cssi/SciSciGPT-SciSciNet huggingface dataset:
Improving Prediction Accuracy of Protein-DNA Docking with GPU Computing

Protein-DNA docking is a very challenging problem in bioinformatics and has important implications in a number of applications (e.g. rational drug design). This paper presents a computational approach to improve the prediction accuracy of protein-DNA docking. One of the major difficulties in protein-DNA docking is the high cost of sampling the conformational space. To address this problem, we develop a graphics processing unit (GPU)-based approach to accelerate the sampling process, and thereby improving the quality of conformational space sampling. The effectiveness of the our approach is validated against anon-redundant set of 75 protein-DNA complexes, and the results demonstrate improved performance in finding near-native protein-DNA complex structures. To the best of our knowledge, this is the first ad hoc effort of applying GPU or GPU clusters to the protein-DNA docking problem.
A test of thermal-ignition theory in autocatalytic reactions

The Semenov-Frank-Kamenetskii treatment of thermal ignitions has been applied to a complex reaction scheme for the formation of hydrogen chloride in mixtures of hydrogen, chlorine, nitric oxide, and nitrosyl chloride. When conditions are chosen to lead to nonautocatalytic reactions, for example when nitric oxide is added but [NOCl] is low, the simple Frank-Kamenetskii treatment predicts pressure limits of ignition accurately. When nitrosyl chloride is added initially and the reaction is autocatalytic in nature, the basic equations for the rate of heat production and the rates of removal of reactants and additives, with values of the rate constants and other parameters measured in quite independent experiments, can be solved on a computer to derive the pressure limits of ignition accurately for a wide variety of conditions of temperature or additive concentration. The induction periods for the autocatalytic reaction are of the correct order of magnitude, although differences between two sets of experimental values cannot be accounted for. A complete correlation of the limits and of the slow reaction in different vessels requires changes in the values of the rate constants of the surface reactions of chlorine atoms and molecules, or changes in the reaction scheme. It is not possible without further experimental work to decide which are the best changes.
History of extracellular matrix: A personal view☆

Before the early 1800s, the "fibers" of connective tissue were thought to be the basis of life, which arose by spontaneous generation. With the discovery of cells in connective tissue, the cellular theory became accepted as the basis of life in about 1850. Material outside cells, but presumably made by cells, was recognized as the extracellular matrix. In the period from 1930 to 1975, the components of extracellular matrix were characterized by physical chemical, chemical and cell biological methods. For the major collagen of skin, tendon and bone, the molecular and fibril structures were determined; the aldehydederived crosslinks were discovered; its polypeptide chains were sequenced; and its biosynthesis and degradation were defined. This collagen, now type I collagen, was shown to be one of many types. The events of this period are described from the author's perspective. Since 1975, molecular and cell biological techniques have shown that the extracellular matrix is not the passive residence of cells but is highly interactive and plays a major role in health and disease.
AuAg)144(SR)60 alloy nanomolecules

(Au-Ag)144(SR)60 alloy nanomolecules were synthesized and characterized by ESI mass spectrometry to atomic precision. The number of Ag atoms can be varied by changing the incoming metal ratio and plateaus at ∼60. UV-vis data demonstrates that the electronic structure of the nanomolecules can be tuned by incorporation of silver atoms. Based on the proposed 3-shell structure of Au144(SR)60, we hypothesize that the Ag atoms are selectively incorporated in to the symmetry equivalent 60-atom shell—having Au12, Au42, Ag60 concentric shells with 30 –SR–Au–SR– protecting units.
Gas flow through rotameters

Using data available for small rotameters that use spherical floats in gas flow, a linear relationship is derived. It is noted that the relationship provides a good fit for variable volumetric flow, density, and viscosity at constant flow height. With low Reynolds numbers (Re being less than 1), the product of the variable volumetric flow and the viscosity becomes constant; at high Reynolds numbers (Re being greater than 2000), the product of the variable volumetric flow and the square root of the density becomes constant. It is pointed out that the equation given here can be used to obtain an indirect calibration with any gas of known density and viscosity. The constancy of the product of the variable volumetric flow and viscosity at low variable volumetric flows is seen as suggesting the development of simple, inexpensive gas viscometers using rotameter technology.
Barriers to enrollment in a state child health insurance program.

Objective. —To identify barriers to enrollment into Colorado's Child Health Insurance Plan (CHP+) for non-Hispanic (NH), Hispanic (H), and uninsured families. Design. —Telephone survey of 1) random samples of families who requested an application but did not complete it (N = 273 NH, N=159 H) and 2) families with uninsured children identified by random-digit-dial statewide surveys (N = 165). Results. —Major reasons for not enrolling included 1) got other insurance (NH 16.5%; H 27.2% P P = .01), and 3) paperwork (NH 13.4%; H 14.7%, P = NS). Of those who thought their income was too high (N = 76, 17.6%), 58.5% appeared eligible based on reported income. Of uninsured families, only 41.7% had heard of CHP+. Of those who had never applied, major remediable reasons included not knowing enough about the program (20.9%) and thinking household income was too high (9.3%). Conclusions. —Effective marketing and education to increase awareness of CHP+ and ensure understanding of eligibility are critical to the success of the program.
Prevalence of axis I disorders in an AIDS cohort: A cross-sectional, controlled study

