bluuebunny/crossref_metadata_2025_split huggingface dataset:
Model-based understanding of single-cell CRISPR screening
Authors: Duan Bin , Zhou Chi , Zhu Chengyu , Yu Yifei , Li Gaoyang , Zhang Shihua , Zhang Chao , Ye Xiangyun , Ma Hanhui , Qu Shen , Zhang Zhiyuan , Wang Ping , Sun Shuyang , Liu Qi 
Published: May 2019

AbstractThe recently developed single-cell CRISPR screening techniques, independently termed Perturb-Seq, CRISP-seq, or CROP-seq, combine pooled CRISPR screening with single-cell RNA-seq to investigate functional CRISPR screening in a single-cell granularity. Here, we present MUSIC, an integrated pipeline for model-based understanding of single-cell CRISPR screening data. Comprehensive tests applied to all the publicly available data revealed that MUSIC accurately quantifies and prioritizes the individual gene perturbation effect on cell phenotypes with tolerance for the substantial noise that exists in such data analysis. MUSIC facilitates the single-cell CRISPR screening from three perspectives, i.e., prioritizing the gene perturbation effect as an overall perturbation effect, in a functional topic-specific way, and quantifying the relationships between different perturbations. In summary, MUSIC provides an effective and applicable solution to elucidate perturbation function and biologic circuits by a model-based quantitative analysis of single-cell-based CRISPR screening data.
DNA-templated synthesis of biomimetic cell wall for nanoencapsulation and protection of mammalian cells
Authors: Shi Peng , Zhao Nan , Coyne James , Wang Yong 
Published: May 2019

AbstractMammalian cells are different from plant and microbial cells, having no exterior cell walls for protection. Environmental assaults can easily damage or destroy mammalian cells. Thus, the ability to develop a biomimetic cell wall (BCW) on their plasma membrane as a shield can advance various applications. Here we demonstrate the synthesis of BCW with a framing template and a crosslinked matrix for shielding live mammalian cells. The framing template is a supramolecular DNA structure. The crosslinked matrix is a polyelectrolyte complex made of alginate and polylysine. As the entire procedure of BCW synthesis is strictly operated under physiological conditions, BCW-covered mammalian cells can maintain high bioactivity. More importantly, the data show that BCW can shield live mammalian cells from not only physical assaults but also biological assaults. Thus, this study has successfully demonstrated the synthesis of BCW on live mammalian cells with great potential of shielding them from environmental assaults.
Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms
Authors: Diamond Spencer , Andeer Peter F. , Li Zhou , Crits-Christoph Alexander , Burstein David , Anantharaman Karthik , Lane Katherine R. , Thomas Brian C. , Pan Chongle , Northen Trent R. , Banfield Jillian F. 
Published: May 2019

AbstractSoil microbial activity drives the carbon and nitrogen cycles and is an important determinant of atmospheric trace gas turnover, yet most soils are dominated by microorganisms with unknown metabolic capacities. Even Acidobacteria, among the most abundant bacteria in soil, remain poorly characterized, and functions across groups such as Verrucomicrobia, Gemmatimonadetes, Chloroflexi and Rokubacteria are understudied. Here, we have resolved 60 metagenomic and 20 proteomic data sets from a Mediterranean grassland soil ecosystem and recovered 793 near-complete microbial genomes from 18 phyla, representing around one-third of all microorganisms detected. Importantly, this enabled extensive genomics-based metabolic predictions for these communities. Acidobacteria from multiple previously unstudied classes have genomes that encode large enzyme complements for complex carbohydrate degradation. Alternatively, most microorganisms encode carbohydrate esterases that strip readily accessible methyl and acetyl groups from polymers like pectin and xylan, forming methanol and acetate, the availability of which could explain the high prevalence of C1metabolism and acetate utilization in genomes. Microorganism abundances among samples collected at three soil depths and under natural and amended rainfall regimes indicate statistically higher associations of inorganic nitrogen metabolism and carbon degradation in deep and shallow soils, respectively. This partitioning decreased in samples under extended spring rainfall, indicating that long-term climate alteration can affect both carbon and nitrogen cycling. Overall, by leveraging natural and experimental gradients with genome-resolved metabolic profiles, we link microorganisms lacking prior genomic characterization to specific roles in complex carbon, C1, nitrate and ammonia transformations, and constrain factors that impact their distributions in soil.
Transcriptomic profiles of 33 opium poppy samples in different tissues, growth phases, and cultivars
Authors: Zhao Yucheng , Zhang Zhaoping , Li Mingzhi , Luo Jun , Chen Fang , Gong Yongfu , Li Yanrong , Wei Yujie , Su Yujie , Kong Lingyi 
Published: May 2019

