cssi/SciSciGPT-SciSciNet huggingface dataset:
The ChrA Response Regulator in Corynebacterium diphtheriae Controls Hemin-Regulated Gene Expression through Binding to the hmuO and hrtAB Promoter Regions

Corynebacterium diphtheriae, the etiologic agent of diphtheria, utilizes heme and hemoglobin (Hb) as iron sources for growth. Heme-iron utilization involves HmuO, a heme oxygenase that degrades cytosolic heme, resulting in the release of heme-associated iron. Expression of the hmuO promoter is under dual regulation, in which transcription is repressed by DtxR and iron and activated by a heme source, such as hemin or Hb. Hemin-dependent activation is mediated primarily by the ChrAS two-component system, in which ChrS is a putative heme-responsive sensor kinase while ChrA is proposed to serve as a response regulator that activates transcription. It was recently shown that the ChrAS system similarly regulates the hrtAB genes, which encode an ABC transporter involved in the protection of C. diphtheriae from hemin toxicity. In this study, we characterized the phosphorelay mechanism in the ChrAS system and provide evidence for the direct regulation of the hmuO and hrtAB promoters by ChrA. A fluorescence staining method was used to show that ChrS undergoes autophosphorylation and that the phosphate moiety is subsequently transferred to ChrA. Promoter fusion studies identified regions upstream of the hmuO and hrtAB promoters that are critical for the heme-dependent regulation by ChrA. Electrophoretic mobility shift assays revealed that ChrA specifically binds at the hmuO and hrtAB promoter regions and that binding is phosphorylation dependent. A phosphorylation-defective mutant of ChrA [ChrA(D50A)] exhibited significantly diminished binding to the hmuO promoter region relative to that of wild-type ChrA. DNase I footprint analysis further defined the sequences in the hmuO and hrtAB promoters that are involved in ChrA binding, and this analysis revealed that the DtxR binding site at the hmuO promoter partially overlaps the binding site for ChrA. DNase I protection studies as well as promoter fusion analysis suggest that ChrA and DtxR compete for binding at the hmuO promoter. Collectively, these data demonstrate that the ChrA response regulator directly controls the expression of hmuO and the hrtAB genes and the binding activity of ChrA is dependent on phosphorylation by its cognate sensor kinase ChrS.
Homologous regulation of gonadotropin-releasing hormone receptors in cultured pituitary cells

Specific receptors for gonadotropin-releasing hormone (GnRH) in cultured rat pituitary cells were increased by subnanomolar concentrations of GnRH agonists and decreased by high concentrations of these peptides. The antagonist [D-Phe2, Pro3, D-Phe6]GnRH did not alter GnRH binding capacity and blocked the increase in sites induced by GnRH. These findings provide direct evidence for the homologous regulation of GnRH receptors by physiological concentrations of the hypothalamic peptide, an action that could mediate the cyclical and postcastration increases in GnRH receptors and responsiveness of the pituitary gonadotrophs.
A phase I dose escalation and pharmacokinetic study of vatalanib (PTK787/ZK 222584) in combination with paclitaxel in patients with advanced solid tumors.

Purpose To define the maximum-tolerated dose (MTD) for weekly paclitaxel administered in combination with daily vatalanib (PTK787/ZK 222584, PTK/ZK) and assess for a drug–drug interaction.
Comparison of mixing model performance for nonpremixed turbulent reactive flow

Abstract A spatially inhomogeneous model problem for studying turbulent nonpremixed reacting flow with reversible reaction is proposed, which admits stationary solutions that are periodic in physical space. The thermochemical state of the fluid is characterized by two composition variables: mixture fraction ξ(x, t) and reaction progress variable Y(x, t). A linear gradient in the mean mixture fraction field is imposed in the x2 direction, so that, in a forced stationary velocity field, the mixture fraction field attains statistical stationarity. The reaction progress variable Y(x, t) is statistically homogeneous in x1 and x3, and is statistically periodic in x2. The flow is called periodic reaction zones. The solutions are parametrized by the Damkohler number and the reaction zone thickness parameter. At sufficiently high Damkohler number there is stable reaction, but as the Damkohler number is decreased below a critical value, global extinction occurs. The range of parameter values is chosen such that the model problem reproduces important phenomena such as stable near-equilibrium reaction, local extinction, and global extinction. Monte Carlo simulations are performed to solve for the joint probability density function of velocity, turbulent frequency, and composition. The predictions for critical Damkohler number are compared for two different mixing models: the interaction by exchange with the mean (IEM) model, and the Euclidean Minimum Spanning Tree (EMST) model. The results obtained using the simpler conditional moment closure (CMC) model are also presented for comparison. The model problem is formulated to permit direct numerical simulations (DNS) using pseudo-spectral methods, which require periodic boundary conditions. The DNS study of this model problem, which is reported in a separate publication, provides additional insight into the phenomenon of extinction in inhomogeneous turbulent reactive flows.
Synthesis of tritium labelled 1-(3,4-dichlorophenyl)-3-(methylamino)propanol hydrochloride

