bluuebunny/crossref_metadata_2025_split huggingface dataset:
Serum NY-ESO-1 antibody as a predictive biomarker for postoperative recurrence of gastric cancer: a multicenter prospective observational study
Authors: Saito Takuro , Kurokawa Yukinori , Fujitani Kazumasa , Kawabata Ryohei , Takeno Atsushi , Mikami Jota , Endo Shunji , Matsuyama Jin , Akamaru Yusuke , Hirota Masashi , Kishi Kentaro , Urakawa Shinya , Yamamoto Kei , Tanaka Koji , Takahashi Tsuyoshi , Oka Mikio , Wada Hisashi , Eguchi Hidetoshi , Doki Yuichiro 
Published: February 2024

Abstract
Background
No reliable marker has been identified to predict postoperative recurrence of gastric cancer. We designed a clinical trial to investigate the utility of serum NY-ESO-1 antibody responses as a predictive marker for postoperative recurrence in gastric cancer.

Methods
A multicenter prospective study was conducted between 2012 and 2021. Patients with resectable cT3-4 gastric cancer were included. Postoperative NY-ESO-1 and p53 antibody responses were serially evaluated every 3 months for 1 year in patients with positive preoperative antibody responses. The recurrence rate was assessed by the positivity of antibody responses at 3 and 12 months postoperatively.

Results
Among 1001 patients, preoperative NY-ESO-1 and p53 antibody responses were positive in 12.6% and 18.1% of patients, respectively. NY-ESO-1 antibody responses became negative postoperatively in non-recurrent patients (negativity rates; 45% and 78% at 3 and 12 months, respectively), but remained positive in recurrent patients (negativity rates; 9% and 8%, respectively). p53 antibody responses remained positive in non-recurrent patients. In multivariate analysis, NY-ESO-1 antibody positivity at 3 months (P  < 0.03) and 12 months (P  < 0.001) were independent prognostic factors for a shorter recurrence-free interval.

Conclusions
Serum NY-ESO-1 antibodies may be a useful predictive marker for postoperative recurrence in gastric cancer.

Clinical trial registration
UMIN000007925.
Process-evaluation of forest aerosol-cloud-climate feedback shows clear evidence from observations and large uncertainty in models
Authors: Blichner Sara M. , Yli-Juuti Taina , Mielonen Tero , Pöhlker Christopher , Holopainen Eemeli , Heikkinen Liine , Mohr Claudia , Artaxo Paulo , Carbone Samara , Meller Bruno Backes , Quaresma Dias-Júnior Cléo , Kulmala Markku , Petäjä Tuukka , Scott Catherine E. , Svenhag Carl , Nieradzik Lars , Sporre Moa , Partridge Daniel G. , Tovazzi Emanuele , Virtanen Annele , Kokkola Harri , Riipinen Ilona 
Published: February 2024

AbstractNatural aerosol feedbacks are expected to become more important in the future, as anthropogenic aerosol emissions decrease due to air quality policy. One such feedback is initiated by the increase in biogenic volatile organic compound (BVOC) emissions with higher temperatures, leading to higher secondary organic aerosol (SOA) production and a cooling of the surface via impacts on cloud radiative properties. Motivated by the considerable spread in feedback strength in Earth System Models (ESMs), we here use two long-term observational datasets from boreal and tropical forests, together with satellite data, for a process-based evaluation of the BVOC-aerosol-cloud feedback in four ESMs. The model evaluation shows that the weakest modelled feedback estimates can likely be excluded, but highlights compensating errors making it difficult to draw conclusions of the strongest estimates. Overall, the method of evaluating along process chains shows promise in pin-pointing sources of uncertainty and constraining modelled aerosol feedbacks.
Visualization-enhanced under-oil open microfluidic system for in situ characterization of multi-phase chemical reactions
Authors: Chen Qiyuan , Zhai Hang , Beebe David J. , Li Chao , Wang Bu 
Published: February 2024

