bluuebunny/crossref_metadata_2025 huggingface dataset:
Physiological basis for atmospheric methane oxidation and methanotrophic growth on air
Authors: Schmider Tilman , Hestnes Anne Grethe , Brzykcy Julia , Schmidt Hannes , Schintlmeister Arno , Roller Benjamin R. K. , Teran Ezequiel Jesús , Söllinger Andrea , Schmidt Oliver , Polz Martin F. , Richter Andreas , Svenning Mette M. , Tveit Alexander T.
Published: May 2024

Atmospheric methane oxidizing bacteria (atmMOB) constitute the sole biological sink for atmospheric methane. Still, the physiological basis allowing atmMOB to grow on air is not well understood. Here we assess the ability and strategies of seven methanotrophic species to grow with air as sole energy, carbon, and nitrogen source. Four species, including three outside the canonical atmMOB group USCα, enduringly oxidized atmospheric methane, carbon monoxide, and hydrogen during 12 months of growth on air. These four species exhibited distinct substrate preferences implying the existence of multiple metabolic strategies to grow on air. The estimated energy yields of the atmMOB were substantially lower than previously assumed necessary for cellular maintenance in atmMOB and other aerobic microorganisms. Moreover, the atmMOB also covered their nitrogen requirements from air. During growth on air, the atmMOB decreased investments in biosynthesis while increasing investments in trace gas oxidation. Furthermore, we confirm that a high apparent specific affinity for methane is a key characteristic of atmMOB. Our work shows that atmMOB grow on the trace concentrations of methane, carbon monoxide, and hydrogen present in air and outlines the metabolic strategies that enable atmMOB to mitigate greenhouse gases.
Direct conversion of cardiac fibroblasts into endothelial-like cells using Sox17 and Erg
Authors: Farber Gregory , Dong Yanhan , Wang Qiaozi , Rathod Mitesh , Wang Haofei , Dixit Michelle , Keepers Benjamin , Xie Yifang , Butz Kendall , Polacheck William J. , Liu Jiandong , Qian Li
Published: May 2024

Endothelial cells are a heterogeneous population with various organ-specific and conserved functions that are critical to organ development, function, and regeneration. Here we report a Sox17-Erg direct reprogramming approach that uses cardiac fibroblasts to create differentiated endothelial cells that demonstrate endothelial-like molecular and physiological functions in vitro and in vivo. Injection of these induced endothelial cells into myocardial infarct sites after injury results in improved vascular perfusion of the scar region. Furthermore, we use genomic analyses to illustrate that Sox17-Erg reprogramming instructs cardiac fibroblasts toward an arterial-like identity. This results in a more efficient direct conversion of fibroblasts into endothelial-like cells when compared to traditional Etv2-based reprogramming. Overall, this Sox17-Erg direct reprogramming strategy offers a robust tool to generate endothelial cells both in vitro and in vivo, and has the potential to be used in repairing injured tissue.
TDP-43 proteinopathy in ALS is triggered by loss of ASRGL1 and associated with HML-2 expression
Authors: Garcia-Montojo Marta , Fathi Saeed , Rastegar Cyrus , Simula Elena Rita , Doucet-O’Hare Tara , Cheng Y. H. Hank , Abrams Rachel P. M. , Pasternack Nicholas , Malik Nasir , Bachani Muzna , Disanza Brianna , Maric Dragan , Lee Myoung-Hwa , Wang Herui , Santamaria Ulisses , Li Wenxue , Sampson Kevon , Lorenzo Juan Ramiro , Sanchez Ignacio E. , Mezghrani Alexandre , Li Yan , Sechi Leonardo Antonio , Pineda Sebastian , Heiman Myriam , Kellis Manolis , Steiner Joseph , Nath Avindra
Published: May 2024

TAR DNA-binding protein 43 (TDP-43) proteinopathy in brain cells is the hallmark of amyotrophic lateral sclerosis (ALS) but its cause remains elusive. Asparaginase-like-1 protein (ASRGL1) cleaves isoaspartates, which alter protein folding and susceptibility to proteolysis. ASRGL1 gene harbors a copy of the human endogenous retrovirus HML-2, whose overexpression contributes to ALS pathogenesis. Here we show that ASRGL1 expression was diminished in ALS brain samples by RNA sequencing, immunohistochemistry, and western blotting. TDP-43 and ASRGL1 colocalized in neurons but, in the absence of ASRGL1, TDP-43 aggregated in the cytoplasm. TDP-43 was found to be prone to isoaspartate formation and a substrate for ASRGL1. ASRGL1 silencing triggered accumulation of misfolded, fragmented, phosphorylated and mislocalized TDP-43 in cultured neurons and motor cortex of female mice. Overexpression of ASRGL1 restored neuronal viability. Overexpression of HML-2 led to ASRGL1 silencing. Loss of ASRGL1 leading to TDP-43 aggregation may be a critical mechanism in ALS pathophysiology.
Systematic review and meta-analysis of ex-post evaluations on the effectiveness of carbon pricing
Authors: Döbbeling-Hildebrandt Niklas , Miersch Klaas , Khanna Tarun M. , Bachelet Marion , Bruns Stephan B. , Callaghan Max , Edenhofer Ottmar , Flachsland Christian , Forster Piers M. , Kalkuhl Matthias , Koch Nicolas , Lamb William F. , Ohlendorf Nils , Steckel Jan Christoph , Minx Jan C.
Published: May 2024

