cssi/SciSciGPT-SciSciNet huggingface dataset:
Ion beam characterization and treatment

Almost every process that occurs when an ion beam hits a solid has been pressed into service as a technique in materials science. Some ions bounce off: backscattering is a routine technique for near-surface analysis in many laboratories. Atoms of the sample are knocked out: sputter profiling is used as an adjunct to many surface science measurements, and analysis of the ejected atoms yields information about the composition of the sample. Ions slow down in a solid, depositing energy in the sample and causing radiation damage. This makes ion beams useful in the development of radiation-resistant materials and has to be understood in order to apply other ion beam techniques. Finally, the ion stops and becomes incorporated into the sample, which is known as “implantation.” As well as being a vital industrial technique in the manufacture of semiconductor devices, implantation can be used in materials science wherever it is useful to change the composition of a near-surface layer. The implanted species doesn’t have to be soluble in the sample.
Greenhouse gas implications of household energy technology in Kenya.

Linkages between household energy technology, indoor air pollution, and greenhouse gas (GHG) emissions have become increasingly important in understanding the local and global environmental and health effects of domestic energy use. We report on GHG emissions from common Kenyan wood and charcoal cookstoves. Our estimations are based on 29 d of measurements under the conditions of actual use in 19 rural Kenyan households. Carbon monoxide (CO), particulate matter (PM10), combustion phase, and fuel mass were measured continuously or in short intervals in day-long monitoring sessions. Emissions of pollutants other than CO and PM10 were estimated using emissions ratios from published literature. We estimated that the daily carbon emissions from charcoal stoves (5202 +/- 2257 g of C: mean +/- SD) were lower than both traditional open fire (5990 +/- 1843 g of C) and improved ceramic woodstoves (5905 +/- 1553 g of C), but the differences were not statistically significant. However, when each pollutant was weighted using a 20-yr global warming potential, charcoal stoves emitted larger amounts of GHGs than either type of woodstove (9850 +/- 4600 g of C for charcoal as compared to 8310 +/- 2400 and 9649 +/- 2207 for open fire and ceramic woodstoves, respectively; differences not statistically significant). Non-CO2 emissions from charcoal stoves were 5549 +/- 2700 g of C in 20-yr CO2 equivalent units, while emissions were 2860 +/- 680 and 4711 +/- 919 for three-stone fires and improved ceramic stoves, respectively, with statistically significant results between charcoal and wood stoves. Therefore in a sustainable fuel-cycle (i.e., excluding CO2), charcoal stoves have larger emissions than woodstoves. When the emissions from charcoal production, measured in a previous study, were included in the assessment, the disparity between the GHG emissions from charcoal and firewood increased significantly, with non-CO2 GHG emissions factors (g of C/kg of fuel burned) for charcoal production and consumption 6-13 times higher than emissions from woodstoves. Policy implications and options for environment and public health are discussed.
The Kinetic Energy Budgets of Two Severe Storm Producing Extratropical Cyclones

Abstract Eulerian kinetic energy budgets for the synoptic-scale flow over North America were computed for two cases of cyclone development associated with severe prefrontal convection. Horizontal flux convergence constitutes the major energy source in both cases and assumes major importance in maintaining the strength of the upper tropospheric jet maxima. Generation of kinetic energy via cross-counter flow is, surprisingly, a persistent sink in one case and only a weak energy source for the cyclone in the second case. Cross-contour flow toward higher heights is generally found ahead of the upper level troughs, where the jet stream is moving through regions in which the contour gradient weakens downstream. Generation of kinetic energy is largely confined to the lower troposphere, reflecting frictional influence near the earth's surface. Dissipation of kinetic energy, computed as a residual, has local maxima both in the lower troposphere (nearly balancing the generation) and near the jet stream level. Subgr...
A unique myosin isoform transition in cat striated external anal sphincter muscle induced by denervation

Denervation of limb and trunk muscles leads to characteristic changes in their biochemical properties. However, the effects of denervation of the striated external anal sphincter (EAS) muscle have not been studied, even though denervation is a common etiology for fecal incontinence. The present study reports effects ofdenervation of the cat EAS and compares them with changes in a denervated limb muscle [cat extensor digitorum longus (EDL)]. Nerves supplying the EAS and the EDL were sectioned in anesthetized cats, which were allowed to recover and live for 10, 30, or 60 days. Their muscles were then excised, and myofibrillar proteins were isolated. Myosin heavy chain (MHC) isoform composition was measured by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The EDL and EAS showed progressive increases in MHC type IIA and progressive decreases in MHC type IIB at 10, 30, and 60 days. MHC type I progressively increased in the EDL but showed no change in the EAS. We hypothesize that this distinctive transition is related to the unique embryological origin and function of the EAS.
How to avoid inconsistent idealizations

