cssi/SciSciGPT-SciSciNet huggingface dataset:
Multi-way association extraction and visualization from biological text documents using hyper-graphs: Applications to genetic association studies for diseases

Objectives: Biological research literature, as in many other domains of human endeavor, represents a rich, ever growing source of knowledge. An important form of such biological knowledge constitutes associations among biological entities such as genes, proteins, diseases, drugs and chemicals, etc. There has been a considerable amount of recent research in extraction of various kinds of binary associations (e.g., gene-gene, gene-protein, protein-protein, etc.) using different text mining approaches. However, an important aspect of such associations (e.g., ''gene A activates protein B'') is identifying the context in which such associations occur (e.g., ''gene A activates protein B in the context of disease C in organ D under the influence of chemical E''). Such contexts can be represented appropriately by a multi-way relationship involving more than two objects (e.g., objects A, B, C, D, E) rather than usual binary relationship (objects A and B). Methods: Such multi-way relations naturally lead to a hyper-graph representation of the knowledge rather than a binary graph. The hyper-graph based multi-way knowledge extraction from biological text literature represents a computationally difficult problem (due to its combinatorial nature) which has not received much attention from the Bioinformatics research community. In this paper, we describe and compare two different approaches to such multi-way hyper-graph extraction: one based on an exhaustive enumeration of all multi-way hyper-edges and the other based on an extension of the well-known A Priori algorithm for structured data to the case unstructured textual data. We also present a representative graph based approach towards visualizing these genetic association hyper-graphs. Results: Two case studies are conducted for two biomedical problems (related to the diseases of lung cancer and colorectal cancer respectively), illustrating that the latter approach (using the text-based A Priori method) identifies the same hyper-edges as the former approach (the exhaustive method), but at a much less computational cost. The extracted hyper-relations are presented in the paper as cognition-rich representative graphs, representing the corresponding hyper-graphs. Conclusions: The text-based A Priori algorithm is a practical, useful method to extract hyper-graphs representing multi-way associations among biological objects. These hyper-graphs and their visualization using representative graphs can provide important contextual information for understanding gene-gene associations relevant to specific diseases.
Systematic empirical research versus clinical case studies: A valid antagonism?

This paper considers the issue of systematic empirical research versus clinical case studies raised by Hoffman (2009). A rebuttal of Hoffman's arguments is offered, followed by an argument that each method addresses itself to different questions and that posing them in opposition is not fruitful. Finally, criteria and requirements of the case study method are proposed that, if met, would enhance its evidential value.
Retro Modern or Revolutionary: Scale Shifts and Political Reaction in Twenty–First Century Urbanism

This paper Speculates about some trends in the shape and development of twenty–first century cities. The central shift involved in new urban development concerns the altered functions and scale at which cities are constituted with the fruition of global capitalism. Stylistically the next generation of urban development will revisit modernism, and this theme is explored via a critical discussion of new urbanism and of contemporary reconstruction in Berlin. Yet the capitalist revolution that will mark the first years of the twenty-first century may itself be vulnerable, and the possibility exists for revolutionary change in the social relations that give rise to specific patterns and processes of urban development and therefore to equally revolutionary urban forms. [Scale, modernism, revolution, Berlin, revanchism, new urbanism]
Ixabepilone: a new antimitotic for the treatment of metastatic breast cancer.

Objective:To evaluate the safety and efficacy of ixabepilone as a new antimitotic chemotherapeutic agent for the treatment of breast cancer.Data Sources:Data were identified by searches of MEDLINE, PubMed, and American Society of Clinical Oncology abstracts from 1966 to March 2008, using the primary search terms ixabepilone, epothilones, BMS-247550, and breast cancer.Study Selection And Data Extraction:Phase 1, Phase 2, and Phase 3 clinical trials examining the safely and efficacy of ixabepilone and its place in cancer treatment were reviewed. Preference was given to large Phase 2 and 3 clinical trials in the breast cancer population. Manufacturer product information was used to supplement data lacking in published trials.Data Synthesis:Ixabepilone belongs to a novel class of drugs, the epothilones, which are nontaxano microtubule-stabilizing agents. Ixabepilone, in combination with capecitabine, has been approved by the Food and Drug Administration for treatment in patients with metastatic or locally adv...
Caribbean Currents: Caribbean Music from Rumba to Reggae

Caribbean Currents: Caribbean Music from Rumba to Reggae. PETER MANUEL. with KENNETH BILBY and MICHAEL LARGEY. Philadelphia: Temple University Press, 1995. xvi. 242 pp., glossary, illustrations, index, notes.
Preoperative Hydronephrosis Predicts Extravesical and Node Positive Disease in Patients Undergoing Cystectomy for Bladder Cancer

