bluuebunny/crossref_metadata_2025_split huggingface dataset:
Feeding climate and biodiversity goals with novel plant-based meat and milk alternatives
Authors: Kozicka Marta , Havlík Petr , Valin Hugo , Wollenberg Eva , Deppermann Andre , Leclère David , Lauri Pekka , Moses Rebekah , Boere Esther , Frank Stefan , Davis Chris , Park Esther , Gurwick Noel 
Published: September 2023

AbstractPlant-based animal product alternatives are increasingly promoted to achieve more sustainable diets. Here, we use a global economic land use model to assess the food system-wide impacts of a global dietary shift towards these alternatives. We find a substantial reduction in the global environmental impacts by 2050 if globally 50% of the main animal products (pork, chicken, beef and milk) are substituted—net reduction of forest and natural land is almost fully halted and agriculture and land use GHG emissions decline by 31% in 2050 compared to 2020. If spared agricultural land within forest ecosystems is restored to forest, climate benefits could double, reaching 92% of the previously estimated land sector mitigation potential. Furthermore, the restored area could contribute to 13-25% of the estimated global land restoration needs under target 2 from the Kunming Montreal Global Biodiversity Framework by 2030, and future declines in ecosystem integrity by 2050 would be more than halved. The distribution of these impacts varies across regions—the main impacts on agricultural input use are in China and on environmental outcomes in Sub-Saharan Africa and South America. While beef replacement provides the largest impacts, substituting multiple products is synergistic.
Membrane manipulation by free fatty acids improves microbial plant polyphenol synthesis
Authors: Tharmasothirajan Apilaasha , Melcr Josef , Linney John , Gensch Thomas , Krumbach Karin , Ernst Karla Marlen , Brasnett Christopher , Poggi Paola , Pitt Andrew R. , Goddard Alan D. , Chatgilialoglu Alexandros , Marrink Siewert J. , Marienhagen Jan 
Published: September 2023

AbstractMicrobial synthesis of nutraceutically and pharmaceutically interesting plant polyphenols represents a more environmentally friendly alternative to chemical synthesis or plant extraction. However, most polyphenols are cytotoxic for microorganisms as they are believed to negatively affect cell integrity and transport processes. To increase the production performance of engineered cell factories, strategies have to be developed to mitigate these detrimental effects. Here, we examine the accumulation of the stilbenoid resveratrol in the cell membrane and cell wall during its production using Corynebacterium glutamicum and uncover the membrane rigidifying effect of this stilbenoid experimentally and with molecular dynamics simulations. A screen of free fatty acid supplements identifies palmitelaidic acid and linoleic acid as suitable additives to attenuate resveratrol’s cytotoxic effects resulting in a three-fold higher product titer. This cost-effective approach to counteract membrane-damaging effects of product accumulation is transferable to the microbial production of other polyphenols and may represent an engineering target for other membrane-active bioproducts.
Non-invasive assessment of normal and impaired iron homeostasis in the brain
Authors: Filo Shir , Shaharabani Rona , Bar Hanin Daniel , Adam Miriam , Ben-David Eliel , Schoffman Hanan , Margalit Nevo , Habib Naomi , Shahar Tal , Mezer Aviv A. 
Published: September 2023

AbstractStrict iron regulation is essential for normal brain function. The iron homeostasis, determined by the milieu of available iron compounds, is impaired in aging, neurodegenerative diseases and cancer. However, non-invasive assessment of different molecular iron environments implicating brain tissue’s iron homeostasis remains a challenge. We present a magnetic resonance imaging (MRI) technology sensitive to the iron homeostasis of the living brain (the r1-r2* relaxivity). In vitro, our MRI approach reveals the distinct paramagnetic properties of ferritin, transferrin and ferrous iron ions. In the in vivo human brain, we validate our approach against ex vivo iron compounds quantification and gene expression. Our approach varies with the iron mobilization capacity across brain regions and in aging. It reveals brain tumors’ iron homeostasis, and enhances the distinction between tumor tissue and non-pathological tissue without contrast agents. Therefore, our approach may allow for non-invasive research and diagnosis of iron homeostasis in living human brains.
Directed exciton transport highways in organic semiconductors
Authors: Müller Kai , Schellhammer Karl S. , Gräßler Nico , Debnath Bipasha , Liu Fupin , Krupskaya Yulia , Leo Karl , Knupfer Martin , Ortmann Frank 
Published: September 2023

