bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phase‐Modulated Interferometry, Spectroscopy, and Refractometry using Entangled Photon Pairs
Authors: Lavoie Jonathan , Landes Tiemo , Tamimi Amr , Smith Brian J. , Marcus Andrew H. , Raymer Michael G. 
Published: January 2020

AbstractThe authors demonstrate a form of two‐photon‐counting interferometry by measuring the coincidence counts between single‐photon‐counting detectors at an output port of a Mach–Zehnder Interferometer (MZI) following injection of broad‐band time‐frequency‐entangled photon pairs (EPP) generated from collinear spontaneous parametric down conversion into a single input port. Spectroscopy and refractometry are performed on a sample inserted in one internal path of the MZI by scanning the other path in length, which acquires phase and amplitude information about the sample's linear response. Phase modulation and lock‐in detection are introduced to increase detection signal‐to‐noise ratio and implement a “down‐sampling” technique for scanning the interferometer delay, which reduces the sampling requirements needed to reproduce fully the temporal interference pattern. The phase‐modulation technique also allows the contributions of various quantum‐state pathways leading to the final detection outcomes to be extracted individually. Feynman diagrams frequently used in the context of molecular spectroscopy are used to describe the interferences resulting from the coherence properties of time‐frequency EPPs passing through the MZI. These results are an important step toward the implementation of a proposed method for molecular spectroscopy—quantum‐light‐enhanced 2D spectroscopy.
Photocontrolled Hierarchical Self‐Assembly of Anisotropic Micropatterns of Nanofibers onto Isotropic Surfaces
Authors: de Vet Christiaan , Gartzia‐Rivero Leire , Schäfer Philip , Raffy Guillaume , Del Guerzo André 
Published: January 2020

AbstractHierarchical self‐assembly is achieved using a visible light triggered photoreaction. A pro‐gelator, α‐diketone‐2,3‐didecyloxyanthracene, is photoconverted into a low molecular weight gelator, 2,3‐didecyloxyanthracene (DDOA), that self‐assembles into nanofibers. Spatial confinement and patterns of these nanofibers onto a surface are achieved by localizing initial nucleation with a focused laser and photogenerate subsequent fiber growth with the laser or gentler wide‐field irradiation. Remarkably, collective growth of nanofibers results in anisotropic micropatterns with orientation factors (OF) reaching 79%, resulting in collective emission of linearly polarized light. The OF, distance of collective growth and fiber density, are controlled by the photoirradiation conditions and the balance of interactions between DDOA aggregates and the glass surface. An unprecedented juxtaposition of orthogonally oriented nanofiber patterns on an isotropic surface is achieved with individual control of the fibers' main direction. In perspective, this photochemical method can be extended to a large variety of self‐assembling molecules.
Understanding and targeting the disease‐related RNA binding protein human antigen R (HuR)
Authors: Schultz Christopher W. , Preet Ranjan , Dhir Teena , Dixon Dan A. , Brody Jonathan R. 
Published: January 2020

AbstractAltered gene expression is a characteristic feature of many disease states such as tumorigenesis, and in most cancers, it facilitates cancer cell survival and adaptation. Alterations in global gene expression are strongly impacted by post‐transcriptional gene regulation. The RNA binding protein (RBP) HuR (ELAVL1) is an established regulator of post‐transcriptional gene regulation and is overexpressed in most human cancers. In many cancerous settings, HuR is not only overexpressed, but it is “overactive” as denoted by increased subcellular localization within the cytoplasm. This dysregulation of HuR expression and cytoplasmic localization allows HuR to stabilize and increase the translation of various prosurvival messenger RNA (mRNAs) involved in the pathogenesis of numerous cancers and various diseases. Based on almost 20 years of work, HuR is now recognized as a therapeutic target. Herein, we will review the role HuR plays in the pathophysiology of different diseases and ongoing therapeutic strategies to target HuR. We will focus on three ongoing‐targeted strategies: (1) inhibiting HuR's translocation from the nucleus to the cytoplasm; (2) inhibiting the ability of HuR to bind target RNA; and (3) silencing HuR expression levels. In an oncologic setting, HuR has been demonstrated to be critical for a cancer cell's ability to survive a variety of cancer relevant stressors (including drugs and elements of the tumor microenvironment) and targeting this protein has been shown to sensitize cancer cells further to insult. We strongly believe that targeting HuR could be a powerful therapeutic target to treat different diseases, particularly cancer, in the near future.This article is categorized under:
RNA in Disease and Development > RNA in Disease
NRA Turnover and Surveillance > Regulation of RNA Stability
Translation > Translation Regulation
Processing and Analyzing Multiple Genomes Alignments with MafFilter
Authors: Dutheil Julien Y. 
Published: January 2020

