bluuebunny/crossref_metadata_2025_split huggingface dataset:
X-ray phase contrast tomography by tracking near field speckle
Authors: Wang Hongchang , Berujon Sebastien , Herzen Julia , Atwood Robert , Laundy David , Hipp Alexander , Sawhney Kawal 
Published: March 2015

AbstractX-ray imaging techniques that capture variations in the x-ray phase can yield higher contrast images with lower x-ray dose than is possible with conventional absorption radiography. However, the extraction of phase information is often more difficult than the extraction of absorption information and requires a more sophisticated experimental arrangement. We here report a method for three-dimensional (3D) X-ray phase contrast computed tomography (CT) which gives quantitative volumetric information on the real part of the refractive index. The method is based on the recently developed X-ray speckle tracking technique in which the displacement of near field speckle is tracked using a digital image correlation algorithm. In addition to differential phase contrast projection images, the method allows the dark-field images to be simultaneously extracted. After reconstruction, compared to conventional absorption CT images, the 3D phase CT images show greatly enhanced contrast. This new imaging method has advantages compared to other X-ray imaging methods in simplicity of experimental arrangement, speed of measurement and relative insensitivity to beam movements. These features make the technique an attractive candidate for material imaging such as in-vivo imaging of biological systems containing soft tissue.
0.0045 mm2 15.8 µW three‐stage amplifier driving 10×‐wide (0.15–1.5 nF) capacitive loads with >50° phase margin
Authors: Yan Zushu , Mak Pui‐In , Law Man‐Kay , Martins Rui Paulo 
Published: March 2015

A three‐stage amplifier employing embedded capacitor‐multiplier compensation (ECMC) and active parallel compensation (APC) to enhance the area efficiency when driving nF‐range capacitive loads (CL) is presented. Unlike the conventional current‐buffer Miller compensation, ECMC applied to the dominant compensation path saves substantial power and area, while securing a large gain–bandwidth product. The created left‐half‐plane zero also benefits the phase margin (PM). For the APC, unlike the traditional passive parallel compensation, this work benefits from the Miller effect to avoid the area‐consuming resistor, and reduces the entailed capacitances without lowering the parasitic pole position. A multi‐path Gm‐boosting second stage enhances the effective transconductance and DC gain. With 0.0045 mm2 of area and 15.8 µW of power, the 0.18 µm CMOS three‐stage amplifier measures 1.13 MHz unity‐gain frequency, 0.41 V/µs average slew rate and 56.2° PM at 1 nF CL. Stable responses with >50° PM are attained for a 10 × range of CL from 0.15 to 1.5 nF. The achieved figure‐of‐merit accounting for both die area and power compares favourably with the state of the art.
The Association between Stimulant, Opioid, and Multiple Drug use on Behavioral Health Care Utilization in a Safety-Net Health System
Authors: Calcaterra Susan L. , Keniston Angela , Blum Joshua , Crume Tessa , Binswanger Ingrid A. 
Published: March 2015

Background Prior studies show an association between drug use and health care utilization. The relationship between specific drug type and emergent/urgent, inpatient, outpatient, and behavioral health care utilization has not been examined. We aimed to determine if multiple drug use was associated with increased utilization of behavioral health care. Methods To assess health care utilization, we conducted a retrospective cohort study of patients who accessed health care at a safety-net medical center and affiliated clinics. Using electronic health records, we categorized patients who used stimulants, opioids, or multiple drugs based on urine toxicology screening tests and/or International Classification of Diseases, 9th Revision (ICD-9). Remaining patients were categorized as patients without identified drug use. Health care utilization by drug use group and visit type was determined using a negative binomial regression model. Associations were reported as incidence rate ratios. Utilization was described by rates of health care–related visits for inpatient, emergent/urgent, outpatient, and behavioral health care among patients who used drugs, categorized by drug types, compared with patients without identified drug use. Results Of 95,198 index visits, 4.6% ( n = 4340) were by patients who used drugs. Opioid and multiple drug users had significantly higher rates of behavioral health care visits than patients without identified drug use (opioid incidence rate ratio [IRR] = 7.2; 95% confidence interval [CI]: 3.8–13.8; multiple drug use IRR = 5.6, 95% CI: 3.3–9.7). Patients who used stimulants were less likely to use behavioral health services (IRR = 1.3, 95% CI: 0.9–2.0) when compared with opioid and multiple drug users, but were more likely to use inpatient (IRR = 1.6, 95% CI: 1.4–1.8) and emergent/urgent care (IRR = 1.4, 95% CI: 1.3–1.5) services as compared with patients without identified drug use. Conclusions Integrated medical and mental health care and drug treatment may reduce utilization of costly health care services and improve patient outcomes. How to capture and deliver primary care and behavioral health care to patients who use stimulants needs further investigation.
Broadband measurement of coating thermal noise in rigid Fabry–Pérot cavities
Authors: Chalermsongsak Tara , Seifert Frank , Hall Evan D , Arai Koji , Gustafson Eric K , Adhikari Rana X 
Published: March 2015