AbstractOpium poppy is one of the most important medicinal plants and remains the only commercial resource of morphinan-based painkillers. However, little is known about the regulatory mechanisms involved in benzylisoquinoline alkaloids (BIAs) biosynthesis in opium poppy. Herein, the full-length transcriptome dataset of opium poppy was constructed for the first time in accompanied with the 33 samples of Illumina transcriptome data from different tissues, growth phases and cultivars. The long-read sequencing produced 902,140 raw reads with 55,114 high-quality transcripts, and short-read sequencing produced 1,923,679,864 clean reads with an average Q30 rate of 93%. The high-quality transcripts were subsequently quantified using the short reads, and the expression of each unigene among different samples was calculated as reads per kilobase per million mapped reads (RPKM). These data provide a foundation for opium poppy transcriptomic analysis, which may aid in capturing splice variants and some non-coding RNAs involved in the regulation of BIAs biosynthesis. It can also be used for genome assembly and annotation which will favor in new transcript identification.
Characteristics of the regulation of the surprise emotion
Authors: Zhu Chuanlin , Li Ping , Zhang Zhao , Liu Dianzhi , Luo Wenbo 
Published: May 2019

AbstractThis study aimed to assess the characteristics of the regulation of the emotion of surprise. Event-related potentials (ERPs) of college students when using cognitive reappraisal and expressive suppression to regulate their surprise level were recorded. Different contexts were presented to participants, followed by the image of surprised facial expression; subsequently, using a 9-point scale, participants were asked to rate the intensity of their emotional experience. The behavioral results suggest that individuals’ surprise level could be reduced by using both expressive suppression and cognitive reappraisal, in basic and complex conditions. The ERP results showed that (1) the N170 amplitudes were larger in complex than basic contexts, and those elicited by using expressive suppression and cognitive reappraisal showed no significant differences, suggesting that emotion regulation did not occur at this stage; (2) the LPC amplitudes elicited by using cognitive reappraisal and expressive suppression were smaller than those elicited by free viewing in both context conditions, suggesting that the late stage of individuals’ processing of surprised faces was influenced by emotion regulation. This study found that conscious emotional regulation occurred in the late stages when individuals processed surprise, and the regulation effects of cognitive reappraisal and expressive suppression were equivalent.
Privacy-preserving Quantum Sealed-bid Auction Based on Grover’s Search Algorithm
Authors: Shi Run-hua , Zhang Mingwu 
Published: May 2019

AbstractSealed-bid auction is an important tool in modern economic especially concerned with networks. However, the bidders still lack the privacy protection in previously proposed sealed-bid auction schemes. In this paper, we focus on how to further protect the privacy of the bidders, especially the non-winning bidders. We first give a new privacy-preserving model of sealed-bid auction and then present a quantum sealed-bid auction scheme with stronger privacy protection. Our proposed scheme takes a general state in N-dimensional Hilbert space as the message carrier, in which each bidder privately marks his bid in an anonymous way, and further utilizes Grover’s search algorithm to find the current highest bid. By O(lnn) iterations, it can get the highest bid finally. Compared with any classical scheme in theory, our proposed quantum scheme gets the lower communication complexity.
The extrahepatic events of Asian patients with primary biliary cholangitis: A 30-year cohort study
Authors: Lin Cheng-Yu , Cheng Ya-Ting , Chang Ming-Ling , Chien Rong-Nan 
Published: May 2019