AbstractAs the number of available genome sequences from both closely related species and individuals within species increased, theoretical and methodological convergences between the fields of phylogenomics and population genomics emerged. Population genomics typically focuses on the analysis of variants, while phylogenomics heavily relies on genome alignments. However, these are playing an increasingly important role in studies at the population level. Multiple genome alignments of individuals are used when structural variation is of primary interest and when genome architecture permits to assemble de novo genome sequences. Here I describe MafFilter, a command-line-driven program allowing to process genome alignments in the Multiple Alignment Format (MAF). Using concrete examples based on publicly available datasets, I demonstrate how MafFilter can be used to develop efficient and reproducible pipelines with quality assurance for downstream analyses. I further show how MafFilter can be used to perform both basic and advanced population genomic analyses in order to infer the patterns of nucleotide diversity along genomes.
Exploring Population Structure with Admixture Models and Principal Component Analysis
Authors: Liu Chi-Chun , Shringarpure Suyash , Lange Kenneth , Novembre John 
Published: January 2020

AbstractPopulation structure is a commonplace feature of genetic variation data, and it has importance in numerous application areas, including evolutionary genetics, conservation genetics, and human genetics. Understanding the structure in a sample is necessary before more sophisticated analyses are undertaken. Here we provide a protocol for running principal component analysis (PCA) and admixture proportion inference—two of the most commonly used approaches in describing population structure. Along with hands-on examples with CEPH-Human Genome Diversity Panel and pragmatic caveats, readers will learn to analyze and visualize population structure on their own data.
Oronce Fine and Sacrobosco: From the Edition of the Tractatus de sphaera (1516) to the Cosmographia (1532)
Authors: Axworthy Angela 
Published: January 2020

AbstractThis paper considers the contribution of the French mathematician Oronce Fine to the diffusion and transformation of Johannes de Sacrobosco’sTractatus de sphaeraby considering his 1516 edition of theSphaeraand hisCosmographia, sive sphaera mundi(inProtomathesis, 1532). The article first describes Fine’s life and career, as well as his work as editor of theSphaera. In a second part, it considers what Fine, in theCosmographia, has drawn and left aside from theSphaera, revealing the consequent transformations to the teaching of Sacrobosco’s theory of the sphere and its adaptation to the cultural and intellectual environment in which Fine evolved. A last part considers the treatment, in theCosmographia, of the cosmological representations transmitted by Sacrobosco and by subsequent interpreters of Ptolemaic astronomy concerning the number of celestial spheres and its relation to judicial astrology.
Fazit: Klappe zu, Affe(kt) tot?
Authors: Shah Mira 
Published: January 2020

ZusammenfassungDie filmischen Bearbeitungen von Pierre Boulles La planète des Singes fallen durch ihre kreativen Eigenarbeiten und Ergänzungen auf. Häufig geht es dabei darum, die von Ulysse Mérou thematisierte Wissenslücke zu füllen: Wie kam es zum Niedergang der Menschheit und dem Aufstieg der Affenheit? Ob Atomkrieg, Sklaverei, genetische Manipulation und/oder Virus, die Bearbeitungen des von Boulle initiierten Stoffes bemühen sich redlich, diesen auszumalen – daher ist es umso auffälliger, welche Elemente des Urnarrativs sie aussparen: Hartnäckig haben die diversen Verfilmungen und Bearbeitungen ein wesentliches Konstruktionselement des Romans ausgeblendet: Ulysse Mérous Bericht von seiner Zeit auf dem Planeten der Affen erreicht uns nur, weil er im Roman bereits Leser/innen hat. Wie wir aus einer Rahmenerzählung erfahren, findet ein Paar auf Weltraumlustreise, „un couple de riches oisifs […] parcouraient l’univers pour leur plaisir“ (5), im All eine Flaschenpost und darin Ulysses Manuskript.
The lung microbiota: role in maintaining pulmonary immune homeostasis and its implications in cancer development and therapy
Authors: Sommariva Michele , Le Noci Valentino , Bianchi Francesca , Camelliti Simone , Balsari Andrea , Tagliabue Elda , Sfondrini Lucia 
Published: January 2020

