bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparing Methods for Assessing Reliability
Authors: Tourangeau Roger , Sun Hanyu , Yan Ting 
Published: June 2020

AbstractThe usual method for assessing the reliability of survey data has been to conduct reinterviews a short interval (such as one to two weeks) after an initial interview and to use these data to estimate relatively simple statistics, such as gross difference rates (GDRs). More sophisticated approaches have also been used to estimate reliability. These include estimates from multi-trait, multi-method experiments, models applied to longitudinal data, and latent class analyses. To our knowledge, no prior study has systematically compared these different methods for assessing reliability. The Population Assessment of Tobacco and Health Reliability and Validity (PATH-RV) Study, done on a national probability sample, assessed the reliability of answers to the Wave 4 questionnaire from the PATH Study. Respondents in the PATH-RV were interviewed twice about two weeks apart. We examined whether the classic survey approach yielded different conclusions from the more sophisticated methods. We also examined two ex ante methods for assessing problems with survey questions and item nonresponse rates and response times to see how strongly these related to the different reliability estimates. We found that kappa was highly correlated with both GDRs and over-time correlations, but the latter two statistics were less highly correlated, particularly for adult respondents; estimates from longitudinal analyses of the same items in the main PATH study were also highly correlated with the traditional reliability estimates. The latent class analysis results, based on fewer items, also showed a high level of agreement with the traditional measures. The other methods and indicators had at best weak relationships with the reliability estimates derived from the reinterview data. Although the Question Understanding Aid seems to tap a different factor from the other measures, for adult respondents, it did predict item nonresponse and response latencies and thus may be a useful adjunct to the traditional measures.
Trade in clean energy technologies: sliding from protection to protectionism through obligations for technology transfer in climate change law, or Vice Versa?†
Authors: Koskina Anthi , Farah Paolo Davide , Ibrahim Imad Antoine 
Published: June 2020

Abstract
Global regulations involving clean energy technologies have evolved in recent decades. Such evolution came as a result of technological disparities between the North and the South. Such regulatory changes came because of the failure of developed nations to assist developing countries in obtaining said technologies. Since the beginning, international climate change law has attempted to alleviate the discrepancies in technology transfer regulations so as to introduce some form of unity, especially through various legislations, such as a global regulatory framework. In response, this article seeks to answer the following question: did international climate change law provide the necessary regulations to ensure technological accessibility to developing nations? This article will examine the accessibility of clean energy technology in relation to international climate law, especially highlighting the phases characterized by either technological protection or international collaboration. These changes reflect a continuous cycle where both circumstances and events affect international climate change law and the relations with technology state of affairs.
Are judges influenced by legally irrelevant circumstances?
Authors: Bergius My , Ernberg Emelie , Dahlman Christian , Sarwar Farhan 
Published: June 2020

Abstract
Judges should not be influenced by legally irrelevant circumstances in their legal decision making and judges generally believe that they manage legally irrelevant circumstances well. The purpose of this experimental study was to investigate whether this self-image is correct. Swedish judges (N = 256) read a vignette depicting a case of libel, where a female student had claimed on her blog that she had been sexually harassed by a named male professor. The professor had sued the student for libel and the student retracted her claim during the hearing. Half of the judges received irrelevant information - that the professor himself had been convicted of libel a year earlier, while the other half did not receive this information. For the outcome variable, the judges were asked to state how much compensation the student should pay the professor. Those judges who received information about the professor himself having been convicted of libel stated that he should be given significantly less compensation than those who did not receive the irrelevant information. The results show that the judges’ decision was affected by legally irrelevant circumstances. Implications for research and practice are discussed
Analytical solutions of radiative transfer equations in accretion discs with finite optical depth
Authors: Samadi M , Habibi F , Abbassi S 
Published: June 2020

