Topographic influences on the wind-driven exchange between marginal seas and the open ocean

Author Posting. © American Meteorological Society, 2021. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 51(12),(2021): 3663–3678, https://doi.org/10.1175/JPO-D-21-0058.1.The wind-driven exchange through complex ridges and islands between marginal seas and the open ocean is studied using both numerical and analytical models. The models are forced by a steady, spatially uniform northward wind stress intended to represent the large-scale, low-frequency wind patterns typical of the seasonal monsoons in the western Pacific Ocean. There is an eastward surface Ekman transport out of the marginal sea and westward geostrophic inflows into the marginal sea. The interaction between the Ekman transport and an island chain produces strong baroclinic flows along the island boundaries with a vertical depth that scales with the ratio of the inertial boundary layer thickness to the baroclinic deformation radius. The throughflows in the gaps are characterized by maximum transport in the center gap and decreasing transports toward the southern and northern tips of the island chain. An extended island rule theory demonstrates that throughflows are determined by the collective balance between viscosity on the meridional boundaries and the eastern side boundary of the islands. The outflowing transport is balanced primarily by a shallow current that enters the marginal sea along its equatorward boundary. The islands can block some direct exchange and result in a wind-driven overturning cell within the marginal sea, but this is compensated for by eastward zonal jets around the southern and northern tips of the island chain. Topography in the form of a deep slope, a ridge, or shallow shelves around the islands alters the current pathways but ultimately is unable to limit the total wind-driven exchange between the marginal sea and the open ocean.This research is supported in part by the China Scholarship Council (201906330102). H. G. is financially supported by the China Scholarship Council to study at WHOI for 2 years as a guest student. M. A. S. is supported by the National Science Foundation Grant OCE-1922538

Robust model of fresh jujube soluble solids content with near-infrared (NIR) spectroscopy

A robust partial least square (PLS) calibration model with high accuracy and stability was established for the measurement of soluble solids content (SSC) of fresh jujube using near-infrared (NIR) spectroscopytechnique. Fresh jujube samples were collected in different areas of Taigu and Taiyuan cities, central China in 2008 and 2009. A partial least squares (PLS) calibration model was established based on the NIR spectra of 70 fresh jujube samples collected in 2008. A good calibration result was obtained with correlation coefficient (Rc) of 0.9530 and the root mean square error of calibration (RMSEC) of 0.3951 °Brix. Another PLS calibration model was established based on the NIR spectral of 180 samples collected in 2009; it resulted in the Rc of 0.8536 and the RMSEC of 1.1410 °Brix. It could be seen that the accuracy of established PLS models were different when samples harvested in different years were used for the model calibration. In order to improve the accuracy and robustness of model, different numbers (5, 10, 15, 20, 30 and 40) of samples harvested in 2008 were added to the calibration sample set of the model with samples harvested in 2009, respectively. The established PLS models obtained Rc with the range of 0.8846 to 0.8893 and RMSEC with the range of 1.0248 to 0.9645 °Brix. The obtained results werebetter than the result of the model which was established only with samples harvested in 2009. Moreover, the models established using different numbers of added samples had similar results. Therefore, it was concluded that adding samples from another harvest year could improve the accuracy and robustness of the model for SSC prediction of fresh jujube. The overall results proved that the consideration of samples from different harvest places and years would be useful for establishing an accuracy and robustness spectral model.Keywords: Near-infrared (NIR) spectroscopy, Huping jujube, soluble solids content (SSC), partial least squares (PLS), accuracy, stabilit

NQE: N-ary Query Embedding for Complex Query Answering over Hyper-relational Knowledge Graphs

