cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
3'-End processing of histone pre-mRNAs in Drosophila: U7 snRNP is associated with FLASH and polyadenylation factors
Creators: name: Skrajna, A.
name: Yang, X.-c.
name: Dominski, Z.
name: Marzluff, W. F.
name: Sabath, I.
name: Dadlez, M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: 3′-End cleavage of animal replication-dependent histone pre-mRNAs is controlled by the U7 snRNP. Lsm11, the largest component of the U7-specific Sm ring, interacts with FLASH, and in mammalian nuclear extracts these two proteins form a platform that recruits the CPSF73 endonuclease and other polyadenylation factors to the U7 snRNP. FLASH is limiting, and the majority of the U7 snRNP in mammalian extracts exists as a core particle consisting of the U7 snRNA and the Sm ring. Here, we purified the U7 snRNP from Drosophila nuclear extracts and characterized its composition by mass spectrometry. In contrast to the mammalian U7 snRNP, a significant fraction of the Drosophila U7 snRNP contains endogenous FLASH and at least six subunits of the polyadenylation machinery: symplekin, CPSF73, CPSF100, CPSF160, WDR33, and CstF64. The same composite U7 snRNP is recruited to histone pre-mRNA for 3′-end processing. We identified a motif in Drosophila FLASH that is essential for the recruitment of the polyadenylation complex to the U7 snRNP and analyzed the role of other factors, including SLBP and Ars2, in 3′-end processing of Drosophila histone pre-mRNAs. SLBP that binds the upstream stem–loop structure likely recruits a yet-unidentified essential component(s) to the processing machinery. In contrast, Ars2, a protein previously shown to interact with FLASH in mammalian cells, is dispensable for processing in Drosophila. Our studies also demonstrate that Drosophila symplekin and three factors involved in cleavage and polyadenylation—CPSF, CstF, and CF Im—are present in Drosophila nuclear extracts in a stable supercomplex.
Polar Properties and Hysteresis Loops in Multilayered Thin Films Ferroelectric/Virtual Ferroelectric
Creators: name: Eliseev, E. A.
name: Glinchuk, M. D.
name: Morozovska, A. N.
name: Yakovenko, Ya. V.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: In the framework of Landau--Ginzburg--Devonshire (LGD) phenomenological theory, the influence of misfit strains, surface energy, and finite-size effects on phase diagrams, polar properties, and hysteresis loops has been calculated for multilayered thin films of the type ferroelectric/virtual ferroelectric. The influence of elastic deformations that arise at the interface thin film--substrate owing to a mismatch between the lattice constants in the film and the substrate on the phase diagrams of multilayered thin films virtual ferroelectric SrTiO$_{3}$/ferroelectric BaTiO$_{3}$ has been studied for the first time. In contrast to bulk BaTiO$_{3}$, in which only four phases (cubic, tetragonal, orthorhombic, and rhombohedral) can exist, it turned out that six thermodynamically stable BaTiO$_{3}$ phases (paraelectric phase and tetragonal (FEc), two monoclinic (FEaac and FEac), and two orthorhombic (FEa and FEaa) ferroelectric phases) can exist in multilayered SrTiO$_{3}$/BaTiO$_{3}$ films. The main polar properties of hysteresis loops (shape, coercive field, and spontaneous polarization) in thin multilayered SrTiO$_{3}$/BaTiO$_{3}$ films are calculated. It is shown that the system demonstrates a strong dependence of its polar properties on the thickness of SrTiO$_{3}$ and BaTiO$_{3}$ layers, as well as on the elastic misfit strains, with SrTiO$_{3}$ playing the role of dielectric layer: the thicker the layer, the stronger is the depolarization field, which, in its turn, reduces the spontaneous polarization in the BaTiO$_{3}$ film.
description: 9 pages, 5 figures
Circular RNAs are abundant, conserved, and associated with ALU repeats
Creators: name: Sharpless, N. E.
name: Slevin, M. K.
name: Liu, J.
name: Sorrentino, J. A.
name: Burd, C. E.
name: Marzluff, W. F.
name: Jeck, W. R.
name: Wang, K.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Circular RNAs composed of exonic sequence have been described in a small number of genes. Thought to result from splicing errors, circular RNA species possess no known function. To delineate the universe of endogenous circular RNAs, we performed high-throughput sequencing (RNA-seq) of libraries prepared from ribosome-depleted RNA with or without digestion with the RNA exonuclease, RNase R. We identified >25,000 distinct RNA species in human fibroblasts that contained non-colinear exons (a “backsplice”) and were reproducibly enriched by exonuclease degradation of linear RNA. These RNAs were validated as circular RNA (ecircRNA), rather than linear RNA, and were more stable than associated linear mRNAs in vivo. In some cases, the abundance of circular molecules exceeded that of associated linear mRNA by >10-fold. By conservative estimate, we identified ecircRNAs from 14.4% of actively transcribed genes in human fibroblasts. Application of this method to murine testis RNA identified 69 ecircRNAs in precisely orthologous locations to human circular RNAs. Of note, paralogous kinases HIPK2 and HIPK3 produce abundant ecircRNA from their second exon in both humans and mice. Though HIPK3 circular RNAs contain an AUG translation start, it and other ecircRNAs were not bound to ribosomes. Circular RNAs could be degraded by siRNAs and, therefore, may act as competing endogenous RNAs. Bioinformatic analysis revealed shared features of circularized exons, including long bordering introns that contained complementary ALU repeats. These data show that ecircRNAs are abundant, stable, conserved and nonrandom products of RNA splicing that could be involved in control of gene expression.