Purpose: Preoperative hydronephrosis may be associated with a worse outcome in patients who undergo radical cystectomy for invasive bladder cancer. We characterized the prognostic significance of hydronephrosis, and its relationship to cancer stage and outcome. We also evaluated concordance between the side of identifiable hydronephrosis and concomitant pelvic lymph node metastasis.Materials and Methods: We analyzed information from our prospectively collected database of patients who underwent radical cystectomy for bladder cancer from January 2001 to December 2007. We examined the relationship between hydronephrosis and clinical variables as well as survival outcome. Hydronephrosis was diagnosed intraoperatively or by radiographic imaging within 3 months of radical cystectomy.Results: Of 753 patients 244 (32%) were diagnosed with hydronephrosis. Logistic regression modeling revealed that hydronephrosis was an independent predictor of extravesical disease (OR 2.01, 95% CI 1.37 to 2.96, p <0.001) and node...
Lobatto Point Quadrature for Thermal Lubrication Problems Involving Compressible Lubricants

Refined solutions of thermal lubrication problems generally require fine mesh and many iteration steps. To resolve these difficulties, Elrod and Brewe (1) proposed an efficient algorithm based on the use of Lobatto point quadrature. Within this approach, the unknown temperature across the film is written in a series of Legendre polynomials. This paper presents a Lobatto point quadrature algorithm which is applicable for thermal lubrication problems with compressible lubricants. In this case both density and viscosity of the lubricant are taken to be temperature and pressure dependent. The transverse velocity is obtained from the continuity equation. Use of the Labatto point calculation method has resulted in greater accuracy without the use of a large number of grid points.Copyright © 2005 by ASME
Short-term changes in Pinus strobus sapling height/diameter ratios following partial release: testing the acclimative stem-form development hypothesis

Following release, mature trees can acclimatively shift aboveground growth allocation from height to diameter at breast height (DBH) growth to adjust their stem form (reducing height/diameter ratio (HDR)) to better withstand increased wind stress. The purpose of this study was to determine if, over a 6-year period, 7- to 12-year-old eastern white pines (Pinus strobus L.) also responded to different levels of partial release with (i) stem-form adjustments (reduced HDR) through growth-allocation shifts from height to DBH growth and (ii) lower HDR values (shorter heights) than for unreleased trees of the same DBH (“acclimative stem-form development hypothesis”). Over the 6-year postrelease period, juvenile white pine seedlings exhibited unsynchronized height and DBH growth response patterns that depended on their prerelease height growth. Height growth of faster growing white pines was temporarily reduced. Concurrently, DBH growth was enhanced with increasing release intensity. HDR reductions followed a fair...
Taking Research to FLOSS-Curious Engineers and Managers

In 2006 the author undertook to take what I'd learnt from the research on Free, Libre and Open Source Software (FLOSS) both to 'the community' and to those interested in joining 'the community'. I prepared and presented two 3.5 hour tutorials at FLOSS conferences: LinuxAsia in Delhi and O'Reilly's Open Source Conference (OSCON) in Portland. This paper describes these experiences. The author first summarizes the tutorials, pointing out which research was used and what the interests of the participants were and where more research can bridge the gaps. The author then describe an ongoing interaction with a software engineering manager at Microsoft who attended the tutorial and is in the interesting position of taking a Microsoft work group open. Finally the author reflects on this experience for lessons about 'transferable research'.
The role of the right hemisphere in the physiological and cognitive components of emotional processing

Right hemisphere specialization for emotional processing was investigated using behavioral and psychophysiological methods. Fifty undergraduates were shown slides depicting negative emotional and neutral scenes briefly lateralized to the right or left cerebral hemispheres and asked to categorize each as emotional or neutral. Pulse volume and heart rate (HR) measured physiological processing and reaction time measured cognitive processing. The largest vasoconstriction responses and HR deceleration were obtained for emotional items in the right hemisphere. However, reaction time failed to show right hemisphere superiority in perceptual/cognitive processing, demonstrating instead slowest responses to emotional stimuli presented to the right hemisphere together with evidence for left hemisphere competence. Selective right hemispheric activation in autonomic responses, combined with the lack of right hemisphere specialization in the cognitive task, suggests that the physiological response system rather than the perceptual/cognitive system is the locus of the right hemisphere superiority for emotion.
The self-medication hypothesis and psychostimulant treatment of cocaine dependence: an update.

Background: Stimulant medications have shown promise as a treatment for cocaine dependence (CD) for several decades, yet these treatments have not been widely studied and substantial barriers to clinical implementation remain. The “Self‐Medication Hypothesis,” posits that an individual’s choice to use a particular substance is to some degree based on the substance’s effect on subjective painful affects or unpleasant emotional states which may or may not be associated with a psychiatric disorder. Objectives: The Self‐Medication Hypothesis remains relevant, particularly when considering the scenario of cocaine dependence, both with and withoutandco‐occurringattention‐deficit/hyperactivitydisorder(ADHD). Methods: Two case studies (N ¼ 2) and a review of the relevant literature are provided in this clinical update on psychostimulant treatment of cocaine dependence. Results: Two case studies are presented in which psychostimulant treatment of cocaine dependence was associated with a good clinical outcome. Discussion: While the use of psychostimulant medication for the treatment of cocaine dependence is controversial, emerging evidence suggests potential utility for this approach. Conclusions: Cocaine use in individuals with CD may represent self‐ medication, and prescribed psychostimulants may have benefi ti n restoring dopaminergic function. Scientific Significance: Psychostimulant treatment of cocaine dependence is consistent with the Self‐Meidcation Hypothesis and is deserving of further study. (Am J Addict 2013;XX:000–000)
America's looming creativity crisis

