cssi/SciSciGPT-SciSciNet huggingface dataset:
TH-C-BRB-03: On the Suitability of Using NanoDot for Measuring Dose Distributions Resulting from KV-CBCT Acquisitions

Purpose: There is a growing need to determine radiation exposure and dose distributions resulting from an image‐guidance procedure. Although Monte Carlo simulations are capable to calculate the dose distributions experimental measurements remain the gold standards to validate the accuracy of calculations. This study investigated the suitability of nanoDot dosimeters for measuring accumulative dose at several locations simultaneously to determine 3D dose distributions resulting from a kilovoltage cone‐beam CT (kV‐CBCT) scan. Method and Materials: The nanoDot dosimeters read with a microStar reader by Landauer were used in the study. The system can be calibrated to measure dose from kilovoltage to megavoltage energy beams. The manufacturer provides a set of calibration dosimeters for 80 kVp x‐rays. The accuracy of the nanoDot dosimeters for absorbed dose measurements for kV‐CBCT scans was validated by using an ionization chamber in which the air‐kerma calibration factors were traceable to National Standards Laboratory. The relative dose distributions measured with nanoDot were compared with Monte Carlo calculated dose distributions in a PLASTIC WATER® LR phantom. Results: Seven nanoDot dosimeters were placed at different locations to determine dose distributions resulting from each kV‐CBCT scan protocol. There are five different kV‐CBCT scan protocols in the Varian OBI 1.4 system including Head Low‐dose Thorax Pelvis and Pelvis Spot Light with two different Bow‐tie filters. Both absolute and relative dose distributions were investigated. The dose values measured from 35 points generally agree with that of Monte Carlo calculations within 2–4%. Conclusion: The nanoDot dosimeters have been shown to be very suitable detectors for measuring 3D dose distributions resulting from kV‐CBCT scans due to its small size the ease of use good reproducibility and manageable photon energy dependence. Conflict of Interest: The microStar reader used in the research was provided by Landauer Inc. Glenwood IL
The influence of temperature on the rate of root and sprout growth of potatoes

Sprout and root growth of potato seed pieces representing ten varieties was studied in the range of 45–60° F. The critical temperature for growth was in the 48–50° range. No consistent association between early maturity and rapid seed-piece germination could be determined.
Antimicrobial Stewardship as Part of the Infection Prevention Effort

Antimicrobial stewardship programs (ASPs) optimize antimicrobial use to decrease the incidence of infection with multidrug-resistant organisms (MDRO) and the emergence of drug resistance, to improve patient outcomes and safety, and to decrease hospital costs. ASPs achieve these goals through several types of interventions that can occur before or after the antimicrobial has been prescribed; interventions can also be "active" or "passive." We believe that active post-prescription interventions such as post-prescription audit and feedback have the most supportive evidence and most promise. Stewardship activities must be integrated into already established efforts for infection prevention. We believe it is critical that antimicrobial stewardship, infection control, pharmacy, information technology, and clinical microbiology work collaboratively in order to decrease the incidence of infection due to MDRO.
The RNA accordion model for template positioning by telomerase RNA during telomeric DNA synthesis

Telomerase is a ribonucleoprotein (RNP) enzyme that maintains the ends of linear eukaryotic chromosomes and whose activation is a hallmark of 90% of all cancers. This RNP minimally contains a reverse transcriptase protein subunit (TERT) that catalyzes telomeric DNA synthesis and an RNA subunit (TER) that has templating, architectural and protein-scaffolding roles. Telomerase is unique among polymerases in that it synthesizes multiple copies of the template on the 3' end of a primer following a single binding event, a process known as repeat addition processivity (RAP). Using biochemical assays and single-molecule Forster resonance energy transfer (smFRET) experiments on Tetrahymena thermophila telomerase, we now directly demonstrate that TER contributes to template positioning within the active site and to the template translocation required for RAP. We propose that the single-stranded RNA elements flanking the template act as a molecular accordion, undergoing reciprocal extension and compaction during telomerase translocation.
Mind the phenotype gap

This meeting brought together over 100 scientists with a common interest in using genetic approaches in mice to study human biology. One of the strengths of the meeting was the diversity of subject areas covered. Presentations were given on mouse models of both simple and complex human disorders including developmental abnormalities, inflammatory diseases, cancer, and CNS diseases. Mixed in were a number of talks describing the latest techniques currently used to study gene function in the mouse, such as N-ethyl-Nnitrosourea (ENU) mutagenesis screens, DNA microarrays, and gene targeting. It was also readily apparent that Celera’s recent completion of the mouse genome sequence, as well as new programs to analyze this information, have made a significant impact on the speed with which investigators can localize and identify candidate genes that contribute to a particular phenotype. The first two days featured a variety of talks given on models of human disorders and genome analysis technology. The final session was largely focused on ENU mutagenesis screens. Martin Hrabe de Angelis (GSF Research Center for Environment and Health, Munich, Germany) began the session by describing his strategies for solving the ‘phenotype gap’. This term refers to a major problem in mouse genetics, basically that mutations have only been described for only a small number of genes. In his talk, he outlined the Munich-ENU screen, designed to identify both dominant and recessive mutations affecting a variety of organ systems. Over 300 mutant lines have now been generated from this work. A description of the genetically confirmed mutants from this ongoing project is available at http://www.gsf.de/ieg. Shigeharu Wakana (RIKEN Genomics Sciences Center, Yokohama, Japan) gave an overview of the RIKEN mutagenesis project. This effort is focused on identifying late-onset phenotypes such as tumorigenesis, diabetes, hypertension, and neurodegeneration. He also discussed Mind the phenotype gap
Low Frequency Self-Exciting Commutator Generator