The primary purpose of this study was to assess the prevalence of major psychiatric disorders in human immunodeficiency virus-positive (HIV+) men with acquired immune deficiency syndrome (AIDS)-defining conditions. Secondary goals were to identify correlates of distress and psychopathology, and to determine whether there is a gradient of distress associated with progressive HIV illness. One hundred twelve men with AIDS-defining conditions, 61 HIV+ men without AIDS, and 84 HIV-seronegative gay men were assessed. Measures included the Structured Clinical Interview for DSM-IV (SCID), Hamilton Rating Scale for Depression (HAM-D), and other dimensional measures of distress and outlook, as well as laboratory markers of HIV stage, including HIV RNA viral load assays. Rates of major depression, consistent with other findings, were in the 5% to 10% range. Mean scores on dimensional measures of distress and outlook were within the "not depressed" range and did not increase despite increasing HIV illness severity. However, rates of dysthymia were elevated among men with CD4 cell counts less than 500, and the cumulative rates of any current axis I depressive disorder for three of the four study groups were in the range of 15% to 20%. The strongest correlates of dimensional measures of distress were current HIV symptoms and social support, and to a lesser extent, a lifetime history of major depression and current use of antidepressants and/or anxiolytics. Overall, most men displayed effective adaptation to illness, but a significant minority experienced moderate psychological distress, which warrants consideration by health providers who serve this population.
SIR2 calls upon the ER

Resveratrol induces longevity in C. elegans through the action of SIR2. Recently published work shows that resveratrol induces genes of the unfolded protein stress response of the endoplasmic reticulum. Paradoxically, these stress genes are repressed by SIR2, suggesting that resveratrol increases life span by inhibiting this SIR2 action.
Launching a Successful Copyright Education Program

Librarians, and particularly academic librarians, deal with copyright issues on an almost daily basis. It makes sense, therefore, that libraries and librarians should be the “go to” place on campus for copyright information. I am often asked by colleagues for suggestions on launching copyright education programs on their campuses. In this column, I provide steps and ideas to help you get started with a copyright education program, or at least to make you feel more confident in your efforts by providing advice from my own experiences, from educating yourself to implementing local workshops.
Steroid glaucoma: Corticosteroid-induced ocular hypertension in cats

This study was undertaken to develop a feline model of corticosteroid-induced ocular hypertension. In the first experiment, eight cats were selected whose intraocular pressure (17 ± 0.4 mmHg) was consistently below the mean baseline intraocular pressure of our colony (24 ± 0.5) during the preceding 2 months. Unilateral twice or thrice daily topical application of 10 μl 1 % dexamethasone sodium phosphate caused a gradual intraocular pressure increase that became significant (P
Modeling Heart Rate Baroreflex Mechanism and its Application in Predicting Acute Hypotensive Episodes

In this paper a new nonlinear system identification approach is developed for identification of the heart rate (HR) baroreflex mechanism. The developed model in then used in the task of acute hypotensive episodes (AHE) prediction. The AHE is defined as any period of 30 min or more during which at least 90% of the mean arterial pressure (MAP) measurements are below 60 mmHg. The proposed HR baroreflex model is based on inherent features of the autonomic nervous system for which we develop an adaptive neuro-fuzzy inference system (ANFIS) structure. The model showed significant improvement in HR prediction accuracy in terms of the normalized root mean square error (NRMSE) in comparison with previously reported results. We achieved a value of 0.191 in mean NRMSE in prediction of HR in this paper which is about 20% better than the best reported result in other papers. For the task of AHE prediction, since arterial pressure has a direct correlation with heart rate, we could simply find the periods in which HR drops blow a certain level without losing generality. The demonstrated AHE data for twenty patients are selected to validate the proposed algorithm. Results show that the proposed method could truly predict occurrence of the AHE in 9 out of the 10 cases analyzed. Results show reliable accuracy in predicting AHE in these patients.Copyright © 2011 by ASME
Optimal numerical solution of PDEs using the variational Germano identity

The variational Germano identity (VGI) is a condition that must be satisfied if the variational approximation to a partial differential equation is optimal in a user-defined metric. The VGI is useful as it can be utilized to dynamically determine unknown parameters in the variational approximation without any a-priori knowledge of the exact solution. With these values it yields solutions that are close to the optimal solution. In this manuscript we examine the relation between the definition of an optimal solution and the parameters computed using the VGI. We demonstrate that this relation is made precise by a so-called truncated restriction operator that appears in the final expression for the model parameters and is sensitive to the criterion used for selecting the optimal solution. In order to facilitate the use of the VGI for determining model parameters, we derive explicit expressions for this operator when three distinct approaches are used for defining the optimal solution. Through numerical examples that make use of these expressions, we confirm that the VGI does indeed yield model parameters and numerical solutions that are consistent with the choice of the optimal solution. We also observe that the numerical solutions obtained using the VGI are close to the best numerical solution that can be obtained from a given variational approximation, indicating that it yields nearly optimal values for the parameters.
Column height required for continuous chromatographic separation: A probabilistic model

