bluuebunny/crossref_metadata_2025_split huggingface dataset:
A genomic appraisal of invasive Salmonella Typhimurium and associated antibiotic resistance in sub-Saharan Africa
Authors: Van Puyvelde Sandra , de Block Tessa , Sridhar Sushmita , Bawn Matt , Kingsley Robert A. , Ingelbeen Brecht , Beale Mathew A. , Barbé Barbara , Jeon Hyon Jin , Mbuyi-Kalonji Lisette , Phoba Marie-France , Falay Dadi , Martiny Delphine , Vandenberg Olivier , Affolabi Dissou , Rutanga Jean Pierre , Ceyssens Pieter-Jan , Mattheus Wesley , Cuypers Wim L. , van der Sande Marianne A. B. , Park Se Eun , Kariuki Simon , Otieno Kephas , Lusingu John P. A. , Mbwana Joyce R. , Adjei Samuel , Sarfo Anima , Agyei Seth O. , Asante Kwaku P. , Otieno Walter , Otieno Lucas , Tahita Marc C. , Lompo Palpouguini , Hoffman Irving F. , Mvalo Tisungane , Msefula Chisomo , Hassan-Hanga Fatimah , Obaro Stephen , Mackenzie Grant , Deborggraeve Stijn , Feasey Nicholas , Marks Florian , MacLennan Calman A. , Thomson Nicholas R. , Jacobs Jan , Dougan Gordon , Kariuki Samuel , Lunguya Octavie 
Published: October 2023

AbstractInvasive non-typhoidal Salmonella (iNTS) disease manifesting as bloodstream infection with high mortality is responsible for a huge public health burden in sub-Saharan Africa. Salmonella enterica serovar Typhimurium (S. Typhimurium) is the main cause of iNTS disease in Africa. By analysing whole genome sequence data from 1303 S. Typhimurium isolates originating from 19 African countries and isolated between 1979 and 2017, here we show a thorough scaled appraisal of the population structure of iNTS disease caused by S. Typhimurium across many of Africa’s most impacted countries. At least six invasive S. Typhimurium clades have already emerged, with ST313 lineage 2 or ST313-L2 driving the current pandemic. ST313-L2 likely emerged in the Democratic Republic of Congo around 1980 and further spread in the mid 1990s. We observed plasmid-borne as well as chromosomally encoded fluoroquinolone resistance underlying emergences of extensive-drug and pan-drug resistance. Our work provides an overview of the evolution of invasive S. Typhimurium disease, and can be exploited to target control measures.
Hierarchical assembly of tryptophan zipper peptides into stress-relaxing bioactive hydrogels
Authors: Nguyen Ashley K. , Molley Thomas G. , Kardia Egi , Ganda Sylvia , Chakraborty Sudip , Wong Sharon L. , Ruan Juanfang , Yee Bethany E. , Mata Jitendra , Vijayan Abhishek , Kumar Naresh , Tilley Richard D. , Waters Shafagh A. , Kilian Kristopher A. 
Published: October 2023

AbstractSoft materials in nature are formed through reversible supramolecular assembly of biological polymers into dynamic hierarchical networks. Rational design has led to self-assembling peptides with structural similarities to natural materials. However, recreating the dynamic functional properties inherent to natural systems remains challenging. Here we report the discovery of a short peptide based on the tryptophan zipper (trpzip) motif, that shows multiscale hierarchical ordering that leads to emergent dynamic properties. Trpzip hydrogels are antimicrobial and self-healing, with tunable viscoelasticity and unique yield-stress properties that allow immediate harvest of embedded cells through a flick of the wrist. This characteristic makes Trpzip hydrogels amenable to syringe extrusion, which we demonstrate with examples of cell delivery and bioprinting. Trpzip hydrogels display innate bioactivity, allowing propagation of human intestinal organoids with apical-basal polarization. Considering these extensive attributes, we anticipate the Trpzip motif will prove a versatile building block for supramolecular assembly of soft materials for biotechnology and medicine.
Interactions between interfaces dictate stimuli-responsive emulsion behaviour
Authors: Rey Marcel , Kolker Jannis , Richards James A. , Malhotra Isha , Glen Thomas S. , Li N. Y. Denise , Laidlaw Fraser H. J. , Renggli Damian , Vermant Jan , Schofield Andrew B. , Fujii Syuji , Löwen Hartmut , Clegg Paul S. 
Published: October 2023

