cssi/SciSciGPT-SciSciNet huggingface dataset:
Empirical Bayes accomodation of batch-effects in microarray data using identical replicate reference samples: application to RNA expression profiling of blood from Duchenne muscular dystrophy patients

Non-biological experimental error routinely occurs in microarray data collected in different batches. It is often impossible to compare groups of samples from independent experiments because batch effects confound true gene expression differences. Existing methods can correct for batch effects only when samples from all biological groups are represented in every batch. In this report we describe a generalized empirical Bayes approach to correct for cross-experimental batch effects, allowing direct comparisons of gene expression between biological groups from independent experiments. The proposed experimental design uses identical reference samples in each batch in every experiment. These reference samples are from the same tissue as the experimental samples. This design with tissue matched reference samples allows a gene-by-gene correction to be performed using fewer arrays than currently available methods. We examine the effects of non-biological variation within a single experiment and between experiments. Batch correction has a significant impact on which genes are identified as differentially regulated. Using this method, gene expression in the blood of patients with Duchenne Muscular Dystrophy is shown to differ for hundreds of genes when compared to controls. The numbers of specific genes differ depending upon whether between experiment and/or between batch corrections are performed.
Interaction between red cell membranes and fibrinogen.

Abstract We have previously reported that red blood cells interact in fibrin formation to yield altered fibrin. ( 1 ) In these experiments, human red blood cells have been separated into fractions representing walls and a soluble fraction. These components were admixed with fibrinogen to determine whether the N-terminal structure of fibrin would be altered. The components were also admixed with preformed fibrin to determine whether alterations of this substrate could be achieved. It was shown that a primary relationship exists between erythrocyte membranes and fibrinogen. Under these conditions, N-terminal amino acid analysis revealed an alteration of the 4:2 ratio of glycine to tyrosine, and substantial additions of aspartic acid and alanine.
MODULATION OF THE BIOLOGICAL FUNCTIONS OF GALECTIN-3 BY MATRIX METALLOPROTEINASES

Galectin-3 is an important intracellular and extracellular lectin which is presumed to interact with extracellular matrix proteins and cell surface glycoproteins in normal and pathophysiological conditions. The exact physiological role of the protein is presently not known. We have previously demonstrated that recombinant human galectin-3 is a novel substrate for metalloproteinases, particularly MMP-2 and MMP-9. These enzymes are capable of efficiently cleaving the Ala62–Tyr63 bond of the ca. 30 kDa galectin-3, generating a 22 kDa fragment with intact carbohydrate recognition domain and a ca. 9 kDa polypeptide comprising the amino terminal end of the intact galectin-3. In this study, we analyzed interactions of the 22 kDa fragment of galectin-3 with immobilized laminins. We have also compared the hemagglutination as well as homodimerization potentials of this fragment with that of intact galectin-3. Our data suggest that cleavage of galectin-3 by metalloproteinases; (a) alters the carbohydrate recognition domain of the lectin so that it binds more tightly to the glycoconjugates and, (b) reduces selfassociation of the galectin molecules thereby abrogating the biological properties dependent on such associations or homodimerization.
When are persons ‘white’?: on some practical asymmetries of racial reference in talk-in-interaction:

This report contributes to the study of racial discourse by examining some of the practical asymmetries that obtain between different categories of racial membership as they are actually employed in talk-in-interaction. In particular, we identify three interactional environments in which the ordinarily ‘invisible’ racial category ‘white’ is employed overtly, and we describe the mechanisms through which this can occur. These mechanisms include: (1) ‘white’ surfacing ‘just in time’ as an account for action; (2) the occurrence of referential ambiguities with respect to race occasioning repairs that result in overt references to ‘white’; and (3) the operation of a recipient design consideration that we term ‘descriptive adequacy’. These findings demonstrate some ways in which the mundane invisibility of whiteness — or indeed, other locally invisible racial categories — can be both exposed and disturbed as a result of ordinary interactional processes, revealing the importance of the generic machinery of talk-i...
What you need to know about statistics, part II: reliability of diagnostic and screening tests

The intent of this manuscript is to provide guidance and support to clinicians and investigators for reporting the results of screening and diagnostic tests. This article is the first of two parts addressing statistics in imaging research. In this part validity measures are discussed. In part II reliability measures will be discussed. In discussing validity, the following concepts will be introduced: (1) functions of diagnostic tests, (2) statistical characteristics of diagnostic tests and application of validity measures, (3) power and sample size for testing the sensitivity and specificity of the diagnostic test, (4) statistical versus clinical significance and (5) characteristics of a useful diagnostic test.
Magnetic structure and paramagnetic dynamics of chromium and its alloys.

