bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cryptic enzymatic assembly of peptides armed with β-lactone warheads
Authors: Xu Guangcai , Torri Daniele , Cuesta-Hoyos Sebastian , Panda Deepanjan , Yates Luke R. L. , Zallot Rémi , Bian Kehan , Jia Dongxu , Iorgu Andreea I. , Levy Colin , Shepherd Sarah A. , Micklefield Jason 
Published: July 2024

AbstractNature has evolved biosynthetic pathways to molecules possessing reactive warheads that inspired the development of many therapeutic agents, including penicillin antibiotics. Peptides armed with electrophilic warheads have proven to be particularly effective covalent inhibitors, providing essential antimicrobial, antiviral and anticancer agents. Here we provide a full characterization of the pathways that nature deploys to assemble peptides with β-lactone warheads, which are potent proteasome inhibitors with promising anticancer activity. Warhead assembly involves a three-step cryptic methylation sequence, which is likely required to reduce unfavorable electrostatic interactions during the sterically demanding β-lactonization. Amide-bond synthetase and adenosine triphosphate (ATP)-grasp enzymes couple amino acids to the β-lactone warhead, generating the bioactive peptide products. After reconstituting the entire pathway to β-lactone peptides in vitro, we go on to deliver a diverse range of analogs through enzymatic cascade reactions. Our approach is more efficient and cleaner than the synthetic methods currently used to produce clinically important warhead-containing peptides.
Transition transferases prime bacterial capsule polymerization
Authors: Litschko Christa , Di Domenico Valerio , Schulze Julia , Li Sizhe , Ovchinnikova Olga G. , Voskuilen Thijs , Bethe Andrea , Cifuente Javier O. , Marina Alberto , Budde Insa , Mast Tim A. , Sulewska Małgorzata , Berger Monika , Buettner Falk F. R. , Lowary Todd L. , Whitfield Chris , Codée Jeroen D. C. , Schubert Mario , Guerin Marcelo E. , Fiebig Timm 
Published: July 2024

AbstractCapsules are long-chain carbohydrate polymers that envelop the surfaces of many bacteria, protecting them from host immune responses. Capsule biosynthesis enzymes are potential drug targets and valuable biotechnological tools for generating vaccine antigens. Despite their importance, it remains unknown how structurally variable capsule polymers of Gram-negative pathogens are linked to the conserved glycolipid anchoring these virulence factors to the bacterial membrane. Using Actinobacillus pleuropneumoniae as an example, we demonstrate that CpsA and CpsC generate a poly(glycerol-3-phosphate) linker to connect the glycolipid with capsules containing poly(galactosylglycerol-phosphate) backbones. We reconstruct the entire capsule biosynthesis pathway in A. pleuropneumoniae serotypes 3 and 7, solve the X-ray crystal structure of the capsule polymerase CpsD, identify its tetratricopeptide repeat domain as essential for elongating poly(glycerol-3-phosphate) and show that CpsA and CpsC stimulate CpsD to produce longer polymers. We identify the CpsA and CpsC product as a wall teichoic acid homolog, demonstrating similarity between the biosynthesis of Gram-positive wall teichoic acid and Gram-negative capsules.
Role of Pacific Ocean climate in regulating runoff in the source areas of water transfer projects on the Pacific Rim
Authors: Chen Feng , Wang Shijie , Dong Qianjin , Esper Jan , Büntgen Ulf , Meko David , Linderholm Hans W. , Wang Tao , Yue Weipeng , Zhao Xiaoen , Hadad Martín , González-Reyes Álvaro , Chen Fahu 
Published: July 2024

AbstractOver the past two decades, more frequent and intense climate events have seriously threatened the operation of water transfer projects in the Pacific Rim region. However, the role of climatic change in driving runoff variations in the water source areas of these projects is unclear. We used tree-ring data to reconstruct changes in the runoff of the Hanjiang River since 1580 CE representing an important water source area for China’s south-north water transfer project. Comparisons with hydroclimatic reconstructions for the southwestern United States and central Chile indicated that the Pacific Rim region has experienced multiple coinciding droughts related to ENSO activity. Climate simulations indicate an increased likelihood of drought occurrence in the Pacific Rim region in the coming decades. The combination of warming-induced drought stresses with dynamic El Niño (warming ENSO) patterns is a thread to urban agglomerations and agricultural regions that rely on water transfer projects along the Pacific Rim.
Urbanization-induced warming amplifies population exposure to compound heatwaves but narrows exposure inequality between global North and South cities
Authors: Gao Shengjun , Chen Yunhao , Chen Deliang , He Bin , Gong Adu , Hou Peng , Li Kangning , Cui Ying 
Published: July 2024