The strength of the American economy does not rest on its manufacturing prowess, its natural resources, or the size of its market. It turns on one factor--the country's openness to new ideas, which has allowed it to attract the brightest minds from around the world and harness their creative energies. But the United States is on the verge of losing that competitive edge. As the nation tightens its borders to students and scientists and subjects federal research funding to ideological and religious litmus tests, many other countries are stepping in to lure that creative capital away. Ireland, Canada, Australia, New Zealand, Denmark, and others are spending more on research and development and shoring up their universities in an effort to attract the world's best--including Americans. If even a few of these nations draw away just a small percentage of the creative workers from the U.S., the effect on its economy will be enormous. In this article, the author introduces a quantitative measure of the migration of creative capital called the Global Creative-Class Index. It shows that, far from leading the world, the United States doesn't even rank in the top ten in the percentage of its workforce engaged in creative occupations. What's more, the baby boomers will soon retire. And data showing large drops in foreign student applications to U.S. universities and in the number of visas issued to knowledge workers, along with concomitant increases in immigration in other countries, suggest that the erosion of talent from the United States will only intensify. To defend the U.S. economy, the business community must take the lead in ensuring that global talent can move efficiently across borders, that education and research are funded at radically higher levels, and that we tap into the creative potential of more and more workers. Because wherever creativity goes, economic growth is sure to follow.
Efficient out-of-core algorithms for linear relaxation using blocking covers

When a numerical computation fails to fit in the primary memory of a serial or parallel computer, a so-called "out-of-core" algorithm must be used which moves data between primary and secondary memories. In this paper, we study out-of-core algorithms for sparse linear relaxation problems in which each iteration of the algorithm updates the state of every vertex in a graph with a linear combination of the states of its neighbors. We give a general method that can save substantially on the I/O traffic for many problems. For example, our technique allows a computer with M words of primary memory to perform T=/spl Omega/(M/sup 1/5/) cycles of a multigrid algorithm for a two-dimensional elliptic solver over an n-point domain using only /spl Theta/(nT/M/sup 1/5/) I/O transfers, as compared with the naive algorithm which requires /spl Omega/(nT) I/O's. >
Effects of low concentrations of ethanol on the fluidity of spin-labeled erythrocyte and brain membranes.

The effects of ethanol on membrane fluidity at 37° have been assessed by a sensitive electron paramagnetic resonance technique. Erythrocyte and brain membranes from DBA/2J mice were spin-labeled with 5-doxylstearic acid ( N -oxyl-49,49-dimethyloxazolidine derivative of 5-ketostearic acid). The molecular motion of the spin label was measured from the EPR spectrum by determining the order parameter S , an index of membrane fluidity. The fluidity of both erythrocyte and synaptosomal membranes was greater than that of myelin but less than that of mitochondrial membranes. The addition of low concentrations (0.02 or 0.04 M) of ethanol in vitro increased fluidity in erythrocyte, mitochondrial, and synaptosomal membranes. This fluidizing effect of ethanol was dose-related up to 0.35 M in all the membranes except myelin. These data suggest that nonlethal concentrations of ethanol may increase membrane fluidity in vivo .
Can Social Movements Resolve the Crisis of the U.S. Party System

I have argued in other work that the US party system is in a crisis, combining intense partisanship with an inability to handle such major issues as climate change, a democratic foreign policy, or redirection of the economy toward sustainable prosperity. In the past such crises were resolved by intervention of minor parties, leading to realignment of the system. Today, such intervention appears to be blocked by a number of factors. In this paper, I examine the possibility that the crisis might be resolved by non-electoral means, such as the Occupy protests and increased labor militancy. The paper will use twitter feeds, websites, and other ephemeral sources to make a detailed study of the Occupy movement, in particular, to try to determine its real impact on public opinion, and through public opinion on the election of 2012 and the propsect of future electoral impact.
Protection of IB-MECA against myocardial stunning in conscious rabbits is not mediated by the A1 adenosine receptor.

