cssi/SciSciGPT-SciSciNet huggingface dataset:
Proof-of-concept trial with the neurosteroid pregnenolone targeting cognitive and negative symptoms in schizophrenia.

The neurosteroid pregnenolone and its sulfated derivative enhance learning and memory in rodents. Pregnenolone sulfate also positively modulates NMDA receptors and could thus ameliorate hypothesized NMDA receptor hypofunction in schizophrenia. Furthermore, clozapine increases pregnenolone in rodent hippocampus, possibly contributing to its superior efficacy. We therefore investigated adjunctive pregnenolone for cognitive and negative symptoms in patients with schizophrenia or schizoaffective disorder receiving stable doses of second-generation antipsychotics in a pilot randomized, placebo-controlled, double-blind trial. Following a 2-week single-blind placebo lead-in, patients were randomized to pregnenolone (fixed escalating doses to 500 mg/day) or placebo, for 8 weeks. Primary end points were changes in BACS and MCCB composite and total SANS scores. Of 21 patients randomized, 18 completed at least 4 weeks of treatment (n=9/group). Pregnenolone was well tolerated. Patients receiving pregnenolone demonstrated significantly greater improvements in SANS scores (mean change=10.38) compared with patients receiving placebo (mean change=2.33), p=0.048. Mean composite changes in BACS and MCCB scores were not significantly different in patients randomized to pregnenolone compared with placebo. However, serum pregnenolone increases predicted BACS composite scores at 8 weeks in the pregnenolone group (rs=0.81, p=0.022). Increases in allopregnanolone, a GABAergic pregnenolone metabolite, also predicted BACS composite scores (rs=0.74, p=0.046). In addition, baseline pregnenolone (rs=−0.76, p=0.037), pregnenolone sulfate (rs=−0.83, p=0.015), and allopregnanolone levels (rs=−0.83, p=0.015) were inversely correlated with improvements in MCCB composite scores, further supporting a possible role for neurosteroids in cognition. Mean BACS and MCCB composite scores were correlated (rs=0.74, p<0.0001). Pregnenolone may be a promising therapeutic agent for negative symptoms and merits further investigation for cognitive symptoms in schizophrenia.
Hydrogen bonding Part 54. NMR study of the effects of anesthetics on hydration of choline, acetylcholine and tetraethylammonium halides in aqueous solution

Abstract The onset and development of 14 N to CH coupling on sequential dilution of saturated solutions of the chloride and bromide salts of choline, acetylcholine and tetraethylammonium cations were used to determine the effect of the anesthetic substances chloroform, methane, argon and diethyl ether on the formation of primary and secondary hydration structures. The addition of anesthetics tends to reduce the number of H 2 O molecules required to form the primary structure. Anesthetics reduce the number of H 2 O molecules in the secondary structures of salts that form secondary structures in the absence of anesthetics, and promote the formation of secondary structures for salts that do not form secondary structures in the absence of anesthetics. These phenomena are discussed in terms of competition between salt and anesthetic substance as structure formers. Anesthetics appear to disrupt the “iceberg” water of hydration of acetylcholine; this effect might play some role in their action in anesthesia.
Perceptual Characterization and Analysis of Aroma Mixtures Using Gas Chromatography Recomposition-Olfactometry

This paper describes the design of a new instrumental technique, Gas Chromatography Recomposition-Olfactometry (GC-R), that adapts the reconstitution technique used in flavor chemistry studies by extracting volatiles from a sample by headspace solid-phase microextraction (SPME), separating the extract on a capillary GC column, and recombining individual compounds selectively as they elute off of the column into a mixture for sensory analysis (Figure 1). Using the chromatogram of a mixture as a map, the GC-R instrument allows the operator to "cut apart" and recombine the components of the mixture at will, selecting compounds, peaks, or sections based on retention time to include or exclude in a reconstitution for sensory analysis. Selective recombination is accomplished with the installation of a Deans Switch directly in-line with the column, which directs compounds either to waste or to a cryotrap at the operator's discretion. This enables the creation of, for example, aroma reconstitutions incorporating all of the volatiles in a sample, including instrumentally undetectable compounds as well those present at concentrations below sensory thresholds, thus correcting for the "reconstitution discrepancy" sometimes noted in flavor chemistry studies. Using only flowering lavender (Lavandula angustifola 'Hidcote Blue') as a source for volatiles, we used the instrument to build mixtures of subsets of lavender volatiles in-instrument and characterized their aroma qualities with a sensory panel. We showed evidence of additive, masking, and synergistic effects in these mixtures and of "lavender' aroma character as an emergent property of specific mixtures. This was accomplished without the need for chemical standards, reductive aroma models, or calculation of Odor Activity Values, and is broadly applicable to any aroma or flavor.
Some possible theoretical implications of experiments on the chemical transfer of memory.

