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Analytical Chemistry Jun 2017The ability to localize phosphosites to specific amino acid residues is crucial to translating phosphoproteomic data into biological meaningful contexts. In a companion...
The ability to localize phosphosites to specific amino acid residues is crucial to translating phosphoproteomic data into biological meaningful contexts. In a companion manuscript ( Anal. Chem. 2017 , DOI: 10.1021/acs.analchem.7b00213 ), we described a new implementation of activated ion electron transfer dissociation (AI-ETD) on a quadrupole-Orbitrap-linear ion trap hybrid MS system (Orbitrap Fusion Lumos), which greatly improved peptide fragmentation and identification over ETD and other supplemental activation methods. Here we present the performance of AI-ETD for identifying and localizing sites of phosphorylation in both phosphopeptides and intact phosphoproteins. Using 90 min analyses we show that AI-ETD can identify 24,503 localized phosphopeptide spectral matches enriched from mouse brain lysates, which more than triples identifications from standard ETD experiments and outperforms ETcaD and EThcD as well. AI-ETD achieves these gains through improved quality of fragmentation and MS/MS success rates for all precursor charge states, especially for doubly protonated species. We also evaluate the degree to which phosphate neutral loss occurs from phosphopeptide product ions due to the infrared photoactivation of AI-ETD and show that modifying phosphoRS (a phosphosite localization algorithm) to include phosphate neutral losses can significantly improve localization in AI-ETD spectra. Finally, we demonstrate the utility of AI-ETD in localizing phosphosites in α-casein, an ∼23.5 kDa phosphoprotein that showed eight of nine known phosphorylation sites occupied upon intact mass analysis. AI-ETD provided the greatest sequence coverage for all five charge states investigated and was the only fragmentation method to localize all eight phosphosites for each precursor. Overall, this work highlights the analytical value AI-ETD can bring to both bottom-up and top-down phosphoproteomics.
Topics: Animals; Brain; Chromatography, Liquid; Electron Transport; Ions; Mice; Phosphopeptides; Phosphoproteins; Phosphorylation; Proteomics; Tandem Mass Spectrometry
PubMed: 28383256
DOI: 10.1021/acs.analchem.7b00212 -
Wellcome Open Research 2022Single-molecule localisation microscopy (SMLM) uses software to extract super-resolved positions from microscope images of fluorescent molecules. These localisations can...
Single-molecule localisation microscopy (SMLM) uses software to extract super-resolved positions from microscope images of fluorescent molecules. These localisations can then be used to render super-resolution images or analysed to extract information about molecular behaviour. The GDSC SMLM software provides a set of tools for analysing SMLM data in a single cross-platform environment. The software identifies fluorescent molecules in raw microscope images and localises their positions using stages of spot detection, spot fitting and spot rejection. The resulting localisation data set can then be visualised, cropped and filtered. A suite of downstream analysis tools enable the user to perform single-particle tracking, cluster analysis and drift correction. In addition, GDSC SMLM also provides utility tools that enable modelling of EM-CCD and sCMOS cameras as well as point spread functions (PSFs) for data simulation. The software is written in Java and runs as a collection of plugins for the ImageJ software.
PubMed: 37351368
DOI: 10.12688/wellcomeopenres.18327.1 -
The Journal of the Acoustical Society... Apr 2017If an auditory scene consists of many spatially separated sound sources, how many sound sources can be processed by the auditory system? Experiment I determined how many...
If an auditory scene consists of many spatially separated sound sources, how many sound sources can be processed by the auditory system? Experiment I determined how many speech sources could be localized simultaneously on the azimuth plane. Different words were played from multiple loudspeakers, and listeners reported the total number of sound sources and their individual locations. In experiment II the accuracy of localizing one speech source in a mixture of multiple speech sources was determined. An extra sound source was added to an existing set of sound sources, and the task was to localize that extra source. In experiment III the setup and task were the same as in experiment I, except that the sounds were tones. The results showed that the maximum number of sound sources that listeners could perceive was limited to approximately four spatially separated speech signals and three for tonal signals. The localization errors increased along with the increase of total number of sound sources. When four or more speech sources already existed, the accuracy in localizing an additional source was near chance.
