cssi/SciSciGPT-SciSciNet huggingface dataset:
Optogenetic regulation of engineered cellular metabolism for microbial chemical production

The optimization of engineered metabolic pathways requires careful control over the levels and timing of metabolic enzyme expression. Optogenetic tools are ideal for achieving such precise control, as light can be applied and removed instantly without complex media changes. Here we show that light-controlled transcription can be used to enhance the biosynthesis of valuable products in engineered Saccharomyces cerevisiae. We introduce new optogenetic circuits to shift cells from a light-induced growth phase to a darkness-induced production phase, which allows us to control fermentation with only light. Furthermore, optogenetic control of engineered pathways enables a new mode of bioreactor operation using periodic light pulses to tune enzyme expression during the production phase of fermentation to increase yields. Using these advances, we control the mitochondrial isobutanol pathway to produce up to 8.49 ± 0.31 g l-1 of isobutanol and 2.38 ± 0.06 g l-1 of 2-methyl-1-butanol micro-aerobically from glucose. These results make a compelling case for the application of optogenetics to metabolic engineering for the production of valuable products.
Polymorphic exocellular protease expression in clinical isolates of Trichophyton tonsurans.

Tinea capitis continues to be an overwhelmingly prevalent disease in children. Despite the fact that it was recognized over a century ago, the factors that dictate the divergent clinical presentations seen with tinea capitis (e.g., carrier state, chronic non-inflammatory infection, acute severely-inflammatory infection) remain unknown. Given the pathogenicrole of exocellular proteases in dermatophyte infections and their potential immunogenic role, this investigation was designed to characterize strain-specific variability in fungal protease expression and activity in Trichophyton tonsurans isolates identified from children with tinea capitis.
Economic health care costs of blood culture contamination: A systematic review.

Background Blood culture contamination with gram-positive organisms is a common occurrence in patients suspected of bloodstream infections, especially in emergency departments. Although numerous research studies have investigated the cost implications of blood culture contamination, a contemporary systematic review of the literature has not been performed. The aim of this project was to perform a systematic review of the published literature on the economic costs of blood culture contamination. Methods PubMed was searched (January 1, 1978, to July 15, 2018) using the search terms “blood culture contamination” or “false-positive blood cultures.” Articles were title searched and abstracts were reviewed for eligible articles that reported immediate or downstream economic costs of blood culture contamination. Results and Discussion The PubMed search identified 151 relevant articles by title search, with 49 articles included after abstract review. From the studies included, overall blood culture contamination rates ranged from 0.9%-41%. Up to 59% of patients received unnecessary treatment with parenteral vancomycin as a result of blood culture contamination, resulting in increased pharmacy charges between $210 and $12,611 per patient. Increases in total laboratory charges between $2,397 and $11,152 per patient were reported. Attributable hospital length of stay increases due to blood culture contamination ranged from 1-22 days. Conclusions This systematic review of the literature identified several areas of health care expenditure associated with blood culture contamination. Interventions to reduce the risk of blood culture contamination would avoid downstream economic costs.
THE RELATIONSHIP OF DELIVERY METHOD, BIRTH WEIGHT AND RACE ON INFANT MORTALITY [Kennesaw State University]

Infant mortality is defined as the number of deaths per 1000 births. The U.S. infant mortality rate in 2014 was reported as 5.8 which is very high compared to other countries such as Japan where the rate 2.1. It is known that infant mortality is a huge problem, but the challenge right now is finding ways to solve this issue. My research aims to see what factors influence infant mortality to see how it can be reduced. I also wanted to learn about which groups are most vulnerable to experiencing high infant death rates. The purpose of this research is to find out how factors such as delivery method, birth weight, and race affect infant mortality to determine how these factors lead to the reduction of mortality rates. I wanted to see if there is a preferred delivery method for small infants compared to larger infants. To evaluate this, I analyzed 2007-2016 U.S. infant mortality data from the CDC and created bar charts relating race, birth weight, and delivery method to the death rate. I found out that the vaginal delivery method has the lower death rate compared to the C-section delivery method, that American Indians who were born through C-sections have the highest death rate out of all the other races and delivery methods, that the death rate is lower for small infants when they are delivered through the C-section method and that it is preferable to deliver larger infants through the vaginal method since the death rate would be lower. These results can serve as then beginning of a more comprehensive look into infant mortality.
A Smooth Dissipative Particle Dynamics method for nonisothermal liquid and gas flows in bounded domains