Using mean-field theory, we study the dynamics of chromium and its alloys above the N\'eel temperature ${\mathit{T}}_{\mathit{N}}$. Starting with a three-band model of chromium, we recover the two-band model originally developed by Sato and Maki (SM). From the poles of the transverse spin susceptibility, we calculate the wave vector and N\'eel temperature of the spin-density-wave (SDW) state. Like SM, we find that the SDW is commensurate with the lattice when the energy mismatch ${\mathit{z}}_{0}$ between the electron and hole Fermi surfaces is smaller than the critical value ${\mathit{z}}_{0}^{\mathrm{*}}$\ensuremath{\approxeq}365 meV, which may be achieved with the addition of a small fraction of manganese impurities, as observed experimentally. In the incommensurate state above ${\mathit{z}}_{0}^{\mathrm{*}}$, the susceptibility contains two peaks on either side of the wave vector G/2=2\ensuremath{\pi}/a for small frequency and close to ${\mathit{T}}_{\mathit{N}}$. In the commensurate state below ${\mathit{z}}_{0}^{\mathrm{*}}$, the susceptibility contains only a single peak at G/2. Because ${\mathit{z}}_{0}^{\mathrm{*}}$ decreases with the damping energy \ensuremath{\Gamma}, this central peak may split into sidepeaks with the addition of isoelectric impurities such as molybdenum or tungsten. As \ensuremath{\Gamma} increases, ${\mathit{z}}_{0}^{\mathrm{*}}$ reaches a minimum value of about 185 meV. When ${\mathit{z}}_{0}$ is below this minimum value, the SDW is always commensurate for any value of the damping. If \ensuremath{\Gamma} exceeds the critical damping ${\mathrm{\ensuremath{\Gamma}}}_{\mathrm{cr}}$, then the N\'eel temperature vanishes but the susceptibility still contains peaks near the wave vectors of the SDW with \ensuremath{\Gamma}=0. In agreement with experiments by Fawcett et al., we find that the elastic-scattering cross section for paramagnetic chromium alloys vanishes at T=0. We also predict that the elastic-scattering cross section reaches a maximum at a temperature which increases with \ensuremath{\Gamma}.
Hyperkeratosis induced by sunlight degradation products of the major polybrominated biphenyl in Firemaster

Sunlight photodegradation of 2,2', 4,4', 5,5' -hexabromobiphenyl, the major component of Firemaster, gave a mixture that produces severe hyperkeratosis of the rabbit ear. This component in its pure state does not cause hyperkeratosis. One or more of the four major photolysis products must be responsible for this activity. A similar photodegradation pattern was observed for 2,2', 3,4,4', 5,5' -heptabromobiphenyl, the second largest component of Firemaster.
Evidence for deformation associated with the 1998 eruption of Axial Volcano, Juan de Fuca Ridge, from acoustic extensometer measurements

Acoustic extensometer instruments capable of making precise daily measurements of horizontal distance were deployed across the north rift zone of Axial Volcano in June 1996 and were in place when a submarine eruption began on Axial's south rift zone in January 1998. The instruments recorded a gradual 9-cm extension over a 405-m baseline leading up to the eruption, and then an abrupt, 4-cm contraction at the time of the eruption. An elastic point-source deformation model shows that deflation of Axial's summit can explain both the 4-cm distance decrease at the extensometer array and a 3.2-m subsidence measured by another instrument in the caldera, if the pressure source is located at a depth of 3.8 km below the center of the caldera. The 9-cm distance increase may represent pre-eruption spreading across the rift zone.
Rescue and replication signals of the adeno-associated virus 2 genome.

Abstract The adeno-associated virus 2 (AAV) genome is a single-stranded DNA which contains the inverted terminal repeats (ITRs) of 145 nucleotides. The terminal 125 nucleotides of each ITR form palindromic hairpin structures that serve as primers for AAV DNA replication. These hairpin structures also play a crucial role in the integration, as well as the rescue, of the proviral genome from latently-infected cells, or from the recombinant AAV plasmids. However, the ITRs also contain an additional domain, designated the D-sequence, a 20-nucleotide stretch that is not involved in the formation of hairpins. In order to examine the role of the D-sequence in viral DNA rescue and replication, a number of recombinant AAV plasmids were constructed which contained deletions/substitutions in different regions of the ITRs. The results presented here reveal the existence of additional sequences, other than the hairpin structures, which serve as primers for AAV DNA replication. The results also show that whereas the hairpin structures are sufficient for excision and replication of the viral DNA, the D-sequence is crucial for the high efficiency of rescue and replication of the AAV genome. f2
Role of 5-hydroxytryptamine in the modulation of acoustic brainstem (far-field) potentials.

Abstract Acoustic brainstem evoked responses (far-field) were recorded in rats anesthetized witha-chloralose, subsequent to pharmacological modification of serotonergic activity. Reserpine caused an initial decrement followed by an increment in FFP amplitudes, probably as a result of initial displacement followed by depletion of 5HT from its storage sites. Depletion of 5HT by PCPA also caused an amplitude increment, whereas increased 5HT levels following 5HTP administration resulted in an amplitude decrement. It is suggested that 5HT may be an inhibitory transmitter in pontine and mesencephalic brainstem relays of the auditory pathway.
ZnSe-ZnSxSe1−x and ZnSe-Zn1−xMnxSe metal-insulator-semiconductor heterostructure lasers

