Xiaohui Yu

• Shanghai University of Engineering Science

Large language models (LLMs) have revolutionized natural language interfaces for databases, particularly in text-to-SQL conversion. However, current approaches often generate unreliable outputs when faced with ambiguity or insufficient context. We present Reliable Text-to-SQL (RTS), a novel framework that enhances query generation reliability by in...

Large language models (LLMs) have revolutionized natural language interfaces for databases, particularly in text-to-SQL conversion. However, current approaches often generate unreliable outputs when faced with ambiguity or insufficient context. We present Reliable Text-to-SQL (RTS), a novel framework that enhances query generation reliability by in...

Video Database Management Systems (VDBMS) leverage advancements in computer vision and deep learning for efficient video data analysis and retrieval. This paper introduces the concept of user-specified Clues, allowing users to incorporate domain-specific knowledge, referred to as Clues, into query optimization. Clues are expressed as Clue types, ea...

The problem of identifying the k -shortest paths (KSPs for short) in a dynamic road network is essential to many location-based services. Road networks are dynamic in the sense that the weights of the edges in the corresponding graph constantly change over time, representing evolving traffic conditions. Very often such services have to process nu...

In recent years, there has been a growing recognition that high-quality training data is crucial for the performance of machine learning models. This awareness has catalyzed both research endeavors and industrial initiatives dedicated to data acquisition to enhance diverse dimensions of model performance. Among these dimensions, model confidence ho...

While selecting the execution plan for a given query based on a single estimated cost is a generally-adopted strategy, it is usually error-prone and fails to comprehensively profile the plan performance. In this work, we complement existing plan selection methods by proposing a new approach named ET, which produces execution time distributions for...

Objective: Gestational transient thyrotoxicosis (GTT) and Graves' disease (GD) are the most common causes of hyperthyroidism during pregnancy. However, few studies have compared pregnancy outcomes of patients who had GTT to those who had GD in the first trimester of pregnancy. Methods: We conducted a prospective, multicenter cohort study in Chin...

Background Multiple endocrine neoplasia type 1 (MEN1) is a hereditary cancer syndrome caused by germline variants in the MEN1 gene located on chromosome 11q13. We found a Chinese woman who had a pancreatic tumor, parathyroid tumor, adrenal tumor, and suspicion of gastrinoma. Case presentation The proband and her immediate family members underwent...

During evolutionary adaptation, the mechanisms for self-regulation are established between the normal growth and development of plants and environmental stress. The phytohormone jasmonate (JA) is a key tie of plant defence and development, and JASMONATE-ZIM DOMAIN (JAZ) repressor proteins are key components in JA signalling pathways. Here, we show...

Recent advances in Computer Vision (CV) algorithms have improved accuracy and efficiency, making video annotations possible with high accuracy. In this paper, we utilize the annotated data provided by such algorithms and construct graph representations to capture both object labels and spatial-temporal relationships of objects in videos. We define...

Background: Metabolic disorders (MDs) and the Metabolic Syndrome (MetS) may be associated with thyroid diseases. The aim of this study was to investigate the relationship between MDs and various types of thyroid nodules (TNs), according to gender. Methods: We analyzed cross-sectional data from the Thyroid Disorders, Iodine Status, and Diabetes E...

Next location prediction is of great importance for many location-based applications and provides essential intelligence to various businesses. In previous studies, a common approach to next location prediction is to learn the sequential transitions with massive historical trajectories based on conditional probability. Nevertheless, due to the time...

The widespread use of positioning devices has generated large-scale trip data, boosting the study of traffic modeling. For instance, New York City Taxi & Limousine Commission regularly releases over 165 million taxi trip records containing the end-point information of each trip every year. Such big datasets provide us potential new perspectives to...

The growing popularity of location-based social networks gives rise to a tremendous amount of social check-ins data, which are broadly used in previous studies to produce dense venue representations for various trajectory mining tasks. In this work, we focus on the interpretability of venue representations, an essential property that existing metho...