Two-Phase Topology Optimization for Metamaterials with Negative Poisson's Ratio
Creators: name: Akamatsu, Daichi
name: Noguchi, Yuki
name: Matsushima, Kei
name: Sato, Yuji
name: Yanagimoto, Jun
name: Yamada, Takayuki
Publisher: name: arXiv
Year: 2023
Subjects: subject: Applied Physics (physics.app-ph)
subject: FOS: Physical sciences
subject: 74Q05

description: Although recent developments in 3D printing technology have made it possible to fabricate metamaterials with characteristic mechanical properties, it is not easy to fabricate complex shapes containing cavities. In this study, a composite structure comprising two types of materials without a cavity was optimized. Moreover, a mechanical metamaterial with a negative Poisson's ratio that can be fabricated using an additive manufacturing method was developed. First, a homogenization method that characterizes the properties of composite structures was briefly described. Then, an optimization problem to realize a negative Poisson's ratio was formulated, and a level set-based topology optimization method was proposed to solve the abovementioned problem. Next, three-dimensional numerical examples are presented to confirm the effectiveness of the proposed method, and the deformation behaviors of the optimized designs are numerically examined. Furthermore, a sample containing the optimized design with negative Poisson's ratio for the tensile test was fabricated using a 3D printer. We conducted some experiments to evaluate its mechanical performance.
description: 26 pages, 14 figures
Developmental arrest of Drosophila survival motor neuron (Smn) mutants accounts for differences in expression of minor intron-containing genes
Creators: name: Meers, M. P.
name: Lu, Z.
name: Garcia, E. L.
name: Praveen, K.
name: Matera, A. G.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Reduced levels of survival motor neuron (SMN) protein lead to a neuromuscular disease called spinal muscular atrophy (SMA). Animal models of SMA recapitulate many aspects of the human disease, including locomotion and viability defects, but have thus far failed to uncover the causative link between a lack of SMN protein and neuromuscular dysfunction. While SMN is known to assemble small nuclear ribonucleoproteins (snRNPs) that catalyze pre-mRNA splicing, it remains unclear whether disruptions in splicing are etiologic for SMA. To investigate this issue, we carried out RNA deep-sequencing (RNA-seq) on age-matched Drosophila Smn-null and wild-type larvae. Comparison of genome-wide mRNA expression profiles with publicly available data sets revealed the timing of a developmental arrest in the Smn mutants. Furthermore, genome-wide differences in splicing between wild-type and Smn animals did not correlate with changes in mRNA levels. Specifically, we found that mRNA levels of genes that contain minor introns vary more over developmental time than they do between wild-type and Smn mutants. An analysis of reads mapping to minor-class intron–exon junctions revealed only small changes in the splicing of minor introns in Smn larvae, within the normal fluctuations that occur throughout development. In contrast, Smn mutants displayed a prominent increase in levels of stress-responsive transcripts, indicating a systemic response to the developmental arrest induced by loss of SMN protein. These findings not only provide important mechanistic insight into the developmental arrest displayed by Smn mutants, but also argue against a minor-intron-dependent etiology for SMA.
On fusion kernel in Liouville theory
Creators: name: Nemkov, Nikita
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We study fusion kernel for non-degenerate conformal blocks in Liouville theory as a solution to the difference equations originating from the pentagon identity. We suggest an approach to these equations based on 'non-perturbative' series expansion which allows to calculate the fusion kernel iteratively. We also find the exact solutions for the cases when the central charge is $c=1+6(b-b^{-1})^2$ and $b~\in \mathbb{N}$. For $c = 1$ our result reproduces the formula, obtained earlier from analytical continuation via Painlevé equation. However, in our case it appears in a significantly simplified form.
description: 23 pages, version 2 with minor corrections added
Contribution of climate and catchment characteristics to runoff variations in Indian river basins: a climate elasticity approach
Creators: name: Mandal, Nehar
name: Chanda, Kironmala
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Plant Biology

description: The relative influence of climate and catchment characteristics to the variations in runoff in five Indian river basins is assessed using the climate elasticity approach based on the Budyko hypothesis. From 1980 to 1999, catchment characteristics are found to be the main contributor to runoff variation for all of the basins except Upper Mahanadi sub-basin, where climatic factors are the major contributor. Among the climatic factors, runoff is more responsive to changes in precipitation than to changes in potential evapotranspiration. The mean contribution of climate (catchment) to runoff variation is largest at the Cauvery (Krishna) basin. The findings may be useful in planning sustainable water resources infrastructure. Investigation of the relationship between runoff changes in the basins and their land use and land cover changes, as well as the vegetation index, adds to the novelty and usefulness of the study.
