bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of active catalysts for the acceptorless dehydrogenation of alcohols to carbonyls
Authors: Wang Tao , Sha Jin , Sabbe Maarten , Sautet Philippe , Pera-Titus Marc , Michel Carine 
Published: August 2021

AbstractAcceptorless dehydrogenation into carbonyls and molecular hydrogen is an attractive strategy to valorize (biobased) alcohols. Using 2-octanol dehydrogenation as benchmark reaction in a continuous reactor, a library of metal-supported catalysts is tested to validate the predictive level of catalytic activity for combined DFT and micro-kinetic modeling. Based on a series of transition metals, scaling relations are determined as a function of two descriptors, i.e. the surface binding energies of atomic carbon and oxygen. Then, a volcano-shape relation based on both descriptors is derived, paving the way to further optimization of active catalysts. Evaluation of 294 diluted alloys but also a series of carbides and nitrides with the volcano map identified 12 promising candidates with potentially improved activity for alcohol dehydrogenation, which provides useful guidance for experimental catalyst design. Further screening identifies β-Mo2N and γ-Mo2N exposing mostly (001) and (100) facets as potential candidates for alcohol dehydrogenation.
Engineered whole cut meat-like tissue by the assembly of cell fibers using tendon-gel integrated bioprinting
Authors: Kang Dong-Hee , Louis Fiona , Liu Hao , Shimoda Hiroshi , Nishiyama Yasutaka , Nozawa Hajime , Kakitani Makoto , Takagi Daisuke , Kasa Daijiro , Nagamori Eiji , Irie Shinji , Kitano Shiro , Matsusaki Michiya 
Published: August 2021

AbstractWith the current interest in cultured meat, mammalian cell-based meat has mostly been unstructured. There is thus still a high demand for artificial steak-like meat. We demonstrate in vitro construction of engineered steak-like tissue assembled of three types of bovine cell fibers (muscle, fat, and vessel). Because actual meat is an aligned assembly of the fibers connected to the tendon for the actions of contraction and relaxation, tendon-gel integrated bioprinting was developed to construct tendon-like gels. In this study, a total of 72 fibers comprising 42 muscles, 28 adipose tissues, and 2 blood capillaries were constructed by tendon-gel integrated bioprinting and manually assembled to fabricate steak-like meat with a diameter of 5 mm and a length of 10 mm inspired by a meat cut. The developed tendon-gel integrated bioprinting here could be a promising technology for the fabrication of the desired types of steak-like cultured meats.
Deciphering ion transport and ATPase coupling in the intersubunit tunnel of KdpFABC
Authors: Silberberg Jakob M. , Corey Robin A. , Hielkema Lisa , Stock Charlott , Stansfeld Phillip J. , Paulino Cristina , Hänelt Inga 
Published: August 2021

AbstractKdpFABC, a high-affinity K+ pump, combines the ion channel KdpA and the P-type ATPase KdpB to secure survival at K+ limitation. Here, we apply a combination of cryo-EM, biochemical assays, and MD simulations to illuminate the mechanisms underlying transport and the coupling to ATP hydrolysis. We show that ions are transported via an intersubunit tunnel through KdpA and KdpB. At the subunit interface, the tunnel is constricted by a phenylalanine, which, by polarized cation-π stacking, controls K+ entry into the canonical substrate binding site (CBS) of KdpB. Within the CBS, ATPase coupling is mediated by the charge distribution between an aspartate and a lysine. Interestingly, individual elements of the ion translocation mechanism of KdpFABC identified here are conserved among a wide variety of P-type ATPases from different families. This leads us to the hypothesis that KdpB might represent an early descendant of a common ancestor of cation pumps.
Inertial and viscous flywheel sensing of nanoparticles
Authors: Katsikis Georgios , Collis Jesse F. , Knudsen Scott M. , Agache Vincent , Sader John E. , Manalis Scott R. 
Published: August 2021

