bluuebunny/crossref_metadata_2025_split huggingface dataset:
The ABL2 kinase regulates an HSF1-dependent transcriptional program required for lung adenocarcinoma brain metastasis
Authors: Hoj Jacob P. , Mayro Benjamin , Pendergast Ann Marie 
Published: December 2020

Significance
Among all cancer types, lung cancer patients exhibit the highest prevalence of brain metastasis, often associated with cognitive impairment, seizures, decline in quality of life, and decreased survival. Limited therapeutic options are currently available to treat brain metastasis. A comprehensive understanding of the signaling pathways and transcriptional networks required for survival and growth of brain-metastatic cancer cells is needed to develop effective strategies to treat this disease. Here, we report that the Heat Shock Transcription Factor 1 (HSF1) is upregulated in brain-metastatic lung cancer cells and is required for brain metastasis in mice. Importantly, we show that the HSF1-dependent expression of E2F target genes implicated in cell cycle progression and survival is decreased by blood–brain barrier-penetrant ABL allosteric inhibitors.
Towards the molecular architecture of the peroxisomal receptor docking complex
Authors: Lill Pascal , Hansen Tobias , Wendscheck Daniel , Klink Bjoern Udo , Jeziorek Tomasz , Vismpas Dimitrios , Miehling Jonas , Bender Julian , Schummer Andreas , Drepper Friedel , Girzalsky Wolfgang , Warscheid Bettina , Erdmann Ralf , Gatsogiannis Christos 
Published: December 2020

Significance
Peroxisomal matrix enzymes are synthesized in the cytosol and carry targeting signals. These are recognized and bound by an import receptor in the cytosol. The cargo-loaded receptor further binds to the “docking” complex at the peroxisomal membrane. The docking events are expected to trigger the formation of a transient pore allowing import of the cargo into the peroxisomal matrix. Here using cryoelectron microscopy complemented by native MS, cross-linking MS, SEC MALS, and immunogold labeling, we provide the structural characterization of the major components of the yeast peroxisomal docking complex. Pex14p/Pex17p assemble in a parallel 3:1 bundle arrangement to form intriguingly long flexible rods that emanate into the cytosol to recruit the cargo-loaded receptor for further translocation events.
Fluorine assembly nanocluster breaks the shackles of immunosuppression to turn the cold tumor hot
Authors: Li Zhaoting , Zhu Lianghan , Sun Honghao , Shen Yuexin , Hu Dandan , Wu Wenhao , Wang Yixin , Qian Chenggen , Sun Minjie 
Published: December 2020

Significance
“Cold” tumors are good at camouflaging themselves, thus making it difficult for the immune system to recognize and to construct a great barrier for cancer immunotherapies. New methods that could awaken the immune system, enhance T cells and antigen-presenting cells (APCs) trafficking, and relieve immunosuppression to treat cold tumors are urgently in need. Here, we first report a chemically ingenious nanocluster FS@PMPt assembly by fluorine–fluorine interaction to regulate the immune process. The nanocluster not only increased the infiltration of immunopositive cells from the outside but also decreased the immunosuppressive cells from the inside to break the shackles of immunosuppression, which provides a promising paradigm for improving the anti–cold tumor immunotherapy.
A general fragment-based approach to identify and optimize bioactive ligands targeting RNA
Authors: Suresh Blessy M. , Li Weichao , Zhang Peiyuan , Wang Kye Won , Yildirim Ilyas , Parker Christopher G. , Disney Matthew D. 
Published: December 2020

SignificanceThe development of selective bioactive compounds that target RNA structures is difficult. Here we report an approach to identify low molecular weight fragments that bind to a cancer-causing RNA. By determining where the fragments bind within an RNA target, they can be assembled to provide a high-affinity and potent inhibitor. This approach could be a general way to develop bioactive small molecules that target RNA, which previously was considered “undruggable.” It was applied to provide a precision lead medicine against an RNA that contributes to cancer metastasis.
An isolated water droplet in the aqueous solution of a supramolecular tetrahedral cage
Authors: Sebastiani Federico , Bender Trandon A. , Pezzotti Simone , Li Wan-Lu , Schwaab Gerhard , Bergman Robert G. , Raymond Kenneth N. , Toste F. Dean , Head-Gordon Teresa , Havenith Martina 
Published: December 2020

