GenDrux: A biomedical literature search system to identify gene expression-based drug sensitivity in breast cancer

Background This paper describes the development of a web-based tool, GenDrux, which extracts and presents (over the Internet) information related to the disease-gene-drug nexus. This information is archived from the relevant biomedical literature using automated methods. GenDrux is designed to alleviate the difficulties of manually processing the vast biomedical literature to identify disease-gene-drug relationships. GenDrux will evolve with the literature without additional algorithmic modifications. Results GenDrux, a pilot system, is developed in the domain of breast cancer and can be accessed at http://www.microarray.uab.edu/drug_gene.pl. GenDrux can be queried based on drug, gene and/or disease name. From over 8,000 relevant abstracts from the biomedical literature related to breast cancer, we have archived a corpus of more than 4,000 articles that depict gene expression-drug activity relationships for breast cancer and related cancers. The archiving process has been automated. Conclusions The successful development, implementation, and evaluation of this and similar systems when created may provide clinicians with a tool for literature management, clinical decision making, thus setting the platform for personalized therapy in the future

GenDrux: A biomedical literature search system to identify gene expression-based drug sensitivity in breast cancer

Background This paper describes the development of a web-based tool, GenDrux, which extracts and presents (over the Internet) information related to the disease-gene-drug nexus. This information is archived from the relevant biomedical literature using automated methods. GenDrux is designed to alleviate the difficulties of manually processing the vast biomedical literature to identify disease-gene-drug relationships. GenDrux will evolve with the literature without additional algorithmic modifications. Results GenDrux, a pilot system, is developed in the domain of breast cancer and can be accessed at http://www.microarray.uab.edu/drug_gene.pl. GenDrux can be queried based on drug, gene and/or disease name. From over 8,000 relevant abstracts from the biomedical literature related to breast cancer, we have archived a corpus of more than 4,000 articles that depict gene expression-drug activity relationships for breast cancer and related cancers. The archiving process has been automated. Conclusions The successful development, implementation, and evaluation of this and similar systems when created may provide clinicians with a tool for literature management, clinical decision making, thus setting the platform for personalized therapy in the future

Electronic health record: integrating evidence-based information at the point of clinical decision making

The authors created two tools to achieve the goals of providing physicians with a way to review alternative diagnoses and improving access to relevant evidence-based library resources without disrupting established workflows. The “diagnostic decision support tool” lifted terms from standard, coded fields in the electronic health record and sent them to Isabel, which produced a list of possible diagnoses. The physicians chose their diagnoses and were presented with the “knowledge page,” a collection of evidence-based library resources. Each resource was automatically populated with search results based on the chosen diagnosis. Physicians responded positively to the “knowledge page.

PEDSnet: a National Pediatric Learning Health System

A learning health system (LHS) integrates research done in routine care settings, structured data capture during every encounter, and quality improvement processes to rapidly implement advances in new knowledge, all with active and meaningful patient participation. While disease-specific pediatric LHSs have shown tremendous impact on improved clinical outcomes, a national digital architecture to rapidly implement LHSs across multiple pediatric conditions does not exist. PEDSnet is a clinical data research network that provides the infrastructure to support a national pediatric LHS. A consortium consisting of PEDSnet, which includes eight academic medical centers, two existing disease-specific pediatric networks, and two national data partners form the initial partners in the National Pediatric Learning Health System (NPLHS). PEDSnet is implementing a flexible dual data architecture that incorporates two widely used data models and national terminology standards to support multi-institutional data integration, cohort discovery, and advanced analytics that enable rapid learning

Monolayer 1T-NbSe2 as a 2D-correlated magnetic insulator

Monolayer group V transition metal dichalcogenides in their 1T phase have recently emerged as a platform to investigate rich phases of matter, such as spin liquid and ferromagnetism, resulting from strong electron correla- tions. Newly emerging 1T-NbSe2 has inspired theoretical investigations predicting collective phenomena such as charge transfer gap and ferromagnetism in two dimensions; however, the experimental evidence is still lacking. Here, by controlling the molecular beam epitaxy growth parameters, we demonstrate the successful growth of high-quality single-phase 1T-NbSe2. By combining scanning tunneling microscopy/spectroscopy and ab initio calculations, we show that this system is a charge transfer insulator with the upper Hubbard band located above the valence band maximum. To demonstrate the electron correlation resulted magnetic property, we create a vertical 1T/2H NbSe2 heterostructure, and we find unambiguous evidence of exchange interactions between the localized magnetic moments in 1T phase and the metallic/superconducting phase exemplified by Kondo reso- nances and Yu-Shiba-Rusinov–like bound states.Center for Dynamics and Control of Materials: an NSF MRSEC under cooperative agreement no. DMR-1720595. J.L. and F.G. were supported by the Robert A. Welch Foundation under award number F-1990-20190330. Other supports were from NSF grant nos. DMR-1808751 and DMR-1949701, the Welch Foundation F-1672, F-1814, and the National Natural Science Foundation of China (grant nos. 11774268 and 11974012).Center for Dynamics and Control of Material

Occurrence of new neurons in the piriform cortex

Adult neurogenesis has been well studied in hippocampus and subventricular zone; while this is much less appreciated in other brain regions, including amygdala, hypothalamus and piriform cortex. The present review aims at summarizing recent advances on the occurrence of new neurons in the piriform cortex, their potential origin and migration route from the subventricular zone. We further discuss the relevant implications in olfactory dysfunction accompanying the neuro-degenerative diseases

Dark sectors 2016 Workshop: community report

This report, based on the Dark Sectors workshop at SLAC in April 2016, summarizes the scientific importance of searches for dark sector dark matter and forces at masses beneath the weak-scale, the status of this broad international field, the important milestones motivating future exploration, and promising experimental opportunities to reach these milestones over the next 5-10 years

A Molecular Switch between Mammalian MLL Complexes Dictates Response to Menin-MLL Inhibition

Menin interacts with oncogenic MLL1-fusion proteins, and small molecules that disrupt these associations are in clinical trials for leukemia treatment. By integrating chromatin-focused and genome-wide CRISPR screens with genetic, pharmacologic, and biochemical approaches, we discovered a conserved molecular switch between the MLL1-Menin and MLL3/4-UTX chromatin-modifying complexes that dictates response to Menin-MLL inhibitors. MLL1-Menin safeguards leukemia survival by impeding the binding of the MLL3/4-UTX complex at a subset of target gene promoters. Disrupting the Menin-MLL1 interaction triggers UTX-dependent transcriptional activation of a tumor-suppressive program that dictates therapeutic responses in murine and human leukemia. Therapeutic reactivation of this program using CDK4/6 inhibitors mitigates treatment resistance in leukemia cells that are insensitive to Menin inhibitors. These findings shed light on novel functions of evolutionarily conserved epigenetic mediators like MLL1-Menin and MLL3/4-UTX and are relevant to understand and target molecular pathways determining therapeutic responses in ongoing clinical trials