AbstractThe extrahepatic complications of primary biliary cholangitis (PBC) in Asian patients remain elusive. A 30-year cohort study of 150 Taiwanese PBC patients treated with ursodeoxycholic acid (UDCA) was conducted. Patients with alkaline phosphatase levels >1.67 × ULN after 1-year treatment were considered suboptimal responders. At baseline, of 150 patients (mean age: 53.75 years), 128 (85.3%) were females, and 34 (22.8%) had cirrhosis. The cumulative incidences of various incident events were all-cause mortality or liver transplantation: 46.7%; extrahepatic mortality: 24.5%; extrahepatic malignancies: 8.1%; hypertension: 46.2%; dyslipidemia: 44.1%; diabetes: 30.6%; hyperuricemia: 11.2%; acute coronary syndrome: 3.1%; cerebral vascular accident (CVA): 8.9%; autoimmune diseases: 16%; and osteoporosis: 20.9%. The 5- to 20-year cumulative incidences for all-cause mortality or liver transplantation and extrahepatic mortality were 16.2–41.3% and 3.1–11.9%, respectively. Baseline associations were age and alpha-fetoprotein levels with extrahepatic mortality, 80% due to sepsis; age with extrahepatic malignancies and hypertension; gender and hyperuricemia with CVA; and UDCA response with autoimmune disease. Conclusions: Sepsis accounted for most extrahepatic mortality in PBC patients, and the longer the follow-up was, the higher the extrahepatic/all-cause mortality ratio. Baseline age is crucial for incident extrahepatic events and only CVA shows gender-dimorphism; the association between UDCA response and autoimmune disease requires further investigation.
Clinical features for diagnosis of pneumonia among adults in primary care setting: A systematic and meta-review
Authors: Htun Tha Pyai , Sun Yinxiaohe , Chua Hui Lan , Pang Junxiong 
Published: May 2019

AbstractPneumonia results in significant morbidity and mortality worldwide. However, chest radiography may not be accessible in primary care setting. We aimed to evaluate clinical features and its diagnostic value to identify pneumonia among adults in primary care settings. Three academic databases were searched and included studies that assessed clinical predictors of pneumonia, adults without serious illness, have CXR and have conducted in primary care settings. We calculated sensitivity, specificity, positive and negative likelihood ratios, diagnostic odds ratio of each index test and the pool estimates for index tests. We identified 2,397 articles, of which 13 articles were included. In our meta-analysis, clinical features with the best pooled positive likelihood ratios were respiratory rate ≥20 min−1 (3.47; 1.46–7.23), temperature ≥38 °C (3.21; 2.36–4.23), pulse rate >100 min−1 (2.79; 1.71–4.33), and crackles (2.42; 1.19–4.69). Laboratory testing showed highest pooled positive likelihood ratios with PCT >0.25 ng/ml (7.61; 3.28–15.1) and CRP > 20 mg/l (3.76; 2.3–5.91). Cough, pyrexia, tachycardia, tachypnea, and crackles are limited as a single predictor for diagnosis of radiographic pneumonia among adults. Development of clinical decision rule that combine these clinical features together with molecular biomarkers may further increase overall accuracy for diagnosis of radiographic pneumonia among adults in primary care setting.
Genetic analyses of human fetal retinal pigment epithelium gene expression suggest ocular disease mechanisms
Authors: Liu Boxiang , Calton Melissa A. , Abell Nathan S. , Benchorin Gillie , Gloudemans Michael J. , Chen Ming , Hu Jane , Li Xin , Balliu Brunilda , Bok Dean , Montgomery Stephen B. , Vollrath Douglas 
Published: May 2019

AbstractThe retinal pigment epithelium (RPE) serves vital roles in ocular development and retinal homeostasis but has limited representation in large-scale functional genomics datasets. Understanding how common human genetic variants affect RPE gene expression could elucidate the sources of phenotypic variability in selected monogenic ocular diseases and pinpoint causal genes at genome-wide association study (GWAS) loci. We interrogated the genetics of gene expression of cultured human fetal RPE (fRPE) cells under two metabolic conditions and discovered hundreds of shared or condition-specific expression or splice quantitative trait loci (e/sQTLs). Co-localizations of fRPE e/sQTLs with age-related macular degeneration (AMD) and myopia GWAS data suggest new candidate genes, and mechanisms by which a common RDH5 allele contributes to both increased AMD risk and decreased myopia risk. Our study highlights the unique transcriptomic characteristics of fRPE and provides a resource to connect e/sQTLs in a critical ocular cell type to monogenic and complex eye disorders.
Sum of peak intensities outperforms peak area integration in iTRAQ protein expression measurement by LC-MS/MS using a TripleTOF 5600+ platform
Authors: Burat Bastien , Gonzalez Julien , Sauvage François-Ludovic , Aouad Hassan , Arnion Hélène , Pinault Emilie , Marquet Pierre , Essig Marie 
Published: May 2019

