bluuebunny/crossref_metadata_2025_split huggingface dataset:
Named Entity Recognition Datasets: A Classification Framework
Authors: Zhang Ying , Xiao Gang 
Published: March 2024

AbstractNamed entity recognition as a fundamental task plays a crucial role in accomplishing some of the tasks and applications in natural language processing. In the age of Internet information, as far as computer applications are concerned, a huge proportion of information is stored in structured and unstructured forms and used for language and text processing. Before neural networks were widely used in natural language processing tasks, research in the field of named entity recognition usually focused on leveraging lexical and syntactic knowledge to improve the performance of models or methods. To promote the development of named entity recognition, researchers have been creating named entity recognition datasets through conferences, projects, and competitions for many years, based on various research goals, and training entity recognition models with increasing accuracy on this basis. However, there has not been much exploration of named entity recognition datasets. Particularly, there have been many datasets available since the introduction of the named entity recognition task, but there is no clear framework to summarize the development of these seemingly independent datasets. A closer look at the context of the development of each dataset and the features it contains reveals that these datasets share some common features to varying degrees. In this thesis, we review the development of named entity recognition datasets over the years and describe them in terms of the language of the dataset, the domain of research, the type of entity, the granularity of the entity, and the annotation of the entity. Finally, we provide an idea for the creation of subsequent named entity recognition datasets.
Increasing Trust in Climate Vulnerability Projections
Authors: Ford James D. 
Published: March 2024

AbstractProjecting future trends is emerging as a key focus of community‐based climate vulnerability assessments. In these mostly qualitative studies, understanding of current vulnerability processes is used as a basis for identifying who and what are vulnerable to future changes, where, and why, and characterizing the key drivers of vulnerability and how they might change. Few, if any, of these studies engage with approaches for validating findings, reflecting the difficulties of validating mostly qualitative projections of highly uncertain futures, absence of directly measurable vulnerability outcomes, and lack of data on vulnerability drivers. Given the challenges of projecting future trends, this absence undermines trust in such work and limits opportunities to learn. This paper illustrates, with examples, how validation can be incorporated into the study design of community‐based climate vulnerability assessments through: (a) examination of retrospective projections to assess projection skill, (b) evaluation of projections made for future time periods which have since passed for consistency with what actually happened, (c) comparison of projections with empirical research that attempts to understand and constrain the effects of climate change using observed effects of weather variation, and (d) incorporation of demonstrated “best practices” into projection development, such as acknowledgment of areas of uncertainty, integration of diverse viewpoints, and utilization of multiple sources of information.
Saltation‐Induced Dust Emission of Dust Devils in the Convective Boundary Layer—An LES Study on the Meter Scale
Authors: Klamt J. , Giersch S. , Raasch S. 
Published: March 2024

AbstractDust devils are vertically oriented, columnar vortices that form within the atmospheric convective boundary layer (CBL) of dry regions. They are able to lift a sufficient amount of soil particles including dust to become visible and are considered as a potentially important dust source for the atmosphere. Mineral dust, a key component of atmospheric aerosols, influences the climate by affecting the radiation budget and cloud formation. Current estimates of the contribution of dust devils to the global, regional, and local dust release vary considerably from less than 1% to more than 50%. To address this uncertainty, we perform the highest resolved large‐eddy simulation (LES) study on dust emission in the CBL to date, using the PALM model system and the saltation‐based Air Force Weather Agency (AFWA) dust emission scheme. Our results show that under desert‐like conditions, dust devils are responsible for an average of 5% of regional dust emissions, with temporary maxima of up to 15%. This contrasts with previous measurement‐based (>35%) and LES‐based estimates (∼0.1%). Local emissions of dust devils (up to 10 mg m−2 s−1) are 1–3 orders of magnitude higher than the emission in the surroundings. This makes dust devils important for air quality and visibility. Additionally, our study reveals previously unknown large‐scale convective dust emission patterns. These patterns are tied to the CBL's cellular flow structure and are the main cause of dust release. Contrary to other studies, our findings clarify the important role of saltation‐induced dust emission.
Fabrication of Mie-resonant silicon nanoparticles using laser annealing for surface-enhanced fluorescence spectroscopy
Authors: Fukuta Tatsuya , Kato Ryo , Tanaka Takuo , Yano Taka-aki 
Published: March 2024

