cssi/SciSciGPT-SciSciNet huggingface dataset:
Scientific evidence based rare disease research discovery with research funding data in knowledge graph.

BACKGROUND Limited knowledge and unclear underlying biology of many rare diseases pose significant challenges to patients, clinicians, and scientists. To address these challenges, there is an urgent need to inspire and encourage scientists to propose and pursue innovative research studies that aim to uncover the genetic and molecular causes of more rare diseases and ultimately to identify effective therapeutic solutions. A clear understanding of current research efforts, knowledge/research gaps, and funding patterns as scientific evidence is crucial to systematically accelerate the pace of research discovery in rare diseases, which is an overarching goal of this study. METHODS To semantically represent NIH funding data for rare diseases and advance its use of effectively promoting rare disease research, we identified NIH funded projects for rare diseases by mapping GARD diseases to the project based on project titles; subsequently we presented and managed those identified projects in a knowledge graph using Neo4j software, hosted at NCATS, based on a pre-defined data model that captures semantics among the data. With this developed knowledge graph, we were able to perform several case studies to demonstrate scientific evidence generation for supporting rare disease research discovery. RESULTS Of 5001 rare diseases belonging to 32 distinct disease categories, we identified 1294 diseases that are mapped to 45,647 distinct, NIH-funded projects obtained from the NIH ExPORTER by implementing semantic annotation of project titles. To capture semantic relationships presenting amongst mapped research funding data, we defined a data model comprised of seven primary classes and corresponding object and data properties. A Neo4j knowledge graph based on this predefined data model has been developed, and we performed multiple case studies over this knowledge graph to demonstrate its use in directing and promoting rare disease research. CONCLUSION We developed an integrative knowledge graph with rare disease funding data and demonstrated its use as a source from where we can effectively identify and generate scientific evidence to support rare disease research. With the success of this preliminary study, we plan to implement advanced computational approaches for analyzing more funding related data, e.g., project abstracts and PubMed article abstracts, and linking to other types of biomedical data to perform more sophisticated research gap analysis and identify opportunities for future research in rare diseases.
Breast cancer vaccines for treatment and prevention

Breast cancer is immunogenic and a variety of vaccines have been designed to boost immunity directed against the disease. The components of a breast cancer vaccine, the antigen, the delivery system, and the adjuvant, can have a significant impact on vaccine immunogenicity. There have been numerous immunogenic proteins identified in all subtypes of breast cancer. The majority of these antigens are weakly immunogenic nonmutated tumor-associated proteins. Mutated proteins and neoantigen epitopes are found only in a small minority of patients and are enriched in the triple negative subtype. Several vaccines have advanced to large randomized Phase II or Phase III clinical trials. None of these trials met their primary endpoint of either progression-free or overall survival. Despite these set-backs investigators have learned important lessons regarding the clinical application of breast cancer vaccines from the type of immune response needed for tumor eradication, Type I T-cell immunity, to the patient populations most likely to benefit from vaccination. Many therapeutic breast cancer vaccines are now being tested in combination with other forms of immune therapy or chemotherapy and radiation. Breast cancer vaccines as single agents are now studied in the context of the prevention of relapse or development of disease. Newer approaches are designing vaccines to prevent breast cancer by intercepting high-risk lesions such as ductal carcinoma in situ to limit the progression of these tumors to invasive cancer. There are also several efforts to develop vaccines for the primary prevention of breast cancer by targeting antigens expressed during breast cancer initiation.
Sparse Proximal Support Vector Machines for feature selection in high dimensional datasets

Sparse Proximal Support Vector Machines is an embedded feature selection method.sPSVMs removes more than 98% of features in many high dimensional datasets.An efficient alternating optimization technique is proposed.sPSVMs induces class-specific local sparsity. Classification of High Dimension Low Sample Size (HDLSS) datasets is a challenging task in supervised learning. Such datasets are prevalent in various areas including biomedical applications and business analytics. In this paper, a new embedded feature selection method for HDLSS datasets is introduced by incorporating sparsity in Proximal Support Vector Machines (PSVMs). Our method, called Sparse Proximal Support Vector Machines (sPSVMs), learns a sparse representation of PSVMs by first casting it as an equivalent least squares problem and then introducing the l1-norm for sparsity. An efficient algorithm based on alternating optimization techniques is proposed. sPSVMs remove more than 98% of features in many high dimensional datasets without compromising on generalization performance. Stability in the feature selection process of sPSVMs is also studied and compared with other univariate filter techniques. Additionally, sPSVMs offer the advantage of interpreting the selected features in the context of the classes by inducing class-specific local sparsity instead of global sparsity like other embedded methods. sPSVMs appear to be robust with respect to data dimensionality. Moreover, sPSVMs are able to perform feature selection and classification in one step, eliminating the need for dimensionality reduction on the data. To that end, sPSVMs can be used for preprocessing free classification tasks.
Midsize and SUV Vehicle Simulation Results for Plug-In HEV Component Requirements

