bluuebunny/crossref_metadata_2025_split huggingface dataset:
Magnetic droplet soliton pairs
Authors: Jiang S. , Chung S. , Ahlberg M. , Frisk A. , Khymyn R. , Le Q. Tuan , Mazraati H. , Houshang A. , Heinonen O. , Åkerman J. 
Published: March 2024

AbstractWe demonstrate magnetic droplet soliton pairs in all-perpendicular spin-torque nano-oscillators (STNOs), where one droplet resides in the STNO free layer (FL) and the other in the reference layer (RL). Typically, theoretical, numerical, and experimental droplet studies have focused on the FL, with any additional dynamics in the RL entirely ignored. Here we show that there is not only significant magnetodynamics in the RL, but the RL itself can host a droplet driven by, and coexisting with, the FL droplet. Both single droplets and pairs are observed experimentally as stepwise changes and sharp peaks in the dc and differential resistance, respectively. While the single FL droplet is highly stable, the coexistence state exhibits high-power broadband microwave noise. Furthermore, micromagnetic simulations reveal that the pair dynamics display periodic, quasi-periodic, and chaotic signatures controlled by applied field and current. The strongly interacting and closely spaced droplet pair offers a unique platform for fundamental studies of highly non-linear soliton pair dynamics.
Acidity-activatable upconversion afterglow luminescence cocktail nanoparticles for ultrasensitive in vivo imaging
Authors: Jiang Yue , Zhao Min , Miao Jia , Chen Wan , Zhang Yuan , Miao Minqian , Yang Li , Li Qing , Miao Qingqing 
Published: March 2024

AbstractActivatable afterglow luminescence nanoprobes enabling switched “off-on” signals in response to biomarkers have recently emerged to achieve reduced unspecific signals and improved imaging fidelity. However, such nanoprobes always use a biomarker-interrupted energy transfer to obtain an activatable signal, which necessitates a strict distance requisition between a donor and an acceptor moiety (<10 nm) and hence induces low efficiency and non-feasibility. Herein, we report organic upconversion afterglow luminescence cocktail nanoparticles (ALCNs) that instead utilize acidity-manipulated singlet oxygen (1O2) transfer between a donor and an acceptor moiety with enlarged distance and thus possess more efficiency and flexibility to achieve an activatable afterglow signal. After in vitro validation of acidity-activated afterglow luminescence, ALCNs achieve in vivo imaging of 4T1-xenograft subcutaneous tumors in female mice and orthotopic liver tumors in male mice with a high signal-to-noise ratio (SNR). As a representative targeting trial, Bio-ALCNs with biotin modification prove the enhanced targeting ability, sensitivity, and specificity for pulmonary metastasis and subcutaneous tumor imaging via systemic administration of nanoparticles in female mice, which also implies the potential broad utility of ALCNs for tumor imaging with diverse design flexibility. Therefore, this study provides an innovative and general approach for activatable afterglow imaging with better imaging performance than fluorescence imaging.
N-Acetyltransferase 10 represses Uqcr11 and Uqcrb independently of ac4C modification to promote heart regeneration
Authors: Ma Wenya , Tian Yanan , Shi Leping , Liang Jing , Ouyang Qimeng , Li Jianglong , Chen Hongyang , Sun Hongyue , Ji Haoyu , Liu Xu , Huang Wei , Gao Xinlu , Jin Xiaoyan , Wang Xiuxiu , Liu Yining , Yu Yang , Guo Xiaofei , Tian Ye , Yang Fan , Li Faqian , Wang Ning , Cai Benzhi 
Published: March 2024

AbstractTranslational control is crucial for protein production in various biological contexts. Here, we use Ribo-seq and RNA-seq to show that genes related to oxidative phosphorylation are translationally downregulated during heart regeneration. We find that Nat10 regulates the expression of Uqcr11 and Uqcrb mRNAs in mouse and human cardiomyocytes. In mice, overexpression of Nat10 in cardiomyocytes promotes cardiac regeneration and improves cardiac function after injury. Conversely, treating neonatal mice with Remodelin—a Nat10 pharmacological inhibitor—or genetically removing Nat10 from their cardiomyocytes both inhibit heart regeneration. Mechanistically, Nat10 suppresses the expression of Uqcr11 and Uqcrb independently of its ac4C enzyme activity. This suppression weakens mitochondrial respiration and enhances the glycolytic capacity of the cardiomyocytes, leading to metabolic reprogramming. We also observe that the expression of Nat10 is downregulated in the cardiomyocytes of P7 male pig hearts compared to P1 controls. The levels of Nat10 are also lower in female human failing hearts than non-failing hearts. We further identify the specific binding regions of Nat10, and validate the pro-proliferative effects of Nat10 in cardiomyocytes derived from human embryonic stem cells. Our findings indicate that Nat10 is an epigenetic regulator during heart regeneration and could potentially become a clinical target.
The global speciation continuum of the cyanobacterium Microcoleus
Authors: Stanojković Aleksandar , Skoupý Svatopluk , Johannesson Hanna , Dvořák Petr 
Published: March 2024

