bluuebunny/crossref_metadata_2025_split huggingface dataset:
Laying the experimental foundation for corrosion inhibitor discovery through machine learning
Authors: Özkan Can , Sahlmann Lisa , Feiler Christian , Zheludkevich Mikhail , Lamaka Sviatlana , Sewlikar Parth , Kooijman Agnieszka , Taheri Peyman , Mol Arjan 
Published: February 2024

AbstractCreating durable, eco-friendly coatings for long-term corrosion protection requires innovative strategies to streamline design and development processes, conserve resources, and decrease maintenance costs. In this pursuit, machine learning emerges as a promising catalyst, despite the challenges presented by the scarcity of high-quality datasets in the field of corrosion inhibition research. To address this obstacle, we have created an extensive electrochemical library of around 80 inhibitor candidates. The electrochemical behaviour of inhibitor-exposed AA2024-T3 substrates was captured using linear polarisation resistance, electrochemical impedance spectroscopy, and potentiodynamic polarisation techniques at different exposure times to obtain the most comprehensive electrochemical picture of the corrosion inhibition over a 24-h period. The experimental results yield target parameters and additional input features that can be combined with computational descriptors to develop quantitative structure–property relationship (QSPR) models augmented by mechanistic input features.
Asymmetric oligomerization state and sequence patterning can tune multiphase condensate miscibility
Authors: Rana Ushnish , Xu Ke , Narayanan Amal , Walls Mackenzie T. , Panagiotopoulos Athanassios Z. , Avalos José L. , Brangwynne Clifford P. 
Published: February 2024

AbstractEndogenous biomolecular condensates, composed of a multitude of proteins and RNAs, can organize into multiphasic structures with compositionally distinct phases. This multiphasic organization is generally understood to be critical for facilitating their proper biological function. However, the biophysical principles driving multiphase formation are not completely understood. Here we use in vivo condensate reconstitution experiments and coarse-grained molecular simulations to investigate how oligomerization and sequence interactions modulate multiphase organization in biomolecular condensates. We demonstrate that increasing the oligomerization state of an intrinsically disordered protein results in enhanced immiscibility and multiphase formation. Interestingly, we find that oligomerization tunes the miscibility of intrinsically disordered proteins in an asymmetric manner, with the effect being more pronounced when the intrinsically disordered protein, exhibiting stronger homotypic interactions, is oligomerized. Our findings suggest that oligomerization is a flexible biophysical mechanism that cells can exploit to tune the internal organization of biomolecular condensates and their associated biological functions.
Making cities mental health friendly for adolescents and young adults
Authors: Collins Pamela Y. , Sinha Moitreyee , Concepcion Tessa , Patton George , Way Thaisa , McCay Layla , Mensa-Kwao Augustina , Herrman Helen , de Leeuw Evelyne , Anand Nalini , Atwoli Lukoye , Bardikoff Nicole , Booysen Chantelle , Bustamante Inés , Chen Yajun , Davis Kelly , Dua Tarun , Foote Nathaniel , Hughsam Matthew , Juma Damian , Khanal Shisir , Kumar Manasi , Lefkowitz Bina , McDermott Peter , Moitra Modhurima , Ochieng Yvonne , Omigbodun Olayinka , Queen Emily , Unützer Jürgen , Uribe-Restrepo José Miguel , Wolpert Miranda , Zeitz Lian 
Published: February 2024

