bluuebunny/crossref_metadata_2025_split huggingface dataset:
Zero-shot visual reasoning through probabilistic analogical mapping
Authors: Webb Taylor , Fu Shuhao , Bihl Trevor , Holyoak Keith J. , Lu Hongjing 
Published: August 2023

AbstractHuman reasoning is grounded in an ability to identify highly abstract commonalities governing superficially dissimilar visual inputs. Recent efforts to develop algorithms with this capacity have largely focused on approaches that require extensive direct training on visual reasoning tasks, and yield limited generalization to problems with novel content. In contrast, a long tradition of research in cognitive science has focused on elucidating the computational principles underlying human analogical reasoning; however, this work has generally relied on manually constructed representations. Here we present visiPAM (visual Probabilistic Analogical Mapping), a model of visual reasoning that synthesizes these two approaches. VisiPAM employs learned representations derived directly from naturalistic visual inputs, coupled with a similarity-based mapping operation derived from cognitive theories of human reasoning. We show that without any direct training, visiPAM outperforms a state-of-the-art deep learning model on an analogical mapping task. In addition, visiPAM closely matches the pattern of human performance on a novel task involving mapping of 3D objects across disparate categories.
Biosynthesized gold nanoparticles that activate Toll-like receptors and elicit localized light-converting hyperthermia for pleiotropic tumor immunoregulation
Authors: Qin Hao , Chen Yang , Wang Zeming , Li Nan , Sun Qing , Lin Yixuan , Qiu Wenyi , Qin Yuting , Chen Long , Chen Hanqing , Li Yiye , Shi Jian , Nie Guangjun , Zhao Ruifang 
Published: August 2023

AbstractManipulating the tumor immune contexture towards a more active state can result in better therapeutic outcomes. Here we describe an easily accessible bacterial biomineralization-generated immunomodulator, which we name Ausome (Au + [exo]some). Ausome comprises a gold nanoparticle core covered by bacterial components; the former affords an inducible hyperthermia effect, while the latter mobilizes diverse immune responses. Multiple pattern recognition receptors actively participate in Ausome-initiated immune responses, which lead to the release of a broad spectrum of pro-inflammatory cytokines and the activation of effector immune cells. Upon laser irradiation, tumor-accumulated Ausome elicits a hyperthermic response, which improves tissue blood perfusion and contributes to enhanced infiltration of immunostimulatory modules, including cytokines and effector lymphocytes. This immune-modulating strategy mediated by Ausome ultimately brings about a comprehensive immune reaction and selectively amplifies the effects of local antitumor immunity, enhancing the efficacy of well-established chemo- or immuno-therapies in preclinical cancer models in female mice.
Human forebrain organoid-based multi-omics analyses of PCCB as a schizophrenia associated gene linked to GABAergic pathways
Authors: Zhang Wendiao , Zhang Ming , Xu Zhenhong , Yan Hongye , Wang Huimin , Jiang Jiamei , Wan Juan , Tang Beisha , Liu Chunyu , Chen Chao , Meng Qingtuan 
Published: August 2023

AbstractIdentifying genes whose expression is associated with schizophrenia (SCZ) risk by transcriptome-wide association studies (TWAS) facilitates downstream experimental studies. Here, we integrated multiple published datasets of TWAS, gene coexpression, and differential gene expression analysis to prioritize SCZ candidate genes for functional study. Convergent evidence prioritized Propionyl-CoA Carboxylase Subunit Beta (PCCB), a nuclear-encoded mitochondrial gene, as an SCZ risk gene. However, the PCCB’s contribution to SCZ risk has not been investigated before. Using dual luciferase reporter assay, we identified that SCZ-associated SNPs rs6791142 and rs35874192, two eQTL SNPs for PCCB, showed differential allelic effects on transcriptional activities. PCCB knockdown in human forebrain organoids (hFOs) followed by RNA sequencing analysis revealed dysregulation of genes enriched with multiple neuronal functions including gamma-aminobutyric acid (GABA)-ergic synapse. The metabolomic and mitochondrial function analyses confirmed the decreased GABA levels resulted from inhibited tricarboxylic acid cycle in PCCB knockdown hFOs. Multielectrode array recording analysis showed that PCCB knockdown in hFOs resulted into SCZ-related phenotypes including hyper-neuroactivities and decreased synchronization of neural network. In summary, this study utilized hFOs-based multi-omics analyses and revealed that PCCB downregulation may contribute to SCZ risk through regulating GABAergic pathways, highlighting the mitochondrial function in SCZ.
Long-read whole-genome analysis of human single cells
Authors: Hård Joanna , Mold Jeff E. , Eisfeldt Jesper , Tellgren-Roth Christian , Häggqvist Susana , Bunikis Ignas , Contreras-Lopez Orlando , Chin Chen-Shan , Nordlund Jessica , Rubin Carl-Johan , Feuk Lars , Michaëlsson Jakob , Ameur Adam 
Published: August 2023