AbstractUnder-oil open microfluidic system, utilizing liquid-liquid boundaries for confinements, offers inherent advantages including clogging-free flow channels, flexible access to samples, and adjustable gas permeation, making it well-suited for studying multi-phase chemical reactions that are challenging for closed microfluidics. However, reports on the novel system have primarily focused on device fabrication and functionality demonstrations within biology, leaving their application in broader chemical analysis underexplored. Here, we present a visualization-enhanced under-oil open microfluidic system for in situ characterization of multi-phase chemical reactions with Raman spectroscopy. The enhanced system utilizes a semi-transparent silicon (Si) nanolayer over the substrate to enhance visualization in both inverted and upright microscope setups while reducing Raman noise from the substrate. We validated the system’s chemical stability and capability to monitor gas evolution and gas-liquid reactions in situ. The enhanced under-oil open microfluidic system, integrating Raman spectroscopy, offers a robust open-microfluidic platform for label-free molecular sensing and real-time chemical/biochemical process monitoring in multi-phase systems.
The role of extracellular vesicle fusion with target cells in triggering systemic inflammation
Authors: Papareddy Praveen , Tapken Ines , Kroh Keshia , Varma Bhongir Ravi Kiran , Rahman Milladur , Baumgarten Maria , Cim Eda Irem , Györffy Lilla , Smeds Emanuel , Neumann Ariane , Veerla Srinivas , Olinder Jon , Thorlacus Henrik , Ryden Cecilia , Bartakova Eva , Holub Michal , Herwald Heiko 
Published: February 2024

AbstractExtracellular vesicles (EVs) play a crucial role in intercellular communication by transferring bioactive molecules from donor to recipient cells. As a result, EV fusion leads to the modulation of cellular functions and has an impact on both physiological and pathological processes in the recipient cell. This study explores the impact of EV fusion on cellular responses to inflammatory signaling. Our findings reveal that fusion renders non-responsive cells susceptible to inflammatory signaling, as evidenced by increased NF-κB activation and the release of inflammatory mediators. Syntaxin-binding protein 1 is essential for the merge and activation of intracellular signaling. Subsequent analysis show that EVs transfer their functionally active receptors to target cells, making them prone to an otherwise unresponsive state. EVs in complex with their agonist, require no further stimulation of the target cells to trigger mobilization of NF-κB. While receptor antagonists were unable to inhibit NF-κB activation, blocking of the fusion between EVs and their target cells with heparin mitigated inflammation in mice challenged with EVs.
Hormonal steroids induce multidrug resistance and stress response genes in Neisseria gonorrhoeae by binding to MtrR
Authors: Hooks Grace M. , Ayala Julio C. , Holley Concerta L. , Dhulipala Vijaya , Beggs Grace A. , Perfect John R. , Schumacher Maria A. , Shafer William M. , Brennan Richard G. 
Published: February 2024

AbstractTranscriptional regulator MtrR inhibits the expression of the multidrug efflux pump operon mtrCDE in the pathogenic bacterium Neisseria gonorrhoeae. Here, we show that MtrR binds the hormonal steroids progesterone, β-estradiol, and testosterone, which are present at urogenital infection sites, as well as ethinyl estrogen, a component of some hormonal contraceptives. Steroid binding leads to the decreased affinity of MtrR for cognate DNA, increased mtrCDE expression, and enhanced antimicrobial resistance. Furthermore, we solve crystal structures of MtrR bound to each steroid, thus revealing their binding mechanisms and the conformational changes that induce MtrR.
Realization of large-area ultraflat chiral blue phosphorene
Authors: Song Ye-Heng , Muzaffar M. U. , Wang Qi , Wang Yunhui , Jia Yu , Cui Ping , Zhang Weifeng , Wang Xue-Sen , Zhang Zhenyu 
Published: February 2024

AbstractBlue phosphorene (BlueP), a theoretically proposed phosphorous allotrope with buckled honeycomb lattice, has attracted considerable interest due to its intriguing properties. Introducing chirality into BlueP can further enrich its physical and chemical properties, expanding its potential for applications. However, the synthesis of chiral BlueP remains elusive. Here, we demonstrate the growth of large-area BlueP films on Cu(111), with lateral size limited by the wafer dimensions. Importantly, we discovered that the BlueP is characterized by an ultraflat honeycomb lattice, rather than the prevailing buckled structure, and develops highly ordered spatial chirality plausibly resulting from the rotational stacking with the substrate and interface strain release, as further confirmed by the geometric phase analysis. Moreover, spectroscopic measurements reveal its intrinsic metallic nature and different characteristic quantum oscillations in the image-potential states, which can be exploited for a range of potential applications including polarization optics, spintronics, and chiral catalysis.
Memristor-based storage system with convolutional autoencoder-based image compression network
Authors: Feng Yulin , Zhang Yizhou , Zhou Zheng , Huang Peng , Liu Lifeng , Liu Xiaoyan , Kang Jinfeng 
Published: February 2024