AbstractUrban life shapes the mental health of city dwellers, and although cities provide access to health, education and economic gain, urban environments are often detrimental to mental health1,2. Increasing urbanization over the next three decades will be accompanied by a growing population of children and adolescents living in cities3. Shaping the aspects of urban life that influence youth mental health could have an enormous impact on adolescent well-being and adult trajectories4. We invited a multidisciplinary, global group of researchers, practitioners, advocates and young people to complete sequential surveys to identify and prioritize the characteristics of a mental health-friendly city for young people. Here we show a set of ranked characteristic statements, grouped by personal, interpersonal, community, organizational, policy and environmental domains of intervention. Life skills for personal development, valuing and accepting young people’s ideas and choices, providing safe public space for social connection, employment and job security, centring youth input in urban planning and design, and addressing adverse social determinants were priorities by domain. We report the adversities that COVID-19 generated and link relevant actions to these data. Our findings highlight the need for intersectoral, multilevel intervention and for inclusive, equitable, participatory design of cities that support youth mental health.
Avoiding fusion plasma tearing instability with deep reinforcement learning
Authors: Seo Jaemin , Kim SangKyeun , Jalalvand Azarakhsh , Conlin Rory , Rothstein Andrew , Abbate Joseph , Erickson Keith , Wai Josiah , Shousha Ricardo , Kolemen Egemen 
Published: February 2024

AbstractFor stable and efficient fusion energy production using a tokamak reactor, it is essential to maintain a high-pressure hydrogenic plasma without plasma disruption. Therefore, it is necessary to actively control the tokamak based on the observed plasma state, to manoeuvre high-pressure plasma while avoiding tearing instability, the leading cause of disruptions. This presents an obstacle-avoidance problem for which artificial intelligence based on reinforcement learning has recently shown remarkable performance1–4. However, the obstacle here, the tearing instability, is difficult to forecast and is highly prone to terminating plasma operations, especially in the ITER baseline scenario. Previously, we developed a multimodal dynamic model that estimates the likelihood of future tearing instability based on signals from multiple diagnostics and actuators5. Here we harness this dynamic model as a training environment for reinforcement-learning artificial intelligence, facilitating automated instability prevention. We demonstrate artificial intelligence control to lower the possibility of disruptive tearing instabilities in DIII-D6, the largest magnetic fusion facility in the United States. The controller maintained the tearing likelihood under a given threshold, even under relatively unfavourable conditions of low safety factor and low torque. In particular, it allowed the plasma to actively track the stable path within the time-varying operational space while maintaining H-mode performance, which was challenging with traditional preprogrammed control. This controller paves the path to developing stable high-performance operational scenarios for future use in ITER.
The UFM1 E3 ligase recognizes and releases 60S ribosomes from ER translocons
Authors: Makhlouf Linda , Peter Joshua J. , Magnussen Helge M. , Thakur Rohan , Millrine David , Minshull Thomas C. , Harrison Grace , Varghese Joby , Lamoliatte Frederic , Foglizzo Martina , Macartney Thomas , Calabrese Antonio N. , Zeqiraj Elton , Kulathu Yogesh 
Published: February 2024

AbstractStalled ribosomes at the endoplasmic reticulum (ER) are covalently modified with the ubiquitin-like protein UFM1 on the 60S ribosomal subunit protein RPL26 (also known as uL24)1,2. This modification, which is known as UFMylation, is orchestrated by the UFM1 ribosome E3 ligase (UREL) complex, comprising UFL1, UFBP1 and CDK5RAP3 (ref. 3). However, the catalytic mechanism of UREL and the functional consequences of UFMylation are unclear. Here we present cryo-electron microscopy structures of UREL bound to 60S ribosomes, revealing the basis of its substrate specificity. UREL wraps around the 60S subunit to form a C-shaped clamp architecture that blocks the tRNA-binding sites at one end, and the peptide exit tunnel at the other. A UFL1 loop inserts into and remodels the peptidyl transferase centre. These features of UREL suggest a crucial function for UFMylation in the release and recycling of stalled or terminated ribosomes from the ER membrane. In the absence of functional UREL, 60S–SEC61 translocon complexes accumulate at the ER membrane, demonstrating that UFMylation is necessary for releasing SEC61 from 60S subunits. Notably, this release is facilitated by a functional switch of UREL from a ‘writer’ to a ‘reader’ module that recognizes its product—UFMylated 60S ribosomes. Collectively, we identify a fundamental role for UREL in dissociating 60S subunits from the SEC61 translocon and the basis for UFMylation in regulating protein homeostasis at the ER.
IL-10 constrains sphingolipid metabolism to limit inflammation
Authors: York Autumn G. , Skadow Mathias H. , Oh Joonseok , Qu Rihao , Zhou Quan D. , Hsieh Wei-Yuan , Mowel Walter K. , Brewer J. Richard , Kaffe Eleanna , Williams Kevin J. , Kluger Yuval , Smale Stephen T. , Crawford Jason M. , Bensinger Steven J. , Flavell Richard A. 
Published: February 2024

