bluuebunny/crossref_metadata_2025 huggingface dataset:
Thermal retention of atomic layer deposited Hf0.5Zr0.52 films using H2O and O2–H2 plasma oxidation methods
Authors: Walters Glen , Chojecki Paul , Forrester Zane , Nishida Toshikazu
Published: January 2021

Thermal retention of ferroelectric hafnium zirconium oxide (HZO) is a critical reliability concern impacting its use in applications such as ferroelectric field-effect transistors, ferroelectric random-access memory, and ferroelectric tunnel junctions. Thermal depolarization and thermal imprint are explored for 10 nm thick Hf0.5Zr0.5O2 films. The HZO films were fabricated through atomic layer deposition with two different oxidizing conditions, H2O or sequential O2 and H2-plasmas. A similar virgin state switched polarization of ∼30 μC/cm2 was found by annealing the H2O films at 700 °C and the O2–H2 plasma films at 500 °C. Both O2–H2 plasma and H2O films exhibited same state P–U and |N–D| switched polarization values above 25 μC/cm2 after 100 h at 125 °C. For opposite state switched polarization, however, O2–H2 plasma films showed asymmetric shifts in the coercive fields and subsequent loss of P–U and |N–D| retention after 100 h at 125 °C, while the H2O films exhibited symmetric shifts in the coercive fields, and P–U and |N–D| opposite state thermal retention above 25 μC/cm2 after 100 h at 125 °C.
Oxide semiconductor-based ferroelectric thin-film transistors for advanced neuromorphic computing
Authors: Kim Min-Kyu , Kim Ik-Jyae , Lee Jang-Sik
Published: January 2021

Neuromorphic computing that mimics the biological brain has been demonstrated as a next-generation computing method due to its low power consumption and parallel data processing characteristics. To realize neuromorphic computing, diverse neural networks such as deep neural networks (DNNs) and spiking neural networks (SNNs) have been introduced. DNNs require artificial synapses that have analog conductance modulation characteristics, whereas SNNs require artificial synapses that have conductance modulation characteristics controlled by temporal relationships between signals, so the development of a multifunctional artificial synapse is required. In this work, we report a ferroelectric thin-film transistor (FeTFT) that uses zirconium-doped hafnia (HfZrOx) and indium zinc tin oxide (IZTO) for neuromorphic applications. With reliable conductance modulation characteristics, we suggest that the FeTFT with HfZrOx and IZTO can be used as an artificial synapse for both DNNs and SNNs. The linear and symmetric conductance modulation characteristics in FeTFTs result in high recognition accuracy (93.1%) of hand-written images, which is close to the accuracy (94.1%) of an ideal neural network. Also, we show that the FeTFTs can emulate diverse forms of spike-time-dependent plasticity, which is an important learning rule for SNNs. These results suggest that FeTFT is a promising candidate to realize neuromorphic computing hardware.
Collective locomotion of two uncoordinated undulatory self-propelled foils
Authors: Yu Huiyang , Lu Xi-Yun , Huang Haibo
Published: January 2021

Fish schooling with stable configurations is intriguing. How individuals benefit from hydrodynamic interactions is still an open question. Here, fish are modeled as undulatory self-propelled foils, which is more realistic. The collective locomotion of two foils in a tandem configuration with different amplitude ratios Ar and frequency ratios Fr is considered. Depending on Ar and Fr, the two foils without lateral or yaw motion may spontaneously form stable configurations, separate, or collide with each other. The phase diagram of the locomotion modes in the (Fr, Ar) plane is obtained, which is significantly different from that in Newbolt et al. [“Flow interactions between uncoordinated flapping swimmers give rise to group cohesion,” Proc. Natl. Acad. Sci. U. S. A. 116, 2419 (2019)]. For stable configurations, the gap spacing may be almost constant [stable position (SP) mode] or change dynamically and periodically [stable cycle (SC) mode]. In our diagram, the fast SP mode is found. Besides, the border between the separation and SP/SC modes is more realistic. In the fast SP cases, analyses of hydrodynamic force show the phenomenon of inverted drafting, in which the leader achieves hydrodynamic advantages. For the SC mode, the cruising speed increases piecewise linearly with FrAr. When Ar < 1, the linear slope is identical to that of the isolated leader, and the follower-control mechanism is revealed. Our result sheds some light on fish schooling and predating.
Exciton transfer in organic photovoltaic cells: A role of local and nonlocal electron–phonon interactions in a donor domain
Authors: Cainelli Mauro , Tanimura Yoshitaka
Published: January 2021

We theoretically investigate an exciton transfer process in a donor domain of organic photovoltaic cells focusing on the roles of local and nonlocal electron–phonon interactions. Our model consists of a three-level system described by the Holstein–Peierls Hamiltonian coupled to multiple heat baths for local and nonlocal molecular modes characterized by Brownian spectral distribution functions. We chose tetracene as a reference donor molecule, where the spectral distribution functions of the local and nonlocal modes are available. We then employ the reduced hierarchical equations of motion approach to simulate the dynamics of the system under the influence of the environment as a function of the electron–phonon coupling strength and temperature. We rigorously calculate the reduced density matrix elements to explain the time scale of dynamics under the influence of the dissipative local and nonlocal modes. The results indicate that the strong nonlocal electron–phonon interaction under high temperature conditions favors the exciton transfer process and enhances the efficiency of organic photovoltaic materials, while the lifetime of the exciton becomes shorter due to a low-frequency local mode.
Self-diffusion micromechanism in Nafion studied by 2H NMR relaxation dispersion
Authors: Galitskaya Elena A. , Privalov Alexei F. , Vogel Michael , Ryzhkin Ivan A. , Sinitsyn Vitaly V.
Published: January 2021

