cssi/SciSciGPT-SciSciNet huggingface dataset:
15N2–DNA–stable isotope probing of diazotrophic methanotrophs in soil

Abstract Nucleic acid stable isotope probing (SIP) is a powerful tool that can identify and characterize the microorganisms that mediate specific soil processes and explore the flow of C and N through functional groups in the soil food web. While 13 C–SIP has been used successfully in a range of applications, methodological constraints have limited the applicability of 15 N-labelled compounds in nucleic acid SIP. However, 15 N–DNA–SIP can now be achieved and this method when used with 15 N 2 provides a powerful new tool for characterizing free-living diazotrophs in natural ecosystems. A diverse array of non-cultivated diazotrophs have been observed in soil and yet the characteristics of these organisms and their environmental significance remain almost completely unknown. 15 N 2 –DNA–SIP can identify those diazotrophs that are active in situ while providing access to gene sequences and genome fragments that can yield insights on their evolutionary history and functional capacities. Further insights on the ecology of free-living diazotrophs in soil can be provided by performing 15 N 2 –DNA–SIP on microcosms in which the response of the diazotrophic community is determined in relation to experimental manipulation. We describe the use of 15 N 2 –DNA–SIP to explore linkages between different C sources and N-fixation by specific diazotroph populations in soil. Methane addition to soil was observed to stimulate N-fixation and the organisms that were found to be responsible for this activity were Type II methanotrophs most closely related to the genus Methylocystis . This report provides insights on the use of nucleic acid SIP to identify and characterize microorganisms that mediate specific soil processes and represents the first time that a specific group of methanotrophs has been shown to mediate N-fixation while in the soil environment.
Training the school psychologist for consultation

Abstract New models of service delivery are needed in order that school psychologists can apply their knowledge and skills to the urgent educational and social problems which are disrupting today's schools. Consultation methods have the potential for significantly extending professional impact, but the consultative skills of most school psychologists are limited; school psychology training programs typically provide no systematic training in consultation theory and methods. In this paper multiple models of consultation and their implications for professional training are discussed. A school psychology consultation training program is described and related training issues are raised.
A new distributed sensor and actuator theory for “Intelligent” shells

An “intelligent” shell is a shell structure with a self-sensation and action/reaction capabilities contributed by built-in sensors, actuators and control electronic systems. In this study, a new intelligent shell structure composed of a conventional elastic shell, a distributed piezoelectric sensor and a distributed piezoelectric actuator is proposed. The distributed sensor provides a self-monitoring capability to sense shell oscillation and the distributed actuator contributes a self-correction (control) capability to counteract the oscillation. A new generic theory for the intelligent shell system is developed. System equations of motion coupling sensing and control effects are derived. From the theory derived, it is concluded that the distributed sensor is (theoretically) capable of sensing all shell vibration modes and the distributed actuator controlling all shell modes. However, the sensing or control effort of each mode could be different. Two feedback control algorithms, namely direct feedback control and Lyapunov control, are proposed in the paper. The generic theory can be simplified to account for other general geometries, such as cylinder, plates, beams, etc. Applications of the theory are also demonstrated.
Assessment of the Microbiological Potential for the Natural Attenuation of Petroleum Hydrocarbons in a Shallow Aquifer System.

A multidisciplinary field study investigating the fate and transport of petroleum hydrocarbons commonly associated with jet-fuel contamination is currently underway at Columbus Air Force Base (AFB), Mississippi. Sixty sediment cores from 12 boreholes were recovered from the study aquifer. The goal of this initial sampling was to characterize the potential microbial activity using 14C-labeled substrates, as well as the presence, abundance, and distribution of specific hydrocarbon degrading genotypes using DNA:DNA hybridization. Enumeration of total microbial abundance using a 16S rDNA universal oligonucleotide probe was compared to traditional enumeration methods. Total culturable populations determined by spread plate analysis ranged from a low of 104 to more than 106 organisms per gram sediment. Microbial abundance estimated by DNA hybridization studies with 16S rDNA genes ranged from 107 to 108 organisms per gram sediment. Molecular analysis of aquifer samples using DNA probes targeting genes encoding the degradative enzymes alkane hydroxylase (alkB), catechol 2,3-dioxygenase (nahH), naphthalene dioxygenase (nahA), toluene dioxygenase (todC1C2), toluene monooxygenase (tomA), and xylene monooxygenase (xylA), as well as two probes measuring methanogenic microorganisms, codh (carbon monoxide dehydrogenase) and mcr (methyl coenzyme reductase), revealed that each target gene sequence was present in nearly all 60 samples. The presence of organisms demonstrating the phenotype to degrade BTEX and naphthalene was further supported using mineralization assays with 14C-labeled benzene, toluene, naphthalene, and phenanthrene. Minimal activity occurred during the first 24 hours. After a period of 5–7 days, greater than 40% of the target compounds were mineralized in aquifer sediments.
An ab initio study of di- and trifluorobenzene–benzene complexes as relevant to carbonic anhydrase II–drug interactions

