bluuebunny/crossref_metadata_2025 huggingface dataset:
Climatic Drivers for the Variation of Gross Primary Productivity Across Terrestrial Ecosystems in the United States
Authors: Chen Yan , Wang Guiling , Seth Anji
Published: August 2024

Temperature and water stress are important factors limiting the gross primary productivity (GPP) in terrestrial ecosystems, yet the extent of their influence across ecosystems remains uncertain. This study examines how surface air temperature, soil water availability (SWA) and vapor pressure deficit (VPD) influence ecosystem light use efficiency (LUE), a critical metric for assessing GPP, across different ecosystems and climatic zones at 80 flux tower sites based on in situ measurements and data assimilation products. Results indicate that LUE increases with temperature in spring, with higher correlation coefficients in colder regions (0.79–0.82) than in warmer regions (0.68–0.78). LUE reaches a plateau earlier in the season in warmer regions. LUE variations in summer are mainly driven by SWA, exhibiting a positive correlation indicative of a water‐limited regime. The relationship between the daily LUE and daytime temperature shows a clear seasonal hysteresis at many sites, with a higher LUE in spring than in fall under the same temperature, likely resulting from younger leaves being more efficient in photosynthesis. Drought stress influences LUE through SWA in all ranges of water availability; VPD variation under moderate conditions does not have a clear influence on LUE, but extremely high VPD (exceeding the threshold of 1.6 kPa, often observed during extreme drought‐heat events) causes a dramatic reduction of LUE. Our findings provide insight into how ecosystem productivities respond to climate variability and how they may change under the influence of more frequent and severe heat and drought events projected for the future.
Machine Learning‐Based Hydrofacies Classification: Effects of Noise and Regularization
Authors: Oladeji Emmanuel , Parsekian Andrew , Grana Dario
Published: August 2024

This study utilizes an unsupervised ML approach, the expectation‐maximization (EM) algorithm using Gaussian Mixture Models (GMM), to integrate near‐surface geophysics measurements for hydrofacies classification. We examined the impact of noise and noise estimation on classification across two synthetic models with varying lateral heterogeneity, simulating and inverting resistivity and seismic data with noise levels ranging from minimal to very high. The algorithm proved robust in accurately reconstructing hydrofacies when noise was correctly estimated or not significantly underestimated, showing minimal misclassification in shallow hydrofacies. However, severe underestimation of noise during inversion led to increased misclassifications and artifact‐laden hydrofacies models, especially in shallow regions. Higher lateral heterogeneity lessened the negative impact of noise, slightly improving algorithm performance when noise was correctly estimated. We also explored the influence of geophysical measurement uncertainties on classification uncertainty through hydrofacies probability maps, noting the greatest impact when noise was underestimated. Additionally, we investigated the effect of the regularization trade‐off parameter on the hydrofacies classification and show how the performance of the algorithm can be evaluated in the absence of ground truth data using the average silhouette score of the classification with data obtained from a basement complex field site. We found that moderate regularization (λ = 200) yielded the best hydrofacies model, as indicated by the highest average silhouette score. Our findings underscore the effectiveness of unsupervised ML for facies classification and emphasizes the critical role of accurate noise characterization in geophysical data processing for enhancing the integration of subsurface heterogeneity information into hydrological models.
A dual inhibitor of PIP5K1C and PIKfyve prevents SARS-CoV-2 entry into cells
Authors: Seo Yuri , Jang Yejin , Lee Seon-gyeong , Rhlee Joon Ho , Kong Sukyeong , Vo Thi Tuyet Hanh , Kim Myung hun , Lee Myoung Kyu , Kim Byungil , Hong Sung You , Kim Meehyein , Lee Joo-Yong , Myung Kyungjae
Published: August 2024

The SARS-CoV-2 pandemic has had an unprecedented impact on global public health and the economy. Although vaccines and antivirals have provided effective protection and treatment, the development of new small molecule-based antiviral candidates is imperative to improve clinical outcomes against SARS-CoV-2. In this study, we identified UNI418, a dual PIKfyve and PIP5K1C inhibitor, as a new chemical agent that inhibits SARS-CoV-2 entry into host cells. UNI418 inhibited the proteolytic activation of cathepsins, which is regulated by PIKfyve, resulting in the inhibition of cathepsin L-dependent proteolytic cleavage of the SARS-CoV-2 spike protein into its mature form, a critical step for viral endosomal escape. We also demonstrated that UNI418 prevented ACE2-mediated endocytosis of the virus via PIP5K1C inhibition. Our results identified PIKfyve and PIP5K1C as potential antiviral targets and UNI418 as a putative therapeutic compound against SARS-CoV-2.
Astrocytic 5-HT1A receptor mediates age-dependent hippocampal LTD and fear memory extinction in male mice
Authors: Wu Qian-Yun , Lin Lian-Hong , Lu Kun , Deng Si-Fu , Li Wei-Min , Xu Yuan , Zhang Bin , Liu Ji-Hong
Published: August 2024

