewhat variable in the 3-5 m. y. interval (upper Pliocene), sinistral in the 5-7 m. y. interval (middle Pliocene), dextral in the 7-10 m. y. interval (lower Pliocene and uppermost Miocene), sinistral in the 10-11 m. y. interval (upper Mohnian-Delmontian transition), and dextral in its earliest occurrences of about 11-12 m. y. B.P. (within the Mohnian). End_of_Article - Last_Page 454------------
Central neural circuits for the light-mediated reflexive control of choroidal blood flow in the pigeon eye: a laser Doppler study.

Electrical stimulation in pigeons of the input from the medial subdivision of the nucleus of Edinger-Westphal (EWM) to the choroidal neurons of the ipsilateral ciliary ganglion, which themselves have input to the choroidal blood vessels of the ipsilateral eye, increases choroidal blood flow (ChBF). Since the EWM receives input from the contralateral suprachiasmatic nucleus (SCN), which in turn receives contralateral retinal input, the present study sought to determine if activation of the SCN by microstimulation or by retinal illumination of the contralateral eye would also yield increases in ChBF in that same eye. Using laser Doppler flowmetry (LDF) to measure ChBF, we found that electrical activation of the contralateral SCN by 100-Hz anodal pulse trains yielded increases in ChBF that were stimulus related and proportional to the stimulating current. These increases in ChBF elicited by the SCN stimulation were accompanied by increases in choroidal volume (vasodilation), but not by increases in systemic blood pressure. Furthermore, the increases could be blocked reversibly by lidocaine injection into the EWM. These results suggest that the increases in ChBF in the eye contralateral to the SCN stimulation were specifically mediated by the SCN-EWM pathway. Retinal illumination with a fiber optic light source was also found to increase ChBF in the illuminated eye, and these effects too could be blocked reversibly with lidocaine injection into the EWM or permanently by the EWM lesion. Control studies confirmed that the light-elicited increases were mediated by increases in choroidal volume (i.e. vasodilation), were not accompanied by systemic blood pressure increases, and were not artifactually generated by transocular illumination of the LDF probe. Thus, the SCN-EWM circuit may be involved in regulating ChBF in response to the level of retinal illumination and/or the visual patterns falling on the retina.
Shifting Cultivation and Deforestation in Tropical Africa: Critical Reflections

Shifting cultivation is the agricultural technique employed by the majority of farmers in the tropical regions of Africa. The dominant narrative recited by policy experts, non-governmental organizations and many scientists is that this practice is a principal cause of deforestation in tropical Africa. This article unpacks the various elements of this narrative and explores whether there is any evidence to substantiate it in West and Central Africa. The results challenge the conventional wisdom that shifting cultivation is leading to accelerating deforestation in tropical Africa.
Complex Serology and Immune Response of Mice to Variant High-Molecular-Weight O Polysaccharides Isolated from Pseudomonas aeruginosa Serogroup O2 Strains

The O antigen of the Pseudomonas aeruginosa lipopolysaccharide is the optimal target for protective antibodies, but the unusual and complex nature of their sugar substituents has made it difficult to define the range of these structures needed in an effective vaccine. Most clinical isolates of P. aeruginosa can be classified into 10 O-antigen serogroups, but slight chemical differences among O polysaccharides within a serogroup give rise to subtype epitopes. These epitopes could impact the reactivity of O-antigen-specific antibodies, as well as the susceptibility of a target strain to protective, opsonic antibodies. To define parameters of serogroup and subtype-epitope immunogenicity, antigenicity, and surface expression on P. aeruginosa cells, we prepared high-molecular-weight O-polysaccharide vaccines from strains of P. aeruginosa serogroup O2, for which eight structurally variant O antigens expressing six defined subtype epitopes (O2a to O2f) have been identified. A complex pattern of immune responses to these antigens was observed following vaccination of mice. The high-molecular-weight O polysaccharides were generally more immunogenic at low doses (1 and 10 μg) than at a high dose (50 μg) and usually elicited antibodies that opsonized the homologous strain for phagocytic killing. Some of the individual polysaccharides elicited cross-opsonic antibodies to a variable number of strains that express all of the defined serogroup O2 subtype epitopes. Combination into one vaccine of two antigens that individually elicited cross-reactive opsonic antibodies to most members of the O2 serogroup inhibited, instead of enhanced, the production of antibodies broadly reactive with most serogroup O2 subtype strains. Thus, immune responses to P. aeruginosa O antigens may be restricted to a limited range of epitopes on structurally complex O antigens, and combining multiple related antigens into a single vaccine formulation may inhibit the production of those antibodies best able to protect against most P. aeruginosa strains within a given O-antigen serogroup.