PMC-VQA: Visual Instruction Tuning for Medical Visual Question Answering

In this paper, we focus on the problem of Medical Visual Question Answering (MedVQA), which is crucial in efficiently interpreting medical images with vital clinic-relevant information. Firstly, we reframe the problem of MedVQA as a generation task that naturally follows the human-machine interaction, we propose a generative-based model for medical visual understanding by aligning visual information from a pre-trained vision encoder with a large language model. Secondly, we establish a scalable pipeline to construct a large-scale medical visual question-answering dataset, named PMC-VQA, which contains 227k VQA pairs of 149k images that cover various modalities or diseases. Thirdly, we pre-train our proposed model on PMC-VQA and then fine-tune it on multiple public benchmarks, e.g., VQA-RAD and SLAKE, outperforming existing work by a large margin. Additionally, we propose a test set that has undergone manual verification, which is significantly more challenging, even the best models struggle to solve

Interactions of the apolipoprotein C-III 3238C>G polymorphism and alcohol consumption on serum triglyceride levels

<p>Abstract</p> <p>Background</p> <p>Both apolipoprotein (Apo) C-III gene polymorphism and alcohol consumption have been associated with increased serum triglyceride (TG) levels, but their interactions on serum TG levels are not well known. The present study was undertaken to detect the interactions of the ApoC-III 3238C>G (rs5128) polymorphism and alcohol consumption on serum TG levels.</p> <p>Methods</p> <p>A total of 516 unrelated nondrinkers and 514 drinkers aged 15-89 were randomly selected from our previous stratified randomized cluster samples. Genotyping of the ApoC-III 3238C>G was performed by polymerase chain reaction and restriction fragment length polymorphism combined with gel electrophoresis, and then confirmed by direct sequencing. Interactions of the ApoC-III 3238C>G genotype and alcohol consumption was assessed by using a cross-product term between genotypes and the aforementioned factor.</p> <p>Results</p> <p>Serum total cholesterol (TC), TG, high-density lipoprotein cholesterol (HDL-C), ApoA-I and ApoB levels were higher in drinkers than in nondrinkers (<it>P </it>< 0.05-0.001). There was no significant difference in the genotypic and allelic frequencies between the two groups. Serum TG levels in nondrinkers were higher in CG genotype than in CC genotype (<it>P </it>< 0.01). Serum TC, TG, low-density lipoprotein cholesterol (LDL-C) and ApoB levels in drinkers were higher in GG genotype than in CC or CG genotype (<it>P </it>< 0.01 for all). Serum HDL-C levels in drinkers were higher in CG genotype than in CC genotype (<it>P </it>< 0.01). Serum TC, TG, HDL-C and ApoA-I levels in CC genotype, TC, HDL-C, ApoA-I levels and the ratio of ApoA-I to ApoB in CG genotype, and TC, TG, LDL-C, ApoA-I and ApoB levels in GG genotype were higher in drinkers than in nondrinkers (<it>P </it>< 0.05-0.01). But the ratio of ApoA-I to ApoB in GG genotype was lower in drinkers than in nondrinkers (<it>P </it>< 0.01). Multivariate logistic regression analysis showed that the levels of TC, TG and ApoB were correlated with genotype in nondrinkers (<it>P </it>< 0.05 for all). The levels of TC, LDL-C and ApoB were associated with genotype in drinkers (<it>P </it>< 0.01 for all). Serum lipid parameters were also correlated with age, sex, alcohol consumption, cigarette smoking, blood pressure, body weight, and body mass index in both groups.</p> <p>Conclusions</p> <p>This study suggests that the ApoC-III 3238CG heterozygotes benefited more from alcohol consumption than CC and GG homozygotes in increasing serum levels of HDL-C, ApoA-I, and the ratio of ApoA-I to ApoB, and lowering serum levels of TC and TG.</p

Preparation and Application of Starch/Polyvinyl Alcohol/Citric Acid Ternary Blend Antimicrobial Functional Food Packaging Films

