Large Language Models for Information Retrieval: A Survey

As a primary means of information acquisition, information retrieval (IR) systems, such as search engines, have integrated themselves into our daily lives. These systems also serve as components of dialogue, question-answering, and recommender systems. The trajectory of IR has evolved dynamically from its origins in term-based methods to its integration with advanced neural models. While the neural models excel at capturing complex contextual signals and semantic nuances, thereby reshaping the IR landscape, they still face challenges such as data scarcity, interpretability, and the generation of contextually plausible yet potentially inaccurate responses. This evolution requires a combination of both traditional methods (such as term-based sparse retrieval methods with rapid response) and modern neural architectures (such as language models with powerful language understanding capacity). Meanwhile, the emergence of large language models (LLMs), typified by ChatGPT and GPT-4, has revolutionized natural language processing due to their remarkable language understanding, generation, generalization, and reasoning abilities. Consequently, recent research has sought to leverage LLMs to improve IR systems. Given the rapid evolution of this research trajectory, it is necessary to consolidate existing methodologies and provide nuanced insights through a comprehensive overview. In this survey, we delve into the confluence of LLMs and IR systems, including crucial aspects such as query rewriters, retrievers, rerankers, and readers. Additionally, we explore promising directions within this expanding field

Renin–angiotensin system inhibition is associated with reduced risk of left atrial appendage thrombosis formation in patients with atrial fibrillation

Background: Inhibition of the renin–angiotensin axis can reduce the likelihood of atrial fibrillation (AF). However, the effects of angiotensin-converting-enzyme inhibitors (ACEIs) or angiotensin II receptor blockers (ARBs) on thrombogenicity in AF remain incompletely elucidated. Thisretrospective case-control study was conducted to evaluate whether the use of ACEI or ARB could reduce the incidence of left atrial appendage thrombus (LAAT) and spontaneous echocardiographic contrast (SEC) in patients with AF. Methods: A total of 199 AF patients who received both transesophageal echocardiogram (TEE) and transthoracic echocardiogram (TTE) successively on the same day from 2012 to 2016 were enrolled. Left atrial dimension, maximal left atrial volume (LAVmax), left ventricular end-diastolic dimension, left ventricular ejection fraction, and the ratio of the early transmitral flow velocity and the early mitral annular velocity (E/e’) were determined. Longitudinal LA strain was evaluated using two-dimensional speckle tracking imaging at each LA segment. Peak systolic strain was calculated by averaging total segments. LAAT, LAA emptying flow velocity (LAAeV) and SEC were evaluated by TEE. Risk factors for LAAT and usage of ACEIs or ARBs were recorded. Results: The incidence of LAAT was 27.6%. Among the patients with renin–angiotensin system (RAS) inhibitors, 20.5% were demonstrated to have LAAT, compared with 33.3% in the nonuser group (p = 0.044). LA peak systolic strain and LAAeV were significantly increased in patients with RAS inhibitors compared to the nonuser group (p = 0.002, p = 0.047, respectively). Patients with LAAT had higher CHA2DS2-VASc scores and evident SEC comparedwith those without LAAT (p = 0.000, p = 0.000, respectively). Usage of ACEIs/ARBs and antiplatelet drugs were frequent in patients with LAAT than in those without LAAT (p = 0.044, p = 0.000, respectively). Even after controlling for LAAT-related risk factors (age, body mass index, AF type, hypertension, diabetes mellitus, prior stroke or transient ischemic attack, drinking history and usage of antiplatelet drugs and LAVmax), use of RAS inhibitors remained significantly associated with a lower risk of LAAT (OR = 0.222; 95% CI 0.084–0.585, p = 0.002). Conclusions: This study shows that RAS inhibitors may be effective in reducing the risk of LAAT in patients with AF through atrial reverse remodeling

Uptake of maternal care and childhood immunization among ethnic minority and Han populations in Sichuan province: a study based on the 2003, 2008 and 2013 health service surveys.