AbstractUrban populations face heightened extreme heat risks attributed to urban heat islands and high population densities. Although previous studies have examined global urban population exposure to heatwaves, the influence of urbanization-induced warming is still not quantified. Here, leveraging satellite-derived near-surface air temperature data, we assess the impacts of urbanization-induced warming on heat exposure in 1028 cities worldwide. Additionally, we investigate its role in shaping disparities in heat exposure between global North and South cities. Our findings reveal that urbanization-amplified compound heatwaves exacerbate heat exposure risk in more than 90% of cities, and that this amplification is stronger in high urbanization areas. Moreover, our analysis highlights the potential for overestimating disparities between global North and South cities if urbanization-induced warming is overlooked. The inequality of higher heat exposure in the global South cities than in the global North cities will be narrowed in real scenarios due to more intense urbanization-induced warming in the global North cities. We emphasize the pivotal role of urbanization-induced heatwave intensification in heat exposure assessments and call for its inclusion in future population vulnerability evaluations to extreme heat.
CCL11/CCR3-dependent eosinophilia alleviates malignant pleural effusions and improves prognosis
Authors: Zhang Min , Xia Lixia , Peng Wenbei , Xie Guogang , Li Fei , Zhang Chao , Syeda Madiha Zahra , Hu Yue , Lan Fen , Yan Fugui , Jin Zhangchu , Du Xufei , Han Yinling , Lv Baihui , Wang Yuejue , Li Miao , Fei Xia , Zhao Yun , Chen Kaijun , Chen Yan , Li Wen , Chen Zhihua , Zhou Qiong , Zhang Min , Ying Songmin , Shen Huahao 
Published: July 2024

AbstractMalignant pleural effusion (MPE) is a common occurrence in advanced cancer and is often linked with a poor prognosis. Eosinophils were reported to involve in the development of MPE. However, the role of eosinophils in MPE remains unclear. To investigate this, we conducted studies using both human samples and mouse models. Increased eosinophil counts were observed in patients with MPE, indicating that the higher the number of eosinophils is, the lower the LENT score is. In our animal models, eosinophils were found to migrate to pleural cavity actively upon exposure to tumor cells. Intriguingly, we discovered that a deficiency in eosinophils exacerbated MPE, possibly due to their anti-tumor effects generated by modifying the microenvironment of MPE. Furthermore, our experiments explored the role of the C-C motif chemokine ligand 11 (CCL11) and its receptor C-C motif chemokine receptor 3 (CCR3) in MPE pathology. As a conclusion, our study underscores the protective potential of eosinophils against the development of MPE, and that an increase in eosinophils through adoptive transfer of eosinophils or increasing their numbers improved MPE.
Male and female contributions to diversity among birdwing butterfly images
Authors: Hoyal Cuthill Jennifer F. , Guttenberg Nicholas , Huertas Blanca 
Published: July 2024

AbstractMachine learning (ML) newly enables tests for higher inter-species diversity in visible phenotype (disparity) among males versus females, predictions made from Darwinian sexual selection versus Wallacean natural selection, respectively. Here, we use ML to quantify variation across a sample of > 16,000 dorsal and ventral photographs of the sexually dimorphic birdwing butterflies (Lepidoptera: Papilionidae). Validation of image embedding distances, learnt by a triplet-trained, deep convolutional neural network, shows ML can be used for automated reconstruction of phenotypic evolution achieving measures of phylogenetic congruence to genetic species trees within a range sampled among genetic trees themselves. Quantification of sexual disparity difference (male versus female embedding distance), shows sexually and phylogenetically variable inter-species disparity. Ornithoptera exemplify high embedded male image disparity, diversification of selective optima in fitted multi-peak OU models and accelerated divergence, with cases of extreme divergence in allopatry and sympatry. However, genus Troides shows inverted patterns, including comparatively static male embedded phenotype, and higher female than male disparity – though within an inferred selective regime common to these females. Birdwing shapes and colour patterns that are most phenotypically distinctive in ML similarity are generally those of males. However, either sex can contribute majoritively to observed phenotypic diversity among species.
Proton-pumping photoreceptor controls expression of ABC transporter by regulating transcription factor through light
Authors: Shim Jin-gon , Chuon Kimleng , Kim Ji‐Hyun , Lee Sang-ji , Song Myung-chul , Cho Shin-Gyu , Hour Chenda , Jung Kwang-Hwan 
Published: July 2024

