bluuebunny/crossref_metadata_2025_split huggingface dataset:
DeepPASTA: deep neural network based polyadenylation site analysis
Authors: Arefeen Ashraful , Xiao Xinshu , Jiang Tao 
Published: April 2019

Abstract

Motivation
Alternative polyadenylation (polyA) sites near the 3′ end of a pre-mRNA create multiple mRNA transcripts with different 3′ untranslated regions (3′ UTRs). The sequence elements of a 3′ UTR are essential for many biological activities such as mRNA stability, sub-cellular localization, protein translation, protein binding and translation efficiency. Moreover, numerous studies in the literature have reported the correlation between diseases and the shortening (or lengthening) of 3′ UTRs. As alternative polyA sites are common in mammalian genes, several machine learning tools have been published for predicting polyA sites from sequence data. These tools either consider limited sequence features or use relatively old algorithms for polyA site prediction. Moreover, none of the previous tools consider RNA secondary structures as a feature to predict polyA sites.

Results
In this paper, we propose a new deep learning model, called DeepPASTA, for predicting polyA sites from both sequence and RNA secondary structure data. The model is then extended to predict tissue-specific polyA sites. Moreover, the tool can predict the most dominant (i.e. frequently used) polyA site of a gene in a specific tissue and relative dominance when two polyA sites of the same gene are given. Our extensive experiments demonstrate that DeepPASTA signisficantly outperforms the existing tools for polyA site prediction and tissue-specific relative and absolute dominant polyA site prediction.

Availability and implementation
https://github.com/arefeen/DeepPASTA

Supplementary information
Supplementary data are available at Bioinformatics online.
Religious service attendance, health behaviors and well-being—an outcome-wide longitudinal analysis
Authors: Pawlikowski Jakub , Białowolski Piotr , Węziak-Białowolska Dorota , VanderWeele Tyler J 
Published: April 2019

Abstract

Background
Previous studies of relationship between religiosity, health behaviors and well-being have showed mainly positive relationships, however, are very often limited to results of associative nature and subject to unmeasured confounding. This study focused on evaluating evidence for a positive association between religious service attendance (RSA), health behaviors and well-being in a longitudinal setting and robustness of these associations to unmeasured confounding.

Methods
Three waves (2009, 2011 and 2015) of the biennial longitudinal Polish household panel study with response from 6400 respondents were analyzed. Evidence for a positive and robust association between RSA and outcome variables was evaluated using outcome-wide regression analysis with control of all variables temporally prior to the exposure and sensitivity measures (E-values) to give information on the extent to which an unmeasured confounder would need to be associated with both the exposure and the outcomes.

Results
RSA is associated with reduced risk of unhealthy behaviors (smoking, alcohol use) and higher emotional well-being. These relationships are robust to substantial unmeasured confounding and difficult to explain by reference to other, unknown, variables. Evidence for a positive relationship between RSA and other well-being variables (social, physical) was less clear.

Conclusions
Religiosity may play an important role in public health, particularly in prevention of non-communicable diseases. The strong and robust associations between RSA and some health behaviors (i.e. tobacco use, alcohol abuse) and emotional well-being should arguably be taken into account in health education, health promotion programs, health prevention policy and psychotherapeutic approaches, particularly in more religious populations.
Commemorating Jules Michelet, 1876, 1882, 1898: The productivity of banality
Authors: Creyghton Camille 
Published: April 2019

Abstract
Between 1870 and 1900 three commemorative events for Jules Michelet took place in France: his burial at the Père Lachaise cemetery in 1876, the unveiling of his monument in 1882 and the national commemoration of his centenary in 1898. The republican historian was thus a major figure in Third Republic memory culture, while he was also considered one of its sources of inspiration. This article examines how throughout successive commemorations Michelet’s legacy was appropriated and popularized by the regime and how this resulted in what can be called a ‘banalizing of memory’. Furthermore, it argues that this banalizing process, despite criticism based on Michelet’s own work, was productive and led to an expansion of the public’s awareness of Michelet. Rather than being a sign of declining memory, banality in some contexts was the most viable option for realizing the aims of a commemoration.
Barents Sea cod (Gadus morhua) diet composition: long-term interannual, seasonal, and ontogenetic patterns
Authors: Holt Rebecca E , Bogstad Bjarte , Durant Joël M , Dolgov Andrey V , Ottersen Geir 
Published: April 2019