Ab initio calculations at the MP2/6-31G* level have shown that variously substituted di- and trifluorobenzenes form non-covalent complexes with benzene that adopt either aromatic–aromatic or H---F binding, the choice being determined by the pattern of fluorination. The binding energies of these structures are from 3.4 to 4.5 kcal mol−1. This range is large enough to account for observed variations in the binding affinity of a library of fluoroaromatic inhibitors of carbonic anhydrase. This enzyme has an aromatic amino acid at a central position in the active site. The diverse modes of binding of the dimers also suggest that aggregates of fluorobenzenes might adopt specified 3-dimensional shapes in the solid state.
Charged particle Q values for reactions on C, Cr, Fe, Co, and Ni

$Q$ values were measured for 27 reactions on targets of $^{12}\mathrm{C}$, $^{54}\mathrm{Cr}$, $^{54,56}\mathrm{Fe}$, $^{59}\mathrm{Co}$, and $^{58,\phantom{\rule{0ex}{0ex}}60,\phantom{\rule{0ex}{0ex}}62,\phantom{\rule{0ex}{0ex}}64}\mathrm{Ni}$ with resulting uncertainties of 0.7 to 3.2 keV. Care was taken to define sources of error. A ${\ensuremath{\chi}}^{2}$ test on an interconnected set of 19 measurements indicates internal consistency and a comparison of eight ($d,p$) $Q$ values with ($n,\ensuremath{\gamma}$) numbers shows excellent agreement. A mass evaluation was performed on a truncated region centered on Co. The results indicate that the 1971 values for the masses of $^{55}\mathrm{Cr}$ and $^{55}\mathrm{Co}$ are in error. The uncertainties of the masses of $^{53}\mathrm{Fe}$ and $^{61}\mathrm{Co}$ are greatly reduced. The question of the $^{57}\mathrm{Fe}$ mass raised in The 1971 Atomic Mass Evaluation is not entirely resolved and consequently the absolute values of some masses in this region are still uncertain to about 5 keV although the $Q$ values are improved.
Some solution strategies for automated highway exit bottleneck problems

Abstract Transportation planners are exploring methods to ease congestion on urban freeways. The Automated Highway System (AHS) is a potential solution that could triple current freeway capacity. A three-fold increase in freeway capacity would translate into a significant increase in peak freeway traffic flow. The corresponding increase of flow on urban roads due to exiting AHS vehicles could quickly overwhelm the capacity of urban streets and lead to critical bottlenecking of AHS flow. If exiting AHS vehicles cannot sufficiently clear AHS exits because the local streets are jammed, traffic will spill onto the AHS mainline and reduce AHS capacity. The loss of AHS capacity due to congestion in urban destinations and the resulting back spill of traffic onto the AHS will greatly detract from the AHS system.The following Non-Intermodal Interface (NII) and Intermodal Interface (II) strategies are proposed as solutions to this critical problem: 1. (1) the dispersion of flow through AHS networks; 2. (2) the dispersion of flow at commuter destinations; 3. (3) the consolidation of flow at central locations. Specifically, smart street signals and prioritized street design, intermodal terminals, and automated garages are identified as potential solutions. This paper qualitatively discusses the advantages and disadvantages of each of the three general strategies, and quantitatively discusses the advantages and disadvantages of each of the four specific solutions through simulated scenarios which account for varying ramp volumes, trip attraction patterns, and urban structures. Our investigation shows that creative combinations of these methods can be useful to integrate future AHS with local road networks. Without such integration, the AHS cannot succeed.
Analyses of tomato peel and seed byproducts and their use as a source of carotenoids

Commercial tomato canning yields two different byproducts. One is the material that results from peeling tomatoes, while the other results from removing the seeds. The peel byproduct contained 100.8 g protein, 256.4 g ash and 299.4 g acid detergent fiber kg−1. Ash content was high because the peel byproduct contained 83.8 g kg−1 sodium as a result of using a sodium hydroxide solution to peel the tomatoes. The seed byproduct contained 202.3 g protein, 51.8 g ash, and 537.9 g acid detergent fiber kg−1. An amino acid analysis of seeds indicated that approximately 60% of the protein results from amino acids. Both byproducts were analyzed for carotenoid content. The lycopene content of peel byproduct was 734 µg g−1 of dry material. Significant amounts of lutein, β-carotene, and cis-β-carotene were also present. Seed byproduct contained 130 µg lycopene kg−1 of dry matter. The content of other carotenoids was approximately half of that present in the peels. Peel and seed byproducts were included at 75 g kg−1 in hen diets to determine the transfer of carotenoids to the yolk. When fed at this concentration, the lycopene content of dry egg yolk was approximately 0.9 µg g−1. Approximately 0.1% of the lycopene in peel byproduct and approximately 0.7% of the lycopene in the seed byproduct was transferred from the feed to the yolk. Lycopene appears more similar to carotene than to oxycarotenoids in its transfer to the yolk. Copyright © 2005 Society of Chemical Industry
Web-Based Network Sampling: Efficiency and Efficacy of Respondent-Driven Sampling for Online Research

This study tests the feasibility, effectiveness, and efficiency of respondent-driven sampling (RDS) as a Web-based sampling method. Web-based RDS (WebRDS) is found to be highly efficient and effective. The online nature of WebRDS allows referral chains to progress very quickly, such that studies with large samples can be expected to proceed up to 20 times faster than with traditional sampling methods. Additionally, the unhidden nature of the study population allows comparison of RDS estimators to institutional data. Results indicate that RDS estimates are reasonable but not precise. This is likely due to bias associated with the random recruitment assumption and small sample size of the study. Finally, this article presents methods for testing the validity of assumptions required by RDS estimation.
A Direct Approach to Deriving Filtering Equations for Diffusion Processes