Idealized scientific representations result from employing claims that we take to be false. It is not surprising, then, that idealizations are a prime example of allegedly inconsistent scientific representations. I argue that the claim that an idealization requires inconsistent beliefs is often incorrect and that it turns out that a more mathematical perspective allows us to understand how the idealization can be interpreted consistently. The main example discussed is the claim that models of ocean waves typically involve the false assumption that the ocean is infinitely deep. While it is true that the variable associated with depth is often taken to infinity in the representation of ocean waves, I explain how this mathematical transformation of the original equations does not require the belief that the ocean being modeled is infinitely deep. More generally, as a mathematical representation is manipulated, some of its components are decoupled from their original physical interpretation.
A 68-NUCLEOTIDE SEQUENCE WITHIN THE 3' NONCODING REGION OF SIMIAN HEMORRHAGIC FEVER VIRUS NEGATIVE-STRAND RNA BINDS TO FOUR MA104 CELL PROTEINS

The 3' noncoding region (NCR) of the negative-strand RNA [3'(-)NCR RNA] of the arterivirus simian hemorrhagic fever virus (SHFV) is 209 nucleotides (nt) in length. Since this 3' region, designated 3'(-)209, is the site of initiation of full-length positive-strand RNA and is the template for the synthesis of the 5' leader sequence, which is found on both full-length and subgenomic mRNAs, it is likely to contain cis-acting signals for RNA synthesis and to interact with cellular and viral proteins to form replication complexes. Gel mobility shift assays showed that cellular proteins in MA104 S100 cytoplasmic extracts formed two complexes with the SHFV 3'(-)209 RNA, and results from competition gel mobility shift assays demonstrated that these interactions were specific. Four proteins with molecular masses of 103, 86, 55, and 36 kDa were detected in UV-induced cross-linking assays, and three of these proteins (103, 55, and 36 kDa) were also detected by Northwestern blotting assays. Identical gel mobility shift and UV-induced cross-linking patterns were obtained with uninfected and SHFV-infected extracts, indicating that the four proteins detected are cellular, not viral, proteins. The binding sites for the four cellular proteins were mapped to the region between nt 117 and 184 (68-nt sequence) from the 3' end of the SHFV negative-strand RNA. This 68-nt sequence was predicted to form two stem-loops, SL4 and SL5. The 3'(-)NCR RNA of another arterivirus, lactate dehydrogenase-elevating virus C (LDV-C), competed with the SHFV 3'(-)209 RNA in competition gel mobility shift assays. UV-induced cross-linking assays showed that four MA104 cellular proteins with the same molecular masses as those that bind to the SHFV 3'(-)209 RNA also bind to the LDV-C 3'(-)NCR RNA and equine arteritis virus 3'(-)NCR RNA. However, each of these viral RNAs also bound to an additional MA104 protein. The binding sites for the MA104 cellular proteins were shown to be located in similar positions in the LDV-C 3'(-)NCR and SHFV 3'(-)209 RNAs. These data suggest that the binding sites for a set of the cellular proteins are conserved in all arterivirus RNAs and that these cell proteins may be utilized as components of viral replication complexes.
A 0.8 V asynchronous ADC for energy constrained sensing applications

This paper discusses the design of an asynchronous analog-to-digital converter targeted for low-power sensing applications. The asynchronous sampling scheme will save power because it only samples the input signal when it is changing. The idea of using an adaptive resolution to increase the maximum input frequency of the ADC is introduced. A prototype chip has been fabricated in a 0.18 mum CMOS process. Initial measurement results are presented.
A fractal-based image block-coding algorithm

A novel block-coding algorithm for grey-scale images based on a fractal approximation is presented. Image blocks are approximated by a linear combination of a set of almost orthogonal basis blocks made up of a set of simple image-independent blocks and a set of image-dependent blocks generated from transformed blocks of bigger size in the same image. To find the approximation for each block, the block is projected onto the space spanned by the set of basis blocks. For each block, the biggest coefficients plus the index of the corresponding basis blocks and the number of basis blocks used make the code. The number of basis vectors used for coding each block is the number of basis blocks needed to approximate the block within a given error limit. The results of a study of the effect of variations on Jacquin's fractal-based image coding algorithm are also presented. >
A wireless, remote query magnetoelastic CO2 sensor.

This paper presents a wireless, passive, remote query CO2 sensor comprising a ribbon-like magnetoelastic thick-film coated with a mass-changing CO2 responsive polymer synthesized from acrylamide and isooctylacrylate. In response to a magnetic field impulse, the magnetostrictive magnetoelastic sensor vibrates at a characteristic resonant frequency that is inversely dependent upon the mass of the attached CO2 responsive polymer. The mechanical vibrations of the magnetostrictive sensor launch magnetic flux, which can be detected remotely using a pickup coil. By monitoring the resonant frequency of the passive sensor, the atmospheric CO2 concentration can be determined without the need for physical connections to the sensor or specific alignment requirements. The effect of humidity and the CO2 responsive copolymer composition on the measurement sensitivity are reported. Greatest sensitivity is achieved with a polymer comprising a 1 ∶ 1 mole ratio of acrylamide to isooctyl acrylate. A 0.7% change in atmospheric CO2 concentration can be detected for a 20 µm thick polymer coated sensor.
BLMST: a scalable, power-efficient broadcast algorithm for wireless networks

