bluuebunny/crossref_metadata_2025_split huggingface dataset:
Testing modified gravity with wide binaries in Gaia DR2
Authors: Pittordis Charalambos , Sutherland Will 
Published: July 2019

ABSTRACT
Several recent studies have shown that very wide binary stars can potentially provide an interesting test for modified-gravity theories which attempt to emulate dark matter; these systems should be almost Newtonian according to standard dark-matter theories, while the predictions for MOND-like theories are distinctly different, if the various observational issues can be overcome. Here we explore an observational application of the test from the recent Gaia DR2 data release: we select a large sample of ∼24 000 candidate wide binary stars with distance $\lt 200 \, {\rm pc}$ and magnitudes G < 16 from Gaia DR2, and estimated component masses using a main-sequence mass–luminosity relation. We then compare the frequency distribution of pairwise relative projected velocity (relative to circular-orbit value) as a function of projected separation; these distributions show a clear peak at a value close to Newtonian expectations, along with a long ‘tail’ which extends to much larger velocity ratios; the ‘tail’ is considerably more numerous than in control samples constructed from DR2 with randomized positions, so its origin is unclear. Comparing the velocity histograms with simulated data, we conclude that MOND-like theories without an external field effect (ExFE) are strongly inconsistent with the observed data since they predict a peak-shift in clear disagreement with the data; testing MOND-like theories with an ExFE is not decisive at present, but has good prospects to become decisive in future with improved modelling or understanding of the high-velocity tail, and additional spectroscopic data.
NGC 326: X-shaped no more
Authors: Hardcastle M J , Croston J H , Shimwell T W , Tasse C , Gürkan G , Morganti R , Murgia M , Röttgering H J A , van Weeren R J , Williams W L 
Published: July 2019

ABSTRACT
We present new 144-MHz Low-Frequency Array (LOFAR) observations of the prototypical ‘X-shaped’ radio galaxy NGC 326, which show that the formerly known wings of the radio lobes extend smoothly into a large-scale, complex radio structure. We argue that this structure is most likely the result of hydrodynamical effects in an ongoing group or cluster merger, for which pre-existing X-ray and optical data provide independent evidence. The large-scale radio structure is hard to explain purely in terms of jet reorientation due to the merger of binary black holes, a previously proposed explanation for the inner structure of NGC 326. For this reason, we suggest that the simplest model is one in which the merger-related hydrodynamical processes account for all the source structure, though we do not rule out the possibility that a black hole merger has occurred. Inference of the black hole–black hole merger rate from observations of X-shaped sources should be carried out with caution in the absence of deep, sensitive low-frequency observations. Some X-shaped sources may be signposts of cluster merger activity, and it would be useful to investigate the environments of these objects more generally.
Impact of galaxy mergers on the colours of cluster galaxies
Authors: Oh Sree , Kim Keunho , Lee Joon Hyeop , Kim Minjin , Sheen Yun-Kyeong , Rhee Jinsu , Ree Chang H , Jeong Hyunjin , Ho Luis C , Kyeong Jaemann , Sung Eon-Chang , Park Byeong-Gon , Yi Sukyoung K 
Published: July 2019

ABSTRACT
We examine the ultraviolet and optical colours of 906 cluster galaxies from the KASI-Yonsei Deep Imaging Survey of Clusters (KYDISC). The sample has been divided into two categories, morphologically disturbed and undisturbed galaxies, based on the visual signatures related to recent mergers. We find that galaxies with signatures of recent mergers show significantly bluer colours than undisturbed galaxies. Disturbed galaxies populate more on the cluster outskirts, suggesting recent accretion into the cluster environment, which implies that disturbed galaxies can be less influenced by the environmental quenching process and remain blue. However, we still detect bluer colours of disturbed galaxies in all locations (cluster core and outskirts) for the fixed morphology, which is difficult to understand just considering the difference in time since infall into a cluster. Moreover, blue disturbed galaxies show features seemingly related to recent star formation. Therefore, we suspect that mergers make disturbed galaxies keep their blue colour longer than undisturbed galaxies under the effect of the environmental quenching through either merger-induced star formation or central gas concentration which is less vulnerable for gas stripping.
Do the planets in the HD 34445 system really exist?
Authors: Georgakarakos Nikolaos , Dobbs-Dixon Ian 
Published: July 2019

