cssi/SciSciGPT-SciSciNet huggingface dataset:
Enzymatic synthesis of periodic DNA nanoribbons for intracellular pH sensing and gene silencing.

We report the construction of periodic DNA nanoribbons (DNRs) by a modified DNA origami method. Unlike the conventional DNA origami, the DNR scaffold is a long, single-stranded DNA of tandem repeats, originating from the rolling circular amplification (RCA). Consequently, the number of folding staple strands tremendously decreases from hundreds to a few, which makes the DNR production scalable and cost-effective, thus potentially removing the barrier for practical applications of DNA nanostructures. Moreover, the co-replicational synthesis of scaffold and staple strands by RCA-based enzymatic reactions allows the generation of DNRs in one pot, further reducing the cost. Due to their unique periodicity, rigidity, and high aspect ratio, DNRs are efficiently internalized into cells and escape from endosomal entrapment, making them potential nanocarriers for imaging agents and biological therapeutics. We demonstrated proof-of-concept applications of DNRs as an intracellular pH sensor and an efficient small in...
Drug screening in the athletic setting.

Abstract Considerable energy and money are being spent on drug screening nationally, both in the workplace and the athletic arena. Many legal questions remain unanswered because there are so many different kinds of drug screening programs, and many of the issues have not been tested in court. Unfortunately, there is not a “gold standard” for screening for AOD in student-athletes or in any other setting. The efficacy and detrimental effects of drug screening on student athletes has not been examined in any scientific fashion, and further longitudinal studies are needed to determine efficacy.
Diabetic glomerulopathy in the uninephrectomized rat resists amelioration following islet transplantation.

Uninephrectomy is known to accelerate the development of both functional and morphological changes seen with experimental diabetic nephropathy in the rat. The present experiments utilized electron and light microscopic morphometric techniques to assess glomerular basement membrane width and the volumes of the total mesangium and its cellular and matrix components of inbred Lewis rats made diabetic at 6 weeks of age and uninephrectomized 9 days later. Immunofluorescent microscopy was used to evaluate IgG and C3 in the mesangium. The reversibility of established diabetic glomerular lesions in uninephrectomized diabetic rats after 7 months of diabetes was studied by performing intraportal transplant of neonatal pancreatic tissue. Renal biopsies were taken 2 months later in transplanted and non-transplanted animals. Islet transplantation lowered plasma glucose to normal levels (29.6 to 7.3 mmol/l) and raised plasma insulin values (6.3 to 53 μU/l). Glomerular basement membrane width in transplanted rats (268 nm) still exceeded the same measure (226 nm) in nondiabetic uninephrectomized rats. In transplanted animals volumes of the mesangium (0.51 × 106 μm3) and of its cellular (0.27 × 106 μm3) and matrix (0.24 × 106 μm3) components remained higher than similar measures in control rats (0.32 × 106, 0.17 × 106 and 0.15 × 106 μm3, respectively). Mesangial IgG in treated animals approached normal, but mesangial C3 remained similar to levels in non-transplanted diabetic control animals. These observations in uninephrectomized-diabetic rats contrast with previous observations in intact diabetic rats in which mesangial volumes and localization of immunoglobulins and complement returned to normal levels following islet transplantation.
Bacterial lipopolysaccharide shifts fasted plasma ghrelin to postprandial levels in rats

Lipopolysaccharide (LPS) injected intraperitoneally (i.p.) is known to decrease food intake. Ghrelin is a peptide hormone produced by the stomach with a potent orexigenic effect and plasma levels that are inversely correlated with the fed state. We examined changes in plasma ghrelin levels 3 h after LPS (100 microg/kg, i.p.) in fasted rats with or without a 1 h re-feeding period. LPS injection decreased the fasting levels of ghrelin by 51+/-5% compared with preinjection values while i.p. vehicle did not modify ghrelin levels in fasted rats. LPS at this dose reduced fasting-induced food intake by 60% compared with the i.p. vehicle group. Re-feeding decreased plasma ghrelin levels by 58+/-3% compared with pre-feeding fasting values in i.p. vehicle group. These data provide the first evidence that LPS shifts fasting ghrelin levels to those observed postprandially.
High Resolution Vapor Analysis for Fruit Variety and Fruit Product Comparisons

SUMMARY By using a system incorporating large-bore open-tubular gas chromatographic columns, high resolution vapor analyses of five fresh apple products were run. The improved peak separation attainable with such a system permits more detailed comparisons between different samples. This is a considerable aid in varietal studies and in following loss and change of volatiles during processing. The apple varieties examined appear to differ mostly in the relative proportions of individual components rather than in the presence or absence of certain constituents.
A simple membrane reactor to obtain high cell density and plasmid encoded protein production from Escherichia coli

A relatively simple system is described which yields high concentrations of cell mass and plasmid encoded protein. The maximum concentrations of cell mass and of a plasmid encoded protein, β-lactamase, obtained were: 49 g/L dry weight and 1.4 g/L, respectively.
Working with the private sector for child health.

