cssi/SciSciGPT-SciSciNet huggingface dataset:
Storm-induced response of a nearshore-bar system

Abstract A nearshore-bar system was surveyed periodically through a storm and the following recovery period. The data showed a very rapid response of morphology to changing wave conditions and allowed various models on bar formation to be tested. Under low-energy conditions prior to the storm a small bar was surveyed 13 m offshore. Both the high reflectivity of the beach and the cross-shore distance to the bar are consistent with a model of sediment convergence at the node or antinode of a standing wave of incident period. Such a small-scale bar may be a common feature on beaches with steep foreshores and more gentle offshore slopes. With the increase in wave height during the storm, the bar became better developed and migrated offshore at rates up to 2.2 m h−1. The bar maintained its form in that the ratio of trough depth to crest depth ( h t h c ) remained roughly constant. The bar was in no way related to processes which would cause the convergence of sediment in the breaker zone; through most of the storm the bar-crest distance offshore was typically only 10% of the surf-zone width. Analysis of the bar distance offshore in terms of a standing wave motion showed that the causative wave period must have been much longer than that of incident waves, probably on the order of a minute. Surf-zone wave data showed significant energy in the infragravity band at these periods although no definite link has been made. After the height of the storm, the bar had a crescentic morphology. The development of this morphology occurred very rapidly with parts of the bar migrating onshore at rates up to 1.2 m h−1. In contrast to the storm, during the recovery period h t h c varied by nearly a factor of three. Analysis of the offshore and longshore length scales showed the bar to be similar to one which would be generated by a standing mode 1 edge wave of period on the order of one minute.
Variation in Type Appraisal Scores Due to Sire and Herd Effects

Summary Type appraisal scores on about 1,400 two-year-old and 4,080 older cows for 34 management and type characteristics were analyzed to determine the relative influence of sire and herd effects. Most traits could be scored in from three to Five categories. Estimates of within herd heritability were less than 10% for most traits. Components of variance for herd effects were also less than 10% for most traits. Exceptions are listed below. The management traits of resistance to mastitis and ketosis and of milking speed had heritabilities of about 25%. The body characteristics of dairy character, shoulder tightness, depth of body, and upstandingness also had heritability estimates of 20% or slightly greater. Heritability estimates for levelness of udder floor, depth of udder, strength of rear and fore udder attachment also were in the region of 25%.
A Role for the Geomagnetic Field in Cell Regulation

We advance the hypothesis that biological systems utilize the geomagnetic field (GMF) for functional purposes by means of ion cyclotron resonance-like (ICR) mechanisms. Numerous ICR-designed experiments have demonstrated that living things are sensitive, in varying degrees, to magnetic fields that are equivalent to both changes in the general magnetostatic intensity of the GMF, as well as its temporal perturbations. We propose the existence of ICR-like cell regulation processes, homologous to the way that biochemical messengers alter the net biological state through competing processes of enhancement and inhibition. In like manner, combinations of different resonance frequencies all coupled to the same local magnetic field provide a unique means for cell regulation. Recent work on ultraweak ICR magnetic fields by Zhadin and others fits into our proposed framework if one assumes that cellular systems generate time-varying electric fields of the order 100 mV/cm with bandwidths that include relevant ICR freq...
Digital calibration of inter-stage nonlinear errors in pipelined SAR ADCs

Two digital calibration techniques to linearize the residue amplifier in pipelined SAR ADCs are presented. The proposed techniques utilize a single, one-bit pseudorandom noise (PN) to simultaneously identify all coefficients of a correction polynomial. Behavioral simulation results demonstrate the effectiveness of the two proposed techniques, in which the SNDR and SFDR of a 12-bit pipelined SAR ADC are improved from 54 and 69 dB to 72 and 100 dB, respectively. Some circuit design details are included for the PN injection circuit as well as the digital calibration logic.
The development of thermoregulation in two species of woodrats, Neotoma lepida and Neotoma albigula

Abstract o 1. Comparative thermoregulatory development was studied in two species of woodrats. Neotoma lepida and Neotoma albigula. These species experienced a similar temperature loss when exposed to low ambient temperatures during the pre-weaning period. 2. Assuming identical physiological systems and temperature loss as it relates to physical mass, N. albigula would be expected to have a lower cooling rate than N. lepida, because N. albigula is larger in mass at comparable ages. 3. The results of this experiment show the reverse to be true, and this suggests that N. lepida develops thermoregulatory capabilities faster than does N. albigula. This is presumptive evidence that N. albigula, which develops more rapidly, expends proportionately less energy for thermoregulation and more for growth during the pre-weaning period than does N. lepida.
Practical and Cost-Effective Bias Line Implementations for Reconfigurable Antennas

Bias lines form an integral part of the reconfigurable antenna design process. Current methodologies for bias lines are either too narrowband or require a relatively large amount of real-estate that may not be available. Also, metallic lines are unsuitable for designs with strong fields in the bias line location. Bias lines using resistive materials are often prototyped using microfabrication facilities, but these facilities might not always be accessible. This letter investigates a novel, practical, and cost-effective bias line solution using conductive adhesives. These resistive lines effectively attenuate the RF signals providing good isolation between the RF and the dc signals while still passing a dc voltage to activate the switches. The reconfigurable E-shaped patch antenna is used as a case study in this letter, and some issues when using metallic lines in this type of antenna are also presented. The newly proposed bias line aims to minimize those issues shown hereafter. The fabrication process is also enumerated for those interested in repeating these designs for other applications. Overall, the S11 and pattern measurements show good agreement with the simulations and prove their effectiveness experimentally.
Mapping the interaction of DNA with the Escherichia coli DNA polymerase clamp loader complex.