1-(3,4-Dichlorophenyl)-3-(methylamino)propanol hydrochloride, 1, a potential antidepressant, was synthesized by a two-step method in the [3H]-labelled form with specific activity 12.5 mCi/mmol suitable for drug metabolism and disposition studies (1).
Magnetic resonance imaging and computed tomography utilization trends in an academic ED

Abstract Objective The objective of this study is to examine the annual utilization trends of emergency department (ED)–ordered magnetic resonance imaging (MRI) and computed tomography (CT) at an urban academic hospital from 2007 to 2011. We hypothesized that MRI and CT use would increase annually over the study period. Methods This was a retrospective observational study of ED encounters between January 1, 2007, and December 31, 2011. All patients seen by a provider were identified, and demographics were abstracted. Type of CT and/or MRI examination, clinical indication, and final disposition were collected. Records of patients with an ED-ordered MRI were also examined for presence of a CT within ±3 days of their encounter date. Unadjusted linear regression was used to assess for differences among years for both CT and MRI. Secondary outcomes were descriptively summarized. Results A total of 7089 MRI (20 per 1000) and 85673 CT (243 per 1000) examinations were ordered over a 60-month period. Computed tomography use decreased significantly ( P = .021). Magnetic resonance imaging use significantly increased (2.2 per 1000 ED visits each year, P = .005). Magnetic resonance imaging of the head was ordered most frequently (10.7 per 1000). The overwhelming majority of MRI images were completed for acute neurologic/behavioral problem. Of patients with an MRI completed, 89.4% had a CT completed within 3 calendar days with most of the CT examinations (81%) completed during the encounter. Conclusion There was a steady increase in MRI testing in our academic ED, with most MRIs ordered for acute neurologic or behavioral changes. There was a corresponding decreasing trend for CT scans.
Discrete spectral peak estimation in incoherent backscatter heterodyne lidar. II. Correlogram accumulation

For pt.I see ibid., vol.31, no.1, p.16-27 (1993). The correlogram, an alternative to formation of the periodogram from the time series data sample. is described. The correlogram consists of a set of autocorrelation estimates for some number of lags obtained directly from the data sample. Correlogram accumulation entails adding or averaging the sets of autocorrelation estimates prior to the spectral estimation stage. The correlogram is formed in the time domain directly from the data, using a minimal number of multiplications and additions so that it may be formed and accumulated at the speed that the data are acquired. >
Various continuous harmony search algorithms for web-based hydrologic parameter optimisation

This study compares five different harmony search algorithms that consider continuous variables inherently for the hydrologic parameter calibration. A rainfall intensity assessing model, which can provide stochastic rainfall sizes used for various structure designs, is optimally calibrated with the harmony search algorithms. The results showed that three different harmony search algorithms found better parameter values for the rainfall intensity model than mathematical optimisation technique (Powell method) and evolutionary computation technique (genetic algorithm) with respect to root mean square error (RMSE). Also, in order to enhance user-friendliness in utilising this technique, a web-based technique was developed, which optimally performs parameter calibration and presents its result on a digital map without requiring software installation.
Immediate breast reconstruction with prolonged overexpansion using the Becker permanent expander prosthesis

Immediate breast reconstruction following modified radical mastectomy for breast carcinoma will be described. The method which is favored is an insertion of a Becker permanent expander prosthesis. This is overexpanded and left in this situation for 6 months if possible. It is then deflated and the filling valve is left for another month to carry out further adjustments as necessary. Ninety-six patients with 146 implants with an average follow-up of 3.2 years have been reviewed. The vast majority of patients have been satisfied with their results and the plastic surgeon has also been pleased and has judged this to be the best method for reconstruction available at this time. There have been complications of cellulitis, implant exposure, capsule formation, silicone and fluid leaks, but these have not been unduly significant when compared with the total number of implants inserted.
On the correspondence between fermion and boson states and operators

Abstract Mapping of shell-model (fermion) Hamiltonians onto boson Hamiltonians which underly the interaction boson model 1–5 ) is investigated. A simple correspondence is defined and a sufficient condition given for shell-model Hamiltonians to simply correspond to finite hermitian boson Hamiltonians. A special case is discussed where diagonalization of a shell-model Hamiltonian for valence protons and neutrons can be exactly carried out in an equivalent (but different) boson space. If, however, the proton Hamiltonian and neutron Hamiltonian are diagonal in the seniority scheme, mapping of fermion states onto orthogonal boson states cannot be a simple correspondence. In that case the boson quadrupole operators equivalent to fermion guadrupole operators cannot be single-boson operators but must be more complicated, ones.
Retinal features predictive of progressive stage 4 retinopathy of prematurity.