Abstract A Smoothed Dissipative Particle Dynamics formulation with dynamic virtual particle allocation (SDPD-DV) is developed for the simulation of mesoscale nonisothermal flows with non-slip, constant temperature and constant heat flux boundary conditions. For liquids, the particle internal energy is evaluated through a first-order expansion from an initial volume and entropy state. For liquids, the particle pressure and temperature are evaluated using the coefficients of adiabatic compressibility, volumetric thermal expansion and heat capacity. For monatomic and diatomic gases, the fluid particle internal energy is evaluated through a Sackur-Tetrode type of equation. For both liquids and gases, the viscosity and thermal conductivity are modeled by a power law. Integration of position and momentum equations is performed with a velocity-Verlet method and bounce-forward reflection. Integration of the entropy equation is performed with a Runge-Kutta method. Verification of SDPD-DV is performed for planar isothermal Couette, planar Fourier, and planar nonisothermal Couette flows of liquid H 2 O and gaseous N 2 , and for a nonisothermal planar Poiseuille flow of a fluid with an exponential temperature-depended viscosity. SDPD-DV simulations for liquid H 2 O, gaseous Ar and N 2 systems under thermal equilibrium assess the impact of the ratio of particle mass ( m i ) over the real molecular mass and the size of smoothing length ( h ) on fluid properties, hydrodynamic fluctuations and transport coefficients. For liquid systems the density fluctuations exhibit scatter about the analytical estimates and the temperature fluctuations follow the analytical estimates for mass ratios smaller than 10,000. The velocity fluctuations are in excellent agreement with theoretical estimates. For gases, the density fluctuations exhibit scatter about the analytical estimates and the pressure fluctuations agree with the analytical estimates for mass ratios smaller than 10,000. The temperature and velocity fluctuations are in excellent agreement with the analytical estimates. The self-diffusivity evaluated from SDPD-DV simulations for liquid and gases is shown to increase with smoothing length for a given mass ratio, scales with h 2 / m i and is in excellent agreement with analytical estimates. The shear viscosity evaluated from SDPD-DV simulations for liquid and gases exhibits scatter around the experimental values and is shown to be scale free.
The RNA world: receptors and their cognate ligands in Archaea, Bacteria, and Choanoflagellates

Abstract For life to exist it is necessary to have two essential classes of molecules in a primitive cell. One is RNA, a molecule that can catalyze its own replication. The other is a fatty acid, which can form a bilayer and also divide. Archaea, the ancestors of all species, contained receptors that carried out numerous important functions. An Archaea, Halobacterium halobium , contains a plasma membrane receptor, Bacteriorhodopsin. It uses photons to open a channel allowing H + ions to escape from the cell; thereby producing the universal energy molecule, ATP. Other roles played by receptors in protists (unicellular organisms) are to control the direction of flagella movement to escape from prey, and to form multilayered colonies called biofilms. Choanoflagellates, the ancestors of all animal species, contain collar cells, homologous to similar cells in sponges and other simple multicellular organisms. They also contain 10 G-protein coupled receptors while simple multicellular species contain over 100.
The Historical Prevalence of Infectious Diseases and Global Innovation

Nations with historically high levels of infectious diseases are less innovative today than countries with lower levels. Building on the Parasite Stress Theory of Values, we contend and provide sup...
Correcting Deletions in Multiple-Heads Racetrack Memories

One of the main challenges in developing racetrack memory systems is the limited precision in controlling the track shifts, that in turn affects the reliability of reading and writing the data. The current proposal for combating deletions in racetrack memories is to use redundant heads per-track resulting in multiple copies (potentially erroneous) and solving a specialized version of a sequence reconstruction problem. Using this approach, k-deletion correcting codes of length n, with d heads per-track, with redundancy log log n + 4 were constructed. However, the code construction requires that k ≤ d. For k > d, the best known construction improves slightly over the classic one head deletion code. Here we address the question: What is the best redundancy that can be achieved for a k-deletion code (k is a constant) if the number of heads is fixed at d (due to area limitations)? Our key result is an answer to this question, namely, we construct codes that can correct k deletions, for any k beyond the known limit of d. The code has O(k4dlog log n) redundancy for the case when k ≤ 2d − 1. In addition, when k ≥ 2d, the code has 2⌊k/d⌋ log n + o(log n) redundancy.
Quantitative 3-Dimensional Photographic Assessment of Breast Cosmesis After Whole Breast Irradiation for Early Stage Breast Cancer: A Secondary Analysis of a Randomized Clinical Trial.

Abstract Purpose Our purpose was to use 3-dimensional (3D) surface photography to quantitatively measure breast cosmesis within the framework of a randomized clinical trial of conventionally fractionated (CF) and hypofractionated (HF) whole breast irradiation (WBI); to identify how 3D measurements are associated with patient- and physician-reported cosmesis; and to determine whether objective measures of breast symmetry varied by WBI treatment arm or transforming growth factor β 1 (TGFβ1) status. Methods and Materials From 2011 to 2014, 287 women age ≥40 with ductal carcinoma in situ or early-stage invasive breast cancer were enrolled in a multicenter trial and randomized to HF-WBI or CF-WBI with a boost. Three-dimensional surface photography was performed at 3 years posttreatment. Patient-reported cosmetic outcomes were recorded with the Breast Cancer Treatment Outcome Scale. Physician-reported cosmetic outcomes were assessed by the Radiation Therapy Oncology Group scale. Volume ratios and 6 quantitative measures of breast symmetry, termed F1-6C, were calculated using the breast contour and fiducial points assessed on 3D surface images. Associations between all metrics, patient- and physician-reported cosmesis, treatment arm, and TGFβ1 genotype were performed using the Kruskal-Wallis test and multivariable logistic regression models. Results Among 77 (39 CF-WBI and 38 HF-WBI) evaluable patients, both patient- and physician-reported cosmetic outcomes were significantly associated with the F1C vertical symmetry measure (both P Conclusions Quantitative 3D image-derived measures revealed comparable cosmetic outcomes with HF-WBI compared with CF-WBI. Our findings suggest that 3D surface imaging may be a more sensitive method for measuring subtle cosmetic changes than global patient- or physician-reported assessments.
Osimertinib in non-small cell lung cancer (NSCLC) with atypical EGFR activating mutations: A retrospective multicenter study.

