bluuebunny/crossref_metadata_2025_split huggingface dataset:
First Estimation of the Spontaneous Mutation Rate in Diatoms
Authors: Krasovec Marc , Sanchez-Brosseau Sophie , Piganeau Gwenael 
Published: June 2019

AbstractMutations are the origin of genetic diversity, and the mutation rate is a fundamental parameter to understand all aspects of molecular evolution. The combination of mutation–accumulation experiments and high-throughput sequencing enabled the estimation of mutation rates in most model organisms, but several major eukaryotic lineages remain unexplored. Here, we report the first estimation of the spontaneous mutation rate in a model unicellular eukaryote from the Stramenopile kingdom, the diatom Phaeodactylum tricornutum (strain RCC2967). We sequenced 36 mutation accumulation lines for an average of 181 generations per line and identified 156 de novo mutations. The base substitution mutation rate per site per generation is μbs = 4.77 × 10−10 and the insertion–deletion mutation rate is μid = 1.58 × 10−11. The mutation rate varies as a function of the nucleotide context and is biased toward an excess of mutations from GC to AT, consistent with previous observations in other species. Interestingly, the mutation rates between the genomes of organelles and the nucleus differ, with a significantly higher mutation rate in the mitochondria. This confirms previous claims based on indirect estimations of the mutation rate in mitochondria of photosynthetic eukaryotes that acquired their plastid through a secondary endosymbiosis. This novel estimate enables us to infer the effective population size of P. tricornutum to be Ne∼8.72 × 106.
Quantifying the estimation error of principal component vectors
Authors: Hauser Raphael , Lember Jüri , Matzinger Heinrich , Kangro Raul 
Published: June 2019

Abstract
Principal component analysis (PCA) is an important pattern recognition and dimensionality reduction tool in many applications. Principal components are computed as eigenvectors of a maximum likelihood covariance $\widehat{\varSigma }$ that approximates a population covariance $\varSigma$, and these eigenvectors are often used to extract structural information about the variables (or attributes) of the studied population. Since PCA is based on the eigendecomposition of the proxy covariance $\widehat{\varSigma }$ rather than the ground-truth $\varSigma$, it is important to understand the approximation error in each individual eigenvector as a function of the number of available samples. The combination of recent results of Koltchinskii & Lounici (2017, Bernoulli, 23, 110–133) and Yu et al. (2015, Biometrika, 102, 315–323) yields such bounds. In the present paper we sharpen these bounds and show that eigenvectors can often be reconstructed to a required accuracy from a sample of strictly smaller size order.
First Record of Quill Mites (Acariformes: Syringophilidae: Picobiinae) Living in the Quill Walls of Parrots
Authors: Skoracki Maciej , Sikora Bozena , Hromada Martin 
Published: June 2019

Abstract
Quill mites (Acariformes: Prostigmata: Syringophilidae) are a family of about 400 ectoparasite species known to infest birds for over 140 yr. All previously identified quill mites occur in the calamus, a cavity of the bird feather, where they spent their entire life except for a short dispersion period. In this study, we report the first record of quill mites dwelling in the quill walls during their entire life cycle. In short, we found all of the different life stages of the species Lawrencipicobia poicephali (Skoracki & Dabert 2002) (Acariformes: Syringophilidae) in the quill wall in 33 host individuals of six different host species from many different locations in Sub-Saharan Africa. Hosts were collected over a time period spanning more than 70 yr. Lastly, we report six new avian hosts for this ectoparasite species.
Dark Hope: Notes on Uncertain Futures
Authors: Van Horn O’neil 
Published: June 2019

Abstract
In the midst of the Anthropocene, what might it mean to have hope? This article intends not to ‘answer’ such a question, but instead sketch possibilities for an alternative, cloudier, indeed livable understanding of ‘hope’. As an exercise in theopoetics, this piece offers the concept of ‘dark hope’ as a viable symbol for the purpose of eco-activisms—entangled, intersectional. To achieve a blurred illustration of this vision of ‘dark hope’, this article will trace relations between Karmen MacKendrick’s work on the haunting affects of memory, Paul Tillich’s confrontation with ‘non-being’, and queer visions of possible, and ever troubling, futures on a rapidly shifting planet. If nothing else, this project strives toward an understanding of hope that can stand up to the woes of anthropogenic climate change, that can be practiced in the face of disaster, that can be lived even in the midst of ruins.
The evolution of sizes and specific angular momenta in hierarchical models of galaxy formation and evolution
Authors: Zoldan Anna , De Lucia Gabriella , Xie Lizhi , Fontanot Fabio , Hirschmann Michaela 
Published: June 2019

