bluuebunny/crossref_metadata_2025_split huggingface dataset:
Potent latency reversal by Tat RNA-containing nanoparticle enables multi-omic analysis of the HIV-1 reservoir
Authors: Pardons Marion , Cole Basiel , Lambrechts Laurens , van Snippenberg Willem , Rutsaert Sofie , Noppe Ytse , De Langhe Nele , Dhondt Annemieke , Vega Jerel , Eyassu Filmon , Nijs Erik , Van Gulck Ellen , Boden Daniel , Vandekerckhove Linos 
Published: December 2023

AbstractThe development of latency reversing agents that potently reactivate HIV without inducing global T cell activation would benefit the field of HIV reservoir research and could pave the way to a functional cure. Here, we explore the reactivation capacity of a lipid nanoparticle containing Tat mRNA (Tat-LNP) in CD4 T cells from people living with HIV undergoing antiretroviral therapy (ART). When combined with panobinostat, Tat-LNP induces latency reversal in a significantly higher proportion of latently infected cells compared to PMA/ionomycin (≈ 4-fold higher). We demonstrate that Tat-LNP does not alter the transcriptome of CD4 T cells, enabling the characterization of latently infected cells in their near-native state. Upon latency reversal, we identify transcriptomic differences between infected cells carrying an inducible provirus and non-infected cells (e.g. LINC02964, GZMA, CCL5). We confirm the transcriptomic differences at the protein level and provide evidence that the long non-coding RNA LINC02964 plays a role in active HIV infection. Furthermore, p24+ cells exhibit heightened PI3K/Akt signaling, along with downregulation of protein translation, suggesting that HIV-infected cells display distinct signatures facilitating their long-term persistence. Tat-LNP represents a valuable research tool for in vitro reservoir studies as it greatly facilitates the in-depth characterization of HIV reservoir cells’ transcriptome and proteome profiles.
Orbital perspective on high-harmonic generation from solids
Authors: Jiménez-Galán Álvaro , Bossaer Chandler , Ernotte Guilmot , Parks Andrew M. , Silva Rui E. F. , Villeneuve David M. , Staudte André , Brabec Thomas , Luican-Mayer Adina , Vampa Giulio 
Published: December 2023

AbstractHigh-harmonic generation in solids allows probing and controlling electron dynamics in crystals on few femtosecond timescales, paving the way to lightwave electronics. In the spatial domain, recent advances in the real-space interpretation of high-harmonic emission in solids allows imaging the field-free, static, potential of the valence electrons with picometer resolution. The combination of such extreme spatial and temporal resolutions to measure and control strong-field dynamics in solids at the atomic scale is poised to unlock a new frontier of lightwave electronics. Here, we report a strong intensity-dependent anisotropy in the high-harmonic generation from ReS2 that we attribute to angle-dependent interference of currents from the different atoms in the unit cell. Furthermore, we demonstrate how the laser parameters control the relative contribution of these atoms to the high-harmonic emission. Our findings provide an unprecedented atomic perspective on strong-field dynamics in crystals, revealing key factors to consider in the route towards developing efficient harmonic emitters.
iMUT-seq: high-resolution DSB-induced mutation profiling reveals prevalent homologous-recombination dependent mutagenesis
Authors: Bader Aldo S. , Bushell Martin 
Published: December 2023

AbstractDNA double-strand breaks (DSBs) are the most mutagenic form of DNA damage, and play a significant role in cancer biology, neurodegeneration and aging. However, studying DSB-induced mutagenesis is limited by our current approaches. Here, we describe iMUT-seq, a technique that profiles DSB-induced mutations at high-sensitivity and single-nucleotide resolution around endogenous DSBs. By depleting or inhibiting 20 DSB-repair factors we define their mutational signatures in detail, revealing insights into the mechanisms of DSB-induced mutagenesis. Notably, we find that homologous-recombination (HR) is more mutagenic than previously thought, inducing prevalent base substitutions and mononucleotide deletions at distance from the break due to DNA-polymerase errors. Simultaneously, HR reduces translocations, suggesting a primary role of HR is specifically the prevention of genomic rearrangements. The results presented here offer fundamental insights into DSB-induced mutagenesis and have significant implications for our understanding of cancer biology and the development of DDR-targeting chemotherapeutics.
Strain-driven Kovacs-like memory effect in glasses
Authors: Tong Yu , Song Lijian , Gao Yurong , Fan Longlong , Li Fucheng , Yang Yiming , Mo Guang , Liu Yanhui , Shui Xiaoxue , Zhang Yan , Gao Meng , Huo Juntao , Qiao Jichao , Pineda Eloi , Wang Jun-Qiang 
Published: December 2023