9570Background: Osimertinib (osi) is a 3rd generation EGFR tyrosine kinase inhibitor (TKI) approved for first line (1L) treatment of metastatic NSCLC harboring EGFR Exon 19 del and L858R (represent...
Peace, Unity, and Purity and the Presbyterian Church’s Fifty-Year Journey on Human Sexuality:

Recent ordination controversies have served as barometers for how denominations have addressed matters of human sexuality, and LGBTQ sexuality in particular. Using the Presbyterian Church (U.S.A.)’...
American Exceptionalism, Human Resource Management, and the Contract State:

With the nature, scope, and pace of public sector contracting accelerating significantly during the Bush administration, and with the Obama administration promising to curb the contracting excesses of its predecessors, it is useful to take stock and ponder the consequences of this movement to date for human resource management. This article puts public sector contracting and its effects in a larger historical, political, and democratic context by (a) reviewing the American propensity for market-based solutions (including contracting) to government problems, a disposition rooted in American exceptionalist values; (b) chronicling how that predisposition has manifested itself in four successive and now overlapping expansions of contracting (from products, to services, to core governmental functions, to human resource management functions); and (c) showing how these developments have had significant consequences not only for the future of the public service but also for the values associated with democratic c...
Pandemic and Post-Pandemic Digital Pedagogy in Hospitality Education for Generations Z, Alpha, and Beyond:

Facilitating hospitality and tourism education in the pandemic and post-pandemic eras call for change, as the need for faculty members to deliver the curriculum digitally using multiple modalities,...
Erratum: ``Heteroepitaxy of rare-earth hexa-aluminates on sapphire'' [J. Mater. Res. 9, 410-419 (1994)]

“Heteroepitaxy of rare-earth hexa-aluminates on sapphire” [J. Mater. Res. 9, 410-419 (1994)]
Indicators of Assessing the Effectiveness of the Accounting Information System for Business Organizations

The development that occurred in the activities of business organizations recently and continuous complexity facing these organizations, led to appeared a set of challenges for these organizations, the most important of which is the testing of ability for these companies to formulating and building an effective and useful accounting information system in a manner that keeps pace with the developments and meets the requirements of parties that depend on the outputs of this system. In fact, it cannot say that, all accounting information systems are considered as successful systems and achieve the goals required of it due to many problems located within the structure of this system and the accounting staff who responsible for operating this system. In the context of this problem, the study seeks to clarify the most important duties and tasks of the distinguished system and the indicators through which it can judge the level of success of that system in the expected range.
Why is calcite a strong phosphorus sink in freshwater? Investigating the adsorption mechanism using batch experiments and surface complexation modeling.

Abstract One of the primary drivers of Phosphorus (P) limitation in aquatic systems is P adsorption to sediments. Sediments adsorb more P in freshwater compared to other natural solutions, but the mechanism driving this difference is poorly understood. To provide insights into the mechanism, we conducted batch experiments of P adsorption to calcite in freshwater and seawater, and used computer software to develop complexation models. Our simulations revealed three main reasons that, combining together, may explain the greater P adsorption to calcite in freshwater vs. seawater. First, aqueous speciation of P makes a difference. The ion pair CaPO4− is much more abundant in freshwater; although seawater has more Ca2+ ions, MgHPO40 and NaHPO40 are more thermodynamically favored. Second, the adsorbing species of P make a difference. The ion pair CaPO4− (the preferred adsorbate in freshwater) is able to access adsorption sites that are not available to HPO42− (the preferred adsorbate in seawater), thereby raising the maximum concentration of P that can adsorb to the calcite surface in freshwater. Third, water chemistry affects the competition among ions for surface sites. Other ions (including P) compete more effectively against CO32− when immersed in freshwater vs. seawater, even when the concentration of HCO3−/CO32− is higher in freshwater vs. seawater. In addition, we found that under oligotrophic conditions, P adsorption is driven by the higher energy adsorption sites, and by the lower energy sites in eutrophic conditions. This study is the first to model P adsorption mechanisms to calcite in freshwater and seawater.
Conditioned-based robust nonlinear control of plug-in hybrid electric vehicle with saturated control actions

