Miracle-dz/UniFAR-FTUs huggingface dataset:
Do Stress Responses Promote Leukemia Progression? An Animal Study Suggesting a Role for Epinephrine and Prostaglandin-E2 through Reduced NK Activity

In leukemia patients, stress and anxiety were suggested to predict poorer prognosis. Oncological patients experience ample physiological and psychological stress, potentially leading to increased secretion of stress factors, including epinephrine, corticosteroids, and prostaglandins. Here we tested whether environmental stress and these stress factors impact survival of leukemia-challenged rats, and studied mediating mechanisms. F344 rats were administered with a miniscule dose of 60 CRNK-16 leukemia cells, and were subjected to intermittent forced swim stress or to administration of physiologically relevant doses of epinephrine, prostaglandin-E2 or corticosterone. Stress and each stress factor, and/or their combinations, doubled mortality rates when acutely applied simultaneously with, or two or six days after tumor challenge. Acute administration of the β-adrenergic blocker nadolol diminished the effects of environmental stress, without affecting baseline survival rates. Prolonged β-adrenergic blockade or COX inhibition (using etodolac) also increased baseline survival rates, possibly by blocking tumor-related or normal levels of catecholamines and prostaglandins. Searching for mediating mechanisms, we found that each of the stress factors transiently suppressed NK activity against CRNK-16 and YAC-1 lines on a per NK basis. In contrast, the direct effects of stress factors on CRNK-16 proliferation, vitality, and VEGF secretion could not explain or even contradicted the in vivo survival findings. Overall, it seems that environmental stress, epinephrine, and prostaglandins promote leukemia progression in rats, potentially through suppressing cell mediated immunity. Thus, patients with hematological malignancies, which often exhibit diminished NK activity, may benefit from extended β-blockade and COX inhibition.
A Journey from STEM to STEAM: A Middle School Case Study

ABSTRACT This article examines the initial journey of a middle school in South Carolina from a STEM (science, technology, engineering, and math) curriculum to a STEAM (STEM + art) curriculum. This is the first of a three-year longitudinal study that investigated the perceptions of the effectiveness, relative importance, and sustainability of a STEAM curriculum in which the arts animated learning on a daily basis for both teachers and administrators during the first year of implementation beginning in the fall 2014. The article also investigates the response that the faculty of a STEM-oriented middle school had to the induction of STEAM curriculum training.
Differential Expression of Matrix Metalloproteases in Human Fibroblasts with Different Origins

Fibroblasts are widely distributed cells and are responsible for the deposition of extracellular matrix (ECM) components but also secrete ECM-degrading matrix metalloproteases. A finely balanced equilibrium between deposition and degradation of ECM is essential for structural integrity of tissues. In the past, fibroblasts have typically been understood as a uniform cell population with comparable functions regardless of their origin. Here, we determined growth curves of fibroblasts derived from heart, skin, and lung and clearly show the lowest proliferation rate for cardiac fibroblasts. Furthermore, we examined basal expression levels of collagen and different MMPs in these three types of fibroblasts and compared these concerning their site of origin. Interestingly, we found major differences in basal mRNA expression especially for MMP1 and MMP3. Moreover, we treated fibroblasts with TNF-α and observed different alterations under these proinflammatory conditions. In conclusion, fibroblasts show different properties in proliferation and MMP expression regarding their originated tissue.
Persistence of Skin Contamination and Environmental Shedding of Clostridium difficile during and after Treatment of C. difficile Infection