Because Plug-in Hybrid Electric Vehicles (PHEVs) substitute electrical power from the utility grid for fuel, they have the potential to reduce petroleum use significantly. However, adoption of PHEVs has been hindered by expensive, low-energy batteries. Recent improvements in Li-ion batteries and hybrid control have addressed battery-related issues and have brought PHEVs within reach. The FreedomCAR Office of Vehicle Technology has a program that studies the potential benefit of PHEVs. This program also attempts to clarify and refine the requirements for PHEV components. Because the battery appears to be the main technical barrier, both from a performance and cost perspective, the main efforts have been focused on that component. Working with FreedomCAR energy storage and vehicle experts, Argonne National Laboratory (Argonne) researchers have developed a process to define the requirements of energy storage systems for plug-in applications. This paper describes the impact of All Electric Range (AER), drive cycle, and control strategy on battery requirements for both the midsize and SUV classes of vehicles.
Marginal zone B cells contribute to autoimmunity in the NZM2410 lupus prone mouse model.

Lupus is an autoimmune disease in which the affected individual generates antibodies (Abs) against nuclear antigens such as DNA. Our NZM2410-derived triple congenic (TC) model of lupus expresses 3 previously characterized lupus susceptibility loci. We have previously shown that the breach of follicular exclusion of TC MZB cells is associated with disease progression. The production of nuclear autoAbs occurred in tandem with a large influx of TC MZB cells in the follicles. We also found an expansion of MZB cells in TC mice as compared to non-autoimmune B6 mice that occurs prior to the production of anti-DNA autoAbs, further suggesting that MZB cells may contribute to autoimmunity. MZB cell expansion is associated with the upregulation of Notch2 signaling in these cells. Adoptive transfer of TC or B6 splenic B cells into B6.Rag1-/- recipients indicated no difference in the homeostatic expansion of MZB cells from either donor strain, whether the recipients were treated or not with CpG. However, CpG-treated recipients of TC B cells produced more anti-ssDNA IgM than recipients of B6 B cells. Our transfer results showed that although TC MZB cells do not expand more than B6 MZB cells in a lymphopenic host, TC splenic B cells produce higher level of anti-ssDNA IgM in response to CpG stimulation. Further characterization of the TC MZB cells will determine more precisely how they contribute to autoimmunity.
Biochemical and Biological Characterization of Tumor‐Associated Mutations of p110α

Abstract Signaling by class I phosphatidylinositol 3‐kinase (PI3K) controls cell growth, replication, motility, and metabolism. The PI3K pathway commonly shows gain of function in cancer. Two small GTPases, Rheb (Ras homolog enriched in brain) and Ras (rat sarcoma viral oncogene), play important roles in PI3K signaling. Rheb activates the TOR (target of rapamycin) kinase in a GTP‐dependent manner; it links TOR to upstream signaling components, including the tuberous sclerosis complex (TSC) and Akt (homolog of the Akt8 murine lymphoma viral oncoprotein). Constitutively active, GTP‐bound Rheb is oncogenic in cell culture, and activity that requires farnesylation. Ras activates PI3K by recruitment to the plasma membrane and possibly by inducing a conformational change in the catalytic subunit p110 of PI3K. In return, Ras signaling through the MAP kinase (MAPK) pathway is activated by PIP3, the product of PI3K. Loss of Ras function can interfere with PI3K signaling. Various lines of evidence suggest complementary roles for PI3K and MAPK signaling in oncogenesis.
Individual and Social Cost-of-Living Indexes

Summary The purpose of this paper is to present an econometric approach to cost-of-living measurement. This approach implements the economic theory of individual cost-of-living measurement pioneered by Konus [1939] almost six decades ago. In this paper we develop and implement a completely parallel theory of social cost-of-living measurement. Our approach to cost-of-living measurement is based on an econometric model of aggregate consumer behavior. The novel feature of this model is that systems of individual demand functions can be recovered uniquely from the system of aggregate demand functions. We derive cost-of-living indexes for individual households from systems of individual demand functions. Our key innovation in the economic theory of cost-of-living measurement is the introduction of an explicit social welfare function. Our social welfare function incorporates measures of individual welfare from our econometric model. In addition, this social welfare function employs normative criteria for evaluating transfers among individuals. Given measures of individual welfare from our econometric model, we can express the level of social welfare as a function of prices and of total expenditures of all consuming units. We present methods for translating changes in prices into measures of change in the social cost-of-living. Our definitions of social and individual cost-of-living indexes are perfectly analogous. Finally, we extend the concept of a social cost-of-living index to groups of consuming units with common demographic characteristics. Our definition of the group cost-of-living index is analogous to the definition of a social cost-of-living index. To implement a group cost-of-living index we require a group welfare function that is analogous to a social welfare function.
Integrating‐Ramp A/D Converter

This article has no abstract. Keywords: integrating-ramp A/D converter; pulse-duration signal
Michael Oakeshott, Wendy Brown, and Paradoxes of Anti-moralism

