bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk Estimation with a Time-Varying Probability of Zero Returns
Authors: Sucarrat Genaro , Grønneberg Steffen 
Published: April 2020

AbstractThe probability of an observed financial return being equal to zero is not necessarily zero, or constant. In ordinary models of financial return, however, for example, autoregressive conditional heteroskedasticity, stochastic volatility, Generalized Autoregressive Score, and continuous-time models, the zero probability is zero, constant, or both, thus frequently resulting in biased risk estimates (volatility, value-at-risk [VaR], expected shortfall [ES], etc.). We propose a new class of models that allows for a time-varying zero probability that can either be stationary or nonstationary. The new class is the natural generalization of ordinary models of financial return, so ordinary models are nested and obtained as special cases. The main properties (e.g., volatility, skewness, kurtosis, VaR, ES) of the new model class are derived as functions of the assumed volatility and zero-probability specifications, and estimation methods are proposed and illustrated. In a comprehensive study of the stocks at New York Stock Exchange, we find extensive evidence of time-varying zero probabilities in daily returns, and an out-of-sample experiment shows that corrected risk estimates can provide significantly better forecasts in a large number of instances.
Hematologic adaptation to the subterranean environment by the naked mole-rat, Heterocephalus glaber (Ctenohystrica: Heterocephalidae)
Authors: Holtze Susanne , Koch Rosie , Hildebrandt Thomas Bernd , Lemma Alemayehu , Szafranski Karol , Platzer Matthias , Alemayehu Fitsum , Goeritz Frank , Braude Stan 
Published: April 2020

AbstractOne method burrowing animals are hypothesized to use in adapting to the presumed hypoxic subterranean environment is increasing the oxygen-carrying capacity of blood. A number of recent studies have examined hematologic parameters in laboratory-reared naked mole-rats, but not in animals living under natural atmospheric conditions. To our knowledge, blood chemistry parameters have never been systematically assessed in a fossorial mammal. In this study we examined the blood of wild naked mole-rats in Kenya and Ethiopia to determine whether their blood chemistry differs significantly from naked mole-rats born and living in captivity. We also compared our results to published values for hystricomorphs, other subterranean rodents, and surface-dwelling rodents of similar size.
Internal exposure rate conversion coefficients and absorbed fractions of mouse for 137Cs, 134Cs and 90Sr contamination in body
Authors: Endo Satoru , Matsutani Yuki , Kajimoto Tsuyoshi , Tanaka Kenichi , Suzuki Masatoshi 
Published: April 2020

Abstract
The aim of this study was to determine parameters for estimating the internal exposure of all organs in mouse experiments from the radioactivity concentration in organs. The estimation of internal exposure rate conversion coefficients and absorbed fractions for 137Cs, 134Cs and 90Sr by the Particle and Heavy Ion Transport code System (PHITS) with a voxel-based mouse phantom is presented. The geometry of the voxel phantom is constructed from computer tomography images of a mouse 9 cm in length weighing 23.9 g. The voxel-based mouse phantom has the following organs: brain, skull, heart, lungs, liver, stomach, spleen, kidneys, bladder, testis and tissue (tissue and other organs). Gamma- and beta-rays from 137Cs, 134Cs and 90Sr sources in each source organ are generated and scored for every target organ. The internal exposure rate conversion coefficients and absorbed fractions are calculated from deposition energies in each target organ from each source organ and are used to generate an internal exposure rate conversion coefficient matrix and an absorbed fraction matrix. The absorbed fractions of beta-rays in the source organs are roughly 0.5–0.8 for 137Cs and 134Cs, and the absorbed fractions of gamma-rays are &lt;0.04 for 137Cs and &lt;0.03 for 134Cs. The internal exposure rate conversion coefficient matrix is defined using the absorbed fractions. The calculated internal exposure rate coefficient matrix is tested under a uniform radioactivity concentration of 1 Bq/kg for 137Cs, 134Cs and 90Sr. The estimated internal exposure rates in the mouse whole body for 137Cs, 134Cs and 90Sr are 3.28 × 10−3, 2.55 × 10−3 and 1.20 × 10−2 μGy/d, respectively. These values are very similar to those for an ellipsoid frog (31.4 g) and an ellipsoid crab egg mass (12.6 g) reported in ICRP Publication 108.
Sette’s calculus P1 and some hierarchies of paraconsistent systems
Authors: Ciuciura Janusz 
Published: April 2020