AbstractExciton bandwidths and exciton transport are difficult to control by material design. We showcase the intriguing excitonic properties in an organic semiconductor material with specifically tailored functional groups, in which extremely broad exciton bands in the near-infrared-visible part of the electromagnetic spectrum are observed by electron energy loss spectroscopy and theoretically explained by a close contact between tightly packing molecules and by their strong interactions. This is induced by the donor–acceptor type molecular structure and its resulting crystal packing, which induces a remarkable anisotropy that should lead to a strongly directed transport of excitons. The observations and detailed understanding of the results yield blueprints for the design of molecular structures in which similar molecular features might be used to further explore the tunability of excitonic bands and pave a way for organic materials with strongly enhanced transport and built-in control of the propagation direction.
A nanoscale MOF-based heterogeneous catalytic system for the polymerization of N-carboxyanhydrides enables direct routes toward both polypeptides and related hybrid materials
Authors: Liu Ying , Ren Zhongwu , Zhang Nannan , Yang Xiaoxin , Wu Qihua , Cheng Zehong , Xing Hang , Bai Yugang 
Published: September 2023

AbstractSynthetic polypeptides have emerged as versatile tools in both materials science and biomedical engineering due to their tunable properties and biodegradability. While the advancements of N-carboxyanhydride (NCA) ring-opening polymerization (ROP) techniques have aimed to expedite polymerization and reduce environment sensitivity, the broader implications of such methods remain underexplored, and the integration of ROP products with other materials remains a challenge. Here, we show an approach inspired by the success of many heterogeneous catalysts, using nanoscale metal-organic frameworks (MOFs) as co-catalysts for NCA-ROP accelerated also by peptide helices in proximity. This heterogeneous approach offers multiple advantages, including fast kinetics, low environment sensitivity, catalyst recyclability, and seamless integration with hybrid materials preparation. The catalytic system not only streamlines the preparation of polypeptides and polypeptide-coated MOF complexes (MOF@polypeptide hybrids) but also preserves and enhances their homogeneity, processibility, and overall functionalities inherited from the constituting MOFs and polypeptides.
Phage-microbe dynamics after sterile faecal filtrate transplantation in individuals with metabolic syndrome: a double-blind, randomised, placebo-controlled clinical trial assessing efficacy and safety
Authors: Wortelboer Koen , de Jonge Patrick A. , Scheithauer Torsten P. M. , Attaye Ilias , Kemper E. Marleen , Nieuwdorp Max , Herrema Hilde 
Published: September 2023

AbstractBacteriophages (phages) are bacterial viruses that have been shown to shape microbial communities. Previous studies have shown that faecal virome transplantation can decrease weight gain and normalize blood glucose tolerance in diet-induced obese mice. Therefore, we performed a double-blind, randomised, placebo-controlled pilot study in which 24 individuals with metabolic syndrome were randomised to a faecal filtrate transplantation (FFT) from a lean healthy donor (n = 12) or placebo (n = 12). The primary outcome, change in glucose metabolism, and secondary outcomes, safety and longitudinal changes within the intestinal bacteriome and phageome, were assessed from baseline up to 28 days. All 24 included subjects completed the study and are included in the analyses. While the overall changes in glucose metabolism are not significantly different between both groups, the FFT is well-tolerated and without any serious adverse events. The phage virion composition is significantly altered two days after FFT as compared to placebo, which coincides with more virulent phage-microbe interactions. In conclusion, we provide evidence that gut phages can be safely administered to transiently alter the gut microbiota of recipients.
Langerhans cells shape postnatal oral homeostasis in a mechanical-force-dependent but microbiota and IL17-independent manner
Authors: Jaber Yasmin , Netanely Yasmine , Naamneh Reem , Saar Or , Zubeidat Khaled , Saba Yasmin , Georgiev Olga , Kles Paz , Barel Or , Horev Yael , Yosef Omri , Eli-Berchoer Luba , Nadler Chen , Betser-Cohen Gili , Shapiro Hagit , Elinav Eran , Wilensky Asaf , Hovav Avi-Hai 
Published: September 2023

