bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outcomes of laparoscopic and endoscopic cooperative surgery for gastric submucosal tumors: A retrospective multicenter study at 21 Japanese institutions
Authors: Hashimoto Yoshikazu , Abe Nobutsugu , Nunobe Souya , Kawakubo Hirofumi , Sumiyoshi Tetsuya , Yoshida Naohiro , Morita Yoshinori , Terashima Masanori , Saze Zenichiro , Onimaru Manabu , Otsuji Eigo , Hoteya Shu , Yamashita Haruhiro , Fujimura Takashi , Oyama Tsuneo , Ohata Ken , Shichijo Satoki , Tanabe Kazuaki , Shuto Kiyohiko , Ikeya Takashi , Shinohara Hisashi , Tanabe Satoshi , Hiki Naoki 
Published: March 2024

AbstractAimWe conducted a multicenter study on classical laparoscopic and endoscopic cooperative surgery (LECS) and LECS‐related procedures to retrospectively clarify the safety, problems, and mid‐term outcomes of these methods after their coverage by the national health insurance.MethodsA total of 201 patients who underwent classical LECS/LECS‐related procedures for gastric submucosal tumors (G‐SMTs) in 21 institutions affiliated with the Laparoscopy Endoscopy Cooperative Surgery Study Group from April 2014 to March 2016 were included. Data was retrospectively obtained from the patients' charts.ResultsThe most common surgical procedure was classical LECS (155 patients, 77.1%), non‐exposed endoscopic wall inversion surgery (22 patients, 11.4%), a combination of laparoscopic and endoscopic approaches to neoplasia with non‐exposure technique (16 patients, 8%), and closed LECS (two patients, 1%). Only six (3%) patients underwent LECS with gastrostomy. The mean operative time and blood loss were 188.4 (70–462) minutes and 23.3 (0–793) g, respectively. Ten (5%) patients developed postoperative complications (Clavien–Dindo classification grade II or higher). Two patients needed reoperation due to postoperative bleeding or anastomotic leakage. All tumors were resected with negative margins. A total of 127 (63.2%) patients underwent follow‐up observations for over 36 months, one of whom had a recurrence of peritoneal dissemination and one had poor oral intake.ConclusionClassical LECS and LECS‐related procedures for G‐SMTs have favorable short/mid‐term outcomes.
RNA Control via Redox‐Responsive Acylation
Authors: Guo Junsong , Chen Siqin , Onishi Yoshiyuki , Shi Qi , Song Yangyang , Mei Hui , Chen Leilei , Kool Eric T. , Zhu Ru‐Yi 
Published: March 2024

AbstractIncorporating stimuli‐responsive components into RNA constructs provides precise spatiotemporal control over RNA structures and functions. Despite considerable advancements, the utilization of redox‐responsive stimuli for the activation of caged RNAs remains scarce. In this context, we present a novel strategy that leverages post‐synthetic acylation coupled with redox‐responsive chemistry to exert control over RNA. To achieve this, we design and synthesize a series of acylating reagents specifically tailored for introducing disulfide‐containing acyl adducts into the 2′‐OH groups of RNA (“cloaking”). Our data reveal that these acyl moieties can be readily appended, effectively blocking RNA catalytic activity and folding. We also demonstrate the traceless release and reactivation of caged RNAs (“uncloaking”) through reducing stimuli. By employing this strategy, RNA exhibits rapid cellular uptake, effective distribution and activation in the cytosol without lysosomal entrapment. We anticipate that our methodology will be accessible to laboratories engaged in RNA biology and holds promise as a versatile platform for RNA‐based applications.
Li3PO4‐Enriched SEI on Graphite Anode Boosts Li+ De‐Solvation Enabling Fast‐Charging and Low‐Temperature Lithium‐Ion Batteries
Authors: Wang Chaonan , Xie Yuansen , Huang Yingshan , Zhou Shaoyun , Xie Huanyu , Jin Hongchang , Ji Hengxing 
Published: March 2024