Today, more than 70 carbon pricing schemes have been implemented around the globe, but their contributions to emissions reductions remains a subject of heated debate in science and policy. Here we assess the effectiveness of carbon pricing in reducing emissions using a rigorous, machine-learning assisted systematic review and meta-analysis. Based on 483 effect sizes extracted from 80 causal ex-post evaluations across 21 carbon pricing schemes, we find that introducing a carbon price has yielded immediate and substantial emission reductions for at least 17 of these policies, despite the low level of prices in most instances. Statistically significant emissions reductions range between –5% to –21% across the schemes (–4% to –15% after correcting for publication bias). Our study highlights critical evidence gaps with regard to dozens of unevaluated carbon pricing schemes and the price elasticity of emissions reductions. More rigorous synthesis of carbon pricing and other climate policies is required across a range of outcomes to advance our understanding of “what works” and accelerate learning on climate solutions in science and policy.
The vacuolar fusion regulated by HOPS complex promotes hyphal initiation and penetration in Candida albicans
Authors: Liu Yu , Wang Ruina , Liu Jiacun , Fan Mengting , Ye Zi , Hao Yumeng , Xie Fei , Wang Ting , Jiang Yuanying , Liu Ningning , Cui Xiaoyan , Lv Quanzhen , Yan Lan
Published: May 2024

The transition between yeast and hyphae is crucial for regulating the commensalism and pathogenicity inCandida albicans. The mechanisms that affect the invasion of hyphae in solid media, whose deficiency is more related to the pathogenicity ofC. albicans, have not been elucidated. Here, we found that the disruption ofVAM6orVPS41which are components of the homotypic vacuolar fusion and protein sorting (HOPS) complex, or the Rab GTPaseYPT72, all responsible for vacuole fusion, led to defects in hyphal growth in both liquid and solid media, but more pronounced on solid agar. The phenotypes ofvac8Δ/Δ andGTR1OE-vam6Δ/Δ mutants indicated that these deficiencies are mainly caused by the reduced mechanical forces that drive agar and organs penetration, and confirmed that large vacuoles are required for hyphal mechanical penetration. In summary, our study revealed that large vacuoles generated by vacuolar fusion support hyphal penetration and provided a perspective to refocus attention on the role of solid agar in evaluatingC. albicansinvasion.
High-performance piezoelectric energy harvesting in amorphous perovskite thin films deposited directly on a plastic substrate
Authors: Han Ju , Park Sung Hyun , Jung Ye Seul , Cho Yong Soo
Published: May 2024

Most reported thin-film piezoelectric energy harvesters have been based on cantilever-type crystalline ferroelectric oxide thin films deposited on rigid substrates, which utilize vibrational input sources. Herein, we introduce flexible amorphous thin-film energy harvesters based on perovskite CaCu3Ti4O12 (CCTO) thin films on a plastic substrate for highly competitive electromechanical energy harvesting. The room-temperature sputtering of CCTO thin films enable the use of plastic substrates to secure reliable flexibility, which has not been available thus far. Surprisingly, the resultant amorphous nature of the films results in an output voltage and power density of ~38.7 V and ~2.8 × 106 μW cm−3, respectively, which break the previously reported record for typical polycrystalline ferroelectric oxide thin-film cantilevers. The origin of this excellent electromechanical energy conversion is systematically explored as being related to the localized permanent dipoles of TiO6 octahedra and lowered dielectric constant in the amorphous state, depending on the stoichiometry and defect states. This is the leading example of a high-performance flexible piezoelectric energy harvester based on perovskite oxides not requiring a complex process for transferring films onto a plastic substrate.
Sustained IFN signaling is associated with delayed development of SARS-CoV-2-specific immunity
Authors: Brunet-Ratnasingham Elsa , Morin Sacha , Randolph Haley E. , Labrecque Marjorie , Bélair Justin , Lima-Barbosa Raphaël , Pagliuzza Amélie , Marchitto Lorie , Hultström Michael , Niessl Julia , Cloutier Rose , Sreng Flores Alina M. , Brassard Nathalie , Benlarbi Mehdi , Prévost Jérémie , Ding Shilei , Anand Sai Priya , Sannier Gérémy , Marks Amanda , Wågsäter Dick , Bareke Eric , Zeberg Hugo , Lipcsey Miklos , Frithiof Robert , Larsson Anders , Zhou Sirui , Nakanishi Tomoko , Morrison David , Vezina Dani , Bourassa Catherine , Gendron-Lepage Gabrielle , Medjahed Halima , Point Floriane , Richard Jonathan , Larochelle Catherine , Prat Alexandre , Cunningham Janet L. , Arbour Nathalie , Durand Madeleine , Richards J. Brent , Moon Kevin , Chomont Nicolas , Finzi Andrés , Tétreault Martine , Barreiro Luis , Wolf Guy , Kaufmann Daniel E.
Published: May 2024

Plasma RNAemia, delayed antibody responses and inflammation predict COVID-19 outcomes, but the mechanisms underlying these immunovirological patterns are poorly understood. We profile 782 longitudinal plasma samples from 318 hospitalized patients with COVID-19. Integrated analysis using k-means reveals four patient clusters in a discovery cohort: mechanically ventilated critically-ill cases are subdivided into good prognosis and high-fatality clusters (reproduced in a validation cohort), while non-critical survivors segregate into high and low early antibody responders. Only the high-fatality cluster is enriched for transcriptomic signatures associated with COVID-19 severity, and each cluster has distinct RBD-specific antibody elicitation kinetics. Both critical and non-critical clusters with delayed antibody responses exhibit sustained IFN signatures, which negatively correlate with contemporaneous RBD-specific IgG levels and absolute SARS-CoV-2-specific B and CD4+ T cell frequencies. These data suggest that the “Interferon paradox” previously described in murine LCMV models is operative in COVID-19, with excessive IFN signaling delaying development of adaptive virus-specific immunity.
Correlative single molecule lattice light sheet imaging reveals the dynamic relationship between nucleosomes and the local chromatin environment
Authors: Daugird Timothy A. , Shi Yu , Holland Katie L. , Rostamian Hosein , Liu Zhe , Lavis Luke D. , Rodriguez Joseph , Strahl Brian D. , Legant Wesley R.
Published: May 2024