ABSTRACT
The main purpose of this paper is to obtain analytical solutions for radiative transfer equations related to the vertical structure of accretion discs with finite optical depth. In the non-grey atmosphere, we employ the optical-depth dependent Eddington factor to define the relationship between the mean intensity and radiation stress tensor. Analytical solutions are achieved for two cases: (i) radiative equilibrium, and (ii) a disc with uniform internal heating and both cases are assumed to be in local thermodynamical equilibrium (LTE), too. These solutions enable us to study probable role of scattering and disc optical depth on the emergent intensity and other radiative quantities. Our results show that for the first case, the surface value of mean intensity with constant Eddington factor is three times larger than that with variable factor. Moreover, scattering has no role in the vertical radiative structure of discs with the assumptions of the first case. On the other hand, for the second case, we encounter reductions in all radiative quantities as the photon destruction probability decreases (which is equivalent to increasing scattering). Furthermore, for both cases with total optical depth less than unity, the outward intensity towards the polar direction becomes less than that from the edges of disc which is contrary to limb-darkening. At the end, we apply our results to find the spectrum from accretion systems, based on two dynamical models. Consequently, we can see that how the total optical depth varies with frequency and causes remarkable changes on the emergent spectra.
Scalable Empirical Mixture Models That Account for Across-Site Compositional Heterogeneity
Authors: Schrempf Dominik , Lartillot Nicolas , Szöllősi Gergely 
Published: June 2020

AbstractBiochemical demands constrain the range of amino acids acceptable at specific sites resulting in across-site compositional heterogeneity of the amino acid replacement process. Phylogenetic models that disregard this heterogeneity are prone to systematic errors, which can lead to severe long-branch attraction artifacts. State-of-the-art models accounting for across-site compositional heterogeneity include the CAT model, which is computationally expensive, and empirical distribution mixture models estimated via maximum likelihood (C10–C60 models). Here, we present a new, scalable method EDCluster for finding empirical distribution mixture models involving a simple cluster analysis. The cluster analysis utilizes specific coordinate transformations which allow the detection of specialized amino acid distributions either from curated databases or from the alignment at hand. We apply EDCluster to the HOGENOM and HSSP databases in order to provide universal distribution mixture (UDM) models comprising up to 4,096 components. Detailed analyses of the UDM models demonstrate the removal of various long-branch attraction artifacts and improved performance compared with the C10–C60 models. Ready-to-use implementations of the UDM models are provided for three established software packages (IQ-TREE, Phylobayes, and RevBayes).
Non-parametric estimation and evaluation of capability sets
Authors: Verbunt Pim , Rogge Nicky , Van Puyenbroeck Tom 
Published: June 2020

AbstractA major difficulty for the application of Amartya Sen’s capability approach is that individual capability sets cannot readily be observed. This article proposes a non-parametric framework to construct such sets, on the basis of observed functionings of individuals that are taken to belong to a group sharing the same capability set. Within this framework, the earlier theoretical proposals of Muellbauer to compare different capability sets can be easily implemented. Associated robust empirical estimators are provided and applied to EU-SILC data on household income, material living conditions, housing quality and health; we illustrate our approach with a multilateral comparison of 32 European countries, with a comparison of both a ‘fixed ray’ and a ‘multiple rays’ evaluation metric to compare French and German capability sets, and with a multilateral comparison of socioeconomic sub-groups in France.
Early treatment of bilateral fungal keratitis with corneal cross-linking as adjuvant therapy
Authors: González Castellanos Juan Cruz , Osaba Matías , Reviglio Virginia , Canchi Marcela Tatiana , Arrigone Maitén Cuyén , Reviglio Víctor Eduardo 
Published: June 2020

Abstract
Fungal keratitis is an ocular infection that has no standardized treatment. The etiological agents most frequently reported in the literature are Fusarium spp., Aspergillus spp., Alternaria spp. and Curvularia spp., related to injuries and Candida albicans related to contact lens wear. Here we present a case of bilateral fungal keratitis of a few days of evolution with insufficient response to antifungal pharmacological treatment and with early application of cross-linking in both eyes as an adjuvant therapy. A review of the current status of cross-linking for the treatment of corneal infections is presented.
Endometrial polyp filled with gestational tissues remained undiscovered in an infertile woman for years: a case report
Authors: Dhemesh Najah , Hamsho Maysam , Jarbouh Habib 
Published: June 2020