Probabilistic model equations relating column height, feed location, degree of separation and flow rates for continuous chromatographic column
Acidosis and growth in nonuremic renal disease

Chronic metabolic acidosis is commonly associated with significantly impaired growth in children with kidney disease. In children with diffuse renal disease, chronic acidosis and growth impairment, other factors, e.g., osteodystrophy, uremia and malnutrition, as described elsewhere in this issue, may contribute to impaired growth. The question of whether acidosis alone affects growth in children with renal disease has long been considered. We recently have shown that children with an isolated disorder of renal acidification, type 1 RTA, after prolonged acidosis have short stature; sustained correction of acidosis restores stature to normal. Whether acidosis directly impairs growth in these patients or does so through secondary effects of hypovolemia, potassium deficiency, and disturbances in calcium metabolism is not known. This report reviews the evidence relating acidosis to growth impairment in children with isolated renal disorders. As a direct extension of these results, the question arises whether correction of acidosis benefits growth in nonuremic children with more generalized renal disease; that question, through careful clinical evaluations, is yet to be answered.
Multiscale Finite Element Modeling of Arc Dynamics in a DC Plasma Torch

The dynamics of the electric arc inside a direct current non-transferred arc plasma torch are simulated using a three-dimensional, transient, equilibrium model. The fluid and electromagnetic equations are solved numerically in a fully coupled approach by a multiscale finite element method. Simulations of a torch operating with argon and argon–hydrogen under different operating conditions are presented. The model is able to predict the operation of the torch in steady and takeover modes without any further assumption on the reattachment process except for the use of an artificially high electrical conductivity near the electrodes, needed because of the equilibrium assumption. The results obtained indicate that the reattachment process in these operating modes may be driven by the movement of the arc rather than by a breakdown-like process. It is also found that, for a torch operating in these modes and using straight gas injection, the arc will tend to re-attach to the opposite side of its original attachment. This phenomenon seems to be produced by a net angular momentum on the arc due to the imbalance between magnetic and fluid drag forces.
Computerized facility layout with graph theory

Abstract This paper describes a plant layout procedure based on graph theory. Given a relationship chart for the departments of the layout, the branch and bound technique is used to obtain an optimal relationship diagram. The planar representation of this relationship diagram is next obtained via a single planarity testing procedure. The planar graph's dual graph is found which gives the topology of the proposed final layout. Due to the time and complexities involved, the entire layout procedure described to this point is computerized. Using the topology of the dual graph, one can place the departments into the final layout. An example is presented to demonstrate the plant layout procedure in its entirely.
Bridges and Barriers: Adolescent Perceptions of Student–Teacher Relationships

In urban secondary schools where underpreparation and dropping out are real world concerns, students understand that their relationships with teachers affect their learning. Using descriptive coding and thematic analysis of focus group data, we explore adolescents’ perceptions of the bridges that foster and the barriers that inhibit supportive relationships with teachers, and the boundary expectations that function as both. The characteristics of supportive student–teacher relationships identified by youth participants suggest a number of teacher practices capable of meeting adolescents’ developmental needs and, as such, are likely to positively influence adolescents’ developmental and academic trajectories.
Very Short Quasi-Periodic And Aperiodic Mode Converters For 60 And 140 GHz Gyrotrons

Very short, broad bandwidth designs will be discussed for varying-radius mode transducers for TE02-TE01 and TE03-TE02 mode conversion in a 2.779 cm diameter circular waveguide at 60 and 140 GHz and for TE15, 2-TE15, 1 mode conversion in 2.54 cm diameter waveguide at 14'0 GHz.
Brief Fuzzy wide-range control of fossil power plants for life extension and robust performance

This paper presents a fuzzy-logic-based methodology of life extending control (LEC) for robust wide-range operation of fossil power plants including load-following, scheduled shutdown, and hot startup. The objectives of the LEC are performance enhancement and structural durability of both aging and new fossil power plants. The proposed control system has a two-tier architecture, which explores and optimizes the plant performance and structural durability trade-off. The lower tier consists of a feedforward control policy and a family of linear multivariable robust feedback controllers, which are gain-scheduled for wide-range operation. The sampled-data feedback control laws are synthesized based on an induced L"2-norm technique that minimizes the worst-case gain between the energy of the exogenous inputs and the energy of the regulated outputs. The supervisory controller at the upper tier makes decisions on plant operations with due consideration to structural durability of critical plant components (e.g., steam generators, steam headers, and turbines). The supervisory controller is synthesized based on approximate reasoning embedded with rule-based expert knowledge of the power plant and analytical models of structural damage. Using the fuzzy logic, the plant operation strategy is modified on-line for trade-off between plant performance and structural damage in critical components. The fuzzy algorithm facilitates bumpless controller switching for gain scheduling under wide-range operation and control. It also adds robustness to the control system especially if the lower tier of gain-scheduled controllers is not able to maintain stability under plant perturbations.
Modulation of gene-specific epigenetic states and transcription by non-coding RNAs