Field Cycling (FC) 2H nuclear magnetic resonance (NMR) relaxometry was applied to study dynamics in Nafion NR 212 in the temperature range from 300 K to 190 K and water content of λ = 8.2. The sensitive time window of FC was extended up to eight decades using the temperature–frequency superposition principle and master curve. The rotational correlation times obtained from 2H FC NMR coincide with translational correlation times gained from static field 2H NMR diffusometry in the temperature range applied. This fact means that a long-range mass transport in Nafion is coupled to molecular rotations. It is assumed that confined water in Nafion has more ordered oxygen sublattices as compared with bulk water, on a short range is similar to ice. We discuss the possible role of D and L defects, typical for the ordered ice structure and using this concept to describe the processes of self-diffusion of confined water in Nafion, as well as the similarity of temperature and humidity dependence of self-diffusion and proton conductivity.
Hydrodynamic analysis of nanofluid’s convective heat transfer in channels with extended surfaces
Authors: Soleimani Rasa , Zargartalebi Mohammad , Azaiez Jalel , Gates Ian D.
Published: January 2021

The effects of nanoparticles (NPs) on heat transfer in extended surface channels have been analyzed using a two-component (TC) model. The results show that unlike the single-component model, the TC model leads to more accurate predictions of the system’s heat transfer performance as a result of the direct influence of the NPs’ distribution on the hydrodynamics. It is found that the average Nusselt number varies non-monotonically with the block’s heights, and the trend is explained by the interplay between heat transfer mechanisms and the hydrodynamics. A similar non-monotonic trend observed in the case of the friction factor has been explained by the variations of the concentration- and temperature-dependent viscosity of the nanofluids. A guideline for an optimum design based on the combination of the variation of average Nusselt number and friction factor with respect to the geometrical parameters has also been presented.
Quasi-indirect measurement of electrocaloric temperature change in PbSc0.5Ta0.5O3 via comparison of adiabatic and isothermal electrical polarization data
Authors: Crossley S. , Whatmore R. W. , Mathur N. D. , Moya X.
Published: January 2021

Electrically driven adiabatic changes of temperature are identified in the archetypal electrocaloric material PbSc0.5Ta0.5O3 by comparing isothermal changes of electrical polarization due to the slow variation of electric field and adiabatic changes of electrical polarization due to the fast variation of electric field. By obtaining isothermal (adiabatic) electrical polarization data at measurement (starting) temperatures separated by <0.4 K, we identify a maximum temperature change of ∼2 K due to a maximum field change of 26 kV cm−1 for starting temperatures in the range of 300 K–315 K. These quasi-indirect measurements combine with their direct, indirect, and quasi-direct counterparts to complete the set and could find routine use in the future.
Drop-on-demand assessment of microdrops of dilute ZnO–water nanofluids
Authors: Elcioglu Elif Begum , Murshed S. M. Sohel
Published: January 2021

Shrinking device dimensions demand a high level of control and manipulation of materials at microscale and nanoscale. Microfluidics has a diverse application spectrum including thermal management of chips, point-of-care diagnostics, and biomedical analysis, to name a few. Inkjet printing (IJP) is a manufacturing method used for micro-/nanofabrication and surface restructuring, and liquid inks are characterized based on their density, surface tension, and viscosity for their printability. Nanofluids as colloidal dispersions of nanoparticles hold potential in various heating, cooling, lubricating, and biomedical applications with the premise of nanoparticles’ size and concentration effects and interactions between nanoparticle–nanoparticle and nanoparticle–base fluid. In order to explore the microfluidic behavior of nanofluids, using micro-volumes of nanofluids and/or confining them in a micro-system is essential. With this motivation, we present a printability assessment on the potential of low concentration ZnO–water nanofluids by utilizing a combined theoretical and experimental approach. For 0.05 vol. %–0.4 vol. % of ZnO–water nanofluids, results showed that for a nozzle diameter of 25 μm, the samples do not exhibit the energy necessary for drop formation, while for 50 μm and 100 μm nozzle diameters, the samples behave as satellite droplets. Although satellite droplets were generally not desirable for IJP, the recently introduced satellite droplet printing concept may be applicable to the printing of aqueous nano-ZnO dispersions considered in this work.
Studying the flow dynamics and heat transfer of stranded conductor cables using large eddy simulations
Authors: Abdelhady Mohamed , Wood David H.
Published: January 2021

