cssi/SciSciGPT-SciSciNet huggingface dataset:
Comparative analysis of the XopD type III secretion (T3S) effector family in plant pathogenic bacteria

SUMMARY XopD is a type III effector protein that is required for Xanthomonas campestris pathovar vesicatoria (Xcv) growth in tomato. It is a modular protein consisting of an N-terminal DNA-binding domain, two ethylene-responsive element binding factor-associated amphiphilic repression (EAR) transcriptional repressor motifs and a C-terminal small ubiquitin-related modifier (SUMO) protease. In tomato, XopD functions as a transcriptional repressor, resulting in the suppression of defence responses at late stages of infection. A survey of available genome sequences for phytopathogenic bacteria revealed that XopD homologues are limited to species within three genera of Proteobacteria—Xanthomonas, Acidovorax and Pseudomonas. Although the EAR motif(s) and SUMO protease domain are conserved in all XopD-like proteins, variation exists in the length and sequence identity of the N-terminal domains. Comparative analysis of the DNA sequences surrounding xopD and xopD-like genes led to revised annotation of the xopD gene. Edman degradation sequence analysis and functional complementation studies confirmed that the xopD gene from Xcv encodes a 760-amino-acid protein with a longer N-terminal domain than previously predicted. None of the XopD-like proteins studied complemented Xcv ΔxopD mutant phenotypes in tomato leaves, suggesting that the N-terminus of XopD defines functional specificity. Xcv ΔxopD strains expressing chimeric fusion proteins containing the N-terminus of XopD fused to the EAR motif(s) and SUMO protease domain of the XopD-like protein from X. campestris pathovar campestris strain B100 were fully virulent in tomato, demonstrating that the N-terminus of XopD controls specificity in tomato.
Differentiation of O-H and C-H bond scission mechanisms of ethylene glycol on Pt and Ni/Pt using theory and isotopic labeling experiments.

Understanding and controlling bond-breaking sequences of oxygenates on transition metal catalysts can greatly impact the utilization of biomass feedstocks for fuels and chemicals. The decomposition...
Solitarial premotor neuron projections to the rat esophagus and pharynx: Implications for control of swallowing

Background & Aims: The buccopharyngeal and esophageal phases of swallowing are controlled by distinct networks of premotor neurons localized in the nucleus tractus solitarius. The neuronal circuitry coordinating the two phases was investigated using a combination of central and peripheral tracing techniques. Methods: Using pseudorabies virus, a transsynaptic tracer, in anesthetized rats, third-order esophageal neurons (neurons projecting to premotor neurons) were identified. In a separate protocol that combined transsynaptic and retrograde fluorescent tracing, third-order esophageal neurons projecting to pharyngeal motoneurons (buccopharyngeal premotor neurons) were then identified. Results: Third-order esophageal neurons were identified in the interstitial and intermediate subnuclei of the nucleus tractus solitarius and in other medullary, pontine, midbrain, and forebrain nuclei. A subpopulation of these neurons (double labeled) in the interstitial and intermediate subnuclei were found to project to pharyngeal motoneurons (buccopharyngeal premotor neurons) and to be linked synaptically to esophageal premotor neurons. Conclusions: The synaptic link between buccopharyngeal and esophageal premotor neurons provides an anatomic pathway for the central initiation of esophageal peristalsis and its coordination with the pharyngeal phase of swallowing. This neural circuitry within the nucleus tractus solitarius is consistent with a complex central control mechanism for the swallowing motor sequence that can function independently of afferent feedback.
A Comparative Study of Circular Cylindrical Absorbing Terminations

The performance of various material-based absorbers as well as absorbing boundary conditions is examined when applied to circular cylindrical boundaries. The canonical problem of scattering from a pec cylinder together with an error criterion are used to illustrate the relative absorption of the mathematical as well as the material terminations. Even though the use of an anisotropic material does not result in a perfectly matched interface, it is shown that a metal-backed layer may still outperform a second order absorbing boundary condition.
Constitutive CXCL12 expression induces anoikis in colorectal carcinoma cells.

Background & Aims: CXCL12 and CXCR4 signaling plays critical roles in development, homeostasis, and tumor metastasis. Previously, we have shown that epigenetic silencing of CXCL12 in colorectal and mammary carcinomas promotes metastasis. Anoikis is an essential process of colonic epithelial turnover and limits the metastatic progression of carcinoma. We sought to determine the role for anoikis in limiting tumor metastasis following reexpression of CXCL12 in human colorectal carcinoma cells. Methods: Tumor formation and metastasis of colonic carcinoma cells was monitored using in vivo bioluminescence imaging. Anoikis was defined by using caspase-3/7, focal adhesion kinase (FAK) and p130Cas cleavage, DNA fragmentation, and cell survival assays. Phosphorylation of extracellular-regulated kinase-1/2 (ERK1/2) was monitored by immunoblot and immunohistochemistry, and activity was inhibited by using U0126. Results: Constitutive expression of CXCL12 in human colorectal carcinoma cells reduced orthotopic tumor formation and inhibited metastasis in severe combined immunodeficient mice. Further, CXCL12 expression induced apoptosis specifically in nonadherent colorectal carcinoma cells. Apoptotic cell death was preceded by hypophosphorylation and cleavage of FAK and p130Cas, leading to increased cellular detachment in culture, and depended on alterations in the extracellular matrix. Similar to in vivo colonic epithelium, CXCL12-induced anoikis of carcinoma cells depended on basal ERK1/2 activation. Conclusions: These data significantly expand the current paradigm of chemokine signaling in carcinogenesis by showing that endogenous CXCL12, in marked contrast to exogenous ligand, inhibits tumor metastasis through increased anoikis. Altered ERK1/2 signaling provides a mechanism for the dichotomy between the physiologic and pathophysiologic roles of CXCL12-CXCR4 signaling in the intestinal epithelium.
Prevalence and sociodemographic correlates of spiritual healer use: Findings from the National Survey of American Life

