cssi/SciSciGPT-SciSciNet huggingface dataset:
How to Approach Śūnyatā as the Quantum Reality Through Biological Consciousness

Although there is a dispute as to who discovered the concept of śūnyatā, there is an agreement that the symbol of śūnya was available in India in the fifth century AD. The dot symbol and its subsequent form of the open circle indicate not only nothingness as we know the meaning of śūnya, but it symbolizes infinity as well as there is no beginning or end in the symbol. Therein lies a major symbolic meaning on how the śūnya explains infinite from nothing. Mathematically also the śūnya represents the whole as it cannot be divided by anything. The concept of quantum was basically developed to explain observed reality that was not possible to examine by material science laws that were created in the nineteenth cent ury. It ended up describing the whatness of the reality, without addressing the whyness. It has nevertheless become a major concept in physics today, and its mathematical expressions are being employed to many observations, from origin of the universe to functioning of atoms. However, it is worth noting that the quantum concept is a system developed by admitting the failure to comprehend and making that as the basis to attempt explaining all the physical phenomena. It has obviously succeeded in explaining and predictive verification of many processes to a certain extent. However, it has also become limited when applied more broadly. In other words, it has failed to develop a unified principle for even all things physical.
Pan cancer patterns of allelic imbalance from chromosomal aberrations in 33 tumor types

ABSTRACT Somatic copy number alterations (SCNAs), including deletions and duplications, serve as hallmarks of tumorigenesis. SCNAs may span entire chromosomes and typically result in deviations from an expected one-to-one ratio of alleles at heterozygous loci, leading to allelic imbalance (AI). The Cancer Genome Atlas (TCGA) reports SCNAs identified using a circular binary segmentation (CBS) algorithm, providing segment mean copy number estimates from Affymetrix single-nucleotide polymorphism DNA microarray total (log R ratio) intensities, but not allele-specific (“B allele”) intensities that inform of AI. Here we seek to provide a TCGA-wide description of AI in tumor genomes, including AI induced by SCNAs and copy-neutral loss-of-heterozygosity (cnLOH), using a powerful haplotype-based method applied to allele-specific intensities. We present AI summaries for all 33 tumor sites and propose an automated adjustment procedure to improve calibration of existing SCNA calls in TCGA for tumors with high levels of aneuploidy where baseline intensities were difficult to establish without annotation of AI. Overall, 94% of tumor samples exhibited AI. Recurrent events included deletions of 17p, 9q, 3p, amplifications of 8q, 1q, 7p as well as mixed event types on 8p and 13q. The AI-based approach identified frequent cnLOH on 17p across multiple tumor sites, with additional site-specific cnLOH patterns. Our findings support the exploration of additional methods for robust automated inference procedures and to aid empirical discoveries across TCGA.
Impulsivity and aggression: A meta-analysis using the UPPS model of impulsivity

Abstract Trait impulsivity has long been proposed to play a role in aggression, but the results across studies have been mixed. One possible explanation for the mixed results is that impulsivity is a multifaceted construct and some, but not all, facets are related to aggression. The goal of the current meta-analysis was to determine the relation between the different facets of impulsivity (i.e., negative urgency, positive urgency, lack of premeditation, lack of perseverance, and sensation seeking) and aggression. The results from 93 papers with 105 unique samples (N = 36, 215) showed significant and small-to-medium correlations between each facet of impulsivity and aggression across several different forms of aggression, with more impulsivity being associated with more aggression. Moreover, negative urgency (r = 0.24, 95% [0.18, 0.29]), positive urgency (r = 0.34, 95% [0.19, 0.44]), and lack of premeditation (r = 0.23, 95% [0.20, 0.26]) had significantly stronger associations with aggression than the other scales (rs
Regulatory Roles of Human Surfactant Protein B Variants on Genetic Susceptibility to Pseudomonas Aeruginosa Pneumonia-Induced Sepsis.

Surfactant protein B (SP-B) is essential for life and plays critical roles in host defense and lowering alveolar surface tension. A single-nucleotide polymorphism (SNP rs1130866) of human SP-B (hSP-B) alters the N-linked glycosylation, thus presumably affecting SP-B function. This study has investigated the regulatory roles of hSP-B genetic variants on lung injury in pneumonia-induced sepsis. METHODS Wild-type (WT) FVB/NJ and humanized transgenic SP-B-T and SP-B-C mice (expressing either hSP-B C or T allele without mouse SP-B gene) were infected intratracheally with 50 μL (4 × 10 colony-forming units [CFUs]/mouse) Pseudomonas aeruginosa Xen5 or saline, and then killed 24 or 48 h after infection. Bacterial dynamic growths were monitored from 0 to 48 h postinfection by in vivo imaging. Histopathological, cellular, and molecular changes of lung tissues and bronchoalveolar lavage fluid (BALF) were analyzed. Surface tension of surfactants was determined with constrained drop surfactometry. RESULTS SP-B-C mice showed higher bioluminescence and CFUs, increased inflammation and mortality, the higher score of lung injury, and reduced numbers of lamellar bodies in type II cells compared with SP-B-T or WT (P SP-B-T > WT. Levels of multiple cytokines in the lung of infected SP-B-C were higher than those of SP-B-T and WT (P < 0.01). Furthermore, compared with SP-B-T or WT, SP-B-C exhibited lower SP-B, higher NF-κB and NLRP3 inflammasome activation, and higher activated caspase-3. CONCLUSIONS hSP-B variants differentially regulate susceptibility through modulating the surface activity of surfactant, cell death, and inflammatory signaling in sepsis.
Biko: Exploring Black Identity in Brazil Through a U.S. Lens:

This article analyzes how Black Consciousness and Citizenship (CCN), a curriculum produced at the Steve Biko Cultural Institute (Biko) in Salvador, Bahia, Brazil, is influential to the production o...
The New Zealand white rabbit animal model of acute radiation syndrome: hematopoietic and coagulation-based parameters by radiation dose following supportive care.