ABSTRACTWe extend our previous work focused at z ∼ 0, studying the redshift evolution of galaxy dynamical properties using the state-of-the-art semi-analytic model GAEA (GAlaxy Evolution and Assembly): we show that the predicted size–mass relation for discy/star-forming and quiescent galaxies is in good agreement with observational estimates, up to z ∼ 2. Bulge-dominated galaxies have sizes that are offset low with respect to observational estimates, mainly due to our implementation of disc instability at high redshift. At large masses, both quiescent and bulge-dominated galaxies have sizes smaller than observed. We interpret this as a consequence of our most massive galaxies having larger gas masses than observed, and therefore being more affected by dissipation. We argue that a proper treatment of quasar-driven winds is needed to alleviate this problem. Our model compact galaxies have number densities in agreement with observational estimates and they form most of their stars in small and low angular momentum high-z haloes. GAEA predicts that a significant fraction of compact galaxies forming at high-z is bound to merge with larger structures at lower redshifts: therefore they are not the progenitors of normal-size passive galaxies at z = 0. Our model also predicts a stellar–halo size relation that is in good agreement with observational estimates. The ratio between stellar size and halo size is proportional to the halo spin and does not depend on stellar mass but for the most massive galaxies, where active galactic nucleus feedback leads to a significant decrease of the retention factor (from about 80 per cent to 20 per cent).
Interplay of transcriptional signaling by progesterone, cyclic AMP, and inflammation in myometrial cells: implications for the control of human parturition
Authors: Stanfield Zachary , Amini Peyvand , Wang Junye , Yi Lijuan , Tan Huiqing , Chance Mark R , Koyutürk Mehmet , Mesiano Sam 
Published: June 2019

Abstract
Parturition involves cellular signaling changes driven by the complex interplay between progesterone (P4), inflammation, and the cyclic adenosine monophosphate (cAMP) pathway. To characterize this interplay, we performed comprehensive transcriptomic studies utilizing eight treatment combinations on myometrial cell lines and tissue samples from pregnant women. We performed genome-wide RNA-sequencing on the hTERT-HM${}^{A/B}$ cell line treated with all combinations of P4, forskolin (FSK) (induces cAMP), and interleukin-1$\beta$ (IL-1$\beta$). We then performed gene set enrichment and regulatory network analyses to identify pathways commonly, differentially, or synergistically regulated by these treatments. Finally, we used tissue similarity index (TSI) to characterize the correspondence between cell lines and tissue phenotypes. We observed that in addition to their individual anti-inflammatory effects, P4 and cAMP synergistically blocked specific inflammatory pathways/regulators including STAT3/6, CEBPA/B, and OCT1/7, but not NF$\kappa$B. TSI analysis indicated that FSK + P4- and IL-1$\beta$-treated cells exhibit transcriptional signatures highly similar to non-laboring and laboring term myometrium, respectively. Our results identify potential therapeutic targets to prevent preterm birth and show that the hTERT-HM${}^{A/B}$ cell line provides an accurate transcriptional model for term myometrial tissue.
CNBP controls transcription by unfolding DNA G-quadruplex structures
Authors: David Aldana P , Pipier Angélique , Pascutti Federico , Binolfi Andrés , Weiner Andrea M J , Challier Emilse , Heckel Sofía , Calsou Patrick , Gomez Dennis , Calcaterra Nora B , Armas Pablo 
Published: June 2019

