bluuebunny/crossref_metadata_2025_split huggingface dataset:
ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R
Authors: Paradis Emmanuel , Schliep Klaus 
Published: July 2018

Abstract

Summary
After more than fifteen years of existence, the R package ape has continuously grown its contents, and has been used by a growing community of users. The release of version 5.0 has marked a leap towards a modern software for evolutionary analyses. Efforts have been put to improve efficiency, flexibility, support for ‘big data’ (R’s long vectors), ease of use and quality check before a new release. These changes will hopefully make ape a useful software for the study of biodiversity and evolution in a context of increasing data quantity.

Availability and implementation
ape is distributed through the Comprehensive R Archive Network: http://cran.r-project.org/package=ape. Further information may be found at http://ape-package.ird.fr/.
Absolute quantitation of poly(R)-3-hydroxybutyric acid using spectrofluorometry in recombinant Escherichia coli
Authors: Rajankar Mayooreshwar P , Ravindranathan Sapna , Rajamohanan P R , Raghunathan Anu 
Published: July 2018

AbstractPoly(R)-3-hydroxybutyric acid (PHB) is a biodegradable natural polymer produced by microorganisms and plants under nitrogen deprivation and physiological stress. Metabolic engineering and synthetic biology approaches are underway to develop strains that can produce PHB and its co-polymers. One of the major limitations to the scaling and success of strain development for biosynthesis of PHB is the absence of fast, accurate, quantitative and scalable methods to estimate PHB in polymer producing cells. In this study, a Nile red-based spectrofluorometric method is developed for absolute quantitation of PHB in recombinant Escherichia coli. The method is a modification of an existing Nile red-based method currently only used for relative quantitation. The two added steps of sonication and ethanol extraction increase the dynamic range of the assay and limit of detection/quantitation. Sonication of PHB standards provides uniform distribution of surface area to volume ratios. This ensures reproducibility and accuracy (lower %relative error) of quantitative staining of granules by Nile red even in a higher dynamic concentration range of 125–1000 µg/ml. Ethanolic extraction of the PHB bound Nile red allows higher recovery and accurate absolute quantitation. To reproduce high recovery and ensure accuracy and precision of the analytical method directly using cells, a protein digestion step was added. This accounted for fluorescence from over-expressed protein and resulted in screening of nonproducers of PHB amongst samples. Thus, the method developed is rapid, accurate, and reproducible, requires low sample volumes and processing compared to other conventional methods. This method is scalable to other PHA’s and diverse plastics.
Hybrid principal components analysis for region-referenced longitudinal functional EEG data
Authors: Scheffler Aaron , Telesca Donatello , Li Qian , Sugar Catherine A , Distefano Charlotte , Jeste Shafali , Şentürk Damla 
Published: July 2018

Summary
Electroencephalography (EEG) data possess a complex structure that includes regional, functional, and longitudinal dimensions. Our motivating example is a word segmentation paradigm in which typically developing (TD) children, and children with autism spectrum disorder (ASD) were exposed to a continuous speech stream. For each subject, continuous EEG signals recorded at each electrode were divided into one-second segments and projected into the frequency domain via fast Fourier transform. Following a spectral principal components analysis, the resulting data consist of region-referenced principal power indexed regionally by scalp location, functionally across frequencies, and longitudinally by one-second segments. Standard EEG power analyses often collapse information across the longitudinal and functional dimensions by averaging power across segments and concentrating on specific frequency bands. We propose a hybrid principal components analysis for region-referenced longitudinal functional EEG data, which utilizes both vector and functional principal components analyses and does not collapse information along any of the three dimensions of the data. The proposed decomposition only assumes weak separability of the higher-dimensional covariance process and utilizes a product of one dimensional eigenvectors and eigenfunctions, obtained from the regional, functional, and longitudinal marginal covariances, to represent the observed data, providing a computationally feasible non-parametric approach. A mixed effects framework is proposed to estimate the model components coupled with a bootstrap test for group level inference, both geared towards sparse data applications. Analysis of the data from the word segmentation paradigm leads to valuable insights about group-region differences among the TD and verbal and minimally verbal children with ASD. Finite sample properties of the proposed estimation framework and bootstrap inference procedure are further studied via extensive simulations.
Learning to Read Increases the Informativeness of Distributed Ventral Temporal Responses
Authors: Nordt Marisa , Gomez Jesse , Natu Vaidehi , Jeska Brianna , Barnett Michael , Grill-Spector Kalanit 
Published: July 2018