Recent experiments on so-called chemical transfer of memory may indicate at first glance that the possibility of transfer of the memory of a large number of reaction patterns in this manner requires the assumption of a correspondingly large number of specific chemical substances. It is shown that this is not necessarily the case. A mechanism is conceivable in which a single substance is responsible for “memory” transfer for a large number of distinct patterns. Mechanisms involving only about one hundred different specific substances could conceivably be responsible for chemical transfer of memory of some 1050 spatial patterns.
Minimally Invasive Anterolateral Corpectomy for Spinal Tumors

Traditional open anterior and posterior approaches for the thoracic and thoracolumbar spine are associated with approach-related morbidity and limited surgical access to the level of abnormality. This article describes the minimally invasive anterolateral corpectomy for the treatment of spinal tumors, and reviews the current literature.
Effect of quasi-static prestrain on the formability of dual phase steels in electrohydraulic forming

Abstract Dual phase steels derive their name from their microstructure, which consists of islands of martensite surrounded by a ferrite matrix. These steels are increasingly being used in automobile structures in order to reduce weight, improve fuel economy, and maintain crash safety performance. The higher strength grades of dual phase steels, such as DP780 and DP980, often present significant formability challenges in sheet stamping operations, and therefore any technologies which could alleviate these issues would be of significant value to the automotive industry. Electrohydraulic forming (EHF) is based upon the electro-hydraulic effect: a complex phenomenon related to the discharge of high voltage electrical current through a liquid. In EHF, electrical energy is stored in a bank of capacitors and is converted into the kinetic energy needed to form sheet metal by rapidly discharging that energy across a pair of electrodes submerged in a fluid. During such a discharge, a high pressure, high temperature plasma channel is created between the tips of the electrodes. The resulting shockwave in the liquid, initiated by the expansion of the plasma channel, is propagated toward the blank at the acoustic velocity of the fluid, and the mass and momentum of the water in the shock wave accelerates the sheet metal blank toward the die. The objective of this paper is to report the results of formability testing of dual phase steels under three basic conditions: (1) conventional limiting dome height (LDH) testing; (2) starting with a flat blank and using one pulse of EHF to fill the desired die geometry; and (3) starting with a quasi-static preforming step to partially fill the die cavity and then using one pulse of EHF to fill the remaining area of the die cavity. A hybrid process which combines sheet hydroforming (HF) and EHF as described herein has the potential to reduce the cycle time of the EHF process by replacing the initial EHF forming increments with one quasi-static preforming step. Additionally, a numerical model was developed and employed in order to better understand the sheet deformation process within EHF. The numerical model consists of four distinct models that are integrated into one: (1) an electrical model of the discharge channel, (2) a model of the plasma, (3) a model of the liquid as a pressure-transmitting medium, and (4) a deformable sheet metal blank in contact with a rigid die. Significant improvements in formability were confirmed experimentally for DP780 and DP980 by forming into conical and v-shape dies using EHF from a flat sheet and by using EHF combined with a quasi-static preforming step. Numerical modeling showed that the peak strain rates occurring in both single-pulse EHF the hybrid HF-EHF process are approximately 17,000 units per second.
Protection Zone for Buildings Against Lighning Strokes Using Transmission Line Protection Practice

The nature of the zone of protection of structures from an elevated rod or wire, inadequately defined in the past, can be determined with high reliability using data developed by E.R.Whitehead of the Illinois Institute of Technology under contract from the Edison Electric Institute for the protection of high-voltage electric transmission lines. The vertical boundary of this zone of protection is not linear, as has been believed in the past, but is a circular arc, tangent to the ground, of 150-ft radius for 99.5 percent protection and 125-ft radius for 99.9 percent protection.
Regulation of Androstenedione Production by Adenosine 3′,5′-Monophosphate and Phorbol Myristate Acetate in Ovarian Thecal Cells of the Domestic Hen*

Although factors that regulate cAMP and steroid production in granulosa cells of hen preovulatory follicles have been well studied, much less is known of the mechanisms that control steroidogenesis in the adjacent thecal layer. These studies were conducted to examine the involvement and interaction of cAMP and protein kinase-C in modulating androstenedione output from isolated ovarian thecal cells collected from the second largest preovulatory follicle. Treatment of thecal cells with ovine LH (0.01-100 ng/tube) caused a dose-dependent increase in androstenedione secretion. Although coincubation of cells with the phosphodiesterase inhibitor 3-isobutyl-1-methylxanthine (0.1 mM) potentiated the effects of LH on steroid production, cAMP levels increased only in response to the higher doses of LH (10-100 ng/tube). Small but significant increases in cAMP accumulation and androstenedione production were observed in response to vasoactive intestinal peptide (0.1 and 1.0 microM), but not to 100 ng/tube chicken FSH, in the presence of 0.1 mM 3-isobutyl-1-methylxanthine. Treatment of thecal cells with cholera toxin (0.001-100 ng/tube) or forskolin (0.001-10 microM) resulted in a dose-dependent increase in cellular cAMP levels and androstenedione secretion. Thecal cell androstenedione production was also stimulated by the cAMP analog 8-bromo-cAMP (0.1-1.0 mM). Incubation of thecal cells with phorbol 12-myristate 13-acetate (PMA; 0.32-162 nM) or 1-oleoyl-2-acetylglycerol (OAG; 2.5-126 microM) increased basal steroidogenesis (progesterone and androstenedione production) in the absence of a rise in cAMP levels. By contrast, the stimulatory effects of 1 ng/tube LH on androstenedione, but not progesterone, production were attenuated by the presence of PMA (3.2-162 nM) or OAG (25-126 microM). Only a high concentration of OAG (126 microM) suppressed cAMP accumulation stimulated by LH (50 ng/tube). Phorbol ester treatment (32-162 nM PMA) also inhibited androstenedione production in thecal cells stimulated by the presence of 8-bromo-cAMP (1 mM), indicating a post-cAMP effect of protein kinase-C activity on steroidogenesis. In contrast to the effects of PMA, phorbol 13-monoacetate (162 nM), a nontumor-promoting analog of PMA which does not activate protein kinase-C, did not alter basal steroidogenesis, nor did it affect androstenedione secretion stimulated by LH or 8-bromo-cAMP. Data from the present studies indicate that the adenylyl cyclase-cAMP pathway can mediate the induction of thecal cell steroidogenesis by extracellular signals (i.e. LH and vasoactive intestinal peptide), whereas activated protein kinase-C can both stimulate and inhibit androstenedione production, depending upon the hormonal environment.(ABSTRACT TRUNCATED AT 400 WORDS)
Light and death: photons and apoptosis.