AbstractSilicon nanostructures with unique Mie resonances have garnered considerable attention in the field of nanophotonics. Here, we present a simple and efficient method for the fabrication of silicon (Si) nanoparticle substrates using continuous-wave (CW) laser annealing. The resulting silicon nanoparticles exhibit Mie resonances in the visible region, and their resonant wavelengths can be precisely controlled. Notably, laser-annealed silicon nanoparticle substrates show a 60-fold enhancement in fluorescence. This tunable and fluorescence-enhancing silicon nanoparticle platform has tremendous potential for highly sensitive fluorescence sensing and biomedical imaging applications.
Genome-Wide Association Study of Obsessive-Compulsive Symptoms including 33,943 individuals from the general population
Authors: Strom Nora I. , Burton Christie L. , Iyegbe Conrad , Silzer Talisa , Antonyan Lilit , Pool René , Lemire Mathieu , Crowley James J. , Hottenga Jouke-Jan , Ivanov Volen Z. , Larsson Henrik , Lichtenstein Paul , Magnusson Patrik , Rück Christian , Schachar Russell , Wu Hei Man , Cath Danielle , Crosbie Jennifer , Mataix-Cols David , Boomsma Dorret I. , Mattheisen Manuel , Meier Sandra M. , Smit Dirk J. A. , Arnold Paul D. 
Published: March 2024

AbstractWhile 1–2% of individuals meet the criteria for a clinical diagnosis of obsessive-compulsive disorder (OCD), many more (~13–38%) experience subclinical obsessive-compulsive symptoms (OCS) during their life. To characterize the genetic underpinnings of OCS and its genetic relationship to OCD, we conducted the largest genome-wide association study (GWAS) meta-analysis of parent- or self-reported OCS to date (N = 33,943 with complete phenotypic and genome-wide data), combining the results from seven large-scale population-based cohorts from Sweden, the Netherlands, England, and Canada (including six twin cohorts and one cohort of unrelated individuals). We found no genome-wide significant associations at the single-nucleotide polymorphism (SNP) or gene-level, but a polygenic risk score (PRS) based on the OCD GWAS previously published by the Psychiatric Genetics Consortium (PGC-OCD) was significantly associated with OCS (Pfixed = 3.06 × 10−5). Also, one curated gene set (Mootha Gluconeogenesis) reached Bonferroni-corrected significance (Ngenes = 28, Beta = 0.79, SE = 0.16, Pbon = 0.008). Expression of genes in this set is high at sites of insulin mediated glucose disposal. Dysregulated insulin signaling in the etiology of OCS has been suggested by a previous study describing a genetic overlap of OCS with insulin signaling-related traits in children and adolescents. We report a SNP heritability of 4.1% (P = 0.0044) in the meta-analyzed GWAS, and heritability estimates based on the twin cohorts of 33–43%. Genetic correlation analysis showed that OCS were most strongly associated with OCD (rG = 0.72, p = 0.0007) among all tested psychiatric disorders (N = 11). Of all 97 tested phenotypes, 24 showed a significant genetic correlation with OCS, and 66 traits showed concordant directions of effect with OCS and OCD. OCS have a significant polygenic contribution and share genetic risk with diagnosed OCD, supporting the hypothesis that OCD represents the extreme end of widely distributed OCS in the population.
ZBP1 and TRIF trigger lethal necroptosis in mice lacking caspase-8 and TNFR1
Authors: Solon Margaret , Ge Nianfeng , Hambro Shannon , Haller Susan , Jiang Jian , Baca Miriam , Preston Jessica , Maltzman Allie , Wickliffe Katherine E. , Liang Yuxin , Reja Rohit , Nickles Dorothee , Newton Kim , Webster Joshua D. 
Published: March 2024

AbstractNecroptosis is a lytic form of cell death that is mediated by the kinase RIPK3 and the pseudokinase MLKL when caspase-8 is inhibited downstream of death receptors, toll-like receptor 3 (TLR3), TLR4, and the intracellular Z-form nucleic acid sensor ZBP1. Oligomerization and activation of RIPK3 is driven by interactions with the kinase RIPK1, the TLR adaptor TRIF, or ZBP1. In this study, we use immunohistochemistry (IHC) and in situ hybridization (ISH) assays to generate a tissue atlas characterizing RIPK1, RIPK3, Mlkl, and ZBP1 expression in mouse tissues. RIPK1, RIPK3, and Mlkl were co-expressed in most immune cell populations, endothelial cells, and many barrier epithelia. ZBP1 was expressed in many immune populations, but had more variable expression in epithelia compared to RIPK1, RIPK3, and Mlkl. Intriguingly, expression of ZBP1 was elevated in Casp8−/−Tnfr1−/− embryos prior to their succumbing to aberrant necroptosis around embryonic day 15 (E15). ZBP1 contributed to this embryonic lethality because rare Casp8−/−Tnfr1−/−Zbp1−/− mice survived until after birth. Necroptosis mediated by TRIF contributed to the demise of Casp8−/−Tnfr1−/−Zbp1−/− pups in the perinatal period. Of note, Casp8−/−Tnfr1−/−Trif−/−Zbp1−/− mice exhibited autoinflammation and morbidity, typically within 5–7 weeks of being born, which is not seen in Casp8−/−Ripk1−/−Trif−/−Zbp1−/−, Casp8−/−Ripk3−/−, or Casp8−/−Mlkl−/− mice. Therefore, after birth, loss of caspase-8 probably unleashes RIPK1-dependent necroptosis driven by death receptors other than TNFR1.
Ocular and orbital manifestations in VEXAS syndrome
Authors: Abumanhal Muhammad , Leibovitch Igal , Zisapel Michael , Eviatar Tali , Edel Yonatan , Ben Cnaan Ran 
Published: March 2024

