cssi/SciSciGPT-SciSciNet huggingface dataset:
Probabilistic error correction for RNA sequencing

Sequencing of RNAs (RNA-Seq) has revolutionized the field of transcriptomics, but the reads obtained often contain errors. Read error correction can have a large impact on our ability to accurately assemble transcripts. This is especially true for de novo transcriptome analysis, where a reference genome is not available. Current read error correction methods, developed for DNA sequence data, cannot handle the overlapping effects of non-uniform abundance, polymorphisms and alternative splicing. Here we present SEquencing Error CorrEction in Rna-seq data (SEECER), a hidden Markov Model (HMM)–based method, which is the first to successfully address these problems. SEECER efficiently learns hundreds of thousands of HMMs and uses these to correct sequencing errors. Using human RNA-Seq data, we show that SEECER greatly improves on previous methods in terms of quality of read alignment to the genome and assembly accuracy. To illustrate the usefulness of SEECER for de novo transcriptome studies, we generated new RNA-Seq data to study the development of the sea cucumber Parastichopus parvimensis. Our corrected assembled transcripts shed new light on two important stages in sea cucumber development. Comparison of the assembled transcripts to known transcripts in other species has also revealed novel transcripts that are unique to sea cucumber, some of which we have experimentally validated. Supporting website: http://sb.cs.cmu.edu/seecer/.
Efficient operation of a cavity dumped Q-switched and mode-locked YAG laser

Abstract Successful operation of a cavity dumped, cw pumped, Q-switched and mode locked YAG laser has been achieved. The laser system is capable of providing single pulse energies in excess of 1.5 mj (20 MW peak power) at repetition rates up to 500 Hz. The single pulse amplitude stability is better than 2% for operating periods of several hundred hours.
Running on Empty: Families, Time, and Workplace Injuries

Over the past 5 decades, more women have entered the labor force, and more households have been headed by single parents. Both trends have substantially reduced parents' free time, creating added strain in the event of family health problems, including work-related injuries and illnesses. This commentary presents evidence about the impact of occupational injuries on today's families. In addition to losing considerable income, injured parents are less able to do household work, and other family members are often called on to care for them. Family members cut back on their paid, school, and household work to fill in for the injured parent. This suggests the importance of policies to help today's time-strapped families cope with major family health events.
POB1 over-expression inhibits RLIP76-mediated transport of glutathione-conjugates, drugs and promotes apoptosis.

Abstract RLIP76 (RALBP1) is a Ral-binding nucleotidase which functions as an energy-dependent transporter for glutathione (GSH)-conjugates as well as structurally unrelated xenobiotics. Partner of RALBP1 (POB1), also referred to as REPS2, was identified as the human RLIP76-binding protein, which contains a coiled-coil C-terminal region that binds with the RLIP76. Recent studies show that over-expression of POB1 in prostate cancer cells induces apoptosis. In present studies, we have purified POB1 and one of its deletion mutants POB11–512 (lacking the RLIP76-binding domain), and examined their effect on the transport activity of RLIP76. Both doxorubicin and a model GSH-conjugate, dinitrophenyl-S-glutathione (DNP-SG), transport were inhibited by POB1 in a concentration-dependent manner but not by POB11–512, lacking RLIP76-binding site. Liposomal delivery of recombinant POB1 to H358 (NSCLC) cancer cells caused apoptosis in a concentration-dependent manner, whereas the POB1 mutant deficient in RLIP76-binding site did not exert this effect. Augmentation of cellular POB1 resulted in increased intracellular DOX-accumulation as well as decreased rate of efflux from cells. These results show for the first time that POB1 can regulate the transport function of RLIP76 and are consistent with our previous studies showing that inhibition of RLIP76 induces apoptosis in cancer cells through the accumulation of endogenously formed GSH-conjugates.
Intraspecies competition for niches in the distal gut dictate transmission during persistent Salmonella infection

In order to be transmitted, a pathogen must first successfully colonize and multiply within a host. Ecological principles can be applied to study host-pathogen interactions to predict transmission dynamics. Little is known about the population biology of Salmonella during persistent infection. To define Salmonella enterica serovar Typhimurium population structure in this context, 129SvJ mice were oral gavaged with a mixture of eight wild-type isogenic tagged Salmonella (WITS) strains. Distinct subpopulations arose within intestinal and systemic tissues after 35 days, and clonal expansion of the cecal and colonic subpopulation was responsible for increases in Salmonella fecal shedding. A co-infection system utilizing differentially marked isogenic strains was developed in which each mouse received one strain orally and the other systemically by intraperitoneal (IP) injection. Co-infections demonstrated that the intestinal subpopulation exerted intraspecies priority effects by excluding systemic S. Typhimurium from colonizing an extracellular niche within the cecum and colon. Importantly, the systemic strain was excluded from these distal gut sites and was not transmitted to naive hosts. In addition, S. Typhimurium required hydrogenase, an enzyme that mediates acquisition of hydrogen from the gut microbiota, during the first week of infection to exert priority effects in the gut. Thus, early inhibitory priority effects are facilitated by the acquisition of nutrients, which allow S. Typhimurium to successfully compete for a nutritional niche in the distal gut. We also show that intraspecies colonization resistance is maintained by Salmonella Pathogenicity Islands SPI1 and SPI2 during persistent distal gut infection. Thus, important virulence effectors not only modulate interactions with host cells, but are crucial for Salmonella colonization of an extracellular intestinal niche and thereby also shape intraspecies dynamics. We conclude that priority effects and intraspecies competition for colonization niches in the distal gut control Salmonella population assembly and transmission.
When Teenagers Leave Home