Abstract
Guanine-rich DNA strands can fold into non-canonical four-stranded secondary structures named G-quadruplexes (G4). Experimental evidences suggest that G4-DNA surrounding transcription start sites act as cis-regulatory elements by either stimulating or inhibiting gene transcription. Therefore, proteins able to target and regulate specific G4 formation/unfolding are crucial for G4-mediated transcriptional control. Here we present data revealing that CNBP acts in vitro as a G4-unfolding protein over a tetramolecular G4 formed by the TG4T oligonucleotide, as well as over the G4 folded in the promoters of several oncogenes. CNBP depletion in cellulo led to a reduction in the transcription of endogenous KRAS, suggesting a regulatory role of CNBP in relieving the transcriptional abrogation due to G4 formation. CNBP activity was also assayed over the evolutionary conserved G4 enhancing the transcription of NOGGIN (NOG) developmental gene. CNBP unfolded in vitro NOG G4 and experiments performed in cellulo and in vivo in developing zebrafish showed a repressive role of CNBP on the transcription of this gene by G4 unwinding. Our results shed light on the mechanisms underlying CNBP way of action, as well as reinforce the notion about the existence and function of G4s in whole living organisms.
Trends in Diagnosed Chronic Hepatitis B in a US Health System Population, 2006–2015
Authors: Lu Mei , Zhou Yueren , Holmberg Scott D , Moorman Anne C , Spradling Philip R , Teshale Eyasu H , Boscarino Joseph A , Daida Yihe G , Schmidt Mark A , Li Jia , Rupp Loralee B , Trudeau Sheri , Gordon Stuart C ,   Chronic Hepatitis Cohort Study Investigators
Published: June 2019

Abstract

Background
Trends in the epidemiology of chronic hepatitis B (CHB) among routine clinical care patients in the United States are not well documented. We used data from the Chronic Hepatitis Cohort Study to investigate changes in prevalence and newly recorded cases of CHB from 2006 to 2015.

Methods
Annual percentage changes (APCs) were estimated using join point Poisson regression. Analyses were adjusted by study site; when an interaction with the trend was observed, APCs were estimated by subgroups. Differences in rates based on race, age, and sex were calculated with rate ratios.

Results
We identified 5492 patients with CHB within select health systems with total populations that ranged from 1.9 to 2.4 million persons. From 2006 to 2014, the prevalence of diagnosed CHB increased from 181.3 to 253.0 per 100 000 persons in the health system population; from 2014 to 2015, it declined to 237.0 per 100 000 persons. APC was +3.7%/y through 131 December 2014 (P &lt; .001) and −15.0%/y (P &lt; .001) thereafter. The rate of newly reported cases of CHB did not change significantly across the study period (APC, −1.1%/y; P = .07). The rates of newly reported cases were 20.5 times higher among patients in the Asian American/American Indian/Pacific Islander (ASINPI) category, compared with white patients, and 2.8 times higher among African American patients. The ratio of male to female patients was roughly 3:2.

Conclusions
The prevalence of diagnosed CHB in this US patient population increased from 2006 to 2014, after which it decreased significantly. Rates declined most rapidly among patients ≤40 or 61–70 years old, as well as among ASINPI patients. The rate of newly reported cases remained steady over the study period.
Poisson vs. Gaussian statistics for sparse X-ray data: Application to the soft X-ray spectrometer
Authors: Yamada Shinya , Axelsson Magnus , Ishisaki Yoshitaka , Konami Saori , Takemura Nozomi , Kelley Richard L , Kilbourne Caroline A , Leutenegger Maurice A , Porter F Scott , Eckart Megan E , Szymkowiak Andrew 
Published: June 2019

Abstract
Reliable results when fitting X-ray data require proper consideration of the statistics involved. We probe the impact of Gaussian versus Poisson statistics at low count levels using both the standard χ2 method and maximum likelihood based on Poisson (C) statistics. The difference is studied and quantified through simulated spectra with known properties. We then test the results through analysis of Mn Kα calibration data taken with the flight spare microcalorimeter for the Hitomi soft X-ray spectrometer. Through comparison with simulations, our results show that the χ2 method tends to give overly optimistic estimates of the detector energy resolution, in particular when there are few counts. Given an energy resolution of ∼5 eV and a line with about 100 photons, the line width becomes ∼10% lower in the χ2 method than in Poisson statistics. This is a consequence of the uncertainties being dominated by counting statistics, and therefore highlights the need to choose the appropriate fit statistic.
A case report and literature review: Factitious disorder imposed on another and malingering by proxy
Authors: Walters Ilana C , MacIntosh Rachel , Blake Kim D 
Published: June 2019

