bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the prognostic value of S100A11 and its association with immune infiltration in breast cancer
Authors: He Junfang , Lei Yuxi , Li Xiabin , Wu Bin , Tang Yan 
Published: December 2023

AbstractBreast cancer (BC) is a severe danger to women’s lives and health globally. S100A11 is aberrantly expressed in many carcinomas and serves a crucial function in cancer development. However, the role of S100A11 in BC is unclear. In this study, we utilized multiple databases and online tools, including the TCGA database, cBioPortal, and STRING, to evaluate the significance of S100A11 in BC prognosis and immune infiltration. We found that S100A11 was considerably more abundant in BC tissues. Survival analysis indicated that individuals with S100A11 high expression of BC had shorter overall survival. Multivariate Cox regression analysis revealed that high S100A11 expression independently influenced the poor outcome of patients with BC (HR = 1.738, 95%CI 1.197–2.524). Our nomogram incorporating five factors, including S100A11, age, clinical stage, N, and M, was developed to anticipate the survival probability in BC prognosis. The model demonstrated good consistency and accuracy. Furthermore, the mutation rete of S100A11 was 14%. Survival analysis suggested that breast cancer patients with S100A11 mutation had a worse prognosis. KEGG pathway enrichment analysis revealed that S100A11 may be mainly involved in the IL-17 signaling pathway. Finally, we discovered a correlation between S100A11 expression and immune cell infiltration on BC. S100A11 expression was positively associated with 17 immune checkpoint-related genes. In conclusion, this study indicates that S100A11 may contribute to a worse prognosis for BC and potentially has a significant impact through its influence on immune cell infiltration and the IL-17 signaling pathway.
Immunomodulatory drugs have divergent effects on humoral and cellular immune responses to SARS-CoV-2 vaccination in people living with rheumatoid arthritis
Authors: Benoit Jenna M. , Breznik Jessica A. , Ang Jann C. , Bhakta Hina , Huynh Angela , Cowbrough Braeden , Baker Barbara , Heessels Lauren , Lodhi Sumiya , Yan Elizabeth , Ewusie Joycelyne , Nazy Ishac , Bramson Jonathan , Miller Matthew S. , Bernatsky Sasha , Larché Maggie J. , Bowdish Dawn M. E. ,   the SUCCEED Investigator Group
Published: December 2023

AbstractUnderstanding the efficacy of SARS-CoV-2 vaccination in people on immunosuppressive drugs, including those with rheumatoid arthritis (RA), is critical for their protection. Vaccine induced protection requires antibodies, CD4+ T cells, and CD8+ T cells, but it is unclear if these are equally affected by immunomodulatory drugs. Here, we determined how humoral and cellular SARS-CoV-2 vaccination responses differed between people with RA and controls, and which drug classes impacted these responses. Blood was collected from participants with RA on immunomodulatory drugs and controls after their second, third, and fourth SARS-CoV-2 vaccinations. Receptor binding domain (RBD)-specific antibodies were quantified by ELISA. Spike-specific memory T cells were quantitated using flow cytometry. Linear mixed models assessed the impact of age, sex, and immunomodulatory drug classes on SARS-CoV-2 vaccination responses. Compared to non-RA controls (n = 35), participants with RA on immunomodulatory drugs (n = 62) had lower anti-RBD IgG and spike-specific CD4+ T cell levels, but no deficits in spike-specific CD8+ T cells, following SARS-CoV-2 vaccination. Use of costimulation inhibitors was associated with lower humoral responses. JAK inhibitors were associated with fewer spike-specific CD4+ T cells. Participants with RA on immunomodulatory drugs mounted weaker responses to SARS-CoV-2 vaccination, with different drug classes impacting the cellular and humoral compartments.
Anthelmintic efficacy evaluation and mechanism of N-methylbenzo[d]oxazol-2-amine
Authors: Prangthip Pattaneeya , Tummatorn Jumreang , Adisakwattana Poom , Uthailak Naphatsamon , Boonyuen Usa , Tipthara Phornpimon , Tarning Joel , Laohapaisan Pavitra , Thongsornkleeb Charnsak , Ruchirawat Somsak , Reamtong Onrapak 
Published: December 2023