NMDA receptor-dependent long-term depression (LTD) in the hippocampus is a well-known form of synaptic plasticity that has been linked to different cognitive functions. Although the underlying mechanisms remain unclear, this form of LTD cannot be induced by low-frequency stimulation (LFS) in adult mice. In this study, we found that LFS-induced LTD was not easily induced in adult animals and was age dependent. Interestingly, the level of the 5-HT1A receptor was correspondingly increased and exhibited an inverse correlation with the magnitude of LFS-LTD during development. Knockout or pharmacological inhibition of the 5-HT1A receptor reversed impaired LFS-LTD in adult mice (P60), while activation or inhibition of this receptor disturbed or enhanced LFS-LTD in adolescent mice (P21), respectively. Furthermore, the astrocytic 5-HT1A receptor in the hippocampus predominantly mediated age-dependent LFS-LTD through enhancing GABAergic neurotransmission. Finally, fear memory extinction differed among the above conditions. These observations enrich our knowledge of LTD at the cellular level and suggest a therapeutic approach for LTD-related psychiatric disorders.
Tailored antisense oligonucleotides designed to correct aberrant splicing reveal actionable groups of mutations for rare genetic disorders
Authors: Wai Htoo A. , Svobodova Eliska , Herrera Natalia Romero , Douglas Andrew G. L. , Holloway John W. , Baralle Francisco E. , Baralle Marco , Baralle Diana
Published: August 2024

Effective translation of rare disease diagnosis knowledge into therapeutic applications is achievable within a reasonable timeframe; where mutations are amenable to current antisense oligonucleotide technology. In our study, we identified five distinct types of abnormal splice-causing mutations in patients with rare genetic disorders and developed a tailored antisense oligonucleotide for each mutation type using phosphorodiamidate morpholino oligomers with or without octa-guanidine dendrimers and 2′-O-methoxyethyl phosphorothioate. We observed variations in treatment effects and efficiencies, influenced by both the chosen chemistry and the specific nature of the aberrant splicing patterns targeted for correction. Our study demonstrated the successful correction of all five different types of aberrant splicing. Our findings reveal that effective correction of aberrant splicing can depend on altering the chemical composition of oligonucleotides and suggest a fast, efficient, and feasible approach for developing personalized therapeutic interventions for genetic disorders within short time frames.
Towards mixed physical node reservoir computing: light-emitting synaptic reservoir system with dual photoelectric output
Authors: Lian Minrui , Gao Changsong , Lin Zhenyuan , Shan Liuting , Chen Cong , Zou Yi , Cheng Enping , Liu Changfei , Guo Tailiang , Chen Wei , Chen Huipeng
Published: August 2024

Memristor-based physical reservoir computing holds significant potential for efficiently processing complex spatiotemporal data, which is crucial for advancing artificial intelligence. However, owing to the single physical node mapping characteristic of traditional memristor reservoir computing, it inevitably induces high repeatability of eigenvalues to a certain extent and significantly limits the efficiency and performance of memristor-based reservoir computing for complex tasks. Hence, this work firstly reports an artificial light-emitting synaptic (LES) device with dual photoelectric output for reservoir computing, and a reservoir system with mixed physical nodes is proposed. The system effectively transforms the input signal into two eigenvalue outputs using a mixed physical node reservoir comprising distinct physical quantities, namely optical output with nonlinear optical effects and electrical output with memory characteristics. Unlike previously reported memristor-based reservoir systems, which pursue rich reservoir states in one physical dimension, our mixed physical node reservoir system can obtain reservoir states in two physical dimensions with one input without increasing the number and types of devices. The recognition rate of the artificial light-emitting synaptic reservoir system can achieve 97.22% in MNIST recognition. Furthermore, the recognition task of multichannel images can be realized through the nonlinear mapping of the photoelectric dual reservoir, resulting in a recognition accuracy of 99.25%. The mixed physical node reservoir computing proposed in this work is promising for implementing the development of photoelectric mixed neural networks and material-algorithm collaborative design.
Upconversion-based chiral nanoprobe for highly selective dual-mode sensing and bioimaging of hydrogen sulfide in vitro and in vivo
Authors: Lu Yang , Zhao Xu , Yan Dongmei , Mi Yingqian , Sun Peng , Yan Xu , Liu Xiaomin , Lu Geyu
Published: August 2024

Chiral assemblies have become one of the most active research areas due to their versatility, playing an increasingly important role in bio-detection, imaging and therapy. In this work, chiral UCNPs/CuxOS@ZIF nanoprobes are prepared by encapsulating upconversion nanoparticles (UCNPs) and CuxOS nanoparticles (NPs) into zeolitic imidazolate framework-8 (ZIF-8). The novel excited-state energy distribution-modulated upconversion nanostructure (NaYbF4@NaYF4: Yb, Er) is selected as the fluorescence source and energy donor for highly efficient fluorescence resonance energy transfer (FRET). CuxOS NP is employed as chiral source and energy acceptor to quench upconversion luminescence (UCL) and provide circular dichroism (CD) signal. Utilizing the natural adsorption and sorting advantages of ZIF-8, the designed nanoprobe can isolate the influence of other common disruptors, thus achieve ultra-sensitive and highly selective UCL/CD dual-mode quantification of H2S in aqueous solution and in living cells. Notably, the nanoprobe is also capable of in vivo intra-tumoral H2S tracking. Our work highlights the multifunctional properties of chiral nanocomposites in sensing and opens a new vision and idea for the preparation and application of chiral nanomaterials in biomedical and biological analysis.
Anisotropic phonon dynamics in Dirac semimetal PtTe2 thin films enabled by helicity-dependent ultrafast light excitation
Authors: Li Ziyang , Chen Yequan , Song Anke , Zhang Jinzhong , Zhang Rong , Zhang Zongzhi , Wang Xuefeng
Published: August 2024