AbstractSpeciation is a continuous process driven by genetic, geographic, and ecological barriers to gene flow. It is widely investigated in multicellular eukaryotes, yet we are only beginning to comprehend the relative importance of mechanisms driving the emergence of barriers to gene flow in microbial populations. Here, we explored the diversification of the nearly ubiquitous soil cyanobacteriumMicrocoleus. Our dataset consisted of 291 genomes, of which 202 strains and eight herbarium specimens were sequenced for this study. We found thatMicrocoleusrepresents a global speciation continuum of at least 12 lineages, which radiated during Eocene/Oligocene aridification and exhibit varying degrees of divergence and gene flow. The lineage divergence has been driven by selection, geographical distance, and the environment. Evidence of genetic divergence and selection was widespread across the genome, but we identified regions of exceptional differentiation containing candidate genes associated with stress response and biosynthesis of secondary metabolites.
Antiviral responses induced by Tdap-IPV vaccination are associated with persistent humoral immunity to Bordetella pertussis
Authors: Gillard Joshua , Suffiotti Madeleine , Brazda Peter , Venkatasubramanian Prashanna B. , Versteegen Pauline , de Jonge Marien I. , Kelly Dominic , Bibi Sagida , Pinto Marta Valente , Simonetti Elles , Babiceanu Mihaela , Kettring Andrew , Teodosio Cristina , de Groot Ronald , Berbers Guy , Stunnenberg Hendrik G. , Schanen Brian , Fenwick Craig , Huynen Martijn A. , Diavatopoulos Dimitri A. 
Published: March 2024

AbstractMany countries continue to experience pertussis epidemics despite widespread vaccination. Waning protection after booster vaccination has highlighted the need for a better understanding of the immunological factors that promote durable protection. Here we apply systems vaccinology to investigate antibody responses in adolescents in the Netherlands (N = 14; NL) and the United Kingdom (N = 12; UK) receiving a tetanus-diphtheria-acellular pertussis-inactivated poliovirus (Tdap-IPV) vaccine. We report that early antiviral and interferon gene expression signatures in blood correlate to persistence of pertussis-specific antibody responses. Single-cell analyses of the innate response identified monocytes and myeloid dendritic cells (MoDC) as principal responders that upregulate antiviral gene expression and type-I interferon cytokine production. With public data, we show that Tdap vaccination stimulates significantly lower antiviral/type-I interferon responses than Tdap-IPV, suggesting that IPV may promote antiviral gene expression. Subsequent in vitro stimulation experiments demonstrate TLR-dependent, IPV-specific activation of the pro-inflammatory p38 MAP kinase pathway in MoDCs. Together, our data provide insights into the molecular host response to pertussis booster vaccination and demonstrate that IPV enhances innate immune activity associated with persistent, pertussis-specific antibody responses.
Dynamic feedback bit-level image privacy protection based on chaos and information hiding
Authors: Zhang Jinlong , Wen Heping 
Published: March 2024

