bluuebunny/crossref_metadata_2025_split huggingface dataset:
A proximity biotinylation-based approach to identify protein-E3 ligase interactions induced by PROTACs and molecular glues
Authors: Yamanaka Satoshi , Horiuchi Yuto , Matsuoka Saya , Kido Kohki , Nishino Kohei , Maeno Mayaka , Shibata Norio , Kosako Hidetaka , Sawasaki Tatsuya 
Published: January 2022

AbstractProteolysis-targeting chimaeras (PROTACs) as well as molecular glues such as immunomodulatory drugs (IMiDs) and indisulam are drugs that induce interactions between substrate proteins and an E3 ubiquitin ligases for targeted protein degradation. Here, we develop a workflow based on proximity-dependent biotinylation by AirID to identify drug-induced neo-substrates of the E3 ligase cereblon (CRBN). Using AirID-CRBN, we detect IMiD-dependent biotinylation of CRBN neo-substrates in vitro and identify biotinylated peptides of well-known neo-substrates by mass spectrometry with high specificity and selectivity. Additional analyses reveal ZMYM2 and ZMYM2-FGFR1 fusion protein—responsible for the 8p11 syndrome involved in acute myeloid leukaemia—as CRBN neo-substrates. Furthermore, AirID-DCAF15 and AirID-CRBN biotinylate neo-substrates targeted by indisulam and PROTACs, respectively, suggesting that this approach has the potential to serve as a general strategy for characterizing drug-inducible protein–protein interactions in cells.
Alloy information helps prioritize material criticality lists
Authors: Graedel T. E. , Reck Barbara K. , Miatto Alessio 
Published: January 2022

AbstractMaterials scientists employ metals and alloys that involve most of the periodic table. Nonetheless, materials scientists rarely take material criticality and reuse potential into account. In this work, we expand upon lists of “critical materials” generated by national and regional governments by showing that many materials are employed predominantly as alloying elements, which can be a deterrent to recovery and reuse at end of product life and, likely as a consequence, have low functional end-of-life recycling rates, among other problematic characteristics. We thereby single out six metals for enhanced concern: dysprosium, samarium, vanadium, niobium, tellurium, and gallium. From that perspective, the use of critical metals in low concentrations in alloys unlikely to be routinely recycled should be avoided if possible. If not, provision should be made for better identification and more efficient recycling so that materials designated as critical can have increased potential for more than a single functional use.
Targeted editing and evolution of engineered ribosomes in vivo by filtered editing
Authors: Radford Felix , Elliott Shane D. , Schepartz Alanna , Isaacs Farren J. 
Published: January 2022

AbstractGenome editing technologies introduce targeted chromosomal modifications in organisms yet are constrained by the inability to selectively modify repetitive genetic elements. Here we describe filtered editing, a genome editing method that embeds group 1 self-splicing introns into repetitive genetic elements to construct unique genetic addresses that can be selectively modified. We introduce intron-containing ribosomes into the E. coli genome and perform targeted modifications of these ribosomes using CRISPR/Cas9 and multiplex automated genome engineering. Self-splicing of introns post-transcription yields scarless RNA molecules, generating a complex library of targeted combinatorial variants. We use filtered editing to co-evolve the 16S rRNA to tune the ribosome’s translational efficiency and the 23S rRNA to isolate antibiotic-resistant ribosome variants without interfering with native translation. This work sets the stage to engineer mutant ribosomes that polymerize abiological monomers with diverse chemistries and expands the scope of genome engineering for precise editing and evolution of repetitive DNA sequences.
Suppressing electrolyte-lithium metal reactivity via Li+-desolvation in uniform nano-porous separator
Authors: Sheng Li , Wang Qianqian , Liu Xiang , Cui Hao , Wang Xiaolin , Xu Yulong , Li Zonglong , Wang Li , Chen Zonghai , Xu Gui-Liang , Wang Jianlong , Tang Yaping , Amine Khalil , Xu Hong , He Xiangming 
Published: January 2022