Abstract
Recurrent pregnancy loss (RPL) is a common disease, which presents as two, three or more failed pregnancies. It is attributed to many risk factors, yet half of the cases are idiopathic. In this report, we present a case of a 44-year-old woman with a complaint of secondary infertility for 10 years and a history of three spontaneous abortions. Blood tests and images showed no abnormalities, except for hysteroscopy which showed a polyp-like mass. Pathology revealed an endometrial stroma showing severe decidualization with a lot of gestational villi showing fibrosis and hyaline degeneration, features of old gestational product death, with no glands crowding or cellular atypia. In this case, the conception products were not preceded with a miscarriage and did not cause any symptoms indicating its existing. The asymptomatic endometrial polyp filled with fibrotic gestational villi without a prior miscarriage is an unprecedented case in the medical literature.
Prognosis of adult idiopathic inflammatory myopathy-associated interstitial lung disease: a retrospective study of 679 adult cases
Authors: Li Shan , Sun Yuxin , Shao Chi , Huang Hui , Wang Qian , Xu Kai , Zhang Xin , Liu Peng , Zeng Xiaofeng , Xu Zuojun 
Published: June 2020

Abstract

Objectives
Few studies have investigated the prognostic factors for idiopathic inflammatory myopathy-associated interstitial lung disease (IIM-ILD) across different clinical/serological phenotypes.

Methods
We conducted a retrospective analysis of patients diagnosed with IIM between January 2012 and December 2017.

Results
Of the 760 IIM cases registered, 679 adult cases were included in this study. ILD was present in 508 cases, and the presence of ILD in the clinically amyopathic DM, DM and PM groups was 92.7, 73.6 and 55.1%, respectively (P &lt; 0.01). The prevalence of ILD in the anti-synthetase antibody (ASA)+-IIM group was higher than that in ASA–-IIM group (95.2 vs 72.4%, P &lt; 0.01); no such difference was found between the anti-histidyl-tRNA synthetase (Jo-1)+-IIM and Jo-1–ASA+-IIM groups (93.0 vs 98.5%, P &gt; 0.05). The prevalence of ILD in the melanoma differentiation-associated protein-5 (MDA-5)+-IIM group was higher than that in MDA-5–-IIM group (97.8 vs 72.1%, P &lt; 0.01). Among adults with IIM, men with concurrent ILD, who were older than 50 years, were most likely to die. No significant difference was found in the all-cause mortality rates between DM-ILD and clinically amyopathic DM-ILD groups (33.3 vs 23%, P &gt; 0.05), although both were higher than that in PM group (13.2%, P = 0.01 and P &lt; 0.05, respectively). No difference was found in the all-cause mortality rates between MDA5–ASA–-IM-ILD and MDA5–ASA+-IM-ILD groups (17.2 vs 12.8%, P &gt; 0.05), and both were lower than that in MDA5+ASA–-IM-ILD group (33.7%, P &lt; 0.05).

Conclusion
The prevalence of ILD in IIM and the prognosis of IIM-ILD patients may vary depending on the statuses of the ASA and MDA-5 antibodies.
Diffusion vs. direct transport in the precision of morphogen readout
Authors: Fancher Sean , Mugler Andrew 
Published: June 2020

AbstractMorphogen profiles allow cells to determine their position within a developing organism, but not all morphogen profiles form by the same mechanism. Here we derive fundamental limits to the precision of morphogen concentration sensing for two canonical mechanisms: the diffusion of morphogen through extracellular space and the direct transport of morphogen from source cell to target cell, e.g., via cytonemes. We find that direct transport establishes a morphogen profile without adding noise in the process. Despite this advantage, we find that for suffciently large values of profile length, the diffusion mechanism is many times more precise due to a higher refresh rate of morphogen molecules. We predict a profile lengthscale below which direct transport is more precise, and above which diffusion is more precise. This prediction is supported by data from a wide variety of morphogens in developing organisms.
A targeted e-learning approach to reduce student mixing during a pandemic
Authors: Yeo Sing Chen , Lai Clin K.Y. , Tan Jacinda , Gooley Joshua J. 
Published: June 2020