Abstract Plug-in hybrid electric vehicles (PHEVs) are considered to be a better choice than conventional hybrid electric vehicles due to environmental concerns. There are two main subsystems in the PHEVs power system namely: integrated charging unit (ICU) and hybrid energy storage system (HESS). In this work three energy sources fuel cell (FC), battery and ultra-capacitor (UC) are considered. Keeping in view of different challenging aspects like actuator limits and nonlinear nature of power conditioning circuits in ICU and HESS, design of robust nonlinear controller is still a challenge. Conventional Supertwisting Algorithm (STA) based controller exhibits wind-up effects when control signal is saturated which deteriorates the dynamic response of the controller. In order to resolve this issue, conditioning technique is used to propose conditioned Supertwisting algorithm (CSTA) based controller which mitigates the wind-up phenomenon when the control signal is saturated and exhibits better dynamic performance in the presence of external disturbances. Moreover, energy management algorithm in HESS is also presented in which State of Charge (SoC) of the battery and UC is taken as a decisive factor for the execution of rule-based strategy. Asymptotic stability of the system is proved using Lyapunov stability criterion. Simulations are performed in Matlab/Simulink ODE 45 environment which show the comparison of the proposed controller with conventional STA-based controller. The results show better performance of proposed controller when the control signals are saturated but at the same time conventional STA does not exhibit good response due to integrator wind-up. For the real-time control of PHEV, hardware in loop (HIL)-based experimental verification is also done.
Characterization of the low energy conformations and differential reactivities of D-glucose and D-mannose based oxepines

Carbohydrate-based oxepines are valuable intermediates for the synthesis of septanose carbohydrates. Here we report the characterization of the preferred conformations of D-glucose and D-mannose based oxepines 1 and 2 using computational chemistry and NMR spectroscopy. Monte Carlo conformational searches on 1 and 2 were performed, followed by DFT optimization and single-point energy calculations were performed on the low energy conformations of each oxepine. Coupling constants were computed for all unique conformations at a B3LYP/6-31G(d,p)u+1s level of theory and weighted based on a Boltzmann distribution. These values were then compared to the experimental values collected using 3JH,H values collected from 1H NMR spectra. Information from the MC/DFT approach was then used in a least-squares method that correlated DFT calculated and observed 3JH,H coupling constants. The conformations of 1 and 2 are largely governed by a combination of the rigidifying enol ether element in combination with the reduction of unfavorable interactions. The vinylogous anomeric effect (VAE) emerged as a consequence, rather than a driver of conformations. Oxepine 1, with a conformational profile the led to a greater %VAE, correlated with increased reactivity for Ferrier rearrangement reactions relative to oxepine 2.
Laparoscopic Abdominoperineal Resection

Low rectal adenocarcinoma; location precludes adequate 1 cm distal margin for a sphincter preserving procedure. Melanoma of the anorectum involving the sphincters. Anal carcinoma recurrence after Nigro protocol.
Evaluation of Agnique MMF in man-made ponds for the control of pestiferous chironomid midges (Diptera: Chironomidae).

The efficacy of a monomolecular surface film, Agnique® MMF (a liquid isostearyl alcohol ethoxylate containing 2 oxyethylene groups [ISA-2OE]) in suppressing emergence of adult Chironomidae from man-made earthen ponds was studied. Three replicated rates, 0.23, 0.47, and 0.94 ml/m 2 (or 0.25, 0.5, and 1.0 gal/acre) of Agnique MMF were applied. Pretreatment and periodic posttreatment samples of adult chironomids were collected by employing submerged metal-cone traps as well as floating traps. Concurrently, water pH, dissolved oxygen, specific conductance, and water temperature were measured. Tanytarsini (>82%), Chironomini (16%), and Tanypodinae (1%) midges were collected during the study period. Midge adult collections in floating traps were not significantly reduced by the 0.23-ml/m 2 treatment rate, but were significantly reduced (73-93%) for 1-2 wk posttreatment at 0.47 and 0.94 ml/m 2 of Agnique MMF. The lowest rate significantly reduced midge adult emergence for 1 day posttreatment as measured by metal-cone traps, whereas the 2 higher rates reduced emergence by 78.6-97% for I wk posttreatment. Using either trap, the highest rate of Agnique MMF did not produce suppression of adult midges of any greater magnitude or duration than the middle rate. Agnique MMF was not detected by the indicator oil in any treated pond after 7 days posttreatment. Water pH, dissolved oxygen, specific conductance, and water temperature in the ponds were not significantly influenced by Agnique MMF treatments. Analysis of these data supports the possible use of Agnique MMF for chironomid control in areas where the surface film of this material can be maintained for sufficient time to interfere with adult emergence.
Rheological study of different mashed potato preparations using large amplitude oscillatory shear and confocal microscopy

Abstract Texture is a major driver for mashed potato products. Measuring food texture via descriptive sensory analysis can be expensive and timeconsuming, so rheometry is often used as a method of estimating food texture. The objective of this study was to determine small- and largestrain rheological behavior of different mashed potato formulations. Rheological data, including large amplitude oscillatory shear data, and confocal microscopy images were collected. Comparison of rheological data and confocal images showed relationships between sample rheological behavior and sample structural damage were found. With the exception of freeze-dried samples, samples exhibiting greater starch damage exhibited more linear, fluid-like rheological behavior. Freeze-dried samples showed microfractures on the surface of the starch granules. It was hypothesized that these microfractures allowed amylose strands to leach from the granules without destroying structural integrity. Based on these results, mashed potato rheological behavior, and therefore texture, can be controlled by controlling extent of starch damage.
Influence of Electron Donor/Acceptor Concentrations on Hydrous Ferric Oxide (HFO) Bioreduction

