bluuebunny/crossref_metadata_2025_split huggingface dataset:
Light-induced stress as a primary evolutionary driver of eye origins
Authors: Swafford Andrew J M , Oakley Todd H 
Published: September 2019

AbstractEyes are quintessential complex traits and our understanding of their evolution guides models of trait evolution in general. A long-standing account of eye evolution argues natural selection favors morphological variations that allow increased functionality for sensing light. While certainly true in part, this focus on visual performance does not entirely explain why diffuse photosensitivity persists even after eyes evolve, or why eyes evolved many times, each time using similar building blocks. Here, we briefly review a vast literature indicating most genetic components of eyes historically responded to stress caused directly by light, including ultraviolet damage of DNA, oxidative stress, and production of aldehydes. We propose light-induced stress had a direct and prominent role in the evolution of eyes by bringing together genes to repair and prevent damage from light-stress, both before and during the evolution of eyes themselves. Stress-repair and stress-prevention genes were perhaps originally deployed as plastic responses to light and/or as beneficial mutations genetically driving expression where light was prominent. These stress-response genes sense, shield, and refract light but only as reactions to ongoing light stress. Once under regulatory-genetic control, they could be expressed before light stress appeared, evolve as a module, and be influenced by natural selection to increase functionality for sensing light, ultimately leading to complex eyes and behaviors. Recognizing the potentially prominent role of stress in eye evolution invites discussions of plasticity and assimilation and provides a hypothesis for why similar genes are repeatedly used in convergent eyes. Broadening the drivers of eye evolution encourages consideration of multi-faceted mechanisms of plasticity/assimilation and mutation/selection for complex novelties and innovations in general.
Boolean Product Polynomials, Schur Positivity, and Chern Plethysm
Authors: Billey Sara C , Rhoades Brendon , Tewari Vasu 
Published: September 2019

AbstractLet $k \leq n$ be positive integers, and let $X_n = (x_1, \dots , x_n)$ be a list of $n$ variables. The Boolean product polynomial $B_{n,k}(X_n)$ is the product of the linear forms $\sum _{i \in S} x_i$, where $S$ ranges over all $k$-element subsets of $\{1, 2, \dots , n\}$. We prove that Boolean product polynomials are Schur positive. We do this via a new method of proving Schur positivity using vector bundles and a symmetric function operation we call Chern plethysm. This gives a geometric method for producing a vast array of Schur positive polynomials whose Schur positivity lacks (at present) a combinatorial or representation theoretic proof. We relate the polynomials $B_{n,k}(X_n)$ for certain $k$ to other combinatorial objects including derangements, positroids, alternating sign matrices, and reverse flagged fillings of a partition shape. We also relate $B_{n,n-1}(X_n)$ to a bigraded action of the symmetric group ${\mathfrak{S}}_n$ on a divergence free quotient of superspace.
Prevalence, Incidence, and Clearance of Human Papillomavirus Types Covered by Current Vaccines in Men With Human Immunodeficiency Virus in the SUN Study
Authors: Patel Pragna , Bush Tim , Conley Lois , Unger Elizabeth R , Darragh Teresa M , Henry Keith , Escota Gerome , Brooks John T , Kojic Erna Milunka 
Published: September 2019

AbstractBackgroundHigh-risk anal human papillomavirus (HPV) infection is prevalent among men living with human immunodeficiency virus (HIV); the association between 9-valent (9v) high-risk HPV (HR-HPV) vaccine types and abnormal cytology has not been well characterized.MethodsWe followed a prospective cohort study of persons with HIV at 7 HIV clinics in 4 US cities from March 2004 through June 2012. Annually, providers collected separate anal swabs for HPV detection and cytopathologic examination. Among men, we examined prevalence, incidence, and clearance of 9v HR-HPV vaccine types, compared with other HR types, and associations with abnormal cytology to assess potential vaccine impact.ResultsBaseline prevalence of any anal 9v HR-HPV type among men who have sex with men (MSM) and men who have sex with women (MSW) was 74% and 25% (P &lt; .001), respectively. Among 299 MSM, abnormal cytology was detected in 161 (54%) MSM and was associated with the presence of any 9v HR-HPV (relative risk [RR], 1.8 [95% confidence interval {CI}, 1.3–2.6]; P &lt; .001). Among 61 MSW, abnormal anal cytology was detected in 12 (20%) and was associated with the presence of any 9v HR-HPV (RR, 4.3 [95% CI, 1.6–11.5]; P &lt; .001).ConclusionsAmong men with HIV, the prevalence of the 7 HR-HPV types in the 9v vaccine was high and was associated with abnormal cytology. These findings indicate that men with HIV could benefit from prophylactic administration of the 9v HPV vaccine.
A combined computational pipeline to detect circular RNAs in human cancer cells under hypoxic stress
Authors: Di Liddo Antonella , de Oliveira Freitas Machado Camila , Fischer Sandra , Ebersberger Stefanie , Heumüller Andreas W , Weigand Julia E , Müller-McNicoll Michaela , Zarnack Kathi 
Published: September 2019