ABSTRACT
In 2010 the first planet was discovered around star HD 34445. Recently, another five planets were announced orbiting the same star. It is a rather dense multiplanet system with some of its planets having separations of fractions of an au and minimum masses ranging from Neptune to sub-Jupiter ones. Given the number of planets and the various uncertainties in their masses and orbital elements, the HD 34445 planetary system is quite interesting as there is the potential for mean motion and secular resonances that could render the outcome of its dynamical evolution and fate an open question. In this paper we investigate the dynamical stability of the six-planet system in order to check the validity of the orbital solution acquired. This is achieved by a series of numerical experiments, where the dynamical evolution of the system is tested on different time-scales. We vary the orbital elements and masses of the system within the error ranges provided. We find that for a large area of the parameter space we can produce stable configurations and therefore conclude it is very likely that the HD 34445 planetary system is real. Some discussion about the potential habitability of the system is also done.
Speciation in Howea Palms Occurred in Sympatry, Was Preceded by Ancestral Admixture, and Was Associated with Edaphic and Phenological Adaptation
Authors: Osborne Owen G , Ciezarek Adam , Wilson Trevor , Crayn Darren , Hutton Ian , Baker William J , Turnbull Colin G N , Savolainen Vincent 
Published: July 2019

AbstractHowea palms are viewed as one of the most clear-cut cases of speciation in sympatry. The sister species Howea belmoreana and H. forsteriana are endemic to the oceanic Lord Howe Island, Australia, where they have overlapping distributions and are reproductively isolated mainly by flowering time differences. However, the potential role of introgression from Australian mainland relatives had not previously been investigated, a process that has recently put other examples of sympatric speciation into question. Furthermore, the drivers of flowering time-based reproductive isolation remain unclear. We sequenced an RNA-seq data set that comprehensively sampled Howea and their closest mainland relatives (Linospadix, Laccospadix), and collected detailed soil chemistry data on Lord Howe Island to evaluate whether secondary gene flow had taken place and to examine the role of soil preference in speciation. D-statistics analyses strongly support a scenario whereby ancestral Howea hybridized frequently with its mainland relatives, but this only occurred prior to speciation. Expression analysis, population genetic and phylogenetic tests of selection, identified several flowering time genes with evidence of adaptive divergence between the Howea species. We found expression plasticity in flowering time genes in response to soil chemistry as well as adaptive expression and sequence divergence in genes pleiotropically linked to soil adaptation and flowering time. Ancestral hybridization may have provided the genetic diversity that promoted their subsequent adaptive divergence and speciation, a process that may be common for rapid ecological speciation.
Metabolic alterations of uterine grafts after extended cold ischemic storage: experimental study in ewes
Authors: Tholance Yannick , Tricard Jeremy , Chianea Thierry , Marquet Pierre , Ponsonnard Sébastien , Sturtz Franck , Piccardo Alessandro , Gauthier Tristan 
Published: July 2019

Abstract
Uterine transplantation from a deceased donor could become an available option for widely treating uterine infertility. However, this procedure requires more precise knowledge about the graft’s tolerance to extended cold ischemia. Here, we sought to assess the uterine metabolic alterations after extended cold ischemic storage in a model of auto-transplantation in ewe. A total of 14 uterine auto-transplantations were performed, divided into 2 groups: 7 after 3 h of cold ischemia time (CIT) and 7 after 24 h. Venous uterine blood was collected before uterus retrieval and during reperfusion (30, 60 and 90 min); thereafter, blood gases, lactate, glucose and amino acids (AAs) were analyzed. Apoptosis analyses were performed before uterus retrieval and following reperfusion in uterus biopsies. A total of 12 uterine auto-transplantations were successfully performed and 7 ewes were alive ≥8 days after transplantation. After reperfusion, a decrease in pH, a rise of lactate and lactate/glucose ratio and a delayed decrease of pO2 were found in the 3 h CIT group. No significant variation of these parameters was observed in the 24 h CIT group. Significant decreases of AAs were observed during reperfusion and these decreases were more pronounced and concerned a larger number of compounds in the 24 h CIT group than in the 3 h CIT group. There was no significant uterine apoptotic signal in either group. Overall, these results suggest that extended CIT storage delayed restoration of aerobic glycolysis and induced an increase in AA requirements of the uterus after reperfusion. However, this biochemical alteration did not reduce success rate for uterine transplantation.
A role for the Saccharomyces cerevisiae ABCF protein New1 in translation termination/recycling
Authors: Kasari Villu , Pochopien Agnieszka A , Margus Tõnu , Murina Victoriia , Turnbull Kathryn , Zhou Yang , Nissan Tracy , Graf Michael , Nováček Jiří , Atkinson Gemma C , Johansson Marcus J O , Wilson Daniel N , Hauryliuk Vasili 
Published: July 2019

