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The Continued Impact and Possibilities of AI in Medical and Pharmaceutical Industry Practices
Reporter: Adam P. Tubman, MSc Biotechnology, Research Associate 3, Computer Graphics and AI in Drug Discovery
Researchers have been able to discover many ways to incorporate AI into the practices of healthcare, both in terms of medical healthcare and also in pharmaceutical drug development. For example, given the situation where a doctor provides an inaccurate diagnosis to a patient because the doctor had an incomplete or inaccurate medical record/history, AI presents a solution that has the potential to rapidly and correctly account for human error and predict the correct diagnosis based on the patterns identified in other patient’s medical history to disease diagnosis indication. In the pharmaceutical industry, companies are changing and expanding approaches to drug discovery and development given the possibilities that AI can offer. One company, Reverie Labs, located in Cambridge, MA, is a pharmaceutical company utilizing AI for application of machine learning and computational chemistry to discover new possible compounds to be used in the development of cancer treatments.
Today, AI uses have had many other applications in medicine including managing healthcare data and performing robotic surgery, both of which transform the in-person patient and doctor experience. AI has even been used to change in-person cancer patient experiences. For example, Freenome, a company in San Francisco, CA uses AI in initial screenings, blood tests and diagnostic tests when a patient is being initially tested for cancer. The hope is that this technology will aide in speeding up cancer diagnoses and lead to new treatment developments.
The future will continue to bring many possibilities of AI, provided an acceptable level of accuracy is still maintained by AI technologies and that the technology remains beneficial. If research continues to focus on diagnosing diseases at a faster rate given the potential human errors in having an inaccurate or incomplete medical record upon diagnosis, AI could provide an improved experience for patients given the quicker diagnosis and treatment combined with less time spent either treating the wrong underlying condition or not knowing what condition to treat when accounting for an incomplete medical record. If this technology is proven to be successful not just in theory, but in practice, technology would then be available and could be beneficially applied to all diagnoses and treatment plans, across the world.
However, the reality regarding AI development is that its evolution depends on how much human effort is involved in its development. Therefore, the world won’t know or see the full benefits of AI until it is developed and actively applied. Similarly, the impact that AI will have in medical and pharmaceutical practices won’t be known until scientists fully develop and apply the technologies. Many possibilities, including a possible drastic lowering of the cost for pharmaceutical drugs across the board once drugs are much more readily discovered and produced, may carry a profound benefit to patients who currently struggle to afford their own treatment plans. Additionally, unforeseen advances in the medicinal and pharmaceutical fields because of AI development will lead to unforeseen effects on the global economy and many other life changing variables for the entire world.
For more information on this topic, please check out the article below.
The Use of ChatGPT in the World of BioInformatics and Cancer Research and Development of BioGPT by MIT
Curator: Stephen J. Williams, Ph.D.
Chatbots are being used in multiple interdisciplanary areas in research and medicine and so it was a natural progression to incorporate artificial intelligence (AI), natural language processing (NLP), and chatbot technology like ChatGPT into bioinformatic analysis.
“In domains like informatics, management and marketing, media and communication science, languages and philosophy, psychology and sociology, engineering, design, and human-computer interaction, the fast expanding body of chatbot study is clearly interdisciplinary.
The field of bioinformatics is a natural fit for incorporting this technology. The curated information below shows some use examples of this technology in bioinformatics related to cancer research.
How ChatGPT can be used in bioinformatics research?
ChatGPT is a variant of the GPT (Generative Pre-trained Transformer) language model that was designed to generate human-like text in a conversational setting. It is not directly related to bioinformatics, which is the field of study that deals with the storage, retrieval, and analysis of biological data, particularly in the context of genetics and genomics. However, ChatGPT could potentially be used in a bioinformatics context as a tool for generating natural language descriptions of genetic or genomic data, or for generating responses to queries about such data.
For example, a researcher could use ChatGPT to generate descriptions of genetic variants or gene expression patterns based on input data. This could be useful for generating summaries of results for reports or papers, or for generating explanations of complex concepts for non-expert audiences. ChatGPT could also be used to generate responses to queries about genetic or genomic data, such as “What is the function of gene X?” or “What are the potential consequences of variant Y?”
It’s worth noting that ChatGPT is just one of many tools and techniques that can be used in bioinformatics, and it is unlikely to be the most suitable or effective option in every situation. There are many specialized tools and resources available for working with biological data, and it is often necessary to use a combination of these tools to fully analyze and understand the data.
Generating descriptions of genetic or genomic data: ChatGPT could be used to generate natural language descriptions of genetic or genomic data based on input data. For example, suppose a researcher has a dataset containing information about gene expression levels in different tissues. The researcher could use ChatGPT to generate a description of the data, such as:
“Gene X is highly expressed in the liver and kidney, with moderate expression in the brain and heart. Gene Y, on the other hand, shows low expression in all tissues except for the lung, where it is highly expressed.”
Thereby ChatGPT, at its simplest level, could be used to ask general questions like “What is the function of gene product X?” and a ChatGPT could give a reasonable response without the scientist having to browse through even highly curated databases lie GeneCards or UniProt or GenBank. Or even “What are potential interactors of Gene X, validated by yeast two hybrid?” without even going to the curated InterActome databases or using expensive software like Genie.
Summarizing results: ChatGPT could be used to generate summaries of results from genetic or genomic studies. For example, a researcher might use ChatGPT to generate a summary of a study that found a association between a particular genetic variant and a particular disease. The summary might look something like this:
“Our study found that individuals with the variant form of gene X are more likely to develop disease Y. Further analysis revealed that this variant is associated with changes in gene expression that may contribute to the development of the disease.”
It’s worth noting that ChatGPT is just one tool that could potentially be used in these types of applications, and it is likely to be most effective when used in combination with other bioinformatics tools and resources. For example, a researcher might use ChatGPT to generate a summary of results, but would also need to use other tools to analyze the data and confirm the findings.
ChatGPT is a variant of the GPT (Generative Pre-training Transformer) language model that is designed for open-domain conversation. It is not specifically designed for generating descriptions of genetic variants or gene expression patterns, but it can potentially be used for this purpose if you provide it with a sufficient amount of relevant training data and fine-tune it appropriately.
To use ChatGPT to generate descriptions of genetic variants or gene expression patterns, you would first need to obtain a large dataset of examples of descriptions of genetic variants or gene expression patterns. You could use this dataset to fine-tune the ChatGPT model on the task of generating descriptions of genetic variants or gene expression patterns.
Here’s an example of how you might use ChatGPT to generate a description of a genetic variant:
First, you would need to pre-process your dataset of descriptions of genetic variants to prepare it for use with ChatGPT. This might involve splitting the descriptions into individual sentences or phrases, and encoding them using a suitable natural language processing (NLP) library or tool.
Next, you would need to fine-tune the ChatGPT model on the task of generating descriptions of genetic variants. This could involve using a tool like Hugging Face’s Transformers library to load the ChatGPT model and your pre-processed dataset, and then training the model on the task of generating descriptions of genetic variants using an appropriate optimization algorithm.
Once the model has been fine-tuned, you can use it to generate descriptions of genetic variants by providing it with a prompt or seed text and asking it to generate a response. For example, you might provide the model with the prompt “Generate a description of a genetic variant associated with increased risk of breast cancer,” and ask it to generate a response. The model should then generate a description of a genetic variant that is associated with increased risk of breast cancer.
It’s worth noting that generating high-quality descriptions of genetic variants or gene expression patterns is a challenging task, and it may be difficult to achieve good results using a language model like ChatGPT without a large amount of relevant training data and careful fine-tuning.