AbstractLight is a significant factor for living organisms with photosystems, like microbial rhodopsin—a retinal protein that functions as an ion pump, channel, and sensory transduction. Gloeobacter violaceus PCC7421, has a proton-pumping rhodopsin gene, the Gloeobacter rhodopsin (GR). The helix-turn-helix family of transcriptional regulators has various motifs, and they regulate gene expression in the presence of various metal ions. Here, we report that active proton outward pumping rhodopsin interacted with the helix-turn-helix transcription regulator and regulated gene expression. This interaction is confirmed using ITC analysis (KD of 8 μM) and determined the charged residues required. During in vitro experiments using fluorescent and luciferase reporter systems, ATP-binding cassette (ABC) transporters and the self-regulation of G. violaceus transcriptional regulator (GvTcR) are regulated by light, and gene regulation is observed in G. violaceus using the real-time polymerase chain reaction. These results expand our understanding of the natural potential and limitations of microbial rhodopsin function.
Universal mechanism of shear thinning in supercooled liquids
Authors: Mizuno Hideyuki , Ikeda Atsushi , Kawasaki Takeshi , Miyazaki Kunimasa 
Published: July 2024

AbstractSoft glassy materials experience a significant reduction in viscosity η when subjected to shear flow, known as shear thinning. This phenomenon is characterized by a power-law scaling of η with the shear rate $$\dot{\gamma }$$

γ

°

, $$\eta \propto {\dot{\gamma }}^{-\nu }$$
η
∝

γ

°

−
ν

, where the exponent ν is typically around 0.7 to 0.8 across different materials. Two decades ago, the mode-coupling theory (MCT) suggested that shear thinning occurs due to the advection. However, it predicts too large ν = 1 ( > 0.7 to 0.8) and overestimates the onset shear rate by orders of magnitude. Recently, it was claimed that a minute distortion of the particle configuration is responsible for shear thinning. Here we extend the MCT to include the distortion, and find that both advection and distortion contribute to shear thinning, but the latter is dominant. Our formulation works quantitatively for several different glass formers. We explain why shear thinning is universal for many glassy materials.
Machine learning of knot topology in non-Hermitian band braids
Authors: Chen Jiangzhi , Wang Zi , Tan Yu-Tao , Wang Ce , Ren Jie 
Published: July 2024

AbstractThe deep connection among braids, knots and topological physics has provided valuable insights into studying topological states in various physical systems. However, identifying distinct braid groups and knot topology embedded in non-Hermitian systems is challenging and requires significant efforts. Here, we demonstrate that an unsupervised learning with the representation basis of su(n) Lie algebra on n-fold extended non-Hermitian bands can fully classify braid group and knot topology therein, without requiring any prior mathematical knowledge or any pre-defined topological invariants. We demonstrate that the approach successfully identifies different topological elements, such as unlink, unknot, Hopf link, Solomon ring, trefoil, and so on, by employing generalized Gell-Mann matrices in non-Hermitian models with n=2 and n=3 energy bands. Moreover, since eigenstate information of non-Hermitian bands is incorporated in addition to eigenvalues, the approach distinguishes the different parity-time symmetry and breaking phases, recognizes the opposite chirality of braids and knots, and identifies out distinct topological phases that were overlooked before. Our study shows significant potential of machine learning in classification of knots, braid groups, and non-Hermitian topological phases.
Healthy dietary patterns are associated with exposure to environmental chemicals in a pregnancy cohort
Authors: Yu Guoqi , Lu Ruijin , Yang Jiaxi , Rahman Mohammad L. , Li Ling-Jun , Wang Dong D. , Sun Qi , Pang Wei Wei , Guivarch Claire , Birukov Anna , Grewal Jagteshwar , Chen Zhen , Zhang Cuilin 
Published: July 2024

