bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cation-induced kinetic heterogeneity of the intron–exon recognition in single group II introns
Authors: Kowerko Danny , König Sebastian L. B. , Skilandat Miriam , Kruschel Daniela , Hadzic Mélodie C. A. S. , Cardo Lucia , Sigel Roland K. O. 
Published: March 2015

Significance
RNAs are involved in numerous aspects of cellular metabolism, and correct folding is crucial for their functionality. Folding of single RNA molecules can be followed by single-molecule spectroscopy. Surprisingly, it has been found that chemically identical RNA molecules do often not behave identically. The molecular origin of this heterogeneity is difficult to rationalize and the subject of ongoing debate. By combining single-molecule spectroscopy with NMR, we show that heterogeneity is likely to stem from a subset of microscopically different RNA structures that differ with regard to the occupation of divalent metal ion binding sites.
Effects of Suspended Sediment on Early‐Life Stage Survivalof Yaqui Chub, an Endangered USA–Mexico Borderlands Cyprinid
Authors: Clark Barkalow Stephani L. , Bonar Scott A. 
Published: March 2015

AbstractHigh levels of total suspended sediment (TSS) can have negative consequences on fishes, such as altering food supply, lowering food acquisition, clogging gills, and disrupting reproduction. While effects of TSS on salmonids and estuarine fish are well studied, less is known about possible negative impacts of suspended sediment on desert fishes. Several imperiled desert fishes inhabit streams and springs near the U.S.–Mexico border and are potentially threatened by increased sediment loads from borderlands activity such as livestock grazing, road building, illegal traffic, and law enforcement patrols. One such species is the Yaqui Chub Gila purpurea, a federally listed endangered cyprinid. We exposed Yaqui Chub embryos and fry (mean TL = 12.6 mm; SE = 0.42) to a range of TSS levels commonly found in one of the only streams they inhabit, Black Draw, which crosses the Arizona–Mexico border. We tested effects of 0; 300; 500; 1,000; 5,000; and 10,000 mg/L TSS loads on fry and embryos over a 5‐d period in three replicate containers for each treatment. Fifty percent hatch rate (i.e., median lethal concentration, LC50) was 3,977 mg/L for embryos. The LC50 for fry (concentration at which half died) was 8,372 mg/L after 12 h of exposure; however, after 5‐d exposure, LC50 leveled at 1,197 mg/L. The TL of fry did not change significantly in any treatment over the 5‐d period. Suspended sediment in Black Draw reached concentrations lethal to Yaqui Chub embryo and fry during four floods in 2012. Although some desert fishes have evolved in rivers and streams subject to elevated TSS and are tolerant to high TSS concentrations, other fish species are less tolerant and may be impacted by land practices which increase erosion into stream systems. Management of critically endangered desert fishes should include considerations of the effects of increased suspended sediment.Received September 5, 2014; accepted November 10, 2014
Feasibility of Implementing Shared Medical Appointments (SMAs) for Office-Based Opioid Treatment with Buprenorphine: A Pilot Study
Authors: Suzuki Joji , Zinser Jennifer , Klaiber Brenda , Hannon Melanie , Grassi Hope , Spinosa Madeline , Ramirez Altagracia , Issa Mohammed , Chin Feman Siu Ping 
Published: March 2015

Background Shared medical appointments (SMAs) are designed to improve patient satisfaction and increase access to treatment. In a typical SMA, 6–12 patients with similar diagnoses attend a group appointment with their health care providers, often lasting 60–120 minutes. All components of an individual visit are completed, and additional time is spent providing education and facilitating peer support. The aim of this study was to report on patient and program outcomes after implementation of SMA-based office-based opioid treatment with buprenorphine. Methods The study was conducted at a hospital-based outpatient psychiatric clinic that previously did not offer any office-based opioid treatment with buprenorphine. Demographic and clinical data (treatment retention, depression, anxiety, craving scores, and urine toxicology results) were extracted from the medical records. Patients were recruited to complete a survey assessing their experience. Results Ninety-three patients enrolled in the program, and 52.7% remained in treatment at 6 months. The proportion of aberrant opioid urine results, depression, anxiety, and craving decreased significantly from baseline to 6 months. Twenty-two patients completed the survey, who generally agreed that the SMA format allowed for more time with physicians, more support from peers, better coordination of care, and more predictable times for visits. Conclusions Implementation of an SMA-based buprenorphine program was feasible, with treatment outcomes comparable to traditional models of care. More research is needed to explore the impact of SMA on buprenorphine treatment.
Analysis of a free boundary at contact points with Lipschitz data
Authors: Karakhanyan A. , Shahgholian H. 
Published: March 2015