Stranded cables are widely used in applications where their heat transfer and fluid dynamics are important, but they have not been extensively studied. This paper investigates, using large eddy simulations with the dynamic Smagorinsky sub-grid scale model, a helically wound stranded conductor cable in comparison to a circular cylinder at a Reynolds number of 1000 and Prandtl number of 0.7. The cylinder and the cable were normal to the flow. The triply decomposed heat transport equations were derived, and proper orthogonal decomposition was applied to the fluctuating vorticity and temperature fields to determine the total, coherent, and incoherent terms in the heat transport equations. The results showed that the stranded cable, relative to circular cylinder, has (i) three-dimensional mean flow and heat transfer, especially within and around recirculation region, (ii) 9% higher drag and 8% higher base pressure magnitude, (iii) near-stagnant flow in the gaps between the strands, which results in a significant variation in the local Nusselt number, (iv) ∼15% lower span-wise averaged local Nusselt number in the attached boundary layer, suggesting that surface modifications should be addressed to enhance heat transfer, (v) ∼36° variation in the separation angle along the span, (vi) 12% higher turbulent kinetic energy and 39% higher spanwise normal Reynolds stresses, (vii) insignificant difference in shedding frequency, suggesting similar flow induced vibrations to the cylinder, (viii) asymmetry in the flow and heat fields around the x axis, (ix) significantly different coherent temperature fields and dynamics, and (x) in general, high heat energy transport close to the cable rear side.
Collisional excitation of interstellar PN by H2: New interaction potential and scattering calculations
Authors: Desrousseaux Benjamin , Quintas-Sánchez Ernesto , Dawes Richard , Marinakis Sarantos , Lique François
Published: January 2021

Rotational excitation of interstellar PN molecules induced by collisions with H2 is investigated. We present the first ab initio four-dimensional potential energy surface (PES) for the PN–H2 van der Waals system. The PES was obtained using an explicitly correlated coupled cluster approach with single, double, and perturbative triple excitations [CCSD(T)-F12b]. The method of interpolating moving least squares was used to construct an analytical PES from these data. The equilibrium structure of the complex was found to be linear, with H2 aligned at the N end of the PN molecule, at an intermolecular separation of 4.2 Å. The corresponding well-depth is 224.3 cm−1. The dissociation energies were found to be 40.19 cm−1 and 75.05 cm−1 for complexes of PN with ortho-H2 and para-H2, respectively. Integral cross sections for rotational excitation in PN–H2 collisions were calculated using the new PES and were found to be strongly dependent on the rotational level of the H2 molecule. These new collisional data will be crucial to improve the estimation of PN abundance in the interstellar medium from observational spectra.
Design of modern magnetic materials with giant coercivity
Authors: Gorbachev Evgeny A. , Kozlyakova Ekaterina S. , Trusov Lev A. , Sleptsova Anastasia E. , Zykin Mikhail A. , Kazin Pavel E.
Published: January 2021

The review is devoted to compounds and materials demonstrating extremely high magnetic hardness. The recent advances in the synthesis of modern materials for permanent magnets are considered, and a range of exotic compounds interesting for fundamental research is described. The key details of chemical composition, crystal structure and magnetic microstructure responsible for the appearance of high magnetic anisotropy and giant coercivity are analyzed. The challenges of developing the title materials are noted and strategies for their solution are discussed.

The bibliography includes 389 references.
The effect of environmental conditions on seasonal and inter-annual abundance of two species in the Yangtze River estuary
Authors: Kindong Richard , Chen Jinhui , Dai Libin , Gao Chunxia , Han Dongyan , Tian Siquan , Wu Jianhui , Ma Qiuyun , Tang Jianye
Published: January 2021

It is important in fisheries management to evaluate the effects of environmental factors on changes in the abundance of species, particularly those inhabiting estuaries. The Yangtze River estuary is the largest in the western Pacific Ocean and serves as a spawning, feeding and nursery ground to species of economic and ecological importance, such as Collichthys lucidus and Lophiogobius ocellicauda. By using 3 years of environmental variables and data on the abundance of C. lucidus and L. ocellicauda gathered seasonally through trawl surveys, we compared four generalised additive models (GAMs), each comprising different spline terms, to analyse the influence of the measured variables on the abundance of both species. Deviance explained, Akaike information criterion and generalised cross-validation were used to select the optimal GAM after evaluating the fit and predictive performance of the models. Generalised additive model (GAM) with spline ‘te’ was the optimal model, and predicted that the abundance of both species was influenced by season and by variables temperature, salinity and chlorophyll-a concentration. For C. lucidus, abundance increased during spring and summer, and, for L. ocellicauda, it was higher during winter. Given the socioeconomic importance of both species, we contend that determining the drivers causing abundance fluctuations of estuarine species can support the putting in place of robust monitoring and assessment plans for such fisheries.
Mdm2 phosphorylation by Akt regulates the p53 response to oxidative stress to promote cell proliferation and tumorigenesis
Authors: Chibaya Loretah , Karim Baktiar , Zhang Hong , Jones Stephen N.
Published: January 2021

Significance

We demonstrate that Akt phosphorylation of Mdm2 protein at Ser183 inhibits p53-mediated senescence and promotes ROS-induced tumorigenesis. Thus, different effector kinases can modify Mdm2 and selectively regulate the p53-mediated response to stress. Our study suggests that targeted inhibition of Mdm2 Ser183 phosphorylation would activate p53-mediated senescence and delay tumor progression.
Pathogenic role of delta 2 tubulin in bortezomib-induced peripheral neuropathy
Authors: Pero Maria Elena , Meregalli Cristina , Qu Xiaoyi , Shin Grace Ji-eun , Kumar Atul , Shorey Matthew , Rolls Melissa M. , Tanji Kurenai , Brannagan Thomas H. , Alberti Paola , Fumagalli Giulia , Monza Laura , Grueber Wesley B. , Cavaletti Guido , Bartolini Francesca
Published: January 2021

