cssi/SciSciGPT-SciSciNet huggingface dataset:
Network-based Analysis of Time Series RNA-Seq Gene Expression Data by Integrating the Interactome and Gene Ontology Information

Monitoring the changes in gene expression patterns over time provides the distinct possibility of unraveling the mechanistic drivers characterizing cellular responses. Such time series gene expression data allow us to broadly "watch" the dynamics of the system. However, one challenge in the analysis of time series data is to establish and characterize the interplay between genes that are activated, deactivated or sustained in the context of a biological process or functional category. To address such challenges, novel algorithms are required to improve the interpretation of these data by integrating multi-source prior functional evidence. In this paper, we introduced a novel network-based approach to extract functional knowledge from time-dependent biological processes at a system level using time series mRNA deep sequencing data. First, a list of differentially expressed genes (DEGs) at each time point was identified. Second, GO terms that are enriched in each DEG list were identified. Third, the significance of interactions between DEGs in these GO terms at consecutive time points was measured. Finally, the significant interactions between DEGs in different GO terms were used to construct the interaction networks among GO terms between two consecutive time points, called GO networks. The proposed method was applied to investigate 1α, 25(OH)2D3- altered mechanisms in zebrafish embryo development. GO networks were constructed over 4 consecutive time points. Results suggest that biological processes such as cartilage development and one-carbon compound metabolic process are temporally regulated by 1α,25(OH)2D3. Such discoveries could not have been identified with canonical gene set enrichment analyses. These results demonstrate that the proposed approach can provide insight on the molecular mechanisms taking place in vertebrate embryo development upon treatment with 1α,25(OH)2D3. Our approach enables the monitoring of biological processes that can serve as a basis for generating new testable hypotheses. Such network-based integration approach can be easily extended to any temporal- or condition-dependent genomic data analyses.
The Laser Film Digitizer: Density, Contrast, and Resolution

This work evaluates differences in density linearity, contrast, and resolution of digital images acquired from a laser film scanner. A calibrated photographic step tablet tested linearity of diffuse optical density (OD). It was digitized within center openings of a dark and light film. The 14- × 17-inch films were scanned into 1024 × 1280 picture elements of 8 bits. A photographic tapered resolution guide evaluated the scanner’s detail resolution. A single characteristic curve adequately represents the rate of change of OD per pixel value, but two piecewise linear functions are better. One ranges in light OD and a second in dark OD. Contrast shows a steeper slope in a light film rather than a dark film, yet a greater difference exists between two identical digitizers. The resolution test diminishes at 1.3 line pairs per mm (LP/mm), which compares to a Nyquist limit of 1.44 LP/mm. Such density, contrast, and resolution tests yield a benchmark to assure quality operations.
Knowledge Level of HIV/AIDS among High School Drop-Outs.

Abstract This study was conducted to assess knowledge of HIV/AIDS among high school dropouts enrolled at Lincoln's Challenge Program (LCP), a military structured At-Risk Youth Program. The program was established to give high school drop-outs a second chance. LCP follows eight corps objectives, including education. By examining demographic characteristics, perceptions, and knowledge of drop-outs, educational programs can be designed to better meet needs of these youth. Involvement in this study was anonymous and voluntary for the 495 corpsmembers who participated. A quantitative research design using a survey for data collection was selected for this descriptive study. The survey consisted of two parts: (1) Demographics section, and (2) Reducing AIDS through Community Education (RACE) baseline knowledge instrument. Face and content validity were established. A Cronbach alpha reliability coefficient of .87 for the RACE indicated a reliable survey. Statistics Analysis System (SAS) was used for statistical a...
Phase stability in (Ni,Pt)3Al alloys

The primary goal of this study was to produce pseudobinary alloys based on (Ni,Pt)[sub 3]Al, and then test them mechanically as a function of temperature and observe the resulting dislocation structures. The ternary phase diagram has not been established with confidence, but it was hoped that extended solid solubility would exist and that the transition from one type of behavior to another could be captured and understood. These plans were based on the following observations: Ni[sub 3]Al and Pt[sub 3]Al are both L1[sub 2] materials, with similar lattice parameters; Ni and Pt are isomorphous above about 900 K; and a previous study established a preference for Pt to occupy Ni sites in Ni[sub 3]Al. In this paper, the authors present the results of the phase stability study; the mechanical behavior and dislocation structures will be presented later.
Consumer Perception of Web Site Security Attributes

It is known that consumer e-commerce decisions are affected by trust and the perception of security. Two relatively new aspects of Web security have not yet been studied, but have important consequ...
Tyrosine kinase activity of the EGF receptor in murine metanephric organ culture