Dissimilatory metal-reducing bacteria (DMRB) facilitate the reduction of Fe and Mn oxides in anoxic soils and sediments and play an important role in the cycling of these metals and other elements such as carbon in aqueous environments. Previous studies investigating the reduction of Fe(III) oxides by DMRB focused on reactions under constant initial electron donor (lactate) and electron acceptor (Fe oxide) concentrations. Because the concentrations of these reactants can vary greatly in the environment and would be expected to influence the rate and extent of oxide reduction, the influence of variable electron acceptor and donor concentrations on hydrous ferric oxide (HFO) bioreduction was investigated. Batch experiments were conducted in pH 7 HCO − buffered media usingShewanella putrefaciens strain CN32. In general, the rate of Fe(III) reduction decreased with increasing HFO:lactate ratios, resulting in a relatively greater proportion of crystalline Fe(III) oxides of relatively low availability for DMRB. HFO was transformed to a variety of crystalline minerals including goethite, lepidocrocite, and siderite but was almost completely dissolved at high lactate to HFO ratios. These results indicate that electron donor and acceptor concentrations can greatly impact the bioreduction of HFO and the suite of Fe minerals formed as a result of reduction. The respiration driven rate of Fe(II) formation from HFO is believed to be a primary factor governing the array of ferrous and ferric iron phases formed during reduction.
The Reform of the Fiscal Institutions in Latin America

Fiscal deficits on average only 1.4% of GDP; debt coefficients on the decline; early debt repayments to the International Monetary Fund and massive repurchases of Brady bonds that 15 years ago were the last salvation for overly endebted governments. This doesn't look like Latin America, the region with the strongest tradition of macroeconomic instability in the world and the longest history of noncompliance with its public debt commitments. However, these are some of the fiscal events that have been occurring since the beginning of 2006, a particularly favorable time for the region.
Effect of CO2 Concentration on Intermediates of the Embden-Myerhof Pathway and the Citric Acid Cycle in Isolated Perfused Rat Liver

Abstract The effect of variation of total CO2 concentration at constant pH on the intermediates of the Embden-Meyerhof pathway and citric acid cycle in the isolated perfused liver has been studied. Total CO2 concentration of the perfusate was changed either from 10 to 34 mm or from 34 to 10 mm at pH 7.40 at the midpoint of 2-hour liver perfusions. In livers perfused with a medium containing 14 mm glycerol and 17 mm glucose, the liver concentration of glucose-6-P, fructose-6-P, fructose diphosphate, pyruvate, malate, and citrate was found to have increased when CO2 concentration was increased, and decreased when CO2 concentration was decreased, in a range of 6 to 59%, when compared to control values. The tissue concentration of 3-P-glycerate, P-enolpyruvate, and aspartate changed in an inverse manner, decreasing and increasing in a range of 12 to 104% as the CO2 concentration of the liver perfusate was increased and decreased, respectively. Livers perfused with a medium to which glucose (5.8 mm) was the only added substrate were found to have generally similar changes in metabolite concentrations with change in CO2 concentration. Citrate and pyruvate concentrations were, however, more markedly altered and the change in malate concentration was opposite in direction, with respect to the change in the CO2 concentration of the perfusate, and greater than that observed when both glycerol (14 mm) and glucose (17 mm) were present in the perfusate. Livers perfused with medium containing the combined higher concentrations of glycerol and glucose had higher absolute levels of glucose-6-P, fructose-6-P, fructose diphosphate, 3-P-glycerate, P-enolpyruvate, and pyruvate and lower malate, aspartate, and citrate concentrations at both CO2 concentrations. The results of this study support the concept that physiological changes in extracellular CO2 concentration markedly alter the concentration of metabolic intermediates associated directly with carbohydrate and lipid metabolism.
Toward flexible control of the temporal mapping from concurrent program events to animations

As parallel and distributed computers become more widely available and used, the already important process of understanding and debugging concurrent programs will rake on even greater importance. We believe that visualization can help in the process. We discuss heretofore unaddressed issues in the visualization of concurrent programs, and present the Animation Choreographer. The Animation Choreographer allows users to view, manipulate, and explore the set of alternate feasible orderings of the program execution under study, both through the Choreographer interface and in the context of the selected visualizations, thus providing the user with a variety of temporal perspectives on the computation. >
Identification of a signal for nuclear targeting in platelet-derived-growth-factor-related molecules.

