NeuroART: Real-Time Analysis and Targeting of Neuronal Population Activity during Calcium Imaging for Informed Closed-Loop Experiments.

Two-photon calcium imaging allows for the activity readout of large populations of neurons at single cell resolution in living organisms, yielding new insights into how the brain processes information. Holographic optogenetics allows us to trigger activity of this population directly, raising the possibility of injecting information into a living brain. Optogenetic triggering of activity that mimics "natural" information, however, requires identification of stimulation targets based on real-time analysis of the functional network.

Reproducible mass spectrometry data processing and compound annotation in MZmine 3.

Untargeted mass spectrometry (MS) experiments produce complex, multidimensional data that are practically impossible to investigate manually. For this reason, computational pipelines are needed to extract relevant information from raw spectral data and convert it into a more comprehensible format. Depending on the sample type and/or goal of the study, a variety of MS platforms can be used for such analysis.

Synthesis of silicon carbide in a matrix of graphite-like carbon prepared via carbonization of rigid-rod polyimide Langmuir-Blodgett films on silicon substrate.

Silicon carbide (SiC) is a wide-band gap semiconductor that exceeds other semiconducting materials (except diamond) in electrical, mechanical, chemical, and radiation stability. In this paper, we report a novel approach to fabrication of SiC nano films on a Si substrate, which is based on the endotaxial growth of a SiC crystalline phase in a graphite-like carbon (GLC) matrix. GLC films were formed by carbonization of rigid rod polyimide (PI) Langmuir-Blodgett (LB) films on a Si substrate at 1000 °C in vacuum.

NeuroWRAP: integrating, validating, and sharing neurodata analysis workflows.

Multiphoton calcium imaging is one of the most powerful tools in modern neuroscience. However, multiphoton data require significant pre-processing of images and post-processing of extracted signals. As a result, many algorithms and pipelines have been developed for the analysis of multiphoton data, particularly two-photon imaging data.

Memory-Efficient Searching of Gas-Chromatography Mass Spectra Accelerated by Prescreening.

The number of metabolomics studies and spectral libraries for compound annotation (i.e., assigning possible compound identities to a fragmentation spectrum) has been growing steadily in recent years.

ADAP-KDB: A Spectral Knowledgebase for Tracking and Prioritizing Unknown GC-MS Spectra in the NIH's Metabolomics Data Repository.

We report the development of a spectral knowledgebase named ADAP-KDB for tracking and prioritizing unknown gas chromatography-mass spectrometry (GC-MS) spectra in the NIH's Metabolomics Data Repository-a national and international repository for metabolomics data. ADAP-KDB consists of two parts. One part is a computational workflow that preprocesses raw mass spectrometry data and derives consensus mass spectra.

Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data.

We engineered a machine learning approach, MSHub, to enable auto-deconvolution of gas chromatography-mass spectrometry (GC-MS) data. We then designed workflows to enable the community to store, process, share, annotate, compare and perform molecular networking of GC-MS data within the Global Natural Product Social (GNPS) Molecular Networking analysis platform. MSHub/GNPS performs auto-deconvolution of compound fragmentation patterns via unsupervised non-negative matrix factorization and quantifies the reproducibility of fragmentation patterns across samples.

Metabolomics Data Preprocessing Using ADAP and MZmine 2.

The informatics pipeline for making sense of untargeted LC-MS or GC-MS data starts with preprocessing the raw data. Results from data preprocessing undergo statistical analysis and subsequently mapped to metabolic pathways for placing untargeted metabolomics data in the biological context. ADAP is a suite of computational algorithms that has been developed specifically for preprocessing LC-MS and GC-MS data.

Submucosal Tunneling Muscle Biopsy for Esophageal Motility Disorders: A Case Report.

Submucosal tunneling endoscopic technique can be useful in obtaining esophageal muscle specimens in patients with esophageal motility disorders. Here, we describe the case of a patient with systemic sclerosis. Histological verification of the esophageal involvement in the pathological process was required for the treatment.

ADAP-GC 4.0: Application of Clustering-Assisted Multivariate Curve Resolution to Spectral Deconvolution of Gas Chromatography-Mass Spectrometry Metabolomics Data.

We report a multivariate curve resolution (MCR)-based spectral deconvolution workflow for untargeted gas chromatography-mass spectrometry metabolomics. As an essential step in preprocessing such data, spectral deconvolution computationally separates ions that are in the same mass spectrum but belong to coeluting compounds that are not resolved completely by chromatography. As a result of this computational separation, spectral deconvolution produces pure fragmentation mass spectra.

Global analysis and Decay Associated Images (DAI) derived from Fluorescence Lifetime Imaging Microscopy (FLIM).

The extraction of fluorophore lifetimes in a biological sample provides useful information about the probe environment that is not readily available from fluorescence intensity alone. Cell membrane potential, pH, concentration of oxygen ([O]), calcium ([Ca]), NADH and other ions and metabolites are all regularly measured by lifetime-based techniques. These measurements provide invaluable knowledge about cell homeostasis, metabolism and communication with the cell environment.

ADAP-GC 3.2: Graphical Software Tool for Efficient Spectral Deconvolution of Gas Chromatography-High-Resolution Mass Spectrometry Metabolomics Data.

ADAP-GC is an automated computational workflow for extracting metabolite information from raw, untargeted gas chromatography-mass spectrometry metabolomics data. Deconvolution of coeluting analytes is a critical step in the workflow, and the underlying algorithm is able to extract fragmentation mass spectra of coeluting analytes with high accuracy. However, its latest version ADAP-GC 3.

Multiscale BerEp4 molecular imaging of microtumor phantoms: toward theranostics for basal cell carcinoma.