British philosopher Michael Oakeshott is well-known for a critique of rationalistic moral idealism. He has sometimes been charged with conservatism, since some of the moralisms he criticizes are leftist or socialist. Yet self-described progressive thinker Wendy Brown also criticizes moralism in politics, on some of the same grounds. Contributors to recent debates about moralism have attempted to give advice on how to avoid it, but it is one of those vices one is much more likely to see in others than identify in oneself. A return to some aspects of Oakeshott’s philosophy helps clear up what the problems are and provide some advice to the ongoing debate.
She makes me brave: The emergence of intimacy in gameplay

This paper investigates the complex relationship between intimacy and play, and offers an empirical analysis of how intimacy emerges in a playful digital environment (i.e., Audition). Audition is a non-violent, non-fantasy dance battle Multiplayer Online Game (MOG) that has many Asian and female players, and provides a sophisticated in-game marriage system. Based on players’ self-reports posted on public online forums and in-depth interview data from 35 Audition players, this study shows that Audition marriage is more than a playful game feature for many players. Instead, players experience genuine, meaningful intimate relationships there, and consider their in-game marriage an emergent learning process to satisfy their social and emotional needs. This study contributes to understanding interpersonal dynamics forged around technological objects in digital environments, which is important for designing Intimate (Ubiquitous) Computing and the next generation of ICTs.
Degree-one maps of handlebodies

Abstract The major result of this paper answers a question raised by Waldhausen in 1970 by showing that if M and N are orientable three-dimensional handlebodies with genus(M) ⪢ genus(N) ⪢ 1, then there exist an infinite number of inequivalent proper degree-one maps from M to N.
Acquired Aortic Cusp Fusion After Chronic Left Ventricular Assist Device Support

Explanted hearts from patients with chronic left ventricular assist device (LVAD) support have shown the presence of aortic cusp fusion, which results in valvular stenosis and may complicate weaning of a LVAD. This is the first report of aortic cusp fusion diagnosed solely by transesophageal echocardiography (TEE) in vivo in a patient on chronic LVAD support. Under intraoperative TEE guidance, a 41-year-old woman underwent an attempted explantation of a LVAD, which had been implanted 8 months before for dilated cardiomyopathy. When LVAD support was discontinued, previously normal left ventricular function deteriorated, and aortic stenosis from aortic valve cusp fusion was documented by TEE. The explantation procedure was abandoned. This case demonstrates the utility of intraoperative TEE in the evaluation of aortic valvular anatomy and function in patients wtih chronic LVAD support.
Oriental beetles (Coleoptera : Scarabaeidae) : Current distribution in the United States and optimization of monitoring traps

Cooperators in 20 states used traps baited with (Z) -7-tetradecen-2-one to determine the current distribution of oriental beetles in the United States. New areas where beetles were found include Cape Cod and central Massachusetts (widespread), Delaware, (widespread), southeastern New Hampshire, North Carolina (around Asheville), Ohio (around Painesville on Lake Erie), Maryland (widespread), New Jersey (widespread in blueberry plantings), and Virginia (around Richmond and Arlington). Studies on pheromone concentration and release methods showed that there was no significant difference in beetle captures between 1,000 μg released from rubber septa and 3,000 μg released from polyethylene pellets. Significantly fewer beetles were caught in traps baited with 10 or 100 μg than in traps baited with 1,000 μg released from rubber septa or and 3,000 μg released from polyethylene pellets. There was no significant difference in captures between Trece and Fuji trap designs where 3,000 μg was released from polyethylene pellets in 7 out of 8 comparisons. There was no significant difference in beetle captures where 100 or 1,000 μg pheromone was released from rubber versus polyethylene septa. There was a significant increase in beetle captures where the funnel rims of traps were placed at ground level versus 30 cm above ground level.
Distinctive local features of visual patterns

Random polygons were generated in a manner that permitted tests of whether unfamiliar patterns were discriminated on the basis of their longest lines or most complex local features. Results showed that subjects tended to base discrimination on the most complex local features of complex visual patterns. This tendency may reflect the greater variability and higher information content of those features.
Woody biomass in the U.S. Cornbelt? Constraints and opportunities in the supply.

The U.S. is clearly entering a new era of liquid fuel production; one that will be characterized by increasing degrees of renewable raw materials. Woody biomass is an especially compelling feedstock choice where available. Significant questions, however, exist regarding the potential of some landscapes to provide this feedstock. In an effort to answer these questions, we performed an exploratory spatial assessment of woody biomass production and supply capabilities in two-ecoregions Mississippi River corridor within the US Cornbelt. We used existing forest/timber inventories and conducted in-depth interviews with large regional sawmills to understand the accessibility of woody biomass from natural forests, availability of and general costs associated with woody biomass in the existing timber industry, and potential for production from short-rotation woody crop plantations. On an annual basis, taking into account only the annual net growth of non-sawlog species the Midwest Driftless Area currently produces 3.14 times the raw material required by a hypothetical facility using one-half million dry tons of woody biomass per year. Although allocated over a larger area, the Central Dissected Till Plain produces 3.94 times the required material. Throughout the entire region there would be an additional lower bound estimate of 107,000 dry Mg from easily transportable sawmill residues. The ecological state of US Cornbelt forests stand to gain from a developed market for woody biomass as proper woodland management to harvest trees, preserve wildlife, and reduce risk from disease, pests, and invasive species typically involves harvesting the low-value trees that will by and large drive the woody biomass system.
Methylation of H3-Lysine 79 Is Mediated by a New Family of HMTases without a SET Domain