AbstractThe exponential growth of various complex images is putting tremendous pressure on storage systems. Here, we propose a memristor-based storage system with an integrated near-storage in-memory computing-based convolutional autoencoder compression network to boost the energy efficiency and speed of the image compression/retrieval and improve the storage density. We adopt the 4-bit memristor arrays to experimentally demonstrate the functions of the system. We propose a step-by-step quantization aware training scheme and an equivalent transformation for transpose convolution to improve the system performance. The system exhibits a high (>33 dB) peak signal-to-noise ratio in the compression and decompression of the ImageNet and Kodak24 datasets. Benchmark comparison results show that the 4-bit memristor-based storage system could reduce the latency and energy consumption by over 20×/5.6× and 180×/91×, respectively, compared with the server-grade central processing unit-based/the graphics processing unit-based processing system, and improve the storage density by more than 3 times.
A multicenter clinical AI system study for detection and diagnosis of focal liver lesions
Authors: Ying Hanning , Liu Xiaoqing , Zhang Min , Ren Yiyue , Zhen Shihui , Wang Xiaojie , Liu Bo , Hu Peng , Duan Lian , Cai Mingzhi , Jiang Ming , Cheng Xiangdong , Gong Xiangyang , Jiang Haitao , Jiang Jianshuai , Zheng Jianjun , Zhu Kelei , Zhou Wei , Lu Baochun , Zhou Hongkun , Shen Yiyu , Du Jinlin , Ying Mingliang , Hong Qiang , Mo Jingang , Li Jianfeng , Ye Guanxiong , Zhang Shizheng , Hu Hongjie , Sun Jihong , Liu Hui , Li Yiming , Xu Xingxin , Bai Huiping , Wang Shuxin , Cheng Xin , Xu Xiaoyin , Jiao Long , Yu Risheng , Lau Wan Yee , Yu Yizhou , Cai Xiujun 
Published: February 2024

AbstractEarly and accurate diagnosis of focal liver lesions is crucial for effective treatment and prognosis. We developed and validated a fully automated diagnostic system named Liver Artificial Intelligence Diagnosis System (LiAIDS) based on a diverse sample of 12,610 patients from 18 hospitals, both retrospectively and prospectively. In this study, LiAIDS achieved an F1-score of 0.940 for benign and 0.692 for malignant lesions, outperforming junior radiologists (benign: 0.830-0.890, malignant: 0.230-0.360) and being on par with senior radiologists (benign: 0.920-0.950, malignant: 0.550-0.650). Furthermore, with the assistance of LiAIDS, the diagnostic accuracy of all radiologists improved. For benign and malignant lesions, junior radiologists’ F1-scores improved to 0.936-0.946 and 0.667-0.680 respectively, while seniors improved to 0.950-0.961 and 0.679-0.753. Additionally, in a triage study of 13,192 consecutive patients, LiAIDS automatically classified 76.46% of patients as low risk with a high NPV of 99.0%. The evidence suggests that LiAIDS can serve as a routine diagnostic tool and enhance the diagnostic capabilities of radiologists for liver lesions.
Protein degradation by human 20S proteasomes elucidates the interplay between peptide hydrolysis and splicing
Authors: Soh Wai Tuck , Roetschke Hanna P. , Cormican John A. , Teo Bei Fang , Chiam Nyet Cheng , Raabe Monika , Pflanz Ralf , Henneberg Fabian , Becker Stefan , Chari Ashwin , Liu Haiyan , Urlaub Henning , Liepe Juliane , Mishto Michele 
Published: February 2024

AbstractIf and how proteasomes catalyze not only peptide hydrolysis but also peptide splicing is an open question that has divided the scientific community. The debate has so far been based on immunopeptidomics, in vitro digestions of synthetic polypeptides as well as ex vivo and in vivo experiments, which could only indirectly describe proteasome-catalyzed peptide splicing of full-length proteins. Here we develop a workflow—and cognate software - to analyze proteasome-generated non-spliced and spliced peptides produced from entire proteins and apply it to in vitro digestions of 15 proteins, including well-known intrinsically disordered proteins such as human tau and α-Synuclein. The results confirm that 20S proteasomes produce a sizeable variety of cis-spliced peptides, whereas trans-spliced peptides are a minority. Both peptide hydrolysis and splicing produce peptides with well-defined characteristics, which hint toward an intricate regulation of both catalytic activities. At protein level, both non-spliced and spliced peptides are not randomly localized within protein sequences, but rather concentrated in hotspots of peptide products, in part driven by protein sequence motifs and proteasomal preferences. At sequence level, the different peptide sequence preference of peptide hydrolysis and peptide splicing suggests a competition between the two catalytic activities of 20S proteasomes during protein degradation.
Integrating leiomyoma genetics, epigenomics, and single-cell transcriptomics reveals causal genetic variants, genes, and cell types
Authors: Buyukcelebi Kadir , Duval Alexander J. , Abdula Fatih , Elkafas Hoda , Seker-Polat Fidan , Adli Mazhar 
Published: February 2024