This document assesses the current importance and potential of the private sector in contributing to child health. In many countries private and non-governmental providers are more commonly consulted for child health illnesses than public providers are. Even poor families often use private sector services. Families spend relatively large amounts of money for curative services in the private sector, even when there are cheaper public sector alternatives available. However, in many settings private providers are poorly regulated and the technical quality of the services they provide is questionable. This document focuses on the role of the private sector in the direct provision of child health services. The private sector clearly has a much broader potential role in many other areas related to and supporting the provision of child health services-including the provision of ancillary services, training of health professionals (both pre-service and in-service), communication services, and financing of health care. The potential of the private sector in each of these areas is touched on in this document, but a detailed treatment of each of these important topics is beyond the scope of the paper. Financing of health care and services is a particularly complex topic. In most countries, the private sector has an important role to play in financing both recurrent health service costs and investment costs.
The compositio of bovine cartilage and bone

Abstract 1. 1. Articular and epiphyseal plate cartilage, primary and secondary spongiosa of metaphyses and compact cortical bone from bovine long bones were analyzed for their content of nitrogen, water, ash, calcium, phosphorus, chondroitin sulfate, keratan sulfate, sialic acid and protein-polysaccharides. 2. 2. The collagen content of the organic matrix of calf articular cartilage (63.7%) is greater than epiphyseal plate cartilage (56.2%), but less than primary spongiosa (75.8%), secondary spongiosa (79.5%), or cortex (79.2%). The collagen content of the organic matrix of fetal articulawr cartilage (46.%) was less than that of the calf. 3. 3. The chondroitin sulfate content of the organic matrix of calf epiphyseal plate cartilage (33.9%) is greater than articular cartilage (25.3%), primary spongiosa (.9%), secondary spongiosa (1.1%), or cortex (0.8%); the concentration in the calf of keratan sulfate (4.36, 3.69, 3.29, 0.70, 0.86%) and sialic acid (0.69, 0.52, 0.41, 0.35, 0.25%) decreased in the same anatomical order. These polysaccharide materials were present in greater amounts in the fetal tissues. 4. 4. The protein-polysaccharide light fraction (PP-l) isolated from articular and epiphyseal plate cartilage of calves and fetuses does not vary greatly, but fetal PP-L fraction contained less protein than that of the calf, and articular PP-L fraction contained less protein than that from epiphyseal plate cartilage. 5. 5. Protein-polysaccharide isolated from spongiosa following collagenase digestion is similar to the PP-L fraction from other sources except for its lower content protein (6.9%).
Late Cretaceous basement foundering of the Rosario embayment, Peninsular Ranges forearc basin: backstripping of the El Gallo Formation, Baja California Norte, Mexico

Excellent exposure, well-controlled palaeobathymetry, and tightly-spaced, high-precision radiometric age control in the El Gallo Fm. permit rigorous quantitative analysis. Backstripping of these proximal nonmarine, forearc basin deposits reveals that, during the Late Cretaceous, the Rosario embayment of the Peninsular Ranges forearc was undergoing an episode of rapid tectonic subsidence. This subsidence had several marked effects on the sedimentology of the Rosario embayment: formation of a broad alluvial plain consisting of coarse-grained clastics; rapid (∼ 600 m Myr-1) aggradation of sediments; and a retrogradational succession of facies, capped by a marine transgression, as deposition failed to keep pace with eustatic rise and subsidence. Long-term sedimentation is driven by some combination of two allocyclic mechanisms: tectonic subsidence and eustatic sea-level rise. In order to evaluate which force predominated during deposition of the El Gallo Fm., the processes of sedimentation, compaction, and isostasy are evaluated through the interval in question. A sensitivity analysis is performed, in which the maximum tectonic and maximum eustatic contributions are estimated, along with the best-fit model. These results are qualitatively the same: tectonic subsidence was the major driving force of sedimentation in the Rosario embayment in late Campanian time. Regional sedimentological similarities suggest that this tectonic subsidence may have characterized the Peninsular Ranges forearc margin at this time, reflecting an episode of active down-faulting during the Late Cretaceous.
Application of a dipole-dipole coupling model to the carbonyl stretching spectra of some dinuclear metal carbonyls

Abstract A simplified treatment of the carbonyl stretching vibrations is described. The interactions between carbonyl groups, particularly intermolecular coupling and coupling between carbonyls bonded to different metal atoms, are described as being principally due to dipole- dipole forces. This force field allows a consistent interpretation of the solution and solid state spectra of a series of dinuclear metal carbonyl complexes. The molecules discussed are: [ h 5 -C 5 H 5 ) M (CO) 2 ] 2 , where M = Fe, Ru; [RhX(CO) 2 ] 2 , where X = Cl, Br, I; Ru 2 (O 2 CCH 3 ) 2 (CO) 4 (C 5 H 5 ) 2 ; and Os 2 (O 2 CCH 3 ) 2 (CO) 6 .
Region-based statistical analysis of 2D PAGE images