AbstractLithium reactivity with electrolytes leads to their continuous consumption and dendrite growth, which constitute major obstacles to harnessing the tremendous energy of lithium-metal anode in a reversible manner. Considerable attention has been focused on inhibiting dendrite via interface and electrolyte engineering, while admitting electrolyte-lithium metal reactivity as a thermodynamic inevitability. Here, we report the effective suppression of such reactivity through a nano-porous separator. Calculation assisted by diversified characterizations reveals that the separator partially desolvates Li+ in confinement created by its uniform nanopores, and deactivates solvents for electrochemical reduction before Li0-deposition occurs. The consequence of such deactivation is realizing dendrite-free lithium-metal electrode, which even retaining its metallic lustre after long-term cycling in both Li-symmetric cell and high-voltage Li-metal battery with LiNi0.6Mn0.2Co0.2O2 as cathode. The discovery that a nano-structured separator alters both bulk and interfacial behaviors of electrolytes points us toward a new direction to harness lithium-metal as the most promising anode.
Alteration of ribosome function upon 5-fluorouracil treatment favors cancer cell drug-tolerance
Authors: Therizols Gabriel , Bash-Imam Zeina , Panthu Baptiste , Machon Christelle , Vincent Anne , Ripoll Julie , Nait-Slimane Sophie , Chalabi-Dchar Mounira , Gaucherot Angéline , Garcia Maxime , Laforêts Florian , Marcel Virginie , Boubaker-Vitre Jihane , Monet Marie-Ambre , Bouclier Céline , Vanbelle Christophe , Souahlia Guillaume , Berthel Elise , Albaret Marie Alexandra , Mertani Hichem C. , Prudhomme Michel , Bertrand Martin , David Alexandre , Saurin Jean-Christophe , Bouvet Philippe , Rivals Eric , Ohlmann Théophile , Guitton Jérôme , Dalla Venezia Nicole , Pannequin Julie , Catez Frédéric , Diaz Jean-Jacques 
Published: January 2022

AbstractMechanisms of drug-tolerance remain poorly understood and have been linked to genomic but also to non-genomic processes. 5-fluorouracil (5-FU), the most widely used chemotherapy in oncology is associated with resistance. While prescribed as an inhibitor of DNA replication, 5-FU alters all RNA pathways. Here, we show that 5-FU treatment leads to the production of fluorinated ribosomes exhibiting altered translational activities. 5-FU is incorporated into ribosomal RNAs of mature ribosomes in cancer cell lines, colorectal xenografts, and human tumors. Fluorinated ribosomes appear to be functional, yet, they display a selective translational activity towards mRNAs depending on the nature of their 5′-untranslated region. As a result, we find that sustained translation ofIGF-1RmRNA, which encodes one of the most potent cell survival effectors, promotes the survival of 5-FU-treated colorectal cancer cells. Altogether, our results demonstrate that “man-made” fluorinated ribosomes favor the drug-tolerant cellular phenotype by promoting translation of survival genes.
Nutrient supply controls the linkage between species abundance and ecological interactions in marine bacterial communities
Authors: Dai Tianjiao , Wen Donghui , Bates Colin T. , Wu Linwei , Guo Xue , Liu Suo , Su Yifan , Lei Jiesi , Zhou Jizhong , Yang Yunfeng 
Published: January 2022

AbstractNutrient scarcity is pervasive for natural microbial communities, affecting species reproduction and co-existence. However, it remains unclear whether there are general rules of how microbial species abundances are shaped by biotic and abiotic factors. Here we show that the ribosomal RNA gene operon (rrn) copy number, a genomic trait related to bacterial growth rate and nutrient demand, decreases from the abundant to the rare biosphere in the nutrient-rich coastal sediment but exhibits the opposite pattern in the nutrient-scarce pelagic zone of the global ocean. Both patterns are underlain by positive correlations between community-level rrn copy number and nutrients. Furthermore, inter-species co-exclusion inferred by negative network associations is observed more in coastal sediment than in ocean water samples. Nutrient manipulation experiments yield effects of nutrient availability on rrn copy numbers and network associations that are consistent with our field observations. Based on these results, we propose a “hunger games” hypothesis to define microbial species abundance rules using the rrn copy number, ecological interaction, and nutrient availability.
Cooperation in a fluid swarm of fuel-free micro-swimmers
Authors: Ben Zion Matan Yah , Caba Yaelin , Modin Alvin , Chaikin Paul M. 
Published: January 2022