The goal of this study was to determine whether the protective effects of the A3AR agonist N6-(3-iodobenzyl)adenosine-5'-N-methylcarboxamide (IB-MECA) against myocardial stunning are mediated by the A1AR. Six groups of conscious rabbits underwent a sequence of six 4-minute coronary occlusion (O)/4-minute reperfusion (R) cycles for three consecutive days (days 1, 2, and 3). In vehicle-treated rabbits (group I), the recovery of systolic wall thickening (WTh) in the ischemic/reperfused region was markedly depressed on day 1, indicating the presence of severe myocardial stunning. On days 2 and 3, however, the recovery of systolic WTh was markedly accelerated, indicating the presence of late ischemic preconditioning (PC). When rabbits were pretreated with the A1AR agonist 2-chloro-N6-cyclopentyladenosine (CCPA, 100 μg/kg i.v.) or with IB-MECA (100 μg/kg i.v.) 10 min prior to the first sequence of O/R cycles on day 1 (group III and V, respectively), the recovery of systolic WTh was markedly accelerated compared to vehicle-treated animals (reflected as an ∼48 % decrease in the total deficit of systolic WTh). The magnitude of the protection afforded by adenosine receptor agonists was equivalent to that provided by late ischemic PC. Pre-treating rabbits with the A1AR antagonist N-0861 completely blocked both the hemodynamic and the cardioprotective effects of CCPA (group IV). However, the same dose of N-0861 did not block the cardioprotective actions of IB-MECA (group VI). Importantly, N-0861 did not influence the degree of myocardial stunning in the absence of PC (group II) and it did not block the development of late ischemic PC. Taken together, these results provide conclusive evidence that the cardioprotective effects of IB-MECA are not mediated via the A1AR, supporting the concept that activation of A3ARs prior to an ischemic challenge provides protection against ischemia/reperfusion injury.
Characterization of Emissions from Grass Pellet Combustion

Emission factors of pollutants from combustion of five different types of grass pellets with ash content ranging from 3% to 13% were measured and compared to a premium type wood pellet with ash con...
[Die Republik gegen das Kollektiv: Zwei Geschichten von Kollaboration und Konkurrenz in der modernen Wissenschaft].

Kollaboration und Konkurrenz gibt es in der Wissenschaft zwischen Individuen oder verschiedenen Gruppen, groseren Organisationen, Schauplatzen und Nationalstaaten. Die Spannung zwischen individuellem Ansehen und Gruppenmeriten oder individuellem Ehrgeiz und Gruppenleistung ist der wissenschaftlichen Arbeit inharent und tragt zu ihrem Erfolg bei. Die Autorin vergleicht zwei soziale Modelle der Wissenschaft, die entwickelt wurden, als Wissenschaftler im 20. Jahrhundert zunehmend begannen kollaborativ zu forschen: Michael Polanyis individualistische Freie-Markt-Republik der Wissenschaft und Ludwik Flecks Denkkollektiv. Diese beiden Modelle sollten Praktiken beschreiben und Ideale fur die Wissenschaft im allgemeinen auf der Grundlage der Erfahrungen spezialisierter Forschungsgruppen vorschreiben. Die Arbeitsgruppen von Linus Pauling und Dorothy Crowfoot Hodgkin dienen hier der Erlauterung der beiden Modelle. Die Autorin untersucht verschiedene Auswirkungen von Paulings und Hodgkins Praktiken auf das personliche Ansehen des Direktors und der Mitarbeiter, und schliest mit der Frage, ob eine kollektive Wissenschaft moglich ist.
Effect of porcine parvovirus on development of fertilized pig eggs in vitro.

SUMMARY Fertilized eggs, collected from four oestrus-synchronized gilts 32 h after presumed ovulation, were cultured for five days in a synthetic culture medium with or without porcine parvovirus (PPV). The proportion of virus-exposed eggs which developed to the blastocyst stage was significantly lower than the proportion of controls (53% v . 80%). Examination by the direct fluorescent antibody technique at the end of culture showed that viral antigen had adhered to the outer surface of the zona pellucida but the virus did not seem to have penetrated into the blastocyst itself. It is concluded that although PPV may not seriously interfere with development of the intact fertilized pig egg up to the early blastocyst stage in vitro , the presence of the virus on the zona pellucida could pose a threat to development after hatching occurs.
Multiple reactive sulfhydryl groups modulate the function of adenylate cyclase coupled beta-adrenergic receptors.

The beta -adrenergic receptor adenylate cyclase complex in the frog erythrocyte contains at least two reactive sulfhydryl groups, which have been identified by their different sensitivities to N-ethylmaleimide (NEM). Adenylate cyclase catalytic activity is completely inhibited by [NEM] = 1 mM. In contrast, ability of beta -adrenergic agonists to form a high affinity guanine nucleotide sensitive state is reduced by NEM only at concentrations ≥ 1 mM. The inhibition of cyclase activity did not affect high affinity agonist binding nor perturb the ability of guanine nucleotides to reduce agonist affinity as determined in direct radioligand binding assays utilizing the beta -adrenergic agonist [ 3 H]hydroxybenzylisoproterenol and (-)isoproterenol competition for antagonist [ 3 H]dihydroalprenolol binding. Preincubation of frog erythrocyte membranes with antagonists or guanine nucleotide did not alter the effect of NEM on agonist affinity. However, once formed by preincubation of membranes with agonist, the high affinity state is resistant to the effects of NEM. The data suggest that the sulfhydryl group modulating agonist affinity 1) is located on the receptor complex but distal to the hormonal binding site and 2) may be associated with guanine nucleotide regulation of agonist affinity. The widely different sensitivities of adenylate cyclase activity and agonist binding affinity toward NEM have been exploited to investigate the mechanism of desensitization in frog erythrocytes. Incubation of intact erythrocytes with NEM under appropriate conditions inactivates the cyclase enzyme without altering the ability of membranes prepared from these cells to bind agonist with high affinity. This NEM treatment prior to prolonged exposure to (-)isoproterenol prevents receptor desensitization in frog erythrocytes, suggesting that agonist occupancy of a nucleotide-sensitive receptor is insufficient, by itself, to initiate the receptor regulation process.
An Incision for Extended Suprahilar Retroperitoneal Lymphadenectomy