Phototherapies like photodynamic therapy (PDT), UVA1, UVB, and PUVA treat skin diseases. These phototherapies work because they alter cytokine profiles, change immune cytotoxicity in the skin, and directly kill diseased cells by apoptosis. Apoptosis is a term that only describes the morphologic changes a cell undergoes during this mode of cell death. The terms "immediate", "intermediate", and "delayed" apoptosis segregate the different apoptotic mechanisms into three kinetic categories, whereas the terms preprogrammed cell death (pre-PCD) and programmed cell death (PCD) describe the underlying mechanisms. Immediate apoptosis (T 0.5 h) is initiated by receptor cross-linking on the plasma membrane, which can be achieved using high doses of UVB or UVC radiation. It is also a pre-PCD mechanism. Delayed apoptosis (T>4 h) is induced by DNA damage that can be caused by X-rays, PUVA, UVC, UVB, UVA, and PDT. It is a PCD mechanism of apoptosis, i.e., protein synthesis is required post-insult. These three apoptotic mechanisms each access one of two "points-of-no-return" located on the mitochondrial membrane, which activate different, but not mutually exclusive, final pathways of apoptosis. This review discusses the latest findings on these apoptotic mechanisms and their implications in phototherapies.
Presynaptic localization of a truncated isoform of the type 2 corticotropin releasing factor receptor in the cerebellum

Abstract It is now well established that corticotropin releasing factor is present in two major excitatory afferent systems to the cerebellum, namely climbing fibers and mossy fibers. Two major classes of corticotropin releasing factor receptors, each with unique binding characteristics, have been identified as type 1 and type 2. In this study we used an antibody made to the n-terminus of the type 2 corticotropin releasing factor receptor. Characterization of this antibody showed that it strongly labeled a protein with a molecular weight of 16–32 kDa and only faintly labels a 62–83 kDa protein. The lower molecular weight protein corresponds to the weight of a recently described truncated isoform of this receptor that is designated corticotropin releasing factor-type 2α-truncated isoform. We carried out transfection paradigms using corticotropin releasing factor-type 2α-truncated isoform constructs and confirmed that the antibody recognized the truncated isoform of the type 2 corticotropin releasing factor receptor. Further, light and electron microscopic studies were carried out in mice and rats to define the distribution of the truncated receptor. Immunoreactivity is evident in the basal region of many, but not all Purkinje cell bodies and their initial axonal segments, as well as the initial axonal segments of isolated Golgi cells, and cerebellar nuclear neurons. In addition, punctate elements in the molecular layer were immunolabeled. The localization of the receptor to the initial segment of Purkinje cells was confirmed with electron microscopy. Further, the punctate labeling in the molecular layer was localized to parallel fibers and their terminals. In conclusion, evidence has been presented to show that distinct isoforms of the corticotropin releasing factor receptor are present in the cerebellum. The complex interactions between corticotropin releasing factor and other members of the corticotropin releasing factor family of peptides with both pre- and postsynaptic receptors support a growing concept that corticotropin releasing factor plays an important role in modulating activity in cerebellar circuits and ultimately in controlling motor behavior.
Epidermal nevus syndrome with maxillary involvement.

Abstract The epidermal nevus syndrome is discussed, and the case of a 7-year-old boy with this syndrome, which included numerous compound composite odontomas of the left maxilla, is presented.
Selectivity of the acaricide, Bifenazate, and aphicide, pymetrozine, to spider mite predators in Washington hops

Abstract Toxicity of an acaricide, bifenazate, and an aphicide, pymetrozine, to the phytoseiid mites, Galendromus occidentalis Nesbitt, Neoseiulus fallacis Garman and Amblyseius andersoni (Chant), and the coccinellid spider mite predators, Stethorus punctum picipes Casey and Harmonia axyridis Pallas, was examined in laboratory bioassays. The impact of applications of these pesticides on phytoseiids and a guild of spider mite/aphid predators in commercial hop yards in Washington was also evaluated. In bioassays, bifenazate at the full field rate was moderately toxic to the phytoseiids and coccinellids (37-81% mortality) but less toxic at half and quarter rates (0-44% and 0-11%, respectively). Pymetrozine was non-toxic to all predators at all rates. Phytoseiid (G. occidentalis/N. fallacis) populations and a guild of non-phytoseiid spider mite/aphid predators in hop yards appeared unaffected by single applications of half or three-quarter rates of bifenazate and the full rate of pymetrozine. Bifenazate and p...
A case for a parallelizable hash

