bluuebunny/crossref_metadata_2025_split huggingface dataset:
The actin cytoskeleton plays multiple roles in structural colour formation in butterfly wing scales
Authors: Lloyd Victoria J. , Burg Stephanie L. , Harizanova Jana , Garcia Esther , Hill Olivia , Enciso-Romero Juan , Cooper Rory L. , Flenner Silja , Longo Elena , Greving Imke , Nadeau Nicola J. , Parnell Andrew J. 
Published: May 2024

AbstractVivid structural colours in butterflies are caused by photonic nanostructures scattering light. Structural colours evolved for numerous biological signalling functions and have important technological applications. Optically, such structures are well understood, however insight into their development in vivo remains scarce. We show that actin is intimately involved in structural colour formation in butterfly wing scales. Using comparisons between iridescent (structurally coloured) and non-iridescent scales in adult and developing H. sara, we show that iridescent scales have more densely packed actin bundles leading to an increased density of reflective ridges. Super-resolution microscopy across three distantly related butterfly species reveals that actin is repeatedly re-arranged during scale development and crucially when the optical nanostructures are forming. Furthermore, actin perturbation experiments at these later developmental stages resulted in near total loss of structural colour in H. sara. Overall, this shows that actin plays a vital and direct templating role during structural colour formation in butterfly scales, providing ridge patterning mechanisms that are likely universal across lepidoptera.
Preserving ester-linked modifications reveals glutamate and aspartate mono-ADP-ribosylation by PARP1 and its reversal by PARG
Authors: Longarini Edoardo José , Matić Ivan 
Published: May 2024

AbstractEster-linked post-translational modifications, including serine and threonine ubiquitination, have gained recognition as important cellular signals. However, their detection remains a significant challenge due to the chemical lability of the ester bond. This is the case even for long-known modifications, such as ADP-ribosylation on aspartate and glutamate, whose role in PARP1 signaling has recently been questioned. Here, we present easily implementable methods for preserving ester-linked modifications. When combined with a specific and sensitive modular antibody and mass spectrometry, these approaches reveal DNA damage-induced aspartate/glutamate mono-ADP-ribosylation. This previously elusive signal represents an initial wave of PARP1 signaling, contrasting with the more enduring nature of serine mono-ADP-ribosylation. Unexpectedly, we show that the poly-ADP-ribose hydrolase PARG is capable of reversing ester-linked mono-ADP-ribosylation in cells. Our methodology enables broad investigations of various ADP-ribosylation writers and, as illustrated here for noncanonical ubiquitination, it paves the way for exploring other emerging ester-linked modifications.
Droplet-based mechanical transducers modulated by the symmetry of wettability patterns
Authors: Xue Luanluan , Li An , Li Huizeng , Yu Xinye , Li Kaixuan , Yuan Renxuan , Deng Xiao , Li Rujun , Liu Quan , Song Yanlin 
Published: May 2024

AbstractAsymmetric mechanical transducers have important applications in energy harvesting, signal transmission, and micro-mechanics. To achieve asymmetric transformation of mechanical motion or energy, active robotic metamaterials, as well as materials with asymmetric microstructures or internal orientation, are usually employed. However, these strategies usually require continuous energy supplement and laborious fabrication, and limited transformation modes are achieved. Herein, utilizing wettability patterned surfaces for precise control of the droplet contact line and inner flow, we demonstrate a droplet-based mechanical transducer system, and achieve multimodal responses to specific vibrations. By virtue of the synergistic effect of surface tension and solid-liquid adhesion on the liquid dynamics, the droplet on the patterned substrate can exhibit symmetric/asymmetric vibration transformation when the substrate vibrates horizontally. Based on this, we construct arrayed patterns with distinct arrangements on the substrate, and employ the swarm effect of the arrayed droplets to achieve three-dimensional and multimodal actuation of the target plate under a fixed input vibration. Further, we demonstrate the utilization of the mechanical transducers for vibration management, object transport, and laser modulation. These findings provide a simple yet efficient strategy to realize a multimodal mechanical transducer, which shows significant potential for aseismic design, optical molding, as well as micro-electromechanical systems (MEMS).
Production of deoxycholic acid by low-abundant microbial species is associated with impaired glucose metabolism
Authors: Wahlström Annika , Brumbaugh Ariel , Sjöland Wilhelm , Olsson Lisa , Wu Hao , Henricsson Marcus , Lundqvist Annika , Makki Kassem , Hazen Stanley L. , Bergström Göran , Marschall Hanns-Ulrich , Fischbach Michael A. , Bäckhed Fredrik 
Published: May 2024

