cssi/SciSciGPT-SciSciNet huggingface dataset:
In situ hybridization detection of varicella zoster virus in paraffin-embedded skin biopsy samples

Abstract Background: When virologic and molecular diagnostic techniques are unavailable, the diagnosis of varicella zoster virus (VZV) infection depends on clinical criteria and histologic evaluation of skin biopsy specimens or Tzank preparations. These methods can misdiagnose chickenpox and zoster, particularly when the clinical manifestations are atypical. Objective: To improve diagnosis in these settings, we developed an in situ hybridization technique for the detection of VZV utilizing a fluorescein-labeled oligonucleotide probe visualized with anti-fluorescein alkaline phosphatase-conjugated antibody. Study design: We retrospectively examined 26 paraffin-embedded skin biopsy specimens with histologic features consistent with VZV or herpes simplex virus (HSV) infection and 11 control cases by in situ hybridization. In situ hybridization for VZV and HSV-1 was compared with polymerase chain reaction (PCR) for VZV and HSV-1 and clinical and histologic examination. Results: Thirteen of the 26 study cases and two of the 11 control cases were positive for VZV by in situ hybridization. When compared with PCR, in situ hybridization was 92% sensitive and 88% specific. When compared with clinical diagnosis, in situ hybridization was 86% sensitive and 87% specific. All cases of chickenpox had VZV-positive inflammatory cells in the dermis but this finding was less frequent among the cases of zoster. Conclusions: This in situ hybridization technique is a sensitive and specific method for the diagnosis of VZV in skin lesions that is applicable to most histopathology laboratory settings. In addition, in situ hybridization reveals individual infected cells and may provide insight into the pathogenesis of VZV skin infection.
Rutile solubility and mobility in supercritical aqueous fluids

Experimental and thermodynamic data and the apparent immobility of Ti under metamorphic conditions suggest that rutile is very insoluble in aqueous fluids at upper crustal conditions. New solubility measurements at 1.0–2.93 GPa and 800–1200°C show, however, that under certain pressure and temperature conditions rutile is quite soluble in H2O. Solubilities were estimated from the measured weight loss of a single crystal equilibrated with a known mass of fluid in a piston cylinder apparatus. Measured solubilities in H2O range from 0.15 wt% (wt loss crystal/wt fluid) at 2.93 GPa and 1000°C to 1.9% at 1.0 GPa and 1100°C. Solubility increases with increasing temperature and with decreasing pressure in a manner given by the following fit to the experimental data: $$\log _{10} m_{Ti} = - 7049/T - (0.589* P)/T + 5.14$$ wherem Ti is the molality of Ti in the fluid,T is in degress Kelvin andP is in MPa. The effect of fluid composition on rutile solubility was also examined at 1.0 GPa and 1000°C for H2O-CO2, 1m NaCl, and 1m HF fluids. Kesults suggest that solubility depends on the mole fraction of H2O in the fluid but is independent of ionic strength and fluid pH. This behavior implies that Ti dissolves as the neutrally-charged hydrolysis product Ti(OH)4. The free energy of this species was calculated for each set of experimental conditions. TheP-T dependence of rutile solubility suggests that aqueous fluids derived from subducted oceanic lithosphere would dissolve rutile or other Ti-rich minerals from the deepest portion of the mantle wedge and precipitate them at higher levels. Subsequent melting of the base of the mantle wedge would form HFSE-depleted IAB.
Risk Implications of the New CKD Epidemiology Collaboration (CKD-EPI) Equation Compared With the MDRD Study Equation for Estimated GFR: The Atherosclerosis Risk in Communities (ARIC) Study

Background The Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) recently published an equation for estimated glomerular filtration rate (eGFR) using the same variables (serum creatinine level, age, sex, and race) as the Modification of Diet in Renal Disease (MDRD) Study equation. Although the CKD-EPI equation estimates GFR more precisely compared with the MDRD Study equation, whether this equation improves risk prediction is unknown. Study Design Prospective cohort study, the Atherosclerosis Risk in Communities (ARIC) Study. Setting & Participants 13,905 middle-aged participants without a history of cardiovascular disease with median follow-up of 16.9 years. Predictor eGFR. Outcomes & Measurements We compared the association of eGFR in categories (≥120, 90-119, 60-89, 30-59, and 2 ) using the CKD-EPI and MDRD Study equations with risk of incident end-stage renal disease, all-cause mortality, coronary heart disease, and stroke. Results The median value for eGFR CKD-EPI was higher than that for eGFR MDRD (97.6 vs 88.8 mL/min/1.73 m 2 ; P MDRD of 60-89 and 30-59 mL/min/1.73 m 2 , respectively, upward to a higher eGFR category, but reclassified no one with eGFR MDRD of 90-119 or 2 , decreasing the prevalence of CKD stages 3-5 from 2.7% to 1.6%. Participants with eGFR MDRD of 30-59 mL/min/1.73 m 2 who were reclassified upward had lower risk compared with those who were not reclassified (end-stage renal disease incidence rate ratio, 0.10 [95% CI, 0.03-0.33]; all-cause mortality, 0.30 [95% CI, 0.19-0.48]; coronary heart disease, 0.36 [95% CI, 0.21-0.61]; and stroke, 0.50 [95% CI, 0.24-1.02]). Similar results were observed for participants with eGFR MDRD of 60-89 mL/min/1.73 m 2 . More frequent reclassification of younger, female, and white participants explained some of these trends. Net reclassification improvement in participants with eGFR 2 was positive for all outcomes ( P Limitations Limited number of cases with eGFR 2 and no measurement of albuminuria. Conclusions The CKD-EPI equation more appropriately categorized individuals with respect to long-term clinical risk compared with the MDRD Study equation, suggesting improved clinical usefulness in this middle-aged population.
Premature osteoarthrosis in professional dancers.

