bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prior infection with unrelated neurotropic virus exacerbates influenza disease and impairs lung T cell responses
Authors: Foo Isabelle Jia-Hui , Chua Brendon Y. , Clemens E. Bridie , Chang So Young , Jia Xiaoxiao , McQuilten Hayley A. , Yap Ashley Huey Yiing , Cabug Aira F. , Ashayeripanah Mitra , McWilliam Hamish E. G. , Villadangos Jose A. , Evrard Maximilien , Mackay Laura K. , Wakim Linda M. , Fazakerley John K. , Kedzierska Katherine , Kedzierski Lukasz 
Published: March 2024

AbstractImmunity to infectious diseases is predominantly studied by measuring immune responses towards a single pathogen, although co-infections are common. In-depth mechanisms on how co-infections impact anti-viral immunity are lacking, but are highly relevant to treatment and prevention. We established a mouse model of co-infection with unrelated viruses, influenza A (IAV) and Semliki Forest virus (SFV), causing disease in different organ systems. SFV infection eight days before IAV infection results in prolonged IAV replication, elevated cytokine/chemokine levels and exacerbated lung pathology. This is associated with impaired lung IAV-specific CD8+ T cell responses, stemming from suboptimal CD8+ T cell activation and proliferation in draining lymph nodes, and dendritic cell paralysis. Prior SFV infection leads to increased blood brain barrier permeability and presence of IAV RNA in brain, associated with increased trafficking of IAV-specific CD8+ T cells and establishment of long-term tissue-resident memory. Relative to lung IAV-specific CD8+ T cells, brain memory IAV-specific CD8+ T cells have increased TCR repertoire diversity within immunodominant DbNP366+CD8+ and DbPA224+CD8+ responses, featuring suboptimal TCR clonotypes. Overall, our study demonstrates that infection with an unrelated neurotropic virus perturbs IAV-specific immune responses and exacerbates IAV disease. Our work provides key insights into therapy and vaccine regimens directed against unrelated pathogens.
Demonstration of hypergraph-state quantum information processing
Authors: Huang Jieshan , Li Xudong , Chen Xiaojiong , Zhai Chonghao , Zheng Yun , Chi Yulin , Li Yan , He Qiongyi , Gong Qihuang , Wang Jianwei 
Published: March 2024

AbstractComplex entangled states are the key resources for measurement-based quantum computations, which is realised by performing a sequence of measurements on initially entangled qubits. Executable quantum algorithms in the graph-state quantum computing model are determined by the entanglement structure and the connectivity of entangled qubits. By generalisation from graph-type entanglement in which only the nearest qubits interact to a new type of hypergraph entanglement in which any subset of qubits can be arbitrarily entangled via hyperedges, hypergraph states represent more general resource states that allow arbitrary quantum computation with Pauli universality. Here we report experimental preparation, certification and processing of complete categories of four-qubit hypergraph states under the principle of local unitary equivalence, on a fully reprogrammable silicon-photonic quantum chip. Genuine multipartite entanglement for hypergraph states is certificated by the characterisation of entanglement witness, and the observation of violations of Mermin inequalities without any closure of distance or detection loopholes. A basic measurement-based protocol and an efficient resource state verification by color-encoding stabilizers are implemented with local Pauli measurement to benchmark the building blocks for hypergraph-state quantum computation. Our work prototypes hypergraph entanglement as a general resource for quantum information processing.
Non-catalytic role of phosphoinositide 3-kinase in mesenchymal cell migration through non-canonical induction of p85β/AP2-mediated endocytosis
Authors: Matsubayashi Hideaki T. , Mountain Jack , Takahashi Nozomi , Deb Roy Abhijit , Yao Tony , Peterson Amy F. , Saez Gonzalez Cristian , Kawamata Ibuki , Inoue Takanari 
Published: March 2024

