cssi/SciSciGPT-SciSciNet huggingface dataset:
Left ventricular dysfunction due to chronic right ventricular pressure overload: Resolution following percutaneous balloon valvuloplasty for pulmonic stenosis

Left ventricular dysfunction due to chronic right ventricular pressure overload is well documented in experimental animals, but is controversial in humans. Whether left ventricular dysfunction resolves following the relief of chronic right ventricular pressure overload has not been studied. In this report, rapid improvement in both right and left ventricular function following successful percutaneous balloon valvuloplasty is described in a patient with severe isolated valvular pulmonic stenosis and biventricular dysfunction. It appears that: (1) geometric distortion played a major role in his reversible left ventricular dysfunction, and (2) severe biventricular dysfunction should not be a contraindication to valvuloplasty for valvular pulmonic stenosis.
Style changes in time-coded stream-of-consciousness handwriting identifies real-time mood fluctuations in mania (728.19)

Methods to experimentally assess changes in mood are limited. In this case study real-time mood fluctuations in mania were measured by evaluating, without regard to content, changes in time-coded stream-of-consciousness writing style during a 29-day manic episode experienced and recorded by one of the authors (nlc). Mood was judged to be in flux when text script changed from linear to non-linear with the time point of the change being the cusp between the two writing styles. Handwritten in 13 bound journals were 54,580 words, with 21,918 of them (40%) written in the episode’s first quadrant, 16,287 (30%) in the second, 10,475 (20%) in the third, and 5,900 (10%) in the final quadrant. There were 195 writing style cusps, with 17% occurring in the first quadrant, 48% in the second, 30% in the third, and 5% in the fourth. These time-coded writing style cusps denoted real-time mood fluctuations during the manic episode. Even though the most words were written in the first quadrant, mood fluctuations as measure...
Hamiltonian Medicine: Why the Social Lives of Pathogens Matter

The virulence of bacterial colonies often increases when the members of the colony are more highly related. Foster explains how kin selection theory can be used to analyze this phenomenon and discusses the characteristics of bacteria that enable them to benefit from living among their relatives.
From Flat to Round: Changing Portrayals of the Judge in American Popular Culture

American judges are not only important government functionaries but also familiar pop cultural figures. However, the portrayal of judges in American film, television, and inexpensive literature appears to be changing. Judge Harlan Weaver in Otto Preminger's Anatomy of a Murder (1959) illustrates the way the pop culture judge were once "flat," symbolic representations of the rule of law. Since the 1970s, meanwhile, judges have increasingly been portrayed as crazy, villainous, and complexly sympathetic. Examples of this new "round" characterization include Judges Rayford and Fleming in And Justice for All (1979); assorted judicial characters in novels by Scott Turow and John Grisham; Judge Amy Gray from the television series Judging Amy (1999-2005); and Judge Judith Scheindlin and her irksome judicial colleagues from daytime television. The alterations in characterization ominously suggest larger changes in the culture of postmodern America.
Solving Nonlinear Economic Planning Models Using GRG Algorithms

With the concept of optimization being such a central theme in economic theory, planning economists have always been attracted to mathematical programming as it provides a natural framework of analysis for theoretical and applied work. Although, nonlinear optimizing economic planning models have been specified and studied for more than 20 years [4, 17] few were ever solved on a routine basis. This stands in sharp contrast to linear programming models which, due to highly reliable (commercial) software are the workhorses of many planning agencies. Even today, most large-scale nonlinear planning models are solved with specifically designed algorithms, tailored around some high performance LP system [9, 14, 16].
Pumping of nutrients to ocean surface waters by the action of propagating planetary waves

Primary productivity in the oceans is limited by the lack of nutrients in surface waters. These nutrients are mostly supplied from nutrient-rich subsurface waters through upwelling and vertical mixing1, but in the ocean gyres these mechanisms do not fully account for the observed productivity2. Recently, the upward pumping of nutrients, through the action of eddies, has been shown to account for the remainder of the primary productivity; however, these were regional studies which focused on mesoscale (100-km-scale) eddies3,4,5,6. Here we analyse remotely sensed chlorophyll and sea-surface-height data collected over two years and show that 1,000-km-scale planetary waves, which propagate in a westward direction in the oceans, are associated with about 5 to 20% of the observed variability in chlorophyll concentration (after low-frequency and large-scale variations are removed from the data). Enhanced primary production is the likely explanation for this observation, and if that is the case, propagating disturbances introduce nutrients to surface waters on a global scale—similar to the nutrient pumping that occurs within distinct eddies.
Dynamic compression of chondrocytes induces a Rho kinase-dependent reorganization of the actin cytoskeleton