AbstractParasitic roundworms cause significant sickness and mortality in animals and humans. In livestock, these nematodes have severe economic impact and result in losses in food production on a global scale. None of the currently available drugs ideally suit all treatment circumstances, and the development of drug-resistant nematode strains has become a challenge to control the infection. There is an urgent need to develop novel anthelmintic compounds. According to our previous report, N-methylbenzo[d]oxazol-2-amine (1) showed anthelmintic activity and lowest cytotoxicity. In this study, in vivo anthelmintic properties were evaluated using Trichinella spiralis infected mice. Toxicity was evaluated using the rats and mode of action using molecular docking and metabolomics approaches. The in vivo results demonstrate that a dose of 250 mg/kg reduced the T. spiralis abundance in the digestive tract by 49%. The 250 mg/kg Albendazole was served as control. The relatively low acute toxicity was categorized into chemical category 5, with an LD50 greater than 2000 mg/kg body. Molecular docking analysis showed the T. spiralis tubulin beta chain and glutamate-gated channels might not be the main targets of compound 1. Metabolomics analysis was used to explain the effects of compound 1 on the T. spiralis adult worm. The results demonstrated that compound 1 significantly up-regulated the metabolism of purine, pyrimidine and down-regulated sphingolipid metabolism. In conclusion, compound 1 could be a potential molecule for anthelmintic development. The bioavailability, pharmacokinetics, and absorption of this compound should be studied further to provide information for its future efficacy improvement.
Immuno-SPR biosensor for the detection of Brucella abortus
Authors: Pasquardini Laura , Cennamo Nunzio , Arcadio Francesco , Perri Chiara , Chiodi Alessandro , D’agostino Girolamo , Zeni Luigi 
Published: December 2023

AbstractA proof of principle biosensor for the Brucella abortus recognition onsite is presented. The system is based on a plasmonic optical fiber probe functionalized with an oriented antibody layer immobilized on a short polyethyleneglycol (PEG) interface through carbodiimide chemistry and protein G as an intermediate layer. The biosensor is inserted in a holder built in 3D printing technology, obtaining a custom holder useful for housing the sample to be measured and the equipment. The removable sensor chip is a low-cost Surface Plasmon Resonance (SPR) platform based on D-shaped plastic optical fibers (POFs), built-in in 3D printed connectors, used here for the first time to detect bacteria via a bio-receptor layer specific for its membrane protein. The performances of the biosensor in Brucella abortus recognition are tested by using two different SPR-POF probes combined with the same bio-receptor layer. The best sensor configuration has presented a sensitivity at low concentrations of one order of magnitude greater than the other. A limit of detection (LoD) of 2.8 bacteria/mL is achieved well competitive with other systems but without the need for amplification or special sample treatments. Specificity has been tested using Salmonella bacteria, and reproducibility, regenerability and stability are moreover evaluated. These experimental results pave the way for building an efficient and specific biosensor system for Brucella abortus detection onsite and in a few minutes. Moreover, the proposed POF-based SPR biosensor device, with respect to the already available technologies, could be a Point-of-care-test (POCT), simple to use, small-size and portable, low-cost, don’t necessary of a microfluidic system, and can be connected to the Internet (IoT).
The impact of digital economy on green total factor productivity considering the labor-technology-pollution factors
Authors: Huang Yipeng , Chen Zhiguo , Li Huiru , Yin Shi 
Published: December 2023

AbstractThe digital economy provides new impetus for the high-quality development of manufacturing industry. Through the DEA-Malmquist model and panel regression model, this paper confirmed that there is a positive and significant relationship between the development of digital economy and the green total factor productivity (GTFP) of manufacturing industry. The research result is as follows: (1) the development of digital economy can enhance the overall GTFP of manufacturing industry. (2) The green technology progress brought by the development of digital economy is the main path to promote the GTFP of manufacturing industry. (3) The heterogeneity analysis shows that the impact of digital economy on GTFP of high pollution manufacturing industry is significantly positive, the impact of labor-intensive manufacturing industry is significantly negative, and the impact of technology intensive manufacturing industry is not obvious. The contributions of this study are as follow. In terms of theory, this study theoretically continues Solow’s classical theory, demonstrating the scientific nature of digital technology progress in promoting GTFP growth. In empirical analysis, this study build a new digital economy development level evaluation index system based on the perspective of manufacturing industry. In addition, this study also add a labor-technology-pollution perspective for the development of relevant policies.
Exogenous moisture deficit fuels drought risks across China
Authors: Wang Gang , Zhang Qiang , Pokhrel Yadu , Farinotti Daniel , Wang Jida , Singh Vijay P. , Xu Chong-Yu 
Published: December 2023