AbstractAlterations in gut microbiota composition are suggested to contribute to cardiometabolic diseases, in part by producing bioactive molecules. Some of the metabolites are produced by very low abundant bacterial taxa, which largely have been neglected due to limits of detection. However, the concentration of microbially produced metabolites from these taxa can still reach high levels and have substantial impact on host physiology. To explore this concept, we focused on the generation of secondary bile acids by 7α-dehydroxylating bacteria and demonstrated that addition of a very low abundant bacteria to a community can change the metabolic output dramatically. We show that Clostridium scindens converts cholic acid into the secondary bile acid deoxycholic acid (DCA) very efficiently even though the abundance of C. scindens is low, but still detectable by digital droplet PCR. We also show that colonization of germ-free female mice with a community containing C. scindens induces DCA production and affects host metabolism. Finally, we show that DCA correlates with impaired glucose metabolism and a worsened lipid profile in individuals with type 2 diabetes, which implies that this metabolic pathway may contribute to the development of cardiometabolic disease.
Establishing flood thresholds for sea level rise impact communication
Authors: Mahmoudi Sadaf , Moftakhari Hamed , Muñoz David F. , Sweet William , Moradkhani Hamid 
Published: May 2024

AbstractSea level rise (SLR) affects coastal flood regimes and poses serious challenges to flood risk management, particularly on ungauged coasts. To address the challenge of monitoring SLR at local scales, we propose a high tide flood (HTF) thresholding system that leverages machine learning (ML) techniques to estimate SLR and HTF thresholds at a relatively fine spatial resolution (10 km) along the United States’ coastlines. The proposed system, complementing conventional linear- and point-based estimations of HTF thresholds and SLR rates, can estimate these values at ungauged stretches of the coast. Trained and validated against National Oceanic and Atmospheric Administration (NOAA) gauge data, our system demonstrates promising skills with an average Kling-Gupta Efficiency (KGE) of 0.77. The results can raise community awareness about SLR impacts by documenting the chronic signal of HTF and providing useful information for adaptation planning. The findings encourage further application of ML in achieving spatially distributed thresholds.
Thermoelectric active cooling for transient hot spots in microprocessors
Authors: Liu Yihan , Cheng Hao-Yuan , Malen Jonathan A. , Xiong Feng 
Published: May 2024

AbstractModern microprocessor performance is limited by local hot spots induced at high frequency by busy integrated circuit elements such as the clock generator. Locally embedded thermoelectric devices (TEDs) are proposed to perform active cooling whereby thermoelectric effects enhance passive cooling by the Fourier law in removing heat from the hot spot to colder regions. To mitigate transient heating events and improve temperature stability, we propose a novel analytical solution that describes the temperature response of a periodically heated hot spot that is actively cooled by a TED driven electrically at the same frequency. The analytical solution that we present is validated by experimental data from frequency domain thermal reflectance (FDTR) measurements made directly on an actively cooled Si thermoelectric device where the pump laser replicates the transient hot spot. We herein demonstrate a practical method to actively cancel the transient temperature variations on circuit elements with TEDs. This result opens a new path to optimize the design of cooling systems for transient localized hot spots in integrated circuits.
Vascular endothelial-derived SPARCL1 exacerbates viral pneumonia through pro-inflammatory macrophage activation
Authors: Zhao Gan , Gentile Maria E. , Xue Lulu , Cosgriff Christopher V. , Weiner Aaron I. , Adams-Tzivelekidis Stephanie , Wong Joanna , Li Xinyuan , Kass-Gergi Sara , Holcomb Nicolas P. , Basal Maria C. , Stewart Kathleen M. , Planer Joseph D. , Cantu Edward , Christie Jason D. , Crespo Maria M. , Mitchell Michael J. , Meyer Nuala J. , Vaughan Andrew E. 
Published: May 2024