AbstractLong-read sequencing has dramatically increased our understanding of human genome variation. Here, we demonstrate that long-read technology can give new insights into the genomic architecture of individual cells. Clonally expanded CD8+ T-cells from a human donor were subjected to droplet-based multiple displacement amplification (dMDA) to generate long molecules with reduced bias. PacBio sequencing generated up to 40% genome coverage per single-cell, enabling detection of single nucleotide variants (SNVs), structural variants (SVs), and tandem repeats, also in regions inaccessible by short reads. 28 somatic SNVs were detected, including one case of mitochondrial heteroplasmy. 5473 high-confidence SVs/cell were discovered, a sixteen-fold increase compared to Illumina-based results from clonally related cells. Single-cell de novo assembly generated a genome size of up to 598 Mb and 1762 (12.8%) complete gene models. In summary, our work shows the promise of long-read sequencing toward characterization of the full spectrum of genetic variation in single cells.
Diurnal rhythms of wrist temperature are associated with future disease risk in the UK Biobank
Authors: Brooks Thomas G. , Lahens Nicholas F. , Grant Gregory R. , Sheline Yvette I. , FitzGerald Garret A. , Skarke Carsten 
Published: August 2023

AbstractMany chronic disease symptomatologies involve desynchronized sleep-wake cycles, indicative of disrupted biorhythms. This can be interrogated using body temperature rhythms, which have circadian as well as sleep-wake behavior/environmental evoked components. Here, we investigated the association of wrist temperature amplitudes with a future onset of disease in the UK Biobank one year after actigraphy. Among 425 disease conditions (range n = 200-6728) compared to controls (range n = 62,107-91,134), a total of 73 (17%) disease phenotypes were significantly associated with decreased amplitudes of wrist temperature (Benjamini-Hochberg FDR q < 0.05) and 26 (6.1%) PheCODEs passed a more stringent significance level (Bonferroni-correction α < 0.05). A two-standard deviation (1.8° Celsius) lower wrist temperature amplitude corresponded to hazard ratios of 1.91 (1.58-2.31 95% CI) for NAFLD, 1.69 (1.53-1.88) for type 2 diabetes, 1.25 (1.14-1.37) for renal failure, 1.23 (1.17-1.3) for hypertension, and 1.22 (1.11-1.33) for pneumonia (phenome-wide atlas available at http://bioinf.itmat.upenn.edu/biorhythm_atlas/). This work suggests peripheral thermoregulation as a digital biomarker.
An anti-LpqH human monoclonal antibody from an asymptomatic individual mediates protection against Mycobacterium tuberculosis
Authors: Krishnananthasivam Shivankari , Li Hao , Bouzeyen Rania , Shunmuganathan Bhuvaneshwari , Purushotorman Kiren , Liao Xinlei , Du Fengjiao , Friis Claudia Guldager Kring , Crawshay-Williams Felicity , Boon Low Heng , Xinlei Qian , Chan Conrad En Zuo , Sobota Radoslaw , Kozma Mary , Barcelli Valeria , Wang Guirong , Huang Hairong , Floto Andreas , Bifani Pablo , Javid Babak , MacAry Paul A. 
Published: August 2023