AbstractThe postnatal interaction between microbiota and the immune system establishes lifelong homeostasis at mucosal epithelial barriers, however, the barrier-specific physiological activities that drive the equilibrium are hardly known. During weaning, the oral epithelium, which is monitored by Langerhans cells (LC), is challenged by the development of a microbial plaque and the initiation of masticatory forces capable of damaging the epithelium. Here we show that microbial colonization following birth facilitates the differentiation of oral LCs, setting the stage for the weaning period, in which adaptive immunity develops. Despite the presence of the challenging microbial plaque, LCs mainly respond to masticatory mechanical forces, inducing adaptive immunity, to maintain epithelial integrity that is also associated with naturally occurring alveolar bone loss. Mechanistically, masticatory forces induce the migration of LCs to the lymph nodes, and in return, LCs support the development of immunity to maintain epithelial integrity in a microbiota-independent manner. Unlike in adult life, this bone loss is IL-17-independent, suggesting that the establishment of oral mucosal homeostasis after birth and its maintenance in adult life involve distinct mechanisms.
SHIELD: a platform for high-throughput screening of barrier-type DNA elements in human cells
Authors: Zhang Meng , Ehmann Mary Elisabeth , Matukumalli Srija , Boob Aashutosh Girish , Gilbert David M. , Zhao Huimin 
Published: September 2023

AbstractChromatin boundary elements contribute to the partitioning of mammalian genomes into topological domains to regulate gene expression. Certain boundary elements are adopted as DNA insulators for safe and stable transgene expression in mammalian cells. These elements, however, are ill-defined and less characterized in the non-coding genome, partially due to the lack of a platform to readily evaluate boundary-associated activities of putative DNA sequences. Here we report SHIELD (Site-specific Heterochromatin Insertion of Elements at Lamina-associated Domains), a platform tailored for the high-throughput screening of barrier-type DNA elements in human cells. SHIELD takes advantage of the high specificity of serine integrase at heterochromatin, and exploits the natural heterochromatin spreading inside lamina-associated domains (LADs) for the discovery of potent barrier elements. We adopt SHIELD to evaluate the barrier activity of 1000 DNA elements in a high-throughput manner and identify 8 candidates with barrier activities comparable to the core region of cHS4 element in human HCT116 cells. We anticipate SHIELD could facilitate the discovery of novel barrier DNA elements from the non-coding genome in human cells.
Quantum computation of reactions on surfaces using local embedding
Authors: Gujarati Tanvi P. , Motta Mario , Friedhoff Triet Nguyen , Rice Julia E. , Nguyen Nam , Barkoutsos Panagiotis Kl. , Thompson Richard J. , Smith Tyler , Kagele Marna , Brei Mark , Jones Barbara A. , Williams Kristen 
Published: September 2023

AbstractModeling electronic systems is an important application for quantum computers. In the context of materials science, an important open problem is the computational description of chemical reactions on surfaces. In this work, we outline a workflow to model the adsorption and reaction of molecules on surfaces using quantum computing algorithms. We develop and compare two local embedding methods for the systematic determination of active spaces. These methods are automated and based on the physics of molecule-surface interactions and yield systematically improvable active spaces. Furthermore, to reduce the quantum resources required for the simulation of the selected active spaces using quantum algorithms, we introduce a technique for exact and automated circuit simplification. This technique is applicable to a broad class of quantum circuits and critical to enable demonstration on near-term quantum devices. We apply the proposed combination of active-space selection and circuit simplification to the dissociation of water on a magnesium surface using classical simulators and quantum hardware. Our study identifies reactions of molecules on surfaces, in conjunction with the proposed algorithmic workflow, as a promising research direction in the field of quantum computing applied to materials science.
Counterfactual communication without a trace in the transmission channel
Authors: Pan Wei-Wei , Liu Xiao , Xu Xiao-Ye , Wang Qin-Qin , Cheng Ze-Di , Wang Jian , Liu Zhao-Di , Chen Geng , Zhou Zong-Quan , Li Chuan-Feng , Guo Guang-Can , Dressel Justin , Vaidman Lev 
Published: September 2023