Abstract
Factitious disorder imposed on another (FDIA) and malingering by proxy (MAL-BP) are two forms of underreported child maltreatment that should remain on physicians’ differential. This case of a 2-year-old boy, which spans 6 years, reveals the complexity in and difficulties with diagnosis. Key features include the patient’s mother using advanced medical jargon to report multiple disconnected concerns and visits to numerous providers. As a result, the patient underwent many investigations which often revealed normal findings. FDIA was suspected by the paediatrician, especially following corroboration with the child’s day care and past primary health care provider. This case demonstrates the possible overlap in diagnoses, which are characterized by a lack of consistent presentation and deceitful caregivers, often complicated by true underlying illness. The authors use clinical experience and limited existing literature to empower paediatricians to confidently diagnose and report FDIA and MAL-BP to limit future harm to children.
From Research Partner to Embedded Criminologist: A Synthesized Taxonomy and Reflections From the Field
Authors: Guerette Rob T , Lee-Silcox Joelle , Przeszlowski Kimberly 
Published: June 2019

Abstract
Perhaps never before has the need for collaboration between academic researchers and police agencies been more salient. Technological advances have brought advanced hardware systems into daily policing operations, and analytical software and information systems have assembled massive volumes of data repositories. To produce usable knowledge from these information troves, advanced analytical knowledge has become necessary. At the same time, the evidence-based policy movement requires that police agencies equip themselves with the ability to interpret and produce evaluations of new policing initiatives using sound scientific evaluation methods, something which also requires specialized and advanced knowledge not usually housed within policing organizations. In response to these demands, researcher–police collaborations have become more prevalent. Yet, the specific nature of these researcher–police relationships can take many forms. This article synthesizes previous literature and develops a taxonomy for classifying researcher–police partnerships and discusses the experiences of moving from an external research partner to an embedded criminological ‘unit’ within the Miami Police Department.
Deformation of neutron stars due to poloidal magnetic fields
Authors: Yanase K , Yoshinaga N , Nakano E , Watanabe C 
Published: June 2019

Abstract
The mass–radius (MR) relation of deformed neutron stars in the axially symmetric poloidal magnetic field is calculated. The MR relation is obtained by solving the Hartle equations, whereas the one for spherical stars is obtained by the Tolman–Oppenheimer–Volkoff equations. The anisotropic effects of the poloidal magnetic fields are found to be non-negligible for a strong magnetic field more than $3\times10^{18}$ G at the center of a neutron star.
Changes in Public Opinion Polling: How Newspaper Polls Gained Political Clout
Authors: MAEDA Yukio 
Published: June 2019

Abstract
Approval in public opinion polling is an important resource for prime ministers in contemporary Japanese politics. Though it is widely agreed that cabinet approval ratings increased in political significance after the electoral reform and the restructuring of government agencies, little attention has been paid to the fact that public opinion polling in the mass media also experienced a transformation during the same period. This article surveys the history of public opinion polling since 1945. It argues that changes in survey methodology enabled newspapers to conduct and report opinion polling quickly and frequently, which has strengthened the link between approval ratings and ongoing political processes.
Enhancing the adoption of stockpiling tall fescue and managed grazing
Authors: Freeman Sharon , Poore Matthew , Shaeffer April 
Published: June 2019

Abstract
One of the primary goals of extension is to encourage and support adoption of improved technologies. Managed grazing and stockpiling forage are two such technologies. The goal of this project was to encourage adoption of these practices by providing on-farm demonstrations of the technologies. We also collected forage and soil data and held workshops at each of the demonstration sites. Host producers were selected, given a basic kit of temporary fencing supplies for use during the demonstration, and instructed on their proper use during the winter stockpiling season. Forage yield and quality data were collected and soil tests made to show the economic advantages of proper fertilization and grazing fresh forage in contrast to feeding stored forage and concentrate. The nutritive value of the forage stockpiled in September through November (67% total digestible nutrients [TDN] and 14% crude protein, CP) exceeded the needs of the cattle and was greater than the nutrient content of hay present on the farms (59% TDN and 11% CP, P &lt; 0.01). The mean quantity of available forage (2,856 ± 164 kg dry matter per hectare) provided an average of 260 (±81.8) standard cow (545 kg) grazing days per hectare of stockpiled forage. Taking into account the higher nutritive value of the fresh forage when compared with hay and the savings of time and equipment costs by grazing, we estimated that grazing stockpiled forage saved $1.28 per standard cow per day. The grazing management skills gained during this project and the temporary fencing technology were adopted by 93% of the demonstration farms that responded to our follow-up survey (78% of demonstration sites), and the area managed with these technologies increased on these sites more than 350%. Having the hosts share personal experiences played an important role in encouraging their peers to adopt the technologies.
Get Rich or Die Tryin’: Perceived Earnings, Perceived Mortality Rates, and Migration Decisions of Potential Work Migrants from Nepal
Authors: Shrestha Maheshwor 
Published: June 2019