Emerging evidence points to a role for long non-coding RNAs in the modulation of epigenetic states and transcription in human cells. New insights, using various forms of small non-coding RNAs, suggest that a mechanism of action is operative in human cells, which utilizes non-coding RNAs to direct epigenetic marks to homology containing loci resulting ultimately in the epigenetic-based modulation of gene transcription. Importantly, insights into this mechanism of action have allowed for certain target sequences, which are either actively involved in RNA mediated epigenetic regulation or targets for non-coding RNA based epigenetic regulation, to be selected. As such, it is now feasible to utilize small antisense RNAs to either epigenetically silence a gene expression or remove epigenetic silencing of endogenous non-coding RNAs and essentially turn on a gene expression. Knowledge of this emerging RNA-based epigenetic regulatory network and our ability to cognitively control gene expression has deep implications in the development of an entirely new area of pharmacopeia.
Solution of the Schrödinger equation by a spectral method

Abstract A new computational method for determining the eigenvalues and eigenfunctions of the Schrodinger equation is described. Conventional methods for solving this problem rely on diagonalization of a Hamiltonian matrix or iterative numerical solutions of a time independent wave equation. The new method, in contrast, is based on the spectral properties of solutions to the time-dependent Schrodinger equation. The method requires the computation of a correlation function 〈ψ( r , 0)| ψ( r , t )〉 from a numerical solution ψ( r , t ). Fourier analysis of this correlation function reveals a set of resonant peaks that correspond to the stationary states of the system. Analysis of the location of these peaks reveals the eigenvalues with high accuracy. Additional Fourier transforms of ψ( r , t ) with respect to time generate the eigenfunctions. The effectiveness of the method is demonstrated for a one-dimensional asymmetric double well potential and for the two-dimensional Henon-Heiles potential.
Reduction of isoquinoline and pyridine-containing heterocycles with lithium triethylborohydride (Super-Hydride®)

Abstract Isoquinolines, quinoline and pyridines are effectively reduced to 1,2,3,4-tetrahydroisoquinolines, 1,2,3,4-tetrahydroquinolines and piperidines respectively with lithium triethylborohydride (Super-Hydride®). The mechanism of the reduction was explored by reduction of isoquinoline and pyridine with lithium triethylborodeuteride (Super-Deuteride®).
Amino Acids Regulate Expression of Antizyme-1 to Modulate Ornithine Decarboxylase Activity

In a glucose-salt solution (Earle's balanced salt solution), asparagine (Asn) stimulates ornithine decarboxylase (ODC) activity in a dose-dependent manner, and the addition of epidermal growth factor (EGF) potentiates the effect of Asn. However, EGF alone fails to activate ODC. Thus, the mechanism by which Asn activates ODC is important for understanding the regulation of ODC activity. Asn reduced antizyme-1 (AZ1) mRNA and protein. Among the amino acids tested, Asn and glutamine (Gln) effectively inhibited AZ1 expression, suggesting a differential role for amino acids in the regulation of ODC activity. Asn decreased the putrescine-induced AZ1 translation. The absence of amino acids increased the binding of eukaryotic initiation factor 4E-binding protein (4EBP1) to 5′-mRNA cap and thereby inhibited global protein synthesis. Asn failed to prevent the binding of 4EBP1 to mRNA, and the bound 4EBP1 was unphosphorylated, suggesting the involvement of the mammalian target of rapamycin (mTOR) in the regulation of AZ1 synthesis. Rapamycin treatment (4 h) failed to alter the expression of AZ1. However, extending the treatment (24 h) allowed expression in the presence of amino acids, indicating that AZ1 is expressed when TORC1 signaling is decreased. This suggests the involvement of cap-independent translation. However, transient inhibition of mTORC2 by PP242 completely abolished the phosphorylation of 4EBP1 and decreased basal as well as putrescine-induced AZ1 expression. Asn decreased the phosphorylation of mTOR-Ser2448 and AKT-Ser473, suggesting the inhibition of mTORC2. In the absence of amino acids, mTORC1 is inhibited, whereas mTORC2 is activated, leading to the inhibition of global protein synthesis and increased AZ1 synthesis via a cap-independent mechanism.
Studies on the intestinal absorption of a medium chain fat (trioctanoin) in normal and pancreatectomized dogs.

1. The absorption of intraduodenally administered carboxyl-14C glyceryl trioctanoate (RATO) was studied in 20 normal dogs, in 9 after pancreatectomy and in 4 after pancreatectomy and thoracic duct fistula. 2. The rate of absorption was estimated by continuously monitoring the expired14CO2 after RATO administration. In 20 control animals, an average of 26.7% ± 5.2% of the administered dose of radioactivity was recovered as14CO2 in 150 min. Following pancreatectomy,14CO2 recovery rates diminished significantly in all dogs. 3. The route of absorption was investigated by thin-layer and gas lipid chromatography of lymph collected from 4 of the pancreatectomized dogs after RATO and unlabeled trioctanoin administration. No 8-carbon fatty acids or glycerides were detected in the lymph by these techniques. 4. These results indicate that trioctanoin absorption is retarded in the absence of pancreatic lipase, but that fractional amounts of this lipid are absorbed via the portal route. Probable mechanisms for trioctanoin absorption in pancreatectomized dogs are discussed.
Numerical Simulation of Induced Seismicity in Carbon Capture and Storage Projects