It is always intriguing to read different qualitative studies of similar settings. Will alternative observers confirm one another’s insights or will they offer divergent portraits and interpretations? These two books both provide qualitative interview studies of young people who have left home; however, their two populations are not the same. Clydesdale began with a panel study that interviewed about 75 high school seniors from suburban public schools across the Northeastern USA, and then re-interviewed them about a year later, when most were in college. About one-quarter was African American and there were small numbers of Latinos, but most were white. They spanned much of the SES spectrum from working-class to upper-middle class; but neither the inner city poor nor the upperclass were included. Although two longitudinal waves of interviews yielded rich information about the ‘first year out,’ Clydesdale then added an ethnographic year in one New Jersey public high school, beginning with lunchroom hanging out, transforming into a confidant who interviewed individual students. Clydesdale comes from a Christian fundamentalist background, and he entered into this research with a strong interest in the religious and ethical views and practices of his subjects. However, while his teenage subjects mirror the American population in their belief in God and their commitment to ethical precepts, religion was not uppermost on their minds as they left home for the first time. The ethnographer wisely chose to follow their development and their interests, even if that required a shift in topical emphasis. Clydesdale’s impressive study yielded a rich and entertainingly told story of what young people are up to in their first year beyond the family nest. It is a superb book, convincing in its ethnographic realism, surprising in its findings, insightful in its analyses and discussion. Qual Sociol (2008) 31:207–210 DOI 10.1007/s11133-008-9092-2
Phase diagram compressibility and resistance of americium as a function of pressure

Abstract The compressibility at room temperature and pressure-temperature phase diagram of americium were measured to 35 kbar, and the electrical resistance at room temperature was measured to 120 kbar. Americium exhibits a higher compressibility than other actinides; in general, the physical properties of americium resemble rare earths more closely than the other actinides. The melting curve of americium obeyed the Kraut and Kennedy melting relation. Details of the phase diagram were in good agreement with recent work of Wade and Wolf. The melting point at 1 atm is 1173°C. There was an anomaly in the curve of resistance vs. pressure at 90 kbar; the effect may be due to a phase transition.
Design and Analysis of a Dynamically Configured Log-based Distributed Security Event Detection Methodology

Military and defense organizations rely upon the security of data stored in, and communicated through, their cyber infrastructure to fulfill their mission objectives. It is essential to identify threats to the cyber infrastructure in a timely manner, so that mission risks can be recognized and mitigated. Centralized event logging and correlation is a proven method for identifying threats to cyber resources. However, centralized event logging is inflexible and does not scale well, because it consumes excessive network bandwidth and imposes significant storage and processing requirements on the central event log server. In this paper, we present a flexible, distributed event correlation system designed to overcome these limitations by distributing the event correlation workload across the network of event-producing systems. To demonstrate the utility of the methodology, we model and simulate centralized, decentralized, and hybrid log analysis environments over three accountability levels and compare their p...
The cytochrome P450 genes of channel catfish: their involvement in disease defense responses as revealed by meta-analysis of RNA-Seq data sets.

Background Cytochrome P450s (CYPs) encode one of the most diverse enzyme superfamily in nature. They catalyze oxidative reactions of endogenous molecules and exogenous chemicals.
The Substituent Effect of 1‐Arylazonaphthen‐2‐ols on Azo‐hydrazone Tautomerization According to NMR Analysis

The substituent effect on azo-hydrazone tautomerization of 1-arylazonaphthen-ols is studied by means of NMR analysis. Among the 13C chemical shifts, the C(2) of this series compound is the most sensitive to the variation in the nature of substituent on the phenyl ring. Therefore, the variation in the chemical shifts of C(2) is used to probe the substituent effect by using the substituent chemical shifts and free energy vs. Hammett’s constant (χρ+). Both methods give a negative correlation slope, indicating the electron-with- drawing groups favor the hydrazone tautomer form. The effect on the chemical shifts of C(2) of compound 8 in ten solvents can be classified as the solvent with a proton-donor, proton-acceptor and arenes system. The substituent with electron-donating character is more sensitive to the nature of solvent and it favors the hydrazone form. Free energy obtained from the dynamic NMR technique indicates the tautomerization favors the hydrazone-form for the substituent with electron-withdrawing character.
Differential impact of age, sex steroid hormones, and obesity on basal versus pulsatile growth hormone secretion in men as assessed in an ultrasensitive chemiluminescence assay.