AbstractInterleukin-10 (IL-10) is a key anti-inflammatory cytokine that can limit immune cell activation and cytokine production in innate immune cell types1. Loss of IL-10 signalling results in life-threatening inflammatory bowel disease in humans and mice—however, the exact mechanism by which IL-10 signalling subdues inflammation remains unclear2–5. Here we find that increased saturated very long chain (VLC) ceramides are critical for the heightened inflammatory gene expression that is a hallmark of IL-10 deficiency. Accordingly, genetic deletion of ceramide synthase 2 (encoded by Cers2), the enzyme responsible for VLC ceramide production, limited the exacerbated inflammatory gene expression programme associated with IL-10 deficiency both in vitro and in vivo. The accumulation of saturated VLC ceramides was regulated by a decrease in metabolic flux through the de novo mono-unsaturated fatty acid synthesis pathway. Restoring mono-unsaturated fatty acid availability to cells deficient in IL-10 signalling limited saturated VLC ceramide production and the associated inflammation. Mechanistically, we find that persistent inflammation mediated by VLC ceramides is largely dependent on sustained activity of REL, an immuno-modulatory transcription factor. Together, these data indicate that an IL-10-driven fatty acid desaturation programme rewires VLC ceramide accumulation and aberrant activation of REL. These studies support the idea that fatty acid homeostasis in innate immune cells serves as a key regulatory node to control pathologic inflammation and suggests that ‘metabolic correction’ of VLC homeostasis could be an important strategy to normalize dysregulated inflammation caused by the absence of IL-10.
Mechanisms of action and resistance in histone methylation-targeted therapy
Authors: Yamagishi Makoto , Kuze Yuta , Kobayashi Seiichiro , Nakashima Makoto , Morishima Satoko , Kawamata Toyotaka , Makiyama Junya , Suzuki Kako , Seki Masahide , Abe Kazumi , Imamura Kiyomi , Watanabe Eri , Tsuchiya Kazumi , Yasumatsu Isao , Takayama Gensuke , Hizukuri Yoshiyuki , Ito Kazumi , Taira Yukihiro , Nannya Yasuhito , Tojo Arinobu , Watanabe Toshiki , Tsutsumi Shinji , Suzuki Yutaka , Uchimaru Kaoru 
Published: February 2024

AbstractEpigenomes enable the rectification of disordered cancer gene expression, thereby providing new targets for pharmacological interventions. The clinical utility of targeting histone H3 lysine trimethylation (H3K27me3) as an epigenetic hallmark has been demonstrated1–7. However, in actual therapeutic settings, the mechanism by which H3K27me3-targeting therapies exert their effects and the response of tumour cells remain unclear. Here we show the potency and mechanisms of action and resistance of the EZH1–EZH2 dual inhibitor valemetostat in clinical trials of patients with adult T cell leukaemia/lymphoma. Administration of valemetostat reduced tumour size and demonstrated durable clinical response in aggressive lymphomas with multiple genetic mutations. Integrative single-cell analyses showed that valemetostat abolishes the highly condensed chromatin structure formed by the plastic H3K27me3 and neutralizes multiple gene loci, including tumour suppressor genes. Nevertheless, subsequent long-term treatment encounters the emergence of resistant clones with reconstructed aggregate chromatin that closely resemble the pre-dose state. Acquired mutations at the PRC2–compound interface result in the propagation of clones with increased H3K27me3 expression. In patients free of PRC2 mutations, TET2 mutation or elevated DNMT3A expression causes similar chromatin recondensation through de novo DNA methylation in the H3K27me3-associated regions. We identified subpopulations with distinct metabolic and gene translation characteristics implicated in primary susceptibility until the acquisition of the heritable (epi)mutations. Targeting epigenetic drivers and chromatin homeostasis may provide opportunities for further sustained epigenetic cancer therapies.
Quality assessment of gene repertoire annotations with OMArk
Authors: Nevers Yannis , Warwick Vesztrocy Alex , Rossier Victor , Train Clément-Marie , Altenhoff Adrian , Dessimoz Christophe , Glover Natasha M. 
Published: February 2024