AbstractBit is the most basic unit of a digital image in the spatial domain, and bit-level encryption is regarded as an important technical means for digital image privacy protection. To address the vulnerability of image privacy protection to cryptographic attacks, in this paper, a bit-level image privacy protection scheme using Zigzag and chain-diffusion is proposed. The scheme uses a combination of Zigzag interleaving scrambling with chaotic sequences and chain-diffusion method images are encrypted at each bit level, while using non-sequential encryption to achieve efficient and secure encryption. To balance security and efficiency, the encryption strategy for each bit layer is weighted. The chaos-based sequences used for encryption depend on the previous hash value, thus the effect of chain-diffusion is achieved. To further enhance the encryption effect, a non-sequential encryption technique by non-linearly rearranging the bit cipher image is employed, so that the attacker cannot crack the protection scheme by analyzing the encrypted image. The ciphertext image hidden by discrete wavelet transform (DWT) also provides efficient encryption, higher level of security and robustness to attacks. This technology provides indistinguishable secret data embedding, making it difficult for attackers to detect or extract hidden information. Experimental results show that this scheme can effectively protect the confidentiality of the image and can resist various common cryptographic attacks. The scheme proposed in this paper is a preferred digital image privacy protection technology, so it has broad application prospects in image secure transmission occasions.
Aryl hydrocarbon receptor suppresses STING-mediated type I IFN expression in triple-negative breast cancer
Authors: Martin Jeffrey C. , da Silva Fernandes Tatiane , Chaudhry Kanita A. , Oshi Masanori , Abrams Scott I. , Takabe Kazuaki , Rosario Spencer R. , Bianchi-Smiraglia Anna 
Published: March 2024

AbstractTriple-negative breast cancer (TNBC) is one of the most aggressive types of cancer. Despite decades of intense investigation, treatment options remain limited, and rapid recurrence with distant metastases remains a significant challenge. Cancer cell-intrinsic production of cytokines such as type I interferons (IFN-I) is a known potent modulator of response to therapy in many cancers, including TNBC, and can influence therapeutic outcome. Here, we report that, in TNBC systems, the aryl hydrocarbon receptor (AhR) suppresses IFN-I expression via inhibition of STImulator of Interferon Genes (STING), a key mediator of interferon production. Intratumoral STING activity is essential in mediating the efficacy of PARP inhibitors (PARPi) which are used in the treatment of cancers harboring BRCA1 deficiency. We find that, in TNBC cells, PARPi treatment activates AhR in a BRCA1 deficiency-dependent manner, thus suggesting the presence of a negative feedback loop aimed at modulating PARPi efficacy. Importantly, our results indicate that the combined inhibition of PARP and AhR is superior in elevating IFN-I expression as compared to PARPi-alone. Thus, AhR inhibition may allow for enhanced IFN-I production upon PARPi in BRCA1-deficient breast cancers, most of which are of TNBC origin, and may represent a therapeutically viable strategy to enhance PARPi efficacy.
High gain antipodal meander line antenna for point-to-point WLAN/WiMAX applications
Authors: Gad Mohamed M. , Sallam Mai O. 
Published: March 2024

AbstractThis paper introduces a planar antipodal meander line antenna fabricated using RO3003 substrate. The proposed antenna is designed to radiate in the end-fire direction, achieving a maximum measured gain of 10.43 dBi within its working bandwidth, which ranges from 2.24 GHz to 2.7 GHz, covering long-range WLAN/WiMAX applications. A systematic procedure is adopted in the design process to prove its tunability to cover other application requirements in terms of gain and bandwidth. The proposed design steps show that the bandwidth and the gain can independently be controlled by adjusting specific design parameters such as the number of radiators and the scaling factor. The antenna is fine-tuned using sensitivity analysis and parametric study to guarantee optimum operation at the desired bandwidth. Experimental measurements of the fabricated design demonstrate a high degree of correlation with simulations conducted using CST and HFSS. In comparison to other end-fire antennas presented in the literature, the proposed design manifests its capability to provide high gain for WLAN/WiMAX nodes connectivity. The measurements show that the proposed traveling wave antenna exhibits a high radiation efficiency with maximum value of 99.8% at 2.35 GHz. The measured side lobe level is found to be below $$-18$$

-
18

dB and $$-20$$

-
20

dB at 2.45 GHz along the $$E$$
E
- and $$H$$
H
-planes, respectively. Apart from its excellent radiation performance, the antenna is characterized by its low profile and fabrication simplicity.
The clinical relevance of a polygenic risk score for type 2 diabetes mellitus in the Korean population
Authors: Kim Na Yeon , Lee Haekyung , Kim Sehee , Kim Ye-Jee , Lee Hyunsuk , Lee Junhyeong , Kwak Soo Heon , Lee Seunggeun 
Published: March 2024