Ternary blend films were prepared with different ratios of starch/polyvinyl alcohol (PVA)/citric acid. The films were characterized by field emission scanning electron microscopy (FE-SEM), thermogravimetric analysis, as well as Fourier transform infrared (FTIR) analysis. The influence of different ratios of starch/polyvinyl alcohol (PVA)/citric acid and different drying times on the performance properties, transparency, tensile strength (TS), water vapor permeability (WVP), water solubility (WS), color difference (ΔE), and antimicrobial activity of the ternary blends films were investigated. The starch/polyvinyl alcohol/citric acid (S/P/C1:1:0, S/P/C3:1:0.08, and S/P/C3:3:0.08) films were all highly transparent. The S/P/C3:3:0.08 had a 54.31 times water-holding capacity of its own weight and its mechanical tensile strength was 46.45 MPa. In addition, its surface had good uniformity and compactness. The S/P/C3:1:0.08 and S/P/C3:3:0.08 showed strong antimicrobial activity to Listeria monocytogenes and Escherichia coli, which were the food-borne pathogenic bacteria used. The freshness test results of fresh figs showed that all of the blends prevented the formation of condensed water on the surface of the film, and the S/P/C3:1:0.08 and S/P/C3:3:0.08 prevented the deterioration of figs during storage. The films can be used as an active food packaging system due to their strong antibacterial effect

Effect of the 3'APOB-VNTR polymorphism on the lipid profiles in the Guangxi Hei Yi Zhuang and Han populations

<p>Abstract</p> <p>Background</p> <p>Apolipoprotein (Apo) B is the major component of low-density lipoprotein (LDL), very low-density lipoprotein (VLDL) and chylomicrons. Many genetic polymorphisms of the Apo B have been described, associated with variation of lipid levels. However, very few studies have evaluated the effect of the variable number of tandem repeats region 3' of the Apo B gene (3'APOB-VNTR) polymorphism on the lipid profiles in the special minority subgroups in China. Thus, the present study was undertaken to study the effect of the 3'APOB-VNTR polymorphism on the serum lipid levels in the Guangxi Hei Yi Zhuang and Han populations.</p> <p>Methods</p> <p>A total of 548 people of Hei Yi Zhuang were surveyed by a stratified randomized cluster sampling. The epidemiological survey was performed using internationally standardized methods. Serum lipid and apolipoprotein levels were measured. The 3'APOB-VNTR alleles were determined by polymerase chain reaction (PCR) followed by electrophoresis in polyacrylamide gels, and classified according to the number of repeats of a 15-bp hypervariable elements (HVE). The sequence of the most common allele was determined using the PCR and direct sequencing. The possible association between alleles of the 3'APOB-VNTR and lipid variables was examined. The results were compared with those in 496 people of Han who also live in that district.</p> <p>Results</p> <p>Nineteen alleles ranging from 24 to 64 repeats were detected in both Hei Yi Zhuang and Han. HVE56 and HVE58 were not be detected in Hei Yi Zhuang whereas HVE48 and HVE62 were totally absent in Han. The frequencies of HVE26, HVE30, HVE46, heterozygote, and short alleles (< 38 repeats) were higher in Hei Yi Zhuang than in Han. But the frequencies of HVE34, HVE38, HVE40, homozygote, and long alleles (≥ 38 repeats) were lower in Hei Yi Zhuang than in Han (<it>P </it>< 0.05–0.01). The levels of total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C) and Apo B in Hei Yi Zhuang but not in Han were higher in VNTR-LS (carrier of one long and one short alleles) than in VNTR-LL (the individual carrying two long alleles) genotypes. The levels of TC, triglycerides (TG), LDL cholesterol, and Apo B in Hei Yi Zhuang were higher in both HVE34 and HVE36 alleles than in HVE32 allele. The levels of TC, TG, HDL-C and Apo B in Hei Yi Zhuang were also higher in homozygotes than in heterozygotes. There were no significant differences in the detected lipid parameters between the VNTR-SS (carrier of two short alleles) and VNTR-LS or VNTR-LL genotypes in both ethnic groups.</p> <p>Conclusion</p> <p>There were significant differences of the 3'APOB-VNTR polymorphism between the Hei Yi Zhuang and Han populations. An association between the 3'APOB-VNTR polymorphism and serum lipid levels was observed in the Hei Yi Zhuang but not in the Han populations.</p