Carbon capture and storage (CCS) technology offers a promising solution to control and reduce CO2 emissions. Changes in pore fluid pressure within the injection zone can induce low-magnitude seismic events. The induced seismicity associated with CCS needs to be properly addressed in order to obtain public acceptance for the technology and also to prevent possible CO2 leakage from the storage site due to fractures or fault-slip in the faults which can be reactivated due to injection. Simulation of CO2 injection inherently poses a multi-physics problem coupling thermal, hydrologic, and geomechanical processes. In this paper, a set of 2D coupled thermo-hydro-mechanical modeling was performed to simulate stress changes and resulting geomechanical deformations in the reservoir, caprock and fault due to CO2 injection. The model included a limited-dimension pre-existing fault which cannot be easily detected by surveys. The fault slip obtained from the numerical model was then used along with seismological theories to estimate the maximum magnitude of induced earthquake. A parametric study was performed to investigate the effects of reservoir properties as well as thermal stresses on geomechanical deformation, fault slip, pore pressure generation versus time, rupture time, and magnitude of induced events. The effects of permeability, porosity, and thickness of the reservoir were discussed. It was shown that thinner reservoirs have higher probability of fault reactivation and will result in larger induced seismic events. Reservoirs with higher porosity were shown to have longer rupture time and induce larger events. A higher permeable reservoir can decrease the potential of fault reactivation by generating lower buildup pore pressure and smaller fault slip. In general, for the given model geometry and injection characteristics, the heat flux never reached the fault by the time that the fault slip occurred and had no apparent effect on the results.
Timing and Specificity of Feed-Forward Inhibition within the LGN

Local interneurons provide feed-forward inhibition from retinal ganglion cells (RGCs) to thalamocortical (TC) neurons, but questions remain regarding the timing, magnitude, and functions of this inhibition. Here, we identify two types of inhibition that are suited to play distinctive roles. We recorded excitatory and inhibitory postsynaptic currents (EPSCs/IPSCs) in TC neurons in mouse brain slices and activated individual RGC inputs. In 34% of TC neurons, we identified EPSCs and IPSCs with identical thresholds that were tightly correlated, indicating activation by the same RGC. Such "locked" IPSCs occurred 1 ms after EPSC onset. The remaining neurons had only "nonlocked" inhibition, in which EPSCs and IPSCs had different thresholds, indicating activation by different RGCs. Nonlocked inhibition may refine receptive fields within the LGN by providing surround inhibition. In contrast, dynamic-clamp recordings suggest that locked inhibition improves the precision of synaptically evoked responses in individual TC neurons by eliminating secondary spikes.
Sperm DNA and sex chromosome differences between two geographical populations of the creeping vole, Microtus oregoni

The relative DNA content of the "O" and Y chromosome-bearing sperm is presented for the creeping vole, Microtus oregoni. The animals had been trapped in Oregon and in Washington State. The two populations had very similar autosomal chromosome relationships but differed greatly in the size of their X chromosome (which is not carried by vole sperm) and in their Y chromosome. The greater size and banding differences of the Y chromosome of the Washington State vole compared to the Oregon vole paralleled the greater differences in sperm DNA between the Y-bearing sperm and the sperm carrying no sex chromosome (O). The actual DNA differences between O and Y sperm was 12.5% for the sperm from the Washington State voles and 9.1% for sperm from the Oregon voles. The difference in sperm DNA content (12.5%) for Washington State voles was far greater than the difference shown for other voles or other mammals.
Early-Holocene geochemical evolution of saline Medicine Lake, South Dakota

Medicine Lake is a highly saline, meromictic, magnesium sulfate, closed-basin lake in northeastern South Dakota. The geochemical, mineralogical, and magnetic stratigraphies of sediments deposited from about 10.8 to 4.5 ka B.P. document the evolution of the saline brine in response to climatic change in the early to mid-Holocene. During the spruce occupation of the Medicine Lake catchment (10.8–10.0 ka B.P.), dark-grey massive basal sediments with low total-sulfur and carbonate content, upwardly increasing organic-carbon content, and high magnetic susceptibility were deposited in a deep freshwater lake. As the vegetation in the area changed from spruce to birch to oak and elm and finally to prairie between 10.0 and 9.2 ka B.P., and as the lake became shallow and salinity increased from 10%, light-and dark-grey calcareous and organic-carbon-rich banded sediments with low total-sulfur content and low magnetic susceptibility were deposited. Previous studies have shown that during the forest/prairie transition the lake then changed abruptly from fresh to saline as it lost a substantial portion of its volume. During the early prairie period (9.2–5.5 ka B.P.), alternating sections of aragonite-rich laminae and grey massive sediments with high total-sulfur content and multiple gypsum layers were deposited in a meromictic environment under conditions of fluctuating lake levels and salinity. Continued aridity during the mid-Holocene (5.5–4.5 ka B.P.) probably maintained the lake at relatively low levels and high salinity as dark-grey generally massive sediments with moderate total-sulfur, carbonate, and organic-carbon content and no measurable magnetic susceptibility were deposited.
Glucocorticoid repression of the mouse gonadotropin-releasing hormone gene is mediated by promoter elements that are recognized by heteromeric complexes containing glucocorticoid receptor

