cssi/SciSciGPT-SciSciNet huggingface dataset:
Assembly-associated structural changes of bacteriophage T7 capsids. Detection by use of a protein-specific probe

To detect changes in capsid structure that occur when a preassembled bacteriophage T7 capsid both packages and cleaves to mature-size longer (concatameric) DNA, the kinetics and thermodynamics are determined here for the binding of the protein-specific probe, 1,1'-bi(4-anilino)naphthalene-5,5'-di-sulfonic acid (bis-ANS), to bacteriophage T7, a T7 DNA deletion (8.4%) mutant, and a DNA-free T7 capsid (metrizamide low density capsid II) known to be a DNA packaging intermediate that has a permeability barrier not present in a related capsid (metrizamide high density capsid II). Initially, some binding to either bacteriophage or metrizamide low density capsid II occurs too rapidly to quantify (phase 1, duration
Oxidative stress in alcoholic liver disease: Role of NADPH oxidase complex

Alcohol is a well-known risk factor for liver damage and is one of the major causes of liver disease worldwide. Chronic intake of alcohol, over a certain limit, inevitably leads to hepatic steatosis. If the injury persists, steatosis with concomitant tumor necrosis factor-alpha and other cytokines, progresses to steatohepatitis, fibrosis and finally cirrhosis. Among the multiple factors involved in the process of alcohol-induced liver injury, a crucial role is played by oxidative stress. Several mechanisms during ethanol metabolism result in reactive oxygen species (ROS) production. Although the main site of ethanol metabolism is hepatocytes, other mechanisms are involved in alcohol-induced liver injury. Specifically, in the ROS production activity, an important role is played by the NADPH oxidase complex. NADPH oxidase is expressed in hepatocytes, hepatic stellate cells and Kupffer cells in the liver. Studying NADPH oxidase gives new insights into alcohol-induced liver damage and provides new direction for future therapeutic strategies.
Automatic approaches to clustering occupational description data for prediction of probability of workplace exposure to beryllium

We investigated automatic approaches for clustering data that describes occupations related to hazardous airborne exposure (beryllium). The regulatory compliance data from Occupational Safety and Health Administration includes records containing short free text job descriptions and associated numerical exposure levels. Researchers in public health domain need to map job descriptions to Standard Occupational Classification (SOC) nomenclature for estimating occupational health risks. Previous manual process was time-consuming and did not advance so far to linkage to SOC. We investigated alternative automatic approaches for clustering job descriptions. The clustering results are the first essential step towards discovery of corresponding SOC terms. Our study indicated that the Tolerance Rough Set with Jaccard similarity was a better combination overall. The utility of the algorithm was further verified by applying logistic regression and validating that the predictive power of the automatically generated classifications, in terms of association of “job” with probability of exposure to beryllium above certain threshold, closely approached that of the manually assembled classification of the same 12,148 records.
Micropreconcentration units based on carbon nanotubes (CNT)

Carbon nanotubes (CNT) have some highly desirable sorbent characteristics which make them attractive for a variety of analytical applications. High adsorption capacity and rapid desorbability make CNT excellent candidates for micro-scale devices for gas and liquid-phase analysis. In gas-phase analysis one can implement a micro-concentrator or a micro-sorbent trap, which have been used in a variety of on-line chromatography and sensing applications. Interesting liquid-phase microtrapping applications include micro-scale solid-phase extraction (μ-SPE) and solid-phase micro extraction (SPME). In addition, the ease of surface functionalization, self assembly by chemical vapor deposition, and the formation of diverse polymer composites may well make CNT the high-performance sorbent of the future.
Contrasting patterns in the acquisition of spatial/temporal terms.

Abstract Competing hypotheses about the acquisition of terms that refer to relationships in both time and space are tested. One hypothesis is that the language of time is acquired as a spatial metaphor; consequently, such terms will be acquired in their spatial sense first. The competing hypothesis is that differential experience with the dual senses of each term will result in different patterns of acquisition, depending upon which sense is dominant in actual usage. Comprehension of before-after, first-last , and ahead-behind by 4- to 6-year-olds was assessed in spatial, temporal, and spatial-temporal meaning tasks. Results support the second view: there is no consistent order of acquisition; the sense acquired first is the dominant sense, as determined by both linguistic evidence and empirical survey.
Exploring College Students' Mental Representations of Inferential Statistics.

