bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using regulatory variants to detect gene–gene interactions identifies networks of genes linked to cell immortalisation
Authors: Wragg D. , Liu Q. , Lin Z. , Riggio V. , Pugh C. A. , Beveridge A. J. , Brown H. , Hume D. A. , Harris S. E. , Deary I. J. , Tenesa A. , Prendergast J. G. D. 
Published: January 2020

AbstractThe extent to which the impact of regulatory genetic variants may depend on other factors, such as the expression levels of upstream transcription factors, remains poorly understood. Here we report a framework in which regulatory variants are first aggregated into sets, and using these as estimates of the total cis-genetic effects on a gene we model their non-additive interactions with the expression of other genes in the genome. Using 1220 lymphoblastoid cell lines across platforms and independent datasets we identify 74 genes where the impact of their regulatory variant-set is linked to the expression levels of networks of distal genes. We show that these networks are predominantly associated with tumourigenesis pathways, through which immortalised cells are able to rapidly proliferate. We consequently present an approach to define gene interaction networks underlying important cellular pathways such as cell immortalisation.
Plasmon–emitter interactions at the nanoscale
Authors: Gonçalves P. A. D. , Christensen Thomas , Rivera Nicholas , Jauho Antti-Pekka , Mortensen N. Asger , Soljačić Marin 
Published: January 2020

AbstractPlasmon–emitter interactions are of central importance in modern nanoplasmonics and are generally maximal at short emitter–surface separations. However, when the separation falls below 10–20 nm, the classical theory deteriorates progressively due to its neglect of quantum effects such as nonlocality, electronic spill-out, and Landau damping. Here we show how this neglect can be remedied in a unified theoretical treatment of mesoscopic electrodynamics incorporating Feibelman $$d$$
d
-parameters. Our approach incorporates nonclassical resonance shifts and surface-enabled Landau damping—a nonlocal damping effect—which have a dramatic impact on the amplitude and spectral distribution of plasmon–emitter interactions. We consider a broad array of plasmon–emitter interactions ranging from dipolar and multipolar spontaneous emission enhancement, to plasmon-assisted energy transfer and enhancement of two-photon transitions. The formalism gives a complete account of both plasmons and plasmon–emitter interactions at the nanoscale, constituting a simple yet rigorous platform to include nonclassical effects in plasmon-enabled nanophotonic phenomena.
Self-assembled single-atom nanozyme for enhanced photodynamic therapy treatment of tumor
Authors: Wang Dongdong , Wu Huihui , Phua Soo Zeng Fiona , Yang Guangbao , Qi Lim Wei , Gu Long , Qian Cheng , Wang Haibao , Guo Zhen , Chen Hongzhong , Zhao Yanli 
Published: January 2020

AbstractHypoxia of solid tumor compromises the therapeutic outcome of photodynamic therapy (PDT) that relies on localized O2 molecules to produce highly cytotoxic singlet oxygen (1O2) species. Herein, we present a safe and versatile self-assembled PDT nanoagent, i.e., OxgeMCC-r single-atom enzyme (SAE), consisting of single-atom ruthenium as the active catalytic site anchored in a metal-organic framework Mn3[Co(CN)6]2 with encapsulated chlorin e6 (Ce6), which serves as a catalase-like nanozyme for oxygen generation. Coordination-driven self-assembly of organic linkers and metal ions in the presence of a biocompatible polymer generates a nanoscale network that adaptively encapsulates Ce6. The resulted OxgeMCC-r SAE possesses well-defined morphology, uniform size distribution and high loading capacity. When conducting the in situ O2 generation through the reaction between endogenous H2O2 and single-atom Ru species of OxgeMCC-r SAE, the hypoxia in tumor microenvironment is relieved. Our study demonstrates a promising self-assembled nanozyme with highly efficient single-atom catalytic sites for cancer treatment.
The shift of phosphorus transfers in global fisheries and aquaculture
Authors: Huang Yuanyuan , Ciais Phillipe , Goll Daniel S. , Sardans Jordi , Peñuelas Josep , Cresto-Aleina Fabio , Zhang Haicheng 
Published: January 2020