In the nucleus, biological processes are driven by proteins that diffuse through and bind to a meshwork of nucleic acid polymers. To better understand this interplay, we present an imaging platform to simultaneously visualize single protein dynamics together with the local chromatin environment in live cells. Together with super-resolution imaging, new fluorescent probes, and biophysical modeling, we demonstrate that nucleosomes display differential diffusion and packing arrangements as chromatin density increases whereas the viscoelastic properties and accessibility of the interchromatin space remain constant. Perturbing nuclear functions impacts nucleosome diffusive properties in a manner that is dependent both on local chromatin density and on relative location within the nucleus. Our results support a model wherein transcription locally stabilizes nucleosomes while simultaneously allowing for the free exchange of nuclear proteins. Additionally, they reveal that nuclear heterogeneity arises from both active and passive processes and highlight the need to account for different organizational principles when modeling different chromatin environments.
Serological evidence of zoonotic filovirus exposure among bushmeat hunters in Guinea
Authors: Akoi Boré Joseph , Timothy Joseph W. S. , Tipton Tom , Kekoura Ifono , Hall Yper , Hood Grace , Longet Stephanie , Fornace Kimberly , Lucien Millimono S. , Fehling Sarah Katarina , Koivogui Beatrice K. , Coggins Si’Ana A. , Laing Eric D. , Broder Christopher C. , Magassouba N’ Faly , Strecker Thomas , Rossman Jeremy , Konde Kader , Carroll Miles W.
Published: May 2024

Human Ebola virus (EBOV) outbreaks caused by persistent EBOV infection raises questions on the role of zoonotic spillover in filovirus epidemiology. To characterise filovirus zoonotic exposure, we collected cross-sectional serum samples from bushmeat hunters (n = 498) in Macenta Prefecture Guinea, adjacent to the index site of the 2013 EBOV-Makona spillover event. We identified distinct immune signatures (20/498, 4.0%) to multiple EBOV antigens (GP, NP, VP40) using stepwise ELISA and Western blot analysis and, live EBOV neutralisation (5/20; 25%). Using comparative serological data from PCR-confirmed survivors of the 2013-2016 EBOV outbreak, we demonstrated that most signatures (15/20) were not plausibly explained by prior EBOV-Makona exposure. Subsequent data-driven modelling of EBOV immunological outcomes to remote-sensing environmental data also revealed consistent associations with intact closed canopy forest. Together our findings suggest exposure to other closely related filoviruses prior to the 2013-2016 West Africa epidemic and highlight future surveillance priorities.
Spatial transition tensor of single cells
Authors: Zhou Peijie , Bocci Federico , Li Tiejun , Nie Qing
Published: May 2024

Spatial transcriptomics and messenger RNA splicing encode extensive spatiotemporal information for cell states and transitions. The current lineage-inference methods either lack spatial dynamics for state transition or cannot capture different dynamics associated with multiple cell states and transition paths. Here we present spatial transition tensor (STT), a method that uses messenger RNA splicing and spatial transcriptomes through a multiscale dynamical model to characterize multistability in space. By learning a four-dimensional transition tensor and spatial-constrained random walk, STT reconstructs cell-state-specific dynamics and spatial state transitions via both short-time local tensor streamlines between cells and long-time transition paths among attractors. Benchmarking and applications of STT on several transcriptome datasets via multiple technologies on epithelial–mesenchymal transitions, blood development, spatially resolved mouse brain and chicken heart development, indicate STT’s capability in recovering cell-state-specific dynamics and their associated genes not seen using existing methods. Overall, STT provides a consistent multiscale description of single-cell transcriptome data across multiple spatiotemporal scales.
Prostate intra-fraction motion recorded by transperineal ultrasound
Authors: Ballhausen Hendrik , Belka Claus , Li Minglun
Published: May 2024

Infra-fraction motion of the prostate was recorded during 3.423 fractions of image guided radiotherapy (IGRT) in 191 patients, 14 of which were treated by intensity modulated radiation therapy (IMRT), and 177 of which were treated by volumetric arc therapy (VMAT). The prostate was imaged by three-dimensional and time-resolved transperineal ultrasound (4D-US) of type Clarity by Elekta AB, Stockholm, Sweden. The prostate volume was registered and the prostate position (center of volume) was recorded at a frequency of 2.0 samples per second. This raw data set contains a total of 1.985.392 prostate and patient couch positions over a time span of 272 hours, 52 minutes and 34 seconds of life radiotherapy as exported by the instrument software. This data set has been used for the validation of models of prostate intra-fraction motion and for the estimation of the dosimetric impact of actual intra-fraction motion on treatment quality and side effects. We hope that this data set may be reused by other groups for similar purposes.
Improving the sustainability and effectiveness of photovoltaic evaporative cooling greenhouse in the Sahel
Authors: Djibrilla Alio Sanda M. , Rabani Adamou , Illyassou Karimoun M. , Abdoulkader Atto H. , Aissetou Drame Yaye
Published: May 2024

