cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Dynamic Control of Plasmonic Colors by Voltage Actuation MEMS Cantilevers for Optical Display Applications
Creators: name: Han, Zhengli
name: Frydendahl, Christian
name: Mazurski, Noa
name: Levy, Uriel
Publisher: name: arXiv
Year: 2021
Subjects: subject: Applied Physics (physics.app-ph)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: Conventional optical displays using ITO (indium tin oxide) and LC (liquid crystal) materials present a lot of challenges in terms of long-term sustainability. We show here how it is possible to generate a cost effective and CMOS compatible fast and full range electrically controlled RGB color display by combining transmission based plasmonic metasurfaces with MEMS (Microelectromechanical systems) technology, using only two common materials: Aluminum and silicon oxide. White light is filtered into red, green, and blue components by plasmonic metasurfaces made of aluminum nanohole arrays, and the transmission through each color filter is modulated by MEMS miniaturized cantilevers fabricated with aluminum and silicon oxide on top of the color filters. We show that the relative transmission of a color subpixel can be freely modulated from 35% to 100%. Our pixels can also operate well above 800Hz, enabling future ultrafast displays. Our work provides a road to future circular economic goals by exploiting advances in structural colors and MEMS technologies to innovate optical displays.
description: 13 pages, 4 figures
The RNA recognition motif of NIFK is required for rRNA maturation during cell cycle progression
Creators: name: Wen-An Pan
name: Hsin-Yue Tsai
name: Shun-Chang Wang
name: Hsiao, Michael
name: Wu, Pei-Yu
name: Ming-Daw Tsai
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: Hematology
subject: Computational Biology

description: Ribosome biogenesis governs protein synthesis. NIFK is transactivated by c-Myc, the key regulator of ribosome biogenesis. The biological function of human NIFK is not well established, except that it has been shown to interact with Ki67 and NPM1. Here we report that NIFK is required for cell cycle progression and participates in the ribosome biogenesis via its RNA recognition motif (RRM). We show that silencing of NIFK inhibits cell proliferation through a reversible p53-dependent G1 arrest, possibly by induction of the RPL5/RPL11-mediated nucleolar stress. Mechanistically it is the consequence of impaired maturation of 28S and 5.8S rRNA resulting from inefficient cleavage of internal transcribed spacer (ITS) 1, a critical step in the separation of pre-ribosome to small and large subunits. Complementation of NIFK silencing by mutants shows that RNA-binding ability of RRM is essential for the pre-rRNA processing and G1 progression. More specifically, we validate that the RRM of NIFK preferentially binds to the 5′-region of ITS2 rRNA likely in both sequence specific and secondary structure dependent manners. Our results show how NIFK is involved in cell cycle progression through RRM-dependent pre-rRNA maturation, which could enhance our understanding of the function of NIFK in cell proliferation, and potentially also cancer and ribosomopathies.
Two related trypanosomatid eIF4G homologues have functional differences compatible with distinct roles during translation initiation
Creators: name: Moura, Danielle MN
name: Reis, Christian RS
name: Xavier, Camila C
name: Lima, Tamara D Da Costa
name: Lima, Rodrigo P
name: Carrington, Mark
name: Neto, Osvaldo P De Melo
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: In higher eukaryotes, eIF4A, eIF4E and eIF4G homologues interact to enable mRNA recruitment to the ribosome. eIF4G acts as a scaffold for these interactions and also interacts with other proteins of the translational machinery. Trypanosomatid protozoa have multiple homologues of eIF4E and eIF4G and the precise function of each remains unclear. Here, 2 previously described eIF4G homologues, EIF4G3 and EIF4G4, were further investigated. In vitro, both homologues bound EIF4AI, but with different interaction properties. Binding to distinct eIF4Es was also confirmed; EIF4G3 bound EIF4E4 while EIF4G4 bound EIF4E3, both these interactions required similar binding motifs. EIF4G3, but not EIF4G4, interacted with PABP1, a poly-A binding protein homolog. Work in vivo with Trypanosoma brucei showed that both EIF4G3 and EIF4G4 are cytoplasmic and essential for viability. Depletion of EIF4G3 caused a rapid reduction in total translation while EIF4G4 depletion led to changes in morphology but no substantial inhibition of translation. Site-directed mutagenesis was used to disrupt interactions of the eIF4Gs with either eIF4E or eIF4A, causing different levels of growth inhibition. Overall the results show that only EIF4G3, with its cap binding partner EIF4E4, plays a major role in translational initiation.
No One Representation to Rule Them All: Overlapping Features of Training Methods
Creators: name: Gontijo-Lopes, Raphael
name: Dauphin, Yann
name: Cubuk, Ekin D.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Despite being able to capture a range of features of the data, high accuracy models trained with supervision tend to make similar predictions. This seemingly implies that high-performing models share similar biases regardless of training methodology, which would limit ensembling benefits and render low-accuracy models as having little practical use. Against this backdrop, recent work has developed quite different training techniques, such as large-scale contrastive learning, yielding competitively high accuracy on generalization and robustness benchmarks. This motivates us to revisit the assumption that models necessarily learn similar functions. We conduct a large-scale empirical study of models across hyper-parameters, architectures, frameworks, and datasets. We find that model pairs that diverge more in training methodology display categorically different generalization behavior, producing increasingly uncorrelated errors. We show these models specialize in subdomains of the data, leading to higher ensemble performance: with just 2 models (each with ImageNet accuracy ~76.5%), we can create ensembles with 83.4% (+7% boost). Surprisingly, we find that even significantly low-accuracy models can be used to improve high-accuracy models. Finally, we show diverging training methodology yield representations that capture overlapping (but not supersetting) feature sets which, when combined, lead to increased downstream performance.
Translation attenuation via 3′ terminal codon usage in bovine csn1s2 is responsible for the difference in αs2- and β-casein profile in milk
Creators: name: Kim, Julie J
name: Jaeju Yu
name: Jnanankur Bag
name: Bakovic, Marica
name: Cant, John P
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: Cancer
subject: Computational Biology