AbstractTo fulfill the necessary criteria for adequate exposure for extended suprahilar retroperitoneal lymphadenectomy we have used a thoracoabdominal midline extraperitoneal incision that affords the high exposure of a thoracoabdominal incision without sacrificing the broad exposure afforded by a midline incision and maintains the advantages of the extraperitoneal approach.
Monopoles, Gauge Fields, and Anomalies

The possible catalysis of baryon disintegration by magnetic poles is a beautiful example of the way in which monopoles illuminate fundamental concepts of physics. This hypothetical process is followed step by step, with an effort to minimize arbitrary hypotheses and to state clearly those which remain, as well as the consequences of changing them. The conclusions are that there should be a large cross section for catalysis in collisions of slow monopoles with nucleons, though not with large nuclei, but the intrinsic rate for destruction of a nucleon captured by a pole could be many orders of magnitude below the 1023 per second which characterizes strong interactions. It is argued that Rubakov’s and Callan’s pictures of catalysis are compatible but distinct, and either permits a strong rate but requires at least a weak rate.
Cortical thickness in relation to clinical symptom onset in preclinical AD.

Mild cognitive impairment (MCI) and Alzheimer's disease (AD) dementia are preceded by a phase of disease, referred to as ‘preclinical AD’, during which cognitively normal individuals have evidence of AD pathology in the absence of clinical impairment. This study examined whether a magnetic resonance imaging (MRI) measure of cortical thickness in brain regions, collectively known as ‘AD vulnerable’ regions, predicted the time to onset of clinical symptoms associated with MCI and whether cortical thickness was similarly predictive of clinical symptom onset within 7 years post baseline versus progression at a later point in time. These analyses included 240 participants from the BIOCARD study, a cohort of longitudinally followed individuals who were cognitively normal at the time of their MRI (mean age = 56 years). Participants have been followed for up to 18 years (M follow-up = 11.8 years) and 50 participants with MRIs at baseline have developed MCI or dementia over time (mean time to clinical symptom onset = 7 years). Cortical thickness in AD vulnerable regions was based on the mean thickness of eight cortical regions. Using Cox regression models, we found that lower mean cortical thickness was associated with an increased risk of progression from normal cognition to clinical symptom onset within 7 years of baseline (p = 0.03), but not with progression > 7 years from baseline (p = 0.30). Lower cortical thickness was also associated with higher levels of phosphorylated tau, measured in cerebrospinal fluid at baseline. These results suggest that cortical thinning in AD vulnerable regions is detectable in cognitively normal individuals several years prior to the onset of clinical symptoms that are a harbinger of a diagnosis of MCI, and that the changes are more likely to be evident in the years proximal to clinical symptom onset, consistent with hypothetical AD biomarker models.
Characteristics and adaptive strategies linked with falls in stroke survivors from analysis of laboratory-induced falls.

Falls are the most common and expensive medical complication in stroke survivors. There is remarkably little information about what factors lead to a fall in stroke survivors. With few exceptions, the falls literature in stroke has focused on relating metrics of static balance and impairment to fall outcomes in the acute care setting or in community. While informative, these studies provide little information about what specific impairments in a stroke-survivor’s response to dynamic balance challenges lead to a fall. We identified the key kinematic characteristics of stroke survivors’ stepping responses following a balance disturbance that are associated with a fall following dynamic balance challenges. Stroke survivors were exposed to posteriorly-directed translations of a treadmill belt that elicited a stepping response. Kinematics were compared between successful and failed recovery attempts (i.e. a fall). We found that the ability to arrest and reverse trunk flexion and the ability to perform an appropriate initial compensatory step were the most critical response contributors to a successful recovery. We also identified 2 compensatory strategies utilized by stroke survivors to avoid a fall. Despite significant post-stroke functional impairments, the biomechanical causes of trip-related falls by stroke survivors appear to be similar to those of unimpaired older adults and lower extremity amputees. However, compensatory strategies (pivot, hopping) were observed.
Answering Questions with Questions: A Personal Take on Gödel’s Incompleteness Theorem as It Relates to Architecture and Design