Animal models that accurately reflect human responses to radiation injury are needed for advanced mechanistic investigation and development of effective therapeutics. The rabbit is an established a...
Ionic Effects on the Equilibrium Conformation of Catenated DNA Networks

In this work, we study the ionic effects on the equilibrium size and shape of kinetoplasts, a two-dimensional (2D) network of catenated DNA rings. With increasing ionic strength from 5 to 200 mM, we observe a decrease in kinetoplast size, primarily driven by the long-range electrostatic interactions that give rise to a change in effective DNA width. A fit of the experimentally measured kinetoplast size versus effective width yields a scaling exponent of 0.38. To probe the quantitative effects of ionic strength on kinetoplast size, we develop a scaling argument based on a generalized Flory approach for a 2D polymer represented as monomers on an open lattice. Interestingly, while ionic strength has a significant effect on kinetoplast size, we find that it does not impact the kinetoplast shape.
Optimal Control in Fluid Models of nxn Input-Queued Switches under Linear Fluid-Flow Costs

We consider a fluid model of n x n input-queued switches with associated fluid-flow costs and derive an optimal scheduling control policy to an infinite horizon discounted control problem with a general linear objective function of fluid cost. Our optimal policy coincides with the cμ-rule in certain parameter domains, but more generally, takes the form of the solution to a flow maximization problem. Computational experiments demonstrate the benefits of our optimal scheduling policy over variants of max-weight scheduling and the cμ-rule.
A single GnRH challenge promotes paternal care, changing nestling growth for one day.

Abstract Decades of comparative and experimental work suggest that testosterone (T) promotes mating effort at the expense of parental effort in many vertebrates. There is abundant evidence that T-mediated trade-offs span both evolutionary and seasonal timescales, as T is often higher in species or breeding stages with greater mating competition and lower in association with parental effort. However, it is less clear whether transient elevations in T within a male's own reactive scope can affect parental effort in the same way, with effects that are visible to natural selection. Here, we injected free-living male tree swallows (Tachycineta bicolor) with gonadotropin-releasing hormone (GnRH), thus temporarily maximizing T production within an individual's own limit. Passive loggers at each nest showed that GnRH-injected males provisioned more frequently than saline males for the subsequent day, and their offspring gained more mass during that time. The degree of offspring growth was positively correlated with the father's degree of T elevation, but provisioning was not proportional to changes in T, and GnRH- and saline-injected males did not differ in corticosterone secretion. These results suggest that prior knowledge of T-mediated trade-offs garnered from seasonal, evolutionary, and experimental research cannot necessarily be generalized to the timescale of transient fluctuations in T secretion within an individual. Instead, we propose that GnRH-induced T fluctuations may not result in visible trade-offs if selection has already sculpted an individual male's reactive scope based on his ability to handle the competing demands of mating and parental care.
Realization of a Model-Based DevOps Process for Industrial Safety Critical Cyber Physical Systems

Safety critical Industrial Cyber Physical Systems (CPS) have stringent safety and security requirements and need assurance of deterministic behavior during system operation. In many safety critical application domains, runtime monitors (or runtime verification) are used to enforce operational safety and security. One of the challenges in runtime verification is to identify the critical safety properties that we want to monitor at runtime. In this paper, we explore how structural verification activities in a Model Based Design and Engineering (MBDE) context help formulate more effective monitoring specifications to cover vulnerable areas in a system. We assert that leveraging synergy between design and runtime verification produces more informed runtime safety monitors. This approach of integrating design assurance and runtime safety and security is an important aspect of the dependable DevOps continuum process. To demonstrate this, we perform verification of an Emergency Diesel Generator Startup Sequencer (EDGSS) implemented on an FPGA overlay architecture using model-based verification techniques. We present our key findings on synergy between runtime verification and design processes to support a more inclusive safety case.
The AMP-dependent kinase pathway is upregulated in BAP1 mutant uveal melanoma