Abstract We report a case study that explored how three college students mentally represented the knowledge they held of inferential statistics, how this knowledge was connected, and how it was applied in two problem solving situations. A concept map task and two problem categorization tasks were used along with interviews to gather the data. We found that the students’ representations were based on incomplete statistical understanding. Although they grasped various concepts and inferential tests, the students rarely linked key concepts together or to tests nor did they accurately apply that knowledge to categorize word problems. We suggest that one reason the students had difficulty applying their knowledge is that it was not sufficiently integrated. In addition, we found that varying the instruction for the categorization task elicited different mental representations. One instruction was particularly effective in revealing students’ partial understandings. This finding suggests that modifying the task format as we have done could be a useful diagnostic tool.
Bacillus licheniformis isolated during a fish kill is non-pathogenic

= 7,meanweight = 18.2 g)atﬁshkillsitesinthe river. Dead ﬁsh captured and examined in theareaexhibitedanadvancedstateofautolysis,sonodead ﬁsh were used in this study.The approximatemean water quality parameters at the samplingsites were: temperature 20.22°C, dissolved oxygen8.26 mg/L, salinity 7.6 and pH 8.36. Blood glucoseat the time of capture was measured using themethods of Evans
Modeling of long term behavior of ablation plumes produced with ultrashort laser pulses

Expansion of ablation plumes created by intense ultrashort lasers is determined by various complicated physical processes which have very different spatial and time scales. Since complete simulation by one model is practically impossible, the authors suggest using two models describing initial and final stages that can be matched at an intermediate time. The proposed modeling procedure connects laser parameters to plume properties far away from the ablation spot. Laser material interaction and beginning of the expansion are simulated with a one-dimensional hydrodynamics code and the final stage is modeled using an analytical solution for an expanding three-dimensional ellipsoidal gas cloud.
Intracellular trafficking/membrane targeting of human reduced folate carrier expressed in Xenopus oocytes

The major cellular pathway for uptake of the vitamin folic acid, including its absorption in the intestine, is via a plasma membrane carrier system, the reduced folate carrier (RFC). Very little is known about the mechanisms that control intracellular trafficking and plasma membrane targeting of RFC. To begin addressing these issues, we used Xenopus oocyte as a model system and examined whether the signal that targets the protein to the plasma membrane is located in the COOH-terminal cytoplasmic tail or in the backbone of the polypeptide. We also examined the role of microtubules and microfilaments in intracellular trafficking of the protein. Confocal imaging of human RFC (hRFC) fused to the enhanced green fluorescent protein (hRFC-EGFP) showed that the protein was expressed at the plasma membrane, with expression confined almost entirely to the animal pole of the oocyte. Localization of hRFC at the plasma membrane was not affected by partial or total truncation of the COOH-terminal tail of the polypeptide, whereas a construct of the cytoplasmic tail fused to EGFP was not found at the plasma membrane. Disruption of microtubules, but not microfilaments, prevented hRFC expression at the plasma membrane. These results demonstrate that the molecular determinant(s) that directs plasma membrane targeting of hRFC is located within the backbone of the polypeptide and that intact microtubules, but not microfilaments, are essential for intracellular trafficking of the protein.
Porometric properties of siliciclastic marine sand: a comparison of traditional laboratory measurements with image analysis and effective medium modeling

During the 1999 sediment acoustics experiment (SAX99), porometric properties were measured and predicted for a well sorted, medium sand using standard laboratory geotechnical methods and image analysis of resin-impregnated sediments. Sediment porosity measured by laboratory water-weight-loss methods (0.372 /spl plusmn/ 0.0073 for mean /spl plusmn/1 standard deviation) is 0.026 lower than determined by microscopic image analysis of resin-impregnated sediments (0.398 /spl plusmn/ 0.029). Values of intrinsic permeability (m/sup 2/) determined from constant-head permeameter measurements (3.29 /spl times/ 10/sup -11/ /spl plusmn/ 0.60 /spl times/ 10/sup -11/) and by microscopic image analysis coupled with effective medium theory modeling (2.78 /spl times/ 10/sup -11/ /spl plusmn/ 1.01 /spl times/ 10/sup -11/) are nearly identical within measurement error. The mean value of tortuosity factor measured from images is 1.49 /spl plusmn/ 0.09, which is in agreement with tortuosity factor determined from electrical resistivity measurements. Slight heterogeneity and anisotropy are apparent in the top three centimeters of sediment as determined by image-based porometric property measurements. However, the overall similarity for both measured and predicted values of porosity and permeability among and within SAX99 sites indicates sediments are primarily homogeneous and isotropic and pore size distributions are fairly uniform. The results indicate that an effective medium theory technique and two-dimensional image analysis accurately predicts bulk permeability in resin-impregnated sands.
Identifying noise in an attribute of interest

One of the most significant issues facing the data mining community is that of low-quality data. Real-world datasets are often inundated with various types of data integrity issues, particularly noisy data. In response to the difficulties created by low-quality data, we propose a novel technique to detect noisy instances relative to an attribute of interest (AOI). Any attribute in the dataset can be defined by the user as the attribute of interest. A noise ranking of instances relative to the chosen attribute is output. This approach can be iterated for any number of user-specified attributes of interest. The case study described in this work demonstrates how our technique may be used to detect class noise, which occurs when errors are present in the class or dependent variable. In this scenario the class is declared to be the attribute of interest and an instance noise ranking relative to the class is provided. Our technique is compared to the well-known ensemble and classification filters which have been previously proposed for class noise detection. The results of this study demonstrate the effectiveness of our approach and show that our procedure is a useful tool for improving data quality.
Institutional design and information revelation: Evidence from environmental right-to-know