AbstractTranslation is controlled by numerous accessory proteins and translation factors. In the yeast Saccharomyces cerevisiae, translation elongation requires an essential elongation factor, the ABCF ATPase eEF3. A closely related protein, New1, is encoded by a non-essential gene with cold sensitivity and ribosome assembly defect knock-out phenotypes. Since the exact molecular function of New1 is unknown, it is unclear if the ribosome assembly defect is direct, i.e. New1 is a bona fide assembly factor, or indirect, for instance due to a defect in protein synthesis. To investigate this, we employed yeast genetics, cryo-electron microscopy (cryo-EM) and ribosome profiling (Ribo-Seq) to interrogate the molecular function of New1. Overexpression of New1 rescues the inviability of a yeast strain lacking the otherwise strictly essential translation factor eEF3. The structure of the ATPase-deficient (EQ2) New1 mutant locked on the 80S ribosome reveals that New1 binds analogously to the ribosome as eEF3. Finally, Ribo-Seq analysis revealed that loss of New1 leads to ribosome queuing upstream of 3′-terminal lysine and arginine codons, including those genes encoding proteins of the cytoplasmic translational machinery. Our results suggest that New1 is a translation factor that fine-tunes the efficiency of translation termination or ribosome recycling.
DNA sequence models of genome-wide Drosophila melanogaster Polycomb binding sites improve generalization to independent Polycomb Response Elements
Authors: Bredesen Bjørn André , Rehmsmeier Marc 
Published: July 2019

AbstractPolycomb Response Elements (PREs) are cis-regulatory DNA elements that maintain gene transcription states through DNA replication and mitosis. PREs have little sequence similarity, but are enriched in a number of sequence motifs. Previous methods for modelling Drosophila melanogaster PRE sequences (PREdictor and EpiPredictor) have used a set of 7 motifs and a training set of 12 PREs and 16-23 non-PREs. Advances in experimental methods for mapping chromatin binding factors and modifications has led to the publication of several genome-wide sets of Polycomb targets. In addition to the seven motifs previously used, PREs are enriched in the GTGT motif, recently associated with the sequence-specific DNA binding protein Combgap. We investigated whether models trained on genome-wide Polycomb sites generalize to independent PREs when trained with control sequences generated by naive PRE models and including the GTGT motif. We also developed a new PRE predictor: SVM-MOCCA. Training PRE predictors with genome-wide experimental data improves generalization to independent data, and SVM-MOCCA predicts the majority of PREs in three independent experimental sets. We present 2908 candidate PREs enriched in sequence and chromatin signatures. 2412 of these are also enriched in H3K4me1, a mark of Trithorax activated chromatin, suggesting that PREs/TREs have a common sequence code.
DNA complexes with human apurinic/apyrimidinic endonuclease 1: structural insights revealed by pulsed dipolar EPR with orthogonal spin labeling
Authors: Krumkacheva Olesya A , Shevelev Georgiy Yu , Lomzov Alexander A , Dyrkheeva Nadezhda S , Kuzhelev Andrey A , Koval Vladimir V , Tormyshev Victor M , Polienko Yuliya F , Fedin Matvey V , Pyshnyi Dmitrii V , Lavrik Olga I , Bagryanskaya Elena G 
Published: July 2019

