bluuebunny/crossref_metadata_2025_split huggingface dataset:
Confronting missing observations with probability weights: Fourier space and generalized formalism
Authors: Bianchi Davide , Verde Licia 
Published: May 2020

ABSTRACT
Due to instrumental limitations, spectroscopic galaxy surveys usually do not collect redshifts for the whole population of potential targets. Especially problematic is the entanglement between this incompleteness and the true cosmological signal, arising from the fact that the proportion of successful observations is typically lower in regions with higher galaxy density. The result is a fictitious suppression of the galaxy clustering that can impact severely on cosmological parameter inference. Recent developments have shown that an unbiased estimate of the two-point correlation in the presence of missing observations can be obtained by weighting each pair by its inverse probability of being targeted. In this work, we expand on the concept of probability weights by developing a more mature statistical formalism, which provides us with a deeper understanding of their fundamental properties. We take advantage of this novel perspective to handle the problem of estimating the inverse probability, specifically, we discuss how to efficiently determine the weights from a finite set of realizations of the targeting and how to model exactly the resulting sampling effects. This allows us to derive an inverse-probability-based power-spectrum estimator, which is the main result of this work, but also to improve robustness and computational efficiency of the already existing configuration-space estimator. Finally, we propose a strategy to further extend the inverse-probability prescription, providing examples of how traditional missing-observation countermeasures can be included in this more general picture. The effectiveness of models and weighting schemes discussed in this work is demonstrated using realizations of an idealized survey strategy.
Asteroseismology of 36Keplersubgiants – II. Determining ages from detailed modelling
Authors: Li Tanda , Bedding Timothy R , Christensen-Dalsgaard Jørgen , Stello Dennis , Li Yaguang , Keen Matthew A 
Published: May 2020

ABSTRACTDetailed modelling of stellar oscillations is able to give precise estimates for stellar ages, but the inferred results typically depend on the adopted model parameters used for the age inference. High-quality asteroseismic data with precise measurements of mixed modes are available for 36 Kepler subgiants. To obtain a handle on the robustness of the ages for these stars, we first study the dependencies of seismic ages on three model input parameters. We find that inferred ages do not change systematically with the helium fraction (Y) or the mixing-length parameter (αMLT) but depend strongly on the metallicity ([M/H]) of the model. The results indicate that age estimates of subgiants have less model dependence and hence are more reliable than those of main-sequence stars or red giants. We then model individual oscillation frequencies of the same 36 Kepler subgiants, using observed metallicities, and obtain their ages with an average precision of ${\sim}15{{\ \rm per\ cent}}$. The comparison with previous age estimates with different stellar codes or input physics shows good agreement (mostly within 2σ). We hence suggest that seismology-determined ages of subgiants are not greatly model dependent.
Genetically encoded betaxanthin-based small-molecular fluorescent reporter for mammalian cells
Authors: Stücheli Pascal , Sieber Simon , Fuchs David W , Scheller Leo , Strittmatter Tobias , Saxena Pratik , Gademann Karl , Fussenegger Martin 
Published: May 2020

Abstract
We designed and engineered a dye production cassette encoding a heterologous pathway, including human tyrosine hydroxylase and Amanita muscaria 4,5-DOPA dioxygenase, for the biosynthesis of the betaxanthin family of plant and fungal pigments in mammalian cells. The system does not impair cell viability, and can be used as a non-protein reporter system to directly visualize the dynamics of gene expression by profiling absorbance or fluorescence in the supernatant of cell cultures, as well as for fluorescence labeling of individual cells. Pigment profiling can also be multiplexed with reporter proteins such as mCherry or the human model glycoprotein SEAP (secreted alkaline phosphatase). Furthermore, absorbance measurement with a smartphone camera using standard application software enables inexpensive, low-tech reporter quantification.
Modular protein-oligonucleotide signal exchange
Authors: Agrawal Deepak K , Schulman Rebecca 
Published: May 2020