To train a language model like chatGPT to extract information about specific genes or diseases from research papers, you would need to follow these steps:
Gather a large dataset of research papers that contain information about the specific genes or diseases you are interested in. This dataset should be diverse and representative of the types of papers you want the model to be able to extract information from.
Preprocess the text data in the research papers by tokenizing the text and creating a vocabulary. You may also want to consider lemmatizing or stemming the text to reduce the dimensionality of the dataset.
Train the language model on the preprocessed text data. You may want to fine-tune a pre-trained model such as chatGPT on your specific dataset, or you can train a new model from scratch.
ChatGPT could also be useful for sequence analysis
A few examples of sequence analysis a ChatGPT could be useful include:
Protein structure
Identifying functional regions of a protein
Predicting protein-protein interactions
Identifying protein homologs
Generating Protein alignments
All this could be done without having access to UNIX servers or proprietary software or knowing GCG coding
ChatGPT in biomedical research
There are several potential ways that ChatGPT or other natural language processing (NLP) models could be applied in biomedical research:
Text summarization: ChatGPT or other NLP models could be used to summarize large amounts of text, such as research papers or clinical notes, in order to extract key information and insights more quickly.
Data extraction: ChatGPT or other NLP models could be used to extract structured data from unstructured text sources, such as research papers or clinical notes. For example, the model could be trained to extract information about specific genes or diseases from research papers, and then used to create a database of this information for further analysis.
Literature review: ChatGPT or other NLP models could be used to assist with literature review tasks, such as identifying relevant papers, extracting key information from papers, or summarizing the main findings of a group of papers.
Predictive modeling: ChatGPT or other NLP models could be used to build predictive models based on large amounts of text data, such as electronic health records or research papers. For example, the model could be trained to predict the likelihood of a patient developing a particular disease based on their medical history and other factors.
It’s worth noting that while NLP models like ChatGPT have the potential to be useful tools in biomedical research, they are only as good as the data they are trained on, and it is important to carefully evaluate the quality and reliability of any results generated by these models.
ChatGPT in text mining of biomedical data
ChatGPT could potentially be used for text mining in the biomedical field in a number of ways. Here are a few examples:
Extracting information from scientific papers: ChatGPT could be trained on a large dataset of scientific papers in the biomedical field, and then used to extract specific pieces of information from these papers, such as the names of compounds, their structures, and their potential uses.
Generating summaries of scientific papers: ChatGPT could be used to generate concise summaries of scientific papers in the biomedical field, highlighting the main findings and implications of the research.
Identifying trends and patterns in scientific literature: ChatGPT could be used to analyze large datasets of scientific papers in the biomedical field and identify trends and patterns in the data, such as emerging areas of research or common themes among different papers.
Generating questions for further research: ChatGPT could be used to suggest questions for further research in the biomedical field based on existing scientific literature, by identifying gaps in current knowledge or areas where further investigation is needed.
Generating hypotheses for scientific experiments: ChatGPT could be used to generate hypotheses for scientific experiments in the biomedical field based on existing scientific literature and data, by identifying potential relationships or associations that could be tested in future research.
PLEASE WATCH VIDEO
In this video, a bioinformatician describes the ways he uses ChatGPT to increase his productivity in writing bioinformatic code and conducting bioinformatic analyses.
He describes a series of uses of ChatGPT in his day to day work as a bioinformatian:
Using ChatGPT as a search engine: He finds more useful and relevant search results than a standard Google or Yahoo search. This saves time as one does not have to pour through multiple pages to find information. However, a caveat is ChatGPT does NOT return sources, as highlighted in previous postings on this page. This feature of ChatGPT is probably why Microsoft bought OpenAI in order to incorporate ChatGPT in their Bing search engine, as well as Office Suite programs
ChatGPT to help with coding projects: Bioinformaticians will spend multiple hours searching for and altering open access available code in order to run certain function like determining the G/C content of DNA (although there are many UNIX based code that has already been established for these purposes). One can use ChatGPT to find such a code and then assist in debugging that code for any flaws
ChatGPT to document and add coding comments: When writing code it is useful to add comments periodically to assist other users to determine how the code works and also how the program flow works as well, including returned variables.
One of the comments was interesting and directed one to use BIOGPT instead of ChatGPT
0:54 oh dear. You cannot use chatgpt like that in Bioinformatics as it is rn without double checking the info from it. You should be using biogpt instead for paper summarisation. ChatGPT goes for human-like responses over precise information recal. It is quite good for debugging though and automating boring awkward scripts
The BioGPT model was proposed in BioGPT: generative pre-trained transformer for biomedical text generation and mining by Renqian Luo, Liai Sun, Yingce Xia, Tao Qin, Sheng Zhang, Hoifung Poon and Tie-Yan Liu. BioGPT is a domain-specific generative pre-trained Transformer language model for biomedical text generation and mining. BioGPT follows the Transformer language model backbone, and is pre-trained on 15M PubMed abstracts from scratch.
The abstract from the paper is the following:
Pre-trained language models have attracted increasing attention in the biomedical domain, inspired by their great success in the general natural language domain. Among the two main branches of pre-trained language models in the general language domain, i.e. BERT (and its variants) and GPT (and its variants), the first one has been extensively studied in the biomedical domain, such as BioBERT and PubMedBERT. While they have achieved great success on a variety of discriminative downstream biomedical tasks, the lack of generation ability constrains their application scope. In this paper, we propose BioGPT, a domain-specific generative Transformer language model pre-trained on large-scale biomedical literature. We evaluate BioGPT on six biomedical natural language processing tasks and demonstrate that our model outperforms previous models on most tasks. Especially, we get 44.98%, 38.42% and 40.76% F1 score on BC5CDR, KD-DTI and DDI end-to-end relation extraction tasks, respectively, and 78.2% accuracy on PubMedQA, creating a new record. Our case study on text generation further demonstrates the advantage of BioGPT on biomedical literature to generate fluent descriptions for biomedical terms.
Tips:
BioGPT is a model with absolute position embeddings so it’s usually advised to pad the inputs on the right rather than the left.
BioGPT was trained with a causal language modeling (CLM) objective and is therefore powerful at predicting the next token in a sequence. Leveraging this feature allows BioGPT to generate syntactically coherent text as it can be observed in the run_generation.py example script.
The model can take the past_key_values (for PyTorch) as input, which is the previously computed key/value attention pairs. Using this (past_key_values or past) value prevents the model from re-computing pre-computed values in the context of text generation. For PyTorch, see past_key_values argument of the BioGptForCausalLM.forward() method for more information on its usage.
This model was contributed by kamalkraj. The original code can be found here.
BioGPT is MIT-licensed. The license applies to the pre-trained models as well.
Contributing
This project welcomes contributions and suggestions. Most contributions require you to agree to a Contributor License Agreement (CLA) declaring that you have the right to, and actually do, grant us the rights to use your contribution. For details, visit https://cla.opensource.microsoft.com.
When you submit a pull request, a CLA bot will automatically determine whether you need to provide a CLA and decorate the PR appropriately (e.g., status check, comment). Simply follow the instructions provided by the bot. You will only need to do this once across all repos using our CLA.
As of right now this does not seem Open Access, however a sign up is required!
We provide our pre-trained BioGPT model checkpoints along with fine-tuned checkpoints for downstream tasks, available both through URL download as well as through the Hugging Face 🤗 Hub.
