Biomedical Data Commons (BMDC) prioritizes B-lymphocyte non-coding genetic variants in Type 1 Diabetes.

The repurposing of biomedical data is inhibited by its fragmented and multi-formatted nature that requires redundant investment of time and resources by data scientists. This is particularly true for Type 1 Diabetes (T1D), one of the most intensely studied common childhood diseases. Intense investigation of the contribution of pancreatic ß-islet and T-lymphocytes in T1D has been made. However, genetic contributions from B-lymphocytes, which are known to play a role in a subset of T1D patients, remain relatively understudied. We have addressed this issue through the creation of Biomedical Data Commons (BMDC), a knowledge graph that integrates data from multiple sources into a single queryable format. This increases the speed of analysis by multiple orders of magnitude. We develop a pipeline using B-lymphocyte multi-dimensional epigenome and connectome data and deploy BMDC to assess genetic variants in the context of Type 1 Diabetes (T1D). Pipeline-identified variants are primarily common, non-coding, poorly conserved, and are of unknown clinical significance. While variants and their chromatin connectivity are cell-type specific, they are associated with well-studied disease genes in T-lymphocytes. Candidates include established variants in the HLA-DQB1 and HLA-DRB1 and IL2RA loci that have previously been demonstrated to protect against T1D in humans and mice providing validation for this method. Others are included in the well-established T1D GRS2 genetic risk scoring method. More intriguingly, other prioritized variants are completely novel and form the basis for future mechanistic and clinical validation studies The BMDC community-based platform can be expanded and repurposed to increase the accessibility, reproducibility, and productivity of biomedical information for diverse applications including the prioritization of cell type-specific disease alleles from complex phenotypes.

Strong-field ionization of CH3Cl: proton migration and association.

Strong-field ionization of CH3Cl using femtosecond laser pulses, and the subsequent two-body dissociation of CH3Cl2+ along Hn+ (n = 1-3) and HCl+ forming pathways, have been experimentally studied in a home-built COLTRIMS (cold target recoil ion momentum spectrometer) setup. The single ionization rate of CH3Cl was obtained experimentally by varying the laser intensity from 1.6 × 1013 W cm-2 to 2.4 × 1014 W cm-2 and fitted with the rate obtained using the MO-ADK model. Additionally, the yield of Hn+ ions resulting from the dissociation of all charge states of CH3Cl was determined as a function of intensity and pulse duration (and chirp). Next, we identified four two-body breakup pathways of CH3Cl2+, which are H+ + CH2Cl+, H2+ + CHCl+, H3+ + CCl+, and CH2+ + HCl+, using photoion-photoion coincidence. The yields of the four pathways were found to decrease on increasing the intensity from I = 4.2 × 1013 W cm-2 to 2I = 8.5 × 1013 W cm-2, which was attributed to enhanced ionization of the dication before it can dissociate. As a function of pulse duration (and chirp), the Hn+ forming pathways were suppressed, while the HCl+ forming pathway was enhanced. To understand the excited state dynamics of the CH3Cl dication, which controls the outcome of dissociation, we obtained the total kinetic energy release distributions of the pathways and the two-dimensional coincidence momentum images and angular distributions of the fragments. We inferred that the Hn+ forming pathways originate from the dissociation of CH3Cl dications from weakly attractive metastable excited states having a long dissociation time, while for the HCl+ forming pathway, the dication dissociates from repulsive states and therefore, undergoes rapid dissociation. Finally, quantum chemical calculations have been performed to understand the intramolecular proton migration and dissociation of the CH3Cl dication along the pathways mentioned above. Our study explains the mechanism of Hn+ and HCl+ formation and confirms that intensity and pulse duration can serve as parameters to influence the excited state dynamics and hence, the outcome of the two-body dissociation of CH3Cl2+.

Strong-field ionization of polyatomic molecules: ultrafast H atom migration and bond formation in the photodissociation of CH3OH.

Strong-field ionization induces various complex phenomena like bond breaking, intramolecular hydrogen migration, and bond association in polyatomic molecules. The H-atom migration and bond formation in CH3OH induced by intense femtosecond laser pulses are investigated using a Velocity Map Imaging (VMI) spectrometer. Various laser parameters like intensity (1.5 × 1013 W cm-2-12.5 × 1013 W cm-2), pulse duration (29 fs and 195 fs), wavelength (800 nm and 1300 nm), and polarization (linear and circular) can serve as a quantum control for hydrogen migration and the yield of Hn+ (n = 1-3) ions which have been observed in this study. Further, in order to understand the ejection mechanism of the hydrogen molecular ions H2+ and H3+ from singly-ionized CH3OH, quantum chemical calculations were employed. The dissociation processes of CH3OH+ occurring by four dissociative channels to form CHO+ + H3, H3+ + CHO, CH2+ + H2O, and H2O+ + CH2 are studied. Using the combined approach of experiments and theory, we have successfully explained the mechanism of intramolecular hydrogen migration and predicted the dissociative channels of singly-ionized CH3OH.