We have identified two regions of the mouse gonadotropin-releasing hormone (GnRH) promoter, one between -237 and -201 (distal element) and the other between -184 and -150 (proximal element), which are required for glucocorticoid repression in transiently transfected GT1-7 cells. These sequences show no similarity to known positive or negative glucocorticoid response elements (nGREs) and do not function when placed upstream of heterologous viral promoters. The glucocorticoid receptor (GR) does not bind directly to the distal or proximal promoter elements but may participate in glucocorticoid repression of GnRH gene transcription by virtue of its association within multiprotein complexes at these nGREs. Electrophoretic mobility shift assays with GT1-7 nuclear extract demonstrate the presence of GR-containing protein complexes on GnRH nGREs. One protein that co-occupies the distal nGRE in vitro along with GR is the POU domain transcription factor Oct-1. Thus, the tethering of GR to the GnRH distal nGRE, by virtue of a direct or indirect association with DNA-bound Oct-1, could play a role in hormone-dependent transcriptional repression of the GnRH gene. In contrast, Oct-1 does not appear to be a component of the GR-containing protein complex that is bound to the proximal nGRE.
Generating functional and Green's function hierarchy of the Ising model

Abstract The generating functional of the Ising model is studied. Equations of motion for the generating functional and the hierarchy of Green's functions are derived. These equations resemble a scalar field theory with nonlinear derivative coupling. Such a formulation bridges the gap between the Ising model as a configurational problem and field theoretic models of phase transitions. Only for the one dimensional lattice one can solve the equations exactly. In two and three dimensions several decoupling schemes are investigated: lowest order Hartree, Hartree approximation and a truncation, which includes also the four point function. The results are compared with graphical summations and other approximate theories.
Mobilization of hematopoietic stem cells

Hematopoietic stem cell transplantation has been extensively exploited as a therapeutic and research modality and has revolutionized current patient care. At present, more and more medical centers use peripheral blood progenitor cells for transplantation by mobilizing hematopoietic stem cells from bone marrow to peripheral blood because of potential advantages of peripheral blood stem cell transplantation over bone-marrow transplantation. Different effective mobilization regimens have been developed recently with chemotherapeutic agents, hematopoietic growth factors or their combination. This article reviews current developments related to hematopoietic stem cell mobilization including the biology of hematopoietic stem cells, strategies for mobilization, management for mobilization failure, mechanisms of mobilization, and side effects during mobilization. Finally, the Initiation-Amplification-Emigration-Adaptation Model is proposed to help aid understanding of the mechanisms of hematopoietic stem cell mobilization and to stimulate development of novel and optimal mobilization strategies for patient care.
Implementing PBB: Conflicting Views of Success

A modern budget reform, performance-based budgeting (PBB) emphasizes the measurement of government performance by agencies and public servants. In this article we define PBB as requiring strategic planning regarding agency mission, goals and objectives, and a process that requests quantifiable data that provide meaningful information about program outcomes. Performance-based budgeting requirements are now pervasive in the states. Of forty-seven states with PBB requirements, thirty-one have legislated the process to be conducted, while sixteen have initiated the reform through budget guidelines or instructions.1What remains unknown, yet of vital interest to state administrators, their staff, legislators, and citizens, regards implementation status of PBB systems. How many states are utilizing a PBB process as prescribed by law or administrative directive? And if PBB has been implemented, has it been successful regarding improvement of agency effectiveness and decision making about spending? Perhaps most importantly, has PBB influenced appropriation decisions?. This research is based on responses to a mail survey of executive and legislative budgeters regarding the PBB system established in their state. Results discussed in this article consider budgeters’ response about PBB implementation status and effectiveness as conducted. We find that there are differing perceptions across the branches of government regarding both the extent of PBB implementation as well as its success. Results show that states with better-known PBB systems have not necessarily realized greater success in terms of effectiveness from this budget reform than states with less popularly known systems, at least as perceived by the budgeters included in this article.
Postnatal development of phosphorylase kinase in mouse skeletal muscle