Coherent phonons have aroused considerable attention in condensed matter physics owing to their extraordinary capacity of reflecting and controlling the physical properties of matter. However, the investigation on the interaction between coherent phonons and other microscopic particles on the ultrafast timescale within topological systems continues to be an active and unresolved area. Here, we show the energy transfer of coherent optical phonons (COP) in Dirac semimetal PtTe2 thin films using ultrafast optical pump-probe spectroscopy. Specifically, the helicity-dependent light-driven anisotropic COP signals disclose their direct connection with the light-excited anisotropic spin-polarized electrons via an angular momentum transfer. Furthermore, we observe the notable decreases in the COP oscillation frequency and the decay rate with increasing temperatures due to the anharmonic phonon-phonon scattering and electron-phonon scattering in the COP dissipation process, respectively. Our work paves the way for uncovering the coherent phonons in Dirac semimetals for the potential applications in optoelectronics and opto-spintronics.
Opioid use disorder risk alleles in self-reported assigned African American/Afro-Caribbean and European biogeographical genetic ancestry groups and in males and females
Authors: Sprague Jon E. , Freiermuth Caroline E. , Lambert Joshua , Braun Robert , Frey Jennifer A. , Bachmann Daniel J. , Bischof Jason J. , Beaumont Lauren , Lyons Michael S. , Pantalon Michael V. , Punches Brittany E. , Ancona Rachel , Kisor David F.
Published: August 2024

The influence of genetic variants related to opioid use disorder (OUD) was evaluated using multiple logistic regression analysis in self-reported assigned African American/Afro-Caribbean and European biogeographical ancestry groups (BGAGs) and by sex. From a sample size of 1301 adult patients (>18 years of age) seen in emergency departments of three medical centers in Ohio, six variants were found to be associated with OUD. Two of the variants, rs2740574 (CYP3A4) and rs324029 (DRD3), were included in the analysis having met criteria of at least five subjects for each BGAG, variant carrier status, and OUD status combinations. Variant carriers in the African/Afro-Caribbean BGAG had slightly lower predicted probabilities of OUD. Variant carriers in the European BGAG had slightly higher predicted probabilities of OUD. Relative to sex, all the six variants met evaluation criteria (five subjects for all sex, variant, and OUD status combinations). No statistically significant interactions were found between a given variant, BGAGs and sex. Findings suggest variant testing relative to OUD risk can be applied across BGAGs and sex, however, studies in larger populations are needed.
M6A-methylated circPOLR2B forms an R-loop and regulates the biological behavior of glioma stem cells through positive feedback loops
Authors: Lin Hongda , Cui Zheng , E Tiange , Xu Hailing , Wang Di , Wang Ping , Ruan Xuelei , Liu Libo , Xue Yixue
Published: August 2024

Glioma is the most common primary brain tumor, and targeting glioma stem cells (GSCs) has become a key aspect of glioma treatment. In this study, we discovered a molecular network in which circRNA forms an R-loop structure with its parental gene to regulate the biological behavior of GSCs. Genes with abnormal expression in GSCs were screened using RNA-seq and circRNA microarray analyses. The study results showed that high expression of YTHDC1 in GSCs promoted the transportation of N6-methyladenosine (m6A)-modified circPOLR2B from the nucleus to the cytoplasm. Decreased circPOLR2B levels in the nucleus resulted in fewer R-loop structures formed with its parental gene POLR2B. This reduction in R-loop structures relieved the inhibitory effect on POLR2B transcription and upregulated PBX1 expression through alternative polyadenylation (APA) action, thereby promoting the malignant biological behavior of GSCs. Knockdown of YTHDC1, POLR2B, and PBX1 reduced xenograft tumor volume and prolonged the survival of nude mice. The YTHDC1/circPOLR2B/POLR2B/PBX1 axis plays a regulatory role in the biological behavior of GSCs, offering potential targets and novel strategies for the treatment of glioma.
Systemic mechanisms of necrotic cell debris clearance
Authors: Schuermans Sara , Kestens Caine , Marques Pedro Elias
Published: August 2024

Necrosis is an overarching term that describes cell death modalities caused by (extreme) adverse conditions in which cells lose structural integrity. A guaranteed consequence of necrosis is the production of necrotic cell remnants, or debris. Necrotic cell debris is a strong trigger of inflammation, and although inflammatory responses are required for tissue healing, necrotic debris may lead to uncontrolled immune responses and collateral damage. Besides local phagocytosis by recruited leukocytes, there is accumulating evidence that extracellular mechanisms are also involved in necrotic debris clearance. In this review, we focused on systemic clearance mechanisms present in the bloodstream and vasculature that often cooperate to drive the clearance of cell debris. We reviewed the contribution and cooperation of extracellular DNases, the actin-scavenger system, the fibrinolytic system and reticuloendothelial cells in performing clearance of necrotic debris. Moreover, associations of the (mis)functioning of these clearance systems with a variety of diseases were provided, illustrating the importance of the mechanisms of clearance of dead cells in the organism.
Achieving net zero greenhouse gas emissions critical to limit climate tipping risks
Authors: Möller Tessa , Högner Annika Ernest , Schleussner Carl-Friedrich , Bien Samuel , Kitzmann Niklas H. , Lamboll Robin D. , Rogelj Joeri , Donges Jonathan F. , Rockström Johan , Wunderling Nico
Published: August 2024