Luo R, Sun L, Xia Y, Qin T, Zhang S, Poon H, Liu TY.Brief Bioinform. 2022 Nov 19;23(6):bbac409. doi: 10.1093/bib/bbac409.PMID: 36156661
We evaluate BioGPT on six biomedical natural language processing tasks and demonstrate that our model outperforms previous models on most tasks. …Our case study on text generation further demonstrates the advantage of BioGPT on biomedical literature to generate fl …
Here they show the advantages of BioGPT over BioBERT and ChatGPT in an example of text extraction and question answer
Table 7. Example of generated text
Input Model Text
Bicalutamide GPT-2 Bicalutamide, a synthetic bicalutamide derivative, was found to increase the cellular proliferation
of C. elegans cells. This effect was not observed with the other synthetic bicalutamide derivatives. This is in line with our previous work which showed that bicalutamide increases the proliferation of C. elegans cells but not in the presence of synthetic bicalutamide.
BioGPT Bicalutamide (Casodex) is an androgen receptor (AR) antagonist approved for the treatment of metastatic castration-resistant prostate cancer (mCRPC) in patients who have progressed on or are ineligible for docetaxel chemotherapy, as well as for the treatment of early-stage prostate cancer in men who have not progressed on or are ineligible for docetaxel chemotherapy, as well as for the treatment of metastatic castration-sensitive prostate cancer (mCSPC) in men who have not progressed on or are ineligible for docetaxel chemotherapy.
Janus kinase 3 (JAK-3) GPT-2 Janus kinase 3 (JAK-3) mediates the conversion of glucose to glycogen in skeletal muscle. The
increase in glucose uptake by skeletal muscle is believed to be associated with a reduction in muscle protein breakdown and with the release of ketone bodies, which contribute to the metabolism of glucose.
BioGPT Janus kinase 3 (JAK-3) is a member of the Janus kinase (JAK) family of non-receptor tyrosine kinases and plays an important role in the regulation of cell proliferation, differentiation, survival, migration and angiogenesis.
Apricitabine GPT-2 Apricitabine, duloxetine and citalopram) were investigated in patients with a history of
treatment-resistant depression (n = 10). We found that treatment with the three drugs significantly decreased depressive symptoms, but not depressive symptoms over the next 12 weeks. We conclude that antidepressant drugs that reduce depressive symptoms and reduce depressive symptoms over time may be beneficial in patients with recurrent depression.
BioGPT Apricitabine is an oral prodrug of 5-aza-2 ’-deoxycytidine (5-aza-CdR), a DNA methyltransferase (DNMT) inhibitor, which has been approved by the US Food and Drug Administration (FDA) for the treatment of myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) in combination with low-dose cytarabine (Ara-C) and granulocyte colony-stimulating factor (G-CSF) for patients with intermediate-2 or high-risk MDS or AML.
Xylazine GPT-2 Xylazine, the ‘active ingredient’ in ‘bath salts’ (see above) has been linked to numerous deaths,
including those of former University of California, Berkeley, professor Andrew Anglin, who posted
a video of himself having a bath filled with it.
BioGPT Xylazine is an alpha 2-adrenoceptor agonist which has been used as a sedative and analgesic in veterinary medicine for many years, but its effects on the cardiovascular system have not been extensively studied in the dog, and its effects on the central nervous system (CNS) have not been well characterized in the dog, despite the fact that xylazine has been widely used as a sedative and analgesic in veterinary medicine for more than 30 years.
Psoralen GPT-2 Psoralen, the city of the spiritualist, and had been given to him by God, who wished to show him
the way of salvation, and to draw him back to the true life of Christ, and to bring him into communion with his fellow-man.
BioGPT Psoralen photochemotherapy (PUVA) is a well-established treatment for psoriasis, but its use is limited by the risk of skin cancer, particularly squamous cell carcinoma (SCC) of the head and neck (H & N), which is the most common site of skin cancer in the United States (US)
CP-673451 GPT-2 CP-673451) and 4-5-6-3-1-2-3-4-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22-23-24-25-26-27-
BioGPT CP-673451 is a potent, selective, and orally active inhibitor of human neutrophil elastase (HNE) and human cathepsin G (CatG) with in vitro and in vivo anti-inflammatory activity in a variety of animal models of inflammation and in a model of acute lung injury (ALI) in the rat induced by intratracheal instillation of lipopolysaccharide (LPS) and tumor necrosis factor-alpha (TNF-alpha), a model of acute lung injury (ALI) in which neutrophils play an important role.
BIIB-021 GPT-2 BIIB-021A-2-1.pdf. Wright, C. (2002). ‘The War on Terror: A Legal Theory of Terrorist Attacks,’ in
L.E.R. Wright, S.R. Warrick and J.H. Rothman (Eds.), The War on Terror: Essays in Honor of Michael T. Klare (New York: Oxford University Press), 143-57.
BioGPT BIIB-021 is a novel, orally active, non-peptide bradykinin B2 receptor antagonist with potent and long-lasting anti-inflammatory activity in animal models of acute and chronic inflammation and in a rat model of adjuvant-induced arthritis (AIA), an animal model of rheumatoid arthritis (RA) and in a rat model of collagen-induced arthritis (CIA), an animal model of collagen-induced arthritis (CIA), in which arthritis is induced by immunization with bovine type II collagen (CII).
Huang L, Lin J, Li X, Song L, Zheng Z, Wong KC.Brief Bioinform. 2022 Jan 17;23(1):bbab451. doi: 10.1093/bib/bbab451.PMID: 34791012
The rapid growth in literature accumulates diverse and yet comprehensive biomedical knowledge hidden to be mined such as drug interactions. However, it is difficult to extract the heterogeneous knowledge to retrieve or even discover the latest and novel knowledge in an efficient manner. To address such a problem, we propose EGFI for extracting and consolidating drug interactions from large-scale medical literature text data. Specifically, EGFI consists of two parts: classification and generation. In the classification part, EGFI encompasses the language model BioBERT which has been comprehensively pretrained on biomedical corpus. In particular, we propose the multihead self-attention mechanism and packed BiGRU to fuse multiple semantic information for rigorous context modeling. In the generation part, EGFI utilizes another pretrained language model BioGPT-2 where the generation sentences are selected based on filtering rules.
Results: We evaluated the classification part on ‘DDIs 2013’ dataset and ‘DTIs’ dataset, achieving the F1 scores of 0.842 and 0.720 respectively. Moreover, we applied the classification part to distinguish high-quality generated sentences and verified with the existing growth truth to confirm the filtered sentences. The generated sentences that are not recorded in DrugBank and DDIs 2013 dataset demonstrated the potential of EGFI to identify novel drug relationships.
Jin Q, Yang Y, Chen Q, Lu Z.ArXiv. 2023 May 16:arXiv:2304.09667v3. Preprint.PMID: 37131884 Free PMC article.
While large language models (LLMs) have been successfully applied to various tasks, they still face challenges with hallucinations. Augmenting LLMs with domain-specific tools such as database utilities can facilitate easier and more precise access to specialized knowledge. In this paper, we present GeneGPT, a novel method for teaching LLMs to use the Web APIs of the National Center for Biotechnology Information (NCBI) for answering genomics questions. Specifically, we prompt Codex to solve the GeneTuring tests with NCBI Web APIs by in-context learning and an augmented decoding algorithm that can detect and execute API calls. Experimental results show that GeneGPT achieves state-of-the-art performance on eight tasks in the GeneTuring benchmark with an average score of 0.83, largely surpassing retrieval-augmented LLMs such as the new Bing (0.44), biomedical LLMs such as BioMedLM (0.08) and BioGPT (0.04), as well as GPT-3 (0.16) and ChatGPT (0.12). Our further analyses suggest that: (1) API demonstrations have good cross-task generalizability and are more useful than documentations for in-context learning; (2) GeneGPT can generalize to longer chains of API calls and answer multi-hop questions in GeneHop, a novel dataset introduced in this work; (3) Different types of errors are enriched in different tasks, providing valuable insights for future improvements.