The power-efficient broadcast for multi-hop wireless networks is discussed in this paper. We first investigate the trade-off between (i) using larger transmission power to reach more nodes in one hop and (ii) using smaller power and relaying broadcast messages through multiple hops. Analysis indicates that multi-hop broadcast is more power-efficient if /spl alpha/ /spl ges/ 2.2, where the power consumption model is P(r, /spl alpha/) = c/sub 0/ /spl middot/ r/sup /spl alpha// + c/sub 1/. Based on the analysis, we propose broadcast on local minimum spanning tree (BLMST). An underlying topology is first derived using local minimum spanning tree (LMST), a localized topology control algorithm. Broadcast messages are then simply relayed through the derived topology in a constrained flooding fashion. BLMST is fully localized, scalable, and power-efficient. Simulation results show that the performance of BLMST is comparable to that of existing centralized algorithms.
An Analysis of the Concept of Hope in the Adolescent With Cancer

Nursing application of the concept of hope in the pediatric oncology clinical setting is currently in its infancy. This article presents a systematic analysis of the concept of hope for use by the pediatric oncology nurse in the care of the pediatric adolescent oncology patient. The literature review addresses health and illness states as areas significant to the analysis and application of hope. This article defines critical attributes, antecedents, and consequences of hope; constructs case examples (a model, a borderline, and contrary cases); includes an operational definition of adolescent hopefulness; and summarizes empirical referents of hope. Through clinical assessment of hope in the pediatric adolescent oncology patient and ongoing research of hope in this population, evaluation of the potential benefits of hope to this population's adaptation to varying health states will be further demonstrated.
Pesticides in mountain yellow-legged frogs (Rana muscosa) from the Sierra Nevada Mountains of California, USA

In 1997, pesticide concentrations were measured in mountain yellow-legged frogs (Rana muscosa) from two areas in the Sierra Nevada Mountains of California, USA. One area (Sixty Lakes Basin, Kings Canyon National Park) had large, apparently healthy populations of frogs. A second area (Tablelands, Sequoia National Park) once had large populations, but the species had been extirpated from this area by the early 1980s. The Tablelands is exposed directly to prevailing winds from agricultural regions to the west. When an experimental reintroduction of R. muscosa in 1994 to 1995 was deemed unsuccessful in 1997, the last 20 (reintroduced) frogs that could be found were collected from the Tablelands, and pesticide concentrations in both frog tissue and the water were measured at both the Tablelands and at reference sites at Sixty Lakes. In frog tissues, dichlorodiphenyldichloroethylene (DDE) concentration was one to two orders of magnitude higher than the other organochlorines (46 ± 20 ng/g wet wt at Tablelands and 17 ± 8 Sixty Lakes). Both γ-chlordane and trans-nonachlor were found in significantly greater concentrations in Tablelands frog tissues compared with Sixty Lakes. Organophosphate insecticides, chlorpyrifos, and diazinon were observed primarily in surface water with higher concentrations at the Tablelands sites. No contaminants were significantly higher in our Sixty Lakes samples.
Application of a coupled discontinuous–continuous Galerkin finite element shallow water model to coastal ocean dynamics

Abstract A coupled discontinuous–continuous Galerkin (DG–CG) shallow water model is compared to a continuous Galerkin generalized wave-continuity equation (GWCE) based model for the coastal ocean, whereby local mass imbalance typical of GWCE-based solutions is eliminated using the coupled DG–CG approach. Two mass imbalance indicators for the GWCE-based model are presented and analyzed. The indicators motivate discussion on the suitability of using a GWCE-based model versus the locally conservative coupled DG–CG model. Both realistic and idealized test problems for tide, wind, and wave-driven circulation form the basis of the study. For the problems studied, coupled DG–CG solutions retain the robustness of well-documented solutions from GWCE-based models and also capture the dynamics driven by small-scale, highly advective processes which are problematic for GWCE-based models. Issues associated with the coupled DG–CG model are explored, including increased cost due to increased degrees of freedom, the necessary application of slope limiters, as well as the actual coupling process.
A Method to Determine Stroke Trial Success Using Multidimensional Pooled Control Functions

Background and Purpose— Many early phase trials in stroke have not been subsequently confirmed. Randomization balance in baseline factors that influence outcome are difficult to achieve and may be partly responsible for misleading early results. We hypothesized that comparison with an outcome function derived from a large number of pooled control arms would mitigate these randomization problems and provide a reliable predictor for decision-making before proceeding to later phase trials. We developed such a model and added a novel feature of generation of multidimensional 95% prediction surfaces by which individual studies could be compared. We performed a proof-of-principle study with published clinical trials, determining whether our method correctly identified known outcomes. Methods— The control arms from all randomized, controlled trials for acute stroke with ≥10 subjects, including baseline National Institute of Health Stroke Scale, age, and 3-month outcomes published between 1994 and May 2008, were ...
Projecting Political Correctness: The Divorce of Affect and Signifier

Etude de la manifestation historique de la rupture entre l'affect et le signifiant qui consitute un aspect formatif du dualisme esprit-corps sur lequel reposent les debats feministes sur la distinction sexe/genre. Se referant au dernier ouvrage de R. Feldstein intitule «Political correctness: a response from the cultural left» (1997), l'A. montre que la rupture entre l'affect et la pensee se realise dans la masquarade du politiquement correct que l'on retrouve dans la droite politique comme dans les arguments de la gauche sur la signification
The Use of Vaginal Tampons for the Absorption of Menstrual Discharges