AbstractLike other body districts, lungs present a complex bacteria community. An emerging function of lung microbiota is to promote and maintain a state of immune tolerance, to prevent uncontrolled and not desirable inflammatory response caused by inhalation of harmless environmental stimuli. This effect is mediated by a continuous dialog between commensal bacteria and immune cells resident in lungs, which express a repertoire of sensors able to detect microorganisms. The same receptors are also involved in the recognition of pathogens and in mounting a proper immune response. Due to its important role in preserving lung homeostasis, the lung microbiota can be also considered a mirror of lung health status. Indeed, several studies indicate that lung bacterial composition drastically changes during the occurrence of pulmonary pathologies, such as lung cancer, and the available data suggest that the modifications of lung microbiota can be part of the etiology of tumors in lungs and can influence their progression and response to therapy. These results provide the scientific rationale to analyze lung microbiota composition as biomarker for lung cancer and to consider lung microbiota a new potential target for therapeutic intervention to reprogram the antitumor immune microenvironment. In the present review, we discussed about the role of lung microbiota in lung physiology and summarized the most relevant data about the relationship between lung microbiota and cancer.
Stent-Assisted Angioplasty (SAA) at the Level of the Common Femoral Artery Bifurcation: Long-Term Outcomes
Authors: Stricker H. , Spinedi L. , Limoni C. , Giovannacci L. 
Published: January 2020

Abstract
Background
The objective of this retrospective single-center study was to report the initial and the long-term outcome after stent-assisted angioplasty of occlusive disease at the common femoral artery.

Materials and Methods
Between 1995 and 2015, 94 limbs in 79 consecutive patients (54 men; mean age 70 ± 8.6 years) underwent angioplasty with self-expanding stent implantation in 94 common femoral arteries. Critical limb ischemia was present in 15 limbs (16%); the other patients had claudication.

Results
Technical success was 99%. Complications occurred in 5/94 interventions (5.3%): puncture site hematomas (2), arteriovenous fistula (1), cholesterol embolism (1), and dissection of the access site artery (1). The intervention was outpatient-based in 98%. Median follow-up was 53 months. Ankle–brachial index (ABI) rose from 0.71 ± 0.17 to 1.0 ± 0.2 (p < .001) immediately after the intervention and was 1.03 ± 0.2 after 1 year and 0.96 ± 0.21 at the last follow-up visit (p < .001 compared to pre-interventional ABI). During follow-up, restenosis was found in 23/94 limbs (25%); 15 limbs were treated by angioplasty, 3 by surgery, and 5 conservatively. One limb was amputated below the knee 6 months after stent-assisted angioplasty (SAA). Death rate during follow-up was 35/79 patients (44%).

Conclusions
SAA of the CFA resulted in high immediate success and a low complication rate. Restenosis rate was moderate, and target lesions could easily be retreated by angioplasty. The main hazard was not restenosis, but death during follow-up.
Quantifying the dynamics of the interannual variabilities of the wintertime East Asian Jet Core
Authors: Chan Duo , Zhang Yang , Wu Qigang , Dai Xianglin 
Published: January 2020

AbstractThe East Asian jet has evident interannual variability in strength and position and has broad impacts on weather and climate in the Asian-Pacific-American region. In this study, we quantify the relative contributions of distinct dynamical processes responsible for the wintertime interannual variability of the East Asian jet core. The quantification is based on analyzing the zonal momentum budgets. Our budget analyses show distinct up- and downstream controls for the interannual intensification of the jet. Over the upstream, the jet intensification is predominantly driven by enhanced upper-level angular momentum transport associated with local convective-driven Hadley-cells. In addition to convections over the Tropical Pacific, those over the Bay of Bengal–South China Sea are found responsible for a distinct local Hadley cell over 80$$^\circ$$∘–100$$^\circ$$∘ E, which accelerates the jet from its very upstream. Over the downstream, angular momentum advected by the mean flow from the upstream is the first-order term responsible for the jet intensification, whereas synoptic eddies play a secondary role. For the interannual meridional displacement of the jet, synoptic eddy activities over the North Pacific are found to contribute predominantly. For both the intensification and the meridional displacement, the upper-tropospheric jet covaries closely with changes in the Subtropical Oceanic Frontal Zone in the North Pacific. Such a strong covariation implies the contributions of the air–sea interactions to the downstream jet variability.
The influence of ENSO events on the stratospheric QBO in a multi-model ensemble
Authors: Serva Federico , Cagnazzo Chiara , Christiansen Bo , Yang Shuting 
Published: January 2020