Summary Objectives This study investigates sociodemographic and health-related correlates of use of a spiritual healer for medical help. A large national, multiracial–multiethnic data source permits a more comprehensive investigation than was possible in previous studies. It also enables a closer focus on socioeconomic disadvantage and health need as determinants of utilization. Design and setting Respondents are from the National Survey of American Life: Coping with Stress in the 21st Century (NSAL), a nationally representative multi-stage area-probability survey of U.S. adult African Americans, Caribbean Blacks, and non-Hispanic Whites conducted from 2001 to 2003. The sample contains 6082 adults aged 18 and over. Main outcome measures NSAL respondents were surveyed about lifetime use of alternative providers for medical care or advice. Response categories included two types of spiritual healers: faith healers and psychics. These outcomes were logistically regressed, separately, onto 10 sociodemographic or health-related indicators: race/ethnicity, age, gender, marital status, education, household income, region, medical care use, insurance coverage, and self-rated health. Results Lifetime utilization of a faith healer is more prevalent among respondents in good health and less prevalent among Caribbean Blacks and never married persons. Users of a psychic healer are more likely to be educated, residents of the Northeast or West, and previously married, and less likely to report excellent health. Conclusions Use a spiritual healer is not due, on average, to poor education, marginal racial/ethnic or socioeconomic status, dire health straits, or lack of other healthcare options. To some extent, the opposite appears to be true. Use of a spiritual healer is not associated with fewer social and personal resources or limitations in health or healthcare.
Stellar convection. III - Convection at large Rayleigh numbers

A three dimensional study of convection in a self gravitating sphere of Boussinesq fluid with a Rayleigh number of 10 to the 10th power and a Prandtl of 1 is presented. The velocity and temperature of the fluid are computed at the largest wavelengths using spectral methods. A confirmation that the fluid is anisotropic and that the energy spectra are not smooth functions of wavelength but have a large amount of fine structure is discussed. The parameterization of the transport properties of the unresolvable inertial subrange with eddy viscosities and diffusivities is described. The time dependent fluctuations in the energy spectra and how they cascade from large to small wavelengths is examined.
Short communication: Evaluation of confirmatory stains used for direct microscopic somatic cell counting of sheep milk

Current FDA regulatory screening and confirmatory methods, electronic cell counting and the direct microscopic somatic cell count (DMSCC), differ for the detection of abnormal milk in sheep and goats. The DNA-specific electronic SCC screening methods such as Fossomatic (Foss, Hillerod, Denmark) can be used for both sheep and goat milk; however, the nonspecific methylene blue-based stains used for DMSCC in sheep cannot be used for goats as they nonspecifically stain cytoplasmic particles naturally present in goat milk. The DNA-specific stain pyronin Y-methyl green (PMG) is currently used for DMSCC in goats. Sheep also shed cytoplasmic particles during the milk secretory process, but in fewer numbers than goats. The objective of this study was to determine whether the nonspecific, methylene blue-based Levowitz-Weber (L-W) stain is the appropriate regulatory stain to use for DMSCC in sheep milk. Composite milk samples from 42 commercial dairy ewes were collected every 4 wk for the duration of each ewe's lactation for a total of 10 sample days. Milk samples were subjected to 3 methods of SCC determination: automated Fossomatic counting, DMSCC with L-W stain, and DMSCC with PMG stain conducted according to FDA regulatory procedures (2400 series forms). The DMSCC from milk smears stained with L-W were greater than those from smears stained with PMG and those from the Fossomatic analysis on 6 of the 10 sampling days. Milk smears stained with PMG did not differ from Fossomatic analysis at any sampling. The average milk SCC for L-W, PMG, and Fossomatic were (mean±SE) 275±36×10(3), 174±24×10(3), and 164±24×10(3) cells/mL, respectively. The DMSCC for milk stained with L-W was 58% greater than that with PMG and 68% greater than that obtained with the Fossomatic analysis. In conclusion, DMSCC of sheep milk stained with the nonspecific, methylene blue L-W stain resulted in a marked increase in SCC over that of the DNA-specific stain PMG and Fossomatic SCC analysis. The findings of this study support the continued use of Fossomatic SCC but recommend the replacement of the methylene blue-based stains with DNA-specific PMG for determination of DMSCC in sheep milk.
Posttraumatic Growth in Latina Immigrants

Abstract This study used a Spanish version of the Posttraumatic Growth Inventory to examine the extent to which Latinas report post-traumatic growth (PTG) following the stressful experiences of immigration and explored demographic, stress-related and social context correlates of this growth (N = 100). Findings indicate a moderate level of stress and a high level of PTG but no association between stress and growth variables. Level of stressfulness was related to type of separation and to participation in counseling. Overall, posttraumatic growth was related to participation in counseling and the Philosophy of Life factor was related to the importance of religion. Findings support using a strength perspective to study and service Latina immigrants.
Evaluation of polyethylene glycol method in determining rumen fluid volume in dairy cows fed different diets.