AbstractHypoxia is associated with several diseases, including cancer. Cells that are deprived of adequate oxygen supply trigger transcriptional and post-transcriptional responses, which control cellular pathways such as angiogenesis, proliferation, and metabolic adaptation. Circular RNAs (circRNAs) are a novel class of mainly non-coding RNAs, which have been implicated in multiple cancers and attract increasing attention as potential biomarkers. Here, we characterize the circRNA signatures of three different cancer cell lines from cervical (HeLa), breast (MCF-7), and lung (A549) cancer under hypoxia. In order to reliably detect circRNAs, we integrate available tools with custom approaches for quantification and statistical analysis. Using this consolidated computational pipeline, we identify ~12000 circRNAs in the three cancer cell lines. Their molecular characteristics point to an involvement of complementary RNA sequences as well as trans-acting factors in circRNA biogenesis, such as the RNA-binding protein HNRNPC. Notably, we detect a number of circRNAs that are more abundant than their linear counterparts. In addition, 64 circRNAs significantly change in abundance upon hypoxia, in most cases in a cell type-specific manner. In summary, we present a comparative circRNA profiling in human cancer cell lines, which promises novel insights into the biogenesis and function of circRNAs under hypoxic stress.
Single-Arm Phase II Trials of Combination Therapies: A Review of the CTEP Experience 2008–2017
Authors: Foster Jared C , Freidlin Boris , Kunos Charles A , Korn Edward L 
Published: September 2019

AbstractDesigning and interpreting single-arm phase II trials of combinations of agents is challenging because it can be difficult, based on historical data, to identify levels of activity for which the combination would be worth pursuing. We identified Cancer Therapy Evaluation Program single-arm combination trials that were activated in 2008–2017 and tabulated their design characteristics and results. Positive trials were evaluated as to whether they provided credible evidence that the combination was better than its constituents. A total of 125 trials were identified, and 120 trials had results available. Twelve had designs where eligible patients were required to be resistant or refractory to all but one element of the combination. Only 17.8% of the 45 positive trials were deemed to provide credible evidence that the combination was better than its constituents. Of the 10 positive trials with observed rates 10 percentage points higher than their upper (alternative hypothesis) targets, only five were deemed to provide such credible evidence. Many trials were definitively negative, with observed clinical activity at or below their lower (null hypothesis) targets. Ideally, use of single-arm combination trials should be restricted to settings where each agent is known to have minimal monotherapy activity (and a randomized trial is infeasible). In these settings, an observed signal is attributable to synergy and thus could be used to decide whether the combination is worth pursuing. In other settings, credible evidence can still be obtained if the observed activity is much higher than expected, but experience suggests that this is a rare occurrence.
Alterations in GABAA Receptor Subunit Expression in the Amygdala and Entorhinal Cortex in Human Temporal Lobe Epilepsy
Authors: Stefanits Harald , Milenkovic Ivan , Mahr Nina , Pataraia Ekaterina , Baumgartner Christoph , Hainfellner Johannes A , Kovacs Gabor G , Kasprian Gregor , Sieghart Werner , Yilmazer-Hanke Deniz , Czech Thomas 
Published: September 2019