SELF-EXCITING a-c commutator generators have for some time been considered as sources of electrical power. However, what is probably the first commercial use of this type of generator as the prime source of energy for a power machine has recently been made. It is a 6-pole 1,200-rpm 3-phase machine rated 40 kva, 235 volts, 2.5 cycles, and is driven by a squirrel cage induction motor. The set supplies power to one or more 200 hp super-calender induction motors in order to secure threading operation at very low stable speeds. The generator is compounded for approximately flat voltage and frequency. Commutation has been found to be excellent and the voltage wave form is satisfactory.
The apoptotic response in HCT116BAX-/- cancer cells becomes rapidly saturated with increasing expression of a GFP-BAX fusion protein

Background: Many chemotherapeutic agents promote tumor cell death by activating the intrinsic pathway of apoptosis. Intrinsic apoptosis involves permeabilization of the mitochondrial outer membrane and the release of cytochrome c, a process that is controlled by proteins of the BCL2 gene family. Chemoresistance is often associated with abnormalities in concentrations of BCL2 family proteins. Although stoichiometirc interactions between antiapoptotic and BH3-only BCL2 family proteins have been well documented as affecting cell death, the association between changes in BAX concentration and intrinsic apoptosis are poorly understood. Methods: Exogenous GFP-murine Bax fusion constructs were transfected into BAX-deficient HCT116 cells. To titrate the expression of the fusion protein, GFP-BAX was cloned into a tetracycline sensitive expression cassette and cotransfected with a plasmid expressing the rtTA transcription factor into HCT116 BAX-/- cells. Linear expression of the fusion gene was induced with doxycycline and monitored by quantitative PCR and immunoblotting. Cell death was assayed by DAPI staining cells after exposure to indomethacin, and scoring nuclei for condensed chromatin and fragmented nuclei. Results: HCT116 BAX-/- cells were resistant to indomethacin, but susceptibility could be recovered in cells expressing a GFP-BAX fusion protein. Titration of GFP-BAX expression revealed that the concentration of BAX required to induce a saturating apoptosis response from baseline, was rapidly achieved. Increased levels of GFP-BAX were unable to stimulate higher levels of cell death. Examination of GFP-BAX distribution before and after indomethacin treatment indicated that BAX protein did not form aggregates when present at sub-lethal concentrations. Conclusion: Within the limitations of this experimental system, BAX-dependent apoptosis in HCT116 cells exhibits an all-or-none response depending on the level of BAX protein present. The lack of BAX aggregation at subsaturation levels suggests that the translocation step of BAX activation may be impaired.
IQ and nonplanning impulsivity are independently associated with delay discounting in middle-aged adults

Abstract Impulsivity is a complex and multidimensional construct measured using both self-report measures and objective behavioral tasks. However, most studies using behavioral tasks have utilized relatively small homogeneous populations. In this project we examined both self-reported impulsivity, using the Barratt Impulsiveness Scale (BIS), and delay discounting, a behavioral measure of preference for immediate over delayed rewards, in a large sample of adults (N = 606). Performance on the self-report and behavioral measures was examined in relation to demographic characteristics including age, sex, race, IQ, years of school and family income. Using hierarchical multiple regression we found that preference for immediate rewards was related to the Nonplanning impulsiveness subscale of the BIS and, after controlling for other variables, also related to intelligence. The finding that delay discounting, or preference for immediate rewards, is related to intelligence even after taking into account other variables, including socioeconomic indicators, suggests that there may be previously unrecognized links between this form of impulsivity and intelligence. This also suggests that intelligence should be taken into account in studies designed to measure impulsive behaviors.
Deletion of Ile1 changes the mechanism of streptokinase: evidence for the molecular sexuality hypothesis.

Plasminogen (Plgn) is usually activated by proteolytic cleavage of Arg561−Val562. The new N-terminal amino group of Val562 forms a salt bridge with Asp740, creating the active protease plasmin (Pm). However, streptokinase (SK) binds to Plgn, generating an active protease in a poorly understood, nonproteolytic process. We hypothesized that the N-terminus of SK, Ile1, substitutes for the N-terminal Val562 of Pm, forming an analogous salt bridge with Asp740. SK initially forms an inactive complex with Plgn, which subsequently rearranges to create an active complex; this rearrangement is rate limiting at 4 °C. SK·Plgn efficiently hydrolyzes amide substrates at 4 °C, although ΔIle1−SK·Plgn has no amidolytic activity. ΔIle1−SK prevents formation of wild-type SK·Plgn. These results indicate that ΔIle1−SK forms the initial inactive complex with plasminogen, but cannot form the active complex. However, when the experiment is performed at 37 °C, amidolytic activity is observed when ΔIle1−SK is added to plasminogen....
WE‐E‐204B‐03: Feasibility of Bench‐Top Polychromatic Cone‐Beam X‐Ray Fluorescence Computed Tomography (XFCT) for In‐Phantom Detection of Gold Nanoparticles