Topics: Acoustic Stimulation; Audiometry, Speech; Auditory Threshold; Environment; Environmental Exposure; Female; Humans; Male; Noise; Perceptual Masking; Signal Detection, Psychological; Sound Localization; Speech Perception
PubMed: 28464690
DOI: 10.1121/1.4981118 -
Scientific Reports Mar 2021Magnetic localizers have been widely investigated in the biomedical field, especially for intra-body applications, because they don't require a free line-of-sight...
Magnetic localizers have been widely investigated in the biomedical field, especially for intra-body applications, because they don't require a free line-of-sight between the implanted magnets and the magnetic field sensors. However, while researchers have focused on narrow and specific aspects of the localization problem, no one has comprehensively searched for general design rules for accurately localizing multiple magnetic objectives. In this study, we sought to systematically analyse the effects of remanent magnetization, number of sensors, and geometrical configuration (i.e. distance among magnets-L-and between magnets and sensors-L) on the accuracy of the localizer in order to unveil the basic principles of the localization problem. Specifically, through simulations validated with a physical system, we observed that the accuracy of the localization was mainly affected by a specific angle ([Formula: see text] = tan(L / L)), descriptive of the system geometry. In particular, while tracking nine magnets, errors below ~ 1 mm (10% of the length of the simulated trajectory) and around 9° were obtained if θ ≥ ~ 31°. The latter proved a general rule across all tested conditions, also when the number of magnets was doubled. Our results are interesting for a whole range of biomedical engineering applications exploiting multiple-magnets tracking, such as human-machine interfaces, capsule endoscopy, ventriculostomy interventions, and endovascular catheter navigation.
PubMed: 33649463
DOI: 10.1038/s41598-021-84390-8 -
The New Phytologist Sep 2020Morphogenesis and adaptive tropic growth in plants depend on gradients of the phytohormone auxin, mediated by the membrane-based PIN-FORMED (PIN) auxin transporters....
Morphogenesis and adaptive tropic growth in plants depend on gradients of the phytohormone auxin, mediated by the membrane-based PIN-FORMED (PIN) auxin transporters. PINs localize to a particular side of the plasma membrane (PM) or to the endoplasmic reticulum (ER) to directionally transport auxin and maintain intercellular and intracellular auxin homeostasis, respectively. However, the molecular cues that confer their diverse cellular localizations remain largely unknown. In this study, we systematically swapped the domains between ER- and PM-localized PIN proteins, as well as between apical and basal PM-localized PINs from Arabidopsis thaliana, to shed light on why PIN family members with similar topological structures reside at different membrane compartments within cells. Our results show that not only do the N- and C-terminal transmembrane domains (TMDs) and central hydrophilic loop contribute to their differential subcellular localizations and cellular polarity, but that the pairwise-matched N- and C-terminal TMDs resulting from intramolecular domain-domain coevolution are also crucial for their divergent patterns of localization. These findings illustrate the complexity of the evolutionary path of PIN proteins in acquiring their plethora of developmental functions and adaptive growth in plants.
Topics: Arabidopsis; Arabidopsis Proteins; Biological Transport; Indoleacetic Acids; Membrane Transport Proteins; Plant Growth Regulators
PubMed: 32350870
DOI: 10.1111/nph.16629 -
Frontiers in Neurology 2021Conventional EEG-fMRI methods have been proven to be of limited use in the sense that they cannot reveal the information existing in between the spikes. To resolve this...
Conventional EEG-fMRI methods have been proven to be of limited use in the sense that they cannot reveal the information existing in between the spikes. To resolve this issue, the current study obtains the epileptic components time series detected on EEG and uses them to fit the Generalized Linear Model (GLM), as a substitution for classical regressors. This approach allows for a more precise localization, and equally importantly, the prediction of the future behavior of the epileptic generators. The proposed method approaches the localization process in the component domain, rather than the electrode domain (EEG), and localizes the generators through investigating the spatial correlation between the candidate components and the spike template, as well as the medical records of the patient. To evaluate the contribution of EEG-fMRI and concordance between fMRI and EEG, this method was applied on the data of 30 patients with refractory epilepsy. The results demonstrated the significant numbers of 29 and 24 for concordance and contribution, respectively, which mark improvement as compared to the existing literature. This study also shows that while conventional methods often fail to properly localize the epileptogenic zones in deep brain structures, the proposed method can be of particular use. For further evaluation, the concordance level between IED-related BOLD clusters and Seizure Onset Zone (SOZ) has been quantitatively investigated by measuring the distance between IED/SOZ locations and the BOLD clusters in all patients. The results showed the superiority of the proposed method in delineating the spike-generating network compared to conventional EEG-fMRI approaches. In all, the proposed method goes beyond the conventional methods by breaking the dependency on spikes and using the outside-the-scanner spike templates and the selected components, achieving an accuracy of 97%. Doing so, this method contributes to improving the yield of EEG-fMRI and creates a more realistic perception of the neural behavior of epileptic generators which is almost without precedent in the literature.