Tyrosine kinase activity of the EGF receptor in murine metanephric organ culture. Epidermal growth factor (EGF) and its fetal form, transforming growth factor alpha (TGF-α) are renal mitogens which induce epithelial hyperplasia, proximal tubular cyst formation (TC), and accelerated distal nephron differentiation in metanephric organ culture. To delineate the intracellular mechanisms mediating these growth factor effects, we studied the specific role of the epidermal growth factor receptor (EGF-R), the common receptor for both ligands, as an activated tyrosine kinase in TC formation and nephrogenesis. Fetal murine metanephric explants were incubated for 120 hours in control, and EGF (15 ng/ml)/TGF-α (10 ng/ml) supplemented medium with and without EGF-R blocking monoclonal antibody (50 mg/ml), or tyrosine kinase inhibitor. EGF-R tyrosine kinase inhibition was achieved by incubation with a synthetic tyrphostin (TP B42) (0.1 µM) or genestein (5.5 µg/ml). The following parameters were assessed: (a) segment-specific nephron development using morphometry and immunohistology; (b) tubular epithelial hyperplasia by protein content and BrdU uptake; and (c) TC formation by morphometric cystic index. Both growth factors produced hyperplastic proximal TC, significantly increased explant growth, and significantly increased distal nephron differentiation. Inhibiting the ligand-EGF-R interaction with EGF-R blocking monoclonal antibody abolished all growth factor-induced effects and resulted in increased amounts of undifferentiated mesenchyme and decreased distal nephron differentiation. Inhibition of EGF-R tyrosine kinase activity with either Tyrphostin B42 or genestein blocked TC formation and produced nodular blastemal hyperplasia and decreased distal nephron differentiation. Inhibition of EGF-R tyrosine kinase activity may provide a target for pharmacological therapy in human cystic disease, in which there are both qualitative and quantitative abnormalities of EGF-R expression.
Out of the ordinary? British cities in the world city network

Abstract Over the past 20 years, world cities research has made a worthy attempt at mapping out the epistemological terra incognita in relation to the interface between contemporary globalization processes and an elite group of economically powerful cities. However, this has resulted in the construction of a theoretical object that seems inadequate when faced with the reality of global economic processes as they relate to less powerful, ‘ordinary’ cities throughout the world. Using relevant examples from the literature and introducing British provincial cities as a case study in order to contextualise the argument, this paper is intended to contribute to the growing body of work that seeks to challenge the conceptual and methodological approaches of the dominant world cities literature.
Quantum Dot/Plasmonic Nanoparticle Metachromophores with Quantum Yields That Vary with Excitation Wavelength

Coupled plasmonic/chromophore systems are of interest in applications ranging from fluorescent biosensors to solar photovoltaics and photoelectrochemical cells because near-field coupling to metal nanostructures can dramatically alter the optical performance of nearby materials. We show that CdSe quantum dots (QDs) near single silver nanoprisms can exhibit photoluminescence lifetimes and quantum yields that depend on the excitation wavelength, in apparent violation of the Kasha–Vavilov rule. We attribute the variation in QD lifetime with excitation wavelength to the wavelength-dependent coupling of higher-order plasmon modes to different spatial subpopulations of nearby QDs. At the QD emission wavelength, these subpopulations are coupled to far-field radiation with varying efficiency by the nanoprism dipolar resonance. These results offer an easily accessible new route to design metachromophores with tailored optical properties.
A prototype 8 × 8 pixel array X-ray detector for protein crystallography

Abstract An 8 × 8 pixel array X-ray detector prototype ( 1 100 maximum is less than 1 pixel width (150 μm), which is less than ( 1 2 ) that of a CCD and ( 1 7 ) that of an imaging plate detector [1].
Predictability of repeated challenge: effects on cardiovascular activity in the type A (coronary prone) behavior pattern.

Fifty-two healthy young adults classified either as Type A (coronary prone) or Type B were randomly assigned to a vigilance task during which observing responses produced targets according to either a predictable (i.e., fixed-interval 90-sec) or a nonpredictable (i.e., random-interval 90-sec) reinforcement schedule. During the task, blood volume pulse, interbeat interval, masseter (EMG) activity, and blood pressure were monitored. Transient peripheral vasomotor constriction and heart rate increases were initiated within an 8- to 12-sec period following target detection with the predictable schedule, with subjects evincing greater responsivity than their nonpredictable schedule counterparts. Type A subjects assigned to the random-schedule evinced significantly shorter heart rate and blood volume pulse response durations than did Type B subjects. Longer postevent EMG elevations were evidenced by subjects assigned to the predictable schedule. No significant blood pressure differences were found among the groups. The impact of challenge-contingent behavior on cardiovascular responsivity and the relevance of attentional processes to this relationship and to cardiovascular risk are discussed.
Adenosine 3',5'-Monophosphate: Electrophysiological Evidence for a Role in Synaptic Transmission

Synaptic potentials and changes in resting membrane potentials of superior cervical ganglia of the rabbit were measured in the presence of adenosine 3',5'-monophosphate and agents that affect its metabolism. Adenosine 3',5'-monophosphate and its mono- and dibutyryl derivatives caused a hyperpolarization of the postganglionic neurons. Theophylline potentiated the slow inhibitory postsynaptic potential that follows synaptic transmission, as well as the hyperpolarization of postganglionic neurons caused by exogenous dopamine. Conversely, prostaglandin E1 inhibited both the slow inhibitory postsynaptic potential and the dopamine-induced hyperpolarization. We hypothesize that the slow inhibitory postsynaptic potential as well as the dopamine-induced hyperpolarization result from increased amounts of adenosine 3'5'-monophosphate in the postganglionic neurons. The dibutyryl derivative of guanosine 3'5'-monophosphate caused a depolarization of the postganglionic neurons, which is consistent with the possibility that guanosine 3'5'-monophosphate mediates synaptic transmission at muscarinic cholinergic synapses.
Effects of the β2-adrenoceptor agonist clenbuterol on tyrosine and tryptophan in plasma and brain of the rat