AbstractStimuli-responsive emulsions offer a dual advantage, combining long-term storage with controlled release triggered by external cues such as pH or temperature changes. This study establishes that thermo-responsive emulsion behaviour is primarily determined by interactions between, rather than within, interfaces. Consequently, the stability of these emulsions is intricately tied to the nature of the stabilizing microgel particles - whether they are more polymeric or colloidal, and the morphology they assume at the liquid interface. The colloidal properties of the microgels provide the foundation for the long-term stability of Pickering emulsions. However, limited deformability can lead to non-responsive emulsions. Conversely, the polymeric properties of the microgels enable them to spread and flatten at the liquid interface, enabling stimuli-responsive behaviour. Furthermore, microgels shared between two emulsion droplets in flocculated emulsions facilitate stimuli-responsiveness, regardless of their internal architecture. This underscores the pivotal role of microgel morphology and the forces they exert on liquid interfaces in the control and design of stimuli-responsive emulsions and interfaces.
Dual targeted extracellular vesicles regulate oncogenic genes in advanced pancreatic cancer
Authors: Chiang Chi-Ling , Ma Yifan , Hou Ya-Chin , Pan Junjie , Chen Sin-Yu , Chien Ming-Hsien , Zhang Zhi-Xuan , Hsu Wei-Hsiang , Wang Xinyu , Zhang Jingjing , Li Hong , Sun Lili , Fallen Shannon , Lee Inyoul , Chen Xing-Yu , Chu Yeh-Shiu , Zhang Chi , Cheng Tai-Shan , Jiang Wen , Kim Betty Y. S. , Reategui Eduardo , Lee Robert , Yuan Yuan , Liu Hsiao-Chun , Wang Kai , Hsiao Michael , Huang Chi-Ying F. , Shan Yan-Shen , Lee Andrew S. , James Lee L. 
Published: October 2023

AbstractPancreatic ductal adenocarcinoma (PDAC) tumours carry multiple gene mutations and respond poorly to treatments. There is currently an unmet need for drug carriers that can deliver multiple gene cargoes to target high solid tumour burden like PDAC. Here, we report a dual targeted extracellular vesicle (dtEV) carrying high loads of therapeutic RNA that effectively suppresses large PDAC tumours in mice. The EV surface contains a CD64 protein that has a tissue targeting peptide and a humanized monoclonal antibody. Cells sequentially transfected with plasmid DNAs encoding for the RNA and protein of interest by Transwell®-based asymmetric cell electroporation release abundant targeted EVs with high RNA loading. Together with a low dose chemotherapy drug, Gemcitabine, dtEVs suppress large orthotopic PANC-1 and patient derived xenograft tumours and metastasis in mice and extended animal survival. Our work presents a clinically accessible and scalable way to produce abundant EVs for delivering multiple gene cargoes to large solid tumours.
SARS-CoV-2 infection establishes a stable and age-independent CD8+ T cell response against a dominant nucleocapsid epitope using restricted T cell receptors
Authors: Choy Cecily , Chen Joseph , Li Jiangyuan , Gallagher D. Travis , Lu Jian , Wu Daichao , Zou Ainslee , Hemani Humza , Baptiste Beverly A. , Wichmann Emily , Yang Qian , Ciffelo Jeffrey , Yin Rui , McKelvy Julia , Melvin Denise , Wallace Tonya , Dunn Christopher , Nguyen Cuong , Chia Chee W. , Fan Jinshui , Ruffolo Jeannie , Zukley Linda , Shi Guixin , Amano Tomokazu , An Yang , Meirelles Osorio , Wu Wells W. , Chou Chao-Kai , Shen Rong-Fong , Willis Richard A. , Ko Minoru S. H. , Liu Yu-Tsueng , De Supriyo , Pierce Brian G. , Ferrucci Luigi , Egan Josephine , Mariuzza Roy , Weng Nan-Ping 
Published: October 2023