AbstractWhile many methods are available to measure the concentrations of proteins in solution, the development of a method to quantitatively report both increases and decreases in different protein concentrations in real-time using changes in the concentrations of other molecules, such as DNA outputs, has remained a challenge. Here, we present a biomolecular reaction process that reports the concentration of an input protein in situ as the concentration of an output DNA oligonucleotide strand. This method uses DNA oligonucleotide aptamers that bind either to a specific protein selectively or to a complementary DNA oligonucleotide reversibly using toehold-mediated DNA strand-displacement. It is possible to choose the sequence of output strand almost independent of the sensing protein. Using this strategy, we implemented four different exchange processes to report the concentrations of clinically relevant human α-thrombin and vascular endothelial growth factor using changes in concentrations of DNA oligonucleotide outputs. These exchange processes can operate in tandem such that the same or different output signals can indicate changes in concentration of distinct or identical input proteins. The simplicity of our approach suggests a pathway to build devices that can direct diverse output responses in response to changes in concentrations of specific proteins.
Translation at first sight: the influence of leading codons
Authors: Osterman Ilya A , Chervontseva Zoe S , Evfratov Sergey A , Sorokina Alena V , Rodin Vladimir A , Rubtsova Maria P , Komarova Ekaterina S , Zatsepin Timofei S , Kabilov Marsel R , Bogdanov Alexey A , Gelfand Mikhail S , Dontsova Olga A , Sergiev Petr V 
Published: May 2020

Abstract
First triplets of mRNA coding region affect the yield of translation. We have applied the flowseq method to analyze &gt;30 000 variants of the codons 2–11 of the fluorescent protein reporter to identify factors affecting the protein synthesis. While the negative influence of mRNA secondary structure on translation has been confirmed, a positive role of rare codons at the beginning of a coding sequence for gene expression has not been observed. The identity of triplets proximal to the start codon contributes more to the protein yield then more distant ones. Additional in-frame start codons enhance translation, while Shine–Dalgarno-like motifs downstream the initiation codon are inhibitory. The metabolic cost of amino acids affects the yield of protein in the poor medium. The most efficient translation was observed for variants with features resembling those of native Escherichia coli genes.
PaCRISPR: a server for predicting and visualizing anti-CRISPR proteins
Authors: Wang Jiawei , Dai Wei , Li Jiahui , Xie Ruopeng , Dunstan Rhys A , Stubenrauch Christopher , Zhang Yanju , Lithgow Trevor 
Published: May 2020

AbstractAnti-CRISPRs are widespread amongst bacteriophage and promote bacteriophage infection by inactivating the bacterial host's CRISPR–Cas defence system. Identifying and characterizing anti-CRISPR proteins opens an avenue to explore and control CRISPR–Cas machineries for the development of new CRISPR–Cas based biotechnological and therapeutic tools. Past studies have identified anti-CRISPRs in several model phage genomes, but a challenge exists to comprehensively screen for anti-CRISPRs accurately and efficiently from genome and metagenome sequence data. Here, we have developed an ensemble learning based predictor, PaCRISPR, to accurately identify anti-CRISPRs from protein datasets derived from genome and metagenome sequencing projects. PaCRISPR employs different types of feature recognition united within an ensemble framework. Extensive cross-validation and independent tests show that PaCRISPR achieves a significantly more accurate performance compared with homology-based baseline predictors and an existing toolkit. The performance of PaCRISPR was further validated in discovering anti-CRISPRs that were not part of the training for PaCRISPR, but which were recently demonstrated to function as anti-CRISPRs for phage infections. Data visualization on anti-CRISPR relationships, highlighting sequence similarity and phylogenetic considerations, is part of the output from the PaCRISPR toolkit, which is freely available at http://pacrispr.erc.monash.edu/.
GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins
Authors: Brůna Tomáš , Lomsadze Alexandre , Borodovsky Mark 
Published: May 2020