Summary One hundred and ten subjects using vaginal tampons for the absorption of the menstrual flow throughout each period were interviewed and examined every two months over periods of time varying from a minimum of one year (30 subjects) to a maximum of two years (56 subjects). There was no evidence of any irritation of the cervix or vagina by the tampon. There were 3.63 per cent of the subjects who had Trichomonas vaginalis organisms in the vaginal discharge. (This incidence of infection is lower than the average given in most statistical studies of groups of 100.) There were 3.63 per cent of the subjects who had Monilia albicans present in the vaginal discharge. No subjects acquired trichomonas or yeast infections during the period of study. There was no evidence of any other pelvic infection during this period. There was no evidence that the use of the tampon caused obstruction to the menstrual. flow. Because of the greater comfort experienced, 103 subjects preferred to continue to use the tampons through part or all of the menstrual period rather than to return to the use of the perineal pad alone.
Unwed Fathers and Adoption: A Theoretical Analysis in Context

This Article investigates the theoretical framework underlying the law's treatment of unwed fathers' rights in adoption and explores alternative theories to approach these cases. It further analyzes the theoretical and doctrinal basis for defining unwed fathers' rights as set forth in the Supreme Court's jurisprudence of fatherhood and explores the range of theoretical options for constructing fatherhood in these cases. The author scrutinizes the historical view of fatherhood which defines fatherhood exclusively in terms of marital status and declares that unwed fathers have few, if any, legal rights concerning their children. Although the Supreme Court has shifted away from this approach, proponents of this theory persist. This theory is juxtaposed with a theory of fatherhood that would grant men the same rights as women regarding adoption based solely on their biological relationship to the child. The author then reviews a third theory that premises father's rights on meeting certain threshold requirements, most notably by demonstrating a substantial commitment to parenthood. In the final sections, the author argues that courts must apply this theory in a more sensitive and nuanced way and suggests some practical ways of addressing the theory's limitations.
Trips and Treaties of Adhesion Part II: Back to the Past or a Small Step Forward?

Some in the international community have proclaimed that the international intellectual property system in general, and the Trade Related Aspects of Intellectual Property Rights (TRIPS) specifically, is falling apart. Such proclamations are misplaced. To be sure, TRIPS has generated turmoil and has been attacked from all sides. But, dissatisfaction with the system and efforts to reshape TRIPS reflects the push and pull on an evolving system; indeed, we are experiencing, arguably for the first time in international IP, a legitimate "push" from developing countries seeking fairness in the system. All of this suggests that we take a second look at TRIPS, from the viewpoint of addressing both sides' needs and making the system "fair." If we accept that the international intellectual property system is unfair, a host of questions arises, including how we can consider fairness. I have argued elsewhere that one way to address the inherent unfairness is to embrace a treaty of adhesion doctrine. The doctrine refers to a treaty that was procured through coercion as a result of unequal bargaining power. Applying the doctrine to TRIPS will allow WTO jurists to interpret ambiguous TRIPS provisions in favor of developing countries. This article continues that theme but responds to the potential criticism that adopting a treaty of adhesion doctrine will result in developed countries "regime shifting," that is, leaving the WTO for other favorable forums where they can exploit power asymmetries. A variety of reasons controvert this outcome, including the huge effort involved in procuring TRIPS and the accession of China, a new WTO emerging player with an attractive large trade market. The doctrine will have a positive effect on future bargaining leverage, as developing countries are now more knowledgeable about intellectual property, particularly as to adverse spillover effects in areas such as agriculture, health, and education.
Abstract 77: MicroRNA-34a Accelerates Aging in Vascular Smooth Muscle Cells (SMCs) Isolated from Transgenic Mice Overexpressing Nox1 in SMCs

Background: Aging increases cardiovascular morbidity. Aging in vascular smooth muscle cells (VSMC) induces cell senescence, leading to impaired vasodilation with decreased vascular compliance, increased inflammation and oxidative stress. MicroRNA-34a (miR-34a) has been reported as a biomarker of aging. Methods and Results: After screening for a group of miRs, there was a > 2 fold of miR-34a in aortic SMCs isolated from transgenic mice overexpressing Nox1 in SMCs (Nox-1 SMCs). Therefore, we hypothesized that miR34 contributes to VSMC aging. TaqMan miR assay confirmed an increased miR-34a by 2.1 fold in young NOX-1 SMCs (passage 3-7) with an increase by 5.25 fold in activity of senescence-associated β-galactosidase (SA-β-Gal ) compared to WT. miR-34a in old NOX-1 and WT SMCs (passage 14-16) was increased by 3.8 fold and 2.1 fold, respectively, compared to young SMCs (both P Conclusion: Increased NOX-1 in SMCs induces miR-34a that accelerates SMC senescence. The pathway may involve downregulation of Nrf2 and increased P21 through P53 pathway. This provides potential targets for protecting against vascular aging.
Effects of protein solution composition on the time-dependent functional activity of fibrinogen on surfaces.