Abstract The N-terminal tails of core histones are subjected to multiple covalent modifications, including acetylation, methylation, and phosphorylation [1]. Similar to acetylation, histone methylation has emerged as an important player in regulating chromatin dynamics and gene activity [2–4]. Histone methylation occurs on arginine and lysine residues and is catalyzed by two families of proteins, the protein arginine methyltransferase family and the SET-domain-containing methyltransferase family [3]. Here, we report that lysine 79 (K79) of H3, located in the globular domain, can be methylated. K79 methylation occurs in a variety of organisms ranging from yeast to human. In budding yeast, K79 methylation is mediated by the silencing protein DOT1. Consistent with conservation of K79 methylation, DOT1 homologs can be found in a variety of eukaryotic organisms. We identified a human DOT1-like (DOT1L) protein and demonstrated that this protein possesses intrinsic H3-K79-specific histone methyltransferase (HMTase) activity in vitro and in vivo. Furthermore, we found that K79 methylation level is regulated throughout the cell cycle. Thus, our studies reveal a new methylation site and define a novel family of histone lysine methyltransferase.
Edge Detection In Cytology Using Morphological Filters

ABSTRACT A technique for the semi-automatic detection of cell and nuclear contours in cytological specimens is presented. Gray level images are viewed as stacked binary bit plane images with each bit plane image representing the effect of thresholding the gray level image with multiple gray level windows. A binary morphological edge detector is employed to identify edges on selected bit planes. A simple contour tracking algorithm is used to identify the most likely cell and nuclear contours which are presented to the user for verification._K_ INTRODUCTIONThe main purpose of cytology is to differentiate between normal, reactive and malignant cells; if malignant cells have been found, to determine the precise type of tumor and the prognosis of optimal treatment. This is routinely done by trained pathologist observing the cell morphology under a microscope and applying years of accumulated experience.Features which trained pathologist indicate are important in diagnostic processes are the size and shape of the nucleus, ratio of nuclear area to cytoplasm area, texture of the chromatin, and coloration of the cytoplasm. Accurate segmentation of the cell and its nucleus is important because the contours so identified are used to extract the quantitative features used for classification. Thus, errors in the contours will result in greater parameter variance derived from the contour and may result in classification errors.2^ BACKGROUNDMathematical morphology is an approach to image processing based on set theoretic concepts of shape. It was formalize at the Ecole de Mine in Paris in the mid 1970! s by G. Matheron (1975) and extended by J. Serra (1982). Basically, morphological image processing is the analysis of the geometrical relationship between the image and a
VERIFICATION OF ANAEROBIC BIOFILM MODEL FOR PHENOL DEGRADATION WITH SULFATE REDUCTION

A mathematical model was developed to describe phenol degradation with sulfate reduction in an anaerobic biofilm process. The model incorporates the mechanisms of diffusive mass transport and Monod kinetics. The model was solved using a combination of the orthogonal collocation method and Gear's method. A pilot-scale column reactor was conducted to verify the model. The batch kinetic tests were independently conducted to determine nine biokinetic coefficients used in the model while shear loss and initial thickness of the biofilm were assumed so that the model simulated the substrate concentration results very well. The removal efficiencies for phenol and sulfate are 98 and 88%, respectively. At a steady-state condition, the experimental data of phenol and sulfate concentrations were higher than those obtained from the model. The reason was that the effect of shear loss became significant as the biofilm grew thicker. The higher shear loss resulted in the more-suspended biomass. The suspended biomass decomposed and released soluble microbial products which increased the substrate effluent concentrations. The procedures presented in this paper could be employed for the design of anaerobic biofilm reactor systems for the biodegradation of multiple substrates.
Effect of manganese on the nuclear magnetic relaxivity of water protons in chloroplast suspensions

Abstract Field dispersion profiles of the proton spin-lattice relaxation rate, T1−1, in chloroplast suspensions show a local maximum near 20 MHz, probably due to bound Mn(II); EDTA extraction eliminates, and MnCl2 addition restores, the paramagnetic relaxivity. Since neither treatment affects water oxidation, the Mn(II) site monitored appears to lie outside the water-splitting enzyme. Intense illumination almost totally suppresses the paramagnetic relaxivity through an electron-transport-dependent mechanism. Previous reports that chloroplast nuclear magnetic relaxivity varies cyclically in flash experiments require reevaluation in terms of the probable role of Mn(II) that is nonfunctional in water oxidation.
The Analytic Hierarchy Process in an uncertain environment: A simulation approach