Metastatic uveal melanoma (UM) responds poorly to targeted therapies and immune checkpoint inhibitors. Loss of BRCA1-associated protein 1 (BAP1) via inactivating mutations in the BAP1 gene is associated with UM progression. Thus, molecular alterations caused by BAP1 dysfunction may be novel therapeutic targets for metastatic UM. Here, we found that phosphorylation of AMP-dependent kinase (AMPK) was elevated in BAP1 altered (or mutant) compared to BAP1 unaltered (or wild-type (WT)) UM tumors. As a readout of AMPK pathway activation, phosphorylation of an AMPK downstream effector, acetyl-CoA-carboxylase (ACC), was also elevated. BAP1 re-expression in BAP1-null UM cell lines decreased phospho-AMPK (pAMPK) and phospho-ACC (pACC) levels. AMPK phosphorylation is mediated by calcium/calmodulin dependent protein kinase kinase 2 (CaMKK2) and potentially liver kinase B1 (LKB1) in BAP1 mutant UM cells. Knockdown of AMPKα1/2 reduced the viability of BAP1 mutant UM cells, indicating a survival function of AMPK in BAP1 mutant UM. Our data suggest that the AMPK pathway is an important mechanism mediating the survival of BAP1 mutant UM. Targeting the AMPK pathway may be a novel therapeutic strategy for metastatic UM.
Safe Sampling-Based Air-Ground Rendezvous Algorithm for Dense Street Maps

Demand for fast and economical parcel deliveries in urban environments has risen considerably in recent years. A framework envisions efficient last-mile delivery in urban environments by leveraging a network of ride-sharing vehicles, where Unmanned Aerial Systems (UASs) drop packages on said vehicles, which then cover the majority of the distance before final aerial delivery. Notably, we consider the problem of planning a rendezvous path for the UAS to reach a human driver, who may choose between $N$ possible paths and has uncertain behavior, while meeting strict safety constraints. The long planning horizon and safety constraints require robust heuristics that combine learning and optimal control using Gaussian Process Regression, sampling-based optimization, and Model Predictive Control. The resulting algorithm is computationally efficient and shown to be effective in a variety of qualitative scenarios.
Defining competition vectors in a temperate alley cropping system in the midwestern USA: 1. Production physiology

With renewed interest in the use of ecologically-designed, sustainable agricultural systems for temperate regions of the world, agroforestry is being proposed as an alternative to intensive production of crops in monocultures. However, the knowledge-base for understanding and managing complex, multi-strata systems worldwide is limited, particularly so for temperate regions. We examined an alley cropping system in the midwestern US where maize (Zea mays L.) is grown in alleys between tree rows of either black walnut (Juglans nigra L.) or red oak (Quercus rubra L.). During a course of ten years, crop yields in rows adjacent to tree rows declined by 50% or more. With the experimental introduction of barriers to separate tree and crop root systems, yields in the rows near trees were equal to those of the center row (and monoculture). Irrespective of a high correlation between photosynthetically active radiation and net photosynthesis, shading did not have a major influence on crop yield. At this stage of system development (11 year old trees), influence of incident PAR on crop yield seems to be minimal. Subsequent papers in this series examine the sharing of belowground resources between trees and crops to quantify the competitive interactions that impact crop yields and their implications for economic return to the farmer.
Disruption of sphingolipid metabolism and stimulation of DNA synthesis by fumonisin B1. A molecular mechanism for carcinogenesis associated with Fusarium moniliforme.

Consumption of grains contaminated with Fusarium moniliforme (Sheldon) causes liver cancer in rats and has been correlated with esophageal cancer in humans. The causative agents are believed to be a family of compounds known as fumonisins, which bear remarkable structural resemblances to sphingosine and sphinganine, the long-chain (sphingoid) base backbones of sphingolipids. Recently, fumonisin B1 has been shown to block de novo synthesis of sphingolipids by inhibiting sphingosine (sphinganine) N-acyltransferase, which leads to accumulation of sphingoid bases. Because the exogenous addition of sphingosine and sphingosine 1-phosphate to Swiss 3T3 cells has been shown to stimulate DNA synthesis (Zhang, H., Buckley, N.E., Gibson, K., and Spiegel, S. (1990) J. Biol. Chem. 265, 76-81; Zhang, H., Desai, N.N., Olivera, A., Seki, T., Brooker, G., and Spiegel, S. (1991) J. Cell Biol. 114, 155-167), we hypothesized that fumonisins might stimulate DNA synthesis by disrupting sphingolipid metabolism. Fumonisin B1 caused accumulation of sphinganine and sphingosine in Swiss 3T3 fibroblasts and, as occurred when these sphingoid bases were added exogenously, stimulated thymidine incorporation into DNA and augmented the mitogenic effect of insulin in a concentration-dependent manner. The mechanism underlying the mitogenic effect of fumonisin B1 was further investigated by using beta-fluoroalanine to block the initial step of sphingolipid biosynthesis catalyzed by serine palmitoyltransferase. beta-Fluoroalanine reduced sphingoid base accumulation in fumonisin B1-treated fibroblasts and inhibited fumonisin B1-stimulated DNA synthesis, but had no effect on mitogenesis when added alone. Fumonisin B1 did not cause accumulation of sphinganine 1-phosphate; therefore, it appears that sphingoid bases per se can stimulate DNA synthesis. To prove that the 1-phosphate is not obligatory, a 1-deoxysphinganine was synthesized, and it was as potent as sphinganine in stimulating DNA synthesis. These results establish that fumonisin B1 is mitogenic via accumulation of sphingoid bases rather than inhibition of complex sphingolipid biosynthesis per se. Because mitogens can often affect cell transformation, this provides a plausible molecular mechanism to explain the carcinogenicity of fumonisins.
narI region of the Escherichia coli nitrate reductase (nar) operon contains two genes.