AbstractTuberculosis (TB) is an airborne disease caused by Mycobacterium tuberculosis (Mtb). Whilst a functional role for humoral immunity in Mtb protection remains poorly defined, previous studies have suggested that antibodies can contribute towards host defense. Thus, identifying the critical components in the antibody repertoires from immune, chronically exposed, healthy individuals represents an approach for identifying new determinants for natural protection. In this study, we performed a thorough analysis of the IgG/IgA memory B cell repertoire from occupationally exposed, immune volunteers. We detail the identification and selection of a human monoclonal antibody that exhibits protective activity in vivo and show that it targets a virulence factor LpqH. Intriguingly, protection in both human ex vivo and murine challenge experiments was isotype dependent, with most robust protection being mediated via IgG2 and IgA. These data have important implications for our understanding of natural mucosal immunity for Mtb and highlight a new target for future vaccine development.
Shortwave-infrared-light-emitting probes for the in vivo tracking of cancer vaccines and the elicited immune responses
Authors: Ren Fuqiang , Wang Feifei , Baghdasaryan Ani , Li Ying , Liu Haoran , Hsu RuSiou , Wang Chuchu , Li Jiachen , Zhong Yeteng , Salazar Felix , Xu Chun , Jiang Yingying , Ma Zhuoran , Zhu Guanzhou , Zhao Xiang , Wong Kerry Kaili , Willis Richard , Christopher Garcia K. , Wu Anna , Mellins Elizabeth , Dai Hongjie 
Published: August 2023

AbstractTracking and imaging immune cells in vivo non-invasively would offer insights into the immune responses induced by vaccination. Here we report a cancer vaccine consisting of polymer-coated NaErF4/NaYF4 core–shell down-conversion nanoparticles emitting luminescence in the near-infrared spectral window IIb (1,500–1,700 nm in wavelength) and with surface-conjugated antigen (ovalbumin) and electrostatically complexed adjuvant (class-B cytosine–phosphate–guanine). Whole-body wide-field imaging of the subcutaneously injected vaccine in tumour-bearing mice revealed rapid migration of the nanoparticles to lymph nodes through lymphatic vessels, with two doses of the vaccine leading to the complete eradication of pre-existing tumours and to the prophylactic inhibition of tumour growth. The abundance of antigen-specific CD8+ T lymphocytes in the tumour microenvironment correlated with vaccine efficacy, as we show via continuous-wave imaging and lifetime imaging of two intravenously injected near-infrared-emitting probes (CD8+-T-cell-targeted NaYbF4/NaYF4 nanoparticles and H-2Kb/ovalbumin257-264 tetramer/PbS/CdS quantum dots) excited at different wavelengths, and by volumetrically visualizing the three nanoparticles via light-sheet microscopy with structured illumination. Nanoparticle-based vaccines and imaging probes emitting infrared light may facilitate the design and optimization of immunotherapies.
Associations between extracurricular arts activities, school-based arts engagement, and subsequent externalising behaviours in the Early Childhood Longitudinal Study
Authors: Fluharty Meg E. , Bone Jessica K. , Bu Feifei , Sonke Jill K. , Fancourt Daisy , Paul Elise 
Published: August 2023

AbstractAdolescent externalising behaviours are associated with numerous long-term negative outcomes, although most research is intervention-based as opposed to risk reduction. Arts engagement has been associated with numerous beneficial factors linked to externalising behaviours, yet direct evidence linking them in longitudinal studies is lacking. Data from the Early Childhood Longitudinal Study were used, with baseline at 5th grade and outcomes measured at 8th grade. Ordinary least squares (OLS) regression was used to examine individual-level associations between extracurricular and school-based arts engagement with externalising behaviours. OLS regression was also used to examine associations between school-level arts classes and facilities with an administrator-reported index of externalising behaviours in the school. All models were adjusted for sociodemographic factors. Individual-level analyses were clustered by school. At the individual level, engaging in a greater number of extracurricular arts activities was associated with fewer externalising behaviours, although there was no association for school-based arts engagement. There were no school-level associations between arts classes or adequate arts facilities and externalising behaviours. Our results suggest extracurricular arts activities may be beneficial in reducing the risk for externalising behaviours, but the relationship is seen at an individual-level of engagement rather than based on school-level provision or facilities.
Characterization of small abdominal aortic aneurysms' growth status using spatial pattern analysis of aneurismal hemodynamics
Authors: Rezaeitaleshmahalleh Mostafa , Lyu Zonghan , Mu Nan , Zhang Xiaoming , Rasmussen Todd E. , McBane Robert D. , Jiang Jingfeng 
Published: August 2023