Abstract The use of polyethylene glycol in determining rumen fluid volume of cows fed liberal amounts of roughage and grain (control) or high-grain, low-fiber diets was studied. The polyethylene glycol method accurately measured rumen fluid volume in cows fed either diet. The rumen fluid turnover time was 5.0 and 11.2 hr for animals fed control and high-grain, low-fiber diets. For cows fed the control diet, 20.6% of the rumen fluid volume turned over every hour while the mean for cows fed the high-grain, low-fiber diet was 9.6%.
Who's Afraid of Rap: Differential Reactions to Music Lyrics1

This research examines the recent public outcry against violent rap songs. It was hypothesized that rap music receives more negative criticism than do other types of music, regardless of the actual content of the lyrics. Participants read a violent lyrical passage and were led to believe that it was either a rap song or a country song. They then responded to how offensive and dangerous they thought the song was. The results support the hypothesis. When a violent lyrical passage was represented as a rap song, reactions to the lyrics were significantly more negative. Age, whether or not the participants had children, and the participants’ music tastes and buying habits were all significantly related to whether or not this biased judgment occurred. The findings are briefly discussed in terms of various models of racism and stereotyping.
Occlusive therapy in atopic dermatitis: Overview

Introduction: Occlusive therapy, including both dry and wet (‘wet-wrap therapy’) offers a treatment option in atopic dermatitis (AD) which may be underutilized in clinical practice due to concerns ...
Calcium-induced Modification of Protein Conformation Demonstrated by Immunohistochemistry: What Is the Signal?:

A recent study by Morgan et al. on the mechanism of the heating antigen retrieval (AR) has raised an interesting issue concerning calcium-induced modification of protein conformation demonstrated by immunohistochemistry (IHC). The current study is based on calcium-induced modification of thrombospondin (TSP) and Ki-67, as demonstrated by IHC using seven monoclonal antibodies (MAbs) to TSP and an MAb MIB1. Experiments were carried out on frozen tissue sections of bladder carcinoma and lymph node. Frozen sections were incubated with solutions of 50 mM CaCl2 and/or 10 mM EDTA at 4C overnight before formalin or acetone fixation for TSP and Ki-67, respectively. Sections were then fixed in 10% neutral buffered formalin or acetone before immunostaining. Seven MAbs to TSP, named Ab1 to 7 representing clone numbers of A4.1, D4.6, C6.7, A6.1, B5.2, A2.5, and HB8432, respectively, and MIB1 were utilized as primary antibodies. ABC was used as the detection system and AEC as the chromogen for immunohistochemical staining. An extracellular immunostaining pattern represented a positive result for TSP, and nuclear staining for MIB1. Frozen sections preincubated in 50 mM CaCl2 overnight at 4C showed significant loss of staining and/or altered staining pattern for six of the seven antibodies to TSP and MIB1 compared to positive controls not exposed to CaCl2. Lack of immunostaining of TSP and MIB1 attributable to exposure to CaCl2 could be partially recovered by incubating the frozen sections in EDTA. Calcium-induced modification of protein structure was demonstrated more than 10 years ago on the basis of immunochemical techniques. In this study, similar calcium-induced modification of protein was detectable by IHC in frozen tissue sections, suggesting that calcium-induced modification of protein structure may occur independently of fixation-induced modification. The fact that calcium binding may affect IHC staining is not surprising in view of the fact that antibody/antigen interactions are protein structure-dependent. However, in this experiment the change occurred before and independent of formalin fixation and does not necessarily imply a role for calcium in AR. There may be a valuable role for the use of chemical modification in visualization of protein structure changes in tissue sections by IHC. (J Histochem Cytochem 47:463-469, 1999)
Polymer–leather composites. III. Morphology and water absorptivities of selected acrylic polymer–leather composite materials

The morphology of composite materials made by polymerizing methyl methacrylate into chrome-tanned cattlehide was examined by both light and scanning electron microscopy. The composites were selected from a series previously prepared and characterized, and their kinetics were reported. Micrographs of the polymer phase of the composites, prepared by preferential removal of collageneous material with 6N hydrochloric acid, yielded negative replicas of the fiber conformations. These provided evidence in support of proposed mechanisms of polymer deposition for two different methods of composite preparation. One method involved emulsion polymerization of monomer into hydrated leather and the other, preferentially filling leather free space. Both light and scanning electron microscopy of all composites and replicas revealed poly(methyl methacrylate) deposited largely in coarse aggregates around individual fibers. In emulsion systems, fiber bundles expanded with continuous deposition. No difference was observed in the morphology of bound and deposited polymers. However, high magnification of bound-polymer replicas exposed polymer surrounding some fibril traces. Deposition of polymer in the fine structure of bulk or solution prepared composites was not found; instead, all free space was occupied. A theory specifying polymer location in previous publications of this series, and extended here to define replica parameters, was abundantly supported by measured physical properties. A dominant grafting mechanism was precluded because the large domains limited points of possible attachment. Water absorptivities of emulsion prepared composites and controls were identical when the data were corrected to neat leather, although the rates were slightly perturbed. In contrast, both rate and equilibrium absorption data of the bulk and solution composites were retarded by polymer presence.
Raman spectroscopic study on pressure-induced amorphization in nanocrystalline anatase (TiO 2 )

