-
A Survey on Cyber-Resilience Approaches for Cyber-Physical Systems ACM Comput. Surv. (IF 16.6) Pub Date : 2024-03-16 Mariana Segovia-Ferreira, Jose Rubio-Hernan, Ana Rosa Cavalli, Joaquin Garcia-Alfaro
Concerns for the resilience of Cyber-Physical Systems (CPS) in critical infrastructure are growing. CPS integrate sensing, computation, control, and networking into physical objects and mission-critical services, connecting traditional infrastructure to internet technologies. While this integration increases service efficiency, it has to face the possibility of new threats posed by the new functionalities
-
Mobile Near-Infrared Sensing - A Systematic Review on Devices, Data, Modeling and Applications ACM Comput. Surv. (IF 16.6) Pub Date : 2024-03-16 Weiwei Jiang, Jorge Goncalves, Vassilis Kostakos
Mobile near-infrared sensing is becoming an increasingly important method in many research and industrial areas. To help consolidate progress in this area, we use the PRISMA guidelines to conduct a systematic review of mobile near-infrared sensing, including 1) existing prototypes and commercial products; 2) data collection techniques; 3) machine learning methods; 4) relevant application areas. Our
-
Local Interpretations for Explainable Natural Language Processing: A Survey ACM Comput. Surv. (IF 16.6) Pub Date : 2024-03-15 Siwen Luo, Hamish Ivison, Soyeon Caren Han, Josiah Poon
As the use of deep learning techniques has grown across various fields over the past decade, complaints about the opaqueness of the black-box models have increased, resulting in an increased focus on transparency in deep learning models. This work investigates various methods to improve the interpretability of deep neural networks for Natural Language Processing (NLP) tasks, including machine translation
-
The temporal and genomic scale of selection following hybridization Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-15 Jeffrey S. Groh, Graham Coop
Genomic evidence supports an important role for selection in shaping patterns of introgression along the genome, but frameworks for understanding the evolutionary dynamics within hybrid populations that underlie these patterns have been lacking. Due to the clock-like effect of recombination in hybrids breaking up parental haplotypes, drift and selection produce predictable patterns of ancestry variation
-
Frequent winners explain apparent skewness preferences in experience-based decisions Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-15 Sebastian Olschewski, Mikhail S. Spektor, Gaël Le Mens
Do people’s attitudes toward the (a)symmetry of an outcome distribution affect their choices? Financial investors seek return distributions with frequent small returns but few large ones, consistent with leading models of choice in economics and finance that assume right-skewed preferences. In contrast, many experiments in which decision-makers learn about choice options through experience find the
-
Dependence on relative humidity in the formation of reactive oxygen species in water droplets Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-15 Mohammad Mofidfar, Masoud A. Mehrgardi, Yu Xia, Richard N. Zare
Water microdroplets (7 to 11 µm average diameter, depending on flow rate) are sprayed in a closed chamber at ambient temperature, whose relative humidity (RH) is controlled. The resulting concentration of ROS (reactive oxygen species) formed in the microdroplets, measured by the amount of hydrogen peroxide (H 2 O 2 ), is determined by nuclear magnetic resonance (NMR) and by spectrofluorimetric assays
-
Transcription-induced active forces suppress chromatin motion Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-15 Sucheol Shin, Guang Shi, Hyun Woo Cho, D. Thirumalai
The organization of interphase chromosomes in a number of species is starting to emerge thanks to advances in a variety of experimental techniques. However, much less is known about the dynamics, especially in the functional states of chromatin. Some experiments have shown that the motility of individual loci in human interphase chromosome decreases during transcription and increases upon inhibiting
-
Photo-neuro-immuno-endocrinology: How the ultraviolet radiation regulates the body, brain, and immune system Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-15 Radomir M. Slominski, Jake Y. Chen, Chander Raman, Andrzej T. Slominski
Ultraviolet radiation (UVR) is primarily recognized for its detrimental effects such as cancerogenesis, skin aging, eye damage, and autoimmune disorders. With exception of ultraviolet B (UVB) requirement in the production of vitamin D3, the positive role of UVR in modulation of homeostasis is underappreciated. Skin exposure to UVR triggers local responses secondary to the induction of chemical, hormonal
-