Protein function affects subsequent biological processes such as cell adhesion and thrombus formation. We have developed tools to detect the biological activity of fibrinogen using AFM techniques. ...
Suppression of Late-Season Argentine Ant (Hymenoptera: Formicidae) Field Populations Using a Perimeter Treatment with Containerized Baits

The efficacy of containerized ant baits used in a perimeter treatment in suppressing late-season Argentine ant, Linepithema humile (Mayr), foraging populations was evaluated. Three different containerized ant baits containing either 0.9% hydramethylnon or 0.5% sulfluramid in 2 different bait matrix formulations were placed around buildings of the complex. Semiweekly ant counts at honey water monitors, biweekly bait consumption, and monthly tenant complaint log requests served as evaluation criteria. Bait consumption was slightly less for one of 2 sulfuramid baits tested. However, ant foraging activity, as measured at honey water monitors, was reduced by 84-88% within 2 wk of exposure to baits regardless of bait type. Tenant complaints remained unchanged at untreated buildings but were 4 times less than those from treatment buildings by the end of the 8-wk trial.
Fluoroscopy-guided placement of nasoenteral tubes in children using intermittent digital pulse fluoroscopy and last image save/grab technique

Aim To document the radiation exposure metrics, including fluoroscopic radiation time and radiation dose–area product, in children Materials and methods Following institutional review board approval, the age, gender, anatomical information, immediate procedure-related complications if any, fluoroscopy time, and radiation dose–area product were collected retrospectively in all paediatric patients who underwent fluoroscopically guided nasoenteral tube placement during a 5-year period. Three paediatric radiology faculty members, a radiologist assistant, and trainee residents during their paediatric radiology rotation performed the procedures on two different digital fluoroscopic machines using radiation-minimising techniques. Median values of the fluoroscopy time and radiation dose–area product were calculated and compared to values reported in the literature using the Wilcoxon procedure. Results There were 41 male and 33 female patients with a median age of 4 years and 6 months. Median fluoroscopy time used for placing a nasoenteral tube was 1.25 minutes with a median radiation exposure dose–area product of 0.245 Gy·cm 2 . All patients had successful placement of nasoenteral tube without immediate procedure-related complications. Conclusion Fluoroscopy-guided nasoenteral feeding tube placement can be performed successfully with minimal radiation exposure without compromising procedural success.
Enteral β-hydroxy-β-methylbutyrate supplementation increases protein synthesis in skeletal muscle of neonatal pigs

Many low-birth weight infants are at risk for poor growth due to an inability to achieve adequate protein intake. Administration of the amino acid leucine stimulates protein synthesis in skeletal m...
Health status attributes of older African-American adults with hearing loss

This article describes a study that examined hearing loss and health-related quality of life (HRQoL) attributes of 71 African-American older adults ranging in age from 60 to 89 years. Demographic profiles were used to obtain pertinent case histories, audiometric testing was used to obtain estimates of peripheral hearing sensitivity, and middle-ear integrity was assessed via tympanometry. The health status (i.e., HRQoL) attributes were determined via self-report scores on the Medical Outcomes Study 36-Item Short-Form Health Survey (SF-36). Results from bivariate analyses determined statistically significant correlations between hearing loss and lower SF-36 scores across subscales. Multivariate regression models revealed a statistically significant impact between hearing loss and lower SF-36 scores across subscales, even after controlling for experimental confounds. These findings suggest that hearing loss is capable of contributing to HRQoL deficits in African-American older adults. The importance of these data in terms of pre-existing attitudes of African-American older adults towards hearing healthcare services and long-term effects of untreated hearing loss are considered.
Karma and the Problem of Evil

The doctrine of karma continues to be significant because it provides an explanation for both pain, suffering and misfortune on the one hand, and pleasure, happiness and good fortune on the other. Consequently, an assessment of the success of the doctrine in resolving the problem of good and evil will go a long way in enabling us to evaluate the doctrine itself, for should it fail to resolve satisfactorily the problem which it is intended to meet, since as we have seen the law is an explanatory hypothesis proposed to resolve a problem and not empirically verifiable, there would seem to be little reason to advocate the doctrine.
Algorithms and interfaces for automated non-visual skimming

In our information-driven web-based society, we are all gradually falling victims to information overload [9]. However, while sighted people are finding ways to sift through information faster, computer users who are blind are experiencing an even greater information overload. These users access computers and Internet using screen-reader software, which reads the information on a computer screen sequentially using computer-generated speech through an audio interface and allows users to navigate using keyboard shortcuts or gestures. This interface does not give them an opportunity to know what content to skip and what to listen to. So, they either listen to all of the content or listen to the first part of each sentence/paragraph before they skip to the next one. In this dissertation, I investigate and develop methods for non-visual skimming that will empower visually impaired users to access digitized information significantly faster and, thus, reduce the cognitive load associated with non-visual browsing. Visual skimming involves quickly looking through content while picking out words and phrases that are emphasized visually and/or carry the most meaning. My preliminary user study with 20 visually impaired participants who were blind has shown that users were able to skim and comprehend text much better if the summary included connected word phrases, as opposed to separate unrelated words, e.g., "hands down" instead of "hands". In this dissertation, I investigate the techniques employed by sighted users to skim web content, and design algorithmic methods to enable a computer-assisted skimming experience for screen-reader users. I design and evaluate algorithms for generating variable-length summaries to support skimming text at different levels of granularity and speed. I also design and evaluate a touch-based and shortcut driven screen-reader interfaces to support non-visual skimming. I have used participatory design approaches to devise all user interfaces. I conducted controlled and in-situ real-world experiments to evaluate the approach and interfaces. The Major contributions of this thesis include: (1) novel interfaces for non-visual skimming on regular computers and touch-screen devices; (2) novel computer algorithms that support skimming interfaces.
Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq)