AbstractHealthy dietary patterns, such as the alternate Mediterranean diet and alternate Healthy Eating Index, benefit cardiometabolic health. However, several food components of these dietary patterns are primary sources of environmental chemicals. Here, using data from a racially and ethnically diverse US cohort, we show that healthy dietary pattern scores were positively associated with plasma chemical exposure in pregnancy, particularly for the alternate Mediterranean diet and alternate Healthy Eating Index with polychlorinated biphenyls and per- and poly-fluoroalkyl substances. The associations appeared stronger among Asian and Pacific Islanders. These findings suggest that optimizing the benefits of a healthy diet requires concerted regulatory efforts aimed at lowering environmental chemical exposure.
The challenge of closing the climate adaptation gap for water supply utilities
Authors: Becher Olivia , Smilovic Mikhail , Verschuur Jasper , Pant Raghav , Tramberend Sylvia , Hall Jim 
Published: July 2024

AbstractMany drinking water utilities face immense challenges in supplying sustainable, drought-resilient services to households. Here we propose a quantified framework to perform drought risk analysis on ~5600 potable water supply utilities and evaluate the benefit of adaptation actions. We identify global hotspots of present-day and mid-century drought risk under future scenarios of climate change and demand growth (namely, SSP1-2.6, SSP3-7.0, SSP5-8.5). We estimate the mean rate of unsustainable or disrupted utility supply at 15% (interquartile range, 0–26%) and project a global increase in risk of between 30–45% under future scenarios. Implementing the most cost-effective adaptation action identified per utility would mitigate additional future risk by 75–80%. However, implementing the subset of cost-effective options that generate sufficient tariff revenue to provide a benefit-cost ratio that is greater than 1 would only achieve 5–20% of this benefit. The results underline the challenge of attracting the financing required to close the climate adaptation gap for water supply utilities.
Investment funds are responsible for substantial environmental and social impacts
Authors: Popescu Ioana-Stefania , Schaubroeck Thomas , Gibon Thomas , Petucco Claudio , Benetto Enrico 
Published: July 2024

AbstractSustainable investing is under risk of being watered down by greenwashing given the lack of standardized and reliable indicators for measuring impact at financial product level. Here we propose 13 environmental and 13 social life-cycle-based, ready-to-use, and policy-relevant impact indicators that can be adapted for sustainability assessment of financial products. These indicators are aligned primarily with the EU Sustainable Finance Disclosure Regulation (SFDR) for investment funds. As practical application, we estimate the impacts of a sample of 230 self-labeled sustainable investment funds for all indicators. Their total estimated environmental impacts and social impacts are large and vary between 2.1 and 28.4 times the impacts associated with the consumption of a one million EU citizens, depending on the indicator. Moreover, we have found similar impact ranges within a sample of conventional funds, given the heterogeneity of funds. However, when comparing two funds that are equivalent sustainable/non-sustainable pairs, we find that the sustainable fund is better on specific impact categories, but not all of these, therefore hinting towards trade-offs in terms of impact categories also for sustainable funds.
Compound hazard mapping for tropical cyclone-induced concurrent wind and rainfall extremes over India
Authors: Ranjan Ravi , Karmakar Subhankar 
Published: July 2024

AbstractIndia is the worst affected region in the world by tropical cyclones (TCs), causing an average 2% annual GDP loss. TCs instigate many other natural hazards that have a compounding effect on the adversely affected population and present significant challenges to the resilience of emergency response systems and infrastructure. Hence, any risk assessment on TC is inherently multivariate/compound in nature. This study investigates co-occurring wind and rainfall extremes during TCs across India (1979–2020) using a novel quasi-Lagrangian approach, focusing on location-specific hazards. Eastern coastal states and adjacent inland areas experience the highest frequency (≥10 cyclones in 40 years) of concurrent extremes (wind gusts ≥ 16 m/s and rainfall ≥ 18 mm/h). Whereas duration-wise, the eastern coastal states and Gujarat state experience frequent concurrent extremes lasting more than a day annually, with the Krishna–Godavari delta region particularly vulnerable to highly severe events (duration of concurrent extremes ≥ 24 h). This study provides a high-resolution cartographic product of compound hazard from TC-induced extremes for the first time over the entire India, highlighting regional heterogeneity and aiding targeted national-level risk mitigation and adaptation planning.
Inferring intrahalo light from stellar kinematics
Authors: Marini I. , Saro A. , Borgani S. , Boi M. 
Published: July 2024