How governments design institutions for the revelation of information depends on how the costs and benefits are distributed across affected groups. In this study I examine the incidence of different kinds of constituencies and how governments give citizens access to information that affects them. A number of important studies have sought to understand the effect of such rules on the revelation of private information and policy outcomes, but we know little about the sources of those rules. Do the rules coincide with constituencies that benefit from their existence? Are they absent when strong constituencies can avoid bearing the costs of the rules? Using data on community “right-to-know” protections regarding environmental hazards, I compare the incidence of the benefits and costs of these design choices in the context of rules that reveal information and charge the cost of information revelation to the regulated community. The models show that the incidence of right-to-know protections depends on the presence or absence of constituencies that would enjoy their benefits or bear their costs. However, organizational costs limit the ability of affected constituencies to obtain institutional designs that reflect their interests.
Optimality for completely observed controlled jump processes

A very simple derivation of optimality conditions for completely observable controlled jump processes is given.
A joint radar-acoustic particle filter tracker with acoustic propagation delay compensation

In this paper, a novel particle filter tracker is presented for target tracking using collocated radar and acoustic sensors. Real-time tracking of the target's position and velocity in Cartesian coordinates is performed using batches of range and direction-of-arrival estimates. For robustness, the filter aligns the radar and acoustic data streams to account for acoustic propagation delays. The filter proposal function uses a Gaussian approximation to the full tracking posterior for improved efficiency. To incorporate the aligned acoustic data into the tracker, a two-stage weighting strategy is proposed. Computer simulations are provided to demonstrate the effectiveness of the algorithm.
Calcium Bioavailability of Vegetarian Diets in Rats: Potential Application in a Bioregenerative Life‐Support System

Calcium bioavailability of vegetarian diets containing various proportions of candidate crops for a controlled ecological life-support system (CELSS) was determined by femur 45Ca uptake. Three vegetarian diets and a control diet were labeled extrinsically with 45Ca and fed to 5-wk old male rats. A fifth group of rats fed an unlabeled control diet received an intraperitoneal (IP) injection of 45Ca. There was no significant difference in mean calcium absorption of vegetarian diets (90.80 +/- 5.23%) and control diet (87.85 +/- 5.25%) when calculated as the percent of an IP dose. The amounts of phytate, oxalate, and dietary fiber in the diets did not affect calcium absorption.
A new approach to surface energy characterization for adhesive performance prediction

A new approach to qualitatively predicting adhesion at a solid/solid interface is described. It is based on thermodynamic compatibility of the two adhering surfaces, but it overcomes the weaknesses of existing methods by using a full set of contact angle data and by assembling the data to reveal the main features of the set without loss of information. Adhesive performance data to support this approach are presented.
Network integration and graph analysis in mammalian molecular systems biology

Abstraction of intracellular biomolecular interactions into networks is useful for data integration and graph analysis. Network analysis tools facilitate predictions of novel functions for proteins, prediction of functional interactions and identification of intracellular modules. These efforts are linked with drug and phenotype data to accelerate drug-target and biomarker discovery. This review highlights the currently available varieties of mammalian biomolecular networks, and surveys methods and tools to construct, compare, integrate, visualise and analyse such networks.
Availability and Analysis of Proprietary Dent Corn Inbred Lines with Expired U.S. Plant Variety Protection

Current U.S. commercial hybrid corn (Zea mays L.) is produced using proprietary inbred corn lines as parents. Most proprietary corn inbred lines have been protected by the U.S. Patent and/or U.S. Plant Variety Protection Act (PVPA) since approximately 1980. Currently there are 89 dent inbred corn lines (with more each year) whose intellectual proprietary protection has expired. These inbred lines are now available from the U.S. National Plant Germplasm System with freedom to operate for applications in research, plant breeding, and direct commercial use. This study facilitates an understanding of this germplasm by utilizing detailed pedigree and phenotypic information available from U.S. Patent and PVPA records to enhance their application to research and product development. This germplasm is mostly yellow dent and ranges in maturity from early (1000 heat units to mid-silk) to full (1708 heat units to mid-silk) season. These proprietary lines are from diverse backgrounds that include Iowa Stiff Stalk Synthetic, Argentine Maiz Amargo, Oh43, Minnesota 13, Iodent, Lancaster, Oh07Midland, Commercial Hybrid derived, and uncharacterized broad base sources from exotic, synthetic, and open pollinated populations.
Poor Women's Moral Economies of Nonprofit Social Service Use: Conspicuous Constraint and Empowerment in the Hollow State:

This article explores the moral economy through which poor women apply shared understandings of what is fair, just, and appropriate to their use of nonprofit services. The findings suggest that suc...
Some Reliability Considerations of Large Hybrids

I assume that we all agree that a component does not become inherently less reliable when combined with other components, as in a hybrid, than it is singly. To think otherwise would be unscientific and perhaps even unAmerican. A component that has a particular failure rate when individually packaged should not have a higher failure rate in a hybrid assembly all things being equal. Unfortunately, not all things remain equal and perhaps that is the substance of the question before the panel.
Comparative control study of ideal and methyl acetate reactive distillation