Anthropogenic climate change has caused worldwide extreme weather events including droughts, floods and heatwaves. It disproportionately affects developing countries through food insecurity. Greenhouse is important and relevant to the food-energy-water security in many regions. This study investigates the thermal behavior of photovoltaic evaporative cooling greenhouse made with eco-friendly coolers. The cooling potential of local plant materials was assessed under ambient conditions. Experimental thermal data obtained from optimized evaporative cooling system equipped withHyphaene thebaicafibers (HF-pad) and conventional Celdek pad (C-pad), were used in heat and mass transfer equations to derive the greenhouse cooling performances. Computational fluid dynamics analysis software was used to investigate the refrigerant fluid distribution in the greenhouse. Cooler using HF-pad allows to keep the microclimate below 25 °C, with maximum moisture rate up to 80%, under harsh ambient conditions (temperature: 30–45 °C, humidity: 10–15%). HF-pad had the highest cooling coefficient of performance (COP = 9 against 6 for C-pad), the best cost to efficiency ratio (CER = 5; 4 times less than C-pad) and the lowest outlet temperature (20.0 °C). Due to higher outlet air velocity (1.116 m/s against 0.825 m/s for HF-pad), C-pad cooler spread cool air (20.5 °C) up to 1.25 m farther than its counterpart, creating higher pressure in the atmosphere (1.42 Pa against 0.71 Pa), with 2 times turbulent kinetic energy (0.014 J/kg). HF-pad presented cooling performances that compete with conventional pads. Moreover, optimization of HF-pad frame engineering and the technology scaling up to industrial level can allow better thermal and economic performances.
Formation of hydrogen bonding network of methane sulfonic acid at low degree of hydration (MSA)m·(H2O)n (m = 1–2 and n = 1–5)
Authors: Telfah Ahmad , Charifi Z. , latelli N. , Qattan Issam A. , Baaziz H. , Al-Bataineh Qais M. , Alsaad A. M. , Sabirianov R. F.
Published: May 2024

This study employs ab initio calculations based on density functional theory (DFT) to investigate the structural properties, 1H-NMR spectra, and vibrational spectra of methane sulfonic acid (MSA) at low degree of hydration. The findings reveal that energetically stable structures are formed by small clusters consisting of one or two MSA molecules (m = 1 and 2) and one or two water molecules in (MSA)m·(H2O)n (m = 1–2 and n = 1–5).These stable structures arise from the formation of strong cyclic hydrogen bonds between the proton of the hydroxyl (OH) group in MSA and the water molecules. However, clusters containing three or more water molecules (n > 2) exhibit proton transfer from MSA to water, resulting in the formation of ion-pairs composed of CH3SO3− and H3O+species. The measured 1H-NMR spectra demonstrate the presence of hydrogen-bonded interactions between MSA and water, with a single MSA molecule interacting with water molecules. This interaction model accurately represents the hydrogen bonding network, as supported by the agreement between the experimental and calculated NMR chemical shift results.
Telomere length is longer following diapause in two solitary bee species
Authors: Grula Courtney C. , Rinehart Joshua D. , Anacleto Angelo , Kittilson Jeffrey D. , Heidinger Britt J. , Greenlee Kendra J. , Rinehart Joseph P. , Bowsher Julia H.
Published: May 2024

The mechanisms that underlie senescence are not well understood in insects. Telomeres are conserved repetitive sequences at chromosome ends that protect DNA during replication. In many vertebrates, telomeres shorten during cell division and in response to stress and are often used as a cellular marker of senescence. However, little is known about telomere dynamics across the lifespan in invertebrates. We measured telomere length in larvae, prepupae, pupae, and adults of two species of solitary bees, Osmia lignaria and Megachile rotundata. Contrary to our predictions, telomere length was longer in later developmental stages in both O. lignaria and M. rotundata. Longer telomeres occurred after emergence from diapause, which is a physiological state with increased tolerance to stress. In O. lignaria, telomeres were longer in adults when they emerged following diapause. In M. rotundata, telomeres were longer in the pupal stage and subsequent adult stage, which occurs after prepupal diapause. In both species, telomere length did not change during the 8 months of diapause. Telomere length did not differ by mass similarly across species or sex. We also did not see a difference in telomere length after adult O. lignaria were exposed to a nutritional stress, nor did length change during their adult lifespan. Taken together, these results suggest that telomere dynamics in solitary bees differ from what is commonly reported in vertebrates and suggest that insect diapause may influence telomere dynamics.
Impact of the COVID-19 pandemic on pediatric out-of-hospital cardiac arrest outcomes in Japan
Authors: Chida-Nagai Ayako , Sato Hiroki , Yamazawa Hirokuni , Takeda Atsuhito , Yonemoto Naohiro , Tahara Yoshio , lkeda Takanori
Published: May 2024

This study investigates the impact of the COVID-19 pandemic on pediatric out-of-hospital cardiac arrest (OHCA) outcomes in Japan, aiming to address a critical research gap. Analyzing data from the All-Japan Utstein registry covering pediatric OHCA cases from 2018 to 2021, the study observed no significant changes in one-month survival, neurological outcomes, or overall performance when comparing the pre-pandemic (2018–2019) and pandemic (2020–2021) periods among 6765 cases. However, a notable reduction in pre-hospital return of spontaneous circulation (ROSC) during the pandemic (15.1–13.1%, p = .020) was identified. Bystander-initiated chest compressions and rescue breaths declined (71.1–65.8%, 22.3–13.0%, respectively; both p < .001), while bystander-initiated automated external defibrillator (AED) use increased (3.7–4.9%, p = .029). Multivariate logistic regression analyses identified factors associated with reduced pre-hospital ROSC during the pandemic. Post-pandemic, there was no noticeable change in the one-month survival rate. The lack of significant change in survival may be attributed to the negative effects of reduced chest compressions and ventilation being offset by the positive impact of widespread AED availability in Japan. These findings underscore the importance of innovative tools and systems for safe bystander cardiopulmonary resuscitation during a pandemic, providing insights to optimize pediatric OHCA care.
Impaired signaling pathways on Berardinelli–Seip congenital lipodystrophy macrophages during Leishmania infantum infection
Authors: Nogueira Viviane Brito , de Oliveira Mendes-Aguiar Carolina , Teixeira Diego Gomes , Freire-Neto Francisco Paulo , Tassi Leo Zenon , Ferreira Leonardo Capistrano , Wilson Mary Edythe , Lima Josivan Gomes , Jeronimo Selma Maria Bezerra
Published: May 2024