Abstract
Atlantic cod (Gadus morhua) is an ecologically and commercially important species in the North-Atlantic region. Cod is a top predator and information on its trophic ecology is integral for understanding predator–prey relationships and food-web dynamics. We present an analysis of the trophic patterns of Barents Sea (BS) cod using a unique 33-year time-series of stomach-content data from 1984 to 2016. We assessed patterns in diet (prey) composition across years, between seasons, as well as ontogenetic trends in diet, including predator–prey size relationships. Ontogenetic shifts in diet were observed, with fish becoming more important prey with increasing cod size. A very early onset of piscivory was found in &lt;20 cm cod. Cannibalism was found in cod &gt; 20 cm and increased with size. Juvenile cod exhibit a tendency towards consuming prey up to 33% of their body length, whereas larger cod feed on all prey sizes, resulting in asymmetric predator–prey size distributions. Diet varied significantly during 1984–2016, consistent with changes in both prey, cod abundance, and distribution. Seasonal differences were observed; capelin dominated the winter diet, whereas cod, polar cod, and other fish species were prevalent in summer/autumn months. This work represents an important step towards understanding trophic linkages that determine BS ecosystem dynamics.
Impact of ART-induced viral suppression on the HIV epidemic in Italy
Authors: Papa Federico , Felici Giovanni , Franzetti Marco , Gandolfi Alberto , Sinisgalli Carmela 
Published: April 2019

Abstract
The present study aims to clarify the role of the fraction of patients under antiretroviral therapy (ART) achieving viral suppression (VS) (i.e. having plasma viral load below the detectability threshold) on the human immunodeficiency virus (HIV) epidemic in Italy. Based on the hypothesis that VS makes the virus untransmittable, we extend a previous model and we develop a time-varying ordinary differential equation model with immigration and treatment, where the naive and non-naive populations of infected are distinguished, and different compartments account for treated subjects virally suppressed and not suppressed. Moreover, naive and non-naive individuals with acquired immune deficiency syndrome (AIDS) are considered separately. Clinical data stored in the nationwide database Antiviral Response Cohort Analysis are used to reconstruct the history of the fraction of virally suppressed patients since highly active ART introduction, as well as to assess some model parameters. Other parameters are set according to the literature and the final model calibration is obtained by fitting epidemic data over the years 2003–2015. Predictions on the evolution of the HIV epidemic up to the end of 2035 are made assuming different future trends of the fraction of virally suppressed patients and different eligibility criteria for treatment. Increasing the VS fraction is found to reduce the incidence, the new cases of AIDS and the deaths from AIDS per year, especially in combination with early ART initiation. The asymptotic properties of a time-invariant formulation of the model are studied, and the existence and global asymptotic stability of a unique positive equilibrium are proved.
Linezolid resistance in patients with drug-resistant TB and treatment failure in South Africa
Authors: Wasserman Sean , Louw Gail , Ramangoaela Limpho , Barber Garrick , Hayes Cindy , Omar Shaheed Vally , Maartens Gary , Barry Clifton , Song Taeksun , Meintjes Graeme 
Published: April 2019

Abstract

Objectives
Limited data exist on clinical associations and genotypic correlates of linezolid resistance in Mycobacterium tuberculosis. We aimed to describe mutations and clinical factors associated with phenotypic linezolid resistance from patients with drug-resistant TB at two public sector facilities in South Africa.

Methods
Adults and adolescents with treatment failure (culture positivity ≥4 months) on a linezolid-containing regimen were retrospectively identified. Phenotypic resistance, as defined by a linezolid MIC >1 mg/L, was assessed for retrieved isolates using broth microdilution. Targeted sequencing of rrl and rplC was performed, irrespective of growth on subculture.