Abstract Traditionally, decision makers were forced to converge ambiguous judgments to a single point estimate in order to describe a pairwise relationship between alternatives relative to some criterion for use in the Analytic Hierarchy Process (AHP). Since many circumstances exist which make such a convergence difficult, confidence in the outcome of an ensuing AHP synthesis may be reduced. Likewise, when a group of decision makers cannot arrive at a consensus regarding a judgment, some members of the group may simply lose confidence in the overall synthesis if they lack faith in some of the judgments. The AHP utilizes point estimates in order to derive the relative weights of criteria, sub-criteria, and alternatives which govern a decision problem. However, when point estimates are difficult to determine, distributions describing feasible judgments may be more appropriate. Using simulation, we will demonstrate that levels of confidence can be developed, expected weights can be calculated and expected ranks can be determined. It will also be shown that the simulation approach is far more revealing than traditional sensitivity analysis.
Living the sweet (d)Life: public relations, IMC, and diabetes

Purpose – This paper aims to analyze dLife, an integrated media network dedicated to empowering Americans living with diabetes. It shows how dLife's use of integrated marketing communications (IMC), particularly the public relations component, represents an emerging direction in health product and services marketing. Although some have been skeptical about IMC and specifically the public relations role within it, the paper aims to argue that public relations, through sponsorships, helps organizations interested in IMC to create new types of relationships with marketers and patients.Design/methodology/approach – To demonstrate public relations' importance in IMC, dLife's relationship with the changing health marketing landscape is contextualized. Constitutive and empowerment theory is employed to frame a rhetorical analysis of dLife's efforts to target marketers and patients. The rhetorical analysis demonstrates how dLife's rhetorical choices help to shape marketer strategy, patient identity and discursive...
Effect of saving motives and horizon on saving behaviors

Abstract The purpose of this research is to explore saving motives and saving horizon using a large, nationally representative dataset, the Survey of Consumer Finances. The framework is based on prospect theory, in which consumption and saving decisions are based on a reference point rather than on lifetime income. Prospect theory also posits that individuals construct various mental accounts, thereby allowing for households to have multiple saving motives. Since prospect theory does not assume that saving decisions are based on lifetime income, saving horizons are allowed to vary. The emergency and retirement saving motives are found to significantly increase the likelihood of saving regularly. Longer saving horizons are also found to have a highly significant effect on the likelihood of saving, while poor health is shown to have a significantly negative effect on the likelihood of saving. The results show that the saving motives held by households differ by saving horizon, but the exact relationships are unclear. Further research on the link between saving motives, saving horizon, and saving behaviors is needed. It is important for financial professionals and educators to consider a household’s saving goals, saving horizon, and health status when making recommendations or developing financial plans.
Three-dimensional localization of the α and β subunits and of the II-III loop in the skeletal muscle L-type Ca2+ channel.

The L-type Ca2+ channel (dihydropyridine receptor (DHPR) in skeletal muscle acts as the voltage sensor for excitation-contraction coupling. To better resolve the spatial organization of the DHPR subunits (α1s or CaV1.1, α2, β1a, δ1, and γ), we created transgenic mice expressing a recombinant β1a subunit with YFP and a biotin acceptor domain attached to its N- and C- termini, respectively. DHPR complexes were purified from skeletal muscle, negatively stained, imaged by electron microscopy, and subjected to single-particle image analysis. The resulting 19.1-Å resolution, three-dimensional reconstruction shows a main body of 17 × 11 × 8 nm with five corners along its perimeter. Two protrusions emerge from either face of the main body: the larger one attributed to the α2-δ1 subunit that forms a flexible hook-shaped feature and a smaller protrusion on the opposite side that corresponds to the II-III loop of CaV1.1 as revealed by antibody labeling. Novel features discernible in the electron density accommodate the atomic coordinates of a voltage-gated sodium channel and of the β subunit in a single docking possibility that defines the α1-β interaction. The β subunit appears more closely associated to the membrane than expected, which may better account for both its role in localizing the α1s subunit to the membrane and its suggested role in excitation-contraction coupling.
A Unique Case of Malignant Pleuropericardial Effusion: HHV-8-Unrelated PEL-Like Lymphoma-A Case Report and Review of the Literature.

Primary effusion lymphoma (PEL) or body cavity lymphoma is a rare type of extra nodal lymphoma of B-cell origin that presents as lymphomatous effusion(s) without any nodal enlargement or tumor masses. It belongs to the group of AIDS related non-Hodgkin's lymphomas. First described in 1996 in HIV infected individuals who were coinfected with Kaposi's sarcoma-associated herpesvirus (KSHV) or HHV-8 virus, it was included as a separate entity in WHO classification of tumors of hematopoietic and lymphoid tissue in the year 2001. The definition included association with HHV-8 virus as a mandatory diagnostic criterion. However, cases were later reported where PEL-like disease process was diagnosed in HHV-8 negative patients. This was eventually recognized as a rare but distinct entity termed as “HHV-8-unrelated PEL-like lymphoma”. Herein, we are reporting a case of an elderly patient who presented with a large pleuropericardial effusion and was eventually diagnosed with this entity. Till date, only around 50 cases of HHV-8-unrelated PEL-like lymphoma have been reported and our case being EBV, HIV, and Hepatitis C negative makes it very unique and rare occurrence. We are also presenting a review of relevant literature focused mainly on comparing outcomes in patients treated with and without chemotherapy.
Convection Initiation by Density Currents: Role of Convergence, Shear, and Dynamical Organization

