bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rationalizing the Influence of the Binding Affinity on the Activity of Phosphoserine Phosphatases
Authors: Chiba Yoko , Ooka Hideshi , Wintzer Marie E. , Tsunematsu Nao , Nogawa Toshihiko , Suzuki Takehiro , Dohmae Naoshi , Nakamura Ryuhei 
Published: February 2024

AbstractThe Sabatier principle states that catalytic activity can be maximized when the substrate binding affinity is neither too strong nor too weak. Recent studies have shown that the activity of several hydrolases is maximized at intermediate values of the binding affinity (Michaelis–Menten constant: Km). However, it remains unclear whether this concept of artificial catalysis is applicable to enzymes in general, especially for those which have evolved under different reaction environments. Herein, we show that the activity of phosphoserine phosphatase is also enhanced at an intermediate Km value of approximately 0.5 mM. Within our dataset, the variation of Km by three orders of magnitude accounted for a roughly 18‐fold variation in the activity. Owing to the high phylogenetic and physiological diversity of our dataset, our results support the importance of optimizing Km for enzymes in general. On the other hand, a 77‐fold variation in the activity was attributed to other physicochemical parameters, such as the Arrhenius prefactor of kcat, and could not be explained by the Sabatier principle. Therefore, while tuning the binding affinity according to the Sabatier principle is an important consideration, the Km value is only one of many physicochemical parameters which must be optimized to maximize enzymatic activity.
Engineering Anti‐CRISPR Proteins to Create CRISPR‐Cas Protein Switches for Activatable Genome Editing and Viral Protease Detection
Authors: Kang Wenyuan , Xiao Fei , Zhu Xi , Ling Xinyu , Xie Shiyi , Li Ruimiao , Yu Peihang , Cao Linxin , Lei Chunyang , Qiu Ye , Liu Tao , Nie Zhou 
Published: February 2024

AbstractProteins capable of switching between distinct active states in response to biochemical cues are ideal for sensing and controlling biological processes. Activatable CRISPR‐Cas systems are significant in precise genetic manipulation and sensitive molecular diagnostics, yet directly controlling Cas protein function remains challenging. Herein, we explore anti‐CRISPR (Acr) proteins as modules to create synthetic Cas protein switches (CasPSs) based on computational chemistry‐directed rational protein interface engineering. Guided by molecular fingerprint analysis, electrostatic potential mapping, and binding free energy calculations, we rationally engineer the molecular interaction interface between Cas12a and its cognate Acr proteins (AcrVA4 and AcrVA5) to generate a series of orthogonal protease‐responsive CasPSs. These CasPSs enable the conversion of specific proteolytic events into activation of Cas12a function with high switching ratios (up to 34.3‐fold). These advancements enable specific proteolysis‐inducible genome editing in mammalian cells and sensitive detection of viral protease activities during virus infection. This work provides a promising strategy for developing CRISPR‐Cas tools for controllable gene manipulation and regulation and clinical diagnostics.
A Vitrimer Acts as a Compatibilizer for Polyethylene and Polypropylene Blends
Authors: Yokoyama Kosuke , Guan Zhibin 
Published: February 2024

AbstractPolymer compatibilization plays a critical role in achieving polymer blends with favorable mechanical properties and enabling efficient recycling of mixed plastic wastes. Nonetheless, traditional compatibilization methods often require tailored designs based on the specific chemical compositions of the blends. In this study, we propose a new approach for compatibilizing polymer blends using a dynamically crosslinked polymer network, known as vitrimers. By adding a relatively small amount (1–5 w/w%) of a vitrimer made of siloxane‐crosslinked high‐density polyethylene (HDPE), we successfully compatibilized unmodified HDPE and isotactic polypropylene (iPP). The vitrimer‐compatibilized blend exhibited enhanced elongation at break (120 %) and smaller iPP domain sizes (0.4 μm) compared to the control blend (22 % elongation at break, 0.9 μm iPP droplet size). Moreover, the vitrimer‐compatibilized blend showed significantly improved microphase stability during annealing at 180 °C. This straightforward method shows promise for applications across various polymer blend systems.
RNA‐Templated Peptide Bond Formation Promotes L‐Homochirality
Authors: Węgrzyn Ewa , Mejdrová Ivana , Müller Felix M. , Nainytė Milda , Escobar Luis , Carell Thomas 
Published: February 2024

