bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mapping global dynamics of benchmark creation and saturation in artificial intelligence
Authors: Ott Simon , Barbosa-Silva Adriano , Blagec Kathrin , Brauner Jan , Samwald Matthias 
Published: November 2022

AbstractBenchmarks are crucial to measuring and steering progress in artificial intelligence (AI). However, recent studies raised concerns over the state of AI benchmarking, reporting issues such as benchmark overfitting, benchmark saturation and increasing centralization of benchmark dataset creation. To facilitate monitoring of the health of the AI benchmarking ecosystem, we introduce methodologies for creating condensed maps of the global dynamics of benchmark creation and saturation. We curate data for 3765 benchmarks covering the entire domains of computer vision and natural language processing, and show that a large fraction of benchmarks quickly trends towards near-saturation, that many benchmarks fail to find widespread utilization, and that benchmark performance gains for different AI tasks are prone to unforeseen bursts. We analyze attributes associated with benchmark popularity, and conclude that future benchmarks should emphasize versatility, breadth and real-world utility.
The deubiquitinase OTUD1 regulates immunoglobulin production and proteasome inhibitor sensitivity in multiple myeloma
Authors: Vdovin Alexander , Jelinek Tomas , Zihala David , Sevcikova Tereza , Durech Michal , Sahinbegovic Hana , Snaurova Renata , Radhakrishnan Dhwani , Turi Marcello , Chyra Zuzana , Popkova Tereza , Venglar Ondrej , Hrdinka Matous , Hajek Roman , Simicek Michal 
Published: November 2022

AbstractSerum monoclonal immunoglobulin (Ig) is the main diagnostic factor for patients with multiple myeloma (MM), however its prognostic potential remains unclear. On a large MM patient cohort (n = 4146), we observe no correlation between serum Ig levels and patient survival, while amount of intracellular Ig has a strong predictive effect. Focused CRISPR screen, transcriptional and proteomic analysis identify deubiquitinase OTUD1 as a critical mediator of Ig synthesis, proteasome inhibitor sensitivity and tumor burden in MM. Mechanistically, OTUD1 deubiquitinates peroxiredoxin 4 (PRDX4), protecting it from endoplasmic reticulum (ER)-associated degradation. In turn, PRDX4 facilitates Ig production which coincides with the accumulation of unfolded proteins and higher ER stress. The elevated load on proteasome ultimately potentiates myeloma response to proteasome inhibitors providing a window for a rational therapy. Collectively, our findings support the significance of the Ig production machinery as a biomarker and target in the combinatory treatment of MM patients.
Fully-exposed Pt-Fe cluster for efficient preferential oxidation of CO towards hydrogen purification
Authors: Jia Zhimin , Qin Xuetao , Chen Yunlei , Cai Xiangbin , Gao Zirui , Peng Mi , Huang Fei , Xiao Dequan , Wen Xiaodong , Wang Ning , Jiang Zheng , Zhou Wu , Liu Hongyang , Ma Ding 
Published: November 2022

AbstractHydrogen is increasingly being discussed as clean energy for the goal of net-zero carbon emissions, applied in the proton-exchange-membrane fuel cells (PEMFC). The preferential oxidation of CO (PROX) in hydrogen is a promising solution for hydrogen purification to avoid catalysts from being poisoned by the trace amount of CO in hydrogen-rich fuel gas. Here, we report the fabrication of a novel bimetallic Pt-Fe catalyst with ultralow metal loading, in which fully-exposed Pt clusters bonded with neighbor atomically dispersed Fe atoms on the defective graphene surface. The fully-exposed PtFe cluster catalyst could achieve complete elimination of CO through PROX reaction and almost 100% CO selectivity, while maintaining good stability for a long period. It has the mass-specific activity of 6.19 (molCO)*(gPt)−1*h−1at room temperature, which surpasses those reported in literatures. The exhaustive experimental results and theoretical calculations reveal that the construction of fully-exposed bimetallic Pt-Fe cluster catalysts with maximized atomic efficiency and abundant interfacial sites could facilitate oxygen activation on unsaturated Fe species and CO adsorption on electron-rich Pt clusters to hence the probability of CO oxidation, leading to excellent reactivity in practical applications.
Enormous-stiffness-changing polymer networks by glass transition mediated microphase separation
Authors: Chen Lie , Zhao Cong , Huang Jin , Zhou Jiajia , Liu Mingjie 
Published: November 2022