PLEASE WATCH THE FOLLOWING VIDEOS ON BIOGPT
This one entitled
Microsoft’s BioGPT Shows Promise as the Best Biomedical NLP
gives a good general description of this new MIT/Microsoft project and its usefullness in scanning 15 million articles on PubMed while returning ChatGPT like answers.
Please note one of the comments which is VERY IMPORTANT
bioGPT is difficult for non-developers to use, and Microsoft researchers seem to default that all users are proficient in Python and ML.
Much like Microsoft Azure it seems this BioGPT is meant for developers who have advanced programming skill. Seems odd then to be paying programmers multiK salaries when one or two Key Opinion Leaders from the medical field might suffice but I would be sure Microsoft will figure this out.
ALSO VIEW VIDEO
This is a talk from Microsoft on BioGPT
Other Relevant Articles on Natural Language Processing in BioInformatics, Healthcare and ChatGPT for Medicine on this Open Access Scientific Journal Include
Acinetobacter baumannii bacteria that are resistant to important antibiotics called carbapenems. Acinetobacter baumannii are highly-drug resistant bacteria that can cause a range of infections for hospitalized patients, including pneumonia, wound, or blood infections.
Pseudomonas aeruginosa, which are resistant to carbapenems. Pseudomonas aeruginosa can cause skin rashes and ear infectious in healthy people but also severe blood infections and pneumonia when contracted by sick people in the hospital.
Enterobacteriaceae — a family of bacteria that live in the human gut — that are resistant to both carbepenems and another class of antibiotics, cephalosporins.
It has been designated critical need for development of antibiotics to these pathogens. Now researchers at Mcmaster University and others in the US had used artificial intelligence (AI) to screen libraries of over 7,000 chemicals to find a drug that could be repurposed to kill off the pathogen.
Liu et. Al. (1) published their results of an AI screen to narrow down potential chemicals that could work against Acinetobacter baumanii in Nature Chemical Biology recently.
Abstract
Acinetobacter baumannii is a nosocomial Gram-negative pathogen that often displays multidrug resistance. Discovering new antibiotics against A. baumannii has proven challenging through conventional screening approaches. Fortunately, machine learning methods allow for the rapid exploration of chemical space, increasing the probability of discovering new antibacterial molecules. Here we screened ~7,500 molecules for those that inhibited the growth of A. baumannii in vitro. We trained a neural network with this growth inhibition dataset and performed in silico predictions for structurally new molecules with activity against A. baumannii. Through this approach, we discovered abaucin, an antibacterial compound with narrow-spectrum activity against A. baumannii. Further investigations revealed that abaucin perturbs lipoprotein trafficking through a mechanism involving LolE. Moreover, abaucin could control an A. baumannii infection in a mouse wound model. This work highlights the utility of machine learning in antibiotic discovery and describes a promising lead with targeted activity against a challenging Gram-negative pathogen.
Schematic workflow for incorporation of AI for antibiotic drug discovery for A. baumannii from 1. Liu, G., Catacutan, D.B., Rathod, K. et al. Deep learning-guided discovery of an antibiotic targeting Acinetobacter baumannii. Nat Chem Biol (2023). https://doi.org/10.1038/s41589-023-01349-8
Antibiotics kill bacteria. However, there has been a lack of new drugs for decades and bacteria are becoming harder to treat, as they evolve resistance to the ones we have.
More than a million people a year are estimated to die from infections that resist treatment with antibiotics.The researchers focused on one of the most problematic species of bacteria – Acinetobacter baumannii, which can infect wounds and cause pneumonia.
You may not have heard of it, but it is one of the three superbugs the World Health Organization has identified as a “critical” threat.
It is often able to shrug off multiple antibiotics and is a problem in hospitals and care homes, where it can survive on surfaces and medical equipment.
Dr Jonathan Stokes, from McMaster University, describes the bug as “public enemy number one” as it’s “really common” to find cases where it is “resistant to nearly every antibiotic”.
Artificial intelligence
To find a new antibiotic, the researchers first had to train the AI. They took thousands of drugs where the precise chemical structure was known, and manually tested them on Acinetobacter baumannii to see which could slow it down or kill it.
This information was fed into the AI so it could learn the chemical features of drugs that could attack the problematic bacterium.
The AI was then unleashed on a list of 6,680 compounds whose effectiveness was unknown. The results – published in Nature Chemical Biology – showed it took the AI an hour and a half to produce a shortlist.
The researchers tested 240 in the laboratory, and found nine potential antibiotics. One of them was the incredibly potent antibiotic abaucin.
Laboratory experiments showed it could treat infected wounds in mice and was able to kill A. baumannii samples from patients.
However, Dr Stokes told me: “This is when the work starts.”
The next step is to perfect the drug in the laboratory and then perform clinical trials. He expects the first AI antibiotics could take until 2030 until they are available to be prescribed.
Curiously, this experimental antibiotic had no effect on other species of bacteria, and works only on A. baumannii.
Many antibiotics kill bacteria indiscriminately. The researchers believe the precision of abaucin will make it harder for drug-resistance to emerge, and could lead to fewer side-effects.
In principle, the AI could screen tens of millions of potential compounds – something that would be impractical to do manually.
“AI enhances the rate, and in a perfect world decreases the cost, with which we can discover these new classes of antibiotic that we desperately need,” Dr Stokes told me.
The researchers tested the principles of AI-aided antibiotic discovery in E. coli in 2020, but have now used that knowledge to focus on the big nasties. They plan to look at Staphylococcus aureus and Pseudomonas aeruginosa next.
“This finding further supports the premise that AI can significantly accelerate and expand our search for novel antibiotics,” said Prof James Collins, from the Massachusetts Institute of Technology.
He added: “I’m excited that this work shows that we can use AI to help combat problematic pathogens such as A. baumannii.”
Prof Dame Sally Davies, the former chief medical officer for England and government envoy on anti-microbial resistance, told Radio 4’s The World Tonight: “We’re onto a winner.”
She said the idea of using AI was “a big game-changer, I’m thrilled to see the work he (Dr Stokes) is doing, it will save lives”.
Other related articles and books published in this Online Scientific Journal include the following:
Series D: e-Books on BioMedicine – Metabolomics, Immunology, Infectious Diseases, Reproductive Genomic Endocrinology
The female reproductive lifespan is regulated by the menstrual cycle. Defined as the interval between the menarche and menopause, it is approximately 35 years in length on average. Based on current average human life expectancy figures, and excluding fertility issues, this means that the female body can bear children for almost half of its lifetime. Thus, within this time span many individuals may consider contraception at some point in their reproductive life. A wide variety of contraceptive methods are now available, which are broadly classified into hormonal and non-hormonal approaches. A normal menstrual cycle is controlled by a delicate interplay of hormones, including estrogen, progesterone, follicle-stimulating hormone (FSH) and luteinizing hormone (LH), among others. These molecules are produced by the various glands in the body that make up the endocrine system.
Hormonal contraceptives – including the contraceptive pill, some intrauterine devices (IUDs) and hormonal implants – utilize exogenous (or synthetic) hormones to block or suppress ovulation, the phase of the menstrual cycle where an egg is released into the uterus. Beyond their use as methods to prevent pregnancy, hormonal contraceptives are also being increasingly used to suppress ovulation as a method for treating premenstrual syndromes. Hormonal contraceptives composed of exogenous estrogen and/or progesterone are commonly administered artificial means of birth control. Despite many benefits, adverse side effects associated with high doses such as thrombosis and myocardial infarction, cause hesitation to usage.