This paper discusses the role of prototyping as a vehicle to integrate electronic media technology, materiality, and physical computing into architectural design process and education. It connects a creating-making approach to a broader maker and hacker culture through adaptive and autonomous assemblies and embedded electronic systems. It recognizes the need for a new conceptual discourse on what constitutes effective design methodology that nurtures innovation and considers all design factors: social, cultural, and technological.
Establishing Informative Prior for Gene Expression Variance from Public Databases

Identifying differential expressed genes across various conditions or genotypes is the most typical approach to studying the regulation of gene expression. An estimate of gene-specific variance is often needed for the assessment of statistical significance in most differential expression (DE) detection methods, including linear models (e.g., for transformed and normalized microarray data) and generalized linear models (e.g., for count data in RNAseq). Due to a common limit in sample size, the variance estimate is often unstable in small experiments. Shrinkage estimates using empirical Bayes methods have proven useful in improving the variance estimate, hence improving the detection of DE. The most widely used empirical Bayes methods borrow information across genes within the same experiments. In these methods, genes are considered exchangeable or exchangeable conditioning on expression level. We propose, with the increasing accumulation of expression data, borrowing information from historical data on the same gene can provide better estimate of gene-specific variance, thus further improve DE detection. Specifically, we show that the variation of gene expression is truly gene-specific and reproducible between different experiments. We present a new method to establish informative gene-specific prior on the variance of expression using existing public data, and illustrate how to shrink the variance estimate and detect DE. We demonstrate improvement in DE detection under our strategy compared to leading DE detection methods.
SHOCK PRESSURE OF BREAKING WAVES

Most of you have observed waves breaking against rocks or structures, and have noted that water is frequently thrown high in the air. The pressure required to project water in a vertical direction is about one half pound per square inch for each foot of height. We may therefore expect to find substantial pressure involved in the mechanics of a wave breaking against a structure.
SU( 4)C × SU( 2)L × SU( 2)R models with C-parity

Abstract We construct supersymmetric SU ( 4 ) C × SU ( 2 ) L × SU ( 2 ) R models with spontaneously broken left–right symmetry ( C -parity). The minimal supersymmetric standard model (MSSM) can be recovered at low scales by exploiting the missing partner mechanism. The field content is compatible with realistic fermion masses and mixings, proton lifetime is close to or exceeds the current experimental bounds, and supersymmetric hybrid inflation can be implemented to take care of C -parity domain walls as well as magnetic monopoles, and to realize the observed baryon asymmetry via non-thermal leptogenesis.
Weak protein–protein interactions in live cells are quantified by cell-volume modulation

Weakly bound protein complexes play a crucial role in metabolic, regulatory, and signaling pathways, due in part to the high tunability of their bound and unbound populations. This tunability makes weak binding (micromolar to millimolar dissociation constants) difficult to quantify under biologically relevant conditions. Here, we use rapid perturbation of cell volume to modulate the concentration of weakly bound protein complexes, allowing us to detect their dissociation constant and stoichiometry directly inside the cell. We control cell volume by modulating media osmotic pressure and observe the resulting complex association and dissociation by FRET microscopy. We quantitatively examine the interaction between GAPDH and PGK, two sequential enzymes in the glycolysis catalytic cycle. GAPDH and PGK have been shown to interact weakly, but the interaction has not been quantified in vivo. A quantitative model fits our experimental results with log Kd = -9.7 ± 0.3 and a 2:1 prevalent stoichiometry of the GAPDH:PGK complex. Cellular volume perturbation is a widely applicable tool to detect transient protein interactions and other biomolecular interactions in situ. Our results also suggest that cells could use volume change (e.g., as occurs upon entry to mitosis) to regulate function by altering biomolecular complex concentrations.
Improving Access to Healthcare: Models of Adaptive Behavior

Patient access to healthcare is a major problem area due to inadequate supplies and misallocation of resources including physicians, nurses, and hospital beds. Increasing patient demands due to an aging and more chronically ill population will exacerbate this situation, leading to longer delays for care, hurried treatment times, and adverse clinical outcomes. Though there is a significant operations literature focused on methods to mitigate these effects, suggested remedies may be ineffective due to adaptive behavior by both physicians and patients. This chapter will focus on the quantification and impact of such adaptive behavior on the ability to provide timely patient access to limited health services.
Evaluation emerging PV Performance Rating under indoor lighting simulator

The measured I-V hysteresis is complicated by the vast array of different materials, lighting sources, and device architectures. In our study, we used RTOS method for I-V then the results showed better accuracy by eliminating in real time the acceptance effect. We also used this method to compare emerging PV cells with the latter cells exhibited promising power conversion efficiency and no hysteresis behavior under indoor lighting simulator. In this study, we defined a performance ratio to compare between indoor lighting and solar and the results will be show different performance trend for the different type PV in indoor/outdoor, which depends on device. That’s will be shown what’s type PV have the application of energy harvesting for indoor.
CEO power, product market competition and the acquisition motive for going public