Complex query answering (CQA) is an essential task for multi-hop and logical reasoning on knowledge graphs (KGs). Currently, most approaches are limited to queries among binary relational facts and pay less attention to n-ary facts (n>=2) containing more than two entities, which are more prevalent in the real world. Moreover, previous CQA methods can only make predictions for a few given types of queries and cannot be flexibly extended to more complex logical queries, which significantly limits their applications. To overcome these challenges, in this work, we propose a novel N-ary Query Embedding (NQE) model for CQA over hyper-relational knowledge graphs (HKGs), which include massive n-ary facts. The NQE utilizes a dual-heterogeneous Transformer encoder and fuzzy logic theory to satisfy all n-ary FOL queries, including existential quantifiers, conjunction, disjunction, and negation. We also propose a parallel processing algorithm that can train or predict arbitrary n-ary FOL queries in a single batch, regardless of the kind of each query, with good flexibility and extensibility. In addition, we generate a new CQA dataset WD50K-NFOL, including diverse n-ary FOL queries over WD50K. Experimental results on WD50K-NFOL and other standard CQA datasets show that NQE is the state-of-the-art CQA method over HKGs with good generalization capability. Our code and dataset are publicly available.Comment: Accepted by the 37th AAAI Conference on Artificial Intelligence (AAAI-2023

Genome plasticity of Vibrio parahaemolyticus: microevolution of the 'pandemic group'

<p>Abstract</p> <p>Background</p> <p>Outbreak of <it>V. parahaemolyticus </it>infections occurred since 1996 was linked to a proposed clonal complex, the pandemic group. The whole genome sequence provides an unprecedented opportunity for dissecting genome plasticity and phylogeny of the populations of <it>V. parahaemolyticus</it>. In the present work, a whole-genome cDNA microarray was constructed to compare the genomic contents of a collection of 174 strains of <it>V. parahaemolyticus</it>.</p> <p>Results</p> <p>Genes that present variably in the genome accounted for about 22% of the whole gene pool on the genome. The phylogenetic analysis of microarray data generated a minimum spanning tree that depicted the phylogenetic structure of the 174 strains. Strains were assigned into five complexes (C1 to C5), and those in each complex were related genetically and phylogenetically. C3 and C4 represented highly virulent clinical clones. C2 and C3 constituted two different clonal complexes 'old-O3:K6 clone' and 'pandemic clone', respectively. C3 included all the 39 pandemic strains tested (<it>trh</it>^-, <it>tdh</it>⁺and GS-PCR⁺), while C2 contained 12 pre-1996 'old' O3:K6 strains (<it>trh</it>⁺, <it>tdh</it>^-and GS-PCR^-) tested herein. The pandemic clone (post-1996 'new' O3:K6 and its derivates O4:K68, O1:K25, O1:KUT and O6:K18) might be emerged from the old-O3:K6 clone, which was promoted by acquisition of <it>toxRS</it>/new sequence and genomic islands. A phylogenetic intermediate O3:K6 clade (<it>trh</it>^-, <it>tdh</it>^-and GS-PCR⁺) was identified between the pandemic and old-O3:K6 clones.</p> <p>Conclusion</p> <p>A comprehensive overview of genomic contents in a large collection of global isolates from the microarray-based comparative genomic hybridization data enabled us to construct a phylogenetic structure of <it>V. parahaemolyticus </it>and an evolutionary history of the pandemic group (clone) of this pathogen.</p

Acute and chronic effects of betel quid chewing on brain functional connectivity

Background: The active alkaloid in Betel quid is arecoline. Consumption of betel quid is associated with both acute effects and longer-term addictive effects. Despite growing evidence that betel quid use is linked with altered brain function and connectivity, the neurobiology of this psychoactive substance in initial acute chewing, and long-term dependence, is not clear. Methods: In this observational study, functional magnetic resonance imaging in a resting-state was performed in 24 male betel quid-dependent chewers and 28 male controls prior to and promptly after betel quid chewing. Network-based statistics were employed to determine significant differences in functional connectivity between brain networks for both acute effects and in long-term betel users versus controls. A support vector machine was employed for pattern classification analysis. Results: Before chewing betel quid, higher functional connectivity in betel quid-dependent chewers than in controls was found between the temporal, parietal and frontal brain regions (right medial orbitofrontal cortex, right lateral orbital frontal cortex, right angular gyrus, bilateral inferior temporal gyrus, superior parietal gyrus, and right medial superior frontal gyrus). In controls, the effect of betel quid chewing was significantly increased functional connectivity between the subcortical regions (caudate, putamen, pallidum, and thalamus), and the visual cortex (superior occipital gyrus and right middle occipital gyrus). Conclusion: These findings show that individuals who chronically use betel quid have higher functional connectivity than controls of the orbitofrontal cortex, and inferior temporal and angular gyri. Acute effects of betel quid are to increase the functional connectivity of some visual cortical areas (which may relate to the acute symptoms) and the basal ganglia and thalamus