BACKGROUND: China has made remarkable progress in maternal and child health (MCH) over the last thirty years, but socio-economic inequalities persist. Ethnicity has become an important determinant of poor MCH outcomes, but little rigorous analytical work has been done in this area. To understand the socio-economic factors that explain ethnic variation in uptake of MCH care, we report the findings from an analysis in Sichuan province. METHODS: We linked data from the 2003, 2008 and 2013 National Health Service Surveys in Sichuan Province. The ethnic disparities in uptake of maternal care (completing 5 antenatal visits, giving birth in hospital and receiving a caesarean section) and childhood immunization (Bacillus Calmette Guerin (BCG), three doses of diphtheria (DPT) and measles immunization) were examined by geographical (Han district/county vs. ethnic minority county) and individual-based (Han women/children vs. ethnic minority women/children) comparisons. We also examined variation by distance to township and county hospitals, women's education, parity and age using weighted multilevel Poisson regressions with random intercept at district/county level. RESULTS: Ethnic inequalities in maternal care were marked, both at the geographical (district/county) and the individual level. The % of births in hospital was 90.7% among women in Han districts, compared to 83.3% among women living in Han counties (crude RR 0.93; 95% CI 0.75-1.15), 53.8% among Han women living in ethnic minority counties (crude RR 0.57; 95% CI 0.36-0.93), and 13.5% among ethnic minority women living in ethnic minority counties (crude RR 0.18; 95% CI 0.06-0.57). Adjusting the analysis for survey year, education, parity and distance to county level hospital weakened the association between geographical/individual ethnicity and uptake of maternity care, but associations remained remarkably strong. Coverage of childhood immunization was much higher than uptake of maternity care, and inequalities by ethnicity were much less pronounced. CONCLUSION: Lessons can be learned from China's successful immunization programme to further reduce inequalities in access to maternity care among ethnic minority populations in remote areas. Bringing the services closer to the women's homes and strengthening health promotion from the township to the village level may encourage more women to seek antenatal care and give birth in hospital

Identification of common signature genes and pathways underlying the pathogenesis association between nonalcoholic fatty liver disease and atherosclerosis

BackgroundAtherosclerosis (AS) is one of the leading causes of the cardio-cerebral vascular incident. The constantly emerging evidence indicates a close association between nonalcoholic fatty liver disease (NAFLD) and AS. However, the exact molecular mechanisms underlying the correlation between these two diseases remain unclear. This study proposed exploring the common signature genes, pathways, and immune cells among AS and NAFLD.MethodsThe common differentially expressed genes (co-DEGs) with a consistent trend were identified via bioinformatic analyses of the Gene Expression Omnibus (GEO) datasets GSE28829 and GSE49541, respectively. Further, the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed. We utilized machine learning algorithms of lasso and random forest (RF) to identify the common signature genes. Then the diagnostic nomogram models and receiver operator characteristic curve (ROC) analyses were constructed and validated with external verification datasets. The gene interaction network was established via the GeneMANIA database. Additionally, gene set enrichment analysis (GSEA), gene set variation analysis (GSVA), and immune infiltration analysis were performed to explore the co-regulated pathways and immune cells.ResultsA total of 11 co-DEGs were identified. GO and KEGG analyses revealed that co-DEGs were mainly enriched in lipid catabolic process, calcium ion transport, and regulation of cytokine. Moreover, three common signature genes (PLCXD3, CCL19, and PKD2) were defined. Based on these genes, we constructed the efficiently predictable diagnostic models for advanced AS and NAFLD with the nomograms, evaluated with the ROC curves (AUC = 0.995 for advanced AS, 95% CI 0.971–1.0; AUC = 0.973 for advanced NAFLD, 95% CI 0.938–0.998). In addition, the AUC of the verification datasets had a similar trend. The NOD-like receptors (NLRs) signaling pathway might be the most crucial co-regulated pathway, and activated CD4 T cells and central memory CD4 T cells were significantly excessive infiltration in advanced NAFLD and AS.ConclusionWe identified three common signature genes (PLCXD3, CCL19, and PKD2), co-regulated pathways, and shared immune features of NAFLD and AS, which might provide novel insights into the molecular mechanism of NAFLD complicated with AS

Reproducible bubble-induced acoustic microstreaming for bead disaggregation and immunoassay in microfluidics