Berardinelli–Seip congenital lipodystrophy (CGL), a rare autosomal recessive disorder, is characterized by a lack of adipose tissue. Infections are one of the major causes of CGL individuals’ premature death. The mechanisms that predispose to infections are poorly understood. We used Leishmania infantum as an in vitro model of intracellular infection to explore mechanisms underlying the CGL infection processes, and to understand the impact of host mutations on Leishmania survival, since this pathogen enters macrophages through specialized membrane lipid domains. The transcriptomic profiles of both uninfected and infected monocyte-derived macrophages (MDMs) from CGL (types 1 and 2) and controls were studied. MDMs infected with L. infantum showed significantly downregulated expression of genes associated with infection-response pathways (MHC-I, TCR-CD3, and granzymes). There was a transcriptomic signature in CGL cells associated with impaired membrane trafficking and signaling in response to infection, with concomitant changes in the expression of membrane-associated genes in parasites (e.g. δ-amastins). We identified pathways suggesting the lipid storage dysfunction led to changes in phospholipids expression and impaired responses to infection, including immune synapse (antigen presentation, IFN-γ signaling, JAK/STAT); endocytosis; NF-kappaB signaling; and phosphatidylinositol biosynthesis. In summary, lipid metabolism of the host plays an important role in determining antigen presentation pathways.
Entanglement and quantum coherence of two YIG spheres in a hybrid Laguerre–Gaussian cavity optomechanics
Authors: Hidki Abdelkader , Peng Jia-Xin , Singh S. K. , Khalid M. , Asjad M.
Published: May 2024

We theoretically investigate continuous variable entanglement and macroscopic quantum coherence in the hybrid L–G rotational cavity optomechanical system containing two YIG spheres. In this system, a single L–G cavity mode and both magnon modes (which are due to the collective excitation of spins in two YIG spheres) are coupled through the magnetic dipole interaction whereas the L–G cavity mode can also exchange orbital angular momentum (OAM) with the rotating mirror (RM). We study in detail the effects of various physical parameters like cavity and both magnon detunings, environment temperature, optorotational and magnon coupling strengths on the bipartite entanglement and the macroscopic quantum coherence as well. We also explore parameter regimes to achieve maximum values for both of these quantum correlations. We also observed that the parameters regime for achieving maximum bipartite entanglement is completely different from macroscopic quantum coherence. So, our present study shall provide a method to control various nonclassical quantum correlations of macroscopic objects in the hybrid L–G rotational cavity optomechanical system and have potential applications in quantum sensing, quantum meteorology, and quantum information science.
Water-dispersable photoreactors based on core–shell mesoporous silica particles
Authors: Baliś Andrzej , Lorens Dominika , Gut Arkadiusz , Zapotoczny Szczepan
Published: May 2024

Robust solid-core silica particles with submicrometer size and anthracene-containing mesoporous shell were obtained and studied as model water-dispersable photoreactors. An anthracene derivative containing a triethoxysilyl group was synthesized and co-condensed with tetraethoxysilane in various ratios to form a photoactive mesoporous shell with a thickness up to approximately 80 nm on previously prepared solid silica particles. Mesopores of as-synthesized particles, without a commonly applied removal of the micellar templates, offered a confined space for solubilization of hydrophobic molecules. Efficient excitation energy transfer from anthracene chromophores to both hydrophobic (perylene) and hydrophilic (fluoresceine) encapsulated acceptors was observed in an aqueous dispersion of the particles. Photosensitized oxidation of encapsulated perylene was shown to proceed efficiently in such systems serving as water-dispersable photoreactors. Importantly, the designed core–shell systems were found to be stable for a long time (at least 24 months) and robust enough, thanks to the presence of solid cores, to be handled by centrifugation in aqueous dispersions. All these features make them promising candidates for reusable systems for the photosensitized degradation of water pollutants, especially hydrophobic pollutants.
Revealing the hierarchical structure of microbial communities
Authors: Ruth Beatrice , Peter Stephan , Ibrahim Bashar , Dittrich Peter
Published: May 2024

Measuring the dynamics of microbial communities results in high-dimensional measurements of taxa abundances over time and space, which is difficult to analyze due to complex changes in taxonomic compositions. This paper presents a new method to investigate and visualize the intrinsic hierarchical community structure implied by the measurements. The basic idea is to identify significant intersection sets, which can be seen as sub-communities making up the measured communities. Using the subset relationship, the intersection sets together with the measurements form a hierarchical structure visualized as a Hasse diagram. Chemical organization theory (COT) is used to relate the hierarchy of the sets of taxa to potential taxa interactions and to their potential dynamical persistence. The approach is demonstrated on a data set of community data obtained from bacterial 16S rRNA gene sequencing for samples collected monthly from four groundwater wells over a nearly 3-year period (n = 114) along a hillslope area. The significance of the hierarchies derived from the data is evaluated by showing that they significantly deviate from a random model. Furthermore, it is demonstrated how the hierarchy is related to temporal and spatial factors; and how the idea of a core microbiome can be extended to a set of interrelated core microbiomes. Together the results suggest that the approach can support developing models of taxa interactions in the future.
Immune profiling of dedifferentiated liposarcoma and identification of novel antigens for targeted immunotherapy
Authors: Jirovec Anna , Flaman Ashley , Godbout Elena , Serrano Daniel , Werier Joel , Purgina Bibianna , Diallo Jean-Simon
Published: May 2024

