bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeting pro-inflammatory T cells as a novel therapeutic approach to potentially resolve atherosclerosis in humans
Authors: Fan Lin , Liu Junwei , Hu Wei , Chen Zexin , Lan Jie , Zhang Tongtong , Zhang Yang , Wu Xianpeng , Zhong Zhiwei , Zhang Danyang , Zhang Jinlong , Qin Rui , Chen Hui , Zong Yunfeng , Zhang Jianmin , Chen Bing , Jiang Jun , Cheng Jifang , Zhou Jingyi , Gao Zhiwei , Liu Zhenjie , Chai Ying , Fan Junqiang , Wu Pin , Chen Yinxuan , Zhu Yuefeng , Wang Kai , Yuan Ying , Huang Pintong , Zhang Ying , Feng Huiqin , Song Kaichen , Zeng Xun , Zhu Wei , Hu Xinyang , Yin Weiwei , Chen Wei , Wang Jian’an 
Published: March 2024

AbstractAtherosclerosis (AS), a leading cause of cardio-cerebrovascular disease worldwide, is driven by the accumulation of lipid contents and chronic inflammation. Traditional strategies primarily focus on lipid reduction to control AS progression, leaving residual inflammatory risks for major adverse cardiovascular events (MACEs). While anti-inflammatory therapies targeting innate immunity have reduced MACEs, many patients continue to face significant risks. Another key component in AS progression is adaptive immunity, but its potential role in preventing AS remains unclear. To investigate this, we conducted a retrospective cohort study on tumor patients with AS plaques. We found that anti-programmed cell death protein 1 (PD-1) monoclonal antibody (mAb) significantly reduces AS plaque size. With multi-omics single-cell analyses, we comprehensively characterized AS plaque-specific PD-1+ T cells, which are activated and pro-inflammatory. We demonstrated that anti-PD-1 mAb, when captured by myeloid-expressed Fc gamma receptors (FcγRs), interacts with PD-1 expressed on T cells. This interaction turns the anti-PD-1 mAb into a substitute PD-1 ligand, suppressing T-cell functions in the PD-1 ligands-deficient context of AS plaques. Further, we conducted a prospective cohort study on tumor patients treated with anti-PD-1 mAb with or without FcγR-binding capability. Our analysis shows that anti-PD-1 mAb with FcγR-binding capability effectively reduces AS plaque size, while anti-PD-1 mAb without FcγR-binding capability does not. Our work suggests that T cell-targeting immunotherapy can be an effective strategy to resolve AS in humans.
Early exposure to sugar sweetened beverages or fruit juice differentially influences adult adiposity
Authors: Benton David , Young Hayley A. 
Published: March 2024

Abstract
Objective
To examine associations between different types of sweet drinks consumed in early life and adult adiposity.

Design
The analysis involved the secondary analysis of the Avon Longitudinal Study of Parents and Children which followed children from birth to 24 years. Adiposity was measured using Dual-energy X-ray absorptiometry while food frequency questionnaires and diaries monitored diet. ‘Early exposure’ to sweet drinks was defined as giving a sugar-sweetened beverage or 100% fruit juice (FJ), before two years of age.

Results
Early exposure to cola was associated with higher fat mass, android fat mass and BMI at age 24 years; whereas early exposure to apple juice was associated with lower adult adiposity in females but not males. When age three, exposure to cola was associated with a greater intake of energy, carbohydrates, protein, fat, and less fruit and more fried foods. In contrast, early exposure to apple juice was associated with higher protein and lower fat intakes and consuming more fruits/vegetables and less fried foods. Parental education, adiposity and socio-economic status influenced whether SSB or FJ was given to a child.

Conclusions
Early drinking of sugar sweetened beverages was associated with a less healthy dietary pattern, and greater adult adiposity. Early drinking of apple juice was associated with a healthier dietary pattern, and lower fat mass in adult females. The choice of drink was associated with social deprivation. As the dietary causes of adult obesity begin in early childhood, increased attention should be given to diet in the first years of life.
Biobased and biodegradable films exhibiting circularly polarized room temperature phosphorescence
Authors: Cao Mengnan , Ren Yiran , Wu Yue , Shen Jingjie , Li Shujun , Yu Zhen-Qiang , Liu Shouxin , Li Jian , Rojas Orlando J. , Chen Zhijun 
Published: March 2024