description: The rate of secretion of αs2-casein into bovine milk is approximately 25% of that of β-casein, yet mammary expression of their respective mRNA transcripts (csn1s2 and csn2) is not different. Our objective was to identify molecular mechanisms that explain the difference in translation efficiency between csn1s2 and csn2. Cell-free translational efficiency of csn2 was 5 times that of csn1s2. Transcripts of csn1s2 distributed into heavier polysomes than csn2 transcripts, indicating an attenuation of elongation and/or termination. Stimulatory and inhibitory effects of the 5′ and 3′ UTRs on translational efficiency were different with luciferase and casein sequences in the coding regions. Substituting the 5′ and 3′ UTRs from csn2 into csn1s2 did not improve csn1s2 translation, implicating the coding region itself in the translation difference. Deletion of a 28-codon fragment from the 3′ terminus of the csn1s2 coding region, which displays codons with low correlations to cell fitness, increased translation to a par with csn2. We conclude that the usage of the last 28 codons of csn1s2 is the main regulatory element that attenuates its expression and is responsible for the differential translational expression of csn1s2 and csn2.
“Probing the closed-loop model of mRNA translation in living cells”
Creators: name: Archer, Stuart K
name: Shirokikh, Nikolay E
name: Hallwirth, Claus V
name: Beilharz, Traude H
name: Preiss, Thomas
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: 60506 Virology
subject: FOS: Biological sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Cancer
subject: Biological Sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Chemistry
subject: Earth and Environmental Sciences
subject: Physiology
subject: Molecular Biology
subject: Biochemistry
subject: Biophysics