Level set-based multiscale topology optimization for a thermal cloak design problem using the homogenization method
Creators: name: Nakagawa, Makoto
name: Noguchi, Yuki
name: Matsushima, Kei
name: Yamada, Takayuki
Publisher: name: arXiv
Year: 2023
Subjects: subject: Computational Engineering, Finance, and Science (cs.CE)
subject: FOS: Computer and information sciences

description: Artificially designed composite materials consist of microstructures, that exhibit various thermal properties depending on their shapes, such as anisotropic thermal conductivity. One of the representative applications of such composite materials for thermal control is the thermal cloak. This study proposed a topology optimization method based on a level set method for a heat conduction problem to optimally design composite materials that achieve a thermal cloak. The homogenization method was introduced to evaluate its effective thermal conductivity coefficient. Then, we formulated a multiscale topology optimization method for the composite materials in the framework of the homogenization method, where the microstructures were optimized to minimize objective functions defined using the macroscopic temperature field. We presented examples of optimal structures in a two-dimensional problem and discussed the validity of the obtained structures.
mRNAs containing the histone 3' stem-loop are degraded primarily by decapping mediated by oligouridylation of the 3' end
Creators: name: Rhoads, R. E.
name: Darzynkiewicz, E.
name: Su, W.
name: Ziemniak, M.
name: Kowalska, J.
name: Slevin, M. K.
name: Jemielity, J.
name: Slepenkov, S. V.
name: Lyons, S. M.
name: Marzluff, W. F.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Metazoan replication-dependent histone mRNAs are only present in S-phase, due partly to changes in their stability. These mRNAs end in a unique stem–loop (SL) that is required for both translation and cell-cycle regulation. Previous studies showed that histone mRNA degradation occurs through both 5′→3′ and 3′→5′ processes, but the relative contributions are not known. The 3′ end of histone mRNA is oligouridylated during its degradation, although it is not known whether this is an essential step. We introduced firefly luciferase reporter mRNAs containing the histone 3′ UTR SL (Luc-SL) and either a normal or hDcp2-resistant cap into S-phase HeLa cells. Both mRNAs were translated, and translation initially protected the mRNAs from degradation, but there was a lag of ∼40 min with the uncleavable cap compared to ∼8 min for the normal cap before rapid decay. Knockdown of hDcp2 resulted in a similar longer lag for Luc-SL containing a normal cap, indicating that 5′→3′ decay is important in this system. Inhibition of DNA replication with hydroxyurea accelerated the degradation of Luc-SL. Knockdown of terminal uridyltransferase (TUTase) 4 but not TUTase 3 slowed the decay process, but TUTase 4 knockdown had no effect on destabilization of the mRNA by hydroxyurea. Both Luc-SL and its 5′ decay intermediates were oligouridylated. Preventing oligouridylation by 3′-deoxyadenosine (cordycepin) addition to the mRNA slowed degradation, in the presence or absence of hydroxyurea, suggesting oligouridylation initiates degradation. The spectrum of oligouridylated fragments suggests the 3′→5′ degradation machinery stalls during initial degradation, whereupon reuridylation occurs.
Exchange bias in molecule/Fe3GeTe2 van der Waals heterostructures via spinterface effects
Creators: name: Jo, Junhyeon
name: Calavalle, Francesco
name: Martín-García, Beatriz
name: Casanova, Fèlix
name: Chuvilin, Andrey
name: Hueso, Luis E.
name: Gobbi, Marco
Publisher: name: arXiv
Year: 2023
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: The exfoliation of layered magnetic materials generates atomically thin flakes characterized by an ultrahigh surface sensitivity, which makes their magnetic properties tunable via external stimuli, such as electrostatic gating and proximity effects. Another powerful approach to tailor magnetic materials is molecular functionalization, which leads to hybrid interface states with peculiar magnetic properties, called spinterfaces. However, spinterface effects have not yet been explored on layered magnetic materials. Here, we demonstrate the emergence of spinterface effects at the interface between flakes of the prototypical layered magnetic metal Fe3GeTe2 and thin films of paramagnetic Co-phthalocyanine. Magnetotransport measurements show that the molecular layer induces a magnetic exchange bias in Fe3GeTe2, indicating that the unpaired spins in Co-phthalocyanine develop antiferromagnetic ordering by proximity and pin the magnetization reversal of Fe3GeTe2. The effect is strongest for a Fe3GeTe2 thickness of 20 nm, for which the exchange bias field reaches -840 Oe and is measurable up to approximately 110 K. This value compares very favorably with previous exchange bias fields reported for Fe3GeTe2 in all-inorganic van der Waals heterostructures, demonstrating the potential of molecular functionalization to tailor the magnetism of van der Waals layered materials.