Under current emission trajectories, temporarily overshooting the Paris global warming limit of 1.5 °C is a distinct possibility. Permanently exceeding this limit would substantially increase the probability of triggering climate tipping elements. Here, we investigate the tipping risks associated with several policy-relevant future emission scenarios, using a stylised Earth system model of four interconnected climate tipping elements. We show that following current policies this century would commit to a 45% tipping risk by 2300 (median, 10–90% range: 23–71%), even if temperatures are brought back to below 1.5 °C. We find that tipping risk by 2300 increases with every additional 0.1 °C of overshoot above 1.5 °C and strongly accelerates for peak warming above 2.0 °C. Achieving and maintaining at least net zero greenhouse gas emissions by 2100 is paramount to minimise tipping risk in the long term. Our results underscore that stringent emission reductions in the current decade are critical for planetary stability.
Anchoring PdOx clusters on defective alumina for improved catalytic methane oxidation
Authors: Yu Xiang , Genz Nina S. , Mendes Rafael G. , Ye Xinwei , Meirer Florian , Nachtegaal Maarten , Monai Matteo , Weckhuysen Bert M.
Published: August 2024

Evolution of the Pd active centers in size and spatial distribution leads to an irreversible deactivation in many high-temperature catalytic processes. This research demonstrates the use of a defective alumina (Al2O3-x) as catalyst support to anchor Pd atoms and suppress the growth of Pd clusters in catalytic methane oxidation. A combination of operando spectroscopy and density functional theory (DFT) calculations provide insights into the evolution of Pd species and reveals distinct catalytic methane oxidation mechanisms on Pd single atoms, clusters, and nanoparticles (NPs). Among these Pd species, the cluster active centers are found to be the most favorable participants in methane oxidation due to their high dispersion, high content of Pd2+ oxidation state, and resistance to deactivation by carbonates, bicarbonates, and water. The Pd/Al2O3-x catalyst shows increased stability with respect to a Pd/Al2O3 counterpart during simulated aging in alternating reducing and oxidizing conditions due to stronger interactions with the support. This study demonstrates that defect engineering of non-reducible supports can constrain the evolution of active centers, which holds promising potential for widespread utilization across diverse industrial catalytic processes, including various hydrogenation and oxidation reactions.
Neural representational geometries reflect behavioral differences in monkeys and recurrent neural networks
Authors: Fascianelli Valeria , Battista Aldo , Stefanini Fabio , Tsujimoto Satoshi , Genovesio Aldo , Fusi Stefano
Published: August 2024

Animals likely use a variety of strategies to solve laboratory tasks. Traditionally, combined analysis of behavioral and neural recording data across subjects employing different strategies may obscure important signals and give confusing results. Hence, it is essential to develop techniques that can infer strategy at the single-subject level. We analyzed an experiment in which two male monkeys performed a visually cued rule-based task. The analysis of their performance shows no indication that they used a different strategy. However, when we examined the geometry of stimulus representations in the state space of the neural activities recorded in dorsolateral prefrontal cortex, we found striking differences between the two monkeys. Our purely neural results induced us to reanalyze the behavior. The new analysis showed that the differences in representational geometry are associated with differences in the reaction times, revealing behavioral differences we were unaware of. All these analyses suggest that the monkeys are using different strategies. Finally, using recurrent neural network models trained to perform the same task, we show that these strategies correlate with the amount of training, suggesting a possible explanation for the observed neural and behavioral differences.
Yu-Shiba-Rusinov bands in a self-assembled kagome lattice of magnetic molecules
Authors: Farinacci Laëtitia , Reecht Gaël , von Oppen Felix , Franke Katharina J.
Published: August 2024

Kagome lattices constitute versatile platforms for studying paradigmatic correlated phases. While molecular self-assembly of kagome structures on metallic substrates is promising, it is challenging to realize pristine kagome properties because of hybridization with the bulk degrees of freedom and modified electron-electron interactions. We suggest that a superconducting substrate offers an compelling platform for realizing a magnetic kagome lattice. Exchange coupling induces kagome-derived bands at the interface, which are protected from the bulk by the superconducting energy gap. We realize a magnetic kagome lattice on a superconductor by depositing Fe-porphin-chloride molecules on Pb(111) and using temperature-activated de-chlorination and self-assembly. This allows us to control the formation of smaller kagome precursors and long-range ordered kagome islands. Using scanning tunneling microscopy and spectroscopy at 1.6 K, we identify Yu-Shiba-Rusinov states inside the superconducting energy gap and track their hybridization from the precursors to larger islands, where the kagome lattice induces extended YSR bands. These YSR-derived kagome bands inside the superconducting energy gap allow for long-range coupling and induced pairing correlations, motivating further studies to resolve possible spin-liquid or Kondo-lattice-type behavior.
Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in COVID-19
Authors: Essex Morgan , Millet Pascual-Leone Belén , Löber Ulrike , Kuhring Mathias , Zhang Bowen , Brüning Ulrike , Fritsche-Guenther Raphaela , Krzanowski Marta , Fiocca Vernengo Facundo , Brumhard Sophia , Röwekamp Ivo , Anna Bielecka Agata , Lesker Till Robin , Wyler Emanuel , Landthaler Markus , Mantei Andrej , Meisel Christian , Caesar Sandra , Thibeault Charlotte , Corman Victor M. , Marko Lajos , Suttorp Norbert , Strowig Till , Kurth Florian , Sander Leif E. , Li Yang , Kirwan Jennifer A. , Forslund Sofia K. , Opitz Bastian
Published: August 2024