We provide a protocol for precision nuclear run-on sequencing (PRO-seq) and its variant, PRO-cap, which map the location of active RNA polymerases (PRO-seq) or transcription start sites (TSSs) (PRO-cap) genome-wide at high resolution. The density of RNA polymerases at a particular genomic locus directly reflects the level of nascent transcription at that region. Nuclei are isolated from cells and, under nuclear run-on conditions, transcriptionally engaged RNA polymerases incorporate one or, at most, a few biotin-labeled nucleotide triphosphates (biotin-NTPs) into the 3' end of nascent RNA. The biotin-labeled nascent RNA is used to prepare sequencing libraries, which are sequenced from the 3' end to provide high-resolution positional information for the RNA polymerases. PRO-seq provides much higher sensitivity than ChIP-seq, and it generates a much larger fraction of usable sequence reads than ChIP-seq or NET-seq (native elongating transcript sequencing). Similarly to NET-seq, PRO-seq maps the RNA polymerase at up to base-pair resolution with strand specificity, but unlike NET-seq it does not require immunoprecipitation. With the protocol provided here, PRO-seq (or PRO-cap) libraries for high-throughput sequencing can be generated in 4-5 working days. The method has been applied to human, mouse, Drosophila melanogaster and Caenorhabditis elegans cells and, with slight modifications, to yeast.
Limiting behavior of asymptotically flat gravitational fields

Couch and Torrence suggest that the vacuum Einstein equations admit a larger class of asymptotically flat solutions than those exhibiting the peeling property. Starting with the assumption that\(\Psi _0 = O(r^{ - 2 - \varepsilon _0 } )\), (d/dr)\(\Psi _0 = O(r^{ - 3 - \varepsilon _0 } )\) and (δ/δx A )\(\Psi _1 = O(r^{ - 2 - \varepsilon _0 } )\), wherex A (A = 2, 3) are angular coordinates, they show that\(\Psi _1 = O(r^{ - 2 - \varepsilon _1 } )\), where e1⩽ 2 and e1<e0;\(< \varepsilon _0 ;\Psi _2 = O(r^{ - 2 - \varepsilon _2 } )\), where e2 ⩽ 1 and e1< e1; and Ψ4 and Ψ3 peel as they would under the stronger peeling conditions. The Winicour-Tamburino energy-momentun and angular momentum integrals for these solutions, in general, diverge. In fact, since Couch and Torrence determine only the radial dependence of the solution, it is not clear that the solutions are well defined. We find that the stronger assumption\(\Psi _0 = O(r^{ - 3 - \varepsilon _0 } )\), (d/dr)\(\Psi _0 = O(r^{ - 4 - \varepsilon _0 } )\), and (δ/δx A )\(\Psi _0 = O(r^{ - 3 - \varepsilon _0 } )\) does result in well-defined solutions for which both the energy-momentum and angular momentum intergrals are not only finite but result in the same expressions as are obtained for peeling space-times. This assumption appears to be the minimal assumption that is necessary for investigating outgoing radiation at null infinity.
Probiotic treatment restores protection against lethal fungal infection lost during amphibian captivity

Host-associated microbiomes perform many beneficial functions including resisting pathogens and training the immune system. Here, we show that amphibians developing in captivity lose substantial skin bacterial diversity, primarily due to reduced ongoing input from environmental sources. We combined studies of wild and captive amphibians with a database of over 1 000 strains that allows us to examine antifungal function of the skin microbiome. We tracked skin bacterial communities of 62 endangered boreal toads, Anaxyrus boreas , across 18 time points, four probiotic treatments, and two exposures to the lethal fungal pathogen Batrachochytrium dendrobatidis ( Bd ) in captivity, and compared these to 33 samples collected from wild populations at the same life stage. As the amphibians in captivity lost the Bd -inhibitory bacteria through time, the proportion of individuals exposed to Bd that became infected rose from 33% to 100% in subsequent exposures. Inoculations of the Bd -inhibitory probiotic Janthinobacterium lividum resulted in a 40% increase in survival during the second Bd challenge, indicating that the effect of microbiome depletion was reversible by restoring Bd -inhibitory bacteria. Taken together, this study highlights the functional role of ongoing environmental inputs of skin-associated bacteria in mitigating a devastating amphibian pathogen, and that long-term captivity decreases this defensive function.
Aristotle on Eudaimonia: On the Virtue of Returning to the Source