Abstract The postnatal development of phosphorylase kinase activity was studied in mouse (strain Ha ICR ) skeletal muscle, and the properties of the enzymes from skeletal muscle of 6- to 10-day-old and adult mice were compared. Phosphorylase kinase activity in skeletal muscle was found to increase more than 12-fold during postnatal development with over 80% of the increase occurring after the second week of life. Comparison of the phosphorylase kinase activity in muscle from 6- to 10-day-old and adult mice showed the two enzymes to have similar kinetic properties, but three lines of evidence indicated that they have different structures: (i) They differed in their cross-reactivity in quantitative immunotitrations using antisera prepared to purified rabbit skeletal muscle phosphorylase kinase. (ii) They differed in their heat lability at 42.5 °C. (iii) They differed in their subunit structure as determined by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. The phosphorylase kinase from muscle of 6- to 10-day-old mice had only the α′,β, and γ subunits, while the enzyme from adults showed α,α′,β, and γ subunits. These results indicate that skeletal muscle of adult mice has a different phosphorylase kinase isozyme(s) from that present in muscle of newborn mice.
Prevention of Bromobenzene Toxicity by N-Acetylmethionine: Correlation between Toxicity and the Impairment in O-Methylation and S-Methylation of Bromothiocatechols

Bromobenzene (800 mg/kg, ip) caused severe liver necrosis with massive hemorrhage in the golden Syrian hamster within the first 24 hr. Kidney injury was also observed. Treatment with N-acetylmethionine (NAM) at an ip dose of 1200 mg/kg at 5 hr after bromobenzene administration significantly protected the liver and kidney against injuries. Plasma glutamate pyruvate transaminase and blood urea nitrogen levels were substantially decreased in the NAM-treated animals. Histological evaluations confirmed these results. When the urinary neutral and phenolic metabolites of bromobenzene from NAM-treated and untreated hamsters were isolated and compared by GC and GC/ MS, a striking result was observed in terms of 0- and S-methylated thiol-containing metabolite formation. The NAM-treated animals showed approximately a 8- to 14-fold increase in the excretion of the four isomeric O and S-methylated bromothiocatechols. These thiocatechols, which are now known to be the 3,4- series metabolites of bromobenzene, can undergo methylation at either the thiol or the hydroxyl functional group. The excretion of 3-S- and 4-S-methylated bromodihydrobenzene thiolols was also increased significantly in the NAM-treated hamster, but other neutral and phenolic metabolites were relatively unchanged. These results suggest that bromobenzene toxicity in the Syrian hamster may be associated with impaired methylation capabilities, an impairment that could be due to methionine and glutathione depletion.
Cladistic analysis of Reduviidae (Heteroptera: Cimicomorpha) based on morphological characters

Abstract With more than 6600 species worldwide, Reduviidae (Insecta: Heteroptera), or assassin bugs, form the second largest and one of the most diverse groups of true bugs. The poor condition of the higher-level classification of Reduviidae is reflected by the facts that different authors recognize between 21 and 32 subfamily-level names and that Reduviidae were never subjected to a rigorous cladistic analysis using an exemplar approach. In the present study, a cladistic analysis of higher-level taxa of Reduviidae based on 162 morphological characters and 75 ingroup and outgroup species is presented. Twenty-one subfamily-level taxa of Reduviidae were examined, accounting for 28 tribes. In addition to characters previously used for diagnosis in Reduviidae, information on recently published character complexes is used in the present analysis, supplemented with new character information gathered specifically for this project. Reduviidae are supported as a monophyletic group with Pachynomidae as their sister taxon. The major results of this study are the support of a sistergroup relationship of Hammacerinae with the remaining Reduviidae, the monophyly of the Phymatine Complex, the relatively basal position of Harpactorinae within Reduviidae as well as a novel hypothesis on the relationships within this group, and the sistergroup relationship of Ectrichodiinae + Tribelocephalinae and their placement in a clade that also contains Emesinae, Saicinae, and Visayanocorinae. The analysis further supports a clade formed by paraphyletic Salyavatinae + Sphaeridopinae, renders Vesciinae non-monophyletic, and demonstrates the polyphyly of Reduviinae. Pseudocetherinae are shown to group with some Reduviinae. Triatominae are supported as a monophyletic group and are nested among additional Reduviinae and Stenopodainae.
The autoignition of C8H10 aromatics at moderate temperatures and elevated pressures

Abstract The autoignition of C8H10 aromatic/air mixtures (ortho-xylene, meta-xylene, para-xylene, and ethylbenzene in air) has been studied in a shock tube at temperatures of 941–1408 K, pressures of 9–45 atm, and equivalence ratios of Φ = 1.0 and 0.5. Ignition times were determined using electronically excited OH emission and pressure measurements. The measurements illustrate the differences in reactivity for the C8H10 aromatics under the studied conditions. Ethylbenzene was by far the most reactive C8H10 aromatic with ignition times a factor of two to three shorter than the xylenes. The xylene isomers exhibited ignition times that were similar, with o-xylene the most reactive, p-xylene the least reactive, and m-xylene just slightly more reactive than p-xylene. The p-xylene ignition times are almost identical to previous measurements for toluene at the same conditions. The differences in reactivity can be attributed to the C–H and C–C bond strengths in the alkyl side chains and the proximity of the methyl groups in the xylenes. These results represent the first ignition measurements for C8H10 aromatics at the elevated-pressure moderate-temperature conditions studied, providing needed targets for kinetic modeling at engine-relevant conditions. Kinetic modeling illustrates the importance of the methylbenzyl + HO2 reaction and indicates further study of this reaction is warranted.
Changes in student goal orientation across the semester in undergraduate computer science courses