More on Soft Theorems: Trees, Loops and Strings
Creators: name: Bianchi, Massimo
name: He, Song
name: Huang, Yu-tin
name: Wen, Congkao
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We study soft theorems in a broader context, addressing their fate at loop level and their universality in effective field theories and string theory. We argue that for gauge theories in the planar limit, loop-level soft gluon theorems can be made manifest already at the integrand level. In particular, we show that the planar integrand for N=4 SYM satisfies the tree-level soft theorem to all orders in perturbation theory and provide strong evidence to this effect for integrands in N<4 SYM. We consider soft theorems for non-supersymmetric Yang-Mills theories and gravity, and show the validity of integrand soft theorem, while loop corrections to the integrated soft theorems are intimately tied to the presence of conformal anomalies. We then address the question of universality of the soft theorems for various theories. In effective field theories with F^3 and R^3 interactions, the soft theorems are not modified. However for gravity theories with R^2 phi interactions, the sub-sub-leading order soft graviton theorem, which is beyond what is implied by the extended BMS symmetry, requires modifications at tree level for non-supersymmetric theories, and at loop level for N<5 supergravity due to anomalies. Finally, for superstring amplitudes at finite alpha', via explicit calculation for lower-point examples as well as world-sheet OPE analysis for arbitrary multiplicity, we show that the superstring amplitudes satisfy the same soft theorem as its field-theory counterpart. This is no longer true for bosonic closed strings due to the presence of R^2 phi interactions.
description: 40 pages. V2, typos and references corrected
title: Necropolitics Beyond the Eexception : Parapolicing, Milícia Urbanism, and the Assassination of Marielle Franco in Rio de Janeiro
Creators: name: Hutta, Jan Simon
Publisher: name: University of Bayreuth
Year: 2022
Subjects: subject: Necropolitics
subject: Violence
subject: Rio de Janeiro
subject: Urban governance
subject: Sovereignty
subject: Brazil
subject: 100
subject: 300
subject: 320
subject: 900

description: Engaging with the assassination of black city councillor Marielle Franco, the paper discusses how “milícia urbanism”, a formation of power and capital accumulation driven by parapolice networks, intensifies the necropolitical governance of Rio de Janeiro. Specifically, this necropolitics is characterised by liaisons among armed, political, institutional and economic actors that enable acts of violence with impunity, aggravating the conditions of violence for subaltern populations. Dialoguing with the Black Studies debate on necropolitics and works on violent democracies, the paper situates milícia urbanism within a postcolonial genealogy of parapolicing. Ever since the colonial plantation, it is argued, parapolicing has been integral to a power technology that avoids sovereign accountability while serving white capital interests. Whereas previous accounts of necropolitics have centred on the sovereign exception, this genealogy furthers an understanding of necropolitics “beyond the exception”. The paper concludes that Marielle Franco’s black-feminist politics has been vital to contestations of this necropolitics.
QuShape: Rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis
Creators: name: Weeks, K. M.
name: McGinnis, J. L.
name: Favorov, O. V.
name: Karabiber, F.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Chemical probing of RNA and DNA structure is a widely used and highly informative approach for examining nucleic acid structure and for evaluating interactions with protein and small-molecule ligands. Use of capillary electrophoresis to analyze chemical probing experiments yields hundreds of nucleotides of information per experiment and can be performed on automated instruments. Extraction of the information from capillary electrophoresis electropherograms is a computationally intensive multistep analytical process, and no current software provides rapid, automated, and accurate data analysis. To overcome this bottleneck, we developed a platform-independent, user-friendly software package, QuShape, that yields quantitatively accurate nucleotide reactivity information with minimal user supervision. QuShape incorporates newly developed algorithms for signal decay correction, alignment of time-varying signals within and across capillaries and relative to the RNA nucleotide sequence, and signal scaling across channels or experiments. An analysis-by-reference option enables multiple, related experiments to be fully analyzed in minutes. We illustrate the usefulness and robustness of QuShape by analysis of RNA SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) experiments.
Two-dimensional LWR model for lane-free traffic
Creators: name: Agrawal, Shrey
name: Kanagaraj, Venkatesan
name: Treiber, Martin
Publisher: name: arXiv
Year: 2023
Subjects: subject: Physics and Society (physics.soc-ph)
subject: Adaptation and Self-Organizing Systems (nlin.AO)
subject: FOS: Physical sciences

description: While macroscopic models for single or multi-lane traffic flow are well established, these models are not applicable to the dynamics and characteristics of disordered traffic which is characterized by widely different types of vehicles and no lane discipline. We propose a first-order two-dimensional Lighthill-Whitham-Richards (LWR) model for the continuous macroscopic longitudinal and lateral dynamics of this type of traffic flow. The continuity equation is extended into two dimensions and the equation is closed by assuming a longitudinal flow-density relationship as in traditional one-dimensional models while the lateral dynamics is based on boundary repulsion and a desire of a majority of the drivers to go to less dense regions. This is equivalent to Fick's law giving rise to a lateral diffusion term. Using the proposed model, several numerical tests were conducted under different traffic scenarios representing a wide range of traffic conditions. Even for extreme initial conditions, the model's outcome turned out to be plausible and consistent with observed traffic flow dynamics. Moreover, the numerical convergence test is performed using an analytical solution for lateral steady-state conditions. The model was applied for bicycle simulation and reproduced the evolution of lateral density profile with asymmetric behavior.