A new comprehensive procedure for statistical analysis of two-dimensional polyacrylamide gel electrophoresis (2D PAGE) images is proposed, including protein region quantification, normalization and statistical analysis. Protein regions are defined by the master watershed map that is obtained from the mean gel. By working with these protein regions, the approach bypasses the current bottleneck in the analysis of 2D PAGE images: it does not require spot matching. Background correction is implemented in each protein region by local segmentation. Two-dimensional locally weighted smoothing (LOESS) is proposed to remove any systematic bias after quantification of protein regions. Proteins are separated into mutually independent sets based on detected correlations, and a multivariate analysis is used on each set to detect the group effect. A strategy for multiple hypothesis testing based on this multivariate approach combined with the usual Benjamini-Hochberg FDR procedure is formulated and applied to the differential analysis of 2D PAGE images. Each step in the analytical protocol is shown by using an actual dataset. The effectiveness of the proposed methodology is shown using simulated gels in comparison with the commercial software packages PDQuest and Dymension. We also introduce a new procedure for simulating gel images.
A recursive algorithm to compute the wave‐scattering solution of a finite‐strip array using an efficient plane‐wave basis

A truncated, nonuniform, finite array of strips does not have a closed-form solution. Using translational symmetry, a recursive algorithm that calculates the scattering solution with N log2 N computational complexity is described. The current distribution for the Hz polarization shows small-length-scale oscillations not present in the Ez polarization.
Gender and Modes of Collaboration in a Chemical Engineering Design Course

Modes of collaboration are gendered in the sense that they define power relationships among members of a group. In this study, the authors define three collaborative modes: dialogic, asymmetrical, and hierarchical. Dialogic and asymmetrical modes are emancipating and characterized by flexibility, open-ended inquiry, and concern for the growth and development of the individuals involved. Hierarchical modes are oppressive and are characterized by rigidity and suppression of the voices of others in the group. Two collaborative writing groups in a chemical engineering design course exemplify these modes. The first, composed of two women and two men, was primarily dialogic, and the second, composed of two women and three men, exhibited characteristics of all three modes.
Collisionally Activated Dissociation of Transition Metal Ion/Polyether Complexes in a Quadrupole Ion Trap

For a series of polyether/transition metal ion complexes, collisionally activated dissociation reactions that are mediated by the flexibility of the polyether and the number of coordination sites are reported. The metal ions are generated by a pulsed laser desorption technique, and collision-activated dissociation methods are used to characterize the structures of the resulting metal/polyether complexes. The CAD patterns for the different polyether/metal ion complexes show striking variations depending on the flexibility of the ether, its number of coordination sites, and the type of metal ion. For example, (18-crown-6 + Co+) dissociates by loss of CHCH• or C2H3O• radicals, each pathway in conjunction with multiple losses of C2H4O, and resulting in products incorporating one covalent or ionic bond between the Co+ ion and the crown ether. In contrast, (12-crown-4 + Co+) dissociates by loss of CH2CH2 or C2H4O closed shell neutrals, each pathway in conjunction with additional losses of C2H4O and resulting in...
Science and technology for a general audience: The personal essay

To increase general readers' understanding and sympathy for scientific and technical subject matter, authors need a literary form that allows the material to be effectively related to common human experience. The imposing formality of scientific papers and technical reports must yield to the organic form and rhetorical richness of the personal essay. Stephen Jay Gould's essay “Of Bamboos, Cicadas, and the Economy of Adam Smith” demonstrates how the use of organic form and rhetorical techniques like examples, analogies, metaphors, historical background, and general personalism can enhance communication with nonspecialists. Excellence in essay writing is achieved only through careful planning, writing, and rewriting, but effective interpretation of science and technology for the intelligent general reader is worth the effort.
Differential O-glycosylation of a conserved domain expressed in murine and human ZP3.

Murine sperm initiate fertilization by binding to the zona pellucida (mZP), the specialized extracellular matrix of their homologous eggs. O-Glycans occupying two highly conserved vicinal glycosylation sites (Ser-332 and Ser-334) on the mZP glycoprotein designated mZP3 were previously implicated in this interaction. However, recent biophysical analyses confirm that neither site is occupied, implying that an alternate O-glycosylation domain may be operational in native mZP3. Since human ZP3 (huZP3) can substitute for mZP3 in rescue mice to mediate sperm binding, the site specificity of O-glycosylation in both native mZP3 and huZP3 was analyzed using ultrasensitive mass spectrometric techniques. Two O-glycosylation sites in native mZP3, one at Thr-155 and the other within the glycopeptide at positions 161−168 (ATVSSEEK), are conserved in huZP3 derived from transgenic mice. Thus, there is a specific O-glycosylation domain within native mZP3 expressing two closely spaced O-glycans that is very well conserved ...
Target discovery in small-molecule cell-based screens by in situ proteome reactivity profiling

Chemical genomics aims to discover small molecules that affect biological processes through the perturbation of protein function. However, determining the protein targets of bioactive compounds remains a formidable challenge. We address this problem here through the creation of a natural product-inspired small-molecule library bearing protein-reactive elements. Cell-based screening identified a compound, MJE3, that inhibits breast cancer cell proliferation. In situ proteome reactivity profiling revealed that MJE3, but not other library members, covalently labeled the glycolytic enzyme phosphoglycerate mutase 1 (PGAM1), resulting in enzyme inhibition. Interestingly, MJE3 labeling and inhibition of PGAM1 were observed exclusively in intact cells. These results support the hypothesis that cancer cells depend on glycolysis for viability and promote PGAM1 as a potential therapeutic target. More generally, the incorporation of protein-reactive compounds into chemical genomics screens offers a means to discover targets of bioactive small molecules in living systems, thereby enabling downstream mechanistic investigations.
A Synthesis of the World Literature of Ice Hockey Injuries: Epidemiologic Principles and Future Directions