AbstractWe report an experimental realization of a modified counterfactual communication protocol that eliminates the dominant environmental trace left by photons passing through the transmission channel. Compared to Wheeler’s criterion for inferring past particle paths, as used in prior protocols, our trace criterion provides stronger support for the claim of the counterfactuality of the communication. We verify the lack of trace left by transmitted photons via tagging the propagation arms of an interferometric device by distinct frequency-shifts and finding that the collected photons have no frequency shift which corresponds to the transmission channel. As a proof of principle, we counterfactually transfer a quick response code image with sufficient fidelity to be scanned with a cell phone.
Open access dataset integrating EEG and fNIRS during Stroop tasks
Authors: Chen Zemeng , Gao Chenyang , Li Ting , Ji Xiang , Liu Shuyu , Xiao Ming 
Published: September 2023

AbstractConflict monitoring and processing are crucial components of the human cognitive system, with significant implications for daily life and the diagnosis of cognitive disorders. The Stroop task, combined with brain function detection technology, has been widely employed as a classical paradigm for investigating conflict processing. However, there remains a lack of public datasets that integrate Electroencephalogram (EEG) and functional Near-infrared Spectroscopy (fNIRS) to simultaneously record brain activity during a Stroop task. We introduce a dual-modality Stroop task dataset incorporating 34-channel EEG (sampling frequency is 1000 Hz) and 20-channel high temporal resolution fNIRS (sampling frequency is 100 Hz) measurements covering the whole frontal cerebral cortex from 21 participants (9 females/12 males, aged 23.0 ± 2.3 years). Event-related potential analysis of EEG recordings and activation analysis of fNIRS recordings were performed to show the significant Stroop effect. We expected that the data provided would be utilized to investigate multimodal data processing algorithms during cognitive processing.
Exploring the dynamics of viscoelastic adhesion in rough line contacts
Authors: Afferrante Luciano , Violano Guido , Carbone Giuseppe 
Published: September 2023

AbstractModeling the adhesion of viscoelastic rough surfaces is a recent challenge in contact mechanics. Existing models have primarily focused on simple systems with smooth topography or single roughness scale due to the co-action of roughness and viscoelasticity leading to elastic instabilities and rate-dependent behavior, resulting in complex adhesion dynamics. In this study, we propose a numerical model based on a finite element methodology to investigate the adhesion between a randomly rough profile and a viscoelastic half-plane. Approach-retraction simulations are performed under controlled displacement conditions of the rough indenter. The results demonstrate that viscous effects dampen the roughness-induced instabilities in both the approach and retraction phases. Interestingly, even when viscous effects are negligible, the pull-off stress, i.e., the maximum tensile stress required to detach the surfaces, is found to depend on the stiffness modulus and maximum load reached during the approach. Furthermore, when unloading is performed from a relaxed state of the viscoelastic half-plane, both adhesion hysteresis and pull-off stress are monotonic increasing functions of the speed. Conversely, when retraction begins from an unrelaxed state of the material, the maximum pull-off stress and hysteretic loss are obtained at intermediate velocities.
Bayesian framework for analyzing adsorption processes observed via time-resolved X-ray diffraction
Authors: Yokoyama Yuichi , Kawaguchi Shogo , Mizumaki Masaichiro 
Published: September 2023