AbstractAneurysm hemodynamics is known for its crucial role in the natural history of abdominal aortic aneurysms (AAA). However, there is a lack of well-developed quantitative assessments for disturbed aneurysmal flow. Therefore, we aimed to develop innovative metrics for quantifying disturbed aneurysm hemodynamics and evaluate their effectiveness in predicting the growth status of AAAs, specifically distinguishing between fast-growing and slowly-growing aneurysms. The growth status of aneurysms was classified as fast (≥ 5 mm/year) or slow (< 5 mm/year) based on serial imaging over time. We conducted computational fluid dynamics (CFD) simulations on 70 patients with computed tomography (CT) angiography findings. By converting hemodynamics data (wall shear stress and velocity) located on unstructured meshes into image-like data, we enabled spatial pattern analysis using Radiomics methods, referred to as "Hemodynamics-informatics" (i.e., using informatics techniques to analyze hemodynamic data). Our best model achieved an AUROC of 0.93 and an accuracy of 87.83%, correctly identifying 82.00% of fast-growing and 90.75% of slowly-growing AAAs. Compared with six classification methods, the models incorporating hemodynamics-informatics exhibited an average improvement of 8.40% in AUROC and 7.95% in total accuracy. These preliminary results indicate that hemodynamics-informatics correlates with AAAs' growth status and aids in assessing their progression.
Investigation of microstructural failure in the human cornea through fracture tests
Authors: Chittajallu Sai Naga Sri Harsha , Gururani Himanshu , Tse Kwong Ming , Rath Subha Narayan , Basu Sayan , Chinthapenta Viswanath 
Published: August 2023

AbstractFracture toughness of the human cornea is one of the critical parameters in suture-involved corneal surgeries and the development of bioengineered mimetics of the human cornea. The present article systematically studied the fracture characteristics of the human cornea to evaluate its resistance to tear in the opening (Mode-I) and trouser tear mode (Mode-III). Tear experiments reveal the dependency of the fracture behavior on the notch size and its location created in the corneal specimens. The findings indicate lamellar tear and collagen fiber pull-out as a failure mechanism in trouser tear and opening mode tests, respectively. Experimental results have shown a localized variation of tear behavior in trouser tear mode and indicated an increasing resistance to tear from the corneal center to the periphery. This article demonstrated the complications of evaluating fracture toughness in opening mode and showed that the limbus was weaker than the cornea and sclera against tearing. The overall outcomes of the present study help in designing experiments to understand the toughness of the diseased tissues, understanding the effect of the suturing location and donor placement, and creating numerical models to study parameters affecting corneal replacement surgery.
Analysis of subcellular RNA fractions demonstrates significant genetic regulation of gene expression in human brain post-transcriptionally
Authors: D’Sa Karishma , Guelfi Sebastian , Vandrovcova Jana , Reynolds Regina H. , Zhang David , Hardy John , Botía Juan A. , Weale Michael E. , Taliun Sarah A. Gagliano , Small Kerrin S. , Ryten Mina 
Published: August 2023

AbstractGaining insight into the genetic regulation of gene expression in human brain is key to the interpretation of genome-wide association studies for major neurological and neuropsychiatric diseases. Expression quantitative trait loci (eQTL) analyses have largely been used to achieve this, providing valuable insights into the genetic regulation of steady-state RNA in human brain, but not distinguishing between molecular processes regulating transcription and stability. RNA quantification within cellular fractions can disentangle these processes in cell types and tissues which are challenging to model in vitro. We investigated the underlying molecular processes driving the genetic regulation of gene expression specific to a cellular fraction using allele-specific expression (ASE). Applying ASE analysis to genomic and transcriptomic data from paired nuclear and cytoplasmic fractions of anterior prefrontal cortex, cerebellar cortex and putamen tissues from 4 post-mortem neuropathologically-confirmed control human brains, we demonstrate that a significant proportion of genetic regulation of gene expression occurs post-transcriptionally in the cytoplasm, with genes undergoing this form of regulation more likely to be synaptic. These findings have implications for understanding the structure of gene expression regulation in human brain, and importantly the interpretation of rapidly growing single-nucleus brain RNA-sequencing and eQTL datasets, where cytoplasm-specific regulatory events could be missed.
Unveiling the contourite depositional system in the Vema Fracture Zone (Central Atlantic)
Authors: Borisov Dmitrii G. , Frey Dmitry I. , Ivanova Elena V. , Dmitrevskiy Nikolay N. , Levchenko Oleg V. , Fomin Vladimir V. , Ligi Marco 
Published: August 2023

