cssi/SciSciGPT-SciSciNet huggingface dataset:
SHI7 Is a Self-Learning Pipeline for Multipurpose Short-Read DNA Quality Control.

ABSTRACT Next-generation sequencing technology is of great importance for many biological disciplines; however, due to technical and biological limitations, the short DNA sequences produced by modern sequencers require numerous quality control (QC) measures to reduce errors, remove technical contaminants, or merge paired-end reads together into longer or higher-quality contigs. Many tools for each step exist, but choosing the appropriate methods and usage parameters can be challenging because the parameterization of each step depends on the particularities of the sequencing technology used, the type of samples being analyzed, and the stochasticity of the instrumentation and sample preparation. Furthermore, end users may not know all of the relevant information about how their data were generated, such as the expected overlap for paired-end sequences or type of adaptors used to make informed choices. This increasing complexity and nuance demand a pipeline that combines existing steps together in a user-friendly way and, when possible, learns reasonable quality parameters from the data automatically. We propose a user-friendly quality control pipeline called SHI7 (canonically pronounced “shizen”), which aims to simplify quality control of short-read data for the end user by predicting presence and/or type of common sequencing adaptors, what quality scores to trim, whether the data set is shotgun or amplicon sequencing, whether reads are paired end or single end, and whether pairs are stitchable, including the expected amount of pair overlap. We hope that SHI7 will make it easier for all researchers, expert and novice alike, to follow reasonable practices for short-read data quality control. IMPORTANCE Quality control of high-throughput DNA sequencing data is an important but sometimes laborious task requiring background knowledge of the sequencing protocol used (such as adaptor type, sequencing technology, insert size/stitchability, paired-endedness, etc.). Quality control protocols typically require applying this background knowledge to selecting and executing numerous quality control steps with the appropriate parameters, which is especially difficult when working with public data or data from collaborators who use different protocols. We have created a streamlined quality control pipeline intended to substantially simplify the process of DNA quality control from raw machine output files to actionable sequence data. In contrast to other methods, our proposed pipeline is easy to install and use and attempts to learn the necessary parameters from the data automatically with a single command.
Sharing and reusing cell image data

The rapid growth in content and complexity of cell image data creates an opportunity for synergy between experimental and computational scientists. Sharing microscopy data enables computational scientists to develop algorithms and tools for data analysis, integration, and mining. These tools can be applied by experimentalists to promote hypothesis-generation and discovery. We are now at the dawn of this revolution: infrastructure is being developed for data standardization, deposition, sharing, and analysis; some journals and funding agencies mandate data deposition; data journals publish high-content microscopy data sets; quantification becomes standard in scientific publications; new analytic tools are being developed and dispatched to the community; and huge data sets are being generated by individual labs and philanthropic initiatives. In this Perspective, I reflect on sharing and reusing cell image data and the opportunities that will come along with it.
A Comparative Assessment of the Response of Two Species of Cucumber Beetles (Coleoptera: Chrysomelidae) to Visual and Olfactory Cues and Prospects for Mass Trapping.

Spotted (Diabrotica undecimpunctata howardii) and striped (Acalymma vittatum) cucumber beetles (Coleoptera: Chrysomelidae) are serious pests of field-grown cucurbits in most areas of the United States where these crops are grown. This study aimed at quantifying, using a comparative approach, the behavioral response of A. vittatum and D. u. howardii to visual and olfactory cues associated with different trap types. In a first field study, Pherocon corn rootworm (CRW) traps baited with a 5-component floral-based lure (= AgBio lure) captured significantly more A. vittatum than traps baited with any other commercial lure. When used in combination with yellow sticky cards, the AgBio lure outperformed the other lures except for the Trece lure TRE8274. Subsequent tests revealed that the response of both cucumber beetle species to the AgBio lure was positively associated with increases in the amount of lure used. In the last series of tests that involved color discrimination by the beetles, traps constructed using 3.8-liter jugs painted yellow outperformed the CRW trap. Results from on-farm research, conducted at a commercial vegetable farm, confirmed the beetles' visual preference for yellow, and also revealed an excellent performance of the mass trapping system, which kept cucumber beetle densities in the cash crop below economic thresholds. Combined findings indicate that the mass trapping system developed can be implemented as part of a broader IPM program aimed at managing cucumber beetles.
Effect of Primary Breast Tumor Location on Axillary Nodal Positivity

Variables such as tumor size, histology, and grade, tumor biology, presence of lymphovascular invasion, and patient age have been shown to impact likelihood of nodal positivity. The aim of this study is to determine whether primary location of invasive disease within the breast is associated with nodal positivity. Patients with invasive breast cancer undergoing axillary staging from 2010 to 2014 were identified from the National Cancer Data Base. Rates of axillary nodal positivity by primary tumor locations were compared, and multivariable analysis performed using logistic regression to control for factors known to impact nodal positivity. A total of 599,722 patients met inclusion criteria. Likelihood of nodal positivity was greatest with primary tumors located in the nipple (43.8%), followed by multicentric disease (40.8%), central breast lesions (39.4%), and axillary tail lesions (38.4%). Tumor location remained independently associated with nodal positivity on multivariable analysis adjusting for variables known to affect nodal positivity with odds ratio 2.8 for tumors in the nipple [95% confidence interval (CI) 2.5–3.1], 2.2 for central breast (95% CI: 2.2–2.3), and 2.7 for axillary tail (95% CI: 2.4–2.9). When restricted to patients with clinically negative nodes (n = 430,949), a similar association was seen. Patients with invasive breast cancer located in the nipple, central breast, and axillary tail have the highest risk of positive axillary lymph nodes independent of patient age, tumor grade, biologic subtype, histology, and size. This should be considered along with other factors in preoperative counseling and decision-making regarding plans for axillary lymph node staging.
Modelli diretti: La teoria del raggio sismico