The beta 2-adrenoceptor agonist, clenbuterol (initially 5 mg/kg), was found to significantly reduce plasma tyrosine and raise brain tryptophan levels (P less than 0.01). By comparison, decreases in plasma tryptophan and increases in brain tyrosine were small and often nonsignificant. Amino acid levels measured in different brain regions revealed that the elevations were similar among the cerebellum, striatum, and cortex. These effects were partially blocked by propanolol but not by atenolol. The ED50 was estimated from dose-response curves to be about 0.05 mg/kg for both the decrease in plasma tyrosine and the increase in brain tryptophan. The effects of low doses of clenbuterol were prevented completely by propranolol. Peripheral organs displayed strikingly different patterns of change in amino acid concentrations. Only the spleen had any accumulation of tryptophan, but that was much less than in brain. In contrast, tyrosine and tryptophan were decreased in heart and unaltered in liver; tyrosine was decreased in lung. The elevation in brain tryptophan levels was attenuated by the beta 2-antagonist, ICI 118,551, but not by the beta 1-antagonist, betaxolol; but the reduction in plasma tyrosine was unaffected by either drug. The serotonin antagonist, methysergide, failed to block the effects of clenbuterol. We conclude that changes in amino acid concentrations produced by clenbuterol are mediated by beta 2-adrenoceptor stimulation. Although the increases in brain tyrosine and tryptophan were similar to increases in the plasma ratios of these amino acids to the sum of the other large neutral amino acids competing for transport into the brain, the disparity between the effects of ICI 118,551 in brain and plasma suggests that clenbuterol may also have a direct action in brain to regulate levels of aromatic amino acids. Since clenbuterol has been purported to have an antidepressant effect and since other antidepressants also increase brain tryptophan, this may be a common feature of antidepressant drug action.
Sequence of an avian non-muscle caldesmon

We have sequenced a cloned cDNA from a chicken gizzard library which encodes a short version of caldesmon with the properties expected for the non-muscle protein. The predicted protein is 524 amino acids long with a molecular mass of 60174 daltons. Expression in bacteria produces a protein with an apparent molecular weight on SDS gels of 75–77000, that comigrates with human platelet caldesmon. The expressed protein binds to F-actin and is retained on calmodulin-Sepharose in the presence, but not absence of Ca2+. This non-muscle caldesmon isoform is identical to the smooth muscle protein at the N- and C-terminal ends, but is missing 232 amino acids from the centre. This central segment is thought to be helical, suggesting that non-muscle caldesmon is approximately 35 nm shorter, about 40 nm overall length, than smooth muscle caldesmon.
Midlife vs Late-Life Depressive Symptoms and Risk of Dementia: Differential Effects for Alzheimer Disease and Vascular Dementia

Context Depression and dementia are common in older adults and often co-occur, but it is unclear whether depression is an etiologic risk factor for dementia. Objective To clarify the timing and nature of the association between depression and dementia. Design We examined depressive symptoms assessed in midlife (1964-1973) and late life (1994-2000) and the risks of dementia, Alzheimer disease (AD), and vascular dementia (VaD) (2003-2009) in a retrospective cohort study. Depressive symptoms were categorized as none, midlife only, late life only, or both. Cox proportional hazards models (age as timescale) adjusted for demographics and medical comorbidities were used to examine depressive symptom category and risk of dementia, AD, or VaD. Setting Kaiser Permanente Medical Care Program of Northern California. Participants Thirteen thousand five hundred thirty-five long-term Kaiser Permanente members. Main Outcome Measure Any medical record diagnosis of dementia or neurology clinic diagnosis of AD or VaD. Results Subjects had a mean (SD) age of 81.1 (4.5) years in 2003, 57.9% were women, and 24.2% were nonwhite. Depressive symptoms were present in 14.1% of subjects in midlife only, 9.2% in late life only, and 4.2% in both. During 6 years of follow-up, 22.5% were diagnosed with dementia (5.5% with AD and 2.3% with VaD). The adjusted hazard of dementia was increased by approximately 20% for midlife depressive symptoms only (hazard ratio, 1.19 [95% CI, 1.07-1.32]), 70% for late-life symptoms only (1.72 [1.54-1.92]), and 80% for both (1.77 [1.52-2.06]). When we examined AD and VaD separately, subjects with late-life depressive symptoms only had a 2-fold increase in AD risk (hazard ratio, 2.06 [95% CI, 1.67-2.55]), whereas subjects with midlife and late-life symptoms had more than a 3-fold increase in VaD risk (3.51 [2.44-5.05]). Conclusions Depressive symptoms in midlife or in late life are associated with an increased risk of developing dementia. Depression that begins in late life may be part of the AD prodrome, while recurrent depression may be etiologically associated with increased risk of VaD.
EFFECTS OF GnRH TREATMENT ON SUPEROVULATORY RESPONSES OF DAIRY COWS