Abstract
The necessary condition for a calculus to be paraconsistent is that its consequence relation is not explosive. This results in rejection of the principle of ex contradictione sequitur quodlibet. In 1973, Sette presented a calculus, denoted as $P^1$, which is paraconsistent only at the atomic level, i.e. $\alpha $ and ${\sim }\alpha $ yield any $\beta $ if, and only if the formula $\alpha $ is not a propositional variable. The calculus has been viewed as one of the noteworthy paraconsistent calculi since then. The objective of this paper is to propose a new semantics for Sette’s calculus and present some hierarchies of the paraconsistent calculi, which are based on $P^1$. We demonstrate that $P^1$ is sound and complete with respect to the semantics and so are all the calculi under consideration.
Multicenter evaluation of three different MALDI-TOF MS systems for identification of clinically relevant filamentous fungi
Authors: Sun Yue , Guo Jian , Chen Rong , Hu Liang , Xia Qihang , Wu Wenjuan , Wang Jinghua , Hu Fupin 
Published: April 2020

AbstractMatrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) holds promise as a potential tool for clinical identification of filamentous fungi. However, due to the lack of an appropriate extraction protocol and the difficulty of database building, the identification power of each system differs. In this study, we selected 126 clinical mould isolates comprising 28 species identified using internal transcribed spacer (ITS) sequencing as the reference method to evaluate three MALDI-TOF MS systems. When using cultures and sample preparation as recommended by the respective vendors, of the 126 strains tested, VITEK MS identified 121 (96.0%) to species-level and 124 (98.4%) to genus-level; Biotyper identified 53 (42.1%) to species-level and 54 (42.9%) to genus-level; Autof identified 74 (58.7%) to species-level and 76 (60.3%) to genus-level. For the Autof system, the tube extraction method recommended by the vendor performed better (59%) than the on-plate lysis (51%). Our study demonstrates that MALDI-TOF MS systems can successfully identify most clinically relevant fungi, while performance is still highly dependent on the database and sample preparation protocol.
High-redshift cosmology with oxygen lines from Hα surveys
Authors: Fonseca José , Camera Stefano 
Published: April 2020

ABSTRACT
A new generation of cosmological experiments will spectroscopically detect the Hα line from emission-line galaxies at optical/near-infrared frequencies. Other emission lines will also be present, which may come from the same Hα sample or constitute a new galaxy sample altogether. Our goal is to assess the value, for cosmological investigation, of galaxies at z ≳ 2 present in Hα galaxy surveys and identifiable by the highly redshifted ultraviolet and optical lines – namely the O ii line and the O iii doublet in combination with the Hβ line. We use state-of-the-art luminosity functions to estimate the number density of O iii + Hβ and O ii ELGs. We study the constraining power of these high-redshift galaxy samples on cosmological parameters such as the baryon acoustic oscillation (BAO) amplitude, H(z), DA(z), fσ8(z), and bσ8(z) for different survey designs. We present a strong science case for extracting the O iii + Hβ sample, which we consider as an independent probe of the Universe in the redshift range 2−3. Moreover, we show that the O ii sample can be used to measure the BAO and growth of structure above z = 3; albeit it may be shot-noise dominated, it will none the less provide valuable tomographic information. We discuss the scientific potential of a sample of galaxies, which, so far, has been mainly considered as a contaminant in Hα galaxy surveys. Our findings indicate that planed Hα surveys should include the extraction of these oxygen-line samples in their pipeline, to enhance their scientific impact on cosmology.
Most stars (and planets?) are born in intense radiation fields
Authors: Lee Eve J , Hopkins Philip F 
Published: April 2020