AbstractClarifying dynamic processes of materials is an important research topic in materials science. Time-resolved X-ray diffraction is a powerful technique for probing dynamic processes. To understand the dynamics, it is essential to analyze time-series data using appropriate time-evolution models and accurate start times of dynamic processes. However, conventional analyses based on non-linear least-squares fitting have difficulty both evaluating time-evolution models and estimating start times. Here, we establish a Bayesian framework including time-evolution models. We investigate an adsorption process, which is a representative dynamic process, and extract information about the time-evolution model and adsorption start time. The information enables us to estimate adsorption properties such as rate constants more accurately, thus achieving more precise understanding of dynamic adsorption processes. Our framework is highly versatile, can be applied to other dynamic processes such as chemical reactions, and is expected to be utilized in various areas of materials science.
Construction of a novel circRNA-miRNA-ferroptosis related mRNA network in ischemic stroke
Authors: Xie Huirong , Huang Yijie , Zhan Yanli 
Published: September 2023

AbstractMolecule alterations are important to explore the pathological mechanism of ischemic stroke (IS). Ferroptosis, a newly recognized type of regulated cell death, is related to IS. Identification of the interactions between circular RNA (circRNA), microRNA (miRNA) and ferroptosis related mRNA may be useful to understand the molecular mechanism of IS. The circRNA, miRNA and mRNA transcriptome data in IS, downloaded from the Gene Expression Omnibus (GEO) database, was used for differential expression analysis. Ferroptosis related mRNAs were identified from the FerrDb database, followed by construction of circRNA-miRNA-ferroptosis related mRNA network. Enrichment and protein–protein interaction analysis of mRNAs in circRNA-miRNA-mRNA network was performed, followed by expression validation by reverse transcriptase polymerase chain reaction and online dataset. A total of 694, 41 and 104 differentially expressed circRNAs, miRNAs and mRNAs were respectively identified in IS. Among which, dual specificity phosphatase 1 (DUSP1), nuclear receptor coactivator 4 (NCOA4) and solute carrier family 2 member 3 (SLC2A3) were the only three up-regulated ferroptosis related mRNAs. Moreover, DUSP1, NCOA4 and SLC2A3 were significantly up-regulated in IS after 3, 5 and 24 h of the attack. Based on these three ferroptosis related mRNAs, 4 circRNA-miRNA-ferroptosis related mRNA regulatory relationship pairs were identified in IS, including hsa_circ_0071036/hsa_circ_0039365/hsa_circ_0079347/hsa_circ_0008857-hsa-miR-122-5p-DUSP1, hsa_circ_0067717/hsa_circ_0003956/hsa_circ_0013729-hsa-miR-4446-3p-SLC2A3, hsa_circ_0059347/hsa_circ_0001414/hsa_circ_0049637-hsa-miR-885-3p-SLC2A3, and hsa_circ_0005633/hsa_circ_0004479-hsa-miR-4435-NCOA4. In addition, DUSP1 is involved in the signaling pathway of fluid shear stress and atherosclerosis. Relationship of regulatory action between circRNAs, miRNAs and ferroptosis related mRNAs may be associated with the development of IS.
Klotho increases antioxidant defenses in astrocytes and ubiquitin–proteasome activity in neurons
Authors: Orellana Ana Maria , Mazucanti Caio Henrique , dos Anjos Leticia Pavan , de Sá Lima Larissa , Kawamoto Elisa Mitiko , Scavone Cristoforo 
Published: September 2023

AbstractKlotho is an antiaging protein, and its levels decline with age and chronic stress. The exogenous administration of Klotho can enhance cognitive performance in mice and negatively modulate the Insulin/IGF1/PI3K/AKT pathway in terms of metabolism. In humans, insulin sensitivity is a hallmark of healthy longevity. Therefore, this study aimed to determine if exogenous Klotho, when added to neuronal and astrocytic cell cultures, could reduce the phosphorylation levels of certain insulin signaling effectors and enhance antioxidant strategies in these cells. Primary cell cultures of cortical astrocytes and neurons from mice were exposed to 1 nM Klotho for 24 h, with or without glucose. Klotho decreased pAKT and mTOR levels. However, in astrocytes, Klotho increased FOXO-3a activity and catalase levels, shielding them from intermediate oxidative stress. In neurons, Klotho did not alter FOXO-3 phosphorylation levels but increased proteasome activity, maintaining lower levels of PFKFB3. This study offers new insights into the roles of Klotho in regulating energy metabolism and the redox state in the brain.