The signal transduction mechanisms in chondrocytes that recognize applied forces and elicit the appropriate bio- chemical cellular responses are not well characterized. A current theory is that the actin cytoskeleton provides an intracellular framework onto which mechanosensation mechanisms are assembled. The actin cytoskeleton is linked to the extracellular matrix at multi-protein complexes called focal adhesions, and evidence exists that focal adhesions mediate the conversion of external physical forces into appropriate biochemical signal transduction events. The Rho GTPases affect the arrangement of actin cytoskeletal structures, and enhance the formation of focal adhesions, which link the cytoskeleton to the extracellular matrix. A major effector pathway downstream of Rho is the activation of Rho kinase (ROCK), which phosphorylates and activates Lim kinase, which in turn phosphorylates and inhibits the actin-depolymerizing protein cofilin. The objectives of this study were threefold: first, to quantify the actin reorganization in response to dynamic compression of agarose-embedded chondrocytes. Second, to test whether Rho kinase is required for the actin cytoskeletal reorganization induced by dynamic compression. Third, to test whether dynamic compression alters the intracellular localization of Rho kinase and actin remodeling proteins in chondrocytes. Dynamic compression of agarose-embedded chondrocytes induced actin cytoskeletal remodeling causing a significant in- crease in punctate F-actin structures. Rho kinase activity was required for these cytoskeletal changes. Dynamic compression increased the amount of phosphorylated Rho kinase. The chemokine CCL20 and inducible nitric oxide synthase (iNOS) were the most highly upregulated genes by dynamic compression and this response was reduced by the Rho kinase inhibitors. In conclusion, we show that dynamic compression induces changes in the actin cytoskeleton of agarose-embedded chondro- cytes, and we establish methodology to quantify these changes. Furthermore, we show that Rho kinase activity is required for this actin reorganization and gene expression induced by dynamic compression.
Analysis of aminoacyl- and peptidyl-tRNAs by gel electrophoresis

During protein synthesis, ribosomes translate the genetic information encoded within messenger RNAs into defined amino acid sequences. Transfer RNAs (tRNAs) are crucial adaptor molecules in this process, delivering amino acid residues to the ribosome and holding the nascent peptide chain as it is assembled. Here, we present methods for the analysis of aminoacyl- and peptidyl-tRNA species isolated from Escherichia coli. These approaches utilize denaturing gel electrophoresis at acidic pH to preserve the labile ester bonds that link amino acids to tRNA. Specific aminoacyl- and peptidyl-tRNAs are detected by Northern blot hybridization using probes for tRNA isoacceptors. Small peptidyl-tRNAs can be differentiated from aminoacyl-tRNA through selective deacylation of the latter with copper sulfate. Additionally, peptidyl-tRNAs can be detected through metabolic labeling of the nascent peptide. This approach is amenable to pulse-chase analysis to examine peptidyl-tRNA turnover in vivo. We have applied these methods to study programmed translational arrests and the kinetics of paused ribosome turnover.
Requisite of high-capacity transmission technology for future optical internet

This paper reviews the key requirements for the high-capacity optical transmission that supports the exponential growth of global IP traffic. The requirements include total data rate, transmission distance, flexibility, reliability, and cost.
Understanding system of systems development using an agent-based wave model

Abstract System of Systems (SoS) development is a complex process that depends on the cooperation of various independent Systems [1] . SoS acquisition and development differs from that typical for a single System; it has been shown to follow a wave paradigm known as the Wave Model [2] . Agent based models (ABMs) consist of a set of abstracted entities referred to as agents, and a framework using simplified rules for simulating agent decisions and interactions. Agents have their own goals and are capable of perceiving changes in the environment. Systemic (global) behavior emerges from the decisions and interactions of the agents. This research provides a generic model of SoS development with a genetic algorithm and fuzzy assessor implemented in an agent based model. The generic SoS development follows the Wave Model. The genetic algorithm provides an initial SoS meta- architecture. The fuzzy assessor qualitatively evaluates SoS meta-architectures. The agent-based model implements the generic SoS development, the genetic algorithm, the fuzzy assessor, and independent SoS and system agents and shows the SoS development based on an initial set of conditions. A prototype model is developed to test the concept on a sample from the DoD Intelligence, Surveillance, and Reconnaissance (ISR) domain.
Comparison of the effects of acute and chronic beta-blockade on infarct size in the dog after circumflex occlusion.

In order to compare the effects of acute and chronic beta-blockade on infact size, the left circumflex coronary artery was occluded for 6 hours in 33 anesthetized dogs. The dogs (18 to 22 kg) were divided in to three groups; group 1 (N=10) served as controls, group 2 received intravenous nadolol (average dose 1.25 mg/kg) just prior to coronary occlusion, and group 3 received oral nadolol (80 mg) twice daily for 16 days prior to coronary occlusion. To ensure equivalent degrees of beta-blockade at the time of occlusion, group 2 and 3 dogs were given incremental doses of intravenous nadolol to abolish the chronotropic response to isoproterenol (2 μ/kg IV). Left ventricular pressure, its first derivative (dP/dt), and heart rate were monitored. The anatomic risk region was determined antemortem by Evan's blue staining while the infarct zone was delineated postmortem by tetrazoleum staining. Compared to Group 1, heart rate was 22% lower in group 2 and 15% lower in group 3 dogs 6 hours after occlusion (p<0.05). There were no differences among groups in peak left ventricular systolic pressure or mean arterial pressure. Infarct size as a function of the area at risk was 68±3% in group 1, 52±7% in group 2, and 44±8% in group 3. A significant difference was found only between groups 3 and 1. The data suggest that chronic beta-blockade provides greater protection against ischemic-induced necrosis than does acute beta-blockade. The greater protective effect of chronic beta-blockade may be due to chronic adaptive changes in either blood flow or metabolism.
Atomic Structure of the DNA Repair [4Fe-4S] Enzyme Endonuclease III