The bead-based immunoassay requires not only efficient mixing but also good control of bead-surface-area-to-sample-volume ratio to realise accurate and reproducible detection of low concentration samples. This paper reports the development of a microfluidic platform with the reproducible and efficient bubble-induced micromixing for bead disaggregation and immunoassay of prostate-specific antigen (PSA). The platform consists of a microfluidic chip with a microchamber and rectangular traps for capturing air bubbles and a home-made controller to generate sound wave using an external piezo transducer. Methods for reproducible bubble formation and bubble size control during mixing are explored. The influence of driving voltage, PDMS thickness and the substrate material on the mixing efficiency is characterised by mixing a fluorescence dye and a buffer solution. The optimised acoustic microstreaming is able to break clusters with hundreds of beads and homogenise individual beads over the microchamber. Immunoassay with efficient micromixing has been applied to PSA immunoassay with greatly reduced detection time. This study provides a practical guide for the design and development of the bubble-induced acoustic micromixers for bead disaggregation and on-chip immunoassays

Development of a novel magnetophoresis-assisted hydrophoresis microdevice for rapid particle ordering

Focusing and ordering of micro- or nanoparticles is an essential ability in microfluidic platforms for bio-sample processing. Hydrophoresis is an effective method utilising hydrodynamic force to focus microparticles, but it is limited by the fixed operational range and the lack of flexibility. Here, we report a work to tune and improve the dynamic range of hydrophoresis device using magnetophoresis. In this work, a novel approach was presented to fabricate the lateral fluidic ports, which allow the flipped chip to remain stable on the stage of microscope. Diamagnetic polystyrene microparticles suspended in a ferrofluidic medium were repelled to the lower level of the channel by negative magnetophoretic force, and then interact with grooves of microchannel to obtain an excellent hydrophoretic ordering. The effects of (i) flow rate, (ii) particle size, (iii) magnetic susceptibility of the medium, and (iv) number of magnets on the particle focusing efficiency were also reported. As the proposed magnetophorsis-assisted hydrophoretic device is tuneable and simple, it holds great potential to be integrated with other microfluidic components to form an integrated sample-to-answer system

The Role of the Dysregulated JNK Signaling Pathway in the Pathogenesis of Human Diseases and Its Potential Therapeutic Strategies: A Comprehensive Review

JNK is named after c-Jun N-terminal kinase, as it is responsible for phosphorylating c-Jun. As a member of the mitogen-activated protein kinase (MAPK) family, JNK is also known as stress-activated kinase (SAPK) because it can be activated by extracellular stresses including growth factor, UV irradiation, and virus infection. Functionally, JNK regulates various cell behaviors such as cell differentiation, proliferation, survival, and metabolic reprogramming. Dysregulated JNK signaling contributes to several types of human diseases. Although the role of the JNK pathway in a single disease has been summarized in several previous publications, a comprehensive review of its role in multiple kinds of human diseases is missing. In this review, we begin by introducing the landmark discoveries, structures, tissue expression, and activation mechanisms of the JNK pathway. Next, we come to the focus of this work: a comprehensive summary of the role of the deregulated JNK pathway in multiple kinds of diseases. Beyond that, we also discuss the current strategies for targeting the JNK pathway for therapeutic intervention and summarize the application of JNK inhibitors as well as several challenges now faced. We expect that this review can provide a more comprehensive insight into the critical role of the JNK pathway in the pathogenesis of human diseases and hope that it also provides important clues for ameliorating disease conditions

Cross-Scale Vector Quantization for Scalable Neural Speech Coding

Bitrate scalability is a desirable feature for audio coding in real-time communications. Existing neural audio codecs usually enforce a specific bitrate during training, so different models need to be trained for each target bitrate, which increases the memory footprint at the sender and the receiver side and transcoding is often needed to support multiple receivers. In this paper, we introduce a cross-scale scalable vector quantization scheme (CSVQ), in which multi-scale features are encoded progressively with stepwise feature fusion and refinement. In this way, a coarse-level signal is reconstructed if only a portion of the bitstream is received, and progressively improves the quality as more bits are available. The proposed CSVQ scheme can be flexibly applied to any neural audio coding network with a mirrored auto-encoder structure to achieve bitrate scalability. Subjective results show that the proposed scheme outperforms the classical residual VQ (RVQ) with scalability. Moreover, the proposed CSVQ at 3 kbps outperforms Opus at 9 kbps and Lyra at 3kbps and it could provide a graceful quality boost with bitrate increase.Comment: INTERSPEECH 2022(Accepted