AbstractStudying complex relaxation behaviors is of critical importance for understanding the nature of glasses. Here we report a Kovacs-like memory effect in glasses, manifested by non-monotonic stress relaxation during two-step high-to-low strains stimulations. During the stress relaxation process, if the strain jumps from a higher state to a lower state, the stress does not continue to decrease, but increases first and then decreases. The memory effect becomes stronger when the atomic motions become highly collective with a large activation energy, e.g. the strain in the first stage is larger, the temperature is higher, and the stimulation is longer. The physical origin of the stress memory effect is studied based on the relaxation kinetics and the in-situ synchrotron X-ray experiments. The stress memory effect is probably a universal phenomenon in different types of glasses.
Behavior of glioblastoma brain tumor stem cells following a suborbital rocket flight: reaching the “edge” of outer space
Authors: Garcia Cesar A. , Suárez-Meade Paola , Brooks Mieu , Bhargav Adip G. , Freeman Michelle L. , Harvey Lawrence M. , Quinn John , Quiñones-Hinojosa Alfredo 
Published: December 2023

AbstractThe emerging arena of space exploration has created opportunities to study cancer cell biology in the environments of microgravity and hypergravity. Studying cellular behavior in altered gravity conditions has allowed researchers to make observations of cell function that would otherwise remain unnoticed. The patient-derived QNS108 brain tumor initiating cell line (BTIC), isolated from glioblastoma (GBM) tissue, was launched on a suborbital, parabolic rocket flight conducted by EXOS Aerospace Systems & Technologies. All biologicals and appropriate ground controls were secured post-launch and transported back to our research facility. Cells from the rocket-flight and ground-based controls were isolated from the culture containers and expanded on adherent flasks for two weeks. In vitro migration, proliferation, and stemness assays were performed. Following cell expansion, male nude mice were intracranially injected with either ground-control (GC) or rocket-flight (RF) exposed cells to assess tumorigenic capacity (n = 5 per group). Patient-derived QNS108 BTICs exposed to RF displayed more aggressive tumor growth than the GC cells in vitro and in vivo. RF cells showed significantly higher migration (p < 0.0000) and stemness profiles (p < 0.01) when compared to GC cells. Further, RF cells, when implanted in vivo in the brain of rodents had larger tumor-associated cystic growth areas (p = 0.00029) and decreased survival (p = 0.0172) as compared to those animals that had GC cells implanted.
Anomalous Nernst effect in the topological and magnetic material MnBi4Te7
Authors: Ceccardi M. , Zeugner A. , Folkers L. C. , Hess C. , Büchner B. , Marré D. , Isaeva A. , Caglieris F. 
Published: December 2023

AbstractThe recently discovered magnetic topological insulators (MnBi2Te4)(Bi2Te3)n, n = 0–4, are an ideal playground to study the influence of magnetic properties on band topology, giving access to diverse quantum states in a single compound. In the low temperature-antiferromagnetic state and vanishing magnetic field, the n = 1 system is a topological insulator protected by a combination of time reversal and a translation symmetries. It has been argued that, when the antiferromagnetic phase is forced to a the fully spin polarized state by the application of an external magnetic field, this system develops Weyl cones in the conduction band, which become accessible in presence of an intrinsic electronic doping. In this work, we experimentally prove the raising of field-induced Weyl state through the detection of an intrinsic anomalous Nernst effect in a bulk single crystal of MnBi4Te7.
Asking the right questions for mutagenicity prediction from BioMedical text
Authors: Acharya Sathwik , Shinada Nicolas K. , Koyama Naoki , Ikemori Megumi , Nishioka Tomoki , Hitaoka Seiji , Hakura Atsushi , Asakura Shoji , Matsuoka Yukiko , Palaniappan Sucheendra K. 
Published: December 2023