AbstractThere is interest in developing sustainable materials displaying circularly polarized room-temperature phosphorescence, which have been scarcely reported. Here, we introduce biobased thin films exhibiting circularly polarized luminescence with simultaneous room-temperature phosphorescence. For this purpose, phosphorescence-active lignosulfonate biomolecules are co-assembled with cellulose nanocrystals in a chiral construct. The lignosulfonate is shown to capture the chirality generated by cellulose nanocrystals within the films, emitting circularly polarized phosphorescence with a 0.21 dissymmetry factor and 103 ms phosphorescence lifetime. By contrast with most organic phosphorescence materials, this chiral-phosphorescent system possesses phosphorescence stability, with no significant recession under extreme chemical environments. Meanwhile, the luminescent films resist water and humid environments but are fully biodegradable (16 days) in soil conditions. The introduced bio-based, environmentally-friendly circularly polarized phosphorescence system is expected to open many opportunities, as demonstrated here for information processing and anti-counterfeiting.
Advancing the scale of synthetic biology via cross-species transfer of cellular functions enabled by iModulon engraftment
Authors: Choe Donghui , Olson Connor A. , Szubin Richard , Yang Hannah , Sung Jaemin , Feist Adam M. , Palsson Bernhard O. 
Published: March 2024

AbstractMachine learning applied to large compendia of transcriptomic data has enabled the decomposition of bacterial transcriptomes to identify independently modulated sets of genes, such iModulons represent specific cellular functions. The identification of iModulons enables accurate identification of genes necessary and sufficient for cross-species transfer of cellular functions. We demonstrate cross-species transfer of: 1) the biotransformation of vanillate to protocatechuate, 2) a malonate catabolic pathway, 3) a catabolic pathway for 2,3-butanediol, and 4) an antimicrobial resistance to ampicillin found in multiple Pseudomonas species to Escherichia coli. iModulon-based engineering is a transformative strategy as it includes all genes comprising the transferred cellular function, including genes without functional annotation. Adaptive laboratory evolution was deployed to optimize the cellular function transferred, revealing mutations in the host. Combining big data analytics and laboratory evolution thus enhances the level of understanding of systems biology, and synthetic biology for strain design and development.
Dislocation Majorana bound states in iron-based superconductors
Authors: Hu Lun-Hui , Zhang Rui-Xing 
Published: March 2024

AbstractWe show that lattice dislocations of topological iron-based superconductors such as FeTe1−xSex will intrinsically trap non-Abelian Majorana quasiparticles, in the absence of any external magnetic field. Our theory is motivated by the recent experimental observations of normal-state weak topology and surface magnetism that coexist with superconductivity in FeTe1−xSex, the combination of which naturally achieves an emergent second-order topological superconductivity in a two-dimensional subsystem spanned by screw or edge dislocations. This exemplifies a new embedded higher-order topological phase in class D, where Majorana zero modes appear around the “corners” of a low-dimensional embedded subsystem, instead of those of the full crystal. A nested domain wall theory is developed to understand the origin of these defect Majorana zero modes. When the surface magnetism is absent, we further find that s± pairing symmetry itself is capable of inducing a different type of class-DIII embedded higher-order topology with defect-bound Majorana Kramers pairs. We also provide detailed discussions on the real-world material candidates for our proposals, including FeTe1−xSex, LiFeAs, β-PdBi2, and heterostructures of bismuth, etc. Our work establishes lattice defects as a new venue to achieve high-temperature topological quantum information processing.
Clearance of persistent SARS-CoV-2 associates with increased neutralizing antibodies in advanced HIV disease post-ART initiation
Authors: Karim Farina , Riou Catherine , Bernstein Mallory , Jule Zesuliwe , Lustig Gila , van Graan Strauss , Keeton Roanne S. , Upton Janine-Lee , Ganga Yashica , Khan Khadija , Reedoy Kajal , Mazibuko Matilda , Govender Katya , Thambu Kershnee , Ngcobo Nokuthula , Venter Elizabeth , Makhado Zanele , Hanekom Willem , von Gottberg Anne , Hoque Monjurul , Karim Quarraisha Abdool , Abdool Karim Salim S. , Manickchund Nithendra , Magula Nombulelo , Gosnell Bernadett I. , Lessells Richard J. , Moore Penny L. , Burgers Wendy A. , de Oliveira Tulio , Moosa Mahomed-Yunus S. , Sigal Alex 
Published: March 2024