Objective The purpose of this study was to determine whether arthrosis begins at an unusually early age in professional dancers; if there is an association between hypermobility and osteoarthrosis in dancers; and if osteoarthrosis is a contributing factor to retirement from a professional career in this population. Design Dance and injury history; physical examinations of back, lower extremities, and ligamentous laxity; and radiographs of lower extremity joints were performed in retired dancers. The dancers' radiographs were compared to those of age-matched nondancers. The radiologist was blinded to the origin of the radiographs. Participants Fourteen retired dancers aged 27 to 46 years who had performed professionally for a minimum of 10 years were included in the study. Thirty-six age-matched nondancers with injuries or pain in various lower extremity joints were used as controls. Main outcome measures This study measured radiographic findings of osteoarthrosis, including sclerosis, joint space narrowing, osteophytes, and subchondral cysts; hypermobility (after Klemp) as manifested by > 3 of 5 tests being positive; and the dancers' reasons for retirement. Results Changes of arthrosis were found in 34 of 56 joints in 14 dancers and in 3 of 36 joints in 36 nondancers. Hip calcifications were found in 10 hips in 7 dancers and in 1 nondancer's hip. None of the participants in this study was hypermobile or had retired because of arthrosis. Conclusions The prevalence of arthrosis in knees, ankles, and first metatarsophalangeal joints in young dancers was increased when compared to that of nondancers in the same age group. Arthrosis does not necessarily cause retirement from a performance career.
In-situ Polymerization of Maleic Acid and Itaconic Acid and Crosslinking of Cotton Fabric:

Polycarboxylic acids have been used as crosslinking agents for cellulosic materials to replace traditional formaldehyde-based reagents. The literature reports that maleic acid (MA) and itaconic acid (ITA) can copolymerize on cotton fabric in the presence of potassium persulfate, and esterification of cotton by the copolymer imparts wrinkle resistance to the treated cotton fabric. Our previous research found that in-situ copoly merization occurs only when both potassium persulfate and sodium hypophosphite are present on the cotton fabric. In this work, we investigate in-situ homopolymerization of maleic acid and itaconic acid on cotton fabric. We use Fourier transform infrared spectroscopy to study the anhydride carbonyls formed on the cotton treated with MA and ITA. We also use a redox titration technique to determine the quantity of the remaining monomers on the treated fabric. The data indicate that MA and ITA can polymerize on the fabric at elevated temperatures when potassium persulfate is present at ...
Src Homology-2 Domain-Containing Protein Tyrosine Phosphatase (SHP) 2 and p38 Regulate the Expression of Chemokine CXCL8 in Human Astrocytes

CXCL8, one of the first chemokines found in the brain, is upregulated in the brains and cerebrospinal fluid of HIV-1 infected individuals suggesting its potential role in human immune deficiency virus (HIV)-associated neuroinflammation. Astrocytes are known to be the major contributors to the CXCL8 pool. Interleukin (IL)-1β activated astrocytes exhibit significant upregulation of CXCL8. In order to determine the signaling pathways involved in CXCL8 regulation in astrocytes, we employed pharmacological inhibitors for non-receptor Src homology-2 domain-containing protein tyrosine phosphatase (SHP) 2 and mitogen-activated protein kinases (MAPK) pathway and observed reduced expression of CXCL8 following IL-1β stimulation. Overexpression of SHP2 and p38 enzymes in astrocytes led to elevated CXCL8 expression; however, inactivating SHP2 and p38 with dominant negative mutants abrogated CXCL8 induction. Furthermore, SHP2 overexpression resulted in higher SHP2 and p38 enzyme activity whereas p38 overexpression resulted in higher p38 but not SHP2 enzyme activity. Phosphorylation of SHP2 was important for phosphorylation of p38, which in turn was critical for phosphorylation of extracellular signal regulated kinase (ERK). Thus, our findings suggest an important role for SHP2 in CXCL8 expression in astrocytes during inflammation, as SHP2, directly or indirectly, modulates p38 and ERK MAPK in the signaling cascade leading to CXCL8 production. This study provides detailed understanding of the mechanisms involved in CXCL8 production during neuroinflammation.
2030 Established cmr methods for left ventricular quantification differ based on variable exclusion of papillary/trabecular volumes: increased diagnostic impact among patients with left ventricular hypertrophy

ss Open Acce Meeting abstract 2030 Established cmr methods for left ventricular quantification differ based on variable exclusion of papillary/trabecular volumes: increased diagnostic impact among patients with left ventricular hypertrophy Matthew Janik*, Matthew D Cham, Michael I Ross, Yi Wang, Noel Codella, James K Min, Shant Manoughagian, Peter M Okin, Richard B Devereux and Jonathan W Weinsaft
A peptide tag system for facile purification and single-molecule immobilization.