AbstractThe resolution of SARS-CoV-2 replication hinges on cell-mediated immunity, wherein CD8+ T cells play a vital role. Nonetheless, the characterization of the specificity and TCR composition of CD8+ T cells targeting non-spike protein of SARS-CoV-2 before and after infection remains incomplete. Here, we analyzed CD8+ T cells recognizing six epitopes from the SARS-CoV-2 nucleocapsid (N) protein and found that SARS-CoV-2 infection slightly increased the frequencies of N-recognizing CD8+ T cells but significantly enhanced activation-induced proliferation compared to that of the uninfected donors. The frequencies of N-specific CD8+ T cells and their proliferative response to stimulation did not decrease over one year. We identified the N222-230 peptide (LLLDRLNQL, referred to as LLL thereafter) as a dominant epitope that elicited the greatest proliferative response from both convalescent and uninfected donors. Single-cell sequencing of T cell receptors (TCR) from LLL-specific CD8+ T cells revealed highly restricted Vα gene usage (TRAV12-2) with limited CDR3α motifs, supported by structural characterization of the TCR–LLL–HLA-A2 complex. Lastly, transcriptome analysis of LLL-specific CD8+ T cells from donors who had expansion (expanders) or no expansion (non-expanders) after in vitro stimulation identified increased chromatin modification and innate immune functions of CD8+ T cells in non-expanders. These results suggests that SARS-CoV-2 infection induces LLL-specific CD8+ T cell responses with a restricted TCR repertoire.
Emergent ferromagnetism with superconductivity in Fe(Te,Se) van der Waals Josephson junctions
Authors: Qiu Gang , Yang Hung-Yu , Hu Lunhui , Zhang Huairuo , Chen Chih-Yen , Lyu Yanfeng , Eckberg Christopher , Deng Peng , Krylyuk Sergiy , Davydov Albert V. , Zhang Ruixing , Wang Kang L. 
Published: October 2023

AbstractFerromagnetism and superconductivity are two key ingredients for topological superconductors, which can serve as building blocks of fault-tolerant quantum computers. Adversely, ferromagnetism and superconductivity are typically also two hostile orderings competing to align spins in different configurations, and thus making the material design and experimental implementation extremely challenging. A single material platform with concurrent ferromagnetism and superconductivity is actively pursued. In this paper, we fabricate van der Waals Josephson junctions made with iron-based superconductor Fe(Te,Se), and report the global device-level transport signatures of interfacial ferromagnetism emerging with superconducting states for the first time. Magnetic hysteresis in the junction resistance is observed only below the superconducting critical temperature, suggesting an inherent correlation between ferromagnetic and superconducting order parameters. The 0-π phase mixing in the Fraunhofer patterns pinpoints the ferromagnetism on the junction interface. More importantly, a stochastic field-free superconducting diode effect was observed in Josephson junction devices, with a significant diode efficiency up to 10%, which unambiguously confirms the spontaneous time-reversal symmetry breaking. Our work demonstrates a new way to search for topological superconductivity in iron-based superconductors for future high Tc fault-tolerant qubit implementations from a device perspective.
Calorimetric evidence for two phase transitions in Ba1−xKxFe2As2 with fermion pairing and quadrupling states
Authors: Shipulin Ilya , Stegani Nadia , Maccari Ilaria , Kihou Kunihiro , Lee Chul-Ho , Hu Quanxin , Zheng Yu , Yang Fazhi , Li Yongwei , Yim Chi-Ming , Hühne Ruben , Klauss Hans-Henning , Putti Marina , Caglieris Federico , Babaev Egor , Grinenko Vadim 
Published: October 2023

AbstractMaterials that break multiple symmetries allow the formation of four-fermion condensates above the superconducting critical temperature (Tc). Such states can be stabilized by phase fluctuations. Recently, a fermionic quadrupling condensate that breaks the Z2 time-reversal symmetry was reported in Ba1−xKxFe2As2. A phase transition to the new state of matter should be accompanied by a specific heat anomaly at the critical temperature where Z2 time-reversal symmetry is broken ($${T}_{{{{{{{{\rm{c}}}}}}}}}^{{{{{{{{\rm{Z2}}}}}}}}} \, > \, {T}_{{{{{{{{\rm{c}}}}}}}}}$$

T

c

Z2

>

T

c

). Here, we report on detecting two anomalies in the specific heat of Ba1−xKxFe2As2 at zero magnetic field. The anomaly at the higher temperature is accompanied by the appearance of a spontaneous Nernst effect, indicating the breakdown of Z2 symmetry. The second anomaly at the lower temperature coincides with the transition to a zero-resistance state, indicating the onset of superconductivity. Our data provide the first example of the appearance of a specific heat anomaly above the superconducting phase transition associated with the broken time-reversal symmetry due to the formation of the novel fermion order.
Metabolic regulation of proteome stability via N-terminal acetylation controls male germline stem cell differentiation and reproduction
Authors: François Charlotte M. , Pihl Thomas , Dunoyer de Segonzac Marion , Hérault Chloé , Hudry Bruno 
Published: October 2023