This study finds that CEO power and product market competition differentially influence post‐IPO growth strategy and its economic consequences. Powerful CEOs are more likely to prefer acquisition growth over internal investment. Further, while CEO power is positively related to the likelihood, frequency and size of post‐IPO acquisitions, it is unrelated to the post‐IPO performance of acquisitive firms. In contrast, product market rivalry does not increase post‐IPO acquisitiveness but is positively related to the performance of acquirers. Finally, CEO power enhances the performance of acquisitive IPO firms only when faced with intense competitive rivalry.
Analytics approaches for the era of 10,000* genomes *and counting

What does it mean to make data available in a world where not everyone is a bioinformatician, but anyone can sequence a genome? As low-cost sequencing democratizes genome sequencing, it is also democratizing data analysis, with predictably uneven results. Can analytics approaches save us from everything from poorly documented analysis protocols to increasingly compressed and confusing visualizations?
Effects on the Heart of Two Forms of Chronic Hypoxia

The physiological effects of chronic exposure to high altitude or carbon monoxide (CO) have been studied intensively in humans and animals, but the effects on the heart of these stressors combined have not been investigated. This research was initiated because theoretical and experimental data suggest that chronic exposure to CO combined with altitude may be more detrimental to the heart than chronic exposure to CO alone and because there are no data on the effects of chronic exposure to CO at altitude.
From rank-seeking to rent-seeking: Changing administrative ethos and corruption in reform China

There are two contrasting images of the contemporaryChinese bureaucracy: the first is one of stiffrevolutionary cadres working under a marginallyreformed mobilization regime; the second is one ofrationalization of administrative institutions withthe transformation of cadres into modern rule-orientedbureaucrats. By examining some prevailing informalbehaviors of Chinese public officials, this articleoffers an alternative image: a neotraditionalistofficialdom with a reconfiguration of somepatrimonial, revolutionary, and legal-rationalinstitutions, ethos, and modes of operation.
Hiring millennial students as software engineers: a study in developing self-confidence and marketable skills

Software engineering courses and internships aim to equip students with skills that are vital in the software engineering industry. Millennial students are expected to emerge from an undergraduate education ready to step directly into software developer positions and succeed. And yet, for a variety of reasons, these experiences often fail to adequately prepare students for the expectations of the industry. The capabilities of a typical undergraduate simply do not align well with the needs of the industry, resulting in disappointed employers, unhappy employees, and a poor reputation for the quality of a higher education in software engineering. This paper describes the Student Software Developers Program, where students are developing real-world applications that solve business needs for departments on campus, leveraging those departments as customers. Students are immersed in the program for a full year, providing them with adequate time to experience both the depth and breadth of skills desired by the curriculum and by industry. Our evaluation shows the program provided students with confidence in their engineering abilities, a wealth of hard and soft skills valuable in industry, all while learning software engineering in a way that aligns with the values of their generation.
“Knower” as an Ethical Concept: From Epistemic Agency to Mutual Recognition

Recent discussions in critical social epistemology have raised the idea that the concept “knower” is not only an epistemological concept but an ethical concept as well. Though this idea plays a central role in these discussions, the theoretical underpinnings of the claim have not received extended scrutiny. This paper explores the idea that “knower” is an irreducibly ethical concept in an effort to defend its use as a critical concept. In section 1, I begin with the claim that “knower” is an irreducibly normative and social concept, drawing from some ideas in Wilfrid Sellars. In section 2, I argue that one’s being a knower involves demands for various sorts of ethically laden recognition. I develop this thought by arguing that Axel Honneth’s threefold typology of recognition—love, respect, and esteem—finds clear expression within the context of socio-epistemic practice. I conclude in section 3 by arguing that Miranda Fricker’s proposed “analogy” between epistemic and moral perception should be modified to indicate a closer relationship than mere analogy.
Plurilingualism and translanguaging: commonalities and divergences

The concepts of plurilingualism and translanguaging are explained and distinguished, showing how each has contributed to transformations in the study of bilingualism and multilingualism. The terms ...
Low noise, near-infrared APDs for laser wavefront monitoring

Avalanche Photodiodes (APDs) that target a wavelength of 1550 nm, have several applications ranging from optical communications to imaging to single photon detection. The DE-JTO will use an array of APDs to image the wavefront of its 1550 nm laser. The distinctive feature of an APD is high sensitivity due to the gain achieved by impact ionization of carriers. Because impact ionization is a stochastic process, it introduces excess noise that limits the signal to noise ratio of an APD. However, the excess noise may be reduced by engineering the k (=β/α) value of the device, where β and α are the impact ionization coefficients of holes and electrons, respectively. k can be engineered by band diagram engineering [1], band structure engineering [2], or dead space effect [3,4]. Combinations of these are also used [5]. Band diagram engineering enables the implementation of Capasso’s channeling APD [1]. In this design, electrons and holes are spatially separated in different channels with distinct materials and bandgaps. These channel materials are designed to minimize the impact ionization of one carrier and promote the other, thereby optimizing the k and excess noise. The two limitations of the Capasso design are (1) the leakage current due to doping the channels and (2) excess noise due to dual carrier injection. Firstly, to spatially separate the carriers between narrow and wide bandgap materials, type I band alignment with doping is suggested by Capasso. However, type II band alignment, due to the valance band offset, may inherently provide the field required for the spatial separation of carriers. And type II alignment avoids the doping that could lead to leakage currents. Secondly, channeling APD is a planar configuration leading to dual carrier injection that increases the excess noise. Using a window injection layer defined by lithography, a channeling APD with single carrier injection is designed.
Abstract 4548: The chemokine receptor CCR1 is involved in microglia stimulated glioblastoma invasion

