bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural dynamics of RAF1-HSP90-CDC37 and HSP90 complexes reveal asymmetric client interactions and key structural elements
Authors: Finci Lorenzo I. , Chakrabarti Mayukh , Gulten Gulcin , Finney Joseph , Grose Carissa , Fox Tara , Yang Renbin , Nissley Dwight V. , McCormick Frank , Esposito Dominic , Balius Trent E. , Simanshu Dhirendra K. 
Published: March 2024

Abstract
RAF kinases are integral to the RAS-MAPK signaling pathway, and proper RAF1 folding relies on its interaction with the chaperone HSP90 and the cochaperone CDC37. Understanding the intricate molecular interactions governing RAF1 folding is crucial for comprehending this process. Here, we present a cryo-EM structure of the closed-state RAF1-HSP90-CDC37 complex, where the C-lobe of the RAF1 kinase domain binds to one side of the HSP90 dimer, and an unfolded N-lobe segment of the RAF1 kinase domain threads through the center of the HSP90 dimer. CDC37 binds to the kinase C-lobe, mimicking the N-lobe with its HxNI motif. We also describe structures of HSP90 dimers without RAF1 and CDC37, displaying only N-terminal and middle domains, which we term the semi-open state. Employing 1 μs atomistic simulations, energetic decomposition, and comparative structural analysis, we elucidate the dynamics and interactions within these complexes. Our quantitative analysis reveals that CDC37 bridges the HSP90-RAF1 interaction, RAF1 binds HSP90 asymmetrically, and that HSP90 structural elements engage RAF1’s unfolded region. Additionally, N- and C-terminal interactions stabilize HSP90 dimers, and molecular interactions in HSP90 dimers rearrange between the closed and semi-open states. Our findings provide valuable insight into the contributions of HSP90 and CDC37 in mediating client folding.
Projecting contributions of marine protected areas to rebuild fish stocks under climate change
Authors: Cheung William W. L. , Palacios-Abrantes Juliano , Roberts Sarah M. 
Published: March 2024

AbstractNo-take marine protected areas (No-take MPAs) are considered as a major tool for conserving marine biodiversity and ecosystem services. No-take MPAs can also contribute to climate adaptation for exploited fish stocks. Meanwhile, many fish stocks in the world are overfished and management institutions are developing plans to rebuild them. Understanding the potential effects of no-take MPAs on fish stocks under climate change can help develop strategies for climate-resilient stock rebuilding. Here, using a linked climate-fish-fishing model, we undertake simulation experiments to examine the effects of no-take MPAs on biomass and potential catches of 231 exploited fish and invertebrate species in eight marine ecoregions in the Northeast Atlantic under climate change. The simulations include different levels of fishing, no-take MPAs coverage, atmospheric global warming levels, and account for the expected displacement of fishing to the area around the no-take MPAs. Average individual stock biomass is projected to decrease by 5–15% per degree Celsius atmospheric warming. Having 30% of the distribution of over-exploited fish stocks under no-take MPAs together with conservation-focused fisheries management of these stocks are projected to offset the negative impacts on their biomass under 2.6–2.9 °C global warming. Meanwhile, potential catches increase when a portion of the over-exploited fish stocks is protected from fishing as higher biomass in the no-take MPAs spills-over to the surrounding areas. Our findings highlight that no-take MPAs, combined with reducing fishing intensity, can help rebuild over-exploited fish biomass and benefit their dependent fisheries in the Northeast Atlantic under projected climate change in the 21st century.
Two classes of DNA gyrase inhibitors elicit distinct evolutionary trajectories toward resistance in gram-negative pathogens
Authors: Leyn Semen A. , Kent James E. , Zlamal Jaime E. , Elane Marinela L. , Vercruysse Maarten , Osterman Andrei L. 
Published: March 2024