Abstract Metal-insulator-semiconductors (MIS) heterostructures, using ZnSe and ZnSe-based ternary compounds such as ZnSSe and ZnMnSe, have been proposed to obtain efficient blue light emission and lasing action. MIS laser structures are particularly desirable for wide energy gap semiconductors in which the controlled doping of n- and p-type impurities is somewhat difficult to realize. The MIS heterostructure laser is a novel device as an alternative to the conventional p-n double heterojunction laser. In these lasers, efficient minority carrier injection in the active layer is achieved from the MIS interface in place of a p-n heterojunstion emitter. Emitted photons are confined in the active layer as they are reflected by a heterostructure dielectric discontinuity (e.g., ZnSe-ZnS x Se 1- x ) on one side and the perfectly reflecting surface of the barrier metal on the other. Modal analysis of a stripe geometry Au-SiO 2 -n-ZnSe-n-ZnS x Se 1- x -n-ZnSe MIS laser is presented. The output characteristics are compared with a conventional p-n double heterostructure laser. A MIS heterostructure to realize a distributed feedback laser is also discussed.
The anachronism of moral individualism and the responsibility of extended agency

Recent social theory has departed from methodological individualism’s explanation of action according to the motives and dispositions of human individuals in favor of explanation in terms of broader agencies consisting of both human and nonhuman elements described as cyborgs, actor-networks, extended agencies, or distributed cognition. This paper proposes that moral responsibility for action also be vested in extended agencies. It advances a consequentialist view of responsibility that takes moral responsibility to be a species of causal responsibility, and it answers objections that might be raised on the basis of intentions and deserts.
Strategy Orientations, Learner Activity, and Learning Outcomes: Implications for Instructional Support of Learning

Investigated were the differential effects of strategy orientations (memory strategy, organization strategy, application strategy, and read-and-study control) orthogonally crossed with learner activity (guided versus active) and outcomes (memory, organization, and application). Subjects were 136 undergraduates, randomly assigned to 1 of 8 treatments. One day after they studied a passage on the topic of radar, outcome measures were completed. Guided activities were found to be superior to the learner-active counterparts on a composite achievement score. The hypothesized interaction of strategy orientation and kind of measure was supported. Performance was highest, in every comparison, on the outcome measure that paralleled the strategy-orientation treatment. The main effect of strategy orientation on the total achievement score was not significant. These findings were discussed in terms of the transfer-appropriate processing theory, the encoding specificity principle, and generative learning theory, with implications for further research and instructional design.
Effect of a Circumferential Arc Crack on the Vibration Characteristics of a Flexible Spinning Disk

The vibration characteristics of a circumferentially cracked rotating disk are investigated. The disk is assumed to be axisymmetric, flexible and clamped at the center. The crack increases the local flexibility of the disk at the crack location and is modeled as linear and torsional springs, connecting the two segments of the disk. The spring constants are evaluated by considering crack opening displacements due to bending moment and shear force at the crack location. The equations of motion of two segments of the disk, for disk operating in vacuum as well as subjected to shear fluid flow are developed. Using the Finite Difference Technique, the coupled systems of equations are solved and the natural frequencies and mode shapes are obtained. The mode shapes are seen to be comparatively flattened in the inner region of the disk separated by the crack and heightened towards the periphery of the disk. Shear fluid loading reduces the critical speeds and results in a quicker onset of instability. The degree of instability caused by the crack is a function of crack depth and location. Critical speeds increase with increasing crack distance from the central clamp and decrease with increasing crack depth.Copyright © 2007 by ASME
Playing Well with Others: The Discipline in a Pediatric Hospital

This article contains a personal reflection on the way it feels, in fact and in theory, to move from a chaplaincy position in a clinical setting, to one where clinical chaplaincy is relatively new. The article presents the ways a clinically trained chaplain can introduce herself to a new setting, and how she must continually reevaluate her approach.
Risk and Disease

The way that diseases such as high blood pressure (hypertension), high cholesterol, and diabetes are defined is closely tied to ideas about modifiable risk. In particular, the threshold for diagnosing each of these conditions is set at the level where future risk of disease can be reduced by lowering the relevant parameter (of blood pressure, low-density lipoprotein, or blood glucose, respectively). In this article, I make the case that these criteria, and those for diagnosing and treating other "risk- based diseases," reflect an unfortunate trend towards reclassifying risk as disease. I closely examine stage 1 hypertension and high cholesterol and argue that many patients diag - nosed with these "diseases" do not actually have a pathological condition. In addition, though, I argue that the fact that they are risk factors, rather than diseases, does not diminish the importance of treating them, since there is good evidence that such treat - ment can reduce morbidity and mortality. For both philosophical and ethical reasons, however, the conditions should not be labeled as pathological. The tendency to reclas - sify risk factors as diseases is an important trend to examine and critique.
EPR studies of the valence states of thulium in thulium monochalcogenides

We have studied theGd3+ EPR at 9.2 HGz in 0.1 at % GdS inTmS, 1 at %GdTe inTmTe, and 1 at %GdSe inTmSe. From the temperature dependence of theGd3+ linewidth we have concluded thatTm inTmS is trivalent. The temperature variation of theGd3+ linewidth inTmTe has been interpreted as the result of the “delocalization” of the extra electron “localized” aroundGd3+. Theg-value and linewidth data are consistent with the identification thatTm inTmTe is divalent. The linewidth and theg-value of theGd3+ resonance inTmSe have been found to be temperature independent. These striking results have been attributed to the “motional narrowing” effect arising from valence fluctuations ofTm inTmSe.
Synthesis, structure and molecular dynamics of η2-iminoacyl compounds [Cp(ArO)Zr(η2-ButNCCH2Ph)(CH2Ph)] and [Cp(ArO)Zr(η2-ButNCCH2Ph)2]