Abstract Steady-state analytic models establish two key points concerning the impact of vertical shear on density currents and the implication for convection initiation. First, shear decreases the horizontal convergence, and therefore the mean ascent, associated with downshear propagating currents. Second, shear has a basic effect on the dynamical organization. If the downshear current travels at the speed of the ambient flow at a critical (steering) level, an overturning circulation provides deep lifting. Although mean ascent is increased by shear in the case of upshear propagating currents, the lifting is comparatively shallow because jumplike ascent occurs rather than deep overturning. The convection initiation mechanism involving the downshear current is therefore very different from the upshear case. These basic principles are borne out in two-dimensional numerical simulations. Density currents generated by a stationary cold source imposed on an initially horizontally homogeneous, sheared, and neutra...
The phototoxicity of benzo[a]pyrene in the green alga Selenastrum capricornutum

The effects of selected polycyclic aromatic hydrocarbons (PAHs) on the growth of the green alga Selenastrum capricornutum in three light regimens were examined. In gold fluorescent light, benzo[a]pyrene (BaP) at 12 mg/liter (48 mumole/liter), benz[a]anthracene (BaA) at 40 mg/liter (175 mumole/liter), anthracene (A) at 40 mg/liter (224 mumole/liter), and 13 metabolites of BaP each at 40 micrograms/liter had no effect on algal growth. In cool-white fluorescent light, 30% inhibition of algal growth occurred with 0.1 mumole/liter BaP, 8.0 mumole/liter BaA, and 40 mumole/liter A. BaP at 0.16 mg/liter (0.64 mumole/liter) totally inhibited growth. BaP concentrations an order of magnitude lower inhibited algal growth in fluorescent blacklight. In cool-white light, 5 of 13 metabolites of BaP (each 40 micrograms/liter) inhibited algal growth: 3,6-quinone; 6-hydroxy; 9-hydroxy; 3-hydroxy; and 1,6-quinone. Based on these results, PAHs and metabolites of BaP are selectively phototoxic to S. capricornutum due to the incident light intensity below 550 nm.
A mechanism of cyclin D1 action encoded in the patterns of gene expression in human cancer.

Abstract Here we describe how patterns of gene expression in human tumors have been deconvoluted to reveal a mechanism of action for the cyclin D1 oncogene. Computational analysis of the expression patterns of thousands of genes across hundreds of tumor specimens suggested that a transcription factor, C/EBPβ/Nf-Il6, participates in the consequences of cyclin D1 overexpression. Functional analyses confirmed the involvement of C/EBPβ in the regulation of genes affected by cyclin D1 and established this protein as an indispensable effector of a potentially important facet of cyclin D1 biology. This work demonstrates that tumor gene expression databases can be used to study the function of a human oncogene in situ.
Robust antigen specific th17 T cell response to group A Streptococcus is dependent on IL-6 and intranasal route of infection.

Group A streptococcus (GAS, Streptococcus pyogenes) is the cause of a variety of clinical conditions, ranging from pharyngitis to autoimmune disease. Peptide-major histocompatibility complex class II (pMHCII) tetramers have recently emerged as a highly sensitive means to quantify pMHCII-specific CD4+ helper T cells and evaluate their contribution to both protective immunity and autoimmune complications induced by specific bacterial pathogens. In lieu of identifying an immunodominant peptide expressed by GAS, a surrogate peptide (2W) was fused to the highly expressed M1 protein on the surface of GAS to allow in-depth analysis of the CD4+ helper T cell response in C57BL/6 mice that express the I-Ab MHCII molecule. Following intranasal inoculation with GAS-2W, antigen-experienced 2W:I-Ab-specific CD4+ T cells were identified in the nasal-associated lymphoid tissue (NALT) that produced IL-17A or IL-17A and IFN-γ if infection was recurrent. The dominant Th17 response was also dependent on the intranasal route of inoculation; intravenous or subcutaneous inoculations produced primarily IFN-γ+ 2W:I-Ab+ CD4+ T cells. The acquisition of IL-17A production by 2W:I-Ab-specific T cells and the capacity of mice to survive infection depended on the innate cytokine IL-6. IL-6-deficient mice that survived infection became long-term carriers despite the presence of abundant IFN-γ-producing 2W:I-Ab-specific CD4+ T cells. Our results suggest that an imbalance between IL-17- and IFN-γ-producing CD4+ T cells could contribute to GAS carriage in humans.
Esophageal Crohn's disease: medical management and correlation between clinical, endoscopic, and histologic features.