La teoria del raggio sismico e derivata dai principi e dalle metodologie della teoria elettromagnetica. Per ottenere la teoria del raggio sismico si usa la teoria delle onde che e stata sviluppata attraverso l’analisi asintotica. Per questa ragione si chiama teoria del raggio asintotico che fornisce una base teorica per il calcolo delle ampiezze e della polarizzazione. Essa e facile da derivare in un mezzo inomogeneo anisotropo.
Measurement of water vapor diffusion in nanoscale polymer films by frequency-domain probe beam deflection.

We developed an optical pump-probe technique, frequency-domain probe beam deflection (FD-PBD) to measure the diffusion of water vapor in nanoscale polymer films with microsecond temporal resolution and micrometer spatial resolution. We describe the quantitative model of beam deflection for multilayer structures, the experimental approach, and the application of FD-PBD to measure the diffusivity (Dm) of saturated water vapor in various glassy polymer films including polyimide (PI, Dm = 7.0 × 10−13 m2 s−1), poly(methyl methacrylate) (PMMA, Dm = 1.2 × 10−12 m2 s−1), poly-(vinylpyrrolidone) (PVP, Dm = 1.7 × 10−12 m2 s−1), and cellulose acetate (CA, Dm = 2.6 × 10−11 m2 s−1), and the piperazine/trimesoyl chloride (PIP/TMC, Dm = 9 × 10−11 m2 s−1) nanofiltration membrane synthesized by interfacial polymerization. The uncertainty of the measurements is typically ≈8%.
Phosphate glass matrix composites incorporating trisilanol phenyl polyhedral oligomeric silsesquioxane prepared by viscous flow sintering method with enhanced benefits

Abstract The effect of mixing and sintering processes to prepare tin fluorophosphate glass (Pglass) matrix composites incorporating trisilanol phenyl polyhedral oligomeric silsesquioxane (TSP-POSS) was investigated by comparing manual and suspension mixing, one-step and stepwise sintering processes to explore the structure dynamics and physical properties in the composites as a function of the different process conditions used. Energy Dispersive X-ray analysis confirmed optimal homogeneous dispersion of the TSP-POSS molecules in the composites prepared by the suspension method. The observed increase of glass transition temperature and the reduction of non-bridging bonds in the composites are believed to be the reason for the effective dispersion of TSP-POSS molecules in the composites. The chemical reaction between the TSP-POSS and Pglass was strongly influenced by the mixing/dispersion and sintering processes investigated. 13C cross polarized magic angle spinning (CP MAS) solid state nuclear magnetic resonance (NMR) spectroscopy confirmed the chemical stability of the TSP-POSS during the sintering process at elevated temperatures. In addition, a chemical reaction between the TSP-POSS and Pglass was evidenced by 29Si CP MAS NMR analysis. This study will provide a better fundamental understanding of the effective dispersion mechanism of the TSP-POSS molecules in the Pglass matrix that will facilitate tailoring the physicochemical properties of the composites with addition of various small concentrations of TSP-POSS for a number of applications where the pure Pglass is not applicable due to the intrinsic properties of the Pglass.
Technology use and constituting structures: accounting for the consequences of information technology on police organisational change

The influence of information technology on organisational change has long been a concern in policing. Despite the assumption that technology holds great potential for improving police performance, ...
Surgery and survival in patients with stage IV breast cancer.

Background Retrospective studies have shown some improvement in survival for patients receiving surgical management of the intact primary tumor in patients with presenting with Stage IV disease, while prospective studies have revealed mixed results. Methods An examination of the NCDB from 2004-2013 was undertaken to examine factors related to the utilization of surgery and overall survival in patients with de novo Stage IV disease. Univariate and multivariable analyses were conducted to determine factors related to survival. Propensity score matching method was implemented to balance patients' baseline characteristics. Results A total of 11 694 patients with Stage IV breast cancer at diagnosis met inclusion criteria. Surgical intervention occurred in 5202 patients (44.5%), with the use of surgery decreasing throughout the study period (53.6% surgery 2004-2006; 31.8% surgery 2011-2013). Selection for surgical intervention was associated with small tumors (T1) and a higher nodal burden (N2/3). Uninsured patients, those treated at academic centers, those treated in the Northeast, and those with hormone receptor positive tumors were less likely to undergo surgery. Surgery was independently associated with a better overall survival. Propensity score matching revealed a persistent survival advantage for surgical patients receiving surgery, regardless of the receipt of systemic therapy. Conclusions Surgery on the intact primary tumor for patients presenting with de novo Stage IV breast cancer is associated with improved overall survival. Surgical resection in patients with Stage IV breast cancer should be considered for well-selected patients as a part of multimodality therapy.
Spectrally-resolved thermal transport in graphene nanoribbons