The reaction of the substrate [CpZr(CH2Ph)3] with the ligands 2,3,5,6-tetraphenyl- 1, 2-phenyl-4,6-di-tert-butyl- 2 or 2-(1-naphthyl)-4,6-di-tert-butyl-phenol 3 leads to the corresponding compounds [Cp(ArO)Zr(CH2Ph)2] 4–6. Solution studies show that naphthyl rotation is slow on the NMR timescale at ambient temperatures within 6 leading to non-equivalent benzyl groups with diastereotopic methylene protons. The solid-state structure of 5 shows both benzyl ligands to be η1-bound. Compounds 4–6 react with tert-butylisocyanide in hydrocarbon solvents to initially produce the mono(iminoacyl) derivatives [Cp(ArO)Zr(η2-ButNCCH2Ph)(CH2Ph)] 7–9 followed by the bis(iminoacyl) products [Cp(ArO)Zr(η2-ButNCCH2Ph)2] 10–12. In the solution 13C NMR spectra of the iminoacyl derivatives the Zr–CN carbon atom resonates at δ 242–244 ppm (7–9) and δ 229–234 ppm (10–12) consistent with the η2-C,N binding. This was confirmed in the solid state by X-ray diffraction studies of 8, 11 and 12. At ambient temperatures only one set of iminoacyl resonances are observed for 10 and 11, indicating that both iminoacyl rotation and aryloxide rotation are facile. At lower temperatures the iminoacyl ligands in 11 become non-equivalent in the 1H NMR spectrum consistent with restricted rotation about the Zr–O–Ar bond. The iminoacyl ligands in the 2-(1-naphthyl) derivative 12 are non-equivalent in solution NMR spectra from −75 to +85 °C. The solution fluxionality of these molecules as determined by NMR studies is discussed in detail.
Allyl Esters of Crambe-Derived Long-Chain Fatty Acids and Their Polymers

Synopsis Allyl esters of erucic, brassidic, behenic, oleo-erucic, and stearo-behenic acids, prepared by refluxing benzene solutions of the acids with excess allyl alcohol in the presence of p-toluenesulfonic acid monohydrate, polymerize smoothly in the presence of 5 wt. %t -butyl perbenzoate at 120°C for 24 hr. Polymerization of the unsaturated acid esters involves a large portion (ca. 84%) of allylic and a small portion (ca. 26%) of ethylenic bonds. The products, saturated and unsaturated, have a degree of polymerization between 6 and 10 and are soluble in typical polymer solvents. Crystallinity, judged by thermal analysis, decreased with increased cis unsaturation. The oligomers melted between -30°C and 59°C and started decomposing at 200°C.
RCLK-VJ network reduction with Hurwitz polynomial approximation

We propose a new linear network reduction algorithm based on a generalized Y-/spl Delta/ transformation technique in s-domain. Resultant admittance is kept as a rational function of s with a dramatically reduced order. Yet it preserves low-order terms of exact admittance evaluated with traditional symbolic analysis. Stability of transfer functions derived from reduced-order admittance is guaranteed via a Hurwitz polynomial approximation. Such low-order transfer functions are used in pole analysis and time domain waveform evaluation in response to any input signal.
Pericytes prevent regression of endothelial cell tubes by accelerating metabolism of lysophosphatidic acid

Efforts to eradicate pathological vessels in neovascular diseases and induce growth of mature, functional vasculature in ischemic diseases are limited by our incomplete understanding of molecular mechanisms of vessel stabilization. While it is well known that pericytes stabilize blood vessels, the underlying mechanisms have not been fully elucidated. The goal of this study was to further investigate the mechanisms by which pericytes stabilize vessels. In an in vitro model of blood vessels, in which regression is driven by lysophosphatidic acid (LPA), pericyte-mediated stabilization was associated with a decrease in the concentration of LPA. The decline in the concentration of LPA was not caused by a reduction in activity or expression of autotaxin, the main enzyme implicated in LPA production. Rather, pericytes accelerated LPA metabolism. Stabilization of tubes by pericytes correlated with accelerated LPA dephosphorylation and increased expression of lipid phosphate phosphatases (LPPs). Finally, pericytes failed to stabilize tubes exposed to an LPA analogue, which was resistant to degradation. Our results suggest that pericytes stabilize endothelial cell tubes by accelerating the metabolism of LPA.
The impact fracture toughness of plasticized cellulose acetate and the relationship with the secondary loss transition

The impact fracture toughness of plasticized cellulose acetate has been determined by linear elastic fracture mechanics over the temperature range 20–70°C. A major peak in fracture toughness at −10°C has been found to correspond to a secondary loss transition in the dynamic mechanical loss spectrum of plasticized cellulose acetate. At −10°C, the fracture toughness is directly proportional to the log of the maximum strain rate.
A game theory framework for cooperative management of refillable and disposable bottle lifecycles

Abstract Firms engaged in industrial ecology hope to reduce environmental impacts and costs, improve resource efficiency, and create symbiotic relationships that reduce transaction costs and enhance information flow. However, current LCA tools do not explain firms' incentives to implement the principles of industrial ecology, or how an individual or firm can affect the products and processes at other firms. Game theory, on the other hand, allows investigation of the willingness of producers and consumers to seek strategies that promote the common interest of the system while not harming their own interests. This paper applies game theory to the lifecycle of bottle packaging, and presents a framework for analysis of the choice between refillable and disposable bottles. Although refillable bottles may be more cost effective in the long run, bottlers only have incentive to use refillable bottles when they are sure that consumer return rates will be reasonably high. It has been found that consumers who keep or dispose of refillable bottles, or respond to deposit/refund return incentives by reducing their demand, may drive costs up and encourage adoption of disposables. A simple model is provided which finds the optimal bottler strategy as a function of the bottler's expectations for consumer cooperation.
Contribution of feedforward thalamic afferents and corticogeniculate feedback to the spatial summation area of macaque V1 and LGN.