description: The mRNA closed-loop, formed through interactions between the cap structure, poly(A) tail, eIF4E, eIF4G and PAB, features centrally in models of eukaryotic translation initiation, although direct support for its existence in vivo is not well established. Here, we investigated the closed-loop using a combination of mRNP isolation from rapidly cross-linked cells and high-throughput qPCR. Using the interaction between these factors and the opposing ends of mRNAs as a proxy for the closed-loop, we provide evidence that it is prevalent for eIF4E/4G-bound but unexpectedly sparse for PAB1-bound mRNAs, suggesting it primarily occurs during a distinct phase of polysome assembly. We observed mRNA-specific variation in the extent of closed-loop formation, consistent with a role for polysome topology in the control of gene expression.
Nonintrusive Manufactured Solutions for Non-Decomposing Ablation in Two Dimensions
Creators: name: Freno, Brian A.
name: Carnes, Brian R.
name: Brunini, Victor E.
name: Matula, Neil R.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Computational Physics (physics.comp-ph)
subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: Code verification is a necessary step towards establishing credibility in computational physics simulations. It is used to assess the correctness of the implementation of the numerical methods within the code, and it is a continuous part of code development. Code verification is typically performed using exact and manufactured solutions. However, exact solutions are often limited, and manufactured solutions generally require the invasive introduction of an artificial forcing term within the source code, such that the code solves a modified problem for which the solution is known. The equations for some physics phenomena, such as non-decomposing ablation, yield infinite analytic solutions, but the boundary conditions may eliminate these possibilities. For such phenomena, however, we can manufacture the terms that comprise the boundary conditions to obtain exact solutions. In this paper, we present a nonintrusive method for manufacturing solutions for non-decomposing ablation in two dimensions, which does not require the addition of a source term.
Sr-Doped Molecular Hydrogen: Synthesis and Properties of SrH$_{22}$
Creators: name: Semenok, Dmitrii V.
name: Chen, Wuhao
name: Huang, Xiaoli
name: Zhou, Di
name: Kruglov, Ivan A.
name: Mazitov, Arslan B.
name: Galasso, Michele
name: Tantardini, Christian
name: Gonze, Xavier
name: Kvashnin, Alexander G.
name: Oganov, Artem R.
name: Cui, Tian
Publisher: name: arXiv
Year: 2021
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Recently, several research groups announced reaching the point of metallization of hydrogen above 400 GPa. Following the mainstream of extensive investigations of compressed polyhydrides, in this work we demonstrate that small (4 atom %) doping of molecular hydrogen by strontium leads to a dramatic reduction in the metallization pressure to about 200 GPa. Studying the high-pressure chemistry of the Sr-H system at 56-180 GPa, we observed the formation of several previously unknown compounds: C2/m-Sr$_3$H$_{13}$, pseudocubic SrH$_6$, SrH$_9$ with cubic F-43m Sr sublattice, and pseudotetragonal P1-SrH$_{22}$, the metal hydride with the highest hydrogen content discovered so far. Unlike Ca and Y, strontium forms molecular semiconducting polyhydrides, whereas calcium and yttrium polyhydrides are high-Tc superconductors with an atomic H sublattice. The latter phase, SrH$_{22}$ or Sr$_{0.04}$H$_{0.96}$, may be considered as a convenient model of the consistent bandgap closure and metallization of hydrogen. Using the impedance measurements in diamond anvil cells at 300-440 K, we estimated the direct bandgap of the Pm-3n-like compound P1-SrH$_6$ to be 0.44-0.51 eV at 150 GPa, and its metallization pressure to be 220 GPa. Together with the machine learning interatomic potentials, the impedance spectroscopy allowed us to estimate the diffusion coefficients of hydrogen D$_H$ = 1.0-2.8 E-10 m$^2$/s in SrH$_6$ and 1.2-2.1 E-9 m$^2$/s in P1-SrH$_{22}$ at 500-600 K.
description: Supporting information was compressed and reduced by 2 times to 36 figures
Context Meta-Reinforcement Learning via Neuromodulation
Creators: name: Ben-Iwhiwhu, Eseoghene
name: Dick, Jeffery
name: Ketz, Nicholas A.
name: Pilly, Praveen K.
name: Soltoggio, Andrea
Publisher: name: arXiv
Year: 2021
Subjects: subject: Neural and Evolutionary Computing (cs.NE)
subject: Artificial Intelligence (cs.AI)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Meta-reinforcement learning (meta-RL) algorithms enable agents to adapt quickly to tasks from few samples in dynamic environments. Such a feat is achieved through dynamic representations in an agent's policy network (obtained via reasoning about task context, model parameter updates, or both). However, obtaining rich dynamic representations for fast adaptation beyond simple benchmark problems is challenging due to the burden placed on the policy network to accommodate different policies. This paper addresses the challenge by introducing neuromodulation as a modular component to augment a standard policy network that regulates neuronal activities in order to produce efficient dynamic representations for task adaptation. The proposed extension to the policy network is evaluated across multiple discrete and continuous control environments of increasing complexity. To prove the generality and benefits of the extension in meta-RL, the neuromodulated network was applied to two state-of-the-art meta-RL algorithms (CAVIA and PEARL). The result demonstrates that meta-RL augmented with neuromodulation produces significantly better result and richer dynamic representations in comparison to the baselines.
Challenges Faced by the Elderly in the Evolving Indian Context and the Necessity for Social Work Interventions
Creators: name: Dr Mohammad Tahir*
name: Mr. Arham Hasan Rizvi
Publisher: name: Zenodo
Year: 2025
Subjects: Ageing Population, Geriatric Social Work, Successful Ageing, Elderly Care, Social Work Intervention, Multidisciplinary Approach.

description: Abstract: The ageing population and increased life expectancy result from reduced mortality and fertility rates, indicative of a society's socioeconomic advancement. In several nations, the internationally acknowledged threshold for categorising persons as elderly is 60 years. The increasing older demographic heightens apprehensions over physical and functional health, social isolation, and maltreatment. The ageing process is linked to several issues, each arising from multiple factors. Geriatric social workers are essential in augmenting the mobility and autonomy of elderly individuals, thereby raising their quality of life and that of their loved ones. Social work intervention is crucial for successful ageing, encompassing comprehensive evaluation, counselling, crisis intervention, information distribution, and interdisciplinary teamwork. A multidisciplinary strategy, incorporating geriatric social workers, is crucial in the 21st century for guaranteeing a secure living environment and facilitating good ageing.
Structure and motifs of iron oxides from 1 to 3 TPa
Creators: name: Zheng, Feng
name: Sun, Yang
name: Wang, Renhai
name: Fang, Yimei
name: Zhang, Feng
name: Da, Bo
name: Wu, Shunqing
name: Wang, Cai-Zhuang
name: Wentzcovitch, Renata M.
name: Ho, Kai-Ming
Publisher: name: arXiv
Year: 2021
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Iron oxides are fundamental components of planet-forming materials. Understanding the Fe-O system's behavior and properties under high pressure can help us identify many new phases and states possible in exoplanetary interiors, especially terrestrial ones. Using the adaptive genetic algorithm (AGA), we investigate the structure of iron oxides for a wide range of stoichiometries ($0.25\leq x_O \leq 0.8$) at 1, 2, and 3 TPa. Five unreported ground-state structures with Fe$_2$O, FeO, Fe$_3$O$_5$, FeO$_2$, and FeO$_4$ compositions are identified. The calculated density of states (DOS) suggests that, except for FeO$_4$, all phases are metallic, but their carrier densities decrease with increasing pressure and oxygen content. The cluster alignment analysis of stable and metastable phases shows that several motifs may co-exist in a structure of iron oxides with low O content. In contrast, most iron oxides with high O content adopt a simple BCC motif at TPa pressures. Our results provide a crystal structure database of iron oxides for modeling and understanding the interiors of exoplanets.
description: 7 pages, 9 figures
The RNA recognition motif of NIFK is required for rRNA maturation during cell cycle progression
Creators: name: Wen-An Pan
name: Hsin-Yue Tsai
name: Shun-Chang Wang
name: Hsiao, Michael
name: Wu, Pei-Yu
name: Ming-Daw Tsai
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Hematology
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: Cancer
subject: Developmental Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Molecular Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Cell Biology
subject: Medicine
subject: Biochemistry