Background. Current guidelines for control of Clostridium difficile infection (CDI) suggest that contact precautions be discontinued after diarrhea resolves. However, limited information is available regarding the frequency of skin contamination and environmental shedding of C. difficile during and after treatment. Design. We conducted a 9-month prospective, observational study involving 52 patients receiving therapy for CDI. Stool samples, skin (chest and abdomen) samples, and samples from environmental sites were cultured for C. difficile before, during, and after treatment. Polymerase chain reaction ribotyping was performed to determine the relatedness of stool, skin, and environmental isolates. Results. Fifty-two patients with CDI were studied. C. difficile was suppressed to undetectable levels in stool samples from most patients during treatment; however, 1-4 weeks after treatment, 56% of patients who had samples tested were asymptomatic carriers of C. difficile. The frequencies of skin contamination and environmental shedding remained high at the time of resolution of diarrhea (60% and 37%, respectively), were lower at the end of treatment (32% and 14%, respectively), and again increased 1-4 weeks after treatment (58% and 50%, respectively). Skin and environmental contamination after treatment was associated with use of antibiotics for non-CDI indications. Ninety-four percent of skin isolates and 82% of environmental isolates were genetically identical to concurrent stool isolates. Conclusions. Skin contamination and environmental shedding of C. difficile often persist at the time of resolution of diarrhea, and recurrent shedding is common 1-4 weeks after therapy. These results provide support for the recommendation that contact precautions be continued until hospital discharge if rates of CDI remain high despite implementation of standard infection-control measures.
CLASS2: accurate and efficient splice variant annotation from RNA-seq reads

Next generation sequencing of cellular RNA is making it possible to characterize genes and alternative splicing in unprecedented detail. However, designing bioinformatics tools to capture splicing variation accurately has proven difficult. Current programs find major isoforms of a gene but miss finer splicing variations, or are sensitive but highly imprecise. We present CLASS, a novel open source tool for accurate genome-guided transcriptome assembly from RNA-seq reads. CLASS employs a splice graph to represent a gene and its splice variants, combined with a linear program to determine an accurate set of exons and efficient splice graph-based transcript selection algorithms. When compared against reference programs, CLASS had the best overall accuracy and could detect up to twice as many splicing events with precision similar to the best reference program. Notably, it was the only tool that produced consistently reliable transcript models for a wide range of applications and sequencing strategies, including very large data sets and ribosomal RNA-depleted samples. Lightweight and multi-threaded, CLASS required <3GB RAM and less than one day to analyze a 350 million read set, and is an excellent choice for transcriptomics studies, from clinical RNA sequencing, to alternative splicing analyses, and to the annotation of new genomes.
Chapter 4 A role for cytokinin in the onset of leaf senescence by ethylene in Arabidopsis

The expression of several Arabidopsis senescence-associated genes (SAGs) was found to be upregulated during leaf development of the onset of leaf death 9 mutant under standard growth conditions. Treatment of the mutant with ethylene resulted in a severe senescence response both phenotypically as well as on transcript level. A RNAi-based strategy to downregulate the expression of a SAG encoding for a hydroxyproline-rich glycoprotein, attenuated the ethylene induced senescence response of old9. Comparison of the old9 transcriptome revealed that 67% of the differentially expressed genes with wild type are cytokinin responsive. Cytokinins are well known for their effect to retard leaf senescence. However, by applying cytokinin early in development the response to ethylene-induced senescence could be enhanced. We argue that the cytokinin effect we observed is the result of increasing the sink strength of young tissue while opposite to that ethylene promotes source strength of old leaves. Therefore we propose that the balance between sink and source tissue can modulate the progression rate and timing of senescence.
Animals in environmental education research

Abstract Over the past few decades, the increase in public and scholarly attention to human-animal relations has inspired an animal turn in a number of academic disciplines including environmental education research. This paper reviews the literature on animals in environmental education with respect to its theoretical foundations in critical pedagogy, ecofeminism and posthumanism, considers empirical work on formal, nonformal and informal learning spaces and discusses the implications of an animal-focused paradigm for teaching and research. In the conclusion the author suggests some areas for further inquiries from her own research and teaching experience.
CEO Behavior and Firm Performance

We develop a new method to measure CEO behavior in large samples via a survey that collects high-frequency, high-dimensional diary data and a machine learning algorithm that estimates behavioral types. Applying this method to 1,114 CEOs in six countries reveals two types: “leaders,” who do multifunction, high-level meetings, and “managers,” who do individual meetings with core functions. Firms that hire leaders perform better, and it takes three years for a new CEO to make a difference. Structural estimates indicate that productivity differentials are due to mismatches rather than to leaders being better for all firms.
Online object search with a humanoid robot