Purpose: To examine the feasibility of quantifying concentration and spatial distribution of goldnanoparticles (GNPs) present within a small animal‐sized object by applying an x‐ray fluorescencecomputed tomography (XFCT) technique with a bench‐top, polychromatic, cone‐beam x‐ray source. Method and Materials: The Monte Carlo code MCNP5 was used to simulate the acquisition of goldfluorescencephotons under a polychromatic cone‐beam XFCT scenario. Three 1 cm‐diameter columns containing saline solution with GNPs (≤ 2% gold by weight) were inserted into a 5 cm‐diameter cylindrical PMMA phantom. The phantom was irradiated by a 110 kVp x‐ray source, and the resulting goldfluorescence and Compton‐scattered photons were collected by a series of 11 energy‐sensitive tallies. A maximized‐likelihood iterative reconstruction algorithm was implemented to reconstruct the image of GNP distribution. The effects of attenuation of both the primary beam through the phantom and the goldfluorescencephotons en route to the detector were corrected during the image reconstruction. The attenuation map of the phantom was known a priori, although it could have been easily measured with a transmission scan. Results: An accurate image of the GNP‐containing phantom was successfully reconstructed, with both spatial distribution and relative concentration of GNPs well defined. The pixel intensity of regions containing GNPs was linearly proportional to gold concentration, which would allow XFCT technique to quantify the GNP concentration and spatial distribution of an unknown sample. Conclusion: This study shows the feasibility of performing XFCT imaging using a bench‐top, polychromatic, cone‐beam x‐ray source. The current approach would make XFCT imaging accessible to applications where a synchrotron‐based XFCT imaging may be inapplicable, such as in vivo measurements of GNP biodistribution.
Reducing breast biopsies by ultrasonographic analysis and a modified self-organizing map

Recent studies suggest that visual evaluation of ultrasound images could decrease negative biopsies of breast cancer diagnosis. However, visual evaluation requires highly experienced breast sonographers. The objective of this study is to develop computerized radiologist assistant to reduce breast biopsies needed for evaluating suspected breast cancer. The approach of this study utilizes a neural network and tissue features extracted from digital sonographic breast images. The features include texture parameters of breast images: characteristics of echoes within and around breast lesions, and geometrical information of breast tumors. Clusters containing only benign lesions in the feature space are then identified by a modified self- organizing map. This newly developed neural network objectively segments population distributions of lesions and accurately establishes benign and equivocal regions.t eh method was applied to high quality breast sonograms of a large number of patients collected with a controlled procedure at Mayo Clinic. The study showed that the number of biopsies in this group of women could be decreased by 40 percent to 59 percent with high confidence and that no malignancies would have been included in the nonbiopsied group. The advantages of this approach are that it is robust, simple, and effective and does not require highly experienced sonographers.
Speckle interferometry of molecular cloud sources at 4.8 microns

The spatial structure at 4.8 microns has been observed in W3-IRS 5, Mon R2-IRS 3, and S 140-IRS 1, the first two of which are clearly double. In addition, for four compact sources, low upper limits can be set to the angular diameters which are near those for blackbodies having the same fluxes and color temperatures observed for those sources. With a factor-of-2 higher-resolution, one may be able to distinguish between thermal emission or reddening as the source of the observed spectral shape.
Another look at physicians' treatment of men and women with common complaints

A recent study of San Diego patients found that men received more extensive and appropriate diagnostic workups than women did for five common complaints (Arm#age, K. J., Schneiderman, L. J., & Bass, R. A. Journal of the American Medical Association, 1979, 241, 2186-2187). This article is a broader analysis of medical care given to men and women for those complaints (fatigue, headache, vertigo~dizziness, chest pain, back pain), and it uses a national survey of ambulatory-care visits. We find that medical care is usually similar for men and women. When significant sex differences do appear, they often show that women receive more medical care during a visit. To some extent, differential care stems from different medical needs that men and women with a complaint have; when some medically relevant factors are controlled, half of the significant sex differences disappear. But half persist, and this suggests that psychosocial factors also underlie differential care for men and women. These may originate with patients (for example, their requests for particular services) or with physicians (for example stereotypes of men and women patients). In contrast to the San Diego study, the national data show that (1) women sometimes receive more diagnostic workups for the five complaints, and (2) when medical factors are controlled, sex differences in the extent and content of workups disappear. The only exception is that men with vertigo~dizziness receive more appropriate workups.
Surface plasmon amplification under controlled exciton-plasmon coupling in individual carbon nanotubes

We theoretically demonstrate the possibility of low-energy surface plasmon amplification by optically excited excitons in small-diameter carbon nanotubes. The stimulated character of such an energy transfer causes the buildup of the macroscopic population numbers of coherent localized surface plasmons. As a consequence, high-intensity coherent optical-frequency fields are created at nanoscale throughout the nanotube surface. These strong local fields can be used in a variety of new optoelectronic applications of carbon nanotubes, including near-field nonlinear-optical probing and sensing, optical switching, enhanced electromagnetic absorption, and materials nanoscale modification. (© 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
Sodium dodecyl sulfate-capillary gel electrophoresis of proteins using non-cross-linked polyacrylamide