Abstract The v-vis gene encodes p28sis, the transforming protein of simian sarcoma virus. This gene resulted from a fusion of the env gene of simian sarcoma-associated virus and the woolly monkey gene for the B chain of platelet-derived growth factor (PDGF). Previous work has shown that the v-sis gene product undergoes signal sequence cleavage, glycosylation, dimerization, and proteolytic processing to yield a secreted form of the protein. It transport across the endoplasmic reticulum is blocked by the introduction of a charged amino acid residue within the signal sequence, the protein does not dimerize, is not secreted, and is no longer transforming as assayed by focus-forming ability in NIH 3T3 cells. Instead, this mutant protein localizes to the nucleus as demonstrated by both indirect immunofluorescence and cell fractionation. Using a series of deletion mutations, we delimited an amino acid sequence within this protein which is responsible for nuclear localization. This region is completely conserved in the predicted human c-sis protein, although it lies outside of regions required for transformation by the v-sis gene product. This nuclear transport signal is contained within amino acid residues 237 to 255, RVTIRTVRVRRPPKGKHRK. An amino acid sequence containing these residues is capable of directing cytoplasmic v-sis mutant proteins to the nucleus. This sequence is also capable of directing less efficient nuclear transport of a normally cytoplasmic protein, pyruvate kinase. Pulse-chase experiments indicate that the half-lives of nuclear and cytoplasmic v-sis mutant proteins are approximately 35 min. Using the heat-inducible hsp70 promoter from Drosophila melanogaster, we showed that the nuclear v-sis protein accumulates in the nucleus within 30 min of induction. The identification of a nuclear transport signal in the v-sis gene product raises interesting questions regarding the possibility of some function for PDGF or PDGF-related molecules in the nucleus.
DGPort: a web portal for digital government

This paper provides a summary of the initial development of a Web portal for the digital government domain. Information retrieval techniques commonly used to find information on the Internet are discussed along with the problems associated with these techniques that led to the development of the Digital Government Web portal (DGPort). We also discuss the advantages that DGPort could have for researchers in the digital government domain as well as the value-added features that this portal provides. Future evaluation plans for the portal are also described.
Single-Ended and Differential MRAMs Based on Spin Hall Effect: A Layout-Aware Design Perspective

Spin-based memories have shown an immense promise for on-chip memory applications due to the possibilities of introducing non-volatility in caches employing a CMOS compatible process. Non-volatility leads to zero-standby leakage. However, at the same time, exploration of energy-efficient read and write mechanisms is important to lower the overall energy-consumption of an MRAM cache. Magnetization control employing spin-hall effect is one of the most promising approaches to enhance the write energy efficiency. A separate path for the read which comprises of a magnetic tunnel junction (MTJ) offers the benefits of simultaneous optimization of the read and write operations. In fact, spin-hall effect also leads to the possibility of designing cells with differential sensing. However, the advantages of a differential read over a single-ended read in terms of higher read speed and better noise immunity comes at the cost of larger number of access transistors, which may translate to lower integration density. In this paper, we perform a comparative analysis of spin-hall effect (SHE) based MRAM cells with single-ended and differential read mechanisms in terms of the cell area, read performance and read stability. We perform a detailed layout analysis based on Fin FET technology to evaluate the impact of introducing differential sensing on cell area. Our analysis shows that when the layout area is determined by the pitch of the bit-line and source-line metal tracks, the differential cell shows 1.5X increase in the cell area compared to the single-ended SHE MRAM. The area increase is 2X if the read access transistor determines the layout footprint. However, the differential sensing offers the advantages of a#x007E;48% increase in the read performance along with 6% to 9% boost in the read stability compared to the single-ended SHE MRAM. At iso-area, the differential cell shows a#x007E;24% lower read time and 12% higher read disturb margin with a similar write performance and power. Our analysis also presents other layout-driven perspectives on the design of differential and single-ended SHE MRAMs.
A subfemtotesla multichannel atomic magnetometer

The magnetic field is one of the most fundamental and ubiquitous physical observables, carrying information about all electromagnetic phenomena. For the past 30 years, superconducting quantum interference devices (SQUIDs) operating at 4 K have been unchallenged as ultrahigh-sensitivity magnetic field detectors, with a sensitivity reaching down to 1 fT Hz(-1/2) (1 fT = 10(-15) T). They have enabled, for example, mapping of the magnetic fields produced by the brain, and localization of the underlying electrical activity (magnetoencephalography). Atomic magnetometers, based on detection of Larmor spin precession of optically pumped atoms, have approached similar levels of sensitivity using large measurement volumes, but have much lower sensitivity in the more compact designs required for magnetic imaging applications. Higher sensitivity and spatial resolution combined with non-cryogenic operation of atomic magnetometers would enable new applications, including the possibility of mapping non-invasively the cortical modules in the brain. Here we describe a new spin-exchange relaxation-free (SERF) atomic magnetometer, and demonstrate magnetic field sensitivity of 0.54 fT Hz(-1/2) with a measurement volume of only 0.3 cm3. Theoretical analysis shows that fundamental sensitivity limits of this device are below 0.01 fT Hz(-1/2). We also demonstrate simple multichannel operation of the magnetometer, and localization of magnetic field sources with a resolution of 2 mm.
Absolute intensities of CH-stretching overtones in chloroform and deuterochloroform

Abstract Absolute intensities are calculated for the fundamental and overtone bands of the CH-stretching local mode in chloroform and chloroform- d 1 . The transition dipole moment is expanded in terms of displacement of the CH bond length and involves matrix elements of powers of the displacement and dipole moment derivatives. Dipole moment derivatives are determined from sets of dipole moments by a procedure which avoids making assumptions concerning the shape of the dipole moment function. The sets of dipole moments are obtained from ab initio calculations that employ a variety of basis sets. Vibrational states are described in terms of Morse oscillator wavefunctions and their matrix elements are calculated by numerical integration.
Open complex formation in vitro by σ38 (rpoS) RNA polymerase: Roles for region 2 amino acids