Abstract
In the era of biodiversity genomics, it is crucial to ensure that annotations of protein-coding gene repertoires are accurate. State-of-the-art tools to assess genome annotations measure the completeness of a gene repertoire but are blind to other errors, such as gene overprediction or contamination. We introduce OMArk, a software package that relies on fast, alignment-free sequence comparisons between a query proteome and precomputed gene families across the tree of life. OMArk assesses not only the completeness but also the consistency of the gene repertoire as a whole relative to closely related species and reports likely contamination events. Analysis of 1,805 UniProt Eukaryotic Reference Proteomes with OMArk demonstrated strong evidence of contamination in 73 proteomes and identified error propagation in avian gene annotation resulting from the use of a fragmented zebra finch proteome as a reference. This study illustrates the importance of comparing and prioritizing proteomes based on their quality measures.
Direct evidence of plant consumption in Neolithic Eastern Sudan from dental calculus analysis
Authors: Capasso Giusy , Neves Dulce , Sperduti Alessandra , Cristiani Emanuela , Manzo Andrea 
Published: February 2024

AbstractThe Neolithic communities of Eastern Sudan combined intensive pastoralism with plant exploitation as their main subsistence strategies. However, to date, it remains unclear which plant species were part of the human diet during the Neolithic. This contribution presents direct data on plant consumption in Eastern Sudan from the Early to Late Neolithic, obtained through the analysis of microdebris inclusions in the dental calculus of 37 individuals, integrated by dentoalveolar pathology analysis of 78 individuals, from the sites UA53 (4th millennium BCE) and Mahal Teglinos (3rd–2nd millennium BCE), located in the Gash Delta/Kassala region. Dental calculus inclusions indicate a diverse intake of cereals, legumes, and tubers during the Middle Neolithic, thus supporting the hypothesis of high reliance on plant resources. Dentoalveolar pathologies, possibly related to the consumption of carbohydrate-rich foods, have also been recorded. For the Late Neolithic, consistent with the shift towards aridity that occurred in the Middle/Late Holocene, dental calculus exclusively indicates the exploitation of sorghum and tubers—species well adapted to arid conditions—showing how the Neolithic communities modified their subsistence in response to environmental changes. Evidence of plant processing techniques, such as cooking/heating, was also revealed from the dental calculus analysis.
Correction of high-rate motion for photoacoustic microscopy by orthogonal cross-correlation
Authors: Zou Zilong , Mao Qiuqin , Cheng Renxiang , Tao Chao , Liu Xiaojun 
Published: February 2024

AbstractPhotoacoustic imaging is a promising technology for in vivo imaging. However, its imaging performance can be hampered by motion artifacts, especially when dealing with high-rate motion. In this paper, we propose an orthogonal motion correction method that utilizes cross-correlation along orthogonal scan directions to extract accurate motion displacements from the photoacoustic data. The extracted displacements are then applied to remove artifacts and compensate for motion-induced distortions. Phantom experiments demonstrate that the proposed method can extract the motion information and the structural similarity index measurement after correction is increased by 26.5% and 11.2% compared to no correction and the previous correction method. Then the effectiveness of our method is evaluated in vivo imaging of a mouse brain. Our method shows a stable and effective performance under high-rate motion. The high accuracy of the motion correction method makes it valuable in improving the accuracy of photoacoustic imaging.
A novel extension of half-logistic distribution with statistical inference, estimation and applications
Authors: Bhat A. A. , Ahmad S. P. , Gemeay Ahmed M. , Muse Abdisalam Hassan , Bakr M. E. , Balogun Oluwafemi Samson 
Published: February 2024