Proteins with relative molecular masses of 14,000 to 205,000 were separated by sodium dodecyl sulfate-capillary gel electrophoresis (SDS-CGE) using non-cross-linked linear polyacrylamide gels on both coated and uncoated fused-silica capillaries. It was determined that viscosity of the acrylamide solution was a major factor affecting column stability with linear acrylamide gels. When the viscosity of the acrylamide solution reaches 100 cP, electro-osmotically driven displacement of the gels is insignificant. Uncoated capillaries provided better resolution, stability, and reproducibility than surface coated capillaries when the concentration of linear polyacrylamide was greater than 4%. At lower gel concentrations, non-cross-linked polyacrylamide is easily displaced from the columns. A calibration plot of log molecular mass vs. mobility with non-linear polyacrylamide was linear, which indicated that resolution was equivalent to that obtained with cross-linked acrylamide. Separations with model proteins indicated that baseline resolution between protein species that vary 10% in molecular mass can be achieved.
The role of nitrogenous nutrients in the occurrence of harmful algal blooms caused by Cochlodinium polykrikoides in New York estuaries (USA)

Abstract The harmful dinoflagellate Cochlodinium polykrikoides is well known for forming ichthyotoxic blooms around the world, but the nutritional factors supporting and promoting these blooms have not been well studied. To better understand the nitrogen (N) nutritional ecology of C. polykrikoides , the temporal and spatial dynamics of nutrients, C. polykrikoides cells, and co-occurring phytoplankton were monitored within multiple NY (USA) estuaries over a three-year period. Uptake rates of bicarbonate and various N compounds were assessed during blooms and the growth responses of C. polykrikoides relative to co-occurring phytoplankton were quantified during N enrichment bioassays. Finally, the growth kinetics of C. polykrikoides were examined using clonal cultures grown on four N sources (ammonium, glutamic acid, nitrate, urea). Blooms of C. polykrikoides occurred when concentrations of nitrate and ammonium were 20 μM). During blooms, the addition of N compounds (ammonium, glutamic acid, nitrate, or urea) significantly enhanced primary productivity among microphytoplankton (>20 μm; p C. polykrikoides relative to other phytoplankton groups ( p C. polykrikoides (90% of cells) within eutrophic tributaries were nitrate and nitrite while in mesotrophic, open estuarine regions, urea and glutamic acid dominated N uptake. Finally, C. polykrikoides cultures grown on glutamic acid displayed significantly faster growth rates than cultures grown on urea, ammonium, and nitrate ( p C. polykrikoides blooms and that this alga is nutritionally flexible, capable of adapting to differing nutrient regimes and utilizing a variety of N compounds over a range of concentrations to form blooms.
CORRELATION OF HEAT RESISTANCE AND HSP-70A MRNA LEVELS IN HUMAN TUMOR CELLS MEASURED BY COMPETITIVE QUANTITATIVE POLYMERASE CHAIN REACTION

Abstract Purpose: Several HSP-70 genes have been cloned and sequenced in human cells. Among these genes, the HSP-70A mRNA and protein levels correlate best with the development and decay of thermotolerance and intrinsic thermal sensitivity Leukemic and nonleukemic humant unor cells express low levels of the normally heat inducible HSP-70A mRNA in control nonheated cells. Using a competitive quantitative polymerase chain reaction, we have measured the levels of mRNA for this gene and have correlated it with both transient and intrinsic thermal sensitivity of tumor cells. Such studies were also extended to tumor samples obtained from patients. Methods and Materials: In these studies, the plasmid phHSP-70 which contains the entire human HSP-70A gene was modified by the insertion of the T7 promoter at the 5′-end untranslated region as well as the insertion of a 23 bp synthetic linker at the BamH1 site in the promoter region of the HSP-70A gene. The PCR primers were located such that the amplified fragment contained the linker. Using the T7 polymerase, the HSP-70A mRNA was transcribed from this plasmid (phHSP-70L) in vitro . A known amount of HSP-70A mRNA was then added to the total RNA prepared from the cell samples or from the tumor tissues obtained from patients. Using the components of the PCR reaction plus known amounts of HSP-70A mRNA synthesized from phHSP-70L and unknown amounts of total cellular RNA, the samples were amplified and analysed on a denaturing acrylamide gel. The PCR products obtained from phHSP-70L were 23 by larger than the PCR products obtained from the cell samples due to the addition of the synthetic linker to the HSP-70A gene in phHSP-70L and therefore, the two products could be easily distinguished from each other and quantitated. The α- 32 P-dCTP incorporated in each sample was quantitated by AMBIS Scanner. When the 32 P-counts were equal in the known and the unknown samples, the amount of the HSP-70A mRNA was taken to be equal in the known and the unknown sample. Results: The results show that HSP-70A mRNA levels can be used to predict the survival levels during the development and decay of thermotolerance. In nonleukemic human tumor cell lines, there are as much as 40–50-fold induction of FISP-70A mRNA levels during the peak of thermotolerance. In leukemic cell lines, however, HSP-70A mRNA (levels are induced only by three-fold during the same time period. These differences between the levels of HSP-70A mRNA positively correlate with the amount of tolerance development in leukemic and nonleukemic tumor cells. HSP-70A mRNA levels also vary in different tumor cells under nonheated conditions and there is a positive correlation between HSP-70A mRNA levels in nonleukemic human tumor cells and the level of their intrinsic thermal resistance. Conclusion: HSP-70A mRNA levels can be used to predict the intrinsic thermal sensitivity of nonleukemic human tumor cells.
Lateral cervical displacement is associated with endometriosis