Abstract
We have made several steps toward creating a fast and accurate algorithm for gene prediction in eukaryotic genomes. First, we introduced an automated method for efficient ab initio gene finding, GeneMark-ES, with parameters trained in iterative unsupervised mode. Next, in GeneMark-ET we proposed a method of integration of unsupervised training with information on intron positions revealed by mapping short RNA reads. Now we describe GeneMark-EP, a tool that utilizes another source of external information, a protein database, readily available prior to the start of a sequencing project. A new specialized pipeline, ProtHint, initiates massive protein mapping to genome and extracts hints to splice sites and translation start and stop sites of potential genes. GeneMark-EP uses the hints to improve estimation of model parameters as well as to adjust coordinates of predicted genes if they disagree with the most reliable hints (the -EP+ mode). Tests of GeneMark-EP and -EP+ demonstrated improvements in gene prediction accuracy in comparison with GeneMark-ES, while the GeneMark-EP+ showed higher accuracy than GeneMark-ET. We have observed that the most pronounced improvements in gene prediction accuracy happened in large eukaryotic genomes.
Acute kidney injury in patients treated with anti-programmed death receptor-1 for advanced melanoma: a real-life study in a single-centre cohort
Authors: Stein Claire , Burtey Stéphane , Mancini Julien , Pelletier Marion , Sallée Marion , Brunet Philippe , Berbis Philippe , Grob Jean Jacques , Honoré Stéphane , Gaudy Caroline , Jourde-Chiche Noémie 
Published: May 2020

Abstract

Background
Immune checkpoints inhibitors have transformed the prognosis of advanced melanoma but are associated with immune-related adverse events (irAEs). We evaluated the incidence, risk factors and causes of acute kidney injury (AKI) in a monocentric real-life cohort of patients treated with anti-programmed death receptor-1 (anti-PD1) antibodies for advanced melanoma.

Methods
Retrospective collection of medical charts and comprehensive analysis of lab results from patients treated with nivolumab or pembrolizumab for advanced melanoma between 2014 and 2018 was carried out. AKI was defined by Kidney Disease Improving Global Outcomes criteria, and causes were determined by chart review. Overall survival, survival without AKI and impact of AKI on survival were analysed. Risk factors for death and for AKI were identified.

Results
Two hundred and thirty-nine patients were included. Forty-one (17%) had at least one episode of AKI. Independent risk factors for AKI were treatment with renin–angiotensin–aldosterone system inhibitors (RAASi), pre-existing chronic kidney disease (CKD) and cumulated doses of anti-PD1. The main cause of AKI was prerenal, and only eight patients (3.3%) developed acute interstitial nephritis; 8% of patients developed CKD. The median overall survival was 13.4 months and was not affected by AKI. In multivariate analysis, the overall mortality was lower in overweight and obese patients and higher in patients treated with proton-pump inhibitors (PPI) or corticosteroids.

Conclusions
AKI is common in patients treated with anti-PD1 for advanced melanoma but is mostly prerenal and favoured by the use of RAASi; renal irAE is rare. PPI and corticosteroids were associated with poor survival in this population, while overweight/obesity was protective.
Home-Based Outpatient Parenteral Antibiotic Therapy at an Urban Safety Net Hospital: Comparing Outcomes in Persons With and Without Noninjection Drug Use
Authors: Appa Ayesha , Marquez Carina , Jain Vivek 
Published: May 2020

AbstractAs stimulant use and infections among persons using drugs rise nationally, evidence remains limited on how best to deliver outpatient parenteral antimicrobial therapy (OPAT) to persons using noninjection drugs. In an urban safety net population including persons using noninjection drugs, home-based OPAT completion rates were similarly high as those of non-drug-using individuals.
From low-skilled to key workers: the implications of emergencies for immigration policy
Authors: Fernández-Reino Mariña , Sumption Madeleine , Vargas-Silva Carlos 
Published: May 2020

Abstract
The COVID-19 pandemic has increased public awareness of the extent to which the economy relies on a low-wage workforce. Many of those lower-waged occupations that have been recognized as essential in the emergency are heavily dependent on migrant workers. We explore the implications of the COVID-19 pandemic for future immigration policies and provide an example using data for the UK. We suggest that there are three key considerations for governments in this context. First, whether the management of emergencies themselves requires a certain type of immigration policy. Second, whether the experience of the current pandemic brings to light new information about the ‘value’ of certain types of immigration. Finally, whether immigration is the right response to pandemic-driven increases in labour demand.
A numerical light curve model for interaction-powered supernovae
Authors: Takei Yuki , Shigeyama Toshikazu 
Published: May 2020