A peptide fusion tag and accompanying recombinant capture reagents have been developed based on the peptide-PDZ domain interaction and affinity clamps, a new class of affinity reagent. This system allows for single-step purification under mild conditions and stable capture of a tagged protein. The sub-nanomolar affinity, high force resistance (>30 pN), small size (~25kDa, ~1/6 of IgG) and monomeric nature of the affinity clamp are all superior features for many applications, in particular single-molecule measurements. Genetic fusion tags and accompanying capture reagents facilitate detection, purification and immobilization of recombinant proteins, and thus they have become an integral component in biochemical, biophysical and cellular investigations (1). Short peptide tags, often called epitope tags, are minimally invasive and useful for detection and purification. Folded protein tags often serve additional roles in increasing the solubility and expression yields. Together, available tag systems satisfy the requirements for standard applications in protein expression, detection
Sculpting the Analytical Volume in and around Nanoparticle Sensors Using a Multilayer Geometry

The use of structured nanoparticles as optical contrast agents has led to new sensing opportunities in localizing the analytical volume within or outside the particle. Here we examine the use of structured nanoparticles for controlling the sensed analytical volume and figures of merit for their use. Nanolayered alternating metal–dielectric particles (nanoLAMPs), consisting of metal–dielectric nanospheres, are a flexible and highly tunable structure and used here to illustrate the concept of sculpting the analytical volume associated with a nanoparticle. The alternating metal and dielectric shells in LAMPs are designed such that, when illuminated, the plasmonic coupling of metal shells results in amplified electric fields in specific volumes. The strength and extent of regions with amplified fields (hot spots) in and around a LAMP are at the expense of other regions with depleted fields. A rigorous Mie theory formulation is used to model electric field redistributions. A genetic algorithm-based strategy is...
Painful consequences of anger suppression

The authors experimentally examined the effects of anger suppression on pain perception. On the basis of ironic process theory, they proposed that efforts to suppress experiential or expressive components of anger may paradoxically enhance cognitive accessibility of anger-related thoughts and feelings, thereby contaminating perception of succeeding pain in an anger-congruent manner. Participants were randomly assigned to nonsuppression or experiential or expressive suppression conditions during mental arithmetic with or without harassment. A cold-pressor task followed. Results revealed that participants instructed to suppress experiential or expressive components of emotion during harassment not only reported the greatest pain levels, but also rated the anger-specific dimensions of pain uniquely strong. Results suggest that attempts to suppress anger may amplify pain sensitivity by ironically augmenting perception of the irritating and frustrating qualities of pain.
Visually mediated motor planning in the escape response of Drosophila.

A key feature of reactive behaviors is the ability to spatially localize a salient stimulus and act accordingly. Such sensory-motor transformations must be particularly fast and well tuned in escape behaviors, in which both the speed and accuracy of the evasive response determine whether an animal successfully avoids predation [1]. We studied the escape behavior of the fruit fly, Drosophila, and found that flies can use visual information to plan a jump directly away from a looming threat. This is surprising, given the architecture of the pathway thought to mediate escape [2, 3]. Using high-speed videography, we found that approximately 200 ms before takeoff, flies begin a series of postural adjustments that determine the direction of their escape. These movements position their center of mass so that leg extension will push them away from the expanding visual stimulus. These preflight movements are not the result of a simple feed-forward motor program because their magnitude and direction depend on the flies’ initial postural state. Furthermore, flies plan a takeoff direction even in instances when they choose not to jump. This sophisticated motor program is evidence for a form of rapid, visually mediated motor planning in a genetically accessible model organism.
Raptor responses to low-level jet aircraft and sonic booms.

Abstract We estimated effects of low-level military jet aircraft and mid- to high-altitude sonic booms (actual and simulated) on nesting peregrine falcons (Falco peregrinus) and seven other raptors by observing their responses to test stimuli, determining nesting success for the test year, and evaluating site reoccupancy rates for the year following the tests. Frequent and nearby jet aircraft passes: (1) sometimes noticeably alarmed birds, (2) occasionally caused birds to fly from perches or eyries, (3) most often evoked only minimal responses, and (4) were never associated with reproductive failure. Similarly, responses to real and simulated mid- to high-altitude sonic booms were often minimal and never appeared productivity limiting. Eighteen (95%) of 19 nest sites subjected to low-level jet flights and/or simulated sonic booms in 1980 fledged young during that year. Eighteen (95%) of 19 sites disturbed in 1980 were reoccupied by pairs or lone birds of the same species in 1981. We subjected four pairs of prairie falcons (Falco mexicanus) to low-level aircraft at ad libitum levels during the courtship and incubation phases when adults were most likely to abandon: all four eyries fledged young. From heart rate (HR) data taken via a telemetering egg at another prairie falcon eyrie, we determined that stimulus-induced HR alterations were comparable to rate changes for birds settling to incubate following flight. While encouraging, our findings cannot be taken as conclusive evidence that jet flights and/or sonic booms will have no long-term negative effects for other raptor species or for other areas. In addition, we did not experiment with totally naive wild adults, rotary-winged aircraft, or low-level sonic booms.
Membranes of Mammary Gland. XI. Marker Enzyme Distribution Profiles for Membranous Components from Bovine Mammary Gland