The crystal structure of the DNA repair enzyme endonuclease III, which recognizes and cleaves DNA at damaged bases, has been solved to 2.0 angstrom resolution with an R factor of 0.185. This iron-sulfur [4Fe-4S] enzyme is elongated and bilobal with a deep cleft separating two similarly sized domains: a novel, sequence-continuous, six-helix domain (residues 22 to 132) and a Greek-key, four-helix domain formed by the amino-terminal and three carboxyl-terminal helices (residues 1 to 21 and 133 to 211) together with the [4Fe-4S] cluster. The cluster is bound entirely within the carboxyl-terminal loop with a ligation pattern (Cys-X6-Cys-X2-Cys-X5-Cys) distinct from all other known [4Fe-4S] proteins. Sequence conservation and the positive electrostatic potential of conserved regions identify a surface suitable for binding duplex B-DNA across the long axis of the enzyme, matching a 46 angstrom length of protected DNA. The primary role of the [4Fe-4S] cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone. The crystallographically identified inhibitor binding region, which recognizes the damaged base thymine glycol, is a seven-residue beta-hairpin (residues 113 to 119). Location and side chain orientation at the base of the inhibitor binding site implicate Glu112 in the N-glycosylase mechanism and Lys120 in the beta-elimination mechanism. Overall, the structure reveals an unusual fold and a new biological function for [4Fe-4S] clusters and provides a structural basis for studying recognition of damaged DNA and the N-glycosylase and apurinic/apyrimidinic-lyase mechanisms.
Clot injection technique affects thrombolytic efficacy in a rat embolic stroke model: implications for translaboratory collaborations

Current recommendations encourage the use of embolic stroke (ES) models and replication of results across laboratories in preclinical research. Since such endeavors employ different surgeons, we sought to ascertain the impact of injection technique on outcome and response to thrombolysis in an ES model. Embolic stroke was induced in Male Wistar Kyoto rats (n=166) by a fast or a slow clot injection (CI) technique. Saline or recombinant tissue plasminogen activator (rtPA) was given at 1 hour after stroke. Flow rate curves were assessed in 24 animals. Cerebral perfusion was assessed using laser Doppler flowmetry. Edema corrected infarct volume, hemispheric swelling, hemorrhagic transformation, and neurologic outcome were assessed at 24 hours after stroke. Clot burden was estimated in a subset of animals (n=40). Slow CI resulted in significantly smaller infarct volumes (P=0.024) and better neurologic outcomes (P=0.01) compared with fast CI at 24 hours. Unexpectedly, rtPA treatment attenuated infarct size in fast (P<0.001) but not in slow CI experiments (P=0.382), possibly related to reperfusion injury as indicated by greater hemorrhagic transformation (P<0.001) and hemispheric swelling (P<0.05). Outcome and response to thrombolysis after ES are operator dependent, which needs to be considered when comparing results obtained from different laboratories.
Graphene: electrons en masse.

Massless electrons in graphene exhibit a mass when considered as collective excitations known as plasmons.
Fast automatic particle picking from cryo-electron micrographs using a locally normalized cross-correlation function: a case study

Recent progress in single-particle reconstruction methods and cryo-EM techniques has led to the determination of macromolecular structures with unprecedented resolution. The number of particles that goes into the reconstruction is a key determinant in achieving high resolution. Interactive manual picking of particles from an electron micrograph is a very time-consuming, tedious, and inefficient process. We have implemented a fast automatic particle picking procedure in the SPIDER environment. The procedure makes use of template matching schemes and employs a recently developed locally normalized correlation algorithm based on Fourier techniques. As a test, we have used this procedure to pick 70S Escherichia coli ribosomes from a cryo-electron micrograph. Different search strategies including use of a circular mask and asymmetric masks for different orientations of the particle have been explored, and their relative efficiencies are discussed. The results indicate that the procedure can be optimally used to pick ribosomes in a fully automatic way within the limit of selecting less than 10% false positives while missing about 15% of true positives.
Effects of physical disturbance and canopy cover on attached diatom community structure in an Idaho stream

A field experiment was conducted to determine the effect of disturbance frequency on diatom communities established on artificial substrates within an open canopy site and a closed canopy site of a 3rd order stream. The open canopy site (OCS) had a total of 80 diatom taxa colonizing the substrates, while the closed canopy site (CCS) had only 55 taxa. Cluster analysis revealed that the two sites had distinct diatom communities, although the most common species were similar between sites. There was no effect of disturbance frequency on species diversity (H') at OCS, however species diversity significantly decreased as disturbance frequency increased at CCS. At OCS, Amphora perpusilla increased in abundance as disturbance frequency increased, while Navicula lanceolata abundance decreased as disturbance increased. At CCS, Cocconeis placentula v. euglypta remained dominant regardless of disturbance frequency. The results suggest that some diatom species may be ‘shade adapted’, which may explain the site-specific responses. In addition, diatom growth-forms may explain the within site taxon-specific responses to disturbance. For example, Achnanthes sp. and Cocconeis sp., small horizontal forms, were predominant on the high disturbance substrates. Vertical or large horizontal forms may be mechanically removed by frequent physical disturbance allowing such small horizontal forms to become abundant. Frequent disturbance, by maintaining the community in an early stage of development, directly influences the diatom assemblage on rocks in streams.
Molecular Cloning of a Dendritic Cell-associated Transmembrane Protein, DC-HIL, That Promotes RGD-dependent Adhesion of Endothelial Cells through Recognition of Heparan Sulfate Proteoglycans