Abstract In previous studies it has been established that in Escherichia coli the three known subunits of anaerobic nitrate reductase are encoded by the narGHI operon. From the nucleotide sequence of the narI region of the operon we conclude that, in addition to the narG and narH genes, the nar operon contains two other open reading frames (ORFs), ORF1 and ORF2, that encode proteins of 26.5 and 25.5 kilodaltons, respectively. Protein fusions to each of the genes in the operon showed that expression of all four genes was similarly regulated. The reading frames of ORF1 and ORF2 were verified, and the N-terminal sequence for the ORF1 fusion protein was determined. The nar operon therefore contains four genes designated and ordered as narGHJI.
Phosphopantetheinyl transferase inhibition and secondary metabolism.

Efforts to isolate carrier protein-mediated synthases from natural product-producing organisms using reporter-linked post-translational modification have been complicated by the efficiency of the endogenous process. To address this issue, we chose to target endogenous phosphopantetheinyl transferases (PPTases) for inhibitor design to facilitate natural product synthase isolation through a chemical genetics approach. Herein we validate secondary metabolism-associated PPTase for chemical probe development. We synthesized and evaluated a panel of compounds based on the anthranilate 4H-oxazol-5-one pharmacophore previously described to attenuate PPTase activity within bacterial cultures. Through the use of a new high-throughput Forster resonance energy transfer assay, we demonstrated that these compounds exclusively inhibit fatty acid synthase-specific PPTases. In vivo, a lead compound within this panel demonstrated selective antibiotic activity in a Bacillus subtilis model. Further evaluation demonstrated that the compound enhances actinorhodin production in Streptomyces coelicolor, revealing the ability of this class of molecules to stimulate precocious secondary metabolite production.
Saccade target selection in frontal eye field of macaque. I. Visual and premovement activation

We investigated how the brain selects the targets for eye movements, a process in which the outcome of visual processing is converted into guided action. Macaque monkeys were trained to make a saccade to fixate a salient target presented either alone or with multiple distractors during visual search. Neural activity was recorded in the frontal eye field, a cortical area at the interface of visual processing and eye movement production. Neurons discharging after stimulus presentation and before saccade initiation were analyzed. The initial visual response of frontal eye field neurons was modulated by the presence of multiple stimuli and by whether a saccade was going to be produced, but the initial visual response did not discriminate the target of the search array from the distractors. In the latent period before saccade initiation, the activity of most visually responsive cells evolved to signal the location of the target. Target selection occurred through suppression of distractor evoked activity contingent on the location of the target relative to the receptive field. The evolution of a signal specifying the location of the salient target could be dissociated from saccade initiation in some cells and could occur even when fixation was maintained. Neural activity in the frontal eye fields may participate in or be the product of the decision process guiding eye movements.
Ciliary neurotrophic factor-mediated signaling regulates neuronal versus glial differentiation of retinal stem cells/progenitors by concentration-dependent recruitment of mitogen-activated protein kinase and Janus kinase-signal transducer and activator of transcription pathways in conjunction with Notch signaling.

In the retina, as elsewhere in the central nervous system, neurogenesis precedes gliogenesis; that is, the only glia in the retina, Muller cells, are born when the majority of neurons have already been generated. However, our understanding of how the multipotent retinal stem cells/progenitors choose to differentiate along neuronal and glial lineages is unclear. This information is important in promoting directed differentiation of retinal stem cells/progenitors in an ex vivo or in vivo stem cell approach to treating degenerative retinal diseases. Here, using the neurosphere assay, we demonstrate that ciliary neurotrophic factor (CNTF), acting in a concentration-dependent manner, influences the simultaneous differentiation of retinal stem cells/progenitors into neurons or glia. At low CNTF concentrations differentiation of bipolar cells is promoted, whereas high CNTF concentrations facilitate Muller cell differentiation. The two concentrations of CNTF lead to differential activation of mitogen-activated protein kinase and Janus kinase-signal transducer and activator of transcription (Jak-STAT) pathways, with recruitment of the former and the latter for the differentiation of bipolar and Muller cells, respectively. The concentration-dependent recruitment of two disparate pathways toward neurogenesis and gliogenesis occurs in concert with Notch signaling. Furthermore, we demonstrate that the attenuation of Jak-STAT signaling along with Notch signaling facilitates the differentiation of retinal stem cells/progenitors along the rod photoreceptor lineage in vivo. Our observations posit CNTF-mediated signaling as a molecular switch for neuronal versus glial differentiation of retinal stem cells/progenitors and a molecular target for directed neuronal differentiation of retinal stem cells/progenitors as an approach to addressing degenerative changes in the retina. Disclosure of potential conflicts of interest is found at the end of this article.
Was bedeutet Adoleszenz, und wie kann man sie erforschen?

