cssi/SciSciGPT-SciSciNet huggingface dataset:
Rational monitoring of respiratory function during mechanical ventilation of infants and children

Oxygen and carbon dioxide homeostasis (effective pulmonary gas exchange) requires that lung exchange matches tissue exchange. The movement of gas in and out of the lung is determined by the mechanical properties of the system especially resistance and compliance and the work needed to provide this movement is supplied either by the patient's muscles or by the mechanical ventilator. If the latter is required, its optimal use demands that the user understands the relationship between the mechanical device and the mechanical properties of the patient's respiratory system so that optimal gas exchange can be provided. The following discussion provides the minimum physiological information needed for successful use of a mechanical ventilator and suggests that this requires measurement of at least four parameters: alveolar partial pressure of CO2 (PACO2), arterial oxygen saturation (SaO2), the mechanical RC time constant (RC) and functional residual capacity (FRC).
Prevention of cancer by agents that suppress oxygen radical formation.

The prevention of cancer by agents in our diet has led to the concept that oxygen radicals are a necessary component of a variety of human cancers including breast, colon and prostatic cancer. These cancers are putatively promoted by estradiol, bile acids and androgens. Epidemiological studies have shown that these cancers are suppressed in vegetarian populations. Vegetable components that may be responsible for this cancer prevention are Vitamin A, retinoids and protease inhibitors (PIS). These agents have been shown to suppress the formation of hydrogen peroxide in promoter-induced neutrophils. They also have been shown to block two-stage carcinogenesis and breast cancer when fed to animals. PIS also suppress experimentally-induced colon cancer and spontaneous liver cancer. Moreover, a new series of cancer-preventive agents, Sarcophytols (isolated by Fujiki and co-workers), are capable of suppressing two-stage carcinogenesis, breast and colon cancers in rodents when given in low concentrations. Sarcophy...
Regulation of amino acid transport in chicken embryo fibroblasts by purified multiplication-stimulating activity (MSA)

Enhanced amino acid transport is observed when quiescent cultures of chicken embryo fibroblasts are stimulated to proliferate by the addition of purified multiplication-stimulating activity (MSA). This increase in amino acid transport is an early event occurring prior to the onset of DNA synthesis in stimulated cells. Results indicate that the changes in transport activity, as measured by alpha-aminoisobutyric acid (AIB) uptake, are due to stimulation of only the Na+-dependent A transport system. There is little or no change in the activities of transport systems ASC, L, or Ly+ upon exposure to MSA. A kinetic analysis shows this increased activity is due to a change in Vmax while Km remains unaltered. Continuous exposure to the stimulus is required to maintain the increased level of transport activity and the presence of inhibitors of RNA and protein synthesis significantly inhibits the response. Results also indicate that a similar specific increase in the A transport system is initiated when RSV tsNY68 infected cells are shifted to the permissive temperature. It appears that the A system of mediation is emerging as a strategic regulatory site for cell function.
The Effect of Source—Sink Manipulations on Nitrogen Fixation in Peas

The effect on nitrogen fixation of excising leaves or pods in pea {Pisum sativum L. cv. Alaska) was determined over a 60-day period. Flower buds or their subtending leaves were removed, and C2H2 reduction, Hj evolution and N accumulation were measured at weekly intervals. Highest percentage nitrogen content in all treatments coincided with time of maximal C^Hj-reduction rates. Nitrogen fixation, calculated from C2H2-reduction and H2-evolution data, was significantly lower in the partially defoliated and generally higher in the depodded plants than in the controls. Total N accumulation was greatest in the depodded plants and least in the defoliated ones. Percentage nitrogen content and N2-fixation rates in the depodded plants were maximized approximately 10 days later than in the defoliated or control plants. The absolute rates of C2H2 reduction and H2 evolution were significantly altered by plant organ removal, but the relative rates were proportional. As a result the ratios of H2/C2H4 production and the related relative efficiency of N2 fixation in the treatments were not significantly different from the controls.
Effects of Heterogeneous and Clustered Contact Patterns on Infectious Disease Dynamics

The spread of infectious diseases fundamentally depends on the pattern of contacts between individuals. Although studies of contact networks have shown that heterogeneity in the number of contacts and the duration of contacts can have farreaching epidemiological consequences, models often assume that contacts are chosen at random and thereby ignore the sociological, temporal and/or spatial clustering of contacts. Here we investigate the simultaneous effects of heterogeneous and clustered contact patterns on epidemic dynamics. To model population structure, we generalize the configuration model which has a tunable degree distribution (number of contacts per node) and level of clustering (number of three cliques). To model epidemic dynamics for this class of random graph, we derive a tractable, low-dimensional system of ordinary differential equations that accounts for the effects of network structure on the course of the epidemic. We find that the interaction between clustering and the degree distribution is complex. Clustering always slows an epidemic, but simultaneously increasing clustering and the variance of the degree distribution can increase final epidemic size. We also show that bond percolation-based approximations can be highly biased if one incorrectly assumes that infectious periods are homogeneous, and the magnitude of this bias increases with the amount of clustering in the network. We apply this approach to model the high clustering of contacts within households, using contact parameters estimated from survey data of social interactions, and we identify conditions under which network models that do not account for household structure will be biased.
Developmental Regulation of Follicle-Stimulating Hormone Receptor Messenger RNA Expression in the Baboon Fetal Ovary