AbstractThe COVID-19 pandemic has resulted in widespread closure of schools and universities. These institutions have turned to distance learning to provide educational continuity. Schools now face the challenge of how to reopen safely and resume in-class learning. However, there is little empirical evidence to guide decision-makers on how this can be achieved. Here, we show that selectively deploying e-learning for larger classes is highly effective at decreasing campus-wide opportunities for student-to-student contact, while allowing most in-class learning to continue uninterrupted. We conducted a natural experiment at a large university that implemented a series of e-learning interventions during the COVID-19 outbreak. Analyses of >24 million student connections to the university Wi-Fi network revealed that population size can be manipulated by e-learning in a targeted manner according to class size characteristics. Student mixing showed accelerated growth with population size according to a power law distribution. Therefore, a small e-learning dependent decrease in population size resulted in a large reduction in student clustering behaviour. Our results show that e-learning interventions can decrease potential for disease transmission while minimizing disruption to university operations. Universities should consider targeted e-learning a viable strategy for providing educational continuity during early or late stages of a disease outbreak.
Ush regulates hemocyte-specific gene expression, fatty acid metabolism and cell cycle progression and cooperates with dNuRD to orchestrate hematopoiesis
Authors: Lenz Jonathan , Liefke Robert , Funk Julianne , Shoup Samuel , Nist Andrea , Stiewe Thorsten , Schulz Robert , Tokusumi Yumiko , Albert Lea , Raifer Hartmann , Förstemann Klaus , Vázquez Olalla , Tokusumi Tsuyoshi , Fossett Nancy , Brehm Alexander 
Published: June 2020

AbstractThe generation of lineage-specific gene expression programmes that alter proliferation capacity, metabolic profile and cell type-specific functions during differentiation from multipotent stem cells to specialised cell types is crucial for development. During differentiation gene expression programmes are dynamically modulated by a complex interplay between sequence-specific transcription factors, associated cofactors and epigenetic regulators. Here, we study U-shaped (Ush), a multi-zinc finger protein that maintains the multipotency of stem cell-like hemocyte progenitors during Drosophila hematopoiesis. Using genomewide approaches we reveal that Ush binds to promoters and enhancers and that it controls the expression of three gene classes that encode proteins relevant to stem cell-like functions and differentiation: cell cycle regulators, key metabolic enzymes and proteins conferring specific functions of differentiated hemocytes. We employ complementary biochemical approaches to characterise the molecular mechanisms of Ush-mediated gene regulation. We uncover distinct Ush isoforms one of which binds the Nucleosome Remodeling and Deacetylation (NuRD) complex using an evolutionary conserved peptide motif. Remarkably, the Ush/NuRD complex specifically contributes to the repression of lineage-specific genes but does not impact the expression of cell cycle regulators or metabolic genes. This reveals a mechanism that enables specific and concerted modulation of functionally related portions of a wider gene expression programme. Finally, we use genetic assays to demonstrate that Ush and NuRD regulate enhancer activity during hemocyte differentiation in vivo and that both cooperate to suppress the differentiation of lamellocytes, a highly specialised blood cell type. Our findings reveal that Ush coordinates proliferation, metabolism and cell type-specific activities by isoform-specific cooperation with an epigenetic regulator.
In situstructure of the AcrAB-TolC efflux pump at subnanometer resolution
Authors: Chen Muyuan , Shi Xiaodong , Yu Zhili , Fan Guizhen , Serysheva Irina , Baker Matthew L. , Luisi Ben F. , Ludtke Steven J. , Wang Zhao 
Published: June 2020