ChatKBQA: A Generate-then-Retrieve Framework for Knowledge Base Question Answering with Fine-tuned Large Language Models

Knowledge Base Question Answering (KBQA) aims to derive answers to natural language questions over large-scale knowledge bases (KBs), which are generally divided into two research components: knowledge retrieval and semantic parsing. However, three core challenges remain, including inefficient knowledge retrieval, retrieval errors adversely affecting semantic parsing, and the complexity of previous KBQA methods. In the era of large language models (LLMs), we introduce ChatKBQA, a novel generate-then-retrieve KBQA framework built on fine-tuning open-source LLMs such as Llama-2, ChatGLM2 and Baichuan2. ChatKBQA proposes generating the logical form with fine-tuned LLMs first, then retrieving and replacing entities and relations through an unsupervised retrieval method, which improves both generation and retrieval more straightforwardly. Experimental results reveal that ChatKBQA achieves new state-of-the-art performance on standard KBQA datasets, WebQSP, and ComplexWebQuestions (CWQ). This work also provides a new paradigm for combining LLMs with knowledge graphs (KGs) for interpretable and knowledge-required question answering. Our code is publicly available.Comment: Preprin

Text2NKG: Fine-Grained N-ary Relation Extraction for N-ary relational Knowledge Graph Construction

Beyond traditional binary relational facts, n-ary relational knowledge graphs (NKGs) are comprised of n-ary relational facts containing more than two entities, which are closer to real-world facts with broader applications. However, the construction of NKGs still significantly relies on manual labor, and n-ary relation extraction still remains at a course-grained level, which is always in a single schema and fixed arity of entities. To address these restrictions, we propose Text2NKG, a novel fine-grained n-ary relation extraction framework for n-ary relational knowledge graph construction. We introduce a span-tuple classification approach with hetero-ordered merging to accomplish fine-grained n-ary relation extraction in different arity. Furthermore, Text2NKG supports four typical NKG schemas: hyper-relational schema, event-based schema, role-based schema, and hypergraph-based schema, with high flexibility and practicality. Experimental results demonstrate that Text2NKG outperforms the previous state-of-the-art model by nearly 20\% points in the $F_1$ scores on the fine-grained n-ary relation extraction benchmark in the hyper-relational schema. Our code and datasets are publicly available.Comment: Preprin

Epidemiological characteristics analysis of foodborne disease outbreaks caused by takeaway in China’s Mainland from 2010 to 2020

ObjectiveTo analyze the epidemiological characteristics of foodborne disease outbreaks caused by takeaway in China’s Mainland from 2010 to 2020， and put forward relevant regulatory suggestions.MethodsThrough the National Foodborne Disease Outbreak Monitoring System， the data of foodborne disease outbreaks caused by takeaway in China’s Mainland from 2010 to 2020 were collected and analyzed， and descriptive epidemiological characteristics were performed.ResultsA total of 549 foodborne disease outbreaks caused by takeaway were reported in China’s Mainland （except Tibet Autonomous Region） from 2010 to 2020， resulting in 9 285 illnesses and 2 deaths. The largest number of outbreaks and illnesses was in the third quarter， accounting for 41.53% and 44.58% of the total respectively. Except the unknown pathogenic factors， the number of outbreaks and illnesses caused by microbial pathogenic factors were the highest， accounting for 39.16% and 60.26% of the total respectively. Except the unknown suspected food， the number of outbreaks and illnesses caused by mixed food and multiple food were higher， accounting for 21.86% and 15.12% of the outbreaks respectively， and accounting for 20.58% and 13.10% of the number of illnesses respectively. Except the unknown food source， the top 3 food source were school canteens， collective dining delivery units/central kitchens and fast food restaurants， the number of outbreaks accounted for 20.04%， 15.66% and 15.48% respectively， and the number of illnesses accounted for 35.30%， 17.52% and 10.57% respectively. Except the multiple factors and unknown factors， the number of outbreaks caused by improper storage were the highest accounting for 8.74%， and the number of illnesses caused by improper processing accounted for 7.74%.ConclusionMicrobial growth and reproduction due to improper storage and processing is the major cause of foodborne disease outbreaks caused by takeaway. It is suggested that the food safety supervision and administration departments should strengthen the whole process supervision and management of takeaway， establish and ensure catering services strictly abide by the good hygiene operations according to food raw in materials， production， transportation， distribution and other aspects， so as to effectively prevent and control the occurrence foodborne diseases