Abstract
The amygdala has long been implicated in the pathophysiology of human temporal lobe epilepsy (TLE). The different nuclei of this complex structure are interconnected and share reciprocal connections with the hippocampus and other brain structures, partly via the entorhinal cortex. Expression of GABAA receptor subunits α1, α2, α3, α5, β2, β2/3, and γ2 was evaluated by immunohistochemistry in amygdala specimens and the entorhinal cortex of 12 TLE patients and 12 autopsy controls. A substantial decrease in the expression of α1, α2, α3, and β2/3 subunits was found in TLE cases, accompanied by an increase of γ2 subunit expression in many nuclei. In the entorhinal cortex, the expression of all GABAA receptor subunits was decreased except for the α1 subunit, which was increased on cellular somata. The overall reduction in α subunit expression may lead to decreased sensitivity to GABA and its ligands and compromise phasic inhibition, whereas upregulation of the γ2 subunit might influence clustering and kinetics of receptors and impair tonic inhibition. The description of these alterations in the human amygdala is important for the understanding of network changes in TLE as well as the development of subunit-specific therapeutic agents for the treatment of this disease.
THE EFFECTS OF BROADCASTING DIGITIZATION ON EU COMPETITION LAW: A TALE OF EU COPYRIGHT POLICIES
Authors: Bania Konstantina 
Published: September 2019

ABSTRACT
In recent years, buzz terms such as “geo-blocking”, “online content portability”, and “digital copyright” have been making rounds in EU policy circles. This is largely attributed to the “Digital Single Market Strategy”, an ambitious reform the objective of which is to ensure seamless cross-border access to online services. Pursuit of this objective appears to be largely driven by the assumption that limiting the exclusivity of copyright would stimulate intra-Union competition in content markets. Against the background of EU competence limitations in the field of copyright and the increasing popularity of global U.S. firms in European audiovisual markets, this paper argues that EU Competition Law has vainly been instrumentalized to complete a single market for content. More particularly, based on legal and policy developments, which appear to challenge widespread licensing practices, sector-specific economics, and the case law that sets the conditions under which competition enforcement may introduce limits to copyright protection, this study develops the following twofold argument: in an attempt to create a single market for copyright-protected broadcast content, the EU has stretched the boundaries of competition law in an excessive manner and such unjustified interference with copyright is simply inadequate to promote competition and market integration.
eROSITA detection rates for tidal disruptions of white dwarfs by intermediate mass black holes
Authors: Malyali A , Rau A , Nandra K 
Published: September 2019

ABSTRACT
White dwarf black hole tidal disruption events (herein WTDEs) present an opportunity to probe the quiescent intermediate mass black hole population in the Universe. We run an extensive set of Monte Carlo based simulations to explore SRG/eROSITA’s detection sensitivity to WTDEs as a function of black hole mass, redshift, and time offset between event flaring and it first being observed. A novel estimate of WTDE rate densities from globular clusters and dwarf galaxies is also presented. We combine this with estimated detection sensitivities to infer the rate of eROSITA detecting these events. Depending on the estimate of the intrinsic rate of WTDEs, we anticipate that eROSITA may detect three events over its 4 yr all-sky survey. eROSITA will be most sensitive to systems with black hole masses above $10^4\, \mathrm{M}_{\odot }$, and is most likely to catch these within 5 d of flaring.
Non–adiabatic tidal oscillations induced by a planetary companion
Authors: Bunting Andrew , Papaloizou John C B , Terquem Caroline 
Published: September 2019

Abstract
We calculate the dynamical tides raised by a close planetary companion on non–rotating stars of 1 M⊙ and 1.4 M⊙. Using the Henyey method, we solve the fully non–adiabatic equations throughout the star. The horizontal Lagrangian displacement is found to be 10 to 100 times larger than the equilibrium tide value in a thin region near the surface of the star. This is because non–adiabatic effects dominate in a region that extends from below the outer edge of the convection zone up to the stellar surface, and the equilibrium tide approximation is inconsistent with non–adiabaticity. Although this approximation generally applies in the low frequency limit, it also fails in the parts of the convection zone where the forcing frequency is small but larger than the Brunt-Väisälä frequency. We derive analytical estimates which give a good approximation to the numerical values of the magnitude of the ratio of the horizontal and radial displacements at the surface. The relative surface flux perturbation is also significant, on the order of 0.1% for a system modelled on 51 Pegasi b. Observations affected by the horizontal displacement may therefore be more achievable than previously thought, and brightness perturbations may be the result of flux perturbations rather than due to the radial displacement. We discuss the implication of this on the possibility of detecting such tidally excited oscillations, including the prospect of utilising the large horizontal motion for observations of systems such as 51 Pegasi.
VVV-WIT-04: an extragalactic variable source caught by the VVV Survey
Authors: Saito R K , Minniti D , Ivanov V D , Masetti N , Navarro M G , Cid Fernandes R , Ruschel-Dutra D , Smith L C , Lucas P W , Gonzalez-Fernandez C , Contreras Ramos R 
Published: September 2019