Abstract Enzyme distribution profiles of clarified bovine mammary homogenates separated by equilibrium centrifugation on linear sucrose gradients suggested that several of the commonly utilized marker enzymes for rat liver are also valid markers for mammary cellular components. These marker enzymes include: Succinate dehydrogenase (mitochondria), nicotinamide adenine dinucleotide phosphate cytochrome c reductase and, to a lesser extent, retenone insensitive nicotinamide adenine dinucleotide cytochrome c reductase (endoplasmic reticulum), galactosyl transferase (Golgi apparatus), 5′-nucleotidase (plasma membranes), uric acid oxidase (microbodies), and acid phosphatase (lysosomes). Rotenone sensitive nicotinamide adenine dinucleotide cytochrome c reductase and sodium, potassium, magnesium-stimulated adenosine triphosphatase were widely distributed among subcellular fractions and are not valid marker enzymes. The boyant densities determined for the above fractions should aid in design of methods to obtain enriched sources of these components for analysis.
The weak mixing angle and unification mass in supersymmetric SU(5)

We consider the predictions for the weak mixing angle 0w and the scale M of unification in a supersymmetric extension of SU(5). with particular emphasis on the sensitivity to the number of Higgs multiplets. In the one-loop approximation, we also calculate the ratio nrJrn,. We discuss generally the effects of an intermediate threshold between the weak interaction scale and M and estimate the sensitivity of 6’w and M to the scale of supersymmetry breaking The evolution of the coupling constants of the supersymmetric SU(3) 8 SU(2) @ U(1) effective gauge theory is described and the two-loop corrections to 6’, and M are calculated. Supersymmetric unified models (SUMS) offer a potential solution to the unnaturalness or gauge hierarchy puzzle of standard grand unified models (GUMS) of electroweak and strong interactions [ 1,2]. Attempts to build realistic SUMS face theoretical and phenomenological difficulties [2,3], but it has been emphasized [4] that the most naive extension of SU(5) will not substantially alter the successful prediction of the weak mixing angle Bw, whereas the unification mass scale M tends to increase by several orders of magnitude, thereby suppressing the proton decay rate beyond the range of feasible observation. Were this a universal feature of SUMS, the observation of proton decay would discourage further attempts to utilize supersymmetry to render GUMS natural*. In this paper, we reconsider the predictions for 8, and M in SUMS, emphasizing the sensitivity to the number of light Higgs doublets. We also extend the previous lowest order results to two loops, our motivation being twofold: (i) The accuracy of the one-loop approximation depends upon the size of higher order corrections, and, since SUMS generally will contain many more particles than GUMS, one might a priori expect higher order corrections to be relatively more important. (ii) Even a relatively modest change in the unification mass M produces a large change in the proton lifetime r a M4. Another topic treated in the course of this investigation is the change in the prediction of the quark-lepton ratio m,/m, in going from the minimal SU(5) GUM to the minimal SU(5) SUM. Remarkably enough, we find only a small change in this seemingly successful consequence of SU(5) unification. *See note added in proof.
Grafting of syndiotactic polystyrene by branched oligoethene using [Ni(π‐methallyl)(Br)]2/AlCl3 catalyst

The grafting of syndiotactic polystyrene with branched oligoethene was achieved with [Ni(π-methallyl)(Br)]2/AlCl3 as a catalyst. The molar ratio of AlCl3 to Ni(II) is important, and an efficient reaction occurs only with a large excess of AlCl3. The grafted polymers were characterized by NMR, wide-angle X-ray diffraction, and differential scanning calorimetry. The predominant grafts were sec-butyl groups. No melting point was observed for highly grafted polymers, and X-ray diffraction studies indicated that these materials were completely amorphous. © 2001 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 39: 446–451, 2001
ANALYSIS OF BREAKTHROUGH PROFILES BASED ON GAMMA-RAY EMISSION ALONG LOADED PACKED BED COLUMNS: COMPARATIVE EVALUATION OF IONSIV® IE-911 AND CHABAZITE ZEOLITE FOR THE REMOVAL OF RADIOSTRONTIUM AND CESIUM FROM GROUNDWATER