AbstractRotational dynamics often challenge physical intuition while enabling unique realizations, from the rotor of a gyroscope that maintains its orientation regardless of the outer gimbals, to a tennis racket that rotates around its handle when tossed face-up in the air. In the context of inertial sensing, which can measure mass with atomic precision, rotational dynamics are normally considered a complication hindering measurement interpretation. Here, we exploit the rotational dynamics of a microfluidic device to develop a modality in inertial sensing. Combining theory with experiments, we show that this modality measures the volume of a rigid particle while normally being insensitive to its density. Paradoxically, particle density only emerges when fluid viscosity becomes dominant over inertia. We explain this paradox via a viscosity-driven, hydrodynamic coupling between the fluid and the particle that activates the rotational inertia of the particle, converting it into a ‘viscous flywheel’. This modality now enables the simultaneous measurement of particle volume and mass in fluid, using a single, high-throughput measurement.
Global scenarios of resource and emission savings from material efficiency in residential buildings and cars
Authors: Pauliuk Stefan , Heeren Niko , Berrill Peter , Fishman Tomer , Nistad Andrea , Tu Qingshi , Wolfram Paul , Hertwich Edgar G. 
Published: August 2021

AbstractMaterial production accounts for a quarter of global greenhouse gas (GHG) emissions. Resource-efficiency and circular-economy strategies, both industry and demand-focused, promise emission reductions through reducing material use, but detailed assessments of their GHG reduction potential are lacking. We present a global-scale analysis of material efficiency for passenger vehicles and residential buildings. We estimate future changes in material flows and energy use due to increased yields, light design, material substitution, extended service life, and increased service efficiency, reuse, and recycling. Together, these strategies can reduce cumulative global GHG emissions until 2050 by 20–52 Gt CO2-eq (residential buildings) and 13–26 Gt CO2e-eq (passenger vehicles), depending on policy assumptions. Next to energy efficiency and low-carbon energy supply, material efficiency is the third pillar of deep decarbonization for these sectors. For residential buildings, wood construction and reduced floorspace show the highest potential. For passenger vehicles, it is ride sharing and car sharing.
Differentiable sampling of molecular geometries with uncertainty-based adversarial attacks
Authors: Schwalbe-Koda Daniel , Tan Aik Rui , Gómez-Bombarelli Rafael 
Published: August 2021

AbstractNeural network (NN) interatomic potentials provide fast prediction of potential energy surfaces, closely matching the accuracy of the electronic structure methods used to produce the training data. However, NN predictions are only reliable within well-learned training domains, and show volatile behavior when extrapolating. Uncertainty quantification methods can flag atomic configurations for which prediction confidence is low, but arriving at such uncertain regions requires expensive sampling of the NN phase space, often using atomistic simulations. Here, we exploit automatic differentiation to drive atomistic systems towards high-likelihood, high-uncertainty configurations without the need for molecular dynamics simulations. By performing adversarial attacks on an uncertainty metric, informative geometries that expand the training domain of NNs are sampled. When combined with an active learning loop, this approach bootstraps and improves NN potentials while decreasing the number of calls to the ground truth method. This efficiency is demonstrated on sampling of kinetic barriers, collective variables in molecules, and supramolecular chemistry in zeolite-molecule interactions, and can be extended to any NN potential architecture and materials system.
Subpicosecond metamagnetic phase transition in FeRh driven by non-equilibrium electron dynamics
Authors: Pressacco Federico , Sangalli Davide , Uhlíř Vojtěch , Kutnyakhov Dmytro , Arregi Jon Ander , Agustsson Steinn Ymir , Brenner Günter , Redlin Harald , Heber Michael , Vasilyev Dmitry , Demsar Jure , Schönhense Gerd , Gatti Matteo , Marini Andrea , Wurth Wilfried , Sirotti Fausto 
Published: August 2021