Filtering equations are derived for conditional probability density functions in case of partially observable diffusion processes by using results and methods from the L p -theory of SPDEs. The method of derivation is new and does not require any knowledge of filtering theory.
The new politics of voting alignments in the United Nations General Assembly

Voting patterns in the United National General Assembly provide an exceptionally good set of evidence for observing issues and alignments of states in international politics. We analyze those patterns in three post-cold war sessions of the General Assembly and compare them with the alignments and issues that characterized sessions during the cold war. We find new groups and alignments (with most of Eastern Europe now voting with rather than against West European positions) and a new prominence of long-term North-South issues as they now relate to questions of redefining “human security” in the post-cold war world. The predominant General Assembly division is between richer and poorer nations. Key correlates of voting with the North are wealth, democracy, and proportionately low levels of trade with the United States.
Evaluating usability methods: why the current literature fails the practitioner

Practitioners who deal in the business world must find ways to keep up-to-date with best practices in the field and must apply them to their work in cost-effective ways. Research should help to define best practices, but often the worlds of research and of practice can seem too dichotomous. Recently, for instance, the fields of usability and user-centered design generally have seen considerable controversy about the relative effectiveness of different methodologies. In this column, Dennis Wixon argues that we need to look at whether we are evaluating methods by the appropriate criteria. He considers the growing body of literature on evaluation of methods unhelpful, or even irrelevant, to the practitioner. He argues that consideration of the factors that determine success of usability efforts in product development organizations will fundamentally change the terms of the debate. ---David A. Siegel
Issues With the New Developmental Screening and Surveillance Policy Statement: In Reply

In writing the new policy statement on developmental surveillance and screening,1 the American Academy of Pediatrics (AAP) Council on Children With Disabilities, Section on Developmental and Behavioral Pediatrics, Bright Futures Steering Committee, Medical Home Initiatives for Children With Special Needs Project Advisory Committee, and the Partnership for Policy Implementation joined together to forge a new policy that could address the recognized barriers to implementation of screening.2 As is clear from the title of the policy, we chose to highlight the need for early identification and create a system for surveillance and screening for the first 3 years of life. Although we emphasized implementation from birth to 30 months, we stated clearly in the policy that surveillance should continue throughout childhood and that school-readiness screening should be performed at 4 years of age.1(p414) The third edition of the Bright Futures guidelines (in press) also includes the 9-, 18-, and 30-month developmental screening, as recommended in the algorithm for those visits. We support the …
Letter by Bourque et al regarding article, "Changing incidence and survival for heart failure in a well-defined older population, 1970-1974 and 1990-1994".

To the Editor: In the article, “The Changing Incidence and Survival for Heart Failure in a Well-Defined Older Population, 1970–1974 and 1990–1994),”1 Barker et al used an administrative data set to show that the incidence of heart failure has increased 14% during that time period after controlling for population aging. This increase was predominately seen in men and those of advanced age. Interestingly, there was a suggestion of a decrease in the mortality from heart failure among men and not women between those 2 …
Volatile fatty acid profile for grass hay or alfalfa hay fed to alpacas (Vicugna pacos).

Summary The purpose of this study was to determine the diurnal composition and concentration of volatile fatty acids (VFA) and to determine VFA composition and concentration differences between stomach compartment 1 (C1) and caecum of alpacas fed grass and alfalfa hay. The study was divided into two experiments. In Experiment 1 (EXP 1), 10 male alpacas (3+ years old, 65 kg BW) were divided into two groups, housed in drylot pens, provided ad libitum water and fed alfalfa (AH) or grass hay (GH) for 30 days. The alpacas were slaughtered and the digestive tract collected, divided into sub-tract sections, weighed and digesta sampled for pH, dry matter (DM) and NDF. Volatile fatty acid composition and concentration were determined on C1 and caecal material. Four adult male (3+ years old, 60 kg BW), C1 fistulated alpacas were housed in metabolism crates and divided into two forage groups for Experiment 2 (EXP 2). Alpacas were fed the forages as in EXP 1. Diurnal C1 VFA samples were drawn at 1, 3, 6, 9, 12, 18 and 24 h post-feeding. There were no differences between forages for tract weight, C1 and caecum digesta DM or NDF. Differences were noted (p < 0.05) for pH between forages and sub-tract site. Volatile fatty acids concentrations were different (p < 0.05) for forage and site, and total VFA was higher for AH than GH (110.6 and 79.1 mm) and C1 than caecum (40.7 and 27.6 mm). Proportion of VFA was significant (p < 0.05) for forage and site, C1 acetate highest for GH (84.8 vs. 74.0 mm) and caecum acetate 83.7 and 76.2 mm for GH and AH respectively. These data demonstrate the level of VFA produced in C1 and the caecum of alpacas and the diurnal VFA patterns. Composition of VFA is similar to other ruminant species.
Work in Progress: Supporting K-12 Teacher Professional Development through the National Center for Engineering and Technology Education