The control of an ideal reactive distillation column is compared with that of a similar, but somewhat different, real chemical system, the production of methyl acetate. Similarities and differences are observed. Three control structures are evaluated for both systems. A control structure with one internal composition controller and one temperature controller provides effective control of both systems for both high and moderate conversion designs. A two-temperature control structure is effective when the system is overdesigned in terms of number of reactive trays, holdup and/or catalyst load. Direct control of product purity for the high-conversion/high-purity design is difficult because of system nonlinearity and interaction. Tray temperature control avoids the nonlinearity problem.
Isolation, purification, and characterization of Crithidia fasciculata cytochrome c555

Abstract Cytochrome c555 was isolated from Crithidia fasciculata (Anopheles strain; A.T.C.C. No. 11745), and was purified by salt fractionation and chromatography on Amberlite CG-50 cation-exchange resin. The cellular content of cytochrome c555 was estimated to be 1.56 × 105 molecules per cell, accounting for about 25% of the hemin requirement of the organism. Absorbance maxima occurred at 413 mμ for the oxidized form, and at 420, 525, and 555.5 mμ for the reduced form, the extinction coefficient of the latter peak having been determined to be 29.7 m m −1 cm−1. The α-maximum of the pyridine hemochromogen was at 553 mμ. Acid acetone failed to remove the heme moiety from the cytochrome. The mono-heme protein had a minimum molecular weight of 12,051, calculated from the amino acid composition. The value calculated from ultracentrifugation data was 13,200. The mobility of the protein on Amberlite columns and upon electrophoresis in polyacrylamide gels was consistent with that which would have been expected from the amino acid composition. The isoelectric point was at pH 9.9, while the midpoint of the oxidation-reduction potential was +280 mV at pH 7.0. The cytochrome was not autooxidizable, nor did it combine with carbon monoxide at neutral pH. Comparison with other purified cytochromes c from a variety of sources showed that, in most of its properties, cytochrome c555 was similar to cytochromes from certain yeasts.
Speech Recognition Using Neural Networks

It is generally agreed that natural language will become the most common method for interacting with computers, increasing our reliance on natural language processing, the task of understanding written human language, and speech recognition, the task of converting human speech into written form. This chapter will focus on speech recognition — what it is, what speech features are used for recognition, its associated problems, and possible applications. We will also review a sample program for speech recognition, examining what it does, how it works, show sample data, create the training data for a neural network based speech recognition system, and consider ideas for expanding the system.
Gold leaching in cyanide-starved copper solutions in the presence of glycine

Abstract In the cyanidation of copper–gold ores, the presence of copper minerals can lead to soluble gold losses, the production of weak acid dissociable (WAD) cyanide, as well as a number of operational challenges in CIP/CIL circuits with regard to competitive adsorption, and subsequent difficulties associated with elution, electrowinning and smelting. In addition, copper minerals are significant cyanide consumers, leading to higher cost in ore treatment. This paper presents a process to enhance the dissolution of gold using copper–cyanide solutions in the presence of glycine where the solution is cyanide starved. The effect of glycine addition on gold leaching kinetics in copper–cyanide solutions under different leaching conditions was studied. The results show that, in the presence of glycine, gold dissolution rate increases significantly in solutions containing copper–cyanide species at a very low, or zero, free cyanide concentration. In the presence and absence of glycine, gold dissolution rates in solutions containing 10 mM Cu(CN) 3 2 − were 11.1 μmol/m 2 ·s and 0.65 μmol/m 2 ·s, respectively. It is shown that the average gold dissolution rate in a Cu–CN − -glycine system is about 6.5 times higher than the gold dissolution rate in the conventional cyanidation, the presence of cyanide being similar in each system. Kinetic and electrochemical studies were conducted to evaluate the effects of glycine concentration, pH, CN/Cu ratio, and initial copper concentrations on the dissolution of gold. It has also been shown that the gold dissolution rate increases by increasing the glycine concentration up to 1 g/L and any further glycine addition has a negative effect on the dissolution of gold. Increasing leaching pH up to 12 enhances gold dissolution in the copper–cyanide–glycine solutions. However, increasing leaching pH to 13 has an adverse effect on the dissolution of gold.
From Fayols Mechanistic To Todays Organic Functions Of Management

This paper reviews Fayols original five managerial functions, demonstrates that they are still being taught in todays management courses, and offers a new set of organic management functions more applicable to todays turbulent business environment.
Demonstration of renal lithiasis on technetium-99m MDP bone scintigraphy.

Renal lithiasis shown on technetium-99m MDP bone scintigraphy is uncommon. The author reports two cases of this unusual finding. Radiographic, computed tomographic, and sonographic correlation in these instances confirms the presence of kidney stones and their uptake of radiotracer. Renal lithiasis is a rare but possible cause of focal technetium-99m MDP uptake in the kidneys.
Abstract 4275: Production and characterization of ErbB1 (EGFR) associated with nanolipoprotein particles via cell-based and cell-free methods.