Abstract
Becoming a proficient reader requires substantial learning over many years. However, it is unknown how learning to read affects development of distributed visual representations across human ventral temporal cortex (VTC). Using fMRI and a data-driven, computational approach, we quantified the development of distributed VTC responses to characters (pseudowords and numbers) versus other domains in children, preteens, and adults. Results reveal anatomical- and hemisphere-specific development. With development, distributed responses to words and characters became more distinctive and informative in lateral but not medial VTC, and in the left but not right hemisphere. While the development of voxels with both positive and negative preference to words affected distributed information, only development of voxels with positive preference to words (i.e., word-selective) was correlated with reading ability. These data show that developmental increases in informativeness of distributed left lateral VTC responses are related to proficient reading and have important implications for both developmental theories and for elucidating neural mechanisms of reading disabilities.
Exchange protein activated by cyclic-adenosine monophosphate (Epac) regulates atrial fibroblast function and controls cardiac remodelling
Authors: Surinkaew Sirirat , Aflaki Mona , Takawale Abhijit , Chen Yu , Qi Xiao-Yan , Gillis Marc-Antoine , Shi Yan-Fen , Tardif Jean-Claude , Chattipakorn Nipon , Nattel Stanley 
Published: July 2018

Abstract

Aims
Heart failure (HF) produces left atrial (LA)-selective fibrosis and promotes atrial fibrillation. HF also causes adrenergic activation, which contributes to remodelling via a variety of signalling molecules, including the exchange protein activated by cAMP (Epac). Here, we evaluate the effects of Epac1-signalling on LA fibroblast (FB) function and its potential role in HF-related atrial remodelling.

Methods and results
HF was induced in adult male mongrel dogs by ventricular tachypacing (VTP). Epac1-expression decreased in LA-FBs within 12 h (−3.9-fold) of VTP onset. The selective Epac activator, 8-pCPT (50 µM) reduced, whereas the Epac blocker ESI-09 (1 µM) enhanced, collagen expression in LA-FBs. Norepinephrine (1 µM) decreased Epac1-expression, an effect blocked by prazosin, and increased FB collagen production. The β-adrenoceptor (AR) agonist isoproterenol increased Epac1 expression, an effect antagonized by ICI (β2-AR-blocker), but not by CGP (β1-AR-blocker). β-AR-activation with isoproterenol decreased collagen expression, an effect mimicked by the β2-AR-agonist salbutamol and blocked by the Epac1-antagonist ESI-09. Transforming growth factor-β1, known to be activated in HF, suppressed Epac1 expression, an effect blocked by the Smad3-inhibitor SIS3. To evaluate effects on atrial fibrosis in vivo, mice subjected to myocardial infarction (MI) received the Epac-activator Sp-8-pCPT or vehicle for 2 weeks post-MI; Sp-8-pCPT diminished LA fibrosis and attenuated cardiac dysfunction.

Conclusions
HF reduces LA-FB Epac1 expression. Adrenergic activation has complex effects on FBs, with α-AR-activation suppressing Epac1-expression and increasing collagen expression, and β2-AR-activation having opposite effects. Epac1-activation reduces cardiac dysfunction and LA fibrosis post-MI. Thus, Epac1 signalling may be a novel target for the prevention of profibrillatory cardiac remodelling.
Chromosome-level reference genome of the Siamese fighting fish Betta splendens, a model species for the study of aggression
Authors: Fan Guangyi , Chan Judy , Ma Kailong , Yang Binrui , Zhang He , Yang Xianwei , Shi Chengcheng , Chun-Hin Law Henry , Ren Zhitao , Xu Qiwu , Liu Qun , Wang Jiahao , Chen Wenbin , Shao Libin , Gonçalves David , Ramos Andreia , Cardoso Sara D , Guo Min , Cai Jing , Xu Xun , Wang Jian , Yang Huanming , Liu Xin , Wang Yitao 
Published: July 2018

Abstract

Background
Siamese fighting fish Betta splendens are notorious for their aggressiveness and accordingly have been widely used to study aggression. However, the lack of a reference genome has, to date, limited the understanding of the genetic basis of aggression in this species. Here, we present the first reference genome assembly of the Siamese fighting fish.