AbstractFemtosecond light-induced phase transitions between different macroscopic orders provide the possibility to tune the functional properties of condensed matter on ultrafast timescales. In first-order phase transitions, transient non-equilibrium phases and inherent phase coexistence often preclude non-ambiguous detection of transition precursors and their temporal onset. Here, we present a study combining time-resolved photoelectron spectroscopy and ab-initio electron dynamics calculations elucidating the transient subpicosecond processes governing the photoinduced generation of ferromagnetic order in antiferromagnetic FeRh. The transient photoemission spectra are accounted for by assuming that not only the occupation of electronic states is modified during the photoexcitation process. Instead, the photo-generated non-thermal distribution of electrons modifies the electronic band structure. The ferromagnetic phase of FeRh, characterized by a minority band near the Fermi energy, is established 350 ± 30 fs after the laser excitation. Ab-initio calculations indicate that the phase transition is initiated by a photoinduced Rh-to-Fe charge transfer.
Dysregulated cholesterol homeostasis results in resistance to ferroptosis increasing tumorigenicity and metastasis in cancer
Authors: Liu Wen , Chakraborty Binita , Safi Rachid , Kazmin Dmitri , Chang Ching-yi , McDonnell Donald P. 
Published: August 2021

AbstractHypercholesterolemia and dyslipidemia are associated with an increased risk for many cancer types and with poor outcomes in patients with established disease. Whereas the mechanisms by which this occurs are multifactorial we determine that chronic exposure of cells to 27-hydroxycholesterol (27HC), an abundant circulating cholesterol metabolite, selects for cells that exhibit increased cellular uptake and/or lipid biosynthesis. These cells exhibit substantially increased tumorigenic and metastatic capacity. Notably, the metabolic stress imposed upon cells by the accumulated lipids requires sustained expression of GPX4, a negative regulator of ferroptotic cell death. We show that resistance to ferroptosis is a feature of metastatic cells and further demonstrate that GPX4 knockdown attenuates the enhanced tumorigenic and metastatic activity of 27HC resistant cells. These findings highlight the general importance of ferroptosis in tumor growth and metastasis and suggest that dyslipidemia/hypercholesterolemia impacts cancer pathogenesis by selecting for cells that are resistant to ferroptotic cell death.
A host–guest semibiological photosynthesis system coupling artificial and natural enzymes for solar alcohol splitting
Authors: Cai Junkai , Zhao Liang , He Cheng , Li Yanan , Duan Chunying 
Published: August 2021

AbstractDevelopment of a versatile, sustainable and efficient photosynthesis system that integrates intricate catalytic networks and energy modules at the same location is of considerable future value to energy transformation. In the present study, we develop a coenzyme-mediated supramolecular host-guest semibiological system that combines artificial and enzymatic catalysis for photocatalytic hydrogen evolution from alcohol dehydrogenation. This approach involves modification of the microenvironment of a dithiolene-embedded metal-organic cage to trap an organic dye and NADH molecule simultaneously, serving as a hydrogenase analogue to induce effective proton reduction inside the artificial host. This abiotic photocatalytic system is further embedded into the pocket of the alcohol dehydrogenase to couple enzymatic alcohol dehydrogenation. This host-guest approach allows in situ regeneration of NAD+/NADH couple to transfer protons and electrons between the two catalytic cycles, thereby paving a unique avenue for a synergic combination of abiotic and biotic synthetic sequences for photocatalytic fuel and chemical transformation.
A non-enzymatic, isothermal strand displacement and amplification assay for rapid detection of SARS-CoV-2 RNA
Authors: Mohammadniaei Mohsen , Zhang Ming , Ashley Jon , Christensen Ulf Bech , Friis-Hansen Lennart Jan , Gregersen Rasmus , Lisby Jan Gorm , Benfield Thomas Lars , Nielsen Finn Erland , Henning Rasmussen Jens , Pedersen Ellen Bøtker , Olinger Anne Christine Rye , Kolding Lærke Tørring , Naseri Maryam , Zheng Tao , Wang Wentao , Gorodkin Jan , Sun Yi 
Published: August 2021