Scientists at the University of the Philippines and Roskilde University are exploring methods to optimize the dosage of exogenous hormones in such contraceptives. Their overall aim is the creation of patient-specific minimizing dosing schemes, to prevent adverse side effects that can be associated with hormonal contraceptive use and empower individuals in their contraceptive journey. Their research data showed evidence that the doses of exogenous hormones in certain contraceptive methods could be reduced, while still ensuring ovulation is suppressed. Reducing the total exogenous hormone dose by 92% in estrogen-only contraceptives, or the total dose by 43% in progesterone-only contraceptives, prevented ovulation according to the model. In contraceptives combining estrogen and progesterone, the doses could be reduced further.
Verily announced other organizational changes, 1/13/2023
Reporter: Aviva Lev-Ari, PhD, RN
The layoffs come just a few months after Verily raised $1 billion in an investment round led by Alphabet. At the time of the investment round, Verily said the $1 billion would be used to expand its business in precision health.
In addition to the layoffs, Verily announced other organizational changes.
“We are making changes that refine our strategy, prioritize our product portfolio and simplify our operating model,” Gillett said in his email. “We will advance fewer initiatives with greater resources. In doing so, Verily will move from multiple lines of business to one centralized product organization with increasingly connected healthcare solutions.”
The company will specifically focus on AI and data science to accelerate learning and improving outcomes, with advancing precision health being the top overarching goal. In addition, the company will simplify how it works, “designing complexity out of Verily.”
Among its product portfolio, Verily plans to “do fewer things” and focus its efforts within research and care. The company is “discontinuing the development of Verily Value Suite and some early-stage products, including our work in remote patient monitoring for heart failure and microneedles for drug delivery,” Gillet said. By eliminating Verily Value Suite, some staff will be redeployed elsewhere, while others will leave the company, Gillet said.
The 15% of eliminated staff include roles within discontinued programs and redundancy within the new, simplified organization. Gillet also announced leadership changes, including expanding the role of Amy Abernethy to become president of product development and chief medical officer. Scott Burke will expand his responsibilities as chief technology officer, adding hardware engineering and devices teams to his responsibilities, as well as serving as the bridge between product development and customer needs. Lisa Greenbaum will expand her responsibilities in a new chief commercial officer role, overseeing sales, marketing and corporate strategy teams.
Use of Systems Biology for Design of inhibitor of Galectins as Cancer Therapeutic – Strategy and Software
Curator:Stephen J. Williams, Ph.D.
Below is a slide representation of the overall mission 4 to produce a PROTAC to inhibit Galectins 1, 3, and 9.
Using A Priori Knowledge of Galectin Receptor Interaction to Create a BioModel of Galectin 3 Binding
Now after collecting literature from PubMed on “galectin-3” AND “binding” to determine literature containing kinetic data we generate a WordCloud on the articles.
This following file contains the articles needed for BioModels generation.
From the WordCloud we can see that these corpus of articles describe galectin binding to the CRD (carbohydrate recognition domain). Interestingly there are many articles which describe van Der Waals interactions as well as electrostatic interactions. Certain carbohydrate modifictions like Lac NAc and Gal 1,4 may be important. Many articles describe the bonding as well as surface interactions. Many studies have been performed with galectin inhibitors like TDGs (thio-digalactosides) like TAZ TDG (3-deoxy-3-(4-[m-fluorophenyl]-1H-1,2,3-triazol-1-yl)-thio-digalactoside). This led to an interesting article
.
Dual thio-digalactoside-binding modes of human galectins as the structural basis for the design of potent and selective inhibitors
Human galectins are promising targets for cancer immunotherapeutic and fibrotic disease-related drugs. We report herein the binding interactions of three thio-digalactosides (TDGs) including TDG itself, TD139 (3,3′-deoxy-3,3′-bis-(4-[m-fluorophenyl]-1H-1,2,3-triazol-1-yl)-thio-digalactoside, recently approved for the treatment of idiopathic pulmonary fibrosis), and TAZTDG (3-deoxy-3-(4-[m-fluorophenyl]-1H-1,2,3-triazol-1-yl)-thio-digalactoside) with human galectins-1, -3 and -7 as assessed by X-ray crystallography, isothermal titration calorimetry and NMR spectroscopy. Five binding subsites (A-E) make up the carbohydrate-recognition domains of these galectins. We identified novel interactions between an arginine within subsite E of the galectins and an arene group in the ligands. In addition to the interactions contributed by the galactosyl sugar residues bound at subsites C and D, the fluorophenyl group of TAZTDG preferentially bound to subsite B in galectin-3, whereas the same group favored binding at subsite E in galectins-1 and -7. The characterised dual binding modes demonstrate how binding potency, reported as decreased Kd values of the TDG inhibitors from μM to nM, is improved and also offer insights to development of selective inhibitors for individual galectins.
Figures
Figure 1. Chemical structures of L3, TDG…
Figure 2. Structural comparison of the carbohydrate…
Infertility is a major reproductive health issue that affects about 12% of women of reproductive age in the United States. Aneuploidy in eggs accounts for a significant proportion of early miscarriage and in vitro fertilization failure. Recent studies have shown that genetic variants in several genes affect chromosome segregation fidelity and predispose women to a higher incidence of egg aneuploidy. However, the exact genetic causes of aneuploid egg production remain unclear, making it difficult to diagnose infertility based on individual genetic variants in mother’s genome. Although, age is a predictive factor for aneuploidy, it is not a highly accurate gauge because aneuploidy rates within individuals of the same age can vary dramatically.
Researchers described a technique combining genomic sequencing with machine-learning methods to predict the possibility a woman will undergo a miscarriage because of egg aneuploidy—a term describing a human egg with an abnormal number of chromosomes. The scientists were able to examine genetic samples of patients using a technique called “whole exome sequencing,” which allowed researchers to home in on the protein coding sections of the vast human genome. Then they created software using machine learning, an aspect of artificial intelligence in which programs can learn and make predictions without following specific instructions. To do so, the researchers developed algorithms and statistical models that analyzed and drew inferences from patterns in the genetic data.
As a result, the scientists were able to create a specific risk score based on a woman’s genome. The scientists also identified three genes—MCM5, FGGY and DDX60L—that when mutated and are highly associated with a risk of producing eggs with aneuploidy. So, the report demonstrated that sequencing data can be mined to predict patients’ aneuploidy risk thus improving clinical diagnosis. The candidate genes and pathways that were identified in the present study are promising targets for future aneuploidy studies. Identifying genetic variations with more predictive power will serve women and their treating clinicians with better information.
Each of these posts were on the importance of scientific curation of findings within the realm of social media and the Web 2.0; a sub-environment known throughout the scientific communities as Science 2.0, in which expert networks collaborated together to produce massive new corpus of knowledge by sharing their views, insights on peer reviewed scientific findings. And through this new media, this process of curation would, in itself generate new ideas and new directions for research and discovery.
The platform sort of looked like the image below:
This system lied above a platform of the original Science 1.0, made up of all the scientific journals, books, and traditional literature:
In the old Science 1.0 format, scientific dissemination was in the format of hard print journals, and library subscriptions were mandatory (and eventually expensive). Open Access has tried to ameliorate the expense problem.
