bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recent Trends in Squamous Cell Carcinoma of the Anus Incidence and Mortality in the United States, 2001–2015
Authors: Deshmukh Ashish A , Suk Ryan , Shiels Meredith S , Sonawane Kalyani , Nyitray Alan G , Liu Yuxin , Gaisa Michael M , Palefsky Joel M , Sigel Keith 
Published: November 2019

AbstractBackgroundSquamous cell carcinoma of the anus (SCCA) incidence is rising in the United States. Study of incidence trends by stage at diagnosis, age-specific and birth cohort patterns, and trends in mortality could provide evidence for a true increase and etiological clues for the increase in incidence.MethodsUsing the US Cancer Statistics dataset, we examined trends in SCCA incidence (2001–2015) and mortality (2001–2016) rates. Join-point regression was used to compute annual and average annual percentage change (AAPC). Incidence patterns by 5-year age group and birth cohort were evaluated using incidence rate ratios (IRRs) and age-period-cohort modeling.ResultsSCCA incidence increased 2.7% per year (95% confidence interval [CI] = 2.1% to 3.3%), with pronounced increases in age groups 50 years and older. Distant-stage SCCA incidence tripled (AAPC = 8.6%, 95% CI = 5.4% to 12.0%, among men and AAPC = 7.5%, 95% CI = 4.8% to 10.2%, among women) and regional-stage SCCA incidence nearly doubled (AAPC = 4.7% for men and women) in both sexes; the AAPC for localized stage was 1.3% (95% CI = 0.6% to 2.0%) in men and 2.3% (95% CI = 1.8% to 2.8%) in women. Compared with adults born circa 1946, recently born black men (born circa 1986) had a nearly fivefold higher risk (IRR = 4.7, 95% CI = 2.1 to 10.2) of SCCA, and the risk doubled among white men (IRR = 2.0, 95% CI = 1.7 to 2.2) and white women (IRR = 2.1, 95% CI = 1.9 to 2.3) born after circa 1960. Anal cancer mortality rates increased 3.1% per year (95% CI = 2.6% to 3.5%) with statistically significant increases in age groups 50 years and older. SCCA incidence-based mortality increased 1.9% annually (95% CI = 0.5% to 3.4%), with a notable (4.9%, 95% CI = 2.4% to 7.3%, per year) rise in adults ages 60–69 years.ConclusionThe increase in SCCA incidence, particularly advanced-stage disease, and a similar increase in mortality suggest a true increase in the occurrence of SCCA. Future research and improved prevention are urgently needed to mitigate the increasing disease burden.
Efficacy of the AS04-Adjuvanted HPV16/18 Vaccine: Pooled Analysis of the Costa Rica Vaccine and PATRICIA Randomized Controlled Trials
Authors: Tota Joseph E , Struyf Frank , Sampson Joshua N , Gonzalez Paula , Ryser Martin , Herrero Rolando , Schussler John , Karkada Naveen , Rodriguez Ana Cecilia , Folschweiller Nicolas , Porras Carolina , Schiffman Mark , Schiller John T , Quint Wim , Kreimer Aimée R , Wheeler Cosette M , Hildesheim Allan ,   for the Costa Rica Vaccine Trial and PATRICIA Study
Published: November 2019

Abstract

Background
The AS04-adjuvanted HPV16/18 (AS04-HPV16/18) vaccine provides excellent protection against targeted human papillomavirus (HPV) types and a variable degree of cross-protection against others, including types 6/11/31/33/45. High efficacy against any cervical intraepithelial neoplasia grade 3 or greater (CIN3+; &gt;90%) suggests that lower levels of protection may exist for a wide range of oncogenic HPV types, which is difficult to quantify in individual trials. Pooling individual-level data from two randomized controlled trials, we aimed to evaluate AS04-HPV16/18 vaccine efficacy against incident HPV infections and cervical abnormalities .

Methods
Data were available from the Costa Rica Vaccine Trial (NCT00128661) and Papilloma Trial Against Cancer in Young Adults trial (NCT00122681), two large-scale, double-blind randomized controlled trials of the AS04-HPV16/18 vaccine. Primary analyses focused on disease-free women with no detectable cervicovaginal HPV at baseline.