AbstractThe world in which we live is homochiral. The ribose units that form the backbone of DNA and RNA are all D‐configured and the encoded amino acids that comprise the proteins of all living species feature an all‐L‐configuration at the α‐carbon atoms. The homochirality of α‐amino acids is essential for folding of the peptides into well‐defined and functional 3D structures and the homochirality of D‐ribose is crucial for helix formation and base‐pairing. The question of why nature uses only encoded L‐α‐amino acids is not understood. Herein, we show that an RNA‐peptide world, in which peptides grow on RNAs constructed from D‐ribose, leads to the self‐selection of homo‐L‐peptides, which provides a possible explanation for the homo‐D‐ribose and homo‐L‐amino acid combination seen in nature.
Breaking Global Diatropic Current to Tame Diradicaloid Character: Thiele's Hydrocarbon Under Macrocyclic Constraints
Authors: Banachowicz Piotr , Das Mainak , Kruczała Krzysztof , Siczek Miłosz , Sojka Zbigniew , Kijewska Monika , Pawlicki Miłosz 
Published: February 2024

AbstractA diradical/biradical character of organic derivatives is one of the key aspects of contemporary research focusing on the fundamental studies followed by potential applicability relying on the unique optical, electronic, or magnetic properties assigned to unpaired electrons. A precise involvement of two p‐phenylenes into a cyclophane‐like conjugated, diatropic system creates a flexible molecule with the two different characters of both subunits (benzene and quinone) imprinting into the structure a Kekulé delocalized system. A dynamic of both carbocyclic subunits, and their mutual interaction generates a singlet open‐shell state (J=−1.25 kcal/mol) as documented spectroscopically (NMR and EPR). The extended theoretical analysis has proved a correlation between dihedral angle and the diradicaloid character that shifts from a closed‐shell singlet to an open‐shell state, eventually showing the y0=0.86 for 78 degrees and ΔEST=−0.34 kcal/mol.
Redox‐Regulated Synthetic Channels: Enabling Reversible Ion Transport by Modulating the Ion‐Permeation Pathway
Authors: Shi Linlin , Zhao Wen , Jiu Zhihui , Guo Jingjing , Zhu Qiuhui , Sun Yonghui , Zhu Bo , Chang Junbiao , Xin Pengyang 
Published: February 2024

AbstractNatural redox‐regulated channel proteins often utilize disulfide bonds as redox sensors for adaptive regulation of channel conformations in response to diverse physiological environments. In this study, we developed novel synthetic ion channels capable of reversibly switching their ion‐transport capabilities by incorporating multiple disulfide bonds into artificial systems. X‐ray structural analysis and electrophysiological experiments demonstrated that these disulfide‐bridged molecules possess well‐defined tubular cavities and can be efficiently inserted into lipid bilayers to form artificial ion channels. More importantly, the disulfide bonds in these molecules serve as redox‐tunable switches to regulate the formation and disruption of ion‐permeation pathways, thereby achieving a transition in the transmembrane transport process between the ON and OFF states.
Impact of water absorption on the creep performance of epoxy/microcrystalline cellulose composites
Authors: Lavoratti Alessandra , Bianchi Otávio , Cruz Joziel A. , Al‐Maqdasi Zainab , Varna Janis , Amico Sandro Campos , Joffe Roberts 
Published: February 2024

AbstractRecently, considerable effort has been made to study cellulose/epoxy composites. However, there is a gap when it comes to understanding the post‐conditioning anomalous effect of moisture uptake on their mechanical and dynamic‐mechanical properties, and on their creep behavior. In this work, up to 10.0 wt% microcrystalline cellulose (MCC) was incorporated into epoxy resin by simple mixing and sonication. Epoxy/MCC composites were fabricated by casting in rubber silicone molds, and rectangular and dog‐bone test specimens were produced. The moisture uptake, dynamic mechanical, chemical, tensile, and creep behavior were evaluated. The incorporation of MCC increased the water diffusion coefficient. The changes in storage modulus and glass transition temperature, combined with Fourier‐transform infrared spectroscopy analysis, evidenced that water sorption in epoxies causes both plasticization and additional resin crosslinking, although the latter is prevented by the addition of MCC. The creep strain of the composites increased by 60% after conditioning, indicating that plasticization induced by water sorption plays an important role in the long‐term properties of the composites.
CFD evaluation of hydrophobic feedstock bench‐scale fermenters for efficient high agitation volumetric mass transfer
Authors: Marx Richard , Liu Huolong , Yoon Seongkyu , Xie Dongming 
Published: February 2024