Ice hockey is a fast-paced, aggressive sport whose participants are subject to relatively high rates of injury. Although there is a growing emphasis on the epidemiology of ice hockey research and its application towards reducing injuries, the literature has never been organized into an accessible database. Ice hockey is played in North America, Europe, Scandinavia, the U.K., and several other non-English speaking countries, yet injury reports not written in English are often ignored in review articles. The purpose of this project was to synthesize the existing world literature on ice hockey injuries into a framework of epidemiologic criteria, accessible in an organized, retrievable library. An extensive search of the following databases was done: MEDLINE, BIOSIS, EMBASE, NTIS, CURRENT CONTENTS, DISSERTATION ABSTRACTS, SPORT DISCUS, CINAHL, and WEB OF SCIENCE. Key words used were “ice hockey” and “injuries,” and the search range was 1966 to July 2007. Endnote X (Thompson Corp., Stamford, CT) was used for reference compilation. Eight hundred sixty seven documents were catalogued, from 27 countries in 8 languages. Documents were first categorized by type, including injury (226), equipment (45), case reports (94), review articles (294), editorials (39), or as focusing on the physiological, psychological, or medical aspects of ice hockey (169). Documents were then subdivided by study type and whether they were prospective (117) or retrospective (109). Further subdivisions beyond these levels were based on the inclusion of certain critical epidemiological criteria, including exposure time, a clear definition of “injury,” and the level of play, among others. This comprehensive database should make future ice hockey research more efficient, as well as promote sound epidemiology and a more global perspective.
Observation of Quantum Dissipation in the Vortex State of a Highly Disordered Superconducting Thin Film

We present transport measurements on a highly disordered, amorphous thin film superconductor that shows a crossover from activated to temperature independent resistance at low temperatures in the presence of a magnetic field. We interpret the data in terms of quantum tunneling of vortices, and find that within this interpretation the tunneling objects are not single vortices but rather dislocations and antidislocations of the vortex lattice, which nucleate quantum mechanically as unbound pairs. We note, however, that other interpretations of the data may be possible.
Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

Eukaryotic cytosine methylation represses transcription but also occurs in the bodies of active genes, and the extent of methylation biology conservation is unclear. We quantified DNA methylation in 17 eukaryotic genomes and found that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons is not. We show that methylation of plant transposons in the CHG context extends to green algae and that exclusion of histone H2A.Z from methylated DNA is conserved between plants and animals, and we present evidence for RNA-directed DNA methylation of fungal genes. Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes.
Application of LED imager for breast cancer diagnosis

This paper focuses on breast cancer diagnosis using the newly developed low-noise threewavelength (?=730nm, 805nm and 850nm) NIR light emitting diode (LED) continuous-wave (CW) imager. The NIR CW imager has its advantage of simplicity, and potential for a portable instrument. The imaging rate is 5 frame/second. The signal to noise ratio is larger than 2000 when measuring at a breast model ( ?a=0.04/cm, ?'= 8/cm), which corresponds to 4x 10-4 optical density (OD) error. Phantom test was carried out, and indicated good localization of heterogeneity. It was known that cancer has more blood concentration and de-oxygenation than normal tissue, which is the principle of breast cancer detection using NIR spectroscopy. Clinical results of breast cancer studies will be presented. Keywords: LED, Breast Cancer Imaging, CW
Manipulation of particles using dielectrophoresis

Abstract A numerical scheme based on the distributed Lagrange multiplier method (DLM) is used to study the motion of particles of electrorheological suspensions subjected to non-uniform electric fields. At small Reynolds number, the time taken by the particles to collect at the minimums or maximums of the electric field is primarily determined by a parameter defined to be the ratio of the dielectrophoretic and viscous forces. Simulations show that in non-uniform electric fields the collection time is also influenced by a parameter defined by the ratio of the electrostatic particle–particle interaction and dielectrophoretic forces. The collection time decreases as this parameter decreases because when this parameter is less than one, particles move to the regions of high or low electric field regions individually. However, when this parameter is greater than one, particles regroup into chains which then move toward the electric field maximums or minimums without breaking. It is also shown that when the real part of the Clausius–Mosotti factor (β) is negative the positions of the local minimums of the electric field, and thus also the locations where particles collect, can be modified by changing the electric potential boundary conditions.
Comprehensive modeling of ELMs and their effect on plasma-facing surfaces during normal tokamak operation