Results
A total of 12 550 women were included in our primary analyses (HPV arm = 6271, control arm = 6279). Incidence of 6-month persistent oncogenic and nononcogenic infections, excluding known and accepted protected types 6/11/16/18/31/33/45 (focusing on 34/35/39/40/42/43/44/51/52/53/54/56/58/59/66/68/73/70/74), was statistically significantly lower in the HPV arm than in the control arm (efficacy = 9.9%, 95% confidence interval [CI] = 1.7% to 17.4%). Statistically significant efficacy (P &lt; .05) was observed for individual oncogenic types 16/18/31/33/45/52 and nononcogenic types 6/11/53/74. Efficacy against cervical abnormalities (all types) increased with severity, ranging from 27.7% (95% CI = 21.7% to 33.3%) to 58.7% (95% CI = 34.1% to 74.7%) for cytologic outcomes (low-grade squamous intraepithelial neoplasia lesion or greater, and high-grade squamous intraepithelial neoplasia lesion or greater, respectively) and 66.0% (95% CI = 54.4% to 74.9%) to 87.8% (95% CI = 71.1% to 95.7%) for histologic outcomes (CIN2+ and CIN3+, respectively). Comparing Costa Rica Vaccine Trial and Papilloma Trial Against Cancer in Young Adults results, there was no evidence of heterogeneity, except for type 51 (efficacy = −28.6% and 20.7%, respectively; two-sided P = .03).

Conclusions
The AS04-HPV16/18 vaccine provides some additional cross-protection beyond established protected types, which partially explains the high efficacy against CIN3+.
Two SLENDER AND CRINKLY LEAF dioxygenases play an essential role in rice shoot development
Authors: Liu Xiong , Cai Wen-Jing , Yin Xiaoming , Yang Di , Dong Tian , Feng Yu-Qi , Wu Yan 
Published: November 2019

Abstract
It is clear that 2-oxoglutarate-dependent dioxygenases have critical functions in salicylic acid (SA) metabolism in plants, yet their role in SA biosynthesis is poorly understood. Here, we report that two dioxygenase-encoding genes, SLENDER AND CRINKLY LEAF1 (SLC1) and SLC2, play essential roles in shoot development and SA production in rice. Overexpression of SLC1 (SLC1-OE) or SLC2 (SLC2-OE) in rice produced infertile plants with slender and crinkly leaves. Disruption of SLC1 or SLC2 led to dwarf plants, while simultaneous down-regulation of SLC1 and SLC2 resulted in a severe defect in early leaf development. Enhanced SA levels in SLC1-OE plants and decreased SA levels in slc1 and slc2 mutants were observed. Accordingly, these lines all showed altered expression of a set of SA-related genes. We demonstrated that SLC1 interacts with homeobox1 (OSH1), and that either the knotted1-like homeobox (KNOX1) or glutamate, leucine, and lysine (ELK) domain of OSH1 is sufficient for accomplishing this interaction. Collectively, our data reveal the importance of SLC1 and SLC2 in rice shoot development.
A role for Arabidopsis growth-regulating factors 1 and 3 in growth–stress antagonism
Authors: Piya Sarbottam , Liu Jinyi , Burch-Smith Tessa , Baum Thomas J , Hewezi Tarek 
Published: November 2019

Abstract
Growth-regulating factors (GRFs) belong to a small family of transcription factors that are highly conserved in plants. GRFs regulate many developmental processes and plant responses to biotic and abiotic stimuli. Despite the importance of GRFs, a detailed mechanistic understanding of their regulatory functions is still lacking. In this study, we used ChIP sequencing (ChIP-seq) to identify genome-wide binding sites of Arabidopsis GRF1 and GRF3, and correspondingly their direct downstream target genes. RNA-sequencing (RNA-seq) analysis revealed that GRF1 and GRF3 regulate the expression of a significant number of the identified direct targets. The target genes unveiled broad regulatory functions of GRF1 and GRF3 in plant growth and development, phytohormone biosynthesis and signaling, and the cell cycle. Our analyses also revealed that clock core genes and genes with stress- and defense-related functions are most predominant among the GRF1- and GRF3-bound targets, providing insights into a possible role for these transcription factors in mediating growth–defense antagonism and integrating environmental stimuli into developmental programs. Additionally, GRF1 and GRF3 target molecular nodes of growth–defense antagonism and modulate the levels of defense- and development-related hormones in opposite directions. Taken together, our results point to GRF1 and GRF3 as potential key determinants of plant fitness under stress conditions.
Star formation and gas flow history of a dwarf irregular galaxy traced by gas-phase and stellar metallicities
Authors: Fukagawa Nao 
Published: November 2019