AbstractIntensifying droughts under climatic warming are of widespread concern owing to their devastating impacts on water resources, societies and ecosystems. However, the effects of exogeneous drivers on regional droughts remain poorly understood. Using the Lagrangian method, atmospheric reanalysis data and climate projections from the Coupled Model Inter-comparison Project phase 6 (CMIP6), we show how exogenous precipitation minus evaporation (PME) deficit drives droughts across China. More specifically, we demonstrate that four distinct trajectories of such exogenous PME deficit fuel regional droughts. Three of these trajectories relate to oceanic PME deficit originating from the North Atlantic, eastern Bering Sea and Indian Ocean, and one trajectory characterizes exogenous terrestrial PME deficit from the Siberian Plateau. We show that during 1980–2020, droughts induced by exogenous PME deficit account for 45% of all droughts that occurred in China’s coastal region, and for 7% of all droughts in the northwestern regions. Under climate scenario SSP245 (SSP585), limiting warming to 1.5 °C compared to 2 °C above pre-industrial levels could avoid 60% (84%) of exogenous drought exposure. This would in turn reduce population exposure by 40% (49%), and economic exposure by 73% (66%). Our study unravels how exogenous PME deficit drives droughts in China, underscoring the role that external drivers have on regional droughts and associated future prediction.
Chromatin regulator SMARCAL1 modulates cellular lipid metabolism
Authors: Nagai Taylor Hanta , Hartigan Chrissy , Mizoguchi Taiji , Yu Haojie , Deik Amy , Bullock Kevin , Wang Yanyan , Cromley Debra , Schenone Monica , Cowan Chad A. , Rader Daniel J. , Clish Clary B. , Carr Steven A. , Xu Yu-Xin 
Published: December 2023

AbstractBiallelic mutations of the chromatin regulator SMARCAL1 cause Schimke Immunoosseous Dysplasia (SIOD), characterized by severe growth defects and premature mortality. Atherosclerosis and hyperlipidemia are common among SIOD patients, yet their onset and progression are poorly understood. Using an integrative approach involving proteomics, mouse models, and population genetics, we investigated SMARCAL1’s role. We found that SmarcAL1 interacts with angiopoietin-like 3 (Angptl3), a key regulator of lipoprotein metabolism. In vitro and in vivo analyses demonstrate SmarcAL1’s vital role in maintaining cellular lipid homeostasis. The observed translocation of SmarcAL1 to cytoplasmic peroxisomes suggests a potential regulatory role in lipid metabolism through gene expression. SmarcAL1 gene inactivation reduces the expression of key genes in cellular lipid catabolism. Population genetics investigations highlight significant associations between SMARCAL1 genetic variations and body mass index, along with lipid-related traits. This study underscores SMARCAL1’s pivotal role in cellular lipid metabolism, likely contributing to the observed lipid phenotypes in SIOD patients.
Atomistic ensemble of active SHP2 phosphatase
Authors: Anselmi Massimiliano , Hub Jochen S. 
Published: December 2023