AbstractThe Quasi-Biennial Oscillation (QBO) and the El Niño–Southern Oscillation (ENSO) are two dominant modes of climate variability at the Equator. There exist observational evidences of mutual interactions between these two phenomena, but this possibility has not been widely studied using climate model simulations. In this work we assess how current models represent the ENSO/QBO relationship, in terms of the response of the amplitude and descent rate of stratospheric wind regimes, by analyzing atmosphere-only and ocean–atmosphere coupled simulations from a large multi-model ensemble. The annual cycle of the QBO descent rate is well represented in both coupled and uncoupled models. Previous results regarding the phase alignment of the QBO after the 1997/98 strong warm ENSO event are confirmed in a larger ensemble of uncoupled experiments. However, in general we find that a relatively high horizontal resolution is necessary to reproduce the observed modulation of the QBO descent rate under strong ENSO events, while the amplitude response is generally weak at any horizontal resolution. We argue that biases in the mean state and over-dependence on parameterized wave forcing undermine the realism of the simulated coupling between the ocean and the stratosphere in the tropics in current climate models. The modulation of the QBO by the ENSO in a high emission scenario consistently differs from that in the historical period, suggesting that this relationship is sensitive to changes in the large-scale circulation.
Spermidine in dementia
Authors: Pekar Thomas , Wendzel Aribert , Flak Walter , Kremer Alexandra , Pauschenwein-Frantsich Susanne , Gschaider Anna , Wantke Felix , Jarisch Reinhart 
Published: January 2020

SummaryPrevious studies have highlighted that spermidine has the ability to trigger the
important process of dissolving amyloid-beta plaques by autophagy. This manuscript
focuses on the correlation of serum spermidine levels between age and between
performance in mini-mental state examinations. It will serve as a premise for an ongoing
multicentric placebo-controlled study, which focuses on the effect of oral spermidine
supplementation on memory performance. Memory tests were carried out on 80 subjects aged
60–96 years old in 6 nursing homes in Styria. Blood samples were taken for the
determination of spermidine concentration. The results showed a significant correlation
between the spermidine concentration and the mini-mental state examination score
(p = 0.025). On the basis of the dependence
demonstrated it can be concluded that spermidine might be suitable as a biomarker for
the diagnosis of neurocognitive changes (senile dementia or Alzheimer’s disease).
Low and High Nitrogen Deposition Rates in Northern Coniferous Forests Have Different Impacts on Aboveground Litter Production, Soil Respiration, and Soil Carbon Stocks
Authors: Forsmark Benjamin , Nordin Annika , Maaroufi Nadia I. , Lundmark Tomas , Gundale Michael J. 
Published: January 2020

AbstractNitrogen (N) deposition can change the carbon (C) sink of northern coniferous forests by changing the balance between net primary production and soil respiration. We used a field experiment in an N poor Pinus sylvestris forest where five levels of N (0, 3, 6, 12, and 50 kg N ha−1 yr−1, n = 6) had been added annually for 12–13 years to investigate how litter C inputs and soil respiration, divided into its autotrophic and heterotrophic sources, respond to different rates of N input, and its subsequent effect on soil C storage. The highest N addition rate (50 kg N ha−1 yr−1) stimulated soil C accumulation in the organic layer by 22.3 kg C kg−1 N added, increased litter inputs by 46%, and decreased soil respiration per mass unit of soil C by 31.2%, mainly by decreasing autotrophic respiration. Lower N addition rates (≤ 12 kg N ha−1 yr−1) had no effect on litter inputs or soil respiration. These results support previous studies reporting on increased litter inputs coupled to impeded soil C mineralization, contributing to enhancing the soil C sink when N is supplied at high rates, but add observations for lower N addition rates more realistic for N deposition. In doing so, we show that litter production in N poor northern coniferous forests can be relatively unresponsive to low N deposition levels, that stimulation of microbial activity at low N additions is unlikely to reduce the soil C sink, and that high levels of N deposition enhance the soil C sink by increasing litter inputs and decreasing soil respiration.
Mechanisms mediating the relation between reading self-concept and reading comprehension
Authors: Locher Franziska Maria , Becker Sarah , Schiefer Irene , Pfost Maximilian 
Published: January 2020