Dedifferentiated liposarcoma (DDLS) is an aggressive, recurring sarcoma with limited treatments. T-cell immunotherapies selectively target malignant cells, holding promise against DDLS. The development of successful immunotherapy for DDLS requires a thorough evaluation of the tumor immune microenvironment and the identification and characterization of targetable immunogenic tumor antigens. To assess the complexity of the human DDLS tumor immune microenvironment and to identify target antigens, we used the nCounter NanoString platform, analyzing gene expression profiles across 29 DDLS and 10 healthy adipose tissue samples. Hierarchical clustering of tumors based on expression of tumor inflammation signature genes revealed two distinct groups, consisting of 15 inflamed tumors and 14 non-inflamed tumors, demonstrating tumor heterogeneity within this sarcoma subtype. Among the identified antigens, PBK and TTK exhibited substantial upregulation in mRNA expression compared to healthy adipose tissue controls, further corroborated by positive protein expression by IHC. This data shows considerable inter-tumoral heterogeneity of inflammation, which should be taken into consideration when designing an immunotherapy for DDLS, and provides a novel targetable antigen in DDLS. The results of this study lay the groundwork for the development of a novel immunotherapy for this highly aggressive sarcoma.
Influence of Li concentration on structural, morphological and electrochemical properties of anatase-TiO2 nanoparticles
Authors: Putjuso Thanin , Putjuso Sasitorn , Karaphun Attaphol , Swatsitang Ekaphan
Published: May 2024

Lithium-doped anatase-TiO2 nanoparticles (LixTi1-xO2 NPs, x = 0, 0.05, 0.10, 0.15 and 0.20) could be synthesized by a simple sol–gel process. X-ray diffraction (XRD) results displayed the tetragonal (space group: I41/amd) of polycrystalline TiO2 anatase phase. The spectroscopy results of Raman and FT-IR confirmed the anatase phase of TiO2 through the specific modes of metal oxides vibration in the crystalline TiO2. Surfaces micrographs by scanning electron microscope (SEM) of agglomerated LixTi1-xO2 NPs showed a spongy like morphology. Transmission electron microscope (TEM) illustrated a cuboidal shape of dispersed NPs with particle size distributed in a narrow range 5–10 nm. Bruanauer Emmett-Teller (BET) results showed the increased surface area of LixTi1−xO2 NPs with increasing Li content. LixTi1-xO2 NPs (x = 0.05–0.20) working electrodes illustrated a pseudocapacitive behavior with excellent electrochemical properties through the whole cycles of GCD test. Interestingly, Li0.1Ti0.9O2 NPs electrode illustrated a high performance in terms of maximum specific capacitance 822 F g−1 at 1.5 A g−1 in 0.5 M Li2SO4 electrolyte, with excellent capacitive retention 92.6% after 5000 cycles GCD test.
Efficacy and safety of netupitant/palonosetron in preventing nausea and vomiting in diffuse large B cell lymphoma patients undergoing R–CHOP chemotherapy
Authors: Kwak Kunye , Park Yong , Kim Byung Soo , Kang Ka-Won
Published: May 2024

Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin’s lymphoma, for which cyclophosphamide, doxorubicin, vincristine, and prednisone with rituximab(R–CHOP) is one of the standard regimens. Given that R–CHOP is highly emetogenic, chemotherapy-induced nausea and vomiting (CINV) prevention is clinically important. However, there is a paucity of studies focusing on these patients. This study aimed to ascertain the effectiveness of an oral fixed-dose combination of netupitant and palonosetron (NEPA) in preventing CINV in patients with DLBCL undergoing first-line R-CHOP chemotherapy. Seventy patients were enrolled in this single-center prospective non-comparative study conducted between November 2020 and May 2023 in South Korea. NEPA was administered 1 h prior to chemotherapy initiation on day 1. The primary endpoint of the study was the complete response rate (no emesis, and no rescue medication) during the acute, delayed, and overall phases, which were assessed over a period of 120 h post-chemotherapy. The complete response rates for NEPA were 90.0% [95% CI 80.5, 95.9] for the acute phase, 85.7% [95% CI 75.3, 92.9] for the delayed phase, and 84.3% [95% CI 73.6, 91.9] for the overall phase, with no-emesis rates (acute: 97.1% [95% CI 97.1, 99.7], delayed: 95.7% [95% CI 88.0, 99.1], overall: 92.9% [95% CI 84.1, 97.6]). NEPA was well tolerated with no severe treatment-emergent adverse events. NEPA exhibited substantial efficacy in mitigating CINV in DLBCL patients undergoing R–CHOP chemotherapy, demonstrating high CR and no-emesis rates, and favorable safety profiles.
Patient-centricity in digital measure development: co-evolution of best practice and regulatory guidance
Authors: Aryal Suvekshya , Blankenship Jennifer M. , Bachman Shelby L. , Hwang Soohyun , Zhai Yaya , Richards Jennifer C. , Clay Ieuan , Lyden Kate
Published: May 2024