Twenty-eight Holstein cows were randomly divided into two groups. Group received 50 mg of FSH-P intramuscularly in declining doses for five days. Cows in group II received the same treatment as those in Group I but were also administered 250 ug of GnRH on the day of expected estrus. Neither the mean number of corpora lutea palpated nor the mean number of embryos recovered nonsurgically was different (P0.05) between treatments. However, administration of GnRH resulted in a higher fertilization rate and recovery of more developing embryos.
B Hadron Properties Measured in the DØ Experiment

We report on the observation of b-hadron states reconstructed using the DO detector data at the Tevatron Collider. Measurements of the mass and relative rates of neutral excited B d and B s mesons, and the discovery of the Ξ b baryon are described.
Primary erythrocytosis in the cat: Treatment with hydroxyurea

Primary erythrocytosis was diagnosed in six adult neutered domestic cats. All the cats showed varying signs of neurological dysfunction, including seizures, blindness, abnormal behaviour, episodes of ataxia, dilated pupils and foaming at the mouth. Other signs included polyuria, polydipsia, lethargy, wobbly gait, head bobbing and twitching. Affected animals had initially high packed cell volumes (PCV) (0.63 to 0.82 litres/litre) without any identifiable cause of relative or secondary erythrocytosis. Serum erythropoietin concentrations were low or normal in four cats, equivocal in one and undetermined in one. Primary erythrocytosis was diagnosed, rather than polycythaemia vera, as abnormalities often associated with the latter were uncommon (granulocytosis, splenomegaly) or unrecorded (thrombocytosis, hepatomegaly). The six cats were treated with hydroxyurea and five had phlebotomies. All remain well at least 10 months after treatment began, and two have survived more than six years, despite potential complications with hydroxyurea, including neutropenia, anaemia and methaemoglobinaemia.
Constructing American Lives: Biography and Culture in Nineteenth-Century America

Nineteenth-century American authors, critics, and readers believed that biography had the power to shape individuals' characters and to help define the nation's identity. In an age predating radio and television, biography was not simply a genre of writing, says Scott Casper; it was the medium that allowed people to learn about public figures and peer into the lives of strangers. In this pioneering study, Casper examines how Americans wrote, published, and read biographies and how their conceptions of the genre changed over the course of a century. Campaign biographies, memoirs of pious women, patriotic narratives of eminent statesmen, "mug books" that collected the lives of ordinary midwestern farmers--all were labeled "biography," however disparate their contents and the contexts of their creation, publication, and dissemination. Analyzing debates over how these diverse biographies should be written and read, Casper reveals larger disputes over the meaning of character, the definition of American history, and the place of American literary practices in a transatlantic world of letters. As much a personal experience as a literary genre, biography helped Americans imagine their own lives as well as the ones about which they wrote and read. |Nineteenth-century Americans believed that biographies influenced individual character and national identity. This book examines how Americans wrote, published, and read biographies during the 1800s, showing how their conceptions of the genre changed over time.
Network Server Supply Chain at HP: A Case Study

The confluence of several trends in manufacturing organizations has created many opportunities for supply chain management practitioners to apply their skills. These trends include the increasingly ubiquitous implementation of Advanced Planning Systems, the growing complexity of supply chains, and the recognition among managers of the importance of supply chain costs to profitability.
Fine motor activities in Head Start and kindergarten classrooms.

OBJECTIVE. The purpose of this study was to describe and compare the fine motor activities in Head Start and kindergarten classrooms in order to open a dialogue between the two contexts about the fine motor activities children in preschool will face in kindergarten. METHODS. Children in 10 Head Start and 10 kindergarten classrooms were observed for 1 day each. Time spent in activities was categorized into four groups: fine motor activities with no academic purpose, fine motor activities with academic purpose, academic activities with no fine motor component, and nonacademic activities with no fine motor component. Percentages of time were calculated and t tests were used for comparison between contexts. RESULTS. Children in Head Start spent 27%‐46% (mean of 37%) of the in-class day in all fine motor activities whereas children in kindergarten spent 36%‐66% (mean of 46%). For children in kindergarten, 42% of total fine motor activity time involved paper and pencil activities. In contrast, children in Head Start spent 10% of total fine motor activity time in paper and pencil activities. CONCLUSION. The higher mean percent of time spent in fine motor activities in kindergarten classrooms suggests a developmentally appropriate increase in fine motor demands. The percent of paper and pencil activity time the children engaged in substantially increased from Head Start to kindergarten. The findings describe a difference between the two environments, informing Head Start of the fine motor demands their graduates face in kindergarten.
Effective clinical practices for improved FNA biopsy cell block outcomes.