AbstractInflammation induced by lung infection is a double-edged sword, moderating both anti-viral and immune pathogenesis effects; the mechanism of the latter is not fully understood. Previous studies suggest the vasculature is involved in tissue injury. Here, we report that expression of Sparcl1, a secreted matricellular protein, is upregulated in pulmonary capillary endothelial cells (EC) during influenza-induced lung injury. Endothelial overexpression of SPARCL1 promotes detrimental lung inflammation, with SPARCL1 inducing ‘M1-like’ macrophages and related pro-inflammatory cytokines, while SPARCL1 deletion alleviates these effects. Mechanistically, SPARCL1 functions through TLR4 on macrophages in vitro, while TLR4 inhibition in vivo ameliorates excessive inflammation caused by endothelial Sparcl1 overexpression. Finally, SPARCL1 expression is increased in lung ECs from COVID-19 patients when compared with healthy donors, while fatal COVID-19 correlates with higher circulating SPARCL1 protein levels in the plasma. Our results thus implicate SPARCL1 as a potential prognosis biomarker for deadly COVID-19 pneumonia and as a therapeutic target for taming hyperinflammation in pneumonia.
Two telomere-to-telomere gapless genomes reveal insights into Capsicum evolution and capsaicinoid biosynthesis
Authors: Chen Weikai , Wang Xiangfeng , Sun Jie , Wang Xinrui , Zhu Zhangsheng , Ayhan Dilay Hazal , Yi Shu , Yan Ming , Zhang Lili , Meng Tan , Mu Yu , Li Jun , Meng Dian , Bian Jianxin , Wang Ke , Wang Lu , Chen Shaoying , Chen Ruidong , Jin Jingyun , Li Bosheng , Zhang Xingping , Deng Xing Wang , He Hang , Guo Li 
Published: May 2024

AbstractChili pepper (Capsicum) is known for its unique fruit pungency due to the presence of capsaicinoids. The evolutionary history of capsaicinoid biosynthesis and the mechanism of their tissue specificity remain obscure due to the lack of high-quality Capsicum genomes. Here, we report two telomere-to-telomere (T2T) gap-free genomes of C. annuum and its wild nonpungent relative C. rhomboideum to investigate the evolution of fruit pungency in chili peppers. We precisely delineate Capsicum centromeres, which lack high-copy tandem repeats but are extensively invaded by CRM retrotransposons. Through phylogenomic analyses, we estimate the evolutionary timing of capsaicinoid biosynthesis. We reveal disrupted coding and regulatory regions of key biosynthesis genes in nonpungent species. We also find conserved placenta-specific accessible chromatin regions, which likely allow for tissue-specific biosynthetic gene coregulation and capsaicinoid accumulation. These T2T genomic resources will accelerate chili pepper genetic improvement and help to understand Capsicum genome evolution.
A delayed 400 GeV photon from GRB 221009A and implication on the intergalactic magnetic field
Authors: Xia Zi-Qing , Wang Yun , Yuan Qiang , Fan Yi-Zhong 
Published: May 2024

AbstractLarge High Altitude Air Shower Observatory has detected 0.2 − 13 TeV emission of GRB 221009A within 2000 s since the trigger. Here we report the detection of a 400 GeV photon, without accompanying prominent low-energy emission, by Fermi Large Area Telescope in this direction with a 0.4 days’ delay. Given an intergalactic magnetic field strength of about 4 × 10−17 G, which is comparable to limits from TeV blazars, the delayed 400 GeV photon can be explained as the cascade emission of about 10 TeV gamma rays. We estimate the probabilities of the cascade emission that can result in one detectable photon beyond 100 GeV by Fermi Large Area Telescope within 0.3 − 1 days is about 2% whereas it is about 20.5% within 0.3 − 250 days. Our results show that Synchrotron Self-Compton explanation is less favored with probabilities lower by a factor of about 3 − 30 than the cascade scenario.
Atomically dispersed Iridium on Mo2C as an efficient and stable alkaline hydrogen oxidation reaction catalyst
Authors: Fang Jinjie , Wang Haiyong , Dang Qian , Wang Hao , Wang Xingdong , Pei Jiajing , Xu Zhiyuan , Chen Chengjin , Zhu Wei , Li Hui , Yan Yushan , Zhuang Zhongbin 
Published: May 2024