ABSTRACT
Studying the evolution of dwarf galaxies can provide insights into the characteristics of systems that can act as building blocks of massive galaxies. This paper discusses the history of star formation and gas flows (inflow and outflow) of a dwarf irregular galaxy in the Local Group, NGC 6822, from the viewpoint of gas-phase and stellar chemical abundance. Gas-phase oxygen abundance, stellar metallicity distribution, and gas fraction data are compared to chemical evolution models in which continuous star formation and gas flows are assumed. If the galaxy is assumed to be a closed or an accretion-dominated system where steeper stellar initial mass functions are allowed, the observed gas-phase oxygen abundance and gas fraction can be explained simultaneously; however, metallicity distributions predicted by the models seem to be inconsistent with the observed distribution, which suggests that the star formation, gas flows, and/or chemical enrichment are more complex than assumed by the models. When NGC 6822 is assumed to be a system dominated by outflow, the observed values of gas-phase oxygen abundance and gas fraction can be explained, and the metallicity distributions predicted by some of the models are also roughly consistent with the observed distribution in the metallicity range of −2.0 ≲ [Fe/H] ≲ −0.5. It should be noted that this result does not necessarily mean that the accretion of gas is completely ruled out. More observables, such as chemical abundance ratios, and detailed modelling may provide deeper insight into the evolution of the system.
The Sloan Digital Sky Survey extended point spread functions
Authors: Infante-Sainz Raúl , Trujillo Ignacio , Román Javier 
Published: November 2019

ABSTRACT
A robust and extended characterization of the point spread function (PSF) is crucial to extract the photometric information produced by deep imaging surveys. Here, we present the extended PSFs of the Sloan Digital Sky Survey (SDSS), one of the most productive astronomical surveys of all time. By stacking ∼1000 images of individual stars with different brightness, we obtain the bidimensional SDSS PSFs extending over 8 arcmin in radius for all the SDSS filters (u, g, r, i, z). This new characterization of the SDSS PSFs is near a factor of 10 larger in extension than previous PSFs characterizations of the same survey. We found asymmetries in the shape of the PSFs caused by the drift scanning observing mode. The flux of the PSFs is larger along the drift scanning direction. Finally, we illustrate with an example how the PSF models can be used to remove the scattered light field produced by the brightest stars in the central region of the Coma cluster field. This particular example shows the huge importance of PSFs in the study of the low-surface brightness Universe, especially with the upcoming of ultradeep surveys, such as the Large Synoptic Survey Telescope (LSST). Following a reproducible science philosophy, we make all the PSF models and the scripts used to do the analysis of this paper publicly available (snapshot v0.4-0-gd966ad0).
New constraints on the HR 8799 planetary system from mid-infrared direct imaging
Authors: Petit dit de la Roche D J M , van den Ancker M E , Kissler-Patig M , Ivanov V D , Fedele D 
Published: November 2019

ABSTRACT
Direct imaging is a tried and tested method of detecting exoplanets in the near-infrared (IR), but has so far not been extended to longer wavelengths. New data at mid-IR wavelengths (8–20 μm) can provide additional constraints on planetary atmospheric models. We use the VLT Imager and Spectrometer for the mid-IR (VISIR) instrument on the VLT to detect or set stringent limits on the 8.7 μm flux of the four planets surrounding HR 8799, and to search for additional companions. We use a novel circularized point spread function subtraction technique to reduce the stellar signal and obtain instrument limited background levels and obtain optimal flux limits. The BT SETTL isochrones are then used to determine the resulting mass limits. We find flux limits between 0.7 and 3.3 mJy for the J8.9 flux of the different planets at better than 5σ level and derive a new mass limit of 30 MJup for any objects beyond 40 au. While this work has not detected planets in the HR 8799 system at 8.7 μm, it has found that an instrument with the sensitivity of VISIR is sufficient to detect at least four known hot planets around close stars, including β Pictoris b (1700 K, 19 pc), with more than 5σ certainty in 10 h of observing time in the mid-IR.
In situ scattering of warm Jupiters and implications for dynamical histories
Authors: Anderson Kassandra R , Lai Dong , Pu Bonan 
Published: November 2019