AbstractIn the present study, we develop and investigate the odd Frechet Half-Logistic (OFHL) distribution that was developed by incorporating the half-logistic and odd Frechet-G family. The OFHL model has very adaptable probability functions: decreasing, increasing, bathtub and inverted U shapes are shown for the hazard rate functions, illustrating the model’s capacity for flexibility. A comprehensive account of the mathematical and statistical properties of the proposed model is presented. In estimation viewpoint, six distinct estimation methodologies are used to estimate the unknown parameters of the OFHL model. Furthermore, an extensive Monte Carlo simulation analysis is used to evaluate the effectiveness of these estimators. Finally, two applications to real data are used to demonstrate the versatility of the suggested method, and the comparison is made with the half-logistic and some of its well-known extensions. The actual implementation shows that the suggested model performs better than competing models.
Scalable and efficient grating couplers on low-index photonic platforms enabled by cryogenic deep silicon etching
Authors: Lomonte Emma , Stappers Maik , Krämer Linus , Pernice Wolfram H. P. , Lenzini Francesco 
Published: February 2024

AbstractEfficient fiber-to-chip couplers for multi-port access to photonic integrated circuits are paramount for a broad class of applications, ranging, e.g., from telecommunication to photonic computing and quantum technologies. Grating-based approaches are often desirable for providing out-of-plane access to the photonic circuits. However, on photonic platforms characterized by a refractive index ≃ 2 at telecom wavelength, such as silicon nitride or thin-film lithium niobate, the limited scattering strength has thus far hindered the achievement of coupling efficiencies comparable to the ones attainable in silicon photonics. Here we present a flexible strategy for the realization of highly efficient grating couplers on such low-index photonic platforms. To simultaneously reach a high scattering efficiency and a near-unitary modal overlap with optical fibers, we make use of self-imaging gratings designed with a negative diffraction angle. To ensure high directionality of the diffracted light, we take advantage of a metal back-reflector patterned underneath the grating structure by cryogenic deep reactive ion etching of the silicon handle. Using silicon nitride as a testbed material, we experimentally demonstrate coupling efficiency up to − 0.55 dB in the telecom C-band with high chip-scale device yield.
A dynamic fuzzy rule-based inference system using fuzzy inference with semantic reasoning
Authors: Shoaip Nora , El-Sappagh Shaker , Abuhmed Tamer , Elmogy Mohammed 
Published: February 2024

AbstractThe challenge of making flexible, standard, and early medical diagnoses is significant. However, some limitations are not fully overcome. First, the diagnosis rules established by medical experts or learned from a trained dataset prove static and too general. It leads to decisions that lack adaptive flexibility when finding new circumstances. Secondly, medical terminological interoperability is highly critical. It increases realism and medical progress and avoids isolated systems and the difficulty of data exchange, analysis, and interpretation. Third, criteria for diagnosis are often heterogeneous and changeable. It includes symptoms, patient history, demographic, treatment, genetics, biochemistry, and imaging. Symptoms represent a high-impact indicator for early detection. It is important that we deal with these symptoms differently, which have a great relationship with semantics, vary widely, and have linguistic information. This negatively affects early diagnosis decision-making. Depending on the circumstances, the diagnosis is made solo on imaging and some medical tests. In this case, although the accuracy of the diagnosis is very high, can these decisions be considered an early diagnosis or prove the condition is deteriorating? Our contribution in this paper is to present a real medical diagnostic system based on semantics, fuzzy, and dynamic decision rules. We attempt to integrate ontology semantics reasoning and fuzzy inference. It promotes fuzzy reasoning and handles knowledge representation problems. In complications and symptoms, ontological semantic reasoning improves the process of evaluating rules in terms of interpretability, dynamism, and intelligence. A real-world case study, ADNI, is presented involving the field of Alzheimer’s disease (AD). The proposed system has indicated the possibility of the system to diagnose AD with an accuracy of 97.2%, 95.4%, 94.8%, 93.1%, and 96.3% for AD, LMCI, EMCI, SMC, and CN respectively.