The clinical course of COVID-19 is variable and often unpredictable. To test the hypothesis that disease progression and inflammatory responses associate with alterations in the microbiome and metabolome, we analyzed metagenome, metabolome, cytokine, and transcriptome profiles of repeated samples from hospitalized COVID-19 patients and uninfected controls, and leveraged clinical information and post-hoc confounder analysis. Severe COVID-19 was associated with a depletion of beneficial intestinal microbes, whereas oropharyngeal microbiota disturbance was mainly linked to antibiotic use. COVID-19 severity was also associated with enhanced plasma concentrations of kynurenine and reduced levels of several other tryptophan metabolites, lysophosphatidylcholines, and secondary bile acids. Moreover, reduced concentrations of various tryptophan metabolites were associated with depletion of Faecalibacterium, and tryptophan decrease and kynurenine increase were linked to enhanced production of inflammatory cytokines. Collectively, our study identifies correlated microbiome and metabolome alterations as a potential contributor to inflammatory dysregulation in severe COVID-19.
Nanometer-resolution tracking of single cargo reveals dynein motor mechanisms
Authors: Peng Chunte Sam , Zhang Yunxiang , Liu Qian , Marti G. Edward , Huang Yu-Wen Alvin , Südhof Thomas C. , Cui Bianxiao , Chu Steven
Published: August 2024

Cytoplasmic dynein is essential for intracellular transport. Despite extensive in vitro characterizations, how the dynein motors transport vesicles by processive steps in live cells remains unclear. To dissect the molecular mechanisms of dynein, we develop optical probes that enable long-term single-particle tracking in live cells with high spatiotemporal resolution. We find that the number of active dynein motors transporting cargo switches stochastically between one and five dynein motors during long-range transport in neuronal axons. Our very bright optical probes allow the observation of individual molecular steps. Strikingly, these measurements reveal that the dwell times between steps are controlled by two temperature-dependent rate constants in which two ATP molecules are hydrolyzed sequentially during each dynein step. Thus, our observations uncover a previously unknown chemomechanical cycle of dynein-mediated cargo transport in living cells.
The burden of diabetes-associated multiple long-term conditions on years of life spent and lost
Authors: Gregg Edward W. , Pratt Adrian , Owens Alex , Barron Emma , Dunbar-Rees Rupert , Slade Eirion T. , Hafezparast Nasrin , Bakhai Chirag , Chappell Paul , Cornelius Victoria , Johnston Desmond G. , Mathews Jacqueline , Pickles Jason , Bragan Turner Ellie , Wainman Gary , Roberts Kate , Khunti Kamlesh , Valabhji Jonathan
Published: August 2024

Diabetes mellitus is a central driver of multiple long-term conditions (MLTCs), but population-based studies have not clearly characterized the burden across the life course. We estimated the age of onset, years of life spent and loss associated with diabetes-related MLTCs among 46 million English adults. We found that morbidity patterns extend beyond classic diabetes complications and accelerate the onset of severe MLTCs by 20 years earlier in life in women and 15 years earlier in men. By the age of 50 years, one-third of those with diabetes have at least three conditions, spend >20 years with them and die 11 years earlier than the general population. Each additional condition at the age of 50 years is associated with four fewer years of life. Hypertension, depression, cancer and coronary heart disease contribute heavily to MLTCs in older age and create the greatest community-level burden on years spent (813 to 3,908 years per 1,000 individuals) and lost (900 to 1,417 years per 1,000 individuals). However, in younger adulthood, depression, severe mental illness, learning disabilities, alcohol dependence and asthma have larger roles, and when they occur, all except alcohol dependence were associated with long periods of life spent (11–14 years) and all except asthma associated with many years of life lost (11–15 years). These findings provide a baseline for population monitoring and underscore the need to prioritize effective prevention and management approaches.
Recurrent fever of unknown origin and unexplained bacteremia in a patient with a novel 4.5 Mb microdeletion in Xp11.23-p11.22
Authors: Lee Cho-Rong , Kim Man Jin , Park Sang-Heon , Kim Sheehyun , Kim Soo Yeon , Koh Seong-Joon , Lee Seungbok , Choi Murim , Chae Jong Hee , Park Sung-Gyoo , Moon Jangsup
Published: August 2024

Fever of unknown origin (FUO) remains a formidable diagnostic challenge in the field of medicine. Numerous studies suggest an association between FUO and genetic factors, including chromosomal abnormalities. Here, we report a female patient with a 4.5 Mb Xp microdeletion, who presented with recurrent FUO, bacteremia, colitis, and hematochezia. To elucidate the underlying pathogenic mechanism, we employed a comprehensive approach involving single cell RNA sequencing, T cell receptor sequencing, and flow cytometry to evaluate CD4 T cells. Analysis of peripheral blood mononuclear cells revealed augmented Th1, Th2, and Th17 cell populations, and elevated levels of proinflammatory cytokines in serum. Notably, the patient exhibited impaired Treg cell function, possibly related to deletion of genes encoding FOPX3 and WAS. Single cell analysis revealed specific expansion of cytotoxic CD4 T lymphocytes, characterized by upregulation of various signature genes associated with cytotoxicity. Moreover, interferon-stimulated genes were upregulated in the CD4 T effector memory cluster. Further genetic analysis confirmed maternal inheritance of the Xp microdeletion. The patient and her mother exhibited X chromosome-skewed inactivation, a potential protective mechanism against extensive X chromosome deletions; however, the mother exhibited complete skewing and the patient exhibited incomplete skewing (85:15), which may have contributed to emergence of immunological symptoms. In summary, this case report describes an exceptional instance of FUO stemming from an incompletely inactivated X chromosome microdeletion, thereby increasing our understanding of the genetics underpinning FUO.
Adsorption of cationic dye onto Raphanus seeds: optimization, adsorption kinetics, thermodynamic studies
Authors: Hammad W. A. , Darweesh M. A. , Zouli Nasser , Osman Samir M. , Eweida Basant , Amr M. H. A.
Published: August 2024