Background Metabolic syndrome (MetS) has a potential connection with thyroid disease, but its relationship with thyroid nodules (TNs) is still controversial. This study aims to clarify the relationship between MetS and TNs, and this relationship in the subgroup of gender. Methods The recent nationwide cross-sectional study called Thyroid Disorders...

Maternal subclinical hypothyroidism (SCH) during pregnancy can adversely affect the neurodevelopment of the offspring. The balance of nerve growth factor (NGF)-related tropomyosin receptor kinase A/p75 neurotrophin receptor (TrkA/p75 NTR ) signaling in the hippocampus is important in brain development, and whether it affects cognitive function in m...

In reality, the missing of some traffic data is inevitable due to some unexpected errors, which not only affects traffic management but also hinders the development of traffic data research. In this paper, we propose a novel Imputation Model for traffic Congestion data, CIM for short, based on joint matrix factorization. CIM jointly models the char...

Set similarity search is a problem of central interest to a wide variety of applications such as data cleaning and web search. Past approaches on set similarity search utilize either heavy indexing structures, incurring large search costs or indexes that produce large candidate sets. In this paper, we design a learning-based exact set similarity se...

Background Bilateral lesions are common in papillary thyroid carcinoma (PTC). For patients with unilateral PTC, occult carcinoma that is not detected preoperatively, but pathologically after surgery, might remain in the contralateral lobe. In this situation, inadequate surgical extent could cause relapse and even lead to re-operation. Here, we expl...

Set similarity search is a problem of central interest to a wide variety of applications such as data cleaning and web search. Past approaches on set similarity search utilize either heavy indexing structures, incurring large search costs or indexes that produce large candidate sets. In this paper, we design a learning-based exact set similarity se...

Thyroid carcinoma is a solid malignant tumor that has had a fast-growing incidence in recent years. Our research used thyroid carcinoma gene expression profiling from TCGA (The Cancer Genome Atlas) database to identify differentially expressed ceRNAs. Using the gene expression profiling from 502 carcinoma thyroid tissues and 58 normal thyroid tissu...

The vast advances in Machine Learning (ML) over the last ten years have been powered by the availability of suitably prepared data for training purposes. The future of ML-enabled enterprise hinges on data. As such, there is already a vibrant market offering data annotation services to tailor sophisticated ML models. In this paper, inspired by the r...

The vast advances in Machine Learning over the last ten years have been powered by the availability of suitably prepared data for training purposes. The future of ML-enabled enterprise hinges on data. As such, there is already a vibrant market offering data annotation services to tailor sophisticated ML models. In this paper, we present research on...

Machine Learning (ML) applications are proliferating in the enterprise. Relational data which are prevalent in enterprise applications are typically normalized; as a result, data has to be denormalized via primary/foreign-key joins to be provided as input to ML algorithms. In this paper, we study the implementation of popular nonlinear ML models, G...

Background: Antithyroperoxidase (TPOAb) and antithyroglobulin (TgAb) antibodies are associated with abnormal thyrotropin (TSH) levels. However, the effect of dynamic changes in TPOAb and TgAb on incident abnormal TSH is unknown. Methods: A total of 2,387 euthyroid participants aged 18 years or older from three rural areas in northern China were enr...

Purpose: To determine the diagnostic efficiency of the ATA classification and ultrasound-guided fine-needle aspiration (FNA) results in identifying the risk factors of malignancy, we analyzed the thyroid nodules of patients who underwent thyroidectomy and compared preoperative ATA classifications with FNA results. Methods: We retrospectively analyz...

Primary macronodular adrenal hyperplasia (PMAH) is a rare cause of Cushing syndrome (CS). In many cases of the PMAH family, variant in ARMC5, a putative tumor suppressor gene, are thought to induce the disease. The purpose of this study was to report a large Chinese family, in which a new germline heterozygous variant of ARMC5 (c.52C>T (p.Gln18X))...