In this paper we consider a minimization problem for the functional
\[

J
(
u
)
=

∫

B
1
+

|

∇
u

|

2

+

λ

+

2

χ

{
u
>
0
}

+

λ

−

2

χ

{
u
≤
0
}

J(u)=\int _{B_1^+}|\nabla u|^ 2+\lambda _{+}^2\chi _{\{u>0\}}+\lambda _{-}^2\chi _{\{u\leq 0\}}

\]
in the upper half ball

B
1
+

⊂

R

n

,
n
≥
2

B_1^+\subset \mathbb {R}^n, n\geq 2

, subject to a Lipschitz continuous Dirichlet data on

∂

B
1
+

\partial B_1^+

. More precisely we assume that

0
∈
∂
{
u
>
0
}

0\in \partial \{u>0\}

and the derivative of the boundary data has a jump discontinuity. If

0
∈

∂
(
{
u
>
0
}
∩

B
1
+

)

¯

0\in \overline {\partial ( \{u>0\} \cap B_1^+)}

, then (for

n
=
2

n=2

or

n
≥
3

n\geq 3

and the one-phase case) we prove, among other things, that the free boundary

∂
{
u
>
0
}

\partial \{u>0\}

approaches the origin along one of the two possible planes given by
\[

γ

x
1

=
±

x
2

,

\gamma x_1 = \pm x_2,

\]
where

γ
\gamma

is an explicit constant given by the boundary data and

λ
±

\lambda _\pm

the constants seen in the definition of

J
(
u
)

J(u)

. Moreover the speed of the approach to

γ

x
1

=

x
2

\gamma x_1=x_2

is uniform.
WS1: one more new Galactic bona fide luminous blue variable
Authors: Kniazev A. Y. , Gvaramadze V. V. , Berdnikov L. N. 
Published: March 2015

Abstract
In this Letter, we report the results of spectroscopic and photometric monitoring of the candidate luminous blue variable (LBV) WS1, which was discovered in 2011 through the detection of a mid-infrared circular shell and follow-up optical spectroscopy of its central star. Our monitoring showed that WS1 brightened in the B, V and I bands by more than 1 mag during the last three years, while its spectrum revealed dramatic changes during the same time period, indicating that the star became much cooler. The light curve of WS1 demonstrates that the brightness of this star has reached maximum in 2013 December and then starts to decline. These findings unambiguously proved the LBV nature of WS1 and added one more member to the class of Galactic bona fide LBVs, bringing their number to sixteen (an updated census of these objects is provided).
Anachronism
Authors: De Grazia Margreta 
Published: March 2015

Abstract
To an age enjoined to “Always Historicize,” anachronism is an embarrassment. It is not merely getting a date wrong, a chronological error. It is mistaking some aspect of a period’s regulative conceptualization of the world. It typically occurs when we impose our own modern conceptions onto the workings of the past. Sensitivity to anachronism and an understanding of history has generally been regarded as one of the defining features of the Renaissance, much to the detriment of the Medieval, that thereby becomes historically insensitive. This essay works to loosen our disciplinary commitment to chronology and periods by looking at other ways of relating to the past, beginning with a radical reconstrual of Lorenzo Valla’s exposure of the Donation of Constantine. It is not violations of chronology that Valla exposes but bad rhetoric. And it is from the arts of language that the essay hints at alternative ways of relating to the past, through narrative and figuration rather than numerical timelines and metaphysical periods.
Historiography
Authors: Lander Jesse 
Published: March 2015