Abstract We isolated a novel molecule (DC-HIL) expressed abundantly by the XS52 dendritic cell (DC) line and epidermal Langerhans cells, but minimally by other cell lines. DC-HIL is a type I transmembrane protein that contains a heparin-binding motif and an integrin-recognition motif, RGD, in its extracellular domain (ECD). A soluble fusion protein (DC-HIL-Fc) of the ECD and an immunoglobulin Fc bound to the surface of an endothelial cell line (SVEC). This binding induced adhesion of SVEC to its immobilized form. Sulfated polysaccharides (e.g. heparin and fucoidan) inhibited binding of soluble DC-HIL-Fc and adhesion of SVEC. By contrast, an integrin inhibitor (RGDS tetramer) had no effect on binding to SVEC, but prevented adhesion of SVEC. This differential RGD requirement was confirmed by the finding that DC-HIL-Fc mutant lacking the RGD motif can bind to SVEC but is unable to induce adhesion of SVEC. Furthermore, DC-HIL appears to recognize directly these sulfated polysaccharides. These results suggest that DC-HIL binds to SVEC by recognizing heparan sulfate proteoglycans on endothelial cells, thereby inducing adhesion of SVEC in an RGD-dependent manner. We propose that DC-HIL serves as a DC-associated, heparan sulfate proteoglycan-dependent integrin ligand, which may be involved in transendothelial migration of DC.
Gene expression profiling of human diseases by serial analysis of gene expression

Until recently, the approach to understanding the molecular basis of complex syndromes such as cancer, coronary artery disease, and diabetes was to study the behavior of individual genes. However, it is generally recognized that expression of a number of genes is coordinated both spatially and temporally and that this coordination changes during the development and progression of diseases. Newly developed functional genomic approaches, such as serial analysis of gene expression (SAGE) and DNA microarrays have enabled researchers to determine the expression pattern of thousands of genes simultaneously. One attractive feature of SAGE compared to microarrays is its ability to quantify gene expression without prior sequence information or information about genes that are thought to be expressed. SAGE has been successfully applied to the gene expression profiling of a number of human diseases. In this review, we will first discuss SAGE technique and contrast it to microarray. We will then highlight new biological insights that have emerged from its application to the study of human diseases.
Uncertainty and Denial: A Resource-Rational Model of the Value of Information

Classical decision theory predicts that people should be indifferent to information that is not useful for making decisions, but this model often fails to describe human behavior. Here we investigate one such scenario, where people desire information about whether an event (the gain/loss of money) will occur even though there is no obvious decision to be made on the basis of this information. We find a curious dual trend: if information is costless, as the probability of the event increases people want the information more; if information is not costless, people's desire for the information peaks at an intermediate probability. People also want information more as the importance of the event increases, and less as the cost of the information increases. We propose a model that explains these results, based on the assumption that people have limited cognitive resources and obtain information about which events will occur so they can determine whether to expend effort planning for them.
Volatiles in basaltic glasses from the East Pacific Rise at 21°N: implications for MORB sources and submarine lava flow morphology

Pillow-rim glasses from a suite of moderately evolved lavas erupted along the axis of the East Pacific Rise (EPR) at 21°N were analyzed by high-temperature mass spectrometry for volatile content. Concentrations of H2O, F and Cl in the 21°N glasses are low and correlate inversely with Mg# yielding well-defined trends. These and other geochemical data indicate derivation of the 21°N glasses from similar parental magmas produced from a highly depleted, nearly homogeneous source [1]. Total volatile, H2O, F and S contents are lower and CO2 content is somewhat higher in these samples than in previously analyzed Mid-Atlantic Ridge (MAR) glasses. 21°N glasses are similar in volatile content to glasses from the Galapagos Spreading Center (GSC) at 95°W except in Cl (lower) and CO2 (higher). Unlike most MAR and GSC glasses, CO2 is the dominant volatile in all of the 21°N glasses with Mg# > 62. All of the EPR and GSC glasses contain reduced carbon species (CO and CH4), unlike most previously analyzed MAR samples. These data indicate that sources for mid-ocean ridge basalts are extremely volatile-poor (< 0.10 wt.%) and are probably dominantly reduced (below quartz-fayalite-magnetite buffer). Sheet flow and pillow basalts contain identical volatile contents. Thus, volatile abundance is not a factor controlling flow morphology. Extrusion rate and/or surface topography are probably the most important factors influencing flow morphology in submarine basalts. H2O-release patterns are however related to flow morphology. Mass pyrograms for sheet flow and pillow basalt glasses both show bimodal H2O-release behavior at the same temperatures (800°C and1000°C ± 50°C). However, the dominant H2O-release peak for sheet flow glasses is at the lower temperature; for pillow-rim glasses it is at the higher temperature. Infrared spectroscopic studies indicate that H2O in these glasses is present only as hydroxyl groups. Thus, the cause of differences in the bimodal H2O-release and how it is related to flow morphology is unclear.
Maximum entropy and least square error minimizing procedures for estimating missing conditional probabilities in Bayesian networks