Avoiding Ambiguous Framework in Distance-based Formation Control Using Virtual Followers
Creators: name: latifi, Morteza
name: Bayati, Reza
Publisher: name: figshare
Year: 2022
Subjects: subject: 91302 Automation and Control Engineering
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: 90602 Control Systems, Robotics and Automation

description: In this study, we develop a shape formation controller based on regular distance-based control law. As distance rigidity theory may not be successful in achieving desired shape when the control system defined under minimally rigid graph. As a matter of fact, the formation may converge to ambiguous framework when the group of mobile robots did not initialize in proper way. This is a well-known issue with distance-based formation control while there are multiple equilibrium points in the dynamics. We introduce a new controller by adding virtual constraints to the system. The performance of control system is exemplified through numerical simulations and the convergence to the desired formation for all initial conditions validated with stability analysis.
Unveiling the nature of dark matter with high redshift 21 cm line experiments
Creators: name: Evoli, Carmelo
name: Mesinger, Andrei
name: Ferrara, Andrea
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: Observations of the redshifted 21 cm line from neutral hydrogen will open a new window on the early Universe. By influencing the thermal and ionization history of the intergalactic medium (IGM), annihilating dark matter (DM) can leave a detectable imprint in the 21 cm signal. Building on the publicly available 21cmFAST code, we compute the 21 cm signal for a 10 GeV WIMP DM candidate. The most pronounced role of DM annihilations is in heating the IGM earlier and more uniformly than astrophysical sources of X-rays. This leaves several unambiguous, qualitative signatures in the redshift evolution of the large-scale ($k\approx0.1$ Mpc$^{-1}$) 21 cm power amplitude: (i) the local maximum (peak) associated with IGM heating can be lower than the other maxima; (ii) the heating peak can occur while the IGM is in emission against the cosmic microwave background (CMB); (iii) there can be a dramatic drop in power (a global minimum) corresponding to the epoch when the IGM temperature is comparable to the CMB temperature. These signatures are robust to astrophysical uncertainties, and will be easily detectable with second generation interferometers. We also briefly show that decaying warm dark matter has a negligible role in heating the IGM.
description: 17 pages, 5 figures. Published in JCAP
Assessing influential rainfall–runoff variables to simulate daily streamflow using random forest
Creators: name: Vilaseca, Federico
name: Castro, Alberto
name: Chreties, Christian
name: Gorgoglione, Angela
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified

description: This work aims to improve the feature selection for data-driven rainfall–runoff models by assessing the significance of each input variable in the learning process and analysing it from a physical point of view. For this purpose, a set of 14 experiments was carried out in two watersheds of the Santa Lucía Chico basin, Uruguay. A random forest model was trained and tested for daily discharge prediction in each of them using different input variables. A feature importance analysis was carried out for each model, using a non-model-biased method (Shapely additive explanations). Results showed that the most relevant variables were lagged discharges of one and two days, along with seven-day accumulated rainfall, which is interpreted as a proxy of the soil moisture condition of the watershed. The temperature was also relevant and was proven to represent the effect of the whole set of climatic variables (relative humidity, solar radiation, wind speed).
Prevalent RNA recognition motif duplication in the human genome
Creators: name: Tsai, Y. S.
name: Gomez, S. M.
name: Wang, Z.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: The sequence-specific recognition of RNA by proteins is mediated through various RNA binding domains, with the RNA recognition motif (RRM) being the most frequent and present in >50% of RNA-binding proteins (RBPs). Many RBPs contain multiple RRMs, and it is unclear how each RRM contributes to the binding specificity of the entire protein. We found that RRMs within the same RBP (i.e., sibling RRMs) tend to have significantly higher similarity than expected by chance. Sibling RRM pairs from RBPs shared by multiple species tend to have lower similarity than those found only in a single species, suggesting that multiple RRMs within the same protein might arise from domain duplication followed by divergence through random mutations. This finding is exemplified by a recent RRM domain duplication in DAZ proteins and an ancient duplication in PABP proteins. Additionally, we found that different similarities between sibling RRMs are associated with distinct functions of an RBP and that the RBPs tend to contain repetitive sequences with low complexity. Taken together, this study suggests that the number of RBPs with multiple RRMs has expanded in mammals and that the multiple sibling RRMs may recognize similar target motifs in a cooperative manner.
Implementation of a probability matching method in developing intensity–duration–frequency relationships for sub-daily durations using IMERG satellite-based data
Creators: name: Shabankareh, Rahim Najafi Tireh
name: Abedini, Mohammad Javad
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Medicine
Molecular Biology
Environmental Sciences not elsewhere classified
Biological Sciences not elsewhere classified

description: Reliable estimation of design rainfall in time and space can play a significant role in reducing flood-related losses. However, many parts of the world suffer from a lack of dense raingauge networks. Under this condition, the use of satellite-based data can be an alternative solution. In this research, using data from a dense ground-based raingauge network and Integrated Multi-satellitE Retrievals for GPM (IMERG) satellite-based precipitation product, the performance of a probability matching method for satellite-based extreme values has been investigated. The results indicate that the correction model, especially at shorter durations, is able to reduce the error of extreme values of raw satellite-based estimates, and its performance is not affected significantly by the density of the available raingauge network. In conclusion, implementation of the proposed method in poorly gauged regions can play an effective role in providing a reliable estimate of the design rainfall and eventually reducing the financial losses caused by floods.