Thermal transport properties of graphene nanoribbons (GNRs) are investigated using phonon transport studies. Ribbons of varying widths are considered to investigate the transition of key thermal properties with width. The lattice structure of the ribbons is fully resolved, and phonon transport is modeled by accounting for all three-phonon scattering processes using a solution of the linearized Boltzmann transport equation. A 3× reduction in intrinsic thermal conductivity is observed compared to bulk graphene arising from increased strength of three-phonon scattering due to the additional nondegenerate phonon modes that appear due to the finite edges of confined nanoribbons. Strong dependence of thermal conductivity on ribbon width is also observed. The underlying mechanisms for thermal conductivity reduction and width dependence are presented by analyzing frequency- and polarization-resolved phonon transport. The additional scattering pathways present in 1D GNRs lead to a significant reduction in the thermal conductivity of otherwise highly conducting flexural phonons in bulk graphene. In contrast, confinement-induced changes to the density of states, specific heat or group velocity, and the subsequent impact on lattice thermal conductivity are found to be relatively small.
Application of Conditional Adversarial Networks for Automatic Generation of MR-based Attenuation Map in PET/MR

Current PET/MR imaging systems use methods based on MR image segmentation with subsequent assignment of empirical attenuation coefficients for attenuation correction in PET image reconstruction. Delineation of bone in MR images has been challenging, especially in the head and neck areas, due to the difficulty of separating bone from air. In this work, we study deep learning techniques to automatically generate attenuation maps directly from MR images, with focus on the head and neck areas. We use a generative adversarial network (GAN) in a conditional setting for this image translation task. GANs separate the deep learning network into a generator, which tries to generate fake examples, and a discriminator, which learns to distinguish between real and fake examples, and train the two networks simultaneously. The objective function of the conditional GAN is a combination of the generator loss, discriminator loss, and the L1 distance between the label image and the output image from the generator. Image pairs of PET/MR image (input) and corresponding PET/CT based 511 keV photon attenuation map (label) are used to train the network. The network is trained for 6k iterations. The generator loss is trained from 2.0 to 1.4. The discriminator loss is trained from 0.6 to 1.0. The L1 loss is trained from 0.2 to 0.1. In our previous work with a basic autoencoder network for the conversion from MR images to corresponding attenuation maps, if we convert the defined L2 loss for the network to the RMS pixel value prediction error, the autoencoder network, after training, has a pixel prediction error of around 0.2 when all pixel values are scaled from 0 to 1. In this study, the L1 loss also represents this pixel prediction error, which is around 0.1 after the network is trained. This indicates an average reduction of 50% of the pixel prediction error.
Failure Mechanisms in Two-layer Undrained Slopes

This note presents results of stability analyses of two-layer undrained slopes by the finite element method. The study focuses on the circumstances under which either deep or shallow failure mechan...
rcs5-mediated spot blotch resistance in barley is conferred by wall-associated kinases that resist pathogen manipulation

Plant biotrophic pathogen disease resistances rely on immunity receptor-mediated programmed cell death (PCD) responses, but specialized necrotrophic/hemi-biotrophic pathogens hijack these mechanisms to colonize the resulting dead tissue in their necrotrophic phase. Thus, immunity receptors can become necrotrophic pathogen dominant susceptibility targets but resistance mechanisms that resist necrotroph manipulation are recessive resistance genes. The barley rcs5 QTL imparts recessive resistance against the disease spot blotch caused by the hemi-biotrophic fungal pathogen Bipolaris sorokiniana. The rcs5 genetic interval was delimited to ~0.23 cM, representing an ~234 kb genomic region containing four wall-associated kinase (WAK) genes, designated HvWak2, Sbs1, Sbs2 (susceptibility to Bipolaris sorokiniana 1&2), and HvWak5. Post-transcriptional gene silencing of Sbs1&2 in susceptible barley cultivars resulted in resistance showing dominant susceptibility function. Allele analysis of Sbs1&2 from resistant and susceptible barley cultivars identified sequence polymorphisms associated with phenotypes in their primary coding sequence and promoter regions, suggesting differential transcriptional regulation may contribute to susceptibility. Transcript analysis of Sbs1&2 showed nearly undetectable expression in resistant and susceptible cultivars prior to pathogen challenge; however, upregulation of both genes occurred specifically in susceptible cultivars post-inoculation with a virulent isolate. Apoplastic wash fluids collected from barley infected with a virulent isolate induced Sbs1, suggesting regulation by an apoplastic-secreted effector. Thus, Sbs1&2 function as B. sorokiniana susceptibility targets and non-functional alleles or alleles that resist induction by the pathogen mediate rcs5-recessive resistance. The sbs1&2 alleles underlying the rcs5 QTL that the pathogen is unable to manipulate are the first resistance genes identified against spot blotch.
The effect of sex and age on paw use within a large sample of dogs (Canis familiaris)