Abstract
In the field of quantitative proteomics, the Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) technology has demonstrated efficacy for proteome monitoring despite its lack of a consensus for data handling. In the present study, after peptide and protein identification, we compared the widespread quantitation method based on the calculation of MS/MS reporter ion peaks areas ratios (ProteinPilot) to the alternative method based on the calculation of ratios of the sum of peak intensities (jTRAQx [Quant]) and we processed output data with the in-house Customizable iTRAQ Ratios Calculator (CiR-C) algorithm. Quantitation based on peak area ratios displayed no significant linear correlation with Western blot quantitation. In contrast, quantitation based on the sum of peak intensities displayed a significant linear association with Western blot quantitation (non-zero slope; Pearson correlation coefficient test, r = 0.296, P=0.010**) with an average bias of 0.087 ± 0.500 and 95% Limits of Agreement from −0.893 to 1.068. We proposed the Mascot-jTRAQx-CiR-C strategy as a simple yet powerful data processing adjunct to the iTRAQ technology.
Planetesimal formation in an evolving protoplanetary disk with a dead zone
Authors: Charnoz Sébastien , Pignatale Francesco C. , Hyodo Ryuki , Mahan Brandon , Chaussidon Marc , Siebert Julien , Moynier Frédéric 
Published: May 2019

Context. When and where planetesimals form in a protoplanetary disk are highly debated questions. Streaming instability is considered the most promising mechanism, but the conditions for its onset are stringent. Disk studies show that the planet forming region is not turbulent because of the lack of ionization forming possibly dead zones (DZs).
Aims. We investigate planetesimal formation in an evolving disk, including the DZ and thermal evolution.
Methods. We used a 1D time-evolving stratified disk model with composite chemistry grains, gas and dust transport, and dust growth.
Results. Accretion of planetesimals always develops in the DZ around the snow line, due to a combination of water recondensation and creation of dust traps caused by viscosity variations close to the DZ. The width of the planetesimal forming region depends on the disk metallicity. For Z = Z⊙, planetesimals form in a ring of about 1 au width, while for Z > 1.2 Z⊙ planetesimals form from the snow line up to the outer edge of the DZ ≃ 20 au. The efficiency of planetesimal formation in a disk with a DZ is due to the very low effective turbulence in the DZ and to the efficient piling up of material coming from farther away; this material accumulates in region of positive pressure gradients forming a dust trap due to viscosity variations. For Z = Z⊙ the disk is always dominated in terms of mass by pebbles, while for Z > 1.2 Z⊙ planetesimals are always more abundant than pebbles. If it is assumed that silicate dust is sticky and grows up to impact velocities ~10 m s−1, then planetesimals can form down to 0.1 au (close to the inner edge of the DZ). In conclusion the DZ seems to be a sweet spot for the formation of planetesimals: wide scale planetesimal formation is possible for Z > 1.2 Z⊙. If hot silicate dust is as sticky as ice, then it is also possible to form planetesimals well inside the snow line.
Rotation rate of the solar core as a key constraint to magnetic angular momentum transport in stellar interiors
Authors: Eggenberger P. , Buldgen G. , Salmon S. J. A. J. 
Published: May 2019