AbstractThe rapid development of flexible electronics and soft robotics has an urgent demand for materials with wide-range switchable stiffness. Here, we report a polymer network that can isochorically and reversibly switch between soft ionogel and rigid plastic accompanied by a gigantic stiffness change from about 600 Pa to 85 MPa. This transition is realized by introducing polymer vitrification to regulate the liquid–liquid phase separation, namely the Berghmans’ point in the phase diagram of binary gel systems. Regulating the Lewis acid-base interactions between polymer and ionic liquids, the stiffness-changing ratio of polymer network can be tuned from 10 to more than 105. These wide-range stiffness-changing ionogels show excellent shape adaptability and reconfigurability, which can enhance the interfacial adhesion between ionogel and electrode by an order of magnitude and reduce interfacial impedance by 75%.
Emergent ferromagnetism and insulator-metal transition in δ-doped ultrathin ruthenates
Authors: Ali Zeeshan , Saghayezhian Mohammad , Wang Zhen , O’Hara Andrew , Shin Donghan , Ge Wenbo , Chan Ying Ting , Zhu Yimei , Wu Weida , Pantelides Sokrates T. , Zhang Jiandi 
Published: November 2022

AbstractHeterostructures of complex transition metal oxides are known to induce extraordinary emergent quantum states that arise from broken symmetry and other discontinuities at interfaces. Here we report the emergence of unusual, thickness-dependent properties in ultrathin CaRuO3 films by insertion of a single isovalent SrO layer (referred to as δ-doping). While bulk CaRuO3 is metallic and nonmagnetic, films thinner than or equal to ~15-unit cells (u.c.) are insulating though still nonmagnetic. However, δ-doping to middle of such CaRuO3 films induces an insulator-to-metal transition and unusual ferromagnetism with strong magnetoresistive behavior. Atomically resolved imaging and density-functional-theory calculations reveal that the whole δ-doped film preserves the bulk-CaRuO3 orthorhombic structure, while appreciable structural and electronic changes are highly localized near the SrO layer. The results highlight delicate nature of magnetic instability in CaRuO3 and subtle effects that can alter it, especially the role of A-site cation in electronic and magnetic structure additional to lattice distortion in ruthenates. It also provides a practical approach to engineer material systems via highly localized modifications in their structure and composition that may offer new routes to the design of oxide electronics.
Hierarchical optofluidic microreactor for water purification using an array of TiO2 nanostructures
Authors: Kim Hyejeong , Kwon Hyunah , Song Ryungeun , Shin Seonghun , Ham So-Young , Park Hee-Deung , Lee Jinkee , Fischer Peer , Bodenschatz Eberhard 
Published: November 2022

AbstractClean water for human consumption is, in many places, a scarce resource, and efficient schemes to purify water are in great demand. Here, we describe a method to dramatically increase the efficiency of a photocatalytic water purification microreactor. Our hierarchical optofluidic microreactor combines the advantages of a nanostructured photocatalyst with light harvesting by base substrates, together with a herringbone micromixer for the enhanced transport of reactants. The herringbone micromixer further improves the reaction efficiency of the nanostructured photocatalyst by generating counter-rotating vortices along the flow direction. In addition, the use of metal-based substrates underneath the nanostructured catalyst increases the purification capacity by improving the light-harvesting efficiency. The photocatalyst is grown from TiO2 as a nanohelix film, which exhibits a large surface-to-volume ratio and a reactive microstructure. We show that the hierarchical structuring with micro- to nanoscale features results in a device with markedly increased photocatalytic activity as compared with a solid unstructured catalyst surface. This is evidenced by the successful degradation of persistent aqueous contaminants, sulfamethoxazole, and polystyrene microplastics. The design can potentially be implemented with solar photocatalysts in flow-through water purification systems.
Stain-free identification of cell nuclei using tomographic phase microscopy in flow cytometry
Authors: Pirone Daniele , Lim Joowon , Merola Francesco , Miccio Lisa , Mugnano Martina , Bianco Vittorio , Cimmino Flora , Visconte Feliciano , Montella Annalaura , Capasso Mario , Iolascon Achille , Memmolo Pasquale , Psaltis Demetri , Ferraro Pietro 
Published: November 2022