During the normal operation of the high confinement regime (H-mode) in next generation tokamaks, edge-localized modes (ELMs) are a serious concern for divertor plasma-facing components. The periodic relaxation of edge pressure gradient results in pulses of energy and particles transported across the Separatrix to the scrape-off-layer (SOL) and eventually to the divertor surface. ELMs could, therefore, result in cyclic thermal stresses, excessive target erosion, and consequently shorter divertor lifetime. In this study a comprehensive two-fluid model has been developed to integrate SOL parameters during ELMs with divertor surface evolution (melting, vaporization, vapor cloud dynamics, and macroscopic spallation) for different ELM parameters. Calculations were performed using the HEIGHTS numerical simulation package. Initial results indicate that high-power ELMs in ITER-like machines can cause serious damage to divertor components, may terminate plasma in disruptions, and may affect subsequent plasma operations due to extensive contamination.
Characterization of a hollow cathode styled plasma reactor for photovoltaic applications

Heated pocket deposition sources are often used for the rapid manufacture of thin film CdS/CdTe photovoltaic devices, however, new process methods are needed to further improve the quality of the films, increase cell efficiency, and reduce production costs. A plasma-enhanced, close-spacing sublimation (PECSS) technique utilizing a hollow cathode style discharge in a heated pocket has recently been developed as a candidate process method. It has been successfully used to eliminate pin holes, to dope CdS with oxygen, and dope CdTe absorption layers; all of which have resulted in higher device efficiencies. This work presents a characterization of plasma properties inside the hollow cathode style reactor including: plasma density, electron temperature, and plasma potential. Additionally, the uniformity of the ion current flux to the substrate is presented for nitrogen/oxygen and argon feed gases by means of in situ surface probes fabricated by segmenting a transparent conductive oxide film on a glass substrate. A three-dimensional model was developed and used to calculate plasma production and transport processes, and to gain an understanding of the relative roles of energetic primaries and bulk cold electrons on spatial ionization rates that develop within the reactor plasma as a function of gas pressure and geometry. Comparisons between the model and experimental measurements are presented and good agreement has been observed when the appropriate spatially varying ionization rates are estimated.
Energy expenditure by indirect calorimetry in premenopausal women: variation within one menstrual cycle☆☆☆

Energy expenditure in relation to the menstrual cycle was determined by indirect calorimetry in premenopausal women. For each subject, three measurements were made within a single menstrual cycle. Energy expenditure measurements coincided with the subject's expected hormonal fluxes of estradiol and progesterone: menstrual phase-both hormones at basal levels; follicular phase-elevated estradiol; and luteal phase-elevated progesterone. In experiment I, resting energy expenditure of 14 women was determined for 1 hour using a canopy system for calorimetry; in experiment 2, 24-hour energy expenditures of 12 subjects were measured in a room-size calorimeter. Blood from fasted (12 hours) subjects was collected following measurements of energy expenditure and analyzed for serum estradiol-17B and progesterone by radioimmunoassay. In experiment 1, resting energy expenditure did not differ within one menstrual cycle; neither estradiol nor progesterone affected resting energy expenditure. In experiment 2, 24-hour energy expenditure was significantly lower (P < 0.013) during the follicular phase when compared with the menstrual (−3.8%) and luteal (−4.9%) phases. Lowered 24-hour energy expenditure during the follicular phase may in part be due to a decrease in spontaneous activity and exercise. Energy expenditure during sleep, an indicator of metabolic energy expenditure, was significantly greater (P < 0.0001) during the luteal phase than during the menstrual (+6.7%) and follicular (+5.4%) phases; this was a reflection of increased progesterone (P < 0.0001). Twenty-four hour energy expenditure (mean ± SEM) during the menstrual, follicular, and luteal phases was 8.86 ± 0.26, 8.52 ± 0.22, and 8.96 ± 0.21 MJ/d, respectively. Corresponding values for energy expenditure during sleep were 5.49 ± 0.09, 5.56 ± 0.10, and 5.86 ± 0.11 MJ/d. The menstrual cycle is a significant contributor to variation in energy expenditure through progesterone-mediated increases in metabolic rate. Variation in metabolic energy expenditure was detectable when the contributory components of 24-hour energy expenditure were measured.
The factorability of symmetric matrices and some implications for statistical linear models

Abstract General conditions where a symmetric matrix is factorable by Cholesky decomposition are described. While numerical stability is a remaining issue whenever the Cholesky decomposition is used to factor indefinite matrices, the existence of such factors is demonstrated for matrix structures that are commonly found in statistics. Kalman filtering, for example, is rediscovered in the Cholesky decomposition of an indefinite matrix. Moreover, the Cholesky decomposition uniquely defines the likelihood function in linear statistical models, and this includes situations when the variance matrix is singular or when the Cholesky decomposition does not run to completion. Alternative methods of likelihood evaluation (which may involve, for example, the Bunch–Parlett factorization) are available only when the Cholesky decomposition exists. Suggestions are made for computing an adaptive-precision Cholesky decomposition when numerical stability is an issue.
Bullying Among Pediatric Patients With Food Allergy

JA Lieberman, C Weiss, TJ Furlong, M Sicherer, SH Sicherer. Ann Allergy Asthma Immunol. 2010;105(4):282–286 To determine the scope and characteristics of bullying, teasing, or harassment of food-allergic patients because of their food allergies. A specialized questionnaire developed by experts in food allergy and bullying was administered to teenagers and adults with food allergies and parents/caregivers of children with food allergies at conferences …
A method of obturation of an oral-cutaneous fistula.