Digital health technologies (DHTs) have the potential to modernize drug development and clinical trial operations by remotely, passively, and continuously collecting ecologically valid evidence that is meaningful to patients’ lived experiences. Such evidence holds potential for all drug development stakeholders, including regulatory agencies, as it will help create a stronger evidentiary link between approval of new therapeutics and the ultimate aim of improving patient lives. However, only a very small number of novel digital measures have matured from exploratory usage into regulatory qualification or efficacy endpoints. This shows that despite the clear potential, actually gaining regulatory agreement that a new measure is both fit-for-purpose and delivers value remains a serious challenge. One of the key stumbling blocks for developers has been the requirement to demonstrate that a digital measure is meaningful to patients. This viewpoint aims to examine the co-evolution of regulatory guidance in the United States (U.S.) and best practice for integration of DHTs into the development of clinical outcome assessments. Contextualizing guidance on meaningfulness within the larger shift towards a patient-centric drug development approach, this paper reviews the U.S. Food and Drug Administration (FDA) guidance and existing literature surrounding the development of meaningful digital measures and patient engagement, including the recent examples of rejections by the FDA that further emphasize patient-centricity in digital measures. Finally, this paper highlights remaining hurdles and provides insights into the established frameworks for development and adoption of digital measures in clinical research.
Dual function of a highly conserved bacteriophage tail completion protein essential for bacteriophage infectivity
Authors: Auzat Isabelle , Ouldali Malika , Jacquet Eric , Fauler Beatrix , Mielke Thorsten , Tavares Paulo
Published: May 2024

Infection of bacteria by phages is a complex multi-step process that includes specific recognition of the host cell, creation of a temporary breach in the host envelope, and ejection of viral DNA into the bacterial cytoplasm. These steps must be perfectly regulated to ensure efficient infection. Here we report the dual function of the tail completion protein gp16.1 of bacteriophage SPP1. First, gp16.1 has an auxiliary role in assembly of the tail interface that binds to the capsid connector. Second, gp16.1 is necessary to ensure correct routing of phage DNA to the bacterial cytoplasm. Viral particles assembled without gp16.1 are indistinguishable from wild-type virions and eject DNA normally in vitro. However, they release their DNA to the extracellular space upon interaction with the host bacterium. The study shows that a highly conserved tail completion protein has distinct functions at two essential steps of the virus life cycle in long-tailed phages.
Specific DNMT3C flanking sequence preferences facilitate methylation of young murine retrotransposons
Authors: Dossmann Leonie , Emperle Max , Dukatz Michael , de Mendoza Alex , Bashtrykov Pavel , Jeltsch Albert
Published: May 2024

The DNA methyltransferase DNMT3C appeared as a duplication of the DNMT3B gene in muroids and is required for silencing of young retrotransposons in the male germline. Using specialized assay systems, we investigate the flanking sequence preferences of DNMT3C and observe characteristic preferences for cytosine at the -2 and -1 flank that are unique among DNMT3 enzymes. We identify two amino acids in the catalytic domain of DNMT3C (C543 and V547) that are responsible for the DNMT3C-specific flanking sequence preferences and evolutionary conserved in muroids. Reanalysis of published data shows that DNMT3C flanking preferences are consistent with genome-wide methylation patterns in mouse ES cells only expressing DNMT3C. Strikingly, we show that CpG sites with the preferred flanking sequences of DNMT3C are enriched in murine retrotransposons that were previously identified as DNMT3C targets. Finally, we demonstrate experimentally that DNMT3C has elevated methylation activity on substrates derived from these biological targets. Our data show that DNMT3C flanking sequence preferences match the sequences of young murine retrotransposons which facilitates their methylation. By this, our data provide mechanistic insights into the molecular co-evolution of repeat elements and (epi)genetic defense systems dedicated to maintain genomic stability in mammals.
Fibroblasts’ secretome from calcified and non-calcified dermis in Pseudoxanthoma elasticum differently contributes to elastin calcification
Authors: Lofaro Francesco Demetrio , Costa Sonia , Simone Maria Luisa , Quaglino Daniela , Boraldi Federica
Published: May 2024

Pseudoxanthoma elasticum (PXE) is a rare disease characterized by ectopic calcification, however, despite the widely spread effect of pro/anti-calcifying systemic factors associated with this genetic metabolic condition, it is not known why elastic fibers in the same patient are mainly fragmented or highly mineralized in clinically unaffected (CUS) and affected (CAS) skin, respectively. Cellular morphology and secretome are investigated in vitro in CUS and CAS fibroblasts. Here we show that, compared to CUS, CAS fibroblasts exhibit: a) differently distributed and organized focal adhesions and stress fibers; b) modified cell-matrix interactions (i.e., collagen gel retraction); c) imbalance between matrix metalloproteinases and tissue inhibitor of metalloproteinases; d) differentially expressed pro- and anti-calcifying proteoglycans and elastic-fibers associated glycoproteins. These data emphasize that in the development of pathologic mineral deposition fibroblasts play an active role altering the stability of elastic fibers and of the extracellular matrix milieu creating a local microenvironment guiding the level of matrix remodeling at an extent that may lead to degradation (in CUS) or to degradation and calcification (in CAS) of the elastic component. In conclusion, this study contributes to a better understanding of the mechanisms of the mineral deposition that can be also associated with several inherited or age-related diseases (e.g., diabetes, atherosclerosis, chronic kidney diseases).
Cost-competitive decentralized ammonia fertilizer production can increase food security
Authors: Tonelli Davide , Rosa Lorenzo , Gabrielli Paolo , Parente Alessandro , Contino Francesco
Published: May 2024