Abstract Many studies have focused on handedness as proxy for lateralization, highlighting that population-level biases in handedness seem to be characteristic of most animals, although the strength and direction varies between species. Gender has been found to influence handedness in some species; in humans, for instance, males are more likely to be left-handed than females. Another aspect that has been comparatively unexplored is the role of age in shaping functional asymmetries, especially in adulthood. Handedness has been widely explored in dogs (Canis familiaris), although there are contrasting findings about the influence of the dogs’ sex and age, possibly due to the comparatively small sample sizes used in previous studies. Here we overcame this issue by investigating these effects in a unique sample of 17,901 dogs of unknown neutered status. Specifically, this study used pre-collected data from the British Broadcasting Corporation (BBC)’s ‘Test Your Pet’ survey, during which owners tested their dogs’ paw preference in retrieving food from a tube in 3 consecutive trials. Based on the results of these 3 trials, owners were asked to assess whether their dogs used their left or right forepaw most of the time, or if it was difficult to tell. 13,240 dogs were scored as having a paw preference (i.e., were not ambidextrous or ambiguous), representing 74.0 % of the dogs tested. In those dogs that showed a paw preference, there was a population-level right-paw preference in both male and female dogs (60.7 % female and 56.1 % male), however, the proportion of dogs with a right-paw preference was significantly higher in females than males. Elderly dogs also tended to show a stronger right-paw preference than younger dogs. We conclude that the effect of sex on handedness may be influenced by factors such as sex hormones, while age changes may reflect the development of handedness and its maintenance in dog populations.
Machine-learning-based dynamic-importance sampling for adaptive multiscale simulations

Multiscale simulations are a well-accepted way to bridge the length and time scales required for scientific studies with the solution accuracy achievable through available computational resources. Traditional approaches either solve a coarse model with selective refinement or coerce a detailed model into faster sampling, both of which have limitations. Here, we present a paradigm of adaptive, multiscale simulations that couple different scales using a dynamic-importance sampling approach. Our method uses machine learning to dynamically and exhaustively sample the phase space explored by a macro model using microscale simulations and enables an automatic feedback from the micro to the macro scale, leading to a self-healing multiscale simulation. As a result, our approach delivers macro length and time scales, but with the effective precision of the micro scale. Our approach is arbitrarily scalable as well as transferable to many different types of simulations. Our method made possible a multiscale scientific campaign of unprecedented scale to understand the interactions of RAS proteins with a plasma membrane in the context of cancer research running over several days on Sierra, which is currently the second-most-powerful supercomputer in the world. Tackling scientific problems often requires computational models that bridge several spatial and temporal scales. A new simulation framework employing machine learning, which is scalable and can be used on standard laptops as well as supercomputers, promises exhaustive multiscale explorations.
Transfers Prior to Marriage and the Uniform Probate Code's Redesigned Elective Share - Why the Partnership is Not Yet Complete

This Article begins with an examination of the historical background of the common-law doctrine of antenuptial transfers in fraud of marital rights and its relationship to the elective share. Although this Article rejects the specific approach of this doctrine, the author finds that it provides invaluable insights into both intentional and unintentional spousal disinheritance and serves as an important guide in correcting a serious omission in the UPC and other elective share statutes. In the majority of cases invalidating an antenuptial conveyance, the decedent retained an interest in or power over the transferred property, although this element was never a formal requirement of the doctrine. Next, the Article examines several statutory approaches, including certain prenuptial transfers in the forced share, that may serve as alternative models to the common-law doctrine.The Article will then analyze and evaluate the UPC's adoption of the marital-sharing theory of marriage, discuss a total partnership theory as an alternative, and examine the UPC's treatment of prenuptial transfers of property. Specifically, it will focus on whether the exclusion of these prenuptial transfers promotes the goals of marital partnership or support. In the course of its examination of the common-law doctrine and the statutory approaches, the Article will analyze the deficiencies of each model in light of the policies of the elective share. Finally, it will propose guidelines that better accomplish these goals and close a significant loophole in the UPC and other statutory and common-law schemes. The guidelines used should effectively and equitably protect the surviving spouse, produce greater certainty in property arrangements for the benefit of the decedent's family, and reduce the likelihood of litigation.
MANTIS: Multiple Type and Attribute Index Selection using Deep Reinforcement Learning

DBMS performance is dependent on many parameters, such as index selection, cache size, physical layout, and data partitioning. Some combinations of these parameters can lead to optimal performance for a given workload but selecting an optimal or near-optimal combination is challenging, especially for large databases with complex workloads. Among the hundreds of parameters, index selection is arguably the most critical parameter for performance. We propose a self-administered framework, called the Multiple Type and Attribute Index Selector (MANTIS), that automatically selects near-optimal indexes. The framework advances the state-of-the-art index selection by considering both multi-attribute and multiple types of indexes within a bounded storage size constraint, a combination not previously addressed. MANTIS combines supervised and reinforcement learning, a Deep Neural Network recommends the type of index for a given workload while a Deep Q-Learning network recommends the multi-attribute aspect. MANTIS is sensitive to storage cost constraints and incorporates noisy rewards in its reward function for better performance. Our experimental evaluation shows that MANTIS outperforms the current state-of-art methods by an average of 9.53% QphH@size.
Transformation of alliances: Mapping Russia’s close relationships in the era of multivectorism