SUMMARY : Esophageal involvement in patients with Crohn's disease, initially thought to be rare, has been documented with increasing frequency in both retrospective and prospective studies. However, there is no documented standardized medical regimen for treatment of these patients. We report five cases of esophageal Crohn's disease as well as a review of the literature emphasizing therapeutic approach and increased incidence of corticosteroid dependence in these patients. In the past, patients with significant esophageal disease and symptoms have been surgical candidates. We recommend that all patients with symptoms of dysphagia, odynophagia, chest pain, or dyspepsia with documented esophageal Crohn's disease should receive H2 receptor antagonists as part of their medical regimen. In addition, immunosuppressant agents should be considered as adjuvant therapy in steroid-dependent patients with esophageal disease involvement.
Performance analysis of synchronous downlink MC-CDMA with precoding and frequency offset

We analyze the performance of code division multiple access (CDMA) system with multicarrier (MC) that employs precoding in synchronous downlink channels. Even though considerable efforts are undergoing for frequency offset estimation and correction, it is inevitable for the system to bear the remaining frequency offset. Therefore it is important to predict accurately the system performance in the presence of the residual frequency offset. We obtain the bit error rate (BER) performance in terms of the number of users, the spreading factor, the number of sub-carriers, and frequency offset. We assume that the spreading factor is equal to the number of sub-carriers, although we can generalize the case. The simulation results show that the BER of MC-CDMA with precoding shows a performance that varies with frequency offset as well as system loading.
Towards measurement of the time-resolved heat release of protein conformation dynamics

We present a way to observe time-resolved heat release using a laminar flow diffusional mixer coupled with a highly sensitive infrared camera which measures the temperature change of the solvent. There are significant benefits to the use of laminar flow mixers for time-resolved calorimetry: (1) The thermal signal can be made position and time- stationary to allow for signal integration; (2) Extremely small volumes (nl/s) of sample are required for a measurement; (3) The same mixing environment can be observed spectroscopically to obtain state occupation information; (4) The mixer allows one to do out of equilibrium dynamic studies. The hope is that these measurements will allow us probe the non-equilibrium thermodynamics as a protein moves along a free energy trajectory from one state to another.
The role of Al in C-S-H: NMR, XRD, and compositional results for precipitated samples

X-ray diffraction, compositional analysis, and 29Si and 27Al MAS NMR spectroscopy of Al-substituted tobermorite-type C�S�H made by precipitation from solution provide significant new insight into the structural mechanisms of Al-substitution in this important and complicated phase. Al occurs in 4-, 5-, and 6-coordination (Al[4], Al[5], and Al[6]) and plays multiple structural roles. Al[4] occurs on the bridging tetrahedra of the drierkette Al�silicate chains, and Al[5] and Al[6] occur in the interlayer and perhaps on particle surfaces. Al does not enter either the central Ca�O sheet or the pairing tetrahedra of the tobermorite-type layers. Al[4] occurs on three types of bridging sites, Q3 sites that bridge across the interlayer; Q2 sites that are charge balanced by interlayer Ca+2, Na+, or H+; and Q2 sites that are most likely charge balanced by interlayer or surface Al[5] and Al[6] through Al[4]�O�Al[5,6] linkages. Although the data presented here are for relatively well-crystallized tobermorite-type C�S�H with C/S ratios less than or equal to 1.2, comparable spectral features for hydrated white cement pastes indicate the presence of similar structural environments in the C�S�H of such pastes, and by implication OPC pastes.
Brain Heart Infusion Broth May Not Be a Required Component for the Decontamination Process for the Isolation of Mycobacterium Avium Subspecies Paratuberculosis from Fecal Samples using ESP® Broth Cultures:

Based on the authors' laboratory experience indicating that increased bacterial contamination in Mycobacterium avium ssp. paratuberculosis (MAP) cultures may be because of the addition of brain heart infusion broth (BHI) during the decontamination process, this study was designed to examine whether BHI is a required component for the isolation of MAP from ESPH broth cultures. Twenty-six National Veterinary Services Laboratory (NVSL) proficiency test samples supplied for the year 2005 were used for the comparison. Two paired sets of samples were processed in the experiment. In one set, the hexadecylpyridinium chloride monohydrate (HPC) and antibiotic brew were prepared in half strength BHI and for the other set, HPC and antibiotic brew were prepared in sterile distilled water. Culture of the 26 samples using the BHI/HPC decontamination method identified 13 (50%) positives, whereas culture using the water/HPC decontamination method identified 14 (54%) positives. The proportions of samples with a positive result did not differ significantly between the 2 decontamination methods. Although in most cases it took longer to identify a positive result by the BHI method, the difference between methods with respect to the number of days to a positive culture result was not statistically significant. Retrospective data collected from the Animal Disease Diagnostic Laboratory, Ohio also suggest that inclusion of BHI in the decontamination protocol may not have any effect on MAP recovery or contamination rate. Elimination of BHI from broth cultures may increase the sensitivity of MAP isolation, and reduce the cost of testing.
Spectroscopy Of Tryptophan Derivatives In Supersonic Expansions: Addition Of Solvent Molecules

One or more solvent molecules have been added to selected derivatives of the amino acid tryptophan. The preparations are carried out using supersonic gas expansion techniques and the samples are probed via laser induced fluorescence spectra and fluorescence lifetime measurements. In tryptophan derivatives that have a polar side chain at the 3-indole position, the solvent complexes formed are different from those previously observed in indoles. Now it is the case that solvent adducts bind overwhelmingly at the polar sites of the 3-indole side chain and not directly on the indole. For at least one derivative, tryptamine, addition of a single water or alcohol molecule results in formation of one solvent-stabilized conformation independent of the starting conformation of the bare derivative molecule.
Analysis and design of two-arm conical spiral antennas