AbstractThe current nucleic acid signal amplification methods for SARS-CoV-2 RNA detection heavily rely on the functions of biological enzymes which imposes stringent transportation and storage conditions, high cost and global supply shortages. Here, a non-enzymatic whole genome detection method based on a simple isothermal signal amplification approach is developed for rapid detection of SARS-CoV-2 RNA and potentially any types of nucleic acids regardless of their size. The assay, termed non-enzymatic isothermal strand displacement and amplification (NISDA), is able to quantify 10 RNA copies.µL−1. In 164 clinical oropharyngeal RNA samples, NISDA assay is 100 % specific, and it is 96.77% and 100% sensitive when setting up in the laboratory and hospital, respectively. The NISDA assay does not require RNA reverse-transcription step and is fast (<30 min), affordable, highly robust at room temperature (>1 month), isothermal (42 °C) and user-friendly, making it an excellent assay for broad-based testing.
Humans and other commonly used model organisms are resistant to cycloheximide-mediated biases in ribosome profiling experiments
Authors: Sharma Puneet , Wu Jie , Nilges Benedikt S. , Leidel Sebastian A. 
Published: August 2021

AbstractRibosome profiling measures genome-wide translation dynamics at sub-codon resolution. Cycloheximide (CHX), a widely used translation inhibitor to arrest ribosomes in these experiments, has been shown to induce biases in yeast, questioning its use. However, whether such biases are present in datasets of other organisms including humans is unknown. Here we compare different CHX-treatment conditions in human cells and yeast in parallel experiments using an optimized protocol. We find that human ribosomes are not susceptible to conformational restrictions by CHX, nor does it distort gene-level measurements of ribosome occupancy, measured decoding speed or the translational ramp. Furthermore, CHX-induced codon-specific biases on ribosome occupancy are not detectable in human cells or other model organisms. This shows that reported biases of CHX are species-specific and that CHX does not affect the outcome of ribosome profiling experiments in most settings. Our findings provide a solid framework to conduct and analyze ribosome profiling experiments.
PD-L1 degradation is regulated by electrostatic membrane association of its cytoplasmic domain
Authors: Wen Maorong , Cao Yunlei , Wu Bin , Xiao Taoran , Cao Ruiyu , Wang Qian , Liu Xiwei , Xue Hongjuan , Yu Yang , Lin Jialing , Xu Chenqi , Xu Jie , OuYang Bo 
Published: August 2021

AbstractThe cytoplasmic domain of PD-L1 (PD-L1-CD) regulates PD-L1 degradation and stability through various mechanism, making it an attractive target for blocking PD-L1-related cancer signaling. Here, by using NMR and biochemical techniques we find that the membrane association of PD-L1-CD is mediated by electrostatic interactions between acidic phospholipids and basic residues in the N-terminal region. The absence of the acidic phospholipids and replacement of the basic residues with acidic residues abolish the membrane association. Moreover, the basic-to-acidic mutations also decrease the cellular abundance of PD-L1, implicating that the electrostatic interaction with the plasma membrane mediates the cellular levels of PD-L1. Interestingly, distinct from its reported function as an activator of AMPK in tumor cells, the type 2 diabetes drug metformin enhances the membrane dissociation of PD-L1-CD by disrupting the electrostatic interaction, thereby decreasing the cellular abundance of PD-L1. Collectively, our study reveals an unusual regulatory mechanism that controls the PD-L1 level in tumor cells, suggesting an alternative strategy to improve the efficacy of PD-L1-related immunotherapies.
Expanding the binding specificity for RNA recognition by a PUF domain
Authors: Zhou Wei , Melamed Daniel , Banyai Gabor , Meyer Cindy , Tuschl Thomas , Wickens Marvin , Cao Junyue , Fields Stanley 
Published: August 2021

AbstractThe ability to design a protein to bind specifically to a target RNA enables numerous applications, with the modular architecture of the PUF domain lending itself to new RNA-binding specificities. For each repeat of the Pumilio-1 PUF domain, we generate a library that contains the 8,000 possible combinations of amino acid substitutions at residues critical for RNA contact. We carry out yeast three-hybrid selections with each library against the RNA recognition sequence for Pumilio-1, with any possible base present at the position recognized by the randomized repeat. We use sequencing to score the binding of each variant, identifying many variants with highly repeat-specific interactions. From these data, we generate an RNA binding code specific to each repeat and base. We use this code to design PUF domains against 16 RNAs, and find that some of these domains recognize RNAs with two, three or four changes from the wild type sequence.
Behavioral and psychological impact of genome sequencing: a pilot randomized trial of primary care and cardiology patients
Authors: Christensen Kurt D. , Schonman Erica F. , Robinson Jill O. , Roberts J. Scott , Diamond Pamela M. , Lee Kaitlyn B. , Green Robert C. , McGuire Amy L. 
Published: August 2021

