Multivariate Bernoulli distribution

In this paper, we consider the multivariate Bernoulli distribution as a model to estimate the structure of graphs with binary nodes. This distribution is discussed in the framework of the exponential family, and its statistical properties regarding independence of the nodes are demonstrated. Importantly the model can estimate not only the main effects and pairwise interactions among the nodes but also is capable of modeling higher order interactions, allowing for the existence of complex clique effects. We compare the multivariate Bernoulli model with existing graphical inference models - the Ising model and the multivariate Gaussian model, where only the pairwise interactions are considered. On the other hand, the multivariate Bernoulli distribution has an interesting property in that independence and uncorrelatedness of the component random variables are equivalent. Both the marginal and conditional distributions of a subset of variables in the multivariate Bernoulli distribution still follow the multivariate Bernoulli distribution. Furthermore, the multivariate Bernoulli logistic model is developed under generalized linear model theory by utilizing the canonical link function in order to include covariate information on the nodes, edges and cliques. We also consider variable selection techniques such as LASSO in the logistic model to impose sparsity structure on the graph. Finally, we discuss extending the smoothing spline ANOVA approach to the multivariate Bernoulli logistic model to enable estimation of non-linear effects of the predictor variables.Comment: Published in at http://dx.doi.org/10.3150/12-BEJSP10 the Bernoulli (http://isi.cbs.nl/bernoulli/) by the International Statistical Institute/Bernoulli Society (http://isi.cbs.nl/BS/bshome.htm

InstructSeq: Unifying Vision Tasks with Instruction-conditioned Multi-modal Sequence Generation

Empowering models to dynamically accomplish tasks specified through natural language instructions represents a promising path toward more capable and general artificial intelligence. In this work, we introduce InstructSeq, an instruction-conditioned multi-modal modeling framework that unifies diverse vision tasks through flexible natural language control and handling of both visual and textual data. InstructSeq employs a multimodal transformer architecture encompassing visual, language, and sequential modeling. We utilize a visual encoder to extract image features and a text encoder to encode instructions. An autoregressive transformer fuses the representations and generates sequential task outputs. By training with LLM-generated natural language instructions, InstructSeq acquires a strong comprehension of free-form instructions for specifying visual tasks. This provides an intuitive interface for directing capabilities using flexible natural instructions. Without any task-specific tuning, InstructSeq achieves compelling performance on semantic segmentation, referring expression segmentation/comprehension, and image captioning. The flexible control and multi-task unification empower the model with more human-like versatility and generalizability for computer vision. The code will be released soon at https://github.com/rongyaofang/InstructSeq.Comment: 10 page

Efficacy of sorafenib on metastatic renal cell carcinoma in Asian patients: Results from a multicenter study

<p>Abstract</p> <p>Background</p> <p>The effects of sorafenib in the treatment of advanced renal cell carcinoma (RCC) have been confirmed in an international collaborative phase III trial. This study aims to confirm similar efficacy and treatment-induced toxicities of sorafenib in the treatment of metastatic RCC in ethnic Chinese patients.</p> <p>Methods</p> <p>Ninety-eight consecutive and non-selected patients with pathologically confirmed metastatic RCC were treated according to an institutional treatment protocol. All patients were treated with 400 mg of sorafenib orally twice daily on a continuous basis until disease progression or intolerance to treatment occurred. Dose reduction to 400 mg once daily was required if grade 3 or 4 toxicities occurred. All patients except for 7 received nephrectomy in the course of their disease. All patients were assessed for tumor response, progression-free survival (PFS), overall survival (OS), and treatment-induced toxicities.</p> <p>Results</p> <p>The median follow-up time was 76 weeks (range 2–296 weeks) for the entire group of patients. Radiologically confirmed complete response (CR), partial response (PR), stable disease (SD) of more than 4 months, and disease progression as best objective responses were observed in 1 (1%), 23 (23.5%), 62 (63.3%), and 12 (12.2%) patients, respectively. The tumor control rate (CR+PR+SD of >4 months) was 87.8%. The 1-year estimated PFS and OS were 58.4% and 64.6%, respectively. The median progression-free survival (PFS) time was 60 weeks (95% CI 41–79); and the median overall survival (OS) time was not reached with a follow-up of 76 weeks. Reduction of sorafenib dose was required in 26 patients who developed grade 3 or 4 treatment-cause adverse-effects. An additional 9 patients discontinued sorafenib treatment due to severe adverse-effects. No grade 5 toxicity occurred.</p> <p>Multivariate analysis revealed that independent predictive factors for tumor response to sorafenib treatment included ECOG status, presence of lymph node metastasis, and nephrectomy prior to the development of metastasis.</p> <p>Conclusion</p> <p>Sorafenib produced an 87.8% disease control rate for metastatic renal cell carcinoma in Chinese patients, with acceptable rates of toxicity. The medication dosed at 400 mg twice daily is both efficacious and safe in the treatment of metastatic renal cell carcinoma in Chinese patients.</p

A Practical Quality Control Method for Saponins Without UV Absorption by UPLC-QDA

Saponins are a class of important active ingredients. Analysis of saponin-containing herbal medicines is a major challenge for the quality control of medicinal herbs in companies. Taking the medicine Astragali radix (AR) as an example, it has been shown that the existing evaporative light scattering detection (ELSD) methods of astragaloside IV (AG IV) has the disadvantages of time-consuming sample preparation and low sensitivity. The universality of ELSD results in an inapplicable fingerprint with huge signals from primary compounds and smaller signals from saponins. The purpose of this study was to provide a practical and comprehensive method for the quality control of the astragalosides in AR. A simple sample preparation method with sonication extraction and ammonia hydrolyzation was established, which shortens the preparation time from around 2 days to less than 2 h. A UPLC-QDA method with the SIM mode was established for the quantification of AG IV in AR. Methanol extract was subjected to UPLC-QDA for fingerprinting analysis, and the common peaks were assigned simultaneously with the QDA. The results showed that with the newly established method, the preparation time for a set of samples was less than 90 min. The fingerprints can simultaneously detect both saponins and flavonoids in AR. This simple, rapid, and comprehensive UPLC-QDA method is suitable for quality assessment of RA and its products in companies, and also provides references for the quality control of other saponin ingredients without UV absorption