AbstractLi+ de‐solvation at solid‐electrolyte interphase (SEI)‐electrolyte interface stands as a pivotal step that imposes limitations on the fast‐charging capability and low‐temperature performance of lithium‐ion batteries (LIBs). Unraveling the contributions of key constituents in the SEI that facilitate Li+ de‐solvation and deciphering their mechanisms, as a design principle for the interfacial structure of anode materials, is still a challenge. Herein, we conducted a systematic exploration of the influence exerted by various inorganic components (Li2CO3, LiF, Li3PO4) found in the SEI on their role in promoting the Li+ de‐solvation. The findings highlight that Li3PO4‐enriched SEI effectively reduces the de‐solvation energy due to its ability to attenuate the Li+‐solvent interaction, thereby expediting the de‐solvation process. Building on this, we engineer Li3PO4 interphase on graphite (LPO−Gr) anode via a simple solid‐phase coating, facilitating the Li+ de‐solvation and building an inorganic‐rich SEI, resulting in accelerated Li+ transport crossing the electrode interfaces and interphases. Full cells using the LPO−Gr anode can replenish its 80 % capacity in 6.5 minutes, while still retaining 70 % of the room temperature capacity even at −20 °C. Our strategy establishes connection between the de‐solvation characteristics of the SEI components and the interfacial structure design of anode materials for high performance LIBs.
Discovery of Terminal Oxazole‐Bearing Natural Products by a Targeted Metabologenomic Approach
Authors: Park Jiyoon , Shin Yern‐Hyerk , Hwang Sunghoon , Kim Jungwoo , Moon Dong Hyun , Kang Ilnam , Ko Yoon‐Joo , Chung Beomkoo , Nam Hyunsung , Kim Seokhee , Moon Kyuho , Oh Ki‐Bong , Cho Jang‐Cheon , Lee Sang Kook , Oh Dong‐Chan 
Published: March 2024

AbstractA targeted metabologenomic method was developed to selectively discover terminal oxazole‐bearing natural products from bacteria. For this, genes encoding oxazole cyclase, a key enzyme in terminal oxazole biosynthesis, were chosen as the genomic signature to screen bacterial strains that may produce oxazole‐bearing compounds. Sixteen strains were identified from the screening of a bacterial DNA library (1,000 strains) using oxazole cyclase gene‐targeting polymerase chain reaction (PCR) primers. The PCR amplicon sequences were subjected to phylogenetic analysis and classified into nine clades. 1H−13C coupled‐HSQC NMR spectra obtained from the culture extracts of the hit strains enabled the unequivocal detection of the target compounds, including five new oxazole compounds, based on the unique 1JCH values and chemical shifts of oxazole: lenzioxazole (1) possessing an unprecedented cyclopentane, permafroxazole (2) bearing a tetraene conjugated with carboxylic acid, tenebriazine (3) incorporating two modified amino acids, and methyl‐oxazolomycins A and B (4 and 5). Tenebriazine displayed inhibitory activity against pathogenic fungi, whereas methyl‐oxazolomycins A and B (4 and 5) selectively showed anti‐proliferative activity against estrogen receptor‐positive breast cancer cells. This metabologenomic method enables the logical and efficient discovery of new microbial natural products with a target structural motif without the need for isotopic labeling.
Recent Advances in Dearomative Partial Reduction of Benzenoid Arenes
Authors: Liu De‐Hai , Ma Jiajia 
Published: March 2024

AbstractDearomative partial reduction is an extraordinary approach for transforming benzenoid arenes and has been well‐known for many decades, as exemplified by the dehydrogenation of Birch reduction and the hydroarylation of Crich addition. Despite its remarkable importance in synthesis, this field has experienced slow progress over the last half‐century. However, a revival has been observed with the recent introduction of electrochemical and photochemical methods. In this Minireview, we summarize the recent advancements in dearomative partial reduction of benzenoid arenes, including dihydrogenation, hydroalkylation, arylation, alkenylation, amination, borylation and others. Further, the intriguing utilization of dearomative partial reduction in the synthesis of natural products is also emphasized. It is anticipated that this Minireview will stimulate further progress in arene dearomative transformations.
Programming of Supercrystals Using Replicable DNA‐Functionalized Colloids
Authors: Sun Xiaoyun , Hua Wenqiang , Liu Xiaoyu , Jin Jing , Zhang Jianing , Tian Jie , Zheng Bin , Jiang Wei , Yao Dongbao , Liang Haojun 
Published: March 2024