The National Center for Engineering and Technology Education (NCETE) links technology educators with engineering educators to build capacity for research, nurture a cadre of talented, diverse leaders in engineering and technology education and infuse engineering design and analytical skills into K-12 schools. The NSF-funded center (ESI-0426421) links four research universities with five technology teacher education institutions, fifteen K-12 school districts and three education-related societies. In 2005 and 2006 the Center has been involved in on-going delivery of professional development for technology teachers in the partner K-12 schools. Professional development focuses on assessment-driven open-ended problem solving applied to engineering design utilizing mathematics and science concepts. Data is collected from students and teachers to determine if project objectives are met and if the content is effective for technology education students. At the time of the 2006 FIE conference, the project will have collected data from 50 technology teachers designed to assess the value and focus of the professional development workshops. Evaluation survey instruments, designed by the Center's external evaluator in collaboration with the Center's leadership, are used to collect data from students and teachers to assess the extent to which the project met the objectives and whether the content and delivery mechanisms were effective for technology education students.
The frequency distribution of chromosome constituents in cells with chromosome-number dispersion

The frequency distribution in a population of cells of the quantityCD (defined as the amount of some chromosomal substance in a cell which containsC chromosomes) is calculated using the distribution in the population of the amount per chromosome,D, and the distribution of chromosome number,C.
Neutron capture in the giant resonance region of 209Pb

Abstract The giant dipole resonance region of 209 Pb has been studied via the reaction 208 Pb(n, γ) for transitions leading to the ground and first excited states of 209 Pb. Measured angular distributions were used to extract a 2 coefficients at 8 energies and a 1 coefficients at 4 energies between 10 and 13 MeV. The results are compared to direct-semidirect model and pure resonance model calculations using both real and complex form factors. Absolute cross sections at 90° were measured in 200 keV steps from E n ( E x ) = 7.0(10.9) MeV to 13.0(16.9) MeV and are compared to previous data and to DSD and PRM calculations. The transitions to the ground and first excited states exhaust 0.39 % and 0.13 % of the classical dipole sum, respectively, between the excitation energies of 10.9 and 16.9 MeV.
Multiple elastic modules for visual pattern recognition

Fast synaptic plasticity, used to associate topologically ordered features in an input image to those of previously learned objects, has been previously proposed as a possible model for object recognition (von der Malsburg & Bienenstock, 1987, Europhysics Letters, 3(11), 1243–1249). In this paper, it is argued that in addition to rapid link dynamics, fast receptive field size dynamics are necessary to automatically escape from poor local matches and also allow for simultaneous recognition of multiple objects. Furthermore, a feature locking mechanism with a properly designed hysteresis property is needed to handle complex, cluttered, and dynamic scenes. The multiple elastic modules (MEM) model, described in this paper, utilizes newly developed dynamics that locate and recognize a previously learned object based on expected spatial arrangement of local features. The MEM model can be viewed as using a deformable template of an object to search the input scene. Unlike many of the current artificial neural network models, the proposed MEM model attempts to capture many of the functions available in the biological visual system by providing mechanisms for: multi-model feature integration, generation and maintenance of focus of attention, multiresolution hierarchical searching, and top-down expectation driven processing coupled with bottom-up feature activation processing. In addition, the MEM dynamics, unlike similar template matching approaches (Konen et al., 1994, Neural Networks, 7(6/7), 1019–1030; Yuille et al., 1992, International Journal of Computer Vision, 8(2), 99–111), does not converge to false objects when there are no sufficiently familiar objects in the scene. The performance of the MEM model in detection and recognition of objects through a number of computer simulations is demonstrated.
Alternative bleaching methods for Cheddar cheese whey.

: Residual annatto colorant (norbixin) in fluid Cheddar cheese whey can be bleached. The 2 approved chemical bleaching agents for whey, hydrogen peroxide (HP) and benzoyl peroxide (BP), negatively impact the flavor of dried whey protein. The objective of this study was to evaluate alternative methods for bleaching liquid whey: ultraviolet radiation (UV), acid-activated bentonite (BT), and ozone (OZ). Colored Cheddar cheese whey was manufactured followed by pasteurization and fat separation. Liquid whey was subjected to one of 5 treatments: control (CT) (no bleaching; 50 °C, 1 h), HP (250 mg/kg; 50 °C, 1 h), UV (1 min exposure; 50 °C), BT (0.5% w/w; 50 °C, 1 h), or OZ (2.2g/h, 50 °C, 1 h). The treated whey was then ultrafiltered, diafiltered, and spray-dried to 80% whey protein concentrate (WPC80). The entire experiment was replicated 3 times. Color (norbixin extraction and measurement), descriptive sensory, and instrumental volatile analyses were conducted on WPC80. Norbixin elimination was 28%, 79%, 39%, and 15% for HP, BT, UV, and OZ treatments, respectively. WPC80 from bleached whey, regardless of bleaching agent, had lower sweet aromatic and cooked/milky flavors compared to unbleached CT (P < 0.05). The HP and BT WPC80 had higher fatty flavor compared to the CT WPC80 (P < 0.05), and the UV and OZ WPC80 had distinct mushroom/burnt and animal flavors. Volatile compound results were consistent with sensory results and confirmed higher relative abundances of volatile aldehydes in UV, HP, and OZ WPC80 compared to CT and BT WPC80. Based on bleaching efficacy and flavor, BT may be an alternative to chemical bleaching of fluid whey. Practical Application: The 2 approved chemical bleaching agents for whey, hydrogen peroxide (HP) and benzoyl peroxide (BP), negatively impact flavor of dried whey protein, and restrictions on these agents are increasing. This study evaluated 3 alternatives to chemical bleaching of fluid whey: UV radiation, ozone, and bentonite.
Cortical Myoclonus During Lithium Exposure