On November 2, 2007, NIST (United States National Institute of Standards and Technology) announced an initiative to design a new secure hash function for this century, to be called SHA-3. The competition will be open and it is planned to conclude in 2012. These developments are quite similar to the recent history of symmetric block ciphers- breaking of the DES (Data Encryption Standard) and emergence of the AES (Advanced Encryption Standard) in 2001 as the winner of a multiyear NIST competition. In this paper we make a case that parallelizability should be one of the properties sought in the new SHA-3 design. We present a design concept for a parallelizable hash function called PHASH based on a block cipher, and we discuss PHASHpsilas performance and security.
Liquid phase epitaxial growth of InAsxSbyPl-x-y layers on InAs

High quality InAsxSbyPl-x-y quaternary layers, which are lattice matched to InAs, have been grown successfully on InAs substrates by liquid phase epitaxy. Both Graded and constant composition InAsxSbyPl-x-y layers have been grown. In addition, the graded InAsxSbyPl-x-y layer has been used as a buffer layer for the growth of InAsl-xSbx on an InAs substrate.
Study on electrodeposition of Pt

AbstractThe electrodeposition of Pt is investigated experimentally. The nucleation and growth dynamics are studied through cyclic voltammetry and chronoamperometry and the results are analysed by a unified nucleation and growth theory. Surface morphology is investigated by atomic force microscopy. The hydrogen adsorption/desorption method is utilised to determine the roughness factor of the electrodes. Electrochemical impedance spectroscopy and catalytic activity study are carried out to compare the electrochemical behaviours of the electrodes before and after Pt electrodeposition.
Exercise training increases the näive to memory T cell ratio in old mice.

Aging is associated with changes in T cells including involution of the thymus gland and an imbalance in the proportion of naive (CD44lo) and memory (CD44hi) T cells in the periphery. Reversal of these changes may improve immunity in the aged. We sought to determine whether 4 months of moderately intense treadmill running (EXC; 5 days/week, 45 min/day, 13-22 m/min) in 2 month (Y) and 18 month (O) old male Balb/c mice would alter T lymphocyte profiles in the thymus and spleen when compared to sedentary controls (CON). Splenocytes and thymocytes were harvested 24-48 h after the last exercise session and analyzed using immunofluorescence and flow cytometry. While there were significant age-related changes (lower cell number, altered subsets) in the thymuses of O when compared to Y mice, exercise training failed to affect any of these measures in mice of either age. Aged mice exhibited a significantly (p < .05) higher percentage of splenic memory cells and a lower percentage of naive cells in both the CD4 and CD8 T cell subsets. Interestingly, exercise training significantly (p < .05) increased the percentage of naive and decreased the percentage of memory cells in both the CD4+ (69.6+/-1.7% naive and 30.4+/-1.7% memory for OCON vs. 75.0+/-1.5% naive and 25.0+/-1.5% memory in OEXC) and CD8+ (60.0+/-2.6% naive and 40.0+/-2.6% memory in OCON vs. 76.7+/-2.7% naive and 23.3+/-2.7% memory in OEXC) T cells subsets in O, but not Y, mice. This effect was due to a decrease in the absolute number of memory cells and not an increase in the absolute number of naive cells. We conclude that 4 months of EXC has little restorative effect on the thymus in aged mice, but can restore the percentages of naive and memory cells in the spleen towards that of young mice, perhaps due to removal of memory cells.
Molecular evolution of alcohol dehydrogenase 1 in members of the grass family.

Abstract The molecular evolution of the alcohol dehydrogenase 1 (Adh1; alcohol:NAD+ oxidoreductase, EC 1.1.1.1) locus in members of the grass family is analyzed. We report the complete DNA sequence of a genomic clone of Adh1 from Pennisetum glaucum cv. Tift 23DB (pearl millet). The gene is characterized by ten exons and nine introns. The 5' flanking region of the gene contains sequences corresponding to the anaerobic regulatory element as well as sequences corresponding to the TATA box and the CAAT box identified in the maize Adh1-1S flanking regions. Exon sequences from Pennisetum and maize have been subjected to relative rate tests; the maize and Pennisetum Adh1 lineages evolve at equal rates. These results are compared with similar relative rate studies by using the chloroplast DNA encoding the ribulose-1,5-bisphosphate carboxylase (rbcL) gene. Evolutionary rates of Adh1 are estimated. Nonsynonymous rates are found to be 2.50 x 10(-10) substitutions per site per year, whereas synonymous rates are approximately 7.90 x 10(-9) substitutions per site per year. Molecular phylogenies of the Poaceae based upon Adh1 data are presented.
The extinction behavior of small interacting droplets in cross-flow

Abstract Experiments were conducted on monodisperse streams of small ( dY o ,∞ n o / v , where d is the droplet diameter, Y o ,∞ is the oxidizer mass fraction, v is the droplet velocity, and n o is 0.5 and 0.75 for methanol and ethanol, respectively.
Environmental embrittlement of an ordered NiMo alloy