AbstractA DNA molecule is under continuous influence of endogenous and exogenous damaging factors, which produce a variety of DNA lesions. Apurinic/apyrimidinic sites (abasic or AP sites) are among the most common DNA lesions. In this work, we applied pulse dipolar electron paramagnetic resonance (EPR) spectroscopy in combination with molecular dynamics (MD) simulations to investigate in-depth conformational changes in DNA containing an AP site and in a complex of this DNA with AP endonuclease 1 (APE1). For this purpose, triarylmethyl (TAM)-based spin labels were attached to the 5′ ends of an oligonucleotide duplex, and nitroxide spin labels were introduced into APE1. In this way, we created a system that enabled monitoring the conformational changes of the main APE1 substrate by EPR. In addition, we were able to trace substrate-to-product transformation in this system. The use of different (orthogonal) spin labels in the enzyme and in the DNA substrate has a crucial advantage allowing for detailed investigation of local damage and conformational changes in AP-DNA alone and in its complex with APE1.
An expanded landscape of human long noncoding RNA
Authors: Jiang Shuai , Cheng Si-Jin , Ren Li-Chen , Wang Qian , Kang Yu-Jian , Ding Yang , Hou Mei , Yang Xiao-Xu , Lin Yuan , Liang Nan , Gao Ge 
Published: July 2019

Abstract
Long noncoding RNAs (lncRNAs) are emerging as key regulators of multiple essential biological processes involved in physiology and pathology. By analyzing the largest compendium of 14,166 samples from normal and tumor tissues, we significantly expand the landscape of human long noncoding RNA with a high-quality atlas: RefLnc (Reference catalog of LncRNA). Powered by comprehensive annotation across multiple sources, RefLnc helps to pinpoint 275 novel intergenic lncRNAs correlated with sex, age or race as well as 369 novel ones associated with patient survival, clinical stage, tumor metastasis or recurrence. Integrated in a user-friendly online portal, the expanded catalog of human lncRNAs provides a valuable resource for investigating lncRNA function in both human biology and cancer development.
Nonparametric expression analysis using inferential replicate counts
Authors: Zhu Anqi , Srivastava Avi , Ibrahim Joseph G , Patro Rob , Love Michael I 
Published: July 2019

AbstractA primary challenge in the analysis of RNA-seq data is to identify differentially expressed genes or transcripts while controlling for technical biases. Ideally, a statistical testing procedure should incorporate the inherent uncertainty of the abundance estimates arising from the quantification step. Most popular methods for RNA-seq differential expression analysis fit a parametric model to the counts for each gene or transcript, and a subset of methods can incorporate uncertainty. Previous work has shown that nonparametric models for RNA-seq differential expression may have better control of the false discovery rate, and adapt well to new data types without requiring reformulation of a parametric model. Existing nonparametric models do not take into account inferential uncertainty, leading to an inflated false discovery rate, in particular at the transcript level. We propose a nonparametric model for differential expression analysis using inferential replicate counts, extending the existing SAMseq method to account for inferential uncertainty. We compare our method, Swish, with popular differential expression analysis methods. Swish has improved control of the false discovery rate, in particular for transcripts with high inferential uncertainty. We apply Swish to a single-cell RNA-seq dataset, assessing differential expression between sub-populations of cells, and compare its performance to the Wilcoxon test.
Evaluating the pathways linking complementary feeding practices to obesity in early life
Authors: Thompson Amanda L 
Published: July 2019

AbstractThe complementary feeding period, when solids and liquids other than breast milk and formula are added to the infant diet, is an important development window shaping infant growth and weight gain, metabolic development, and lifelong eating practices. Yet, relatively little is known about how the timing and types of foods offered to infants at this stage may shape their growth and subsequent risk of developing obesity. This narrative review describes the existing literature on complementary feeding practices, discusses potential biological and behavioral pathways linking complementary feeding practices to the development of obesity, and offers potential avenues for intervention. While further research is needed to more fully understand optimal complementary feeding practices, existing evidence supports the importance of healthful early feeding practices in the physiological and behavioral regulation of growth and metabolism and the need for early intervention to prevent the development of obesity.
Ventricular Catheter Tract Hemorrhage as a Risk Factor for Ventriculostomy-Related Infection
Authors: Kim Julie , Lee James , Feng Rui , Chartrain Alexander , Sobotka Stanislaw , Griffiths Stephen , Weiss Nirit , Dangayach Neha , Bederson Joshua , Mayer Stephan A , Gordon Errol 
Published: July 2019

Abstract

BACKGROUND
Ventriculostomy-related infection (VRI) is a feared complication of external ventricular drain (EVD) placement. Although many contributing factors to VRI have been examined, little is known whether there is an association between ventriculostomy-related catheter tract hemorrhage (VCTH) and VRI.

OBJECTIVE
To evaluate risk factors for VRI and assess possible correlations with VCTH.