Conditional probability tables (CPT) in many Bayesian networks often contain missing values. The problem of missing values in CPT is a very common problem and occurs due to the lack of data on certain scenarios that are observed in the real world but are missing in the training data. The current approaches of addressing the problem of missing values in CPT are very restrictive in that they assume certain probability distributions for estimating missing values. Recently, maximum entropy (ME) approaches have been used to learn features of probability distribution functions from the observed data. The ME approaches do not require any data distribution assumptions and are shown to work well for several non-parametric distributions. The ME and least square (LS) error minimizing approaches can be used for estimating missing values in CPT for Bayesian networks. The applications of ME and LS approaches for estimating missing CPT require researchers to solve difficult constrained non-linear optimization problems. These difficult constrained non-linear optimization problems can be solved using genetic algorithms.
A New Metal-Binding Site for Yeast Phosphoglycerate Kinase as Determined by the Use of a Metal-ATP Analog

Suicide substrate β, γ-bidentate Rh(III)ATP (RhATP) was used to map the metal ion-binding site in yeast phosphoglycerate kinase (PGK). Cleavage of the RhATP-inactivated enzyme with pepsin and subsequent separation of peptides by reverse-phase high-performance liquid chromatography gave two Rh-nucleotide bound peptides. One of the peptides corresponded to the C-terminal residues of PGK, and the other to a part of helix V. Of the four glutamates present in the C-terminal peptide, Glu 398 may be a likely metal coordination site. Therefore, importance of the C-terminal residues in PGK catalysis may be attributed, in part, to the coordination of metal ion of the metal-ATP substrate. Metal coordination may then align the C-terminal peptide to extend toward the N-terminal domain and form the “closed” active site. Results presented in this paper suggest that one or more side chains of the enzyme may be coordinated to the metal ion in the PGK·3-phospho-D-glycerate·RhATP complex, and that exchange-inert metal-ATP analogs could be used to determine metal coordination sites on kinases and other metal-ATP-utilizing enzymes.
Prediction of late-onset pouch failure in patients with restorative proctocolectomy with a nomogram

Abstract Background A proportion of UC patients with restorative proctocolectomy and IPAA develop pouch failure. Accurate risk assessment is critical for making proper evaluation and treatment. Information on factors that may reliably predict pouch failure for the patients requiring referral to a specialized care unit is minimal. Aim We sought to develop and internally validate a nomogram for the prediction of late-onset pouch failure. Methods The study cohort included all eligible UC patients with restorative proctocolectomy and IPAA at the subspecialty Pouchitis Clinic from 2002 to 2009. Inclusion criteria were patients having: 1) inflammatory bowel disease; 2) ileal pouches; and 3) regular follow-up at the Pouchitis Clinic. Demographic and clinical variables were prospectively collected. Multivariable accelerated failure time regression model was developed to predict pouch failure defined as pouch excision or permanent diversion. Discrimination and calibration of the model were assessed following bootstrapping methods for correcting optimism, and the model was presented as a nomogram. Results A total of 921 patients were included for the model. The mean age for this cohort was 45.5 years old. The mean follow-up at the Pouchitis Clinic was 5.8 years. Kaplan–Meier analysis showed that the probabilities for pouch retention are 0.939, 0.916 and 0.907 at 3, 5 and 7 years, respectively. The predictor variables which were included in the nomogram were smoking, duration of the pouch, baseline pouch diagnosis, and pre- and post-op use of biologics. The concordance index was 0.824. The nomogram seemed well calibrated based on the calibration curve. Conclusions The nomogram model appeared to predict late-onset pouch failure reasonably well with satisfactory concordance index and calibration curve. The nomogram is readily applicable for clinical practice in pouch patients.
The Relationship between Aircraft Count and Controller Workload in Different En Route Workstation Systems

Some air traffic control researchers have reported that the relationship between aircraft count in the sector and controller workload is nonlinear. Other researchers have reported it linear. However, they did not manipulate the number of aircraft separately in their experiments. In our experiment, we gradually increased traffic levels within each experimental run. Our controllers used three different workstation systems with and without data communication. The linear and power models described the relationship well. The proportion of workload variance explained by aircraft count was well above 50%. With these models, we predict controllers could handle about four (13%) more aircraft with data communication than without it with the Display System Replacement (DSR) system that is currently used at Air Route Traffic Control Centers (ARTCCs).
Assimilatory nitrate uptake in Pseudomonas fluorescens studied using nitrogen-13

