Exploring the Value of Pre-trained Language Models for Clinical Named Entity Recognition

The practice of fine-tuning Pre-trained Language Models (PLMs) from general or domain-specific data to a specific task with limited resources, has gained popularity within the field of natural language processing (NLP). In this work, we re-visit this assumption and carry out an investigation in clinical NLP, specifically Named Entity Recognition on drugs and their related attributes. We compare Transformer models that are trained from scratch to fine-tuned BERT-based LLMs namely BERT, BioBERT, and ClinicalBERT. Furthermore, we examine the impact of an additional CRF layer on such models to encourage contextual learning. We use n2c2-2018 shared task data for model development and evaluations. The experimental outcomes show that 1) CRF layers improved all language models; 2) referring to BIO-strict span level evaluation using macro-average F1 score, although the fine-tuned LLMs achieved 0.83+ scores, the TransformerCRF model trained from scratch achieved 0.78+, demonstrating comparable performances with much lower cost - e.g. with 39.80\% less training parameters; 3) referring to BIO-strict span-level evaluation using weighted-average F1 score, ClinicalBERT-CRF, BERT-CRF, and TransformerCRF exhibited lower score differences, with 97.59\%/97.44\%/96.84\% respectively. 4) applying efficient training by down-sampling for better data distribution further reduced the training cost and need for data, while maintaining similar scores - i.e. around 0.02 points lower compared to using the full dataset. Our models will be hosted at \url{https://github.com/HECTA-UoM/TransformerCRF}Comment: working paper - Large Language Models, Fine-tuning LLMs, Clinical NLP, Medication Mining, AI for Healthcar

Pseudogap and weak multifractality in disordered Mott charge-density-wave insulator

The competition, coexistence and cooperation of various orders in low-dimensional materials like spin, charge, topological orders and charge-density-wave has been one of the most intriguing issues in condensed matter physics. In particular, layered transition metal dichalcogenides provide an ideal platform for studying such an interplay with a notable case of 1${T}$-TaS$_{2}$ featuring Mott-insulating ground state, charge-density-wave, spin frustration and emerging superconductivity together. We investigated local electronic states of Se-substituted 1${T}$-TaS$_{2}$ by scanning tunneling microscopy/spectroscopy (STM/STS), where superconductivity emerges from the unique Mott-CDW state. Spatially resolved STS measurements reveal that an apparent V-shape pseudogap forms at the Fermi Level (E$_{F}$), with the origin of the electronic states splitting and transformation from the Mott states, and the CDW gaps are largely preserved. The formation of the pseudogap has little correlation to the variation of local Se concentration, but appears to be a global characteristics. Furthermore, the correlation length of local density of states (LDOS) diverges at the Fermi energy and decays rapidly at high energies. The spatial correlation shows a power-law decay close to the Fermi energy. Our statistics analysis of the LDOS indicates that our system exhibits weak multifractal behavior of the wave functions. These findings strongly support a correlated metallic state induced by disorder in our system, which provides an new insight into the novel mechanism of emerging superconductivity in the two-dimensional correlated electronic systems

Vasohibin-1 suppresses colon cancer

Vasohibin-1 (VASH1) is an endogenous angiogenesis inhibitor. However, the clinical relevance of VASH1 in colon cancer and its regulations on cancer angiogenesis and cancer cell biological characteristics are still unknown. Here we showed that stromal VASH1 levels were negatively correlated with tumor size, advanced clinical stage and distant metastases in colon cancer patients. Overexpression of VASH1 in colon cancer cells induced apoptosis and senescence, inhibiting cancer cell growth and colony formation in vitro and tumor growth in vivo. In addition, knockdown of VASH1 in cancer cells promoted cell growth, adhesion and migration in vitro, and enhanced tumorigenesis and metastasis in vivo

Effects of aluminum diffusion on the adhesive behavior of the Ni(111)/Cr2O3(0001) interface: First principle study

AbstractDensity functional theory was employed to investigate the structure and properties of Ni/Cr2O3 and Ni/Al2O3/Cr2O3. The O-terminated Ni(111)/Cr2O3(0001) interface was firstly found to be the most stable configuration. Based on this construction, the effects of the Al diffusion at the Ni/Cr2O3 interface were further studied. The results of total energies indicate that Al atoms originating from Ni slab prefer to diffuse into Cr2O3 slab through the interface, resulting in the formation of alumina at the Ni/Cr2O3 interface. Due to the presence of Al atoms, there was an amazing increase in the work of adhesion, whereas the Ni/Al2O3/Cr2O3 interface showed the strongest stability. Moreover, this calculated work well agrees with the reported experimental results