AbstractWhile motile bacteria display rich dynamics in dense colonies, the phoretic nature of artificial micro-swimmers restricts their activity when crowded. Here we introduce a new class of synthetic micro-swimmers that are driven solely by light. By coupling a light absorbing particle to a fluid droplet we produce a colloidal chimera that transforms optical power into propulsive thermo-capillary action. The swimmers’ internal drive allows them to operate for a long duration (days) and remain active when crowded, forming a high density fluid phase. We find that above a critical concentration, swimmers form a long lived crowded state that displays internal dynamics. When passive particles are introduced, the dense swimmer phase can re-arrange to spontaneously corral the passive particles. We derive a geometrical, depletion-like condition for corralling by identifying the role the passive particles play in controlling the effective concentration of the micro-swimmers.
Shortcuts to adiabaticity for open systems in circuit quantum electrodynamics
Authors: Yin Zelong , Li Chunzhen , Allcock Jonathan , Zheng Yicong , Gu Xiu , Dai Maochun , Zhang Shengyu , An Shuoming 
Published: January 2022

AbstractShortcuts to adiabaticity are powerful quantum control methods, allowing quick evolution into target states of otherwise slow adiabatic dynamics. Such methods have widespread applications in quantum technologies, and various shortcuts to adiabaticity protocols have been demonstrated in closed systems. However, realizing shortcuts to adiabaticity for open quantum systems has presented a challenge due to the complex controls in existing proposals. Here, we present the experimental demonstration of shortcuts to adiabaticity for open quantum systems, using a superconducting circuit quantum electrodynamics system. By applying a counterdiabatic driving pulse, we reduce the adiabatic evolution time of a single lossy mode from 800 ns to 100 ns. In addition, we propose and implement an optimal control protocol to achieve fast and qubit-unconditional equilibrium of multiple lossy modes. Our results pave the way for precise time-domain control of open quantum systems and have potential applications in designing fast open-system protocols of physical and interdisciplinary interest, such as accelerating bioengineering and chemical reaction dynamics.
Identifying optimal cycles in quantum thermal machines with reinforcement-learning
Authors: Erdman Paolo A. , Noé Frank 
Published: January 2022

AbstractThe optimal control of open quantum systems is a challenging task but has a key role in improving existing quantum information processing technologies. We introduce a general framework based on reinforcement learning to discover optimal thermodynamic cycles that maximize the power of out-of-equilibrium quantum heat engines and refrigerators. We apply our method, based on the soft actor-critic algorithm, to three systems: a benchmark two-level system heat engine, where we find the optimal known cycle; an experimentally realistic refrigerator based on a superconducting qubit that generates coherence, where we find a non-intuitive control sequence that outperforms previous cycles proposed in literature; a heat engine based on a quantum harmonic oscillator, where we find a cycle with an elaborate structure that outperforms the optimized Otto cycle. We then evaluate the corresponding efficiency at maximum power.
Esophageal regeneration following surgical implantation of a tissue engineered esophageal implant in a pediatric model
Authors: Sundaram Sumati , Jensen Todd , Roffidal Tina , Paquin Karissa , Wanczyk Heather , Cockman Michael D. , Shadman Shawyon , Finck Christine , Fodor William 
Published: January 2022