description: Ribosome biogenesis governs protein synthesis. NIFK is transactivated by c-Myc, the key regulator of ribosome biogenesis. The biological function of human NIFK is not well established, except that it has been shown to interact with Ki67 and NPM1. Here we report that NIFK is required for cell cycle progression and participates in the ribosome biogenesis via its RNA recognition motif (RRM). We show that silencing of NIFK inhibits cell proliferation through a reversible p53-dependent G1 arrest, possibly by induction of the RPL5/RPL11-mediated nucleolar stress. Mechanistically it is the consequence of impaired maturation of 28S and 5.8S rRNA resulting from inefficient cleavage of internal transcribed spacer (ITS) 1, a critical step in the separation of pre-ribosome to small and large subunits. Complementation of NIFK silencing by mutants shows that RNA-binding ability of RRM is essential for the pre-rRNA processing and G1 progression. More specifically, we validate that the RRM of NIFK preferentially binds to the 5′-region of ITS2 rRNA likely in both sequence specific and secondary structure dependent manners. Our results show how NIFK is involved in cell cycle progression through RRM-dependent pre-rRNA maturation, which could enhance our understanding of the function of NIFK in cell proliferation, and potentially also cancer and ribosomopathies.
Striatocycloceras in Kroger & Isakar 2006
Creators: name: Kröger, Björn
Publisher: name: Zenodo
Year: 2013
Subjects: Biodiversity
Taxonomy
Animalia
Mollusca
Cephalopoda
Orthocerida
Orthoceratidae
Striatocycloceras

description: Striatocycloceras? sp.
Fig. 15
Material
One specimen: PMU 26699, Kallholn, Siljan District, Sweden; Boda Limestone.
Description
The 90 mm long shell fragment consists in part of a body chamber. The maximum width of the fragment is 57 mm, from which a conch of ca. 70 mm in diameter may be reconstructed, based on the cross section. The conch was slightly curved and annulated with prominent, directly transverse annuli. The distance between the annuli is 10–15 mm, with a tendency to decrease toward the aperture (ca. 0.14–0.2 of conch cross section; seven to five chambers in a distance equal to the corresponding cross section). The shell surface is ornamented by narrowly, irregularly spaced distinctive growth lines (ca. 4 per one millimeter; Fig. 15). Additionally, on the inner surface of the shell, fine inconspicuous longitudinal lirae are visible (ca. one per millimeter).
Remarks
This orthoconic shell fragment is only provisionally assigned within Striatocycloceras. Nothing is known about the internal characters of this specimen. This generic identification is solely based on the annulated orthoconic shell, which is additionally transversally striated, a feature that is known exclusively from Striatocycloceras in the Late Ordovician beds of Baltoscandia.
description: Published as part of Kröger, Björn, 2013, The cephalopods of the Boda Limestone, Late Ordovician, of Dalarna, Sweden, pp. 1-110 in European Journal of Taxonomy 41 on pages 29-30, DOI: 10.5852/ejt.2013.41, http://zenodo.org/record/3814221
Translation attenuation via 3′ terminal codon usage in bovine csn1s2 is responsible for the difference in αs2- and β-casein profile in milk
Creators: name: Kim, Julie J
name: Jaeju Yu
name: Jnanankur Bag
name: Bakovic, Marica
name: Cant, John P
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Computational Biology
subject: Biological Sciences
subject: Ecology
subject: FOS: Biological sciences
subject: Chemistry
subject: Molecular Biology
subject: Genetics
subject: Cell Biology
subject: Physics
subject: Biochemistry
subject: Biophysics