AbstractReading self-concept is an important predictor of reading comprehension and vice versa. However, the mechanisms that are at work in this relation have yet to be identified. In line with the self-enhancement approach, we propose that in the reading domain, amount of reading, book choice (text difficulty and book length), and intrinsic reading motivation should function as mediating variables in the relation between reading self-concept and reading comprehension. We tested this hypothesis with longitudinal data gathered fromN = 405 German students in Grades 7, 8, and 9. The results showed that reading self-concept had a positive effect on reading comprehension, intrinsic motivation, book length, and amount of reading. However, indirect paths between reading self-concept and reading comprehension were found only for intrinsic motivation, not for amount of reading or book choice. The results are discussed in the context of students’ reading comprehension development, and consequences for research and education are derived.
Reaganomics — Wegbereiter des Trumpismus
Authors: Komlos John , Schubert Hermann 
Published: January 2020

ZusammenfassungDie von der Regierung Reagan durchgeführte angebotsorientierte Wirtschaftspolitik hat weder das Wirtschaftswachstum stimuliert noch Investitionsanreize intensiviert. Es ist auch kein Einkommen von den Reichen zu den Armen “durchgesickert”. Der erhoffte Trickle-Down-Effekt blieb aus. Stattdessen profitierten vor allem die obersten 1 % der US-amerikanischen Gesellschaft von den Steuererleichterungen. Die von den Reaganomics ausgelösten wirtschaftlichen Prozesse zeitigten zahlreiche Verlierer, vor allem unter weniger Qualifizierten und Besitzlosen. Schließlich stellten sie sich gegen das Establishment und brachten einen starken Mann an die Macht–komme was wolle. Der Triumph des Trumpismus ist in diesem Sinne das ultimative Vermächtnis von Ronald Reagan und seiner Wirtschafts- und Sozialpolitik.
Gender Identity and Sexual Orientation Identity in Women and Men Prenatally Exposed to Diethylstilbestrol
Authors: Troisi Rebecca , Palmer Julie R. , Hatch Elizabeth E. , Strohsnitter William C. , Huo Dezheng , Hyer Marianne , Fredriksen-Goldsen Karen I. , Hoover Robert , Titus Linda 
Published: January 2020

AbstractWe assessed the associations of prenatal diethylstilbestrol (DES) exposure, a potent estrogen, with sexual orientation and gender identity in 3306 women and 1848 men who participated in a study of prenatal DES exposure. Odds ratios (OR) and 95% confidence intervals (CI) were derived from logistic regression models adjusted for birth year, study cohort, and education. Among women, the OR for DES in relation to reporting sexual orientation identity as nonheterosexual was 0.61 (95% CI 0.40–0.92) primarily due to a strong inverse association with a lesbian identity (OR 0.44, 95% CI 0.25–0.76). Among men, the OR for DES in relation to reporting a nonheterosexual sexual orientation identity was 1.4 (95% CI 0.82–2.4), and ORs were similar for having a gay identity (1.4, 95% CI 0.72–2.85) and bisexual identity (1.4, 95% CI 0.57–3.5). Only five individuals reported a gender identity not conforming to that assigned at birth, preventing meaningful analysis. Women who were prenatally exposed to DES were less likely to have a lesbian or bisexual orientation, while DES-exposed men were somewhat more likely to report being gay or bisexual, but estimates were imprecise.
A set of Yarrowia lipolytica CRISPR/Cas9 vectors for exploiting wild-type strain diversity
Authors: Larroude Macarena , Trabelsi Heykel , Nicaud Jean-Marc , Rossignol Tristan 
Published: January 2020

Abstract
Objectives
The construction and validation of a set of Yarrowia lipolytica CRISPR/Cas9 vectors containing six different markers that allows virtually any genetic background to be edited, including those of wild-type strains.

Results
Using the Golden Gate method, we assembled a set of six CRISPR/Cas9 vectors, each containing a different selection marker, to be used for editing the genome of the industrial yeast Y. lipolytica. This vector set is available via Addgene. Any guide RNA (gRNA) sequence can be easily and rapidly introduced in any of these vectors using Golden Gate assembly. We successfully edited six different genes in a variety of genetic backgrounds, including those of wild-type strains, with five of the six vectors. Use of these vectors strongly improved homologous recombination and cassette integration at a specific locus.

Conclusions
We have created a versatile and modular set of CRISPR/Cas9 vectors that will allow any Y. lipolytica strain to be rapidly edited; this tool will facilitate experimentation with any prototroph wild-type strains displaying interesting features.