ABSTRACT
Protostars and young stars are strongly spatially ‘clustered’ or ‘correlated’ within their natal giant molecular clouds. We demonstrate that such clustering leads to the conclusion that the incident bolometric radiative flux upon a random young star/disc is enhanced (relative to volume-averaged fluxes) by a factor that increases with the total stellar mass of the complex. Because the Galactic cloud mass function is top-heavy, the typical star in our Galaxy experienced a much stronger radiative environment than those forming in well-observed nearby (but relatively small) clouds, exceeding fluxes in the Orion Nebular Cluster by factors of ≳30. Heating of the circumstellar disc around a median young star is dominated by this external radiation beyond $\sim \! 50$ au. And if discs are not well shielded by ambient dust, external ultraviolet irradiation can dominate over the host star down to sub-au scales. Another consequence of stellar clustering is an extremely broad Galaxy-wide distribution of incident flux (spanning &gt;10 decades), with half the Galactic star formation in a substantial ‘tail’ towards even more intense background radiation. We also show that the strength of external irradiation is amplified superlinearly in high-density environments such as the Galactic Centre, starbursts, or high-redshift galaxies.
Understanding the Early Evolutionary Stages of a Tandem Drosophilamelanogaster-Specific Gene Family: A Structural and Functional Population Study
Authors: Clifton Bryan D , Jimenez Jamie , Kimura Ashlyn , Chahine Zeinab , Librado Pablo , Sánchez-Gracia Alejandro , Abbassi Mashya , Carranza Francisco , Chan Carolus , Marchetti Marcella , Zhang Wanting , Shi Mijuan , Vu Christine , Yeh Shudan , Fanti Laura , Xia Xiao-Qin , Rozas Julio , Ranz José M 
Published: April 2020

AbstractGene families underlie genetic innovation and phenotypic diversification. However, our understanding of the early genomic and functional evolution of tandemly arranged gene families remains incomplete as paralog sequence similarity hinders their accurate characterization. The Drosophila melanogaster-specific gene family Sdic is tandemly repeated and impacts sperm competition. We scrutinized Sdic in 20 geographically diverse populations using reference-quality genome assemblies, read-depth methodologies, and qPCR, finding that ∼90% of the individuals harbor 3–7 copies as well as evidence of population differentiation. In strains with reliable gene annotations, copy number variation (CNV) and differential transposable element insertions distinguish one structurally distinct version of the Sdic region per strain. All 31 annotated copies featured protein-coding potential and, based on the protein variant encoded, were categorized into 13 paratypes differing in their 3′ ends, with 3–5 paratypes coexisting in any strain examined. Despite widespread gene conversion, the only copy present in all strains has functionally diverged at both coding and regulatory levels under positive selection. Contrary to artificial tandem duplications of the Sdic region that resulted in increased male expression, CNV in cosmopolitan strains did not correlate with expression levels, likely as a result of differential genome modifier composition. Duplicating the region did not enhance sperm competitiveness, suggesting a fitness cost at high expression levels or a plateau effect. Beyond facilitating a minimally optimal expression level, Sdic CNV acts as a catalyst of protein and regulatory diversity, showcasing a possible evolutionary path recently formed tandem multigene families can follow toward long-term consolidation in eukaryotic genomes.
Behavioural aspects of microhabitat segregation of different age stages in the wetland land snail Vertigo moulinsiana (Eupulmonata: Vertiginidae) in the laboratory
Authors: Książkiewicz-Parulska Zofia 
Published: April 2020

ABSTRACT
This laboratory study investigated behavioural differences between adults and juveniles of the wetland land snail species Vertigo moulinsiana with respect to temperature and humidity. Juveniles of V. moulinsiana, for example, tend to remain within the shaded, humid and cool layer of the litter, while adults usually climb above wet vegetation to a height of over 2 m. Adults are thus exposed to greater variation in temperature and humidity than juveniles. My experiments showed that adults of V. moulinsiana remain active longer than juveniles when subject to high temperature (36 °C) and low relative humidity (RH 30%). Conversely, juveniles stay active longer than adults in high humidity (22 °C, RH 100%). A short period of starvation lengthened the time needed for the juveniles to become active after dormancy, possibly indicating a different response between adults and juveniles to lack of nutritional reserves. These behavioural differences to food availability and the risk of water loss correspond to the microhabitat differences observed between adults and juveniles in the wild.
Can a digital slide scanner and viewing technique assist the visual scoring for the cytokinesis-block micronucleus cytome assay?
Authors: Jaunay Emma L , Dhillon Varinderpal S , Semple Susan J , Simpson Bradley S , Deo Permal , Fenech Michael 
Published: April 2020