Abstract A raman spectroscopic investigation was carried out to study the pressure-induced phase transformation in nanocrystalline anatase (TiO 2 ) up to 37 GPa. As compared to a macrocrystalline solid which transforms to the α-PbO 2 structure at 2.6–4.5 GPa, we found that the nano-anatase phase remains stable to pressures as high as ∼24 GPa, and then transforms to an amorphous phase. The new amorphous phase is quenchable upon release of pressure to ambient condition. An increased surface energy may stabilize the nano-anatase, suppressing the appearance of anatase-to-α-PbO 2 phase transformation (2.6–4.5 GPa in bulk anatase), and then leads to the amorphization of nano-anatase under strong compression.
The one-year prospective prediction of substance abuse and dependence among high-risk adolescents.

The present study examined 1-year prospective predictors of self-reported substance abuse and dependence among a sample of 702 youths at high risk for drug abuse from 21 southern California continuation high schools. Triadic influence theory was used as a theoretical guide. Predictors were selected as measures of triadic influence theory. Among 13 predictors, a drug use and intention index, and concern that one is or will become an addict or alcoholic, were consistently predictive of self-reported substance abuse or substance dependence 1 year later, controlling for baseline abuse or dependence status. In addition, baseline substance abuse, White ethnicity, and relatively poor prosocial coping predicted later substance dependence. Apparently, adolescents can predict their future use, and abuse or dependence status. Also, instruction in prosocial coping (e.g., seeking social support) may help inhibit the transition from substance abuse to substance dependence.
Fetal pyelectasis: is it always "physiologic"?

Abstract OBJECTIVE: Our purpose was to determine the degree of fetal pyelectasis predictive of neonatal renal pathologic processes. STUDY DESIGN: Eighty-four cases of pyelectasis were identified during the study period (1989 through 1993). Fetuses with an anteroposterior diameter of the renal pelvis ≥4 mm before 33 weeks or ≥7 mm after 33 weeks without caliectasis were included. Fetuses with an anteroposterior diameter of >10 mm were excluded. Postnatal evaluation included renal sonogram, voiding cystourethrogram, and renal flow and function studies. RESULTS: Sixteen cases were excluded because of incomplete postnatal workup. Renal pathologic processes were found in 30 of 68 (44%) at birth: the most common were ureteropelvic junction obstruction (37%) and vesicoureteral reflux (33%). Only four cases required surgical intervention (13%), and the remaining 87% were managed conservatively. A normal urinary tract was found in 25% of the infants and the remaining 21 of 68 (31%) had regression of pyelectasis before birth. Fetuses with a dilated anteroposterior diameter ≥8 mm after 28 weeks' gestation were found to have renal pathologic features in two of three of the cases, with sensitivity, specificity, and positive and negative predictive values of 87%, 41%, 66.7% and 70%, respectively. CONCLUSION: Fetuses with an anteroposterior diameter of the renal pelvis ≥8 mm after 28 weeks' gestation require appropriate urologic evaluation after birth.
Modeling long term energy futures after Nordhaus (1973)

Nordhaus’ (1973) prescient analysis is seminal – and has been cited hundreds of times – in part because of the insights it provides about the energy system and also because it serves as a model mod...
Explaining Citizen Support for Trade Liberalization

This paper examines individual attitudes in six industrialized democracies to determine what factors condition citizens' support for trade liberalization. We argue that public support for trade liberalization is influenced by politically driven views and individual economic utilitarian considerations. To test our propositions, we develop and estimate a series of logistic regression models of public support for trade liberalization. That data are derived from The World Values Surveys (1995–1997). We find strong empirical support for the economic utilitarian factors—primarily education, but also gender and income—as the principal factors shaping individual attitudes toward trade liberalization. Conversely, while some empirical support is found for political factors such as one's geographic orientation and level of cognitive mobilization, we find that the political predictors of support are weaker overall than the economic interest predictors.
Energy resolved mass spectrometry of diethyl alkyl phosphonates with an atmospheric pressure ionization tandem mass spectrometer