Black Female Teachers in White-Dominated Educational Spaces: Narratives of Professional Identity
Creators: name: Ramdeo, Janet
Publisher: name: London South Bank University
Year: 2022

description: This study provides a narrative account of the experiences of 10 Black female teachers as they navigate white-dominated educational workspaces and explores how these experiences have shaped their professional identities. Very little research has focussed on Black female teachers’ professional identities specifically in England. This study therefore seeks to address the apparent gap, thus contributing to further understanding Black women as teachers, using Critical Race Theory in education and consciousness of Black feminist thought. The foundations of the two theories led to using narrative inquiry as the methodology. A semi-structured interview approach was used to elicit accounts from participants at various stages of their careers in a range of state-funded schools across England. The data were analysed through both theoretical lenses. Thematic analysis was undertaken to draw out commonalities of experiences to accumulate knowledge from the richness of individual stories. The findings suggested that participants experienced a number of oppressions in their schools, demonstrated through a lack of career progression, being perceived by white colleagues through stereotyped images of Black women and the impact of seeing unjust practices towards Black and minoritised learners. Despite this, participants held a positive view of themselves. They drew their ability to resist hegemonic stereotyped images from their parents’, particularly their fathers’ aspirations for them and their agency maintaining positive professional self-definitions. Further, they drew on an enhanced definition of Du Bois’ double consciousness, that of ‘Blackness’ and ‘gender’, for agentic action to drive for inclusive educational practices and to facilitate positive consequences, especially for minoritised children, their families and staff representation, whilst challenging normative stereotypes of Black women. This study found that participants held a unique experiential positionality in white-dominated school spaces, the implications of which provides a positive counter-narrative to encourage Black women to enter and remain in teaching. Further, it provides evidence of the impact of schools’ practices on their Black female workforce and a rationale for making positive cultural changes.
Trends? Complicated answers to a simple question
Creators: name: Bürger, Gerd
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Ecology
subject: FOS: Biological sciences
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Science Policy

description: Trend significance of time series that are serially correlated is once more addressed. Most conventional techniques to “pre-whiten” the series prior to calculating trends rely on the assumption of autoregressive residual noise, AR(1). Monthly recordings of 40 water level stations in Germany are investigated, revealing strong memory up to lag 2. A new scheme (PW(p)) is introduced that extends pre-whitening to AR(p) with p > 1. It performs well on surrogate series with prescribed trend and memory. For seven series the estimated trends are unrealistically off, raising doubts about the validity of the basic assumptions of short-memory noise. The series are characterized by a hockey stick pattern from which any pre-whitening produces trends that are all but plausible. The pattern also reveals that pre-whitening is not invariant under time reversal. Regardless of the validity of the noise model, these special cases serve as a warning for using pre-whitening in general.
The profinite polynomial automorphism group
Creators: name: Maubach, Stefan
name: Rauf, Abdul
Publisher: name: arXiv
Year: 2014
Subjects: subject: Algebraic Geometry (math.AG)
subject: Commutative Algebra (math.AC)
subject: FOS: Mathematics

description: We introduce an extension of the (tame) polynomial automorphism group over finite fields: the profinite (tame) polynomial automorphism group, which is obtained by putting a natural topology on the automorphism group. We show that most known candidate non-tame automorphisms are inside the profinite tame polynomial automorphism group, giving another result showing that tame maps are potentially "dense" inside the set of automorphisms. We study the profinite tame automorphism group and show that it is not far from the set of bijections obtained by endomorphisms.
description: 24 pages
RNA secondary structure modeling at consistent high accuracy using differential SHAPE
Creators: name: Rice, G. M.
name: Leonard, C. W.
name: Weeks, K. M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: RNA secondary structure modeling is a challenging problem, and recent successes have raised the standards for accuracy, consistency, and tractability. Large increases in accuracy have been achieved by including data on reactivity toward chemical probes: Incorporation of 1M7 SHAPE reactivity data into an mfold-class algorithm results in median accuracies for base pair prediction that exceed 90%. However, a few RNA structures are modeled with significantly lower accuracy. Here, we show that incorporating differential reactivities from the NMIA and 1M6 reagents—which detect noncanonical and tertiary interactions—into prediction algorithms results in highly accurate secondary structure models for RNAs that were previously shown to be difficult to model. For these RNAs, 93% of accepted canonical base pairs were recovered in SHAPE-directed models. Discrepancies between accepted and modeled structures were small and appear to reflect genuine structural differences. Three-reagent SHAPE-directed modeling scales concisely to structurally complex RNAs to resolve the in-solution secondary structure analysis problem for many classes of RNA.