Significance

Chemotherapy-induced peripheral neuropathy (CIPN) is a debilitating “dying back” neuropathy featuring a distal-to-proximal peripheral nerve degeneration seen in cancer patients undergoing chemotherapy. The pathogenenic mechanisms of CIPN are largely unknown. We report that in sensory neurons, the CIPN-inducing drug bortezomib caused axonopathy and disrupted mitochondria motility by increasing delta 2 tubulin (D2), the only irreversible tubulin posttranslational modification and a marker of hyper-stable microtubules. These data provide a new paradigm for the risk associated with enhanced tubulin longevity in peripheral neuropathy and suggest that targeting the enzymes regulating this tubulin modification may provide therapies that prevent the axonal injury observed in bortezomib-induced peripheral neuropathy.
Environment-based object values learned by local network in the striatum tail
Authors: Kunimatsu Jun , Yamamoto Shinya , Maeda Kazutaka , Hikosaka Okihide
Published: January 2021

Significance

Choosing good objects is a fundamental behavior for all animals, to which the basal ganglia (BG) contribute extensively. However, the object choice needs to be changed in different environments. The mechanism of object choice is based on the neuronal circuits originating from output neurons (MSNs) in the striatum. We found that the environment information is provided by fast-spiking interneurons (FSIs) connecting to the MSN circuit. More critically, the experimental reduction of the FSI-input to MSNs disabled the monkey to learn the environment-based object choice. This proved that the object choice controlled by the downstream BG circuit is modulated by the environmental context controlled by the internal circuits in the top of BG circuit. This is important for our flexible decision.
Synthetic protein conjugate vaccines provide protection against
Mycobacterium tuberculosis
in mice
Authors: Hanna Cameron C. , Ashhurst Anneliese S. , Quan Diana , Maxwell Joshua W. C. , Britton Warwick J. , Payne Richard J.
Published: January 2021

Significance

Tuberculosis is the leading cause of death worldwide from a single infectious agent, but vaccines developed to date have limited efficacy and pose safety concerns. Protein-based vaccines are a safe option but usually require powerful adjuvants. We present examples of fully synthetic, self-adjuvanted protein vaccine constructs. These vaccines comprise a low-dose immune-stimulating adjuvant, covalently fused to the ESAT6 protein from
Mycobacterium tuberculosis
, the causative agent of tuberculosis. When administered by inhalation, the vaccines generated powerful immune responses and significant protection from
M. tuberculosis
in the lungs of mice. The synthetic strategy we describe represents a method that could be used to rapidly generate vaccines for preclinical testing against many diseases, including novel pathogens such as SARS-CoV-2.
Photopatterned biomolecule immobilization to guide three-dimensional cell fate in natural protein-based hydrogels
Authors: Batalov Ivan , Stevens Kelly R. , DeForest Cole A.
Published: January 2021

Significance

Over the past two decades, natural protein-based hydrogel biomaterials have catapulted cell biology into the third dimension, becoming the modern workhorses of 3D cell and organoid culture. Although these systems mimic many important aspects of native tissue while permitting matrix remodeling and biological integration, spatiotemporal control over cell fate within these materials has not been demonstrated. Here, we introduce a generalizable strategy to covalently decorate cell-laden natural hydrogels with bioactive proteins including growth factors and then use these methods to anisotropically govern cell fates in ways currently unobtainable in synthetic biomaterials. Enabling 4D biochemical tunability within natural protein-based gels, these approaches are likely to find great utility in probing and directing biological functions and in engineering heterogenous functional tissues.
Nonlinear elasticity and damping govern ultrafast dynamics in click beetles
Authors: Bolmin Ophelia , Socha John J. , Alleyne Marianne , Dunn Alison C. , Fezzaa Kamel , Wissa Aimy A.
Published: January 2021

Significance

Click beetles are among animals that amplify mechanical power output using springs and latches to perform ultrafast movements. Studies involving these animals have been limited to observing the kinematics of the movements. Here, we study the kinematics and dynamics of the extremely fast bending maneuver performed by click beetles (i.e., the clicking motion). First, we identify the latching, loading, and release phases of the clicking motion using high-speed synchrotron X-ray imaging. Second, we discover a portion of the spring mechanism that the beetles use to store and quickly release energy. Finally, using specialized analytical methods, we characterize the damping and elastic forces that govern the release phase, which explains why the beetles can rapidly perform this click without significant damage.
Acceleration of catalysis in dihydrofolate reductase by transient, site-specific photothermal excitation
Authors: Kozlowski Rachel , Zhao Jing , Dyer R. Brian
Published: January 2021

Significance

Direct excitation of specific protein structural dynamics as a test of their role in enzyme catalysis has not yet been possible. Here we show that such motions can be excited photothermally, using a gold nanoparticle attached to a specific site on the enzyme dihydrofolate reductase (DHFR). DHFR is known to adopt multiple ground-state conformations having different kinetics of enzyme turnover. Site-specific photothermal excitation enables the enzyme to sample different reactive basins in the catalytic energy landscape and accelerates catalysis. We postulate that transient, site-specific heating excites a network of coupled motions that form a collective breathing mode of the protein structure near the active site, facilitating redistribution of the population into more reactive conformations.
The Tiger Rattlesnake genome reveals a complex genotype underlying a simple venom phenotype
Authors: Margres Mark J. , Rautsaw Rhett M. , Strickland Jason L. , Mason Andrew J. , Schramer Tristan D. , Hofmann Erich P. , Stiers Erin , Ellsworth Schyler A. , Nystrom Gunnar S. , Hogan Michael P. , Bartlett Daniel A. , Colston Timothy J. , Gilbert David M. , Rokyta Darin R. , Parkinson Christopher L.
Published: January 2021