Energy resolved mass spectrometry (ERMS) was used to characterize the dissociation processes of four diethyl alkyl phosphonates where the alkyl R group attached to the central phosphorus atom ranged from methyl to n-butyl. An atmospheric pressure ionization triple quadrupole mass spectrometer was used in the analyses. Dissociation of the MH+ and further dissociation of the resulting progeny ions was induced between the atmospheric—vacuum sampling orifice and the first ion focusing RF-only quadrupole, Q0, instead of the central Q2 quadrupole. The major dissociation pathways of the four phosphonates could be characterized by two sequential McLafferty rearrangements yielding an alkyl phosphonic acid. This acid further dissociated losing H2O followed by ROH to produce PO+, or the same process occurred but in the reverse order, i.e. first losing ROH followed by H2O to yield PO+. The latter process was the energetically favored process. The alkyl group attached to the phosphorus atom of the protonated alkyl phosphonic acid was observed to have a significant influence on the stability of the protonated alkyl phosphonic acid. As the R group increased in size with a concomitant increase in electron-donating power, the alkyl phosphonic acid was less prone to dissociation than other alkyl phosphonic acids which possessed smaller R groups. A significant difference was also noted in the alkyl phosphonic acid dissociation processes; methyl phosphonic acid dissociated predominantly via H2O loss unlike the other acids which favored the loss of ROH over H2O.
Evidence for the performance prism in higher education

Purpose – This study aims to examine the potential for the Performance Prism (Neely et al., 2001) to influence the perceived outcome of a planned organizational change. General Systems Theory (Ruben, 1979; Thayer, 1968; vonBertalanffy, 1975) is used to understand the differences in stakeholder perception throughout the institution. Design/methodology/approach – Thirty-two participants from four educational support services departments and the senior leadership group of a university were interviewed. A grounded theory, constant comparative method (Glaser and Strauss, 1967) was used to generate themes and codes from transcripts. Findings – Findings suggest that implementers failed to adequately assess all employees’ satisfaction and contributions prior to implementation. Using the Performance Prism could have been the key to perceptions of success about the change effort. Research limitations/implications – Research comparing the Performance Prism to implemented planned change efforts not using the Performa...
Multiple myeloma and FISH (but no CHIPS)

[Comment on Avet-Loiseau et al, page 3489][1]Avet-Loiseau and colleagues present the definitive study of the clinical importance of genetic subtypes of multiple myeloma (MM). These aberrations, detected by interphase fluorescence in situ hybridization (FISH), define subtypes of multiple myeloma (MM
Measurement of in-flight base pressure on an artillery-fired projectile

T HE in-flight base pressure has been measured on conventionally fired artillery projectiles. No previous successful effort for such measurements and projectiles is apparent. A passively actuated base-sealing mechanism provided protection to the sensitive base-pressure instrumentation prior to gun muzzle exit and was released after exit to allow base-pressure sensing in flight. Comparisons are made of flight measurements with base-pressure data from wind-tunnel testing.
An undergraduate parallel processing laboratory

We discuss possibilities for setting up an undergraduate laboratory for parallel processing and how such a laboratory, based on transputers, can be used in a course on parallel processing.
Collusion in second price auctions with heterogeneous bidders

Abstract We show that efficient collusion by any subset of bidders in second price private value auctions is possible, even when the bidders are heterogeneous. An important property of efficient collusion is that a bidder's net payoff from participating in collusion is independent of her valuation. We show that the cooperative game whose characteristic function (evaluated at a coalition) is the ex ante collusive surplus (of that coalition) has a nonempty core. A feature of more technical interest is the mechanism characterization when the private information of agents does not enter in a linear (or even piecewise linear) manner.
Measurements on an Experimental Induction Plasma Accelerator

An experimental arrangement is described which electromagnetically generates and accelerates ionized gas by inductive coupling between the circuit and the gas. Measurements are made of energy coupled from the circuit to the plasma and of energy, momentum, and velocity of the accelerated gas. Energy on the order of 20 to 40 j is transferred to the plasma; this represents about 5 to 10% of the energy available for transfer, and 1/3 to 1/2 of this appears as energy of directed motion of the gas. The gas velocities measured 10 cm beyond the acceleration coil are in the range between 0.5 x 10/sup 4/ and 1.5 x 10/sup 4/ m/sec, whereas the corresponding momenta are from 2 to 11 radial compression of the plasma within the coil indicate that this radial compression is influential in determining the ultimate operating characteristics of this type of accelerator. Suggestions are made concerning improvement of efficiency. (auth)
Poly(C)-binding proteins as transcriptional regulators of gene expression

Poly(C)-binding proteins (PCBPs) are generally known as RNA-binding proteins that interact in a sequence-specific fashion with single-stranded poly(C). They can be divided into two groups: hnRNP K and PCBP1-4. These proteins are involved mainly in various posttranscriptional regulations (e.g., mRNA stabilization or translational activation/silencing). In this review, we summarize and discuss how PCBPs act as transcriptional regulators by binding to specific elements in gene promoters that interact with the RNA polymerase II transcription machinery. Transcriptional regulation of PCBPs might itself be regulated by their localization within the cell. For example, activation by p21-activated kinase 1 induces increased nuclear retention of PCBP1, as well as increased promoter activity. PCBPs can function as a signal-dependent and coordinated regulator of transcription in eukaryotic cells. We address the molecular mechanisms by which PCBPs binding to single- and double-stranded DNA mediates gene expression.
Modeling Complex between FBA and TIM: Functional Motions of FBA and TIM are Preserved in their Complex