A gamma counting system has been assembled that can profile the breakthrough fronts of gamma-emitting radioisotopes longitudinally along a loaded column. This profiling technique has been particularly useful in column studies such as those performed with IONSIV® IE-911, a crystalline silicotitanate (CST) manufactured by UOP, in which long operating times are required to observe cesium effluent breakthrough at the low inlet (10−4 ppm) concentrations studied here. The length of the mass transfer zone and extent of column saturation can be detected by viewing the relative emission of gamma emitters along the length of the column. In this study, gamma scans were used to analyze loaded CST and zeolite columns used in the treatment of process wastewater simulant and actual groundwater. The longitudinal gamma scans for both 90Sr and 137Cs conformed with breakthrough results based on column effluent activity. Although not obvious from data obtained by monitoring effluent activity, the gamma scans indicated that b...
Behavioural correlates of dual diagnosis among women in treatment for substance abuse

While co-occurring disorders induced by mental illness and substance use can be debilitating, prioritizing care for such dually diagnosed individuals remain challenging. Determinants of dual diagnosis among women (n = 299) were examined in a substance-use treatment facility in Midwestern United States. Participants were mostly <40 years old, with histories of unemployment, trauma, and criminal justice involvement. One-third of the participants met DSM-IV criteria for dual diagnosis. Assessments included the Addiction Severity Index, and self-reported risky sexual behaviors. Binary logistic regression analyses revealed transactional sex, lower score on Global Assessment of Functioning (GAF) and low family and social support to be predictive of higher likelihood of dual diagnosis. Practice, policy and research implications are suggestive of holistic and integrated mental health treatment intervention plans for this population.
Effects of sex steroids on cell growth and C-myc oncogene expression in LN-CaP and DU-145 prostatic carcinoma cell lines.

The prostate gland is dependent on androgens for the maintenance of its normal growth and functional integrity. Initially, growth of the majority of prostate tumours can be manipulated by endocrine therapy. In the present study, we evaluated the effects of sex steroids on the cell growth and expression of the C-myc oncogene in two human prostatic adenocarcinoma cell lines. We found that dihydrotestosterone increases the proliferation rate of prostatic cells, and amplification of C-myc oncogene is hormone-dependent. We also demonstrated a positive correlation between the number of cells positive for C-myc oncogene and oncoprotein in hormone-treated prostated cell lines.
Pulling the cart and enjoying the ride.

▪ Abstract I was pleased to receive the invitation to write this prefatory chapter. In doing so, I join a number of physiologists whose work and writings I have often admired. There are two aspects of my experience in physiology that I discuss here. The first concerns my own research accomplishments. The second is my role in developing three departments of physiology and fostering the careers of others. While I take pleasure in the former, the overall contribution of the latter was undoubtedly greater.
Property Rights and Unemployment Insurance Reserves

Unemployment insurance (UI) laws have recently come under considerable criticism for fostering employment disincentives. Imperfections in the experience rating tax schedule has been the primary causal factor behind most of these allegations. In particular, the insurance subsidies created by the tax schedule have been blamed for distorted labor markets and for increased layoffs.
Alignment of Learning Objectives and Assessments in Therapeutics Courses to Foster Higher-Order Thinking

Objective. To determine whether national educational outcomes, course objectives, and classroom assessments for 2 therapeutics courses were aligned for curricular content and cognitive processes, and if they included higher-order thinking. Method. Document analysis and student focus groups were used. Outcomes, objectives, and assessment tasks were matched for specific therapeutics content and cognitive processes. Anderson and Krathwohl’s Taxonomy was used to define higher-order thinking. Students discussed whether assessments tested objectives and described their thinking when responding to assessments. Results. There were 7 outcomes, 31 objectives, and 412 assessment tasks. The alignment for content and cognitive processes was not satisfactory. Twelve students participated in the focus groups. Students thought more short-answer questions than multiple choice questions matched the objectives for content and required higher-order thinking. Conclusion. The alignment analysis provided data that could be used to reveal and strengthen the enacted curriculum and improve student learning.
Array-based assay detects genome-wide 5-mC and 5-hmC in the brains of humans, non-human primates, and mice

Background: Methylation on the fifth position of cytosine (5-mC) is an essential epigenetic mark that is linked to both normal neurodevelopment and neurological diseases. The recent identification of another modified form of cytosine, 5-hydroxymethylcytosine (5-hmC), in both stem cells and post-mitotic neurons, raises new questions as to the role of this base in mediating epigenetic effects. Genomic studies of these marks using model systems are limited, particularly with array-based tools, because the standard method of detecting DNA methylation cannot distinguish between 5-mC and 5-hmC and most methods have been developed to only survey the human genome. Results: We show that non-human data generated using the optimization of a widely used human DNA methylation array, designed only to detect 5-mC, reproducibly distinguishes tissue types within and between chimpanzee, rhesus, and mouse, with correlations near the human DNA level (R 2 > 0.99). Genome-wide methylation analysis, using this approach, reveals 6,102 differentially methylated loci between rhesus placental and fetal tissues with pathways analysis significantly overrepresented for developmental processes. Restricting the analysis to oncogenes and tumor suppressor genes finds 76 differentially methylated loci, suggesting that rhesus placental tissue carries a cancer epigenetic signature. Similarly, adapting the assay to detect 5-hmC finds highly reproducible 5-hmC levels within human, rhesus, and mouse brain tissue that is species-specific with a hierarchical abundance among the three species (human > rhesus >> mouse). Annotation of 5-hmC with respect to gene structure reveals a significant prevalence in the 3'UTR and an association with chromatin-related ontological terms, suggesting an epigenetic feedback loop mechanism for 5-hmC. Conclusions: Together, these data show that this array-based methylation assay is generalizable to all mammals for the detection of both 5-mC and 5-hmC, greatly improving the utility of mammalian model systems to study the role of epigenetics in human health, disease, and evolution.
Influence of water chemistry and travel distance on bacteriophage PRD-1 transport in a sandy aquifer