Vera Kings Buch beschaftigt sich mit der Frage, wie die Adoleszenz in westlichen modernisierten Gesellschaften am besten theoretisch zu verstehen und zu untersuchen sei. In ihrer Analyse der Bedeutung und des Verlaufs der Adoleszenz berucksichtigt King stets die unterschiedlichen Bedingungen und Faktoren, welche auf die Adoleszenz einwirken, so u.a. die Generationszugehorigkeit, Geschlecht und sozialer Hintergrund bzw. soziale Ungleichheit. Wahrend sich der erste Teil des Buches mit wissenschaftsgeschichtlichen und methodologischen Fragen zur Adoleszenzforschung befasst, stellt King im zweiten Teil konkrete Analysen zu drei Schwerpunktthemen vor: Familie, Korperbedeutungen und Peer Group in der Adoleszenz.
Jakarta, drawing the city near

Districts are full of tough guys and tough women, shrewd operators who know how to make a buck out of anything, diligent civil servants who show up for work on time every day, studious children det...
Fuzzy Fractional Error Function Relied Neural Network Approximations

Here we treat the univariate fuzzy fractional quantitative approximation of fuzzy real valued functions on a compact interval by quasi-interpolation error function based fuzzy neural network operators.
Parting the Red Sea: The Religious Case for LGBT Equality

Much of the LGBT legal equality movement has focused on non-religious arguments. While that has netted gains in a purely legal sense, the broader - and more desirable - goal of social equality will remain elusive if the LGBT movement does not turn the religious argument around. In other words, LGBT proponents need to understand how to utilize religion to forward their causes, rather than ignore how opponents use it on the other side.
TGF alpha can act as a chemoattractant to perioptic mesenchymal cells in developing mouse eyes

Growth factors are believed to play an important role in regulating cell fate and cell behavior during embryonic development. Transforming growth factor alpha (TGF alpha), a member of the epidermal growth factor (EGF) superfamily, is a small polypeptide growth factor. Upon binding to its receptor, the EGF receptor (EGFR), TGF alpha can exert diverse biological activities, such as induction of cell proliferation or differentiation. To explore the possibility that TGF alpha might regulate cell fate during murine eye development, we generated transgenic mice that express human TGF alpha in the lens under the control of the mouse alpha A-crystallin promoter. The transgenic mice displayed multiple eye defects, including corneal opacities, cataracts and microphthalmia. At early embryonic stages TGF alpha induced the perioptic mesenchymal cells to migrate abnormally into the eye and accumulate around the lens. In situ hybridization revealed that the EGFR mRNA is highly expressed in the perioptic mesenchyme, suggesting that the migratory response is mediated by receptor activation. In order to test this model, the TGF alpha transgenic mice were bred to EGFR mutant waved-2 (wa-2) mice. We found that the eye defects of the TGF alpha transgenic mice are significantly abated in the wa-2 homozygote background. Because the EGFR mutation in the wa-2 mice is located in the receptor kinase domain, this result indicates that the receptor tyrosine kinase activity is critical for signaling the migratory response. Taken together, our studies demonstrate that TGF alpha is capable of altering the migratory decisions and behavior of perioptic mesenchyme during eye development.
The Public Address and the Rhetoric of Science: Henry Rowland, Epideictic Speech, and Nineteenth-Century American Science

The public address about scientific practice is an understudied genre in the scholarship on the rhetoric of science. Recent scholarship has studied expert-to-layperson addresses but not the relationship between addresses and other science writing. This article analyzes a scientific article and two speeches by Henry Rowland, the first chair of Physics at The Johns Hopkins University, and investigates how the public address supports and develops scientific ethos. Scientific ethos is developed through the genres of the scientific article and the public address, which delineates the mental activities that are presented through more commonly studied rhetorical activities in the scientific article.
Nipple attachment in neonatal rats exposed to alcohol prenatally

Previous work (Chen, Driscoll, & Riley, 1982) has shown that rat pups exposed to alcohol prenatally take longer to attach to the nipple of a test dam than do controls. However, the earliest age at which pups were tested was 3 days, which leaves open the possibility that the increased latencies might be the result of some altered postnatal experience. In the present study, rat pups whose mothers consumed liquid diets containing 35% or 0% ethanol-derived calories or lab chow were tested for nipple attachment before they had had an opportunity to suckle on their biological mothers. In support of previous data, animals exposed to alcohol prenatally were more apt to show longer attachment latencies than were controls.
On the characterization of good economic policy: Is there a consensus?

Abstract Starting from the classic treatment by Meade of the policy mix needed to secure internal and external balance simultaneously, this paper reviews the extent of consensus regarding the proximate objectives of economic policy. It is suggested that policy needs to be assessed in terms of its impact on at least five proximate objectives: the pressure of demand, the balance of payments, the rate of inflation, the expansion in supply capacity, and income distribution. The paper then suggests four policy rules: (1) the pursuit of microeconomic efficiency, to place the economy on the frontier; (2) maintenance of an effective though not necessarily rigid anti- inflationary stance; (3) continuous maintenance of internal balance; and (4) medium-term pursuit of a current balance target guided by thrift and productivity. It is argued that these propositions merit a consensus, and jointly provide a useful basis for policy evaluation, but that it is doubtful whether the area of consensus could be expanded much further.
Evaluating Methods for Modeling Epistasis Networks with Application to Head and Neck Cancer

Epistasis helps to explain how multiple single-nucleotide polymorphisms (SNPs) interact to cause disease. A variety of tools have been developed to detect epistasis. In this article, we explore the strengths and weaknesses of an information theory approach for detecting epistasis and compare it to the logistic regression approach through simulations. We consider several scenarios to simulate the involvement of SNPs in an epistasis network with respect to linkage disequilibrium patterns among them and the presence or absence of main and interaction effects. We conclude that the information theory approach more efficiently detects interaction effects when main effects are absent, whereas, in general, the logistic regression approach is appropriate in all scenarios but results in higher false positives. We compute epistasis networks for SNPs in the FSD1L gene using a two-phase head and neck cancer genome-wide association study involving 2,185 cases and 4,507 controls to demonstrate the practical application of the methods.
Outcome of early surgical complications following ileoanal pouch operation without diverting ileostomy.