AbstractThe development of self‐replicating systems is of great importance in research on the origin of life. As the most iconic molecules, nucleic acids have provided prominent examples of the fabrication of self‐replicating artificial nanostructures. However, it is still challenging to construct sophisticated synthetic systems that can create large‐scale or three‐dimensionally ordered nanomaterials using self‐replicating nanostructures. By integrating a template system containing DNA‐functionalized colloidal seeds with a simplified DNA strand‐displacement circuit programmed subsystem to produce DNA‐functionalized colloidal copies, we developed a facile enthalpy‐mediated strategy to control the replication and catalytic assembly of DNA‐functionalized colloids in a time‐dependent manner. The replication efficiency and crystal quality of the resulting superlattice structures can be effectively increased by regulating the molar ratio of the template to the copy colloids. By constructing binary systems from two types of gold nanoparticles (or proteins), superlattice structures with different crystal symmetries can be obtained through the replication and catalytic assembly processes. This programmable enthalpy‐mediated approach was easily leveraged to achieve the phase transformation and catalytic amplification of colloidal crystals starting from different initial template crystals. This work offers a potential way to construct self‐replicating artificial systems that exhibit complicated phase behaviors and can produce large‐scale superlattice nanomaterials.
6‐Strand to Stable 10/12 Helix Conformational Switch by Incorporating Flexible β‐hGly in the Homooligomers of Camphor Derived β‐Amino Acid: NMR and X‐Ray Crystallographic Evidence
Authors: Sukumar Genji , Rahul  , Nayani Kiranmai , Mainkar Prathama S. , Prashanth Jupally , Sridhar Balasubramanian , Sarma Akella V. S. , Bharatam Jagadeesh , Chandrasekhar Srivari 
Published: March 2024

AbstractRational design of unnatural amino acid building blocks capable of stabilizing predictable secondary structures similar to protein fragments is pivotal for foldamer chemistry/catalysis. Here, we introduce novel β‐amino acid building blocks: [1S,2R,4R]exoCDA and [1S,2S,4R]endoCDA, derived from the abundantly available R(+)‐camphor, which is traditionally known for its medicinal value. Further, we demonstrate that the homooligomers of exoCDA adopt 6‐strand conformation, which switches to a robust 10/12‐helix simply by inserting flexible β‐hGly spacer at alternate positions (1 : 1 β‐hGly/exoCDA heterooligomers), as evident by DFT‐calculations, solution‐state NMR spectroscopy and X‐ray crystallography. To the best of our knowledge, this is the first example of crystalline‐state structure of left‐handed 10/12‐mixed helix, that is free from the conventional approach of employing β‐amino acids of either alternate chirality or alternate β2/β3 substitutions, to access the 10/12‐helix. The results also show that the homooligomers of heterochiral exoCDA don′t adopt helical fold, instead exhibit banana‐shaped strands, whereas the homodimers of the other diastereomer endoCDA, nucleate 8‐membered turns. Furthermore, the homo‐exoCDA and hetero‐[β‐hGly‐exoCDA] oligomers are found to exhibit self‐association properties with distinct morphological features. Overall, the results offer new possibilties of constructing discrete stable secondary and tertiary structures based on CDAs, which can accommodate flexible residues with desired side‐chain substitutions.
Sequencing vs. amplification for the estimation of allele dosages in sugarcane (Saccharum spp.)
Authors: Jaimes Hugo , Londoño Alejandra , Saavedra‐Diaz Carolina , Trujillo‐Montenegro Jhon Henry , López‐Gerena Jershon , Riascos John J. , Aguilar Fernando S. 
Published: March 2024

AbstractPremiseDetecting single‐nucleotide polymorphisms (SNPs) in a cost‐effective way is fundamental in any plant breeding pipeline. Here, we compare three genotyping techniques for their ability to reproduce the allele dosage of SNPs of interest in sugarcane (Saccharum spp.).MethodsTo identify a reproducible technique to estimate allele dosage for the validation of SNP markers, the correlation between Flex‐Seq, kompetitive allele‐specific PCR (KASP), and genotyping‐by‐sequencing and restriction site–associated DNA sequencing (GBS+RADseq) was determined for a set of 76 SNPs. To find alternative methodologies for allele dosage estimation, the KASP and Flex‐Seq techniques were compared for the same set of SNPs. For the three techniques, a population of 53 genotypes from the diverse sugarcane panel of the Centro de Investigación de la Caña de Azúcar (Cenicaña), Colombia, was selected.ResultsThe average Pearson correlation coefficients between GBS+RADseq and Flex‐Seq, GBS+RADseq and KASP, and Flex‐Seq and KASP were 0.62 ± 0.27, 0.38 ± 0.27, and 0.38 ± 0.30, respectively.DiscussionFlex‐Seq reproduced the allele dosages determined using GBS+RADseq with good levels of precision because of its depth of sequencing and ability to target specific positions in the genome. Additionally, Flex‐Seq outperformed KASP by allowing the conversion of a higher number of SNPs and a more accurate estimation of the allele dosage. Flex‐Seq has therefore become the genotyping methodology of choice for marker validation at Cenicaña.
Mixed‐effects regression weights for advice taking and related phenomena of information sampling and utilization
Authors: Rebholz Tobias R. , Biella Marco , Hütter Mandy 
Published: March 2024