A chemiluminescence-based GH assay with 30- to loo-fold increased sensitivity recently disclosed combined basal and pulsatile GH secretion in men. However, how age, sex steroid hormones, and obesity singly and jointly influence the basal us. pulsatile modes of GH release is not known. We used the foregoing assay (detection threshold, 0.002-0.005 pg/L) and high sensitivity and specificity (290% each) deconvolution analysis to quantitate basal and pulsatile GH secretion from 24-h serum GH concentration profiles in 26 healthy lean and obese men, whose ages spanned 18-63 yr and whose percentage body fat ranged from 12-47%. Concentrations of serum insulin-like growth factor I (IGF-I), IGF-I-binding protein-l (IGFBP-l), and IGFBP-3 were related to specific measures of basal or pulsatile GH release. We observed that mean (24-h) serum GH concentrations embraced a 140-fold range from 0.013-1.8 pg/L and were related negatively to age (r = -0.50; P < O.Ol), percentage body fat (r = -0.620; P < 0.011, and their interaction (r = -0.610; P < 0.01). In contrast, testosterone was a robustly positive statistical determinant of mean serum GH values (r = 0.628; P = 0.0006). Stepwise multivariate regression analysis disclosed that percentage body fat alone and jointly with the serum testosterone concentration controlled, respectively, 38% and 50% of the total variability in GH levels (P = 0.0013 and P = 0.0008). As assessed by deconvolution analysis, GH secretory burst mass was negatively related to percentage body fat (r = -0.621; P < 0.01) and positively to serum testosterone (r = 0.529; P = 0.0054). The calculated half-life of GH correlated positively with serum estradiol (r = 0.447; P = 0.0321, and negatively with percentage body fat (r = -0.437; P = 0.048). Basal GH secretion rates were negatively related to serum estradiol (r = -0.485; P = 0.016). In contrast, GH secretory burst frequency and duration were unrelated to age, percentage body fat, or sex steroids. The fraction of total GH secreted in bursts was negatively correlated with the body mass index (r = - 0.540; P < 0.01). Serum IGF-I concentrations were positively related to total pulsatile GH secretion (r = 0.690; P = 0.0011) and negatively to age (r = -0.597; P = 0.007) and percentage body fat (r = -0.611; P = 0.009). Serum IGFBP-3 was inversely proportional to the basal GH secretion rate (r = -0.467; P = 0.044). In contrast, IGFBP-1 concentrations correlated positively with GH secretory burst mass (r = 0.674; P = 0.0016) as well as basal GH secretion (r = 0.519; P = 0.023), and negatively with age, and percentage body fat and their interactions (absolute r values = 0.517-0.653; P 5 0.021). The serial orderliness of GH release, as assessed by a novel approximate entropy (ApEn) statistic, revealed decreased orderliness (higher ApEn) of GH release with increasing age (r = 0.482; P = 0.019) and adiposity (r = 0.505;
Efficient support of delay and rate guarantees in an internet

In this paper, we investigate some issues related to the efficient provision of end-to-end delay guarantees in the context of the Guaranteed (G) Services framework [16]. First, we consider the impact of reshaping traffic within the network on the end-to-end delay, the end-to-end jitter, as well as per-hop buffer requirements. This leads us to examine a class of traffic disciplines that use reshaping at each hop, namely rate-controlled disciplines. In this case, it is known that it is advantageous to use the Earliest Deadline First (EDF) scheduling policy at the link scheduler [8]. For this service discipline, we determine the appropriate values of the parameters that have to be exported, as specified in [16]. Subsequently, with the help of an example, we illustrate how the G service traffic will typically underutilize the network, regardless of the scheduling policy used. We then define a Guaranteed Rate (GR) service, that is synergetic with the G service framework and makes use of this unutilized bandwidth to provide rate guarantees to flows. We outline some of the details of the GR service and explain how it can be supported in conjunction with the G service in an efficient manner.
Nuclear Magnetic Resonance Study of Hyperfine Fields in Dilute Fe Alloys

The hyperfine field spectra of ten Fe alloy systems have been studied. Nuclear magnetic resonance fast-passage techniques have been used to obtain direct plots of the distributions of hyperfine fields. The systems studied were FeAl, FeSi, FeV, FeCr, FeMn, FeCo, FeNi, FeGe, FePd, and FeSn. In general, four alloys of each system were studied, with the impurity concentration varying from 10−3 to 1.5 × 10−2. All the experimental hyperfine field distributions include satellite resonances. These satellites are interpreted as arising from different sets of Fe near-neighbours of an impurity. The intensities and line shapes of the satellites are studied. The results of the study are compared with the results of spin-echo NMR and Mossbauer effect studies to obtain (for most of the alloys) the hyperfine field shifts at the first five near-neighbor sites. Die Hyperfeinfeld-Spektren von zehn Eisenlegierungen wurden untersucht. Kernmagnetische-Resonanz-„fast passage”-Methoden wurden benutzt, um die Verteilung der Hyperfeinfelder direkt aufzuzeichnen. Generell wurden je vier Legierungen der Substanzen FeAl, FeSi, FeV, FeCr, FeMn, FeCo, FeNi, FeGe, FePd und FeSn mit verschiedenen Konzentrationen (zwischen 10−3 und 1,5 × 10−2) des Zusatzelementes untersucht. Die Hyperfeinfeld-Verteilungen zeigen in allen Fallen Satelliten. Diese Nebenresonanzen werden folgendermasen interpretiert: Sie werden durch die unterschiedlichen Anordnungen der nachsten Fe-Nachbarn um die Zusatzatome erzeugt. Die Intensitat und Form der Satellitenlinien werden untersucht. Die Ergebnisse dieser Experimente werden mit Resultaten der Spinecho-Kernresonanz- und Mosbauereffekt-Methoden verglichen, um die Hyperfeinfeld-Verschiebungen an den ersten funf nachsten Nachbarplatzen (fur die meisten Legierungen) abzuleiten.
“DOUBLE-MUSCLE” TRAIT IN CATTLE: A POSSIBLE MODEL FOR WIEDEMANN-BECKWITH SYNDROME