Russia led a key Cold War alliance and is now at the forefront of debates about major power realignments. Yet Russia’s own conceptualization of alliances in the post-Soviet era has received scant a...
Treatment of Lymphocele

Lymphocele occurs following procedures that surgically disrupt channels imbedded within the subcutaneous tissues, most commonly in the extremities. These fluid collections contain an increased concentration of lymph and are associated with painful swelling, prolonged drainage, and infection. Recent advancements in the management of lymphocele include recognition of high-risk patients, preoperative and intraoperative identification of lymphatic channels using radiopharmaceuticals, and newer, improved surgical treatments that utilize a variety of muscle flap transpositions, sometimes prophylactically, to fill dead space and promote wound healing. The increasing popularity of bariatric procedures for obesity has concomitantly led to a larger number of patients seeking thigh lift and brachioplasty enhancements of redundant skin folds. These procedures are particularly prone to causing damage to existing subcutaneous lymphatics.
Information Seeking with Multiple Sources of Conflicting and Unreliable Information

The effects of information conflict, the frequency with which the information is updated, and the reliability of the information sources upon information seeking and decision behavior were studied....
Why Men Won't Ask for Directions: The Seductions of Sociobiology

List of Illustrations ix Acknowledgments xi Chapter 1 Darwinian Paranoia 1 Chapter 2 An Orgasm of One's Own 10 Chapter 3 Sex without SEX 19 Chapter 4 Transgendered 36 Chapter 5 Alternative Lifestyles 51 Chapter 6 Social Inhibitions 75 Chapter 7 Why Does the Mockingbird Mock? 102 Chapter 8 Brain Ecology 124 Chapter 9 Why Men Won't Ask for Directions 150 Chapter 10 A Textbook Case of Penis Envy? 175 Chapter 11 Darwin's Temptress 192 Notes 201 Bibliography 257 Index 311
Coloring Random Graphs

We present an algorithm for coloring random 3-chromatic graphs with edge probabilities below the n−1/2 “barrier”. Our (deterministic) algorithm succeeds with high probability to 3-color a random 3-chromatic graph produced by partitioning the vertex set into three almost equal sets and selecting an edge between two vertices of different sets with probability p≥n− 3/5+e. The method is extended to k-chromatic graphs, succeeding with high probability for p≥n−α+e with α=2k/((k−l)(k+2)) and e>0. The algorithms work also for Blum's balanced semi-random GSB(n,p,k) model where an adversary chooses the edge probability up to a small additive noise p. In particular, our algorithm does not rely on any uniformity in the degree.
The Speech Recognition Virtual Kitchen: An Initial Prototype

This paper describes a “kitchen” environment to promote community sharing of research techniques, foster innovative experimentation, and provide solid reference systems as a tool for education, research, and evaluation with a focus on, but not restricted to, speech and language research. The core of the research infrastructure is the use of virtual machines (VMs) that provide a consistent environment for experimentation. We liken the virtual machines to a “kitchen” because they provide the infrastructure into which one can install “appliances” (e.g., speech recognition toolkits), “recipes” (scripts for creating state-of-the art systems), and “ingredients” (language data). In this demo, we show an initial proposal for a community framework based on VM technology used for teaching classes at CMU and OSU.
Enhanced erosion of frozen H2O films by high energy 19f ions

Abstract We have measured sputtering yields of H2O films with 19F ions at bombarding energies from 1.6 to 25 MeV. The sputtering yield was found to be very sensitive to the incident charge state of the beam, and insensitive to the thickness of the ice film for thicknesses ranging from approximately 20 to 80×l016H2O/cm2. The yield was independent of the target substrate temperature from 10 to 60 K and independent of the F beam current density from < 1 to approximately 5.5 particle nanoamps/mm2. There are several models proposed to explain enhanced sputtering of dielectrics; we have discussed their relevance to our data.
Classical and molecular methods to measure fecal bacteria.

This chapter provides an overview of classical and molecular methods to detect and enumerate fecal indicator bacteria (FIB). It summarizes general field sampling and laboratory considerations for using FIB methods, outlines the more common laboratory approaches to measure FIB, describes methods for certain key FIB, identifies standard methods, and summarizes some considerations for using FIB methods in particular situations or environments. The chapter is limited to providing an overview of some of the more common molecular approaches that have been used to detect FIB. Molecular methods such as Immunological methods, fluorescent in situ hybridization (FISH), PCR and quantitative PCR (qPCR) are also discussed. Although these new molecular methods are likely to remain research tools for years to come, they open up great potential for developing new FIB methods to expand the water quality assessment toolbox in the future. Advances in molecular methods offer potential to enumerate both culturable and non-culturable cells of Escherichia coli. The enterococci are a subgroup of the fecal streptococci. Growth of Pfizer selective enterococcus (PSE) isolates in brain-heart infusion broth confirms presence of enterococci. When collecting water samples, a maximum holding time of 24 hours has been proposed for enumerating Clostridium perfringens. Uncultured organisms that are genetically similar to cultured Bacteroides have gained popularity as indicator bacteria.
Self-Customization of E-Knowledge Using Color Semantics

It is a common practice for readers to highlight portions, clumps, of a printed document deemed important for later use. In this research effort, the benefits of highlighting process are extended to e-Documents. The analysis, design and implementation of a software system, Prospector, is presented, which is able to (1) provide for highlighting of clumps in an e-Document using different colors, (2) enforce color semantics, (3) deliver customized veins of clumps in an e-Document, (4) aggregate the same-color clumps, (5) support dynamic review of the highlighted clumps, and (6) provide for editing of the clumps.
The variant undecapeptide sequence of the Arcanobacterium pyogenes haemolysin, pyolysin, is required for full cytolytic activity.