description: The rate of secretion of αs2-casein into bovine milk is approximately 25% of that of β-casein, yet mammary expression of their respective mRNA transcripts (csn1s2 and csn2) is not different. Our objective was to identify molecular mechanisms that explain the difference in translation efficiency between csn1s2 and csn2. Cell-free translational efficiency of csn2 was 5 times that of csn1s2. Transcripts of csn1s2 distributed into heavier polysomes than csn2 transcripts, indicating an attenuation of elongation and/or termination. Stimulatory and inhibitory effects of the 5′ and 3′ UTRs on translational efficiency were different with luciferase and casein sequences in the coding regions. Substituting the 5′ and 3′ UTRs from csn2 into csn1s2 did not improve csn1s2 translation, implicating the coding region itself in the translation difference. Deletion of a 28-codon fragment from the 3′ terminus of the csn1s2 coding region, which displays codons with low correlations to cell fitness, increased translation to a par with csn2. We conclude that the usage of the last 28 codons of csn1s2 is the main regulatory element that attenuates its expression and is responsible for the differential translational expression of csn1s2 and csn2.
A process evaluation of the new interventions for independence in dementia study family stream (NIDUS-Family)
Creators: name: Wyman, Danielle
Publisher: name: Anglia Ruskin Research Online (ARRO)
Year: 2024

description: The New Interventions for independence in Dementia Study (NIDUS)-Family is an effective Alzheimer’s Society funded manualised psychosocial intervention supporting people living with dementia and their family carers to attain goals they set towards living as independently and as well as possible at home for longer. The aim of this thesis was to conduct a process evaluation embedded into the intervention-arm population of the NIDUS-Family randomised controlled trial (RCT) to understand the causal pathways through which the intervention influenced change.A systematic review of process evaluation methodology for this population informed the design of the NIDUS-Family process evaluation. The Medical Research Council (MRC) Guidance (Moore et al, 2015) recommendations and a theory-driven convergent mixed-method design were applied. Research questions interrogated the theoretical principles and hypothesised causal assumptions to understand how NIDUS-Family influenced goal attainment and wellbeing in practice through identifying core implementation, mechanisms of impact and contextual factors.Overall, findings indicated participants positively experienced the NIDUS-Family intervention, describing it as being transformative, supportive, and having a positive impact on their wellbeing and dyadic relationship. Attrition, reach, adherence, delivery, and fidelity data demonstrated NIDUS-Family was delivered as intended against the protocol to its target audience. Core implementation factors were delivery from the facilitator of the NIDUS-Family approaches, strategies, and values. For dyads, mechanisms of impact were building a respectful, trusting, and impartial relationship with their facilitator which aided the development of meaningful goals and/or actions in which they could work through the modules towards finding manageable solutions. Core contextual factors impacting intervention implementation and mechanisms were dyadic participation and knowledge of dementia.These findings will directly inform the NIDUS-Family implementation study in helping adapt and translate the intervention into practice and widen the knowledge of process evaluation design to ensure more robust applications of frameworks and methods to enable more generalisable outcomes.
Apples and Oranges: Comparing black holes in X-ray binaries and gravitational-wave sources
Creators: name: Fishbach, Maya
name: Kalogera, Vicky
Publisher: name: arXiv
Year: 2021
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: The component black holes (BHs) observed in gravitational-wave (GW) binary black hole (BBH) events tend to be more massive and slower spinning than those observed in black hole X-ray binaries (BH-XRBs). Without modeling their evolutionary histories, we investigate whether these apparent tensions in the BH populations can be explained by GW observational selection effects alone. We find that this is indeed the case for the discrepancy between BH masses in BBHs and the observed high-mass X-ray binaries (HMXBs), when we account for statistical uncertainty from the small sample size of just three HMXBs. On the other hand, the BHs in observed low-mass X-ray binaries (LMXBs) are significantly lighter than the astrophysical BBH population, but this may just be due to a correlation between component masses in a binary system. Given their light stellar companions, we expect light BHs in LMXBs. The observed spins in HMXBs and LMXBs, however, are in tension with the inferred BBH spin distribution at the $>99.9\%$ level. We discuss possible scenarios behind the significantly larger spins in observed BH-XRBs. One possibility is that a small subpopulation (conservatively $<30\%$) of BBHs have rapidly spinning primary components, indicating that they may have followed a similar evolutionary pathway to the observed HMXBs. In LMXBs, it has been suggested that BHs can spin up by accretion. If LMXB natal spins follow the BBH spin distribution, we find LMXBs must gain an average dimensionless spin of $0.47^{+0.10}_{-0.11}$, but if their natal spins follow the observed HMXB spins, the average spinup must be $<0.03$.
description: 13 pages, 6 figures. Updated to match version accepted by ApJL
Two related trypanosomatid eIF4G homologues have functional differences compatible with distinct roles during translation initiation
Creators: name: Moura, Danielle MN
name: Reis, Christian RS
name: Xavier, Camila C
name: Lima, Tamara D Da Costa
name: Lima, Rodrigo P
name: Carrington, Mark
name: Neto, Osvaldo P De Melo
Publisher: name: Taylor & Francis
Year: 2015
Subjects: Biological Sciences
Molecular Biology
Cell Biology
Biochemistry
Biophysics