Significance

A central question in biology is whether trait differences are the result of variation in gene number, sequence, or regulation. Snake venoms are an excellent system for addressing this question because of their genetic tractability, contributions to fitness, and high evolutionary rates. We sequenced and assembled the genome of the Tiger Rattlesnake to determine whether the simplest rattlesnake venom was the product of a simple or complex genotype. The number of venom genes greatly exceeded the number of venom proteins producing the simple phenotype, indicating regulatory mechanisms were responsible for the production of the simplest, but most toxic, rattlesnake venom. We suggest that the retention of genomic complexity may be the result of shared regulatory elements among gene-family members.
Accumulation of styrene oligomers alters lipid membrane phase order and miscibility
Authors: Morandi Mattia I. , Kluzek Monika , Wolff Jean , Schroder André , Thalmann Fabrice , Marques Carlos M.
Published: January 2021

Significance

Accumulation of nanopollutants in lifeforms has become the subject of increasing concern, but effects are not understood. Biological systems are inherently complex, and therefore any small variations on the membrane properties can potentially perturb cell functionality. In this study we observe that the presence of styrene oligomers in lipid membranes alters their phase behavior, with stronger changes occurring in more complex systems, which could translate into potential cellular disruption. This study provides evidence that the presence of nanopollutants in the membrane may alter its fundamental properties and affect cell viability.
DNA origami demonstrate the unique stimulatory power of single pMHCs as T cell antigens
Authors: Hellmeier Joschka , Platzer Rene , Eklund Alexandra S. , Schlichthaerle Thomas , Karner Andreas , Motsch Viktoria , Schneider Magdalena C. , Kurz Elke , Bamieh Victor , Brameshuber Mario , Preiner Johannes , Jungmann Ralf , Stockinger Hannes , Schütz Gerhard J. , Huppa Johannes B. , Sevcsik Eva
Published: January 2021

Significance

The nanoscale organization of ligands and receptors is critical for cellular communication yet inherently challenging to investigate. We have here devised a DNA origami-based biointerface which allows the experimenter to adjust protein distances with nanometer precision as a means to enhance or disturb signaling while being responsive to large-scale reorganization processes during cell activation. Applying this biointerface to study the spatial requirements of T cell activation, we find that the smallest signaling-competent receptor unit consists of two stably ligated T cell receptors (TCRs) within a distance of 20 nanometers. Spatial organization of the physiological ligand pMHC, however, is not a relevant parameter of antigen-mediated T cell activation, as single, well-isolated pMHC molecules efficiently stimulate T cells.
Discovery of a hidden transient state in all bromodomain families
Authors: Raich Lluís , Meier Katharina , Günther Judith , Christ Clara D. , Noé Frank , Olsson Simon
Published: January 2021

Significance

Proteins dynamically shape shift, adopting different three-dimensional structures, called conformations. The conformations fulfill different functions and expose different binding surfaces to drug molecules aiming to inhibit the protein. While structural biology experiments can capture the most frequently occurring conformations, those that are more rarely visited are very difficult to capture but may be functionally important. Using extensive computer simulations, we discover an undocumented conformation present in all families of bromodomains—protein domains crucial for epigenetic regulation and associated with several diseases. We also show that available experimental data confirms the existence of this previously overlooked state. The surprising ubiquity of this new conformation makes it a likely player in biological function and opens up new drug development strategies.
Structurally silent peptide anchor modifications allosterically modulate T cell recognition in a receptor-dependent manner
Authors: Smith Angela R. , Alonso Jesus A. , Ayres Cory M. , Singh Nishant K. , Hellman Lance M. , Baker Brian M.
Published: January 2021

Significance

The strength of peptide binding to class I MHC proteins is a correlate of immunogenicity. However, many peptides of interest, including shared tumor antigens, bind weakly and are poorly immunogenic. Considerable effort has been spent generating stronger-binding variants of these, with the goal of using them as vaccines to elicit responses against the unmodified peptides. We show that common modifications used to improve peptide binding can unpredictably alter T cell recognition. The alterations arise from structurally silent, “through-protein” effects that are sensed differently by different T cell receptors. Our results have implications for the design and use of modified peptides, as well as efforts to predict the immunogenicity of peptides incorporating similar modifications, such as tumor neoantigens.
Bifurcation of excited state trajectories toward energy transfer or electron transfer directed by wave function symmetry
Authors: Oviedo Paola S. , Baraldo Luis M. , Cadranel Alejandro
Published: January 2021

Significance

Electron transfer and energy transfer are the simplest chemical reactions and the key processes involved in cellular respiration, energy conversion schemes like photosynthesis, and photoredox catalysis. In photoreactive systems, any decay cascade to lower excited states that precedes electron or energy transfer dissipates part of the energy absorbed from light. Our findings show that influence of symmetry on energy or electron transfer, related to orbital overlap, can be exploited to avoid detrimental energy losses, decisive for improving energy conversion and expanding the limits of photoredox catalysis.
Live-cell epigenome manipulation by synthetic histone acetylation catalyst system
Authors: Fujiwara Yusuke , Yamanashi Yuki , Fujimura Akiko , Sato Yuko , Kujirai Tomoya , Kurumizaka Hitoshi , Kimura Hiroshi , Yamatsugu Kenzo , Kawashima Shigehiro A. , Kanai Motomu
Published: January 2021