Neurons in the primary visual cortex (V1) respond best to oriented gratings of optimal size within their receptive field (RF) and are suppressed by larger gratings involving the nonclassical RF surround. A V1 neuron's optimal stimulus size is larger at lower stimulus contrast. A central question in visual neuroscience is what circuits generate the size tuning of V1 cells. We recently demonstrated that V1 horizontal connections integrate signals within a region of the RF center corresponding to the V1 neuron's optimal stimulus size at low contrast; extrastriate feedback connections to V1, instead, are longer range and can integrate signals from the most distant regions of the V1 cell's RF surround. Here, we have determined the contribution of geniculocortical feedforward and corticogeniculate feedback connections to the size-tuning of macaque V1 and lateral geniculate (LGN) neurons, respectively. Specifically, we have quantitatively compared the visuotopic extent of geniculate feedforward afferents to V1 with the size of the RF center and surround of neurons in the V1 input layers and the visuotopic extent of V1 feedback connections to the LGN with the RF size of cells in V1 layer 6, where these connections originate. We find geniculate feedforward connections to provide visuotopic information to V1 that is spatially coextensive with the V1 neuron's optimal stimulus size measured with high-contrast gratings. V1 feedback connections restrict their influence to an LGN region visuotopically coextensive with the size of the minimum response field (or classical RF) of V1 layer 6 cells and commensurate with the LGN region from which they receive feedforward connections. J. Comp. Neurol. 498:330–351, 2006. © 2006 Wiley-Liss, Inc.
Factors controlling the photochemical generation of gaseous H2O2 in the Los Angeles atmosphere

The factors for controlling the photochemical generation of gaseous H{sub 2}O{sub 2} were studied on the basis of both field data and model predictions. Field data of the concentration of gaseous H{sub 2}O{sub 2} at ground-level were obtained in west Los Angeles during 1985-88. The results indicate that there is a clear seasonal trend of gaseous H{sub 2}O{sub 2} (0.03-1.35 ppb, n=150) with highest concentrations in the summer. Statistical analyses revealed that the concentration of H{sub 2}O{sub 2} increases with increasing solar radiation at a statistically significant level. A one-dimensional photochemical model, which is based on the prevailing meteorological conditions and primary pollutants loading in Los Angeles, also predicted that solar radiation is the major factor in determining the formation rate of H{sub 2}O{sub 2} in the atmosphere. These results indicate that solar radiation significantly controls the formation of gaseous H{sub 2}O{sub 2}. Considering the low photochemical activity in the winter, H{sub 2}O{sub 2} is probably limiting for the oxidation of SO{sub 2} in the Los Angeles winter atmosphere where the SO{sub 2} content exceeds the H{sub 2}O{sub 2} concentrations. Our results also imply that, if the UV radiation in the troposphere increases due to the depletion of the stratosphericmore » O{sub 3} content, the H{sub 2}O{sub 2} levels will increase and as a result the production of sulfuric acid will increase in the winter atmosphere.« less
Bilateral Renal Artery Involvement of Erdheim–Chester Disease

To report a rare case of nonatherosclerotic renal artery disease (NARAD) in a patient with Erdheim-Chester disease (ECD), a non-Langerhans cell histiocytosis. The patient is a 75-year-old male who presented with 2 years of hypertension secondary to right renal artery occlusion incidentally found on cardiac catheterization. Open bilateral renal revascularization was performed because of improved long-term graft patency demonstrated in other forms of NARAD. Nine months postoperatively, the patient's hypertension was significantly improved and surveillance duplex demonstrated patent bilateral renal artery bypasses. Revascularization in patients with NARAD, such as ECD, should be managed in an open approach because of the superior long-term graft patency and blood pressure control in a disease where progression to vessel fibrosis and atherosclerosis could interfere with endovascular stent patency.
False Positives and Negatives Obtained with PCR-Based Identification of Staphylococcus aureus Clonal Complex 398

Staphylococcus aureus belonging to multilocus sequence type (MLST) 398 (ST398) and their relatives in clonal complex 398 (CC398) have emerged recently as important zoonotic agents worldwide ([1][1]). Livestock, especially swine, are implicated in carriage and transmission of these organisms, as are
Equilibration of Scroll Wave Filaments in the Ventricular Wall and the Minimal Principle

Scroll waves of electrical excitation are self-organized reentrant waveforms circling a filament and are a suspected cause of lethal cardiac arrhythmias. The lack of information about the filaments inside the cardiac wall raises the question of what is the dynamics of scroll waves and what equilibrium shape, if any, can we expect for their filaments. Here, we analyze the filament configuration and describe their equilibration in a curved slab of twisted fibers, a reasonably close model of the ventricular wall. We then generalize our findings by the use of the recently developed minimal principle to show that the filaments are predictable; namely, they are aligned with minimal resistance paths (geodesics) determined by the fiber configuration.
Emission spectrum differences in fluorescent blacklight lamps.