Previous image source: PeerJ.com
To index the massive and voluminous research and papers beyond the old Dewey Decimal system, a process of curation was mandatory. The dissemination of this was a natural for the new social media however the cost had to be spread out among numerous players. Journals, faced with the high costs of subscriptions and their only way to access this new media as an outlet was to become Open Access, a movement first sparked by journals like PLOS and PeerJ but then begrudingly adopted throughout the landscape. But with any movement or new adoption one gets the Good the Bad and the Ugly (as described in my cited, above, Clive Thompson article). The bad side of Open Access Journals were
costs are still assumed by the individual researcher not by the journals
the arise of the numerous Predatory Journals
Even PeerJ, in their column celebrating an anniversary of a year’s worth of Open Access success stories, lamented the key issues still facing Open Access in practice
which included the cost and the rise of predatory journals.
In essence, Open Access and Science 2.0 sprung full force BEFORE anyone thought of a way to defray the costs
Can Web 3.0 Finally Offer a Way to Right the Issues Facing High Costs of Scientific Publishing?
Web 1.0 and Web 2.0 refer to eras in the history of the Internet as it evolved through various technologies and formats. Web 1.0 refers roughly to the period from 1991 to 2004, where most websites were static webpages, and the vast majority of users were consumers, not producers, of content.[6][7] Web 2.0 is based around the idea of “the web as platform”,[8] and centers on user-created content uploaded to social-networking services, blogs, and wikis, among other services.[9] Web 2.0 is generally considered to have begun around 2004, and continues to the current day.[8][10][4]
The term “Web3”, specifically “Web 3.0”, was coined by Ethereum co-founder Gavin Wood in 2014.[1] In 2020 and 2021, the idea of Web3 gained popularity[citation needed]. Particular interest spiked towards the end of 2021, largely due to interest from cryptocurrency enthusiasts and investments from high-profile technologists and companies.[4][5] Executives from venture capital firm Andreessen Horowitz travelled to Washington, D.C. in October 2021 to lobby for the idea as a potential solution to questions about Internet regulation with which policymakers have been grappling.[11]
Web3 is distinct from Tim Berners-Lee‘s 1999 concept for a semantic web, which has also been called “Web 3.0”.[12] Some writers referring to the decentralized concept usually known as “Web3” have used the terminology “Web 3.0”, leading to some confusion between the two concepts.[2][3] Furthermore, some visions of Web3 also incorporate ideas relating to the semantic web.[13][14]
Web3 revolves around the idea of decentralization, which proponents often contrast with Web 2.0, wherein large amounts of the web’s data and content are centralized in the fairly small group of companies often referred to as Big Tech.[4]
Specific visions for Web3 differ, but all are heavily based in blockchain technologies, such as various cryptocurrencies and non-fungible tokens (NFTs).[4]Bloomberg described Web3 as an idea that “would build financial assets, in the form of tokens, into the inner workings of almost anything you do online”.[15] Some visions are based around the concepts of decentralized autonomous organizations (DAOs).[16]Decentralized finance (DeFi) is another key concept; in it, users exchange currency without bank or government involvement.[4]Self-sovereign identity allows users to identify themselves without relying on an authentication system such as OAuth, in which a trusted party has to be reached in order to assess identity.[17]
Technologists and journalists have described Web3 as a possible solution to concerns about the over-centralization of the web in a few “Big Tech” companies.[4][11] Some have expressed the notion that Web3 could improve data security, scalability, and privacy beyond what is currently possible with Web 2.0 platforms.[14]Bloomberg states that sceptics say the idea “is a long way from proving its use beyond niche applications, many of them tools aimed at crypto traders”.[15]The New York Times reported that several investors are betting $27 billion that Web3 “is the future of the internet”.[18][19]
Some companies, including Reddit and Discord, have explored incorporating Web3 technologies into their platforms in late 2021.[4][20] After heavy user backlash, Discord later announced they had no plans to integrate such technologies.[21] The company’s CEO, Jason Citron, tweeted a screenshot suggesting it might be exploring integrating Web3 into their platform. This led some to cancel their paid subscriptions over their distaste for NFTs, and others expressed concerns that such a change might increase the amount of scams and spam they had already experienced on crypto-related Discord servers.[20] Two days later, Citron tweeted that the company had no plans to integrate Web3 technologies into their platform, and said that it was an internal-only concept that had been developed in a company-wide hackathon.[21]
Some legal scholars quoted by The Conversation have expressed concerns over the difficulty of regulating a decentralized web, which they reported might make it more difficult to prevent cybercrime, online harassment, hate speech, and the dissemination of child abuse images.[13] But, the news website also states that, “[decentralized web] represents the cyber-libertarian views and hopes of the past that the internet can empower ordinary people by breaking down existing power structures.” Some other critics of Web3 see the concept as a part of a cryptocurrency bubble, or as an extension of blockchain-based trends that they see as overhyped or harmful, particularly NFTs.[20] Some critics have raised concerns about the environmental impact of cryptocurrencies and NFTs. Others have expressed beliefs that Web3 and the associated technologies are a pyramid scheme.[5]
Kevin Werbach, author of The Blockchain and the New Architecture of Trust,[22] said that “many so-called ‘web3’ solutions are not as decentralized as they seem, while others have yet to show they are scalable, secure and accessible enough for the mass market”, adding that this “may change, but it’s not a given that all these limitations will be overcome”.[23]
David Gerard, author of Attack of the 50 Foot Blockchain,[24] told The Register that “web3 is a marketing buzzword with no technical meaning. It’s a melange of cryptocurrencies, smart contracts with nigh-magical abilities, and NFTs just because they think they can sell some monkeys to morons”.[25]
Below is an article from MarketWatch.com Distributed Ledger series about the different forms and cryptocurrencies involved
by Frances Yue, Editor of Distributed Ledger, Marketwatch.com
Clayton Gardner, co-CEO of crypto investment management firm Titan, told Distributed Ledger that as crypto embraces broader adoption, he expects more institutions to bypass bitcoin and invest in other blockchains, such as Ethereum, Avalanche, and Terra in 2022. which all boast smart-contract features.
Bitcoin traditionally did not support complex smart contracts, which are computer programs stored on blockchains, though a major upgrade in November might have unlocked more potential.
“Bitcoin was originally seen as a macro speculative asset by many funds and for many it still is,” Gardner said. “If anything solidifies its use case, it’s a store of value. It’s not really used as originally intended, perhaps from a medium of exchange perspective.”
For institutions that are looking for blockchains that can “produce utility and some intrinsic value over time,” they might consider some other smart contract blockchains that have been driving the growth of decentralized finance and web 3.0, the third generation of the Internet, according to Gardner.
“Bitcoin is still one of the most secure blockchains, but I think layer-one, layer-two blockchains beyond Bitcoin, will handle the majority of transactions and activities from NFT (nonfungible tokens) to DeFi,“ Gardner said. “So I think institutions see that and insofar as they want to put capital to work in the coming months, I think that could be where they just pump the capital.”
Decentralized social media？
The price of Decentralized Social, or DeSo, a cryptocurrency powering a blockchain that supports decentralized social media applications, surged roughly 74% to about $164 from $94, after Deso was listed at Coinbase Pro on Monday, before it fell to about $95, according to CoinGecko.
In the eyes of Nader Al-Naji, head of the DeSo foundation, decentralized social media has the potential to be “a lot bigger” than decentralized finance.
“Today there are only a few companies that control most of what we see online,” Al-Naji told Distributed Ledger in an interview. But DeSo is “creating a lot of new ways for creators to make money,” Al-Naji said.
“If you find a creator when they’re small, or an influencer, you can invest in that, and then if they become bigger and more popular, you make money and they make and they get capital early on to produce their creative work,” according to AI-Naji.
BitClout, the first application that was created by AI-Naji and his team on the DeSo blockchain, had initially drawn controversy, as some found that they had profiles on the platform without their consent, while the application’s users were buying and selling tokens representing their identities. Such tokens are called “creator coins.”