AbstractSARS-CoV-2 clearance requires adaptive immunity but the contribution of neutralizing antibodies and T cells in different immune states is unclear. Here we ask which adaptive immune responses associate with clearance of long-term SARS-CoV-2 infection in HIV-mediated immunosuppression after suppressive antiretroviral therapy (ART) initiation. We assembled a cohort of SARS-CoV-2 infected people in South Africa (n = 994) including participants with advanced HIV disease characterized by immunosuppression due to T cell depletion. Fifty-four percent of participants with advanced HIV disease had prolonged SARS-CoV-2 infection (>1 month). In the five vaccinated participants with advanced HIV disease tested, SARS-CoV-2 clearance associates with emergence of neutralizing antibodies but not SARS-CoV-2 specific CD8 T cells, while CD4 T cell responses were not determined due to low cell numbers. Further, complete HIV suppression is not required for clearance, although it is necessary for an effective vaccine response. Persistent SARS-CoV-2 infection led to SARS-CoV-2 evolution, including virus with extensive neutralization escape in a Delta variant infected participant. The results provide evidence that neutralizing antibodies are required for SARS-CoV-2 clearance in HIV-mediated immunosuppression recovery, and that suppressive ART is necessary to curtail evolution of co-infecting pathogens to reduce individual health consequences as well as public health risk linked with generation of escape mutants.
Imprint of urbanization on snow precipitation over the continental USA
Authors: Salvi Kaustubh Anil , Kumar Mukesh 
Published: March 2024

AbstractUrbanization can alter the local climate through modifications in land-atmosphere feedback. However, a continental scale evaluation of its influence on precipitation phase remains unknown. Here, we assess the difference in the likelihood of snow dominated events (SDEs) over 7,415 urban and surrounding non-urban (buffer) regions across the continental United States. Among 4,856 urban-buffer pairs that received at least five SDEs per year, 81% of urban regions are characterized by a smaller snow probability, 99% by a lower frequency of SDEs, and 57% by faster declining trends in SDEs compared to their buffer counterparts. Notably, urban (buffer) regions with lower snow probability are often characterized by higher net incoming and sensible energy fluxes as compared to buffer (urban) regions, thus highlighting the influence of land-energy feedback on precipitation phase. Results highlight a clear imprint of urbanization on precipitation phase and underscore the need to consider these influences while projecting hydro-meteorological risks.
Bubble-water/catalyst triphase interface microenvironment accelerates photocatalytic OER via optimizing semi-hydrophobic OH radical
Authors: Ren Guanhua , Zhou Min , Hu Peijun , Chen Jian-Fu , Wang Haifeng 
Published: March 2024

AbstractPhotocatalytic water splitting (PWS) as the holy grail reaction for solar-to-chemical energy conversion is challenged by sluggish oxygen evolution reaction (OER) at water/catalyst interface. Experimental evidence interestingly shows that temperature can significantly accelerate OER, but the atomic-level mechanism remains elusive in both experiment and theory. In contrast to the traditional Arrhenius-type temperature dependence, we quantitatively prove for the first time that the temperature-induced interface microenvironment variation, particularly the formation of bubble-water/TiO2(110) triphase interface, has a drastic influence on optimizing the OER kinetics. We demonstrate that liquid-vapor coexistence state creates a disordered and loose hydrogen-bond network while preserving the proton transfer channel, which greatly facilitates the formation of semi-hydrophobic •OH radical and O-O coupling, thereby accelerating OER. Furthermore, we propose that adding a hydrophobic substance onto TiO2(110) can manipulate the local microenvironment to enhance OER without additional thermal energy input. This result could open new possibilities for PWS catalyst design.
CRISPR-powered quantitative keyword search engine in DNA data storage
Authors: Zhang Jiongyu , Hou Chengyu , Liu Changchun 
Published: March 2024

AbstractDespite the growing interest of archiving information in synthetic DNA to confront data explosion, quantitatively querying the data stored in DNA is still a challenge. Herein, we present Search Enabled by Enzymatic Keyword Recognition (SEEKER), which utilizes CRISPR-Cas12a to rapidly generate visible fluorescence when a DNA target corresponding to the keyword of interest is present. SEEKER achieves quantitative text searching since the growth rate of fluorescence intensity is proportional to keyword frequency. Compatible with SEEKER, we develop non-collision grouping coding, which reduces the size of dictionary and enables lossless compression without disrupting the original order of texts. Using four queries, we correctly identify keywords in 40 files with a background of ~8000 irrelevant terms. Parallel searching with SEEKER can be performed on a 3D-printed microfluidic chip. Overall, SEEKER provides a quantitative approach to conducting parallel searching over the complete content stored in DNA with simple implementation and rapid result generation.
Unconventional superconductivity near a nematic instability in a multi-orbital system
Authors: Islam Kazi Ranjibul , Chubukov Andrey 
Published: March 2024