Abstract
The cytokinesis-block micronucleus cytome (CBMNcyt) assay is a comprehensive method to measure DNA damage, cytostasis and cytotoxicity caused by nutritional, radiation and chemical factors. A slide imaging technique has been identified as a new method to assist with the visual scoring of cells for the CBMNcyt assay. A NanoZoomer S60 Digital Pathology slide scanner was used to view WIL2-NS cells treated with hydrogen peroxide (H2O2) and measure CBMNcyt assay biomarkers using a high-definition desktop computer screen. The H2O2-treated WIL2-NS cells were also scored visually using a standard light microscope, and the two visual scoring methods were compared. Good agreement was found between the scoring methods for all DNA damage indices (micronuclei, nucleoplasmic bridges and nuclear buds) and nuclear division index with correlation R values ranging from 0.438 to 0.789, P &lt; 0.05. Apoptotic and necrotic cell frequency was lower for the NanoZoomer scoring method, but necrotic frequency correlated well with the direct visual microscope method (R = 0.703, P &lt; 0.0001). Considerable advantages of the NanoZoomer scoring method compared to direct visual microscopy includes reduced scoring time, improved ergonomics and a reduction in scorer fatigue. This study indicates that a digital slide scanning and viewing technique may assist with visual scoring for the CBMNcyt assay and provides similar results to conventional direct visual scoring.
Human REXO2 controls short mitochondrial RNAs generated by mtRNA processing and decay machinery to prevent accumulation of double-stranded RNA
Authors: Szewczyk Maciej , Malik Deepshikha , Borowski Lukasz S , Czarnomska Sylwia D , Kotrys Anna V , Klosowska-Kosicka Kamila , Nowotny Marcin , Szczesny Roman J 
Published: April 2020

Abstract
RNA decay is a key element of mitochondrial RNA metabolism. To date, the only well-documented machinery that plays a role in mtRNA decay in humans is the complex of polynucleotide phosphorylase (PNPase) and SUV3 helicase, forming the degradosome. REXO2, a homolog of prokaryotic oligoribonucleases present in humans both in mitochondria and the cytoplasm, was earlier shown to be crucial for maintaining mitochondrial homeostasis, but its function in mitochondria has not been fully elucidated. In the present study, we created a cellular model that enables the clear dissection of mitochondrial and non-mitochondrial functions of human REXO2. We identified a novel mitochondrial short RNA, referred to as ncH2, that massively accumulated upon REXO2 silencing. ncH2 degradation occurred independently of the mitochondrial degradosome, strongly supporting the hypothesis that ncH2 is a primary substrate of REXO2. We also investigated the global impact of REXO2 depletion on mtRNA, revealing the importance of the protein for maintaining low steady-state levels of mitochondrial antisense transcripts and double-stranded RNA. Our detailed biochemical and structural studies provide evidence of sequence specificity of the REXO2 oligoribonuclease. We postulate that REXO2 plays dual roles in human mitochondria, ‘scavenging’ nanoRNAs that are produced by the degradosome and clearing short RNAs that are generated by RNA processing.
Structural basis of the XPB–Bax1 complex as a dynamic helicase–nuclease machinery for DNA repair
Authors: DuPrez Kevin , He Feng , Chen Zhenhang , Hilario Eduardo , Fan Li 
Published: April 2020

AbstractNucleotide excision repair (NER) is a major DNA repair pathway for a variety of DNA lesions. XPB plays a key role in DNA opening at damage sites and coordinating damage incision by nucleases. XPB is conserved from archaea to human. In archaea, XPB is associated with a nuclease Bax1. Here we report crystal structures of XPB in complex with Bax1 from Archaeoglobus fulgidus (Af) and Sulfolobus tokodaii (St). These structures reveal for the first time four domains in Bax1, which interacts with XPB mainly through its N-terminal domain. A Cas2-like domain likely helps to position Bax1 at the forked DNA allowing the nuclease domain to incise one arm of the fork. Bax1 exists in monomer or homodimer but forms a heterodimer exclusively with XPB. StBax1 keeps StXPB in a closed conformation and stimulates ATP hydrolysis by XPB while AfBax1 maintains AfXPB in the open conformation and reduces its ATPase activity. Bax1 contains two distinguished nuclease active sites to presumably incise DNA damage. Our results demonstrate that protein-protein interactions regulate the activities of XPB ATPase and Bax1 nuclease. These structures provide a platform to understand the XPB-nuclease interactions important for the coordination of DNA unwinding and damage incision in eukaryotic NER.
COVTree: Coevolution in OVerlapped sequences by Tree analysis server
Authors: Teppa Elin , Zea Diego J , Oteri Francesco , Carbone Alessandra 
Published: April 2020