Dyes are one of the common contaminants in industrial wastewater. Adsorption is the most widely method which used to treat dye-contaminated water due to their easy use, cost-effectiveness, and their efficiency was high. The aim of this study is the investigating of the utilization of the activated carbon which prepared from Raphanus seeds solid residual (ACRS) as a low cost adsorbent for removing of cationic Methylene Blue dye (MB)from wastewater. measuring the surface area using BET methods and SEM. The FT‒IR and XRD was measured. Different variables (e.g.: initial concentration of the dye, pH, contact time, and dosage) have been studied. Process has been systematically investigated experimentally at (25 ± 1 °C). The % removal of MB reached 99.4% after 90-min MB adsorption (40 mg/L) was observed within 5 min of contact time for the Raphanus seeds solid residual (ACRS) dosage of 4 g/L. MB initial concentration (10 ppm) Raphanus seeds solid residual (ACRS) effectively adsorbed MB (> 99%) over a widely range of pH (from pH 2 to pH 8). However, a swift decline in removal was observed when the pH was set at 7. The results of the adsorption kinetics analysis indicate a strong correlation with the pseudo-second-order model, as evidenced by the high regression coefficients. However, the adsorption capacity diminished with a rise in temperature. Thermodynamic calculations of (MB) onto Raphanus seeds solid residual (ACRS) is an exothermic reaction. The results have been indicated that the effectiveness of MB removal by activated carbon prepared from Raphanus seeds solid residual is favorable under neutral conditions, Raphanus seeds solid residual (ACRS) can be considered an efficient, environmentally friendly, readily available, and economical adsorbent that could treat industrial wastewater contaminated with cationic textile dyes. The objective of the experiments was to investigate the impact of various factors on the response of a process or formulation. To accomplish this goal, response surface methodology (RSM) has employed as a statistical model. RSM is an efficient and effective method for optimizing processes through the use of a quadratic polynomial model. The utilization of RSM allows for a reduction in the number of experiments needed, thus minimizing the associated costs of extensive analysis. This method has been done using Box–Behnken Design (BBD) to optimize % removal of MB. The optimal conditions as obtained from the RSM is pH 7,contact time  120 min, initial concentration  10 ppm, ACRS dosage  1 g, adsorption temperature  45 °C.
An analysis of fertility and fecundity in the Australian sheep flock between 2006 and 2019
Authors: Refshauge G. , Golledge M. , Rickard J. , de Graaf S.
Published: August 2024

After decades of decline, the Australian sheep flock aspires to rebuild its population of breeding ewes. A successful, rebuild will rely on high pregnancy rates and number of lambs born and reared. To examine this potential, a cross-sectional study of historical ultrasound pregnancy scanning records was undertaken using records collated from two experienced sheep pregnancy scanning businesses (years 2006 to 2019) from 15,397 mobs of ewes, totalling 7,443,314 ewes. Client details were de-identified and excluded from analyses, but details describing the mobs were retained when available, such as season of mating, production zone, ewe age, and breed. The key finding was a mean pregnancy rate (ewes pregnant per ewe scanned) of 0.76 ± 0.24, with a median of 0.83. Mobs scanned to identify fetal number had a higher mean (0.84 ± 0.15) and median (0.89) pregnancy rate. The mean reproduction rate (fetuses per ewe scanned) was 1.21 ± 0.27 and the median was 1.25. Differences were observed between the factors including age, breed, season, year or production zone but all results were lower than anticipated. The unexpected findings imply a problem exists with the fertility of many Australian sheep flocks.
Empowering the younger generation increases their willingness for intergenerational reconciliation in the context of climate change
Authors: Stollberg Janine , Bogdan Danja , Jonas Eva
Published: August 2024

Climate change can evoke intergenerational conflict. Structural inequalities and their unequal impact on generations can increase perceptions of collective victimhood among the younger generation (< 30 years) and bear the risk of social tensions between the young and the elderly. An experimental study (N = 434) showed that younger people perceived an increased risk of future victimhood. In line with a needs-based approach, the young reported an increased desire to pursue agentic intergroup goals, indicating a heightened need for agency. However, when the young received empowering messages that affirmed their ingroup agency, their willingness to reconcile with the old generation increased, whereas informing them about non-agentic ingroup behavior did not affect reconciliation (between-subjects manipulation). While empowering messages from the outgroup (“Grannies for Future”) that directly affirmed the young generations’ agency for climate change mitigation as well as empowering messages from the ingroup that indirectly affirmed ingroup agency in domains unrelated to climate change both addressed the need for agency, only outgroup empowerment promoted intergenerational reconciliation. However, empowerment did not affect support for collective climate action. We discuss empowerment as an avenue for resolving intergroup conflict in the context of climate change and possible consequences for climate action and social change.
Whole-genome demography of COVID-19 virus during its pandemic period and on “panvalent” vaccine design
Authors: Kim Byung-Ju , Choi JaeJin , Kim Sung-Hou
Published: August 2024