AbstractGlobal fish production (capture and aquaculture) has increased quickly, which has altered global flows of phosphorus (P). Here we show that in 2016, $$2.04_{1.59}^{3.09}$$
2.0

4

1.59

3.09

Tg P yr−1 (mean and interquartile range) was applied in aquaculture to increase fish production; while $$1.10_{1.04}^{1.14}$$
1.1

0

1.04

1.14

Tg P yr−1 was removed from aquatic systems by fish harvesting. Between 1950 and 1986, P from fish production went from aquatic towards the land-human systems. This landward P peaked at 0.54 Tg P yr−1, representing a large but overlooked P flux that might benefit land activities under P scarcity. After 1986, the landward P flux decreased significantly, and became negative around 2004, meaning that humans spend more P to produce fish than harvest P in fish capture. An idealized pathway to return to the balanced anthropogenic P flow would require the mean phosphorus use efficiency (the ratio of harvested to input P) of aquaculture to be increased from a current value of 20% to at least 48% by 2050 — a big challenge.
Cryo-EM structure of the respiratory syncytial virus RNA polymerase
Authors: Cao Dongdong , Gao Yunrong , Roesler Claire , Rice Samantha , D’Cunha Paul , Zhuang Lisa , Slack Julia , Domke Mason , Antonova Anna , Romanelli Sarah , Keating Shayon , Forero Gabriela , Juneja Puneet , Liang Bo 
Published: January 2020

AbstractThe respiratory syncytial virus (RSV) RNA polymerase, constituted of a 250 kDa large (L) protein and tetrameric phosphoprotein (P), catalyzes three distinct enzymatic activities — nucleotide polymerization, cap addition, and cap methylation. How RSV L and P coordinate these activities is poorly understood. Here, we present a 3.67 Å cryo-EM structure of the RSV polymerase (L:P) complex. The structure reveals that the RNA dependent RNA polymerase (RdRp) and capping (Cap) domains of L interact with the oligomerization domain (POD) and C-terminal domain (PCTD) of a tetramer of P. The density of the methyltransferase (MT) domain of L and the N-terminal domain of P (PNTD) is missing. Further analysis and comparison with other RNA polymerases at different stages suggest the structure we obtained is likely to be at an elongation-compatible stage. Together, these data provide enriched insights into the interrelationship, the inhibitors, and the evolutionary implications of the RSV polymerase.
The origins of acoustic communication in vertebrates
Authors: Chen Zhuo , Wiens John J. 
Published: January 2020

AbstractAcoustic communication is crucial to humans and many other tetrapods, including birds, frogs, crocodilians, and mammals. However, large-scale patterns in its evolution are largely unstudied. Here, we address several fundamental questions about the origins of acoustic communication in terrestrial vertebrates (tetrapods), using phylogenetic methods. We show that origins of acoustic communication are significantly associated with nocturnal activity. We find that acoustic communication does not increase diversification rates, a surprising result given the many speciation-focused studies of frog calls and bird songs. We also demonstrate that the presence of acoustic communication is strongly conserved over time. Finally, we find that acoustic communication evolved independently in most major tetrapod groups, often with remarkably ancient origins (~100–200 million years ago). Overall, we show that the role of ecology in shaping signal evolution applies to surprisingly deep timescales, whereas the role of signal evolution in diversification may not.
Unfolding the complexity of phonon quasi-particle physics in disordered materials
Authors: Mu Sai , Olsen Raina J. , Dutta Biswanath , Lindsay Lucas , Samolyuk German D. , Berlijn Tom , Specht Eliot D. , Jin Ke , Bei Hongbin , Hickel Tilmann , Larson Bennet C. , Stocks George M. 
Published: January 2020