In eyes that develop progressive stage 4 retinopathy of prematurity (ROP) after laser treatment for threshold ROP,1,2 vitreoretinal surgery is considered to prevent or repair retinal detachment.3–7 For the best visual potential, surgery should achieve retinal attachment, be performed before macular detachment,4 and spare the lens to permit visual rehabilitation in the phakic eye.3,7 However, surgical complications of cataract,8 aphakia, and peripheral retinal breaks have vision-threatening consequences, including profound amblyopia and inoperable retinal detachment,5 which are unique to the developing infant compared with the adult. In addition, because approximately 70% of eyes treated for threshold ROP1,2 and some eyes with stage 4A ROP do not progress,9 recognition of retinal features predictive of progression of stage 4 ROP may facilitate early treatment of eyes at risk for vision loss and also minimize treatment of some low-risk eyes. We performed this study to determine the characteristics predictive of progression of stage 4 ROP in infants who had been adequately treated for threshold ROP. We abstracted features from retinal drawings made at the time of examinations performed within 1 week of developing partial retinal detachment (stage 4A ROP) or 2 weeks after laser treatment in eyes that showed regression of disease. We developed a generalized estimating equation (GEE) model that accounted for within-subject variability of the eyes10 to determine predictive features of progressive stage 4 ROP in eyes after laser treatment for threshold ROP.
Acoustic signature recognition technique for Human-Object Interactions (HOI) in persistent surveillance systems

Handling, manipulation, and placement of objects, hereon called Human-Object Interaction (HOI), in the environment generate sounds. Such sounds are readily identifiable by the human hearing. However, in the presence of background environment noises, recognition of minute HOI sounds is challenging, though vital for improvement of multi-modality sensor data fusion in Persistent Surveillance Systems (PSS). Identification of HOI sound signatures can be used as precursors to detection of pertinent threats that otherwise other sensor modalities may miss to detect. In this paper, we present a robust method for detection and classification of HOI events via clustering of extracted features from training of HOI acoustic sound waves. In this approach, salient sound events are preliminary identified and segmented from background via a sound energy tracking method. Upon this segmentation, frequency spectral pattern of each sound event is modeled and its features are extracted to form a feature vector for training. To reduce dimensionality of training feature space, a Principal Component Analysis (PCA) technique is employed to expedite fast classification of test feature vectors, a kd-tree and Random Forest classifiers are trained for rapid classification of training sound waves. Each classifiers employs different similarity distance matching technique for classification. Performance evaluations of classifiers are compared for classification of a batch of training HOI acoustic signatures. Furthermore, to facilitate semantic annotation of acoustic sound events, a scheme based on Transducer Mockup Language (TML) is proposed. The results demonstrate the proposed approach is both reliable and effective, and can be extended to future PSS applications.
On-Line Diagnosis of Unrestricted Faults

A formal model for the study of on-line diagnosis is introduced and used to investigate the diagnosis of unrestricted faults. Within this model a fault of a system S is considered to be a transformation of S into another system S' at some time r. The resulting faulty system is taken to be the system which looks like S up to time r and like S' thereafter. Notions of fault tolerance and error are defined in terms of the resulting system being able to mimic some desired behavior as specified by a system S. A notion of on-line diagnosis is formulated which involves an external detector and a maximum time delay within which every error caused by a fault in a prescribed set must be detected.
From germ theory to germ therapy: skin microbiota, chronic wounds, and probiotics.

Background:Microorganisms living throughout the body comprise the human “microbiota” and play an important role in health and disease. Recent research suggests that alterations in the skin microbiota may underlie chronic wound pathology. Probiotics are bacteria or yeast that confer a health benefit
Evidence for detective repair of cyclobutane pyrimidine dimers with normal repair of other DNA photoproducts in a transcriptionally active gene transfected into Cockayne syndrome cells

Abstract Cockayne syndrome (CS) and xeroderma pigmentosum (XP), autosomal recessive diseases with clinical and cellular hypersensitivity to UV radiation, differ in ability to repair UV DNA photoproducts in their overall genome: normal repair in CS, defective repair in XP. In order to characterize a DNA repair defect in an active gene in CS, we measured the capacity of cells from patients with CS and XP to reactive 2 major types of UV-induced DNA damage, photoreactivatable (i.e., cyclobutane pyrimidine dimers) and non-photoreactivable (primarily pyrimidine-(4–6)pyrimidone photoproducts, in the actively transcribing chloramphenicol acetyltransferase ( cat ) gene of the plasmid expression vector pRSV-cat. Epstein-Barr virus-transformed lymphoblast lines from 4 normal persons and from 3 patients with CS and from two with XP were transiently transfected with the plasmid, and the cat activity in cell extracts was determined. When the cells were transfected with UV-irradiated plasmid, cat expression was abnormally decreased in both the CS and XP cells. When the cyclobutane pyrimidine dimers in the UV-irradiated plasmid were removed by photoreactivation prior to transfection, cat expression in the CS, but not in the XP, lines reached normal levels. These data imply that both XP and CS cells are unable to repair normally the cyclobutane pyrimidine dimer photoproducts which block transcription of cat . However, the CS, but not XP, cells can repair normally the other UV-induced photoproducts which block transcription. The ability of CS, but not XP, cells to repair these non-dimer photoproducts indicates that the active gene repair mechanism treats the cyclobutane pyrimidine dimer differently from the non-dimer photoproducts.
Role of native disulfide bonds in the structure and activity of insulin-like growth factor 1: Genetic models of protein-folding intermediates