Abstract In the adult ovary, pituitary FSH via interaction with its receptor (FSHR) is required for follicular maturation and granulosa cell development. In humans and nonhuman primates, the pool of follicles available for adult ovarian function is established in utero. However, our understanding of the ontogeny and developmental regulation of FSHR in the ovary of the primate fetus is incomplete. Our goal was to determine whether the baboon fetal ovary expresses the full-length FSHR mRNA transcript and whether levels are developmentally regulated. Fetal ovaries were obtained at mid (Day 100) and late (Day 165) gestation (term = Day 184) from untreated baboons and on Day 165 from baboons in which fetal estrogen levels were either decreased by >95% by treatment with the aromatase inhibitor CGS 20267 or restored to 30% of normal by treatment with CGS 20267 plus estradiol benzoate administered s.c. to the mother on Days 100–164. The full-length 2088-base pair FSHR mRNA transcript was expressed in ovaries of a...
Low‐Temperature Atomic Layer Deposition of Tungsten using Tungsten Hexafluoride and Highly‐diluted Silane in Argon

Inherent chemical hazards in atomic layer deposition (ALD) processes can be mitigated significantly by careful selection of precursor materials. This work describes the effect of silane (SiH4) exposure on tungsten ALD growth when the silane is heavily diluted (2 at.-%) in argon. A wide ALD temperature window from 200 to ∼300°C is identified, exhibiting a growth rate of between 5 and 6 A per ALD cycle using SiH4 and tungsten hexafluoride (WF6) exposures of ∼6 × 105 and ∼5 × 105 Langmuirs (L), respectively. For deposition at lower temperature (150°C), growth rates of ∼4.5 A per cycle are obtained using a silane exposure of 30 s per cycle, where the partial pressure of silane at the inlet is controlled at 40 mTorr (corresponding to 1.2 × 106 L of silane). Compositional analysis by secondary ion mass spectroscopy (SIMS) and Auger electron spectroscopy (AES) show less than ∼5 at.-% Si in the W films, with the smallest Si content in films deposited at 300°C. We also describe effects of hot-wall reactor preconditioning on film growth. We conclude that the dilute silane co-reactant offers an alternative to the common disilane, borosilane, or undiluted silane precursors, allowing well-controlled W deposition at 150°C.
A Program for Testing Categorized Data for Normality

Most current statistics packages do not appropriately compute tests for normality on categorized data. This program for personal computers calculates two test statistics and associated significance levels for categorized data: the Kolmogorov-Smimov D, and an omnibus test based on skew and kurtosis. This program would be useful in examining, for example, sample test score or rating distributions.
The Psen1-L166P-knock-in mutation leads to amyloid deposition in human wild-type amyloid precursor protein YAC transgenic mice

Genetically engineered mice have been generated to model cerebral β-amyloidosis, one of the hallmarks of Alzheimer disease (AD) pathology, based on the overexpression of a mutated cDNA of the amyloid-β precursor protein (AβPP) or by knock-in of the murine Aβpp gene alone or with presenilin1 mutations. Here we describe the generation and initial characterization of a new mouse line based on the presence of 2 copies of the human genomic region encoding the wild-type AβPP and the L166P presenilin 1 mutation. At ∼6 mo of age, double-mutant mice develop amyloid pathology, with signs of neuritic dystrophy, intracellular Aβ accumulation, and glial inflammation, an increase in AβPP C-terminal fragments, and an 8 times increase in Aβ42 levels with a 40% decrease in Aβ40 levels, leading to a significant increase (14 times) of Aβ42/Aβ40 ratios, with minimal effects on presenilin or the Notch1 pathway in the brain. We conclude that in mice, neither mutations in AβPP nor overexpression of an AβPP isoform are a prerequisite for Aβ pathology. This model will allow the study of AD pathogenesis and testing of therapeutic strategies in a more relevant environment without experimental artifacts due to the overexpression of a single-mutant AβPP isoform using exogenous promoters.
Reducing glucose infusion safely prevents hyperglycemia in post-surgical children