AbstractThe concept of quasi-particles forms the theoretical basis of our microscopic understanding of emergent phenomena associated with quantum-mechanical many-body interactions. However, the quasi-particle theory in disordered materials has proven difficult, resulting in the predominance of mean-field solutions. Here, we report first-principles phonon calculations and inelastic X-ray and neutron-scattering measurements on equiatomic alloys (NiCo, NiFe, AgPd, and NiFeCo) with force-constant dominant disorder—confronting a key 50-year-old assumption in the Hamiltonian of all mean-field quasi-particle solutions for off-diagonal disorder. Our results have revealed the presence of a large, and heretofore unrecognized, impact of local chemical environments on the distribution of the species-pair-resolved force-constant disorder that can dominate phonon scattering. This discovery not only identifies a critical analysis issue that has broad implications for other elementary excitations, such as magnons and skyrmions in magnetic alloys, but also provides an important tool for the design of materials with ultralow thermal conductivities.
Releasing the hidden shift current in the TTF-CA organic molecular solid via symmetry lowering
Authors: Kim Bumseop , Kim Jeongwoo , Shin Dongbin , Choi Min , Lee Junhee , Park Noejung 
Published: January 2020

AbstractBulk photovoltaic effect, characterized by an excitation-driven unbiased spontaneous photocurrent, has attracted substantial attention mainly due to its potential for harvesting solar energy. Here, we investigate the photovoltaic characteristics of organic molecular solids and focus on the association between the photocurrent and the crystal symmetry in the exemplary case of tetrathiafulvalene-p-chloranil. We perform comprehensive first-principles calculations, including direct evaluations of the excited-state current via real-time propagations of the time-dependent density functional theory. We find that the charge shifting in the low-temperature phase is mainly driven by the intrachain ferroelectricity, which gives rise to a photocurrent not only in the visible-light range but also near the band-edge infrared region. The shift current that is locked in the symmetry of the high-temperature phase can be released by introducing a potential asymmetry. We suggest that organic molecular solids can be exploited via appropriate engineering to lower the symmetry, aiming at room-temperature photovoltaics.
Quantum inverse iteration algorithm for programmable quantum simulators
Authors: Kyriienko Oleksandr 
Published: January 2020

AbstractWe propose a quantum inverse iteration algorithm, which can be used to estimate ground state properties of a programmable quantum device. The method relies on the inverse power iteration technique, where the sequential application of the Hamiltonian inverse to an initial state prepares the approximate ground state. To apply the inverse Hamiltonian operation, we write it as a sum of unitary evolution operators using the Fourier approximation approach. This allows to reformulate the protocol as separate measurements for the overlap of initial and propagated wavefunction. The algorithm thus crucially depends on the ability to run Hamiltonian dynamics with an available quantum device, and can be used for analog quantum simulators. We benchmark the performance using paradigmatic examples of quantum chemistry, corresponding to molecular hydrogen and beryllium hydride. Finally, we show its use for studying the ground state properties of relevant material science models, which can be simulated with existing devices, considering an example of the Bose-Hubbard atomic simulator.
Doping evolution of the charge excitations and electron correlations in electron-doped superconducting La2−xCexCuO4
Authors: Lin Jiaqi , Yuan Jie , Jin Kui , Yin Zhiping , Li Gang , Zhou Ke-Jin , Lu Xingye , Dantz Marcus , Schmitt Thorsten , Ding Hong , Guo Haizhong , Dean Mark P. M. , Liu Xuerong 
Published: January 2020

AbstractElectron correlations play a dominant role in the charge dynamics of the cuprates. We use resonant inelastic X-ray scattering (RIXS) to track the doping dependence of the collective charge excitations in electron doped La$${}_{2-x}$$

2
−
x

Ce$${}_{x}$$

x

CuO$${}_{4}$$

4

(LCCO). From the resonant energy dependence and the out-of-plane momentum dependence, the charge excitations are identified as three-dimensional (3D) plasmons, which reflect the nature of the electronic structure and Coulomb repulsion on both short and long lengthscales. With increasing electron doping, the plasmon excitations increase monotonically in energy, a consequence of the electron correlation effect on electron structure near the Fermi surface (FS). Importantly, the plasmon excitations evolve from a broad feature into a well-defined peak with much increased life time, revealing the evolution of the electrons from incoherent states to coherent quasi-particles near the FS. Such evolution marks the reduction of the short-range electronic correlation, and thus the softening of the Mottness of the system with increasing electron doping.
Spatial Network Connectivity and Spatial Reasoning Ability in Children with Nonverbal Learning Disability
Authors: Banker Sarah M. , Ramphal Bruce , Pagliaccio David , Thomas Lauren , Rosen Elizabeth , Sigel Anika N. , Zeffiro Thomas , Marsh Rachel , Margolis Amy E. 
Published: January 2020