Significance

Chemical methods to install histone posttranslational modifications in live cells promise extraordinary potential in epigenome biology and medicine due to the use of endogenous protein levels and lack of genetic manipulation. In this study, we developed a chemical catalyst, PEG-LANA-DSSMe, that binds with nucleosome’s acidic patch and promotes regioselective, synthetic histone acetylation at H2BK120 in living cells. Importantly, the synthetic acetylation suppressed H2B ubiquitination, a critical epigenome mark in cell physiology. This achievement is an example of epigenome manipulation in living cells, entirely relying on the chemical system. In the long term, our catalyst system with further improvements may contribute to both therapy and elucidation of epigenetic mechanisms.
Impact of transnational land acquisitions on local food security and dietary diversity
Authors: Müller Marc F. , Penny Gopal , Niles Meredith T. , Ricciardi Vincent , Chiarelli Davide Danilo , Davis Kyle Frankel , Dell’Angelo Jampel , D’Odorico Paolo , Rosa Lorenzo , Rulli Maria Cristina , Mueller Nathaniel D.
Published: January 2021

Significance

Foreign investors have acquired vast tracts of land globally since the early 2000s, yet the food security implications of this phenomenon are poorly understood. The ability to close crop yield gaps through commercial agriculture must be weighed against local impacts on food access. We combine agricultural, remote sensing, and household survey data with georeferenced information on land deals to examine their implications on food production and access. Results point to a paradox where land deals simultaneously contribute to closing the global yield gap by increasing crop production, while threatening local food security by redirecting key dietary nutrients toward the export market. This trade-off between food production and food security calls into question the sustainability of current land investment practices.
Results from a 2020 field experiment encouraging voting by mail
Authors: Hopkins Daniel J. , Meredith Marc , Chainani Anjali , Olin Nathaniel , Tse Tiffany
Published: January 2021

The ability to cast a mail ballot can safeguard the franchise. However, because there are often additional procedural protections to ensure that a ballot cast in person counts, voting by mail can also jeopardize people’s ability to cast a recorded vote. An experiment carried out during the COVID-19 pandemic illustrates both forces. Philadelphia officials randomly sent 46,960 Philadelphia registrants postcards encouraging them to apply to vote by mail in the lead-up to the June 2020 primary election. While the intervention increased the likelihood a registrant cast a mail ballot by 0.4 percentage points (
P
= 0.017)—or 3%—many of these additional mail ballots counted only because a last-minute policy intervention allowed most mail ballots postmarked by Election Day to count.
PIAS1 modulates striatal transcription, DNA damage repair, and SUMOylation with relevance to Huntington’s disease
Authors: Morozko Eva L. , Smith-Geater Charlene , Monteys Alejandro Mas , Pradhan Subrata , Lim Ryan G. , Langfelder Peter , Kachemov Marketta , Kulkarni Jayesh A. , Zaifman Josh , Hill Austin , Stocksdale Jennifer T. , Cullis Pieter R. , Wu Jie , Ochaba Joseph , Miramontes Ricardo , Chakraborty Anirban , Hazra Tapas K. , Lau Alice , St-cyr Sophie , Orellana Iliana , Kopan Lexi , Wang Keona Q. , Yeung Sylvia , Leavitt Blair R. , Reidling Jack C. , Yang X. William , Steffan Joan S. , Davidson Beverly L. , Sarkar Partha S. , Thompson Leslie M.
Published: January 2021

Significance

Genetic variants in genes involved in maintenance of genomic stability are modifiers of Huntington’s disease (HD) age of onset. This study shows a connection between the E3 SUMO ligase PIAS1, DNA damage repair protein PNKP, and HD-associated transcriptional dysregulation. Reduction of Pias1 in a knockin HD mouse striatum normalizes disease-associated aberrant transcription, rescues perturbed enzymatic activity of Pnkp, and increases genomic integrity, while also having transcriptional effects in WT animals. PIAS1 reduction in human iPSC neurons alters transcription of synaptic signaling and DNA damage repair, rescues PNKP activity, and increases genomic integrity in HD iPSC-derived neurons. Finally, PIAS1 can modulate SUMO modification of PNKP, which is the first identification of an enzyme that regulates this modification.
Multiple domain interfaces mediate SARM1 autoinhibition
Authors: Shen Chen , Vohra Mihir , Zhang Pengfei , Mao Xianrong , Figley Matthew D. , Zhu Jian , Sasaki Yo , Wu Hao , DiAntonio Aaron , Milbrandt Jeffrey
Published: January 2021