Recent studies have demonstrated that a number of ordered intermetallics containing reactive elements, such as Al, Ti, Si, or V are susceptible to environmental degradation when tested in air at room temperature. This phenomenon is believed to be a hydrogen embrittlement process which involves the reaction of reactive elements in intermetallic alloys with water vapor in air, and subsequent generation of atomic hydrogen that is transported into the interior of the specimen, leading to brittle crack propagation along grain boundaries and/or cleavage planes. Such an embrittlement effect seems to be a common phenomenon, independent of ordered crystal structure and has been observed in intermetallics with various crystal structures. Ni-based alloys containing 26--30 wt.% Mo form the basis for a number of commercial alloys, e.g., HASTELLOY alloy B-2, which is resistant to reducing media such as hydrochloric acid. However, upon exposure to elevated temperatures in the range of 600--800 C, these alloys suffer an almost complete loss of room temperature ductility as a result of long-range ordering to Ni{sub 4}Mo. It is of interest to determine whether the ductility of Ni{sub 4}Mo alloy is intrinsically low, or if some other mechanism such as environmental degradation is the major cause of themore » commonly observed low ductility at ambient temperatures. The objectives of this research is to investigate the environmental effects in an ordered Ni-Mo alloy. The alloy was tested under controlled environments to check the effect of moisture and hydrogen on the ductility of the alloy.« less
A Systematic and Evidence-Based Approach to the Management of Vertebral Metastasis

Diagnosis and management of vertebral metastasis requires a systematic approach to patient identification as well as selection of appropriate therapy. Rapid identification and prompt intervention in the treatment of malignant epidural spinal cord compression (MESCC) is key to maintaining quality of life. This paper provides a series of tools as well as guidance in selecting effective and evidence-based therapy individualized to the specific patient.
A Comparison of Sinus Computed Tomography (CT) Staging Systems for Outcomes Research

The success of outcomes research for sinus disease will depend in part on the utilization of a computed tomography (CT) staging system that meets rigorous statistical criteria. Such a staging syste...
Handbook of isotopes in the cosmos. Hydrogen to gallium, by Donald Clayton

Book Review: Handbook of Isotopes in the Cosmos. Hydrogen to Gallium, Donald Clayton. Cambridge University Press (2003).
Shadow Graphs and 3D Texture Reconstruction

We present methods for recovering surface height fields such as geometric details of 3D textures by incorporating shadow constraints. We introduce shadow graphs which give a new graph-based representation for shadow constraints. It can be shown that the shadow graph alone is sufficient to solve the shape-from-shadow problem from a dense set of images. Shadow graphs provide a simpler and more systematic approach to represent and integrate shadow constraints from multiple images. To recover height fields from a sparse set of images, we propose a method for integrated shadow and shading constraints. Previous shape-from-shadow algorithms do not consider shading constraints while shape-from-shading usually assumes there is no shadow. Our method is based on collecting a set of images from a fixed viewpoint as a known light source changes its position. It first builds a shadow graph from shadow constraints from which an upper bound for each pixel can be derived if the height values of a small number of pixels are initialized correctly. Finally, a constrained optimization procedure is designed to make the results from shape-from-shading consistent with the height bounds derived from the shadow constraints. Our technique is demonstrated on both synthetic and real imagery.
Exploring the Use of Explanatory Models in Nursing Research and Practice

Purpose: To address the lack of information in nursing for delivering culturally appropriate care and provide a framework for nurses to incorporate diverse beliefs and health needs into research and practice. People interpret and react to health and illness events within a cultural system. However, the nursing literature contains little about how to elicit cultural beliefs. Organizing Framework: Use of Kleinman's (1980) concept of explanatory models (EMs) is explored first, by describing the concept as it was developed by Kleinman, and second, by illustrating how it was used in three research studies conducted between 1990 and 1994. Method: Individual in-depth interviews were conducted with community-based convenience samples. Data were analyzed using content analysis. Explanatory models were explored with healthy people, with people following illness, and with people having a condition with potential health risks, to illustrate their usefulness in nursing research and practice. Conclusions: The findings provide a beginning understanding of the complex linkages between beliefs and actions and demonstrate the versatility and usefulness of EMs for nursing research and practice. Assessing models offers one means for researchers and clinicians to explore health beliefs and the linkages between beliefs and behaviors.
Photocurrent in graphene harnessed by tunable intrinsic plasmons

By patterning graphene with sub-wavelength features to introduce plasmonic modes, its optical properties can be tailored. Freitag et al. show how tunable plasmons in graphene nanoribbons can be exploited to form polarization-sensitive graphene photodetectors in the mid-infrared spectral region.
Statistical methods for identifying differentially expressed genes in RNA-Seq experiments

RNA sequencing (RNA-Seq) is rapidly replacing microarrays for profiling gene expression with much improved accuracy and sensitivity. One of the most common questions in a typical gene profiling experiment is how to identify a set of transcripts that are differentially expressed between different experimental conditions. Some of the statistical methods developed for microarray data analysis can be applied to RNA-Seq data with or without modifications. Recently several additional methods have been developed specifically for RNA-Seq data sets. This review attempts to give an in-depth review of these statistical methods, with the goal of providing a comprehensive guide when choosing appropriate metrics for RNA-Seq statistical analyses.
Mass Absorption Coefficient of Tungsten and Tantalum, 1450 eV to 2350 eV: Experiment, Theory, and Application