Significance
Using a supramolecular assembly that catalyzes substrates in water, we show that the nanocage encapsulates a water cluster that is structurally and dynamically distinct from any known phase of water. It plays an important role in the driving force for guest encapsulation: The release of the highly unusual encapsulated water droplet creates a strong thermodynamic drive for the high-affinity binding of guests in aqueous solution for the supramolecular construct.
Direct quantification of in vivo mutagenesis and carcinogenesis using duplex sequencing
Authors: Valentine Charles C. , Young Robert R. , Fielden Mark R. , Kulkarni Rohan , Williams Lindsey N. , Li Tan , Minocherhomji Sheroy , Salk Jesse J. 
Published: December 2020

Significance
Error-corrected next-generation sequencing (ecNGS) can be used to rapidly detect and quantify the in vivo mutagenic impact of environmental exposures or endogenous processes in any tissue, from any species, at any genomic location. The greater speed, higher scalability, richer data outputs, and cross-species and cross-locus applicability of ecNGS compared to existing methods make it a powerful new tool for mutational research, regulatory safety testing, and emerging clinical applications.
A 2020 view of tension-based cortical morphogenesis
Authors: Van Essen David C. 
Published: December 2020

SignificanceBrain structures change shape dramatically during development. Elucidating the mechanisms of morphogenesis provides insights relevant to understanding brain function in health and disease. The tension-based morphogenesis (TBM) hypothesis posits that mechanical tension along axons, dendrites, and glial processes contributes to many aspects of central nervous system morphogenesis. Since TBM was proposed in 1997, extensive evidence supports a role for tension in diverse cellular phenomena, but tension’s role in cortical folding has been controversial. An extensively revised version of the TBM model for cerebral cortex addresses limitations of the original model, incorporates new features, and can be tested by many experimental approaches. For cerebellar cortex, a revised model accounts for many aspects of its development and adult architecture.
Quinine copolymer reporters promote efficient intracellular DNA delivery and illuminate a protein-induced unpackaging mechanism
Authors: Van Bruggen Craig , Punihaole David , Keith Allison R. , Schmitz Andrew J. , Tolar Jakub , Frontiera Renee R. , Reineke Theresa M. 
Published: December 2020

Significance
Polymer-based vehicles that controllably deliver therapeutic nucleic acids to cells show great potential to develop safe and effective gene therapies. Realizing this potential, however, is limited by the lack of understanding of how polymers unpackage their cargo. We developed a quinine-containing polymer that shows exceptional gene delivery activity. A key aspect of this platform is that the quinine serves as a reporter for DNA binding using Raman spectroscopy. This allows us to track cargo release inside the cell using Raman chemical imaging. We find that proteins dominate the unpackaging of DNA encapsulated by these quinine polymers inside cells. This trackable delivery system should be broadly applicable to study nucleic acid delivery mechanisms and to be used for clinical therapy applications.
Large-scale mapping of live corals to guide reef conservation
Authors: Asner Gregory P. , Vaughn Nicholas R. , Heckler Joseph , Knapp David E. , Balzotti Christopher , Shafron Ethan , Martin Roberta E. , Neilson Brian J. , Gove Jamison M. 
Published: December 2020

Significance
Coral reefs are changing at unprecedented rates, and the majority of reefs are undergoing widespread losses in live coral cover. Management and policy development efforts focused on conserving and restoring coral reefs are hampered by a lack of geographically consistent and actionable high-resolution information on the specific location and extent of live coral. Based on an operational airborne technique, we developed and applied a live coral mapping capability across the main Hawaiian islands to identify potential coral refugia as well as reefs for potential coral restoration. Our findings inform current management actions across the archipelago and demonstrate the tactical role that live coral mapping can play to support decision-making at large ecological scales.
Robust identification of investor beliefs
Authors: Chen Xiaohong , Hansen Lars Peter , Hansen Peter G. 
Published: December 2020