This paper presents an object active visual search behavior in a 3D environment performed by a HRP-2 humanoid robot. The search is formalized as an optimization problem in which the goal is to maximize the target detection probability while minimizing the energy/distance and time to achieve the task. Natural constraints on the camera parameter space based on the characteristics of the recognition system are used to reduce the dimension of the problem and to speed up the optimization process to achieve a real time behavior. We present simulation and real experimental results using an HRP-2 robot.
Drug Discrimination in Methamphetamine-Trained Monkeys: Effects of Monoamine Transporter Inhibitors

The involvement of brain monoamine systems in the discriminative stimulus effects of methamphetamine (MA) was studied in squirrel monkeys by evaluating the effects of differentially selective monoamine uptake inhibitors alone and in combination. In monkeys discriminating i.m. injections of 0.3 mg/kg MA from saline, methamphetamine (0.01-0.3 mg/kg), and dopamine transporter (DAT) inhibitors, including 1-{2-(bis(4-fluorophenyl)-methoxy)ethyl}-4-(3-phenylpropyl)piperazine (GBR 12909; 1.0-17.8 mg/kg) and its analogs AM2502 (1.0-17.8 mg/kg), AM2506 (1.0-30.0 mg/kg), AM2515 (1.0-17.8 mg/kg), and AM2517 (1.0-5.6 mg/kg), produced dose-related increases in responding on the MA-associated lever and, at the highest doses, full substitution. The time course of MA-like effects was similar for equivalent (3.0 mg/kg) doses of GBR 12909 and its most potent analog, AM2517. Unlike the DAT blockers, the selective 5-hydroxytryptamine (serotonin) uptake inhibitor clomipramine (1.0-10.0 mg/kg) and the selective norepinepherine (NE) uptake inhibitor desipramine (1.0-10 mg/kg) produced responding primarily on the saline lever. The selective NE uptake inhibitor nisoxetine partially substituted at the highest dose tested (10.0 mg/kg). Pretreatment with GBR 12909 or AM2517 enhanced the discriminative stimulus effects of MA, shifting the dose-effect curve leftward. The NE uptake inhibitors desipramine or nisoxetine also enhanced the discriminative stimulus effects of MA, whereas clomipramine only attenuated them. These results support the view that dopaminergic mechanisms play a prominent role in the discriminative stimulus effects of MA in monkeys, whereas involvement of serotonergic and noradrenergic systems may be limited to a modulatory role.
Discovering Test Set Regularities in Relational Domains

Machine learning typically involves discovering regularities in a training set, then applying these learned regularities to classify objects in a test set. In this paper we present an approach to discovering additional regularities in the test set, and show that in relational domains such test set regularities can be used to improve classification accuracy beyond that achieved using the training set alone. For example, we have previously shown how FOIL, a relational learner, can learn to classify Web pages by discovering training set regularities in the words occurring on target pages, and on other pages related by hyperlinks. Here we show how the classification accuracy of FOIL on this task can be improved by discovering additional regularities on the test set pages that must be classified. Our approach can be seen as an extension to Kleinberg’s Hubs and Authorities algorithm that analyzes hyperlink relations among Web pages. We present evidence that this new algorithm leads to better test set precision and recall on three binary Web classification tasks where the test set Web pages are taken from different Web sites than the training set.
Aerobic Vanillate Degradation and C1 Compound Metabolism in Bradyrhizobium japonicum