Abstract
We construct a numerical light curve model for interaction-powered supernovae that arise from an interaction between the ejecta and the circumstellar matter (CSM). In order to resolve the shocked region of an interaction-powered supernova, we solve the fluid equations and radiative transfer equation assuming steady states in the rest frames of the reverse and forward shocks at each time step. Then we numerically solve the radiative transfer equation and the energy equation in the CSM with the radiative flux obtained from the forward shock as a radiation source. We also compare the results of our models with observational data of two supernovae, 2005kj and 2005ip, classified as type IIn, and discuss the validity of our assumptions. We conclude that our model can predict the physical parameters associated with supernova ejecta and the CSM from the observed features of the light curve as long as the CSM is sufficiently dense. Furthermore, we found that the absorption of radiation in the CSM is an important factor in calculating the luminosity.
Strategy, Structure, and the Administration of Complex Geographies
Authors: Whitford Andrew B 
Published: May 2020

AbstractAll countries with complex geographies must extend national power to local areas. Field administration is a primitive in government: it is inevitable in modern national governments, but its variety and impact is rarely discussed in modern public administration. Building on the work of James Fesler and formal results on agenda-setting in organizations, this article demonstrates dilemmas in the use of historically important, widespread mechanisms for designing the field operations of national governments. The experiences of different nation-states provide context for these dilemmas. How governments address these dilemmas shapes policy implementation and the performance of national governments.
The Taiji program: A concise overview
Authors: Luo Ziren , Wang Yan , Wu Yueliang , Hu Wenrui , Jin Gang 
Published: May 2020

Abstract
Taiji is a Chinese space mission to detect gravitational waves in the frequency band 0.1 mHz to 1.0 Hz, which aims at detecting super (intermediate) mass black hole mergers and extreme (intermediate) mass ratio in-spirals. A brief introduction of its mission overview, scientific objectives, and payload design is presented. A roadmap is also given in which the launching time is set to the 2030s.
Chest wall muscle atrophy as a contributory factor for forced vital capacity decline in systemic sclerosis-associated interstitial lung disease
Authors: Nawata Takashi , Shirai Yuichiro , Suzuki Mikito , Kuwana Masataka 
Published: May 2020

Abstract

Objective
To investigate the potential contribution of accessory respiratory muscle atrophy to the decline of forced vital capacity (FVC) in patients with SSc-associated interstitial lung disease (ILD).

Methods
This single-centre, retrospective study enrolled 36 patients with SSc-ILD who underwent serial pulmonary function tests and chest high-resolution CT (HRCT) simultaneously at an interval of 1–3 years. The total extent of ILD and chest wall muscle area at the level of the ninth thoracic vertebra on CT images were evaluated by two independent evaluators blinded to the patient information. Changes in the FVC, ILD extent, and chest wall muscle area between the two measurements were assessed in terms of their correlations. Multiple regression analysis was conducted to identify the independent contributors to FVC decline.

Results
Interval changes in FVC and total ILD extent were variable among patients, whereas chest wall muscle area decreased significantly with time (P=0.0008). The FVC change was negatively correlated with the change in ILD extent (r=−0.48, P=0.003) and was positively correlated with the change in the chest wall muscle area (r = 0.53, P=0.001). Multivariate analysis revealed that changes in total ILD extent and chest wall muscle area were independent contributors to FVC decline.

Conclusion
In patients with SSc-ILD, FVC decline is attributable not only to the progression of ILD but also to the atrophy of accessory respiratory muscles. Our findings call attention to the interpretation of FVC changes in patients with SSc-ILD.
Predictors of Treatment Response to Electroconvulsive Therapy in Schizophrenia—A Nationwide Registry-Based Study
Authors: Stenmark Linnea , Popiolek Katarzyna , Bodén Robert , Brus Ole , Hammar Åsa , Landén Mikael , Lundberg Johan , Nordanskog Pia , Nordenskjöld Axel 
Published: May 2020