The Wiedemann-Beckwith syndrome (WBS) was first described in 1963 as a group of anomalies involving primarily macrosomia, macroglossia, and omphalocele. Histologic studies of WBS show nesidioblastosis of the pancreas, adrenocortical cytomegaly, and persistent metanephric blastema of the kidney. Multiple lines of evidence indicate that the human 11p15.5 region is the locus of abnormality in WBS. Insulin-like growth factor II (IGF-2) frequently has been considered a candidate gene, and expression of IGF-2 is known to be significantly delayed in fetal skeletal muscle of double-muscle (DM) cattle. Other candidate genes recently have been proposed for WBS. A number of recessive alleles in the bovine myostatin gene (GDF8, mapped to bovine chromosome 2 and apparently orthologous to the human 2q22 region) have been shown to be responsible for DM. Recently the first human case of deficient GDF8 function has been reported, confirming the importance of this gene. Bovine IGF-2 has been sequenced and localized to chromosome 25. The primary purpose of this study was to compare and contrast histologic findings in DM and WBS. Immunohistochemical staining confirms changes similar to nesidioblastosis in the pancreas. Other dysplastic changes of a cystic nature are seen in the adrenal. The renal histology of DM fetuses did not appear significantly different than controls.
Satellite monitoring of sea surface temperatures off China

Satellite measurements of global sea surface temperatures (SST) have been made since 1982 using the multi-channel radiometers (AVHRR) on NOAA polar orbiting satellites. A four year data set was accumulated at daily intervals and a spatial resolution of about 100 kilometers on an interactive computer system. The time lapse evaluation of the data revealed variations of the SST which were related to coastal and equatorial upwelling events as well as to the pronounced equatorial warming associated with the 1982–1983 El Nino. In the present study, satellite time series are used to describe the annual variability of the SST at selected locations along the coast of China, the Yellow Sea, the Sea of Japan and the Equatorial Indian and Pacific Oceans. Further study of the SST off China using higher resolution satellite data are also described.
Scanning tunneling microscopy characterization of organoselenium monolayers on Au(111)

Self-assembled monolayers were formed by immersing Au(111) surfaces into solutions of benzeneselenol and diphenyl diselenide. Chemisorption of benzeneselenol produced numerous gold islands (20−200 A in diameter) on the surface and a selenium-containing monolayer with a fundamental repeat unit of (3√3 × 2√3)R30°. Upon annealing at 60 °C in air, these gold islands coalesce to form larger, hexagonal-shaped islands. Chemisorption of diphenyl diselenide is qualitatively similar and upon annealing appears to produce the same surface structures observed with benzeneselenol. These organoselenium-modified surfaces were investigated by scanning tunneling microscopy (STM) and Auger electron spectroscopy (AES).
Subcellular sizing with polarized light spectroscopy

Abstract We report for the first time that subcellular morphologic information such as the size distribution of mitochondria can be noninvasively measured using polarized light spectroscopic techniques. An in vitro two-layer model was used to demonstrate the techniques, where the top layer consisted of mammalian cells (cervical or breast cancer cells) and the bottom layer was composed of a solid tissue-like phantom of Intralipid and India ink. The methods were first confirmed with 2.065 μm latex spheres as the top layer. A least squared optimization scheme coupled with Mie scattering theory was used to iteratively fit the measured intensity spectra. The results show that the size distributions of mitochondria obtained with our methods are in excellent agreement with that measured by fluorescence microscope.
INVERTED COEXISTENCE OF SPHERICAL AND DEFORMED STATES IN LIGHT NUCLEI.

Abstract The possibility of “inverted” coexistence of spherical and deformed states in 28Si, 32S and 12C is explored.
Differential expression of the α9 nicotinic acetylcholine receptor subunit in neonatal and adult cochlear hair cells

The expression of the alpha9 nicotinic acetylcholine receptor (nAChR) subunit was investigated in perinatal and adult rat cochleae using [35S] labeled cRNA in situ hybridization techniques. In the adult, alpha9 expression showed both longitudinal and radial gradients. The highest expression occurs over outer hair cells (OHCs) in basal regions, and particularly, OHCs in row 1. In contrast, expression over IHCs is lowest in basal regions and highest in apical regions. During embryonic and postnatal ages, the pattern of alpha9 expression differs. Expression of alpha9 was nearly equivalent over IHCs and OHCs. Additionally, the greater epithelial ridge, which is adjacent to IHCs before birth, shows a high level of alpha9 expression. These data are consistent with current models of efferent synaptogenesis and suggest that the expression of the alpha9 nAChR may be influenced by the arrival of efferent axons.
Comparison of the biological effects of thyroxine and triiodothyronine in the rat.