Non-functional mutants of σ38(σS) were studied in vitro to identify the nature of their defects. Mutations in four amino acids led to severe defects in DNA binding and enzyme isomerization with promoter fork junction probes containing single-stranded non-template DNA. The same properties were previously seen with DNA mutations at the fork junction, implying that sigma:DNA interactions at the fork junction are used both for DNA binding and enzyme isomerization. An overlapping set of four mutants had defects that appear to be associated with DNA melting to create the fork junction. When mapped onto the σ70 structure, these groups of mutants suggest motifs used by σ factors to melt DNA and isomerize RNA polymerase to form functional open promoter complexes.
The infrared spectra and structure of [Pd(dien)X]X☆☆☆

Abstract The infrared spectra of [Pd(dien)I]I, [Pd(dien)Br]Br, and [Pd(dien)Cl]Cl have been observed and assignments made in the region 200–4000 cm −1 . The investigation of these spectra is intended to provide the background and basis for the study of the spectra of (dien-H) complexes [where (dien-H) represents a diethylenetriamine ligand from which one proton has been removed] in regard to the character of the bond between the metal ion and the ligand nitrogen atom from which the proton is removed. The assignment of several bands was facilitated by the infrared spectrum (200–4000 cm −1 ) of the new complex [Pd(tmdien)I]I (tmdien = 1,4,7-trimethyldiethylenetriamine).
Statistical analysis of process and composition factors affecting the leaching of heavy metals from fly ash solidified/stabilized wastes

Abstract The results of an extensive series of experimental Toxicity Characteristic Leaching Procedure (TCLP) tests on the leaching behavior of heavy-metal containing wastes solidified/stabilized by compacting the waste with pozzolanic fly ash are given. The test simulates the behavior of the waste by contacting it with an acidic media during 18 h with continuous agitation. The two heavy metals studied (chromium and cadmium) were selected based on the pH at which their minimum solubility occurred. Even though aluminum is not considered a heavy metal, it was also included in this study since its minimum solubility occurred at a lower pH than the other two metals. Six process factors were studied using a combined 2 6–3 fractional factorial design and the composition was studied using an augmented simplex-centroid design. Process factors included acid strength, acid/waste ratio, slurry pH, ash/slurry ratio, pressure, and aging time. Statistical analysis of the TCLP data obtained after 18 h of leaching showed that the factors which significantly affected the results depended on the specific response metal being studied. Only the process factor, aging time, was statistically significant for all of the responses. The composition of the waste did affect only the cadmium response. The results obtained in this study will contribute to understanding the leaching behavior of hazardous materials contained in solidified/stabilized fly ash wastes.
Only One ATP-binding DnaX Subunit Is Required for Initiation Complex Formation by the Escherichia coli DNA Polymerase III Holoenzyme

The DnaX complex (DnaX3δδ′χψ) within the Escherichia coli DNA polymerase III holoenzyme serves to load the dimeric sliding clamp processivity factor, β2, onto DNA. The complex contains three DnaX subunits, which occur in two forms: τ and the shorter γ, produced by translational frameshifting. Ten forms of E. coli DnaX complex containing all possible combinations of wild-type or a Walker A motif K51E variant τ or γ have been reconstituted and rigorously purified. DnaX complexes containing three DnaX K51E subunits do not bind ATP. Comparison of their ability to support formation of initiation complexes, as measured by processive replication by the DNA polymerase III holoenzyme, indicates a minimal requirement for one ATP-binding DnaX subunit. DnaX complexes containing two mutant DnaX subunits support DNA synthesis at about two-thirds the level of their wild-type counterparts. β2 binding (determined functionally) is diminished 12–30-fold for DnaX complexes containing two K51E subunits, suggesting that multiple ATPs must be bound to place the DnaX complex into a conformation with maximal affinity for β2. DNA synthesis activity can be restored by increased concentrations of β2. In contrast, severe defects in ATP hydrolysis are observed upon introduction of a single K51E DnaX subunit. Thus, ATP binding, hydrolysis, and the ability to form initiation complexes are not tightly coupled. These results suggest that although ATP hydrolysis likely enhances β2 loading, it is not absolutely required in a mechanistic sense for formation of functional initiation complexes.
Evaluation of the Role of the Vaccinia Virus Uracil DNA Glycosylase and A20 Proteins as Intrinsic Components of the DNA Polymerase Holoenzyme