Insulin and insulin-related proteins contain three motif-specific disulfide bonds. Here we examine the role of these disulfide bonds in the folding and function of one family member, human insulin-like growth factor 1 (IGF-1). Analogues containing pariwise Cys-->Ser or Cys-->Ala substitutions were expressed in Escherichia coli, purified, and analyzed with respect to receptor-binding, solution structure, and thermodynamic stability. An analogue lacking all three disulfide bonds (designated des-Cys-IGF-1) is inactive and unfolded. Introduction of the [18-61] disulfide bond, previously shown to occur in an early intermediate in oxidative refolding [Miller, J. A., Owers-Narhi, L., Hua, Q. X., Rosenfeld, R., Arakawa, T., Rohde, M., Prestrelski, S., Lauren, S., S. Stoney, K. S., Tsai, L., & Weiss, M. A. (1993) Biochemistry (preceding paper in this issue)], results in a compact partially folded state with low but significant biological activity. Additional but incomplete structural organization and biological activity are observed following introduction of either the [6-48] or the [47-52] disulfide bonds. Native function, structure, and stability require the presence of all three disulfide bonds. These analogues provide genetic models of IGF-1 protein-folding intermediates. Their characterization suggests that bifurcation of the IGF-1 folding pathway reflects alternative late steps in the folding of a molten-globule intermediate.
Restoring legitimacy to the systems approach

The systems approach is a mainstay of engineering theory and practice, but it has been misapplied in the public policy arena and it is now viewed skeptically. This article briefly analyzes the problems that have been encountered with certain prescriptive applications of system concepts in the field of public policy. It then suggests steps that could restore credibility and legitimacy to policy-related applications of the systems approach.
Design and Full-Scale Test for Steel Tubular Tower of UHV and EHV Quadruple-Circuit Transmission Line on the same Tower

State Grid Corporation of China has carried out research on key technology of UHV&EHV AC and DC multi-circuit transmission lines, the research on material and structure of transmission tower is the important part. The SSZT2 tower, on which 1000 kV AC double-circuit and 500 kV AC double-circuit are arranged, is the largest power transmission capacity all over the world. Q420 high-strength tubular steel, the plug-in boards and forging flanges are used in SSZT2 tower,and the forging flange with strength classification is applied for the first time. Through the monographic study on the tower structures, wind vibration coefficient, and biaxial bending of steel tube etc. The success of full-scale test verified the reliability in design and manufacture of multi-circuit steel tubular tower for UHV and EHV. Research results of this paper can be applied in UHV transmission line projects.
Who Are We? Mining Institutional Identities Using n-grams

Disciplines and organizations alike can be defined by the text they produce, the topics they discuss, and the language they employ. Analyzing such large amounts of text is challenging, but is nevertheless needed because it can help stakeholders to understand key themes in, and the evolution of their corporate or disciplinary identity. N-gram analysis is a leading text-mining technique that can be leveraged for this purpose. In this manuscript we present the development and demonstrate the potential utility of an n-gram analysis tool. We focus on revealing several aspects of the identity of an academic journal, namely Communications of the ACM (CACM), through the analysis of over 14 million unique n-grams and their relative frequencies. The results of the study imply that n-gram analyses may be a key tool in resolving the IS identity crisis. Implications for research and practice are discussed.
The Relationship Between Neuropsychological Functioning and Coping Activity Among HIV-Positive Men

Neuropsychological impairment occurs in many persons with AIDS and in a smaller proportion of asymptomatic HIV-1 carriers, but the implications of such impairments in terms of psychosocial functioning are poorly understood. We explored potential differences in coping activity (e.g., cognitive and behavioral efforts to manage, alter, or regulate emotional responses to stressful situations) in a group of 275 medically symptomatic and asymptomatic HIV-positive men stratified on neuropsychological impairment. Regardless of medical symptom status, persons rated as being neuropsychologically impaired in attention/speed of information processing and verbal skills utilized significantly more confrontive coping than did unimpaired subjects. It may be that individuals with difficulty sustaining attention to details or reduced ability to process verbal information resort to impulsive forms of coping because they are less able to assess the precise nature or extent of threat or harm posed by a stressful situation.
DESENSITIZATION AND INSIGHT.

Abstract For many years, awareness of forgotten experiences and conflicts (insight) has been considered necessary for long-lasting beneficial therapeutic results. The author suggests that in cases where insight therapy has been successful the patients were desensitized toward noxious environmental situations and this resulted in changes in verbal behavior which indicated that the patient was aware of possible etiological factors related to the symptom complex. Three cases are presented in which the desensitization procedure of Wolpe was used to achieve a remission of symptoms. While no attempt was made by the therapist to make the patient aware of etiological factors concerning the symptom complex, the patient gave insightful-like statements as the desensitization procedure became effective. The alternate hypothesis that symptom-alleviation causes insight was advanced as a more valid explanation of the situation where insightful-like statements occur concomitant with symptom changes.
Work‐based learning in practice