Summary Background & aims To investigate the effects of two different glucose infusions on glucose homeostasis and amino acid metabolism in post-surgical children. Methods This randomized crossover study evaluated glucose and amino acid metabolism in eight children (age 9.8 ± 1.9 months, weight 9.5 ± 1.1 kg) admitted to a pediatric intensive care unit in a tertiary university hospital after surgical correction for non-syndromal craniosynostosis. Patients were randomized to receive low (LG; 2.5 mg kg −1 min −1 ) and standard (SG; 5.0 mg kg −1 min −1 ) glucose infusion in a crossover setting. After a bolus (4 g kg −1 ) of deuterium oxide, we conducted a primed, constant, 8 h tracer infusion with [6,6- 2 H 2 ]Glucose, [1- 13 C]Leucine, [ring- 2 H 5 ]Phenylalanine and [3,3- 2 H 2 ]Tyrosine. Results SG resulted in hyperglycemia (defined as > 6.1 mmol L −1 ), while during LG plasma glucose levels were normoglycemic (5.9 ± 0.6 vs. 7.5 ± 1.7 mmol L −1 ; LG vs. SG respectively, p = 0.02). Hypoglycemia did not occur during LG infusion. Endogenous glucose production was not fully suppressed during the hyperglycemic state under SG and increased with reduced glucose infusion (2.6 ± 1.5 vs. 1.1 ± 1.4 mg kg −1 min −1 ; LG vs. SG; p = 0.05). Whole body protein balance derived from leucine and phenylalanine kinetics was slightly negative but not further affected with a decrease in glucose infusion. Conclusions The current recommended glucose infusion induces hyperglycemia in post-surgical children. A reduced glucose infusion safely reduced high glucose levels, while children were capable to sustain normoglycemia with increased endogenous glucose production. The reduced glucose infusion did not exacerbate the mild catabolic state in which the patients were.
Hyperosmolar Hyperglycemic State: A Historic Review of the Clinical Presentation, Diagnosis, and Treatment

The hyperosmolar hyperglycemic state (HHS) is the most serious acute hyperglycemic emergency in patients with type 2 diabetes. von Frerichs and Dreschfeld described the first cases of HHS in the 1880s in patients with an “unusual diabetic coma” characterized by severe hyperglycemia and glycosuria in the absence of Kussmaul breathing, with a fruity breath odor or positive acetone test in the urine. Current diagnostic HHS criteria include a plasma glucose level >600 mg/dL and increased effective plasma osmolality >320 mOsm/kg in the absence of ketoacidosis. The incidence of HHS is estimated to be <1% of hospital admissions of patients with diabetes. The reported mortality is between 10 and 20%, which is about 10 times higher than the mortality rate in patients with diabetic ketoacidosis (DKA). Despite the severity of this condition, no prospective, randomized studies have determined best treatment strategies in patients with HHS, and its management has largely been extrapolated from studies of patients with DKA. There are many unresolved questions that need to be addressed in prospective clinical trials regarding the pathogenesis and treatment of pediatric and adult patients with HHS.
Forms of non-suicidal self-injury as a function of trait aggression

To date, the considerable body of research on predictors of non-suicidal self-injury (NSSI) has conceptualized NSSI as a unitary construct despite the fact that NSSI can exist in many forms (e.g., hitting, cutting, burning). The goal of the present study is to examine differential prediction of forms of NSSI. Specifically, we examined trait aggression as a predictor of more aggressive forms of NSSI (i.e., hitting). We hypothesized that higher trait aggression would differentiate those who engaged in hitting forms of NSSI from those who did not, whereas other factors (i.e., emotion regulation and trait anger) would serve as a non-specific predictor of NSSI. We also hypothesized that higher trait aggression would be related to lifetime frequency of hitting NSSI, but not other forms of NSSI, whereas emotion regulation and anger would act as predictors of other forms of NSSI. To test these hypotheses, a large sample of young adults completed measures of trait aggression, trait anger, emotion regulation, and NSSI behaviors. Results were generally in line with our hypotheses. Higher levels of trait aggression differentiated those who engaged in hitting NSSI from those who did not and was also associated with greater frequency of hitting NSSI. These results imply that different factors predict different forms of NSSI and that NSSI may be best examined as a multi-faceted construct.
QuikScan: Facilitating reading and information navigation through innovative document formatting

QuikScan is an innovative document format aimed at facilitating reading and information navigation in documents. It employs multiple within-document summaries formatted as numbered list items to summarize the gist of each section of a document. The presence of the summaries, with a fine level of granularity, enables readers to skim for the superordinate ideas of each section and locate particular items of information quickly and efficiently. This paper focuses on an empirical study of information navigation with QuikScan. Forty participants completed timed information navigating tasks using either a QuikScan or control version of a document with conventional formatting. This study demonstrates intriguing and important findings. Those who read QuikScan were able to locate the superordinate content items significantly faster with a significantly higher accuracy rate. However, QuikScan readers did not perform better on items of lesser importance than those who read the control version.
Effects of discontinuing maintenance digoxin therapy in patients with ischemic heart disease and congestive heart failure in sinus rhythm