Results
Thirty-nine patients with linezolid-based treatment failure were identified, 13 (33%) of whom had phenotypic or genotypic linezolid resistance after a median duration of 22 months (range = 7–32) of linezolid therapy. Paired MIC testing and genotyping was performed on 55 unique isolates. All isolates with phenotypic resistance (n = 16) were associated with known resistance mutations, most frequently due to the T460C substitution in rplC (n = 10); rrl mutations included G2814T, G2270C/T and A2810C. No mutations were detected in isolates with MICs at or below the critical concentration.

Conclusions
Linezolid resistance occurred in a third of patients with drug-resistant TB and treatment failure. Resistance occurred late and was predicted by a limited number of mutations in rrl and rplC. Screening for genotypic resistance should be considered for patients with a positive culture after 4 months of linezolid therapy in order to optimize treatment and avoid the toxicity of ineffective linezolid therapy.
Determination of Quinolone Antibiotic Residues in Human Serum and Urine Using High-Performance Liquid Chromatography/Tandem Mass Spectrometry
Authors: Wang Xiaoli , Guo Tao , Wei Yunbo , Xu Guiju , Li Na , Feng Jinhong , Zhao Rusong 
Published: April 2019

Abstract
Quinolone antibiotic residues may pose potential threat to human health. A rapid and sensitive method was developed for the determination of quinolone residues in human serum and urine. After solid phase extraction (SPE) process, eight quinolone residues were analyzed by high-performance liquid chromatography/tandem mass spectrometry (HPLC-MS/MS) using ciprofloxacin-d8 as the internal standard. The relative standard deviation of intra-day and inter-day precision for the eight quinolones were less than 7.52% and the accuracies ranged from 95.8% to 103% in human serum, and from 94.1% to 104% in human urine. The extraction recoveries for the eight quinolones varied from 80.2% to 113% in human serum and 83.4% to 117% in human urine. The limit of detection for the eight quinolones was 0.50–1.00 ng/mL. Quinolone antibiotic residues in human serum and urine from 12 volunteers were successfully analyzed with the validated method. The SPE-HPLC-MS/MS method was useful for accurate determination of quinolone antibiotic residues in human body.
Trends in the Evolution of Floodplain Management in Australia: Risk Assessment, Precautionary and Robust Decision-Making
Authors: England Philippa 
Published: April 2019

Abstract
This article tracks the evolution of floodplain development policy in Australia and analyses some recent case law in the light of that policy. Although the dominant policy paradigm promotes strategic risk management combined with affordable and proportionate risk mitigation, the case law analysed adopts a more risk averse and normative tone. There seems to be a clear dichotomy between the preferred risk management approach of the main policy documents and actual practice, at least in the courts. The reasons for this divergence and some reflections on the future of the precautionary principle in the light of this evidence are discussed in the final sections.
Noninvasive Sampling Reveals Short-Term Genetic Rescue in an Insular Red Fox Population
Authors: Quinn Cate B , Alden Preston B , Sacks Benjamin N 
Published: April 2019

AbstractGenetic factors in the decline of small populations are extremely difficult to study in nature. We leveraged a natural experiment to investigate evidence of inbreeding depression and genetic rescue in a remnant population of subalpine-specialized Sierra Nevada red foxes (Vulpes vulpes necator) using noninvasive genetic monitoring during 2010–2017. Only 7 individuals were detected in the first 2 years. These individuals assigned genetically to the historical population and exhibited genetic hallmarks of inbreeding and no evidence of reproduction. Two years into the study, we detected 2 first-generation immigrant males from a recently expanding population of red foxes in the Great Basin Desert. Through annual resampling of individuals (634 red fox DNA samples, 41 individuals) and molecular reconstruction of pedigrees, we documented 1–3 litters/year for 5 years, all descended directly or indirectly from matings involving immigrant foxes. The observed heterozygosity and allelic richness of the population nearly doubled in 2 years. Abundance increased, indicative of a rapidly expanding population. Throughout the study, adult survival was high. Restoration of gene flow apparently improved the demographic trajectory of this population in the short term. Whether these benefits continue in the longer term could depend on numerous factors, such as maintenance of any locally adapted alleles. This study highlights the value of noninvasive genetic monitoring to assess rapidly shifting conditions in small populations. Uncertainties about the longer-term trajectory of this population underscore the need to continue monitoring and to research potential for both negative and positive aspects of continued genetic infusion.
From positive PDL to its non-classical extensions
Authors: Sedlár Igor , Punčochář Vít 
Published: April 2019