Abstract
Background
VEXAS (Vacuoles, E1 enzyme, X-linked, Autoinflammatory, Somatic) is a hematoinflammatory disease that typically affects adults. It results from a somatic mutation of the E1 ubiquitin conjugating enzyme encoded by the UBA1 gene. VEXAS is frequently accompanied by myelodysplastic syndrome (MDS). The purpose of this study is to describe the ocular and orbital manifestations of VEXAS patients in a case series in our medical centre.

Methods
A retrospective chart review was performed for all patients who were diagnosed with VEXAS syndrome in a tertiary medical centre over two years.

Results
Eight patients were identified with VEXAS. In six patients, the diagnosis was confirmed by genomic sequencing. Two patients were identified based on their phenotype. All patients were males. The mean age at diagnosis was 78.7 years. In two patients, the ocular manifestation was the presenting symptom for VEXAS. Seven patients (87.5%) had history of MDS. Systemic inflammation manifestations include: skin rash (n = 5), recurrent fevers (n = 2), relapsing polychondritis (n = 2), pleuritis and pleural effusion (n = 2), poly arteritis nodosa- PAN (n = 1) and thrombophlebitis (n = 1). Seven (87%) patients were presented with periorbital oedema. Three patients showed orbital inflammation. Dacryoadenitis was observed in two patients, and extraocular muscle (EOM) myositis was detected in two patients. Four patients demonstrated ocular inflammation such as: episcleritis, scleritis and anterior uveitis.

Conclusion
ocular manifestations in VEXAS include orbital inflammation, dacryoadenitis, myositis, uveitis, scleritis, episcleritis and periorbital oedema. We recommend that in old male patients, with history of haematological disorder, presenting with ocular symptom, VEXAS investigation should be taken into consideration.
Central retinal artery occlusion: a stroke of the eye
Authors: Chen Celia , Singh Gurfarmaan , Madike Reema , Cugati Sudha 
Published: March 2024

AbstractCentral retinal artery occlusion (CRAO), like a stroke in the brain, is a critical eye condition that requiring urgent medical attention. Patients with CRAO present with acute loss of vision and the visual prognosis is poor with low chance of spontaneous visual recovery. Moreover, the risk of developing ischaemic heart disease and cerebral stroke is increased due to the presence of underlying atherosclerotic risk factors. Currently, there is no officially recommended treatment for CRAO. This review will describe the anatomy, pathophysiology, clinical features of CRAO, as well as exploring existing and potential future approaches for managing the condition.
Autophagy-enhancing ATG16L1 polymorphism is associated with improved clinical outcome and T-cell immunity in chronic HIV-1 infection
Authors: Schreurs Renée R. C. E. , Koulis Athanasios , Booiman Thijs , Boeser-Nunnink Brigitte , Cloherty Alexandra P. M. , Rader Anusca G. , Patel Kharishma S. , Kootstra Neeltje A. , Ribeiro Carla M. S. 
Published: March 2024