Background Many surgeons use a diverting ileostomy routinely following ileoanal pouch operation because they fear that complications may lead to permanent unsatisfactory pouch function or even death. We report the outcome of early surgical complications when ileoanal pouch operation is performed without a diverting ileostomy. We performed 74 consecutive ileoanal pouch operations since October 1989 using a transition-zone-sparing stapled J pouch method. Results Of the 74 patients, 68 (92%) underwent the operation without a diverting ileostomy. Five of the 68 patients (7.4%) required reoperation within 30 days of operation. Pouch excision was necessary in 2 patients (3%) for reasons not resulting from omitting the diverting ileostomy, and they now have excellent pouch function. Conclusion Patients who required early reoperation and placement of a temporary diverting ileostomy did not suffer long-term consequences. The fear that early surgical complications following ileoanal pouch operation without diverting ileostomy are permanently detrimental is unjustified.
Measures of Clinical Significance

Behavioral scientists are interested in answering three basic questions when examining the relationships between variables (Kirk, 2001). First, is an observed result real or should it be attributed to chance (i.e., statistical significance)? Second, if the result is real, how large is it (i.e., effect size)? Third, is the result large enough to be meaningful and useful (i.e., clinical or practical significance)? In this last column in the series, we treat clinical significance as equivalent to practical significance. Judgments by the researcher and the consumers (e.g., clinicians and patients) regarding clinical significance consider factors such as clinical benefit, cost, and side effects. Although there is no formal statistical test of clinical significance, researchers suggest using one of three types of effect size measures to assist in interpreting clinical significance. These include the strength of association between variables (r family effect size measures), the magnitude of the difference between treatment and comparison groups (d family effect size measures), and measures of risk potency. In this paper, we review the d and r effect size measures and five measures of risk potency: odds ratio, risk ratio, relative risk reduction, risk difference, and number needed to treat. Finally, we review a relatively new effect size, AUC (which for historical reasons irrelevant to the current discussion stands for area under the receiver operating characteristic [ROC] curve), that integrates many of the others and is directly related to clinical significance. Each of these measures, however, has limitations that require the clinician to be cautious about interpretation. Guidelines are offered to facilitate the interpretation and understanding of clinical significance. Problems With Statistical Significance
Les nouveaux équipements de contrôle pour une maintenance prédictive des vannes

Framatome a developpe une strategie pour la maintenance et le diagnostic de la robinetterie, fondee sur l'experience, ses relations avec les exploitants et la R&D. L'application des concepts de maintenance predictive et l'utilisation de puissants outils de diagnostic et de gestion historique de donnees rencontre les enjeux majeurs des exploitants de centrales nucleaires : reduction des couts, de la dosimetrie, amelioration de la surete et de la disponibilite.
Computing the real roots of a Fourier series-plus-linear-polynomial: A Chebyshev companion matrix approach

Abstract Fourier series often need to be generalized by appending a linear polynomial to the usual series of sines and cosines. The integral of a trigonometric polynomial is one example; another is a time series of climate data where the periodic oscillations of the diurnal and annual cycles are accompanied by a non-periodic trend (global warming). Stock market averages fluctuate about a generally upward trend. Such non-periodic variations with time are commonly called “secular trends”. We borrow “secular” to label a truncated Fourier series plus a linear trend as a “linear”, secular trigonometric polynomial. Standard Fourier rootfinding methods are wrecked by the extra, nonperiodic term. Therefore, we introduce a new algorithm for computing the zeros of a Fourier polynomial-with-secular-trend. First, we expand the linear secular trigonometric polynomial f N ( t ) as a truncated Chebyshev series. Because of the special structure, it is easy to calculate a problem-dependent truncation M such that the error of the truncated Chebyshev series is guaranteed to be less than a user-specified tolerance. We then find the roots of the truncated Chebyshev series as the eigenvalues of the Chebyshev companion matrix. This computes all roots, but we explain why the method is not reliable for complex-valued roots unless these are close to the real axis. No a priori information is required of the user except the coefficients of the linear secular trigonometric polynomial. Numerical examples show that 13 decimal place accuracy for real roots is typical.
Multilateral Labor Relations in the Public Sector: Citizen Involvement:

This article examines institutionalized citizen involvement in the public sector labor relations pro cess, including (1) labor relations referenda, (2) sunshine bargaining, (3) trilateral bargaining, and (4) public hearings. It analyzes labor relations referenda and sunshine bargaining in depth, and gives summary evaluations of all four types of involvement.
Hormones and metabolites which control tracheid differentiation, with or without concomitant effects on growth, in cultured tuber tissue of Helianthus tuberosus L.