BACKGROUND Cell blocks are critically important in fine-needle aspiration (FNA) biopsies and the increasing requirements for personalized medicine testing further highlight their value. When a cell block is inadequate, it can necessitate additional procedures. The objective of the current study was to measure the impact and outcome of dedicated aspirate pass techniques and slide cellularity on cell block quality. METHODS Over a 6-month period, all FNA biopsy cases with cell blocks were identified. Procedural data including the number of dedicated aspirate passes were recorded. Individual cases were retrospectively reviewed and scored for multiple endpoints, including aspirate smear cellularity and cell block quality. RESULTS A total of 605 FNA biopsy and cell block cases were identified. The cell block quality score demonstrated a progressive improvement with an increasing number of dedicated biopsies. The performance of a single dedicated biopsy demonstrated a higher percentage of intermediate to high cell block quality scores in comparison with none (+12.1%; P = .0142). The performance of 3 dedicated biopsies demonstrated a higher percentage of intermediate to high cell block quality scores in comparison with a single pass (+13.5%; P = .0138). An intermediate-quality to high-quality terminal aspirate smear was more likely to have a high cell block quality score (+31.6%; P = .0001). CONCLUSIONS Performing at least 1 dedicated FNA biopsy pass was found to improve cell block quality and multiple dedicated biopsies resulted in nearly one-half having a higher quality score. A high-cellularity terminal FNA biopsy smear contributed significantly to obtaining a high-quality cell block. Performing dedicated FNA biopsies and the use of high-quality aspirate smears are effective clinical practices for improving cell block outcomes. Cancer (Cancer Cytopathol) 2015. © 2015 American Cancer Society.
Integrin-Mediated Transforming Growth Factor-β Activation, a Potential Therapeutic Target in Fibrogenic Disorders

A subset of integrins function as cell surface receptors for the profibrotic cytokine transforming growth factor-β (TGF-β). TGF-β is expressed in an inactive or latent form, and activation of TGF-β is a major mechanism that regulates TGF-β function. Indeed, important TGF-β activation mechanisms involve several of the TGF-β binding integrins. Knockout mice suggest essential roles for integrin-mediated TGF-β activation in vessel and craniofacial morphogenesis during development and in immune homeostasis and the fibrotic wound healing response in the adult. Amplification of integrin-mediated TGF-β activation in fibrotic disorders and data from preclinical models suggest that integrins may therefore represent novel targets for antifibrotic therapies.
The front speed of intrusions into a continuously stratified medium

This paper examines intrusive Boussinesq gravity currents, propagating into a continuously stratified fluid. We develop a model, based on energy arguments, to predict the front speed of such an intrusive gravity current from a lock release. We find that the depth at which the intrusion occurs, which corresponds to the level of neutral buoyancy (i.e. the depth where the intrusion density equals the stratified fluid density), affects the front speed. The maximum speeds occur when the intrusion travels along the top and bottom boundaries and the minimum speed occurs at mid-depth. Experiments and numerical simulations were conducted to compare to the theoretically predicted values, and good agreement was found.
Recognition of handwritten foreign mail

Foreign mail recognition (FMR) is part of the more general problem of recognizing destination addresses in a mail stream. It is defined as the problem of finding the country of destination of a mail piece sent to a foreign address. We discuss some of the differences between FMR and domestic mail recognition (DMR) and present its specific challenges. Two complementary baseline algorithms that use heuristics in combining word, character and digit recognizers are presented. Their performance is improved by reducing the search space for the address elements using address configuration distributions. Preliminary results are presented.
EVALUATING PROGRESS IN BEHAVIORAL PROGRAMS FOR CHILDREN WITH AUTISM SPECTRUM DISORDERS VIA CONTINUOUS AND DISCONTINUOUS MEASUREMENT

We evaluated the influence of two different frequencies of data collection on skill acquisition and maintenance within behavioral treatment programs for children with autism spectrum disorders. Six children were taught multiple skills in up to four different behavioral programs. Half of the skills were measured continuously (i.e., trial by trial), and the other half were measured discontinuously (i.e., first trial only). When differences were detected, quicker acquisition was typically associated with discontinuous measurement, and stronger maintenance was typically associated with continuous measurement.
High-Capacity, Microporous Cu6Sn5 – Sn Anodes for Li-Ion Batteries

Rechargeable lithium-ion batteries are extremely attractive, portable energy storage devices. The world’s increasing dependency on natural oil reserves for transportation has intensified international efforts to use lithium-ion batteries in hybrid-, plug-in hybrid-, and all-electric vehicles to constrain the growth of oil imports. For those goals to be realized, and particularly to increase the electric range of vehicles, the batteries need to store more energy, last longer, and most importantly, be safer than those currently manufactured. Safety limitations of state-of-the-art lithium-ion batteries arise from a number of factors, such as manufacturing defects, metal oxide cathode decomposition, overcharging a fully lithiated graphitic carbon LiC6 anode at or below the potential of metallic lithium, and the high reactivity between charged electrodes and flammable electrolyte solvents, particularly during thermal excursions.
An integrated approach of AHP and NFRs framework