AbstractClass IA phosphoinositide 3-kinase (PI3K) galvanizes fundamental cellular processes such as migration, proliferation, and differentiation. To enable these multifaceted roles, the catalytic subunit p110 utilizes the multi-domain, regulatory subunit p85 through its inter SH2 domain (iSH2). In cell migration, its product PI(3,4,5)P3 generates locomotive activity. While non-catalytic roles are also implicated, underlying mechanisms and their relationship to PI(3,4,5)P3 signaling remain elusive. Here, we report that a disordered region of iSH2 contains AP2 binding motifs which can trigger clathrin and dynamin-mediated endocytosis independent of PI3K catalytic activity. The AP2 binding motif mutants of p85 aberrantly accumulate at focal adhesions and increase both velocity and persistency in fibroblast migration. We thus propose the dual functionality of PI3K in the control of cell motility, catalytic and non-catalytic, arising distinctly from juxtaposed regions within iSH2.
Developing a machine learning model for accurate nucleoside hydrogels prediction based on descriptors
Authors: Li Weiqi , Wen Yinghui , Wang Kaichao , Ding Zihan , Wang Lingfeng , Chen Qianming , Xie Liang , Xu Hao , Zhao Hang 
Published: March 2024

AbstractSupramolecular hydrogels derived from nucleosides have been gaining significant attention in the biomedical field due to their unique properties and excellent biocompatibility. However, a major challenge in this field is that there is no model for predicting whether nucleoside derivative will form a hydrogel. Here, we successfully develop a machine learning model to predict the hydrogel-forming ability of nucleoside derivatives. The optimal model with a 71% (95% Confidence Interval, 0.69−0.73) accuracy is established based on a dataset of 71 reported nucleoside derivatives. 24 molecules are selected via the optimal model external application and the hydrogel-forming ability is experimentally verified. Among these, two rarely reported cation-independent nucleoside hydrogels are found. Based on their self-assemble mechanisms, the cation-independent hydrogel is found to have potential applications in rapid visual detection of Ag+ and cysteine. Here, we show the machine learning model may provide a tool to predict nucleoside derivatives with hydrogel-forming ability.
Multi-omic integration of microbiome data for identifying disease-associated modules
Authors: Muller Efrat , Shiryan Itamar , Borenstein Elhanan 
Published: March 2024

AbstractMulti-omic studies of the human gut microbiome are crucial for understanding its role in disease across multiple functional layers. Nevertheless, integrating and analyzing such complex datasets poses significant challenges. Most notably, current analysis methods often yield extensive lists of disease-associated features (e.g., species, pathways, or metabolites), without capturing the multi-layered structure of the data. Here, we address this challenge by introducing “MintTea”, an intermediate integration-based approach combining canonical correlation analysis extensions, consensus analysis, and an evaluation protocol. MintTea identifies “disease-associated multi-omic modules”, comprising features from multiple omics that shift in concord and that collectively associate with the disease. Applied to diverse cohorts, MintTea captures modules with high predictive power, significant cross-omic correlations, and alignment with known microbiome-disease associations. For example, analyzing samples from a metabolic syndrome study, MintTea identifies a module with serum glutamate- and TCA cycle-related metabolites, along with bacterial species linked to insulin resistance. In another dataset, MintTea identifies a module associated with late-stage colorectal cancer, including Peptostreptococcus and Gemella species and fecal amino acids, in line with these species’ metabolic activity and their coordinated gradual increase with cancer development. This work demonstrates the potential of advanced integration methods in generating systems-level, multifaceted hypotheses underlying microbiome-disease interactions.
Vacancies tailoring lattice anharmonicity of Zintl-type thermoelectrics
Authors: Zhu Jinfeng , Ren Qingyong , Chen Chen , Wang Chen , Shu Mingfang , He Miao , Zhang Cuiping , Le Manh Duc , Torri Shuki , Wang Chin-Wei , Wang Jianli , Cheng Zhenxiang , Li Lisi , Wang Guohua , Jiang Yuxuan , Wu Mingzai , Qu Zhe , Tong Xin , Chen Yue , Zhang Qian , Ma Jie 
Published: March 2024

AbstractWhile phonon anharmonicity affects lattice thermal conductivity intrinsically and is difficult to be modified, controllable lattice defects routinely function only by scattering phonons extrinsically. Here, through a comprehensive study of crystal structure and lattice dynamics of Zintl-type Sr(Cu,Ag,Zn)Sb thermoelectric compounds using neutron scattering techniques and theoretical simulations, we show that the role of vacancies in suppressing lattice thermal conductivity could extend beyond defect scattering. The vacancies in Sr2ZnSb2 significantly enhance lattice anharmonicity, causing a giant softening and broadening of the entire phonon spectrum and, together with defect scattering, leading to a ~ 86% decrease in the maximum lattice thermal conductivity compared to SrCuSb. We show that this huge lattice change arises from charge density reconstruction, which undermines both interlayer and intralayer atomic bonding strength in the hierarchical structure. These microscopic insights demonstrate a promise of artificially tailoring phonon anharmonicity through lattice defect engineering to manipulate lattice thermal conductivity in the design of energy conversion materials.
Thermodynamic driving forces in contact electrification between polymeric materials
Authors: Zhang Hang , Sundaresan Sankaran , Webb Michael A. 
Published: March 2024