Abstract
This article reports on a randomized field experiment in which potential work migrants from Nepal to Malaysia and the Persian Gulf countries are provided with information on wages and mortality incidences at their intended destinations. It is found that, particularly for the group of potential migrants without prior foreign migration experience, the information changes their expectations of earnings and mortality risks abroad, which further changes their actual migration decisions. Using the exogenous variation in expectations, it is estimated that the elasticity of migration with respect to mortality rate expectation is 0.8, and the elasticity of migration with respect to earnings expectation is 1.1.
S118 IMPACT OF PRE‐TRANSPLANT DONOR‐SPECIFIC ANTI‐HLA ANTIBODIES IN CORD BLOOD TRANSPLANTATION ON BEHALF OF THE TRANSPLANT COMPLICATIONS WORKING GROUP OF JSHCT
Authors: Fuji S. , Oshima K. , Ohashi K. , Sawa M. , Saito K. , Eto T. , Tanaka M. , Onizuka M. , Nakamae H. , Shiratori S. , Ozawa Y. , Hidaka M. , Nagamura‐Inoue T. , Tanaka H. , Fukuda T. , Ichinohe T. , Atsuta Y. , Ogata M. 
Published: June 2019

Background:Cord blood transplant (CBT) is an effective treatment for hematological diseases. Graft failure (GF) remains a major complication of CBT. Although presence of pre‐transplant donor‐specific anti‐HLA antibody (DSA) was reported to be associated with an increased risk of GF after CBT, data is still limited.Aims:In order to clarify the impact of pre‐transplant DSA, we conducted a retrospective analysis of recipients of CBT with pre‐transplant anti‐HLA antibody using the database of Japan Society for Hematopoietic Cell Transplantation (JSHCT).Methods:Data for recipients of CBT with pre‐transplant anti‐HLA antibody from 2010 to 2014 were obtained from the Transplant Registry Unified Management Program. Additional data such as detailed information about anti‐HLA antibody were collected. This study was approved by the institutional review boards of the JSHCT and Oita University.Results:In total, 343 patients who received CBT with detailed information about anti‐HLA antibody were included in the further analysis. Median age was 51 years (range, 0 to 71). Regarding DSA, 25 patients had mean fluorescence intensity (MFI) >1000 (DSA‐positive group) and 318 patients had MFI<1000 (DSA‐negative group). Cumulative incidence of neutrophil engraftment at 60 days after CBT was 75.7% (95% CI, 70.6–80.1) in the DSA‐negative group and 56.0% (95% CI, 34.1–73.1) in the DSA‐positive group (P = 0.03, Figure). Grouped according to the HLA class of DSA, cumulative incidence of neutrophil engraftment was 71.4% in patients with DSA against HLA class II antigen (n = 14), 44.4% in those with DSA against HLA class I antigen (n = 9), 0% in those with DSA against both HLA class I and class II antigens (n = 2). Stratified according to the achievement of neutrophil engraftment, the probabilities of overall survival at 1 year after CBT were 62.7% (95% CI, 56.2–68.5) in the engrafted patients and 19.5% (11.8–28.5) in the non‐engrafted patients (P < 0.001).Summary/Conclusion:Our study is a largest cohort of CBT recipients with pre‐transplant anti‐HLA antibody. Pre‐transplant DSA was associated with an increased risk of GF. The importance of target HLA antigen should be clarified in the future study.image