Psychologists are increasingly interested in the topic of eudaimonia, a term adopted from ancient Greek philosophers (with most modern views traceable to Aristotle), referring to human flourishing. Conceptual confusion remains because investigators generally have not clarified how and why they have appropriated Aristotle’s concept of eudaimonia. This chapter presents a close interpretation of Aristotle’s view and explores continuities and discontinuities in psychologists’ application of this original concept to provide a theoretical baseline and increase conceptual clarity. Eudaimonia is explored as an ethical concept referring to the best kind of life, which is an outgrowth of humans’ natural endowments. Eudaimonia is a form of activity (that includes subjective experience, but is not limited to it), comprised by the pursuit of ends that are choiceworthy for human beings. Eudaimonia is a unified way of life, but it has multiple constituents (e.g., belonging, justice, and social harmony). Eudaimonia is related to, but distinct from pleasure (hedonia). Human flourishing is a matter of a complete life that encompasses virtue or excellence, and Aristotle saw it as the ultimate aim of human life. The chapter concludes with several major challenges for eudaimonia researchers.
Machine learning classifiers using stochastic logic

This paper presents novel architectures for machine learning based classifiers using stochastic logic. Two types of classifier architectures are presented. These include: linear support vector machine (SVM) and artificial neural network (ANN). Stochastic computing systems require fewer logic gates and are inherently fault-tolerant. Thus, these structures are well suited for nanoscale CMOS technologies. These architectures are validated using seizure prediction from electroencephalogram (EEG) as an application example. To improve the accuracy of proposed stochastic classifiers, a novel approach based on linear transformation of input data is proposed for EEG signal classification using linear SVM classifiers. Simulation results in terms of the classification accuracy are presented for the proposed stochastic computing and the traditional binary implementations based datasets from one patient. Compared to conventional binary implementation, the accuracy of the proposed stochastic ANN is improved by 5.89%. Synthesis results are also presented for EEG signal classification. Compared to the traditional binary linear SVM, the hardware complexity, power consumption and critical path of the stochastic implementation are reduced by 78%, 74% and 53%, respectively. The hardware complexity, power consumption and critical path of the stochastic ANN classifier are reduced by 92%, 88% and 47%, respectively, compared to the conventional binary implementation.
The effect of saccadic eye movements on the sensor-level magnetoencephalogram.

Abstract Objective We used a combination of simulation and recordings from human subjects to characterize how saccadic eye movements affect the magnetoencephalogram (MEG). Methods We used simulated saccadic eye movements to generate simulated MEG signals. We also recorded the MEG signals from three healthy adults to 5° magnitude saccades that were vertical up and down, and horizontal left and right. Results The signal elicited by the rotating eye dipoles is highly dependent on saccade direction, can cover a large area, can sometimes have a non-intuitive trajectory, but does not significantly extend above approximately 30 Hz in the frequency domain. In contrast, the saccadic spikes (which are primarily monophasic pulses, but can be biphasic) are highly localized to the lateral frontal regions for all saccade directions, and in the frequency domain extend up past 60 Hz. Conclusions Gamma band saccadic artifact is spatially localized to small regions regardless of saccade direction, but beta band and lower frequency saccadic artifact have broader spatial extents that vary strongly as a function of saccade direction. Significance We have here characterized the MEG saccadic artifact in both the spatial and the frequency domains for saccades of different directions. This could be important in ruling in or ruling out artifact in MEG recordings.
Inverse Mapping Theorem

(Tate)Let E, F be complete normed vector spaces. Let f: E → F be a map having the following property. There exists a number C > 0 such that for all x, y ∈ E we have $$\left| {f(x + y) - f(x) - f(y)} \right|C.$$
Image Guidance Systems for Brachytherapy

The evolution of brachytherapy is largely due to advances in image guidance. A wide array of image modalities are being implemented and investigated to better identify and delineate target volumes and critical structures, visualize the implant, and obtain functional information of the target and surrounding organs. This chapter gives an overview of the different imaging modalities available and both their current and future clinical uses. The chapter includes a description of 2D modalities (planar radiography, fluoroscopy, ultrasound), 3D modalities (computed tomography, ultrasound, magnetic resonance imaging, and positron emission tomography), challenges in the 2D to 3D imaging transition, other imaging methods specific to brachytherapy and tools for multi-modality imaging.
Abstract IA23: Enhancing anti-tumor immunity through selective inhibition of IDO1

Tryptophan catabolism serves as an important metabolic immunoregulatory checkpoint, functioning in anti-inflammatory, immunosuppressive and tolerance-inducing processes. Three distinct heme-containing enzymes—indoleamine 2,3-dioxygenase (IDO) 1, IDO2 and tryptophan 2,3-dioxygenase (TDO)—have the capacity to initiate the first and rate-limiting step in this metabolic process, catalyzing the conversion of tryptophan to kynurenine. A growing body of scientific evidence indicates that this pathway, and more specifically, the IDO1 enzyme, may be of fundamental importance to tumor immune evasion. Through the depletion of local tryptophan and the production of kynurenine and other downstream metabolites, IDO1 activity has been shown to have an anti-proliferative effect on T cells, to promote Treg differentiation and to bias dendritic cells and macrophages toward an immunosuppressive phenotype. Further, IDO1 expression is a negative prognostic factor across numerous cancer histologies. Therefore, the selective inhibition of IDO1 has emerged as an attractive therapeutic approach to enhance anti-tumor immunity. This presentation will review the immunologic basis for targeting tryptophan catabolism in cancer, describe the emerging preclinical and clinical data on epacadostat, a novel first-in-class selective IDO1 inhibitor, and discuss the therapeutic rationales for epacadostat-based combination immunotherapies. Citation Format: Reid Huber. Enhancing anti-tumor immunity through selective inhibition of IDO1. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Targeting the Vulnerabilities of Cancer; May 16-19, 2016; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(1_Suppl):Abstract nr IA23.
Multipliers and the Simplex Method