ABSTRACT Bradyrhizobium japonicum, a symbiotic nitrogen-fixing soil bacterium, has multiple gene copies for aromatic degradation on the genome and is able to use low concentrations of vanillate, a methoxylated lignin monomer, as an energy source. A transcriptome analysis indicated that one set of vanA1B, pcaG1H1, and genes for C1 compound catabolism was upregulated in B. japonicum USDA110 cells grown in vanillate (N. Ito, M. Itakura, S. Eda, K. Saeki, H. Oomori, T. Yokoyama, T. Kaneko, S. Tabata, T. Ohwada, S. Tajima, T. Uchiumi, E. Masai, M. Tsuda, H. Mitsui, and K. Minamisawa, Microbes Environ. 21:240-250, 2006). To examine the functions of these genes in vanillate degradation, we tested cell growth and substrate consumption in vanA1B, pcaG1H1, and mxaF mutants of USDA110. The vanA1B and pcaG1H1 mutants were unable to grow in minimal media containing 1 mM vanillate and protocatechuate, respectively, although wild-type USDA110 was able to grow in both media, indicating that the upregulated copies of vanA1B and pcaG1H1 are exclusively responsible for vanillate degradation. Mutating mxaF eliminated expression of gfa and flhA, which contribute to glutathione-dependent C1 metabolism. The mxaF mutant had markedly lower cell growth in medium containing vanillate than the wild-type strain. In the presence of protocatechuate, there was no difference in cell growth between the mxaF mutant and the wild-type strain. These results suggest that the C1 pathway genes are required for efficient vanillate catabolism. In addition, wild-type USDA110 oxidized methanol, whereas the mxaF mutant did not, suggesting that the metabolic capability of the C1 pathway in B. japonicum extends to methanol oxidation. The mxaF mutant showed normal nodulation and N2 fixation phenotypes with soybeans, which was not similar to symbiotic phenotypes of methylotrophic rhizobia.
Hierarchical Beta Processes and the Indian Buffet Process

We show that the beta process is the de Finetti mixing distribution underlying the Indian buffet process of [2]. This result shows that the beta process plays the role for the Indian buffet process that the Dirichlet process plays for the Chinese restaurant process, a parallel that guides us in deriving analogs for the beta process of the many known extensions of the Dirichlet process. In particular we define Bayesian hierarchies of beta processes and use the connection to the beta process to develop posterior inference algorithms for the Indian buffet process. We also present an application to document classification, exploring a relationship between the hierarchical beta process and smoothed naive Bayes models.
Thermodynamics and Lattice Vibrations of Minerals, 4, Application to Chain and Sheet Silicates and Orthosilicates (Paper 80R1044)

This paper is the fourth in a series relating the lattice vibrational properties to the thermodynamic properties of minerals. The temperature dependence of the harmonic lattice heat capacity is calculated from a model which uses only elastic, crystallographic, and spectroscopic data for the following minerals: calcite, zircon, forsterite, grossular, pyrope, almandine, spessartine, andradite, kyanite, andalusite, sillimanite, clinoenstatite, orthoenstatite, jadeite, diopside, tremolite, talc, and muscovite. The heat capacities of these minerals reflect structural and compositional differences. The ‘excess’ entropy of pyrope—compared with that of grossular—is shown to arise from low-frequency optic modes of vibration. The entropy differences between kyanite, andalusite, and sillimanite are well reproduced by the model, although the absolute values calculated are systematically about 3% high. Model values of the heat capacity and entropy are compared with experimental values at 298.15, 700, and 1000°K for the 32 minerals included in papers 1–4 of this series. The average deviation of the entropies at 298°K from well-determined calorimetric values is ±1.5%. A method is given for obtaining greater accuracy in the model thermodynamic functions by fitting one parameter to experimental data when partial calorimetric data (such as the heat capacity at a single temperature in the range 50–100°K) are available; such a method should permit accurate extrapolation of calorimetric data beyond the range of experiment.
Designing Hierarchical Storage Systems for Interactive On-Demand Video Services

1 Designing Hierarchical Storage Systems for Interactive On-Demand Video Services S. -H. Gary Chan Fouad A. Tobagi Department of Electrical Engineering Stanford University Stanford, CA 94305 Abstract|A hierarchical storage system achieves scalable storage in providing on-demand video services. In such a system, video les are stored in a tertiary level (such as a library or jukebox), and transferred to a secondary level (such as magnetic disks) from which it is streamed to the users. In this paper, we study the design of such a system for interactive applications in which a movie has to be completely transferred (or \staged") to the secondary level before it is displayed to its user; thereby incurring some user delay. We specify the required storage and bandwidth to meet a delay goal, given application characteristics. We have developed an accurate and yet simple model for the system, which greatly facilitates the design process and allows us to extract important performance characteristics of the system. We provide some design examples, and study the in uence of video popularity. Keywords|Hierarchical storage systems, interactive video services, tertiary storage, secondary storage, storage system model
Playing Hare and Tortoise: The FigarOS Kernel for Fine-Grained System-Level Energy Optimizations