The current centralized configuration of the ammonia industry makes the production of nitrogen fertilizers susceptible to the volatility of fossil fuel prices and involves complex supply chains with long-distance transport costs. An alternative consists of on-site decentralized ammonia production using small modular technologies, such as electric Haber–Bosch or electrocatalytic reduction. Here we evaluate the cost-competitiveness of producing low-carbon ammonia at the farm scale, from a solar agrivoltaic system, or using electricity from the grid, within a novel global fertilizer industry. Projected costs for decentralized ammonia production are compared with historical market prices from centralized production. We find that the cost-competitiveness of decentralized production relies on transport costs and supply chain disruptions. Taking both factors into account, decentralized production could achieve cost-competitiveness for up to 96% of the global ammonia demand by 2030. These results show the potential of decentralized ammonia technologies in revolutionizing the fertilizer industry, particularly in regions facing food insecurity.
Northern Pacific sea-level pressure controls rain-on-snow in North America
Authors: Rasiya Koya Sinan , Kar Kanak Kanti , Roy Tirthankar
Published: May 2024

Rain-on-snow (ROS) events, a phenomenon of liquid rainfall falling over accumulated snowpack, cause quick melting of snow, often leading to rapid and catastrophic flooding. Here we explore the causal drivers of ROS events across North America. A ROS identification method is proposed, which builds on the existing methods but adds more realism in terms of rain and snow conditions for ROS occurrence. We consider a wide range of observed hydrometeorological variables along with climatic oscillations over the period of 1951 to 2022. Causal linkages between the potential drivers and ROS frequency are explored by implementing Convergent Cross Mapping (CCM). Results suggest a strong causal link between the North-Pacific (NP) Index, a measure of sea-level pressure in the Northern Pacific Ocean, and ROS frequencies in North America, specifically in the eastern and western parts. We show the association of the NP index with the hydroclimatic variables and explain how this association might have contributed to this causal link. Thus, our findings provide valuable insights into the potential mechanisms of ROS events in different regions in North America.
Coded environments: data-driven indoor localisation with reconfigurable intelligent surfaces
Authors: Shah Syed Tariq , Shawky Mahmoud A. , Kazim Jalil ur Rehman , Taha Ahmad , Ansari Shuja , Hasan Syed Faraz , Imran Muhammad Ali , Abbasi Qammer H.
Published: May 2024

Reconfigurable Intelligent Surfaces have recently emerged as a revolutionary next-generation wireless networks paradigm that harnesses engineered electromagnetic environments to reshape radio wave propagation. Pioneering research presented in this article establishes the viability of Reconfigurable Intelligent Surfaces-enhanced indoor localisation and charts a roadmap for its integration into next-generation wireless network architectures. Here, we present a comprehensive experimental analysis of a Reconfigurable Intelligent Surfaces-enabled indoor localisation scheme that evaluates the localisation accuracy of different machine learning algorithms under varying Reconfigurable Intelligent Surfaces states, antenna types, and communication setups. The results indicate that incorporating Reconfigurable Intelligent Surfaces can significantly enhance indoor localisation accuracy, achieving an impressive 82.4% success rate. Moreover, this study delves into system performance across varied communication modes and subcarrier configurations. This research is poised to lay the groundwork for implementing Reconfigurable Intelligent Surfaces-empowered joint sensing and communications in future next-generation wireless networks.
Testing the reliability of an AI-based large language model to extract ecological information from the scientific literature
Authors: Gougherty Andrew V. , Clipp Hannah L.
Published: May 2024

Artificial intelligence-based large language models (LLMs) have the potential to substantially improve the efficiency and scale of ecological research, but their propensity for delivering incorrect information raises significant concern about their usefulness in their current state. Here, we formally test how quickly and accurately an LLM performs in comparison to a human reviewer when tasked with extracting various types of ecological data from the scientific literature. We found the LLM was able to extract relevant data over 50 times faster than the reviewer and had very high accuracy (>90%) in extracting discrete and categorical data, but it performed poorly when extracting certain quantitative data. Our case study shows that LLMs offer great potential for generating large ecological databases at unprecedented speed and scale, but additional quality assurance steps are required to ensure data integrity.
Fragmentation dynamics of the doubly charged aniline: the source of kinetically excited CnH3+ ions
Authors: Selvaraj Muthuamirthambal , Subramani Arun , Ramanathan Karthick , Richter Robert , Pal Nitish , Bolognesi Paola , Avaldi Lorenzo , Kadhane Umesh R.
Published: May 2024

This work is an attempt to decipher if an aniline dication can isomerize to a picoline dication in a given astrochemical environment and if the dissociation of such dications could be a source of kinetically hot fragment ions.
Structural and thermochemical investigation of 1,3-bis(λ4-boraneyl)-1λ4,3λ4-imidazolidine adduct for chemical hydrogen storage
Authors: Irfan Fathima Rifana Mohamed , Masters Sarah L.
Published: May 2024

The structure, thermochemical properties and reaction pathways of a cyclic amine diborane complex (1,3-bis(λ4-boraneyl)-1λ4,3λ4-imidazolidine) were investigated using quantum chemical calculations.
Detection of carbofuran in fruits and vegetables by Raman spectroscopy combined with immunochromatography
Authors: Pei Jiahuan , Jin Yong , Ren Chunsheng , Chen Yan , Zou Mingqiang , Qi Xiaohua
Published: May 2024

It has long been desired to develop rapid methods for the rapid identification and quantification of pesticides and their metabolites.
Observing atomically precise nanocluster aggregates in solution by mass photometry
Authors: Roy Jayoti , Marathe Ila , Wysocki Vicki , Pradeep Thalappil
Published: May 2024

We report the first mass photometric characterization of nanoaggregates of atomically precise nanoclusters (NCs) in solution.