Context. In the context of structure formation, disentangling the central galaxy stellar population from the stellar intrahalo light can help us shed light on the formation history of the halo as a whole, as the properties of the stellar components are expected to retain traces of the formation history. Many approaches are adopted to assess the task, depending on different physical assumptions (e.g. the light profile, chemical composition, and kinematical differences) and depending on whether the full six-dimensional phase-space information is known (much like in simulations) or whether one analyses projected quantities (i.e. observations).
Aims. This paper paves the way for a new approach to bridge the gap between observational and simulation methods. We propose the use of projected kinematical information from stars in simulations in combination with deep learning to create a robust method for identifying intrahalo light in observational data to enhance understanding and consistency in studying the process of galaxy formation.
Methods. Using deep learning techniques, particularly a convolutional neural network called U-Net, we developed a methodology for predicting these contributions in simulated galaxy cluster images. We created a sample of mock images from hydrodynamical simulations (including masking of the interlopers) to train, validate and test the network. Reinforced training (Attention U-Net) was used to improve the first results, as the innermost central regions of the mock images consistently overestimate the stellar intrahalo contribution.
Results. Our work shows that adequate training over a representative sample of mock images can lead to good predictions of the intrahalo light distribution. The model is mildly dependent on the training size and its predictions are less accurate when applied to mock images from different simulations. However, the main features (spatial scales and gradients of the stellar fractions) are recovered for all tests. While the method presented here should be considered as a proof of concept, future work (e.g. generating more realistic mock observations) is required to enable the application of the proposed model to observational data.
GRAVITY for MATISSE
Authors: Woillez J. , Petrov R. , Abuter R. , Allouche F. , Berio P. , Dembet R. , Eisenhauer F. , Frahm R. , Gonté F. , Haubois X. , Houllé M. , Jaffe W. , Lacour S. , Lagarde S. , Leftley J. , Lopez B. , Matter A. , Meilland A. , Millour F. , Nowak M. , Paladini C. , Rivinius T. , Salabert D. , Schuhler N. , Varga J. , Zins G. 
Published: July 2024

Context. MATISSE, the mid-infrared spectro-imaging instrument of VLTI, was designed to deliver its designed performance when paired with an external second-generation fringe tracker. Science observations started in 2019, demonstrating imaging capabilities and faint science target observations. Now, the GRAVITY fringe tracker stabilises the MATISSE fringes, which allows the use of all spectroscopic modes and improves sensitivity and data accuracy.
Aims. We present how the MATISSE and GRAVITY instruments were adapted to make the GRAVITY fringe tracker work with MATISSE, under the umbrella of the aptly named GRA4MAT project, led by ESO in collaboration with the two instrument consortia.
Methods. We detail the software modifications needed to implement an acquisition and observing sequence specific to GRA4MAT, including simultaneous fringe tracking and chopping and a narrow off-axis capability inspired by the Galactic Centre and exoplanet capability of GRAVITY. We explain the modified data collection and reduction processes. We show how we leveraged the recent fringe tracker upgrade to implement features specific to its use with MATISSE, for example mitigation of fringe jumps with an improved group delay control, and simultaneous fringe tracking and chopping with a new state machine.
Results. We successfully demonstrate significant improvements to the MATISSE instrument. Observations can now be performed at higher spectral resolutions of up to R ~ 3300 and across the full LM bands at once. Long detector integration times, made possible with stabilised fringes, have improved the LM-band sensitivity by a factor of 10. Low flux biases in coherently reduced N-band data have been eliminated. The L-band transfer function is now higher and more stable. We finally illustrate the scientific potential of GRA4MAT with a preview of the first exoplanet observation made by MATISSE on β Pictoris b.