description: In higher eukaryotes, eIF4A, eIF4E and eIF4G homologues interact to enable mRNA recruitment to the ribosome. eIF4G acts as a scaffold for these interactions and also interacts with other proteins of the translational machinery. Trypanosomatid protozoa have multiple homologues of eIF4E and eIF4G and the precise function of each remains unclear. Here, 2 previously described eIF4G homologues, EIF4G3 and EIF4G4, were further investigated. In vitro, both homologues bound EIF4AI, but with different interaction properties. Binding to distinct eIF4Es was also confirmed; EIF4G3 bound EIF4E4 while EIF4G4 bound EIF4E3, both these interactions required similar binding motifs. EIF4G3, but not EIF4G4, interacted with PABP1, a poly-A binding protein homolog. Work in vivo with Trypanosoma brucei showed that both EIF4G3 and EIF4G4 are cytoplasmic and essential for viability. Depletion of EIF4G3 caused a rapid reduction in total translation while EIF4G4 depletion led to changes in morphology but no substantial inhibition of translation. Site-directed mutagenesis was used to disrupt interactions of the eIF4Gs with either eIF4E or eIF4A, causing different levels of growth inhibition. Overall the results show that only EIF4G3, with its cap binding partner EIF4E4, plays a major role in translational initiation.
Variational principle for optimal quantum controls in quantum metrology
Creators: name: Yang, Jing
name: Pang, Shengshi
name: Chen, Zekai
name: Jordan, Andrew N.
name: del Campo, Adolfo
Publisher: name: arXiv
Year: 2021
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We develop a variational principle to determine the quantum controls and initial state which optimizes the quantum Fisher information, the quantity characterizing the precision in quantum metrology. When the set of available controls is limited, the exact optimal initial state and the optimal controls are in general dependent on the probe time, a feature missing in the unrestricted case. Yet, for time-independent Hamiltonians with restricted controls, the problem can be approximately reduced to the unconstrained case via the Floquet engineering. In particular, we find for magnetometry with a time-independent spin chain containing three-body interactions, even when the controls are restricted to one and two-body interaction, that the Heisenberg scaling can still be approximately achieved. Our results open the door to investigate quantum metrology under a limited set of available controls, of relevance to many-body quantum metrology in realistic scenarios.
description: Close to the published version
Senatus -- A Fast and Accurate Code-to-Code Recommendation Engine
Creators: name: Silavong, Fran
name: Moran, Sean
name: Georgiadis, Antonios
name: Saphal, Rohan
name: Otter, Robert
Publisher: name: arXiv
Year: 2021
Subjects: subject: Software Engineering (cs.SE)
subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: Machine learning on source code (MLOnCode) is a popular research field that has been driven by the availability of large-scale code repositories and the development of powerful probabilistic and deep learning models for mining source code. Code-to-code recommendation is a task in MLOnCode that aims to recommend relevant, diverse and concise code snippets that usefully extend the code currently being written by a developer in their development environment (IDE). Code-to-code recommendation engines hold the promise of increasing developer productivity by reducing context switching from the IDE and increasing code-reuse. Existing code-to-code recommendation engines do not scale gracefully to large codebases, exhibiting a linear growth in query time as the code repository increases in size. In addition, existing code-to-code recommendation engines fail to account for the global statistics of code repositories in the ranking function, such as the distribution of code snippet lengths, leading to sub-optimal retrieval results. We address both of these weaknesses with \emph{Senatus}, a new code-to-code recommendation engine. At the core of Senatus is \emph{De-Skew} LSH a new locality sensitive hashing (LSH) algorithm that indexes the data for fast (sub-linear time) retrieval while also counteracting the skewness in the snippet length distribution using novel abstract syntax tree-based feature scoring and selection algorithms. We evaluate Senatus and find the recommendations to be of higher quality than competing baselines, while achieving faster search. For example on the CodeSearchNet dataset Senatus improves performance by 31.21\% F1 and 147.9\emph{x} faster query time compared to Facebook Aroma. Senatus also outperforms standard MinHash LSH by 29.2\% F1 and 51.02\emph{x} faster query time.
description: Accepted to MSR 2022
Can we decipher the composition of the core of a neutron star?
Creators: name: Mondal, Chiranjib
name: Gulminelli, Francesca
Publisher: name: arXiv
Year: 2021
Subjects: subject: Nuclear Theory (nucl-th)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Nuclear Experiment (nucl-ex)
subject: FOS: Physical sciences

description: General relativity guarantees a unique one-to-one correspondence between static observables of neutron stars (NSs) accessible by multi-messenger astronomy, such as mass-radius or tidal deformability, and the equation of state (EoS) of beta equilibrated matter. It is well known that these static properties are not enough to discern conventional NSs from hybrid stars. However, if one assumes that hadrons present in the neutron star core are only neutrons and protons, the lepton fraction is in principle determined unequivocally by the condition of chemical equilibrium. Using a simple analytical method based on a polynomial expansion of the EoS, we show that multiple solutions are possible to the beta-equilibrium equation, leading to a characteristic indetermination on the composition of the interiors of NSs, even in the purely nucleonic hypothesis. We further show that additional empirical information on symmetric matter at high densities are not very efficient to pin down the composition, if uncertainties on measurements are accounted for. We conclude that constraints on the symmetry energy at high densities only, can make meaningful impact to decipher the composition of neutron star core. Our results give a lower limit to the uncertainty on the NS core composition that can be obtained with astrophysical and terrestrial experiments.
description: 8 pages, restructured, new figures added
Structural determinants for alternative splicing regulation of the MAPT pre-mRNA
Creators: name: Lisowiec, Jolanta
name: Magner, Dorota
name: Elzbieta Kierzek
name: Elzbieta Lenartowicz
name: Kierzek, Ryszard
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Biophysics
subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology

description: Alternative splicing at the MAPT gene exon 10 yields similar levels of the 3R and 4R tau protein isoforms.1 The presence of mutations, particularly in exon 10 and intron 10–11, changes the quantity of tau isoforms. Domination each of the isoform yields tau protein aggregation and frontotemporal dementia and Parkinsonism linked to chromosome 17 (FTDP-17). Here, we report for the first time the secondary structure of the 194/195 nucleotide region for the wild type (WT) and 10 mutants of the MAPT gene pre-mRNA determined using both chemical and microarray mapping. Thermodynamic analyses indicate that single nucleotide mutations in the splicing regulatory element (SRE) that form a hairpin affect its stability by up to 4 and 7 kcal/mol. Moreover, binding the regulatory hairpin of small molecule ligands (neomycin, kanamycin, tobramycin and mitoxantrone) enhance its stability depending on the nature of the ligands and the RNA mutations. Experiments using the cos-7 cell line indicate that the presence of ligands and modified antisense oligonucleotides affect the quantity of 3R and 4R isoforms. This finding correlates with the thermodynamic stability of the regulatory hairpin. An alternative splicing regulation mechanism for exon 10 is postulated based on our experimental data and on published data.
Dawsonoceras Hyatt 1884
Creators: name: Kröger, Björn
Publisher: name: Zenodo
Year: 2013
Subjects: Biodiversity
Taxonomy
Animalia
Mollusca
Cephalopoda
Orthocerida
Dawsonoceratidae
Dawsonoceras

description: Genus Dawsonoceras Hyatt, 1884
Type species
Orthoceras annulatum Sowerby, 1816, Wenlock Series, Coalbrookdale, Shropshire, England; by original designation.
Diagnosis
Slender, circular or slightly compressed orthocones with symmetrically curved septa and straight transverse sutures; sutures parallel to the annulations in each groove of the annulations; annulations regularly spaced, with fine transverse ornamentation or growth lines; growth lines in some species festooned. In some species with longitudinal ridges that may form nodes at the ridges of the annulations; siphuncle subcentral in early growth stages, central in late growth stages, narrow, but expanded within the chambers; septal necks short suborthochoanitic to achoanitic. Incipient annulosiphuncular deposits.
Remarks
The diagnosis is adopted from Kröger & Isakar (2006). There the genus was revised and discussed in detail.
description: Published as part of Kröger, Björn, 2013, The cephalopods of the Boda Limestone, Late Ordovician, of Dalarna, Sweden, pp. 1-110 in European Journal of Taxonomy 41 on page 30, DOI: 10.5852/ejt.2013.41, http://zenodo.org/record/3814221
Supplementary figures from Extensive simulations assess the performance of genome-wide association mapping in various Saccharomyces cerevisiae subpopulations
Creators: name: Peter, Jackson
name: Friedrich, Anne
name: Liti, Gianni
name: Schacherer, Joseph
Publisher: name: The Royal Society
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences
subject: 60408 Genomics

description: With the advent of high throughput sequencing technologies, genome-wide association studies (GWAS) have become a powerful paradigm for dissecting the genetic origins of the observed phenotypic variation. We recently completely sequenced the genome of 1011 Saccharomyces cerevisiae isolates, laying a strong foundation for GWAS. To assess the feasibility and the limits of this approach, we performed extensive simulations using five selected subpopulations as well as the total set of 1011 genomes. We measured the ability to detect the causal genetic variants involved in Mendelian and more complex traits using a linear mixed model approach. The results showed that population structure is well accounted for and is not the main problem when the sample size is high enough. While the genetic determinant of a Mendelian trait is easily mapped in all studied subpopulations, discrepancies are seen between datasets when performing GWAS on a complex trait in terms of detection, false positive and false negative rate. Finally, we performed GWAS on the different defined subpopulations using a real quantitative trait (resistance to copper sulfate) and showed the feasibility of this approach. The performance of each dataset depends simultaneously on several factors such as sample size, relatedness and population evolutionary history.This article is part of the theme issue ‘Genetic basis of adaptation and speciation: from loci to causative mutations’.
Stabilization of the G-quadruplex at the VEGF IRES represses cap-independent translation
Creators: name: Cammas, Anne
name: Dubrac, Alexandre
name: Morel, Benjamin
name: Assala Lamaa
name: Touriol, Christian
name: Marie-Paule Teulade-Fichou
name: Prats, Hervé
name: Millevoi, Stefania
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: Computational Biology