Sliding clamps are loaded onto DNA by ATP-dependent clamp loader complexes. A recent crystal structure of a clamp loader–clamp complex suggested an unexpected mechanism for DNA recognition, in which the ATPase subunits of the loader spiral around primed DNA. We report the results of fluorescence-based assays that probe the mechanism of the Escherichia coli clamp loader and show that conserved residues clustered within the inner surface of the modeled clamp loader spiral are critical for DNA recognition, DNA-dependent ATPase activity and clamp release. Duplex DNA with a 5′-overhang single-stranded region (corresponding to correctly primed DNA) stimulates clamp release, as does blunt-ended duplex DNA, whereas duplex DNA with a 3′ overhang and single-stranded DNA are ineffective. These results provide evidence for the recognition of DNA within an inner chamber formed by the spiral organization of the ATPase domains of the clamp loader.
Diurnal and seasonal characteristics of particle volatility and chemical composition in the vicinity of a light-duty vehicle freeway

Abstract During the winter of 2005, physicochemical properties of size-fractionated PM 10 particles were analyzed next to State Route 110 (Pasadena freeway in Los Angeles, CA, USA), a light-duty vehicle freeway, closed to heavy-duty traffic. We report volatility of ultrafine particles and chemical characteristics in the coarse, accumulation, and ultrafine modes very close to the freeway and at an urban background site. For measurement of mass and chemical composition, the study employed in each location a Micro-Orifice Uniform Deposit Impactor (MOUDI) and a modified high-volume sampler. Both instruments sampled with the same size cutpoints. A tandem differential mobility analyzer (TDMA) was used at the two sampling sites to analyze the semivolatile fraction of the aerosols. Size distributions of the ambient aerosol were measured using a DMA and total number concentration using a condensation particle counter (CPC). In this study, which was a continuation of a campaign during summer 2004, we compared the seasonal, i.e. winter versus summer, and diurnal, i.e. daytime versus evening, variation in PM characteristics in the vicinity of this freeway. Conditions in winter differed most from those in summer during the evening rush-hour traffic, with much lower temperatures in the winter campaign. Diurnal variations in particle volatility were observed, with higher content of volatile material in aerosols sampled in the evenings. Particle number concentrations were also much higher during the evening hours, increasing from 67,000 to 110,000 cm −3 . The average total number concentration next to the freeway was 80,000 cm −3 during the sampling period, which was higher than in summer, when the average was 46,000 cm −3 . External mixing was observed with increasing nonvolatile fractions for 40, 80, and 120 nm particles (39% of particles). In general the volatility increased in the evenings, while the nonvolatile fraction decreased.
Tools of play: coordinating games, characters, and actions while learning to play video games

This paper describes an individual's role in coordinating a distributed system for learning. The analysis deals with a core issue for CSCL; the mismatch between common measures for learning, which are based on individual traits and outcomes, and learning processes that are distributed across people and artifacts. Rather than bridge this mismatch through an assessment of group performance, we suggest that learning scientists consider assessing an individual's adaptive reorganization in a socio-technical system. We selected video game play as a context for looking at collaborative learning because it represents an emergent social activity young people commonly engage in. Additionally, recent claims that game play involves deep learning have not been thoroughly investigated with ethnographic research; this project begins to address that gap.
A Nonlinear Theory for Elastic Plates With Application to Characterizing Paper Properties

On developpe une theorie des plaques minces physiquement et cinematiquement non lineaire. On l'utilise pour caracteriser le comportement de materiaux elastiques pour des deformations arbitraires en etirement et flexion. On introduit un concept de deformation effective pour simplifier la theorie et on l'applique a la caracterisation du papier
Experiments with a very efficient heuristic for clustering problems

Abstract A method is described for solving certain nonlinear clustering problems. While operating in polynomial time the method is not an algorithm and counter examples are cited, along with a linear programming methodology for constructing them. The success of the procedure when applied to real problems is discussed and some theoretical lines of investigation suggested for establishing circumstances under which convergence may be guaranteed. Finally, applications to important problems in the information sciences are reviewed, and the case of large sets of objects discussed.
Corneal lens goggles and visual space perception.