AbstractThe clinical utility of a type 2 diabetes mellitus (T2DM) polygenic risk score (PRS) in the East Asian population remains underexplored. We aimed to examine the potential prognostic value of a T2DM PRS and assess its viability as a clinical instrument. We first established a T2DM PRS for 5490 Korean individuals using East Asian Biobank data (269,487 samples). Subsequently, we assessed the predictive capability of this T2DM PRS in a prospective longitudinal study with baseline data and data from seven additional follow-ups. Our analysis showed that the T2DM PRS could predict the transition of glucose tolerance stages from normal glucose tolerance to prediabetes and from prediabetes to T2DM. Moreover, T2DM patients in the top-decile PRS group were more likely to be treated with insulin (hazard ratio = 1.69, p value = 2.31E−02) than were those in the remaining PRS groups. T2DM PRS values were significantly high in the severe diabetes subgroup, characterized by insulin resistance and $$\beta$$
β
-cell dysfunction (p value = 0.0012). The prediction models with the T2DM PRS had significantly greater Harrel’s C-indices than did corresponding models without it. By utilizing prospective longitudinal study data and extensive clinical risk factor information, our analysis provides valuable insights into the multifaceted clinical utility of the T2DM PRS.
Effects of macro- and micro-nutrients on momentary and season-long feeding responses by select species of ants
Authors: Renyard Asim , Gooding Claire , Chalissery Jaime M. , Petrov Jonathan , Gries Gerhard 
Published: March 2024

AbstractFew studies have investigated the relative contribution of specific nutrients to momentary and season-long foraging responses by ants. Using western carpenter ants, Camponotus modoc, and European fire ants, Myrmica rubra, as model species, we: (1) tested preferential consumption of various macro- and micro-nutrients; (2) compared consumption of preferred macro-nutrients; (3) investigated seasonal shifts (late May to mid-September) in nutrient preferences; and (4) tested whether nutrient preferences of C. modoc and M. rubra pertain to black garden ants, Lasius niger, and thatching ants, Formica aserva. In laboratory and field experiments, we measured nutrient consumption by weighing Eppendorf tubes containing aqueous nutrient solutions before and after feeding by ants. Laboratory colonies of C. modoc favored nitrogenous urea and essential amino acids (EAAs), whereas M. rubra colonies favored sucrose. Field colonies of C. modoc and M. rubra preferentially consumed EAAs and sucrose, respectively, with no sustained shift in preferred macro-nutrient over the course of the foraging season. The presence of a less preferred macro-nutrient in a nutrient blend did not diminish the blend’s ‘appeal’ to foraging ants. Sucrose and EAAs singly and in combination were equally consumed by L. niger, whereas F. aserva preferred EAAs. Baits containing both sucrose and EAAs were consistently consumed by the ants studied in this project and should be considered for pest ant control.
Viral genome sequencing to decipher in-hospital SARS-CoV-2 transmission events
Authors: Esser Elisabeth , Schulte Eva C. , Graf Alexander , Karollus Alexander , Smith Nicholas H. , Michler Thomas , Dvoretskii Stefan , Angelov Angel , Sonnabend Michael , Peter Silke , Engesser Christina , Radonic Aleksandar , Thürmer Andrea , von Kleist Max , Gebhardt Friedemann , da Costa Clarissa Prazeres , Busch Dirk H. , Muenchhoff Maximilian , Blum Helmut , Keppler Oliver T. , Gagneur Julien , Protzer Ulrike 
Published: March 2024

AbstractThe SARS-CoV-2 pandemic has highlighted the need to better define in-hospital transmissions, a need that extends to all other common infectious diseases encountered in clinical settings. To evaluate how whole viral genome sequencing can contribute to deciphering nosocomial SARS-CoV-2 transmission 926 SARS-CoV-2 viral genomes from 622 staff members and patients were collected between February 2020 and January 2021 at a university hospital in Munich, Germany, and analysed along with the place of work, duration of hospital stay, and ward transfers. Bioinformatically defined transmission clusters inferred from viral genome sequencing were compared to those inferred from interview-based contact tracing. An additional dataset collected at the same time at another university hospital in the same city was used to account for multiple independent introductions. Clustering analysis of 619 viral genomes generated 19 clusters ranging from 3 to 31 individuals. Sequencing-based transmission clusters showed little overlap with those based on contact tracing data. The viral genomes were significantly more closely related to each other than comparable genomes collected simultaneously at other hospitals in the same city (n = 829), suggesting nosocomial transmission. Longitudinal sampling from individual patients suggested possible cross-infection events during the hospital stay in 19.2% of individuals (14 of 73 individuals). Clustering analysis of SARS-CoV-2 whole genome sequences can reveal cryptic transmission events missed by classical, interview-based contact tracing, helping to decipher in-hospital transmissions. These results, in line with other studies, advocate for viral genome sequencing as a pathogen transmission surveillance tool in hospitals.
Kernel Bayesian nonlinear matrix factorization based on variational inference for human–virus protein–protein interaction prediction
Authors: Ma Yingjun , Zhao Yongbiao , Ma Yuanyuan 
Published: March 2024