The mechanism of nitrate uptake for assimilation in procaryotes is not known. We used the radioactive isotope, 13N as NO3 -, to study this process in a prevalent soil bacterium, Pseudomonas fluorescens. Cultures grown on ammonium sulfate or ammonium nitrate failed to take up labeled nitrate, indicating ammonium repressed synthesis of the assimilatory enzymes. Cultures grown on nitrite or under ammonium limitation had measurable nitrate reductase activity, indicating that the assimilatory enzymes need not be induced by nitrate. In cultures with an active nitrate reductase, the form of 13N internally was ammonium and amino acids; the amino acid labeling pattern indicated that 13NO3 - was assimilated via glutamine synthetase and glutamate synthase. Cultures grown on tungstate to inactivate the reductase concentrated NO3 - at least sixfold. Chlorate had no effect on nitrate transport or assimilation, nor on reduction in cell-free extracts. Ammonium inhibited nitrate uptake in cells with and without active nitrate reductases, but had no effect on cell-free nitrate reduction, indicating the site of inhibition was nitrate transport into the cytoplasm. Nitrate assimilation in cells grown on nitrate and nitrate uptake into cells grown with tungstate on nitrite both followed Michaelis-Menten kinetics with similar K mvalues, 7 μM. Both azide and cyanide inhibited nitrate assimilation. Our findings suggest that Pseudomonas fluorescens can take up nitrate via active transport and that nitrate assimilation is both inhibited and repressed by ammonium.
DNA-Thumb Interactions and Processivity of T7 DNA Polymerase in Comparison to Yeast Polymerase η

The replicative polymerase of bacteriophage T7 is structurally and mechanistically well characterized. The crystal structure of T7 DNA polymerase or gene 5 protein complexed to its processivity factor, Escherichia coli thioredoxin, a primer-template, and a dideoxynucleotide reveals how this enzyme interacts with the 3′-end of the primer-template, but does not show how thioredoxin confers processivity to the polymerase. In the crystal structure highly conserved amino acids Asn335 and Ser338 of the thumb subdomain of T7 DNA polymerase are seen to interact with phosphates 7 and 8 of the DNA template strand. Results with a mutant T7 DNA polymerase in which aliphatic residues are substituted for these amino acids and experiments with different length and methylphosphonate-modified primer-templates demonstrate that these interactions are essential for processive synthesis and d(A·T)n tract bypass. Our data with methylphosphonate-modified DNA suggests that thioredoxin confers processivity to T7 DNA polymerase in part by causing an interaction with the phosphate backbone or minor groove of DNA. Residues Asn335 and Ser338 may also function with a nearby helix-loop-helix motif located at residues 339–372 to enclose the DNA during processive synthesis. Our results suggest that this structure must be held close to the DNA by ionic interactions to function. These interactions also allow for DNA sliding but physically block the passage of a 3T bulge in the template. In contrast, yeast polymerase η, a polymerase that non-mutagenically repairs cis-syn thymidine dimers, allows the same bulge to slide past its thumb subdomain during synthesis. A relaxed thumb interaction with the DNA could account for the notably low processivity of polymerase η.
Teaching Gender History to Secondary School Students

Teaching gender history to high school students requires a level of explanation that is usually absent in history survey courses and texts. Thus, students and faculty are unlikely to view the enterprise as basic or necessary knowledge. Although the scholarly world has come a long way toward recognizing gender as a central category of historical analysis, popular attitudes and the consciousness of adolescents lag far behind. So, each time we have taught gender history (and each time we have argued to keep it in the curriculum), we have had to make a case for why gender matters. We argue that gender as a cultural category affects a person's life chances, values, earning power, likelihood of committing or being a victim of crime, chance of being killed in battle, opportunities for education and professional advancement, and even life expectancy. We urge students to question gender prescriptions that they have been taught ("girls are . . . boys are . . ." statements), whether they come from teachers, family members, or public experts. We also invite them to look closely at the variety in gender populations and the motivation behind gender prescription. Though biological determinism in many forms, especially sociobiology, has won new popular audiences since the 1 970s in the United States, high school students can look at the several sides to current debates and compare them to debates that surrounded biology's "just so stories" of the late nineteenth century. They can examine the debates among equality feminists and difference feminists and critics of feminism to explore what they have been taught and what remain their unanswered questions about gender. A basic requirement for making gender studies a presence in a high school is to convince curriculum planners and students that gender systems may be as powerful in shaping people's lives as are economic or governmental systems.1 We take it for granted today that history departments offer courses on gender as a basic element of their curricula. That is, we take it for granted if the departments in question are college or university departments. At the secondary level, such offerings
Author's response: re: findings of nonparentage: a case for autonomy.

We thank both Dr Chandler and Drs Michie and Allyse for their thoughtful and challenging responses to our article, “Incidental Findings of Nonparentage.” The subtle arguments that the authors provide is precisely the kind of debate we hoped to spark in writing this article. We have several responses. The first is directed to Dr Chandler, who makes a principle-based argument regarding truth-telling. Dr Chandler is concerned that our recommendation might undermine the clinician’s obligation of truth-telling, which he holds to be an absolute ethical duty. However, an explicit policy of universal nondisclosure removes both the clinician’s ethical obligation of truth-telling and the parental expectation that information of nonparentage be shared. Consider an analogous case of nondisclosure: if I … E-mail: fiester{at}upenn.edu
Cleidocranial Dysplasia with Neonatal Death Due to Central Nervous System Injury in Utero: Case Report and Literature Review