Night vision goggles are head-mounted, unity-power systems designed to allow the human operator to see and operate at night. Field experience and experimental studies have revealed many drawbacks in conventional designs that impair performance. One major drawback is the poor space perception provided by the goggles. The Hadani et al. [ J. Opt. Soc. Am.70, 60– 65 ( 1980)] model for space perception attributes this drawback to the fact that the conventional designs shift the observer's effective center of perspective ∼15 cm ahead and also predicts the resulting impairments. An innovative redesign is presented in this paper—the corneal lens goggles (CLG)—which brings the effective center of perspective of the goggles to coincide with the center of perspective of the eyes, thus annulling the optical length of the device. Qualitative and quantitative laboratory studies have compared the performance of the CLG and conventional goggles (type AN/PVS-5). These studies have revealed better visual and visual-motor performance with the CLG. The implications to optical design of the Hadani et al. theory and the CLG concept are discussed.
Prediction of changes in memory performance by plasma homovanillic acid levels in clozapine-treated patients with schizophrenia

Rationale Cognitive dysfunction in schizophrenia has been demonstrated to be dependent, in part, on dopaminergic activity. Clozapine has been found to improve some domains of cognition, including verbal memory, in patients with schizophrenia.
Tunable laser pumped 3 mu m Ho:YAlO/sub 3/ laser

The tuning characteristics of the /sup 5/I/sub 6/-/sup 5/I/sub 7/ transition in a Ho:YAlO/sub 3 /laser, intracavity pumped by a 1.079 mu m Nd:YalO/sub 3/ laser, were studied. Operation on seven distinct lines between 2.844 and 3.017 mu m was found, and the threshold and relative slope efficiency of each line was measured. Several of these lines were previously unreported. >
Modifications of the “alarm” pattern by nicotine

Abstract The effect of nicotine on the behavioral and autonomic response pattern, “alarm”, evoked in awake cats implanted with recording devices by stimulation of stereotaxically oriented hypothalamic electrodes was studied. Before stimulation, the lowest effective intravenous infusion rate of nicotine (10 μg/min) induced EEG desynchronization, increased gastrointestinal motility and decreased heart rate. As the infusion rate was raised to 50 {mg/min}, the arterial pressure increased, and moderate iliac and mesenteric vasoconstriction occurred. The effects of nicotine on the response to short hypothalamic stimulation (100–500 msec) were: less tachycardia, a marked post-stimulus enhancement of gastrointestinal motility, a decreased threshold for growling, and an increased number of somatic responses (head turn). The effects of nicotine on the response to long hypothalamic stimulation (1–5 sec) were, in addition, a more marked pressor response and a reduction of the iliac vasodilatation.
A dose-volume histogram based optimization algorithm for ultrasound guided prostate implants.

The task of treatment planning for prostate implants is to find an optimal seed configuration, comprising the target coverage and dosimetric consideration of critical structures such as the rectum and urethra. An efficient method to accomplish this is to use an inverse planning technique that derives the optimized solution from a prescribed treatment goal. The goal can be specified in the voxel domain as the desired doses to the voxels of the target and critical structures, or in the dose volume representation as the desired dose volume histograms (DVHs) of the target and critical structures. The DVH based optimization has been successfully used in plan optimization for intensity-modulated radiation therapy(IMRT) but little attention has been paid to its application in prostate implants. Clinically, it has long been known that some normal structure tolerances are more accurately assessed by volumetric information. Dose-volume histograms are also widely used for plan evaluation. When working in the DVH domain for optimization one has more control over the final DVHs. We have constructed an objective function sensitive to the DVHs of the target and critical structures. The objective function is minimized using an iterative algorithm, starting from a randomly selected initial seed configuration. At each iteration step, a trial position is given to a randomly selected source and the trial position is accepted if the objective function is decreased. To avoid being trapped in a less optimal local minimum, the optimization process is repeated. The final plan is selected from a pool of optimized plans obtained from a series of randomized initial seed configurations.
Teaching Islam at a home school: Muslim women and critical thinking in Uzbekistan

In this article I describe and analyse non-institutionalized religious education among local women in Uzbekistan. I argue that while exhibiting vestiges of ‘traditional’ objectives, methods of teaching, and models of knowledge transmission, and incorporating elements of educational reforms advocated by the Central Asian reformers in the early 1900s, and of Soviet pedagogy, the dynamics of such education foster students' critical thinking. By enabling students to think critically about their lives and social environment, the non-institutionalized religious education does not have one predetermined outcome, but ensures social change that starts on an individual level, whereby a student can, but does not have to, engage politically with the state, which systematically intervenes in shaping its citizens' religious lives.
The Redox State of the Glutathione/Glutathione Disulfide Couple Mediates Intracellular Arginase Activation in HCT-116 Colon Cancer Cells