SignificancePrices in asset markets reflect a combination of investor beliefs and their risk preferences. Researchers, as well as policymakers, look to asset market data as a barometer of public beliefs. Such data are informative because investors must be compensated for exposure to macroeconomic shocks, and thus beliefs about future macroeconomic performance are encoded in asset prices. This paper develops a method informed by data and models to recover information about investor beliefs. Our approach uses information embedded in forward-looking asset prices in conjunction with asset pricing models. We entertain families of potential belief distortions bounded by a statistical measure of divergence. Additionally, our method allows for the direct use of sparse survey evidence to make these bounds more informative.
Rewiring the specificity of extracytoplasmic function sigma factors
Authors: Todor Horia , Osadnik Hendrik , Campbell Elizabeth A. , Myers Kevin S. , Li Hao , Donohue Timothy J. , Gross Carol A. 
Published: December 2020

Significance
Bacterial phenotypes require the concerted expression of multiple genes, usually coordinated by a transcriptional regulator. Although the functions of many genes in sequenced bacterial genomes can be inferred, the regulatory networks that coordinate their expression are only known in a few model systems. Using a bioinformatic and experimental approach, we solve the DNA-specificity code of extracytoplasmic function sigma factors (ECF σs), a major class of bacterial regulators. We develop and use a high-stringency pipeline to predict the genes regulated by 67% of ECF σs in >10,000 species, providing a comprehensive look at the role of a broadly distributed family of gene regulatory proteins. This conceptual and computational framework is potentially applicable to other bacterial regulators.
FXR mediates T cell-intrinsic responses to reduced feeding during infection
Authors: Campbell Clarissa , Marchildon Francois , Michaels Anthony J. , Takemoto Naofumi , van der Veeken Joris , Schizas Michail , Pritykin Yuri , Leslie Christina S. , Intlekofer Andrew M. , Cohen Paul , Rudensky Alexander Y. 
Published: December 2020

Significance
Anorexia or decreased appetite is a common feature of infection. The effects of acute nutritional stress on effector T cells, which are required for pathogen-specific responses and protective immunological memory, are not fully understood. We show that reduced food intake during infection decreases the numbers of effector T cells in a manner dependent on the Farnesoid X Receptor (FXR). FXR was previously implicated in controlling hepatic responses to fasting. Our findings suggest that FXR functions in effector T cells to promote coherent physiological responses to decreased feeding, allowing organisms to scale their immune responses according to food availability.
Formation of high-photoresponsivity BaSi2 films on glass substrate by radio-frequency sputtering for solar cell applications
Authors: Koitabashi Ryota , Nemoto Taira , Yamashita Yudai , Mesuda Masami , Toko Kaoru , Suemasu Takashi 
Published: December 2020

Abstract
The formation of high-photoresponsivity semiconducting films composed of earth-abundant elements on a SiO2 substrate is of particular importance for large-scale deployment of solar cells. We investigated the deposition of high-photoresponsivity BaSi2 films by radio-frequency sputtering on indium-tin-oxide (ITO), Ti, or TiN electrodes formed on a SiO2 substrate. Raman spectroscopy and x-ray diffraction measurements revealed the formation of randomly oriented polycrystalline BaSi2 films only on TiN/SiO2 substrates at 570 °C–650 °C. In contrast, impurity phases such as Ba oxides and TiSi2 were included when ITO and Ti layers were used, respectively. The photoresponsivity of the BaSi2 films on TiN electrodes reached 1.1 A W−1 at a wavelength of 790 nm under a bias voltage of 0.5 V applied between the front ITO and bottom TiN electrodes. This value is equivalent to the highest photoresponsivity ever achieved for BaSi2 epitaxial films on Si(111) substrates by molecular beam epitaxy.
Length-scale independent skyrmion and meron Hall angles
Authors: Bera Sandip , Mandal Sudhansu S 
Published: December 2020

Abstract
Motivated by the recent observation (Zeissler et al 2020 Nature Commun.
11 428) of enigmatic radius-independent skyrmion Hall angle in chiral magnets, we derive skyrmion Hall angle based on the recent solution of skyrmions characterized by the sole length scale determined with the Dzyaloshinskii–Moriya interaction strength and applied magnetic field. We find that the skyrmion Hall angle is independent of input current density and the length-scale which determines the radius of a skyrmion. This is corroborated with the single length-scale dependent skyrmion profile which is the solution of the Euler equation of polar angle representing magnetization. Although the magnitude of Hall angle may change with the change of profile (shape) of the skyrmion, it remains unchanged for a particular profile. With the application of tunable current along mutually perpendicular directions, this property enables us to propose an experimental setup by which the transverse motion of a skyrmion can be restricted so that the skyrmion can only traverse longitudinally. We further find the length-scale and input-current density independent Hall angles for merons where their transverse motion will be opposite depending on whether the spin at their centers are up or down, in agreement with an experiment.
Role of anharmonic strength and number of allowed three-phonon processes in lattice thermal conductivity of SnTe based compounds
Authors: Keshri Sonu Prasad , Medhi Amal 
Published: December 2020