AbstractAdvice taking and related research is dominated by deterministic weighting indices, specifically ratio‐of‐differences‐based formulas for investigating informational influence. Their arithmetic is intuitively simple, but they pose several measurement problems and restrict research to a particular paradigmatic approach. As a solution, we propose to specify how strongly peoples' judgments are influenced by externally provided evidence by fitting corresponding mixed‐effects regression models. Our approach explicitly distinguishes between endogenous components, such as updated beliefs, and exogenous components, such as independent initial judgments and advice. Crucially, mixed‐effects regression coefficients of various exogenous sources of information also reflect individual weighting but are based on a conceptually consistent representation of the endogenous judgment process. The formal derivation of the proposed weighting measures is accompanied by a detailed elaboration on their most important technical and statistical subtleties. We use this modeling approach to revisit empirical findings from several paradigms investigating algorithm aversion, sequential collaboration, and advice taking. In summary, we replicate and extend the original finding of algorithm appreciation and initially demonstrate a lack of evidence for both systematic order effects in sequential collaboration as well as differential weighting of multiple pieces of advice. In addition to opening new avenues for innovative research, appropriate modeling of information sampling and utilization has the potential to increase the reproducibility and replicability of behavioral science. Furthermore, the proposed method is relevant beyond advice taking, as mixed‐effects regression weights can also inform research on related cognitive phenomena such as multidimensional belief updating, anchoring effects, hindsight bias, or attitude change.
Rigid linker peptides improve the stability and anti‐inflammation effect of human serum albumin and α‐melanocyte‐stimulating hormone fusion proteins
Authors: Liu Yiyao , Li Yang , Wei Xueyan , Ullah Inam , Uddin Shahab , Wang Jiatao , Xia Runjie , Wang MeiZhu , Yang Hui , Li Hongyu 
Published: March 2024

AbstractThe anti‐inflammatory effect of α‐melanocyte‐stimulating hormone (α‐MSH) in the central nervous system (CNS) has been reported for 40 years. However, the short half‐life of α‐MSH limits its clinical applications. The previous study has shown that a fusion protein comprising protein transduction domain (PTD), human serum albumin (HSA), and α‐MSH extends the half‐life of α‐MSH, but its anti‐inflammatory effect is not satisfactory. In this study, optimization of the structures of fusion proteins was attempted by changing the linker peptide between HSA and α‐MSH. The optimization resulted in the improvement of various important characteristics, especially the stability and anti‐inflammatory bioactivity, which are important features in protein medicines. Compared to the original linker peptide L0, the 5‐amino‐acid rigid linker peptide L6 (PAPAP) is the best option for further investigation due to its higher expression (increased by 6.27%), improved purification recovery (increased by 60.8%), excellent thermal stability (Tm = 83.5°C) and better inhibition in NF‐κB expression (increased by 81.5%). From this study, the significance of the design of linker peptides in the study of structure–activity relationship of fusion proteins was proved.
Enhanced synthesis of S‐adenosyl‐L‐methionine through combinatorial metabolic engineering and Bayesian optimization in Saccharomyces cerevisiae
Authors: Xiao Wenhan , Shi Xiangliu , Huang Haowei , Wang Xiaogang , Liang Wenshu , Xu Jianguo , Liu Fei , Zhang Xiaomei , Xu Guoqiang , Shi Jinsong , Xu Zhenghong 
Published: March 2024

AbstractS‐Adenosyl‐L‐methionine (SAM) is a substrate for many enzyme‐catalyzed reactions and provides methyl groups in numerous biological methylations, and thus has vast applications in the agriculture and medical field. Saccharomyces cerevisiae has been engineered as a platform with significant potential for producing SAM, but the current production has room for improvement. Thus, a method that consists of a series of metabolic engineering strategies was established in this study. These strategies included enhancing SAM synthesis, increasing ATP supply, down‐regulating SAM metabolism, and down‐regulating competing pathway. After combinatorial metabolic engineering, Bayesian optimization was conducted on the obtained strain C262P6S to optimize the fermentation medium. A final yield of 2972.8 mg·L−1 at 36 h with 29.7% of the L‐Met conversion rate in the shake flask was achieved, which was 26.3 times higher than that of its parent strain and the highest reported production in the shake flask to date. This paper establishes a feasible foundation for the construction of SAM‐producing strains using metabolic engineering strategies and demonstrates the effectiveness of Bayesian optimization in optimizing fermentation medium to enhance the generation of SAM.
Predicting protein retention in ion‐exchange chromatography using an open source QSPR workflow
Authors: Neijenhuis Tim , Le Bussy Olivier , Geldhof Geoffroy , Klijn Marieke E. , Ottens Marcel 
Published: March 2024