Emerging studies have implicated arginase hyperactivity in the dysregulation of nitric oxide synthesis, which can lead to the development of vascular disease and the promotion of tumor cell growth. Recently, we showed that cysteine, in the presence of molecular iron, promotes arginase activity by driving the Fenton reaction. However, the exact mechanism of arginase activation in the cell induced by oxidative stress is unknown. The aim of the present study is to examine whether intracellular arginase is regulated by the cellular redox status of glutathione. To test this hypothesis, the glutathione/glutathione disulfide redox couple was altered in colon cancer cells with the thiol-specific oxidant, diamide, or the glutathione inhibitor, buthionine-(S,R)-sulfoximine, and the activity of the arginase in the cells was assessed. Treatment of cells with diamide, a thiol-specific oxidant, resulted in a dose-dependent decrease in the glutathione/glutathione disulfide ratio that was associated with the loss of glutathione and a coincident increase in arginase activity and arginase-1 levels in drug-treated cells compared with untreated cells. These results show that oxidation-induced redox changes of glutathione are of sufficient magnitude to control the activity of arginase in the cells. Thus, the physiologic modulation of the glutathione/glutathione disulfide ratio could prove to be a fundamental parameter for the control of arginase activity in pathological conditions of increased oxidative stress. This is the first evidence supporting the ex vivo regulation of arginase activity through the redox modulation of intracellular glutathione. The potential adaptive and pathological consequences of glutathione redox regulation of arginase activity are discussed.
Locomotor Patterns in the Evolution of Actinopterygian Fishes

SYNOPSIS. Locomotor adaptations in actinopterygian fishes are described for (a) caudal propulsion, used in cruising and sprint swimming, acceleration, and fast turns and (b) median and paired fin propulsion used for slow swimming and in precise maneuver. Caudal swimming is subdivided into steady (time independent) and unsteady (time dependent acceleration and turning) locomotion. High power caudal propulsion is the major theme in actinopterygian swimming morphology because of its role in predator evasion and food capture. Non-caudal slow swimming appears to be secondary and is not exploited before the Acanthopterygii. Optimal morphological requirements for unsteady swimming are (a) large caudal fin and general body area, (b) deep caudal peduncle, often enhanced by posterior dorsal and anal fins, (c) an anterior stabilizing body mass and\or added mass, (d) flexible body and (e) large ratio of muscle mass to body mass. Optimal morphological requirements for steady swimming are (a) high aspect ratio caudal fin, (b) narrow caudal peduncle, (c) small total caudal area, (d) anterior stabilizing body mass and added mass, and (e) a stiff body. Small changes in morphology can have large effects on performance. Exclusive morphological requirements for steady versus unsteady swimming are partially overcome using collapsible fins, but compromises remain necessary. Morphologies favoring unsteady performance are a recurring theme in actinopterygian evolution. Successive radiations at chondrostean, halecostome and teleostean levels are associated with modifications in the axial and caudal skeleton. Strength of ossified structures probably limited maximum propulsion forces early in actinopterygian evolution, so that specializations for fast cruising (carangiform and thunmform modes) followed structural advances especially in the caudal skeleton. No such limits apply to eel-like forms which consequently recur in successive actinopterygian radiations. Slow swimming using mainly non-caudal propulsion probably first occurred among neopterygians in association with reduced and neutral buoyancy. Slow swimming adaptations can add to and extend the scope of caudal swimming, but specialization is associated with reduced caudal swimming performance. Marked exploitation of slow swimming opportunities does not occur prior to the anterodorsal location of pectoral and pelvic girdles and the vertical rotation of the base of the pectoral fin, as found in the Acanthopterygii.
Quasi-static growth of PbS epitaxic films

Abstract A modified hot-wall method has been used to grow PbS epitaxic films under near-equilibrium conditions. The apparatus is a demountable closed tube type which permits rapid handling of source and substrate materials. Low carrier concentration films were obtained (∼10 17 cm 3 and lower). The high frequency dielectric constant e ∞ and plasma frequency were obtained for different growth rates. Corrections due to the close proximity of the free carrier plasma frequency to the LO phonon frequency were needed and yielded good agreement between conductivity and plasma frequency data. However, Hall data indicated the presence of significant planar carrier type inhomogeneities in one of the films. This suggests that great care must be taken in the analysis of epitaxic films.
Comparison of Anaerobic Susceptibility Results Obtained by Different Methods

Susceptibility tests using 7 antimicrobial agents (carbenicillin, chloramphenicol, clindamycin, penicillin, cephalothin, metronidazole, and tetracycline) were run against 35 anaerobes including Bacteroides fragilis (17), other gram-negative bacilli (7), clostridia (5), peptococci (4), and eubacteria (2). Results in triplicate obtained by the microbroth dilution method and the aerobic modification of the broth disk method were compared with those obtained with an agar dilution method using Wilkins-Chalgren agar. Media used in the microbroth dilution method included Wilkins-Chalgren broth, brain heart infusion broth, brucella broth, tryptic soy broth, thioglycolate broth, and Schaedler's broth. A result differing by more than one dilution from the Wilkins-Chalgren agar result was considered a discrepancy, and when there was a change in susceptibility status this was termed a significant discrepancy. The microbroth dilution method using Wilkins-Chalgren broth and thioglycolate broth produced the fewest total discrepancies (22 and 24, respectively), and Wilkins-Chalgren broth, thioglycolate, and Schaedler's broth had the fewest significant discrepancies (6, 5, and 5, respectively). With the broth disk method, there were 15 significant discrepancies, although half of these were with tetracycline, which was the antimicrobial agent associated with the highest number of significant discrepancies (33), considering all of the test methods and media.
Cell Killing by Simian Virus 40: Protective Effect of Chloroquine