ABSTRACT
Many warm Jupiters (WJs) have substantial eccentricities, which are linked to their formation and migration histories. This paper explores eccentricity excitation of WJs due to planet–planet scattering, beginning with three to four planets in unstable orbits, with the innermost planet placed in the range (0.1−1) au. Such a setup is consistent with either in situ formation or arrival at sub-au orbits due to disc migration. Most previous N-body experiments have focused on ‘cold’ Jupiters at several au, where scattering results in planet ejections, efficiently exciting the eccentricities of surviving planets. In contrast, scattering at sub-au distances results in a mixture of collisions and ejections, and the final eccentricities of surviving planets are unclear. We conduct scattering experiments for a range of planet masses and initial spacings, including the effect of general relativistic apsidal precession, and systematically catalogue the scattering outcomes and properties of surviving planets. A comparable number of one-planet and two-planet systems are produced. Two-planet systems arise exclusively through planet–planet collisions, and tend to have low eccentricities/mutual inclinations and compact configurations. One-planet systems arise through a combination of ejections and collisions, resulting in higher eccentricities. The observed eccentricity distribution of solitary WJs (lacking detection of a giant planet companion) is consistent with roughly $60 {{\ \rm per\ cent}}$ of the systems having undergone in situ scattering, and the remaining experiencing a quiescent history.
A double-stranded RNA platform is required for the interaction between a host restriction factor and the NS1 protein of influenza A virus
Authors: Chen Guifang , Ma Li-Chung , Wang Shanshan , Woltz Ryan L , Grasso Emily M , Montelione Gaetano T , Krug Robert M 
Published: November 2019

Abstract
Influenza A viruses cause widespread human respiratory disease. The viral multifunctional NS1 protein inhibits host antiviral responses. This inhibition results from the binding of specific cellular antiviral proteins at various positions on the NS1 protein. Remarkably, binding of several proteins also requires the two amino-acid residues in the NS1 N-terminal RNA-binding domain (RBD) that are required for binding double-stranded RNA (dsRNA). Here we focus on the host restriction factor DHX30 helicase that is countered by the NS1 protein, and establish why the dsRNA-binding activity of NS1 is required for its binding to DHX30. We show that the N-terminal 152 amino-acid residue segment of DHX30, denoted DHX30N, possesses all the antiviral activity of DHX30 and contains a dsRNA-binding domain, and that the NS1-DHX30 interaction in vivo requires the dsRNA-binding activity of both DHX30N and the NS1 RBD. We demonstrate why this is the case using bacteria-expressed proteins: the DHX30N-NS1 RBD interaction in vitro requires the presence of a dsRNA platform that binds both NS1 RBD and DHX30N. We propose that a similar dsRNA platform functions in interactions of the NS1 protein with other proteins that requires these same two amino-acid residues required for NS1 RBD dsRNA-binding activity.
Geospatial Analyses of Pain Intensity and Opioid Unit Doses Prescribed on the Day of Discharge Following Orthopedic Surgery
Authors: Tighe Patrick , Modave François , Horodyski MaryBeth , Marsik Matthew , Lipori G , Fillingim Roger , Hu Hui , Hagen Jennifer 
Published: November 2019

AbstractObjectiveInappropriate opioid prescribing after surgery contributes to opioid use disorder and risk of opioid overdose. In this cross-sectional analysis of orthopedic surgical patients, we examined the role of patient location on postoperative pain intensity and opioids prescribed on hospital discharge.MethodsWe used geospatial analyses to characterize spatial patterns of mean pain intensity on the day of discharge (PiDoD) and opioid units prescribed on the day of discharge (OuPoD), as well as the effect of regional social deprivation on these outcomes.ResultsAt a 500-km radius from the surgery site, the Global Moran’s I for PiDoD (2.71 × 10−3, variance = 1.67 × 10−6, P = 0.012) and OuPoD (2.19 × 10−3, SD = 1.87, variance = 1.66 × 10−6, P = 0.03) suggested significant spatial autocorrelation within each outcome. Local indicators of spatial autocorrelation, including local Moran’s I, Local Indicator of Spatial Autocorrelation cluster maps, and Getis-Ord Gi* statistics, further demonstrated significant, specific regions of clustering both OuPoD and PiDoD. These spatial patterns were associated with spatial regions of area deprivation.ConclusionsOur results suggest that the outcomes of pain intensity and opioid doses prescribed exhibit varying degrees of clustering of patient locations of residence, at both global and local levels. This indicates that a given patient’s pain intensity on discharge is related to the pain intensity of nearby individuals. Similar interpretations exist for OuPoD, although the relative locations of hot spots of opioids dispensed in a geographic area appear to differ from those of hot spots of pain intensity on discharge.
Maximal efficiency of the collisional Penrose process with a spinning particle. II. Collision with a particle on the innermost stable circular orbit
Authors: Okabayashi Kazumasa , Maeda Kei-ichi 
Published: November 2019