Significance

Axon degeneration is an active program of subcellular self-destruction that drives pathology in the injured and diseased nervous system. SARM1 is an inducible NAD
+
hydrolase and the central executioner of axon loss. In healthy axons, the SARM1 NADase is autoinhibited. With injury or disease, this autoinhibition is relieved and SARM1 depletes NAD
+
, inducing a metabolic crisis and subsequent axon loss. Here we combine peptide screening, cryo-electron microscopy, and site-directed mutagenesis with analysis of axonal metabolomics and axon degeneration to define five domain interactions within and across SARM1 protomers that are required to maintain an inactive SARM1 octamer. These structural insights may enable the development of SARM1 inhibitors that stabilize this autoinhibited conformation and thereby block axon degeneration.
Developing T cells form an immunological synapse for passage through the β-selection checkpoint
Authors: Allam Amr H. , Charnley Mirren , Pham Kim , Russell Sarah M.
Published: January 2021

The β-selection checkpoint of T cell development tests whether the cell has recombined its genomic DNA to produce a functional T cell receptor β (TCRβ). Passage through the β-selection checkpoint requires the nascent TCRβ protein to mediate signaling through a pre-TCR complex. In this study, we show that developing T cells at the β-selection checkpoint establish an immunological synapse in in vitro and in situ, resembling that of the mature T cell. The immunological synapse is dependent on two key signaling pathways known to be critical for the transition beyond the β-selection checkpoint, Notch and CXCR4 signaling. In vitro and in situ analyses indicate that the immunological synapse promotes passage through the β-selection checkpoint. Collectively, these data indicate that developing T cells regulate pre-TCR signaling through the formation of an immunological synapse. This signaling platform integrates cues from Notch, CXCR4, and MHC on the thymic stromal cell to allow transition beyond the β-selection checkpoint.
Direct binding of ESCRT protein Chm7 to phosphatidic acid–rich membranes at nuclear envelope herniations
Authors: Thaller David J. , Tong Danqing , Marklew Christopher J. , Ader Nicholas R. , Mannino Philip J. , Borah Sapan , King Megan C. , Ciani Barbara , Lusk C. Patrick
Published: January 2021

Mechanisms that control nuclear membrane remodeling are essential to maintain the integrity of the nucleus but remain to be fully defined. Here, we identify a phosphatidic acid (PA)–binding capacity in the nuclear envelope (NE)–specific ESCRT, Chm7, in budding yeast. Chm7’s interaction with PA-rich membranes is mediated through a conserved hydrophobic stretch of amino acids, which confers recruitment to the NE in a manner that is independent of but required for Chm7’s interaction with the LAP2-emerin-MAN1 (LEM) domain protein Heh1 (LEM2). Consistent with the functional importance of PA binding, mutation of this region abrogates recruitment of Chm7 to membranes and abolishes Chm7 function in the context of NE herniations that form during defective nuclear pore complex (NPC) biogenesis. In fact, we show that a PA sensor specifically accumulates within these NE herniations. We suggest that local control of PA metabolism is important for ensuring productive NE remodeling and that its dysregulation may contribute to pathologies associated with defective NPC assembly.
LNCcation: lncRNA localization and function
Authors: Bridges Mary Catherine , Daulagala Amanda C. , Kourtidis Antonis
Published: January 2021

Subcellular localization of RNAs has gained attention in recent years as a prevalent phenomenon that influences numerous cellular processes. This is also evident for the large and relatively novel class of long noncoding RNAs (lncRNAs). Because lncRNAs are defined as RNA transcripts >200 nucleotides that do not encode protein, they are themselves the functional units, making their subcellular localization critical to their function. The discovery of tens of thousands of lncRNAs and the cumulative evidence involving them in almost every cellular activity render assessment of their subcellular localization essential to fully understanding their biology. In this review, we summarize current knowledge of lncRNA subcellular localization, factors controlling their localization, emerging themes, including the role of lncRNA isoforms and the involvement of lncRNAs in phase separation bodies, and the implications of lncRNA localization on their function and on cellular behavior. We also discuss gaps in the current knowledge as well as opportunities that these provide for novel avenues of investigation.
Mapping and role of T cell response in SARS-CoV-2–infected mice
Authors: Zhuang Zhen , Lai Xiaomin , Sun Jing , Chen Zhao , Zhang Zhaoyong , Dai Jun , Liu Donglan , Li Yuming , Li Fang , Wang Yanqun , Zhu Airu , Wang Junxiang , Yang Wenhui , Huang Jicheng , Li Xiaobo , Hu Lingfei , Wen Liyan , Zhuo Jianfen , Zhang Yanjun , Chen Dingbin , Li Suxiang , Huang Shuxiang , Shi Yongxia , Zheng Kui , Zhong Nanshan , Zhao Jingxian , Zhou Dongsheng , Zhao Jincun
Published: January 2021

Virus-specific T cells play essential roles in protection against multiple virus infections, including SARS-CoV and MERS-CoV. While SARS-CoV-2–specific T cells have been identified in COVID-19 patients, their role in the protection of SARS-CoV-2–infected mice is not established. Here, using mice sensitized for infection with SARS-CoV-2 by transduction with an adenovirus expressing the human receptor (Ad5-hACE2), we identified SARS-CoV-2–specific T cell epitopes recognized by CD4+ and CD8+ T cells in BALB/c and C57BL/6 mice. Virus-specific T cells were polyfunctional and were able to lyse target cells in vivo. Further, type I interferon pathway was proved to be critical for generating optimal antiviral T cell responses after SARS-CoV-2 infection. T cell vaccination alone partially protected SARS-CoV-2–infected mice from severe disease. In addition, the results demonstrated cross-reactive T cell responses between SARS-CoV and SARS-CoV-2, but not MERS-CoV, in mice. Understanding the role of the T cell response will guide immunopathogenesis studies of COVID-19 and vaccine design and validation.
Pseudoreplication in physiology: More means less
Authors: Eisner David A.
Published: January 2021