AbstractDiseases of the esophagus, damage of the esophagus due to injury or congenital defects during fetal esophageal development, i.e., esophageal atresia (EA), typically require surgical intervention to restore esophageal continuity. The development of tissue engineered tubular structures would improve the treatment options for these conditions by providing an alternative that is organ sparing and can be manufactured to fit the exact dimensions of the defect. An autologous tissue engineered Cellspan Esophageal ImplantTM (CEI) was surgically implanted into piglets that underwent surgical resection of the esophagus. Multiple survival time points, post-implantation, were analyzed histologically to understand the tissue architecture and time course of the regeneration process. In addition, we investigated CT imaging as an “in-life” monitoring protocol to assess tissue regeneration. We also utilized a clinically relevant animal management paradigm that was essential for long term survival. Following implantation, CT imaging revealed early tissue deposition and the formation of a contiguous tissue conduit. Endoscopic evaluation at multiple time points revealed complete epithelialization of the lumenal surface by day 90. Histologic evaluation at several necropsy time points, post-implantation, determined the time course of tissue regeneration and demonstrated that the tissue continues to remodel over the course of a 1-year survival time period, resulting in the development of esophageal structural features, including the mucosal epithelium, muscularis mucosae, lamina propria, as well as smooth muscle proliferation/migration initiating the formation of a laminated adventitia. Long term survival (1 year) demonstrated restoration of oral nutrition, normal animal growth and the overall safety of this treatment regimen.
Passive transfer of Ad26.COV2.S-elicited IgG from humans attenuates SARS-CoV-2 disease in hamsters
Authors: Tostanoski Lisa H. , Chandrashekar Abishek , Patel Shivani , Yu Jingyou , Jacob-Dolan Catherine , Chang Aiquan , Powers Olivia C. , Sellers Daniel , Gardner Sarah , Barrett Julia , Sanborn Owen , Stephenson Kathryn E. , Ansel Jessica L. , Jaegle Kate , Seaman Michael S. , Porto Maciel , Lok Megan , Spence Brittany , Cayer Kathleen , Nase Danielle , Holman Shaikim , Bradette Heath , Kar Swagata , Andersen Hanne , Lewis Mark G. , Cox Freek , Tolboom Jeroen T. B. M. , de Groot Anne Marit , Heerwegh Dirk , Le Gars Mathieu , Sadoff Jerald , Wegmann Frank , Zahn Roland C. , Schuitemaker Hanneke , Barouch Dan H. 
Published: January 2022

AbstractSARS-CoV-2 Spike-specific binding and neutralizing antibodies, elicited either by natural infection or vaccination, have emerged as potential correlates of protection. An important question, however, is whether vaccine-elicited antibodies in humans provide direct, functional protection from SARS-CoV-2 infection and disease. In this study, we explored directly the protective efficacy of human antibodies elicited by Ad26.COV2.S vaccination by adoptive transfer studies. IgG from plasma of Ad26.COV2.S vaccinated individuals was purified and transferred into naïve golden Syrian hamster recipients, followed by intra-nasal challenge of the hamsters with SARS-CoV-2. IgG purified from Ad26.COV2.S-vaccinated individuals provided dose-dependent protection in the recipient hamsters from weight loss following challenge. In contrast, IgG purified from placebo recipients provided no protection in this adoptive transfer model. Attenuation of weight loss correlated with binding and neutralizing antibody titers of the passively transferred IgG. This study suggests that Ad26.COV2.S-elicited antibodies in humans are mechanistically involved in protection against SARS-CoV-2.
Ciliary beating patterns map onto a low-dimensional behavioural space
Authors: Geyer Veikko F. , Howard Jonathon , Sartori Pablo 
Published: January 2022

AbstractBiological systems are robust to perturbations at both the genetic and environmental levels, although these same perturbations can elicit variation in behaviour. The interplay between functional robustness and behavioural variability is exemplified at the organellar level by the beating of cilia and flagella. Cilia are motile despite wide genetic diversity between and within species, differences in intracellular concentrations of ATP and calcium, and considerable environment fluctuations in temperature and viscosity. At the same time, these perturbations result in a variety of spatio-temporal patterns that span a rich behavioural space. To investigate this behavioural space we analysed the dynamics of isolated cilia from the unicellular algae Chlamydomonas reinhardtii under many different environmental and genetic conditions. We found that, despite large changes in beat frequency and amplitude, the space of waveform shapes is low-dimensional in the sense that two features account for 80% of the observed variation. The geometry of this behavioural space accords with the predictions of a simple mechanochemical model in the low-viscosity regime. This allowed us to associate waveform shape variability with changes in only the curvature response coefficients of the dynein motors.
Delivery of affordable and scalable encapsulated allogenic/autologous mesenchymal stem cells in coagulated platelet poor plasma for dental pulp regeneration
Authors: Angelopoulos Ioannis , Trigo Cesar , Ortuzar Maria-Ignacia , Cuenca Jimena , Brizuela Claudia , Khoury Maroun 
Published: January 2022