Summary Two types of fluorescent blacklight lamps with distinctly different emission spectra bear the same code designations. One type, which we refer to as BL-O, has most of its UV radiation emission centered over 350 nm. The other (BL-N) type concentrates more energy around 365 nm. The spectral differences are correlated with the manufacturer's shift in the type of phosphor used in the lamps. Whether this change is detrimental to photobiological experiments depends in part on the user's ability to independently verify emission spectra.
Electroporative transfection with KGF-1 DNA improves wound healing in a diabetic mouse model

We recently demonstrated that electroporation enhances transfection in a mouse wound-healing model. Keratinocyte growth factor (KGF) is an inducer of epithelial cell proliferation and differentiation and has been shown to be under expressed in the wounds of diabetic individuals. We hypothesized that KGF delivered into an excisional wound via naked DNA injection with subsequent electroporation would be a novel and potentially effective method to enhance wound closure in a diabetic mouse model. ELISA assays confirmed production of KGF protein in cultured mouse cells and RT-PCR assays confirmed KGF mRNA in skin samples taken from mice. In all, 32 genetically diabetic mice were given two identical excisional wounds of their dorsum and split into two groups with one group receiving KGF DNA injection and electroporation with the other group receiving no treatment. Over 90% of wounds healed in the presence of KGF and electroporation versus 40% in the untreated group by day 12. Histological analysis of the wounds demonstrated that untreated wounds contained microulcers with thin or incomplete epithelium with unresolved inflammation as compared to treated wounds where intact and mature epithelium was observed. Taken together these findings suggest that a single injection of KGF DNA encoded on a plasmid coupled with electroporation improves and accelerates wound closure in a delayed wound-healing model.
Assessing the Usefulness of 18F-fluorodeoxyglucose PET-CT Scan After Stereotactic Body Radiotherapy for Early-Stage Non-small Cell Lung Cancer

BACKGROUND Although stereotactic body radiation therapy (SBRT) is an established treatment option for early-stage lung cancer, there are no guidelines for reassessing patients for local treatment failure or intrathoracic recurrence after treatment. This study reports the sensitivity, specificity, and positive and negative predictive values for 18 F-fluorodeoxyglucose (FDG) PET-CT scanning when used to evaluate patients after SBRT. METHODS Charts were reviewed of all patients who received SBRT and a subsequent FDG PET-CT scan at a university hospital over a 5-year period. Pretreatment and 3-month posttreatment tumor characteristics on PET-CT scan and outcome data (adverse events from SBRT, need for repeat biopsy, rate of local treatment failure and recurrent disease, and all-cause mortality) were recorded. RESULTS Eighty-eight patients were included in the study. Fourteen percent of patients (12 of 88) had positive 3-month PET scans. Of the positive results, 67% (eight of 12) were true positives. Eighty-six percent (76 of 88 patients) had negative 3-month FDG PET-CT scans, with 89% (68 of 76) true negatives. FDG PET-CT scan performed 3 months after SBRT for non-small cell lung cancer (NSCLC) had a sensitivity of 50% (95% CI, 0.26-0.75), a specificity of 94% (95% CI, 0.89-1.0), a positive predictive value of 67% (95% CI, 0.4-0.93), and a negative predictive value of 89% (95% CI, 0.83- 0.96). CONCLUSIONS FDG PET-CT scan 3 months after treatment of NSCLC with SBRT was a specific but insensitive test for the detection of recurrence or treatment failure. Serial CT scans should be used for early surveillance following SBRT, whereas FDG PET-CT scans should be reserved to define suspected metastatic disease or to evaluate new abnormalities on CT scan, or for possible reassessment later in the follow-up period after radiation-related inflammation subsides.
Black-Box, Round-Efficient Secure Computation via Non-malleability Amplification

We present round-efficient protocols for secure multi-party computation with a dishonest majority that rely on black-box access to the underlying primitives. Our main contributions are as follows: * a O(log^∗ n)-round protocol that relies on black-box access to dense cryptosystems, homomorphic encryption schemes, or lossy encryption schemes. This improves upon the recent O(1)^{log∗ n} -round protocol of Lin, Pass and Venkitasubramaniam (STOC 2009) that relies on non-black-box access to a smaller class of primitives. * a O(1)-round protocol requiring in addition, black-box access to a one-way function with sub-exponential hardness, improving upon the recent work of Pass and Wee (Euro crypt 2010). These are the first black-box constructions for secure computation with sub linear round complexity. Our constructions build on and improve upon the work of Lin and Pass (STOC 2009) on non-malleability amplification, as well as that of Ishai et al. (STOC 2006) on black-box secure computation. In addition to the results on secure computation, we also obtain a simple construction of a O(log^∗ n)-round non-malleable commitment scheme based on one-way functions, improving upon the recent O(1)^{log∗ n}-round protocol of Lin and Pass (STOC 2009). Our construction uses a novel transformation for handling arbitrary man-in-the-middle scheduling strategies which improves upon a previous construction of Barak (FOCS 2002).
Retinal afferent arborization patterns, dendritic field orientations, and the segregation of function in the lateral geniculate nucleus of the monkey