This paper depicts a prototypical learning program based on the author’s model of work‐based learning. The model is premised on the simple idea that learning can be acquired in the midst of practice. It deliberately merges theory with practice and acknowledges the intersection of explicit and tacit forms of knowing. There are eight learning modalities in the model of work‐based learning. The paper concentrates on three somewhat popular action strategies that are typically presented in isolation: action learning, action science, and communities of practice. The paper demonstrates how corporate educators and facilitators might distinguish between these approaches and yet offer them in a meaningful sequence based upon their preferences, skill, and comfort level as well as upon the needs of their managerial clients.
A theory for the high field conductance of polyelectrolytes

Using a theory based on that of Onsager for the dissociation field effect, the authors have shown it is possible to explain the dependence of the Wien effect or polyelectrolyte samples on concentration, molecular weight, and gegenion mobility. The theory has been used to calculate a parameter, q, interpreted as representing a function of polyion size. It has been shown that for samples of polystyrenesulfonic acid the variation of q with increasing neutralization showed a constant polyion size, as would be expected of a fully charged polyion when only the gegenions are exchanged; a sample at a smaller concentration had a larger polyion, as would be expected. For samples of polyacrylic acid, the variation of q with increasing neutralization was initially similar to that revealed by viscosity or light scattering measurements—a rapid increase in polyion size. In our measurements, however, the size remained relatively constant over a considerable range of neutralization and then decreased slightly. This is interpreted as meaning that the ions removed from the polyion are those near the surface, and that the radius of importance in this particular experiment is more nearly the radius of the extended polyion cylinder and not a radius computed from the end-to-end separation of the polyion.
Antihypertensive efficacy of pinacidil--automatic ambulatory blood pressure monitoring.

Forty-three patients with mild essential hypertension were randomized into two double-blind studies: pinacidil vs. placebo or pinacidil vs. hydralazine. Pinacidil (62±18 mg/day) decreased office systolic and diastolic blood pressures from 145 to 137 mm Hg and from 98 to 89 mm Hg, respectively, after 6 weeks of therapy. Similarly, hydralazine (128±28 mg/day) reduced supine systolic blood pressure from 140 to 134 mm Hg and supine diastolic blood pressure from 93 mm Hg to 84 mm Hg. Significant tachycardia was not noted with either drug. Ambulatory blood pressure was monitored for 24 h during the placebo-washout and efficacy phases with both pinacidil and hydralazine. Mean 24-h blood pressure was 128 systolic and 81 diastolic with pinacidil and 121 systolic and 76 diastolic with hydralazine. Reduction in awake hypertensive diastolic blood pressure was significant for both pinacidil and hydralazine. Normal sleep diastolic blood pressure was not reduced by pinacidil but was reduced by hydralazine. Side-effects with both drugs included edema, headache, and palpitations. These data demonstrate that pinacidil is as effective an antihypertensive agent as hydralazine.
Preparation of fused-silica polar stationary phase wallcoated open tubular columns

Abstract Recent methodology, developed in our laboratory for the preparation of Pyrex (borosilicate) wall-coated open tubular (WCOT) gas chromatography columns with the polar stationary phases Superox™-4 (4 · 10 6 molecular weight polyethylene glycol) and SP-1000 (nitroterephthalic acid derivative of Carbowax 2OM), was successfully adapted to the preparation of fused-silica WCOT columns with these phases. Pretreatment of the fused-silica tubing with Superox-4 increased the surface energy, improved the wettability of the surface for polar phases and deactivated the fused-silica surface. The polar stationary phases, Superox-4 and SP-1000, were statically coated onto the Superox-4-treated surface. These polar WCOT columns were found to be efficient, thermally stable, and low in surface activity.
Craft-Based IGERT Experiment in Graduate Macromolecular Studies

The Teaching Craft for Macromolecular Creativity project at Louisiana State University is an experiment in graduate polymer education. With support from the National Science Foundation's Division of Graduate Education, in the form of an IGERT grant, it has affected 36 Ph.D.-intending graduate students from 6 departments using an Apprentice-Artisan-Craftsperson training ladder adapted from the trade arts. After research-driven lecture and lab-based coursework in the synthesis, characterization, processing, and theory of macromolecules, recruits joined an interdisciplinary team including other students, faculty, and off-campus participants. Based on merit, students were elected as Apprentices, who worked side by side at the bench with professors and other on- or off-campus “research craftspersons” for 2–6 weeks. Upon completion of a written report and advancement to Ph.D. candidacy, Apprentices became Artisans. Among other privileges and responsibilities, Artisans were permitted to write minigrants to explo...
Diabetes and poor disease control: is comorbid depression associated with poor medication adherence or lack of treatment intensification?