Fructuose bisphostate aldolase (FBA) and triosephosphate isomerase (TIM) are the fourth and fifth enzymes in the glycolysis pathway and they are known to bind. FBA cleaves the six-carbon fructose 1, 6-bisphosphate into two three-carbon components – dihydroxyacetone phosphate (DHAP) and glyceraldehyde 3-phosphate (GAP). TIM converts DHAP into GAP, a substrate for the subsequent synthetic step. These two alpha/beta barrel proteins have high structural similarity – with a core RMSD 4.8A. These two enzymes have low activity in the monomeric form with the functionally active structures present in higher oligomeric states. By applying Elastic Network Model, we find the modes of motions that are functionally important for these proteins. We build models for the complex between these two proteins to investigate their important motions in their complexes as well as for their different oligomeric states including those that are different in different species to learn their important modes of motions for different functionalities. For each protein, by multiple sequence alignment across the species, we predict the coevolving residues and cluster these residues along the structure. We build the information transfer pathways from the important interface residues to the catalytic residues. Change in these pathways in different oligomeric states maybe be related to the change of motions in the catalytic region in different oligomeric states. We use this knowledge about the changes in motions and the information transfer pathways within the structure of these interacting proteins as constraints for selecting the computational docked models of complexes between these two proteins to preserve their functional motions.
Transport of the Norwegian Atlantic current as determined from satellite altimetry

Relatively warm and salty North Atlantic surface waters flow through the Faeroe-Shetland Channel into the higher latitudes of the Nordic Seas, preserving an ice-free winter environment for much of the exterior coast of northern Europe. This flow was monitored along the Norwegian coast using Geosat altimetry on two ascending arcs during the Exact Repeat Mission in 1987-1989. Concurrent undertrack CTD surveys were used to fix a reference surface for the altimeter-derived SSH anomalies, in effect creating time series of alongtrack surface dynamic height topographies. Climatologic CTD casts were then used, with empirical orthogonal function (EOF) analysis, to derive relationships between historical surface dynamic heights and vertical temperature and salinity profiles. Applying these EOF relationships to the altimeter signals, mean transports of volume, heat, and salt were calculated at approximately 2.9 Sverdrups, 8.1 x 10 exp 11 KCal/s and 1.0 x 10 exp 8 Kg/s, respectively. Maximum transports occurred in February/March and minimum in July/August.
EXPERIMENTS AND MODELING OF CARBON NANOTUBE-BASED NEMS DEVICES

Abstract In this paper, carbon nanotube-based nanoelectromechanical systems (NEMS) are nanofabricated and tested. In-situ scanning electron microscopy measurements of the deflection of the cantilever under electrostatic actuation are reported. In particular, a cantilever nanotube suspended over an electrode (nanoswitch), or two symmetric cantilever nanotubes (nanotweezers), from which a differential in electrical potential is imposed, are studied. The finite deformation regime investigated here is the first of its kind. An analytical model based on the energy method in both small deformation and finite kinematics (large deformation) regimes is used to interpret the measurements. The theory overcomes limitations of prior analysis reported in the literature towards the prediction of the structural behavior of NEMS. Some of the simplifying hypotheses have been removed. Furthermore, the theory takes into account the cylindrical shape of the deflected nanotube in the evaluation of its electrical capacitance, the influence of the van der Waals forces as well as finite kinematics. In addition, tip charge concentration and a quantum correction of the electrical capacitance are also considered. The energy-based method is used to predict the structural behavior and instability of the nanotube, corresponding to the on/off states of the nanoswitch, or to the open/close states of the nanotweezers—at the so-called pull-in voltage. Accuracy of the derived formulas is assessed by comparison of the theoretical prediction and experimental data in both small deformation and finite kinematics regimes. The results reported in this work are particularly useful in the characterization of the electromechanical properties of nanotubes as well as in the optimal design of nanotube-based NEMS devices.
Monitoring regional market systems in prehistory: Models, methods, and metrics

While market systems have long been recognized as key factors in the development and integration of many complex societies, market exchange has been largely ignored in recent studies of archaic states. The underlying causes appear threefold: (1) we overlook the rich conceptual framework developed within economic geography that identifies key differences among regional market systems; (2) we underestimate the degree to which these differences constrain or create distinct opportunities for other productive activities; and/or (3) we lack appropriate measures for monitoring organizational differences in the archaeological record. To understand the role of markets within the ancient economy, measures are needed to model and monitor its regional organization. The method proposed here focuses on the distribution of goods which circulated through the market system. By examining how different types of market systems move goods through the regional system in different ways, distinct patterns of commodity distribution are predicted. Metrics for monitoring exchange based on artifact assemblage similarity are then proposed. As a case study, the analysis applies these insights to characterizing the regional market system in the Aztec heartland, an area where the organization of exchange and the degree of political interference remain topics of active debate.
Concord grape juice supplementation improves memory function in older adults with mild cognitive impairment