Glioblastoma Multiforme (GBM) is the most aggressive form of adult brain tumor with a median survival time of twelve months. GBM is highly resistant to conventional therapy which includes surgical resection of the tumor, radiation treatment and chemotherapy. GBM cells are highly motile and invasive resulting in infiltrative tumors with poorly defined borders. GBM tumors are heavily infiltrated with microglia cells which are known to stimulate GBM cell invasion. Our laboratory has previously demonstrated that microglia strongly stimulates GBM invasion both in-vitro and in orthotopic animal models. This interaction was found to be dependent on CSF-1R which is expressed on all tumor infiltrating macrophages/microglia. Blockade of the CSF-1R using compounds such as pexidartinib (PLX3397) can inhibit microglia/macrophage-stimulated GBM invasion in-vitro and in vivo. A variety of chemokines are upregulated in the GBM tumor microenvironment and facilitate “cross-talk” between microglia and GBM cells eliciting a chemotactic response. We have demonstrated that the chemotactic ligand, CCL3, is similarly upregulated in GBM tumors. We postulated that inhibition of CCL3 associated receptors such as C-C receptor 1 (CCR1) might also inhibit GBM invasion, thus, a CCR1 antagonist could prove efficacious for blockade of microglia-induced glioblastoma invasion in vitro. Many potent CCR1 antagonists have been described in the literature. We chose four of these compounds with two distinct structural cores, all with reported IC50’s of less than 200 nM for inhibition of CCR1 binding versus CCL3. We examined the ability of these antagonists to block microglia-stimulated glioblastoma invasion using an in-vitro coculture invasion assay. Using quantitative PCR arrays, we also show that expression of chemokines and chemokine receptor genes is greatly altered in GBM conditioned media-treated microglia. Understanding the pattern of tumor-associated macrophage/microglia chemokine secretion in GBM may present additional targets for chemotherapeutic intervention and enhance immunotherapy. Citation Format: Salvatore J. Coniglio, Poornema Ramasundaram, Neshama Fournier, Danielle S. Hamilton, Gregory Marshall, Keia Smith, Diana Habib, James R. Merritt. The chemokine receptor CCR1 is involved in microglia stimulated glioblastoma invasion [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4548.
Art and Science in the Thinking of Rudolf Arnheim

In Rudolf Arnheim’s thinking, art and science are two different but complementary modes of knowing the world. In a review of Nelson Goodman’s Languages of Art, he wrote: “science employs and consumes sensory data in order to arrive at the principles governing the operations of physical and mental forces. In art, the sensory data themselves are the ultimate statement because what we are made to see and hear lets us experience the play of forces that govern our existence.” I wish to review Arnheim’s discussions of art and science and reinforce his intuitions with some ontological principles derived from his contemporary Roman Ingarden, in order to flesh out a truly “symmetrical” account of art and science. I will argue that science builds systems of thought to coordinate the determinacies of the world whereas art coordinates a few determinacies of the world to suggest alternative, possible and aspirational worlds. Both serve an orienting role for human cognition.
Cadmium Selective Etching in CdTe Solar Cells Produces Detrimental Narrow-Gap Te in Grain Boundaries

Recent advances in design and processing technology have made possible commercialization of polycrystalline (px)-CdTe as a photovoltaic absorber. Grain boundaries (GBs) are the most prominent struc...
Positron Emission Tomography in Head and Neck Cancer

PET imaging complements CT and MRI in the staging process of head and neck malignancies. It has been shown to be helpful in detection of nodal metastasis, distant metastasis and unknown primary tumors leading to a change in TNM classification in up to 20% of patients. Tumor stage and CT tumor volumes have been well-established variables in the stratification process of patients into favorable and unfavorable treatment groups. PET imaging with its ability to capture biological activity and areas of hypoxia within tumors adds other important variables to consider, with high FDG activities and hypoxia representing unfavorable risk factors. Utilization of FDG activity- or hypoxia-tumor maps facilitates more individualized treatment planning, with the possibility to deliver higher radiation doses to unfavorable tumor areas. Posttreatment PET imaging can help to decide whether lymph node dissection is needed and facilitates the detection of persistent or recurrent tumors, in particular when significant alterations of the soft tissues planes are present. The strengths, weaknesses and limitations of PET imaging prior, during and after treatment will be discussed in this chapter.