The four members of the ErbB family of mammalian receptor tyrosine kinases are essential for the development and maintenance of a variety of tissues. Aberrant activation or over-expression of these receptors leads to the progression of epithelial and brain tumors. An understanding of the mechanistic and structural changes that occur to activate the intracellular receptor tyrosine kinase domain via extracellular ligand binding and receptor dimerization is desirable for identifying specific and efficient methods to inhibit signal transduction. Previous methods to study this process achieved low success due to low protein yield, poor water solubility of the membrane protein, and the large size of receptor. We report progress on overcoming these technical hurdles by forming the ErbB family members in nanolipoprotein particles (NLPs), which are ∼20 nm disc-shaped cell membrane analogs. Here we compare an optimized cell-based method with a novel cell-free method to produce NLPs containing the ErbB1 receptor, also called EGFR. The cell-produced ErbB1-NLPs retain kinase activity compared to cell-free produced material with higher yields. However, the cell-free produced receptors have regions of correct folding and can be produced in less than a day. The cell-free produced constructs can be labeled conveniently with unnatural amino acids to enable characterization of dimerization interactions. These two receptor production systems can be utilized synergistically to enable new studies of conformational changes associated with ligand binding or protein mutations, as well as to identify small molecule inhibitors of these receptors. Citation Format: Tiffany M. Scharadin, Christina Takanishi, Wei He, Matthew Saldano, Kermit L. Carraway, Matthew A. Coleman, Paul T. Henderson. Production and characterization of ErbB1 (EGFR) associated with nanolipoprotein particles via cell-based and cell-free methods. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4275. doi:10.1158/1538-7445.AM2013-4275
System for Multi-agent Based Agile Scheduling in Virtual Enterprises

This paper presents an approach to deal with the conflicts problems in agile scheduling with the exploitation of multi-agent techniques. At first, the agile scheduling in virtual enterprises is discussed, then the connict's happening and type, the resolution methods and the inter-operations among scheduling, planning and supervision are described. Finally. the design of a negotiation mechanism in multi-agent based agile scheduling in virtual enterprises is presented.
Primary Malignant Melanoma of the Female Urethra: A Case Report

A case of primary malignant melanoma of the female urethra is presented. A 65-year-old Japanese woman was referred with dysuria and urethral bleeding. A hemorrhagic blue-black tumor, 3 cm in diameter, was diagnosed as a malignant melanoma by urinary cytology and biopsy. In spite of radical surgery followed by adjuvant immunochemotherapy with beta interferon, dacarbazine, nimustine and vincristine (IFN beta-DAV), the patient died of the disease one year after surgery because of lung metastasis which developed six months after diagnosis. The regional lymph nodes were not involved. In the present paper, we have briefly discussed the diagnostic value of cytological examination for this condition, as well as biopsy, with regard to the risk of hematogeneous tumor spread.
Abstract IA01: T cells as a drug for the personalized immunotherapy of cancer

Adoptive cell transfer (ACT) immunotherapy using T lymphocytes with antitumor activity is a living therapy that can be highly effective in patients with a variety of metastatic cancers. Naturally occurring tumor infiltrating lymphocytes (TIL) expanded in vitro and administered following a lymphodepleting preparative regimen mediated objective regression of metastatic melanoma in 56% of 194 patients including complete regressions in 20% of patients who remain ongoing disease-free 3 to 10 years later. Recent studies have shown that TIL recognized random somatic mutations that served as the targets resulting in complete cancer regressions. To extend ACT immunotherapy to additional patients we developed an approach based on deep exomic sequencing and immunologic testing to generate T cells that recognized immunogenic mutations in a variety of human cancer types including esophageal, colorectal, bile duct, gastric, pancreatic, ovarian and lung cancer. Targeting these unique mutations opens the possibility of using ACT to treat patients with common epithelial cancers. We used this approach to treat a patient with metastatic cholangiocarcinoma using autologous mutation-reactive T cells and mediated regression of lung and liver metastases ongoing at two years. In addition to the use of naturally occurring mutation-reactive cells, we have genetically engineered autologous lymphocytes to express antitumor T-cell receptors (TCR) or chimeric antigen receptors (CAR) for use in ACT immunotherapy. These cells can mediate durable cancer regressions in heavily pretreated patients with refractory lymphomas, sarcomas, and melanoma. Thus autologous T cells can be used to provide a highly personalized therapy for cancer patients refractory to conventional cancer treatments. Citation Format: Steven Rosenberg. T cells as a drug for the personalized immunotherapy of cancer. [abstract]. In: Proceedings of the CRI-CIMT-EATI-AACR Inaugural International Cancer Immunotherapy Conference: Translating Science into Survival; September 16-19, 2015; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(1 Suppl):Abstract nr IA01.
Shut Out: How Barriers Often Prevent Meaningful Access to Emergency Shelter

Most cities fine and even jail homeless people for living outside on the assumption that their alternative is to access homeless shelters. This brief finds that assumption deeply flawed. This first-ever study of shelters discloses that shelters have insufficient beds to meet the demand, and rules that bar entry to many homeless people. Most shelters only serve single males or females — they automatically exclude families, LGBTQ youth, and couples. For many then, shelters are not an alternative. The brief offers several recommendations to encourage cities to stop criminalizing homelessness and to instead pursue non-punitive alternatives.
Characteristics and distribution of Listeria spp., including Listeria species newly described since 2009