AbstractSHP2 phosphatase plays an important role in regulating several intracellular signaling pathways. Pathogenic mutations of SHP2 cause developmental disorders and are linked to hematological malignancies and cancer. SHP2 comprises two tandemly-arranged SH2 domains, a catalytic PTP domain, and a disordered C-terminal tail. Under physiological, non-stimulating conditions, the catalytic site of PTP is occluded by the N-SH2 domain, so that the basal activity of SHP2 is low. Whereas the autoinhibited structure of SHP2 has been known for two decades, its active, open structure still represents a conundrum. Since the oncogenic mutant SHP2E76K almost completely populates the active, open state, this mutant has been extensively studied as a model for activated SHP2. By molecular dynamics simulations and accurate explicit-solvent SAXS curve predictions, we present the heterogeneous atomistic ensemble of constitutively active SHP2E76K in solution, encompassing a set of conformational arrangements and radii of gyration in agreement with experimental SAXS data.
Impaired FADD/BID signaling mediates cross-resistance to immunotherapy in Multiple Myeloma
Authors: Munawar Umair , Zhou Xiang , Prommersberger Sabrina , Nerreter Silvia , Vogt Cornelia , Steinhardt Maximilian J. , Truger Marietta , Mersi Julia , Teufel Eva , Han Seungbin , Haertle Larissa , Banholzer Nicole , Eiring Patrick , Danhof Sophia , Navarro-Aguadero Miguel Angel , Fernandez-Martin Adrian , Ortiz-Ruiz Alejandra , Barrio Santiago , Gallardo Miguel , Valeri Antonio , Castellano Eva , Raab Peter , Rudert Maximilian , Haferlach Claudia , Sauer Markus , Hudecek Michael , Martinez-Lopez J. , Waldschmidt Johannes , Einsele Hermann , Rasche Leo , Kortüm K. Martin 
Published: December 2023

AbstractThe treatment landscape in multiple myeloma (MM) is shifting from genotoxic drugs to immunotherapies. Monoclonal antibodies, immunoconjugates, T-cell engaging antibodies and CART cells have been incorporated into routine treatment algorithms, resulting in improved response rates. Nevertheless, patients continue to relapse and the underlying mechanisms of resistance remain poorly understood. While Impaired death receptor signaling has been reported to mediate resistance to CART in acute lymphoblastic leukemia, this mechanism yet remains to be elucidated in context of novel immunotherapies for MM. Here, we describe impaired death receptor signaling as a novel mechanism of resistance to T-cell mediated immunotherapies in MM. This resistance seems exclusive to novel immunotherapies while sensitivity to conventional anti-tumor therapies being preserved in vitro. As a proof of concept, we present a confirmatory clinical case indicating that the FADD/BID axis is required for meaningful responses to novel immunotherapies thus we report impaired death receptor signaling as a novel resistance mechanism to T-cell mediated immunotherapy in MM.
Optimal tagging strategies for illuminating expression profiles of genes with different abundance in zebrafish
Authors: Liu Jiannan , Li Wenyuan , Jin Xuepu , Lin Fanjia , Han Jiahuai , Zhang Yingying 
Published: December 2023

AbstractCRISPR-mediated knock-in (KI) technology opens a new era of fluorescent-protein labeling in zebrafish, a preferred model organism for in vivo imaging. We described here an optimized zebrafish gene-tagging strategy, which enables easy and high-efficiency KI, ensures high odds of obtaining seamless KI germlines and is suitable for wide applications. Plasmid donors for 3′-labeling were optimized by shortening the microhomologous arms and by reducing the number and reversing the sequence of the consensus Cas9/sgRNA binding sites. To allow for scar-less KI across the genome, linearized dsDNA donors with 5′-chemical modifications were generated and successfully incorporated into our method. To refine the germline screen workflow and expedite the screen process, we combined fluorescence enrichment and caudal-fin junction-PCR. Furthermore, to trace proteins expressed at a low abundance, we developed a fluorescent signal amplifier using the transcriptional activation strategy. Together, our strategies enable efficient gene-tagging and sensitive expression detection for almost every gene in zebrafish.
Efficiency limit of transition metal dichalcogenide solar cells
Authors: Nassiri Nazif Koosha , Nitta Frederick U. , Daus Alwin , Saraswat Krishna C. , Pop Eric 
Published: December 2023

AbstractUltrathin transition metal dichalcogenide (TMD) films show great promise as absorber materials in high-specific-power (i.e., high-power-per-weight) solar cells, due to their high optical absorption, desirable band gaps, and self-passivated surfaces. However, the ultimate performance limits of TMD solar cells remain unknown today. Here, we establish the efficiency limits of multilayer (≥5 nm-thick) MoS2, MoSe2, WS2, and WSe2 solar cells under AM 1.5 G illumination as a function of TMD film thickness and material quality. We use an extended version of the detailed balance method which includes Auger and defect-assisted Shockley-Read-Hall recombination mechanisms in addition to radiative losses, calculated from measured optical absorption spectra. We demonstrate that single-junction solar cells with TMD films as thin as 50 nm could in practice achieve up to 25% power conversion efficiency with the currently available material quality, making them an excellent choice for high-specific-power photovoltaics.
Weak signal extraction in non-stationary channel with weak measurement
Authors: Song Qi , Li Hongjing , Huang Jingzheng , Huang Peng , Tan Xiaorui , Tao Yu , Shi Chunhui , Zeng Guihua 
Published: December 2023