Treatment of CV-1 cells with chloroquine before infection by simian virus 40 resulted in the accumulation of fewer nonviable, trypan blue-stainable cells at 72 h. The drug did not affect the fraction of infected T-antigen-producing cells or the viral yields. It did diminish the apparent redistribution of lysosomal N-acetyl-beta-glucosaminidase from a particulate to a soluble cell fraction, and it caused an increase in the size and number of lysosomes.
Trichothecene genotypes of Gibberella zeae from winter wheat fields in the eastern USA

Fusarium head blight (FHB), caused principally by Gibberella zeae (Fusarium graminearum), is a devastating disease of small grains such as wheat and barley worldwide. Grain infected with G. zeae may be contaminated with trichothecene mycotoxins such as deoxynivalenol (DON) and nivalenol (NIV). Strains of G. zeae that produce DON may also produce acetylated derivatives of DON: 3-acetyl-DON (3-ADON) and 15-acetyl-DON (15-ADON). Gradients (clines) of 3-ADON genotypes in Canada have raised questions about the distribution of G. zeae trichothecene genotypes in wheat fields in the eastern USA. Tri3 and Tri12 genotypes were evaluated in 998 isolates of G. zeae collected from 39 winter wheat fields in New York (NY), Pennsylvania (PA), Maryland (MD), Virginia (VA), Kentucky (KY) and North Carolina (NC). Ninety-two percent (919/998) of the isolates were 15-ADON, 7% (69/998) were 3-ADON, and 1% (10/998) was NIV. A phylogenetic analysis based on portions of three genes (PHO, RED and URA) from 23 isolates revealed two species of Fusarium (F. graminearum sensu stricto and one isolate of F. cerealis (synonym F. crookwellense)). An increasing trend of 3-ADON genotypes was observed from NC (south) to NY (north). Punctuated episodes of atmospheric transport may favour a higher frequency of 3-ADON genotypes in the northeastern USA, near Canada, compared with the mid-Atlantic states. Discoveries of the NIV genotype in NY and NC indicate the need for more intensive sampling in the surrounding regions.
EXACT: the experimental algorithmics computational toolkit

In this paper, we introduce EXACT, the EXperimental Algorithmics Computational Toolkit. EXACT is a software framework for describing, controlling, and analyzing computer experiments. It provides the experimentalist with convenient software tools to ease and organize the entire experimental process, including the description of factors and levels, the design of experiments, the control of experimental runs, the archiving of results, and analysis of results.As a case study for EXACT, we describe its interaction with FAST, the Sandia Framework for Agile Software Testing. EXACT and FAST now manage the nightly testing of several large software projects at Sandia. We also discuss EXACT's advanced features, which include a driver module that controls complex experiments such as comparisons of parallel algorithms.
Infeasible path optimization with sequential modular simulators

Infeasible path optimization algorithms have been effective with equation-solving or simultaneous modular process simulators. Using these simulators, successive quadratic programming is applied to large nonlinear programs. However, the algorithms are not directly applicable to commercial simulators of the sequential modular type. Here an infeasible path algorithm is presented which can easily be integrated with most commercial process simulators. The optimization problem remains small (10 or 20 variables) and the user merely replaces the convergence block with an “optimization” block. A simple process example demonstrates the operation, effectiveness, and potential of this algorithm.
Exercise Echocardiographic Correlates of Transient Dilatation of the Left Ventricular Cavity on Exercise Thallium-201 SPECT Imaging

Transient dilatation of the left ventricular cavity on exercise thallium perfusion imaging is recognized as a marker of significant coronary disease, but the mechanisms that produce this finding are not fully understood. We studied 32 patients who underwent exercise thallium imaging and exercise echocardiography to determine the changes in left ventricular cavity size that underlie transient dilatation. Left ventricular area from the apical four-chamber view was used to approximate left ventricular cavity size. There were 24 patients who did not have transient dilatation (group 1) and 8 patients who did have transient dilatation (group 2) on thallium imaging. Systolic area decreased from rest to exercise in group 1 patients but not in group 2 patients. There was no significant change in diastolic area from rest to exercise in either group 1 or group 2 patients. Thus, exercise-induced systolic dysfunction, manifested as a failure to decrease left ventricular systolic cavity size in exercise, may be an important mechanism in producing scintigraphic transient dilatation.
Troponin I serines 43/45 and regulation of cardiac myofilament function

We studied Ca2+ dependence of tension and actomyosin ATPase rate in detergent extracted fiber bundles isolated from transgenic mice (TG), in which cardiac troponin I (cTnI) serines 43 and 45 were m...
Effect of DNA damage on PCR amplification efficiency with the relative threshold cycle method