Abstract Optic tract fibers and cell bodies in the lateral geniculate nucleus of the monkey were studied intracellularly with micropipette electrodes containing the marker enzyme horseradish peroxidase. Single optic-tract fibers always projected to only one of the six geniculate layers. The majority of the axons innervating the four parvocellular laminae were red/green opponent color units; their terminations formed cylindrical columns that were perpendicular to the layers. In similar fashion, the geniculate cells in the parvocellular layers were mostly red/green units with narrow, bipolar dendritic fields oriented normal to the laminar borders. The majority of the retinal axons ending in parvocellular layers 6 and 5 were on-center units; nearly all geniculate cells in these two laminae were also on-center neurons. In layers 4 and 3 most terminating optic-tract fibers, as well as the geniculate cells themselves, were off-center units. All axons projecting to the magnocellular layers were broad-band units with spherical terminal arborizations. The magnocellular geniculate neurons, which were also broad band, had extensive spherical dendritic fields that often crossed laminar borders. Thus, the terminal patterns of each class of retinogeniculate axon closely resembled the dendritic orientations of the functionally related geniculate target cells.
A View through Faraday’s Fog. II. Parsec-Scale Rotation Measures in 40 Active Galactic Nuclei

Results from a survey of the parsec-scale Faraday rotation measure (RM) properties for 40 quasars, radio galaxies, and BL Lac objects are presented. Core RMs for quasars vary from approximately 500 to several thousand rad m-2. Quasar jets have RMs that are typically 500 rad m-2 or less. The cores and jets of the BL Lac objects have RMs similar to those found in quasar jets. The jets of radio galaxies exhibit a range of RMs from a few hundred to almost 10,000 rad m-2 for the jet of M87. Radio galaxy cores are generally depolarized, and only one of four radio galaxies (3C 120) has a detectable RM in the core. Several potential identities for the foreground Faraday screen are considered, and we believe the most promising candidate for all the active galactic nucleus types considered is a screen in close proximity to the jet. This constrains the path length to approximately 10 pc, and magnetic field strengths of approximately 1 μG can account for the observed RMs. For 27 out of 34 quasars and BL Lac objects, their optically thick cores have good agreement with a λ2 law. This requires the different τ = 1 surfaces to have the same intrinsic polarization angle independent of the observed frequency and distance from the black hole.
Viral FLIPping Autophagy for Longevity

Tumor-causing γ-herpesviruses have evolved elaborate mechanisms to deal with almost every aspect of host cell defense. In this issue of Cell Host & Microbe, Leidal et al. (2012) report an oncogenic synergy between the latent KSHV proteins v-FLIP and v-cyclin during KSHV persistent infection that reshapes autophagy.
Delayed action control problems

In this paper modifications to be made in the theory of optimal control are given for the case when the controlled system model has dependence on both the previous history of state variables and control variables. More specifically, systems which are modeled by linear functional differential equations are considered. The systems may have additional side constraints or multiple cost functionals. The question of the existence of an optimal controller is studied, and the necessary and sufficient conditions for an optimal controller are derived.
HIV-1 infection of the developing nervous system: central role of astrocytes in pathogenesis

Abstract Recent studies in our laboratory and that of Dr. Howard Gendelman have revealed two important pathways for neuronal damage during HIV-1 encephalopathy in children. First, substantial numbers of astrocytes are actively or latently infected with HIV-1. Astrocyte infection may lead to neuronal dysfunction through loss of supporting growth factors, excitotoxicity due to dysregulation of neurotransmitter reuptake, and loosening of the blood-brain barrier permitting further seeding of HIV-1 in the CNS. Significantly, infection of astrocytes is marked by near-exclusive synthesis of early regulatory gene products of HIV-1, while structural proteins characteristic of productive infection are found in macrophages, microglia and multinucleated giant cells. We propose the term ‘restricted’ to denote the non-productive infection found in astrocytes. Second, HIV-1-infected macrophages initiate inflammatory processes which are amplified through cell-cell interactions with astrocytes. Macrophage-astrocyte interactions produce arachidonic metabolites and potentially neurotoxic cytokines (TNF-α and IL-1β), leading to astroglial activation and proliferation which then amplifies these cellular processes. These new findings suggest that two major pathways leading to neurotoxicity in pediatric AIDS encephalopathy are linked to HIV-1 infection through astrocyte-mediated processes, and help explain how small numbers of productively infected cells indirectly cause widespread tissue pathology and elicit profound neurological impairment.
Structured contraceptive counseling provided by the Contraceptive CHOICE Project

Background We describe the contraceptive counseling provided by the Contraceptive CHOICE Project (CHOICE) and compare contraceptive methods selected between the university research site and community partner clinics.
IDTT therapy in cadaveric lumbar spine: temperature and thermal dose distributions