Background: Multiple endocrine neoplasia type 1 (MEN1) is a hereditary cancer syndrome caused by germline mutations in the MEN1 gene located on chromosome 11q13. The three main endocrine tissues affected most frequently by tumors in MEN1 are the parathyroid (95%), enteropancreatic neuroendocrine tissues (50%), and anterior pituitary (40%). The purp...

Background: Multiple endocrine neoplasia type 1 (MEN1) is a hereditary cancer syndrome caused by germline mutations in the MEN1 gene located on chromosome 11q13. The three main endocrine tissues affected most frequently by tumors in MEN1 are the parathyroid (95%), enteropancreatic neuroendocrine tissues (50%), and anterior pituitary (40%). The purp...

Background: Multiple endocrine neoplasia type 1 (MEN1) is a hereditary cancer syndrome caused by germline mutations in the MEN1 gene located on chromosome 11q13. The three main endocrine tissues affected most frequently by tumors in MEN1 are the parathyroid (95%), enteropancreatic neuroendocrine tissues (50%), and anterior pituitary (40%). The purp...

The widespread use of positioning devices has given rise to many trajectories, with each having three explicit attributes: user ID , location ID , and time-stamp and an implicit attribute: activity type (akin to “topic” in text mining). To model these trajectories, existing works learn different attribute representations by either introduci...

The widespread use of positioning devices and cameras has given rise to a deluge of trajectory data (e.g., vehicle passage records and check-in data), offering great opportunities for location prediction. One problem that has received much attention recently is predicting next locations for an object given previous locations. Several location predi...

The problem of identifying the k-shortest paths (KSPs for short) in a dynamic road network is essential to many location-based services. Road networks are dynamic in the sense that the weights of the edges in the corresponding graph constantly change over time, representing evolving traffic conditions. Very often such services have to process numer...

Many location-based services are supported by the moving k-nearest neighbour (k-NN) query, which continuously returns the k-nearest data objects for a query point. Most of existing approaches to this problem have focused on a centralized setting, which show poor scalability to work around massive-scale and distributed data sets. In this paper, we p...

Recent advances in social and mobile technology have enabled an abundance of digital traces (in the form of mobile check-ins, association of mobile devices to specific WiFi hotspots, etc.) revealing the physical presence history of diverse sets of entities (e.g., humans, devices, and vehicles). One challenging yet important task is to identify k en...

With the booming of personalized recipe sharing networks (e.g., Yummly), a deluge of recipes from different cuisines could be obtained easily. In this paper, we aim to solve a problem which many home-cooks encounter when searching for recipes online. Namely, finding recipes which best fit a handy set of ingredients while at the same time follow hea...

Next location prediction is of great importance for many location-based applications and provides essential intelligence to business and governments. In existing studies, a common approach to next location prediction is to learn the sequential transitions with massive historical trajectories based on conditional probability. Unfortunately, due to t...

The wide spread use of positioning and photographing devices gives rise to a deluge of traffic trajectory data (e.g., vehicle passage records and taxi trajectory data), with each record having at least three attributes: object ID, location ID, and time-stamp. In this paper, we propose a novel mobility pattern embedding model called MPE to shed the...

Recent advances in Computer Vision and Deep Learning made possible the efficient extraction of a schema from frames of streaming video. As such, a stream of objects and their associated classes along with unique object identifiers derived via object tracking can be generated, providing unique objects as they are captured across frames. In this pape...

S100A12 belongs to the S100 family and acts as a vital regulator in different types of tumors. However, the function of S100A12 in thyroid carcinoma has not yet been investigated. In this study, we analyzed the expression of S100A12 in human papillary thyroid cancer (PTC) samples and two PTC cell lines. In addition, we explored the effects of S100A...