The vaccinia virus DNA polymerase is inherently distributive but acquires processivity by associating with a heterodimeric processivity factor comprised of the viral A20 and D4 proteins. D4 is also an enzymatically active uracil DNA glycosylase (UDG). The presence of an active repair protein as an essential component of the polymerase holoenzyme is a unique feature of the replication machinery. We have shown previously that the A20-UDG complex has a stoichiometry of ∼1:1, and our data suggest that A20 serves as a bridge between polymerase and UDG. Here we show that conserved hydrophobic residues in the N′ terminus of A20 are important for its binding to UDG. Our data argue against the assembly of D4 into higher order multimers, suggesting that the processivity factor does not form a toroidal ring around the DNA. Instead, we hypothesize that the intrinsic, processive DNA scanning activity of UDG tethers the holoenzyme to the DNA template. The inclusion of UDG as an essential holoenzyme component suggests that replication and base excision repair may be coupled. Here we show that the DNA polymerase can utilize dUTP as a substrate in vitro. Moreover, uracil moieties incorporated into the nascent strand during holoenzyme-mediated DNA synthesis can be excised by the viral UDG present within this holoenzyme, leaving abasic sites. Finally, we show that the polymerase stalls upon encountering an abasic site in the template strand, indicating that, like many replicative polymerases, the poxviral holoenzyme cannot perform translesion synthesis across an abasic site.
Two‐dimensional dielectric imaging for dermatologic screening: a feasibility study

Background/purpose The diagnosis of skin neoplasia can be very challenging, given the low sensitivity and specificity of traditional methods of diagnosis which are based on visual appearance. Techniques which are based on the dielectric properties of cells can improve the diagnostic accuracy of screening techniques; as an example, point-contact coaxial probes for dielectric measurement can improve diagnostic accuracy. Unfortunately, these probes are not well suited for two-dimensional spatial imaging of the skin surface, given that they must be manually scanned over the skin surface. Methods/Results An electronic scanning probe was developed and fabricated to simulate an open-ended coaxial probe suitable for two-dimensional dielectric imaging of human skin in real time. A clinical study was undertaken to demonstrate proof-of-concept for the instrumentation. A select group of normal healthy subjects as well as a subject with diagnosed squamous cell carcinoma participated in this study. The electronic scanning probe was found to be a potentially useful tool for providing two-dimensional images from diseased skin. Conclusion The electronic scanning probe used for the present study addresses existing limitations with current coaxial probes. Measurements of healthy and diseased areas of skin are provided to illustrate the feasibility of the approach.
Rolling partial prefix-sums to speedup evaluation of uniform and affine recurrence equations

As multithreaded and reconfigurable logic architectures play an increasing role in high-performance computing (HPC), the scientific community is in need for new programming models for efficiently mapping existing applications to the new parallel platforms. In this paper, we show how we can effectively exploit tightly coupled fine-grained parallelism in architectures such as GPU and FPGA to speedup applications described by uniform recurrence equations. We introduce the concept of rolling partial-prefix sums to dynamically keep track of and resolve multiple dependencies without having to evaluate intermediary values. Rolling partial-prefix sums are applicable in low-latency evaluation of dynamic programming problems expressed as uniform or affine equations. To assess our approach, we consider two common problems in computational biology, hidden Markov models (HMMER) for protein motif finding and the Smith-Waterman algorithm. We present a platform independent, linear time solution to HMMER, which is traditionally solved in bilinear time, and a platform independent, sub-linear time solution to Smith-Waterman, which is normally solved in linear time.
Maturation success of pink salmon (Oncorhynchus gorbuscha) and coho salmon (O. kisutch) held under three salinity regimes

Abstract Adult pink salmon ( Oncorhynchus gorbuscha ) and coho salmon ( Oncorhynchus kisutch ) were held in freshwater, seawater (28–32%%.), and in an estuary (24–31‰ with a low-salinity surface lens) to determine the effects of salinity on survival to spawning and gamete viability. Gamete viability was determined by individual matings. Samples of blood plasma and gonadal fluids were analyzed for osmolality and potassium. Capture location of the brood fish affected time of spawning and maturation success. The low-salinity lens in the estuary eliminated or reduced the detrimental effects on final maturation of pink salmon and coho salmon in seawater. Viability of gametes from pink salmon was inversely correlated to blood plasma osmolality of males and females, osmolality and potassium concentration of ovarian fluid, and blood-plasma potassium concentration of males. Viability of gametes of coho salmon was inversely correlated with the osmolality of blood plasma, ovarian fluid, and seminal fluid.
THE EFFECTS of SOLUTION COMPOSITION and DRYING TEMPERATURE ON CRYSTALLINITY, PERMEABILITY and MECHANICAL PROPERTIES of METHYLCELLULOSE FILMS

The effects of film drying temperature (100C for 35 min, 80C for 1 h, 50C for 1.5 h or room temperature overnight) and ethanol concentration (0, 25, 50 or 75%) in the aqueous film solution on the physical properties of methylcellulose (MC) films were investigated. Increased drying temperatures increased crystallinity in all films. MC films prepared from a 75% water-25% ethanol solvent exhibited smaller permeabilities to oxygen and water vapor, greater crystallinity (when the higher drying temperatures were used), greater tensile strength, and greater percent elongation than films prepared from other water or water/ethanol solvents. Ethanol, at a 25% concentration, may enhance intermolecular hydrogen bonding of MC, while higher concentrations of ethanol may have prevented complete hydration of MC. Extensive association of MC by hydrogen bonding and hydrophobic association (which induces crystallization) likely reinforces the film matrix and presumably produces a film with greater resistance to oxygen and water vapor.