Abstract
During the Reformation, arguments over the near and distant past are crucial for making people increasingly aware of the plurality of competing, even contradictory, accounts of the past. This article examines the way in which historical accounts of Richard III’s reign point to the emergence of a historiographical consciousness, an awareness that written history is partial in both senses of the word. It considers the extent of John Foxe’s influence on English history writing and how he made revisionist history mainstream. It analyses chronicle history plays, especially The True Tragedie of Richard III, as evidence that historiographical consciousness was widespread in the period. It also treats the connection between dissimulation and conspiracy in Thomas More’s History and cites George Buck’s The History of King Richard III(1619) as a remarkable example of revisionism that deploys historical learning against received opinion.
Literary Histories
Authors: Lerer Seth 
Published: March 2015

Abstract
Literary history has had a mixed history among the readers and the writers of the European traditions. For William Warburton, an eighteenth-century ecclesiast and critic, literary history was “the most agreeable subject in the world.” However, the early nineteenth-century German poet Heinrich Heine describes literary history as a “morgue where each seeks out the friend he most loved.” The complex connotation of literary history stems in part from the modern European understanding of the place of literature in the formation of national identity. This article examines how the history of medieval literature was received during the Renaissance. It first looks at the regulations of late Henrician reading, particularly the 1543 Act for the Advancement of True Religion, before focusing on Miles Hogarde and his poetry. It then discusses Richard Tottel’s Miscellany in the context of English literature and its past, along with the poetry of love and loss that follows Tottel.
Enclosed Spaces
Authors: Staley Lynn 
Published: March 2015

Abstract
Bede described Britain as a bountiful and beautiful island characterized by ethnic diversity, whereas Gildas viewed it as a fallen garden or bride. Bede and Gildas established the foundations of a nation whose boundaries enclosed people or peoples, a site of the struggles between individuals and of individuals. English historians from Gervase of Canterbury to Ralph of Diceto, William of Malmesbury, and William of Newburgh look at the history of Britain as a history instituted by Bede and Gildas, whose impulses to write geography as narrative are evident in the two most important histories of the later Middle Ages: Brut and Ranulf Higden’s Polychronicon. This article examines Britain as an enclosed space protected by the sea. It begins with an analysis of Andrew Marvell’s poem “Upon Appleton House” and locates Marvell within the company of those who wrote Britain’s history through its geography, particularly William Langland and Geoffrey Chaucer. It then describes the Wilton Diptych as an icon of sacred kingship and sacred geography.
The Eucharist
Authors: Aers David , Beckwith Sarah 
Published: March 2015

Abstract
This chapter explores theological and ethical dimensions of the Eucharist in the later Middle Ages and in the Reformation. The exploration introduces a number of genres and practices, because the Eucharist was a central and pervasive presence in Christian cultures, including those opposing medieval liturgy and teaching. One of the focal points of the study is the emergence of the doctrine and practice of transubstantiation, a language that became enshrined in thirteenth century orthodoxy. The chapter sets out with St. Augustine, who did not know either this doctrine, or the theological questions it sponsored (such as, what happens when a mouse eats the consecrated host), or its practice, together with its rich visionary accompaniments (such as bleeding hosts and manifestations of bleeding parts of the body of Christ or the Infant Jesus). After Augustine, a cluster of medieval writers and performances are addressed. The chapter concludes with commentary on the Reformation, and some rumination of Shakespeare, especially The Tempest.
Folly
Authors: Walker Greg 
Published: March 2015