The mass absorption coefficients of tungsten and tantalum were measured with soft x-ray photons from 1450 eV to 2350 eV using an undulator source. This region includes the M3, M4, and M5 absorption edges. X-ray absorption fine structure was calculated within a real-space multiple scattering formalism; the predicted structure was observed for tungsten and to a lesser degree tantalum as well. Separately, the effects of dynamic screening were observed as shown by an atomic calculation within the relativistic time-dependent local-density approximation. Dynamic screening effects influence the spectra at the 25 % level and are observed for both tungsten and tantalum. We applied these results to characterize spatially-resolved spectra of a tungsten integrated circuit interconnect obtained using a scanning transmission x-ray microscope. The results indicate tungsten fiducial markers were deposited into silica trenches with a depths of 50 % and 60 % of the markers' heights.
Particle migration in pressure-driven flow of a Brownian suspension

Shear induced particle migration of 2 µm diameter spherical col- loidal particles flowing through rectangular capillary tubes (50 µm × 500 µm cross section) is studied by confocal microscopy. The confocal microscope allows imaging of the flowing particles far from the walls of the tube, at particle velocities up to 8000 µm s 1 . The particle volume fraction is varied from � = 0.05-0.34, and the flow rate is also varied, which results in a bulk Peclet number (Pe) which varies by two orders of magnitude. Concentration profiles are measured across the narrow dimension of the tube; particles at the larger volume frac- tions migrate toward the centreline, with the migration progressively stronger as Pe increases. The flow has been analyzed using an existing mixture flow model under the assumption of fully-developed flow and a proposed constitu- tive law which describes the suspension normal stresses as a function of bothand Pe, the latter of which is defined as a variable quantity through the local shear rate. Shear thinning and shear thickening are not included. Comparisons made with the experimental data indicate that the dependence of the extent of migration upon Pe is well cap- tured but discrepancies arise, at least in part because the assumption of full development is not valid for these experiments.
Estimation of the Bid-Ask Spread and Its Components: A New Approach

We show that time variation in expected returns and/or partial price adjustments lead to a downward bias in previous estimators of both the spread and its components. We introduce a new approach that provides unbiased and efficient estimators of the components of the spread. We find that between 77 and 97 percent of the downward bias in previous spread estimates is caused by time variation in expected returns. More importantly, the adverse-selection component, though significant, accounts for a much smaller proportion (8 to 13 percent) of the quoted spread, at least for small trades, than the proportion (over 40 percent) previously reported in the literature. Order processing costs are the predominant component of quoted spreads. Article published by Oxford University Press on behalf of the Society for Financial Studies in its journal, The Review of Financial Studies.
The effects of dexamethasone on plasma steroid levels and fetal adrenal histology in the pregnant rhesus monkey.

Dexamethasone (8 mg/day im) has been administered to rhesus monkeys (Macaca mulatto) from days 146–156 of pregnancy, until term. This treatment was ineffective in precipitating premature delivery, and the monkeys delivered spontaneously at the expected time (day 166–176). Maternal peripheral plasma progesterone concentrations were unaffected by the dexamethasone treatment. However, administration of the synthetic glucocorticoid resulted in a marked suppression of the maternal plasma estrone and estradiol-17β concentrations in all animals. In the 4 monkeys in which injections of dexamethasone were initiated earliest (days 146–150), the plasma unconjugated estrogen levels at term were 15–40% of those found prior to the start of treatment. At autopsy, the adrenal glands from the fetuses of dexamethasone-treated monkeys had markedly atrophied, and showed appreciable regression of the fetal zone. It is suggested that dexamethasone crosses the placenta and inhibits fetal ACTH release, resulting in regression of...
Buying science and selling science: gender differences in the market for commercial science

Growing opportunities for academic scientists to commercialize their science has led to a new commercial marketplace. Recent evidence suggests that “commercial science” participation is characterized by gender stratification. Using interviews with life science faculty at one high-status university we examine the mechanisms that instituted, reinforced, and reduced the gender gap in commercial science between 1975 and 2005. We find gender differences from processes on both the demand—(opportunity) and supply—(interest) sides; of deeper significance are the intersections between these sides of the market. Specifically, explicit early exclusion of women left them with fewer opportunities in the marketplace, weakening their socialization and skills in commercial science. This uneven opportunity structure left senior/mid-career women with fewer chances to confront the ambiguities of this new practice, resulting in their greater ambivalence. Gender differences remain significant among junior faculty but we find their decline prompted by greater gender-equality in advisor mentoring and the presence of institutional support which together have started to reshape the supply-side of commercial science.
Hox, Wnt, and the evolution of the primary body axis: insights from the early-divergent phyla