One of the challenging areas in dealing with Non-Functional Requirements (NFRs) is the need for a decision support system which helps in a better trade-off among alternative operationalizations in the potential solution space for the NFRs. Dealing with such a trade-off is popularly treated with a qualitative fashion through the NFRs framework. In this paper, we propose the incorporation of the mathematical based trade-off technique: Analytical Hierarchy Process (AHP) to quantitatively deal with ambiguities, trade-offs, priorities and interdependencies among NFRs and operationalizations when using the NFRs framework. Such usage of the AHP technique within the NFRs framework will bring the benefits of the mathematically based trade-off techniques to the NFRs framework and eliminates the drawbacks associated with model-based trade-off techniques which the NFRs framework belongs to.
Evaluating mixture adsorption models using molecular simulation

The design of adsorption-based separation processes using novel adsorbents requires reliable data for the adsorption of fluid mixtures on candidate adsorbents. Due to the difficulty of generating sufficient data across possible operating conditions, process designs generally rely on interpolation of pure-component data using a model, most commonly ideal adsorbed solution theory (IAST), and related theories. There are many cases where IAST fails to provide an adequate description of mixture adsorption, usually due to the fact that practical adsorbents do not have uniform surfaces. We have evaluated the use of a segregated version of IAST, where competition is assumed to occur at isolated adsorption sites. This simple modification can provide the correct description of adsorption across a large range of pressures using ideal isotherm models. We also demonstrate the importance of identifying multiple sites even for weakly adsorbing components to provide the correct behavior at high pressure. © 2013 American Institute of Chemical Engineers.
Theory of high-temperature superconductivity and effective gravity

We argue that an approach involving effective gravity could play a crucial role in elucidating the properties of the high temperature superconducting materials. In particular we propose that the high critical temperature might be naturally explained in a framework constructed as a direct condensed matter analog of the Randall-Sundrum approach to a geometrization of the hierarchy problem in high-energy physics.
Quantum Optics and Quantum Information Processing with Photonic Crystal Devices

We have demonstrated classical and quantum information processing devices enabled by strong light-matter interaction in photonic crystals, including quantum dot-photonic crystal single photon source, ultrafast photonic crystal nanocavity laser, and small quantum network on chip.
Certainty and Circularity in Evolutionary Taxonomy

After a considerable period of uncritical acceptance, the principles and procedures of evolutionary taxonomy have been subjected to careful scrutiny and, none too surprisingly, have been found not completely adequate or totally free from vagueness and ambiguity. One of the more serious criticisms currently popular is that evolutionary reasoning is inherently circular. For example, Robert R. Sokal and P. H. A. Sneath (1963) say:
False Estrus in Human Females: Sexual Manipulation without Conception

Variations in human arousal independent of ovulation suggest that females use nonreproductive sex to manipulate interactions with males.
Response to 2'-deoxycoformycin after failure of interferon-alpha in nonsplenectomized patients with hairy cell leukemia.

Two patients with hairy cell leukemia with massive splenomegaly and severe pancytopenia were treated with recombinant alpha-A interferon (IFN-alpha-2a). There was no significant response to a trial of IFN- alpha-2a (11 and 20 weeks) with respect to blood counts or spleen size. Subsequent treatment with 2′-deoxycoformycin (dCF) for 8 consecutive weeks (4 mg/m2/wk) resulted in normalization of spleen size and a normalization of peripheral blood counts and bone marrow in one patient. The second patient demonstrated a reduction in spleen size and improved blood counts following 9 weeks of dCF therapy but eventually became refractory. This demonstrates that dCF is non-cross-resistant with interferon and confirms the efficacy of dCF in nonsplenectomized patients.
CHARMM-GUI 10 Years for Biomolecular Modeling and Simulation

CHARMM-GUI, http://www.charmm-gui.org, is a web-based graphical user interface to prepare complex molecular simulation systems and input files (CHARMM, NAMD, GROMACS, AMBER, OpenMM, CHARMM/OpenMM) to facilitate the usage of common and advanced simulation techniques. Since its original development in 2006, CHARMM-GUI has been widely adopted for various purposes and now contains a number of different modules designed to setup a broad range of simulations: PDB Reader & Manipulator for reading PDB structure files and modifying side chains (e.g., mutation, phosphorylation, protonation, lipid-tail linkers, spin labels, fluorophores, and unnatural amino acids), Glycan Reader for preparation of simulation systems containing carbohydrates or glycoproteins, Quick MD Simulator for solution simulation system generation, Membrane Builder for bilayer simulation system generation, HMMM Builder for HMMM-based bilayer system generation, Monolayer Builder for monolayer simulation system generation, Micelle Builder for micelle simulation system generation, PACE CG Builder for coarse-grained simulation system preparation using the PACE force field. Martini Maker for coarse-grained simulation system preparation using the Martini force field, PBEQ-Solver for electrostatic potential visualization, Ligand Binder for free energy perturbation molecular dynamics simulations for protein-ligand binding affinity calculations, Drude Prepper for conversion of CHARMM additive FF-based systems to Drude polarizable FF-based systems, and GCMC/BD ion simulator for Brownian dynamics of ions across ion channels. Recently, new modules have been integrated into CHARMM-GUI, such as Ligand Reader & Modeler for generation of the CHARMM-compatible topology and parameter files of ligands, Glycolipid Modeler for generation of various glycolipid structures, LPS Modeler for generation of various lipopolysaccharide structures. These new features together with existing modules are expected to be useful in advanced biomolecular modeling and simulation.
1003 Group and organisational safety climate in the fire service: psychometric pilot study results