AbstractUterine fibroids (UF), that can disrupt normal uterine function and cause significant physical and psychological health problems, are observed in nearly 70% of women of reproductive age. Although heritable genetics is a significant risk factor, specific genetic variations and gene targets causally associated with UF are poorly understood. Here, we performed a meta-analysis on existing fibroid genome-wide association studies (GWAS) and integrated the identified risk loci and potentially causal single nucleotide polymorphisms (SNPs) with epigenomics, transcriptomics, 3D chromatin organization from diverse cell types as well as primary UF patient’s samples. This integrative analysis identifies 24 UF-associated risk loci that potentially target 394 genes, of which 168 are differentially expressed in UF tumors. Critically, integrating this data with single-cell gene expression data from UF patients reveales the causal cell types with aberrant expression of these target genes. Lastly, CRISPR-based epigenetic repression (dCas9-KRAB) or activation (dCas9-p300) in a UF disease-relevant cell type further refines and narrows down the potential gene targets. Our findings and the methodological approach indicate the effectiveness of integrating multi-omics data with locus-specific epigenetic editing approaches for identifying gene- and celt type-targets of disease-relevant risk loci.
Capacitive tendency concept alongside supervised machine-learning toward classifying electrochemical behavior of battery and pseudocapacitor materials
Authors: Deebansok Siraprapha , Deng Jie , Le Calvez Etienne , Zhu Yachao , Crosnier Olivier , Brousse Thierry , Fontaine Olivier 
Published: February 2024

AbstractIn recent decades, more than 100,000 scientific articles have been devoted to the development of electrode materials for supercapacitors and batteries. However, there is still intense debate surrounding the criteria for determining the electrochemical behavior involved in Faradaic reactions, as the issue is often complicated by the electrochemical signals produced by various electrode materials and their different physicochemical properties. The difficulty lies in the inability to determine which electrode type (battery vs. pseudocapacitor) these materials belong to via simple binary classification. To overcome this difficulty, we apply supervised machine learning for image classification to electrochemical shape analysis (over 5500 Cyclic Voltammetry curves and 2900 Galvanostatic Charge-Discharge curves), with the predicted confidence percentage reflecting the shape trend of the curve and thus defined as a manufacturer. It’s called “capacitive tendency”. This predictor not only transcends the limitations of human-based classification but also provides statistical trends regarding electrochemical behavior. Of note, and of particular importance to the electrochemical energy storage community, which publishes over a hundred articles per week, we have created an online tool to easily categorize their data.
Challenging thermodynamics: combining immiscible elements in a single-phase nano-ceramic
Authors: Liu Shuo , Dun Chaochao , Jiang Qike , Xuan Zhengxi , Yang Feipeng , Guo Jinghua , Urban Jeffrey J. , Swihart Mark T. 
Published: February 2024

AbstractThe Hume-Rothery rules governing solid-state miscibility limit the compositional space for new inorganic material discovery. Here, we report a non-equilibrium, one-step, and scalable flame synthesis method to overcome thermodynamic limits and incorporate immiscible elements into single phase ceramic nanoshells. Starting from prototype examples including (NiMg)O, (NiAl)Ox, and (NiZr)Ox, we then extend this method to a broad range of Ni-containing ceramic solid solutions, and finally to general binary combinations of elements. Furthermore, we report an “encapsulated exsolution” phenomenon observed upon reducing the metastable porous (Ni0.07Al0.93)Ox to create ultra-stable Ni nanoparticles embedded within the walls of porous Al2O3 nanoshells. This nanoconfined structure demonstrated high sintering resistance during 640 h of catalysis of CO2 reforming of methane, maintaining constant 96% CH4 and CO2 conversion at 800 °C and dramatically outperforming conventional catalysts. Our findings could greatly expand opportunities to develop novel inorganic energy, structural, and functional materials.
Steep-slope vertical-transport transistors built from sub-5 nm Thin van der Waals heterostructures
Authors: Yang Qiyu , Luo Zheng-Dong , Duan Huali , Gan Xuetao , Zhang Dawei , Li Yuewen , Tan Dongxin , Seidel Jan , Chen Wenchao , Liu Yan , Hao Yue , Han Genquan 
Published: February 2024