Basal cell carcinoma (BCC), the most common cancer in humans, appears macroscopically and microscopically similar to many other skin lesions, which makes differential diagnosis difficult. We are developing an approach for quantitative molecular imaging of BerEP4, a transmembrane biomarker for BCC, with the goal of increasing the precision and accuracy of diagnosis. This pilot study was conducted to assess the affinity and selectivity of BerEp4 antibody and assess its possible use in designing theranostic probes for BCC.

Compact non-contact total emission detection for in vivo multiphoton excitation microscopy.

We describe a compact, non-contact design for a total emission detection (c-TED) system for intra-vital multiphoton imaging. To conform to a standard upright two-photon microscope design, this system uses a parabolic mirror surrounding a standard microscope objective in concert with an optical path that does not interfere with normal microscope operation. The non-contact design of this device allows for maximal light collection without disrupting the physiology of the specimen being examined.

Nanostructures formed by displacement of porous silicon with copper: from nanoparticles to porous membranes.

The application of porous silicon as a template for the fabrication of nanosized copper objects is reported. Three different types of nanostructures were formed by displacement deposition of copper on porous silicon from hydrofluoric acid-based solutions of copper sulphate: (1) copper nanoparticles, (2) quasi-continuous copper films, and (3) free porous copper membranes. Managing the parameters of porous silicon (pore sizes, porosity), deposition time, and wettability of the copper sulphate solution has allowed to achieve such variety of the copper structures.

In vivo fluorescence lifetime imaging monitors binding of specific probes to cancer biomarkers.

One of the most important factors in choosing a treatment strategy for cancer is characterization of biomarkers in cancer cells. Particularly, recent advances in Monoclonal Antibodies (MAB) as primary-specific drugs targeting tumor receptors show that their efficacy depends strongly on characterization of tumor biomarkers. Assessment of their status in individual patients would facilitate selection of an optimal treatment strategy, and the continuous monitoring of those biomarkers and their binding process to the therapy would provide a means for early evaluation of the efficacy of therapeutic intervention.

Conformational heterogeneity and quasi-static self-quenching in DNA containing a fluorescent guanine analogue, 3MI or 6MI.

Two different microenvironments in the DNA sequence 5'-act aGa gat ccc tca gac cct ttt agt cag tGt gga-3' (in both single- and double-stranded forms) are explored using two similar fluorescent nucleoside analogues, 3MI and 6MI. Each probe was evaluated in two environments, one strand with the probe flanked by thymines (PTRT) and the other by adenines (PTRA) with positions indicated by G's in the sequence. Both time-resolved anisotropies and lifetimes of the probes depend upon local interactions, and these are altered by duplex formation.

Optimization of multiphoton excitation microscopy by total emission detection using a parabolic light reflector.

We have constructed a device that maximizes the probability of collecting all of the scattered and ballistic light isotropically generated at the focal spot of multiphoton excited emissions (MPE) to optimize the signal-to-noise ratio (SNR) for micro-imaging. This was accomplished by optically coupling a parabolic reflector (that surrounds the sample and top of the objective) to a pair of collimating lenses (above the sample) that redirects emitted light to a separate detector. These additional optics, combined with the objective, allow the total emission detection (TED) condition to be approached.

Quantitative detection of the ligand-dependent interaction between the androgen receptor and the co-activator, Tif2, in live cells using two color, two photon fluorescence cross-correlation spectroscopy.

Two-photon, two-color fluorescence cross-correlation spectroscopy (TPTCFCCS) was used to directly detect ligand-dependent interaction between an eCFP-fusion of the androgen receptor (eCFP-AR) and an eYFP fusion of the nuclear receptor co-activator, Tif2 (eYFP-Tif2) in live cells. As expected, these two proteins were co-localized in the nucleus in the presence of ligand. Analysis of the cross-correlation amplitude revealed that AR was on average 81% bound to Tif2 in the presence of agonist, whereas the fractional complex formation decreased to 56% in the presence of antagonist.

Combined spectral karyotyping, comparative genomic hybridization, and in vitro apoptyping of a panel of Burkitt's lymphoma-derived B cell lines reveals an unexpected complexity of chromosomal aberrations and a recurrence of specific abnormalities in chemoresistant cell lines.

The comprehensive cytogenetic profiles of a panel of 10 Burkitt's lymphoma (BL)-derived B cell lines, designated Akata, BL-28, BL-41, Daudi, DG-75, Mutu I, Mutu III, Namalwa, Rael, and Ramos, respectively, are reported herein. The unique origin of each cell line was established using multiplex quantitative fluorescence polymerase chain reaction (QF-PCR). Spectral karyotyping (SKY) revealed a large number of structural and numerical chromosomal aberrations, many of which had not been previously identified or resolved by conventional G-banding techniques.

Betulinic acid, a natural cytotoxic agent, fails to trigger apoptosis in human Burkitt's lymphoma-derived B-cell lines.

Betulinic acid (BA), a pentacyclic triterpene of natural origin, effectively induces apoptosis in neuroectodermal tumors and was recently shown to be a potent trigger of cell death in human leukemia-derived cell lines. To explore the potential of BA in the treatment of hematologic malignancies, we tested a panel of 10 Burkitt's lymphoma (BL)-derived B-cell lines for sensitivity to BA. The human Jurkat T leukemia cell line was included as a positive control.

Watching a protein as it functions with 150-ps time-resolved x-ray crystallography.

We report picosecond time-resolved x-ray diffraction from the myoglobin (Mb) mutant in which Leu29 is replaced by Phe (L29Fmutant). The frame-by-frame structural evolution, resolved to 1.8 angstroms, allows one to literally "watch" the protein as it executes its function.