Objectives Research related to safety climate in fire service organisations is limited. The researchers initiated a large-scale safety climate study in the fire service in the eastern and western United States. Methods The researchers have completed extensive qualitative research to identify and refine the dimensions of safety climate in the fire service and to refine the model guiding the research. Pilot data were collected from 208 firefighters in Georgia. Psychometric analyses were completed to assess reliability and validity. Results Psychometric analyses identified reliable scales. Group-level factors derived include supervisor support (α = 0.91), vertical cohesion (α = 0.92), and horizontal cohesion (α = 0.94). Key organisational factors derived include management commitment (α = 0.95) and programs/policies (α = 0.95). Other organisational factors included human resource management (α = 0.85) and incident command (α = 0.92). Safety behaviour scales were also derived, including safe work practices (α = 0.79), personal protective equipment use (α = 0.85), safety citizenship behaviour (α = 0.96), safety voice (α = 0.87) and employee rights and responsibilities (α = 0.79). Correlations between these latent factors were mostly highly significant. The only relationships not significant were between human resource management and safety citizenship behaviour and human resource management and personal protective equipment. Discussion Research within fire service organisations has been limited. This novel work provides some initial exploration into safety climate factors within the American fire service. The initial factors, which were psychometrically determined and analysed, provide initial guidance for future safety climate research in the fire service and provide information that practitioners can use to explore safety climate within fire and emergency service organisations.
Screening CT Angiography of the Aorta, Visceral Branch Vessels, and Pelvic Arteries in Fibromuscular Dysplasia

Abstract Objectives This study sought to evaluate the diagnostic yield of a dedicated computed tomography angiography (CTA) protocol of the chest, abdomen, and pelvis in patients with fibromuscular dysplasia (FMD). Background FMD is an uncommon vascular disease that may result in stenosis, dissection, or aneurysm of nearly all arterial distributions, typically affecting medium-sized arteries. Findings from the United States Registry for Fibromuscular Dysplasia have suggested the potential need to perform screening imaging of the aorta and medium branch vessels. Methods A total of 113 consecutive patients enrolled in our institutional FMD registry who received a tailored CTA protocol at our institution between March 2013 and June 2015 were included in this study. Arterial phase contrast-enhanced images were obtained on a dual-source scanner using high pitch and electrocardiogram trigger. Images were analyzed by 2 readers. Results Abnormalities including beading, aneurysm, dissection, and stenosis/occlusion were noted in aortic, renal, mesenteric, and iliac distributions. The most commonly affected vessels were the renal arteries (n = 76 [67%]), followed by the lower extremity/iliac arteries (n = 37 [32%]). Aortic abnormalities were less frequently encountered (n = 3 [3%]), including 1 case with mild dilation (4.2 cm) of the ascending aorta and 2 cases of dissection involving the descending aorta, 1 with mild dilation (4.4 cm). Incremental findings beyond those known at patient intake were commonly noted, including new areas of arterial beading (n = 55 [49%]), new aneurysms (n = 21 [19%]), and new dissections (n = 3 [3%]). Reformatted images were crucial, affecting final assessment in 56% of cases evaluated by reader 1 and 36% evaluated by reader 2. Conclusions Screening chest, abdomen, and pelvis CTA in patients with FMD showed substantial and incremental diagnostic yield. Reformatted images should routinely be included in imaging analysis. Abnormalities in the aorta were not common, so screening of the thoracic aorta may not be indicated.
Breathing while altricial: the ontogeny of ventilatory chemosensitivity in red-winged blackbird (Agelaius phoeniceus) nestlings

Altricial bird species, like red-winged blackbirds, hatch at an immature state of functional maturity with limited aerobic capacity and no endothermic capacity. Over the next 10–12 days in the nest...
FATETHICS: Response to Erich Goode

The general issues of ethics and fieldwork have been addressed in several rather good compendia (Sjoberg 1968; Klockars and O’Conner 1979; Social Problems 1980; Gubrium and Silverman 1989; Punch 1986, 1998). Each attempts to blend case studies and experiences that are highly contextual and occasioned— a particular experience by a person (of a given age, gender and education) doing fieldwork in a specific site in a specific period with general issues. Such exercises confront immediately the type-token problem—how does a given example or case fit a typology containing subheads like “personality,” “deception,” “privacy and harm”. . .? Many of the issues raised here are ethical, that is, standards of individuals, whereas social scientists seek guidelines for collective standards, or norms, morals and morality. That one is embarrassed, or ashamed, or guilty of some action is less important than whether one has violated a general rule of good conduct. In that sense, I am afraid we must cling to a vague and blurred idea about good conduct and sensitivity to violations of it. There is perhaps more agreement on unacceptable conduct than on the range of the acceptable. Goode’s essay may suggest possible harm to informants, but my concern is the absence of a clear research purpose or motivational account emphasizing scientific work.
Adventures in Communism: Counterculture and Camp in East Berlin