Abstract To evaluate the importance of oral maintenance digoxin therapy in chronic congestive heart failure (CHF), 24 patients in sinus rhythm on maintenance digoxin for documented CHF were studied prospectively on and off the drug. The average duration of therapy was 39 months (range 2 to 180). All 24 patients had documented coronary artery disease (CAD): 22 were in New York Heart Association functional class III and 2 in class II. Twenty-one patients (88%) were receiving diuretic or vasodilator therapy, or both, before digoxin discontinuance. At 1 month off digoxin and with no increase in doses of other medications excepting minor increases in antianginal therapy in 2 patients, no difference was observed in the group as a whole in symptoms, resting heart rate, arterial blood pressure, physical findings, weight, cardiothoracic ratio, radiographic signs of pulmonary congestion, radionuclide left ventricular ejection fraction (LVEF), duration of symptom-limited treadmill exercise (14 patients), or CHF score, compared with evaluation during maintenance digoxin therapy. Similar results were obtained in a subgroup of 9 patients with a resting LVEF
Atmospheric Disturbances Caused by Human Modification of the Landscape

This study documents significant atmospheric effects over the U.S. central plains caused by human modification of the landscape. Using observations and an atmospheric model, it is shown here that diurnal, thermally induced circulations occur during summer over a 250 × 250 km region in Oklahoma and Kansas. Furthermore, it is shown that the driving force behind these circulations is the landscape heterogeneity resulting from differential land use patterns, that such atmospheric phenomena are characteristic of surfaces with this type of heterogeneity and not limited to infrequent days when unusual wind or other meteorological conditions prevail, and that the net effect of these motions is significant, not only locally, but also at the regional and global scales.
THERMO-BIMORPH MICROCILIA ARRAYS FOR SMALL SPACECRAFT DOCKING

Microelectromechanical system (MEMS) technology promises to improve performance of future spacecraft components while reducing mass, cost, and manufacture time. Arrays of microcilia actuators offer a lightweight alternative to conventional docking systems for miniature satellites. Instead of mechanical guiding structures, such a system uses a surface tiled with MEMS actuators to guide the satellite to its docking site. This paper describes an experimental setup for precision docking of a “picosatellite” with the help of MEMS cilia arrays. Microgravity is simulated with an aluminum puck on an airtable. A series of experiments is performed to characterize the cilia, with the goal to understand the influence of normal force, picosat mass, docking velocity, cilia frequency, interface material, and actuation strategy (“gait”) on the performance of the MEMS docking system. We demonstrate a 4 cm
The bacterial cell cycle regulator GcrA is a σ70 cofactor that drives gene expression from a subset of methylated promoters

Cell cycle progression in most organisms requires tightly regulated programs of gene expression. The transcription factors involved typically stimulate gene expression by binding specific DNA sequences in promoters and recruiting RNA polymerase. Here, we found that the essential cell cycle regulator GcrA in Caulobacter crescentus activates the transcription of target genes in a fundamentally different manner. GcrA forms a stable complex with RNA polymerase and localizes to almost all active σ(70)-dependent promoters in vivo but activates transcription primarily at promoters harboring certain DNA methylation sites. Whereas most transcription factors that contact σ(70) interact with domain 4, GcrA interfaces with domain 2, the region that binds the -10 element during strand separation. Using kinetic analyses and a reconstituted in vitro transcription assay, we demonstrated that GcrA can stabilize RNA polymerase binding and directly stimulate open complex formation to activate transcription. Guided by these studies, we identified a regulon of ∼ 200 genes, providing new insight into the essential functions of GcrA. Collectively, our work reveals a new mechanism for transcriptional regulation, and we discuss the potential benefits of activating transcription by promoting RNA polymerase isomerization rather than recruitment exclusively.
Fundamental Investigation of Wax Diffusion Characteristics in Water-in-Oil Emulsion

Although multiphase transportation of petroleum fluids commonly occurs in the field, investigations of wax deposition have been limited in the case of single-phase oil flow for the past few decades. The main complication for wax deposition research in multiphase flow is the variety of flow regimes and one has to analyze the transport characteristics in each flow regime. In the area of water-in-oil dispersed phase flow, previous studies provide limited information on the effects of water droplets on the mass transfer of wax. This study discusses the increase in the wax diffusion path to reach the pipe wall caused by the water droplets. The impact of the water droplets on wax molecular diffusion in water-in-oil dispersions is quantified using NMR diffusometry. Two commonly used empirical approaches for wax diffusivity calculation in single-phase flow have been evaluated for water-in-oil dispersed flow and neither provides consistent predictions compared to experimental measurements. Finally, a fundamental a...
Some Computational Problems of Transonic Aerodynamics

Different levels of approximations for transonic flow simulations are discussed together with the corresponding assumptions for both inviscid and viscous flows. The role of artificial viscosity in excluding expansion shocks is studied and formulas for evaluating wave drag are obtained. Some comments on viscous/inviscid interaction are made. Finally numerical results of a parametric study using existing codes are presented.
Older women's responses and decisions after a fall: the work of getting "back to normal"