Background Many patients with diabetes fail to achieve American Diabetes Association Guidelines for glycemic, blood pressure and lipid control. Depression is a common comorbidity and may affect disease control through adverse effects on adherence and physician intensification of treatment.
Photovoltage Mechanism for Room Light Conversion of Citrate Stabilized Silver Nanocrystal Seeds to Large Nanoprisms

We investigate the photoconversion of aqueous 8 nm Ag nanocrystal seeds into 70 nm single crystal plate nanoprisms. The process relies on the excitation of Ag surface plasmons. The process requires dioxygen, and the transformation rate is first-order in seed concentration. Although citrate is necessary for the conversion, and is consumed, the transformation rate is independent of citrate concentration. We propose a mechanism that accounts for these features by coupling the oxidative etching of the seed and the subsequent photoreduction of aqueous Ag+. The reduced Ag deposits onto a Ag prism of specific size that has a cathodic photovoltage resulting from plasmon “hot hole” citrate photo-oxidation. This photovoltage mechanism also explains recent experimental results involving single and dual wavelength irradiation and the core/shell synthesis of Ag layers on Au seeds.
A novel semi-supervised learning approach to analyzing metagenomic reads

A novel semi-supervised learning approach is proposed to partition metagenomic reads by combining supervised learning method and unsupervised learning method. In this paper, corresponding analytic methods and dedicated simulating studies were conducted within the scope of a controlled framework emphasizing performance improvement, especially when reads from similar species are applied. According to the experimentation and the learning deliverables, the proposed method outperforms the existing algorithms in the case that the reads partitioning has a considerable number of similar species.
PHONY: A Heuristic Phonological Analyzer

PHONY is a program to do phonological analysis. Within the generative model of grammar the function of the phonological component is to assign a phonetic representation to an utterance by modifying the underlying representations (URs) of its constituent morphemes. Morphemes are the minimal meaning units of language, i.e. the smallest units in the expression system which can be correlated with any part of the content system, e.g. un+tir+ing+ly. URs are abstract entities which contain the idiosyncratic information about pronounciations of morphemes.
Zeta-Potential Measurements of Surfactant-Wrapped Individual Single-Walled Carbon Nanotubes

A systematic study of the zeta (ζ)-potential distribution of surfactant-wrapped individual single-walled carbon nanotubes (SWNTs) dissolved in water is presented here. The surface charge on the SWNT micelles, as measured by the ζ-potential, has implications for the stability of the dispersions and for the electrophoretic and dielectrophoretic assembly and alignment of SWNTs. Very highly charged SWNTs are obtained by dispersing the nanotubes in high concentrations of anionic and cationic surfactants, whereas almost neutral SWNTs are obtained by using non-ionic surfactants. The ζ-potential of the dissolved SWNTs is tuned by adjusting the surfactant concentration, the alkyl chain length of the surfactant molecule, and the solution pH in different surfactant−SWNT systems.
High density plasma source for plasma lens experiments

Experimental results of the study of a candidate source for high-energy particle beam underdense plasma lens experiments are presented. The high density plasma is based an the operation of the back-lighted thyratron. A 100% ionized hydrogen plasma with density of 1.7/spl times/10/sup 16/ cm/sup -3/ homogeneous in space and monotonically varying in time with a time scale on the order of /spl mu/secs is straightforwardly achievable. The desired plasma density for lens experiments can be achieved very simply by controlling either the applied voltage, the beam entry time or other parameters. This scheme presents a simple device with the ability to support a plasma with density ranging from 10/sup 12/ cm/sup -3/ to above 10/sup 16/ cm/sup -3/. The structure also facilitates the particle beam entry and the components are vacuum compatible. The device is small, simple, robust,easy to adjust, can be operated at high repetition rates, and has a long life time. >
Structure-based enzyme inhibitor design: modeling studies and crystal structure analysis of Pneumocystis carinii dihydrofolate reductase ternary complex with PT653 and NADPH

Structural data are reported for N-(2,4-diaminopteridin-6-yl)methyldibenz[b,f]azepine (PT653), an example of structure-based inhibitor design with 21-fold selectivity for Pneumocystis carinii dihydrofolate reductase (pcDHFR) relative to rat liver dihydrofolate reductase (rlDHFR). These data test the hypothesis that 2,4-diaminopteridines with a bulky N,N-diarylaminomethyl side chain at the 6-position could fit better into the larger active site of pcDHFR than into that of mammalian DHFR. The crystal structure of the ternary complex of NADPH, PT653 and pcDHFR, refined to 2.4 A resolution, reveals that PT653 binds in a different orientation than predicted from modeling studies reported previously [Rosowsky et al. (1999), J. Med. Chem. 42, 4853–4860]. These crystal data show that the pteridine-ring plane is tilted compared with that observed in the crystal structure of the pcDHFR methotrexate (MTX) NADPH ternary complex used as a template to model PT653 binding. Also, as a result of this tilt, the dibenzoazepine ring is bound deeper into the p-­aminobenzoyl folate binding pocket of pcDHFR, thereby relieving close intermolecular contacts predicted from the modeling data. By far the most significant structural change, but more subtle in magnitude, is the ligand-induced conformational shift of 1.2 A away from the inhibitor of residues 61–­66 in helix C. The other major effect is the unwinding of the short helical segment involving loop 47 which has a different conformation to that observed in other pcDHFR complexes [Cody et al. (1999), Biochemistry, 38, 4303–4312]. The favorable pcDHFR selectivity of PT653 could be a result of ligand-induced fit of the large hydrophobic dibenzazepine ring which occupies regions of the enzyme active site not probed by other antifolates and which take advantage of sequence and conformational differences between the structures of human and pcDHFR. These data suggest that such hydrophobic analogs could be used as lead compounds in the design of more pcDHFR-selective antifolates. Enzyme inhibition data also show that PT653 is 102-fold selective for Toxoplasma gondii (tg) DHFR relative to rlDHFR. Homology-modeling studies of the tgDHFR structure suggest that differences in ligand-binding orientation and enzyme sequence could influence the enhanced selectivity of PT653 for tgDHFR.
Respiratory metabolism of normal and divisionless strains of Candida albicans.