The tableau-based simplex method in Chapter 4 masks a relationship between the data in the initial tableau and in the tableaus that result from sequences of pivots. That relationship is now brought into view. Each tableau encountered by the simplex method will be shown to have at least one set of “multipliers,” one per constraint.
Layer transfer of bulk gallium nitride by controlled spalling

Successful wafer-scale layer transfer from high-quality 2-in. diameter bulk gallium nitride substrates was demonstrated using the Controlled Spalling technique. The crystal quality of both the as-fractured bulk substrate and the spalled GaN film was assessed using transmission electron microscopy analysis, and the defect density was below the detection limit (mid 107 cm−2) for both samples. By using the experimentally determined critical conditions for tensile stress and thickness of the Ni stressor layer, an effective fracture toughness KIC of 1.7 MPa m could be calculated for [0001] fracture using the Suo and Hutchinson mechanical model. The resulting in-plane contraction of the GaN film after spalling permitted a novel method for measuring film strain without knowledge of the elastic properties of the material. This was used to measure the Raman E2(high) peak shift coefficient of Δω(cm−1) = 1411e which, when converted to a stress coefficient (2.95 cm−1/GPa), was in agreement with only one other literat...
Voltage control of magnetism in NiZn ferrite/mica/PMNPT heterostructure with giant tunability and narrow linewidth

Recently, large magnetoelectric coupling of a spinel/piezoelectric heterostructure has been reported. However, the linewidth of the spinel is very large due to lattice mismatch when ferrite is directly deposited on piezoelectric substrates. This indicates a large magnetic loss, which impedes the spinel/piezoelectric heterostructure from useful device applications. Mica is a well-known 2D material, which can be split manually layer by layer without the substrate clamping effect. In this report, NiZn ferrite was deposited on a mica substrate by a spin-spray deposition technique. Spin-spray deposition is a wet chemical synthesis technique involving several chemical reactions for generating high-quality crystalline spinel ferrite films with various compositions directly from an aqueous solution. The thickness of ferrite is 2 μm, and the linewidth of the ferromagnetic resonance (FMR) is 115 Oe which is suitable for RF/microwave devices. The large FMR field tuning of 605 Oe was observed in NiZn ferrite/mica/PMN-PT heterostructures with minimal substrate clamping effect by reducing the thickness of the mica substrate. These multiferroic heterostructures exhibiting combined giant magnetoelectric coupling and narrow ferromagnetic resonance linewidth offer great opportunities for flexible RF magnetic devices.
Robust Classification in RSVP Keyboard

To use in the Rapid Serial Visual Presentation (RSVP) KeyboardTM, a brain computer interface (BCI) typing system developed by our group, we propose a robust classification method of handling non-stationarity in the electroencephelography (EEG) data that is caused by artifacts and/or sensor failure. Considering the effect of these non-stationarities, we build a mixture data model to use as EEG evidence in the fusion with an n-gram language model to develop a robust classification algorithm. Using Monte Carlo simulations on the pre-recorded EEG data containing sections with or without intentionally generated artifacts we compare the typing performances of non-robust and robust classification methods in terms of speed and accuracy.
Formation of Ocean Surface Patterns by Cetacean Fluke Oscillations

This paper presents a theory describing the fluid mechanics of whale flukeprints. It contains excerpts of a longer paper recently published in the International Journal of Non-Linear Mechanics special issue on biological structures. Whale flukeprints are smooth oval-shaped water patches that form on the surface of the ocean behind a swimming or diving whale. The prints persist up to several minutes and can be used to track whales cruising near the ocean surface. The motion of the fluke provides a mechanism for shedding vortex rings. The subsequent interaction of the vortex ring with the ocean surface damps the short wavelength capillary waves in the print. The theory suggests that the role of natural surfactants are of secondary importance in the early formation of flukeprints. We describe potential directions for future research, including collection of quantitative data from real flukeprints.
Literary Device: Invisible Light and a Photo of Photography

In 1844, in the first photographically illustrated book, The Pencil of Nature, Fox Talbot includes a perplexing chapter, “A Scene in a Library,” which couples a photograph of a bookshelf with a seemingly unrelated passage of text. Here, Talbot speculates about a fantastical voyeuristic scenario involving a proto-night vision device and its literary possibilities. In this chapter, it is shown that the vexing nature of “A Scene in a Library,” particularly Talbot’s pairing of invisible light with books, stems from the challenge that light beyond the visible range of the spectrum, such as ultraviolet and infrared, posed to the dominant epistemology of the time. His recourse to a literary form of invisibility was an attempt to reconcile the incommensurability of invisible light with the prevailing episteme structured around tropes of visible light and the eye.