This article reviews how to analyze data from experiments designed to compare the cellular physiology of two or more groups of animals or people. This is commonly done by measuring data from several cells from each animal and using simple t tests or ANOVA to compare between groups. I use simulations to illustrate that this method can give erroneous positive results by assuming that the cells from each animal are independent of each other. This problem, which may be responsible for much of the lack of reproducibility in the literature, can be easily avoided by using a hierarchical, nested statistics approach.
Steady state entropy production rate for scalar Langevin field theories
Authors: Li Yuting I , Cates Michael E
Published: January 2021

The entropy production rate (EPR) offers a quantitative measure of time reversal symmetry breaking in non-equilibrium systems. It can be defined either at particle level or at the level of coarse-grained fields such as density; the EPR for the latter quantifies the extent to which these coarse-grained fields behave irreversibly. In this work, we first develop a general method to compute the EPR of scalar Langevin field theories with additive noise. This large class of theories includes active versions of model A (non-conserved density dynamics) and model B (conserved) and also models where both types of dynamics are simultaneously present (such as model AB (2020 J. Stat. Mech. 05206)). Treating the scalar field ϕ (and its time derivative

ϕ

̇

) as the sole observable(s), we arrive at an expression for the EPR that is non-negative for every field configuration and is quadratic in the time-antisymmetric component of the dynamics. Our general expression is a function of the quasipotential, which determines the full probability distribution for configurations, and is not generally calculable. To alleviate this difficulty, we present a small-noise expansion of the EPR, which only requires knowledge of the deterministic (mean-field) solution for the scalar field in steady state, which generally is calculable, at least numerically. We demonstrate this calculation for the case of model AB (2020 J. Stat. Mech. 05206). We then present a similar EPR calculation for model AB with the conservative and non-conservative contributions to

ϕ

̇

=

ϕ

̇

A

+

ϕ

̇

B

viewed as separately observable quantities. The results are qualitatively different, confirming that the field-level EPR depends on the choice of coarse-grained information retained within the dynamical description.
Non-monotonic nucleus-nucleus potential and incompressibility of infinite cold nuclear matter
Authors: Basak A K , Hossain S , Uddin M A , Tariq A S B
Published: January 2021

A novel method for the determination of the yet not well-known quantity of nuclear incompressibility, K is presented. Non-monotonic (NM) nucleus-nucleus potentials from the energy-density functional (EDF) theory including the Pauli principle have been considered for K in the range 188-266 MeV. The experimental cross sections of 16O+16O elastic scattering over the 31-350 MeV incident energies have been analyzed in the optical model using the NM potentials. Sensitivity of K on the elastic scattering data is studied and its value for infinite cold nuclear matter deduced to be 222 ± 5 MeV
Remarkable class of materials: Band structures and optical properties of non-superconducting and superconducting MAX phases
Authors: Islam A K M A
Published: January 2021

The MAX phases, due to their nanolaminated crystal structure, are found to be exciting materials which combine certain best attributes of metals (good electrical and thermal conductivity, low hardness, machinability, damage tolerance and thermal shock resistance) with those of ceramics (high temperature strength, high elastic moduli, oxidation and corrosion resistance). Over 70 MAX phases are in existence, amongst which there are eight low-temperature superconductors. Thus a vast majority of the MAX phases are not superconductors. In the present review, emphasis will be made on the theoretical works conducted in recent years in our laboratory to understand the band structure and optical properties of several non-superconducting (particularly Zr-metal based phases) and the available superconducting MAX phases.
Bose condensation and the Casimir effects of an imperfect Bose gas in a d-dimensional configuration space
Authors: Bhuiyan G M
Published: January 2021

Some properties of an ideal gas of massive bosons in a mean field potential and, confined between two infinite parallel slabs in a d-dimensional configuration space are investigated systematically. Here, one particle density of states approach is employed to study the critical temperature, shift of density, Casimir effects and critical exponents, starting from the evaluation of the grand canonical free energy in d-dimension. We have found that, the shift of density, Casimir force and the critical temperature depend on the space dimensionality. But the Casimir force decays as an inverse power law of the distance between two slabs in the condensate and, decays exponentially in the non-condensed state situated very close to the point of phase transition. Specifically, this study enabled us to predict the shift of the density of boson in the excited states due to mean field potential, and also the dimensional dependence of the critical exponent. The form of the critical exponent is found to be

1

d
−
2

for the imperfect Bose gas. This leads to a value of critical exponent 1 for d = 3. Most interestingly, in the limit when the mean field potential goes to zero the resulting expressions for the above properties coincide with those of the ideal Bose gas.
Non-monotonic potential description of alpha-40Carefractive elastic scattering
Authors: Shahinur Islam M , Billah M M , Basak A K
Published: January 2021

Experimental differential cross sections of elastic scattering by 40Ca, over a wide range of incident energies, have been analyzed in terms of non-monotonic (NM) potentials, generated from the energy density functional (EDF) theory using a realistic two-nucleon potential coupled with an appropriate consideration of the Pauli principle. The Airy structure of the nuclear rainbow scattering data in the energy range of 36.1–42.6 MeV is well accounted for the first time by the shallow NM potential.