In this descriptive qualitative research, we examined older women's responses and decisions after experiencing a fall. Falls were unexpected, sudden events that heightened these women's awareness of their physical, emotional, spiritual, and social independence. Interviewees reported assessing personal, physical, and emotional needs; feeling burdened by the extra work; trying to get back to normal; seeking and obtaining assistance and spiritual support; avoiding specific people, objects, and places; planning ahead; and putting the fall out of mind. Consideration of older women's post-fall responses and decisions should be incorporated into fall prevention and management programs, services, and clinical recommendations.
Approximate Decoupling of Continuous Modes and Mode Interaction in High-speed Boundary-layer Transition

An excessively large entropy mode is produced when Orr-Sommerfeld type disturbances are sought. Strong inter-mode coupling is thought to cause this behavior. A method to approximately decouple eigenmodes is proposed to circumvent this anomaly. By this procedure, horizontal and normal vorticity modes and entropy modes are obtained separately. Direct numerical simulation shows that under the oblique horizontal vorticity mode prescribed at the inlet, boundary layer streaks are produced. Low frequency vorticity mode alone are found to induce transition through a spontaneously generated, two-dimensional Mack second mode. The second mode is non-linearly excited at high harmonics of the forcing frequency. Adding a second mode on the top of the vorticity mode causes even earlier transition suggesting that the Mack second mode plays a crucial role in the break-down of boundary layer streaks.
Dispatches from the “Viejo” New South: Historicizing recent Latino migrations

Latino migration to the US South is not a new phenomenon. Claims of a “Nuevo New South” are thus products of the scholarly and popular imaginations rather than the historical record. Indeed, the claim of a rupture with the past has the potential to obscure the fact that contemporary relationships of race and class have their roots in the dilemmas that have confronted white and black Southerners since Emancipation. If the times and places of “the New South” meant something different to African Americans than it did to white observers and boosters, what have the times and places of the “Nuevo” South meant to Latino immigrants? Do those meanings, in fact, originate in a novel globalizing moment at the turn of the twenty-first century? And how can teasing out Latino immigrants’ own narratives about the region help social scientists and historians find more appropriate ways of conceptualizing Latino immigration's meaning for the South as a whole?
Optimality Criteria for Flowshop Schedules

Abstract This article considers the problem of scheduling n jobs on M machines in a flowshop and examines the present formulation of the problem. To understand the true nature of the problem, this article provides economic interpretations of various optimality criteria which are being used for solving the scheduling problem. A general optimization criterion, called minimization of opportunity cost, is proposed for flow-shop scheduling problems and the results of the sensitivity analysis of various optimality criteria are reported which indicate the need to reformulate the scheduling problem.
Substrate Specificity of the Lanthipeptide Peptidase ElxP and the Oxidoreductase ElxO

The final step in lanthipeptide biosynthesis involves the proteolytic removal of an N-terminal leader peptide. In the class I lanthipeptide epilancin 15X, this step is performed by the subtilisin-like serine peptidase ElxP. Bioinformatic, kinetic, and mass spectrometric analysis revealed that ElxP recognizes the stretch of amino acids DLNPQS located near the proteolytic cleavage site of its substrate, ElxA. When the ElxP recognition motif was inserted into the noncognate lanthipeptide precursor NisA, ElxP was able to proteolytically remove the leader peptide from NisA. Proteolytic removal of the leader peptide by ElxP during the biosynthesis of epilancin 15X exposes an N-terminal dehydroalanine on the core peptide of ElxA that hydrolyzes to a pyruvyl group. The short-chain dehydrogenase ElxO reduces the pyruvyl group to a lactyl moiety in the final step of epilancin 15X maturation. Using synthetic peptides, we also investigated the substrate specificity of ElxO and determined the 1.85 A resolution X-ray c...
Inferring species divergence times using pairwise sequential Markovian coalescent modelling and low-coverage genomic data

Understanding when species diverged aids in identifying the drivers of speciation, but the end of gene flow between populations can be difficult to ascertain from genetic data. We explore the use of pairwise sequential Markovian coalescent (PSMC) modelling to infer the timing of divergence between species and populations. PSMC plots generated using artificial hybrid genomes show rapid increases in effective population size at the time when the two parent lineages diverge, and this approach has been used previously to infer divergence between human lineages. We show that, even without high coverage or phased input data, PSMC can detect the end of significant gene flow between populations by comparing the PSMC output from artificial hybrids to the output of simulations with known demographic histories. We then apply PSMC to detect divergence times among lineages within two real datasets: great apes and bears within the genus Ursus Our results confirm most previously proposed divergence times for these lineages, and suggest that gene flow between recently diverged lineages may have been common among bears and great apes, including up to one million years of continued gene flow between chimpanzees and bonobos after the formation of the Congo River.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.
Assessment of recent HIV testing among older adults in the United States