AbstractQuantitative phase imaging has gained popularity in bioimaging because it can avoid the need for cell staining, which, in some cases, is difficult or impossible. However, as a result, quantitative phase imaging does not provide the labelling of various specific intracellular structures. Here we show a novel computational segmentation method based on statistical inference that makes it possible for quantitative phase imaging techniques to identify the cell nucleus. We demonstrate the approach with refractive index tomograms of stain-free cells reconstructed using tomographic phase microscopy in the flow cytometry mode. In particular, by means of numerical simulations and two cancer cell lines, we demonstrate that the nucleus can be accurately distinguished within the stain-free tomograms. We show that our experimental results are consistent with confocal fluorescence microscopy data and microfluidic cyto-fluorimeter outputs. This is a remarkable step towards directly extracting specific three-dimensional intracellular structures from the phase contrast data in a typical flow cytometry configuration.
Detection of m6A from direct RNA sequencing using a multiple instance learning framework
Authors: Hendra Christopher , Pratanwanich Ploy N. , Wan Yuk Kei , Goh W. S. Sho , Thiery Alexandre , Göke Jonathan 
Published: November 2022

AbstractRNA modifications such as m6A methylation form an additional layer of complexity in the transcriptome. Nanopore direct RNA sequencing can capture this information in the raw current signal for each RNA molecule, enabling the detection of RNA modifications using supervised machine learning. However, experimental approaches provide only site-level training data, whereas the modification status for each single RNA molecule is missing. Here we present m6Anet, a neural-network-based method that leverages the multiple instance learning framework to specifically handle missing read-level modification labels in site-level training data. m6Anet outperforms existing computational methods, shows similar accuracy as experimental approaches, and generalizes with high accuracy to different cell lines and species without retraining model parameters. In addition, we demonstrate that m6Anet captures the underlying read-level stoichiometry, which can be used to approximate differences in modification rates. Overall, m6Anet offers a tool to capture the transcriptome-wide identification and quantification of m6A from a single run of direct RNA sequencing.
A global dataset of pandemic- and epidemic-prone disease outbreaks
Authors: Torres Munguía Juan Armando , Badarau Florina Cristina , Díaz Pavez Luis Rodrigo , Martínez-Zarzoso Inmaculada , Wacker Konstantin M. 
Published: November 2022

AbstractThis paper presents a new dataset of infectious disease outbreaks collected from the Disease Outbreak News and the Coronavirus Dashboard produced by the World Health Organization. The dataset contains information on 70 infectious diseases and 2227 public health events that occurred over the period from January 1996 to March 2022 in 233 countries and territories around the world. We illustrate the potential use of this dataset to the research community by analysing the spatial distribution of disease outbreaks. We find evidence of spatial clusters of high incidences (“hot spots”) in Africa, America, and Asia. This spatial analysis enables policymakers to identify the regions with the greatest likelihood of suffering from disease outbreaks and, taking into account their degree of preparedness and vulnerability, to develop policies that may help contain the spreading of future outbreaks. Further applications could focus on combining our data with other information sources to study, for instance, the link between environmental, globalization, and/or socioeconomic factors with disease outbreaks.
Bacterial plasmid-associated and chromosomal proteins have fundamentally different properties in protein interaction networks
Authors: Downing Tim , Rahm Alexander 
Published: November 2022