AbstractIn Gram-negative bacteria, tripartite efflux pump AcrAB-TolC plays a prominent role in antibiotic resistance. We have used high resolution cryo-ET to visualize the structure ofEscherichia coliAcrAB-TolC at a 7 Å resolution in intact cells. The resulting structures show the detailed architecture of the assembled complex embedded into cell envelope. Interactions with the inner membrane enable crosstalk between AcrB and TolC through AcrA, suggesting that assembly in the native cellular environment is critical for the pump activation mechanism, where the allosteric activating signal is triggered by the alternate binding of AcrA to the lipid membrane and AcrB porter domain. We establish a platform for high resolutionin situstructural studies of bacteria efflux pump, which can yield critical information in understanding complex assemblies’ function.One sentence summaryA 7 Åin situstructure of the AcrAB-TolC pump from bacteria by cryo-ET reveals mechanisms for active efflux.
Broad-Range Virus Detection and Discovery Using Microfluidic PCR Coupled with High-throughput Sequencing
Authors: Tao Ying , Paden Clinton R. , Queen Krista , Zhang Jing , Tyagi Eishita , Tong Suxiang 
Published: June 2020

AbstractThere is a need for a comprehensive and sensitive method to test for a broad range of viral pathogens in samples without any identifiable pathogen detected. Real-time PCR assays are sensitive and rapid, but their specificity limits their utility in detecting divergent agents. Shotgun high-throughput sequencing methods provide unbiased sequence identification, however, they have limited sensitivity and require complex analyses. In order to meet the need for a sensitive, high-throughput virus detection and discovery platform with good sensitivity, we combine two existing technologies, broadly-reactive consensus-degenerate pan-viral group PCR and the MiSeq sequencer (Illumina), using the Access Array (Fluidigm), a commercially-available microfluidic PCR system. Pan-viral group primers target conserved regions of virus taxonomic groups and can amplify known and potentially novel species. The Access Array employs dozens of these assays in parallel, which are then sequenced all at once on the MiSeq. In this study, we run a respiratory panel of pan-viral group PCR assays using AA-PCR-Seq. We validate the panel on a collection of representative human and animal samples, comparing it to qPCR and shotgun next-generation sequencing (NGS). AA-PCR-Seq provides a robust, straightforward method for screening large numbers of samples for virus detection and discovery.
Computation noise promotes cognitive resilience to adverse conditions during decision-making
Authors: Findling Charles , Wyart Valentin 
Published: June 2020

SummaryRandom noise in information processing systems is widely seen as detrimental to function. But despite the large trial-to-trial variability of neural activity and behavior, humans and other animals show a remarkable adaptability to unexpected adverse events occurring during task execution. This cognitive ability, described as constitutive of general intelligence, is missing from current artificial intelligence (AI) systems which feature exact (noise-free) computations. Here we show that implementing computation noise in recurrent neural networks boosts their cognitive resilience to a variety of adverse conditions entirely unseen during training, in a way that resembles human and animal cognition. In contrast to artificial agents with exact computations, noisy agents exhibit hallmarks of Bayesian inference acquired in a ‘zero-shot’ fashion – without prior experience with conditions that require these computations for maximizing rewards. We further demonstrate that these cognitive benefits result from free-standing regularization of activity patterns in noisy neural networks. Together, these findings suggest that intelligence may ride on computation noise to promote near-optimal decision-making in adverse conditions without any engineered cognitive sophistication.
Lyophilized cell-free systems display tolerance to organic solvent exposure
Authors: Lee Marilyn S. , Raig Rebecca M. , Gupta Maneesh K. , Lux Matthew W. 
Published: June 2020

AbstractCell-free systems offer a powerful way to deliver biochemical activity to the field without cold chain storage. These systems are capable of sensing as well as biosynthesis of useful molecules at the point of need. So far, cell-free protein synthesis (CFPS) reactions have been studied as aqueous solutions in test tubes or absorbed into paper or cloth. Embedding biological functionality into broadly-used materials, such as plastic polymers, represents an attractive goal. Unfortunately, this goal has for the most part remained out of reach, presumably due to the fragility of biological systems outside of aqueous environments. Here, we describe a surprising and useful feature of lyophilized cell-free lysate systems: tolerance to a variety of organic solvents. Screens of individual CFPS reagents and different CFPS methods reveal that solvent tolerance varies by CFPS reagent composition. Tolerance to suspension in organic solvents may facilitate the use of polymers to deliver dry cell-free reactions in the form of coatings or fibers, or allow dosing of analytes or substrates dissolved in non-aqueous solvents, among other processing possibilities.