Older adults are the fastest growing segment of people living with HIV, and unfortunately many are unaware of their HIV status. Many providers are reluctant to ask older adults about their sexual histories, evaluate their risk factors, and test for HIV, and older adults have low perception of HIV risk. Using data from the 2013 to 2014 National Health and Nutrition Examination Survey, this study assessed the prevalence of recent HIV testing among older adults in the United States (n = 1,056) and identified predictors and barriers to recent HIV testing. The prevalence of recent HIV testing was 28%. Recent HIV testing was associated positively with male gender, education level, having public insurance, having same sex sexual behavior, African, and Hispanic ethnicity, whereas age, income-to-poverty ratio, and Asian ethnicity were associated negatively with recent HIV testing. Public health social workers are advised that targeted HIV testing for Asian, economically disadvantaged, female older adults is needed to increase HIV awareness and detection and to decrease late diagnosis of HIV. Provided public insurance was identified as a predictor of recent HIV testing, facilitating economically disadvantaged older adults' eligibility for public insurance that will likely improve access to HIV testing services and increase HIV testing rates.
Spectral science: tracing the conflict zones of Uruguayan lead poisoning

Lead poisoning, one of the most researched and ‘settled’ domains of global biomedical science, has only been collectively acknowledged as a significant environmental health risk in Uruguay from 200...
NanoAsPipe: A transcriptome analysis and alternative splicing detection pipeline for MinION long-read RNA-seq

After the next-generation sequencing technology, long-read sequencing technologies were developed. Both the advantages and the drawbacks of long-read sequencing technologies are obvious. Here, we take advantages of long-read sequencing technology, MinION, to develop a comprehensive and user-friendly pipeline, NanoAsPipe, to identify the transcriptomic profiles, isoform profiles, and alternative splicing (AS) events of long-read RNA-seq data on the Open Science Grid (OSG). NanoAsPipe includes RNA-seq data preprocessing, mapping and alternative splicing analysis to simultaneously account for AS events. NanoAsPipe was applied to two long-read datasets and its performance was evaluated by comparing discovered AS events with gene annotation and results from short-read RNA-seq data. Majority of predicted AS events by NanoAsPipe was confirmed by the gene annotation and there is a high correlation between results from long-read data and short-read data. NanoAsPipe was implemented as a software package, which is available for academic research at http://sysbio.unl.edu/NanoAsPipe. The user may run the workflow based on the OSG environment or switch it to other computing setup environments.
Equations for the Extension and Flexure of Relatively Thin Thermopiezoelectric Plates Subjected to Large Electric Fields

A system of approximate two-dimensional equations for the extensional and flexural motion of thermopiezoelectric plates subject to large electric fields is derived from the three-dimensional equations of thermopiezoelectricity for small strains, small temperature variations, and strong electric fields. The two-dimensional equations are derived by introducing an appropriate expansion for the mechanical displacement, temperature field, and electric potential in the thickness-coordinate and integrating the balance laws and constitutive relations.
Nasal mites from specimens of the brown-headed cowbird (Icteridae: Molothrus ater) from Texas and Arkansas, U.S.A.

Avian nasal mites are obligate parasites that spend their entire life in the respiratory system of birds. In North America, four families in three orders parasitize birds: Rhinonyssidae (Mesostigmata), Ereynetidae (Prostigmata), Cytoditidae (Astigmata) and Turbinoptidae (Astigmata). Mechanisms of nasal mite transmission among hosts is still unclear and brood parasites like the Brown-headed Cowbird (Molothrus ater Boddaert, 1783), which utilize multiple bird species as hosts, are interesting for the study of parasites such as nasal mites. We examined 126 cowbirds for nasal mites and found 84 individuals (66.6 %) to be infested. The most common nasal mite species recovered was Ptilonyssus icteridius Strandmann and Furman, 1956. The presence of P. richmondenae George, 1961, in Brown-headed Cowbird represents a new host association, and a potential new species of Ptilonyssus was also recovered. The ereynetid species Boydaia quiscali Clark, 1960 was found in two Brown-headed Cowbirds, both times a co-infestation with species of Ptilonyssus.
Multi-physics simulation of CO2 gas coolers using equivalence modelling

Abstract A CFD model to simulate CO2 gas coolers is presented: the adoption of an equivalent approach allows to reproduce the effects of an extended finned surface while drastically reducing the computational effort. The model is validated against experimental results available in the open literature. The contemporary solution of both convection and conduction allows highlighting the impact of conduction along the tubes and the supporting end plates. The model provides satisfactory matching with experimental results: total heating power is forecast within 2.5%, while the maximum temperature deviation between the simulated and experimental heat exchanger curves temperature is 3.8 °C, when the CO2 temperature is as high as 108 °C. This thermal CFD model allows evaluating the 3D effects of the air maldistribution in terms of temperature, heat transfer coefficients, and cooling power, thus opening the way to the simulation and optimisation of complete ventilated finned coil and gas cooling systems.
An efficient spectral method for acoustic scattering from rough surfaces