The purpose of this study was to perform extensive temperature mapping throughout human cadaveric disc (n=12) specimens during Intradiscal Thermal Therapy IDTT using the SpineCath applicator. Temperature distributions and accumulated thermal dose or thermal damage calculated from the temperature-time history are used to define probable regions of thermal necrosis (destruction of nerves) or thermal coagulation (induced structural changes). The IDTT procedure using SpineCath (5 cm resistive heating segment) and the current standard heating protocol (∼17 min) produces intra-discal temperatures which are too low to generate appreciable regions of thermal coagulation and resultant changes in biomechanical properties. This finding was supported by temperature measurements which were mostly below the critical temperature of 60-65°C, except for regions within 1-2 mm of the SpineCath applicator. Furthermore, the analysis of the thermal dose profiles indicate that sufficient thermal doses (240-640 EM 43°C ) capable of generating complete thermal damage to the nociceptive nerves fibers infiltrating the disc are limited to within ∼6 mm of the nucleus and IDTT probe heating segment.
A Boundary Element Cavitation Algorithm

In this paper, a new numerical algorithm is presented to predict gaseous cavitation in various fluid film bearings. Elrod's universal differential equation is transformed into a generalized boundary integral equation, which is valid throughout both the full film and the cavitated regions. The mathematical development of the algorithm couples the boundary discrete element and internal integral cell techniques. A computer code for linear elements is developed. Three types of bearings, a parabolic slider bearing, a submerged journal bearing, and a grooved journal bearing, are investigated. The results are compared with those obtained by use of the finite difference method. The advantage of the algorithm is clearly demonstrated by its computational accuracy and solution speed. Presented as a Society of Tribologists and Lubrication Engineers paper at the STLE/ASME Tribology Conference in New Orleans, Louisiana, October 24–27, 1993
Hereditary properties of graphs

Let αo(G) denote the point coverning number of a graph G, let βo(G) denote the point independence number of G. In 1959, Gallai [1] proved that, for any graph G having p points, αo(G)+βo(G)=p. This paper contains several generalizations of Gallai's Theorem of the form αo(P)+βo(P)=p, where αo(P) and βo(P) denote generalizations of αo(G) and βo(G) to a broad class of properties P which are called hereditary. A property P of a graph G is hereditary if, whenever G has property P and G′ is a subgraph of G, then G′ also has property P.
Studies on the blood sugar of Octopus dofleini

Abstract 1. 1. Blood glucose levels (4·5–65·5) mg per cent) have been determined in Octopus dofleini for the period February–July. Both sexes show a rise in blood sugar over this period. It appears that, at any given time during the first half of the year, the sexes do not differ significantly in blood glucose concentration. 2. 2. Insulin has been assayed at concentrations of 15–51 units/kg. In some of the assays hypoglycaemia was observed, but it is questionable whether this was a specific response to the hormone. 3. 3. Glucagon, nor-epinephrine, octopamine, dopamine and serotonin have been assayed for glycaemic effects. At the concentrations tested none brought about a change in the blood sugar level, but some of the assays are unsatisfactory and the negative results are not conclusive. 4. 4. Hyperglycaemia was established by infusion of glucose. It appears that about 3 hr is required for distribution of the sugar throughout the exra-cellular fluid. Return to the pre-infusion blood sugar level is slow. 5. 5. Dietary hyperglycaemia (after feeding) has been observed. Its duration indicates that a considerable time is required for complete digestion and absorption of a meal.
Hyporeninemic normoaldosteronism in severe autonomic failure

Sympathetic mechanisms play an important role in the acute regulation of renin release in humans. On the other hand, the effect of chronic sympathetic deprivation on the renin-aldosterone system has not been fully evaluated. We, therefore, studied 24 patients with severe autonomic failure due to pure autonomic failure (n = 14) or to multiple system atrophy (n = 10). Supine plasma renin activity (PRA) was low (0.09 +/- 0.01 ng/(L*s)) and remained virtually unchanged in the upright posture (0.10 +/- 0.01 ng/(L*s)) despite profound orthostatic hypotension to levels that should activate renal baroreceptors. Isoproterenol, at doses that produced significant tachycardia and hypotension, also failed to stimulate PRA. Furthermore, renin-producing cells were absent in the kidneys of two autopsy cases. Norepinephrine depletion alone could not explain these findings because no correlation was found between plasma norepinephrine and PRA, and because PRA was normal in patients with intact sympathetic innervation but c...
Direct measurement of the reversal potential and current-voltage characteristics in the acid and alkaline regions of Chara corallina.

A new vibrating probe-current voltage measuring system is described which enabled us to detect current-voltage curves in the acid and alkaline regions of Chara corallina (Klein ex Willd., em. R.D.W.). Extracellular current analysis, performed before and after the measurement of a current-voltage curve, established that the voltage-clamp protocol had no significant effect on the transport function of the plasma membrane, provided no action potential was triggered. This validated experimental system was then used to determine the reversal potential (- 450 mV) and the stoichiometry (1 H(+):ATP hydrolyzed) of the Chara H(+)-ATPase, which dominates the acid regions. Current-voltage curves of the acid regions almost saturated at values close to the resting potential, in the absence of exogenous buffer. Introduction of artificial buffers and-or HCO 3 (-) shifted the reversal potential of this area to more positive values. Furthermore, it was shown that the reversal potential (-120 mV) of the extracellular current in the alkaline band (passive H(+) channel) coincided with the threshold for the action potential. We propose that the action potential functions as a component of the spatial control system in the Chara cell.