The two-arm, conical spiral antenna is analyzed using the finite-difference time-domain method. The analysis is validated by comparison with measurements of the input impedance and the realized gain. A parametric study is performed with the analysis, and the results from the study are used to produce new design graphs for this antenna. These graphs supplement and extend the existing, mainly empirical, design base for this antenna. Two resistive terminations, intended to improve the low-frequency performance, are examined. One is a termination formed from two lumped resistors, and the other is a new termination formed from a thin disc of resistive material. These terminations are shown to improve the front-to-back ratio and axial ratio for the antenna.
Hormonal determinants of apolipoprotein B,E receptor expression in human liver. Positive association of receptor expression with plasma estrone concentration in middle-aged/elderly women

The relationships of the expression of hepatic low-density lipoprotein (LDL) receptors (apo B,E receptors) to several plasma hormone concentrations were examined in 15 fasted women aged 37-75 years (mean, 57 years), who were undergoing laparotomy for non-neoplastic disease. No subject had clinical or biochemical evidence of familial hypercholesterolemia, renal disease, hepatic disease, or endocrine disease. Hepatic apo B,E receptor expression was quantified in vitro as the EDTA-suppressible binding of 125I-labeled human LDL (15 micrograms protein/ml) by liver homogenate at 37 degrees C; values were 23-75 ng LDL protein/mg cell protein (mean, 47 ng/mg). Receptor expression was strongly correlated with plasma estrone concentration (rs = +0.70, P = 0.035), but was unrelated to the concentrations of testosterone, thyroxine, free triiodothyronine, cortisol, sex hormone-binding globulin (SHBG) or cortisol-binding globulin. Insulin and estradiol concentrations were mostly very low. The correlation of receptor expression with plasma total estrone concentration reflected associations with both the albumin-bound (rs = +0.78, P = 0.014) and unbound (rs = +0.80, P = 0.009) fractions, but not with the SHBG-bound fraction (rs = -0.22, P = 0.574), of this hormone. As the non-SHBG-bound fractions of gonadal steroids are considered to be the biologically active components, these results are consistent with experimental evidence that the synthesis of apo B,E receptors in hepatocytes is stimulated by estrogens, and suggest that circulating estrone may be the major hormonal determinant of receptor expression in fasted middle-aged/elderly women.
Behavior, Consequences, and the Seff: Is all Well that Ends Well?

This study contrasts the consistency, the self-concept, and the new look formulations of cognitive dissonance. Individuals varying in self-concept positivity engaged in either consistent or inconsistent behavior that produced either positive or negative consequences. Individuals with extremely positive self-concepts experienced more dissonance when their inconsistent behavior resulted in positive rather than negative consequences. Individuals with mildly positive self-concepts experienced equally intense dissonance following positive consequences of both inconsistent and consistent behavior Dissonance-reducing activities appeared to be aimed at verification of the initial beliefs about the self;
The effect of order on hydrogen embrittlement of Ni3Fe

Abstract The susceptibility of a cold pressed and sintered Ni 3 Fe alloy to hydrogen embrittlement has been investigated by means of room temperature tensile tests in air and with hydrogen charging in both fully ordered and disordered conditions. Pre-charging with hydrogen and simultaneous charging with hydrogen resulted in a fracture morphology which ranged from a mixed transgranular/intergranular mode to a totally intergranular depending on the type of exposure to hydrogen and the degree of ordering. Associated reductions in the tensile elongations as well as in the ultimate tensile strengths were also observed. Hydrogen diffusion along the grain boundaries led to intergranular fracture concentrated near the surfaces of the alloy when cathodic pre-charging conditions were used, with a deeper penetration due to higher hydrogen diffusivity in the case of the disordered alloy. Susceptibility to hydrogen embrittlement has been found to be largely promoted by ordering under simultaneous charging conditions with a resulting totally intergranular fracture. The results suggest that enhanced diffusitivity of hydrogen to grain boundaries, associated with dislocation transport, occurs in combination with planar slip in the ordered alloy.
A simulation model of the infection cycle of Leishmania mexicana in Neotoma micropus

Abstract A simulation model of transmission of Leishmania mexicana among Neotoma micropus by Lutzomyia anthophora was developed to predict the threshold vector density below which L. mexicana would be eliminated from a population of N. micropus within 2 years. Model results supported the hypothesis that N. micropus is a reservoir of L. mexicana . Leishmania mexicana could be maintained in a focus with an initial annual prevalence of 5.7%, which approximated the lowest non-zero prevalence found in field studies, and a peak annual vector density of only 11.4 female sand flies/woodrat. At a peak density of 2.8 female sand flies/woodrat, the prevalence declined below 1% (0.69%) at the end of 2 years. Simulations indicated that if the initial prevalence of infection was 27%, the highest annual prevalence found in the field studies, prevalence would remain > 1% (1.27%) after 2 years even if there was no sand fly activity.