Cleidocranial dysplasia (CCD), an uncommon disorder involving membranous bones, is rarely lethal in early life. The calvaria is defective and wormian bones are present. Abnormalities of the clavicles vary in severity from a minor unilateral defect to bilateral absence. This report concerns pre- and postmortem anatomical and radiological findings in a 15-day-old female neonate with CCD. Her postnatal course was characterized by seizures and recognition of hydrocephalus during the first day of life. The calvaria was hypoplastic with numerous wormian bones. A pseudofracture of the right clavicle was present. Hydrocephalus was present in the brachycephalic brain which had a severely thinned cerebral cortex. Hemosiderin in the ventricular lining and marked subependymal gliosis were interpreted as evidence of old intraventricular hemorrhage that had occurred in utero. A CCD-related condition, Yunis-Varon syndrome (YVS), is noted for early lethality and for developmental and secondary abnormalities of the central nervous system. The present case only partially matches the phenotype of YVS and might represent a part of a spectrum of phenotypic variants ranging from viable CCD to lethal YVS.
The principle of BRS symmetry: An alternative approach to Yang-Mills theories

Abstract Postulating BRS and anti-BRS symmetry of the quantum Yang-Mills lagrangian and of the measure of the functional integral, we prove gauge invariance and renormalizability and recover the classical theory from the quantum one. We also give a heuristic interpretation of the BRS and anti-BRS symmetry. The most general BRS and anti-BRS admissible gauges are linear in the gauge field, but may depend non-linearly on the ghost fields.
A herpes simplex virus ribonucleotide reductase deletion mutant is defective for productive acute and reactivatable latent infections of mice and for replication in mouse cells.

Abstract Herpes simplex virus encodes a ribonucleotide reductase that is not essential for virus growth in dividing cells at 37°. This enzyme has been proposed as a target for antiviral drugs; its utility in this regard could depend upon its importance in vivo . To test the requirement of viral ribonucleotide reductase in a mammalian host, we tested a mutant virus, lacking most of the gene encoding the ribonucleotide reductase large subunit, in a mouse eye model of pathogenesis and latency where the wild-type virus establishes reactivatable latent infections in trigeminal ganglia following corneal inoculation. The deletion mutant was severely impaired in its ability to replicate acutely in the eye and in the trigeminal ganglion and failed to establish reactivatable latent infections. In contrast, a recombinant virus in which the deleted sequences were restored was competent for both acute and latent infections. The defects of the deletion mutant in the mouse may be related to its severely impaired growth at 38° in mouse cells relative to its growth in Vero cells. These results indicate that ribonucleotide reductase is critical for productive acute and reactivatable latent infections in mice and replication in mouse cells at 38° and suggest that caution be exercised in extrapolating from studies conducted in mice to human infections when judging the utility of this enzyme as a target for antiviral chemotherapy.
The prevalence and perceived health consequences of Hunger in emergency department patient populations

Objectives: Hunger is associated with chronic poor health and may force patients to make choices that acutely impact their health. This study was conducted to determine the prevalence of hunger, some of the choices it forces, and its perceived health effects among emergency department (ED) patients. Methods: A validated survey about hunger, choosing between food and medicine, and perceived adverse health outcomes was administered in English, Spanish, and Somali to non-critically ill ED patients or their parents. Demographics, rates of hunger, numbers of yearly ED visits, and decisions between buying commodities or medications were assessed. Relationships between variables were summarized with odds ratios (ORs), 95% confidence intervals, and logistic regression. Results: Of 930 respondents, 23.7% screened positive for hunger and 17.6% bought food instead of medications. Among the hunger-positive respondents, 44% believed this choice caused illness, and of these, 69% sought ED assessment and 35% believed they were hospitalized because of this choice. Predictors of hunger were low income (OR = 3.3), illicit drug use (OR = 5.5), chronic illness (OR = 2.1), Hispanic ethnicity (OR = 1.9), and lack of insurance (OR = 1.8). Buying food instead of medicine was predicted by low income (OR = 2.5), chronic illness (OR = 2.4), and lack of insurance (OR = 3.4). Predictors of illness were chronic illness (OR = 1.8), lack of insurance (OR = 2.8), African American race (OR = 2.0), and "poor" health (OR = 1.9). Conclusions: These ED patients have high rates of hunger and often choose to buy food instead of medications. Many believe that this choice results in ED visits and hospitalizations. Socioeconomic factors may predict hunger and subsequent ill health.
Wave Functions and Transition Probabilities in Scaled Thomas-Fermi Ion Potentials

A semiempirical method for computing atomic and ionic wave functions is described. The method uses a one-electron potential obtained from a scaled Thomas-Fermi ionic charge distribution. The scale factors are chosen to make the one-electron binding energies agree with experimental ionization potentials. A number of oscillator strengths have been evaluated and are found to agree well with results of alternative methods of calculation. The method has a wider range of applicability than that of Bates and Damgaard, and calculations are much shorter than those using the self-consistent-field methods.
Use of an ultraviolet light at point-of-dispense faucet to eliminate Pseudomonas aeruginosa