Background Myoclonus can occur in association with lithium therapy at toxic and therapeutic dosages, and can be a predominant and disabling adverse effect. Moreover, myoclonus has been reported when lithium has been combined with cyclic antidepressants and with the neuroleptic clozapine. Although clinical case reports exist, no electrophysiologic data are available that provide a source or a neurophysiological mechanism for the myoclonus seen in lithium therapy. Objective To describe the electrophysiologic characteristics and source of the myoclonus associated with lithium therapy. Design and Methods We retrospectively analyzed 5 cases of myoclonus during lithium therapy. We reviewed the clinical features and results of previous electrophysiologic testing. Four patients received lithium monotherapy; and 1, sertraline hydrochloride and nefazodone hydrochloride in addition to lithium. The electrophysiologic data that had been gathered included multichannel surface electromyographic (EMG) recordings with simultaneous electroencephalography (EEG), somatosensory evoked potentials, and elicitation of long-latency EMG reflexes to median and digital nerve stimulation. Results All 5 patients showed multifocal action myoclonus without reflex activation and only rare occurrence at rest. In each case, back-averaging created a focal EEG transient over the contralateral sensorimotor area preceding the myoclonus EMG discharge. In 2 of the patients receiving lithium monotherapy, the therapy was discontinued and the myoclonus disappeared. Conclusions Lithium, by itself, can be associated with prominent clinical myoclonus, short-duration (
Spatially-resolved spectroscopy at 1.6 μm of Titan's atmosphere and surface

[1] We present spatially-resolved, low-resolution (λ/Δλ ∼ 1,500) spectroscopy of the leading hemisphere of Titan in the H-band (1.5–1.7 μm) using adaptive optics. Spatial variations of surface albedo are observed in images at 1.55–1.57 μm, which are clearly distinct from stratospheric haze. There is a significant increase in albedo around the southern (summer) pole at 1.62 μm. Using a plane-parallel radiative transfer model to fit the observed spectra, we find a 61% increase in tropopause haze opacity (τ = 0.100 from 30–40 km) around the southern pole relative to the rest of the disk (where τ = 0.062 from 30–40 km).
Police Administrators' Ambivalence towards Professionalism

The reasons for the traditional ambivalence of police administrators towards the development of police professionalism are explored. The analysis takes account of variables along several dimensions: formal organization, the characteristics of the professional, and the distinction between the rhetoric of professionalism and professional action. Several concerns, intrinsic to the administrative role of assuring continuity and integrity of the organization over time, are cited to explain ambivalence toward professionalism. Reluctance to utilize the rhetoric of professionalism is largely based on the administrator's recognition that the credibility of the rhetoric ultimately depends on the presence of professional activities. Activitating professionalism, rather than utilizing professionalism rhetoric, emerges as the real issue. Several factors associated with professional action create concern for police administrators. These include automony, performance accountability, role taking by the individual, organi...
The Political Economy of Nominal Macroeconomic Pathologies

Recognizing that inflation and the macroeconomic policies that affect it can emanate from distributional conflicts in society, we examine the deep determinants of several nominal pathologies and related policy variables from a distributional perspective. We develop new instruments and use well-established existing instruments for these deep determinants and find that two deep determinants—societal divisions and democratic institutions—have a powerful and robust causal impact on nominal macroeconomic outcomes. Surprisingly, given the widespread attention accorded to the effects of populist democracy on inflation, democracy robustly serves to reduce inflation over the long term. A one standard deviation increase in democracy reduces inflation nearly fourfold. A similar increase in societal divisions increases inflation more than twofold. Our results are robust to alternative measures of democracy, samples, covariates, and definitions of societal division. It is particularly noteworthy that a variety of nominal pathologies and their proximate policy causes discussed in the recent macroeconomic literature, such as procyclical policy, absence of central bank independence, original sin, and debt intolerance, have common origins in societal divisions and undemocratic political institutions.
Arginine methyltransferase activity in chronic erythremic myelosis (Diguglielmo syndrome)

Activity of S-adenosylmethionine-dependent arginine methyltransferase was substantially higher in sonicated bone marrow samples from 6 patients with chronic erythremic myelosis than in bone marrow from 3 patients with untreated pernicious anemia, 2 patients with autoimmune hemolytic anemia, and 4 normal persons. Increased activity of this enzyme may be one of the factors contributing to the pathogenesis fo methylated arginines in histones of erythroblasts from patients with chronic erythremic myelosis.
Avidity modulation activates adhesion under flow and requires cooperativity among adhesion receptors.