Abstract Objective: To report on a series of cases of lateral cervical displacement and uterosacral ligament scarring associated with endometriosis. Design: Case series. Setting: Academic medical center. Patient(s): Three nulliparous women with chronic pelvic pain, lateral cervical displacement, and uterosacral nodularity. Intervention(s): Physical examination to evaluate for lateral cervical displacement. Laparoscopic surgery to evaluate for endometriosis and uterosacral ligament involvement. Main Outcome Measure(s): Displacement of the entire cervix lateral to the midline of the vagina. Presence of endometriosis on the affected uterosacral ligament. Result(s): All three patients had lateral cervical displacement and implants of endometriosis and scarring on the uterosacral ligament ipsilateral to the displaced cervix. Conclusion(s): In women with pelvic pain, lateral cervical displacement due to uterosacral scarring may be a physical finding associated with endometriosis.
Benzodiazepines protect hippocampal neurons from degeneration after transient cerebral ischemia: an ultrastructural study.

Abstract The ability of full and partial benzodiazepine receptor agonists to prevent DNA fragmentation and neuronal death after transient cerebral ischemia was investigated in the Mongolian gerbil. Diazepam (10 mg/kg, i.p.) or the partial agonist imidazenil (3 mg/kg, i.p.) was administered 30 and 90 min after transient forebrain ischemia produced by occlusion of the carotid arteries for 5 min. Treatment with diazepam completely protected CA1b hippocampal pyramidal neurons in 94% of the animals and partially protected pyramidal neurons in 6% of the animals, as assessed with a standard Nissl stain three and four days after ischemia. DNA fragmentation was examined by the terminal dUTP nick-end labeling (TUNEL) reaction. Prior to cell death, there were no TUNEL-positive neurons in area CA1b. By three days after ischemia, when neuronal degeneration was nearly complete, 14 out of 16 gerbils exhibited a positive TUNEL reaction throughout area CA1b stratum pyramidale. In 13 out of 14 gerbils treated with diazepam, no TUNEL-positive neurons were observed in this region. Imidazenil was less effective than diazepam with respect to both neuroprotection and prevention of DNA fragmentation. Three days after ischemia, six out of eight gerbils treated with imidazenil showed partial to complete neuroprotection. Imidazenil completely prevented DNA fragmentation in only one of the animals; varying degrees of TUNEL reaction persisted in the remainder. To determine whether the neurons protected by diazepam had a normal ultrastructure, gerbils were killed two to 30 days after ischemia and the hippocampal neurons in area CA1b were examined by electron microscopy. Within the first 48 h after ischemia, early cytoplasmic changes of varying degrees (e.g., vacuolation, rough endoplasmic reticulum stacking, swollen mitochondria) and electron-dense dendrites were observed in gerbils not treated with diazepam. Degeneration was nearly complete by three days after ischemia. In contrast, pyramidal neuron ultrastructure appeared normal in gerbils that exhibited complete area CA1b neuroprotection (defined at the light microscope level) by diazepam when studied two, seven or 30 days after ischemia. In gerbils with partial protection of area CA1b, most of the remaining neurons exhibited varying degrees of necrosis when studied 30 days after ischemia. No apoptotic bodies were observed. We conclude that: (i) diazepam can fully protect CA1 pyramidal cells from the toxic effects of transient cerebral ischemia; (ii) when diazepam affords only partial neuroprotection, the residual CA1 pyramidal cells exhibit ultrastructural abnormalities consistent with necrotic damage; and (iii) diazepam is a more efficacious neuroprotectant than the partial benzodiazepine receptor agonist, imidazenil.
5.3.2 Integrating the Life‐cycle Process Utilizing SysML

Sandia National Laboratories is developing and applying an Integrated Phase Gate (IPG) project structure to execute critical programs such as nuclear weapon Life Extension Projects (LEP) that require the utmost attention to reliability, function and other stakeholder requirements including safety and security. This emphasis on project rigor reflects a new directive from the Department of Energy's National Nuclear Security Agency (NNSA) to develop robust processes in order to ensure that the nation's nuclear deterrence will be effective and available for decades to come. To this end, Sandia's Advanced and Exploratory Systems Department is developing a SysML model of an integrated Product Lifecycle Management (PLM) environment with the intent of providing project teams with direct access to program templates, requirements, tools (both program and technical) and related databases. This paper will describe the current state and future direction of the integrated PLM environment SysML model.
How Do You Tell Whether a Change in Surgical Technique Leads to a Change in Outcome