Abstract
We analyze the collisional Penrose process between a particle on the innermost stable circular orbit (ISCO) orbit around an extreme Kerr black hole and a particle impinging from infinity. We consider both cases with non-spinning and spinning particles. We evaluate the maximal efficiency, $\eta_{\text{max}}=(\text{extracted energy})/(\text{input energy})$, for the elastic collision of two massive particles and for the photoemission process, in which the ISCO particle will escape to infinity after a collision with a massless impinging particle. For non-spinning particles, the maximum efficiency is $\eta_{\text{max}} \approx 2.562$ for the elastic collision and $\eta_{\text{max}} \approx 7$ for the photoemission process. For spinning particles we obtain the maximal efficiency $\eta_{\text{max}} \approx 8.442$ for the elastic collision and $\eta_{\text{max}} \approx 12.54$ for the photoemission process.
Representation of Partisan, Territorial, and Institutional Interests in Second Chambers: Evidence from the German Bundesrat and its Committees
Authors: Finke Patrick , Müller Markus M , Souris Antonios , Sturm Roland 
Published: November 2019

Abstract
Revisiting the longstanding debate on interest representation in federal second chambers, this article investigates the influence of partisanship vis-à-vis territorial and other interests such as institutional concerns on deliberations. We argue that committees as the actual place of policy- and decision-making provide an instructive approach to understand interest representation in second chambers, just as in first chambers. For the empirical part of our study, we focus on the German Bundesrat and its committees. Based on the protocols of their meetings, we developed a new dataset that contains information on more than 51,000 roll call votes, the largest-ever empirical basis to study interest representation and decision-making in the Bundesrat. Above all, we find that partisanship plays a role, yet a minor one. The representatives prioritize individual or joint sub-state interests over their political party affiliations, just like the founding fathers of the Federal Republic have envisaged it in the German constitution.
MRP8/14 and neutrophil elastase for predicting treatment response and occurrence of flare in patients with juvenile idiopathic arthritis
Authors: Barendregt Anouk M , Veldkamp Saskia R , Hissink Muller Petra C E , van de Geer Annemarie , Aarts Cathelijn , van Gulik E Charlotte , Schilham Marco W , Kessel Christoph , Keizer Mischa P , Hemke Robert , Nassar-Sheikh Rashid Amara , Dolman Koert M , Schonenberg-Meinema Dieneke , ten Cate Rebecca , van den Berg J Merlijn , Maas Mario , Kuijpers Taco W 
Published: November 2019

Abstract

Objective
To study two neutrophil activation markers, myeloid-related protein (MRP) 8/14 and neutrophil elastase (NE), for their ability to predict treatment response and flare in patients with JIA.

Methods
Using samples from two cohorts (I and II), we determined MRP8/14 and NE levels of 32 (I) and 81 (II) patients with new-onset, DMARD-naïve arthritis and compared patients who responded to treatment (defined as fulfilling ≥ adjusted ACRpedi50 response and/or inactive disease) with non-responders (defined as fulfilling &lt; adjusted ACRpedi50 response and/or active disease) at 6 and 12 months. Secondly, we compared biomarker levels of 54 (I) and 34 (II) patients with clinically inactive disease who did or did not suffer from a flare of arthritis after 6 or 12 months. Receiver operating characteristic analyses were carried out to study the predictive value of MRP8/14 and NE for treatment response and flare.

Results
For both cohorts, baseline MRP8/14 and NE levels for patients who did or did not respond to treatment were not different. Also, MRP8/14 and NE levels were not different in patients who did or did not flare. Receiver operating characteristic analysis of MRP8/14 and NE demonstrated areas under the curve &lt;0.7 in both cohorts.

Conclusion
In our cohorts, MRP8/14 and NE could not predict treatment response. Also, when patients had inactive disease, neither marker could predict flares.