AbstractIntroductionUp to 30% of patients with schizophrenia respond insufficiently to antipsychotic drugs. Electroconvulsive therapy (ECT) has been reported to effectively augment the effects of antipsychotics in some of these patients. To date, there are few established predictors of treatment response to ECT in patients with schizophrenia.AimsThe primary aim was to determine the response rate to ECT in patients with schizophrenia. The secondary aim was to investigate predictors of treatment response.MethodsAll patients admitted to any Swedish hospital for schizophrenia from 2011 to 2017, who were treated with ECT while in inpatient care, were included in the Swedish National Quality Registry for ECT (Q-ECT), and were assessed using the Clinical Global Impression – Improvement (CGI-I) scale after treatment were included. CGI-I scores of 1 or 2 were considered a response to treatment. Multiple national registries were used to obtain information on demographics and clinical variables.ResultsThe study included 285 patients who were concurrently treated with antipsychotic drugs. The response rate to ECT was 73.0%. Among those patients with outcome data, treatment with long-acting injectable antipsychotics was predictive of a better response, whereas comorbid substance use disorders were predictive of a worse response.ConclusionThis study provides new evidence on predictors of who might respond among patients with schizophrenia treated by ECT. Additional studies of ECT in schizophrenia are needed.
Social Stratification and Choice-Based Policy Programs: The Case of Early Withdrawal of Retirement Savings during the Great Recession
Authors: Kline Zachary D , Pais Jeremy 
Published: May 2020

AbstractAccess to emergency funds during times of need is increasingly dependent on a “choice-based” retirement system in the United States. This study examines the operation of this choice-based retirement system across a socioeconomically stratified population impacted by the Great Recession. Using data from the Panel Study of Income Dynamics collected between 2005 and 2011, we first assess how socioeconomic status shapes access to different types of retirement plans. We then examine the varied pathways that lead to the early withdrawal of retirement savings. The results depict a multistage selection process through which socioeconomic resources structure the process of withdrawal. This occurs first through the availability of retirement funds and the makeup of the retirement portfolio and then through the likelihood of hardship. The results also reveal the importance of education in getting access to retirement savings during a hardship. The general implications for choice-based programs are discussed.
Effects of agomelatine and mirtazapine on sleep disturbances in major depressive disorder: evidence from polysomnographic and resting-state functional connectivity analyses
Authors: Mi Wei-Feng , Tabarak Serik , Wang Li , Zhang Su-Zhen , Lin Xiao , Du Lan-Ting , Liu Zhen , Bao Yan-Ping , Gao Xue-Jiao , Zhang Wei-Hua , Wang Xue-Qin , Fan Teng-Teng , Li Ling-Zhi , Hao Xiao-Nan , Fu Yi , Shi Ying , Guo Li-Hua , Sun Hong-Qiang , Liu Lin , Si Tian-Mei , Zhang Hong-Yan , Lu Lin , Li Su-Xia 
Published: May 2020

AbstractTo investigate effects of agomelatine and mirtazapine on sleep disturbances in patients with major depressive disorder. A total of 30 depressed patients with sleep disturbances, 27 of which completed the study, took agomelatine or mirtazapine for 8 weeks. Subjective scales were administered, and polysomnography was performed at baseline and at the end of week 1 and 8. Functional magnetic resonance imaging was performed at baseline and at the end of week 8. Compared with baseline, scores on the Hamilton Depression Scale, Hamilton Anxiety Scale, Pittsburgh Sleep Quality Index, Sleep Dysfunction Rating Scale, and Insomnia Severity Index after 8 weeks of treatment significantly decreased in both groups, with no significant differences between groups, accompanied by significant increases in total sleep time, sleep efficiency, and rapid eye movement (REM) sleep and significant decrease in wake after sleep onset. Mirtazapine treatment increased N3 sleep at week 1 compared with agomelatine treatment, but this difference disappeared at week 8. The increases in the percentage and duration of N3 sleep were positively correlated with increases in connectivity between right dorsal lateral prefrontal cortex (dlPFC) and right precuneus and between left posterior cingulate cortex and right precuneus in both groups, respectively. Functional connectivity (FC) between right dlPFC and left precuneus in mirtazapine group was higher compared with agomelatine group after 8 weeks of treatment. These findings indicated that both agomelatine and mirtazapine improved sleep in depressed patients, and the effect of mirtazapine was greater than agomelatine with regard to rapidly increasing N3 sleep and gradually improving FC in the brain.