Molecular Structure Extraction from Documents Using Deep Learning.

Chemical structure extraction from documents remains a hard problem because of both false positive identification of structures during segmentation and errors in the predicted structures. Current approaches rely on handcrafted rules and subroutines that perform reasonably well generally but still routinely encounter situations where recognition rates are not yet satisfactory and systematic improvement is challenging. Complications impacting the performance of current approaches include the diversity in visual styles used by various software to render structures, the frequent use of ad hoc annotations, and other challenges related to image quality, including resolution and noise.

Structure-specific recognition protein 1 facilitates microtubule growth and bundling required for mitosis.

Tight regulation of microtubule (MT) dynamics is essential for proper chromosome movement during mitosis. Here we show, using mammalian cells, that structure-specific recognition protein 1 (SSRP1) is a novel regulator of MT dynamics. SSRP1 colocalizes with the spindle and midbody MTs, and associates with MTs both in vitro and in vivo.

Investigating lipid interactions and the process of raft formation in cellular membranes using ToF-SIMS.

There is an increased interest in how lipids interact with each other, especially in the lateral separation of lipids into coexisting liquid phases as this is believed to be an attribute of raft formation in cell membranes. ToF-SIMS has shown itself to be an excellent tool for investigating cellular and model membrane systems and will be perhaps the most powerful one for investigating raft formation. Results from our laboratory show the capability of ToF-SIMS at identifying unequivocally the content of coexisting liquid lipid phases.

Sphingomyelin/phosphatidylcholine and cholesterol interactions studied by imaging mass spectrometry.

Label-free imaging mass spectrometry is utilized the first time to study lipid-lipid interactions in a model membrane system. Ternary lipid mixtures of cholesterol (CH), sphingomyelin (SM), and phosphatidylcholine (PC) on supported Langmuir-Blodgett films are investigated as a mimic of the cellular membrane. The unique chemical specificity and imaging capability allow identification and localization of each lipid molecule in the membranes.

Localization of sphingomyelin in cholesterol domains by imaging mass spectrometry.

The location of each lipid in a palmitoyloleoylphosphatidylcholine/18:0 sphingomyelin/cholesterol monolayer system is laterally resolved using imaging time-of-flight secondary ion mass spectrometry (TOF-SIMS) without the necessity of adding fluorescent labels. This system of coexisting immiscible liquid phases shows cholesterol domains with sizes and shapes comparable to those in the fluorescence microscopy literature. The results show that SM localizes with cholesterol and that palmitoyloleoylphosphatidylcholine is excluded.

Influence of molecular environment on the analysis of phospholipids by time-of-flight secondary ion mass spectrometry.

Understanding the influence of molecular environment on phospholipids is important in time-of-flight secondary ion mass spectrometry (TOF-SIMS) studies of complex systems such as cellular membranes. Varying the molecular environment of model membrane Langmuir-Blodgett (LB) films is shown to affect the TOF-SIMS signal of the phospholipids in the films. The molecular environment of a LB film of dipalmitoylphosphatidylcholine (DPPC) is changed by varying the film density, varying the sample substrate, and the addition of cholesterol.

Lateral heterogeneity of dipalmitoylphosphatidylethanolamine-cholesterol Langmuir-Blodgett films investigated with imaging time-of-flight secondary ion mass spectrometry and atomic force microscopy.

To better understand the influence of cholesterol (CH) on dipalmitoylphosphatidylethanolamine (DPPE), Langmuir-Blodgett (LB) model membranes of DPPE with varying amounts of cholesterol were imaged by time-of-flight secondary ion mass spectrometry (ToF-SIMS) and atomic force microscopy (AFM). Cholesterol has a condensing effect on DPPE that at low cholesterol concentrations results in lateral heterogeneity of the LB monolayer. At 4:1 DPPE/CH, islands of DPPE/CH phase exist with a connected DPPE phase.

Depth profiling of Langmuir-Blodgett films with a buckminsterfullerene probe.

Bombardment with C60+ primary ions of monolayer and multilayer barium arachidate Langmuir-Blodgett (LB) films is investigated. The behavior of cluster versus atomic (Ga+) bombardment is monitored by the barium-cationized arachidate ion (mass-to-charge ratio (m/z) 449) and a characteristic fragment ion (m/z 209) using 1-, 7-, and 15-layer model systems. The removal rate of material from the films is shown to be on the order of several hundred molecules per C60 impact, a value 100-fold larger than Ga+ impact.

Phosphatidylethanolamine-induced cholesterol domains chemically identified with mass spectrometric imaging.

Coexisting liquid phases of model membrane systems are chemically identified using imaging time-of-flight secondary ion mass spectrometry (TOF-SIMS). The systems studied were Langmuir-Blodgett (LB) model membranes of cholesterol (CH) with two different phospholipids, one a major component in the outer plasma membrane bilayer leaflet (dipalmitoylphosphatidylcholine (PC)) and the other a major component in the inner leaflet (dipalmitoylphosphatidylethanolamine (PE)). Binary mixtures of CH with each of the phospholipids were investigated, as well as a ternary system.