AbstractWe analyze superconductivity in a multi-orbital fermionic system near the onset of a nematic order, using doped FeSe as an example. We associate nematicity with spontaneous polarization between dxz and dyz orbitals. We derive pairing interaction, mediated by soft nematic fluctuations, and show that it is attractive, and its strength depends on the position on the Fermi surface. As the consequence, right at the nematic quantum-critical point (QCP), superconducting gap opens up at Tc only at special points and extends into finite arcs at T < Tc. In between the arcs the Fermi surface remains intact. This leads to highly unconventional behavior of the specific heat, with no jump at Tc and seemingly finite offset at T = 0. We discuss gap structure and pairing symmetry away from a QCP and compare nematic and spin-fluctuation scenarios. We apply the results to FeSe1−xSx and FeSe1−xTex.
Test for BCS-BEC crossover in the cuprate superconductors
Authors: Chen Qijin , Wang Zhiqiang , Boyack Rufus , Levin K. 
Published: March 2024

AbstractIn this paper we address the question of whether high-temperature superconductors have anything in common with BCS-BEC crossover theory. Towards this goal, we present a proposal and related predictions which provide a concrete test for the applicability of this theoretical framework. These predictions characterize the behavior of the Ginzburg-Landau coherence length, $${\xi }_{0}^{{{{\rm{coh}}}}}$$

ξ

0

coh

, near the transition temperature Tc, and across the entire superconducting Tc dome in the phase diagram. That we are lacking a systematic characterization of $${\xi }_{0}^{{{{\rm{coh}}}}}$$

ξ

0

coh

in the entire class of cuprate superconductors is perhaps surprising, as it is one of the most fundamental properties of any superconductor. This paper is written to motivate further experiments and, thus, address this shortcoming. Here we show how measurements of $${\xi }_{0}^{{{{\rm{coh}}}}}$$

ξ

0

coh

contain direct indications for whether or not the cuprates are associated with BCS-BEC crossover and, if so, where within the crossover spectrum a particular superconductor lies.
Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance
Authors: Ma Peng-Fei , Liu Yun-Long , Guo Cen , Jin Guihua , Guo Zhen-Hua , Mao Ling , Yang Yi-Zhou , Niu Liang-Zhong , Wang Yu-Jiao , Clark Lynn G. , Kellogg Elizabeth A. , Xu Zu-Chang , Ye Xia-Ying , Liu Jing-Xia , Zhou Meng-Yuan , Luo Yan , Yang Yang , Soltis Douglas E. , Bennetzen Jeffrey L. , Soltis Pamela S. , Li De-Zhu 
Published: March 2024

AbstractPolyploidy (genome duplication) is a pivotal force in evolution. However, the interactions between parental genomes in a polyploid nucleus, frequently involving subgenome dominance, are poorly understood. Here we showcase analyses of a bamboo system (Poaceae: Bambusoideae) comprising a series of lineages from diploid (herbaceous) to tetraploid and hexaploid (woody), with 11 chromosome-level de novo genome assemblies and 476 transcriptome samples. We find that woody bamboo subgenomes exhibit stunning karyotype stability, with parallel subgenome dominance in the two tetraploid clades and a gradual shift of dominance in the hexaploid clade. Allopolyploidization and subgenome dominance have shaped the evolution of tree-like lignified culms, rapid growth and synchronous flowering characteristic of woody bamboos as large grasses. Our work provides insights into genome dominance in a remarkable polyploid system, including its dependence on genomic context and its ability to switch which subgenomes are dominant over evolutionary time.
Prevalence, outcomes and associated factors of SARS-CoV-2 infection in psoriasis patients of Southwest China: a cross-sectional survey
Authors: Zou Yang , Xu Jing , Chen Ai-Jun , Huang Kun , Zhu Shou-Min , Li Jian-Jun , He Jin , Li Jun-Zhi , Xiong Jian-Xia , Fan Yu-Kun , Liu Chuan , Pan Yun , Wang Ping 
Published: March 2024