Experiments were conducted to evaluate the impact of groundwater chemistry and travel distance on the transport and fate behavior of PRD-1, a bacteriophage employed as a surrogate tracer for pathogenic enteric viruses. The experiments were conducted in the unconfined aquifer at the United States Geological Survey Cape Cod ToxicSubstances Hydrology Research Site in Falmouth, Massachusetts. The transport behavior of bromide (Br � ) and PRD-1 were evaluated in a sewage-effluent contaminated zone and a shallower uncontaminated zone at this site. Several multilevel sampling devices located along a 13-m transect were used to collect vertically discrete samples to examine longitudinal and vertical variability of PRD-1 retardation and attenuation. The concentration of viable bacteriophage in the aqueous phase decreased greatly during the first few meters of transport. This decrease is attributed to a combination of colloid filtration (attachment) and inactivation. The removal was greater (10 � 12 relative recovery) and occurred within the first meter for the uncontaminated zone, whereas it was lesser (10 � 9 relative recovery) and occurred over 4 m in the contaminated zone. The lesser removal observed for the contaminated zone is attributed to the influence of sorbed and dissolved organic matter, phosphate, and other anions, which are present in higher concentrations in the contaminated zone, on PRD-1 attachment. After the initialdecrease, the aqueous PRD-1 concentrations remained essentially constant in both zones for the remainder of the tests (total travel distances of 13 m), irrespective of variations in geochemical properties within and between the two zones. The viable, mobile PRD-1 particles traveled at nearly the rate of bromide, which was used as a non-reactive tracer. The results of this study indicate that a small fraction of viable virus particles may persist in the aqueous phase and travel significant distances in the subsurface environment. r 2005 Elsevier Ltd. All rights reserved.
Large-scale neural systems for vision and cognition

Consideration of how people respond to the question What is this? has suggested new problem frontiers for pattern recognition and information fusion, as well as neural systems that embody the cognitive transformation of declarative information into relational knowledge. In contrast to traditional classification methods, which aim to find the single correct label for each exemplar (This is a car), the new approach discovers rules that embody coherent relationships among labels which would otherwise appear contradictory to a learning system (This is a car, that is a vehicle, over there is a sedan). This talk will describe how an individual who experiences exemplars in real time, with each exemplar trained on at most one category label, can autonomously discover a hierarchy of cognitive rules, thereby converting local information into global knowledge. Computational examples are based on the observation that sensors working at different times, locations, and spatial scales, and experts with different goals, languages, and situations, may produce apparently inconsistent image labels, which are reconciled by implicit underlying relationships that the network's learning process discovers. The ARTMAP information fusion system can, moreover, integrate multiple separate knowledge hierarchies, by fusing independent domains into a unified structure. In the process, the system discovers cross-domain rules, inferring multilevel relationships among groups of output classes, without any supervised labeling of these relationships. In order to self-organize its expert system, the ARTMAP information fusion network features distributed code representations which exploit the model's intrinsic capacity for one-to-many learning (This is a car and a vehicle and a sedan) as well as many-to-one learning (Each of those vehicles is a car). Fusion system software, testbed datasets, and articles are available from http://cns.bu.edu/techlab .
A knowledge scoring engine (KSE) for real-time knowledge base generation used in intelligent tutoring systems

This paper provides a detailed account of a tool developed to facilitate the development of individual computational cognitive models to be used in intelligent tutoring systems (ITS). A generic tool that is called the knowledge scoring engine (KSE) reads eye tracking and human performance data in real-time, parses the data into discrete events, and uses a knowledge inference generator to build and update student knowledge bases. Student knowledge bases are generated by interpreting actions in real-time based on the context in which the actions take place. The knowledge bases generated by KSE are used by ADAPT, a comprehension-based framework construction-integration model of pilot action planning. This paper provides a detailed description of KSE, the current ADAPT architecture, how the ADAPT model interacts with KSE, and the potential for future developments.
Thermal diffusivity of aluminous spinels and magnetite at elevated temperature with implications for heat transport in Earth’s transition zone