Findings
Frist, we sequenced and de novo assembled a 465.24-Mb genome for the B. splendens variety Giant, with a weighted average (N50) scaffold size of 949.03 Kb and an N50 contig size of 19.01 Kb, covering 99.93% of the estimated genome size. To obtain a chromosome-level genome assembly, we constructed one Hi-C library and sequenced 75.24 Gb reads using the BGISEQ-500 platform. We anchored approximately 93% of the scaffold sequences into 21 chromosomes and evaluated the quality of our assembly using the high-contact frequency heat map and Benchmarking Universal Single-Copy Orthologs. We also performed comparative chromosome analyses between Oryzias latipes and B. splendens, revealing a chromosome conservation evolution in B. splendens. We predicted 23,981 genes assisted by RNA-sequencing data generated from brain, liver, muscle, and heart tissues of Giant and annotated 15% repetitive sequences in the genome. Additionally, we resequenced five other B. splendens varieties and detected ~3.4 M single-nucleotide variations and 27,305 insertions and deletions.

Conclusions
We provide the first chromosome-level genome for the Siamese fighting fish. The genome will lay a valuable foundation for future research on aggression in B. splendens.
Spatial and temporal dynamics of European hake (Merluccius merluccius) in the North Sea
Authors: Staby Arved , Skjæraasen Jon Egil , Geffen Audrey J , Howell Daniel 
Published: July 2018

Abstract
Catches of European hake (Merluccius merluccius) in the North Sea have increased substantially during the last decade, even though there is no directed commercial fishery of hake in this area. We analysed the spatial distributions of hake in the northern the parts of its range, (where it is less well-studied), using ICES international bottom trawl survey data from 1997 to 2015. We examine length-frequency distributions for (i) distinct modes enabling the assignment of fish into categories which likely corresponded to the ages 1, 2, and 3+ and (ii) patterns of seasonal spatial distribution for the different groups. Age categories 1 and 2 fish were most abundant in the northern North Sea, and appear to remain in the North Sea until 2 years of age, when they move into deeper waters. Their distribution has expanded into the western-central North Sea in the last decade. Age category 3+ fish were most abundant in the northern and central North Sea during summer, indicating a seasonal influx of large individuals into this area likely associated with spawning activity. The distribution of these older fish has gradually expanded westward in both seasons.
Topologically Nontrivial Counterexamples to Sard’s Theorem
Authors: Goldstein Paweł , Hajłasz Piotr , Pankka Pekka 
Published: July 2018

Abstract
We prove the following dichotomy: if $n=2,3$ and $f\in C^1(\mathbb{S}^{n+1},\mathbb{S}^n)$ is not homotopic to a constant map, then there is an open set $\Omega \subset \mathbb{S}^{n+1}$ such that $\operatorname{rank} df=n$ on $\Omega $ and $f(\Omega )$ is dense in $\mathbb{S}^n$, while for any $n\geq 4$, there is a map $f\in C^1(\mathbb{S}^{n+1},\mathbb{S}^n)$ that is not homotopic to a constant map and such that $\operatorname{rank} df&lt;n$ everywhere. The result in the case $n\geq 4$ answers a question of Larry Guth.
Nonlinear Weakly Sequentially Continuous Embeddings Between Banach Spaces
Authors: Braga B M 
Published: July 2018

Abstract
In these notes, we study nonlinear embeddings between Banach spaces that are also weakly sequentially continuous. In particular, our main result implies that if a Banach space $X$ coarsely (resp. uniformly) embeds into a Banach space $Y$ by a weakly sequentially continuous map, then every spreading model $(e_n)_n$ of a normalized weakly null sequence in $X$ satisfies $$ \|e_1+\ldots+e_k\|_{\overline{\delta}_Y}\lesssim\|e_1+\ldots+e_k\|_S,$$where $\overline{\delta }_Y$ is the modulus of asymptotic uniform convexity of $Y$. Among other results, we obtain Banach spaces $X$ and $Y$ so that $X$ coarsely (resp. uniformly) embeds into $Y$, but so that $X$ cannot be mapped into $Y$ by a weakly sequentially continuous coarse (resp. uniform) embedding.
Vanishing Estimates for Fully Bubbling Solutions of SU (n + 1) Toda Systems at a Singular Source
Authors: Zhang Lei 
Published: July 2018