AbstractAn emerging challenge of integrated communication and sensing is the extraction of weak sensing signals transmitted through an unknown non-stationary channel. In this work, we propose a weak signal extraction method with weak measurement. Taking advantage of time division multiplexing, we preliminarily estimate the channel via adjustable finite impulse response filter, further suppressing the interfering signal caused by background noises via spectrum shift. By subsequently using the time-varying phase estimation method via weak measurement, the real-time detection of weak signals in the non-stationary channel is achieved. We demonstrate via theoretical analysis and confirmatory experiment that our method is able to amplify the phase shift, to suppress technical noise and to improve detection resolution limit, while proving robust against light source fluctuations, initial phase differences and detector saturation. The method hence enables weak sensing signal extraction with a low signal-to-noise ratio non-stationary channel. Furthermore, we interface our measurement method to squeezed light sources, offering the possibility of surpassing standard quantum limit.
Nonlinear electrical transport phenomena as fingerprints of a topological phase transition in ZrTe5
Authors: Salawu Yusuff Adeyemi , Adhikari Dilanath , Kim Jin Hee , Rhyee Jong-Soo , Sasaki Minoru , Kim Ki-Seok , Kim Heon-Jung 
Published: December 2023

AbstractTopological phase transitions, influenced by magnetic fields, dopants, pressure, and temperature, create Berry curvature in band structures, challenging to detect due to resolution and scattering issues in spectroscopy and transport. Here, we propose nonlinear electrical transport phenomena as fingerprints of a topological phase transition in ZrTe5 under magnetic fields. Both a nonlinear longitudinal conductivity ΔσL in a magnetic-field-aligned electric field and a third-order nonlinear Hall (transverse) conductivity Δσxy in a magnetic-field-perpendicular electric field arise below a characteristic temperature T*. The sensitivity of nonlinear transport to the band topology allows the detection of a subtle change in the band topology hidden in linear transport coefficients. Extending the previous scaling theory between linear transport coefficients (σxx and σxy), we also propose scaling relations for both linear (σxx and σxy) and nonlinear (ΔσL and Δσxy) transport coefficients. These scaling relations will help understand the interplay between the mechanisms of nonlinear transport coefficients and the influence of Berry curvature.
Biochar-plant interactions enhance nonbiochar carbon sequestration in a rice paddy soil
Authors: Liu Zhiwei , Zhang Wei , Ma Ruiling , Li Shixian , Song Kaiyue , Zheng Jufeng , Wang Yan , Bian Rongjun , Zhang Xuhui , Pan Genxing 
Published: December 2023

AbstractSoil amendment with biochar is being promoted as a promising strategy for carbon (C) stabilization and accrual, which are key to climate change mitigation. However, it remains elusive on how biochar addition influences nonbiochar C in soils and its mechanisms, especially in the presence of plants. Here we conducted a 365-day soil microcosm experiment with and without adding 13C-labeled biochar into topsoil to quantify changes in nonbiochar C in the topsoil and subsoil in the presence or absence of rice plants and to determine the mechanisms by which biochar controls nonbiochar C accrual in the soil profile. The nonbiochar C content of topsoil was not affected by biochar addition in the absence of rice plants, but was significantly increased by 4.5% in the presence of rice plants, which could result from increases in the soil macroaggregate fraction, iron (Fe)-bound nonbiochar organic C content, and fungal biomass collectively. However, biochar amendment had no effect on the content of nonbiochar organic C in the subsoil. Overall, biochar-plant interactions drive more nonbiochar C sequestration in the topsoil, and the changes of nonbiochar C in planted soils following biochar addition should be quantified to better assess the soil C sequestration potential in agricultural lands.