The phonon component of thermal diffusivity ( D ) from 12 single crystals in the spinel family was measured at temperatures ( T ) of up to ~2000 K, using laser-flash analysis. Synthetic disordered spinel, 4 gemstones near MgAl 2 O 4 , nearly ZnAl 2 O 4 , 4 “hercynites” [(Mg,Fe 2+ )(Al,Fe 3+ ) 2 O 4 ], and 2 magnetites (nearly Fe 3 O 4 ) were characterized using optical spectroscopy and electron microprobe analysis. The magnetic transition in Fe 3 O 4 is manifest as a lambda curve in 1/ D , but otherwise, D decreases with increasing T and approaches a constant ( D sat ) at high T . Part of the decrease in D as T increases results from disordering above ~700 K: these two effects were distinguished by making multiple heating runs. At 298 K, D decreases strongly as either cation substitution or Mg-Al disorder increases, whereas D sat is moderately perturbed by substitutions. For both ordered and (equilibrium) disordered spinels and hercynites, the temperature dependence of 1/ D is best described by low-order polynomial fits. For spinel, combining our data with previous cryogenic studies of thermal conductivity ( k ) constrains the T dependence of D and k from ~0 K to melting. The response of D to disorder, impurity content, and cation mass for the aluminates is used to constrain D ( T ) for γ-Mg 2 SiO 4 and ringwoodite. Pressure derivatives are provided by relationships such as ∂ln( k lat )/∂ P = ∂ln( K T )/∂ P . Our results show that the phonon contribution to heat transport in Earth’s transition zone is high, particularly for large proportions of ringwoodite.
POLAR 2.0: An Effective Routability-Driven Placer

A wirelength-driven placer without considering routability would lead to unroutable results. To mitigate routing congestion, there are two basic approaches: (1) minimizing the routing demand; (2) distributing the routing demand properly. In this paper, we propose a new placer POLAR 2.0 emphasizing both approaches. To minimize the routing demand, POLAR 2.0 attaches very high importance to maintaining a good wirelength-driven placement in the global placement stage. To distribute the routing demand, cells in congested regions are spread out by a novel routability-driven rough legalization in a global manner and by a history based cell inflation technique in a local manner. The experimental results based on ICCAD 2012 contest benchmark suite show that POLAR 2.0 outperforms all published academic routability-driven placers both in runtime and quality.
Generation of feasible set points and control of a cable robot

Cable-suspended robots are structurally similar to parallel-actuated robots, but with the fundamental difference that cables can only pull the end-effector, but not push it. These input constraints make feedback control of cable-suspended robots a lot more challenging than their counterpart parallel-actuated robots. In this paper, we present a computationally efficient control design procedure for a cable robot with six cables, which is kinematically determined as long as all cables are in tension. The control strategy is based on dynamic aspects of statically feasible workspace. The basic idea suggested in this paper is to represent the reachable domain in terms of achievable set points under a specified control law that respects the input constraints. This computational framework is recursively used to find a set of reachable domains, using which, we are able to expand the region of feasibility by connecting adjacent domains through common points. The salient feature of the technique is that it is computationally efficient, or online implementable, for the control of a cable robot with positive input constraints. However, due to the complexity of the dynamics of general motion of a cable robot, we consider only translations. No cable interference is considered in this paper. Finally, the effectiveness of the proposed method is illustrated by numerical simulations and laboratory experiments on a six-degree-of-freedom cable-suspended robot.
Paired single cell co-culture microenvironments isolated by two-phase flow with continuous nutrient renewal

Cancer–stromal cell interactions are a critical process in tumorigenesis. Conventional dish-based assays, which simply mix two cell types, have limitations in three aspects: 1) limited control of the cell microenvironment; 2) inability to study cell behavior in a single-cell manner; and 3) have difficulties in characterizing single cell behavior within a highly heterogeneous cell population (e.g. tumor). An innovative use of microfluidic technology is for improving the spatial resolution for single cell assays. However, it is challenging to isolate the paired interacting cells while maintaining nutrient renewal. In this work, two-phase flow was used as a simple isolation method, separating the microenvironment of each individual chamber. As nutrients in an isolated chamber are consumed by cells, media exchange is required. To connect the cell culture chamber to the media exchange layer, we demonstrated a 3D microsystem integration technique using vertical connections fabricated by deep reactive-ion etching (DRIE). Compared to previous approaches, the presented process allows area reduction of vertical connections by an order of magnitude, enabling compact 3D integration. A semi-permeable membrane was sandwiched between the cell culture layer and the media exchange layer. The selectivity of the semi-permeable membrane results in the retention of the signaling proteins within the chamber while allowing free diffusion of nutrients (e.g., glucose and amino acids). Thus, paracrine signals are accumulated inside the chamber without cross-talk between cells in other chambers. Utilizing these innovations, we co-cultured UM-SCC-1 (head and neck squamous cell carcinoma) cells and endothelial cells to simulate tumor proliferation enhancement in the vascular endothelial niche.
A multiresolution generalized maximum likelihood approach for the detection of unknown transient multichannel signals in colored noise with unknown covariance

The problem of detecting transient signals of unknown waveforms has been widely studied in recent years due to the numerous applications associated with it. In particular, the detection of neural spikes using a recording array of closely spaced sensors in the brain is one such application. In this paper, we propose a new approach for solving this problem when no apriori knowledge is given about the signal and/or the noise processes. By extending our previous multiresolution analysis framework for noise suppression and source identification [1,2], we show that it is feasible to achieve reasonable detection performance in low SNR scenarios. Comparison to traditional detection schemes is presented and the overall performance is evaluated.
Is obesity un-American? Disease concerns bias implicit perceptions of national identity