AbstractTwo-dimensional (2D) semiconductor-based vertical-transport field-effect transistors (VTFETs) – in which the current flows perpendicularly to the substrate surface direction – are in the drive to surmount the stringent downscaling constraints faced by the conventional planar FETs. However, low-power device operation with a sub-60 mV/dec subthreshold swing (SS) at room temperature along with an ultra-scaled channel length remains challenging for 2D semiconductor-based VTFETs. Here, we report steep-slope VTFETs that combine a gate-controllable van der Waals heterojunction and a metal-filamentary threshold switch (TS), featuring a vertical transport channel thinner than 5 nm and sub-thermionic turn-on characteristics. The integrated TS-VTFETs were realised with efficient current switching behaviours, exhibiting a current modulation ratio exceeding 1 × 108 and an average sub-60 mV/dec SS over 6 decades of drain current. The proposed TS-VTFETs with excellent area- and energy-efficiency could help to tackle the performance degradation-device downscaling dilemma faced by logic transistor technologies.
Spatial transcriptomics reveal neuron–astrocyte synergy in long-term memory
Authors: Sun Wenfei , Liu Zhihui , Jiang Xian , Chen Michelle B. , Dong Hua , Liu Jonathan , Südhof Thomas C. , Quake Stephen R. 
Published: February 2024

AbstractMemory encodes past experiences, thereby enabling future plans. The basolateral amygdala is a centre of salience networks that underlie emotional experiences and thus has a key role in long-term fear memory formation1. Here we used spatial and single-cell transcriptomics to illuminate the cellular and molecular architecture of the role of the basolateral amygdala in long-term memory. We identified transcriptional signatures in subpopulations of neurons and astrocytes that were memory-specific and persisted for weeks. These transcriptional signatures implicate neuropeptide and BDNF signalling, MAPK and CREB activation, ubiquitination pathways, and synaptic connectivity as key components of long-term memory. Notably, upon long-term memory formation, a neuronal subpopulation defined by increased Penk and decreased Tac expression constituted the most prominent component of the memory engram of the basolateral amygdala. These transcriptional changes were observed both with single-cell RNA sequencing and with single-molecule spatial transcriptomics in intact slices, thereby providing a rich spatial map of a memory engram. The spatial data enabled us to determine that this neuronal subpopulation interacts with adjacent astrocytes, and functional experiments show that neurons require interactions with astrocytes to encode long-term memory.
Circulating myeloid-derived MMP8 in stress susceptibility and depression
Authors: Cathomas Flurin , Lin Hsiao-Yun , Chan Kenny L. , Li Long , Parise Lyonna F. , Alvarez Johana , Durand-de Cuttoli Romain , Aubry Antonio V. , Muhareb Samer , Desland Fiona , Shimo Yusuke , Ramakrishnan Aarthi , Estill Molly , Ferrer-Pérez Carmen , Parise Eric M. , Wilk C. Matthias , Kaster Manuella P. , Wang Jun , Sowa Allison , Janssen William G. , Costi Sara , Rahman Adeeb , Fernandez Nicolas , Campbell Matthew , Swirski Filip K. , Nestler Eric J. , Shen Li , Merad Miriam , Murrough James W. , Russo Scott J. 
Published: February 2024

AbstractPsychosocial stress has profound effects on the body, including the immune system and the brain1,2. Although a large number of pre-clinical and clinical studies have linked peripheral immune system alterations to stress-related disorders such as major depressive disorder (MDD)3, the underlying mechanisms are not well understood. Here we show that expression of a circulating myeloid cell-specific proteinase, matrix metalloproteinase 8 (MMP8), is increased in the serum of humans with MDD as well as in stress-susceptible mice following chronic social defeat stress (CSDS). In mice, we show that this increase leads to alterations in extracellular space and neurophysiological changes in the nucleus accumbens (NAc), as well as altered social behaviour. Using a combination of mass cytometry and single-cell RNA sequencing, we performed high-dimensional phenotyping of immune cells in circulation and in the brain and demonstrate that peripheral monocytes are strongly affected by stress. In stress-susceptible mice, both circulating monocytes and monocytes that traffic to the brain showed increased Mmp8 expression following chronic social defeat stress. We further demonstrate that circulating MMP8 directly infiltrates the NAc parenchyma and controls the ultrastructure of the extracellular space. Depleting MMP8 prevented stress-induced social avoidance behaviour and alterations in NAc neurophysiology and extracellular space. Collectively, these data establish a mechanism by which peripheral immune factors can affect central nervous system function and behaviour in the context of stress. Targeting specific peripheral immune cell-derived matrix metalloproteinases could constitute novel therapeutic targets for stress-related neuropsychiatric disorders.