A redox switch allows binding of Fe(II) and Fe(III) ions in the cyanobacterial iron-binding protein FutA from Prochlorococcus Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-15 Rachel Bolton, Moritz M. Machelett, Jack Stubbs, Danny Axford, Nicolas Caramello, Lucrezia Catapano, Martin Malý, Matthew J. Rodrigues, Charlotte Cordery, Graham J. Tizzard, Fraser MacMillan, Sylvain Engilberge, David von Stetten, Takehiko Tosha, Hiroshi Sugimoto, Jonathan A. R. Worrall, Jeremy S. Webb, Mike Zubkov, Simon Coles, Eric Mathieu, Roberto A. Steiner, Garib Murshudov, Tobias E. Schrader
The marine cyanobacterium Prochlorococcus is a main contributor to global photosynthesis, whilst being limited by iron availability. Cyanobacterial genomes generally encode two different types of FutA iron-binding proteins: periplasmic FutA2 ABC transporter subunits bind Fe(III), while cytosolic FutA1 binds Fe(II). Owing to their small size and their economized genome Prochlorococcus ecotypes typically
-
KCTD10 regulates brain development by destabilizing brain disorder–associated protein KCTD13 Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-15 Jianbo Cheng, Zhen Wang, Manpei Tang, Wen Zhang, Guozhong Li, Senwei Tan, Chenjun Mu, Mengyuan Hu, Dan Zhang, Xiangbin Jia, Yangxuan Wen, Hui Guo, Dan Xu, Liang Liu, Jiada Li, Kun Xia, Faxiang Li, Ranhui Duan, Zhiheng Xu, Ling Yuan
KCTD10 belongs to the KCTD (potassiumchannel tetramerization domain) family, many members of which are associated with neuropsychiatric disorders. However, the biological function underlying the association with brain disorders remains to be explored. Here, we reveal that Kctd10 is highly expressed in neuronal progenitors and layer V neurons throughout brain development. Kctd10 deficiency triggers
-
A minimal physical model for curvotaxis driven by curved protein complexes at the cell’s leading edge Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-15 Raj Kumar Sadhu, Marine Luciano, Wang Xi, Cristina Martinez-Torres, Marcel Schröder, Christoph Blum, Marco Tarantola, Stefano Villa, Samo Penič, Aleš Iglič, Carsten Beta, Oliver Steinbock, Eberhard Bodenschatz, Benoît Ladoux, Sylvain Gabriele, Nir S. Gov
Cells often migrate on curved surfaces inside the body, such as curved tissues, blood vessels, or highly curved protrusions of other cells. Recent in vitro experiments provide clear evidence that motile cells are affected by the curvature of the substrate on which they migrate, preferring certain curvatures to others, termed “curvotaxis.” The origin and underlying mechanism that gives rise to this
-
Changes in spatial self-consciousness elicit grid cell–like representation in the entorhinal cortex Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-15 Hyuk-June Moon, Louis Albert, Emanuela De Falco, Corentin Tasu, Baptiste Gauthier, Hyeong-Dong Park, Olaf Blanke
Grid cells in the entorhinal cortex (EC) encode an individual’s location in space, integrating both environmental and multisensory bodily cues. Notably, body-derived signals are also primary signals for the sense of self. While studies have demonstrated that continuous application of visuo-tactile bodily stimuli can induce perceptual shifts in self-location, it remains unexplored whether these illusory
-
Heterogeneous elasticity drives ripening and controls bursting kinetics of transcriptional condensates Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-15 Lingyu Meng, Sheng Mao, Jie Lin
Many biomolecular condensates, including transcriptional condensates, are formed in elastic mediums. In this work, we study the nonequilibrium condensate dynamics in a chromatin-like environment modeled as a heterogeneous elastic medium. We demonstrate that the ripening process in such an elastic medium exhibits a temporal power-law scaling of the average condensate radius, depending on the local stiffness
-
Extended Reality (XR) Toward Building Immersive Solutions: The Key to Unlocking Industry 4.0 ACM Comput. Surv. (IF 16.6) Pub Date : 2024-03-14 A’aeshah Alhakamy
When developing XR applications for Industry 4.0, it is important to consider the integration of visual displays, hardware components, and multimodal interaction techniques that are compatible with the entire system. The potential use of multimodal interactions in industrial applications has been recognized as a significant factor in enhancing humans’ ability to perform tasks and make informed decisions
-
Intel TDX Demystified: A Top-Down Approach ACM Comput. Surv. (IF 16.6) Pub Date : 2024-03-14 Pau-Chen Cheng, Wojciech Ozga, Enriquillo Valdez, Salman Ahmed, Zhongshu Gu, Hani Jamjoom, Hubertus Franke, James Bottomley
Intel Trust Domain Extensions (TDX) is an architectural extension in the 4th Generation Intel Xeon Scalable Processor that supports confidential computing. TDX allows the deployment of virtual machines in the Secure-Arbitration Mode (SEAM) with encrypted CPU state and memory, integrity protection, and remote attestation. TDX aims to enforce hardware-assisted isolation for virtual machines and minimize
-