AbstractContact electrification, or contact charging, refers to the process of static charge accumulation after rubbing, or even simple touching, of two materials. Despite its relevance in static electricity, various natural phenomena, and numerous technologies, contact charging remains poorly understood. For insulating materials, even the species of charge carrier may be unknown, and the direction of charge-transfer lacks firm molecular-level explanation. Here, we use all-atom molecular dynamics simulations to investigate whether thermodynamics can explain contact charging between insulating polymers. Based on prior work suggesting that water-ions, such as hydronium and hydroxide ions, are potential charge carriers, we predict preferred directions of charge-transfer between polymer surfaces according to the free energy of water-ions within water droplets on such surfaces. Broad agreement between our predictions and experimental triboelectric series indicate that thermodynamically driven ion-transfer likely influences contact charging of polymers. Furthermore, simulation analyses reveal how specific interactions of water and water-ions proximate to the polymer-water interface explain observed trends. This study establishes relevance of thermodynamic driving forces in contact charging of insulators with new evidence informed by molecular-level interactions. These insights have direct implications for future mechanistic studies and applications of contact charging involving polymeric materials.
Outcome differences by sex in oncology clinical trials
Authors: Kammula Ashwin V. , Schäffer Alejandro A. , Rajagopal Padma Sheila , Kurzrock Razelle , Ruppin Eytan 
Published: March 2024

Abstract
Identifying sex differences in outcomes and toxicity between males and females in oncology clinical trials is important and has also been mandated by National Institutes of Health policies. Here we analyze the Trialtrove database, finding that, strikingly, only 472/89,221 oncology clinical trials (0.5%) had curated post-treatment sex comparisons. Among 288 trials with comparisons of survival, outcome, or response, 16% report males having statistically significant better survival outcome or response, while 42% reported significantly better survival outcome or response for females. The strongest differences are in trials of EGFR inhibitors in lung cancer and rituximab in non-Hodgkin’s lymphoma (both favoring females). Among 44 trials with side effect comparisons, more trials report significantly lesser side effects in males (N = 22) than in females (N = 13). Thus, while statistical comparisons between sexes in oncology trials are rarely reported, important differences in outcome and toxicity exist. These considerable outcome and toxicity differences highlight the need for reporting sex differences more thoroughly going forward.
Ultra-fast green hydrogen production from municipal wastewater by an integrated forward osmosis-alkaline water electrolysis system
Authors: Cassol Gabriela Scheibel , Shang Chii , An Alicia Kyoungjin , Khanzada Noman Khalid , Ciucci Francesco , Manzotti Alessandro , Westerhoff Paul , Song Yinghao , Ling Li 
Published: March 2024

AbstractRecent advancements in membrane-assisted seawater electrolysis powered by renewable energy offer a sustainable path to green hydrogen production. However, its large-scale implementation faces challenges due to slow power-to-hydrogen (P2H) conversion rates. Here we report a modular forward osmosis-water splitting (FOWS) system that integrates a thin-film composite FO membrane for water extraction with alkaline water electrolysis (AWE), denoted as FOWSAWE. This system generates high-purity hydrogen directly from wastewater at a rate of 448 Nm3 day−1 m−2 of membrane area, over 14 times faster than the state-of-the-art practice, with specific energy consumption as low as 3.96 kWh Nm−3. The rapid hydrogen production rate results from the utilisation of 1 M potassium hydroxide as a draw solution to extract water from wastewater, and as the electrolyte of AWE to split water and produce hydrogen. The current system enables this through the use of a potassium hydroxide-tolerant and hydrophilic FO membrane. The established water-hydrogen balance model can be applied to design modular FO and AWE units to meet demands at various scales, from households to cities, and from different water sources. The FOWSAWE system is a sustainable and an economical approach for producing hydrogen at a record-high rate directly from wastewater, marking a significant leap in P2H practice.
Activation of the insulin receptor by insulin-like growth factor 2
Authors: An Weidong , Hall Catherine , Li Jie , Hung Albert , Wu Jiayi , Park Junhee , Wang Liwei , Bai Xiao-chen , Choi Eunhee 
Published: March 2024