Abstract
Overlapping genes are commonplace in viruses and play an important role in their function and evolution. For these genes, molecular coevolution may be seen as a mechanism to decrease the evolutionary constraints of amino acid positions in the overlapping regions and to tolerate or compensate unfavorable mutations. Tracing these mutational sites, could help to gain insight on the direct or indirect effect of the mutations in the corresponding overlapping proteins. In the past, coevolution analysis has been used to identify residue pairs and coevolutionary signatures within or between proteins that served as markers of physical interactions and/or functional relationships. Coevolution in OVerlapped sequences by Tree analysis (COVTree) is a web server providing the online analysis of coevolving amino-acid pairs in overlapping genes, where residues might be located inside or outside the overlapping region. COVTree is designed to handle protein families with various characteristics, among which those that typically display a small number of highly conserved sequences. It is based on BIS2, a fast version of the coevolution analysis tool Blocks in Sequences (BIS). COVTree provides a rich and interactive graphical interface to ease biological interpretation of the results and it is openly accessible at http://www.lcqb.upmc.fr/COVTree/.
Regulation of mRNA export through API5 and nuclear FGF2 interaction
Authors: Bong Seoung Min , Bae Seung-Hyun , Song Bomin , Gwak HyeRan , Yang Seung-Won , Kim Sunshin , Nam Seungyoon , Rajalingam Krishnaraj , Oh Se Jin , Kim Tae Woo , Park SangYoun , Jang Hyonchol , Lee Byung Il 
Published: April 2020

Abstract
API5 (APoptosis Inhibitor 5) and nuclear FGF2 (Fibroblast Growth Factor 2) are upregulated in various human cancers and are correlated with poor prognosis. Although their physical interaction has been identified, the function related to the resulting complex is unknown. Here, we determined the crystal structure of the API5–FGF2 complex and identified critical residues driving the protein interaction. These findings provided a structural basis for the nuclear localization of the FGF2 isoform lacking a canonical nuclear localization signal and identified a cryptic nuclear localization sequence in FGF2. The interaction between API5 and FGF2 was important for mRNA nuclear export through both the TREX and eIF4E/LRPPRC mRNA export complexes, thus regulating the export of bulk mRNA and specific mRNAs containing eIF4E sensitivity elements, such as c-MYC and cyclin D1. These data show the newly identified molecular function of API5 and nuclear FGF2, and provide a clue to understanding the dynamic regulation of mRNA export.
Fine-tune control of targeted RNAi efficacy by plant artificial small RNAs
Authors: López-Dolz Lucio , Spada Maria , Daròs José-Antonio , Carbonell Alberto 
Published: April 2020

AbstractEukaryotic RNA interference (RNAi) results in gene silencing upon the sequence-specific degradation of target transcripts by complementary small RNAs (sRNAs). In plants, RNAi-based tools have been optimized for high efficacy and high specificity, and are extensively used in gene function studies and for crop improvement. However, efficient methods for finely adjusting the degree of induced silencing are missing. Here, we present two different strategies based on artificial sRNAs for fine-tuning targeted RNAi efficacy in plants. First, the degree of silencing induced by synthetic-trans-acting small interfering RNAs (syn-tasiRNAs) can be adjusted by modifying the precursor position from which the syn-tasiRNA is expressed. The accumulation and efficacy of Arabidopsis TAS1c-based syn-tasiRNAs progressively decrease as the syn-tasiRNA is expressed from positions more distal to the trigger miR173 target site. And second, syn-tasiRNA activity can also be tweaked by modifying the degree of base-pairing between the 3′ end of the syn-tasiRNA and the 5′ end of the target RNA. Both strategies were used to finely modulate the degree of silencing of endogenous and exogenous target genes in Arabidopsis thaliana and Nicotiana benthamiana. New high-throughput syn-tasiRNA vectors were developed and functionally analyzed, and should facilitate the precise control of gene expression in multiple plant species.