Pigment intensity and patterns are important factors that determine the nutritional and market values of tomato fruits. The acropetal manner of light-dependent anthocyanin accumulation with the highest levels at the stem end of the fruit makes Pro35S:BrTT8 tomato plants an ideal system for investigating the effects of light intensity on anthocyanin...

Neural attention, an emerging technique used to identify important inputs within neural networks, have become increasingly popular in the area of recommender systems. Not only allowing to better identify what defines users and items, attention-based recommender systems are further able to provide accompanying explanations. However, these representa...

The wide spread use of positioning and photographing devices gives rise to a deluge of traffic trajectory data (e.g., vehicle passage records and taxi trajectory data), with each record having at least three attributes: object ID, location ID, and time-stamp. In this paper, we propose a novel mobility pattern embedding model called MPE to shed the...

Key message Overexpression of SlMBP9 reduced auxin biosynthesis and transport, and negatively regulated lateral root formation and apical dominance. Abstract MADS-box transcription factors play a critical role in plant development. In this study, we describe SlMBP9, a novel MADS-box gene that is expressed in the roots of tomato plants. Tomato line...

Recommender systems provide an important tool for users to find interested items from the massive amount of user-generated contents. As user interests often change over time and contents become available in a streaming fashion, it is highly desirable to support real-time recommendation that can adapt to changes in user interests and contents. If we...

Recent advances in social and mobile technology have enabled an abundance of digital traces (in the form of mobile check-ins, association of mobile devices to specific WiFi hotspots, etc.) revealing the physical presence history of diverse sets of entities (e.g., humans, devices, and vehicles). One challenging yet important task is to identify k en...

With the booming of personalized recipe sharing networks (e.g., Yummly), a deluge of recipes from different cuisines could be obtained easily. In this paper, we aim to solve a problem which many home-cooks encounter when searching for recipes online. Namely, finding recipes which best fit a handy set of ingredients while at the same time follow hea...

Using query logs to enhance user experience has been extensively studied in the Web IR literature. However, in the area of keyword search on structured data (relational databases in particular), most existing works have focused on improving search result quality via designing better scoring functions, without giving explicit consideration to query...

The widespread use of positioning devices (e.g., GPS) has given rise to a vast body of human movement data, often in the form of trajectories. Understanding human mobility patterns could benefit many location-based applications. In this paper, we propose a novel generative model called TraLFM via latent factor modeling to mine human mobility patter...

AGAMOUS (AG) MADS-box transcription factors have been shown to play crucial roles in floral organ and fruit development in angiosperms. Here, a tomato AG MADS-box gene, SlMBP3, was isolated. SlMBP3 is preferentially expressed in flowers and early fruit developmental stages in wild type (WT), Nr and rin mutants. Its transcripts are notably accumulat...

Background: The fact that serum thyrotropin (TSH) levels increase with age may influence the diagnosis of thyroid diseases in older adults. This study aimed to establish an age-specific serum TSH reference range, examine the prevalence of thyroid diseases in older adults ≥65 years, and analyze the risk factors. Methods: A cross-sectional study o...

Papillary thyroid cancer is a prevalent endocrine malignancy. Although alterations in glutamine metabolism have been reported in several types of hematological and solid tumors, little is known about the functions of glutamine and glutaminolysis-associated proteins in papillary thyroid cancer. Here, we demonstrated the glutamine dependence of papil...

MADS-box genes have been demonstrated to participate in a number of processes in tomato development, especially fruit ripening. In this study, we reported a novel MADS-box gene, SlMBP15, which is implicated in fruit ripening. Based on statistical analysis, the ripening time of SlMBP15-silenced tomato was delayed by 2–4 days compared with that of th...

Gene information for SlMBP15.

Accession numbers of SlMBP15 and the transcript variants.

Alignment of the protein sequences of SlMBP15 and the transcript variants.

The accession numbers of proteins contained in multiple sequence alignment and phylogenic analysis.

Primers used for Quantitative PCR analysis.