Respiration of a normal strain of Candida albicans was compared with that of a divisionless mutant which has a biochemical lesion such that metabolically generated hydrogen "spills over," during growth, for non-specific dye reduction. This waste is not at expense of growth, since both strains grow at essentially similar rates, nor at expense of respiration, since the mutant reduces oxygen more rapidly than the normal strain. Respiration in both strains is qualitatively similar, and seemingly unique among highly aerobic organisms in that it is not mediated by cytochrome oxidase. In resting ceils of both strains, respiration is not only resistant to, but markedly stimulated by, high concentrations of cyanide, carbon monoxide, and azide. In contrast, growth of these yeasts is inhibited by low concentrations of cyanide and azide. Cytochrome oxidase Could not be detected in cell-free preparations; reduced cytochrome c was not oxidized by such preparations. Cytochrome bands could not be observed in thick ceil suspensions treated with reducing agents. However, incorporation of superoptimal levels of zinc and iron into the culture medium resulted in growth of cells possessing distinct cytochrome bands; respiration of these cells remained insensitive to cyanide, monoxide, and azide, and the bands were maintained in a reduced form on oxygenation. In the divisionless yeast, tetrazolium dyes compete with oxygen for reduction; this is not the case in the normal strain. The firmness with which hydrogen transfer is channeled in the latter for reduction of disulfide bonds (of importance in the division mechanism) and of oxygen, is contrasted with the lack of such control in the mutant.
Inflammatory cytokine levels correlate with amyloid load in transgenic mouse models of Alzheimer's disease

BACKGROUND: Inflammation is believed to play an important role in the pathology of Alzheimer's disease (AD) and cytokine production is a key pathologic event in the progression of inflammatory cascades. The current study characterizes the cytokine expression profile in the brain of two transgenic mouse models of AD (TgAPPsw and PS1/APPsw) and explores the correlations between cytokine production and the level of soluble and insoluble forms of Abeta. METHODS: Organotypic brain slice cultures from 15-month-old mice (TgAPPsw, PS1/APPsw and control littermates) were established and multiple cytokine levels were analyzed using the Bio-plex multiple cytokine assay system. Soluble and insoluble forms of Abeta were quantified and Abeta-cytokine relationships were analyzed. RESULTS: Compared to control littermates, transgenic mice showed a significant increase in the following pro-inflammatory cytokines: TNF-alpha, IL-6, IL-12p40, IL-1beta, IL-1alpha and GM-CSF. TNF-alpha, IL-6, IL-1alpha and GM-CSF showed a sequential increase from control to TgAPPsw to PS1/APPsw suggesting that the amplitude of this cytokine response is dependent on brain Abeta levels, since PS1/APPsw mouse brains accumulate more Abeta than TgAPPsw mouse brains. Quantification of Abeta levels in the same slices showed a wide range of Abeta soluble:insoluble ratio values across TgAPPsw and PS1/APPsw brain slices. Abeta-cytokine correlations revealed significant relationships between Abeta1-40, 1-42 (both soluble and insoluble) and all the above cytokines that changed in the brain slices. CONCLUSION: Our data confirm that the brains of transgenic APPsw and PS1/APPsw mice are under an active inflammatory stress, and that the levels of particular cytokines may be directly related to the amount of soluble and insoluble Abeta present in the brain suggesting that pathological accumulation of Abeta is a key driver of the neuroinflammatory response.
Deep Brain Stimulation for the Control of Pain

Abstract The most common sites of deep brain stimulation (DBS) for relief of pain are the periaqueductal gray (PAG) for nociceptive pain and the principal sensory nucleus of the thalamus (Vc) for control of neuropathic pain. The mechanism of action of PAG stimulation seems to involve release of endogenous opiates, whereas the mechanism of Vc stimulation may involve either antidromic activation of the spinothalamic tract or orthodromic activation of thalamocortical relay cells. Success rates are higher for PAG stimulation than for Vc stimulation, but long-term success rates for both are in the range 40 to 60%. The rate of complications with DBS is lower in recent literature of DBS for movement disorders than in earlier literature of DBS for pain, suggesting that hardware modifications have decreased the rate of complications. DBS is an option in patients with chronic pain who are refractory to other modes of medical and surgical therapy.
Nonlinear Dynamics Modeling of Correlated Functional Process Variables for Condition Monitoring in Chemical–Mechanical Planarization