The subkingdom Bilateria encompasses the overwhelming majority of animals, including all but four early-branching phyla: Porifera, Ctenophora, Placozoa, and Cnidaria. On average, these early-branching phyla have fewer cell types, tissues, and organs, and are considered to be significantly less specialized along their primary body axis. As such, they present an attractive outgroup from which to investigate how evolutionary changes in the genetic toolkit may have contributed to the emergence of the complex animal body plans of the Bilateria. This review offers an up-to-date glimpse of genome-scale comparisons between bilaterians and these early-diverging taxa. Specifically, we examine these data in the context of how they may explain the evolutionary development of primary body axes and axial symmetry across the Metazoa. Next, we re-evaluate the validity and evolutionary genomic relevance of the zootype hypothesis, which defines an animal by a specific spatial pattern of gene expression. Finally, we extend the hypothesis that Wnt genes may be the earliest primary body axis patterning mechanism by suggesting that Hox genes were co-opted into this patterning network prior to the last common ancestor of cnidarians and bilaterians.
A CMOS multi-channel IC for pulse timing measurements with 1 mV sensitivity

This CMOS data acquisition channel measures the leading-edge timing of pulses relative to a 62.5 MHz system clock, where the input pulses have peak amplitudes in the range of 1 to 10 mV. Such "time-of-occurrence" measurements are required in applications such as laser range-finding, electronics testing, and particle-physics experiments. In this case, the channel is designed for use in a particle-physics instrumentation application requiring a large number (>100,000) of channels with a timing measurement error of less than 0.75 ns r.m.s. The channel consists of a wideband amplifier, a tail-cancellation filter, a timing discriminator, and a time digitizer. For reasons of cost, size, and power dissipation, it is desirable to integrate multiple channels in a single integrated circuit. This implies that the individual subcircuits comprising each channel must be designed so as to generate minimal amounts of switching noise.
Aggregation Improves Learning: Experiments in Natural Language Generation for Intelligent Tutoring Systems

To improve the interaction between students and an intelligent tutoring system, we developed two Natural Language generators, that we systematically evaluated in a three way comparison that included the original system as well. We found that the generator which intuitively produces the best language does engender the most learning. Specifically, it appears that functional aggregation is responsible for the improvement.
The sensitivity of idealized hurricane structure and development to the distribution of vertical levels in MM5

Abstract In the course of studying the development of hurricanes using the fifth-generation Pennsylvania State University–National Center for Atmospheric Research Mesoscale Model (MM5), a relationship between storm intensity and the distribution of vertical levels became apparent, even when the same total number of sigma levels was used. A specific case of an idealized hurricane, on an f plane, in a quiescent environment, with constant and uniform SST of 28°C, was used to study the sensitivity of hurricane structure and evolution to the distribution of sigma levels. The distribution of vertical levels in the inflow, outflow, and middle layers of the atmosphere clearly affects the intensity, size, and structure of the storms, causing certain physical processes to be under- or overresolved. A well-resolved outflow layer is found to be necessary for proper storm intensification, while a well-resolved inflow layer does not necessarily correspond to an intense storm. In fact, when a well-resolved inflow layer ...
Proper prior marginalization of the conditional ML model for combined model selection/source localization

We present a Bayesian evidence technique for the parameter estimation/model selection problem within the conditional maximum likelihood (CML) framework. The CML is chosen because of its flexibility: it allows for a wide range of source amplitude models (e.g., no unreasonable or restrictive assumptions, such as Gaussian signals are necessary). In contrast to other CML studies, we eliminate the large number of unknown amplitude parameters by marginalization with a proper (normalizable), yet every broad prior. The resulting marginal is used to derive a new model selection/parameter estimation procedure, based on the Bayesian evidence of each considered model, given the observed data. Monte Carlo simulations for a scenario consisting of two narrowband, far-field sources demonstrate the effectiveness of the proposed method in low SNR, small temporal/spatial sample situations.
Depletion of type IA regulatory subunit (RIα) of protein kinase A (PKA) in mammalian cells and tissues activates mTOR and causes autophagic deficiency

The human PRKAR1A gene encodes the regulatory subunit 1-alpha (RIalpha) of the cAMP-dependent protein kinase A (PKA) holoenzyme. Regulation of the catalytic activity of PKA is the only well-studied function of RIalpha. Inactivating PRKAR1A mutations cause primary pigmented nodular adrenocortical disease (PPNAD) or Carney complex (CNC), an inherited syndrome associated with abnormal skin pigmentation and multiple neoplasias, including PPNAD. Histochemistry of tissues from CNC patients is indicative of autophagic deficiency and this led us to investigate the relationship between RIalpha and mammalian autophagy. We found that fluorescently tagged RIalpha associates with late endosomes and autophagosomes in cultured cells. The number of autophagosomes in prkar1a-/- mouse embryonic fibroblasts (MEFs) was reduced compared with wild-type MEFs. RIalpha co-immunoprecipitated with mTOR kinase, a major regulator of autophagy. Phosphorylated-mTOR levels and mTOR activity were dramatically increased in prkar1a-/- mouse cells, and in HEK 293 cells with RIalpha levels reduced by siRNA. Finally, phosphorylated-mTOR levels and mTOR activity were increased in CNC cells and in PPNAD tissues. These data suggest that RIalpha deficiency decreases autophagy by the activation of mTOR, providing a molecular basis to autophagic deficiency in PPNAD.
Substrate specificity of schistosome versus human legumain determined by P1–P3 peptide libraries