Abstract | This essay examines the encounter between Western countercultural groups and the urban landscape of East Berlin in the years immediately following the fall of the Berlin Wall in 1989. Focusing on squatted houses, the underground techno scene, and experimental art projects, the essay argues that countercultural groups who were active in East Berlin in the early 1990s developed a peculiar set of practices that were characterized both by their campy aesthetics and by their temporal indeterminacy. The essay posits that these experimental temporal practices were only possible due to the layered historicity of urban space in the dilapidated, inner-city neighbourhoods of East Berlin. Resume | Cet essai etudie la rencontre entre les groupes contre-culturels Occidentaux et le paysage urbain de Berlin-Est suite a la chute du Mur de Berlin en 1989. A travers une analyse des squats, de la scene techno « underground » et des projets d’art experimental, l’essai soutient que les groupes contre-culturels actifs dans le Berlin-Est du debut des annees 1990 ont developpe un ensemble de pratiques caracterise a la fois par leur esthetique manieree et leur indetermination temporelle. L’essai avance que seule l’historicite imbriquee de l’espace urbain dans les quartiers pauvres et dilapides du Berlin-Est a rendu possible ces pratiques temporelles experimentales.
Real-Time Control Architecture for Sauvim 1

Abstract This paper provides an overview of hardware and software architecture of SAUVIM (Semi-Autonomous Underwater Vehicle for Intervention Missions) which has been developed at the Autonomous Systems Laboratory (ASL). Unlike other autonomous underwater vehicles (AUVs), SAUVIM is equipped with an electric motor-driven dexterous robotic manipulator for underwater tasks requiring physical contacts with underwater objects. The overall vehicle-manipulator system becomes a high degrees-of-freedom multi-body nonlinear dynamic system. To effectively control this complex robotic system, distributed real-time hardware architecture and modified hierarchical software architecture with Sensor Data Bus (SDB) were used. The SDB makes it possible to get a prompt response from high-level control with respect to low-level sensor data. SAUVIM Task Description Language (STDL) was also developed to increase the flexibility of the vehicle tasks. Using STDL, any modification of control software is not required for various tasks. The user can also easily describe a task with various sensor data and handle multiple actuators.
An interactive generative abstraction system for the archetype-based pre-ideation process (IGATY)

Archetype in Greek means an original basis that prevails in all later forms. In the field of design, types and archetypes have been used as analytical tools; unfortunately, they have not been perceived as promising prospects in the search for creative ideas, and the dynamic transformative quality embedded in archetypes has not been fully utilized in the ideation process. This research is an exploration of re-establishing the value of implementing archetypes as generative abstractions in the initial phase of the ideation process. The fundamental structure of archetypes was redefined based on the dual structure of a core signal and a peripheral, and an interactive genetic algorithm (IGA) was implemented to visualize the transformative quality embedded in archetypes. In order to emphasize the experiential property of archetypes, the proposed system was designed to offer users the opportunity to view their exploration in a virtual environment (VE). Emphasis was placed on the artful use of technology in the pre-logical stage of the ideation process based on the theory of archetypes. This paper reports on the results from the experiment based on six museum archetypes focusing on (1) the system’s generative quality; (2) the synthesis evolution function; and (3) VE integration.
Dead Presidents: An American Adventure into the Strange Deaths and Surprising Afterlives of Our Nation's Leaders. By Brady Carlson. (New York, NY: W. W. Norton, 2016. Pp. 324. $26.95.)

Today's libraries contain hundreds of scholarly and popular books that examine the lives of American presidents. In covering a president's death, these works often move to a bigger picture to specu...
Principles of skin regeneration

Abstract: Partial regeneration of adult organs has been accomplished by induction. This is increasingly an alternative to organ transplantation. Skin was the first adult organ to be induced to regenerate partly in animals and in humans. Skin regeneration was induced following grafting of a highly porous scaffold based on a graft copolymer of type I collagen and chondroitin 6-sulfate (CG scaffold). Peripheral nerves and the conjunctiva have been similarly induced to regenerate. The structural determinants of active CG scaffolds have been determined. The data support a theory of induced regeneration in which contraction of a severe wound in an organ is blocked by the CG scaffold. Contraction blocking appears to require reduction of MFB (myofibroblasts) density in the wound as well as integrin-specific binding of contractile fibroblasts (MFB) on the extensive surface of the CG scaffold. When present in such reduced numbers and oriented quasi-randomly in the plane of the wound, MFB appear to lose their ability to contract wounds. Active CG scaffolds are powerful insoluble regulators of cell function. They appear to modify the adult wound healing to a process that resembles early fetal healing.
MEMS-Based Electrodynamic Synthetic Jet Actuators for Flow Control Applications

Synthetic jet actuators are used in various applications, such as separation control, mixing enhancement, and thermal management. Each of these requires the design to be optimized to meet specific performance requirements. This paper presents a design and scaling analysis of an electrodynamic synthetic jet actuator using a lumped element modeling approach. Various performance parameters, such as the resonant frequency, output volumetric flow rate and velocity, and jet formation, are studied as a function of device scale and current density. The viability and potential advantages of microscale synthetic jets are discussed.