description: The activation of translation contributes to malignant transformation and is an emerging target for cancer therapies. RNA G-quadruplex structures are general inhibitors of cap-dependent mRNA translation and were recently shown to be targeted for oncoprotein translational activation. In contrast however, the G-quadruplex within the 5'UTR of the human vascular endothelial growth factor A (VEGF) has been shown to be essential for IRES-mediated translation. Since VEGF has a pivotal role in tumor angiogenesis and is a major target of anti-tumoral therapies, we investigated the structure/function relationship of the VEGF G-quadruplex and defined whether it could have a therapeutic potential. We found that the G-quadruplex within the VEGF IRES is dispensable for cap-independent function and activation in stress conditions. However, stabilization of the VEGF G-quadruplex by increasing the G-stretches length or by replacing it with the one of NRAS results in strong inhibition of IRES-mediated translation of VEGF. We also demonstrate that G-quadruplex ligands stabilize the VEGF G-quadruplex and inhibit cap-independent translation in vitro. Importantly, the amount of human VEGF mRNA associated with polysomes decreases in the presence of a highly selective stabilizing G-quadruplex ligand, resulting in reduced VEGF protein expression. Together, our results uncover the existence of functionally silent G-quadruplex structures that are susceptible to conversion into efficient repressors of cap-independent mRNA translation. These findings have implications for the in vivo applications of G-quadruplex-targeting compounds and for anti-angiogenic therapies.
Structural determinants for alternative splicing regulation of the MAPT pre-mRNA
Creators: name: Lisowiec, Jolanta
name: Magner, Dorota
name: Elzbieta Kierzek
name: Elzbieta Lenartowicz
name: Kierzek, Ryszard
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Biological Sciences
subject: Pharmacology
subject: Molecular Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Biochemistry
subject: Biophysics

description: Alternative splicing at the MAPT gene exon 10 yields similar levels of the 3R and 4R tau protein isoforms.1 The presence of mutations, particularly in exon 10 and intron 10–11, changes the quantity of tau isoforms. Domination each of the isoform yields tau protein aggregation and frontotemporal dementia and Parkinsonism linked to chromosome 17 (FTDP-17). Here, we report for the first time the secondary structure of the 194/195 nucleotide region for the wild type (WT) and 10 mutants of the MAPT gene pre-mRNA determined using both chemical and microarray mapping. Thermodynamic analyses indicate that single nucleotide mutations in the splicing regulatory element (SRE) that form a hairpin affect its stability by up to 4 and 7 kcal/mol. Moreover, binding the regulatory hairpin of small molecule ligands (neomycin, kanamycin, tobramycin and mitoxantrone) enhance its stability depending on the nature of the ligands and the RNA mutations. Experiments using the cos-7 cell line indicate that the presence of ligands and modified antisense oligonucleotides affect the quantity of 3R and 4R isoforms. This finding correlates with the thermodynamic stability of the regulatory hairpin. An alternative splicing regulation mechanism for exon 10 is postulated based on our experimental data and on published data.
D5.5 Prospective energy citizenship scenarios with recommendations
Creators: name: Hajdinjak, Marko
name: Asenova, Desislava
name: Brizga, Janis
name: Damianova, Zoya
name: Dimova, Adriana
name: Georgieva, Rositsa
name: Lydon, Michael
name: Thalberg, Karin
Publisher: name: Zenodo
Year: 2024

description: This report presents several scenarios for development, consolidation and transformation of energy citizenship in the EU. The scenarios are based on the relevant findings from PESTEL analysis (study of the political, economic, social, technological, environmental and legal conditions that have an impact on the emergence and development of energy citizenship in the European countries; see Debourdeau et al, 2023 and Hajdinjak et al, 2023) and an online survey, in which 10,071 citizens from 19 European countries participated (see Hajdinjak et al, 2024). The three scenarios explore possible developments for energy citizenship in the EU until 2030. The first scenario considers the combined impact of the most relevant economic developments and societal characteristics that shape the scope and options for involvement of citizens in the energy transition. The second scenario examines the wider political and legal environment in which energy citizenship forms and is manifested. The third scenario looks at the opportunities for energy citizenship emerging from the interaction between technological advances (seen as a tool or enabler of energy citizenship) and environmental consciousness and concerns (considered as motivation for citizens to act).
Parametric and nonparametric methods hint dark energy evolution
Creators: name: Bernardo, Reginald Christian
name: Grandón, Daniela
name: Said, Jackson Levi
name: Cárdenas, Víctor H.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We study dark energy through the viewpoints of parametric and nonparametric analyses of late-time cosmological data. We consider four Hubble parameter priors reflecting the Hubble tension and make use of two phenomenological functions, namely, a normalized dark energy density and a compactified dark energy equation of state. We predict the shape of both functions and present new constraints on the dark energy equation of state. The results hint at dark energy evolution regardless of the choice of the method and of the priors. The fact that similar evolutions for the dark energy densities are found through drastically different approaches suggests that the features found in this paper are driven by the data, and are not artifact of the reconstruction methods applied.
description: 39 pages, 14 figures, 3 tables, v3: discussion improved, new figure added, to appear in Phys. Dark Universe