AbstractComprehensive knowledge of mechanisms driving the acquisition of antimicrobial resistance is essential for the development of new drugs with minimized resistibility. To gain this knowledge, we combine experimental evolution in a continuous culturing device, the morbidostat, with whole genome sequencing of evolving cultures followed by characterization of drug-resistant isolates. Here, this approach was used to assess evolutionary dynamics of resistance acquisition against DNA gyrase/topoisomerase TriBE inhibitor GP6 in Escherichia coli and Acinetobacter baumannii. The evolution of GP6 resistance in both species was driven by a combination of two classes of mutational events: (i) amino acid substitutions near the ATP-binding site of the GyrB subunit of the DNA gyrase target; and (ii) various mutations and genomic rearrangements leading to upregulation of efflux pumps, species-specific (AcrAB/TolC in E. coli and AdeIJK in A. baumannii) and shared by both species (MdtK). A comparison with the experimental evolution of resistance to ciprofloxacin (CIP), previously performed using the same workflow and strains, revealed fundamental differences between these two distinct classes of compounds. Most notable were non-overlapping spectra of target mutations and distinct evolutionary trajectories that, in the case of GP6, were dominated by upregulation of efflux machinery prior to (or even in lieu) of target modification. Most of the efflux-driven GP6-resistant isolates of both species displayed a robust cross-resistance to CIP, while CIP-resistant clones showed no appreciable increase in GP6-resistance.
MDU‐sampling: Multi‐domain uniform sampling method for large‐scale outdoor LiDAR point cloud registration
Authors: Ou Wengjun , Zheng Mingkui , Zheng Haifeng 
Published: March 2024

AbstractSampling is a crucial concern for outdoor light detection and ranging (LiDAR) point cloud registration due to the large amounts of point cloud. Numerous algorithms have been devised to tackle this issue by selecting key points. However, these approaches often necessitate extensive computations, giving rise to challenges related to computational time and complexity. This letter proposes a multi‐domain uniform sampling method (MDU‐sampling) for large‐scale outdoor LiDAR point cloud registration. The feature extraction based on deep learning aggregates information from the neighbourhood, so there is redundancy between adjacent features. The sampling method in this paper is carried out in the spatial and feature domains. First, uniform sampling is executed in the spatial domain, maintaining local point cloud uniformity. This is believed to preserve more potential point correspondences and is beneficial for subsequent neighbourhood information aggregation and feature sampling. Subsequently, a secondary sampling in the feature domain is performed to reduce redundancy among the features of neighbouring points. Notably, only points on the same ring in LiDAR data are considered as neighbouring points, eliminating the need for additional neighbouring point search and thereby speeding up processing rates. Experimental results demonstrate that the approach enhances accuracy and robustness compared with benchmarks.
PCQD‐AR: Subjective quality assessment of compressed point clouds with head‐mounted augmented reality
Authors: Fan Chunling , Zhang Yun , Zhu Linwei , Wu Xinju 
Published: March 2024

AbstractThis letter fully studies the coloured point cloud quality assessment in augmented reality (AR) environment through subjective test. Firstly, a point cloud dataset, named point cloud quality dataset‐AR, including ten reference point clouds and their 90 distorted versions is presented, which were generated using the reference software of video‐based point cloud compression across various combinations of geometry and texture quantization parameters. Then, the impact of geometry and texture distortions on perceived quality of point clouds in AR environment was discussed in detail. Moreover, the performance of existing objective point cloud quality assessment metrics on the proposed dataset is evaluated. The subjective dataset including the values of mean opinion score were released to public.
Recovery strategy of distribution network based on dynamic island rescue under extreme weather
Authors: Liu Xinrui , Meng Qingkun , Wang Rui , Dong Chaoyu , Sun Qiuye 
Published: March 2024

AbstractThe frequent occurrence of various extreme weather has a great influence on the normal and stable operation of the distribution network. In order to minimise the large‐scale power loss of the distribution network caused by extreme weather, considering that most of the practical disasters are concurrent with various weather types, and each disaster is independent of each other. A unified failure rate calculation model is proposed, which includes line break, short circuit, tower fall, insulator flashover etc., to realise disaster scenario prediction. Secondly, a resilience evaluation index of island rescue based on mobile energy storage system (IR‐MESS) is proposed. Thirdly, considering the flexibility of MESS, the pre‐disaster scheduling of MESS is carried out according to the predicted disaster scenario. After the disaster occurs, a spatio‐temporal optimisation scheduling model based on the rescue state and charge state of MESS is proposed, and a dynamic IR‐MESS is formed to provide power supply for important loads in out‐of‐load areas of the distribution network. Finally, taking the actual ice disaster in northeast China as an example, the results show that the rescue strategy based on IR‐MESS proposed in this paper can effectively elevate the resilience of the distribution network.
Capacitor sizing of three‐level neutral point clamped voltage source inverter for electric vehicles: Effects of modulation and motor characteristics
Authors: Ogan Serhat Emir , Bostanci Emine 
Published: March 2024