To compare the biological effects of thyroxine (T4) and triiodothyronine (T3), the results of varying the production rates of T3 and T4 independently were evaluated. In one set of experiments, the responses of hypothyroid rats to thyroid hormones were measured in terms of weight gain, hepatic mitochondrial alpha-glycerophosphate dehydrogenase (alphaGPD) and serum TSH. T4 was given with, and without, 6-n-propylthiouracil (PTU) and alphaGPD activity paralleled, and could completely be accounted for, by the effect of the quantities of the T3 produced. The direct role of T3 production in the maintenance of hepatic alphaGPD activity was supported by finding normal serum T3 and alphaGPD activities, but reduced T4, in rats on low iodine diet for 2 months. Only after 4 months of iodine deficiency was alphaGPD reduced in the presence of a normal serum T3. These results suggest that T4 per se plays minimal role in this system. In contrast, there were significant effects of T4 administration on stimulation of weight gain and suppression of TSH release in hypothyroid animals which were not due to the T3 produced by peripheral conversion. While T3 given parenterally was about tenfold more potent than T4 in acute suppression of TSH, PTU retreatment did not alter the acute decrease in TSH after T4 which lasted for at least 22 h, as opposed to less than 7 h for T3. Despite the direct effect of T4 on TSH suppression , acute reduction in T3 in normal rats resulted in an elevation of serum TSH even though serum T4 concentrations were unchanged or even increased at this time. The results indicate that the thyrotroph, unlike the hepatocyte, can respond acutely to both increases and decreases in either T3 or T4 production. The differential sensitivities of various tissues to T3 and T4 indicate that the relative potencies of these two hormones must be defined experimentally in terms of a specific biological effect.
Glucose dehydrogenase is required for normal sperm storage and utilization in female Drosophila melanogaster

Female sperm storage is a key factor for reproductive success in a variety of organisms, including Drosophila melanogaster. The spermathecae, one of the Drosophila sperm storage organs, has been suggested as a long-term storage organ because its secreted substances may enhance the quality of sperm storage. Glucose dehydrogenase (GLD) is widely expressed and secreted in the spermathecal ducts among species of the genus Drosophila. This highly conserved expression pattern suggests that this enzyme might have an important role in female fertility. Here, we examine the function of GLD in sperm storage and utilization using Gld-null mutant females. The absence of GLD reduced the amount of sperm stored in the spermathecae and led to a highly asymmetrical sperm distribution in the two spermathecal capsules of the mutant females. The storage defect was especially severe when the mutant females were crossed to a Gld-mutant male that had previously mated a few hours before the experimental cross. Under this mating condition, the mutant females stored in the spermathecae only one-third of the sperm amount of the wild-type control females. In addition, the mutant females used stored sperm at a slower rate over a longer period compared with wild-type females. Thus, our results indicate that GLD facilitates both sperm uptake and release through the spermathecal ducts.
Sources of Support for Mandatory Military Service in the Context of the War on Terrorism: Survey Evidence Pre- and Post-September 11, 2001*

Objectives. The advent of the War on Terrorism raises the question of the short-term impacts on public opinion of terrorist attacks with respect to the idea of universal military service in the United States. Previous studies indicate that international crises tend to produce a polarizing effect on public opinion with respect to military service. Methods. Multinomial logistic regression analysis is used here to analyze an archival data set featuring survey data collected among 18,000+ citizens in 18 major U.S. metropolitan areas in 2000, 2001, and 2002. Results and Conclusions. This article offers further support for previous analyses into the principal sources of support for military service. However, the analysis also indicates that the initial impact of the War on Terrorism may have been to produce a decline in support for mandatory military service and a mild unifying effect on the distribution of attitudes rather than the expected polarization. Attitudes toward military service were more polarized in 2000 and 2001 than in the post-9/11 2002 studies.
Optical frequency domain reflectometry with high sensitivity and resolution using optical synchronous detection with coded modulators

A new optical frequency domain reflectometry (OFDR) method is demonstrated. Two broadband, coded, travellingwave electro-optic LiNbO3 modulators are used over a 25.6GHz frequency range, one as a source and the other as an optical synchronous detector. A 4 mm resolution in fibre is achieved, along with a dynamic range improvement of ⋍18dB (optical) over previous OFDR results.
Neutral gas free molecular flow algorithm including ionization and walls for use in plasma simulations

Several plasma devices, including Hall and ion thrusters, operate by ionizing a low density neutral gas for which the mean free path between collisions of gas molecules is greater than typical device dimensions. In general, the discrete-particle algorithms used to calculate the neutral gas ignore velocity changes due to collisions between gas molecules. However, particle algorithms are a source of unphysical statistical noise that may detract from the study of the plasma physics, the prime purpose of most simulations. In this paper we present a new neutral gas algorithm for use in plasma simulation codes that exploits the fact that very few collisions change the velocity of neutral gas molecules. The algorithm assumes that the particle velocity distribution function for neutrals emitted from a given surface remains unchanged except for a scale factor that reflects the loss of neutrals to ionization. The sources of neutrals may be gas inlets, and isotropic, thermally accommodated, gas molecules coming off chamber surfaces including recombined ions. The algorithm is implemented in two dimensions (R-Z) with emitting surfaces represented as surfaces of revolution. The advantage of this algorithm over the conventional particle approach is the absence of statistical noise.
Identification in nonparametric limited dependent variable models with simultaneity and unobserved heterogeneity

We extend the identification results for nonparametric simultaneous equations models in Matzkin (2008) to situations where the observations on the vector of dependent variables might be limited, and where the number of exogenous unobservable variables is larger than the number of dependent variables.
Oxidation and glycolytic cleavage of etheno and propano DNA base adducts.