AbstractThe main goal of regenerative endodontics procedures (REPs) is to revitalize teeth by the regeneration of healthy dental pulp. In this study, we evaluated the potential of combining a natural and accessible biomaterial based on Platelet Poor Plasma (PPP) as a support for dental pulp stem cells (DPSC) and umbilical cord mesenchymal stem cells (UC-MSC). A comparison study between the two cell sources revealed compatibility with the PPP based scaffold with differences noted in the proliferation and angiogenic properties in vitro. Additionally, the release of growth factors including VEGF, HGF and DMP-1, was detected in the media of cultured PPP and was enhanced by the presence of the encapsulated MSCs. Dentin-Discs from human molars were filled with PPP alone or with MSCs and implanted subcutaneously for 4 weeks in mice. Histological analysis of the MSC-PPP implants revealed a newly formed dentin-like structure evidenced by the expression of Dentin sialophosphoprotein (DSPP). Finally, DPSC induced more vessel formation around the dental discs. This study provides evidence of a cost-effective, xenofree scaffold that is compatible with either autologous or allogenic strategy for dental pulp regeneration. This attempt if successfully implemented, could make REPs treatment widely accessible, contributing in improving global health conditions.
Water availability, bedrock, disturbance by herbivores, and climate determine plant diversity in South-African savanna
Authors: Hejda Martin , Čuda Jan , Pyšková Klára , Zambatis Guin , Foxcroft Llewellyn C. , MacFadyen Sandra , Storch David , Tropek Robert , Pyšek Petr 
Published: January 2022

AbstractTo identify factors that drive plant species richness in South-African savanna and explore their relative importance, we sampled plant communities across habitats differing in water availability, disturbance, and bedrock, using the Kruger National Park as a model system. We made plant inventories in 60 plots of 50 × 50 m, located in three distinct habitats: (i) at perennial rivers, (ii) at seasonal rivers with water available only during the rainy season, and (iii) on crests, at least ~ 5 km away from any water source. We predicted that large herbivores would utilise seasonal rivers’ habitats less intensely than those along perennial rivers where water is available throughout the year, including dry periods. Plots on granite harboured more herbaceous and shrub species than plots on basalt. The dry crests were poorer in herb species than both seasonal and perennial rivers. Seasonal rivers harboured the highest numbers of shrub species, in accordance with the prediction of the highest species richness at relatively low levels of disturbance and low stress from the lack of water. The crests, exposed to relatively low pressure from grazing but stressed by the lack of water, are important from the conservation perspective because they harbour typical, sometimes rare savanna species, and so are seasonal rivers whose shrub richness is stimulated and maintained by the combination of moderate disturbance imposed by herbivores and position in the middle of the water availability gradient. To capture the complexity of determinants of species richness in KNP, we complemented the analysis of the above local factors by exploring large-scale factors related to climate, vegetation productivity, the character of dominant vegetation, and landscape features. The strongest factor was temperature; areas with the highest temperatures reveal lower species richness. Our results also suggest thatColophospermum mopane, a dominant woody species in the north of KNP is not the ultimate cause of the lower plant diversity in this part of the park.
Acoustic-level and language-specific processing of native and non-native phonological sequence onsets in the low gamma and theta-frequency bands
Authors: Wagner Monica , Ortiz-Mantilla Silvia , Rusiniak Mateusz , Benasich April A. , Shafer Valerie L. , Steinschneider Mitchell 
Published: January 2022

AbstractAcoustic structures associated with native-language phonological sequences are enhanced within auditory pathways for perception, although the underlying mechanisms are not well understood. To elucidate processes that facilitate perception, time–frequency (T–F) analyses of EEGs obtained from native speakers of English and Polish were conducted. Participants listened to same and different nonword pairs within counterbalanced attend and passive conditions. Nonwords contained the onsets /pt/, /pət/, /st/, and /sət/ that occur in both the Polish and English languages with the exception of /pt/, which never occurs in the English language in word onset. Measures of spectral power and inter-trial phase locking (ITPL) in the low gamma (LG) and theta-frequency bands were analyzed from two bilateral, auditory source-level channels, created through source localization modeling. Results revealed significantly larger spectral power in LG for the English listeners to the unfamiliar /pt/ onsets from the right hemisphere at early cortical stages, during the passive condition. Further, ITPL values revealed distinctive responses in high and low-theta to acoustic characteristics of the onsets, which were modulated by language exposure. These findings, language-specific processing in LG and acoustic-level and language-specific processing in theta, support the view that multi scale temporal processing in the LG and theta-frequency bands facilitates speech perception.