AbstractPlasmids facilitate horizontal gene transfer, which enables the diversification of pathogens into new anatomical and environmental niches, implying that plasmid-encoded genes can cooperate well with chromosomal genes. We hypothesise that such mobile genes are functionally different to chromosomal ones due to this ability to encode proteins performing non-essential functions like antimicrobial resistance and traverse distinct host cells. The effect of plasmid-driven gene gain on protein–protein interaction network topology is an important question in this area. Moreover, the extent to which these chromosomally- and plasmid-encoded proteins interact with proteins from their own groups compared to the levels with the other group remains unclear. Here, we examined the incidence and protein–protein interactions of all known plasmid-encoded proteins across representative specimens from most bacteria using all available plasmids. We found that plasmid-encoded genes constitute ~ 0.65% of the total number of genes per bacterial sample, and that plasmid genes are preferentially associated with different species but had limited taxonomical power beyond this. Surprisingly, plasmid-encoded proteins had both more protein–protein interactions compared to chromosomal proteins, countering the hypothesis that genes with higher mobility rates should have fewer protein-level interactions. Nonetheless, topological analysis and investigation of the protein–protein interaction networks' connectivity and change in the number of independent components demonstrated that the plasmid-encoded proteins had limited overall impact in > 96% of samples. This paper assembled extensive data on plasmid-encoded proteins, their interactions and associations with diverse bacterial specimens that is available for the community to investigate in more detail.
Evidence for compositionality in baboons (Papio papio) through the test case of negation
Authors: Dautriche Isabelle , Buccola Brian , Berthet Melissa , Fagot Joel , Chemla Emmanuel 
Published: November 2022

AbstractCan non-human animals combine abstract representations much like humans do with language? In particular, can they entertain a compositional representation such as ‘not blue’? Across two experiments, we demonstrate that baboons (Papio papio) show a capacity for compositionality. Experiment 1 showed that baboons can entertain negative, compositional, representations: they can learn to associate a cue with iconically related referents (e.g., a blue patch referring to all blue objects), but also to the complement set associated with it (e.g., a blue patch referring to all non-blue objects). Strikingly, Experiment 2 showed that baboons not only learn to associate a cue with iconically related referents, but can learn to associate complex cues (composed of the same cue and an additional visual element) with the complement object set. Thus, they can learn an operation, instantiated by this additional visual element, that can be compositionally combined with previously learned cues. These results significantly reduce any claim that would make the manipulation and combination of abstract representations a solely human privilege.
Simplified inelastic electron tunneling spectroscopy based on low-noise derivatives
Authors: Kesarwani Shankar , Misra Shobhna , Saha Dipankar , Della Rocca Maria Luisa , Roy Indrajit , Ganguly Swaroop , Mahajan Ashutosh 
Published: November 2022

AbstractA standard experimental setup for Inelastic Electron Tunneling Spectroscopy (IETS) performs the measurement of the second derivative of the current with respect to the voltage ($$d^2I/dV^2$$

d
2

I
/
d

V
2

) using a small AC signal and a lock-in based second harmonic detection. This avoids noise arising from direct differentiation of the current-voltage characteristics (I–V) by standard numerical methods. Here we demonstrate a noise-filtering algorithm based on Tikhonov Regularization to obtain IET spectra (i.e. $$d^2I/dV^2$$

d
2

I
/
d

V
2

vs. V) from measured DC I–V curves. This leads to a simple and effective numerical method for IETS extraction. We apply the algorithm to I–V data from a molecular junction and a metal-insulator-semiconductor tunneling device, demonstrating that the computed first/second derivatives have a workable match with those obtained from our lock-in measurements; the computed IET spectral peaks also correlate well with reported experimental ones. Finally, we present a scheme for automated tuning of the algorithm parameters well-suited for the use of this numerical protocol in real applications.
Characteristics of site-specific response using the measured data from seismic accelerometers in Pohang Yeongil New Port under 9.12 and Pohang earthquakes
Authors: Seo Jihye , Won Deokhee 
Published: November 2022