Warm-Starting and Quantum Computing: A Systematic Mapping Study ACM Comput. Surv. (IF 16.6) Pub Date : 2024-03-13 Felix Truger, Johanna Barzen, Marvin Bechtold, Martin Beisel, Frank Leymann, Alexander Mandl, Vladimir Yussupov
Due to low numbers of qubits and their error-proneness, Noisy Intermediate-Scale Quantum (NISQ) computers impose constraints on the size of quantum algorithms they can successfully execute. State-of-the-art research introduces various techniques addressing these limitations by utilizing known or inexpensively generated approximations, solutions, or models as a starting point to approach a task instead
-
Drug–Drug Interaction Relation Extraction Based on Deep Learning: A Review ACM Comput. Surv. (IF 16.6) Pub Date : 2024-03-13 Mingliang Dou, Jijun Tang, Prayag Tiwari, Yijie Ding, Fei Guo
Drug–drug interaction (DDI) is an important part of drug development and pharmacovigilance. At the same time, DDI is an important factor in treatment planning, monitoring effects of medicine and patient safety, and has a significant impact on public health. Therefore, using deep learning technology to extract DDI from scientific literature has become a valuable research direction to researchers. In
-
On Trust Recommendations in the Social Internet of Things – A Survey ACM Comput. Surv. (IF 16.6) Pub Date : 2024-03-13 Marius Becherer, Omar Khadeer Hussain, Yu Zhang, Frank den Hartog, Elizabeth Chang
The novel paradigm Social Internet of Things (SIoT) improves the network navigability, identifies suitable service providers, and addresses scalability concerns. Ensuring trustworthy collaborations among devices is a key aspect in SIoT and can be realized through trust recommendations. However, the outcome of trust recommendations depends on multiple factors related to the context-dependent nature
-
Learning to Expand/Contract Pareto Sets in Dynamic Multi-Objective Optimization With a Changing Number of Objectives IEEE T. Evolut. Comput. (IF 14.3) Pub Date : 2024-03-14 Gan Ruan, Leandro L. Minku, Stefan Menzel, Bernhard Sendhoff, Xin Yao
-
SRF transcriptionally regulates the oligodendrocyte cytoskeleton during CNS myelination Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-14 Tal Iram, Miguel A. Garcia, Jérémy Amand, Achint Kaur, Micaiah Atkins, Manasi Iyer, Mable Lam, Nicholas Ambiel, Danielle M. Jorgens, Andreas Keller, Tony Wyss-Coray, Fabian Kern, J. Bradley Zuchero
Myelination of neuronal axons is essential for nervous system development. Myelination requires dramatic cytoskeletal dynamics in oligodendrocytes, but how actin is regulated during myelination is poorly understood. We recently identified serum response factor (SRF)—a transcription factor known to regulate expression of actin and actin regulators in other cell types—as a critical driver of myelination
-
Endogenous retrovirus HERVH-derived lncRNA UCA1 controls human trophoblast development Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-14 Xuhui Kong, Ruiqi Li, Manqi Chen, Rongyan Zheng, Jichang Wang, Chuanbo Sun, Yuliang Qu
Endogenous retroviruses (ERVs) are frequently reactivated in mammalian placenta. It has been proposed that ERVs contribute to shaping the gene regulatory network of mammalian trophoblasts, dominantly acting as species- and placental-specific enhancers. However, whether and how ERVs control human trophoblast development through alternative pathways remains poorly understood. Besides the well-recognized
-
Molecular and structural basis of the dual regulation of the polycystin-2 ion channel by small-molecule ligands Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-14 Zhifei Wang, Mengying Chen, Qiang Su, Tiago D. C. Morais, Yan Wang, Elianna Nazginov, Akhilraj R. Pillai, Feng Qian, Yigong Shi, Yong Yu
Mutations in the PKD2 gene, which encodes the polycystin-2 (PC2, also called TRPP2) protein, lead to autosomal dominant polycystic kidney disease (ADPKD). As a member of the transient receptor potential (TRP) channel superfamily, PC2 functions as a non-selective cation channel. The activation and regulation of the PC2 channel are largely unknown, and direct binding of small-molecule ligands to this
-
Neuronal IL-17 controls Caenorhabditis elegans developmental diapause through CEP-1/p53 Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-14 Abhishiktha Godthi, Sehee Min, Srijit Das, Johnny Cruz-Corchado, Andrew Deonarine, Kara Misel-Wuchter, Priya D. Issuree, Veena Prahlad
During metazoan development, how cell division and metabolic programs are coordinated with nutrient availability remains unclear. Here, we show that nutrient availability signaled by the neuronal cytokine, ILC-17.1, switches Caenorhabditis elegans development between reproductive growth and dormancy by controlling the activity of the tumor suppressor p53 ortholog, CEP-1. Specifically, upon food availability
-