AbstractFor Gauss curvature equation (or more general Toda systems) defined on 2D spaces, the vanishing rate of certain curvature functions on blowup points is a key estimate for numerous applications. However, if these equations have singular sources, very few vanishing estimates can be found. In this article we consider a Toda system with singular sources defined on a Riemann surface and we prove a very surprising vanishing estimates and a reflection phenomenon for certain functions involving the Gauss curvature.
Almost Finiteness for General Étale Groupoids and Its Applications to Stable Rank of Crossed Products
Authors: Suzuki Yuhei 
Published: July 2018

AbstractWe extend Matui’s notion of almost finiteness to general étale groupoids and show that the reduced groupoid C$^{\ast }$-algebras of minimal almost finite groupoids have stable rank 1. The proof follows a new strategy, which can be regarded as a local version of the large subalgebra argument. The following three are the main consequences of our result: (1) for any group of (local) subexponential growth and for any its minimal action admitting a totally disconnected free factor, the crossed product has stable rank 1; (2) any countable amenable group admits a minimal action on the Cantor set, all whose minimal extensions form the crossed product of stable rank 1; and (3) for any amenable group, the crossed product of the universal minimal action has stable rank 1.
Association Between Plasma Antibody Responses and Risk for Cryptococcus-Associated Immune Reconstitution Inflammatory Syndrome
Authors: Yoon Hyun Ah , Nakouzi Antonio , Chang Christina C , Kuniholm Mark H , Carreño Leandro J , Wang Tao , Ndung’u Thumbi , Lewin Sharon R , French Martyn A , Pirofski Liise-anne 
Published: July 2018

AbstractBackgroundInitiation of antiretroviral therapy (ART) in human immunodeficiency virus (HIV)-infected individuals with cryptococcal meningitis places them at risk for Cryptococcus-associated immune reconstitution inflammatory syndrome (C-IRIS). The relationship between antibody immunity and C-IRIS risk has not been investigated.MethodsWe compared plasma levels of immunoglobulins, C. neoformans glucuronoxylomannan (GXM) capsule-specific and laminarin (Lam)-binding IgM and IgG, and percentages of peripheral blood total and memory B cells between 27 HIV-infected patients with CM who developed C-IRIS and 63 who did not, and evaluated associations of these parameters with risk of C-IRIS.ResultsPrior to initiation of ART, plasma IgM, Lam-binding IgM (Lam-IgM), Lam-IgG, and GXM-IgM levels were significantly lower in patients who developed C-IRIS than those who did not. Multivariate analysis revealed significant inverse associations between C-IRIS and IgM (P = .0003), Lam-IgM (P = .0005), Lam-IgG (P = .002), and GXM-IgM (P = .002) independent of age, sex, HIV viral load, CD4+ T-cell count, and cerebrospinal fluid fungal burden. There were no associations between C-IRIS and total or memory B cells.DiscussionAntibody profiles that include plasma IgM, Lam-IgM, Lam-IgG, and/or GXM-IgM may have value in furthering our understanding of C-IRIS pathogenesis and hold promise as candidate biomarkers of C-IRIS risk.
Immunological association of inducible bronchus-associated lymphoid tissue organogenesis in Ag85B-rHPIV2 vaccine-induced anti-tuberculosis mucosal immune responses in mice
Authors: Nagatake Takahiro , Suzuki Hidehiko , Hirata So-ichiro , Matsumoto Naomi , Wada Yasuko , Morimoto Sakiko , Nasu Ayaka , Shimojou Michiko , Kawano Mitsuo , Ogami Kentaro , Tsujimura Yusuke , Kuroda Etsushi , Iijima Norifumi , Hosomi Koji , Ishii Ken J , Nosaka Tetsuya , Yasutomi Yasuhiro , Kunisawa Jun 
Published: July 2018