AbstractChronic HIV-1 infection is characterized by T-cell dysregulation that is partly restored by antiretroviral therapy. Autophagy is a critical regulator of T-cell function. Here, we demonstrate a protective role for autophagy in HIV-1 disease pathogenesis. Targeted analysis of genetic variation in core autophagy geneATG16L1reveals the previously unidentified rs6861 polymorphism, which correlates functionally with enhanced autophagy and clinically with improved survival of untreated HIV-1-infected individuals. T-cells carryingATG16L1rs6861(TT) genotype display improved antiviral immunity, evidenced by increased proliferation, revamped immune responsiveness, and suppressed exhaustion/immunosenescence features. In-depth flow-cytometric and transcriptional profiling reveal T-helper-cell-signatures unique to rs6861(TT) individuals with enriched regulation of pro-inflammatory networks and skewing towards immunoregulatory phenotype. Therapeutic enhancement of autophagy recapitulates the rs6861(TT)-associated T-cell traits in non-carriers. These data underscore the in vivo relevance of autophagy for longer-lasting T-cell-mediated HIV-1 control, with implications towards development of host-directed antivirals targeting autophagy to restore immune function in chronic HIV-1 infection.
A midbrain GABAergic circuit constrains wakefulness in a mouse model of stress
Authors: Ren Shuancheng , Zhang Cai , Yue Faguo , Tang Jinxiang , Zhang Wei , Zheng Yue , Fang Yuanyuan , Wang Na , Song Zhenbo , Zhang Zehui , Zhang Xiaolong , Qin Han , Wang Yaling , Xia Jianxia , Jiang Chenggang , He Chao , Luo Fenlan , Hu Zhian 
Published: March 2024

AbstractEnhancement of wakefulness is a prerequisite for adaptive behaviors to cope with acute stress, but hyperarousal is associated with impaired behavioral performance. Although the neural circuitries promoting wakefulness in acute stress conditions have been extensively identified, less is known about the circuit mechanisms constraining wakefulness to prevent hyperarousal. Here, we found that chemogenetic or optogenetic activation of GAD2-positive GABAergic neurons in the midbrain dorsal raphe nucleus (DRNGAD2) decreased wakefulness, while inhibition or ablation of these neurons produced an increase in wakefulness along with hyperactivity. Surprisingly, DRNGAD2 neurons were paradoxically wakefulness-active and were further activated by acute stress. Bidirectional manipulations revealed that DRNGAD2 neurons constrained the increase of wakefulness and arousal level in a mouse model of stress. Circuit-specific investigations demonstrated that DRNGAD2 neurons constrained wakefulness via inhibition of the wakefulness-promoting paraventricular thalamus. Therefore, the present study identified a wakefulness-constraining role DRNGAD2 neurons in acute stress conditions.
Efficient excitation and control of integrated photonic circuits with virtual critical coupling
Authors: Hinney Jakob , Kim Seunghwi , Flatt Graydon J. K. , Datta Ipshita , Alù Andrea , Lipson Michal 
Published: March 2024

AbstractCritical coupling in integrated photonic devices enables the efficient transfer of energy from a waveguide to a resonator, a key operation for many applications. This condition is achieved when the resonator loss rate is equal to the coupling rate to the bus waveguide. Carefully matching these quantities is challenging in practice, due to variations in the resonator properties resulting from fabrication and external conditions. Here, we demonstrate that efficient energy transfer to a non-critically coupled resonator can be achieved by tailoring the excitation signal in time. We rely on excitations oscillating at complex frequencies to load an otherwise overcoupled resonator, demonstrating that a virtual critical coupling condition is achieved if the imaginary part of the complex frequency equals the mismatch between loss and coupling rate. We probe a microring resonator with tailored pulses and observe a minimum intensity transmission $$T=0.11$$
T
=
0.11
in contrast to a continuous-wave transmission $$T=0.58$$
T
=
0.58
, corresponding to 8 times enhancement of intracavity intensity. Our technique opens opportunities for enhancing and controlling on-demand light-matter interactions for linear and nonlinear photonic platforms.
Understanding the effect of spatially separated Cu and acid sites in zeolite catalysts on oxidation of methane
Authors: Xiao Peipei , Wang Yong , Wang Lizhuo , Toyoda Hiroto , Nakamura Kengo , Bekhti Samya , Lu Yao , Huang Jun , Gies Hermann , Yokoi Toshiyuki 
Published: March 2024

AbstractUnraveling the effect of spatially separated bifunctional sites on catalytic reactions is significant yet challenging. In this report, we investigate the role of spatial separation on the oxidation of methane in a series of Cu-exchanged aluminosilicate zeolites. Regulation of the bifunctional sites is done either through studying a physical mixture of Cu-exchanged zeolites and acidic zeolites or by systematically varying the Cu and acid density within a family of zeolite materials. We show that separated Cu and acid sites are beneficial for the formation of hydrocarbons while high-density Cu sites, which are closer together, facilitate the production of CO2. By contrast, a balance of the spatial separation of Cu and acid sites shows more favorable formation of methanol. This work will further guide approaches to methane oxidation to methanol and open an avenue for promoting hydrocarbon synthesis using methanol as an intermediate.
Direct observation of a crescent-shape chromosome in expanded Bacillus subtilis cells
Authors: Tišma Miloš , Bock Florian Patrick , Kerssemakers Jacob , Antar Hammam , Japaridze Aleksandre , Gruber Stephan , Dekker Cees 
Published: March 2024