Identification of a negative-strand RNA virus with natural plant and fungal hosts Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-14 Ruoyin Dai, Shian Yang, Tianxing Pang, Mengyuan Tian, Hao Wang, Dong Zhang, Yunfeng Wu, Hideki Kondo, Ida Bagus Andika, Zhensheng Kang, Liying Sun
The presence of viruses that spread to both plant and fungal populations in nature has posed intriguingly scientific question. We found a negative-strand RNA virus related to members of the family Phenuiviridae , named Valsa mali negative-strand RNA virus 1 (VmNSRV1), which induced strong hypovirulence and was prevalent in a population of the phytopathogenic fungus of apple Valsa canker ( Valsa mali
-
Network of epistatic interactions in an enzyme active site revealed by large-scale deep mutational scanning Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-14 Allison Judge, Banumathi Sankaran, Liya Hu, Murugesan Palaniappan, André Birgy, B. V. Venkataram Prasad, Timothy Palzkill
Cooperative interactions between amino acids are critical for protein function. A genetic reflection of cooperativity is epistasis, which is when a change in the amino acid at one position changes the sequence requirements at another position. To assess epistasis within an enzyme active site, we utilized CTX-M β-lactamase as a model system. CTX-M hydrolyzes β-lactam antibiotics to provide antibiotic
-
Distinct early role of PTEN regulation during HCMV infection of monocytes Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-14 Liudmila S. Chesnokova, Bailey S. Mosher, Heather L. Fulkerson, Hyung W. Nam, Akhalesh K. Shakya, Andrew D. Yurochko
Human cytomegalovirus (HCMV) infection of monocytes is essential for viral dissemination and persistence. We previously identified that HCMV entry/internalization and subsequent productive infection of this clinically relevant cell type is distinct when compared to other infected cells. We showed that internalization and productive infection required activation of epidermal growth factor receptor (EGFR)
-
Predation without direction selectivity Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-14 Jenna Krizan, Xiayingfang Song, Michael J. Fitzpatrick, Ning Shen, Florentina Soto, Daniel Kerschensteiner
Across the animal kingdom, visual predation relies on motion-sensing neurons in the superior colliculus (SC) and its orthologs. These neurons exhibit complex stimulus preferences, including direction selectivity, which is thought to be critical for tracking the unpredictable escape routes of prey. The source of direction selectivity in the SC is contested, and its contributions to predation have not
-
Structural transitions modulate the chaperone activities of Grp94 Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-14 Yaa S. Amankwah, Yasmeen Fleifil, Erin Unruh, Preston Collins, Yi Wang, Katherine Vitou, Alison Bates, Ikponwmosa Obaseki, Meghana Sugoor, John Paul Alao, Robert M. McCarrick, Daniel T. Gewirth, Indra D. Sahu, Zihai Li, Gary. A. Lorigan, Andrea N. Kravats
Hsp90s are ATP-dependent chaperones that collaborate with co-chaperones and Hsp70s to remodel client proteins. Grp94 is the ER Hsp90 homolog essential for folding multiple secretory and membrane proteins. Grp94 interacts with the ER Hsp70, BiP, although the collaboration of the ER chaperones in protein remodeling is not well understood. Grp94 undergoes large-scale conformational changes that are coupled
-
Large nonlinear optical magnetoelectric response in a noncentrosymmetric magnetic Weyl semimetal Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-14 Kentaro Shoriki, Keigo Moriishi, Yoshihiro Okamura, Kohei Yokoi, Hidetomo Usui, Hiroshi Murakawa, Hideaki Sakai, Noriaki Hanasaki, Yoshinori Tokura, Youtarou Takahashi
Weyl semimetals resulting from either inversion ( P ) or time-reversal ( T ) symmetry breaking have been revealed to show the record-breaking large optical response due to intense Berry curvature of Weyl-node pairs. Different classes of Weyl semimetals with both P and T symmetry breaking potentially exhibit optical magnetoelectric (ME) responses, which are essentially distinct from the previously observed
-
East Asian summer monsoon delivers large abundances of very-short-lived organic chlorine substances to the lower stratosphere Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-14 Laura L. Pan, Elliot L. Atlas, Shawn B. Honomichl, Warren P. Smith, Douglas E. Kinnison, Susan Solomon, Michelle L. Santee, Alfonso Saiz-Lopez, Johannes C. Laube, Bin Wang, Rei Ueyama, James F. Bresch, Rebecca S. Hornbrook, Eric C. Apel, Alan J. Hills, Victoria Treadaway, Katie Smith, Sue Schauffler, Stephen Donnelly, Roger Hendershot, Richard Lueb, Teresa Campos, Silvia Viciani, Francesco D’Amato
Deep convection in the Asian summer monsoon is a significant transport process for lifting pollutants from the planetary boundary layer to the tropopause level. This process enables efficient injection into the stratosphere of reactive species such as chlorinated very-short-lived substances (Cl-VSLSs) that deplete ozone. Past studies of convective transport associated with the Asian summer monsoon