Context. The internal rotation of the Sun constitutes a fundamental constraint when modelling angular momentum transport in stellar interiors. In addition to the more external regions of the solar radiative zone probed by pressure modes, measurements of rotational splittings of gravity modes would offer an invaluable constraint on the rotation of the solar core.
Aims. We study the constraints that a measurement of the core rotation rate of the Sun could bring on magnetic angular momentum transport in stellar radiative zones.
Methods. Solar models accounting for angular momentum transport by hydrodynamic and magnetic instabilities were computed for different initial velocities and disc lifetimes on the pre-main sequence to reproduce the surface rotation velocities observed for solar-type stars in open clusters. The internal rotation of these solar models was then compared to helioseismic measurements.
Results. We first show that models computed with angular momentum transport by magnetic instabilities and a recent prescription for the braking of the stellar surface by magnetized winds can reproduce the observations of surface velocities of stars in open clusters. These solar models predict both a flat rotation profile in the external part of the solar radiative zone probed by pressure modes and an increase in the rotation rate in the solar core, where the stabilizing effect of chemical gradients plays a key role. A rapid rotation of the core of the Sun, as suggested by reported detections of gravity modes, is thus found to be compatible with angular momentum transport by magnetic instabilities. Moreover, we show that the efficiency of magnetic angular momentum transport in regions of strong chemical gradients can be calibrated by the solar core rotation rate independently from the unknown rotational history of the Sun. In particular, we find that a recent revised prescription for the transport of angular momentum by the Tayler instability can be easily distinguished from the original Tayler–Spruit dynamo, with a faster rotating solar core supporting the original prescription.
Conclusions. By calibrating the efficiency of magnetic angular momentum transport in regions of strong chemical gradients, a determination of the solar core rotation rate through gravity modes is of prime relevance not only for the Sun, but for stars in general, since radial differential rotation precisely develops in these regions during the more advanced stages of evolution.
Interpolation of equation-of-state data
Authors: Baturin V. A. , Däppen W. , Oreshina A. V. , Ayukov S. V. , Gorshkov A. B. 
Published: May 2019

Aims. We use Hermite splines to interpolate pressure and its derivatives simultaneously, thereby preserving mathematical relations between the derivatives. The method therefore guarantees that thermodynamic identities are obeyed even between mesh points. In addition, our method enables an estimation of the precision of the interpolation by comparing the Hermite-spline results with those of frequent cubic (B-) spline interpolation.
Methods. We have interpolated pressure as a function of temperature and density with quintic Hermite 2D-splines. The Hermite interpolation requires knowledge of pressure and its first and second derivatives at every mesh point. To obtain the partial derivatives at the mesh points, we used tabulated values if given or else thermodynamic equalities, or, if not available, values obtained by differentiating B-splines.
Results. The results were obtained with the grid of the SAHA-S equation-of-state (EOS) tables. The maximum lgP difference lies in the range from 10−9 to 10−4, and Γ1 difference varies from 10−9 to 10−3. Specifically, for the points of a solar model, the maximum differences are one order of magnitude smaller than the aforementioned values. The poorest precision is found in the dissociation and ionization regions, occurring at T ∼ 1.5 × 103−105 K. The best precision is achieved at higher temperatures, T >  105 K. To discuss the significance of the interpolation errors we compare them with the corresponding difference between two different equation-of-state formalisms, SAHA-S and OPAL 2005. We find that the interpolation errors of the pressure are a few orders of magnitude less than the differences from between the physical formalisms, which is particularly true for the solar-model points.
Risikokommunikation in gesundheitsbedrohlichen Krisensituationen: Zusammenfassung einer WHO-Leitlinie
Authors: Christof Claudia , Nußbaumer-Streit Barbara , Gartlehner Gerald 
Published: May 2019

Zusammenfassung
Hintergrund Risikokommunikation ist ein wesentlicher Bestandteil, um auf Notfälle und Katastrophen, die die Gesundheit der Bevölkerung gefährden, angemessen reagieren zu können.
Ziel Die Weltgesundheitsorganisation (WHO) entwickelte diese Leitlinie, um WHO-Mitgliedsstaaten, sowie Stakeholdern aus dem Bereich Notfallschutz und -bekämpfung evidenzbasierte, aktuelle und systemorientierte Handlungsempfehlungen zur Risikokommunikation bereitzustellen.
Methode Die Leitlinie wurde gemäß WHO-Standards entwickelt.
Ergebnisse Die Leitlinie beinhaltet Empfehlungen zu den Bereichen (1) Vertrauen aufbauen, Unsicherheiten kommunizieren und die betroffene Bevölkerung einbinden, (2) Integration von Risikokommunikation in bestehende Strukturen des Notfallschutz- und der Notfallbekämpfung und (3) Planung, Umsetzung und Evaluierung von Risikokommunikation in der Praxis.
Schlussfolgerung Diese Leitlinie gibt Empfehlungen für den Auf- und Ausbau von Risikokommunikation, enthält aber keine Schritt-für-Schritt Anleitungen. Solche detaillierten Anleitungen werden zukünftig in anderer Form von der WHO bereitgestellt.