An efficient and accurate spectral method is presented for scattering problems with rough surfaces. A probabilistic framework is adopted by modeling the surface roughness as random process. An improved boundary perturbation technique is employed to transform the original Helmholtz equation in a random domain into a stochastic Helmholtz equation in a fixed domain. The generalized polynomial chaos (gPC) is then used to discretize the random space; and a Fourier-Legendre method to discretize the physical space. These result in a highly efficient and accurate spectral algorithm for acoustic scattering from rough surfaces. Numerical examples are presented to illustrate the accuracy and efficiency of the present algorithm.
Contraception Before and After GDM

Increasing parity is a risk factor for GDM. For women with a history of GDM, a subsequent pregnancy increases 3-fold the risk of progressing to type 2 diabetes. Therefore, the proper use of contraception to prevent unwanted pregnancies in young women both before and after a pregnancy complicated by GDM is essential. There are several forms of hormonal contraceptives available that offer effective contraception. Some forms of hormonal contraceptives also have unwanted metabolic side effects, and the risks associated with the use of individual contraceptives should be weighed against their benefits. Women with a history of GDM may be particularly vulnerable to metabolic side effects. This chapter summarizes hormonal contraceptive use before pregnancy and its effect on risk of GDM and reviews family planning methods in women after a GDM pregnancy, including postpartum lactational amenorrhea, barrier methods, combination oral contraceptives, progesterone-only contraception, and intrauterine devices. We will review the risks and benefits of each method, as the effect of the method in preventing unintended pregnancies may outweigh any adverse impacts on glucose tolerance and lipid metabolism.
Understanding Self-Report of Sexual Abuse in an Initial Clinical Interview

Publisher Summary This chapter focuses on understanding self-report of sexual abuse in an initial interview. The limitations inherent in the information obtained are reviewed in light of additional challenges understanding sexual abuse. These are pointed, but not atypical, examples of the limitations of all information gathered in mental health services. All assessment information simultaneously serves a therapeutic function (and vice versa); the interplay between these is explored. Since sexual abuse history is typically embedded in the symptoms it generates, effectively managing such symptoms is the necessary initial strategy in working with sexual abuse. A goal-oriented, directive approach is offered with justification for its recommended use. It may appear in this approach that more preparation for addressing sexual abuse clinically than actual resolution has occurred. In fact, such “preparation” constitutes much of the actual clinical work and parallels the ways in which sexual abuse affects individual patterns of vulnerability and resiliency.
Host regulation of the replication of the yeast retrotransposon Ty5

viii CHAPTER L GENERAL INTRODUCnON 1 Genomic organization of retrotransposons 1 Life cycle of LTR-retrotransposons 3 Ty elements of Sacchairomyces cerevisiae 5 Transcriptional regulation 6 Translational regulation 7 Post-translational regulation 8 Integration and recombination of cDNA 8 The effects of flanking sequences on Ty transcription 9 Ty5 elements are associated preferentially with silent chromatin 10 Dissertation organization 10 References 11 CHAPTER n. LIFE IN SILENT CHROMATIN: TRANSCRIPTIONAL REGULATION OF THE SACCHAROMYCES RETROTRANSPOSON TY5 17 Abstract 17 Introduction 18 Results 21 Transcription of Ty5 is repressed by silent chromatin 21 Ty5 transcription is under pheromone and cell type regulation 22 Cis-acting sequences mediates pheromone and cell type regulation 23 a-factor induced transcription of Ty5 insertions located in silent chromatin 24
Constructive induction on decision trees

Selective induction techniques perform poorly when the features are inappropriate for the target concept. One solution is to have the learning system construct new features automatically; unfortunately feature construction is a difficult and poorly understood problem. In this paper we present a definition of feature construction in concept learning, and offer a framework for its study based on four aspects: detection, selection, generalization, and evaluation. This framework is used in the analysis of existing learning systems and as the basis for the design of a new system, CITRE. CITRE performs feature construction using decision trees and simple domain knowledge as constructive biases. Initial results on a set of spatial-dependent problems suggest the importance of domain knowledge and feature generalization, i.e., constructive induction.
Transformation and Tumorigenesis Mediated by the Adenovirus E1A and E1B Oncogenes

Adenoviruses and other small DNA tumor viruses, e.g., SV40 virus and papillomaviruses, have evolved efficient strategies for replicating their genomes on entry into their host cells. Because these viruses have limited coding capacities, they cannot produce all of the protein products required to synthesize their new double-stranded DNA genomes and, therefore, must utilize many components of the host-cell machinery. In naturally occurring infections, adenovirus frequently enters noncycling, differentiated epithelial cells. This presents adenovirus with the problem of how to stimulate these quiescent cells to an active growth state in order to create a cellular environment in which viral propagation can take place. The small DNA viruses have devised strategies in which certain of their early viral proteins, i.e., adenovirus E1A and E1B, SV40 T antigen, and papilloma E6 and E7, physically target specific cellular proteins whose function it is to regulate cellular growth.
Mid-infrared quantum cascade laser arrays with electrical switching of emission frequencies