-
On-the-fly Raman microscopy guaranteeing the accuracy of discrimination Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-14 Koji Tabata, Hiroyuki Kawagoe, J. Nicholas Taylor, Kentaro Mochizuki, Toshiki Kubo, Jean-Emmanuel Clement, Yasuaki Kumamoto, Yoshinori Harada, Atsuyoshi Nakamura, Katsumasa Fujita, Tamiki Komatsuzaki
Accelerating the measurement for discrimination of samples, such as classification of cell phenotype, is crucial when faced with significant time and cost constraints. Spontaneous Raman microscopy offers label-free, rich chemical information but suffers from long acquisition time due to extremely small scattering cross-sections. One possible approach to accelerate the measurement is by measuring necessary
-
Thermodynamic properties and enhancement of diamagnetism in nitrogen doped lutetium hydride synthesized at high pressure Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-14 Yifeng Han, Yunbo Ou, Hualei Sun, Jan Kopaczek, Gerson J. Leonel, Xin Guo, Benjamin L. Brugman, Kurt Leinenweber, Hongwu Xu, Meng Wang, Sefaattin Tongay, Alexandra Navrotsky
Nitrogen doped lutetium hydride has drawn global attention in the pursuit of room-temperature superconductivity near ambient pressure and temperature. However, variable synthesis techniques and uncertainty surrounding nitrogen concentration have contributed to extensive debate within the scientific community about this material and its properties. We used a solid-state approach to synthesize nitrogen
-
Structural insights reveal interplay between LAG-3 homodimerization, ligand binding, and function Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-14 John L. Silberstein, Jasper Du, Kun-Wei Chan, Jessica A. Frank, Irimpan I. Mathews, Yong Bin Kim, Jia You, Qiao Lu, Jia Liu, Elliot A. Philips, Phillip Liu, Eric Rao, Daniel Fernandez, Grayson E. Rodriguez, Xiang-Peng Kong, Jun Wang, Jennifer R. Cochran
Lymphocyte activation gene-3 (LAG-3) is an inhibitory receptor expressed on activated T cells and an emerging immunotherapy target. Domain 1 (D1) of LAG-3, which has been purported to directly interact with major histocompatibility complex class II (MHCII) and fibrinogen-like protein 1 (FGL1), has been the major focus for the development of therapeutic antibodies that inhibit LAG-3 receptor-ligand
-
Epidermal growth factor receptor (EGFR) is a target of the tumor-suppressor E3 ligase FBXW7 Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-14 Matteo Boretto, Maarten H. Geurts, Shashank Gandhi, Ziliang Ma, Nadzeya Staliarova, Martina Celotti, Sangho Lim, Gui-Wei He, Rosemary Millen, Else Driehuis, Harry Begthel, Lidwien Smabers, Jeanine Roodhart, Johan van Es, Wei Wu, Hans Clevers
FBXW7 is an E3 ubiquitin ligase that targets proteins for proteasome-mediated degradation and is mutated in various cancer types. Here, we use CRISPR base editors to introduce different FBXW7 hotspot mutations in human colon organoids. Functionally, FBXW7 mutation reduces EGF dependency of organoid growth by ~10,000-fold. Combined transcriptomic and proteomic analyses revealed increased EGFR protein
-
DevOps Metrics and KPIs: A Multivocal Literature Review ACM Comput. Surv. (IF 16.6) Pub Date : 2024-03-13 Ricardo Amaro, Rúben Pereira, Miguel Mira da Silva
Context: Information Technology (IT) organizations are aiming to implement DevOps capabilities in order to fulfill market, customers and internal needs. While many are successful with DevOps implementation, others still have difficulty to measure DevOps success in their organization. As a result, the effectiveness of assessing DevOps remains erratic. This emphasizes the need to withstand management
-
Knowledge Graph Embedding: A Survey from the Perspective of Representation Spaces ACM Comput. Surv. (IF 16.6) Pub Date : 2024-03-13 Jiahang Cao, Jinyuan Fang, Zaiqiao Meng, Shangsong Liang
Knowledge graph embedding (KGE) is an increasingly popular technique that aims to represent entities and relations of knowledge graphs into low-dimensional semantic spaces for a wide spectrum of applications such as link prediction, knowledge reasoning and knowledge completion. In this article, we provide a systematic review of existing KGE techniques based on representation spaces. Particularly, we
-
Symbolic Knowledge Extraction and Injection with Sub-symbolic Predictors: A Systematic Literature Review ACM Comput. Surv. (IF 16.6) Pub Date : 2024-03-13 Giovanni Ciatto, Federico Sabbatini, Andrea Agiollo, Matteo Magnini, Andrea Omicini
In this article, we focus on the opacity issue of sub-symbolic machine learning predictors by promoting two complementary activities—symbolic knowledge extraction (SKE) and symbolic knowledge injection (SKI)—from and into sub-symbolic predictors. We consider as symbolic any language being intelligible and interpretable for both humans and computers. Accordingly, we propose general meta-models for both