A fluorescence-switchable luminogen in the solid state: a sensitive and selective sensor for the fast "turn-on" detection of primary amine gas

The emission of pyrrole-substituted benzoic acid can be repeatedly switched between the dark and bright states in the solid state by chemical fuming and heating processes, enabling it to work as a rapid sensitive fluorescent sensor for primary amine detection

Spatial-Temporal Variation of Aridity Index of China during 1960–2013

Aridity index, as the ration of potential evapotranspiration and precipitation, is an important indicator of regional climate. GIS technology, Morlet wavelet, Mann-Kendall test, and principal component analysis are utilized to investigate the spatial-temporal variation of aridity index and its impacting factors in China on basis of climate data from 599 stations during 1960–2013. Results show the following. (1) Boundaries between humid and semihumid region, and semihumid and semiarid region coincide with 400 mm and 800 mm precipitation contour lines. (2) Average annual aridity index is between 3.4 and 7.5 and shows decrease trend with a tendency of –0.236 per decade at 99% confidence level. (3) The driest and wettest month appear in December and July, respectively, in one year. (4) Periods of longitudinal and latitudinal shift of aridity index 1, 1.5, and 4 contours coordinate are 10 and 25 years, 6 and 26 years, and 5 and 25 years, respectively. (5) Four principal components which affect aridity index are thermodynamic factors, water and radiation factors, geographical and air dynamic factors, and evaluation factor, respectively

Analysis of the vp2 gene sequence of a new mutated mink enteritis parvovirus strain in PR China

<p>Abstract</p> <p>Background</p> <p>Mink enteritis virus (MEV) causes a highly contagious viral disease of mink with a worldwide distribution. MEV has a linear, single-stranded, negative-sense DNA with a genome length of approximately 5,000 bp. The VP2 protein is the major structural protein of the parvovirus encoded by the <it>vp</it>2 gene. VP2 is highly antigenic and plays important roles in determining viral host ranges and tissue tropisms. This study describes the bionomics and <it>vp</it>2 gene analysis of a mutated strain, MEV-DL, which was isolated recently in China and outlines its homologous relationships with other selected strains registered in Genbank.</p> <p>Results</p> <p>The MEV-DL strain can infect F81 cells with cytopathic effects. Pig erythrocytes were agglutinated by the MEV-DL strain. The generation of MEV-DL in F81 cells could infect mink within three months and cause a disease that was similar to that caused by wild-type MEV. A comparative analysis of the <it>vp</it>2 gene nucleotide (nt) sequence of MEV-DL showed that this was more than 99% homologous with other mink enteritis parvoviruses in Genbank. However, the nucleotide residues at positions 1,065 and 1,238 in the MEV-DL strain of the <it>vp</it>2 gene differed from those of all the other MEV strains described previously. It is noteworthy that the mutation at the nucleotide residues position 1,238 led to Asp/Gly replacement. This may lead to structural changes. A phylogenetic tree and sequence distance table were obtained, which showed that the MEV-DL and ZYL-1 strains had the closest inheritance distance.</p> <p>Conclusions</p> <p>A new variation of the <it>vp</it>2 gene exists in the MEV-DL strain, which may lead to structural changes of the VP2 protein. Phylogenetic analysis showed that MEV-DL may originate from the ZYL-1 strain in DaLian.</p

Water resource security evaluation and barrier analysis in Henan Province utilizing the DPSIR framework

Water resource health is one of the necessary conditions for society to achieve sustainable development. Due to the predominant focus of most studies on relatively short time spans, with limited attention to long time series and spatial trends, this study, using various regions of Henan Province as a case study, constructs a water resource security assessment framework based on the DPSIR model encompassing Drivers (D), Pressures (P), State (S), Impact (I), and Response (R) dimensions, with a selection of 19 evaluation indicators. Based on this evaluation index system, the CRITIC-TOPSIS evaluation method is formulated by integrating the CRITIC (Criteria Importance Through Intercriteria Correlation) and TOPSIS (Technique for Order Preference by Similarity to Ideal Solution) models. This method is employed to assess the degree of water resource security in Henan Province from 2013 to 2022. And the Obstruction Degree Model is introduced to diagnose the water resource security levels in various regions of Henan Province. The assessment results indicate that over the past decade, the overall level of water resource security in various regions of Henan Province has shown an increasing trend. Irrigated area, per capita water resources, water consumption per unit of industrial value added, per acre water consumption for agricultural irrigation, the ratio of river length meeting water quality standards, groundwater supply proportion, and sewage treatment rate are identified as the primary obstacles influencing the water resource security levels in different regions of Henan Province. The research outcomes of this study can serve as theoretical foundations to enhance urban water resource security globally, ultimately facilitating sustainable development