Abstract The current research examined whether Americans incorporate obesity into their national identity, and further investigated the role an evolved behavioral immune system plays in shaping Americans' perceptions of obesity and national identity. Two studies revealed that obesity is not, on the whole, incorporated into the American identity at an implicit level. Moreover, when disease concerns were salient, either because of an experimental priming manipulation (Study 1) or due to recent illness (Study 2), thin individuals (for whom obesity may represent a particularly atypical morphology and thus a heuristic cue to disease) implicitly excluded obesity from the American identity to a greater degree. Thus, implicitly categorizing a subgroup of people as an outgroup pathogen threat may promote behavioral avoidance, exclusion, or stigmatization. This behavioral avoidance, could, in turn lead to less risk of fitness-reducing disease contraction. Further implications for evolutionary theories of disease avoidance, group identity, and discrimination are discussed.
Low-boiling-point solvent additives can also enable morphological control in polymer solar cells

Abstract Processing organic photovoltaic (OPV) blend solutions with high-boiling-point solvent additives has recently been used for morphological control in bulk-heterojunction OPV cells. Here we show that even low-boiling-point solvents can be effective additives. When P3HT:PCBM OPV cells were processed with a low-boiling-point solvent tetrahydrafuran as an additive in parent solvent o-dichlorobenzene, charge extraction increased leading to fill factors as high as 69.5%, without low work-function cathodes, electrode buffer layers or thermal treatment. This was attributed to PCBM demixing from P3HT domains and better vertical phase separation, as indicated by photoluminescence lifetimes, hole mobilities, and shunt leakage currents. Dependence on solvent parameters and applicability beyond P3HT system was also investigated.
Mediation: The Effects of Mediator Proposals, Number of Issues, and Altered Negotiator Aspirations

This study investigated the effects that a mediator's proposals, the number of issues, and the mediator's alteration of the negotiators' aspirations have upon negotiators' bargaining outcomes. In the study subjects bargained face to face while a confederate acted as the mediator. The results revealed that (a) mediator proposals improve negotiators' outcomes, (b) proposals are more effective when few issues are under negotiation, and (c) raised negotiator aspirations result in higher payoffs only when there are few bargaining issues.
Association of gene polymorphisms with development of cancer risk or their protective role associated with some mutant alleles.

Over the past decade, due to the advent of human genome project and its overwhelming success, there has been a great deal of interest in defining genetic polymorphisms and finding their associations with development of disease risks. However, to keep a consistent and balanced growth in this arena, one needs to have an in-depth knowledge about the extent of variations in phenotypes and their potential. Answers must be sought for questions, such as “In their ability to handle and rectify the DNA damage, how much do each individual vary from one another? To what extent do these variations play a role in making any individual susceptible to developing a higher cancer risk? And lastly, but more importantly, how far and to what limit genetic polymorphism can be held responsible for such variations?”.
Negative Refraction in a Cut-Off Parallel-Plate Waveguide Loaded with Two-Dimensional Lattice of Dielectric Resonators

A two-dimensional (2-D) negative-refractive-index metamaterial is proposed, which is composed of a parallel-plate waveguide and a square lattice of dielectric resonators (DR) inserted in it. The collective and macroscopic behavior of the DR lattice under TE resonance gives negative effective permeability whereas the parallel-plate waveguide below the cut-off for fundamental TE modes shows negative effective permittivity, which leads to the left-handedness. The 2-D triangular prism of the proposed left-handed waveguide that is sandwiched by right-handed parallel-plate waveguides provides the numerical and experimental demonstrations of the negative refraction for the propagated waves.
Minimal energy dissipation in logic

Minimal energy dissipations for the logic process based on thermodynamics and general phase space considerations are known. The actual availability of these minimal dissipations has not, however, been demonstrated. These minimal dissipation sources in a computing system also act as noise sources and thereby lead to questions about the ultimate available reliability of the computing process. A new and hypothetical device is presented in this paper and used to construct a physically analyzable computing system. It is demonstrated that this system has dissipations larger than, but of the same order of magnitude as, the original minimal quantities. It is also shown that any required reliability can be obtained with this device, without increased energy expenditure, but at the expense of an increasing time per computational step.
Experimental Results From a Two-Turn 40 mm Railgun

The Institute for Advanced Technology (IAT) has tested a high-inductance-gradient series-connected two-turn railgun. The primary goal of these experiments was to launch a dual-armature launch package in the two-turn configuration while maintaining electrical isolation between the rail and armature pairs. Two tests with the dual-armature launch package on a single-turn configuration independently examined the performance of the launch package. Results of those tests showed good thermal and structural performance of the armature assembly and no melt transfer between the armature contact regions. Five tests were then conducted on the two-turn rail configuration. During the second test, the crossover that connects the two rail pairs at the breech suffered arcing damage at the rail contacts. A new crossover was fabricated, and all subsequent tests were successful with no crossover arcing. The final system had a propulsive inductance gradient of 1.8 mu H/m, with projectiles successfully launched in excess of 400 m/s at linear current densities up to 35 kA/mm.