Polymerase stop assays used to quantify DNA damage assume that single lesions are sufficient to block polymerase progression. To test the effect of specific lesions on PCR amplification efficiency, we amplified synthetic 90 base oligonucleotides containing normal or modified DNA bases using real-time PCR and determined the relative threshold cycle amplification efficiency of each template. We found that while the amplification efficiencies of templates containing a single 8-oxo-7,8-dihydro-2 0 -deoxyguanosine (8-oxodG) were not significantly perturbed, the presence of a single 8-oxo-7,8-dihydro-2 0 -deoxyadenosine, abasic site, or a cis–syn thymidine dimer dramatically reduced amplification efficiency. In addition, while templates containing two 8-oxodGs separated by 13 bases amplified as well as the unmodified template, the presence of two tandem 8-oxodGs substantially hindered amplification. From these findings, we conclude that the reduction in polymerase progression is dependent on the type of damage and the relative position of lesions within the template. � 2004 Elsevier Inc. All rights reserved.
Reply to William A. Green's “The Perils of Comparative History”

The preceding article by William A. Green does not make clear the basis upon which he criticizes my October 1981 comparison of Belize and the British sugar colonies. He begins by saying that the "phenomena compared must possess important and comprehensive unities of character" and writes later that "it is the presence of similar people performing similar functions under similar circumstances that renders comparative analysis valuable. These identities did not prevail between Belize and the British sugar colonies." Belize, he writes, had a "unique system of domination" (his emphasis). Is the problem, then, that there are no "unities of character," that "identities did not prevail," or that Belize was "unique"? Every case is unique, surely, yet comparisons are made in social, as in natural, science between selected common factors which appear under similar, but not identical, conditions. There exists a range between John Stuart Mill's formulae called The Method of Agreement, in which one compares two situations which differ in every respect save one, and The Method of Difference, in which one compares two situations which are alike except in one respect, but Green seems to think only the latter is acceptable. I agree with Stanislav Andreski, who emphasizes "that comparing does not amount to equating, and that there are no logical reasons why a comparison should be focused on resemblances rather than differences."' Consider, for example, a classic of comparative analysis of two nineteenth-century Caribbean societies in which there are striking contrasts of situation but which reveal "certain significant similarities of process": Sidney Mintz's "Labor and Sugar in Puerto Rico and in Jamaica, 1800-1850."2 That is the kind of broad comparative history with which I associate my study of the control of land and labor in the British West Indies after 1838.
Low Coverage Analysis using dynamic un-testability debug in ATPG

In this paper, we propose an automated technique to identify the reasons for un-testable faults and, an interactive Low Coverage Analysis flow to expedite the coverage analysis step, in scan ATPG. We seamlessly use an implication graph to keep track of the reasons that are responsible for each conflict encountered during ATPG. As ATPG progresses, for each fault, all the reasons arising from ATPG constraints are logged systematically. Then, we use a low coverage analysis flow to cumulatively analyze the faults and reasons / ATPG constraints. We integrated the proposed technique into the production scan ATPG flow at Intel. The proposed technique resolved up to 15% coverage gap on real micro-processor designs in a few hours. Potentially, this would have, otherwise, taken a few days of manual effort with considerable design knowledge.
DISTRIBUTIONS OF QUADRATIC FORMS

Abstract : For independent chi-square variables x squared sub m and x squared sub n with m and n degrees of freedom, respectively, we consider the quadratic form where the positive ci are distinct. This paper gives exact finite expressions for the distribution of Q in terms of available functions such as the distribution function of chi-square random variables, modified Bessel Functions, Dawson's integral. These formulas are useful for checking the accuracy of approximations and tables of the distribution of Q and provide a simple alternative in their absence. For large m and n, reasonable approximations to the distribution of Q are available. For the general quadratic form Williams (1984) compares algorithms for truncations of infinite series expansions of the distribution.
Comparative pathology of Astragalus (locoweed) and Swainsona poisoning in sheep.

The toxic effect on pregnant two of Swainsona galegifolia (collected in Australia) and of Astragalus pubentissimus and A. Ientiginosus (collected in the United States) were compared. The signs of intoxication, vacuolar lesions, and clinicopathologic changes were similar. These similarities suggest that the toxic agent or agents may be the same in both genera. Some sheep fed Astragalus aborted and some delivered deformed lambs while those fed Swainsona did not.
Analysis of the effects of cover crop residue on hyperspectral reflectance discrimination of soybean and weeds via Haar transform

A Haar-based automatic classification system is designed to discriminate between the hyperspectral reflectance curves of soybean and weeds. The study focuses on whether or not the cover crop residue influences the ability to distinguish grass from soybean when using hyperspectral reflectance curves. Four sets of experiments with or without cover crop residue associated with using or not using conventional tillage are designed and conducted. In each experiment, a three-class classification problem is solved using the leave-one-out test method based on the nearest mean classifier. The classification accuracies and the associated confidence intervals are computed to evaluate the classification performance of the system. The experimental results show that both cover crop residue and conventional tillage have little influence on overall classification accuracies of the automated classification system. In general, the system provides a classification accuracy of over 90%, which indicates a promising discrimination capability of the automated Haar-based classification system.
The pH of Activation of the Hemagglutinin Protein Regulates H5N1 Influenza Virus Pathogenicity and Transmissibility in Ducks