An early step in activation of leukocyte adhesion is a release of integrins from cytoskeletal constraints on their diffusion, leading to rearrangement and, consequently, increased avidity. Static adhesion assays using purified ligand as a substrate have demonstrated that very low doses of cytochalasin D disconnect β2-integrins from their cytoskeletal links, allowing rearrangement and activating adhesion. The adhesion process in blood vessels is poorly simulated by these assays, however, for two reasons: leukocyte adhesion to endothelium 1), occurs in the presence of blood flow and 2), involves the simultaneous interactions of multiple sets of adhesion molecules. We investigated the effect of cytochalasin D, at concentrations that increase integrin diffusion but do not alter leukocyte shape and surface features, on adhesion of leukocytes to endothelial cells under flow. Cytochalasin D increased the number of rolling cells, the number of firmly adherent cells, and the duration of both rolling and firm adhesion. These effects required endothelial cell expression of ICAM-1, the ligand for leukocyte β2-integrins. The β2-integrin–ICAM-1 interaction alone was not sufficient, however. Experiments using purified substrates demonstrated that avidity effects on activation of adhesion under flow require functional cooperativity between integrins and other adhesion receptors.
Formulation of Zeeman modulation as a signal filter.

Abstract The Bloch equation containing a Zeeman modulation field is solved analytically by treating the Zeeman modulation frequency as a perturbation. The absorption and dispersion signals at both 0° and 90° modulation phase are obtained. The solutions are valid to first order in the modulation frequency, but are otherwise valid for any value of modulation amplitude or microwave amplitude. A first order treatment of modulation frequency is shown to be a valid approximation over a wide range of typical experimental EPR conditions. The solutions derived from the Bloch equation suggest that the effect of over-modulation on first and second harmonic EPR spectra can be formulated as a mathematical filter that smoothes and broadens the under-modulated signal. The only adjustable filter parameter is a width that is equivalent to the applied peak-to-peak modulation amplitude. The true spin–spin and spin–lattice relaxation rates are completely determined from the under-modulated spectrum. The filters derived from the analytic solutions of the Bloch equation in the linear limit of modulation frequency are tested against numerical solutions of the Bloch equation that are valid for any modulation frequency to show their applicability. The filters are further tested using experimental EPR spectra. Experimental under-modulated spectra are mathematically filtered and compared with the experimental over-modulated spectra. The application of modulation filters to STEPR spectra is explored and limitations are discussed.
Prostate cancer vaccines in combination with additional treatment modalities

Immunotherapy has been investigated in both preclinical studies and clinical trials as a new therapy for prostate cancer. Vaccines, including those that utilize dendritic cells, viruses, or DNA, immunize against prostate-specific antigen and prostatic acid phosphatase. The vaccines have long been studied as monotherapy for the cancer, but increasingly more trials have been initiated in combination with other modalities. These include radiation, chemotherapy, and androgen deprivation therapy. This review describes and discusses the various combinations of vaccine immunotherapies.
Murine DNA Cytosine-C5 Methyltransferase: Pre-Steady- and Steady-State Kinetic Analysis with Regulatory DNA Sequences†

We present the first description of KmDNA, KdDNA, Kcat, and Kmethylation for a mammalian DNA methyltransferase. Homogeneous, 190 000 MTDNA (cytosine-5-)-methyltransferase isolated from mouse erythroleukemia cells has turnover constants of 0.15-0.59 h-1 with single-stranded and unmethylated double-stranded oligonucleotides containing a single CpG dinucleotide. These substrates were designed to mimic DNA transcriptional cis elements previously reported to have cytosine C-5-methylated regulation. The rate-limiting step for these substrates is the methylation step itself. In contrast, hemimethylated double-stranded substrates show burst kinetics, consistent with a rapid methylation event (3 h-1) followed by a slower step which determines steady-state Kcat. Hemimethylated and unmethylated double-stranded DNA shows similar binding affinities; these results reveal the molecular basis for the enzyme's preference for hemimethylated DNA to be the methyl transfer step. Substrates with multiple recognition sites do not show burst kinetics and have turnover rate constants of 6 h-1. Catalytic turnover for the mammalian enzyme is thus approximately 10-fold slower than that for the related bacterial enzymes. Our combined results show quantitatively that one enzyme is certainly capable of both maintenance and de novo methylation and that maintenance of the genomic methylation pattern is preferred over the de novo establishment of new patterns. Direct comparison of the mammalian enzyme with the bacterial DNA cytosine-C5 methyltransferase, M.SssI, indicates dramatic differences in preferences for single-stranded, double-stranded, and hemimethylated double-stranded substrates. Moreover, the specificity hierarchy shown for the M.SssI is derived from very different changes in K(m) and catalysis than those observed for the mammalian DCMTase. These results demonstrate that the M.SssI, and perhaps other DNA cytosine methyltransferases from bacteria, is functionally dissimilar to the mammalian enzyme.
New specimens of Protocetidae (Mammalia, Cetacea) from New Jersey and South Carolina