AbstractInsulin receptor (IR) controls growth and metabolism. Insulin-like growth factor 2 (IGF2) has different binding properties on two IR isoforms, mimicking insulin’s function. However, the molecular mechanism underlying IGF2-induced IR activation remains unclear. Here, we present cryo-EM structures of full-length human long isoform IR (IR-B) in both the inactive and IGF2-bound active states, and short isoform IR (IR-A) in the IGF2-bound active state. Under saturated IGF2 concentrations, both the IR-A and IR-B adopt predominantly asymmetric conformations with two or three IGF2s bound at site-1 and site-2, which differs from that insulin saturated IR forms an exclusively T-shaped symmetric conformation. IGF2 exhibits a relatively weak binding to IR site-2 compared to insulin, making it less potent in promoting full IR activation. Cell-based experiments validated the functional importance of IGF2 binding to two distinct binding sites in optimal IR signaling and trafficking. In the inactive state, the C-terminus of α-CT of IR-B contacts FnIII-2 domain of the same protomer, hindering its threading into the C-loop of IGF2, thus reducing the association rate of IGF2 with IR-B. Collectively, our studies demonstrate the activation mechanism of IR by IGF2 and reveal the molecular basis underlying the different affinity of IGF2 to IR-A and IR-B.
Long non-coding RNA-NONMMMUT004552.2 regulates the unloading-induced bone loss through the miRNA-15b-5p/Syne1 in mice
Authors: Zhang Zheng , Jing Yu , Zhang Ang , Liu JiShan , Yang Heming , Lou Xiaotong , Xu Liyan , Liu Min , Zhang Yikun , Gu Jianwen 
Published: March 2024

AbstractExercise-induced mechanical loading can increase bone strength whilst mechanical unloading enhances bone-loss. Here, we investigated the role of lncRNA NONMMUT004552.2 in unloading-induced bone-loss. Knockout of lncRNA NONMMUT004552.2 in hindlimb-unloaded mice caused an increase in the bone formation and osteoblast activity. The silencing of lncRNA NONMMUT004552.2 also decreased the osteoblast apoptosis and expression of Bax and cleaved caspase-3, increased Bcl-2 protein expression in MC3T3-E1 cells. Mechanistic investigations demonstrated that NONMMUT004552.2 functions as a competing endogenous RNA (ceRNA) to facilitate the protein expression of spectrin repeat containing, nuclear envelope 1 (Syne1) by competitively binding miR-15b-5p and subsequently inhibits the osteoblast differentiation and bone formation in the microgravity unloading environment. These data highlight the importance of the lncRNA NONMMUT004552.2/miR-15b-5p/Syne1 axis for the treatment of osteoporosis.
Potential use of sludge from El Ferrol Bay (Chimbote, Peru) for the production of lipids in the culture of Scenedesmus acutus (Meyen, 1829)
Authors: Merino Fernando , Mendoza Sorayda , Carhuapoma-Garay Juan , Campoverde-Vigo Luis , Huamancondor-Paz Yolanda P. , Choque-Quispe Yudith , Buleje Campos Dianeth , Choque-Quispe David , Rodriguez-Cardenas Liliana , Saldaña-Rojas Guillermo B. , Loayza-Aguilar Rómulo E. , Olivos-Ramirez Gustavo E. 
Published: March 2024