While the molecular mechanism of membrane fusion by the influenza virus hemagglutinin (HA) protein has been studied extensively in vitro, the role of acid-dependent HA protein activation in virus replication, pathogenesis, and transmission in vivo has not been characterized. To investigate the biological significance of the pH of activation of the HA protein, we compared the properties of four recombinant viruses with altered HA protein acid stability to those of wild-type influenza virus A/chicken/Vietnam/C58/04 (H5N1) in vitro and in mallards. Membrane fusion by wild-type virus was activated at pH 5.9. Wild-type virus had a calculated environmental persistence of 62 days and caused extensive morbidity, mortality, shedding, and transmission in mallards. An N114K mutation that increased the pH of HA activation by 0.5 unit resulted in decreased replication, genetic stability, and environmental stability. Changes of +0.4 and -0.5 unit in the pH of activation by Y23H and K58I mutations, respectively, reduced weight loss, mortality, shedding, and transmission in mallards. An H24Q mutation that decreased the pH of activation by 0.3 unit resulted in weight loss, mortality, clinical symptoms, and shedding similar to those of the wild type. However, the HA-H24(1)Q virus was shed more extensively into drinking water and persisted longer in the environment. The pH of activation of the H5 HA protein plays a key role in the propagation of H5N1 influenza viruses in ducks and may be a novel molecular factor in the ecology of influenza viruses. The data also demonstrate that H5N1 neuraminidase activity increases the pH of activation of the HA protein in vitro.
Prediction of Lifetime Relative Net Income from First Lactation Production and Individual Type Traits in Holstein Cows

Abstract Official type classification data and Dairy Herd Improvement Registry production records of Holstein cows calving between January 1, 1967, and June 1, 1976, were used to estimate contributions of individual descriptive type traits evaluated in first lactation to lifetime profitability as measured by a profit function, relative net income. Relative net income estimated total profit from variables available through Dairy Herd Improvement. Contributions of individual type components to profitability were estimated from least squares constants adjusted for all descriptive type traits and for linear and quadratic effects of final score, first lactation production, age at first calving, herdlife opportunity, stage of lactation, and age when classified. For the model to predict total profit, regressions were most significant for udder traits. Significant positive regressions were for plain or coarse head; firmly attached high and wide rear udder; and desirable teat size and placement. Significant negative regressions were for narrow and pinched, loose or broken rear udder; lack of defined udder support; and winged shoulders. Differences in total profit for body, feet, and hind legs were relatively unimportant as compared with alternative codes for udder traits. Codes considered conformationally most desirable for rear udder, udder support, and teats were also most desirable for total profit.
The effects of aromatase inhibitors and selective estrogen receptor modulators on eye development in the zebrafish (Danio rerio).

Purpose: It has been shown that the steroid hormone estrogen plays an important role in the development of the central nervous system. The purpose of these studies was to determine the effect of estrogen on zebrafish eye maturation. Methods: In these experiments, the estrogen receptor blockers tamoxifen and clomiphene, selective estrogen receptor modulators (SERMs), were used to determine the role of estrogen in the developing eye by morphometric microscopic techniques. Also, in this study the synthesis of estrogen was inhibited with aminoglutethimide or 4-hydgoxyandrostenedione treatments, both of which are aromatase inhibitors (AIs). Results: After these various treatments, the zebrafish were analyzed for eye maturation and growth rates, which were significantly diminished with both AI and SERM treatments. In a competition assay, where tamoxifen and excess estrogen were added at the same time normal eye development and body growth took place, indicating that estrogen out-competed tamoxifen and that thes...
The reaction of influenza viruses with guinea pig polymorphonuclear leucocytes. III. Studies on the mechanism by which influenza viruses inhibit phagocytosis.

Abstract The degree of phagocytosis of heat-killed yeast cells by guinea pig polymorphonuclear leucocytes was shown to depend on the presence in the reaction mixture of guinea pig serum and an added substrate such as glucose, glucose-6-phosphate, or fructose-6-phosphate. The concentration of carbohydrate was important in order to obtain maximum phagocytosis. Phagocytosis by polymorphonuclear leucocytes was reduced when the cells had reacted with partially purified Lee virus and were incubated in the presence of serum and glucose or glucose-6-phosphate. When fructose-6-phosphate served as the added substrate, there was no inhibition of phagocytosis. The observed inhibition of phagocytosis by leucocytes to which influenza virus had been adsorbed was postulated to be due to the block in the energy yielding mechanisms of virus-treated cells.
Student Learning: What Has Instruction Got to Do With It?