Abstract
We report on the relative length fluctuation of two fixed-spacer Fabry–Pérot cavities with mirrors fabricated from silica/tantala dielectric coatings on fused silica substrates. By locking a laser to each cavity and reading out the beat note

of the transmitted beams, we find that, for frequencies from 10 Hz to 1 kHz, the power spectral density of beat note fluctuation is

. By careful budgeting of noise sources contributing to the beat note, we find that our measurement is consistent with the fluctuation in this band being dominated by the Brownian noise of the mirror coatings. Fitting for the coating loss angle ϕ
c, we find it equal to 4 × 10−4. We then use a Bayesian analysis to combine our measurement with previous observations, and thereby extract estimates for the individual loss angles of the silica and tantala constituents of these coatings. With minor upgrades, the testbed described in this article can be used in the future to measure the length noise of cavities formed with novel mirror coating materials and geometries.
Estimating the proportion of true null hypotheses when the statistics are discrete
Authors: Dialsingh Isaac , Austin Stefanie R. , Altman Naomi S. 
Published: March 2015

AbstractMotivation: In high-dimensional testing problems π0, the proportion of null hypotheses that are true is an important parameter. For discrete test statistics, the P values come from a discrete distribution with finite support and the null distribution may depend on an ancillary statistic such as a table margin that varies among the test statistics. Methods for estimating π0 developed for continuous test statistics, which depend on a uniform or identical null distribution of P values, may not perform well when applied to discrete testing problems.Results: This article introduces a number of π0 estimators, the regression and ‘T’ methods that perform well with discrete test statistics and also assesses how well methods developed for or adapted from continuous tests perform with discrete tests. We demonstrate the usefulness of these estimators in the analysis of high-throughput biological RNA-seq and single-nucleotide polymorphism data.Availability and implementation: implemented in RContact: nsa1@psu.edu or naomi@psu.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Despair
Authors: Watson Nicholas 
Published: March 2015

Abstract
The terrain of the Christian psyche and the theological structure within which Christians directed their lives towards salvation were both reconfigured during the Reformation. William Langland’s Piers Plowman offers an account of despair as a phenomenon associated with the deathbed. In the late medieval period, despair was also seen as a spiritual problem affecting religious specialists engaged in contemplative living, rather than ordinary people on their deathbeds. This article explores despair as it was understood in the late medieval period and as a key concern of Protestant theology and narrative after Reformation. It considers two sets of works written in England: a series of narrative treatments of despair related to the death of the apostate Francesco Spiera in 1548 and a set of “remedy” texts that include the Augustinian Friar William Flete’s De remediis contra temptaciones from the 1350s. It also examines the doctrine of “double election” proposed by John Calvin during the 1540s based on a tradition of thinking about divine omnipotence.
‘Literature’
Authors: Teskey Gordon 
Published: March 2015

Abstract
The long Tudor Century (1485-1603) saw the rise of a concept of literature which endures today. Printing and Protestantism had two transformative effects on the social existence of stories: 1. the isolation of individual stories as ‘works’ shaped by artists instead of authorities; 2. the dematerialization of stories as imaginative productions, abstracting them from the medium of the ‘bok’ and according them a transcendent status. Chaucer’s dream poems, Shakespeare’s “Venus and Adonis,” and Spenser’s Faerie Queene are cited. Two works on either side of the change are read closely: Robert Henryson’s Testament of Cresseid (late 15th c) and Thomas Lodge’s Scillae’s Metamorphosis (1589).
London Books and London Readers
Authors: Boffey Julia 
Published: March 2015

AbstractThis article examines the city of London—its history, topography, governance, people—as a most fruitful subject of books in the late medieval period. It considers a poem that praises London’s “renown, riches and royalte” as an example of metropolitan textual production and transmission during the period. It also explores some of the contexts in which manuscript and print were brought together, or conversely kept apart, in the decades which immediately followed the introduction of printing to England by William Caxton in c.1476. In addition, it looks at London readers as a significant audience for texts of wider national significance, the interpenetration of different forms of book production in London at the start of the sixteenth century, and three manuscripts: the two separate volumes of the New cronycles plus the Guildhall manuscript of the Great Chronicle.
The Reformation of the Household
Authors: Burrow Colin 
Published: March 2015