Abstract
According to the chronicler Edward Hall, the execution of Sir Thomas More, who was sentenced to die on the gallows for refusing to acknowledge the Royal Supremacy, was characterized by a characteristically frivolous lack of decorum on the part of More himself, most notably on the scaffold itself. Both More’s evangelical opponents and his catholic allies noted his merry disposition. This article examines how the ideas of mirth and folly are woven through both More’s public career and the life of his close contemporary and nephew, the Catholic writer and playwright John Heywood. It considers the two men’s adoption and adaptation of classical and medieval notions of foolishness and comedy for their own ends in the dangerous years of Henry VIII’s Reformation. To understand More’s alleged lapse in judgment during his own execution and what this might suggest about the uses of mirth in pre-modern culture more generally, the article analyzes it in the context of his attitude towards theater and his Utopia as a satire for and of humanists.
Passion
Authors: Targoff Ramie 
Published: March 2015

Abstract
During the Renaissance, erotic love emerged as a favorite theme of Italian intellectuals. From the Neoplatonic treatises of Marsilio Ficino and Pico della Mirandola, to the works of Petrarch and Dante, the paintings of Botticelli and Raphael, the trattati d’amore (treatises of love) by Pietro Bembo and Leone Ebreo, the learned commentaries on the sonnets of Michelangelo and Lorenzo de Medici, or the medical writings on lovesickness, Italy’s obsession with the subject of love was evident. Italian poets such as Dante were particularly preoccupied with the female beloved, whom they typically idealized as a kind of angelic lady (donna angelicata), a heavenly character, rather than an object of sensual appetite and affection. Thomas Wyatt translated Petrarch’s sonnets, including Rime Sparse, by stripping from them one of their most fundamental features: the idea that erotic love could transcend the beloved’s death. This article examines Wyatt’s erotic poetry, how his Protestantism influenced his translations of Petrarchan lyrics, and his attitude toward Neoplatonism.
Information Structure and Presupposition
Authors: Sæbø Kjell Johan 
Published: March 2015

AbstractThis article surveys and discusses the core points of contact between notions of information structure and notions of presupposition. Section 1 is devoted to the ‘weak’ presuppositional semantics for focus developed by Mats Rooth, describing its properties with regard to verification and accommodation and showing that it can successfully account for a wide range of phenomena. Section 2 examines the stronger thesis that focus–background structures give rise to existential presuppositions, and finds the counterarguments that have been raised to carry considerable weight. Section 3 looks into the relationship between Givenness and run-of-the-mill presuppositions, finding that this relationship is looser than might be expected, mainly because a presupposition may be in need of focus marking instead of givenness marking.
Discourse Functions
Authors: Kiss Katalin É. 
Published: March 2015

AbstractThe chapter first summarizes the syntactic, semantic, and pragmatic properties of the topic–comment structure in the Hungarian sentence. It describes the topic as a constituent external to the extended verbal projection, binding an empty argument in the comment, derived by topic movement or base-generated in situ. The topic functions as the logical subject of predication. Then the chapter discusses the focus–background articulation of the comment. The Hungarian sentence structure contains a designated focus position at the left edge of the comment. The focus elicits verb movement. The Hungarian focus construction, expressing exhaustive identification, is analysed as a predication structure both syntactically and semantically. It is claimed to represent specificational predication, with the background determining a set, and the focus referentially identifying its members.
Freedom of the Press
Authors: Graber Doris A. 
Published: March 2015

Abstract
Freedom of the press has become a popular idea throughout the world. The promise of free expression, however, is not necessarily realized when governments feel that security and stability are threatened. This chapter explains the concept of freedom of the press. The theories and assumptions about freedom of the press, balancing conflicting rights, and societal constraints are reviewed. The chapter then shows how that concept is implemented, discussing legal, political, and economic factors for evaluation. The environmental factors are compared, and the reason behind press freedom violations by governments is discussed. Questions for the future of research on freedom of the press are offered.
Sensitivity analysis of Wntβ-catenin based transcription complex might bolster power-logarithmic psychophysical law & reveal preserved gene gene interactions
Authors: Sinha Shriprakash 
Published: March 2015