A seemingly unending controversy in the field of instruction science concerns how much instructional guidance needs to be provided in a learning environment. At the one extreme lies the claim that it is important for students to explore and construct knowledge for themselves, which is often called discovery learning, and at the other extreme lies the claim that providing direct instruction is more beneficial than withholding it. In this article, evidence and arguments that support either of the approaches are reviewed. Also, we review how different instructional approaches interact with other instructional factors that have been known to be important, such as individual difference, self-explanation, and comparison. The efforts to combine different instructional approaches suggest alternative ways to conceive of learning and to test it.
Increase of extracellular corticotropin-releasing factor-like immunoreactivity levels in the amygdala of awake rats during restraint stress and ethanol withdrawal as measured by microdialysis

Previous research has suggested a role for corticotropin-releasing factor (CRF) in the anxiogenic effects of stressful stimuli and ethanol withdrawal. This hypothesis was explored in a series of experiments using intracranial microdialysis to monitor CRF-like immunoreactivity (CRF-IR) in the extracellular compartment of the rat amygdala. The synaptic origin of CRF-IR release in the amygdala was determined in vitro by assessing the Ca2+ dependency of 4-aminopyridine stimulated CRF-IR release from tissue preparations of rat amygdala. In vivo experiments were performed in awake rats after the placement of microdialysis probes in the amygdala. In the first experiment, transient restraint stress (20 min) produced an increase of CRF-IR release (basal levels, 1.19 +/- 0.15 fmol/50 microliters; stress levels, 4.54 +/- 1.33 fmol/50 microliters; p
Amino Acid Metabolic Origin as an Evolutionary Influence on Protein Sequence in Yeast

The metabolic cycle of Saccharomyces cerevisiae consists of alternating oxidative (respiration) and reductive (glycolysis) energy-yielding reactions. The intracellular concentrations of amino acid precursors generated by these reactions oscillate accordingly, attaining maximal concentration during the middle of their respective yeast metabolic cycle phases. Typically, the amino acids themselves are most abundant at the end of their precursor’s phase. We show that this metabolic cycling has likely biased the amino acid composition of proteins across the S. cerevisiae genome. In particular, we observed that the metabolic source of amino acids is the single most important source of variation in the amino acid compositions of functionally related proteins and that this signal appears only in (facultative) organisms using both oxidative and reductive metabolism. Periodically expressed proteins are enriched for amino acids generated in the preceding phase of the metabolic cycle. Proteins expressed during the oxidative phase contain more glycolysis-derived amino acids, whereas proteins expressed during the reductive phase contain more respiration-derived amino acids. Rare amino acids (e.g., tryptophan) are greatly overrepresented or underrepresented, relative to the proteomic average, in periodically expressed proteins, whereas common amino acids vary by a few percent. Genome-wide, we infer that 20,000 to 60,000 residues have been modified by this previously unappreciated pressure. This trend is strongest in ancient proteins, suggesting that oscillating endogenous amino acid availability exerted genome-wide selective pressure on protein sequences across evolutionary time.
Genital warts and sexual abuse in children

Genital warts in children indicate the possibility of sexual abuse. If sexual child abuse is recognized or suspected, then the law in all states requires that the physician report this to the appropriate authority. The dermatologist may be the first person to suspect the problem and can be of great help in protecting the child from future harm.
Putative Precursors of Gallbladder Dysplasia A Review of 400 Routinely Resected Specimens

Abstract Context.—Dysplasia is thought to be a precursor of invasive gallbladder carcinoma, but it is unsettled whether dysplasia arises from other precursor lesions. Objective.—To ascertain the presence and nature of precursors of dysplasia in the gallbladder. Design.—Four hundred consecutive cholecystectomy specimens were processed and stained routinely for diagnosis. We retrospectively reviewed these cases to look for the presence of epithelial changes, including antral-type metaplasia, intestinal metaplasia, and dysplasia. Results.—Antral-type metaplasia, intestinal metaplasia, and dysplasia were found in 238 (59.5%), 39 (9.8%), and 20 (5.0%) cases, respectively. The mean patient age was 47.7 years (range, 15–93 years). The mean ages for patients with antral-type metaplasia, intestinal metaplasia, and dysplasia were 49.4, 50.9, and 52.6 years, respectively. Statistically significant associations were found between antral-type metaplasia and intestinal metaplasia (P = .007, χ2 test) and between intesti...
A biosensor of local kinesin activity reveals roles of PKC and EB1 in KIF17 activation.

We showed previously that the kinesin-2 motor KIF17 regulates microtubule (MT) dynamics and organization to promote epithelial differentiation. How KIF17 activity is regulated during this process remains unclear. Several kinesins, including KIF17, adopt compact and extended conformations that reflect autoinhibited and active states, respectively. We designed biosensors of KIF17 to monitor its activity directly in single cells using fluorescence lifetime imaging to detect Forster resonance energy transfer. Lifetime data are mapped on a phasor plot, allowing us to resolve populations of active and inactive motors in individual cells. Using this biosensor, we demonstrate that PKC contributes to the activation of KIF17 and that this is required for KIF17 to stabilize MTs in epithelia. Furthermore, we show that EB1 recruits KIF17 to dynamic MTs, enabling its accumulation at MT ends and thus promoting MT stabilization at discrete cellular domains.