Purpose: Surgeons routinely evaluate and modify their surgical technique to improve patient outcome. It is also common for surgeons to analyze results before and after a change in technique to determine whether the change led to better results. Simple comparison of results before and after surgical modification may be confounded by the surgical learning curve. We developed a statistical method applicable to analyzing before/after surgical studies.Materials and Methods: We used simulation studies to compare different statistical analyses of before/after studies. We evaluated a simple 2-group comparison of results before and after the modification by the chi-square test and a novel bootstrap method that adjusts for the surgical learning curve.Results: In the presence of the learning curve a simple 2-group comparison almost always showed an ineffective surgical modification to be of benefit. When the surgical modification was harmful, leading to a 10% decrease in the success rate, 2-group comparison nonethel...
Studies on the thermal decarboxylation of 1‐alkoxycarbonylbenzotriazoles

1-Alkoxycarbonylbenzotriazoles on thermolysis lose carbon dioxide; the decarboxylation is accompanied by the formation of a mixture of 1- and 2-alkylbenzotriazoles, with the N-1 isomer predominating over the N-2 isomer in all cases. A cross-over experiment, in which heating equimolar amounts of 1-benzyloxycarbonylbenzotriazole and 1-(4-methylbenzyloxycarbonyl)-5,6-dimethylbenzotriazole gave almost all the cross-over products, supports the proposed intermolecular mechanism for this decarboxylation and the formation of 1- and 2-alkylbenzotriazoles. No decarboxylation was observed for 1-phenoxycarbonylbenzotriazole.
The Comer Intervention Model and School Reform in Chicago: Implications of Two Models of Change.

An analysis of twopublic reform efforts: the Comer intervention by mutual cooperation and political mobilization in Chicago.
Target Counting under Minimal Sensing: Complexity and Approximations

We consider the problem of counting a set of discrete point targets using a network of sensors under a minimalistic model. Each sensor outputs a single integer, the number of distinct targets in its range, but targets are otherwise indistinguishable to sensors: no angles, distances, coordinates, or other target-identifying measurements are available. This minimalistic model serves to explore the fundamental performance limits of low-cost sensors for such surveillance tasks as estimating the number of people, vehicles or ships in a field of interest to first degree of approximation, to be followed by more expensive sensing and localization if needed. This simple abstract setting allows us to explore the intrinsic complexity of a fundamental problem, and derive rigorous worst-case performance bounds. We show that even in the 1-dimensional setting (for instance, sensors counting vehicles on a road), the problem is non-trivial: target count can be estimated within relative accuracy of factor $\sqrt{2}$ and this is the best possible in the worst-case. We then address additional questions related to constructing feasible target placements, and noisy counters. In two dimensions, the problem is considerably more complicated: a constant-factor approximation is impossible. Our algorithms and analysis can easily handle some of the non-idealities of real sensors, such as asymmetric ranges and non-exact target counts.
First metatarsophalangeal joint arthrodesis: quantitative mechanical testing of six-hole dorsal plate versus crossed screw fixation in cadaveric specimens.

Quantitative strength analysis of first metatarsophalangeal joint arthrodesis was performed using two fixation techniques: a small 6-hole plate with an interfragmentary screw or two crossed lag screws. Twelve matched-pair fresh-frozen cadaveric specimens (24 trials) were used for direct comparison of each of the two fixation techniques. All joint surfaces were prepared with power conical reamers utilizing a standard technique. The fixation construct was stressed to failure on each specimen using a computer-integrated materials tester. Fixation stiffness defined as force (load) over displacement and point of ultimate failure was evaluated. The six-hole plate and interfragmentary screw fixation method was a statistically stiff er form of fixation (p > .01) and displayed a greater point of ultimate failure (p > .002) under the laboratory conditions.
Performance Driven Decoupling Capacitor Allocation Considering Data and Clock Interactions

We propose a sensitivity-based method to allocate decoupling capacitors (decaps) incorporating leakage constraints and tighter data and clock interactions. The proposed approach attempts to allocate decaps not only based on the power grid integrity criteria, but also based on the impact of power grid noise on timing criticality and robustness. The resulting algorithm reduces the power grid noise to below a threshold and improves the performance or timing robustness of the circuit at the same time.
The nucleotide receptor P2X7 mediates actin reorganization and membrane blebbing in RAW 264.7 macrophages via p38 MAP kinase and Rho

Extracellular nucleotides regulate macrophage function via P2X nucleotide receptors that form ligand-gated ion channels. In particular, P2X7 activation is characterized by pore formation, membrane blebbing, and cytokine release. P2X7 is also linked to mitogen-activated protein kinases (MAPK) and Rho-dependent pathways, which are known to affect cytoskeletal structure in other systems. As cytoskeletal function is critical for macrophage behavior, we have tested the importance of these pathways in actin filament reorganization during P2X7 stimulation in RAW 264.7 macrophages. We observed that the P2X7 agonists adenosine 5'-triphosphate (ATP) and 3'-O-(4-benzoylbenzoyl) ATP (BzATP) stimulated actin reorganization and concomitant membrane blebbing within 5 min. Disruption of actin filaments with cytochalasin D attenuated membrane blebbing but not P2X7-dependent pore formation or extracellular-regulated kinase (ERK)1/ERK2 and p38 activation, suggesting that these latter processes do not require intact actin filaments. However, we provide evidence that p38 MAPK and Rho activation but not ERK1/ERK2 activation is important for P2X7-mediated actin reorganization and membrane blebbing. First, activation of p38 and Rho was detected within 5 min of BzATP treatment, which is coincident with membrane blebbing. Second, the p38 inhibitors SB202190 and SB203580 reduced nucleotide-induced blebbing and actin reorganization, whereas the MAPK kinase-1/2 inhibitor U0126, which blocks ERK1/ERK2 activation, had no discernable effect. Third, the Rho-selective inhibitor C3 exoenzyme and the Rho effector kinase, Rho-associated coiled-coil kinase, inhibitor Y-27632, markedly attenuated BzATP-stimulated actin reorganization and membrane blebbing. These data support a model wherein p38- and Rho-dependent pathways are critical for P2X7-dependent actin reorganization and membrane blebbing, thereby facilitating P2X7 involvement in macrophage inflammatory responses.
Quantitative Proteomic Analysis of Host-virus Interactions Reveals a Role for Golgi Brefeldin A Resistance Factor 1 (GBF1) in Dengue Infection