AbstractA new biomanufacturing platform combining intracellular metabolic engineering of the oleaginous yeast Yarrowia lipolytica and extracellular bioreaction engineering provides efficient bioconversion of plant oils/animal fats into high‐value products. However, predicting the hydrodynamics and mass transfer parameters is difficult due to the high agitation and sparging required to create dispersed oil droplets in an aqueous medium for efficient yeast fermentation. In the current study, commercial computational fluid dynamic (CFD) solver Ansys CFX coupled with the MUSIG model first predicts two‐phase system (oil/water and air/water) mixing dynamics and their particle size distributions. Then, a three‐phase model (oil, air, and water) utilizing dispersed air bubbles and a polydispersed oil phase was implemented to explore fermenter mixing, gas dispersion efficiency, and volumetric mass transfer coefficient estimations (kLa). The study analyzed the effect of the impeller type, agitation speed, and power input on the tank's flow field and revealed that upward‐pumping pitched blade impellers (PBI) in the top two positions (compared to Rushton‐type) provided advantageous oil phase homogeneity and similar estimated kLa values with reduced power. These results show good agreement with the experimental mixing and kLa data.
Engineering CREB‐activated promoters for adenosine‐induced gene expression
Authors: Cox John Robert , Fox Andrea , Lenahan Conor , Pivnik Liza , Manion Matthew , Blazeck John 
Published: February 2024

AbstractAccumulation of the ribonucleoside, adenosine (ADO), triggers a cAMP response element binding protein (CREB)‐mediated signaling pathway to suppress the function of immune cells in tumors. Here, we describe a collection of CREB‐activated promoters that allow for strong and tunable ADO‐induced gene expression in human cells. By optimizing number of CREB transcription factor binding sites and altering the core promoter region of CREB‐based hybrid promoters, we created synthetic constructs that drive gene expression to higher levels than strong, endogenous mammalian promoters in the presence of ADO. These synthetic promoters are induced up to 47‐fold by ADO, with minimal expression in their “off” state. We further determine that our CREB‐based promoters are activated by other compounds that act as signaling analogs, and that combinatorial addition of ADO and these compounds has a synergistic impact on gene expression. Surprisingly, we also detail how background ADO degradation caused by the common cell culture media additive, fetal bovine serum (FBS), confounds experiments designed to determine ADO dose‐responsiveness. We show that only after long‐term heat deactivation of FBS can our synthetic promoters enable gene expression induction at physiologically relevant levels of ADO. Finally, we demonstrate that the strength of a CREB‐based promoter is enhanced by incorporating other transcription factor binding sites.
Filtration of a multi‐serotype glycoconjugate vaccine drug product through sterilizing grade 0.2/0.22 µm pore size filters
Authors: Du Zhuoshi , Qiu Siyi , Gill Kanwal , Toprani Vishal , Zydney Andrew L. 
Published: February 2024

AbstractGlycoconjugate vaccines containing multiple serotypes of a bacterial capsular polysaccharide can provide strong immune protection against pathogenic infections. Sterile filtration is an important component of the fill and finish operations in the preparation of these vaccines, with the capacity of the sterile filter limited by membrane fouling. The objective of this study was to examine the performance of a range of commercial 0.2/0.22 µm nominal pore size sterilizing grade filters with both single‐layer and dual‐layer structures during filtration of a glycoconjugate vaccine drug product consisting of four polysaccharide serotypes. The highly asymmetric Millipore Express showed much higher capacity than the more homogeneous filters, with the support structure of the Express acting as a prefilter that was able to remove foulants thereby protecting the small pores in the size‐selective skin layer. This behavior was confirmed by performing experiments with different batch prefilters and by examining the location of foulant deposition within the sterile filters using confocal microscopy. These results provide important insights into the factors controlling fouling by these multiserotype vaccines as well as a framework for increasing the capacity of the sterile filter.
Removal of phenolic compounds from sugarcane syrup and impact on Saccharomyces cerevisiae fermentation for β‐farnesene production
Authors: Carvalho Luís Carlos , Oliveira Ana L. S. , Carsanba Erdem , Lopes Ana , Leal Tânia , Ribeiro Mónica , Fernandes Sara , Pintado Manuela , Oliveira Carla 
Published: February 2024