Concord grape juice contains polyphenol compounds, which have antioxidant and anti-inflammatory properties and influence neuronal signalling. Concord grape juice supplementation has been shown to reduce inflammation, blood pressure and vascular pathology in individuals with CVD, and consumption of such flavonoid-containing foods is associated with a reduced risk for dementia. In addition, preliminary animal data have indicated improvement in memory and motor function with grape juice supplementation, suggesting potential for cognitive benefit in ageing humans. In this initial investigation of neurocognitive effects, we enrolled twelve older adults with memory decline but not dementia in a randomised, placebo-controlled, double-blind trial with Concord grape juice supplementation for 12 weeks. We observed significant improvement in a measure of verbal learning and non-significant enhancement of verbal and spatial recall. There was no appreciable effect of the intervention on depressive symptoms and no effect on weight or waist circumference. A small increase in fasting insulin was observed for those consuming grape juice. These preliminary findings suggest that supplementation with Concord grape juice may enhance cognitive function for older adults with early memory decline and establish a basis for more comprehensive investigations to evaluate potential benefit and assess mechanisms of action.
Adverse and beneficial effects of tocolytic therapy

In addition to questions raised about the efficacy of many tocolytics, appropriate concern has been voice about the safety of these potent drugs. Although some degree of risk for adverse effects with drugs promising a strong therapeutic effect can be accepted, caution needs to be exercised when benefits are marginal or unproven. Unfortunately, some of the tocolytics, most notably the betamimetics and magnesium sulfate, have been found to have considerable potential for adverse maternal cardiovascular and respiratory effects. Although less clearly established, the use of indomethacin appears to be associated with increased fetal and neonatal risks. Concerning magnesium sulfate, in addition to the well-known maternal effects, the accumulating evidence showing an increased frequency of adverse outcomes in the fetus and neonate has led to the recommendations to abandon its use entirely as a tocolytic. Given the limitations of our current state of knowledge, nifedipine would appear to be among the more efficacious and safer tocolytics available to use when properly indicated.
E. coli aspartate transcarbamylase: Part II: Structure and allosteric interactions

Abstract Aspartate transcarbamylase catalyses and regulates the committed step in the pyrimidine biosynthesis pathway in E. coli . The combination of biochemical information together with the high resolution X-ray structure of this enzyme, makes possible an initial understanding of these functions on the molecular level.
Electron microscopic evidence of two stalks linking the F1 and F0 parts of the Escherichia coli ATP synthase

The structure of monodisperse ATP synthase from Escherichia coli (ECF1F0) has been examined by electron microscopy after negative staining of specimens. The F1 part is seen to be connected by two stalks. One is more centrally located and includes the γ and ϵ subunits. The second stalk, observed here in ECF1F0, is arranged peripherally. It probably contains the δ and b subunits which, in addition to γ and ϵ, are required for binding of the F1 and F0 parts of the complex. Other novel features of the F1F0 complex can be discerned. There is a cap at the top of the F1 part at which the second stalk may bind. This likely includes N-terminal stretches of the three copies of the α subunit and a part of the δ subunit. The F0 part is clearly asymmetric. The presence of two stalks in the complex has important functional implications. There is good evidence that the more central stalk of γ and ϵ subunits is a mobile domain that rotates to link the three catalytic sites on β subunits in turn, with the proton channel of the F0 part. The second stalk of δ and b subunits is then the stator which makes this rotation possible.
Behavioral dynamics of the affordance "graspable".

On a daily basis, one perceives whether an object affords grasping with one hand or with both hands. In experiments in which differently sized objects of a fixed type have been presented, the transition from using one manual mode to the other has depended on both the ratio of object size to hand span and the presentation sequence—that is, size increasing versus decreasing. The transitions and their observed hysteresis (i.e., a transition ratio larger for the increasing sequence) can be accommodated by the order parameter dynamics typifying self-organizing systems. Here, we show that hysteresis magnitude depends on (a) the interaction between the attractors (one hand vs. two hands) and (b) the strength of the two-hands attractor. Through modeling and experimental results, we extend the investigation of affordance perception within dynamical-systems theory.
Characterization of human migration inhibitory factor (MIF) from antigen-stimulated lymphocytes.

Abstract Migration inhibitory factor (MIF) obtained from sensitized human lymphocytes stimulated by specific antigen streptokinase-streptodornase (SK-SD) was characterized by Sephadex gel filtration, disc electrophoresis, isopyknic centrifugation, and enzymatic treatment. MIF activity was found after Sephadex gel filtration in fractions containing molecules the size of chymotrypsinogen (MW 23,000). On disc electrophoresis at pH 9.1, peak MIF activity was eluted from the fraction containing molecules that migrate with albumin. In isopyknic centrifugation, human MIF showed a buoyant density similar to that of the reference protein. Human MIF was inactivated by treatment with chymotrypsin but not with neuraminidase. The characteristics of human MIF in comparison to those of guinea pig MIF are discussed.
A study of iron smelting at Lopanzo, Equateur Province, Zaïre

Abstract The equatorial rain forests of Zaire, central Africa, were once home to an apparently unique variant of the bloomery iron smelting furnace—the slag tapping bowl furnace. The few recorded examples of this type are 50–100 cm in diameter, and have a single tuyere blown by two or more sets of valveless drum bellows. A second pit is dug alongside to receive the slag, which is tapped through a slit or tunnel linking the bowl furnace and slag pit. All three recorded examples of this technology are instances of “salvage ethnography”—reconstructions of extinct processes by former practitioners—and are certainly less productive than they once were. We report here the results of petrographic and metallographic examination of specimens of ore, slag and bloom from reconstructions undertaken in 1973 and 1989 in the village of Lopanzo.
Dynamical Gauge Symmetry Breaking as the Casimir Effect