Abstract An immediate solution to the patient's problem was achieved. Long-term success or failure of the prosthesis is dependent upon the patient's attitude, cooperation, and adaptability (Figs. 7 to 9).
Marine nutrient transport: anadromous fish migration linked to the freshwater amphipod Gammarus fasciatus

Migrating anadromous fish may transfer marine-derived nutrients to oligotrophic tidal fresh water. River herrings (genus Alosa Linck, 1790) are the dominant anadromous genus in Virginia, USA. This study investigates whether marine nutrients derived from spawning Alosa spp. were incorporated into benthic invertebrates by using the stable isotopes of carbon and nitrogen. Spawning Alosa spp. had higher δ13C and δ15N values (–18.5‰ and 13.9‰, respectively) than resident freshwater omnivorous fishes (–25.7‰ and 11.8‰, respectively). In a tidal stream supporting abundant spawning Alosa spp., 13C and 15N enrichment was observed in stream amphipods (Gammarus fasciatus Say, 1818) coincident with the spawning migration of Alosa spp. The δ13C value for G. fasciatus increased from –28.5‰ to –26.0‰ from early to late April then fell to –28.1‰ in early June. A similar trend was observed in mayflies (Heptageniidae). Particulate organic matter and sediments from both streams remained depleted in 13C (between –29‰ and –28...
Mechanism-based cofactor derivatization of a copper amine oxidase by a branched primary amine recruits the oxidase activity of the enzyme to turn inactivator into substrate.

The copper amine oxidases (CAOs) have evolved to catalyze oxidative deamination of unbranched primary amines to aldehydes. We report that a branched primary amine bearing an aromatization-prone moiety, ethyl 4-amino-4,5-dihydrothiophene-2-carboxylate (1), is recognized enantioselectively (S ≫ R) by bovine plasma amine oxidase (BPAO) both as a temporary inactivator and as a substrate. Substrate activity results from an O2-dependent turnover of the covalently modified enzyme, with release of 4-aminothiophene-2-carboxylate (2) as ultimate product. Interaction of (S)-1 with BPAO occurs within the enzyme active site with a dissociation constant of 0.76 μM. Evidence from kinetic and spectroscopic studies, and HPLC analysis of stoichiometric reactions of BPAO with (S)-1, combined with a model study using a quinone cofactor mimic, establishes that the enzyme metabolizes 1 according to a transamination mechanism. Following the initial isomerization of substrate Schiff base to product Schiff base, a facile aromatiz...
Irreversible electroporation of the liver and liver hilum in swine

Background Irreversible electroporation (IRE) is a novel, non-thermal form of ablation. We studied the safety and efficacy of IRE for the ablation of liver tissue around the liver hilum. We also studied the ability of triphenyltetrazolium chloride staining (TTC) to predict the zone of ablation after IRE.
Abstract 120: Cellular import of the inhibitor of apoptosis (IAP) protein survivin

The inhibitor of apoptosis (IAP) protein survivin is found overexpressed in virtually all human cancers and has been shown to correlate with poor prognosis. Recent work performed by our laboratory and that of others has demonstrated that survivin, when found or expressed extracellularly, is associated with a more aggressive disease form. In a variety of cancer cell lines grown in conditioned medium, rich with a flag/HA-tagged form of survivin, intracellular accumulation was readily detected. We found that survivin was internalized constitutively at a rate that was not affected by chelation of the conditioned medium in HeLa S cervical cancer cells. Instead, survivin internalization was modestly affected by lipid membrane stasis, induced by cooling the cells and the conditioned medium prior to and during incubation leading us to investigate if survivin9s intracellular accumulation was dependent upon clathrin-coated pit-dependent endocytosis. Using dual-affinity protein purification and mass-spectrometry, survivin was found associating directly with clathrin, TNFR1, and the transferrin receptor (TfR), indicating that the process of survivin uptake may be through endocytosis. In addition, short-inhibitory RNA (siRNA) knockdown of TNFR1 and TfR as well as antibody blocking of these receptors significantly reduced survivin9s intracellular accumulation. Further characterization of this novel survivin pool and its intracellular accumulation may reveal new strategies for the downregulation of survivin in cancer and ultimately better treatment strategies. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 120.
New Ideas on Amphibian Immunity: The Lymph Gland: A Generator of both T and B Cells

Anuran amphibian larvae of the genus Rana possess three major lymphoid organs: the thymus, the lymph gland, and the spleen. Other accumulations of lymphocytes are present in the kidney, liver, and intestine. The thymus develops lymphocytes first followed by peripheral differentiation of other lymphoid centers. Since bone marrow is absent in larvae, there must be an alternative source of stem cells that differentiate into T cells under thymic influence or B cells under the influence of some other organ(s). We are concerned with the source of B cells after bullfrog larvae become immunologically mature. Such an organ should possess stem cells, and, to qualify further, it should play a major role in antibody synthesis. The lymph gland seems to fulfill this requirement. Contrary to our expectations, lymph glands can restore not only antibody synthesis but also transplantation immunity in a significant number of larvae. Thus, the lymph gland may house stem cells that can differentiate into B cells and T cells.
Thermodynamic Studies of the Solvent Effects in Chromatography on Molecularly Imprinted Polymers. 3. Nature of the Organic Mobile Phase