Identification and characterization of a novel gene involved in glandular trichome development in Nepeta tenuifolia

Nepeta tenuifolia is a medicinal plant rich in terpenoids and flavonoids with antiviral, immunoregulatory, and anti-inflammatory activities. The peltate glandular trichome (PGT) is a multicellular structure considered to be the primary storage organ for monoterpenes; it may serve as an ideal model for studying cell differentiation and the development of glandular trichomes (GTs). The genes that regulate the development of GTs have not yet been well studied. In this study, we identified NtMIXTA1, a GT development-associated gene from the R2R3 MYB SBG9 family. NtMIXTA1 overexpression in tobacco resulted in the production of longer and denser GTs. Virus-induced gene silencing of NtMIXTA1 resulted in lower PGT density, a significant reduction in monoterpene concentration, and the decreased expression of genes related to monoterpene biosynthesis. Comparative transcriptome and widely targeted metabolic analyses revealed that silencing NtMIXTA1 significantly influenced the expression of genes, and the production of metabolites involved in the biosynthesis of terpenoids, flavonoids, and lipids. This study provides a solid foundation describing a mechanism underlying the regulation of GT development. In addition, this study further deepens our understanding of the regulatory networks involved in GT development and GT development-associated metabolite flux, as well as provides valuable reference data for studying plants with a high medicinal value without genetic transformation

Genome-wide identification and characterization of novel genes involved in terpenoid biosynthesis in Salvia miltiorrhiza

Terpenoids are the largest class of plant secondary metabolites and have attracted widespread interest. Salvia miltiorrhiza, belonging to the largest and most widely distributed genus in the mint family, is a model medicinal plant with great economic and medicinal value. Diterpenoid tanshinones are the major lipophilic bioactive components in S. miltiorrhiza. Systematic analysis of genes involved in terpenoid biosynthesis has not been reported to date. Searching the recently available working draft of the S. miltiorrhiza genome, 40 terpenoid biosynthesis-related genes were identified, of which 27 are novel. These genes are members of 19 families, which encode all of the enzymes involved in the biosynthesis of the universal isoprene precursor isopentenyl diphosphate and its isomer dimethylallyl diphosphate, and two enzymes associated with the biosynthesis of labdane-related diterpenoids. Through a systematic analysis, it was found that 20 of the 40 genes could be involved in tanshinone biosynthesis. Using a comprehensive approach, the intron/exon structures and expression patterns of all identified genes and their responses to methyl jasmonate treatment were analysed. The conserved domains and phylogenetic relationships among the deduced S. miltiorrhiza proteins and their homologues isolated from other plant species were revealed. It was discovered that some of the key enzymes, such as 1-deoxy-D-xylulose 5-phosphate synthase, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase, hydroxymethylglutaryl-CoA reductase, and geranylgeranyl diphosphate synthase, are encoded by multiple gene members with different expression patterns and subcellular localizations, and both homomeric and heteromeric geranyl diphosphate synthases exist in S. miltiorrhiza. The results suggest the complexity of terpenoid biosynthesis and the existence of metabolic channels for diverse terpenoids in S. miltiorrhiza and provide useful information for improving tanshinone production through genetic engineering

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Perceived facilitators and barriers to intentions of receiving the COVID-19 vaccines among elderly Chinese adults

Elderly adults hold different beliefs regarding vaccination and are at higher risks for COVID-19 related illnesses and deaths. The current study aims to explore elderly (aged 65 or above) Chinese adults\u27 intentions to get vaccinated against COVID-19 and the facilitators and barriers to vaccination intentions. We conducted in-depth interviews with 35 elderly adults in China through the lens of the integrative model of behavioral prediction. The results identified a number of facilitators, including convenience (both individual and collective), psychological and physiological wellbeing, collective wellbeing, supportive normative referents, and trust in the government, and some barriers, including vaccine ineffectiveness, side effects, safety, unsupportive normative referents, and the accessibility, affordability, and availability of COVID-19 vaccines. In addition, the results revealed participants\u27 decision-making process: collective wellbeing and trust in the government overrode perceived barriers and perceived individual-level risks, which eventually overwhelmingly led to a high level of intentions to get vaccinated. Practical implications related to vaccine promotion and trust in the government were discussed

Do Messages Matter? Investigating the Combined Effects of Framing, Outcome Uncertainty, and Number Format on COVID-19 Vaccination Attitudes and Intention

Guided by prospect theory, the current study aims to explore Chinese adults’ attitudes and intention to get vaccinated against COVID-19 and investigate the effects of message frames (gain vs. loss), outcome uncertainty (certain vs. uncertain), and number format (frequency vs. percentage) on vaccination attitudes and intention. Participants (n = 413) were randomly assigned to one of the eight experimental conditions and participated in the online experiment. The results showed that Chinese adults’ attitudes toward COVID-19 vaccination were highly favorable, and the vaccination intention was high; age and education were positively correlated with attitudes and intention. The results also showed that message frames, outcome uncertainty, and number format did not have significant main or interaction effects on vaccination attitudes and intention. The discussion focused on how Chinese culture and contextual factors may have influenced the results of the study, as well as the implications and suggestions for future studies