Students' goal orientations impact their self-regulation, engagement, and achievement in post-secondary STEM courses. But, how students' goal orientations change across a semester and the impacts of these changes have not been extensively studied. Study purposes were to investigate goal orientation change across the semester, associations of goal change with achievement and self-regulation, and associations of classroom climate with goal change. Participants were 175 students from college introductory computer science courses. MANOVA identified significant during semester decreases for all goal orientations except task-avoid (Wilks' λ = .724, F (6, 169.00) = 10.71, p <.001, partial Eta2 = .276). No differences in goal orientation change were found for gender, year in college, or course. Goal orientation change significantly predicted students' course grades, retention of CS content, and strategic self-regulation. Classroom climate significantly predicted goal orientation change. Results indicate that students began the semester with positive goal orientations, but shifted in negative directions over the semester. In college STEM classes, the primary motivational issue may not be motivating students' to initially set learning-and task-approach goals, but rather motivating them to maintain their initial positive goals. Perceptions of course affect and teacher directedness predicted students' goal shifts, suggesting potential avenues for intervention by educators.
Does Diffuse Esophageal Spasm Progress to Achalasia? A Prospective Cohort Study

Diffuse esophageal spasm (DES) and achalasia share both clinical and manometric characteristics. Some reports support the notion of progression of DES to achalasia. However, there are currently no prospective data in support of this theory. To assess prospectively the rate of manometric progression of DES to achalasia. Manometry tracings of DES patients diagnosed between 1992 and 2003 were independently reviewed blindly and agreed on by two esophageal experts. Patients with DES who agreed to undergo repeat esophageal manometry constituted the study cohort. Follow-up manometry tracings were evaluated blindly and independently by the same two interpreters to determine the rate of manometric progression to achalasia. Predictors of manometric progression were assessed. A total of 32 patients were diagnosed with DES between 1992–2003. Twelve patients (9M/3F; median age 62 years) agreed to participate and underwent second manometry (mean ± SD follow-up of 4.8± 3.4 years). Achalasia was diagnosed on follow-up manometry in one patient (8%), seven (58%) patients continued to have DES, three (25%) had normal motility, and one (8%) had nutcracker esophagus. There were no predictors of progression to achalasia based on the initial manometry parameters. A subgroup of DES patients with initial low esophageal body amplitude developed increase in esophageal simultaneous contractions on follow-up similar to the patient who evolved to achalasia. Following were the results. 1) Progression from DES to achalasia is uncommon. 2) DES patients with low esophageal body amplitude may develop increased simultaneous contractions over time. 3) DES remains an elusive diagnosis clinically and manometrically.
Concerted strand exchange and formation of Holliday structures by E. coli RecA protein

RecA protein makes stable joint molecules from fully duplex DNA and molecules that are partially single-stranded; the latter may be either duplex molecules with an internal gap in one strand or molecules with single-stranded ends. Stable joint molecules form only when the end of at least one strand is in a homologous region. When RecA protein pairs linear duplex molecules and tailed molecules that share the same sequence end to end, the joints, which are located away from the single-stranded tails in most instances, have the electron microscopic appearance associated with the Holliday structure resulting from the reciprocal exchange of strands. The reaction leading to reciprocal strand exchange involves the concerted displacement of a strand from the end of the duplex molecule. These observations support the view that RecA protein makes stable joint molecules only by transferring strands and not by the side-by-side pairing of duplex regions.
Tandem Placement of a Coronavirus Promoter Results in Enhanced mRNA Synthesis from the Downstream-Most Initiation Site

Insertion of the 17-nucleotide promoter region for the bovine coronavirus N gene as part of a 27-nucleotide cassette into the open reading frame of a cloned synthetic defective-interfering (DI) RNA resulted in synthesis of subDI RNA transcripts from the replicating DI RNA genome. Duplicating and triplicating the promoter sequence in tandem caused a progressive increase in the efficiency of subgenomic mRNA synthesis despite a concurrent decrease in the rate of DI RNA accumulation that was not specific to the promoter sequences being added. Although initiation of transcription (leader fusion) occurred at each of the three promoter sites in the tandem construct, almost all of the transcripts were found as a product of the most downstream (3'-most on the genome) promoter. These results show that enhancement of subgenomic mRNA synthesis is a property that can reside within sequence situated near the promoter. A possible role for the plus strand in the downstream promoter choice is suggested.
Direct Behavior Rating: A Review of the Issues and Research in Its Development

The conceptual foundation for Direct Behavior Rating as a behavior assessment method is reviewed. A contemporary definition of Direct Behavior Rating is framed as combining strengths of systematic direct observation and behavior rating scales, which may result in a usable and defensible assessment tool for educators engaged in formative purposes. The rationale behind development of Direct Behavior Rating Single Item Scales as general outcome measures for school-based behavioral risk is provided. Research related to development of instrumentation and procedures for Direct Behavior Rating Single Item Scales is discussed, along with implications for future research and practice.
The Germans of British North America during the French and Indian War

(1957). The Germans of British North America during the French and Indian War. The Social Studies: Vol. 48, No. 7, pp. 227-235.