RNA-Seq Mapping and Detection of Gene Fusions with a Suffix Array Algorithm

High-throughput RNA sequencing enables quantification of transcripts (both known and novel), exon/exon junctions and fusions of exons from different genes. Discovery of gene fusions–particularly those expressed with low abundance– is a challenge with short- and medium-length sequencing reads. To address this challenge, we implemented an RNA-Seq mapping pipeline within the LifeScope software. We introduced new features including filter and junction mapping, annotation-aided pairing rescue and accurate mapping quality values. We combined this pipeline with a Suffix Array Spliced Read (SASR) aligner to detect chimeric transcripts. Performing paired-end RNA-Seq of the breast cancer cell line MCF-7 using the SOLiD system, we called 40 gene fusions among over 120,000 splicing junctions. We validated 36 of these 40 fusions with TaqMan assays, of which 25 were expressed in MCF-7 but not the Human Brain Reference. An intra-chromosomal gene fusion involving the estrogen receptor alpha gene ESR1, and another involving the RPS6KB1 (Ribosomal protein S6 kinase beta-1) were recurrently expressed in a number of breast tumor cell lines and a clinical tumor sample

Speech recognition tool

This project is to study the use of various mathematical or statistical methods and techniques used in speech recognition to identify defects in an aircraft material. Aircraft body is likely to have defects after long hours of flights and it is of utmost importance to detect any defects. There are 24 defects and 1 non defect data inputs in this study and they are presented in a form of sound waves. Therefore techniques used in speech recognition are being explored here. Some of the techniques to be explored are such as Earth Mover’s Distance, Correlation and First Derivative Correlation search, Linear Discriminant Analysis, Dynamic Time Warping and Neural Network. Earth Mover’s Distance can be seen employed in colour and image recognition. It is a kind of dissimilarity assessment technique which is applicable to multi-dimensional distributions. Correlation and First Derivative Correlation Search is a type of statistical measure for relationships between distributions and the result of it will show how related the data is from each other. Linear Discriminant Analysis is often employed in statistics and machine learning. It is most often used to find separation between classes of objects. Dynamic Time Warping is a technique used to measure similarity between two distributions and this method is able to analyse data and compare them disregarding the time and speed difference. Neural Network is a complex analytical method which creates a network from training it. With it, Neural Network is able to recognise trends and patterns from data which humans may be unable to. With these few methods, the aim is to study the plausibility and effectiveness of applying these techniques into defect detection for aircraft material.Bachelor of Engineerin

In Silico Screening of Metal-Organic Frameworks for Formaldehyde Capture with and without Humidity by Molecular Simulation

Capturing formaldehydes (HCHO) from indoor air with porous adsorbents still faces challenges due to their low capacity and poor selectivity. Metal-organic frameworks (MOFs) with tunable pore properties were regarded as promising adsorbents for HCHO removal. However, the water presence in humid air heavily influences the formaldehyde capture performance due to the competition adsorption. To find suitable MOFs for formaldehyde capture and explore the relationship between MOFs structure and performance both in dry air and humid air, we performed grand canonical Monte Carlo (GCMC) molecular simulations to obtain working capacity and selectivity that evaluated the HCHO capture performance of MOFs without humidity. The results reveal that small pore size (~5 &Aring;) and moderate heat of adsorption (40&ndash;50 kJ/mol) are favored for HCHO capture without water. It was found that the structure with a 3D cage instead of a 2D channel benefits the HCHO adsorption. Atoms in these high-performing MOFs should possess relatively small charges, and large Lennard-jones parameters were also preferred. Furthermore, it was indicated that Henry&rsquo;s constant (KH) can reflect the HCHO adsorption performance without humidity, in which the optimal range is 10&minus;2&ndash;101. Hence, Henry&rsquo;s constant selectivity of HCHO over water (SKH HCHO/H2O) and HCHO over mixture components (H2O, N2, and O2) was obtained to screen MOFs at an 80% humidity condition. It was suggested that SKH for the mixture component overestimates the influence of N2 and O2, in which the top structures absorb a quantity of water in GCMC simulation, while SKH HCHO/H2O can efficiently find high-performing MOFs for HCHO capture at humidity in low adsorption pressure. The ECATAT found in this work has 0.64 mol/kg working capacity, and barely adsorbs water during 0&ndash;1 bar, which is the promising candidate MOF for HCHO capture