AbstractA combination of a high sediment input and intense bottom currents often leads to the formation of contourites (sediments deposited or significantly reworked by bottom currents). Both of these components are present in the Vema Fracture Zone valley which is the most important passageway for the distribution of the Antarctic Bottom Water from the West to the North-East of the Atlantic. However, no contourite drifts, moats or contourite channels have been found in this region in more than half a century of research. The prevailing sedimentation paradigm postulates that turbidity currents have predominantly governed sedimentation in this region during the Pleistocene. This work describes the first example of contourite depositional system identified in the Vema Fracture Zone. The discovery was made through detailed high-resolution sub-bottom profiling, as well as numerical modeling and direct measurements of bottom current velocities. Such systems are exceptionally uncommon in fracture zones. This study highlights the importance of further research of contourites along the Vema Fracture Zone based on modern concepts of contourite and mixed depositional systems. The work also emphasizes the need to reevaluate the impact of bottom currents on sedimentation in this region, and particularly in the narrow segments of the fracture zone valley.
Apple metabolism under oxidative stress affects plant cell wall structure and mechanical properties
Authors: Pieczywek Piotr Mariusz , Leszczuk Agata , Kurzyna-Szklarek Magdalena , Cybulska Justyna , Jóźwiak Zbigniew , Rutkowski Krzysztof , Zdunek Artur 
Published: August 2023

AbstractSeveral studies have shown beneficial effects of short exposure to oxidative stress on stored fruit, such as better preservation, increased firmness, preservation of polyphenolic compounds, and reduced risk of postharvest disorders such as bitter pit and superficial scald in apples. In this study the effect of short-term oxidative stress conditions on the physiology of apple fruit was investigated. Apple fruit of three cultivars were exposed to hypoxic storage conditions of various lengths to induce anaerobiosis. The response of apple fruit to short-term oxidative stress was evaluated by means of cell wall immunolabeling and atomic force microscopy. In addition, the antioxidant capacity and antioxidative activity of apple peels was assessed. Through various techniques, it was shown that short-term oxidative stress conditions promote specific enzymatic activity that induces changes in the cell wall of apple fruit cells. Exposure to short-term stress resulted in the remodeling of cell wall pectic polysaccharides, observed as an increase in the size and complexity of extracted oxalate pectin. Structural changes in the cell wall were followed by an increase in Young’s modulus (compressive stiffness of a solid material, expressed as the relationship between stress and axial strain) of the cell wall material. The data presented in this paper show in a novel way how storage under short-term oxidative stress modifies the cell wall of apple fruit at the molecular level.
Simulation and retrofitting of mass exchange networks in fertilizer plants
Authors: Shoaib Abeer M. , Atawia Amr A. , Hassanean Mohamed H. , Bhran Ahmed A. 
Published: August 2023

AbstractThis paper presents a simulation technique for optimizing a hydrogen integration network. By applying this technique, the minimum fresh hydrogen consumption can be determined. Quantitative relationship between sources and sinks streams were studied to get the flow rates of coupled source and sink, hydrogen consumption and hydrogen concentration in each stream. The introduced technique was applied on twelve sources and twelve sinks with any purity of hydrogen concentration. The hydrogen integration network was designed through two steps, the first step considers applying the data given in the LINGO program, while the second step considers using the LINGO results in the introduced excel program to obtain the retrofitted hydrogen integration network. The proposed technique was applied on several case studies to achieve the minimum consumption of fresh hydrogen for the obtained hydrogen integrated networks. The introduced model for simulation and retrofitting of mass exchange networks is easy to understand and the results showed that this model is more efficient for fertilizer, petrochemical and refinery plants.