AI-Naji responded to the controversy saying that DeSo now supports more than 200 social-media applications including Bitclout. “I think that if you don’t like those features, you now have the freedom to use any app you want. Some apps don’t have that functionality at all.”
But Before I get to the “selling monkeys to morons” quote,
I want to talk about
THE GOOD, THE BAD, AND THE UGLY
THE GOOD
My foray into Science 2.0 and then pondering what the movement into a Science 3.0 led me to an article by Dr. Vladimir Teif, who studies gene regulation and the nucleosome, as well as creating a worldwide group of scientists who discuss matters on chromatin and gene regulation in a journal club type format.
Fragile Nucleosome is an international community of scientists interested in chromatin and gene regulation. Fragile Nucleosome is active in several spaces: one is the Discord server where several hundred scientists chat informally on scientific matters. You can join the Fragile Nucleosome Discord server. Another activity of the group is the organization of weekly virtual seminars on Zoom. Our webinars are usually conducted on Wednesdays 9am Pacific time (5pm UK, 6pm Central Europe). Most previous seminars have been recorded and can be viewed at our YouTube channel. The schedule of upcoming webinars is shown below. Our third activity is the organization of weekly journal clubs detailed at a separate page (Fragile Nucleosome Journal Club).
This concept of science 3.0 he had coined back in 2009. As Dr Teif had mentioned
So essentially I first introduced this word Science 3.0 in 2009, and since then we did a lot to implement this in practice. The Twitter account @generegulation is also one of examples
This is curious as we still have an ill defined concept of what #science3_0 would look like but it is a good read nonetheless.
The concept of Science 2.0 was introduced almost a decade ago to describe the new generation of online-based tools for researchers allowing easier data sharing, collaboration and publishing. Although technically sound, the concept still does not work as expected. Here we provide a systematic line of arguments to modify the concept of Science 2.0, making it more consistent with the spirit and traditions of science and Internet. Our first correction to the Science 2.0 paradigm concerns the open-access publication models charging fees to the authors. As discussed elsewhere, we show that the monopoly of such publishing models increases biases and inequalities in the representation of scientific ideas based on the author’s income. Our second correction concerns post-publication comments online, which are all essentially non-anonymous in the current Science 2.0 paradigm. We conclude that scientific post-publication discussions require special anonymization systems. We further analyze the reasons of the failure of the current post-publication peer-review models and suggest what needs to be changed in Science 3.0 to convert Internet into a large journal club. [bold face added]
In this paper it is important to note the transition of a science 1.0, which involved hard copy journal publications usually only accessible in libraries to a more digital 2.0 format where data, papers, and ideas could be easily shared among networks of scientists.
As Dr. Teif states, the term “Science 2.0” had been coined back in 2009, and several influential journals including Science, Nature and Scientific American endorsed this term and suggested scientists to move online and their discussions online. However, even at present there are thousands on this science 2.0 platform, Dr Teif notes the number of scientists subscribed to many Science 2.0 networking groups such as on LinkedIn and ResearchGate have seemingly saturated over the years, with little new members in recent times.
The consensus is that science 2.0 networking is:
good because it multiplies the efforts of many scientists, including experts and adds to the scientific discourse unavailable on a 1.0 format
that online data sharing is good because it assists in the process of discovery (can see this evident with preprint servers, bio-curated databases, Github projects)
open-access publishing is beneficial because free access to professional articles and open-access will be the only publishing format in the future (although this is highly debatable as many journals are holding on to a type of “hybrid open access format” which is not truly open access
only sharing of unfinished works and critiques or opinions is good because it creates visibility for scientists where they can receive credit for their expert commentary
There are a few concerns on Science 3.0 Dr. Teif articulates:
A. Science 3.0 Still Needs Peer Review
Peer review of scientific findings will always be an imperative in the dissemination of well-done, properly controlled scientific discovery. As Science 2.0 relies on an army of scientific volunteers, the peer review process also involves an army of scientific experts who give their time to safeguard the credibility of science, by ensuring that findings are reliable and data is presented fairly and properly. It has been very evident, in this time of pandemic and the rapid increase of volumes of preprint server papers on Sars-COV2, that peer review is critical. Many of these papers on such preprint servers were later either retracted or failed a stringent peer review process.
Now many journals of the 1.0 format do not generally reward their peer reviewers other than the self credit that researchers use on their curriculum vitaes. Some journals, like the MDPI journal family, do issues peer reviewer credits which can be used to defray the high publication costs of open access (one area that many scientists lament about the open access movement; where the burden of publication cost lies on the individual researcher).
An issue which is highlighted is the potential for INFORMATION NOISE regarding the ability to self publish on Science 2.0 platforms.
The NEW BREED was born in 4/2012
An ongoing effort on this platform, https://pharmaceuticalintelligence.com/, is to establish a scientific methodology for curating scientific findings where one the goals is to assist to quell the information noise that can result from the massive amounts of new informatics and data occurring in the biomedical literature.
B. Open Access Publishing Model leads to biases and inequalities in the idea selection
The open access publishing model has been compared to the model applied by the advertising industry years ago and publishers then considered the journal articles as “advertisements”. However NOTHING could be further from the truth. In advertising the publishers claim the companies not the consumer pays for the ads. However in scientific open access publishing, although the consumer (libraries) do not pay for access the burden of BOTH the cost of doing the research and publishing the findings is now put on the individual researcher. Some of these publishing costs can be as high as $4000 USD per article, which is very high for most researchers. However many universities try to refund the publishers if they do open access publishing so it still costs the consumer and the individual researcher, limiting the cost savings to either.
However, this sets up a situation in which young researchers, who in general are not well funded, are struggling with the publication costs, and this sets up a bias or inequitable system which rewards the well funded older researchers and bigger academic labs.
C. Post publication comments and discussion require online hubs and anonymization systems
Many recent publications stress the importance of a post-publication review process or system yet, although many big journals like Nature and Science have their own blogs and commentary systems, these are rarely used. In fact they show that there are just 1 comment per 100 views of a journal article on these systems. In the traditional journals editors are the referees of comments and have the ability to censure comments or discourse. The article laments that comments should be easy to do on journals, like how easy it is to make comments on other social sites, however scientists are not offering their comments or opinions on the matter.
In a personal experience,
a well written commentary goes through editors which usually reject a comment like they were rejecting an original research article. Thus many scientists, I believe, after fashioning a well researched and referenced reply, do not get the light of day if not in the editor’s interests.
Therefore the need for anonymity is greatly needed and the lack of this may be the hindrance why scientific discourse is so limited on these types of Science 2.0 platforms. Platforms that have success in this arena include anonymous platforms like Wikipedia or certain closed LinkedIn professional platforms but more open platforms like Google Knowledge has been a failure.
A great example on this platform was a very spirited conversation on LinkedIn on genomics, tumor heterogeneity and personalized medicine which we curated from the LinkedIn discussion (unfortunately LinkedIn has closed many groups) seen here:
In this discussion, it was surprising that over a weekend so many scientists from all over the world contributed to a great discussion on the topic of tumor heterogeneity.
But many feel such discussions would be safer if they were anonymized. However then researchers do not get any credit for their opinions or commentaries.
A Major problem is how to take the intangible and make them into tangible assets which would both promote the discourse as well as reward those who take their time to improve scientific discussion.
This is where something like NFTs or a decentralized network may become important!
Below is an online @TwitterSpace Discussion we had with some young scientists who are just starting out and gave their thoughts on what SCIENCE 3.0 and the future of dissemination of science might look like, in light of this new Meta Verse. However we have to define each of these terms in light of Science and not just the Internet as merely a decentralized marketplace for commonly held goods.