The genus Listeria is currently comprised of 17 species, including 9 Listeria species newly described since 2009. Genomic and phenotypic data clearly define a distinct group of six species (Listeria sensu strictu) that share common phenotypic characteristics (e.g., ability to grow at low temperature, flagellar motility); this group includes the pathogen Listeria monocytogenes. The other 11 species (Listeria sensu lato) represent three distinct monophyletic groups, which may warrant recognition as separate genera. These three proposed genera do not contain pathogens, are non-motile (except for Listeria grayi), are able to reduce nitrate (except for Listeria floridensis), and are negative for the Voges-Proskauer test (except for L. grayi). Unlike all other Listeria species, species in the proposed new genus Mesolisteria are not able to grow below 7 °C. While most new Listeria species have only been identified in a few countries, the availability of molecular tools for rapid characterization of putative Listeria isolates will likely lead to future identification of isolates representing these new species from different sources. Identification of Listeria sensu lato isolates has not only allowed for a better understanding of the evolution of Listeria and virulence characteristics in Listeria but also has practical implications as detection of Listeria species is often used by the food industry as a marker to detect conditions that allow for presence, growth, and persistence of L. monocytogenes. This review will provide a comprehensive critical summary of our current understanding of the characteristics and distribution of the new Listeria species with a focus on Listeria sensu lato.
G-Protein-Coupled Receptors, Signal Fidelity, and Cell Transformation

Publisher Summary G protein-coupled receptors (GPCRs) make up the largest group of transmembrane proteins implicated in signal transduction. These receptors are activated by a large variety of ligands, including cytokines and chemokines, peptide and non-peptide neurotransmitters, hormones, growth factors, odorant molecules and light. This chapter attempts to give a sense of the multiplicity of classical and novel signaling systems that transmit GPCR-mediated changes in cell behavior. The essential molecular events that GPCRs use to govern such a wide range of biological events seem elusive because of their apparent complexity. It emphasizes that the complexity of known GPCR-initiated signals is likely not to exist in one single cell type; that the signaling pathways available to GPCRs in a particular tissue are likely to be much more limited. However, because of the vast signaling potential of GPCRs, these critical cell-specific transduction pathways are in danger of being overridden by deregulated mechanisms that are sensitive to GPCRs. Thus, the study also focuses on mechanisms that enforce GPCR signaling fidelity to physiological pathways as a barrier against GPCR-induced pathological outcomes such as cell transformation. Recently gained understanding of GPCR-driven intracellular signaling networks and how they are organized by scaffolding proteins will provide a more global view of the general systems by which these receptors exert their numerous physiological roles, and elucidate their role in many pathological conditions.
Fast calculation of Laurent expansions for matrix inverses

Previously described algorithms for calculating the Laurent expansion of the inverse of a matrix-valued analytic function become impractical already for singularity orders as low as around p=6, since they require over O(28p) matrix multiplications and correspondingly large amounts of memory. In place of using mathematically exact recursions, we show that, for floating point calculations, a rational approximation approach can avoid this cost barrier without any significant loss in accuracy.
Timing Rules for Synaptic Plasticity Matched to Behavioral Function

It is widely assumed that the complexity of neural circuits enables them to implement diverse learning tasks using just a few generic forms of synaptic plasticity. In contrast, we report that synaptic plasticity can itself be precisely tuned to the requirements of a learning task. We found that the rules for induction of long-term and single-trial plasticity at parallel fiber-to-Purkinje cell synapses vary across cerebellar regions. In the flocculus, associative plasticity in vitro and in vivo is narrowly tuned for an interval of ∼120 ms, which compensates for the specific processing delay for error signals to reach the flocculus during oculomotor learning. In the vermis, which supports a range of behavioral functions, plasticity is induced by a range of intervals, with individual cells tuned for different intervals. Thus, plasticity at a single, anatomically defined type of synapse can have properties that vary in a way that is precisely matched to function.
Accelerated ferumoxytol-enhanced 4D multiphase, steady-state imaging with contrast enhancement (MUSIC) cardiovascular MRI: validation in pediatric congenital heart disease.