Abstract
The lattice heat transport properties of the thermoelectric (TE) material SnTe and the doped Sn7SbTe8 and Sn7BiTe8 are examined using Boltzmann transport theory supplemented with first-principle calculations. We illustrate the microscopic origin of the lattice thermal conductivity, κ
l of the materials by calculating the mode Grüneisen parameters, phase space volume for three-phonon processes, the anharmonic scattering rates (SR), and the phonon group velocities. SnTe is found to be a low κ
l material with a value of ∼3 W mK−1 at room temperature in agreement with experiments. The phonon scatterings in pristine SnTe mainly originates in the strong anharmonicity of the material, as evidenced by the large values of its mode Grüneisen parameters. Doping with Sb or Bi reduces the anharmonic strength. For Sb doped Sn7SbTe8, it results in a drop in the SR and hence a higher κ
l value. However in the Bi doped Sn7BiTe8, the number of allowed three-phonon processes gets greatly enhanced which compensates for the reduction in anharmonicity. This coupled with lower phonon group velocities lowers the κ
l value for the Bi doped system below that of pristine SnTe. In nanowire structures, κ
l values for the doped systems get drastically reduced yielding an ultra-low value of 0.84 W mK−1 at 705 K for the Bi doped material for a nanowire of 10 nm diameter.
Energy and electron drift time measurements in a pixel CCI TlBr detector with 1.3 MeV prompt-gammas
Authors: Ariño-Estrada Gerard , Kim Hadong , Du Junwei , Cirignano Leonard J , Shah Kanai S , Cherry Simon R 
Published: December 2020

Abstract
Assessing the position of the Bragg peak (BP) in hadron radiotherapy utilizing prompt-gamma imaging (PGI) presents many challenges in terms of detector physics. Gamma detectors with the capability of extracting the best energy, timing, and spatial information from each gamma interaction, as well as with high detection efficiency and count rate performance, are needed for this application. In this work we present the characterization of a pixel Čerenkov charge induction (CCI) thallium bromide (TlBr) detector in terms of energy and and electron drift time for its potential use in PGI. The CCI TlBr detector had dimensions of 4 × 4 × 5 mm3 and one of its electrodes was segmented in pixels with 1.7 mm pitch. A silicon photomultiplier (SiPM) was optically coupled to one of the faces of the TlBr slab to read out the Čerenkov light promptly emitted after the interaction of a gamma ray. The detector was operated stand-alone and the 1.275 prompt gammas from a 22Na radioactive source were used for the study. The electron drift time was obtained by combining the Čerenkov and charge induction signals and then used as a measure of the depth of interaction. The electron mobility in TlBr was estimated as ∼27 cm2 V−1 s−1. Energy resolutions between 3.4% and 4.0% at 1.275 MeV were obtained after depth-correction. These values improved to 3.0%–3.3% when events with drift times of 3–6 μs were selected. These results show the potential of pixel CCI TlBr detectors to resolve gamma interactions in the detector with mm-like accuracy in 3D and with excellent energy resolution. Previous studies with CCI TlBr devices have shown a timing resolution of <400 ps full width at half maximum when detecting 511 keV gamma rays, therefore, the timing accuracy is expected to improve with the increased energy of the gamma rays in PGI. While other important detector characteristics such as count rate capability remain to be studied, results from this work combined with other preliminary data show pixel CCI detectors can simultaneously provide excellent energy, timing, and spatial resolution performance and are a very promising option for PGI in hadron therapy.
Iterative time-reversal for multi-frequency hyperthermia
Authors: Zanoli Massimiliano , Trefná Hana Dobšíček 
Published: December 2020