Asparaginyl endopeptidases, or ‘legumains’ have been identified and characterized in plants, the blood fluke parasite Schistosoma , and mammals. The legumains are a novel family of cysteine proteases and display restricted specificity for peptide hydrolysis on the carboxyl side of asparagine residues. Two forms of recombinant asparaginyl endopeptidase from Schistosoma mansoni (C197 Sm32 and N197C Sm32), expressed in Pichia pastoris, have been analyzed for substrate specificity using a positionalscanning synthetic combinatorial library (PS-SCL). We first screened Sm32 using a P1-diverse library. This library demonstrated the absolute specificity of Sm32 for asparagine at P1. To determine the P2/P3 preferences of Sm32, we constructed a library with asparagine fixed at P1, and the P2/P3 positions randomized. The library was screened using the two forms of Sm32, human asparaginyl endopeptidase, and to confirm its diversity, cruzain from Trypanosoma cruzi. The schistosome legumain showed a preference for P3: Thr � /Ala � /Val � /Ile, and P2: Ala� /Thr� /Val� /Asn, with an overall broader specificity at P3 than at P2. Both human and schistosome legumain can accommodate Thr and Ala at P2 and P3. However, optimal substrate sequences differ, with Sm32 preferring Thr-Ala-Asn, and human legumain preferring Pro-Thr-Asn. Predictions of substrate specificity from the library screen were confirmed using single peptide substrates for kinetic assays. # 2002 Published by Elsevier Science B.V.
Transportation, Distance, and Health Care Utilization for Older Adults in Rural and Small Urban Areas

Transportation is vital for access to health care, especially in rural areas, where travel distances are great and access to alternative modes such as transit is less prevalent. This study estimated the impacts of transportation and travel distance on the utilization of health care services for older adults in rural and small urban areas. With data collected from a survey, a model was developed on the basis of the Health Behavior Model, which considered transportation and distance as factors that could enable or impede health care utilization. A random sample of individuals age 60 years and older living in the rural Upper Great Plains states of Montana, North Dakota, South Dakota, and Wyoming were surveyed by mail. Responses were received from 543 individuals (20% response rate). Probit models were used to estimate trip frequency and the likelihood that an individual would miss or would delay a health care trip. Distance and transportation variables were not found to influence significantly the total number of routine or chronic care trips made overall, while emergency care visits were affected by the availability of transportation options. Additional results showed that those who could not drive made more trips if someone in the household could drive and that distance and access to transportation affected the difficulty reported in making trips and the likelihood of missing or delaying a trip. The greatest problems for people using public transportation for health care trips were inconvenient schedules, the need to match transit and medical schedules, and infrequent service.
Synthesized compact models (SCM) of substrate noise coupling analysis and synthesis in mixed-signal ICs

An approach for synthesized compact models (SCM) of substrate noise coupling is presented. The model is formulated using parameterized and scalable Z matrix. The improvement in modeling near field effects results in better substrate noise modeling for analog circuits. The geometrical scalability of the model provides a bi-directional link between noise analysis in the post-layout phase for verification and the noise-aware layout synthesis using convex optimization techniques. The model is validated by rigorous EM and device simulations. Several application examples are used to demonstrate the bi-directional usage of the model.
Statistical Analysis Based H.264 High Profile Deblocking Speedup

This paper proposes a novel scheme to achieve deblocking speedup for H.264 high profile decoders. The proposed approach is to use statistics dependent decoding which takes advantage of the biased statistical distribution in video streams. Specifically, in the proposed scheme, Huffman tree structures are introduced for boundary strength derivation, and hierarchical true edge detection is applied in the boundary filtering process to reduce the computation. As a result, significant computation can be saved in the deblocking process, while bit-exact output is maintained. This platform and encoder independent scheme can be incorporated into both standard conforming encoders and decoders. Since deblocking accounts for a significant percentage of decoding time, the scheme is especially important for decoder implementations. The analyses and experiments show that the proposed scheme could reduce the deblocking computational load by a factor of more than three times.
A Comparison of Immediate Memory Span for Digits, Letters, and Words

(1957). A Comparison of Immediate Memory Span for Digits, Letters, and Words. The Journal of Psychology: Vol. 44, No. 2, pp. 319-327.
Squaric acid sensitization is not required for response in the treatment of alopecia areata

Background Topical immunotherapy using potent contact allergens, such as squaric acid dibutylester (SADBE), can be used to treat alopecia areata. However, there are conflicting reports regarding the best protocol for its administration, particularly with regard to the necessity of an eczematous response after the initial sensitization treatment. Objectives We sought to assess the impact of initial sensitization on subsequent hair regrowth. Methods This is a retrospective review of the use of SADBE in the treatment of alopecia areata in 14 patients. Results Eleven of 14 patients underwent initial sensitization before initiating treatment. Three of these patients had an eczematous reaction after 1 attempt, 5 after ≥2 attempts, and 3 failed to develop a clinical reaction. Four of 14 initiated treatment without a clinical reaction or a previous sensitization. Eleven of 14 patients experienced regrowth, 7 with previous sensitization and 4 without. Limitations This observational study is limited by sample size. Conclusions SADBE sensitization regimens and reactions vary widely, and the absence of an initial eczematous reaction to sensitization does not predict a failed response with continued SADBE treatment.