The cholesterol-dependent cytolysins (CDCs) are characterized by an undecapeptide sequence (ECTGLAWEWWR) that is located near the C terminus and within domain 4 of these proteins. Pyolysin (PLO), the CDC of Arcanobacterium pyogenes, has a variant undecapeptide sequence (EATGLAWDPWW). Site-directed mutants were constructed in undecapeptide residues in a recombinant PLO molecule containing a hexahistidine tag (His-PLO). Mutations in each of the three undecapeptide tryptophan residues resulted in low haemolytic activity, confirming the importance of these residues in the protein. Deletion of a proline residue (P499), inserted in PLO, or substitution of this residue with either phenylalanine or glycine resulted in mutant proteins with undetectable or low haemolytic activities, indicating that P499 is essential for His-PLO haemolytic activity. Substitution of the PLO undecapeptide sequence with a consensus undecapeptide resulted in a His-PLO protein with only 0·1% activity, confirming that the variant PLO undecapeptide is required for the full cytolytic activity of this toxin. The presence of the conserved undecapeptide cysteine residue either alone (His-PLO.C492) or in a consensus sequence resulted in His-PLO molecules which were activated in the presence of reducing compounds, confirming the importance of this residue in the thiol-activated nature of many CDC toxins. The ability of His-PLO mutant proteins to bind cholesterol mimicked haemolytic activity, with the exception of His-PLO.C492, which, despite having reduced haemolytic activity, showed an increased ability to bind cholesterol compared to His-PLO. Despite reductions in haemolytic activity and cholesterol-binding, all mutant proteins were still able to bind to erythrocyte membranes, suggesting that other regions of PLO may recognize host-cell membranes, through receptors other than cholesterol.
Abstract 15599: Klf4 Regulates the Extent of Lung Microvessel Endothelial Cell Regeneration

Rationale: Transcription factor Kruppel like factor (Klf)-4 might regulate endothelial cell (EC) regeneration; however, the underlying mechanisms are poorly understood. Objective: The goal of this study was to delete EC-Klf4 in a timed manner using the lox-P elements, Cdh5 (VE-cadherin) as a promoter to drive the Cre recombinase, and to address the role of Klf4 in adult lung microvessels. Methods and Results: After 12 generations of backcrossing, we transferred Klf4fl to a C57BL background. Male Klf4fl/+ were crossed with female Klf4fl/+ mice to generate Klf4fl/fl (25%) offspring. In the next breeding scheme, Klf4fl/fl mice were crossed with male tg-Cdh5CreERT2 (tamoxifen inducible) mice to produce heterozygous Klf4fl::tg-Cdh5CreERT2 offspring (100%). I then crossed male Klf4fl::tg-Cdh5CreERT2 with female Klf4fl::tg-Cdh5CreERT2 to produce offspring of Klf4fl/fl::tg-Cdh5CreERT2 genotype (25%). Groups of these mice received tamoxifen everyday for 5 days, and on the 10th day, (now called Klf4ECKO mice) all m...
Psychiatric Stress Testing: Novel Strategy for Translational Psychopharmacology

A major focus of clinical neuroscience research today is to elucidate how reactions of brain circuits to stressful loads are regulated by genes and by psychiatric disorders. The study of Salvadore et al (2010) provides a glimpse into how such ‘psychiatric stress tests' may also translate into predictors of who will respond to a specific drug.
A dual criterion account of the development of linguistic judgment in early childhood

Preschool-age children were hypothesized to use one of two criteria, cue recognition or target generation, to make several linguistic judgments. When deciding whether a word is one they know, for example, some were expected to consider whether they recognized its sound form (cue recognition), whereas others were expected to consider whether a meaning came to mind (target generation). The particular criterion that a child adopted was predicted to depend on the efficiency of the phonological or semantic memory processes that supported its use. Fifty-two preschoolers made three linguistic judgments (word familiarity, syntactic acceptability, and object nameability) and received four memory tests. Five correlations between specific memory measures and specific judgments were predicted by the dual criterion account. Five hypotheses about the distinctiveness of these correlations were also tested. The results supported the five predictions as well as three of the distinctiveness hypotheses. The potential of the account for generating new hypotheses about memory and metalinguistic awareness in early childhood was also demonstrated.
Zircon U-Th-Pb and whole-rock Rb-Sr age patterns of lower Mesozoic igneous rocks in the Santa Rita Mountains, southeast Arizona: Implications for Mesozoic magmatism and tectonics in the southern Cordillera