Tap water is believed to be a significant source of Pseudomonas aeruginosa in health care environments. This study evaluated an ultraviolet (UV) light point-of-dispense water treatment system for control of P aeruginosa . No P aeruginosa was detected in 30 different water dispensers in which the UV light device had been operating for 1-34 months. In comparison, P aeruginosa was found in other taps that did not feature this UV light system.
Effect of socialization on adult social preferences in Tilapia mossambica (Sarotherodon mossambicus); Pisces: Cichlidae

Abstract This study investigated the effects of socialization on the sexual preferences of adult Tilapia mossambica . Subjects were reared (1) with mother and siblings for the first month of life and then with siblings until sexual maturity, or (2) with siblings from hatching to sexual maturity, or (3) in social isolation from hatching to sexual maturity. At maturity males were tested with female fish of four different species to determine the range of species they would court and then were subjected to two different preference tests to determine the species they preferred to court. Females were subjected to a ‘proximity to male fish’ preference test. All groups of adult fish preferred to court and ‘stay near’ conspecific fish, regardless of gender or of previous social experience. It was concluded that socialization is not needed for adult T. mossambica to recognize and prefer conspecifics.
Pathophysiology and clinical management of moderate and severe traumatic brain injury in the ICU.

Moderate and severe traumatic brain injury (TBI) is the leading cause of morbidity and mortality among young individuals in high-income countries. Its pathophysiology is divided into two major phases: the initial neuronal injury (or primary injury) followed by secondary insults (secondary injury). Multimodality monitoring now offers neurointensivists the ability to monitor multiple physiologic parameters that act as surrogates of brain ischemia and hypoxia, the major driving forces behind secondary brain injury. The heterogeneity of the pathophysiology of TBI makes it necessary to take into consideration these interacting physiologic factors when recommending for or against any therapies; it may also account for the failure of all the neuroprotective therapies studied so far. In this review, the authors focus on neuroclinicians and neurointensivists, and discuss the developments in therapeutic strategies aimed at optimizing intracranial pressure and cerebral perfusion pressure, and minimizing cerebral hypoxia. The management of moderate to severe TBI in the intensive care unit is moving away from a pure “threshold-based” treatment approach toward consideration of patient-specific characteristics, including the state of cerebral autoregulation. The authors also include a concise discussion on the management of medical and neurologic complications peculiar to TBI as well as an overview of prognostication.
Successful treatment of fibrosing cholestatic hepatitis after liver transplantation.

Abstract Background A minority of liver transplant (OLT) recipients with hepatitis C virus (HCV) develop fibrosing cholestatic hepatitis (FCH), a severe form of HCV recurrence associated with early graft failure and death. There are few reports of successful salvage strategies. In this retrospective study, we sought to determine the characteristics and outcomes for patients with FCH at our transplant center. Methods All cases of HCV-positive OLT recipients from July 2007 through July 2010 were reviewed. Patient demographics, donor characteristics, and the post-OLT clinical course were analyzed. Tacrolimus-based immunosuppression was used. FCH was treated by conversion to cyclosporine A (CsA) and aggressive treatment with pegylated interferon (IFN) alpha2A and ribavirin (RBV). Liver biopsies and HCV RNA were obtained frequently per protocol or for cause. Results The rate of FCH during the study period was 13.5% (5/37). Of the 5 patients with FCH (4 males, 4 Caucasian), mean age was 51 (± 4.8) years and the Model for End-Stage Liver Disease (MELD) score at listing was 26.6 (± 10). Three of the 5 received liver and kidney (L/K) transplants (60%); the rate of L/K transplant in non-FCH patients was 12.5%. HCV RNA levels ranged from 5 to 6.69 log IU/mL pre-OLT; none were on anti-HCV therapy at the time of OLT. Mean ischemic time was 385 (± 152) minutes; donor age was 34.4 (± 13.7) years. No CMV infections developed postoperatively. Time to histologic HCV recurrence was 2 (± 2.23) months (range, 1–6); FCH occurred at 2.2 (± 2.2) months. Patients were converted from tacrolimus to CsA and treated with IFN and RBV; 2 were changed to consensus IFN. HCV RNA increased post-OLT in all, but responded to therapy in 4 of 5. None of the L/K recipients experienced renal graft rejection during treatment. Four of 5 had clinical and histologic improvement; 1 progressed to cirrhosis with minimal inflammation. One-year patient survival after OLT in this group was 80%. Liver allograft rejection occurred in 60% at 4.7 (± 5.5) months and was treated by CsA and prednisone dosage adjustments. In this cohort of patients undergoing OLT for HCV, FCH occurred early after OLT but responded to aggressive management with conversion from tacrolimus to CsA and treatment with pegylated IFN or consensus IFN/RBV. There was a higher rate of combined L/K transplants in the FCH group compared with the non-FCH group. Liver allograft rejection occurred in 60% of cases, but responded to treatment in all; no renal graft rejection occurred in the 3 with L/K transplants while on IFN. One-year graft and patient survival was 80%. Conclusion Better survival with FCH is possible with early initiation of IFN/RBV therapy with close monitoring of biopsies and viral load, and conversion from tacrolimus to CsA. Treatment can be performed even in L/K transplantation recipients, although it is associated with a higher incidence of treatable liver allograft rejection.