ABSTRACT
We report the discovery of VVV-WIT-04, a near-infrared (near-IR) variable source towards the Galactic disc located ∼0.2 arcsec apart from the position of the radio source PMN J1515−5559. The object was found serendipitously in the near-IR data of the ESO public survey VISTA Variables in the Vía Láctea (VVV). Our analysis is based on variability, multicolour, and proper motion data from VVV and VVV eXtended surveys, complemented with archive data at longer wavelengths. We suggest that VVV-WIT-04 has an extragalactic origin as the near-IR counterpart of PMN J1515−5559. The Ks-band light curve of VVV-WIT-04 is highly variable and consistent with that of an optically violent variable quasar. The variability in the near-IR can be interpreted as the redshifted optical variability. Residuals to the proper motion vary with the magnitude suggesting contamination by a blended source. Alternative scenarios, including a transient event such as a nova or supernova, or even a binary microlensing event, are not in agreement with the available data.
RNA binding candidates for human ADAR3 from substrates of a gain of function mutant expressed in neuronal cells
Authors: Wang Yuru , Chung Dong hee , Monteleone Leanna R , Li Jie , Chiang Yao , Toney Michael D , Beal Peter A 
Published: September 2019

AbstractHuman ADAR3 is a catalytically inactive member of the Adenosine Deaminase Acting on RNA (ADAR) protein family, whose active members catalyze A-to-I RNA editing in metazoans. Until now, the reasons for the catalytic incapability of ADAR3 has not been defined and its biological function rarely explored. Yet, its exclusive expression in the brain and involvement in learning and memory suggest a central role in the nervous system. Here we describe the engineering of a catalytically active ADAR3 enzyme using a combination of computational design and functional screening. Five mutations (A389V, V485I, E527Q, Q549R and Q733D) engender RNA deaminase in human ADAR3. By way of its catalytic activity, the ADAR3 pentamutant was used to identify potential binding targets for wild type ADAR3 in a human glioblastoma cell line. Novel ADAR3 binding sites discovered in this manner include the 3′-UTRs of the mRNAs encoding early growth response 1 (EGR1) and dual specificity phosphatase 1 (DUSP1); both known to be activity-dependent immediate early genes that respond to stimuli in the brain. Further studies reveal that the wild type ADAR3 protein can regulate transcript levels for DUSP1 and EGR1, suggesting a novel role ADAR3 may play in brain function.
Can We Justify It? Trends in the Utilization of Spinal Fusions and Associated Reimbursement
Authors: Sheikh Shehryar Rahim , Thompson Nicolas R , Benzel Edward , Steinmetz Michael , Mroz Thomas , Tomic Dennis , Machado Andre , Jehi Lara 
Published: September 2019

Abstract

BACKGROUND
Previous reports have suggested an increasing rate of utilization of spinal fusions, but contemporary data have not been analyzed, and there has been little investigation of putative drivers of increased utilization.

OBJECTIVE
To investigate whether there is an ongoing trend of increased utilization of spinal fusions in recent data, and if there may be associations with an increasing proportion of elderly in the population, changing patterns of payer-types, and changing reimbursement rates.

METHODS
We analyze 7.1 million cases from the National Inpatient Sample between 1998 and 2014. We measure annual utilization per 100 000 persons and conduct trend analyses with subgroup analysis of the senior (65 + ) population. Spine surgery utilization is compared with nonspine surgical procedures (coronary artery bypass grafting, hernia repair, hip, and knee replacement). We assess trends in charges, payer type, Medicare reimbursement rates, and hospital type.