-
Faster nonconvex low-rank matrix learning for image low-level and high-level vision: A unified framework Inform. Fusion (IF 18.6) Pub Date : 2024-03-13 Hengmin Zhang, Jian Yang, Jianjun Qian, Chen Gong, Xin Ning, Zhiyuan Zha, Bihan Wen
This study introduces a unified approach to tackle challenges in both low-level and high-level vision tasks for image processing. The framework integrates faster nonconvex low-rank matrix computations and continuity techniques to yield efficient and high-quality results. In addressing real-world image complexities like noise, variations, and missing data, the framework exploits the intrinsic low-rank
-
Sarcasm driven by sentiment: A sentiment-aware hierarchical fusion network for multimodal sarcasm detection Inform. Fusion (IF 18.6) Pub Date : 2024-03-13 Hao Liu, Runguo Wei, Geng Tu, Jiali Lin, Cheng Liu, Dazhi Jiang
Sarcasm is a form of sentiment expression that highlights the disparity between a person’s true intentions and the content they explicitly present. With the exponential increase in multimodal data on social platforms, the detection of sarcasm across various modes has become a pivotal area of research. Although previous studies have extensively examined multimodal feature extraction, fusion, and the
-
Bayesian Optimisation for Quality Diversity Search With Coupled Descriptor Functions IEEE T. Evolut. Comput. (IF 14.3) Pub Date : 2024-03-13 Paul Kent, Adam Gaier, Jean-Baptiste Mouret, Juergen Branke
-
Competitive Multitasking for Computational Resource Allocation in Evolutionary Constrained Multi-Objective Optimization IEEE T. Evolut. Comput. (IF 14.3) Pub Date : 2024-03-13 Xiaoliang Chu, Fei Ming, Wenyin Gong
-
Multiple retinal isomerizations during the early phase of the bestrhodopsin photoreaction Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-13 Spyridon Kaziannis, Matthias Broser, Ivo H. M. van Stokkum, Jakub Dostal, Wayne Busse, Arno Munhoven, Cesar Bernardo, Miroslav Kloz, Peter Hegemann, John T. M. Kennis
Bestrhodopsins constitute a class of light-regulated pentameric ion channels that consist of one or two rhodopsins in tandem fused with bestrophin ion channel domains. Here, we report on the isomerization dynamics in the rhodopsin tandem domains of Phaeocystis antarctica bestrhodopsin, which binds all-trans retinal Schiff-base (RSB) absorbing at 661 nm and, upon illumination, converts to the meta-stable
-
RN7SL1 may be translated under oncogenic conditions Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-13 Tomoaki Hara, Sikun Meng, Yoshiko Tsuji, Yasuko Arao, Yoshiko Saito, Hiromichi Sato, Daisuke Motooka, Shizuka Uchida, Hideshi Ishii
RN7SL1 (RNA component of signal recognition particle 7SL1), a component of the signal recognition particle, is a non-coding RNA possessing a small ORF (smORF). However, whether it is translated into peptides is unknown. Here, we generated the RN7SL1-Green Fluorescent Protein (GFP) gene, in which the smORF of RN7SL1 was replaced by GFP, introduced it into 293T cells, and observed cells emitting GFP
-
A type I interferon regulatory network for human plasmacytoid dendritic cells based on heparin, membrane-bound and soluble BDCA-2 Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-13 Francisco Venegas-Solis, Laura Staliunaite, Elisa Rudolph, Carina Chan-Song Münch, Philipp Yu, Sven-A. Freibert, Takahiro Maeda, Christine L. Zimmer, Christian Möbs, Christian Keller, Andreas Kaufmann, Stefan Bauer
Plasmacytoid dendritic cells (pDCs) produce type I interferons (IFNs) after sensing viral/bacterial RNA or DNA by toll-like receptor (TLR) 7 or TLR9, respectively. However, aberrant pDCs activation can cause adverse effects on the host and contributes to the pathogenesis of type I IFN-related autoimmune diseases. Here, we show that heparin interacts with the human pDCs-specific blood dendritic cell
-
Grain boundary plasticity initiated by excess volume Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-13 Qi Zhu, Qingkun Zhao, Qishan Huang, Yingbin Chen, Subra Suresh, Wei Yang, Ze Zhang, Haofei Zhou, Huajian Gao, Jiangwei Wang
Grain boundaries (GBs) serve not only as strong barriers to dislocation motion, but also as important carriers to accommodate plastic deformation in crystalline solids. During deformation, the inherent excess volume associated with loose atomic packing in GBs brings about a microscopic degree of freedom that can initiate GB plasticity, which is beyond the classic geometric description of GBs. However
-
Absence of chromosome axis protein recruitment prevents meiotic recombination chromosome-wide in the budding yeast Lachancea kluyveri Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-13 Sylvain Legrand, Asma Saifudeen, Hélène Bordelet, Julien Vernerey, Arnaud Guille, Amaury Bignaud, Agnès Thierry, Laurent Acquaviva, Maxime Gaudin, Aurore Sanchez, Dominic Johnson, Anne Friedrich, Joseph Schacherer, Matthew J. Neale, Valérie Borde, Romain Koszul, Bertrand Llorente