METHODS
We performed a retrospective analysis of patients with EVD placement in a neurocritical care unit between 2011 and 2015. VRI was defined as clinical signs of infection with a positive cerebrospinal fluid gram stain and isolation of cerebrospinal fluid culture. VCTH was diagnosed by computed tomography immediately after EVD insertion.

RESULTS
A total of 247 patients with EVD were identified during the 5-yr study period. An association between VCTH and gram-negative VRI was identified (P = .02). Ten percent (25 of 247 patients) developed a VRI, and 7% (18 of 247 patients) had a VCTH. Of the 25 patients with VRI, 20% (n = 5) had a VCTH, compared to 6% (n = 13) of 222 patients who had an EVD placed but did not develop VRI. There were no significant differences in demographic and clinical factors except for multiple EVD insertions (P < .00001), EVD duration (P < .001), and hospital length of stay (P < .001).

CONCLUSION
VCTH is a potentially significant risk factor for VRI. Further analysis will be needed to confirm the strength of this association, and to delineate the possible mechanisms by which tract hemorrhage may serve as a nidus for bacterial penetration into the central nervous system.
Repeat Resection of a Cavernous Malformation of the Optic Nerve/Chiasm via a Frontotemporal Approach: 2-Dimensional Operative Video
Authors: Gozal Yair M , Alzhrani Gmaan , Abou-Al-Shaar Hussam , Couldwell William T 
Published: July 2019

Abstract
Cavernous malformations are benign vascular lesions that can arise throughout the central nervous system. The occurrence of a cavernous malformation within the optic nerve or chiasm, however, is extremely uncommon. The case described in this video involved a 36-yr-old woman who presented 3 mo after undergoing a left frontotemporal craniotomy for resection of an optic nerve cavernous malformation. She had initially presented to an outside hospital with vision loss, and the left optic nerve lesion was identified and resected. Although her vision had reportedly improved slightly postoperatively, she awoke 3 mo later with bilateral subjective blurriness and new visual field deficits. Magnetic resonance imaging revealed enlargement of the left optic apparatus hemorrhagic lesion, corresponding to residual cavernous malformation. Given the recurrence of hemorrhage and the associated visual symptoms, the patient underwent a redo left frontotemporal craniotomy for resection of the optic nerve and chiasmal lesion. Histopathologic evaluation revealed thick-walled vessels with focal intervening glial tissue, an absence of neoplastic cells, and hemorrhage, consistent with a cavernous malformation. The patient tolerated the procedure well. Postoperatively, she experienced immediate amelioration in her visual symptoms. She was discharged home on postoperative day 3, and her bitemporal visual field deficit continued to progressively improve through her last ophthalmologic appointment 14 mo after surgery. Postoperative and subsequent surveillance neuroimaging demonstrated complete resection of the cavernous malformation without evidence of recurrence. This case demonstrates the techniques utilized to ensure complete resection of the malformation in this very eloquent region. The patient provided consent for publication.
First detection of PSR B1259−63/LS 2883 in the millimeter and submillimeter wavelengths with ALMA
Authors: Fujita Yutaka , Kawachi Akiko , Akahori Takuya , Nagai Hiroshi , Yamaguchi Masaki 
Published: July 2019

Abstract
We report Atacama Large Millimeter/submillimeter Array (ALMA) observations of the binary system containing the pulsar PSR B1259−63 orbiting around a Be star LS 2883 after the 2017 periastron passage. We detected radio continuum emission from the binary system in the millimeter/submillimeter wavelengths for the first time. At Band 3 (97 GHz), the flux 84 days after the periastron is almost the same as that 71 days after the periastron. Although the binary system showed intense GeV gamma-ray flares during our observations, the Band 3 flux did not indicate any time correlation with them. The Band 3 fluxes are consistent with an extrapolation of the radio spectrum at lower frequencies. Assuming that it is synchrotron emission, we constrain magnetic fields (≲0.6 G) and the high-energy cutoff of the electrons (γ ≳ 360). The flux at Band 7 (343 GHz) 69 days after the periastron shows a significant excess from the extrapolation of the radio spectrum at lower frequencies. The flux may be associated with the circumstellar disk around the Be star. We also present the results of Australian Telescope Compact Array (ATCA) observations at 94 GHz for the 2014 periastron passage, which show that the radio spectrum was relatively soft when the pulsar passed the disk.