RESULTS
There was an 88% increase in the utilization rate of spinal fusion procedures from 1998 to 2014 (from 74 to 139 cases per 100 000 persons) with a significant upward trend (P < .001) that persisted in the 65 + subgroup (P < .001). An increasing proportion of spinal fusions is paid for by public payers, but per-procedure reimbursement for spinal fusions by Medicare has decreased recently (5% reduction from 2014 to 2016).

CONCLUSION
Utilization of spinal fusions continues to increase and is not explained by increased proportion of elderly in the population, increased utilization of surgeries across specialties, or increased Medicare reimbursement. In fact, increased utilization of spinal fusions temporally correlated with decreasing per-procedure Medicare reimbursement.
Introduction
Authors: Donahue-Ochoa Thomas J. 
Published: September 2019

Abstract
Among the world’s liberal elites today, a received view answers all five of the questions put by this book, arguing that systematic injustice is, essentially, persecution by a government; that there are no global social injustices; that individuals have a strong reason to challenge injustices only if they perpetrated or were victimized by them; that the individuals made unfree by systematic injustice are only its direct victims; and that the ultimate harm done by oppression is the unjust denial, to the oppressed, of the ability to live as free and equal citizens. Against this, the book’s introduction presents the theory of “Unfreedom for All,” which argues that oppressions are also institutional structures that privilege one group and unjustly harm another; that global systematic injustices of, say, race, gender, and poverty do exist; that all are harmed by oppressions because all are made unfree by them; and that this should be everyone’s main reason for joining in solidarity against them.
How Injustices Harm You
Authors: Donahue-Ochoa Thomas J. 
Published: September 2019

Abstract
Chapter 5 mounts the main argument of the book to show that oppression makes everyone unfree. The main ideas are that oppressions are despotic over their victims, that they can endure only if they try to suppress all actual or potential resistance, that any institutional feature of society that suppresses resistance has established authority, that institutional features with established authority are central social institutions, while suppressing resistance to central social institutions counts as authoritarian tactics used against everyone, that such tactics count as arbitrary power, and that to be subjected to such power is to be subjected to unfreedom of the kind theorized by neo-republicans and Hayekian competitive-order theorists. And since we all have a decent-life interest in freedom from arbitrary power, we are all harmed by such oppression, since it sets back this interest for everyone in society.
The Global Racial Order
Authors: Donahue-Ochoa Thomas J. 
Published: September 2019

Abstract
Chapter 7 offers a differential diagnosis of global racial injustice. Against Charles W. Mills’s theory that we live under global white supremacy, the chapter argues that the white racial group no longer dominates all other racial groups in the world. In particular, those raced as yellow by global society—roughly, East Asians and their descendants—are no longer dominated by racial whites and whiteness. More than this, the supreme political and social status enjoyed by whites over all other racial groups is also waning. The chapter therefore argues that our global racial order is best understood as a system of “partitioned white primacy.” In this system, racial whites exert racial primacy over racial reds, browns, and blacks; but the system is partitioned, because whites do not exert such primacy over those raced as yellow. Moreover, such primacy as whites do exert over other racial groups is less than supremacy, and it is even now being challenged. The chapter then shows how such primacy still suppresses resistance and thereby makes all unfree.
Solidarity, Universal Unfreedom, and You
Authors: Donahue-Ochoa Thomas J. 
Published: September 2019

Abstract
What should be our main reason for resisting oppression? In answer, chapter 9 argues that the universal unfreedom caused by oppression should be that reason, because we should seek a reason that will maximally appeal to the oppression’s non-victims, inducing them to resist and challenge it. For robust solidarity among a critical mass of the victims, the bystanders, and the perpetrators is necessary for abolishing systematic injustice and thus also for ending universal unfreedom. And because of the suspicion and mistrust that are likely to obtain in such a mixed resistance, we need a reason for challenging injustice that describes a shared harm the injustice does them all. The reason is that only a sense of such a shared harm could underwrite the robust and mutual solidarity needed to abolish oppression. Hence those non-victims who join in such solidarity are not allies but rather fellows who are also harmed: they are the scathed.