AbstractBacterial chromosomes are folded into tightly regulated three-dimensional structures to ensure proper transcription, replication, and segregation of the genetic information. Direct visualization of chromosomal shape within bacterial cells is hampered by cell-wall confinement and the optical diffraction limit. Here, we combine cell-shape manipulation strategies, high-resolution fluorescence microscopy techniques, and genetic engineering to visualize the shape of unconfined bacterial chromosome in real-time in live Bacillus subtilis cells that are expanded in volume. We show that the chromosomes predominantly exhibit crescent shapes with a non-uniform DNA density that is increased near the origin of replication (oriC). Additionally, we localized ParB and BsSMC proteins – the key drivers of chromosomal organization – along the contour of the crescent chromosome, showing the highest density near oriC. Opening of the BsSMC ring complex disrupted the crescent chromosome shape and instead yielded a torus shape. These findings help to understand the threedimensional organization of the chromosome and the main protein complexes that underlie its structure.
Single [0001]-oriented zinc metal anode enables sustainable zinc batteries
Authors: Zhang Xiaotan , Li Jiangxu , Liu Yanfen , Lu Bingan , Liang Shuquan , Zhou Jiang 
Published: March 2024

AbstractThe optimization of crystalline orientation of a Zn metal substrate to expose more Zn(0002) planes has been recognized as an effective strategy in pursuit of highly reversible Zn metal anodes. However, the lattice mismatch between substrate and overgrowth crystals has hampered the epitaxial sustainability of Zn metal. Herein, we discover that the presence of crystal grains deviating from [0001] orientation within a Zn(0002) metal anode leads to the failure of epitaxial mechanism. The electrodeposited [0001]-uniaxial oriented Zn metal anodes with a single (0002) texture fundamentally eliminate the lattice mismatch and achieve ultra-sustainable homoepitaxial growth. Using high-angle angular dark-filed scanning transmission electron microscopy, we elucidate the homoepitaxial growth of the deposited Zn following the “~ABABAB~” arrangement on the Zn(0002) metal from an atomic-level perspective. Such consistently epitaxial behavior of Zn metal retards dendrite formation and enables improved cycling, even in Zn||NH4V4O10 pouch cells, with a high capacity of 220 mAh g−1 for over 450 cycles. The insights gained from this work on the [0001]-oriented Zn metal anode and its persistently homoepitaxial mechanism pave the way for other metal electrodes with high reversibility.
SANS-CNN: An automated machine learning technique for spaceflight associated neuro-ocular syndrome with astronaut imaging data
Authors: Kamran Sharif Amit , Hossain Khondker Fariha , Ong Joshua , Zaman Nasif , Waisberg Ethan , Paladugu Phani , Lee Andrew G. , Tavakkoli Alireza 
Published: March 2024

AbstractSpaceflight associated neuro-ocular syndrome (SANS) is one of the largest physiologic barriers to spaceflight and requires evaluation and mitigation for future planetary missions. As the spaceflight environment is a clinically limited environment, the purpose of this research is to provide automated, early detection and prognosis of SANS with a machine learning model trained and validated on astronaut SANS optical coherence tomography (OCT) images. In this study, we present a lightweight convolutional neural network (CNN) incorporating an EfficientNet encoder for detecting SANS from OCT images titled “SANS-CNN.” We used 6303 OCT B-scan images for training/validation (80%/20% split) and 945 for testing with a combination of terrestrial images and astronaut SANS images for both testing and validation. SANS-CNN was validated with SANS images labeled by NASA to evaluate accuracy, specificity, and sensitivity. To evaluate real-world outcomes, two state-of-the-art pre-trained architectures were also employed on this dataset. We use GRAD-CAM to visualize activation maps of intermediate layers to test the interpretability of SANS-CNN’s prediction. SANS-CNN achieved 84.2% accuracy on the test set with an 85.6% specificity, 82.8% sensitivity, and 84.1% F1-score. Moreover, SANS-CNN outperforms two other state-of-the-art pre-trained architectures, ResNet50-v2 and MobileNet-v2, in accuracy by 21.4% and 13.1%, respectively. We also apply two class-activation map techniques to visualize critical SANS features perceived by the model. SANS-CNN represents a CNN model trained and validated with real astronaut OCT images, enabling fast and efficient prediction of SANS-like conditions for spaceflight missions beyond Earth’s orbit in which clinical and computational resources are extremely limited.