Predicted expression profile of SlMBP15.

The predicted expression profile of SlMBP15 in tissues and cells in tomato fruit.

Background: Pregnant women are highly vulnerable to iron deficiency (ID) due to the increased iron needs during pregnancy. ID decreases circulating thyroid hormone concentrations likely through impairment of iron-dependent thyroid peroxidase. The present study aimed to explore the association between ID and hypothyroxinemia in a retrospective coho...

The problem of short-term travel time estimation has been intensively investigated recently. However, accurate travel time predicting is still a challenge due to dynamic changes of the traffic and the difficulty of extracting urban traffic data features. In this paper, we mainly focus on time shifting feature of urban roads, which represents the im...

Traffic problems have seriously affected people's life quality and urban development, and forecasting short-term traffic congestion is of great importance to both individuals and governments. However, understanding and modeling the traffic conditions can be extremely difficult, and our observations from real traffic data reveal that: 1) similar tra...

Objective: Maternal hypothyroidism during pregnancy can affect the neurodevelopment of their offspring. This study aimed to investigate the effects of maternal subclinical hypothyroidism (SCH) on spatial learning and memory, and its relationship with the apoptotic factors in cerebral cortex of the offspring. Methods: Female adult Wistar rats wer...

The SEPALLATA (SEP) MADS-box transcription factors play essential roles in reproductive growth, especially in floral organ differentiation. Here, SlCMB1, a tomato SEP MADS-box gene, was isolated. SlCMB1 is noticeably expressed in inflorescences and flowers. Its transcript levels were higher in sepals than in other floral organs and decreased during...

Papillary thyroid carcinoma (PTC) is the most common type of endocrine malignancy. HS1-associated protein X-1 (HAX-1) is an anti-apoptotic factor involved in the development of many types of cancer. However, its functional role in human PTC remains unclear. Here we investigated HAX-1 overexpression in human PTC samples and correlated with tumor siz...

Previous studies suggest that GRAS transcription factors act as essential regulators, not only in plant growth and development but also in response to biotic and abiotic stresses. Recently, 53 GRAS proteins have been identified, but only a few of them have been functionally studied in tomato. Here, we isolated a novel GRAS transcription factor SlGR...

Mediator complex, a conserved multi-protein, is necessary for controlling RNA polymerase II (Pol II) transcription in eukaryotes. Given little is known about them in tomato, a tomato Mediator subunit 18 gene was isolated and named SlMED18. To further explore the function of SlMED18, the transgenic tomato plants targeting SlMED18 by RNAi-mediated ge...

Histone deacetylation catalyzed by histone deacetylases is an important type of histone modification. Histone deacetylases affect various processes of plant development and involve in responding to hormones and biotic and abiotic stresses. Here, we report a tomato PRD3/HDA1 histone deacetylase gene, SlHDA5, which is expressed ubiquitously in differ...

Key message: SlHDA3 functions as an inhibitor and regulates tomato fruit ripening and carotenoid accumulation. Post-translational modifications, including histones acetylation, play a pivotal role in the changes of chromatin structure dynamic modulation and gene activity. The regulation of histone acetylation is achieved by the action of histone a...

The basic helix-loop-helix (bHLH) proteins are a large family of transcription factors that control various developmental processes in eukaryotes, but the biological roles of most bHLH proteins are not very clear, especially in tomato. In this study, a PRE-like atypical bHLH gene was isolated and designated as SlPRE2 in tomato. SlPRE2 was highly ex...

Most of the traditional top-k algorithms are based on a single-server setting. They may be highly inefficient and/or cause huge communication overhead when applied to a distributed system environment. Therefore, the problem of top-k monitoring in distributed environments has been intensively investigated recently. This paper studies how to monitor...