AbstractIn this study we aimed to investigate the prevalence of SARS-CoV-2 infection in psoriasis patients, and outcomes of SARS-CoV-2 infection and associated risk factors. A cross-sectional survey was conducted from February 2023 to March 2023. Information was obtained with online questionnaire about psoriasis patients on demographic characteristics, clinical characteristics, SARS-CoV-2 infection and outcomes, vaccination, and routine protection against COVID-19. Logistic regression analysis was used to explore risk factors with SARS-CoV-2 infection and exacerbation of psoriasis. A total of 613 participants were recruited. 516 (84.2%) were infected, and associated factors were sex, working status, routine protection against COVID-19, COVID-19 vaccination, impaired nail, infection exacerbate psoriasis, and severity of psoriasis. Among the patients infected with SARS-CoV-2, 30 (5.8%) required hospitalization, 122 (23.6%) had psoriasis exacerbation due to SARS-CoV-2 infection, and associated factors were subtype of psoriasis, discontinuation of psoriasis treatment during SARS-CoV-2 infection, response following COVID-19 vaccination, and severity of psoriasis. Booster dose vaccination contributed a low probability of COVID-19 sequelae. COVID-19 vaccine’s effectiveness was unsatisfactory, while booster dose vaccination reduced the occurrence of COVID-19 sequelae in psoriasis patients of Southwest China. Patients treated with psoriasis shown to be safe, without a higher incidence of SARS-CoV-2 infection or COVID-19hospitalization compared to untreated patients. Stopping treatment during SARS-CoV-2 infection led to psoriasis exacerbation, so psoriasis treatment could be continued except severe adverse reaction.
Statistical detection of selfish mining in proof-of-work blockchain systems
Authors: Li Sheng-Nan , Campajola Carlo , Tessone Claudio J. 
Published: March 2024

AbstractThe core of many cryptocurrencies is the decentralised validation network operating on proof-of-work technology. In these systems, validation is done by so-called miners who can digitally sign blocks once they solve a computationally-hard problem. Conventional wisdom generally considers this protocol as secure and stable as miners are incentivised to follow the behaviour of the majority. However, whether some strategic mining behaviours occur in practice is still a major concern. In this paper we target this question by focusing on a security threat: a selfish mining attack in which malicious miners deviate from protocol by not immediately revealing their newly mined blocks. We propose a statistical test to analyse each miner’s behaviour in five popular cryptocurrencies: Bitcoin, Litecoin, Monacoin, Ethereum and Bitcoin Cash. Our method is based on the realisation that selfish mining behaviour will cause identifiable anomalies in the statistics of miner’s successive blocks discovery. Secondly, we apply heuristics-based address clustering to improve the detectability of this kind of behaviour. We find a marked presence of abnormal miners in Monacoin and Bitcoin Cash, and, to a lesser extent, in Ethereum. Finally, we extend our method to detect coordinated selfish mining attacks, finding mining cartels in Monacoin where miners might secretly share information about newly mined blocks in advance. Our analysis contributes to the research on security in cryptocurrency systems by providing the first empirical evidence that the aforementioned strategic mining behaviours do take place in practice.
A novel trauma induced urethral stricture in rat model
Authors: Wu Ziqiang , Tang Zhengyan , Zheng Zhihuan , Tan Shuo 
Published: March 2024

AbstractUrethral stricture (US) is a longstanding disease, while there has not existed a suitable animal model to mimic the condition. We aimed to establish a trauma-induced US animal model to simulate this clinical scenario. A total of 30 rats were equally distributed into two groups, sham and US group. All rats were anesthetized with isoflurane and undergone cystostomy. In the US group, a 2 mm incision was made in the urethra and sutured to induce US. The sham group only make a skin incision on the ventral side of the anterior urethra. 4 weeks later, ultrasound and cystourethrography were performed to evaluate the degree of urethral stricture, pathological examinations were carried out to evaluate the degree of fibrosis. Urodynamic evaluation and mechanical tissue testing were performed to evaluate the bladder function and urethral tissue stiffness. The results showed that the urethral mucosa was disrupted and urethral lumen was stenosed in the US group. Additionally, the US group showed elevated bladder pressure, prolonged micturition intervals and increased tissue stiffness. In conclusion, the rat urethral stricture model induced by trauma provides a closer representation of the real clinical scenario. This model will significantly contribute to advancing research on the mechanisms underlying traumatic urethral stricture.