Dengue virus is considered to be the most important mosquito-borne virus worldwide and poses formidable economic and health care burdens on many tropical and subtropical countries. Dengue infection induces drastic rearrangement of host endoplasmic reticulum membranes into complex membranous structures housing replication complexes; the contribution(s) of host proteins and pathways to this process is poorly understood but is likely to be mediated by protein-protein interactions. We have developed an approach for obtaining high confidence protein-protein interaction data by employing affinity tags and quantitative proteomics, in the context of viral infection, followed by robust statistical analysis. Using this approach, we identified high confidence interactors of NS5, the viral polymerase, and NS3, the helicase/protease. Quantitative proteomics allowed us to exclude a large number of presumably nonspecific interactors from our data sets and imparted a high level of confidence to our resulting data sets. We identified 53 host proteins reproducibly associated with NS5 and 41 with NS3, with 13 of these candidates present in both data sets. The host factors identified have diverse functions, including retrograde Golgi-to-endoplasmic reticulum transport, biosynthesis of long-chain fatty-acyl-coenzyme As, and in the unfolded protein response. We selected GBF1, a guanine nucleotide exchange factor responsible for ARF activation, from the NS5 data set for follow up and functional validation. We show that GBF1 plays a critical role early in dengue infection that is independent of its role in the maintenance of Golgi structure. Importantly, the approach described here can be applied to virtually any organism/system as a tool for better understanding its molecular interactions.
The genetic basis of head and neck carcinoma

Research over the past few years has pointed to a genetic basis for numerous cancers. Efforts in this regard are ongoing in squamous carcinoma of the head and neck. Today surgeons and residents in training need to stay up to date on molecular biology and the genetic sequences that are necessary to form a malignancy. In addition, these changes offer diagnosticians and therapists novel ways both to diagnose and treat malignancies. An evolution in molecular genetics, tumor virology, and tumor biology has led to our understanding of how malignancies arise. There are two pathways of cancer production: the activation of an oncogene or the mutation of a tumor suppressor gene. This review discusses the interaction of these genetic changes in the development of squamous carcinoma of the head and neck, their relationship to tobacco and alcohol use, as well as methods to detect the presence of malignancy and novel techniques that may be used to treat malignancies in the future.
Human Immunodeficiency Virus Type 1 Matrix Protein Interacts with Cellular Protein HO3

The matrix (MA) protein of human immunodeficiency virus type 1 (HIV-1) plays a critical role in virion morphogenesis and fulfills important functions during the early steps of infection. In an effort to identify cellular partners of MA, a Saccharomyces cerevisiae two-hybrid screen was utilized. A specific interaction between MA and HO3, a putative histidyl-tRNA synthetase, was demonstrated in this system. HO3-specific mRNA was detected in several tissues relevant for HIV infection, such as spleen, thymus, and peripheral blood lymphocytes, as well as in a number of T-lymphoid-cell lines. The binding of MA to HO3 was confirmed in transfected cells by coimmunoprecipitation. This interaction was abrogated by replacing two lysine residues at positions 26 and 27 of MA by threonine (MA(KK27TT)). HO3 localized both to the cytoplasm and to the nucleus of acutely transfected 293T cells. When overexpressed in HIV-1-producing cells, HO3 was incorporated into wild-type virions but not in ones containing the dilysine-mutated variant of MA. Correspondingly, overexpression of HO3 in virus producer cells enhanced the infectivity of wild-type but not MA(KK27AA) HIV-1 particles. The stimulating effect of HO3 was independent from the presence of Envelope, Vpr, or Vpu. Taken together, these results suggest that HO3, through its recognition of MA, plays a role in the life cycle of HIV-1.
Pulsed electron avalanche knife PlasmaBlade

Advances in electrosurgical technology have led to the design of new products with a wider number of applications. Electrosurgical instruments are either monopolar or bipolar devices. The pulsed electron avalanche knife (PEAK) PlasmaBlade™ represents an advancement in monopolar electrosurgical technology. The PEAK PlasmaBlade is a low-temperature tissue-dissection instrument that uses pulsed radiofrequency plasma discharges to cut with simultaneous hemostasis and less collateral thermal damage than traditional electrosurgical instruments.
Semantic similarity in the biomedical domain: an evaluation across knowledge sources