Energy has emerged to be the most important resource for computing systems. Despite the exceptional importance of energy, reducing its demand at application and system level remains a challenging task for programmers and engineers. This is aggravated by the fact that traditional energy-saving approaches are not only error-prone but even lead to adverse consequences (i.e. increased energy consumption). To address this concern, we present the FigarOS operating system for fine-grained system-level energy optimizations. The evaluation of our FigarOS implementation shows that the operating system lowers the energy consumption of processes by up to 2.9 x.
Priming effect in affirmative complex conditional connectives

ABSTRACT We report the results of an experiment that examined the mental representations underlying the comprehension of complex conditional connectives (such as “A, on condition that B”) and the conditional if (such as “A, if B”). The mental representations during the comprehension stage were analysed using a “priming methodology”. The experiment showed that participants read the possibility “A and not-B” faster when it was primed by “A, if B” than when it was primed by “A, on condition that B”. The finding suggests that people understand the sentence “A, on condition that B” as biconditional; other possibilities (“A and B”, “not-A and B”, “not-A and not-B”) were primed equally by both connectives. We discuss the implications of this for current theories of reasoning.
Illusory contours and spatial neglect

IT has been controversial whether the perception of illusory contours arise from higher level cognitive mechanisms that require attention or from early preattentive visual processes. We studied three patients with left spatial neglect who were unable to detect the left inducers of Kanizsa illusory figures in a same/different judgment task but nonetheless showed implicit perception of the figures in a midpoint judgment, in that they made identical bisection for figures with illusory or real contours but very different bisection for other spatially discontinuous figures that did not yield illusory fillingin. Grouping and filling-in mechanisms can thus occur without explicit detection of, or attention to, the inducing features, consistently with the hypothesis that they involve preattentive visual processes.
Determinants of Voltage Attenuation in Neocortical Pyramidal Neuron Dendrites

How effectively synaptic and regenerative potentials propagate within neurons depends critically on the membrane properties and intracellular resistivity of the dendritic tree. These properties therefore are important determinants of neuronal function. Here we use simultaneous whole-cell patch-pipette recordings from the soma and apical dendrite of neocortical layer 5 pyramidal neurons to directly measure voltage attenuation in cortical neurons. When combined with morphologically realistic compartmental models of the same cells, the data suggest that the intracellular resistivity of neocortical pyramidal neurons is relatively low (∼70 to 100 Ωcm), but that voltage attenuation is substantial because of nonuniformly distributed resting conductances present at a higher density in the distal apical dendrites. These conductances, which were largely blocked by bath application of CsCl (5 mm), significantly increased steady-state voltage attenuation and decreased EPSP integral and peak in a manner that depended on the location of the synapse. Together these findings suggest that nonuniformly distributed Cs-sensitive and -insensitive resting conductances generate a “leaky” apical dendrite, which differentially influences the integration of spatially segregated synaptic inputs.
Is it always good to feel valued? The psychological benefits and costs of higher perceived status in one’s ethnic minority group

Two studies (N = 1,048) examined how Blacks’, Asians’, and Latinos’ perceived value within their own ethnic group (ethnic intragroup status) shapes mental health (depression, anxiety, psychological distress). The proposed intragroup status and health (ISAH) model predicts that feeling valued among ethnic ingroup members has benefits for health, but also indirect costs. Costs arise because individuals who feel highly valued in their ethnic group see their ethnicity as more central to their self-concept; with stronger identity-centrality, individuals more frequently view daily social interactions through the “lens” of their ethnicity and ultimately perceive/experience more discrimination. Discrimination, in turn, adversely shapes mental health. Results of structural equation modeling supported these predictions across all groups in both studies. Thus, feeling valued in one’s minority group may be a double-edged sword for mental health. Overall, the ISAH model reveals how intragroup processes, when considered from an intergroup perspective, advance our understanding of minority mental health.