Abstract
Time-reversal (TR) is a known wideband array beam-forming technique that has been suggested as a treatment planning alternative in deep microwave hyperthermia for cancer treatment. While the aim in classic TR is to focus the energy at a specific point within the target, no assumptions are made on secondary lobes that might arise in the healthy tissues. These secondary lobes, together with tissue heterogeneity, may result in hot-spots (HSs), which are known to limit the efficiency of the thermal dose delivery to the tumor. This paper proposes a novel wideband TR focusing method that iteratively shifts the focus away from HSs and towards cold-spots from an initial TR solution, a procedure that improves tumor coverage and reduces HSs. We verify this method on two different applicator topologies and several target volume configurations. The algorithm is deterministic and runs within seconds, enabling its use for real-time applications. At the same time, it yields results comparable to those obtained with global stochastic optimizers such as Particle Swarm.
Magnetic confinement and instability in partially magnetized plasma
Authors: Kim June Young , Jang Jae Young , Choi Jaeyoung , Wang Jong-in , Jeong Won Ik , Elgarhy M A I , Go Geunwoo , Chung Kyoung-Jae , Hwang Y S 
Published: December 2020

Abstract
Discharge with an external magnetic field is promising for various applications of low-temperature plasmas from electric propulsion to semiconductor processes owing to high plasma density. It is essential to understand plasma transport across the magnetic field because plasma confinement under the field is based on strong magnetization of light electrons, maintaining quasi-neutrality through the inertial response of unmagnetized ions. In such a partially magnetized plasma, different degrees of magnetization between electrons and ions can create instability and make the confinement and transport mechanisms more complex. Theoretical studies have suggested a link between the instability of various frequency ranges and plasma confinement, whereas experimental work has not been done so far. Here, we experimentally study the magnetic confinement properties of a partially magnetized plasma considering instability. The plasma properties show non-uniform characteristics as the magnetic field increases, indicating enhanced magnetic confinement. However, the strengthened electric field at the edge of the plasma column gives rise to the Simon–Hoh instability, limiting the plasma confinement. The variation of the edge-to-center plasma density ratio (h-factor) with the magnetic field clearly reveals the transition of the transport regime through triggering of the instability. Eventually, the h-factor reaches an asymptotic value, indicating saturation of magnetic confinement.
Construction of propagators for divisible dynamical maps
Authors: Chakraborty Ujan , Chruściński Dariusz 
Published: December 2020

Abstract
Divisible dynamical maps play an important role in characterizing Markovianity on the level of quantum evolution. Divisible maps provide an important generalization of Markovian semigroups. Usually one analyzes either completely positive or just positive divisibility meaning that the corresponding propagators are defined in terms of completely positive or positive maps, respectively. For maps which are invertible at any moment of time the very existence of propagator is already guaranteed and hence the only issue is (complete) positivity and trace-preservation. However, for maps which are not invertible the problem is much more involved since even the existence of a propagator is not guaranteed. In this paper we propose a simple method to construct propagators of dynamical maps using the concept of generalized inverse. We analyze both time-continuous and time-discrete maps. Since the generalized inverse is not uniquely defined the same applies for the corresponding propagator. In simple examples of qubit evolution we analyze it turns out that the additional requirement of complete positivity possibly makes the propagator unique.
Moses, Noah and Joseph effects in Lévy walks
Authors: Aghion Erez , Meyer Philipp G , Adlakha Vidushi , Kantz Holger , Bassler Kevin E 
Published: December 2020

Abstract
We study a method for detecting the origins of anomalous diffusion, when it is observed in an ensemble of times-series, generated experimentally or numerically, without having knowledge about the exact underlying dynamics. The reasons for anomalous diffusive scaling of the mean-squared displacement are decomposed into three root causes: increment correlations are expressed by the ‘Joseph effect’ (Mandelbrot and Wallis 1968 Water Resour. Res.
4 909), fat-tails of the increment probability density lead to a ‘Noah effect’ (Mandelbrot and Wallis 1968 Water Resour. Res.
4 909), and non-stationarity, to the ‘Moses effect’ (Chen et al 2017 Phys. Rev. E
95 042141). After appropriate rescaling, based on the quantification of these effects, the increment distribution converges at increasing times to a time-invariant asymptotic shape. For different processes, this asymptotic limit can be an equilibrium state, an infinite-invariant, or an infinite-covariant density. We use numerical methods of time-series analysis to quantify the three effects in a model of a non-linearly coupled Lévy walk, compare our results to theoretical predictions, and discuss the generality of the method.