AbstractNonverbal Learning Disability (NVLD) is characterized by deficits in visual-spatial, but not verbal, reasoning. Nevertheless, the functioning of the neural circuits supporting spatial processing have yet to be assessed in children with NVLD. We compared the resting state functional connectivity of a spatial brain network among children with NVLD, children with reading disorder (RD), and typically developing (TD) children. Seventy-five participants (7–15 years old) were included in the study (20 TD, 24 NVLD, and 31 RD). Group differences in global efficiency and functional connectivity among 12 regions comprising a previously defined spatial network were evaluated. Associations with behavior were explored. Global efficiency of the spatial network associated positively with spatial ability and inversely with socioemotional problems. Within the spatial network, associations between left posterior cingulate (PCC) and right retrosplenial cortical activity were reduced in children with NVLD relative to those without spatial deficits (RD and TD). Connectivity between left PCC and right posterior cerebellum (Crus I and II) was reduced in both groups of children with learning disabilities (NVLD and RD) relative to TD children. Functional connectivity of the spatial network was atypically associated with cognitive and socioemotional performance in children with NVLD. Identifying a neurobiological substrate for NVLD provides evidence that it is a discrete clinical entity and suggests targets for treatment.
Ultrastructure of Ediacaran cloudinids suggests diverse taphonomic histories and affinities with non-biomineralized annelids
Authors: Yang Ben , Steiner Michael , Schiffbauer James D. , Selly Tara , Wu Xuwen , Zhang Cong , Liu Pengju 
Published: January 2020

AbstractCloudinids have long been considered the earliest biomineralizing metazoans, but their affinities have remained contentious and undetermined. Based on well-preserved ultrastructures of two taxa, we here propose new interpretations regarding both their extent of original biomineralization and their phylogenetic affinity. One of these taxa is a new cloudinid from Mongolia, Zuunia chimidtsereni gen. et sp. nov., which exhibits key characteristics of submicrometric kerogenous lamellae, plastic tube-wall deformation, and tube-wall delamination. Multiple carbonaceous lamellae are also discovered in Cloudina from Namibia and Paraguay, which we interpret to have originated from chitinous or collagenous fabrics. We deduce that these cloudinids were predominantly originally organic (chitinous or collagenous), and postmortem decay and taphonomic mineralization resulted in the formation of aragonite and/or calcite. Further, based on our ultrastructural characterization and other morphological similarities, we suggest that the cloudinids should most parsimoniously be assigned to annelids with originally organic tubes.
The diversity of recent trends for chondrichthyans in the Mediterranean reflects fishing exploitation and a potential evolutionary pressure towards early maturation
Authors: Ramírez-Amaro Sergio , Ordines Francesc , Esteban Antonio , García Cristina , Guijarro Beatriz , Salmerón Francisca , Terrasa Bàrbara , Massutí Enric 
Published: January 2020

AbstractChondrichthyans are a vulnerable group that has been overexploited for almost half a century in the Mediterranean. Since in this area most chondrichthyans are rarely incorporated into international statistics, the impact of fishing on their populations is difficult to assess. Here, we evaluate temporal trends in order to understand the recent history of chondrichthyans in the western Mediterranean. Fishery-independent data were obtained from scientific surveys carried out from 1994 to 2015 in three geographical sub-areas. Our results reflect fairly stable populations in terms of diversity, with some increase in density and standardized biomass of some species dwelling on the continental shelf, and even for some species dwelling on the slope. In contrast, decreasing trends were observed in some deep-water species. This can be explained by the reduction of the trawling effort on the continental shelf over the last few decades, and the shift of the fleet towards deep waters, along with the greater resilience displayed by some species. Furthermore, a decreasing trend in maturity ofScyliorhinus caniculawas detected, suggesting an evolutionary response to overfishing. These results improve scientific knowledge for developing true adaptive management in the Mediterranean that will implement measures to strengthen or initiate the recovery of chondrichthyans.
Using virtual reality to define the mechanisms linking symptoms with cognitive deficits in attention deficit hyperactivity disorder
Authors: Mangalmurti Aman , Kistler William D. , Quarrie Barrington , Sharp Wendy , Persky Susan , Shaw Philip 
Published: January 2020