Experimental isotherm data of the Fmoc-tryptophan (Fmoc-Trp) enantiomers were measured by frontal analysis on a Fmoc-L-Trp imprinted polymer, using different organic mobile phases, in a wide concentration range. The nonlinear regression of the data and the independent calculation of the affinity energy distributions of the two enantiomers allowed the selection of the isotherm model and the determination of the isotherm parameters. The organic solvents studied were acetonitrile (MeCN), methylene chloride, chloroform, and tetrahydrofuran (THF), all in the presence of the same concentration of acetic acid, used as an organic modifier. It was found that the highest overall affinity and enantiomeric selectivity were obtained in MeCN, which is also the solvent used in the polymerization. In the other solvents, the overall affinity decreases with increasing hydrogen-bonding ability of the solvents but not the enantiomer selectivity. In MeCN, three types of adsorption sites coexist for the two enantiomers on the MIP. The highest energy sites for Fmoc-L-Trp in MeCN are inactive in CH(2)Cl(2), CHCl(3), and THF, and only two types of sites were identified in these solvents. Increasing the acetic acid concentration from 0.2 to 0.9 M causes a large decrease in the association constant of the highest energy sites in CH(2)Cl(2), CHCl(3), and THF but not in MeCN. The overall affinity of Fmoc-L-trp in CH(2)Cl(2), CHCl(3), and THF is dominated by adsorption on the lowest energy sites, the most abundant ones. In contrast, in MeCN, the overall affinity of Fmoc-L-Trp is dominated by adsorption on the highest energy sites, the least abundant sites. In CH(2)Cl(2), CHCl(3), and THF, the number of each type of sites increases with decreasing hydrogen-bonding ability of the solvents while the association constant of the corresponding sites does not change significantly.
Identifying fragment vuv excitations with dissociation channels from the strong-field ionization of N 2

Along with attosecond pulses comes a growing need for broadband amplification in the extreme ultraviolet spectral regime. Ultrafast laser pulses interacting with high symmetry molecules produce electronic excitations that are approaching this energy regime. Although there is some theoretical work regarding such excitation, experimental progress had been hampered in a fundamental way. Ion time-of-flight spectroscopy measures dissociation pathways but provides no specific information regarding the final state of the fragments. Vacuum-ultraviolet spectroscopy provides complete information about excited fragments but says nothing of the dissociation channel. In this paper we measure the internal states of nitrogen ion fragments and we associate them with specific dissociation pathways.
Matrin CYP, an SR-rich Cyclophilin That Associates with the Nuclear Matrix and Splicing Factors

We report the identification and cloning of a nuclear matrix protein termed matrin cyclophilin or matrin CYP. The derived sequence of matrin cyp encodes a protein of 752 amino acids with a predicted mass of 88 kDa. A 172-residue stretch at the amino terminus shows high identity with the ubiquitous family of cyclophilins. Clustered throughout the carboxyl half of the protein are a series of serine-arginine (SR) repeats that are a characteristic feature of many RNA splicing factors. Antibodies raised against matrin CYP recognize a 106-kDa antigen that is detected in isolated nuclei and quantitatively subfractionates in the nuclear matrix. Laser scanning confocal microscopy localizes most of the anti-matrin CYP-specific antigen within the nucleus in a pattern of large bright speckles that co-localize with splicing factors and diffuse nucleoplasmic staining. A strikingly similar pattern of staining is observed in cells extracted for in situ nuclear matrices. A fusion protein containing the cyclophilin domain of matrin CYP exhibits cyclosporin A (CsA)-sensitive, peptidylprolyl cis-trans-isomerase activity that is characteristic of native cyclophilins. Although total rat liver nuclei contains predominantly CsA-resistant PPIase activity, the corresponding activity in the nuclear matrix is largely CsA-sensitive.
Non-Abstinence-Based Supportive Housing for Persons with Co-Occurring Disorders: A Human Rights Perspective

Surveys of providers of social services in Portland, Oregon, in 2003 and 2007 revealed a significant policy shift in meeting the housing needs of chronically mentally ill, homeless persons with ongoing substance-abuse problems. The shift in policy, taking place in Portland, Seattle, Washington, Minneapolis, and other U.S. cities, from a sobriety-first requirement to a housing-first philosophy has occurred largely because of cost-effectiveness. Only when such housing is provided as a human right can we say that a true paradigm shift has occurred.
Social Dimensions of the Human–Avian Bond: Parrots and Their Persons