This paper aims to investigate correlation mechanism among functional process variables (FPVs) for condition monitoring in chemical-mechanical planarization (CMP). During wafer polishing, critical process variables such as coefficient of friction and pad temperature vary with time and present in the shape of functional curves. Our previous work has demonstrated that correlation patterns among these FPVs could be related to polishing conditions. Since correlation is affected by both amplitude fluctuations and phase variability in FPVs, further study of timing correlation of FPVs measured in different units could bring more insight into the physical interactions and thereby enhance CMP condition monitoring. Existing research on FPVs in CMP mainly focuses on individual effects of FPVs and statistical correlations through experimental and theoretical analyses. In this paper, we intend to specifically reveal the timing correlation patterns in CMP. Using nonlinear dynamics, we first established a dynamic phase model to define the strength and patterns of FPV interaction. By monitoring the extracted patterns, we then developed a novel method of detecting CMP condition change and demonstrated the approach via a CMP experiment. The results show that the proposed method has a promising application in identifying the process changes that may not be easily detected otherwise.
Traumatic Fibular Shaft Fractures in Athletes

A direct blow to the leg resulted in fibular shaft fractures in three elite college athletes participating in contact sports. None of the athletes had prior symptoms suggestive of a stress fracture. All three athletes had benign-appearing fractures and were treated nonoperatively. Ultimate healing was delayed, occurring on average at 23 weeks, and each case was complicated by refracture. Fractures of the fibular shaft in athletes may require more aggressive treatment than other simple fractures to allow sufficient healing to withstand the rigors of athletics.
Orderly stimulation of skeletal muscle motor units with tripolar nerve cuff electrode

An electrical nerve stimulation technique, using a single tripolar electrode, was shown to be capable of recruiting motor units according to their size, while allowing simultaneous but independent control of firing rate in the active units. Test paradigms consisting of established fundamental physiological concepts of soleus-gastrocnemius architecture, motor units conduction velocity, firing rate behavior of motor units of different sizes, and their susceptibility to fatigue were used to validate the technique and demonstrate its utility as a basic and applied research tool. >
Laboratory standards and guidelines for population-based cystic fibrosis carrier screening.

In 1997, the National Institutes of Health convened a Consensus Development Conference on Cystic Fibrosis (CF).1 The Consensus Conference recommended that genetic screening for CF mutations should be offered to identify carriers among adults with a positive family history of CF, partners of individuals with CF, couples currently planning a pregnancy, and couples seeking prenatal care. A second NIH-sponsored conference that focused on the implementation of the Consensus Conference recommendations was held in 1998.2 Shortly thereafter, the American College of Medical Genetics (ACMG) and the American College of Obstetricians and Gynecologists (ACOG), in conjunction with the National Human Genome Research Institute, formed a Steering Committee to coordinate the implementation of population-based CF carrier screening and to develop “Clinical and Laboratory Provider Guidelines” for (1) provider education; (2) laboratory testing, interpretation, and genetic counseling; and (3) patient education and informed consent. The ACMG charged the Accreditation of Genetic Services Committee, chaired by Dr. Robert Desnick, to establish a Subcommittee on Cystic Fibrosis Carrier Screening (henceforth the “Committee”) to develop recommendations and guidelines for optimal laboratory testing, interpretation, and counseling. The Subcommittee, cochaired by Drs. Wayne Grody and Garry Cutting, met twice yearly since October 1998. The issues considered by the Committee included (1) the target population to be screened (universal vs. limited to certain high-risk ethnic groups); (2) the screening model to be used (couple-based vs. sequential); (3) criteria for and selection of the standard mutation testing panel; (4) potential value and use of an extended testing panel with additional mutations; (5) whether to test for mutations and variants associated with mild or nonclassical phenotypes (such as congenital bilateral absence of the vas deferens); (6) test interpretation, reporting, and genetic counseling; and (7) laboratory quality assurance. The recommendations detailed here have been incorporated into a joint ACMG/ACOG/NIH Steering Committee document entitled “Preconceptual and Prenatal Carrier Screening for Cystic Fibrosis” which will be widely distributed. This document also will include guidelines for providers, patient education, and informed consent. Patient education materials will include two pamphlets, entitled “Cystic Fibrosis Carrier Testing. . . The Decision is Yours” and “Cystic Fibrosis Testing: What Happens if Both My Partner and I are Carriers?” It is important to note that these guidelines were prepared for population CF carrier screening and that different testing and counseling strategies would be employed for the identification of the mutation(s) in patients diagnosed with CF or in relatives of CF patients. Such diagnostic and prenatal mutation analyses should be referred to a genetics center for appropriate testing and counseling.
Virtually networked housing movement: Hyperlink network structure of housing social movement organizations:

Using such theories as resource mobilization and social capital, this article examines how housing social movement organizations (SMOs) in the USA are connected through hyperlink networks. In doing so, this article employed hyperlink network analysis (HNA) through data collected from 26 national housing SMOs. Results indicate that the more bridging ties an organization has, the more central they are to the network. Results also show that the more incoming hyperlinks that a particular organization has, the more central they are to the network. These results suggest that the utilization of bridging social capital by a housing SMO has the potential to increase the ability to mobilize resources by that organization. Furthermore, increasing the number of bridging hyperlinks available on a website can improve the web presence of the SMO furthering the goals of the overall movement.