Volcanic and plutonic rocks and associated sediments in the Santa Rita Mountains, southeast Arizona, represent one of the most complete Mesozoic sections in the Cordillera. Zircon from the lower member of the Mt. Wrightson Formation, the oldest of the dated units, has lost radiogenic lead and contains a component of older zircon. Accordingly, only an imprecise maximum age of ∼220 Ma could be obtained for an andesite from near the middle of this unit. The lower member is intruded by the Piper Gulch granodiorite, which gave a concordant zircon U-Th-Pb age of 188 ± 2 (2σ) Ma. Complex isotopic systematics of zircon from dacite in the middle member of the Mt. Wrightson Formation allow its age to lie between 172 and 190 Ma. Because the Piper Gulch is interpreted to also cut the base of the middle member, a hiatus of no longer than 30 m.y. is likely to separate the lower and middle members. This stratigraphic break marks the change from early predominantly basaltic and andesitic volcanism to later dacitic to rhyolitic lavas and tuffs. The silty to conglomeratic red beds and minor volcanic rocks of the Gardner Canyon Formation, for which we obtained a nearly concordant U-Th-Pb age of 200 ± 5 Ma on an abraded fraction of zircon, may identify a rift-dominated tectonic regime and mark the transition to felsic volcanism. A second cycle of andesite and rhyolitic volcanism and sedimentation, represented by the Temporal and Bathtub Formations, was dated at 151 ± 5 (2σ) Ma by the whole-rock Rb-Sr isotopic method. Compared to previous age estimates, our results suggest an earlier initiation of arc magmatism in this part of the Cordillera. Apparently, by the Late Triassic, this area was already an uplifted continental arc margin, analogous to the present-day Andes, shedding volcanic material to what is now the Colorado Plateau. The volcanic rocks we dated fall within the range of ages measured for cobbles of similar lithology from the Upper Triassic Chinle Formation in the Colorado Plateau. Therefore, it is not necessary to invoke the tectonic removal of an early Mesozoic arc terrane along the proposed Mojave-Sonora megashear.
Service census caps and unit-based admissions: resident workload, conference attendance, duty hour compliance, and patient safety.

Objective To examine the effect of census caps and unit-based admissions on resident workload, conference attendance, duty hour compliance, and patient safety.
Preoperative virtual screening examination of the airway

A case of a preoperative airway examination performed using telemedicine is presented. The use of this technology has the ability to provide crucial information regarding the feasibility of office-based anesthesia in advance and limit schedule interruptions on the day of surgery.
The Role of Scaling up Research in Designing for and Evaluating Robustness

One of the great strengths of Jim Kaput’s research program was his relentless drive towards scaling up his innovative approach to teaching the mathematics of change and variation. The SimCalc mission, “democratizing access to the mathematics of change,” was enacted by deliberate efforts to reach an increasing number of teachers and students each year. Further, Kaput asked: What can we learn from research at the next level of scale (e.g., beyond a few classrooms at a time) that we cannot learn from other sources? In this article, we develop an argument that scaling up research can contribute important new knowledge by focusing researchers’ attention on the robustness of an innovation when used by varied students, teachers, classrooms, schools, and regions. The concept of robustness requires additional discipline both in the design process and in the conduct of valid research. By examining a progression of three studies in the Scaling Up SimCalc program, we articulate how scaling up research can contribute to designing for and evaluating robustness.
Trabecular organization in mandibular osteodistraction in growing and maturing rats

Purpose Our goal was to investigate the trabecular organization of the distraction regenerate during various consolidation phases and as a result of various distraction rates. Materials and methods One hundred ninety-two growing and maturing rats (96 each) received unilateral mandibular osteotomies and distraction device placement. They were randomly allocated into 4 distraction rate groups (0, 0.2, 0.4, and 0.6 mm/day for 5 days) after a 3-day latency. Eight rats from each rate group were sacrificed at early (10 days), mid (24 days) and late (38 days) consolidation time points. Harvested hemimandibles were embedded in micro-bed resin, sectioned sagittally at 10 μm thickness and stained using the Von Kossa method. The histologic images were captured and processed using Adobe Photoshop (Version 7.0; Adobe Systems Inc, San Jose, CA). Custom-made software (MacAzimuth; written by Prof. J.M. Rensberger, University of Washington) was further used to analyze the orientation (anisotropy and angle distribution) and mass (density and thickness) of trabecular structures in the regenerates. Results Trabecular orientation significantly differed at the mid-consolidation time point with less anisotropy ( P ≤ .000 to .023) and narrower angular distribution ( P ≤ .007 to .021). Trabecular mass increased significantly from early to mid-consolidation ( P ≤ .000 to .002). Growing rats showed greater trabecular organization than maturing rats did at the same time points ( P ≤ .000 to .009). The trabecular organization parameters were associated significantly with bone mineral density and microdensity ( P ≤ .000 to .044). Conclusion The peak change in orientation occurred around the mid-consolidation with a greater increase in trabecular mass. Growing rats showed a greater capacity for trabecular organization at earlier time points. However, distraction rate did not have an effect on trabecular organization. These results suggest that trabecular organization can be used as an important indicator to evaluate bone maturation and quality in the distraction regenerate.
ACT-enabled 100 MHz channel equalizer (for magnetic recording application)