The C-terminal extension of Lsm4 interacts directly with the 3' end of the histone mRNP and is required for efficient histone mRNA degradation
Creators: name: Lyons, S. M.
name: Kambach, C.
name: Ricciardi, A. S.
name: Marzluff, W. F.
name: Guo, A. Y.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Metazoan replication-dependent histone mRNAs are the only known eukaryotic mRNAs that lack a poly(A) tail, ending instead in a conserved stem–loop sequence, which is bound to the stem–loop binding protein (SLBP) on the histone mRNP. Histone mRNAs are rapidly degraded when DNA synthesis is inhibited in S phase in mammalian cells. Rapid degradation of histone mRNAs is initiated by oligouridylation of the 3′ end of histone mRNAs and requires the cytoplasmic Lsm1-7 complex, which can bind to the oligo(U) tail. An exonuclease, 3′hExo, forms a ternary complex with SLBP and the stem–loop and is required for the initiation of histone mRNA degradation. The Lsm1-7 complex is also involved in degradation of polyadenylated mRNAs. It binds to the oligo(A) tail remaining after deadenylation, inhibiting translation and recruiting the enzymes required for decapping. Whether the Lsm1-7 complex interacts directly with other components of the mRNP is not known. We report here that the C-terminal extension of Lsm4 interacts directly with the histone mRNP, contacting both SLBP and 3′hExo. Mutants in the C-terminal tail of Lsm4 that prevent SLBP and 3′hExo binding reduce the rate of histone mRNA degradation when DNA synthesis is inhibited.
Assessing influential rainfall-runoff variables to simulate daily streamflow using random forest
Creators: name: Vilaseca, Federico
name: Castro, Alberto
name: Chreties, Christian
name: Gorgoglione, Angela
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified

description: This work aims to improve the feature selection for data-driven rainfall-runoff models by assessing the significance of each input variable in the learning process and analysing it from a physical point of view. For this purpose, a set of fourteen experiments was carried out in two watersheds of the Santa Lucía Chico basin, Uruguay. A Random Forest model was trained and tested for daily discharge prediction in each of them using different input variables. Furthermore, a feature importance analysis was carried out for each model, using a non-model-biased method based on game theory (SHAP). Results showed that the most relevant variables were lagged discharges of 1 and 2 days, along with 7-day accumulated rainfall, which is interpreted as a proxy of the antecedent soil moisture condition of the watershed. The temperature was also relevant and was proven to represent the effect of the whole set of climatic variables (relative humidity, solar radiation, wind speed).
Effects of planted tree species on biodiversity of conifer plantations in Japan: a systematic review and meta-analysis
Creators: name: Kawamura, Kazuhiro
name: Yamaura, Yuichi
name: Soga, Masashi
name: Spake, Rebecca
name: Nakamura, Futoshi
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Ecology
subject: FOS: Biological sciences
subject: Plant Biology
subject: 60506 Virology

description: Natural forests were increasingly replaced by plantations globally. While plantations support less biodiversity compared to natural forests, they can serve as an important habitat for forest-dependent species. Understanding the key drivers of the habitat function of plantations is necessary to reconcile both forestry and biodiversity. Planted tree species is one of the important factors determining biodiversity of plantations. Here, we systematically collected studies comparing the biodiversity between conifer plantations and natural forests, and conducted meta-analyses to quantify the effects of planted tree family/species (cypress family: Japanese cedar Cryptomeria japonica, Hinoki cypress Chamaecyparis obtuse; pine family: Japanese larch Larix kaempferi, Japanese red pine Pinus densiflora, Todo fir Abies sachalinensis) on abundance and species richness of a wide range of taxa (all taxa, vertebrates, birds, invertebrates, terrestrial arthropods, plants, and understorey plants) in plantations in Japan. Abundance and species richness in plantations relative to natural forests differed among planted tree family/species. In plantations of pine family (mainly larch), abundance or richness did not significantly differ from those in natural forests for many taxa, suggesting the important role as habitats. By contrast, in cypress family (mainly cedar), abundance or richness was significantly lower than in natural forests for all analysis groups except understorey abundance. These results indicate that the habitat function of plantations and its management should be considered for each planted tree species, separately. Nevertheless, since our literature review identifies some research gaps, e.g. studies on vertebrates in western Japan were scarce, more comprehensive research efforts should be made in the future.
A multiprotein occupancy map of the mRNP on the 3′ end of histone mRNAs
Creators: name: Marzluff, William F.
name: Welch, Joshua D.
name: Liu, Zhongle
name: Brooks, Lionel
name: Whitfield, Michael L.