AbstractThis work aimed to study for the first time the effects of phenolic compounds from sugarcane syrup on Saccharomyces cerevisiae β‐farnesene fermentation by removing them from this feedstock. Syrup purification was optimized through a central composite design using five types of activated charcoal: three contact times (1–24 h) and three adsorbent concentrations (10–150 g L−1). The optimal purification condition—charcoal pellets at 115 g L−1 and contact time of 12.5 h—led to 96.7% of phenolic compounds removal and 43.7% of syrup recovery. The effects of reducing phenolic content from approximately 7.0–0.3 mg L−1 in sugarcane syrup on yeast fermentation varied with the scale. An increase in biomolecule productivity was only observed in shake‐flasks (11%) and in biomass productivity only in the 2 L bioreactor (12%). Thus, phenolic compounds from sugarcane syrup do not influence β‐farnesene production at a large scale under the conditions tested.
MCM2 is involved in subtyping and tamoxifen resistance of ERα‐positive breast cancer by acting as the downstream factor of ERα
Authors: Liu Sainan , Liang Zhuoshuai , Wang Yujian , Ren Yaxuan , Gu Yulu , Qiao Yichun , He Huan , Li Yong , Cheng Yi , Liu Yawen 
Published: February 2024

AbstractTamoxifen (TAM) resistance is finally developed in over 40% of patients with estrogen receptor α‐positive breast cancer (ERα+‐BC), documenting that discovering new molecular subtype is needed to confer perception to the heterogeneity of ERα+‐BC. We obtained representative gene sets subtyping ERα+‐BC using gene set variation analysis (GSVA), non‐negative matrix factorization (NMF), and COX regression methods on the basis of METABRIC, TCGA, and GEO databases. Furthermore, the risk score of ERα+‐BC subtyping was established using least absolute shrinkage and selection operator (LASSO) regression on the basis of genes in the representative gene sets, thereby generating the two subtypes of ERα+‐BC. We further found that minichromosome maintenance complex component 2 (MCM2) functioned as the hub gene subtyping ERα+‐BC using GO, KEGG, and MCODE. MCM2 expression was capable for specifically predicting 1‐year overall survival (OS) of ERα+‐BC and correlated with T stage, AJCC stage, and tamoxifen (TAM) sensitivity of ERα+‐BC. The downregulation of MCM2 expression inhibited proliferation, migration, and invasion of TAM‐resistant cells and promoted G0/G1 arrest. Altogether, tamoxifen resistance entails that MCM2 is a hub gene subtyping ERα+‐BC, providing a novel dimension for discovering a potential target of TAM‐resistant BC.
Targeting autophagy overcomes cancer‐intrinsic resistance to CAR‐T immunotherapy in B‐cell malignancies
Authors: Tang Lu , Zhang Huan , Zhou Fen , Wei Qiuzhe , Du Mengyi , Wu Jianghua , Li Chenggong , Luo Wenjing , Zhou Jie , Wang Xindi , Chen Zhaozhao , Zhang Yinqiang , Huang Zhongpei , Wu Zhuolin , Wen Yuxi , Jiang Huiwen , Liao Danying , Kou Haiming , Xiong Wei , Mei Heng , Hu Yu 
Published: February 2024

AbstractBackgroundChimeric antigen receptor T (CAR‐T) therapy has substantially revolutionized the clinical outcomes of patients with hematologic malignancies, but the cancer‐intrinsic mechanisms underlying resistance to CAR‐T cells remain yet to be fully understood. This study aims to explore the molecular determinants of cancer cell sensitivity to CAR‐T cell‐mediated killing and to provide a better understanding of the underlying mechanisms and potential modulation to improve clinical efficacy.MethodsThe human whole‐genome CRISPR/Cas9‐based knockout screening was conducted to identify key genes that enable cancer cells to evade CD19 CAR‐T‐cell‐mediated killing. The in vitro cytotoxicity assays and evaluation of tumor tissue and bone marrow specimens were further conducted to confirm the role of the key genes in cancer cell susceptibility to CAR‐T cells. In addition, the specific mechanisms influencing CAR‐T cell‐mediated cancer clearance were elucidated in mouse and cellular models.ResultsThe CRISPR/Cas9‐based knockout screening showed that the enrichment of autophagy‐related genes (ATG3, BECN1, and RB1CC1) provided protection of cancer cells from CD19 CAR‐T cell‐mediated cytotoxicity. These findings were further validated by in vitro cytotoxicity assays in cells with genetic and pharmacological inhibition of autophagy. Notably, higher expression of the three autophagy‐related proteins in tumor samples was correlated with poorer responsiveness and worse survival in patients with relapsed/refractory B‐cell lymphoma after CD19 CAR‐T therapy. Bulk RNA sequencing analysis of bone marrow samples from B‐cell leukemia patients also suggested the clinical relevance of autophagy to the therapeutic response and relapse after CD19 CAR‐T cell therapy. Pharmacological inhibition of autophagy and knockout of RB1CC1 could dramatically sensitize tumor cells to CD19 CAR‐T cell‐mediated killing in mouse models of both B‐cell leukemia and lymphoma. Moreover, our study revealed that cancer‐intrinsic autophagy mediates evasion of CAR‐T cells via the TNF‐α‐TNFR1 axis‐mediated apoptosis and STAT1/IRF1‐induced chemokine signaling activation.ConclusionsThese findings confirm that autophagy signaling in B‐cell malignancies is essential for the effective cytotoxic function of CAR‐T cells and thereby pave the way for the development of autophagy‐targeting strategies to improve the clinical efficacy of CAR‐T cell immunotherapy.
LiDAR point clouds analysis computer tools for teaching autonomous vehicles perception algorithms
Authors: Jiménez Felipe , Clavijo Miguel 
Published: February 2024