AbstractThe molecular mechanisms connecting cellular metabolism with differentiation remain poorly understood. Here, we find that metabolic signals contribute to stem cell differentiation and germline homeostasis during Drosophila melanogaster spermatogenesis. We discovered that external citrate, originating outside the gonad, fuels the production of Acetyl-coenzyme A by germline ATP-citrate lyase (dACLY). We show that this pathway is essential during the final spermatogenic stages, where a high Acetyl-coenzyme A level promotes NatB-dependent N-terminal protein acetylation. Using genetic and biochemical experiments, we establish that N-terminal acetylation shields key target proteins, essential for spermatid differentiation, from proteasomal degradation by the ubiquitin ligase dUBR1. Our work uncovers crosstalk between metabolism and proteome stability that is mediated via protein post-translational modification. We propose that this system coordinates the metabolic state of the organism with gamete production. More broadly, modulation of proteome turnover by circulating metabolites may be a conserved regulatory mechanism to control cell functions.
Individual level analysis of digital proximity tracing for COVID-19 in Belgium highlights major bottlenecks
Authors: Geenen Caspar , Raymenants Joren , Gorissen Sarah , Thibaut Jonathan , McVernon Jodie , Lorent Natalie , André Emmanuel 
Published: October 2023

AbstractTo complement labour-intensive conventional contact tracing, digital proximity tracing was implemented widely during the COVID-19 pandemic. However, the privacy-centred design of the dominant Google-Apple exposure notification framework has hindered assessment of its effectiveness. Between October 2021 and January 2022, we systematically collected app use and notification receipt data within a test and trace programme targeting around 50,000 university students in Leuven, Belgium. Due to low success rates in each studied step of the digital notification cascade, only 4.3% of exposed contacts (CI: 2.8-6.1%) received such notifications, resulting in 10 times more cases detected through conventional contact tracing. Moreover, the infection risk of digitally traced contacts (5.0%; CI: 3.0–7.7%) was lower than that of conventionally traced non-app users (9.8%; CI: 8.8-10.7%; p = 0.002). Contrary to common perception as near instantaneous, there was a 1.2-day delay (CI: 0.6–2.2) between case PCR result and digital contact notification. These results highlight major limitations of a digital proximity tracing system based on the dominant framework.
Healthy dietary patterns and the risk of individual chronic diseases in community-dwelling adults
Authors: Shang Xianwen , Liu Jiahao , Zhu Zhuoting , Zhang Xueli , Huang Yu , Liu Shunming , Wang Wei , Zhang Xiayin , Tang Shulin , Hu Yijun , Yu Honghua , Ge Zongyuan , He Mingguang 
Published: October 2023

AbstractIt is unclear regarding associations of dietary patterns with a wide range of chronic diseases and which dietary score is more predictive of major chronic diseases. Using the UK Biobank, we examine associations of four individual healthy dietary scores with the risk of 48 individual chronic diseases. Higher Alternate Mediterranean Diet score is associated with a lower risk of 32 (all 8 cardiometabolic disorders, 3 out of 10 types of cancers, 7 out of 10 psychological/neurological disorders, 5 out of 6 digestive disorders, and 9 out of 14 other chronic diseases). Alternate Healthy Eating Index-2010 and Healthful Plant-based Diet Index are inversely associated with the risk of 29 and 23 individual chronic diseases, respectively. A higher Anti-Empirical Dietary Inflammatory Index is associated with a lower risk of 14 individual chronic diseases and a higher incidence of two diseases. Our findings support dietary guidelines for the prevention of most chronic diseases.
Enhanced and synergistic catalytic activation by photoexcitation driven S−scheme heterojunction hydrogel interface electric field
Authors: Wang Aiwen , Du Meng , Ni Jiaxin , Liu Dongqing , Pan Yunhao , Liang Xiongying , Liu Dongmei , Ma Jun , Wang Jing , Wang Wei 
Published: October 2023

AbstractThe regulation of heterogeneous material properties to enhance the peroxymonosulfate (PMS) activation to degrade emerging organic pollutants remains a challenge. To solve this problem, we synthesize S−scheme heterojunction PBA/MoS2@chitosan hydrogel to achieve photoexcitation synergistic PMS activation. The constructed heterojunction photoexcited carriers undergo redox conversion with PMS through S−scheme transfer pathway driven by the directional interface electric field. Multiple synergistic pathways greatly enhance the reactive oxygen species generation, leading to a significant increase in doxycycline degradation rate. Meanwhile, the 3D polymer chain spatial structure of chitosan hydrogel is conducive to rapid PMS capture and electron transport in advanced oxidation process, reducing the use of transition metal activator and limiting the leaching of metal ions. There is reason to believe that the synergistic activation of PMS by S−scheme heterojunction regulated by photoexcitation will provide a new perspective for future material design and research on enhancing heterologous catalysis oxidation process.
The mitochondrial fusion protein OPA1 is dispensable in the liver and its absence induces mitohormesis to protect liver from drug-induced injury
Authors: Lee Hakjoo , Lee Tae Jin , Galloway Chad A. , Zhi Wenbo , Xiao Wei , de Mesy Bentley Karen L. , Sharma Ashok , Teng Yong , Sesaki Hiromi , Yoon Yisang 
Published: October 2023