AbstractA three‐level neutral point clamped (3L‐NPC) voltage source inverter (VSI) topology can be advantageous in electric vehicles with a high DC‐link voltage and a high switching frequency. A bulky DC‐link capacitor is not an option; thus, the DC‐link capacitor's sizing considering the traction system characteristics is an important design step. This paper investigates how the DC‐link capacitor size of a 3L‐NPC VSI gets affected by the combination of the interdependent characteristics of an electric drive, such as its power factor, modulation index, current, and fundamental frequency, with the effects of the modulation methods. Five pulse width modulation (PWM) methods, of which three of them have an active neutral point potential control, are compared in terms of their neutral point potential (NPP) oscillations. Then, the size of the DC‐link capacitor is determined for each PWM method so that the NPP ripple is kept under desired limits at all operating conditions. It is shown that both the modulation technique and the electric machine characteristics influence the capacitor size. For example, electric machine design modifications can introduce more than a 30% reduction in capacitor size. Finally, DC‐link and NPP oscillations with different PWM methods are experimentally validated in a scaled‐down 3L‐NPC inverter.
Research on SSVEP‐EEG feature enhancement algorithm based on fractional differentiation
Authors: Li Zenghui , Wang Wei , Yuan Saijie , Pei Junpeng , Yang Qianqian , Wang Yousong 
Published: March 2024

AbstractSteady‐state visual evoked potentials (SSVEP), significant in brain‐computer interfaces (BCI) and medical diagnostics, benefit from enhanced signal processing for improved analysis and interpretation. This study introduces a novel enhancement algorithm for SSVEP electroencephalogram (EEG) signals, employing fractional‐order differentiation operators combined with image processing techniques. Utilizing fractional‐order differentiation within a Laplace pyramid framework, the algorithm achieves hierarchical signal enhancement, facilitating detailed feature extraction and emphasizing SSVEP signal characteristics. This innovative approach merges the precision of fractional calculus with the structural benefits of the Laplace pyramid, leading to enhanced signal clarity and feature discrimination. The efficacy of this method was validated using canonical correlation analysis (CCA), filter bank CCA (FBCCA), and task‐related component analysis (TRCA) on a public dataset. Compared to conventional methods, our algorithm not only mitigates trend components in SSVEP signals but also significantly boosts the recognition accuracy of CCA, FBCCA, and TRCA algorithms. Experimental results indicate a marked improvement in recognition precision, underscoring the algorithm's potential to advance SSVEP‐based BCI research.
The EDIBLES Survey
Authors: Ebenbichler A. , Smoker J. V. , Lallement R. , Farhang A. , Cox N. L. J. , Joblin C. , van Loon J. Th. , Linnartz H. , Przybilla N. , Ehrenfreund P. , Cami J. , Cordiner M. 
Published: March 2024