AbstractHydroxide exchange membrane fuel cells (HEMFCs) have the advantages of using cost-effective materials, but hindered by the sluggish anodic hydrogen oxidation reaction (HOR) kinetics. Here, we report an atomically dispersed Ir on Mo2C nanoparticles supported on carbon (IrSA-Mo2C/C) as highly active and stable HOR catalysts. The specific exchange current density of IrSA-Mo2C/C is 4.1 mA cm−2ECSA, which is 10 times that of Ir/C. Negligible decay is observed after 30,000-cycle accelerated stability test. Theoretical calculations suggest the high HOR activity is attributed to the unique Mo2C substrate, which makes the Ir sites with optimized H binding and also provides enhanced OH binding sites. By using a low loading (0.05 mgIr cm−2) of IrSA-Mo2C/C as anode, the fabricated HEMFC can deliver a high peak power density of 1.64 W cm−2. This work illustrates that atomically dispersed precious metal on carbides may be a promising strategy for high performance HEMFCs.
Enhanced CD95 and interleukin 18 signalling accompany T cell receptor Vβ21.3+ activation in multi-inflammatory syndrome in children
Authors: Zhang Zhenguang , Kean Iain R. L. , Dratva Lisa M. , Clark John A. , Syrimi Eleni , Khan Naeem , Daubney Esther , White Deborah , O’Neill Lauran , Chisholm Catherine , Payne Caroline , Benkenstein Sarah , Kupiec Klaudia , Galassini Rachel , Wright Victoria , Winmill Helen , Robbins Ceri , Brown Katherine , Ramnarayan Padmanabhan , Scholefield Barnaby , Peters Mark , Klein Nigel , Montgomery Hugh , Meyer Kerstin B. , Teichmann Sarah A. , Bryant Clare , Taylor Graham , Pathan Nazima 
Published: May 2024

AbstractMultisystem inflammatory syndrome in children is a post-infectious presentation SARS-CoV-2 associated with expansion of the T cell receptor Vβ21.3+ T-cell subgroup. Here we apply muti-single cell omics to compare the inflammatory process in children with acute respiratory COVID-19 and those presenting with non SARS-CoV-2 infections in children. Here we show that in Multi-Inflammatory Syndrome in Children (MIS-C), the natural killer cell and monocyte population demonstrate heightened CD95 (Fas) and Interleuking 18 receptor expression. Additionally, TCR Vβ21.3+ CD4+ T-cells exhibit skewed differentiation towards T helper 1, 17 and regulatory T cells, with increased expression of the co-stimulation receptors ICOS, CD28 and interleukin 18 receptor. We observe no functional evidence for NLRP3 inflammasome pathway overactivation, though MIS-C monocytes show elevated active caspase 8. This, coupled with raised IL18 mRNA expression in CD16- NK cells on single cell RNA sequencing analysis, suggests interleukin 18 and CD95 signalling may trigger activation of TCR Vβ21.3+ T-cells in MIS-C, driven by increased IL-18 production from activated monocytes and CD16- Natural Killer cells.
A systematic review and meta-analysis of unimodal and multimodal predation risk assessment in birds
Authors: Mathot Kimberley J. , Arteaga-Torres Josue David , Besson Anne , Hawkshaw Deborah M. , Klappstein Natasha , McKinnon Rebekah A. , Sridharan Sheeraja , Nakagawa Shinichi 
Published: May 2024

AbstractDespite a wealth of studies documenting prey responses to perceived predation risk, researchers have only recently begun to consider how prey integrate information from multiple cues in their assessment of risk. We conduct a systematic review and meta-analysis of studies that experimentally manipulated perceived predation risk in birds and evaluate support for three alternative models of cue integration: redundancy/equivalence, enhancement, and antagonism. One key insight from our analysis is that the current theory, generally applied to study cue integration in animals, is incomplete. These theories specify the effects of increasing information level on mean, but not variance, in responses. In contrast, we show that providing multiple complementary cues of predation risk simultaneously does not affect mean response. Instead, as information richness increases, populations appear to assess risk more accurately, resulting in lower among-population variance in response to manipulations of perceived predation risk. We show that this may arise via a statistical process called maximum-likelihood estimation (MLE) integration. Our meta-analysis illustrates how explicit consideration of variance in responses can yield important biological insights.
Upregulated ECM genes and increased synaptic activity in Parkinson’s human DA neurons with PINK1/ PRKN mutations
Authors: Tripathi Utkarsh , Rosh Idan , Ben Ezer Ran , Nayak Ritu , Hussein Yara , Choudhary Ashwani , Djamus Jose , Manole Andreea , Houlden Henry , Gage Fred H. , Stern Shani 
Published: May 2024