Meiotic recombination shows broad variations across species and along chromosomes and is often suppressed at and around genomic regions determining sexual compatibility such as mating type loci in fungi. Here, we show that the absence of Spo11-DSBs and meiotic recombination on Lakl0C-left, the chromosome arm containing the sex locus of the Lachancea kluyveri budding yeast, results from the absence
-
Harmonizing the cyano-group and Na to enhance selective photocatalytic O 2 activation on carbon nitride for refractory pollutant degradation Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-13 Mingkai Xu, Ruizhao Wang, Haoyang Fu, Yanbiao Shi, Lan Ling
Manipulating exciton dissociation and charge-carrier transfer processes to selectively generate free radicals of more robust photocatalytic oxidation capacity for mineralizing refractory pollutants remains challenging. Herein, we propose a strategy by simultaneously introducing the cyano-group and Na into graphitic carbon nitride (CN) to obtain CN-Cy-Na, which makes the charge-carrier transfer pathways
-
A tale of two topological isomers: Uptuning [Fe IV (O)(Me 4 cyclam)] 2+ for olefin epoxidation Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-13 Bittu Chandra, Faiza Ahsan, Yuan Sheng, Marcel Swart, Lawrence Que
TMC- anti and TMC- syn, the two topological isomers of [Fe IV (O)(TMC)(CH 3 CN)] 2+ (TMC = 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane, or Me 4 cyclam), differ in the orientations of their Fe IV =O units relative to the four methyl groups of the TMC ligand framework. The Fe IV =O unit of TMC- anti points away from the four methyl groups, while that of TMC- syn is surrounded by the methyl
-
4D microvelocimetry reveals multiphase flow field perturbations in porous media Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-13 Tom Bultreys, Sharon Ellman, Christian M. Schlepütz, Matthieu N. Boone, Gülce Kalyoncu Pakkaner, Shan Wang, Mostafa Borji, Stefanie Van Offenwert, Niloofar Moazami Goudarzi, Wannes Goethals, Chandra Widyananda Winardhi, Veerle Cnudde
Many environmental and industrial processes depend on how fluids displace each other in porous materials. However, the flow dynamics that govern this process are still poorly understood, hampered by the lack of methods to measure flows in optically opaque, microscopic geometries. We introduce a 4D microvelocimetry method based on high-resolution X-ray computed tomography with fast imaging rates (up
-
Interpreting chemisorption strength with AutoML-based feature deletion experiments Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-13 Zhuo Li, Changquan Zhao, Haikun Wang, Yanqing Ding, Yechao Chen, Philippe Schwaller, Ke Yang, Cheng Hua, Yulian He
The chemisorption energy of reactants on a catalyst surface, E ads , is among the most informative characteristics of understanding and pinpointing the optimal catalyst. The intrinsic complexity of catalyst surfaces and chemisorption reactions presents significant difficulties in identifying the pivotal physical quantities determining E ads . In response to this, the study proposes a methodology, the
-
Balance and imbalance in biogeochemical cycles reflect the operation of closed, exchange, and open sets Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-13 Preston Cosslett Kemeny, Mark A. Torres, Woodward W. Fischer, Clara L. Blättler
Biogeochemical reactions modulate the chemical composition of the oceans and atmosphere, providing feedbacks that sustain planetary habitability over geological time. Here, we mathematically evaluate a suite of biogeochemical processes to identify combinations of reactions that stabilize atmospheric carbon dioxide by balancing fluxes of chemical species among the ocean, atmosphere, and geosphere. Unlike
-
Predictive phage therapy for Escherichia coli urinary tract infections: Cocktail selection for therapy based on machine learning models Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-13 Marianne Keith, Alba Park de la Torriente, Antonia Chalka, Adriana Vallejo-Trujillo, Sean P. McAteer, Gavin K. Paterson, Alison S. Low, David L. Gally
This study supports the development of predictive bacteriophage (phage) therapy: the concept of phage cocktail selection to treat a bacterial infection based on machine learning (ML) models. For this purpose, ML models were trained on thousands of measured interactions between a panel of phage and sequenced bacterial isolates. The concept was applied to Escherichia coli associated with urinary tract
-
H 2 S preconditioning induces long-lived perturbations in O 2 metabolism Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-13 David A. Hanna, Jutta Diessl, Arkajit Guha, Roshan Kumar, Anthony Andren, Costas Lyssiotis, Ruma Banerjee