AbstractIdentification of potential human–virus protein–protein interactions (PPIs) contributes to the understanding of the mechanisms of viral infection and to the development of antiviral drugs. Existing computational models often have more hyperparameters that need to be adjusted manually, which limits their computational efficiency and generalization ability. Based on this, this study proposes a kernel Bayesian logistic matrix decomposition model with automatic rank determination, VKBNMF, for the prediction of human–virus PPIs. VKBNMF introduces auxiliary information into the logistic matrix decomposition and sets the prior probabilities of the latent variables to build a Bayesian framework for automatic parameter search. In addition, we construct the variational inference framework of VKBNMF to ensure the solution efficiency. The experimental results show that for the scenarios of paired PPIs, VKBNMF achieves an average AUPR of 0.9101, 0.9316, 0.8727, and 0.9517 on the four benchmark datasets, respectively, and for the scenarios of new human (viral) proteins, VKBNMF still achieves a higher hit rate. The case study also further demonstrated that VKBNMF can be used as an effective tool for the prediction of human–virus PPIs.
Mitochondrial DNA mutations in Korean patients with Leber’s hereditary optic neuropathy
Authors: Yang Hee Kyung , Seong Moon-Woo , Hwang Jeong-Min 
Published: March 2024

AbstractIn order to explore the spectrum of mitochondrial DNA (mtDNA) mutations in Korean patients with Leber's hereditary optic neuropathy (LHON), we investigated the spectrum of mtDNA mutations in 145 Korean probands confirmed with the diagnosis of LHON. Total genomic DNA was isolated from the peripheral blood leukocytes of the patients with suspected LHON, and mtDNA mutations were identified by direct sequencing. Analysis of mtDNA mutations revealed seven primary LHON mutations including the nucleotide positions (nps) 11778A (101 probands, 69.2%), 14484C (31 probands, 21.2%), 3460A (5 probands, 3.4%), and G3635A, G3733A, C4171A, and G13051A mutations in one proband each. In addition, two provisional mtDNA mutations at nps T3472C, and G13259A were each found in one proband, respectively. Another provisional mtDNA mutation at np T3394C was found in two probands. In conclusion, the spectrum of mtDNA mutations in Korean patients with LHON may differ from other ethnicities, which is characterized by high prevalence of 11778A and 14484C mutations, and a low prevalence of the 3460A mutation.
Metabolic maturation in the infant urine during the first 3 months of life
Authors: Astono Julie , Poulsen Katrine O. , Larsen Rikke A. , Jessen Emma V. , Sand Chatrine B. , Rasmussen Morten A. , Sundekilde Ulrik K. 
Published: March 2024

AbstractThe infant urine metabolome provides a body metabolic snapshot, and the sample collection can be done without stressing the fragile infant. 424 infant urine samples from 157 infants were sampled longitudinally at 1-, 2-, and 3 months of age. 49 metabolites were detected using proton nuclear magnetic resonance spectroscopy. Data were analyzed with multi- and univariate statistical methods to detect differences related to infant age-stage, gestational age, mother’s pre-pregnancy BMI, C-section, infant birth weight, and infant sex. Significant differences were identified between age-stage (pbonferoni < 0.05) in 30% (15/49) of the detected metabolites. Urine creatinine increased significantly from 1 to 3 months. In addition, myo-inositol, taurine, methionine, and glucose seem to have conserved levels within the individual over time. We calculated a urine metabolic maturation age and found that the metabolic age at 3 months is negatively correlated to weight at 1 year. These results demonstrate that the metabolic maturation can be observed in urine metabolome with implications on infant growth and specifically suggesting that the systematic age effect on creatinine promotes caution in using this as normalization of other urine metabolites.