Secreted nuclear protein DEK regulates hematopoiesis through CXCR2 signaling

The nuclear protein DEK is an endogenous DNA-binding chromatin factor regulating hematopoiesis. DEK is one of only 2 known secreted nuclear chromatin factors, but whether and how extracellular DEK regulates hematopoiesis is not known. We demonstrated that extracellular DEK greatly enhanced ex vivo expansion of cytokine-stimulated human and mouse hematopoietic stem cells (HSCs) and regulated HSC and hematopoietic progenitor cell (HPC) numbers in vivo and in vitro as determined both phenotypically (by flow cytometry) and functionally (through transplantation and colony formation assays). Recombinant DEK increased long-term HSC numbers and decreased HPC numbers through a mechanism mediated by the CXC chemokine receptor CXCR2 and heparan sulfate proteoglycans (HSPGs) (as determined utilizing Cxcr2-/- mice, blocking CXCR2 antibodies, and 3 different HSPG inhibitors) that was associated with enhanced phosphorylation of ERK1/2, AKT, and p38 MAPK. To determine whether extracellular DEK required nuclear function to regulate hematopoiesis, we utilized 2 mutant forms of DEK: one that lacked its nuclear translocation signal and one that lacked DNA-binding ability. Both altered HSC and HPC numbers in vivo or in vitro, suggesting the nuclear function of DEK is not required. Thus, DEK acts as a hematopoietic cytokine, with the potential for clinical applicability

Pathomechanisms of ALS8: altered autophagy and defective RNA binding protein (RBP) homeostasis due to the VAPB P56S mutation.

Mutations in RNA binding proteins (RBPs) and in genes regulating autophagy are frequent causes of familial amyotrophic lateral sclerosis (fALS). The P56S mutation in vesicle-associated membrane protein-associated protein B (VAPB) leads to fALS (ALS8) and spinal muscular atrophy (SMA). While VAPB is primarily involved in the unfolded protein response (UPR), vesicular trafficking and in initial steps of the autophagy pathway, the effect of mutant P56S-VAPB on autophagy regulation in connection with RBP homeostasis has not been explored yet. Examining the muscle biopsy of our index ALS8 patient of European origin revealed globular accumulations of VAPB aggregates co-localised with autophagy markers LC3 and p62 in partially atrophic and atrophic muscle fibres. In line with this skin fibroblasts obtained from the same patient showed accumulation of P56S-VAPB aggregates together with LC3 and p62. Detailed investigations of autophagic flux in cell culture models revealed that P56S-VAPB alters both initial and late steps of the autophagy pathway. Accordingly, electron microscopy complemented with live cell imaging highlighted the impaired fusion of accumulated autophagosomes with lysosomes in cells expressing P56S-VAPB. Consistent with these observations, neuropathological studies of brain and spinal cord of P56S-VAPB transgenic mice revealed signs of neurodegeneration associated with altered protein quality control and defective autophagy. Autophagy and RBP homeostasis are interdependent, as demonstrated by the cytoplasmic mis-localisation of several RBPs including pTDP-43, FUS, Matrin 3 which often sequestered with P56S-VAPB aggregates both in cell culture and in the muscle biopsy of the ALS8 patient. Further confirming the notion that aggregation of the RBPs proceeds through the stress granule (SG) pathway, we found persistent G3BP- and TIAR1-positive SGs in P56S-VAPB expressing cells as well as in the ALS8 patient muscle biopsy. We conclude that P56S-VAPB-ALS8 involves a cohesive pathomechanism of aberrant RBP homeostasis together with dysfunctional autophagy