AbstractWe provide a complete binary implicational axiomatization of the positive fragment of propositional dynamic logic (PDL). The intended application of this result are completeness proofs for non-classical extensions of positive PDL. Two examples are discussed in this article, namely, a paraconsistent extension with modal De Morgan negation and a substructural extension with the residuated operators of the non-associative Lambek calculus. Informal interpretations of these two extensions are outlined.
Tracking reasons with extensions of relevant logics
Authors: Standefer Shawn 
Published: April 2019

AbstractIn relevant logics, necessary truths need not imply each other. In justification logic, necessary truths need not all be justified by the same reason. There is an affinity to these two approaches that suggests their pairing will provide good logics for tracking reasons in a fine-grained way. In this paper, I will show how to extend relevant logics with some of the basic operators of justification logic in order to track justifications or reasons. I will define and study three kinds of frames for these logics. For the first kind of frame, I show soundness and highlight a difficulty in proving completeness. This motivates two alternative kinds of frames, with respect to which completeness results are obtained. Axioms to strengthen the justification logic portions of these logics are considered. I close by developing an analogy between the dot operator of justification logic and theory fusion in relevant logics.
Partiality and its dual in natural implicative expansions of Kleene’s strong 3-valued matrix with only one designated value
Authors: Robles Gemma , Méndez José M 
Published: April 2019

Abstract
Equivalent overdetermined and underdetermined bivalent Belnap–Dunn type semantics for the logics determined by all natural implicative expansions of Kleene’s strong 3-valued matrix with only one designated value are provided.
A unified-models analysis of the development of sexual size dimorphism in Damaraland mole-rats, Fukomys damarensis
Authors: Thorley Jack , Clutton-Brock Tim H 
Published: April 2019

AbstractIndividual variation in growth rates often generates variation in fitness. However, the ability to draw meaningful inferences from growth data depends on the use of growth models that allow for direct comparisons of growth between the sexes, between populations, and between species. Unlike traditional sigmoid functions, a recently parameterized family of unified growth models provides a reliable basis for comparisons since each parameter affects a single curve characteristic and parameters are directly comparable across the unified family. Here, we use the unified-models approach to examine the development of sexual size dimorphism in Damaraland mole-rats (Fukomys damarensis), where breeding males are larger than breeding females. Using skeletal measurements, we show here that the larger size of male Damaraland mole-rats arises from an increased growth rate across the entire period of development, rather than through sex differences in the duration or timing of growth. Male-biased skeletal size dimorphism is not unusual among rodents, and our measures of sex differences in size in captive mole-rats are close to sexual size differences in the wild, where size dimorphism = 1.04 (male:female). We hope our study will encourage the wide use of unified growth models by mammalogists.
ALGORITHMS, MACHINE LEARNING, AND COLLUSION
Authors: Schwalbe Ulrich 
Published: April 2019

AbstractThis paper discusses whether self-learning price-setting algorithms can coordinate their pricing behavior to achieve a collusive outcome that maximizes the joint profits of the firms using them. Although legal scholars have generally assumed that algorithmic collusion is not only possible but also exceptionally easy, computer scientists examining cooperation between algorithms as well as economists investigating collusion in experimental oligopolies have countered that coordinated, tacitly collusive behavior is not as rapid, easy, or even inevitable as often suggested. Research in experimental economics has shown that the exchange of information is vital to collusion when more than two firms operate within a given market. Communication between algorithms is also a topic in research on artificial intelligence, in which some scholars have recently indicated that algorithms can learn to communicate, albeit in somewhat limited ways. Taken together, algorithmic collusion currently seems far more difficult to achieve than legal scholars have often assumed and is thus not a particularly relevant competitive concern at present. Moreover, there are several legal problems associated with algorithmic collusion, including questions of liability, of auditing and monitoring algorithms, and of enforcing competition law.
The Extended Disc Galaxy Exploration Science Survey: description and surface brightness profile properties
Authors: Staudaher Shawn M , Dale Daniel A , van Zee Liese 
Published: April 2019