Context. There have been many attempts to identify families of diffuse interstellar bands (DIBs) with perfectly correlating band strengths. Although major efforts have been made to classify broadly based DIB families and important insights have been gained, no family has been identified with sufficient accuracy or statistical significance to prove that a series of selected DIBs originates from the same carrier. This can be attributed in part to the exclusive use of equivalent widths to establish DIB families.
Aims. In a change of strategy, we search for DIBs that are highly correlated in both band strength and profile shape. This approach increases the chance of correlating DIBs being members of one family and originating from the same carrier molecule. We also search for correlations between DIB profile families and atomic interstellar lines, with the goal of further chemically constraining possible DIB carriers.
Methods. We adapted the well-known method of time-series alignment to perform a spectral alignment; that is, DIB alignment. In a second step, we analysed the alignment results using a clustering analysis. This method required a statistically significant data set of DIB sight lines. The ESO Diffuse Interstellar Bands Large Exploration Survey (EDIBLES) data were perfectly suited for this application.
Results. We report eight DIB families with correlating strengths and profiles, as well as four previously unreported DIBs in the visual range, found using DIB alignment. All profile family members show Pearson correlation coefficients in band strength higher than 0.9. In particular, we report the 6614–6521 Å DIB pair, in which both DIBs show the same triple-peak substructure and an unprecedented band strength Pearson correlation coefficient of 0.9935. The presented approach opens up new perspectives that can guide the laboratory search for DIB carriers.
Anti-Thrombin IgA in a Patient with Multiple Myeloma Leading to In Vitro Interference in Multiple Coagulation Tests and Confounding Diagnosis
Authors: Irsara Christian , Griesmacher Andrea , Loacker Lorin , Feistritzer Clemens , Überbacher Cosima Anna , Amiral Jean 
Published: March 2024

Abstract
Background We report the case of a 59-year-old multiple myeloma patient in whom an anti-human thrombin IgA antibody led to prolonged in vitro coagulation times, suggesting inhibitors to all intrinsic coagulation factors in the absence of spontaneous bleeding.
Methods Routine and extensive special coagulation tests, in vivo bleeding time, and specific antibody testing were performed.
Results Although the patient did not suffer from spontaneous bleeding and had a normal in vivo bleeding time, the anti-human thrombin IgA autoantibody affected all coagulation assays involving human thrombin in vitro, mimicking inhibitors to intrinsic coagulation factors. As the IgA paraprotein and the IgA antibody virtually disappeared after autologous stem cell transplantation, the coagulation tests also largely normalized.
Conclusion Antibodies to human thrombin may interfere with all coagulation assays involving thrombin, imitating a severe coagulopathy. However, in vivo they do not necessarily lead to strongly increased bleeding tendency. Complex and ambiguous coagulation abnormalities should be evaluated and treated in an interdisciplinary setting, including a highly specialized coagulation laboratory, from the beginning.
Committed Lone Fighters And Group Experiences: An International
Survey On Pediatric Hematology And Oncology Training In German-Speaking
Countries
Authors: Barnbrock Anke , Schäfer Kristine , Stursberg Jana , Siebald Benjamin , Graf Norbert , Mücke Urs , Schneider Dominik T. , Bochennek Konrad , Füller Miriam 
Published: March 2024

Abstract
Introduction In German-speaking countries children with cancer are treated
in about 70 hospitals. While national and European curricula for pediatric
oncology and hematology (POH) have been developed, little is known, how far
these curricula have been implemented into daily training and what topics are
deemed urgent by instructors.
Methods and Materials In 2022 the Didactics and Educational working party
of the German Pediatric Hematology/Oncology Society conducted a survey plus
interview by phone call on local educational conditions in POH and needs of
educators.
Results Thirty-two (45%) POH centers answered the questionary, half have
appointed persons overseeing the training. A wide range educational scenarios
were described in some centers. Trainees identified urgent needs in areas such
as hybrid education and demanded training workshops on specific topics and
intensified networking and a general curriculum implemented into daily care as
mandatory.
Conclusion This is the first survey on educational issues in POH in German
speaking centers, describing the current situation before and under pandemic
conditions. Great individual efforts have already been achieved by dedicated
teachers. A comprehensive training program in POH is still missing, which
translates the national curriculum into daily practice, while improving
networking and balancing the resources of the individual centers.
Synthesis of the Cyclohexane Fragment Peculiar to Enacyloxins: Study of Its Assembly and Protective Groups Removal
Authors: Roulland Emmanuel , Christin Orane 
Published: March 2024

AbstractThe enantioselective synthesis of the protected (1S,3R,4S)-3,4-dihydroxycyclohexane-1-carboxylic acid moiety shared among all members of the enacyloxin family has been successfully accomplished. Having obtained this fragment, we devised assembly conditions using models that mimic the enacyloxin acyl chain. Additionally, we assessed conditions for the removal of protective groups, aiming to avoid previously reported detrimental ester shifts.
Sulfonium-Based Activity-Based Probes for Lysine-Selective Protein Profiling under Alkaline Conditions
Authors: Yin Feng , Lu Fei , Li Zigang , Hu Changxing , Wang Rui , An Yuhao , Wan Chuan 
Published: March 2024