Non-invasive strategies for the analysis of endogenous DNA damage are of interest for the purpose of monitoring genomic exposure to biologically produced chemicals. We have focused our research on the biological processing of DNA adducts and how this may impact the observed products in biological matrixes. Preliminary research has revealed that pyrimidopurinone DNA adducts are subject to enzymatic oxidation in vitro and in vivo and that base adducts are better substrates for oxidation than the corresponding 2′-deoxynucleosides. We tested the possibility that structurally similar exocyclic base adducts may be good candidates for enzymatic oxidation in vitro. We investigated the in vitro oxidation of several endogenously occurring etheno adducts [1,N2-e-guanine (1,N2-e-Gua), N2,3-e-Gua, heptanone-1,N2-e-Gua, 1,N6-e-adenine (1,N6-e-Ade), and 3,N4-e-cytosine (3,N4-e-Cyt)] and their corresponding 2′-deoxynucleosides. Both 1,N2-e-Gua and heptanone-1,N2-e-Gua were substrates for enzymatic oxidation in rat liver ...
A Novel Method to Investigate Dependence of SAW Resonator Sensor Signatures on Localized Surface Perturbations

We use a novel method to empirically investigate the dependence of SAW resonator signature on specific perturbation spots. We fabricated two-port SAW resonators and applied mass-loadings on several significant locations on the device surface using the BioChip ArrayerTM, a commercially available micro-dispenser for biomolecules. Frequency characteristics are measured for each SAW resonator sample with a different deposition location for the receptor molecules which represent an acoustic perturbation to the SAW resonator cavity. We could verify that the sensor signature is strongly dependent on the location of these perturbations as well as the concentration of the receptor molecules. We assert that the degree of impact is closely related to the non-uniform acoustic energy distribution on the SAW resonator surface. This study will give insight into how to strategically create the detection layer for the modern SAW resonator sensors by locating the areas where the sensing layer should or should not be deposited.
Nonlinear evolution of the lower hybrid irregularities in artificially created dusty space plasmas

[1] Plasma turbulence associated with the creation of an artificial dust layer in the earth's ionosphere is investigated. The lower hybrid turbulence is considered as the dust is injected across the geomagnetic field into the background plasma, which generates irregularities at times much longer than the dust charging period. A two-dimensional hybrid particle-in-cell model is developed to investigate the lower hybrid instability driven by the streaming charged dust beam. It is shown that turbulence near the lower hybrid frequency is generated which has spatial structure with enhanced electric fields in localized density depletions. The wave saturation involves ion and dust heating. Energization of ions perpendicular to the magnetic field is observed. The ratio of electron plasma frequency to electron gyro frequency plays an important role on the lower hybrid irregularity spatial structure. Important parameters of the dust cloud that impact nonlinear evolution of the waves are discussed for the regimes of upcoming space experiments. Similarities between past observations of lower hybrid turbulence observed during passive space experiments in the auroral region and lower hybrid turbulence generated by such active experiments is discussed.
Numerical transient analysis of Markov models

Abstract We consider the numerical evaluation of Markov model transient behavior. Our research is motivated primarily by computer system dependability modeling. Other application areas include finitecapacity queueing models, closed queueing networks and inventory models. We focus our attention on the general problem of finding the state probability vector of a large, continuous-time, discrete-state Markov chain. Two computational approaches are examined in detail: uniformization and numerical linear multistep methods for ordinary differential equation solution. In general, uniformization provides greater accuracy but deals poorly with stiffness. A special stable ordinary differential equation solver deals well with stiffness, but it provides increased accuracy only at much greater cost. Examples are presented to illustrate the behavior of the techniques discussed as a function of model size, model stiffness, increased accuracy requirements and mission time.
Control on the Acorn User Port

With more students than ever before studying GCSE Technology, an inexpensive and exciting method of teaching controi is to use the Acorn User Port. Moreover, it is not necessary to go shopping for interface boxes: at Rigmer Community College, students have found done it yourself interfaces versatile enough to apply to a range of project ideas.
ACTION SPECTRA FOR THE ABSORBANCE CHANGE AT 880 nm AND FOR P870 FLUORESCENCE FROM A PHOTOSYNTHETIC REACTION CENTER

— Photosynthetic reaction centers isolated from blue-green mutant strain R-26 of Rhodopseudomonas spheroides were used to study the action spectra for the light-induced absorption changes at 880 nm, and for the P870 fluorescence. These spectra indicated that a pigment, possibly bacteriopheophytin, with an absorption maximum at 757 nm is an intrinsic component of the reaction center and transfers energy to P870 with relatively high efficiency.
Financial distress and use of mental health care: Evidence from antidepressant prescription claims