AbstractAssessing the mutagenicity of chemicals is an essential task in the drug development process. Usually, databases and other structured sources for AMES mutagenicity exist, which have been carefully and laboriously curated from scientific publications. As knowledge accumulates over time, updating these databases is always an overhead and impractical. In this paper, we first propose the problem of predicting the mutagenicity of chemicals from textual information in scientific publications. More simply, given a chemical and evidence in the natural language form from publications where the mutagenicity of the chemical is described, the goal of the model/algorithm is to predict if it is potentially mutagenic or not. For this, we first construct a golden standard data set and then propose MutaPredBERT, a prediction model fine-tuned on BioLinkBERT based on a question-answering formulation of the problem. We leverage transfer learning and use the help of large transformer-based models to achieve a Macro F1 score of >0.88 even with relatively small data for fine-tuning. Our work establishes the utility of large language models for the construction of structured sources of knowledge bases directly from scientific publications.
Evidence from Finland and Sweden on the relationship between early-life diseases and lifetime childlessness in men and women
Authors: Liu Aoxing , Akimova Evelina T. , Ding Xuejie , Jukarainen Sakari , Vartiainen Pekka , Kiiskinen Tuomo , Koskelainen Sara , Havulinna Aki S. , Gissler Mika , Lombardi Stefano , Fall Tove , Mills Melinda C. , Ganna Andrea 
Published: December 2023

AbstractThe percentage of people without children over their lifetime is approximately 25% in men and 20% in women. Individual diseases have been linked to childlessness, mostly in women, yet we lack a comprehensive picture of the effect of early-life diseases on lifetime childlessness. We examined all individuals born in 1956–1968 (men) and 1956–1973 (women) in Finland (n = 1,035,928) and Sweden (n = 1,509,092) to the completion of their reproductive lifespan in 2018. Leveraging nationwide registers, we associated sociodemographic and reproductive information with 414 diseases across 16 categories, using a population and matched-pair case–control design of siblings discordant for childlessness (71,524 full sisters and 77,622 full brothers). The strongest associations were mental–behavioural disorders (particularly among men), congenital anomalies and endocrine–nutritional–metabolic disorders (strongest among women). We identified new associations for inflammatory and autoimmune diseases. Associations were dependent on age at onset and mediated by singlehood and education. This evidence can be used to understand how disease contributes to involuntary childlessness.
Unequal climate impacts on global values of natural capital
Authors: Bastien-Olvera B. A. , Conte M. N. , Dong X. , Briceno T. , Batker D. , Emmerling J. , Tavoni M. , Granella F. , Moore F. C. 
Published: December 2023

AbstractEcosystems generate a wide range of benefits for humans, including some market goods as well as other benefits that are not directly reflected in market activity1. Climate change will alter the distribution of ecosystems around the world and change the flow of these benefits2,3. However, the specific implications of ecosystem changes for human welfare remain unclear, as they depend on the nature of these changes, the value of the affected benefits and the extent to which communities rely on natural systems for their well-being4. Here we estimate country-level changes in economic production and the value of non-market ecosystem benefits resulting from climate-change-induced shifts in terrestrial vegetation cover, as projected by dynamic global vegetation models (DGVMs) driven by general circulation climate models. Our results show that the annual population-weighted mean global flow of non-market ecosystem benefits valued in the wealth accounts of the World Bank will be reduced by 9.2% in 2100 under the Shared Socioeconomic Pathway SSP2-6.0 with respect to the baseline no climate change scenario and that the global population-weighted average change in gross domestic product (GDP) by 2100 is −1.3% of the baseline GDP. Because lower-income countries are more reliant on natural capital, these GDP effects are regressive. Approximately 90% of these damages are borne by the poorest 50% of countries and regions, whereas the wealthiest 10% experience only 2% of these losses.
Designer phospholipid capping ligands for soft metal halide nanocrystals
Authors: Morad Viktoriia , Stelmakh Andriy , Svyrydenko Mariia , Feld Leon G. , Boehme Simon C. , Aebli Marcel , Affolter Joel , Kaul Christoph J. , Schrenker Nadine J. , Bals Sara , Sahin Yesim , Dirin Dmitry N. , Cherniukh Ihor , Raino Gabriele , Baumketner Andrij , Kovalenko Maksym V. 
Published: December 2023