With over 16 million submitted genomic sequences, the SARS-CoV-2 (SC2) virus, the cause of the most recent worldwide COVID-19 pandemic, has become the most sequenced genome of all known viruses, revealing, for example, a vast number of expanding viral lineages. Since the pandemic phase appears to be over, we performed a retrospective re-examination of the demographic grouping pattern and their genomic characteristics during the entire pandemic period up to the peak of the last pandemic wave. For our study, we extracted from the NCBI only unique viral sequences and converted each sequence data to a relational vector, indicating the presence/absence of each variational event compared to a “reference” sequence. Our study revealed several genomic features that are unexpected or different from those of previous studies. For example, approximately 44,000 variants with unique sequences emerged during the pandemic period; they group into only four major viral-genomic groups and each has a set of mostly unique highly-conserved variant-genotypes (HCVGs); and a small set from the first (“ancestral”) group was inherited by the three (“descendant”) groups, suggesting that HCVGs in the next group may be predictable from the current group(s). Such a concept may be potentially important in designing “panvalent” vaccines against the current and future waves of viral infections.
Complete de novo assembly of Wolbachia endosymbiont of Drosophila willistoni using long-read genome sequencing
Authors: Jacobs Jodie , Nakamoto Anne , Mastoras Mira , Loucks Hailey , Mirchandani Cade , Karim Lily , Penunuri Gabriel , Wanket Ciara , Russell Shelbi L.
Published: August 2024

Wolbachia is an obligate intracellular α-proteobacterium, which commonly infects arthropods and filarial nematodes. Different strains of Wolbachia are capable of a wide range of regulatory manipulations in their diverse hosts, including the modulation of host cellular differentiation to influence host reproduction. The genetic basis for the majority of these phenotypes is unknown. The wWil strain from the neotropical fruit fly, Drosophila willistoni, exhibits a remarkably high affinity for host germline-derived cells relative to the somatic cells. This trait could be leveraged for understanding how Wolbachia influences the host germline and for controlling host populations in the field. To further the use of this strain in biological and biomedical research, we sequenced the genome of the wWil strain isolated from host cell culture cells. Here, we present the first high quality Nanopore assembly of wWil, the Wolbachia endosymbiont of D. willistoni. Our assembly resulted in a circular genome of 1.27 Mb with a BUSCO completeness score of 99.7%. Consistent with other insect-associated Wolbachia strains, comparative genomic analysis revealed that wWil has a highly mosaic genome relative to the closely related wMel and wAu strains from Drosophila melanogaster and Drosophila simulans, respectively.
Selection for stress tolerance and longevity in Drosophila melanogaster have strong impacts on microbiome profiles
Authors: Kristensen Torsten Nygaard , Schönherz Anna A. , Rohde Palle Duun , Sørensen Jesper Givskov , Loeschcke Volker
Published: August 2024

There is experimental evidence that microbiomes have a strong influence on a range of host traits. Understanding the basis and importance of symbiosis between host and associated microorganisms is a rapidly developing research field, and we still lack a mechanistic understanding of ecological and genetic pressures affecting host-microbiome associations. Here Drosophila melanogaster lines from a large-scale artificial selection experiment were used to investigate whether the microbiota differ in lines selected for different stress resistance traits and longevity. Following multiple generations of artificial selection all selection regimes and corresponding controls had their microbiomes assessed. The microbiome was interrogated based on 16S rRNA sequencing. We found that the microbiome of flies from the different selection regimes differed markedly from that of the unselected control regime, and microbial diversity was consistently higher in selected relative to control regimes. Several common Drosophila bacterial species showed differentially abundance in the different selection regimes despite flies being exposed to similar environmental conditions for two generations prior to assessment. Our findings provide strong evidence for symbiosis between host and microbiomes but we cannot reveal whether the interactions are adaptive, nor whether they are caused by genetic or ecological factors.
Plastic recycling: A panacea or environmental pollution problem
Authors: Singh Nisha , Walker Tony R.
Published: August 2024

Increasing plastic waste is a critical global challenge to ecological and human health requiring focused solutions to reduce omnipresent plastic pollution in the environment. While recycling has been touted as one solution to counter plastic waste and resource utilization, it has been largely ineffective in offsetting the impact of rising global plastic production of more than 400 million metric tonnes annually, due to low global recycling rates of only 9%. Over three decades since implementing plastic resin codes, recycling has favoured thermoplastics, neglecting thermoset plastics. There is a constant need to enhance overall recycling efficiency by exploring advanced methods, as enormous gaps exist in fully unlocking the potential of plastic recycling. We identify critical gaps associated with plastic waste recycling and its potential environmental impacts. We discuss substantial progress in recycling technology, designs-for-recyclability with controlled chemical use, and economic incentives to expand markets for recycled plastics and to curb plastic leakage into the environment. Additionally, we highlight some emerging strategies and legally binding international policy instruments, such as the Global Plastics Treaty that require further development to reduce plastic waste and improve plastic recyclability.
SPIN1 facilitates chemoresistance and HR repair by promoting Tip60 binding to H3K9me3
Authors: Wang Yukun , Li Mengyao , Chen Yuhan , Jiang Yuhan , Zhang Ziyu , Yan Zhenzhen , Liu Xiuhua , Wu Chen
Published: August 2024

The tandem Tudor-like domain-containing protein Spindlin1 (SPIN1) is a transcriptional coactivator with critical functions in embryonic development and emerging roles in cancer. However, the involvement of SPIN1 in DNA damage repair has remained unclear. Our study shows that SPIN1 is recruited to DNA lesions through its N-terminal disordered region that binds to Poly-ADP-ribose (PAR), and facilitates homologous recombination (HR)-mediated DNA damage repair. SPIN1 promotes H3K9me3 accumulation at DNA damage sites and enhances the interaction between H3K9me3 and Tip60, thereby promoting the activation of ATM and HR repair. We also show that SPIN1 increases chemoresistance. These findings reveal a novel role for SPIN1 in the activation of H3K9me3-dependent DNA repair pathways, and suggest that SPIN1 may contribute to cancer chemoresistance by modulating the efficiency of double-strand break (DSB) repair.
Non-invasive diagnostic test for lung cancer using biospectroscopy and variable selection techniques in saliva samples
Authors: Morais Camilo L. M. , Lima Kássio M. G. , Dickinson Andrew W. , Saba Tarek , Bongers Thomas , Singh Maneesh N. , Martin Francis L. , Bury Danielle
Published: August 2024