name: Mahoney, J. Matthew
name: Lyons, Shawn M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: The animal replication-dependent (RD) histone mRNAs are coordinately regulated with chromosome replication. The RD-histone mRNAs are the only known cellular mRNAs that are not polyadenylated. Instead, the mature transcripts end in a conserved stem–loop (SL) structure. This SL structure interacts with the stem–loop binding protein (SLBP), which is involved in all aspects of RD-histone mRNA metabolism. We used several genomic methods, including high-throughput sequencing of cross-linked immunoprecipitate (HITS-CLIP) to analyze the RNA-binding landscape of SLBP. SLBP was not bound to any RNAs other than histone mRNAs. We performed bioinformatic analyses of the HITS-CLIP data that included (i) clustering genes by sequencing read coverage using CVCA, (ii) mapping the bound RNA fragment termini, and (iii) mapping cross-linking induced mutation sites (CIMS) using CLIP-PyL software. These analyses allowed us to identify specific sites of molecular contact between SLBP and its RD-histone mRNA ligands. We performed in vitro crosslinking assays to refine the CIMS mapping and found that uracils one and three in the loop of the histone mRNA SL preferentially crosslink to SLBP, whereas uracil two in the loop preferentially crosslinks to a separate component, likely the 3′hExo. We also performed a secondary analysis of an iCLIP data set to map UPF1 occupancy across the RD-histone mRNAs and found that UPF1 is bound adjacent to the SLBP-binding site. Multiple proteins likely bind the 3′ end of RD-histone mRNAs together with SLBP.
Controlling mRNA stability and translation with the CRISPR endoribonuclease Csy4
Creators: name: Borchardt, Erin K.
name: Huang, Michael
name: Lackey, Patrick E.
name: Vandoros, Leonidas A.
name: Asokan, Aravind
name: Marzluff, William F.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: The bacterial CRISPR endoribonuclease Csy4 has recently been described as a potential RNA processing tool. Csy4 recognizes substrate RNA through a specific 28-nt hairpin sequence and cleaves at the 3′ end of the stem. To further explore applicability in mammalian cells, we introduced this hairpin at various locations in mRNAs derived from reporter transgenes and systematically evaluated the effects of Csy4-mediated processing on transgene expression. Placing the hairpin in the 5′ UTR or immediately after the start codon resulted in efficient degradation of target mRNA by Csy4 and knockdown of transgene expression by 20- to 40-fold. When the hairpin was incorporated in the 3′ UTR prior to the poly(A) signal, the mRNA was cleaved, but only a modest decrease in transgene expression (∼2.5-fold) was observed. In the absence of a poly(A) tail, Csy4 rescued the target mRNA substrate from degradation, resulting in protein expression, which suggests that the cleaved mRNA was successfully translated. In contrast, neither catalytically inactive (H29A) nor binding-deficient (R115A/R119A) Csy4 mutants were able to exert any of the effects described above. Generation of a similar 3′ end by RNase P-mediated cleavage was unable to rescue transgene expression independent of Csy4. These results support the idea that the selective generation of the Csy4/hairpin complex resulting from cleavage of target mRNA might serve as a functional poly(A)/poly(A) binding protein (PABP) surrogate, stabilizing the mRNA and supporting translation. Although the exact mechanism(s) remain to be determined, our studies expand the potential utility of CRISPR nucleases as tools for controlling mRNA stability and translation.
Improved Theory of Neutrino Oscillations in Matter
Creators: name: Kisslinger, Leonard S.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: This is revision of the S-Matrix theory of neutrino oscillations used for many years. We evaluate the transition probability of a $μ$ to $e$ neutrino without an approximation used for many theoretical studies, and find important differences which could improve the extraction of neutrino parameters from experimental data in the future.
description: 4 pages, 1 figure
Role of Ca2+ in the pepsin-induced coagulation and in the dynamic in vitro gastric digestion behavior of casein micelles
Creators: name: Yang, Mengxiao
name: Ye, Aiqian
name: Yang, Zhi
name: Everett, David
name: Gilbert, Elliot
name: Singh, Harjinder
Publisher: name: AgResearch
Year: 2023
Subjects: classificationCode: 3006
subject: Food sciences

description: The effect of Ca2+ on pepsin-induced hydrolysis of κ-casein and subsequent coagulation of casein micelles was studied in a micellar casein (MC) solution at pH ≈ 6.0 at 37 °C without stirring. An NaCl-supplemented MC solution was used as a positive control to assess the effect of increased ionic strength after CaCl2 addition. Quantitative determination of the released para-κ-casein during the reaction using reverse-phase high-performance liquid chromatography showed that specific hydrolysis of κ-casein by pepsin was little affected by the addition of either CaCl2 or NaCl. However, rheological properties and microstructures of curds induced by pepsin hydrolysis depended markedly on the addition of salts. Addition of CaCl2 up to 17.5 mM facilitated coagulation, with decreases in coagulation time and critical hydrolysis degree, and increases in firming rate and maximum storage modulus (G'max); further addition of CaCl2 (22.5 mM) resulted in a lower G'max. Increased ionic strength to 52.5 mM by adding NaCl retarded the coagulation and resulted in a looser curd structure. In a human gastric simulator, MC, without the addition of CaCl2, did not coagulate until the pH decreased to ≈5.0 after ≈50 min of digestion. Addition of CaCl2 facilitated coagulation of casein micelles and resulted in more cohesive curds with dense structures during digestion, which slowed the emptying rate of caseins. At the same CaCl2 concentration, a sample with higher ionic strength coagulated more slowly. This study provides further understanding on the effect of divalent (Ca2+) ions and ionic strength on the coagulation of casein micelles and the digestion behavior of milk.