JAZ (Jasmonate ZIM-domain) proteins are important repressors in JA signaling pathway. JAZs were proved taking part in various development processes and resistance to biotic and abiotic stresses in Arabiodopsis. However, in tomato, the functional study of JAZs is rare, especially on plant growth and development. Here, a typical tomato JAZ gene, SlJA...

The proliferation of location-based social networks, makes it possible to record human mobility using an array of points-of-interest (POIs). Exploring the semantic meanings of POIs can be of great importance to many urban computing applications, e.g., personalized route recommendation and user trajectory clustering. Nonetheless, such information is...

Histone acetylation and deacetylation play an important role in plant growth and development by chromatin modifications. Regulation of histone acetylation and deacetylation is controlled by histone acetyltransferases and histone deacetylases (HDACs) in different tissues and development stages. Knowledge of the importance of genome stability, transc...

Adverse environmental conditions, such as drought, high salinity, and extreme temperature, severely affect the growth and productivity of crop plants. HD-Zip I transcription factors have been described to be involved in stress responses. In the present study, a novel transcription factor gene, SlHB2, from the HD-Zip I subfamily has been cloned from...

Adverse environmental conditions, such as drought, high salinity and extreme temperature, severely affect the growth and productivity of crop plants. MADS-box transcription factors have been described to participate in stress responses. In our study, a MADS-box transcription factor gene, SlMBP8, has been cloned from tomato. The expression of SlMBP8...

The acetylation levels of histones on lysine residues are regulated by histone acetyltransferases and histone deacetylases, which play an important but understudied role in the control of gene expression in plants. There is an increasing research focus on histone deacetylation in crops, but to date, there is little information regarding tomato. Wit...

The problem of distributed monitoring has been intensively investigated recently. This paper studies monitoring the top k data objects with the largest aggregate numeric values from distributed data streams within a fixed-size monitoring window W, while minimizing communication cost across the network. We propose a novel algorithm, which reallocate...

Image sentiment classification, which aims to predict the polarities of sentiments conveyed by the images, has gained a lot of attention. Most existing methods address this problem by training a general classifier with certain visual features, ignoring the discrepancies across domains. In this paper, we propose a novel weighted co-training method f...

Background: TNF-like weak inducer of apoptosis (TWEAK), its receptor fibroblast growth factor-inducible 14 (Fn14) and its scavenger receptor CD163 (sCD163) have known associations with many autoimmune diseases. However, the role of the TWEAK axis in autoimmune thyroid disease (AITD) remains unclear. Therefore, the aim of this study was to investig...

Key message: Silencing SlAGL6 in tomato leads to fused sepal and green petal by influencing the expression of A-, B-class genes. AGAMOUS-LIKE6 (AGL6) lineage is an important clade MADS-box transcription factor and plays essential roles in various developmental programs especially in flower meristem and floral organ development. Here, we isolated a...

[This corrects the article on p. 578 in vol. 7, PMID: 28018345.].

Although much information regarding the chloroplast and chromoplast biosynthesis has been accumulated in recent years, details of the physiological, biochemical, and molecular differences between green tissues and colorful chromoplast tissues are still poorly understood. In this study, the pigment accumulation, plastid ultrastructure, and the expre...

Keyword search over databases, popularized by keyword search in WWW, allows ordinary users to access database information without the knowledge of structured query languages and database schemas. Most of the previous studies in this area use IR-style ranking, which fail to consider the importance of the query answers. In this paper, we propose CI-R...

Objective Autoimmune thyroid disease (AITD) is an organ-specific disorder due to the interplay between environmental and genetic factors. Toll-like receptors (TLRs) are pattern recognition receptors expressed abundantly on monocytes. There is a paucity of data on TLR expression in AITD. The aim of this study was to examine TLR expression, activatio...

In this paper, a data grouping approach based on convolutional neural network (DGCNN) is proposed for forecasting urban short-term traffic flow. This approach includes the consideration of spatial relations between traffic locations, and utilizes such information to train a convolutional neural network for forecasting. There are three advantages of...