When tuber slices of Helianthus tuberosus, are cultured in liquid media containing minerals, thiamine, 2% sucrose, and 1 mg/l α-naphthalene acetic acid (NAA) for 14 days, 3–5% of the cells differentiate into tracheids. Addition of benzylaminopurine (BAP) at 5 mg/l, and 4% starch, which act as xylogenic stimuli, has little effect on growth but results in a yield of over 30% tracheids in the same time period. 70–80% of the tracheids appear between days 8 and 14 of culture. Addition to optimal tracheid media of gibberellic acid (GA3) or abscisic acid (ABA) inhibits tracheid differentiation by 80–90%. GA3 causes a concomitant 20–40% reduction in total cell number while ABA has no effect on growth. In media containing only NAA (lacking BAP and starch), ABA has a large stimulatory effect on the rate of cell division, producing 50% more cells than controls. Sucrose and glucose are equally effective sugars for differentiation, but use of the two in combination results in an unusual interaction leading to substantial inhibition of tracheid formation. There is some indication that the high level of BAP required in tracheid differentiation is acting only at the first regulatory step controlling formation of provascular cells, and not in later steps of cellular development.
COGNITIVE DISSONANCE AND RECALL OF INTERRUPTED AND COMPLETED TASKS

Summary.-The dissonance view of interruption was the basis of a prediction that volition for task commitment and expectation of task completion would affect differential recall of interrupted and completed tasks. 140 university students were randomly assigned to 4 treatment combinations of the 2 independent variables and individually asked to perform 20 paper-and-pencil tasks, half of which were intermpted. It was found that volition and expectation were related to recall of interrupted, but not completed, tasks in an interactive way. That is, higher volition led to better recall of interrupted tasks under low expectation while chere was no differential effect under higher expectation. The interactive results, taken as a whole, suggested an inverted-U relation between magnitude of dissonance and recall of interrupted tasks. In recent years there have been several studies on the relationship between cognitive dissonance and immediate recall of dissonant cognitions or stimuli. Brehrn and Cohen (1962), working directly within the framework of dissonance theory, conducted an experiment in which discrepant fictitious ratings of one's personality characteristics, supposedly made by a friend, were better recalled than consonant ratings. Along the same line, Schlachet (1965) showed that high dissonance (commitment to a greater likelihood of failure) resulted in more recall of dissonant (failure) stimuli in comparison with low dissonance (commitment to less certain failure) or non-dissonance controls. Evidence of the same sort has also been reported by Gerard and Fleischer ( 1967). Starting with a Zeigarnik-effect analogue, these investigators found that the recall of unbalanced stories with a positive P-to-O3 triadic relation in the Heiderian sense took precedence over the recall of balanced ones. Since the concept of imbalance and that of dissonance seem related regardless of whether imbalance is viewed as a kind of dissonance or vice versa (Brown, 1965; Jordan, 1968; Richter, 1965), Gerard and Fleischer's finding may be taken as evidence that dissonance could promote immediate recall of discrepant material. Quite contrary, however, were experimental results obtained by Buss and Brock ( 1963). These investigators had college students who were opposed to 'This article is based upon part of the data collected for a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Psychology from the University of Illinois. Special gratitude is expressed to G. L. Clore, M. E. Fishbein, K. E. Rennet, M. M. Tacsuoka, and K. G. Wia for their helpful suggestions and criticisms. Wow at the National Taiwan University, Taipei, Taiwan, China. 'P-to-0 means that a person (P) has an attitude or sentiment towards some other person (0).
The Role of the Plasma Membrane H+-ATPase in Plant–Microbe Interactions

Plasma membrane (PM) H+-ATPases are the primary pumps responsible for the establishment of cellular membrane potential in plants. In addition to regulating basic aspects of plant cell function, these enzymes contribute to signaling events in response to diverse environmental stimuli. Here, we focus on the roles of the PM H+-ATPase during plant–pathogen interactions. PM H+-ATPases are dynamically regulated during plant immune responses and recent quantitative proteomics studies suggest complex spatial and temporal modulation of PM H+-ATPase activity during early pathogen recognition events. Additional data indicate that PM H+-ATPases cooperate with the plant immune signaling protein RIN4 to regulate stomatal apertures during bacterial invasion of leaf tissue. Furthermore, pathogens have evolved mechanisms to manipulate PM H+-ATPase activity during infection. Thus, these ubiquitous plant enzymes contribute to plant immune responses and are targeted by pathogens to increase plant susceptibility.
Shielding Calculations for the Upgrade of the HFIR HB 2 Beam Line

Experimental facilities at the Oak Ridge National Laboratory's High Flux Isotope Reactor are being upgraded through the redesign of beam tubes supplying neutrons to those facilities. In support of the shield design for one of the beam lines HB-2, calculations were performed to determine dose rates outside the shielding as well as background radiation levels at various locations around the instrumentation. Low-power (10 % power) as well as full-power measurements were made at key locations, and calculated results were compared with corresponding measured results. This paper describes the calculations and compares the measured and calculated results. Most of the measured results, when normalized to the full-operating-power level, compared favorably with the calculated results. One differed by a factor of 2.5, and another differed by a factor of 6. Based on this agreement, one can infer that reasonable calculations for some three-dimensional shield designs can be performed using two-dimensional methods and two-dimensional approximations to the three-dimensional geometry. The results confirmed the adequacy of the design.
Hemodynamic Effects of a Single Intravenous Injection of Synthetic Human Brain Natriuretic Peptide in Patients With Heart Failure Secondary to Ischemic or Idiopathic Dilated Cardiomyopathy