Saliva samples are analysed by using infrared (IR) spectroscopy with computational tools to diagnose lung cancer patients in a screening program study.
Varying the hydrophobic core composition of polymeric nanoparticles affects NLRP3 inflammasome activation
Authors: Malhotra Mehak , Chotaliya Dhruv , Debnath Maharshi , Patel Ruchi , Kulkarni Ashish
Published: August 2024

We have demonstrated the impact of supramolecular polymer nanoparticle (SNP) core composition on NLRP3 inflammasome activation, in vitro and in vivo proinflammatory responses, offering insights for designing nano-immunotherapies.
Transition-metal free, radical oxidation of 1,6-enyne cyclopropanation: synthesis of aza-bicyclo[4.1.0]heptane derivatives
Authors: Meena Shivam A. , Thakur Deepika , Nandy Abhijit , Ranjan Rahul , Rai Anubhav , Banerjee Shibdas , Verma Akhilesh K.
Published: August 2024

A straightforward transition-metal-free sustainable methodology for oxidative cyclopropanation of aza-1,6-enynes has been devised, enabling the synthesis of valuable, functionalized azabicyclo[4.1.0]heptane-2,4,5-triones.
Integrating commercial graphite with network-like carbon fibers for high-rate and long-term cycling K+-storage
Authors: Peng Jiao , Liang Xueying , Mao Zhifei , Wang Rui , He Beibei , Jin Jun , Gong Yansheng , Wang Huanwen
Published: August 2024

Commercial graphite is electrospun into network-like carbon fibers, which can efficiently withstand the volume expansion during K+ insertion and thus achieve excellent cycling stability and fast K+-intercalation kinetics.
Light-induced reversible switching of generation and extinction of an organic radical anion
Authors: Chatterjee Sheelbhadra , Jana Palash , Mahato Samyadeb , Bandyopadhyay Subhajit
Published: August 2024

A dyad system consisting of a dimethyldihydropyrene photochromic unit with a naphthalene diimide (NDI) moiety can reversibly form a radical anion with light in the presence of an electron donor/acceptor.
Structure sensitivity of the low-temperature dehydrogenation of perhydro dibenzyltoluene on supported platinum nanoparticles
Authors: Mahayni Yazan , Maurer Lukas , Auer Franziska , Hutzler Andreas , Wasserscheid Peter , Wolf Moritz
Published: August 2024

In this study, the structure sensitivity of the dehydrogenation reactions of the commonly used liquid organic hydrogen carrier (LOHC) molecules perhydro dibenzyltoluene (H18-DBT) and perhydro benzyltoluene (H12-BT) is investigated.
Suppressing product crossover and C–C bond cleavage in a glycerol membrane electrode assembly reformer
Authors: Dai Chencheng , Wu Qian , Wu Tianze , Zhang Yuwei , Sun Libo , Wang Xin , Fisher Adrian C. , Xu Zhichuan J.
Published: August 2024

An innovative acid–alkali asymmetric cell design to suppress the crossover of liquid products and facilitate glycerol oxidation reaction. It can also impede C–C bond cleavage to promote high-value C3 products generation and reduce carbon emission.
Catalytic combustion of biodiesel wastewater over the Fe2O3 catalyst coupled with a Pt-based catalyst
Authors: Yu Shangzhi , Yuan Wenyu , Bai Jianfeng , Xie Qinglong , Liang Xiaojiang , Nie Yong
Published: August 2024

Continuous and efficient catalytic combustion of biodiesel wastewater with high chemical oxygen demand and sulfur content can be achieved by the Fe2O3 catalyst coupled with the Pt/Al2O3@cordierite catalyst.
Monascus-fermented quinoa alleviates hyperlipidemia in mice by regulating the amino acid metabolism pathway
Authors: Huang Zhiwei , Chen Lichen , Xiao Lishi , Ye Yanfang , Mo Wenlan , Zheng Zhenghuai , Li Xiangyou
Published: August 2024

Monascus-fermented quinoa alleviates the hyperlipidemia in mice induced by a high-fat diet by regulating the metabolic pathways such as phenylalanine, tyrosine, and tryptophan metabolism.
S-Methyl-l-cysteine targeting MsrA attenuates Ang II-induced oxidative stress and atrial remodeling via the p38 MAPK signaling pathway
Authors: Xu Beibei , Xu Yinli , Ren Wenpu , Meng Shan , Hong Tao , Cao Zijun , Xiao Xiong , Guo Xiaodong , Yu Liming , Zhao Jikai , Wang Huishan
Published: August 2024

SMLC protects against atrial remodeling of AF by inhibiting oxidative stress through the mediation of the MsrA/p38 MAPK signaling pathway
Improving DNA aptamers against a heart failure protein biomarker using structure-guided random mutation approaches for colourimetric biosensor development
Authors: Marcius Donny , Ropii Bejo , Safitri Diah Ayu , Ulum Mokhamad Fakhrul , Nugrahapraja Husna , Anshori Isa
Published: August 2024

The optimisation strategy successfully enhanced the DNA aptamer binding capability to its target. The docking, molecular dynamics, and gold nanoparticle aggregation assays showed the performance improvement of optimised aptamer as a bioreceptor.