Using nationwide county-level longitudinal data, we show that recent declines in housing prices are associated with an increased utilization of antidepressant prescriptions among the near elderly. Our results persist in difference-in-difference models using either all non-antidepressant drugs or statins as controls.
Local area radio navigation - a tool for GPS-denied geolocation

Ranger is a local area radio frequency ranging system implemented in the 2.4 GHz Industrial, Scientific and Medical band. Roundtrip time-of-flight measurements are made in a two-stage process: a coarse measurement provides ± 3.4 m accuracy, followed by a fine measurement correction that reduces error to below 20 cm. This innovative approach can be implemented in other parts of the radio frequency spectrum; the 2.4 GHz band was chosen both for regulatory acceptance and availability of commercial components. The Ranger system consists of fixed and mobile radios. Fixed location radios provide the reference from which distances are measured to the mobile radio. A single distance measurement requires approximately 50 ms, therefore with a network of four fixed radios, the position of the mobile can be updated five times per second. Additionally, the digital communications link that is used for distance measurement is also used for concurrent high-bandwidth data communication.
Intracellular recording and labeling of mossy cells and proximal CA3 pyramidal cells in macaque monkeys.

Little is known about the morphological characteristics and intracellular electrophysiological properties of neurons in the primate hippocampus and dentate gyrus. We have therefore begun a program of studies using intracellular recording and biocytin labeling in hippocampal slices from macaque monkeys. In the current study, we investigated mossy cells and proximal CA3 pyramidal cells. As in rats, macaque mossy cells display fundamentally different traits than proximal CA3 pyramidal cells. Interestingly, macaque mossy cells and CA3 pyramidal neurons display some morphological differences from those in rats. Macaque monkey mossy cells extend more dendrites into the molecular layer of the dentate gyrus, have more elaborate thorny excrescences on their proximal dendrites, and project more axon collaterals into the CA3 region. In macaques, three types of proximal CA3 pyramidal cells are found: classical pyramidal cells, neurons with their dendrites confined to the CA3 pyramidal cell layer, and a previously undescribed cell type, the "dentate" CA3 pyramidal cell, whose apical dendrites extend into and ramify within the hilus, granule cell layer, and molecular layer of the dentate gyrus. The basic electrophysiological properties of mossy cells and proximal CA3 cells are similar to those reported for the rodent. Mossy cells have a higher frequency of large amplitude spontaneous depolarizing postsynaptic potentials, and proximal CA3 pyramidal cells are more likely to discharge bursts of action potentials. Although mossy cells and CA3 pyramidal cells in macaque monkeys display many morphological and electrophysiological features described in rodents, these findings highlight significant species differences, with more heterogeneity and the potential for richer interconnections in the primate hippocampus.
Toward a Social Phenomenology of Aging: Studying the Self Process in Biographical Work:

In recent years, the study of aging has come to be increasingly multidisciplinary and to encompass the whole life course. The well established life history approach has been reformulated to include...
The effect of interleukin-2 on parasitemia and myocarditis in experimental Chagas' disease.

Previous investigations showed that interleukin-2 (IL-2) administered in vivo into mice infected with Trypanosoma cruzi reduced levels of parasitemia and increased longevity. Present experiments examined the effect of administration of different doses of IL-2 at different times during infection in mice on parasitemia and histopathoiogy of heart tissue. Two different doses of IL-2 (1,500 or 10,000 U) given at 3 different times during infection were equivalent in reducing parasitemia. All of the IL-2 treated groups of mice had significantly lower numbers of circulating trypomastigotes as compared with controls not receiving this fymphokine. This IL-2 treatment of T. crazi-infected mice resulted also in lower numbers of pseudocysts in all 4 ventricular regions in the hearts. This was particularly evident in the more severely infected right ventricular wall; however, a similar decrease was not as apparent in the less severely infected left ventricular wall. The IL-2 treated, infected mice showed minimal or no effect in reducing inflammation of myocardial cells. However, the mildest inflammation of ventricular wall tended to occur in mice receiving IL-2 treatment either as a low dose (1,500 U) or a high dose (10,000 U) at 5, 7 and 9 days after infection as compared with mice treated later on. It was concluded that IL-2 treatment of infected mice produced a significant decrease in parasitemia and decreased infection of myocardial cells. Key words. Heart, histopathoiogy, inflammation, lymphokine, myocardial cells, pseudocyst, Trypanosoma cruzi.
Nature by Design: People, Natural Process, and Ecological Restoration