Background: Semantic similarity measures estimate the similarity between concepts, and play an important role in many text processing tasks. Approaches to semantic similarity in the biomedical domain can be roughly divided into knowledge based and distributional based methods. Knowledge based approaches utilize knowledge sources such as dictionaries, taxonomies, and semantic networks, and include path finding measures and intrinsic information content (IC) measures. Distributional measures utilize, in addition to a knowledge source, the distribution of concepts within a corpus to compute similarity; these include corpus IC and context vector methods. Prior evaluations of these measures in the biomedical domain showed that distributional measures outperform knowledge based path finding methods; but more recent studies suggested that intrinsic IC based measures exceed the accuracy of distributional approaches. Limitations of previous evaluations of similarity measures in the biomedical domain include their focus on the SNOMED CT ontology, and their reliance on small benchmarks not powered to detect significant differences between measure accuracy. There have been few evaluations of the relative performance of these measures on other biomedical knowledge sources such as the UMLS, and on larger, recently developed semantic similarity benchmarks. Results: We evaluated knowledge based and corpus IC based semantic similarity measures derived from SNOMED CT, MeSH, and the UMLS on recently developed semantic similarity benchmarks. Semantic similarity measures based on the UMLS, which contains SNOMED CT and MeSH, significantly outperformed those based solely on SNOMED CT or MeSH across evaluations. Intrinsic IC based measures significantly outperformed path-based and distributional measures. We released all code required to reproduce our results and all tools developed as part of this study as open source, available under http://code.google.com/p/ytex. We provide a publicly-accessible web service to compute semantic similarity, available under http://informatics.med.yale.edu/ytex.web/. Conclusions: Knowledge based semantic similarity measures are more practical to compute than distributional measures, as they do not require an external corpus. Furthermore, knowledge based measures significantly and meaningfully outperformed distributional measures on large semantic similarity benchmarks, suggesting that they are a practical alternative to distributional measures. Future evaluations of semantic similarity measures should utilize benchmarks powered to detect significant differences in measure accuracy.
Exploring the Energy Profile of the QA - to QB Electron Transfer Reaction in Bacterial Photosynthetic Reaction Centers: pH Dependence of the Conformational Gating Step †

Both large- and small-scale conformational changes are needed as proteins carry out reactions. However, little is known about the identity, energy of, and barriers between functional substates on protein reaction coordinates. In isolated bacterial photosynthetic reaction centers, the electron transfer from the reduced primary quinone, QA - , to the secondary quinone, QB, is rate limited by conformational changes at low pH and by proton binding at high pH. The kinetics and thermodynamics of this reaction were determined between 200 and 300 K from pH 6 to pH 10.5. A model with two substates of the reactant, P + QA - QB, one protonated (state A) and one unprotonated (R), and one state of the product, P + QAQB - (B), was able to simulate the dependence of the rate on temperature and pH fairly well. The equilibrium between the three states were measured in situ at each temperature. Proton binding (R to A transition) has a favorable ¢H and unfavorable ¢S as does the conformational changes required for electron transfer at low pH (A to B). The pK for the A to R transition is 9.7 at room temperature, consistent with previous measurements, and 13.5 at 200 K. The activation barriers were determined for each transition. Both the R to A and the A to B transitions are limited primarily by the activation enthalpy with modest ¢S q .
Identifying critical pathways to high performance PV

The High-Performance Photovoltaic (HiPerf PV) Project was initiated by the US Department of Energy to substantially increase the viability of photovoltaics (PV) for cost-competitive applications so that PV can contribute significantly to our energy supply and our environment in the 21st century. To accomplish this, the NCPV directs in-house and subcontracted research in high-performance polycrystalline thin-film and multijunction concentrator devices. Details of the subcontractor and in-house progress are described toward identifying critical pathways of 25% polycrystalline thin-film tandem cells and developing multijunction concentrator modules to 33%.
Theoretical study of the long-wavelength optical properties of NaCl, KCl, KBr, and KI

We have made a detailed theoretical study of the long-wavelength absorption of NaCl, KCl, KBr, and KI, associated with two-phonon difference processes caused by third-order anharmonic terms in the lattice potential energy. It was found that a simple nearest-neighbor approximation to the anharmonicity, combined with lattice-dynamical eigenfrequencies and eigenvectors generated with the use of a deformation dipole model, can generally account for most of the observed absorption. This agreement was obtained without the use of any disposable parameters, as the form of the first-neighbor potential was predetermined. It was also found that discrepancies between theory and experiment can generally be explained by invoking three-phonon processes and, when these contributions are subtracted from the experimental data, the resultant agreement between theory and experiment is excellent. The effects of lifetime broadening of the final-state phonons were also considered. At the longer wavelengths these may be responsible for part of the discrepancy between theory and experiment. Specifically, for NaCl at 3.09 mm, clear evidence was found of an anomalous contribution to the measured absorption which could have such an origin. However, for KI, which has a "window" in its two-phonon absorption at long wavelengths, it is clear that the three-phonon absorption is dominant at low frequencies. Our findings enable us to present certain criteria as to the requirements necessary for a material to possess high transparency in the millimeter-wavelength region. In addition to obtaining theoretical results for the long-wavelength absorption of the four crystals studied, we have also calculated their damping functions over the whole two-phonon range and we thus present results for both summation and difference processes.