ABSTRACTThough birds are among the most popular companion animals in the United States, little scholarly research has focused on the human– companion parrot relationship. This study uses an ethnographic approach and qualitative analysis to examine the parrot–pet owner relationship. Two and onehalf weeks of ethnographic fieldwork were carried out in a veterinary clinic specializing in avian and exotic medicine. These observations complement the results of quantitative data and qualitative analysis of texts from questionnaires completed by 100 parrot owners outside the clinic. Both textual analysis and observations in the veterinary clinic revealed some interesting insights into the social dimensions of the human–companion parrot relationship, which was rated superior to that of cats and dogs by some bird owners. Various patterns of human–avian interactions emerged from the data, including childhood experience with birds, affection and physical contact with birds, birds as family members and the nature of t...
A high-power NMR probe for narrow-gap magnets

Abstract An NMR probe is described which has the capability of providing high-power cross polarization, high-power decoupling, a variable temperature capability, and magic-angle sample spinning for spectrometers that have narrow-gap electromagnets. The cross-polarization experiments have been carried out using such a design with carbon and proton matching field of 60 kHz and high-power decoupling fields of 60 kHz. Variable temperature capability is provided by virtue of a Dewar which permits low-temperature experiments in excess of −100°C and high-temperature experiments in excess of 150°C. A magic-angle spinning apparatus exists in the literature which is applicable to such a probe. Using this magic-angle spinning device, high-resolution carbon, phosphorus, and silicon NMR spectra of solids are possible. The probe is also useful for lineshape experiments on static powder and oriented samples.
The Paradox of Software Visualization

Software visualization seems like such a logical and helpful concept with obvious benefits and advantages. But after decades of research and work, it has yet to be successful in any mainstream development environment. What is the reason for this paradox? Will software visualization ever be actually widely used? In this paper we argue that most past and current work in the field (our own included) is out of touch with the reality of software development and that new approaches and new ideas are needed
Upregulation of human autophagy-initiation kinase ULK1 by tumor suppressor p53 contributes to DNA-damage-induced cell death

In yeast, activation of ATG1/ATG13 kinase complex initiates autophagy. This mechanism of autophagy initiation is conserved, as unc-51-like kinase 1 (ULK1) and unc-51-like kinase 2 (ULK2) are two mammalian functional homologues of ATG1 and form similar complex with mammalian ATG13. Here, we report that both ULK1 and ULK2 are transcriptional targets of tumor suppressor p53. In response to DNA damage, ULK1 and ULK2 are upregulated by p53. The upregulation of ULK1 (ULK2)/ATG13 complex by p53 is necessary for the sustained autophagy activity induced by DNA damage. In this context, elevated autophagy contributes to subsequent cell death. These findings suggest that ULK1 and ULK2 may mediate part of tumor suppression activity in mammalian cells and contribute to the efficacy of genotoxic chemotherapeutic drugs.
Abstract 1646: Integrative analysis identifies functional prostate cancer risk SNPs in genomic regulatory regions defined as enhancers

Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL Prostate Cancer (PCa) genetic risk has recently been defined in numerous genome-wide association studies (GWASs), which have revealed more than 50 disease-associated single nucleotide polymorphs (SNP), known as tagSNPs, each at a different locus. More than 80% of these tagSNPs are in intergenic regions of the genome for which functionality remains unknown. Taking the 1000 genomes data into consideration, more than 10,000 correlated SNPs are revealed, which each define risk due to linkage disequilibrium (correlated to the tagSNP with an r2>0.5). The above therefore makes the identification of functional and/or causal SNPs not a trivial task. Therefore, we hypothesize that at least some of these SNPs affect non-coding genomic regulatory signatures, such as enhancers, insulators or repressors. In order to reduce the number of candidate functional SNPs, we developed an open-source (R/Bioconductor) package, called FunciSNP (Functional Integration of SNPs), which systematically integrates the 1000 genomes SNP data with chromatin features of interest. To define functionality in non-coding DNA associated with PCa risk we have utilized chromatin features generated by next-generation sequencing technologies, which capture regions genome-wide for which both open chromatin states and enhancers are likely. The open chromatin state (DnaseI, H3K9,14ac), enhancers (H3K4me1), and active/engaged enhancers (H3K27ac) were generated either by our lab, or harvested from the ENCODE project, or retrieved from recent publications. All chromatin features were identified in the same prostate cancer cell line (LNCaP). Thus, we have identified 113 PCa risk correlated SNPs at androgen receptor occupied regions (AROR), 1,545 at DNase1 sensitivity sites and 403 at histone modified regions [H3K4me1 (160 SNPs), H3K9,14 ac (121 SNPs), H3k27ac (122 SNPs)]; all features excluded transcription start sites of known annotated genes. Interestingly, the majority of the identified correlated SNPs (69%) are located in either chromosome 8 or 10. ARORs coinciding with DNase1 sites revealed four novel SNPs correlated with four GWAS tagSNPs. Of the four novel surrogate SNPs, two are located 4kb upstream from KLK3, one is located within the 3′ UTR of NKX3.1 and one is located within an intron of RUVBL1. DNase1 sites coinciding with any histone modification provided 17 novel SNPs correlated with 10 GWAS tagSNPs. Of the 17 novel SNPs, four are located in 8q24 genomic region and each are more than 100kb away from a known annotated gene. Each one of above-mentioned novel SNPs is assessed for effects on potential transcription factor response elements. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1646. doi:1538-7445.AM2012-1646