Abstract
One episode in Edmund Spenser’s Faerie Queene shows a sudden transition of worlds which is paradigmatic of Protestant self-representation. From cannibalistic Catholics to pastoral piety, from a godless outdoors to the small-scale courtesies of the godly household, this shift implies that the act of violent religious Reformation abruptly gives rise to a cultural reformation that profoundly changes the scale and style of social organization. This article argues that Spenser’s Protestant mythology still shapes the understanding of households in the sixteenth century and that it is radically misleading. Royal and magnate households dominate the early part of the century, while representations of small-scale (and sometimes only incidentally Protestant) households richly populate the drama and narrative prose of its end. By focusing on the role played by non-royal households in writing by mid-century Catholics-George Cavendish’s Life and Death of Cardinal Wolsey and William Roper’s The Lyfe of Sir Thomas Moore, Knighte-- this article argues two things: that it is wrong to regard the royal household as the all-encompassing centre of early Tudor writing; and that is incorrect to suggest that the Protestant reformation aided the emergence of smaller-scale domestic institutions. In these mid-century works there is a counter-reformation representation of the household which had a powerful influence on later representations of the household—including even those of Protestants such as Spenser, George Gascoigne and Shakespeare.
Monasticism
Authors: Gillespie Vincent 
Published: March 2015

Abstract
As he faced his own dissolution, Henry VIII repeatedly invoked a religious group who had been absent from his kingdom for seven years: the monks. The 1570s saw an irrevocable change in the nature of English Catholicism as Catholic clergy trained in England died, retired, or conformed. During this period, the first waves of Englishmen trained in the new continental “seminaries” as Catholic secular priests swore allegiance to the universal Church and to the Pope as missionaries for Christ. Moreover, the new orders such as the Theatines, the Capuchins, and the Jesuits eclipsed traditional European and coenobitic monasticism. This article examines the cultural disappearance of monks, monasteries, and monasticism in England during the late medieval period. It also considers how authors such as William Shakespeare, Henry Howard, Earl of Surrey, Thomas Walsingham, Barnabe Googe, John Donne, William Langland, and Geoffrey Chaucer remember the monks in their works.
Revolutionaries, Reactionaries and the Dilemmas of Russian Conservatism
Authors: Martin Alexander M. 
Published: March 2015

Abstract
A peculiarity of the right in imperial Russia was the weakness of conservatism—that portion of the right which equates national identity with the currently dominant cultural values and social hierarchies. Instead, the Russian right was more often palingenetic, that is, it looked to the state to revitalize a nation whose potential was allegedly stifled by the very same cultural values and social hierarchies that conservatives embraced. Russia and its people appeared to lack the rootedness and the matrix of organically evolved local and communal identities that were central to conservatism’s socio-political vision elsewhere. Russians were drawn instead to Utopian schemes resting on palingenetic notions that the nation was capable of, indeed in need of, a ‘regeneration’ that hinged on remaking the collective and individual consciousness. Palingenetic nationalism proved to be a revolutionary force that both destabilized Russia itself and became one of the country’s most explosive exports.
Provincial Russia
Authors: Chulos Chris J. 
Published: March 2015

Abstract
While metropolitan cultural and political elites in the aftermath of the Bolshevik Revolution regarded Voronezh and dozens of provinces like it as backwaters in need of enlightenment, the local perspective (on which this chapter focuses) was different. Despite the problems of pre-revolutionary Russia, educated society in Voronezh considered the province a model of the best the former Empire had to offer: an advancing economy, an accomplished cultural world and a distinctive local identity. In their eyes, the province was not backward, dull or dark, but the soul of what it meant to be Russian at the start of the new revolutionary era.
Victimization and Help-Seeking Among Survivors of Intimate Partner Violence
Authors: Gover Angela R. , Tomsich Elizabeth A. , Richards Tara N. 
Published: March 2015

Abstract
Intimate partner violence (IPV) occurs at high rates in US society and has numerous negative physical, psychological, and economic consequences for victims and survivors. Given the high rates and deleterious consequences of IPV, research has focused added attention on behaviors survivors engage in as a response to the violence. This article discusses help seeking behaviors among victims and survivors of IPV by reviewing the incidence of help-seeking behavior and formal and informal outlets of assistance. The article presents theoretical explanations of help-seeking behaviors and reviews factors associated with the decision to seek help, as well as positive and negative outcomes of help-seeking. Although most victims seek assistance, they are more likely to seek informal rather than formal avenues of support. Barriers to help-seeking behaviors among IPV victims make theoretical evaluations difficult and complicate the development of effective formal resources as a response to those seeking help for IPV.
The Ptolemaic Army
Authors: Fischer-Bovet Christelle 
Published: March 2015