Abstract
The survey description and near-infrared properties for 92 galaxies are presented for the Extended Disc Galaxy Exploration Science (EDGES) Survey, along with an investigation into the properties of the stellar haloes of these galaxies. EDGES is a Spitzer Space Telescope Warm Mission program designed to reach the surface brightness limit (∼0.5 kJy sr−1 or 29 AB mag arcsec−2) of the Infrared Array Camera (IRAC) 3.6 and 4.5 ${\rm \mu}$m bands for a wide range of galaxy types found within the local volume. The surface brightness profiles exhibit a large range in disc scale length, with breaks more frequently seen than in previous studies, owing in large part to the extremely deep near-infrared imaging. A number of these surface brightness profile breaks may be due to stellar haloes, up to seven galaxies out of the full sample of 92 galaxies, and we explore these implications in relation to current cosmological models. We also report the discovery of a new tidal stream near NGC 3953.
Observation of a possible superflare on Proxima Centauri
Authors: Kielkopf John F , Hart Rhodes , Carter Bradley D , Marsden Stephen C 
Published: April 2019

ABSTRACT
We report the observation on ut 2017 July 1 of an unusually powerful flare detected in near-infrared continuum photometry of Proxima Centauri. During a campaign monitoring the star for possible exoplanet transits, we identified an increase in Sloan i’ flux leading to an observed peak at BJD 2457935.996 that was at least 10 per cent over pre-flare flux in this band. It was followed by a two-component rapid decline in the first 100 s that became a slower exponential decay with time constant of 1350 s. A smaller flare event 1300 s after the first added an incremental peak flux increase of 1 per cent of pre-flare flux. Since the onset of the flare was not fully time resolved at a cadence of 62 s, its actual peak value is unknown but greater than the time average over a single exposure of 20 s. The i’ band is representative of broad optical and near-IR continuum flux over which the integrated energy of the flare is 100 times the stellar luminosity. This meets the criteria that established the concept of superflares on similar stars. The resulting implied ultraviolet flux and space weather could have had an extreme effect on the atmospheres of planets within the star’s otherwise habitable zone.
Adaptive Changes in Hemoglobin Function in High-Altitude Tibetan Canids Were Derived via Gene Conversion and Introgression
Authors: Signore Anthony V , Yang Ying-Zhong , Yang Quan-Yu , Qin Ga , Moriyama Hideaki , Ge Ri-Li , Storz Jay F 
Published: April 2019

Abstract
A key question in evolutionary biology concerns the relative importance of different sources of adaptive genetic variation, such as de novo mutations, standing variation, and introgressive hybridization. A corollary question concerns how allelic variants derived from these different sources may influence the molecular basis of phenotypic adaptation. Here, we use a protein-engineering approach to examine the phenotypic effect of putatively adaptive hemoglobin (Hb) mutations in the high-altitude Tibetan wolf that were selectively introgressed into the Tibetan mastiff, a high-altitude dog breed that is renowned for its hypoxia tolerance. Experiments revealed that the introgressed coding variants confer an increased Hb–O2 affinity in conjunction with an enhanced Bohr effect. We also document that affinity-enhancing mutations in the β-globin gene of Tibetan wolf were originally derived via interparalog gene conversion from a tandemly linked β-globin pseudogene. Thus, affinity-enhancing mutations were introduced into the β-globin gene of Tibetan wolf via one form of intragenomic lateral transfer (ectopic gene conversion) and were subsequently introduced into the Tibetan mastiff genome via a second form of lateral transfer (introgression). Site-directed mutagenesis experiments revealed that the increased Hb–O2 affinity requires a specific two-site combination of amino acid replacements, suggesting that the molecular underpinnings of Hb adaptation in Tibetan mastiff (involving mutations that arose in a nonexpressed gene and which originally fixed in Tibetan wolf) may be qualitatively distinct from functionally similar changes in protein function that could have evolved via sequential fixation of de novo mutations during the breed’s relatively short duration of residency at high altitude.