Abstract A new mechanism for dynamical gauge symmetry breaking is found in a class of higher dimensional theories. A system consisting of non-abelian gauge fields and fermions with minimal gauge interactions on a spacetime M2 × S2 is considered, where Mn and S2 are an n-dimensional Minkowski spacetime and a surface of a sphere, respectively. Full analysis is given for odd n. By integrating fermion fields first, we find that gauge symmetry is dynamically broken for n = 4p + 3 (p = 0, 1, 2…), provided that there exists a sufficiently heavy fermion. The phenomenon originates from a shift in fermion zero point energies due to compactness of the extra dimensional space S2, being quite similar to the Casimir effect in electrodynamics.
Network crossover performance on NK landscapes and deceptive problems

Practitioners often have some information about the problem being solved, which may be represented as a graph of dependencies or correlations between problem variables. Similar information can also be obtained automatically, for example by mining the probabilistic models obtained by EDAs or by using other methods for linkage learning. This information can be used to bias variation operators, be it in EDAs (where it can be used to speed up model building) or in GAs (where the linkages can be explored by modifying crossover). This can allow us to solve problems unsolvable with conventional, problem-independent variation operators, or speed up adaptive operators such as those of EDAs. This paper describes a method to build a network crossover operator that can be used in a GA to easily incorporate problem-specific knowledge. The performance of this operator in the simple genetic algorithm(GA) is then compared to other operators as well as the hierarchical Bayesian Optimization Algorithm (hBOA) on several different problem types, all with both elitism replacement and Restricted Tournament Replacement (RTR). The performance of all the algorithms are then analyzed and the results are discussed.
Transgenic Expression of MicroRNA-181d Augments the Stress-Sensitivity of CD4+CD8+ Thymocytes

Physiological stress resulting from infections, trauma, surgery, alcoholism, malnutrition, and/or pregnancy results in a substantial depletion of immature CD4+CD8+ thymocytes. We previously identified 18 distinct stress-responsive microRNAs (miRs) in the thymus upon systemic stress induced by lipopolysaccharide (LPS) or the synthetic glucocorticoid, dexamethasone (Dex). MiRs are short, non-coding RNAs that play critical roles in the immune system by targeting diverse mRNAs, suggesting that their modulation in the thymus in response to stress could impact thymopoiesis. MiR-181d is one such stress-responsive miR, exhibiting a 15-fold down-regulation in expression. We utilized both transgenic and gene-targeting approaches to study the impact of miR-181d on thymopoiesis under normal and stress conditions. The over-expression of miR-181d in developing thymocytes reduced the total number of immature CD4+CD8+ thymocytes. LPS or Dex injections caused a 4-fold greater loss of these cells when compared with the wild type controls. A knockout mouse was developed to selectively eliminate miR-181d, leaving the closely spaced and contiguous family member miR-181c intact. The targeted elimination of just miR-181d resulted in a thymus stress-responsiveness similar to wild-type mice. These experiments suggest that one or more of three other miR-181 family members have overlapping or compensatory functions. Gene expression comparisons of thymocytes from the wild type versus transgenic mice indicated that miR-181d targets a number of stress, metabolic, and signaling pathways. These findings demonstrate that selected miRs enhance stress-mediated thymic involution in vivo.
Physics of excitonic quasiparticles: beyond conventional polaritons☆

Abstract Some aspects of post-conventional polariton physics are discussed. In the framework of quantum statistical properties we demonstrate that polaritons are intrinsically squeezed. The polariton squeezing is frequency tunable, and can be larger than that in usual atomic systems. The new phonoriton excitation, which gives rise to spectrum reconstruction, is reexamined on the basis of a simple model: threshold behavior, new gap structure and related properties are discussed.
Coexistence of bulk superconductivity and charge density wave in CuxZrTe3.

We report the coexistence of bulk superconductivity with ${T}_{c}=3.8\text{ }\text{ }\mathrm{K}$ and charge density wave (CDW) in Cu intercalated quasi-two-dimensional crystals of ${\mathrm{ZrTe}}_{3}$. The Cu intercalation results in the expansion of the unit cell orthogonal to the Zr-Zr metal chains and partial filling of CDW energy gap. We present anisotropic parameters of the superconducting state. We also show that the contribution of CDW to the scattering mechanism is anisotropic in the $\stackrel{^}{a}\mathrm{\text{\ensuremath{-}}}\stackrel{^}{b}$ plane. The dominant scattering mechanism in the normal state for both ${\mathrm{ZrTe}}_{3}$ and ${\mathrm{Cu}}_{0.05}{\mathrm{ZrTe}}_{3}$ along the $\stackrel{^}{b}$ axis is the electron--electron umklapp scattering.
Thermodynamics of the Massive Thirring Model: The Discontinuity in Soliton Mass

A new formulation is presented for the thermodynamics of the massive Thirring model in the attractive-coupling regime. A certain controversy between previous theories is resolved and an overall understanding of the thermodynamics is reached. In particular, it is shown that the soliton mass is discontinuous with the coupling constant at finite temperatures.