AbstractThe success of colloidal semiconductor nanocrystals (NCs) in science and optoelectronics is inextricable from their surfaces. The functionalization of lead halide perovskite NCs1–5 poses a formidable challenge because of their structural lability, unlike the well-established covalent ligand capping of conventional semiconductor NCs6,7. We posited that the vast and facile molecular engineering of phospholipids as zwitterionic surfactants can deliver highly customized surface chemistries for metal halide NCs. Molecular dynamics simulations implied that ligand–NC surface affinity is primarily governed by the structure of the zwitterionic head group, particularly by the geometric fitness of the anionic and cationic moieties into the surface lattice sites, as corroborated by the nuclear magnetic resonance and Fourier-transform infrared spectroscopy data. Lattice-matched primary-ammonium phospholipids enhance the structural and colloidal integrity of hybrid organic–inorganic lead halide perovskites (FAPbBr3 and MAPbBr3 (FA, formamidinium; MA, methylammonium)) and lead-free metal halide NCs. The molecular structure of the organic ligand tail governs the long-term colloidal stability and compatibility with solvents of diverse polarity, from hydrocarbons to acetone and alcohols. These NCs exhibit photoluminescence quantum yield of more than 96% in solution and solids and minimal photoluminescence intermittency at the single particle level with an average ON fraction as high as 94%, as well as bright and high-purity (about 95%) single-photon emission.
A digital health algorithm to guide antibiotic prescription in pediatric outpatient care: a cluster randomized controlled trial
Authors: Tan Rainer , Kavishe Godfrey , Luwanda Lameck B. , Kulinkina Alexandra V. , Renggli Sabine , Mangu Chacha , Ashery Geofrey , Jorram Margaret , Mtebene Ibrahim Evans , Agrea Peter , Mhagama Humphrey , Vonlanthen Alan , Faivre Vincent , Thabard Julien , Levine Gillian , Le Pogam Marie-Annick , Keitel Kristina , Taffé Patrick , Ntinginya Nyanda , Masanja Honorati , D’Acremont Valérie 
Published: December 2023

AbstractExcessive antibiotic use and antimicrobial resistance are major global public health threats. We developed ePOCT+, a digital clinical decision support algorithm in combination with C-reactive protein test, hemoglobin test, pulse oximeter and mentorship, to guide health-care providers in managing acutely sick children under 15 years old. To evaluate the impact of ePOCT+ compared to usual care, we conducted a cluster randomized controlled trial in Tanzanian primary care facilities. Over 11 months, 23,593 consultations were included from 20 ePOCT+ health facilities and 20,713 from 20 usual care facilities. The use of ePOCT+ in intervention facilities resulted in a reduction in the coprimary outcome of antibiotic prescription compared to usual care (23.2% versus 70.1%, adjusted difference −46.4%, 95% confidence interval (CI) −57.6 to −35.2). The coprimary outcome of day 7 clinical failure was noninferior in ePOCT+ facilities compared to usual care facilities (adjusted relative risk 0.97, 95% CI 0.85 to 1.10). There was no difference in the secondary safety outcomes of death and nonreferred secondary hospitalizations by day 7. Using ePOCT+ could help address the urgent problem of antimicrobial resistance by safely reducing antibiotic prescribing. Clinicaltrials.gov Identifier: NCT05144763
Global inventory of species categorized by known underwater sonifery
Authors: Looby Audrey , Erbe Christine , Bravo Santiago , Cox Kieran , Davies Hailey L. , Di Iorio Lucia , Jézéquel Youenn , Juanes Francis , Martin Charles W. , Mooney T. Aran , Radford Craig , Reynolds Laura K. , Rice Aaron N. , Riera Amalis , Rountree Rodney , Spriel Brittnie , Stanley Jenni , Vela Sarah , Parsons Miles J. G. 
Published: December 2023

AbstractA working group from the Global Library of Underwater Biological Sounds effort collaborated with the World Register of Marine Species (WoRMS) to create an inventory of species confirmed or expected to produce sound underwater. We used several existing inventories and additional literature searches to compile a dataset categorizing scientific knowledge of sonifery for 33,462 species and subspecies across marine mammals, other tetrapods, fishes, and invertebrates. We found 729 species documented as producing active and/or passive sounds under natural conditions, with another 21,911 species deemed likely to produce sounds based on evaluated taxonomic relationships. The dataset is available on both figshare and WoRMS where it can be regularly updated as new information becomes available. The data can also be integrated with other databases (e.g., SeaLifeBase, Global Biodiversity Information Facility) to advance future research on the distribution, evolution, ecology, management, and conservation of underwater soniferous species worldwide.
A large-scale dataset of patient summaries for retrieval-based clinical decision support systems
Authors: Zhao Zhengyun , Jin Qiao , Chen Fangyuan , Peng Tuorui , Yu Sheng 
Published: December 2023