AbstractParkinson’s disease (PD) is the second most prevalent neurodegenerative disease. Primary symptoms of PD arise with the loss of dopaminergic (DA) neurons in the Substantia Nigra Pars Compacta, but PD also affects the hippocampus and cortex, usually in its later stage. Approximately 15% of PD cases are familial with a genetic mutation. Two of the most associated genes with autosomal recessive (AR) early-onset familial PD are PINK1 and PRKN. In vitro studies of these genetic mutations are needed to understand the neurophysiological changes in patients’ neurons that may contribute to neurodegeneration. In this work, we generated and differentiated DA and hippocampal neurons from human induced pluripotent stem cells (hiPSCs) derived from two patients with a double mutation in their PINK1 and PRKN (one homozygous and one heterozygous) genes and assessed their neurophysiology compared to two healthy controls. We showed that the synaptic activity of PD neurons generated from patients with the PINK1 and PRKN mutations is impaired in the hippocampus and dopaminergic neurons. Mutant dopaminergic neurons had enhanced excitatory post-synaptic activity. In addition, DA neurons with the homozygous mutation of PINK1 exhibited more pronounced electrophysiological differences compared to the control neurons. Signaling network analysis of RNA sequencing results revealed that Focal adhesion and ECM receptor pathway were the top two upregulated pathways in the mutant PD neurons. Our findings reveal that the phenotypes linked to PINK1 and PRKN mutations differ from those from other PD mutations, suggesting a unique interplay between these two mutations that drives different PD mechanisms.
In vitro selection of DNA aptamers against staphylococcal enterotoxin A
Authors: Oliveira Ricardo , Pinho Eva , Barros Maria Margarida , Azevedo Nuno Filipe , Almeida Carina 
Published: May 2024

AbstractStaphylococcal enterotoxin A (SEA) is the most frequently reported in staphylococcal food poisoning (SFP) outbreaks. Aptamers are single-stranded nucleic acids that are seen as promising alternatives to antibodies in several areas, including diagnostics. In this work, systematic evolution of ligands by exponential enrichment (SELEX) was used to select DNA aptamers against SEA. The SELEX protocol employed magnetic beads as an immobilization matrix for the target molecule and real-time quantitative PCR (qPCR) for monitoring and optimizing sequence enrichment. After 10 selection cycles, the ssDNA pool with the highest affinity was sequenced by next generation sequencing (NGS). Approximately 3 million aptamer candidates were identified, and the most representative cluster sequences were selected for further characterization. The aptamer with the highest affinity showed an experimental dissociation constant (KD) of 13.36 ± 18.62 nM. Increased temperature negatively affected the affinity of the aptamer for the target. Application of the selected aptamers in a lateral flow assay demonstrated their functionality in detecting samples containing 100 ng SEA, the minimum amount capable of causing food poisoning. Overall, the applicability of DNA aptamers in SEA recognition was demonstrated and characterized under different conditions, paving the way for the development of diagnostic tools.
Experimental and computational studies of novel cyclic ammonium based ionic liquids as corrosion inhibitors for carbon steel in acid medium
Authors: El-Nagar Raghda A. , Nessim Maher I. , Khalil N. A. , Elewa Safaa I. 
Published: May 2024

AbstractThe challenge of corrosion posed as a result of acidic sittings is considered as a major industrial concern, wherein ionic liquids serve as crucial in addressing the corrosive impacts on metals. In this study, five selected cyclic ammonium based ionic liquids were synthesized; IL-1MPyrBr, IL-1MPipBr, IL-2PyBr, IL-3MPyBr and IL-4MPyBr and their chemical structures were characterized using a variety of spectroscopic techniques (FT-IR, IH-NMR, 13C-NMR, Elemental analysis and thermal gravimetric analysis (TGA). Their corrosion inhibition efficiency was studied on carbon steel in 1 M HCl via different concentrations at 298 K using chemical and electrochemical parameters (PDP and EIS). DFT quantum parameters were computed, and the noted results were in complete compatible with the experimental. The synthesized ILs recorded excellent inhibition on the carbon steel corrosion in acidic media with increasing efficiency by increasing the inhibitor concentrations from 20 to 100 ppm. Different cations in the synthesized ILs affect the anti-corrosion effect and IL-3MPyBr showed the highest inhibition (ηR); 96.12% using the lowest concentration. Kinetic and thermodynamic considerations were studied and illustrated.