AbstractRecently, medium-sized earthquakes such as the Gyeongju 9.12 earthquake (September 12, 2016, ML = 5.8) and the Pohang earthquake (November 15, 2017, ML = 5.4) occurred in Korea, thereby increasing social concern about earthquakes. Because Korea is not located near the Circum-Pacific Belt, also referred to as the “Ring of Fire”, people in Korea are not used to earthquake disasters. Coastal areas in Korea are lined with multiple mega-cities and major industrial facilities. Most of them constructed on landfill, they have a high threat level to the damage to populations and structures leading to complex disasters in the event of an earthquake. However, studies of seismic hazards in ports is incomplete compared with those of onshore sites. Improving the understanding of seismic hazards and characterizing them catching up with related research from various perspectives being actively conducted. In this study, the site-specific response characteristics of the Pohang International Container Terminal in Pohang Yeongil New Port were analyzed using the S-wave energy of 10 sets of ground motions recorded by seismic accelerometers operated by the Ministry of Oceans and Fisheries based on the horizontal-to-vertical spectral ratio (H/V ratio) method. As a result of analysis, the H/V ratio curves show that the peak frequency values for the target site averages 9 Hz, and the natural period values of the site were preliminarily predicted to average 0.11 s. In addition, site amplification characteristics are different based on the seismic wave calculation method. The result can be used as data for identifying ground dynamic characteristics and verifying the site amplification coefficients and design spectrum in the seismic design.
Loop-mediated isothermal amplification (LAMP) assay for specific and rapid detection of Dickeya fangzhongdai targeting a unique genomic region
Authors: DeLude Anuhea , Wells Riley , Boomla Sherine , Chuang Shu-Cheng , Urena Frank , Shipman Aaron , Rubas Noelle , Kuehu Donna Lee , Bickerton Buster , Peterson Taylor , Dobhal Shefali , Arizala Dario , Klair Diksha , Ochoa-Corona Francisco , Ali Md Emran , Odani Jenee , Bingham Jon-Paul , Jenkins Daniel M. , Fletcher Jacqueline , Stack James P. , Alvarez Anne M. , Arif Mohammad 
Published: November 2022

AbstractDickeya fangzhongdai, a bacterial pathogen of taro (Colocasia esculenta), onion (Allium sp.), and several species in the orchid family (Orchidaceae) causes soft rot and bleeding canker diseases. No field-deployable diagnostic tool is available for specific detection of this pathogen in different plant tissues. Therefore, we developed a field-deployable loop-mediated isothermal amplification (LAMP) assay using a unique genomic region, present exclusively in D. fangzhongdai. Multiple genomes of D. fangzhongdai, and other species of Dickeya, Pectobacterium and unrelated genera were used for comparative genomic analyses to identify an exclusive and conserved target sequence from the major facilitator superfamily (MFS) transporter gene region. This gene region had broad detection capability for D. fangzhongdai and thus was used to design primers for endpoint PCR and LAMP assays. In-silico validation showed high specificity with D. fangzhongdai genome sequences available in the NCBI GenBank genome database as well as the in-house sequenced genome. The specificity of the LAMP assay was determined with 96 strains that included all Dickeya species and Pectobacterium species as well as other closely related genera and 5 hosts; no false positives or false negatives were detected. The detection limit of the assay was determined by performing four sensitivity assays with tenfold serially diluted purified genomic DNA of D. fangzhongdai with and without the presence of crude host extract (taro, orchid, and onion). The detection limit for all sensitivity assays was 100 fg (18–20 genome copies) with no negative interference by host crude extracts. The assays were performed by five independent operators (blind test) and on three instruments (Rotor-Gene, thermocycler and dry bath); the assay results were concordant. The assay consistently detected the target pathogen from artificially inoculated and naturally infected host samples. The developed assay is highly specific for D. fangzhongdai and has applications in routine diagnostics, phytosanitary and seed certification programs, and epidemiological studies.