Abstract
This essay discusses the recruitment and payment of soldiers, as well as the ethnic composition, organization, and training of the Ptolemaic army, through the examination of papyri, of inscriptions, and of Polybius’ account of the Ptolemaic victory against the Seleucids at Raphia. It describes the military reforms that took place between the 220s and 160s BCE in response to external and domestic pressures, in particular the integration of large numbers of Egyptian soldiers. It shows how the development of the socio-economic status of diverse groups of soldiers and cultural exchanges occurring among members of the army, although facilitated by these changes, also shaped them. While the Ptolemaic army is best described as multiethnic, it did not lack coordination on the battlefield, due to skilled leadership and to soldiers’ feeling of attachment to the dynasty, which was reinforced by land grants and other privileges.
The Archaeology of Amarna
Authors: Stevens Anna 
Published: March 2015

AbstractThis essay assesses the body of archaeological research connected to the New Kingdom settlement site of Amarna (ancient Akhetaten), the short-lived capital of Egypt founded by king Akhenaten around 1347 BC as the cult centre for the solar god the Aten. Amarna, by far the largest exposure of pharaonic settlement to survive from Egypt, is unsurpassed as a case site for the study of ancient Egyptian urbanism and daily life. This essay provides an overview of the ancient city, evaluates past and ongoing excavations at the site, and summarizes the archaeological discourse on the city as a physical, functioning and experienced space.
BamHash: a checksum program for verifying the integrity of sequence data
Authors: Óskarsdóttir Arna , Másson Gísli , Melsted Páll 
Published: March 2015

ABSTRACTSummaryLarge resequencing projects require a significant amount of storage for raw sequences, as well as alignment files. Since the raw sequences are redundant once the alignment has been generated, it is possible to keep only the alignment files. We present BamHash, a checksum based method to ensure that the read pairs in FASTQ files match exactly the read pairs stored in BAM files, regardless of the ordering of reads. BamHash can be used to verify the integrity of the files stored and discover any discrepancies. Thus, BamHash can be used to determine if it is safe to delete the FASTQ files storing raw sequencing reads after alignment, without the loss of data.Availability and ImplementationThe software is implemented in C++, GPL licensed and available athttps://github.com/DecodeGenetics/BamHashContactpmelsted@hi.is
Distinctive Features of a Saudi Genome
Authors: Alabdulkareem Ibrahim , Robertson Anthony J. , Garawi Sami Al , Aljumah Mohammed , Al-Turki Saeed , AlBalwi Mohammed A. 
Published: March 2015

SummaryWe have fully sequenced the genome of an individual from the region of Saudi Arabia. In order to facilitate comparative analysis, an initial characterization of the new genome was undertaken based on single nucleotide polymorphism (SNP). The SNP data having associated population statistics, essentially the HapMap, served to identify features that were rare by comparison. Methods were developed and applied to tag observed SNPs as different and were extended to identify strings or clusters of difference in the individual relative to comparison populations to effectively increase the significance over single SNP comparison. Difference strings identified in the individual relative to each comparison population showed a genome location pattern with various levels of overlap between the comparison populations. The SNP frequencies from the HapMap population samples Ceu and Yri showed a difference inversion relative to the sample genome. The total SNP difference count was greatest between the individual and the Yri population sample while the number and total span of SNP difference clusters was greatest in comparison with the Ceu population sample. The final pattern of difference clusters has served to define distinctive features in the individual genome toward preliminary characterization.
Phaseitrials in melanoma: A framework to translate preclinical findings to the clinic
Authors: Kim Eunjung , Rebecca Vito W. , Smalley Keiran S.M. , Anderson Alexander R.A. 
Published: March 2015

AbstractWe present a, mathematical model driven, framework to implement virtual or imaginary clinical trials (phaseitrials) that can be used to bridge the gap between preclinical studies and the clinic. The trial implementation process includes the development of an experimentally validated mathematical model, generation of a cohort of heterogeneous virtual patients, an assessment of stratification factors, and optimization of treatment strategy. We show the detailed process through application to melanoma treatment, using a combination therapy of chemotherapy and an AKT inhibitor, which was recently tested in a phase 1 clinical trial. We developed a mathematical model, composed of ordinary differential equations, based on experimental data showing that such therapies differentially induce autophagy in melanoma cells. Model parameters were estimated using an optimization algorithm that minimizes differences between predicted cell populations and experimentally measured cell numbers. The calibrated model was validated by comparing predicted cell populations with experimentally measured melanoma cell populations in twelve different treatment scheduling conditions. By using this validated model as the foundation for a genetic algorithm, we generated a cohort of virtual patients that mimics the heterogeneous combination therapy responses observed in a companion clinical trial. Sensitivity analysis of this cohort defined parameters that discriminated virtual patients having more favorable versus less favorable outcomes. Finally, the model predicts optimal therapeutic approaches across all virtual patients.One Sentence SummaryWe propose a computational framework to implement phaseitrials (virtual/imaginary yet informed clinical trials) in cancer, using an experimentally calibrated mathematical model of melanoma combination therapy, that can readily capture observed heterogeneous clinical outcomes and be used to optimize future clinical trial design.