AbstractRecently, psychophysical laws have been observed to be functional in certain factors working downstream of the Wnt pathway. This work tests the veracity of the prevalence of such laws, albeit at a coarse level, using sensitivity analysis on biologically inspired epigenetically influenced computational causal models. In this work, the variation in the effect of the predictive behaviour of the transcription complex (TRCMPLX) conditional on the evidences of gene expressions in normal/tumor samples is observed by varying the initially assigned values of conditional probability tables (cpt) for TRCMPLX. Preliminary analysis shows that the variation in predictive behaviour of TRCMPLX follows power-logarithmic psychophysical law, crudely. More recently, wet lab experiments have proved the existence of sensors that behave in a logarithmic fashion thus supporting the earlier proposed postulates based on computational sensitivity analysis of this manuscript regarding the existence of logarithmic behaviour in the signaling pathways. It also signifies the importance of systems biology approach where in silico experiments combined with in vivo/in vitro experiments have the power to explore the deeper mechanisms of a signaling pathway. Additionally, it is hypothesized that these laws are prevalent at gene-gene interaction level also. The interactions were obtained by thresholding the inferred conditional probabilities of a gene activation given the status of another gene activation. The deviation in the interactions in normal/tumor samples was similarly observed by varying the initially assigned values of conditional probability tables (cpt) for TRCMPLX. Analysis of deviation in interactions show prevalence of psychophysical laws and is reported for interaction between elements of pairs (SFRP3, MYC), (SFRP2, CD44) and (DKK1, DACT2). Based on crude static models, it is assumed that dynamic models of Bayesian networks might reveal the phenomena in a better way.
A pan-cancer catalogue of driver protein interaction interfaces
Authors: Porta-Pardo Eduard , Hrabe Thomas , Godzik Adam 
Published: March 2015

AbstractDespite their critical importance in maintaining the integrity of all cellular pathways, the specific role of mutations on protein-protein interaction (PPI) interfaces as cancer drivers, though known for some specific examples, has not been systematically studied. We analyzed missense somatic mutations in a pan-cancer cohort of 5,989 tumors from 23 projects of The Cancer Genome Atlas (TCGA) for enrichment on PPI interfaces using e-Driver, an algorithm to analyze the mutation pattern of specific protein regions such as PPI interfaces. We identified 128 PPI interfaces enriched in somatic cancer mutations. Our results support the notion that many mutations in well-established cancer driver genes, particularly those in critical network positions, act by altering PPI interfaces. Finally, focusing on individual interfaces we are also able to show how tumors driven by the same gene can have different behaviors, including patient outcomes, depending on whether specific interfaces are mutated or not.
Identification of novel transcriptional regulators of PKA subunits inSaccharomyces cerevisiaeby Quantitative Promoter–Reporter Screening
Authors: Pautasso C , Chatfield-Reed K , Chua G , Zaremberg V , Rossi S 
Published: March 2015

AbstractThe cAMP dependent protein kinase (PKA) signaling is a broad specificity pathway that plays important roles in the transduction of environmental signals triggering precise physiological responses. cAMP-signal transduction specificity is achieved and controlled at several levels. TheSaccharomyces cereviciaePKA holoenzyme consists of two catalytic subunits encoded byTPK1,TPK2andTPK3genes, and two regulatory subunits encoded byBCY1gene. In this work we studied the activity of these gene promoters using a reporter-synthetic genetic array screen, with the goal of identifying novel regulators of PKA subunits expression. Gene ontology (GO) analysis of the regulators identified showed that these regulators were enriched for annotations associated with roles in several GO biological process, as lipid and phosphate metabolism or transcription regulation and regulate all or some of the four promoters. Further characterization of the effect of these pathways on promoter activity and mRNA levels pointed to inositol, inositol polyphosphates, choline and phosphate as novel upstream signals that regulate transcription of PKA subunit genes. In addition, within each category there are genes that regulate only one of the promoters and genes that regulate more than one of them at the same time. These results support the role of transcription regulation of each PKA subunit in cAMP specificity signaling. Interestingly, many of the known targets of PKA phosphorylation are associated with the identified pathways, opening the possibility of a reciprocal regulation in which PKA would be coordinating different metabolic pathways and these processes would in turn, regulate expression of the kinase subunits.