Abstract
We previously reported that Ag85B-expressing human parainfluenza type 2 virus (Ag85B-rHPIV2) was effective as a nasal vaccine against tuberculosis in mice; however, the mechanism by which it induces an immune response remains to be investigated. In the present study, we found that organogenesis of inducible bronchus-associated lymphoid tissue (iBALT) played a role in the induction of antigen-specific T cells and IgA antibody responses in the lung of mice intra-nasally administered Ag85B-rHPIV2. We found that expression of Ag85B was dispensable for the development of iBALT, suggesting that HPIV2 acted as an iBALT-inducing vector. When iBALT organogenesis was disrupted in Ag85B-rHPIV2-immunized mice, either by neutralization of the lymphotoxin pathway or depletion of CD11b+ cells, Ag85B-specific immune responses (i.e. IFN γ-producing T cells and IgA antibody) were diminished in the lung. Furthermore, we found that immunization with Ag85B-rHPIV2 induced neutrophil and eosinophil infiltration temporally after the immunization in the lung. Thus, our results show that iBALT organogenesis contributes to the induction of antigen-specific immune responses by Ag85B-rHPIV2 and that Ag85B-rHPIV2 provokes its immune responses without inducing long-lasting inflammation.
The prospects of human rights in US–China relations: a constructivist understanding
Authors: Kim Hun Joon 
Published: July 2018

AbstractWhat are the prospects of U.S.-China relations in the area of human rights? Skeptics maintain that human rights is no longer an issue between the United States and China. A traditional understanding of U.S.–China relations ignores the role of norms, while the constructivist perspective recognizes their independent effects. This paper links the traditional understanding of power politics between the United States and China with the study of constructivist norm research. The three findings of constructivist norm theories are relevant and applied to predict the status of human rights in U.S.-China relations: the historical construction of norms, the long-term and multifaceted effects of norms, and the persistence of norms. Based on these theoretical predictions, it is expected that, although convergence is not completely impossible, the past dynamic of competition and confrontation will continue and human rights will still be a contentious issue in U.S.-China relations.
Chinese views of the United States: evidence from Weibo
Authors: Guan Yichen , Tingley Dustin , Romney David , Jamal Amaney , Keohane Robert 
Published: July 2018

Abstract
We study Chinese attitudes toward the United States, and secondarily toward Japan, Russia, and Vietnam, by analyzing social media discourse on the Chinese social media site, Weibo. We focus separately on a general analysis of attitudes and on Chinese responses to specific international events involving the United States. In general, we find that Chinese netizens are much more interested in US politics than US society. Their views of the United States are characterized by deep ambivalence; they have remarkably favorable attitudes toward many aspects of US influence, whether economic, political, intellectual, or cultural. Attitudes toward the United States become negative when the focus turns to US foreign policy – actions that Chinese netizens view as antithetical to Chinese interests. On the contrary, attitudes toward Japan, Russia, and Vietnam vary a great deal from one another. The contrast between these differentiated Chinese views toward the United States and other countries, on the one hand, and the predominant anti-Americanism in the Middle East, on the other, is striking.
A case study evaluating the portability of an executable computable phenotype algorithm across multiple institutions and electronic health record environments
Authors: Pacheco Jennifer A , Rasmussen Luke V , Kiefer Richard C , Campion Thomas R , Speltz Peter , Carroll Robert J , Stallings Sarah C , Mo Huan , Ahuja Monika , Jiang Guoqian , LaRose Eric R , Peissig Peggy L , Shang Ning , Benoit Barbara , Gainer Vivian S , Borthwick Kenneth , Jackson Kathryn L , Sharma Ambrish , Wu Andy Yizhou , Kho Abel N , Roden Dan M , Pathak Jyotishman , Denny Joshua C , Thompson William K 
Published: July 2018

Abstract
Electronic health record (EHR) algorithms for defining patient cohorts are commonly shared as free-text descriptions that require human intervention both to interpret and implement. We developed the Phenotype Execution and Modeling Architecture (PhEMA, http://projectphema.org) to author and execute standardized computable phenotype algorithms. With PhEMA, we converted an algorithm for benign prostatic hyperplasia, developed for the electronic Medical Records and Genomics network (eMERGE), into a standards-based computable format. Eight sites (7 within eMERGE) received the computable algorithm, and 6 successfully executed it against local data warehouses and/or i2b2 instances. Blinded random chart review of cases selected by the computable algorithm shows PPV ≥90%, and 3 out of 5 sites had &gt;90% overlap of selected cases when comparing the computable algorithm to their original eMERGE implementation. This case study demonstrates potential use of PhEMA computable representations to automate phenotyping across different EHR systems, but also highlights some ongoing challenges.