Ecological restoration is the process of repairing human damage to ecosystems. It involves reintroducing missing plants and animals, rebuilding soils, eliminating hazardous substances, ripping up roads, and returning natural processes such as fire and flooding to places that thrive on their regular occurrence. Thousands of restoration projects take place in North America every year. In Nature by Design, Eric Higgs argues that profound philosophical and cultural shifts accompany these projects. He explores the ethical and philosophical bases of restoration and the question of what constitutes good ecological restoration. Higgs explains how and why the restoration movement came about, where it fits into the array of approaches to human relationships with the land, and how it might be used to secure a sustainable future. Some environmental philosophers and activists worry that restoration will dilute preservation and conservation efforts and lead to an even deeper technological attitude toward nature. They ask whether even well-conceived restoration projects are in fact just expressions of human will. Higgs prefaces his responses to such concerns by distinguishing among several types of ecological restoration. He also describes a growing gulf between professionals and amateurs. Higgs finds much merit in criticism about technological restoration projects, which can cause more damage than they undo. These projects often ignore the fact that changing one thing in a complex system can change the whole system. For restoration projects to be successful, Higgs argues, people at the community level must be engaged. These focal restorations bring communities together, helping volunteers develop a dedication to place and encouraging democracy.
Evidence for a Ca2+ channel within the ryanodine receptor complex from cardiac sarcoplasmic reticulum

The solubilized [3H]ryanodine receptor from cardiac sarcoplasmic reticulum was centrifuged through linear sucrose gradients. A single peak of radioactivity with apparent sedimentation coefficient of approximately 30S specifically comigrated with a high molecular weight protein of apparent relative molecular mass approximately 400,000. Incorporation of the ryanodine receptor into lipid bilayers induced single Ca2+ channel currents with conductance and kinetic behavior almost identical to that of native cardiac Ca2+ release channels. These results suggest that the cardiac ryanodine receptor comprises the Ca2+ release channel involved in excitation-contraction coupling in cardiac muscle.
Timing and direction selectivity of subthalamic and pallidal neurons in patients with Parkinson disease

Current models of basal ganglia function suggest that some manifestations of Parkinson disease (PD) arise from abnormal activity and decreased selectivity of neurons in the subthalamic nucleus (STN) and globus pallidus internus (Gpi). Our goal was to examine the timing and direction selectivity of neuronal activity relative to visually guided movements in the STN and Gpi of patients with PD. Recordings were made from 152 neurons in the STN and 33 neurons in the Gpi of awake subjects undergoing surgery for PD. Corresponding EMG data were obtained for half the cells. We employed a structured behavioral task in which the subjects used a joystick to guide a cursor to one of four targets displayed on a monitor. Each direction was tested over multiple trials. Movement-related modulation of STN activity began on average 264±10 ms before movement initiation and 92±13 ms before initial EMG activity, while modulation of Gpi activity began 204±21 ms before overt movement initiation. In the STN, 40% of cells demonstrated perimovement activity, and of these 64% were directionally selective. In Gpi, 45% of cells showed perimovement activity of which 80% were selective. In both nuclei, directionally selective cells had significantly lower baseline firing rates than nonselective cells (41±5 vs 59±4 spikes/s in STN, and 50±9 vs 74±15 spikes/s in Gpi). These results suggest that STN activity occurs earlier than previously reported, and that higher neuronal firing rates maybe associated with decreased direction selectivity in PD patients.
Spatially extensive reconstructions show variable‐severity fire and heterogeneous structure in historical western United States dry forests

Aim Wildfire is often considered more severe now than historically in dry forests of the western United States. Tree-ring reconstructions, which suggest that historical dry forests were park-like with large, old trees maintained by low-severity fires, are from small, scattered studies. To overcome this limitation, we developed spatially comprehensive reconstructions across 927,000 ha in four landscapes, using a new method based on land surveys from c. 1880. Location Dry forests of the western United States. Methods We reconstructed forest structure for four large dry-forest landscapes using forest descriptions and tree data from historical land surveys. Using multiple elements of historical forest structure from this study along with corroborating information from tree-ring studies, we were able to interpret past forest dynamics. Hypotheses concerning historical structure and dynamics were then tested. Results These reconstructions show that dry forests were structurally variable, containing from 20 to over 1000 trees ha -1 and some dense understoreys of shrubs and small trees. Park-like stands of large trees maintained by low-severity fire predominated only in parts of the study landscapes. Only 3, 12, 40 and 62% of the four landscapes fit a low-severity fire model; 38‐97% had evidence of higherseverity (mixed- and high-severity) fire. Some large modern wildfires (e.g. RodeoChediski), perceived as catastrophic, had fire severity congruent with historical variability.
Self-assembling helical rosette nanotubes for cartilage tissue engineering

Today, one of the limitations associated with cartilage grafting is the lack of bonding between the implanted materials and the natural tissue. Helical rosette nanotubes (HRNs) are novel biomimetic self-assembled supramolecular structures whose basic building blocks are DNA base-pairs, which can solidify into a viscous gel at body temperatures in short periods of time. HRNs are similar in size to collagen in cartilage. In this study, the mechanical properties of select hydrogel/HRN composites were tested. In addition, electrospinning was used to generate three-dimensional, implantable, composite HRN fibers containing fibroblast-like type-B synoviocytes (SFB cells) or chondrocytes. Importantly, results showed that HRNs enhanced hydrogel adhesive strength to fractured collagen and created a scaffold with nanometer-rough surface structures that promoted SFB cell and chondrocyte adhesion and viability. In this manner, this study provided an alternative cartilage regenerative material produced by nanotechnology techniques that can be injected as a liquid, solidify at body temperatures under short periods of time, have suitable mechanical properties to cartilage, and promote SFB cell viability and adhesion.