We present a design of quantum cascade laser arrays made of ridge-waveguide devices in which the emission frequency can be electrically switched between several specified values. Our approach relies on fabricating multiple independently-biased distributed feedback grating sections along the laser ridge waveguides. Switchable single-mode lasing from the laser facet is achieved by balancing the injection pumping of the different grating sections. Our method provides a robust solution that can increase the tuning bandwidth of the quantum cascade laser arrays without increasing the size of the array emission aperture.
Combining multiseismic attributes with an extended octree quantization method

AbstractSeismic interpreters and processors encounter ever-increasing volumes of seismic attributes in geophysical exploration each year. Multiattribute integration and classification improve the a...
Visualizing Classic Synchronization Problems

Classic synchronization problems are often used to introduce students to the subtleties of concurrency and synchronization mechanisms, such as semaphores, monitors, locks, and condition variables. The Dining Philosophers, Producers-Consumers, and Readers-Writers are all classic problems in which a correct solution requires the actions of multiple processes or threads to be synchronized. In this work, we present visualizations for these three problems and demonstrate their use in helping students build accurate mental models of concurrency abstractions. We also present the results of an experiment that indicate students find using these visualizations to be significantly more engaging than reading a textbook, with no significant difference in learning.
Simultaneous isolation and label-free identification of bacteria using contactless dielectrophoresis and Raman spectroscopy.

The traditional bacterial identification method of growing colonies on agar plates can take several days to weeks to complete depending on the growth rate of the bacteria. Successfully decreasing this analysis time requires cell isolation followed by identification. One way to decrease analysis time is by combining dielectrophoresis (DEP), a common technique used for cell sorting and isolation, and Raman spectroscopy for cell identification. DEP-Raman devices have been used for bacterial analysis, however, these devices have a number of drawbacks including sample heating, cell-to-electrode proximity that limits throughput and separation efficiency, electrode fouling, or inability to address sample debris. Presented here is a contactless DEP-Raman device to simultaneously isolate and identify particles from a mixed sample while avoiding common drawbacks associated with other DEP designs. Using the device, a mixed sample of bacteria and 3 μm polystyrene spheres were isolated from each other and a Raman spectrum of the trapped bacteria was acquired, indicating the potential for cDEP-Raman devices to decrease the analysis time of bacteria.
Risk Tolerance and the Investment Behavior of Black and Hispanic Heads of Household

Attitudes toward risk and willingness to hold risky assets are compared for white, Hispanic, and black heads of household using data from the 1998 Survey of Consumer Finances. Results indicate that Hispanic heads of household evidenced a significantly higher level of risk aversion and held a significantly lower percentage of risky assets to net worth. Contrary to prior research, the results for black heads of household were not significant when we control for the level of household wealth suggesting that, although blacks may hold different types of assets than whites, they are not necessarily more risk averse.
A Biochemical Sensor with Artificial 3D Enzyme Network

We report the integration of artificial three-dimensional (3D) enzyme networks into SU-8 photoresist-converted porous carbon electrodes to realize highperformance amperometric nitrate sensors. The sensor provides an improved lifespan that allows for long-term monitoring of nitrate ions. The artificial enzyme is formed by introducing both graphene oxide (GO) and Vitamin B12 (Vit-B12) into the converted porous carbon. The enzymatic electrode serves as the working electrode of the sensor to detect nitrate ions in the sap solution of maize plants. It is demonstrates that the sensor has high sensitivity and selectivity to nitrate ions, as well as high stability over at least seven days with almost no performance degradation.
Physician, know thyself: implicit and explicit decision-making for mechanical thrombectomy in stroke

Few clinical situations in medical practice are as time-sensitive and and have such profound ramifications as selection of patients with acute stroke for mechanical thrombectomy (MT). Emergent large vessel occlusion has become a treatable disease with minimal numbers needed to treat to achieve a functional, long-term neurologic outcome. However, MT carries risk and many patients who are appropriately reperfused continue to have significant neurologic deficits and disability despite a successful procedure. The decision to offer or withhold MT can be complex. Frequently decisions must be made based on incomplete information or emergently while the physician is awoken from sleep or distracted while performing other procedures. A growing number of studies have examined cognitive errors and biases as they pertain to patient diagnosis and treatment in medicine. Dual process theory identifies two decision-making processes as system 1 ('implicit') and system 2 ('explicit') and describes the patterns through which decisions are formulated. The implicit system is the default pathway as it requires little effort or focus, uses mental short cuts, and is rapid; however, this pathway is subject to considerable bias and error. This manuscript reviews the mechanisms underlying the way in which physician decisions about MT are made, specifically highlighting prominent biases that may affect judgment, and reviews other important principles, such as confidence in decisions, aggressiveness to pursue MT, and strategies to improve decisions.
Adaptive Hybrid Molecular Brushes Composed of Chitosan, Polylactide, and Poly(N-vinyl pyrrolidone) for Support and Guiding Human Dermal Fibroblasts

Hybrid molecular brushes (HMBs) are macromolecular constructs made up of a backbone polymer and side-chain polymers with distinct properties. They adapt to changing microenvironment via conformatio...