AbstractDue to their strong nucleophilicities, nucleophilic lysine and cysteine residues can be easily recognized and modified by electrophilic groups, thus, acting as the targets for covalent ligands or drugs. Therefore, the development of site-specific protein-modification chemistry for various nucleophilic residues has been explored to label proteins selectively for many biological and therapeutic applications. In this study, we constructed a series of sulfonium-based small molecules to react with the amine group of lysine residues by utilizing the strong electrophilicity of sulfonium, resulting in lysine-selective labeling via the formation of classical amide bonds under alkaline conditions (pH 9.0–11.0). After systematic optimization of the labeling conditions, this strategy was utilized for protein labeling across various bacteria’s lysates. Finally, combined with the activity-based protein profiling (ABPP) strategy, we successfully identified and analyzed hundreds of labeled lysine residues in the bacterial proteome.
New Guidelines for Severe Community-acquired Pneumonia
Authors: Calabretta Davide , Martìn-Loeches Ignacio , Torres Antoni 
Published: March 2024

AbstractIn 2023, the new European guidelines on severe community-acquired pneumonia, providing clinical practice recommendations for the management of this life-threatening infection, characterized by a high burden of mortality, morbidity, and costs for the society. This review article aims to summarize the principal evidence related to eight different questions covered in the guidelines, by also highlighting the future perspectives for research activity.
Clinicobiochemical Profile and Outcome of Children with Small Molecule Neurometabolic Disorders: A Tertiary Care Hospital Experience from India
Authors: Banerjee Bidisha , Shinde Supriya , Christopher Rita , Acharya Ullas 
Published: March 2024

AbstractInborn Errors of Metabolism (IEM), though heterogenous, are not uncommon. Neurologic manifestations predominate. Without universal newborn screening, early diagnosis and treatment may lessen neuromorbidity. Hence, this study was done to understand small molecule neurometabolic disorders' presentation, diagnostic clues, and outcome. Small molecule neurometabolic disorder was diagnosed in 45 children (postneonatal onset) over 14 years (2008–2022) in a tertiary care hospital. Clinical and laboratory data were retrospectively analyzed. There were 26 boys and 19 girls. The median age at diagnosis was 19 months (interquartile range [IQR]: 8–38 months). The median diagnostic delay was 12 months in chronic encephalopathy (IQR: 1–24 months) and 1 month (IQR: 0.2–5.5 months) in the acute encephalopathy group (p ≤ 0.01). The presentation mode was chronic encephalopathy/myopathy in 29 (64.4%) and acute encephalopathy in 11 (24.4%). Diagnostic clues included unexplained developmental delay (n = 27, 60%), tone abnormalities (n = 26, 57.7%), movement disorder and ataxia (n = 16, 35.5%), acute encephalopathy (n = 11, 24.4%), neuroregression (n = 10, 22.2%), macrocephaly (n = 10, 22.2%), and alopecia (n = 4, 8.9%). Diagnostic/suggestive blood-spot tandem mass spectrometry (TMS) was seen in 34/38 (89.5%) children. Neuroimaging helped clinch the diagnosis in 17 (47%) children. Diagnostic categories were organic acidemias (n = 25, 55.6%), urea cycle disorders (n = 11, 24.4%), aminoacidopathies (n = 5, 11.1%), and fatty acid oxidation disorders (n = 4, 8.9%). The neurodevelopmental outcome was normal in 13 (28.8%), mild delay in 12 (26.6%), severe delay in 11 (24.4%), 3 deaths (6.6%), and 6 (13.3%) children being lost to follow-up. Overall, the outcome was favorable in 55% of cases. Unexplained developmental delay with tone abnormalities with or without movement disorders is a joint presentation of late-onset neurometabolic diseases. Neuroimaging studies and laboratory tests like blood-spot TMS help identify many small molecule disorders.