AbstractMany expect genome sequencing (GS) to become routine in patient care and preventive medicine, but uncertainties remain about its ability to motivate participants to improve health behaviors and the psychological impact of disclosing results. In a pilot trial with exploratory analyses, we randomized 100 apparently healthy, primary-care participants and 100 cardiology participants to receive a review of their family histories of disease, either alone or in addition to GS analyses. GS results included polygenic risk information for eight cardiometabolic conditions. Overall, no differences were observed between the percentage of participants in the GS and control arms, who reported changes to health behaviors such as diet and exercise at 6 months post disclosure (48% vs. 36%, respectively,p = 0.104). In the GS arm, however, the odds of reporting a behavior change increased by 52% per high-risk polygenic prediction (p = 0.032). Mean anxiety and depression scores for GS and control arms had confidence intervals within equivalence margins of ±1.5. Mediation analyses suggested an indirect impact of GS on health behaviors by causing positive psychological responses (p ≤ 0.001). Findings suggest that GS did not distress participants. Future research on GS in more diverse populations is needed to confirm that it does not raise risks for psychological harms and to confirm the ability of polygenic risk predictions to motivate preventive behaviors.
In-silico design of envelope based multi-epitope vaccine candidate against Kyasanur forest disease virus
Authors: Arumugam Sathishkumar , Varamballi Prasad 
Published: August 2021

AbstractKyasanur forest disease virus (KFDV) causing tick-borne hemorrhagic fever which was earlier endemic to western Ghats, southern India, it is now encroaching into new geographic regions, but there is no approved medicine or effective vaccine against this deadly disease. In this study, we did in-silico design of multi-epitope subunit vaccine for KFDV. B-cell and T-cell epitopes were predicted from conserved regions of KFDV envelope protein and two vaccine candidates (VC1 and VC2) were constructed, those were found to be non-allergic and possess good antigenic properties, also gives cross-protection against Alkhurma hemorrhagic fever virus. The 3D structures of vaccine candidates were built and validated. Docking analysis of vaccine candidates with toll-like receptor-2 (TLR-2) by Cluspro and PatchDock revealed strong affinity between VC1 and TLR2. Ligplot tool was identified the intermolecular hydrogen bonds between vaccine candidates and TLR-2, iMOD server confirmed the stability of the docking complexes. JCAT sever ensured cloning efficiency of both vaccine constructs and in-silico cloning into pET30a (+) vector by SnapGene showed successful translation of epitope region. IMMSIM server was identified increased immunological responses. Finally, multi-epitope vaccine candidates were designed and validated their efficiency, it may pave the way for up-coming vaccine and diagnostic kit development.
Wolves, dogs and humans in regular contact can mutually impact each other’s skin microbiota
Authors: Wetzels Stefanie Urimare , Strachan Cameron R. , Conrady Beate , Wagner Martin , Burgener Iwan Anton , Virányi Zsófia , Selberherr Evelyne 
Published: August 2021

AbstractIn contrast to humans and dogs, the skin microbiota of wolves is yet to be described. Here, we investigated the skin microbiota of dogs and wolves kept in outdoor packs at the Wolf Science Center (WSC) via 16S rRNA gene amplicon sequencing. Skin swab samples were also collected from human care takers and their pet dogs. When comparing the three canine groups, representing different degrees of human contact to the care takers and each other, the pet dogs showed the highest level of diversity. Additionally, while human skin was dominated by a few abundant phylotypes, the skin microbiota of the care takers who had particularly close contact with the WSC animals was more similar to the microbiota of dogs and wolves compared to the humans who had less contact with these animals. Our results suggest that domestication may have an impact on the diversity of the skin microbiota, and that the canine skin microbiota can be shared with humans, depending on the level of interaction.