Synthetic human brain natriuretic peptide (sBNP) is a polypeptide with the same amino acid sequence as the naturally occurring hormone. Preclinical studies have demonstrated that BNP has potent hemodynamic, diuretic, and natriuretic effects that might be beneficial in treating patients with heart failure. This study was a randomized, double-blind, placebo-controlled, ascending-dose trial of sBNP administered as a single intravenous bolus in 27 heart failure patients. Six groups of patients received sequentially increasing doses of sBNP (0.3, 1, 3, 10, 15, and 20 micrograms/kg, respectively) as a single intravenous injection, and hemodynamics were assessed by pulmonary artery monitoring catheter. The 10 and 15 micrograms/kg doses of sBNP resulted in significant reductions in pulmonary capillary wedge pressure (-73%, p < 0.001), mean pulmonary artery pressure (-41%, p < 0.001), mean arterial blood pressure (-28%, p = 0.001), and systemic vascular resistance (-53%, p = 0.004). Significant increases occurred in cardiac index (68%, p < 0.001) and stroke volume index (72%, p < 0.001). The magnitude and duration of hemodynamic changes were dose dependent. There were no adverse effects. sBNP injected as a single intravenous bolus in heart failure patients improves hemodynamics in a dose-related fashion. Further clinical investigations to determine the use of sBNP in decompensated heart failure are clearly warranted.
Transforming Growth Factor-Beta (Beta 1, Beta 2, and Beta 3) Gene Expression and Action During Pubertal Development of the Seminiferous Tubule: Potential Role at the Onset of Spermatogenesis

The potential role of transforming growth factor-beta (TGF beta) as a mediator of cell-cell interactions during the pubertal development of the seminiferous tubule was examined. Mesenchymal-derived peritubular cells and epithelial-like Sertoli cells were isolated from prepubertal, midpubertal, and late pubertal rat testes. The developmental expression of the multiple forms of TGF beta (TGF beta 1, -beta 2, and -beta 3) in whole testis and isolated somatic cell types was determined using a nuclease protection analysis. TGF beta 1 and TGF beta 2 mRNA expression was predominant in the immature testis and decreased at the onset of puberty. TGF beta 3 mRNA expression, the most abundant form of TGF beta present, peaked at an early pubertal stage, coincident with the initiation of spermatogenesis. Peritubular and Sertoli cells expressed each isoform of TGF beta during development. Peritubular cell mRNA expression of TGF beta 1, -beta 2, and -beta 3 decreased during pubertal development upon differentiation of th...
Intramyocellular oxygenation during ischemic muscle contractions in vivo.

There is some evidence that the fall in intramyocellular oxygen content during ischemic contractions is less than during ischemia alone. We used proton magnetic resonance spectroscopy to determine whether peak deoxy-myoglobin (dMb) obtained during ischemic ankle dorsiflexion contractions attained the maximal dMb level observed during a separate trial of ischemia alone (resting max). In six healthy young men, the rate of myoglobin desaturation was rapid at the onset of ischemic contractions and then slowed as contractions continued, attaining only 75 ± 3.3% (mean ± SE) of resting max dMb by the end of contractions (p = 0.03). Myoglobin continued to desaturate while ischemia was maintained following contractions, reaching 98 ± 1.8% of resting max within 10 min (p = 0.03 vs. end of contractions). Notably, contractions performed after 10 min of ischemia did not affect dMb (dMb = 100 ± 1.5% of resting max, p > 0.99), suggesting that full desaturation had already been achieved. The blunting of desaturation during ischemic contractions is likely a result of slowed mitochondrial oxygen consumption due to limited oxygen availability.
Coulomb distortion of pion spectra from heavy-ion collisions

The effects of final-state ..pi..-nucleus electromagnetic interactions in heavy-ion collisions are investigated in a covariant classical formulation. Experimentally observed mid-rapidity peaks in ..pi../sup +/ spectra are reproduced by a simple model and are shown to be sensitive to the gross features of the time-dependent nuclear charge distribution.
Intercepting Bacterial Indole Signaling with Flustramine Derivatives

Indole signaling is one of the putative universal signaling networks in bacteria. We have investigated the use of desformylflustrabromine (dFBr) derivatives for the inhibition of biofilm formation ...
Patient characteristics and treatments associated with a decline in upper-body function following breast cancer therapy.

Abstract Breast cancer therapy is often followed by a decline in upper-body function. Women (303) diagnosed with stage I or II breast cancer were interviewed 5 and 21 months after surgery and their medical records were reviewed. Women with cardiopulmonary comorbidity had an odds ratio for decline at the 5-month interview of 2.8 (95% CI 1.3–5.7), relative to women without. Women who received mastectomy (OR = 2.5; 95% CI 0.9–6.7) or breast-conserving surgery with radiation therapy (OR = 2.9; 95% CI 1.0–8.9) were at higher risk for decline at the 5-month interview than women who received only breast-conserving surgery. Women who had axillary dissection were more likely to report numbness or pain in the axilla (OR = 6.4; 95% CI 1.2–33) at the 21-month interview than women who did not. Clinicians should consider the functional consequences of treatment when discussing treatment options and postoperative care with women who have early stage breast cancer.