AbstractRetrieval-based Clinical Decision Support (ReCDS) can aid clinical workflow by providing relevant literature and similar patients for a given patient. However, the development of ReCDS systems has been severely obstructed by the lack of diverse patient collections and publicly available large-scale patient-level annotation datasets. In this paper, we collect a novel dataset of patient summaries and relations called PMC-Patients to benchmark two ReCDS tasks: Patient-to-Article Retrieval (ReCDS-PAR) and Patient-to-Patient Retrieval (ReCDS-PPR). Specifically, we extract patient summaries from PubMed Central articles using simple heuristics and utilize the PubMed citation graph to define patient-article relevance and patient-patient similarity. PMC-Patients contains 167k patient summaries with 3.1 M patient-article relevance annotations and 293k patient-patient similarity annotations, which is the largest-scale resource for ReCDS and also one of the largest patient collections. Human evaluation and analysis show that PMC-Patients is a diverse dataset with high-quality annotations. We also implement and evaluate several ReCDS systems on the PMC-Patients benchmarks to show its challenges and conduct several case studies to show the clinical utility of PMC-Patients.
Long-term gridded land evapotranspiration reconstruction using Deep Forest with high generalizability
Authors: Feng Qiaomei , Shen Junyong , Yang Feng , Liang Shijing , Liu Jiang , Kuang Xingxing , Wang Dashan , Zeng Zhenzhong 
Published: December 2023

AbstractPrevious datasets have limitations in generalizing evapotranspiration (ET) across various land cover types due to the scarcity and spatial heterogeneity of observations, along with the incomplete understanding of underlying physical mechanisms as a deeper contributing factor. To fill in these gaps, here we developed a global Highly Generalized Land (HG-Land) ET dataset at 0.5° spatial resolution with monthly values covering the satellite era (1982–2018). Our approach leverages the power of a Deep Forest machine-learning algorithm, which ensures good generalizability and mitigates overfitting by minimizing hyper-parameterization. Model explanations are further provided to enhance model transparency and gain new insights into the ET process. Validation conducted at both the site and basin scales attests to the dataset’s satisfactory accuracy, with a pronounced emphasis on the Northern Hemisphere. Furthermore, we find that the primary driver of ET predictions varies across different climatic regions. Overall, the HG-Land ET, underpinned by the interpretability of the machine-learning model, emerges as a validated and generalized resource catering to scientific research and various applications.
Novel 3-(pyrazol-4-yl)-2-(1H-indole-3-carbonyl)acrylonitrile derivatives induce intrinsic and extrinsic apoptotic death mediated P53 in HCT116 colon carcinoma
Authors: Mohamed Magda F. , Ibrahim Nada S. , Saddiq Amna A. , Abdelhamid Ismail A. 
Published: December 2023

AbstractA novel series of α-cyano indolylchalcones was prepared, and their chemical structures were confirmed based on the different spectral data. Among them, compound 7f was observed to be the most effective bioactive chalcone with distinguished potency and selectivity against colorectal carcinoma (HCT116) with IC50 value (6.76 µg/mL) relative to the positive control (5 FU) (77.15 µg/mL). In a preliminary action study, the acrylonitrile chalcone 7f was found to enhance apoptotic action via different mechanisms like inhibition of some anti-apoptotic protein expression, regulation of some apoptotic proteins, production of caspases, and cell cycle arrest. All mechanisms suggested that compound 7f could act as a professional chemotherapeutic agent. Also, a molecular docking study was achieved on some selected proteins implicated in cancer (Caspase 9, XIAP, P53 mutant Y220C, and MDM2) which showed variable interactions with compound 7f with good Gibbs free energy scores.
Novel environmental monitoring detector for discriminating fallout and airborne radioactivity
Authors: Holm Philip , Ihantola Sakari , Bogdanoff Ville , Peräjärvi Kari , Dendooven Peter , Tengblad Olof , Muikku Maarit 
Published: December 2023

AbstractEarly warning networks are used for detecting abnormal radioactivity levels in the environment. State-of-the-art networks are equipped with both dose rate detectors and spectrometric stations. Current networks don’t automatically discriminate between radioactivity on the ground and in the air. A novel directional sensing gamma radiation detector utilizing a collimated phoswich scintillator was developed. The signals from the two scintillator materials are separated using a pulse shape discrimination. The separated signals are employed to determine the radioactivity concentrations on the ground and in the air assuming specific concentration distributions. Limitations related to imperfect directional sensing and dead time are discussed.