AbstractMitochondria are critical for metabolic homeostasis of the liver, and their dysfunction is a major cause of liver diseases. Optic atrophy 1 (OPA1) is a mitochondrial fusion protein with a role in cristae shaping. Disruption of OPA1 causes mitochondrial dysfunction. However, the role of OPA1 in liver function is poorly understood. In this study, we delete OPA1 in the fully developed liver of male mice. Unexpectedly, OPA1 liver knockout (LKO) mice are healthy with unaffected mitochondrial respiration, despite disrupted cristae morphology. OPA1 LKO induces a stress response that establishes a new homeostatic state for sustained liver function. Our data show that OPA1 is required for proper complex V assembly and that OPA1 LKO protects the liver from drug toxicity. Mechanistically, OPA1 LKO decreases toxic drug metabolism and confers resistance to the mitochondrial permeability transition. This study demonstrates that OPA1 is dispensable in the liver, and that the mitohormesis induced by OPA1 LKO prevents liver injury and contributes to liver resiliency.
Room-temperature high-speed electrical modulation of excitonic distribution in a monolayer semiconductor
Authors: Zhu Guangpeng , Zhang Lan , Li Wenfei , Shi Xiuqi , Zou Zhen , Guo Qianqian , Li Xiang , Xu Weigao , Jie Jiansheng , Wang Tao , Du Wei , Xiong Qihua 
Published: October 2023

AbstractExcitons in monolayer semiconductors, benefitting from their large binding energies, hold great potential towards excitonic circuits bridging nano-electronics and photonics. However, achieving room-temperature ultrafast on-chip electrical modulation of excitonic distribution and flow in monolayer semiconductors is nontrivial. Here, utilizing lateral bias, we report high-speed electrical modulation of the excitonic distribution in a monolayer semiconductor junction at room temperature. The alternating charge trapping/detrapping at the two monolayer/electrode interfaces induces a non-uniform carrier distribution, leading to controlled in-plane spatial variations of excitonic populations, and mimicking a bias-driven excitonic flow. This modulation increases with the bias amplitude and eventually saturates, relating to the energetic distribution of trap density of states. The switching time of the modulation is down to 5 ns, enabling high-speed excitonic devices. Our findings reveal the trap-assisted exciton engineering in monolayer semiconductors and offer great opportunities for future two-dimensional excitonic devices and circuits.
Photoelectric responsive ionic channel for sustainable energy harvesting
Authors: Guo Qing , Lai Zhuozhi , Zuo Xiuhui , Xian Weipeng , Wu Shaochun , Zheng Liping , Dai Zhifeng , Wang Sai , Sun Qi 
Published: October 2023

AbstractAccess to sustainable energy is paramount in today’s world, with a significant emphasis on solar and water-based energy sources. Herein, we develop photo-responsive ionic dye-sensitized covalent organic framework membranes. These innovative membranes are designed to significantly enhance selective ion transport by exploiting the intricate interplay between photons, electrons, and ions. The nanofluidic devices engineered in our study showcase exceptional cation conductivity. Additionally, they can adeptly convert light into electrical signals due to photoexcitation-triggered ion movement. Combining the effects of salinity gradients with photo-induced ion movement, the efficiency of these devices is notably amplified. Specifically, under a salinity differential of 0.5/0.01 M NaCl and light exposure, the device reaches a peak power density of 129 W m−2, outperforming the current market standard by approximately 26-fold. Beyond introducing the idea of photoelectric activity in ionic membranes, our research highlights a potential pathway to cater to the escalating global energy needs.
Incidence of HER2-expressing brain metastases in patients with HER2-null breast cancer: a matched case analysis
Authors: Moss Nelson S. , Singh Jolene M. , Reiner Anne S. , Drago Joshua Z. , Modi Shanu , Seidman Andrew D. , Chandarlapaty Sarat , Ross Dara S. 
Published: October 2023

AbstractThe HER2-directed antibody-drug conjugate trastuzumab deruxtecan is active against lower levels of HER2 expression than prior-generation therapies. The rate of HER2 expression in brain metastases among patients with initially HER2-null breast cancer is undefined, and receptor discordance in advanced breast cancer with brain metastases may underestimate CNS response potential in the absence of brain metastasis sampling. In this cohort study including 136 patients with 401 samples scored according to ASCO/CAP guidelines, 15/28 patients (54%) with HER2-null primary breast cancer have detectable HER2 expression in subsequently resected brain metastases, a significant discordant population.