The purpose of this work was to validate a parallel imaging (PI) and compressed sensing (CS) combined reconstruction method for a recently proposed 4D non-breath-held, multiphase, steady-state imaging technique (MUSIC) cardiovascular MRI in a cohort of pediatric congenital heart disease patients. We implemented a graphics processing unit accelerated CS-PI combined reconstruction method and applied it in 13 pediatric patients who underwent cardiovascular MRI after ferumoxytol administration. Conventional breath-held contrast-enhanced magnetic resonance angiography (CE-MRA) was first performed during the first pass of ferumoxytol injection, followed by the original MUSIC and the proposed CS-PI MUSIC during the steady-state distribution phase of ferumoxytol. Qualities of acquired images were then evaluated using a four-point scale. Left ventricular volumes and ejection fractions calculated from the original MUSIC and the CS-PI MUSIC were also compared with conventional multi-slice 2D cardiac cine MRI. The proposed CS-PI MUSIC reduced the imaging time of the MUSIC acquisition to 4.6 ± 0.4 min from 8.9 ± 1.2 min. Computationally intensive image reconstruction was completed within 5 min without interruption of sequential clinical scans. The proposed method (mean 3.3-4.0) provided image quality comparable to that of the original MUSIC (3.2-4.0) (all P ≥ 0.42), and better than conventional breath-held first-pass CE-MRA (1.1-3.3) for 13 anatomical structures (all P ≤ 0.0014) with good inter-observer agreement (κ > 0.46). The calculated ventricular volumes and ejection fractions from both original MUSIC (r > 0.90) and CS-PI MUSIC (r > 0.85) correlated well with 2D cine imaging. In conclusion, PI and CS were successfully incorporated into the 4D MUSIC acquisition to further reduce scan time by approximately 50% while maintaining highly comparable image quality in a clinically practical reconstruction time.
Introducing a Text Annotation Tool (OntoMate), Assisting Curation at Rat Genome Database

In model organism databases, one of the important tasks is to convert free text in biomedical literature to a structured data format. Curators in the Rat Genome Database (RGD), the primary source of rat genomic, genetic, and physiological data, spend considerable time and effort curating functional information for genes, QTLs, and strains from the literature. To increase curation efficiency and prioritize literature for data extraction OntoMate was developed at RGD. This tool tags Pubmed abstracts and full papers in PubMed Central with genes, gene names, gene mutations, organism name and terms from 16 ontologies/vocabularies, including synonyms and aliases, used to represent functional information. The tagging process is currently a dictionary based method that is going to be improved by machine learning techniques such as CRF and/or SVM to handle ambiguous terms. An interface allows the user to create a complex query incorporating terms from any of the ontologies, gene symbols, organisms, dates and other parameter. The results return abstracts along with all tagged parameters indicated in the query, along with children of the ontology terms chosen. Results can be further filtered by the user through a panel that lists organisms, genes and diseases with number of paper returned. Abstracts and papers are provided in rank order by relevance to the query. The tool is fully integrated into curation software so citations and abstracts can be automatically entered into the RGD database and given ID and genes and ontology terms in the tags can be checked to create annotations linked to the paper. The system was built with a scalable and open architecture, and literature is updated daily. This tool uses Solr indexing technology and categorizes papers based on a relevance score. It indexes and tags more than two million Pubmed Central papers and more than 23 million abstracts. With the use of bioNLP tools, RGD has added more automation to its curation workflow.
Health Care Resource Use in Patients With and Without 22q11.2 Deletion Syndrome Undergoing Sphincter Pharyngoplasty for Velopharyngeal Insufficiency.

Importance The use of health care resources in patients with velopharyngeal insufficiency undergoing sphincter pharyngoplasty is unknown. Objectives To examine the use of health care resources by patients with velopharyngeal insufficiency who have undergone sphincter pharyngoplasty and investigate whether patients with 22q11.2 deletion syndrome (22qDS) had a longer length of stay, increased cost of admission, and higher number of complications. Design, Setting, and Participants Using data from the Kids’ Inpatient Database for January 1 to December 31, 2012, we retrospectively analyzed all patients undergoing pharyngoplasty for velopharyngeal insufficiency. In addition, patients were analyzed according to whether or not they had 22qDS. Data were analyzed from January 1 to December 31, 2012. Main Outcomes and Measures Total cost of admission, length of stay, number of procedures, and number of complications. Results There were 687 patients: 90 with 22qDS (mean [SD] age, 6.4 [2.7] years; 43 males and 47 females) and 597 without 22qDS (mean [SD] age, 7.5 [4.1] years; 326 males and 271 females). In both groups, patients were predominantly white, had private insurance, were treated in a children’s hospital, and were from either the West or Midwest. The median length of stay (2.0 [interquartile range (IQR), 1.0-3.9] vs 1.0 [IQR, 1.0-2.0] days; 95% CI, 1.0-2.0) and total cost of admission ($9269.24 [IQR, $6800.65-$13 189.25] vs $6936.95 [IQR, $5036.71-$9054.98]; 95% CI, $6791.83-$7542.47) were higher for the group with 22qDS than those without 22qDS, while there was no significant difference in the number of procedures performed. In addition, the median number of diagnoses (5.0 [IQR, 3.0-9.0] vs 3.0 [IQR, 2.0-5.0]; 95% CI, 3.0-4.0) and number of chronic conditions (3.0 [IQR, 2.0-5.0] vs 2.0 [IQR, 1.0-2.0]; 95% CI, 2.0-2.0) were higher for the group with 22qDS than those without 22qDS. Furthermore, results of a multiple regression model showed that 22qDS was positively associated with both length of stay (B = 0.92; 95% CI, 0.59-1.24) and total cost (B = $3458.78; 95% CI, $2051.09-$4866.46). Conclusions and Relevance This study demonstrates that patients with 22qDS undergoing sphincter pharyngoplasty for velopharyngeal insufficiency have more complex medical conditions and require more health care resources than patients without 22qDS.
Improved production of single domain antibodies with two disulfide bonds by co-expression of chaperone proteins in the Escherichia coli periplasm