This online discussion was tweeted out and got a fair amount of impressions (60) as well as interactors (50).
To introduce this discussion first a few startoff material which will fram this discourse
The Intenet and the Web is rapidly adopting a new “Web 3.0” format, with decentralized networks, enhanced virtual experiences, and greater interconnection between people. Here we start the discussion what will the move from Science 2.0, where dissemination of scientific findings was revolutionized and piggybacking on Web 2.0 or social media, to a Science 3.0 format. And what will it involve or what paradigms will be turned upside down?
Old Science 1.0 is still the backbone of all scientific discourse, built on the massive amount of experimental and review literature. However this literature was in analog format, and we moved to a more accesible digital open access format for both publications as well as raw data. However as there was a structure for 1.0, like the Dewey decimal system and indexing, 2.0 made science more accesible and easier to search due to the newer digital formats. Yet both needed an organizing structure; for 1.0 that was the scientific method of data and literature organization with libraries as the indexers. In 2.0 this relied on an army mostly of volunteers who did not have much in the way of incentivization to co-curate and organize the findings and massive literature.
Each version of Science has their caveats: their benefits as well as deficiencies. This curation and the ongoing discussion is meant to solidy the basis for the new format, along with definitions and determination of structure.
We had high hopes for Science 2.0, in particular the smashing of data and knowledge silos. However the digital age along with 2.0 platforms seemed to excaccerbate this somehow. We still are critically short on analysis!
We really need people and organizations to get on top of this new Web 3.0 or metaverse so the similar issues do not get in the way: namely we need to create an organizing structure (maybe as knowledgebases), we need INCENTIVIZED co-curators, and we need ANALYSIS… lots of it!!
Are these new technologies the cure or is it just another headache?
There were a few overarching themes whether one was talking about AI, NLP, Virtual Reality, or other new technologies with respect to this new meta verse and a concensus of Decentralized, Incentivized, and Integrated was commonly expressed among the attendees
The Following are some slides from representative Presentations
Other article of note on this topic on this Open Access Scientific Journal Include:
AI enabled Drug Discovery and Development: The Challenges and the Promise
Reporter:Aviva Lev-Ari, PhD, RN
Early Development
Caroline Kovac (the first IBM GM of Life Sciences) is the one who started in silico development of drugs in 2000 using a big db of substances and computer power. She transformed an idea into $2b business. Most of the money was from big pharma. She was asking what is are the new drugs they are planning to develop and provided the four most probable combinations of substances, based on in Silicon work.
Carol Kovac
General Manager, Healthcare and Life Sciences, IBM
from speaker at conference on 2005
Carol Kovac is General Manager of IBM Healthcare and Life Sciences responsible for the strategic direction of IBM′s global healthcare and life sciences business. Kovac leads her team in developing the latest information technology solutions and services, establishing partnerships and overseeing IBM investment within the healthcare, pharmaceutical and life sciences markets. Starting with only two employees as an emerging business unit in the year 2000, Kovac has successfully grown the life sciences business unit into a multi-billion dollar business and one of IBM′s most successful ventures to date with more than 1500 employees worldwide. Kovac′s prior positions include general manager of IBM Life Sciences, vice president of Technical Strategy and Division Operations, and vice president of Services and Solutions. In the latter role, she was instrumental in launching the Computational Biology Center at IBM Research. Kovac sits on the Board of Directors of Research!America and Africa Harvest. She was inducted into the Women in Technology International Hall of Fame in 2002, and in 2004, Fortune magazine named her one of the 50 most powerful women in business. Kovac earned her Ph.D. in chemistry at the University of Southern California.
The use of artificial intelligence in drug discovery, when coupled with new genetic insights and the increase of patient medical data of the last decade, has the potential to bring novel medicines to patients more efficiently and more predictably.
Jack Fuchs, MBA ’91, an adjunct lecturer who teaches “Principled Entrepreneurial Decisions” at Stanford School of Engineering, moderated and explored how clearly articulated principles can guide the direction of technological advancements like AI-enabled drug discovery.
Kim Branson, Global head of AI and machine learning at GSK.
Russ Altman, the Kenneth Fong Professor of Bioengineering, of genetics, of medicine (general medical discipline), of biomedical data science and, by courtesy, of computer science.
Synthetic Biology Software applied to development of Galectins Inhibitors at LPBI Group
Using Structural Computation Models to Predict Productive PROTAC Ternary Complexes
Ternary complex formation is necessary but not sufficient for target protein degradation. In this research, Bai et al. have addressed questions to better understand the rate-limiting steps between ternary complex formation and target protein degradation. They have developed a structure-based computer model approach to predict the efficiency and sites of target protein ubiquitination by CRNB-binding PROTACs. Such models will allow a more complete understanding of PROTAC-directed degradation and allow crafting of increasingly effective and specific PROTACs for therapeutic applications.
Another major feature of this research is that it a result of collaboration between research groups at Amgen, Inc. and Promega Corporation. In the past commercial research laboratories have shied away from collaboration, but the last several years have found researchers more open to collaborative work. This increased collaboration allows scientists to bring their different expertise to a problem or question and speed up discovery. According to Dr. Kristin Riching, Senior Research Scientist at Promega Corporation, “Targeted protein degraders have broken many of the rules that have guided traditional drug development, but it is exciting to see how the collective learnings we gain from their study can aid the advancement of this new class of molecules to the clinic as effective therapeutics.”
Medical Startups – Artificial Intelligence (AI) Startups in Healthcare
Reporters: Stephen J. Williams, PhD and Aviva Lev-Ari, PhD, RN and Shraga Rottem, MD, DSc,
The motivation for this post is two fold:
First, we are presenting an application of AI, NLP, DL to our own medical text in the Genomics space. Here we present the first section of Part 1 in the following book. Part 1 has six subsections that yielded 12 plots. The entire Book is represented by 38 x 2 = 76 plots.
Second, we bring to the attention of the e-Reader the list of 276 Medical Startups – Artificial Intelligence (AI) Startups in Healthcare as a hot universe of R&D activity in Human Health.
Third, to highlight one academic center with an AI focus
Dear friends of the ETH AI Center,
We would like to provide you with some exciting updates from the ETH AI Center and its growing community.
As the Covid-19 restrictions in Switzerland have recently been lifted, we would like to hear from you what kind of events you would like to see in 2022! Participate in the survey to suggest event formats and topics that you would enjoy being a part of. We are already excited to learn what we can achieve together this year.
We already have many interesting events coming up, we look forward to seeing you at our main and community events!
LPBI Group is applying AI for Medical Text Analysis with Machine Learning and Natural Language Processing: Statistical and Deep Learning
Our Book
Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS & BioInformatics, Simulations and the Genome Ontology
Medical Text Analysis of this Books shows the following results obtained by Madison Davis by applying Wolfram NLP for Biological Languages on our own Text. See below an Example:
2012pharmaceutical
Amandeep Kaur
Aashir Awan, Phd
Abhisar Anand
Adina Hazan
Alan F. Kaul, PharmD., MS, MBA, FCCP
alexcrystal6
anamikasarkar
apreconasia
aptubman
Arav Gandhi
aviralvatsa
David Orchard-Webb, PhD
danutdaagmailcom
Demet Sag, Ph.D., CRA, GCP
Dror Nir
dsmolyar
Ethan Coomber
evelinacohn
FrasonKalapurackal
Gail S Thornton
Irina Robu
jayzmit48
jdpmd
jshertok
kellyperlman
Ed Kislauskis
larryhbern
Madison Davis
marzankhan
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