ABSTRACT The family Protocetidae was first delimited to include Protocetus and Eocetus, the only protocetid genera known at that time. Both are from the middle Eocene of Gebel Mokattam, Egypt. Only three genera were added to the family prior to the 1990s, but since then 16 genera from Indo-Pakistan, North and West Africa, and North America have been added, greatly expanding our knowledge of their diversity, anatomy, behavior, and biogeography. Protocetids are as yet unknown from Europe, Oceania, the North Pacific, or Antarctica. Here, several protocetid teeth are described from New Jersey and South Carolina. The New Jersey specimens represent the northern-most discovery of protocetids in the world. Several were collected by avocational paleontologists, while others were identified in museum collections, where they were previously misidentified. Currently, there are four protocetid species from North America, each in its own genus: Carolinacetus gingerichi, Crenatocetus rayi, Georgiacetus vogtlensis, and N...
Colosplenic Fistula: a Highly Unusual Colonic Fistula

Internal fistulization of the colon to other organs, such as the urinary bladder, vagina, or small bowel is a relatively common complication associated with inflammatory diseases such as diverticulitis, Crohn disease, as well as neoplasia such as colorectal cancer or lymphoma. However, fistulization of the colon to the spleen is an exceedingly rare condition described by few in the literature.
Nucleation control for ZnO nanorods grown by catalyst-driven molecular beam epitaxy

Abstract We report a study of the annealing temperature and time on Ag catalyst size and density for subsequent growth of ZnO nanorods by catalyst-driven molecular beam epitaxy (MBE). Two different substrates (SiO 2 and SiN X ) for the Ag deposition were used and the thickness of the Ag held constant at 25 A. Annealing between 600 and 800 °C produced Ag cluster sizes in the range 8–30 nm diameter on SiO 2 and 10–65 nm on SiN X with a cluster density from 100 to 2500 mm −2 for SiO 2 and 30 to 1900 mm −2 for SiN X . ZnO nanorods grown on these clusters show single-crystal, wurtzite-phase nature and strong band-edge photoluminescence at 380 nm. The nanorods can also be grown selectively on lithographically-patterned dielectric stripes with Ag clusters formed on top by e-beam evaporation and annealing.
3H-5-iodo-2'-deoxyuridine toxicity. Problems in cell proliferation studies.

The toxicity of 3H-5-iodo-2′-deoxyuridine (3H-IUdR) was evaluated by injecting tumor-bearing C3H mice with different concentrations of ethanol (the solvent), different doses of tritium tagged onto either IUdR or thymidine and different chemical doses of IUdR, and then measuring the 3H-IUdR incorporation into duodenal and mammary tumor DNA as well as the cellular kinetics of duodenal crypt cells. Ethanol (37% or less, 0.2 ml/mouse) does not significantly inhibit IUdR incorporation into DNA, and the incorporation after a tritium dose of 75 μCi 3H-IUdR/mouse (about 3 μCi/g body weight) is not less than the incorporation following an injection of 25 μCi 3H-IUdR/mouse when the IUdR dose is below 0.005 μmole per mouse. The toxic effects are primarily due to chemical toxicity from IUdR per se. IUdR, at doses of 0.2 μmoles per mouse does inhibit IUdR incorporation into duodenal and tumor DNA, and the duodenal labeling index and the fraction of labeled mitoses are significantly reduced when 0.013 μmole IUdR per mouse is injected. Also some of the duodenal cells containing IUdR apparently undergo only one post-labeling division and the generation time (Tc) of the cells containing IUdR (25 μCi 3H-IUdR/mouse) is 15.3 hr as compared to 13.3 hr for cells labeled with 3H-T (75 μCi/mouse). This increase in Tc is probably not statistically significant; nevertheless, these results do indicate that one must be exceedingly cautious when using 3H-IUdR as a radiotracer for studies concerned with in vivo cellular kinetics and, at least for C3H mice, the dose should be less than 0.01 μmole per 25 g mouse.
From Trees to Wood and Back: Perspective on Clinical Data Analysis in Thoracic Surgery

General thoracic surgery has been slow to embrace advanced statistical techniques to assess outcome and direct future therapy to individual patients (the "trees") based on aggregating data and discovering informative patterns in them (the "wood"). This is due in part to the nature and complexity of the practice. However, methods exist that deal with problems of small numbers, variable case volume, and heterogeneity of patients, diseases, and therapies. For effective analysis of these multiple variables, modern strategies must be used and pitfalls avoided. For generating new knowledge about appropriateness of therapy, the focus of analyses must include long-term outcome. Quality improvement efforts may be assisted by in-depth analysis of short-term outcome from a select number of centers to inform future universal efforts. Ultimately, these results need to feed back to improved management of the individual patient.
Formulating Chlorinated Hydrocarbon Microemulsions Using Linker Molecules

Previously we reported on the use of lipophilic, hydrophilic, and combined linkers for formulating microemulsions of trichloroethylene and tetrachloroethylene. These linker molecules augment the interaction between the surfactant and oil phase (lipophilic linkers) or between the surfactant and water phase (hydrophilic linkers). Combining both linkers can increase the solubilization capacity several-fold. This formulation technique shows potential advantage in reducing surfactant costs and remedial times, as well as allowing the use of more environmentally friendly additives when designing surfactant-enhanced remediation systems. In this paper, we evaluate the relative importance of the surfactant and each linker in increasing the system's solubilization capacity. This interpretation is based on solubilization curves, partitioning studies, and formulation studies. The solubilization curves show that optimum linker performance is reached at an equimolar ratio of dodecanol, used as a lipophilic linker, and sodium mono and dimethyl naphthalene sulfonate, used as a hydrophilic linker. Furthermore, this equimolar combination was able to replace the anionic surfactant sodium dihexylsulfosuccinate. Dodecanol partitioning at optimum formulation shows that the poor performance of lipophilic linkers alone is due to their low partitioning into the middle phase. Adding hydrophilic linkers into this system increases the fraction of dodecanol in the middle phase, thereby further enhancing the solubilization capacity of the system. A variation of the combined linker approach is introduced by changing a lipophilic linker, oleic acid, into a surfactant (soap), with further increases in the solubilization capacity by 4- to 5-fold.
Energy metabolism of Heliobacterium modesticaldum during phototrophic and chemotrophic growth