AbstractThe mechanisms underpinning attentional deficits are only partially understood. Here we ask if shifts in a child’s field of view (FOV) act as a mediator between symptoms of attention deficit hyperactivity disorder (ADHD) and associated cognitive anomalies, particularly in attentional processes. Real time measurement of shifts in FOV were obtained on 85 children (mean age 9.4 (SD 1.9) years; 45 with DSM 5-defined ADHD) as they completed the continuous performance task in a “virtual classroom”. We extracted measures reflecting focused and selective attention across the task, along with diffusion modelling of latent cognitive processes of information uptake, response conservativeness and non-decision time. Mediation analyses showed that shifts in FOV partially mediated the relationship between hyperactive impulsive symptoms and both poor focused attention and information uptake. Performance accuracy decreased and shifts in FOV increased during the task, but these changes over time did not differ by symptom severity. Employing virtual reality and mediation analysis, we implicate shifts in FOV as a mechanism linking symptoms of ADHD and deficits in focused attention and in the gathering of information to make decisions. The identification of mediating mechanisms might provide new targets for intervention.
Activation of RSK by phosphomimetic substitution in the activation loop is prevented by structural constraints
Authors: Somale Desiana , Di Nardo Giovanna , di Blasio Laura , Puliafito Alberto , Vara-Messler Marianela , Chiaverina Giulia , Palmiero Miriam , Monica Valentina , Gilardi Gianfranco , Primo Luca , Gagliardi Paolo Armando 
Published: January 2020

AbstractThe activation of the majority of AGC kinases is regulated by two phosphorylation events on two conserved serine/threonine residues located on the activation loop and on the hydrophobic motif, respectively. In AGC kinase family, phosphomimetic substitutions with aspartate or glutamate, leading to constitutive activation, have frequently occurred at the hydrophobic motif site. On the contrary, phosphomimetic substitutions in the activation loop are absent across the evolution of AGC kinases. This observation is explained by the failure of aspartate and glutamate to mimic phosphorylatable serine/threonine in this regulatory site. By detailed 3D structural simulations of RSK2 and further biochemical evaluation in cells, we show that the phosphomimetic residue on the activation loop fails to form a critical salt bridge with R114, necessary to reorient the αC-helix and to activate the protein. By a phylogenetic analysis, we point at a possible coevolution of a phosphorylatable activation loop and the presence of a conserved positively charged amino acid on the αC-helix. In sum, our analysis leads to the unfeasibility of phosphomimetic substitution in the activation loop of RSK and, at the same time, highlights the peculiar structural role of activation loop phosphorylation.
Measurement of Prostate Volume with MRI (A Guide for the Perplexed): Biproximate Method with Analysis of Precision and Accuracy
Authors: Wasserman Neil F. , Niendorf Eric , Spilseth Benjamin 
Published: January 2020

AbstractTo review the anatomic basis of prostate boundary selection on T2-weighted magnetic resonance imaging (MRI). To introduce an alternative 3D ellipsoid measuring technique that maximizes precision, report the intra- and inter-observer reliability, and to advocate it’s use for research involving multiple observers. We demonstrate prostate boundary anatomy using gross pathology and MRI examples. This provides background for selecting key boundary marks when measuring prostate volume. An alternative ellipsoid volume method is then proposed using these boundaries in an attempt to improve inter-observer precision. An IRB approved retrospective study of 140 patients with elevated serum prostate specific antigen levels and/or abnormal digital rectal examinations was done with T2-weighted MRI applying a new (Biproximate) technique. Measurements were made by 2 examiners, correlated with each other for inter-observer precision and correlated with an expert observer for accuracy. Correlation statistics, linear regression analysis, and tests of means were applied using p ≤ 0.05 as the threshold for significance. Inter-observer correlation (precision) was 0.95 between observers. Correlation between these observers and the expert (accuracy) was 0.94 and 0.97 respectively. Intra-observer correlation for the expert was 0.98. Means for inter-rater reliability and accuracy were all the same (p = 0.001). We conclude that using more precise reproducible landmarks with biproximate technique, precision and accuracy of total prostate volume is found to be demonstrated.