An acoustic charge transport (ACT) equalizer with 128 taps and a 180-MHz tap sampling rate is demonstrated with a variety of head responses. The standard programmable transversal filter (PTF) product has been modified for magnetic recording applications by the addition of an instrumentation interface and specialized analog circuitry for low-frequency equalization. The resulting module, when combined with controlling software is known as a filter/equalizer development station (FEDS). A laboratory system employing two such FEDS modules for separate amplitude and zero-crossing equalization in a digital saturated magnetic recording peak detection channel is modeled and demonstrated. Equalizer impacts on system speed, packing density, and error rates are predicted with a channel model. >
The goal of monetary reform

The essential reason that a 100-percent-reserve gold standard should be the ultimate goal of monetary reform is that it would secure the economic system against the evils both of inflation and of deflation-depression. In addition, it would be consistent with the fundamental moral-political principle of the absence of the initiation of physical force and thus the positive presence of individual freedom. Indeed, by virtue of the safeguards it imposes against inflation and deflation-depression, it would secure the individual's freedom against the state better than any other monetary system. These are propositions for which I supply far more extensive support in my book Capitalism: A Treatise on Economics than itis possible for me to supply here. 1 Here I will concentrate on the proposition that such a gold standard would be a guarantee against deflation-depression. The security it affords against inflation is relatively obvious and far less controversial and is thus much less urgently in need of explanation. Indeed, the very success of gold in safeguarding against the rising prices that so prominently feature in inflation is what has been made the basis for believing that gold implies defafion-depression. This happens for no other reason than that the typically modest increase in the quantity of money and volume of aggregate spending that takes place under a gold standard is accompanied by actually falling prices whenever greater increases in the production and supply of ordinary, i.e., nonmonetary, commodities take place. Such falling prices occurred in the United States in the generation prior to the discovery of the California gold fields in 1848, and again in the generation GEORGE REISMAN is professor of economics at Pepperdine University. He is the author of Capitalism:A Treatise on Economics (Ottawa, Ill.: Jameson Books, 1996) and is the translator of Ludwig yon Mises's Epistemological Problems of Economics (New York: D. Van Nostrand, 1960). His web site is http://www.capitalism.net. This paper was delivered at the Ludwig yon Mises Institute's AustrianScholar's Conference, March 2000.
Structural Basis for Heart Failure Ventricular Remodeling and Its Pharmacological Inhibition

The syndrome of heart failure has traditionally been viewed as a functional disorder precipitated by impaired left ventricular pump performance. The classification into systolic and diastolic dysfunction has emphasized the functional distinction between abnormalities in contraction and relaxation. Recently, however, attention has been directed toward the possibility that the systolic dysfunction, which has been thought to be related to contractile failure, could be a consequence of a structural increase in ventricular chamber volume. This construct would revise the conventional view—contractile failure leads to chamber dilatation—with a more anatomic basis for heart failure: Chamber dilatation occurs as an early response that results in the reduced wall motion that is mandated to generate a normal stroke volume from a large ventricular end-diastolic volume. This structural alteration is not necessarily related to the underlying etiological cardiac pathology but rather represents an intrinsic morphological change that progresses over time in response to an initiating event. The term “remodeling” often is used to address these structural changes and may be best defined as a change in chamber volume and shape not related to a preload-mediated increase in sarcomere length. In this issue of Circulation , Greenberg and his SOLVD colleagues1 revisit the remodeling issue in chronic heart failure with echocardiographic data collected in the long-term trial of enalapril versus placebo in both symptomatic and asymptomatic patients with left ventricular remodeling. Patients were selected for this study on the basis of an ejection fraction of ≤35%. At the time the study was designed, this low ejection fraction was defined as systolic dysfunction. The implication of that designation is that an impairment of myocardial shortening was the primary abnormality. A more contemporary hypothesis, based on the concept of left ventricular remodeling, is that the low ejection fraction reflects in part a primary increase in chamber volume …
Evaluation of vaccine dosing in patients with solid tumors receiving myelosuppressive chemotherapy

Objective. To provide oncology healthcare providers with information on current vaccine recommendations and discuss the proper timing of vaccination in relation to chemotherapy, to allow for an ade...
Partikelfilter fuer Diesel-Pkw. Beladungs- und Regenerationsverhalten

Als Beitrag zur CO2-Reduktion ist der verbrauchsarme Dieselmotor als Fahrzeugantrieb heute unentbehrlich. Nachteilig sind jedoch seine prinzipbedingt hohen Stickoxid- und Ruspartikelemissionen, denen man abgesehen von motorischen Masnahmen nur durch aufwandige Abgasnachbehandlung begegnen kann. Hier wurden in den letzten Jahren DeNOx-Systeme und Partikelfiltersysteme entwickelt und partiell schon in die Serie gebracht. Bei Tenneco Automotive in Edenkoben lauft zur Zeit ein umfangreiches Untersuchungsprogramm zur Optimierung von Partikelfiltersystemen fur Pkw-Anwendungen.