Hydrogen sulfide exposure in moderate doses can induce profound but reversible hypometabolism in mammals. At a cellular level, H 2 S inhibits the electron transport chain (ETC), augments aerobic glycolysis, and glutamine-dependent carbon utilization via reductive carboxylation; however, the durability of these changes is unknown. We report that despite its volatility, H 2 S preconditioning increases
-
Unsupervised identification of significant lineages of SARS-CoV-2 through scalable machine learning methods Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-13 Roberto Cahuantzi, Katrina A. Lythgoe, Ian Hall, Lorenzo Pellis, Thomas House
Since its emergence in late 2019, SARS-CoV-2 has diversified into a large number of lineages and caused multiple waves of infection globally. Novel lineages have the potential to spread rapidly and internationally if they have higher intrinsic transmissibility and/or can evade host immune responses, as has been seen with the Alpha, Delta, and Omicron variants of concern. They can also cause increased
-
High-throughput measurement of elastic moduli of microfibers by rope coiling Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-13 Yuan Liu, Jack H. Y. Lo, Janine K. Nunes, Howard A. Stone, Ho Cheung Shum
There are many fields where it is of interest to measure the elastic moduli of tiny fragile fibers, such as filamentous bacteria, actin filaments, DNA, carbon nanotubes, and functional microfibers. The elastic modulus is typically deduced from a sophisticated tensile test under a microscope, but the throughput is low and limited by the time-consuming and skill-intensive sample loading/unloading. Here
-
A comprehensive review and new taxonomy on superpixel segmentation ACM Comput. Surv. (IF 16.6) Pub Date : 2024-03-12 Isabela Borlido Barcelos, Felipe de Castro Belém, Leonardo de Melo João, Zenilton K. G. do Patrocínio Jr., Alexandre Xavier Falcão, Silvio Jamil Ferzoli Guimarães
Superpixel segmentation consists of partitioning images into regions composed of similar and connected pixels. Its methods have been widely used in many computer vision applications since it allows for reducing the workload, removing redundant information, and preserving regions with meaningful features. Due to the rapid progress in this area, the literature fails to catch up on more recent works among
-
A novel multi-criteria conflict evidence combination method and its application to pattern recognition Inform. Fusion (IF 18.6) Pub Date : 2024-03-12 Yilin Dong, Ningning Jiang, Rigui Zhou, Changming Zhu, Lei Cao, Tianyu Liu, Yuzhuo Xu, Xinde Li
In recent years, the Dempster–Shafer Theory (DST) has been widely applied in areas such as target classification and multi-modal fusion due to its advantages in uncertain reasoning. However, in DST, when there exists highly conflicts between Sources of Evidence (SoEs), it often leads to counterintuitive fusion results, thereby affecting the performance of the final fused decision-making. To eliminate
-
Aerosolization of viable Mycobacterium tuberculosis bacilli by tuberculosis clinic attendees independent of sputum-Xpert Ultra status Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-12 Benjamin Patterson, Ryan Dinkele, Sophia Gessner, Anastasia Koch, Zeenat Hoosen, Vanessa January, Bryan Leonard, Andrea McKerry, Ronnett Seldon, Andiswa Vazi, Sabine Hermans, Frank Cobelens, Digby F. Warner, Robin Wood
Potential Mycobacterium tuberculosis ( Mtb ) transmission during different pulmonary tuberculosis (TB) disease states is poorly understood. We quantified viable aerosolized Mtb from TB clinic attendees following diagnosis and through six months’ follow-up thereafter. Presumptive TB patients (n=102) were classified by laboratory, radiological, and clinical features into Group A: Sputum-Xpert Ultra-positive
-
The training process of many deep networks explores the same low-dimensional manifold Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-12 Jialin Mao, Itay Griniasty, Han Kheng Teoh, Rahul Ramesh, Rubing Yang, Mark K. Transtrum, James P. Sethna, Pratik Chaudhari
We develop information-geometric techniques to analyze the trajectories of the predictions of deep networks during training. By examining the underlying high-dimensional probabilistic models, we reveal that the training process explores an effectively low-dimensional manifold. Networks with a wide range of architectures, sizes, trained using different optimization methods, regularization techniques
-
Weaker land–atmosphere coupling in global storm-resolving simulation Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-03-12 Junhong Lee, Cathy Hohenegger
The debate on the sign of the soil moisture–precipitation feedback remains open. On the one hand, studies using global coarse-resolution climate models have found strong positive feedback. However, such models cannot represent convection explicitly. On the other hand, studies using km-scale regional climate models and explicit convection have reported negative feedback. Yet, the large-scale circulation