AbstractProtein‐based biopharmaceuticals require high purity before final formulation to ensure product safety, making process development time consuming. Implementation of computational approaches at the initial stages of process development offers a significant reduction in development efforts. By preselecting process conditions, experimental screening can be limited to only a subset. One such computational selection approach is the application of Quantitative Structure Property Relationship (QSPR) models that describe the properties exploited during purification. This work presents a novel open‐source Python tool capable of extracting a range of features from protein 3D models on a local computer allowing total transparency of the calculations. As open‐source tool, it also impacts initial investments in constructing a QSPR workflow for protein property prediction for third parties, making it widely applicable within the field of bioprocess development. The focus of current calculated molecular features is projection onto the protein surface by constructing surface grid representations. Linear regression models were trained with the calculated features to predict chromatographic retention times/volumes. Model validation shows a high accuracy for anion and cation exchange chromatography data (cross‐validated R2 of 0.87 and 0.95). Hence, these models demonstrate the potential of the use of QSPR to accelerate process design.
Recent advances and fundamentals of microalgae cultivation technology
Authors: Rozenberg Julian M. , Sorokin Boris A. , Mukhambetova Amina N. , Emelianova Anna A. , Kuzmin Valentin V. , Belogurova‐Ovchinnikova Oxana Y. , Kuzmin Denis V. 
Published: March 2024

AbstractMicroalgae are considered to be a promising group of organisms for fuel production, waste processing, pharmaceutical applications, and as a source of food components. Unicellular algae are worth being considered because of their capacity to produce comparatively large amounts of lipids, proteins, and vitamins while requiring little room for growth. They can also grow on waste and fix CO2 and nitrogen compounds. However, production costs limit the industrial use of microalgae to the most profitable applications including micronutrient production and fish farming. Therefore, novel microalgae based technologies require an increase of the production efficiencies or values. Here we review the recent studies focused on getting strains with novel characteristics or cultivating techniques that improve production's robustness or efficiency and categorize these findings according to the fundamental factors that determine microalgae growth. Improvements of light and nutrient delivery, as well as other aspects of photobioreactor design, have shown the highest average increase in productivity. Other methods, such as an improvement of phosphorus or CO2 fixation and temperature adaptation have been found to be less effective. Furthermore, interactions with particular bacteria may promote the growth of microalgae, although bacterial and grazer contaminations must be managed to avoid culture failure. The competitiveness of the algal products will increase if these discoveries are applied to industrial settings.
Tuning capsid formation dynamics in recombinant adeno‐associated virus producing synthetic cell lines to enhance full particle productivity
Authors: Lu Min , Lin Yu‐Chieh , Kuo Han‐Jung , Cai Wen , Ye Qian , Zhao Liang , Hu Wei‐Shou 
Published: March 2024

AbstractRecombinant adeno‐associated virus (rAAV) is widely used as an in vivo delivery vector for gene therapy. It is used in a very large dose, and the large quantities required for broad applications present manufacturing challenges. We have developed a synthetic biology platform of constructing cell lines integrated with essential viral genes which can be induced to produce rAAV without plasmid transfection or virus transduction. Through iterative design‐construct‐characterization cycles, we have showcased the potential of this synthetic cell production system. Systems characterization of the dynamics of viral transcripts and proteins as well as virus assembly and packaging revealed that the expression level and balance of viral genome and capsid protein are keys to not only the productivity but also the full particle content, an important product quality attribute. Boosting cap gene expression by sequential transfection and integration of multiple copies of the cap gene elevated the rAAV titer to levels on a par with traditional plasmid transfection and virus infection. However, overexpression of the cap gene shifted the balance and kinetics of the genome and capsid. We independently tuned the dynamics of genome amplification and capsid protein synthesis by modulating the induction concentration as well as the time profile, and significantly enhanced full particle content while maintaining a high productivity. This strategy of constructing an inducible stable producer cell line is readily adaptable to rAAV vectors of different serotypes and payloads. It can greatly facilitate scalable production of gene therapy vectors.