AbstractDespite the extensive development of microalgae biotechnology, it still requires new methodologies to lower production costs, especially in the field of biofuel production. Therefore, innovative methods that facilitate operations and enable cost-effective production are important in driving this industry. In this study, we propose a new low-cost and easy-to-use procedure, addressed to the generation of a culture medium for Scenedesmus acutus. The medium was obtained by thermal reduction of a sludge sample from El Ferrol Bay (Chimbote, Peru), whereby we obtained an aqueous medium. Our results indicated that the aqueous medium incorporates all necessary nutrients for microalgae production; allowing a maximum biomass of 0.75 ± 0.07 g/L with 60% of the medium; while high lipids production (59.42 ± 6.16%) was achieved with 20%. Besides, we quantified, in the experimental medium and at the end of the cultures, the levels of inorganic nutrients such as ammonium, nitrites, nitrates, and phosphates; in addition to COD and TOC, which were significantly reduced ($$p<$$

p
<

0.05) after 7 days of culture, mainly in the treatment with 20%. These results suggest tremendous potential for sludge reuse, which also entails a cost reduction in microalgae biomass production, with additional positive impacts on large-scale application over highly polluted environments.
Community detection in hypergraphs via mutual information maximization
Authors: Kritschgau Jürgen , Kaiser Daniel , Alvarado Rodriguez Oliver , Amburg Ilya , Bolkema Jessalyn , Grubb Thomas , Lan Fangfei , Maleki Sepideh , Chodrow Phil , Kay Bill 
Published: March 2024

AbstractThe hypergraph community detection problem seeks to identify groups of related vertices in hypergraph data. We propose an information-theoretic hypergraph community detection algorithm which compresses the observed data in terms of community labels and community-edge intersections. This algorithm can also be viewed as maximum-likelihood inference in a degree-corrected microcanonical stochastic blockmodel. We perform the compression/inference step via simulated annealing. Unlike several recent algorithms based on canonical models, our microcanonical algorithm does not require inference of statistical parameters such as vertex degrees or pairwise group connection rates. Through synthetic experiments, we find that our algorithm succeeds down to recently-conjectured thresholds for sparse random hypergraphs. We also find competitive performance in cluster recovery tasks on several hypergraph data sets.
Numerical simulation of a fractional stochastic delay differential equations using spectral scheme: a comprehensive stability analysis
Authors: Li Shuo , Khan Sami Ullah , Riaz Muhammad Bilal , AlQahtani Salman A. , Alamri Atif M. 
Published: March 2024

AbstractThe fractional stochastic delay differential equation (FSDDE) is a powerful mathematical tool for modeling complex systems that exhibit both fractional order dynamics and stochasticity with time delays. The purpose of this study is to explore the stability analysis of a system of FSDDEs. Our study emphasizes the interaction between fractional calculus, stochasticity, and time delays in understanding the stability of such systems. Analyzing the moments of the system’s solutions, we investigate stochasticity’s influence on FSDDS. The article provides practical insight into solving FSDDS efficiently using various numerical techniques. Additionally, this research focuses both on asymptotic as well as Lyapunov stability of FSDDS. The local stability conditions are clearly presented and also the effects of a fractional orders with delay on the stability properties are examine. Through a comprehensive test of a stability criteria, practical examples and numerical simulations we demonstrate the complexity and challenges concern with the analyzing FSDDEs.
Diatom-inspired silicification process for development of green flexible silica composite aerogels
Authors: Tan Valerie , Berg Florian , Maleki Hajar 
Published: March 2024

AbstractIn this study, we have developed novel biomimetic silica composite aerogels and cryogels for the first time, drawing inspiration from the natural diatom’s silicification process. Our biomimetic approach involved the modification of tyrosinase-mediated oxidized silk fibroin (SFO) surfaces with polyethyleneimine (PEI). This modification introduced ample amine groups onto the SF polymer, which catalyzed the silicification of the SFO-PEI gel surface with silicic acid. This process emulates the catalytic function of long-chain polyamines and silaffin proteins found in diatoms, resulting in a silica network structure on the primary SFO-PEI network gel’s surface. The SFO-PEI gel matrix played a dual role in this process: (1) It provided numerous amine functional groups that directly catalyzed the silicification of silicic acid on the porous structure’s exterior surface, without encapsulating the created silica network in the gel. (2) It served as a flexible mechanical support facilitating the creation of the silica network. As a result, the final ceramic composite exhibits a mechanically flexible nature (e.g., cyclic compressibility up to 80% strain), distinguishing it from conventional composite aerogels. By mimicking the diatom’s silicification process, we were able to simplify the development of silica-polymer composite aerogels. It eliminates the need for surfactants, multi-step procedures involving solvent exchange, and gel washing. Instead, the reaction occurs under mild conditions, streamlining the composite aerogels fabrication process.