Single domain antibodies are recombinantly expressed variable domains derived from camelid heavy chain antibodies. Natural single domain antibodies can have noncanonical disulfide bonds between their complementarity-determining regions that help position the binding site. In addition, engineering a second disulfide bond serves to tie together β-sheets thereby inhibiting unfolding. Unfortunately, the additional disulfide bond often significantly decreases yield, presumably due to formation of incorrect disulfide bonds during the folding process. Here, we demonstrate that inclusion of the helper plasmid pTUM4, which results in the expression of four chaperones, DsbA, DsbC, FkpA, and SurA, increased yield on average 3.5-fold for the nine multi-disulfide bond single domain antibodies evaluated. No increase in production was observed for single domain antibodies containing only the canonical disulfide bond.
Counselor Perceptions: Let Us Do Our Job!

Elementary and Middle school administrators continually struggle with developing instructional programs that will address the academic and human developmental levels of the students in their care. Addressing the human development and the academic issues related to the elementary and middle school student is only a small percentage of the attention required for that student. Many students at the elementary and middle school levels encounter issues related to social and emotional development that are often overwhelming and many times detrimental to the academic development of those students. School administrators address those issues by utilizing the existing infrastructure of the schools. One of the key components of the school infrastructure is the school counselor. In some situations, school counselors are being required to perform duties outside the realm of their perceived responsibilities. This study was conducted to ascertain school counselor perceptions with respect to job performance, expectations, satisfaction and responsibility. The results of the study indicated that the counselors involved in the study believed that they are being required to perform duties outside the realm of their responsibilities and that the performance of these duties has an impact on their effectiveness as school counselors.
O NACIONAL COSMOPOLITISMO DE MACHADO DE ASSIS

Levando a cabo uma releitura do artigo de Machado de Assis “Noticia da atual literatura brasileira. Instinto de nacionalidade.” engajada nas nocoes de literatura nacional e mundo literario , discutiremos os respectivos regimes de funcionamento e determinacoes mutuas destes conceitos na optica e no contexto historico do autor. Veremos que na sua percepcao do mundo literario do seu tempo estao incluidas as dificuldades ligadas a posicao (periferica) da literatura brasileira e as questoes especificas que tem para resolver nesse espaco, nomeadamente a necessidade de afirmacao nele de um laco constitutivo entre a sua lingua (em rigor, certos linguajares especificos da lingua) e um capital literario de determinada regiao geografica que ainda e pobre e carece de corporizacao.
Effects of K-IBA Rates and Timing on Rooting Percentage and Root Quality of Amelanchier laevis

Abstract Semi-hardwood cuttings of Amelanchier laevis Weig. were taken on May 24, June 15, and July 26 and treated with five different rates of K-IBA: 2,500, 5,000, 10,000, 15,000, and 25,000 ppm. Rooting percentage and root quality were highest in cuttings taken in Mayor June. Root quality was significantly higher when cuttings were treated with higher rates of IBA.
Synthesis of Heat-Induced Separation Networks for Condensation of Volatile Organic Compounds

Mass-exchange operations employ mass-separating agents to induce the transfer of targeted components from the rich phase to the lean phase. Another important class of separations involves the use of energy-separating agents to induce separations. This chapter deals with the optimal design of heat-induced separation networks (HISENs). Examples of HISENs include condensation, crystallization, and drying. The chapter will focus on condensation because of its importance in recovering volatile organic compounds (VOCs), which are among the most serious atmospheric pollutants. A shortcut graphical method will be presented. This method is primarily based on the work of Richburg and El-Halwagi (1995). More generalized procedures and broader applications can be found in the literature.
Braque and Kokoschka: Brain Tissue Injury and Preservation of Artistic Skill.

The neural underpinning of art creation can be gleaned following brain injury in professional artists. Any alteration to their artistic productivity, creativity, skills, talent, and genre can help understand the neural underpinning of art expression. Here, two world-renown and influential artists who sustained brain injury in World War I are the focus, namely the French artist Georges Braque and the Austrian artist Oskar Kokoschka. Braque is particularly associated with Cubism, and Kokoschka with Expressionism. Before enlisting, they were already well-known and highly regarded. Both were wounded in the battlefield where they lost consciousness and treated in European hospitals. Braque’s injury was in the left hemisphere while Kokoschka’s was in the right hemisphere. After the injury, Braque did not paint again for nearly a whole year while Kokoschka commenced his artistic works when still undergoing hospital treatment. Their post-injury art retained the same genre as their pre-injury period, and their artistic skills, talent, creativity, and productivity remained unchanged. The quality of their post-injury artworks remained highly regarded and influential. These neurological cases suggest widely distributed and diffuse neural control by the brain in the creation of art.