Heliobacterium modesticaldum is a gram-positive nitrogen-fixing phototrophic bacterium that can grow either photoheterotrophically or chemotrophically but not photoautotrophically. Surprisingly, this organism is lacking only one gene for the complete reverse tricarboxylic acid (rTCA) cycle required for autotrophic carbon fixation. Along with the genomic information reported recently, we use multiple experimental approaches in this report to address questions regarding energy metabolic pathways in darkness, CO2 fixation, sugar assimilation and acetate metabolism. We present the first experimental evidence that D-ribose, D-fructose and D-glucose can be photoassimilated by H. modesticaldum as sole carbon sources in newly developed defined growth medium. Also, we confirm two non-autotrophic CO2-fixation pathways utilized by H. modesticaldum: reactions catalyzed by pyruvate:ferredoxin oxidoreductase and phosphoenolpyruvate carboxykinase, and report acetate excretion during phototrophic and chemotrophic growth. Further, genes responsible for pyruvate fermentation, which provides reducing power for nitrogen assimilation, carbon metabolism and hydrogen production, are either active or up-regulated during chemotrophic growth. The discovery of ferredoxin-NADP+ oxidoreductase (FNR) activity in cell extracts provides the reducing power required for carbon and nitrogen metabolisms. Moreover, we show that photosynthetic pigments are produced by H. modesticaldum during the chemotrophic growth, and demonstrate that H. modesticaldum performs nitrogen fixation during both phototrophic and chemotrophic growth. Collectively, this report represents the first comprehensive studies for energy metabolism in heliobacteria, which have the simplest known photosynthetic machinery among the entire photosynthetic organisms. Additionally, our studies provide new and essential insights, as well as broaden current knowledge, on the energy metabolism of the thermophilic phototrophic bacterium H. modesticaldum during phototrophic and chemotrophic growth.
Exploring gas permeability of cellular membranes and membrane channels with molecular dynamics.

Abstract Aquaporins are a family of membrane proteins specialized in rapid water conduction across biological membranes. Whether these channels also conduct gas molecules and the physiological significance of this potential function have not been well understood. Here we report 140 ns of molecular dynamics simulations of membrane-embedded AQP1 and of a pure POPE bilayer addressing these questions. The permeability of AQP1 to two types of gas molecules, O2 and CO2, was investigated using two complementary methods, namely, explicit gas diffusion simulation and implicit ligand sampling. The simulations show that the central (tetrameric) pore of AQP1 can be readily used by either gas molecule to permeate the channel. The two approaches produced similar free energy profiles associated with gas permeation through the central pore: a −0.4 to −1.7 kcal/mol energy well in the middle, and a 3.6–4.6 kcal/mol energy barrier in the periplasmic vestibule. The barrier appears to be mainly due to a dense cluster of water molecules anchored in the periplasmic mouth of the central pore by four aspartate residues. Water pores show a very low permeability to O2, but may contribute to the overall permeation of CO2 due to its more hydrophilic nature. Although the central pore of AQP1 is found to be gas permeable, the pure POPE bilayer provides a much larger cross-sectional area, thus exhibiting a much lower free energy barrier for CO2 and O2 permeation. As such, gas conduction through AQP1 may only be physiologically relevant either in membranes of low gas permeability, or in cells where a major fraction of the cellular membrane is occupied by AQPs.
TelEMA: a low-cost and user-friendly telephone assessment platform

Ecological momentary assessment (EMA), or the repeated assessment of individuals’ behaviors and experiences over time, is a methodologically advantageous approach to the study of psychological constructs. Recently, advances in computer technology have allowed for EMA research to be conducted in a more convenient, automated, and secure manner by administering surveys on participants’ telephones and storing the results directly to a central server. The present article introduces TelEMA, an easy-to-use, low-cost telephone assessment platform for clinical and research applications. A single server running TelEMA can be shared among many experimenters, studies, and participants simultaneously. TelEMA routes telephone calls and text messages through a third-party service, so experimenters may conduct studies with no up-front cost or technical expertise. TelEMA provides a secure Web interface for experimenters or clinicians to design studies, enroll participants, monitor compliance, and collate response data from anywhere. Participants complete surveys using their own telephones. Surveys may contain keypress or voice recording questions, and the timing and content of each survey may be randomized and customized. A pilot study was conducted in which individuals used the TelEMA system to complete four randomly timed surveys per day for one week; the surveys assessed state affect and social anxiety. Results indicated that participants found TelEMA easy to use and secure, and compliance rates were on par with other EMA methods using mobile devices. Overall, TelEMA is a practical and robust system that enables fast and inexpensive deployment of EMAs.