AbstractThe technological developments behind autonomous vehicles cover several areas and engineers training in this field represents a challenge. The main layers include perception, decision making, and acting. In the first one, different technologies can be used. The processing of the information provided by the sensors must allow successive modules to understand the environment and Laser imaging Detection and Ranging (LiDAR) technology is one of the most promising ones nowadays for this task. It offers great robustness in detection, but the extraction of information from the point cloud involves the development of complex algorithms that could be very time‐consuming if an experimental teaching is intended. This article presents two educational solutions for deepening in perception algorithms using LiDAR for autonomous driving: a closed ad‐hoc computer application for two‐dimensional (2D) LiDAR point cloud processing and an oriented set of commands for three‐dimensional (3D) LiDARs in Matlab. Their use allows main concept exploration in practical sessions with little time consumption and provides students a general overview of the tasks that must be performed by the perception layer in the autonomous vehicles. Furthermore, these tools provide the possibility of organizing different activities in the classroom related to theoretical and experimental issues, and understanding of results because the most tedious tasks are eased.
Funny things are everywhere: Combatting geographic disparities in aortic stenosis care
Authors: Hashem Anas , Goldsweig Andrew M. 
Published: February 2024

Key points
Only 25%–35% of geographic variation in the use of surgical and transcatheter aortic valve replacement can be attributed to differing patient and hospital characteristics.
To address geographic disparities, the cardiovascular community must address modifiable cardiovascular risk factors, social determinants of health, and healthcare delivery models.
Governmental and professional organizations must study and actively address geographic disparities in access to care for aortic valve disease.
Patient‐specific computer simulation of transcatheter aortic valve replacement in patients with previous mechanical mitral prosthesis: A case series
Authors: Maiani Silvia , Nardi Giulia , Di Mario Carlo , Meucci Francesco 
Published: February 2024

AbstractTranscatheter aortic valve replacement performed in patients with previously implanted mechanical mitral prosthesis represents a high risk procedure with several potential complications. We report a systematic use of a prediction model based on artificial intelligence to plan the interventional strategy in this challenging scenario.
An Overview of Syntheses of Salvinorin A and its Analogues
Authors: Tibouti Soufian , Barriault Louis 
Published: February 2024

AbstractSalvinorin A is a powerful hallucinogen in humans, and a selective, high efficacy agonist of the kappa‐opioid receptor (κ‐OR). Salvinorin A is the first plant‐derived ligand with high selectivity for κ‐OR over other receptors, its structure is unrelated to any known opioid receptor ligands, even lacking any nitrogenous moieties. Mechanistically and pharmacologically, salvinorin A is distinct from other known hallucinogens in humans, making it the only selective κ‐OR ligand to gain wide‐spread interest outside of research. Structurally, salvinorin A bares a highly functionalized trans‐decalin core, containing two quaternary centers, and is fused to a δ‐lactone baring a furan moiety. Synthetic access of salvinorin A has been elusive due to a highly sensitive epimerizable center at carbon 8 (C8). All these features make salvinorin A a highly challenging synthetic target. With multiple synthetic efforts from around the world, only nine completed syntheses have been achieved to date. This review is intended to provide a look at the key strategies used to achieve the syntheses reported to date. We will summarize the efforts towards the syntheses of salvinorin A starting from Evans in 2007 to Barriault in 2023.