PubMed: 34867704
DOI: 10.3389/fneur.2021.695997 -
NeuroImage Aug 2021Functional localizers are invaluable as they can help define regions of interest, provide cross-study comparisons, and most importantly, allow for the aggregation and...
Functional localizers are invaluable as they can help define regions of interest, provide cross-study comparisons, and most importantly, allow for the aggregation and meta-analyses of data across studies and laboratories. To achieve these goals within the non-human primate (NHP) imaging community, there is a pressing need for the use of standardized and validated localizers that can be readily implemented across different groups. The goal of this paper is to provide an overview of the value of localizer protocols to imaging research and we describe a number of commonly used or novel localizers within NHPs, and keys to implement them across studies. As has been shown with the aggregation of resting-state imaging data in the original PRIME-DE submissions, we believe that the field is ready to apply the same initiative for task-based functional localizers in NHP imaging. By coming together to collect large datasets across research group, implementing the same functional localizers, and sharing the localizers and data via PRIME-DE, it is now possible to fully test their robustness, selectivity and specificity. To do this, we reviewed a number of common localizers and we created a repository of well-established localizer that are easily accessible and implemented through the PRIME-RE platform.
Topics: Animals; Behavior, Animal; Brain Mapping; Magnetic Resonance Imaging; Mental Processes; Multicenter Studies as Topic; Neurosciences; Primates; Sensorimotor Cortex
PubMed: 34048898
DOI: 10.1016/j.neuroimage.2021.118203 -
Cureus Jul 2021Image-guidance for frame-based stereotaxis is facilitated by incorporating three to four N-localizers or Sturm-Pastyr localizers into a stereotactic frame. An extant...
Image-guidance for frame-based stereotaxis is facilitated by incorporating three to four N-localizers or Sturm-Pastyr localizers into a stereotactic frame. An extant frame that incorporates only two N-localizers violates the fundamental principle of the N-localizer, which requires three non-colinear points to define a plane in three-dimensional space. Hence, this two N-localizer configuration is susceptible to error. The present article proposes the V-localizer that comprises multiple diagonal bars to provide four or more non-colinear points to minimize error.
PubMed: 34327109
DOI: 10.7759/cureus.16535 -
Seizure Nov 2021To study the accuracy of automated interictal EEG source localisation based on high-density EEG, and to compare it to low-density EEG.
PURPOSE
To study the accuracy of automated interictal EEG source localisation based on high-density EEG, and to compare it to low-density EEG.
METHODS
Thirty patients operated for pharmacoresistant focal epilepsy were retrospectively examined. Twelve months after resective brain surgery, 18 were seizure-free or had 'auras' only, while 12 had persistence of disabling seizures. Presurgical 257-channel EEG lasting 3-20 h was down-sampled to 25, 40, and 204 channels for separate analyses. For each electrode setup, interictal spikes were detected, clustered, and averaged automatically before validation by an expert reviewer. An individual 6-layer finite difference head model and the standardised low-resolution electromagnetic tomography were used to localise the maximum source activity of the most prevalent spike. Sublobar concordance with the resected brain area was visually assessed and related to favourable vs. unfavourable postsurgical outcome.
RESULTS
Depending on the EEG setup, epileptic spikes were detected in 21-24 patients (70-80%). The median number of single spikes per average was 470 (range 17-15,066). Diagnostic sensitivity of EEG source localisation was 58-75%, specificity was 50-67%, and overall accuracy was 55-71%. There were no significant differences between low- and high-density EEG setups with 25 to 257 electrodes.
CONCLUSION
Automated high-density EEG source localisation provides meaningful information in the majority of cases. With hundreds of single spikes averaged, diagnostic accuracy is similar in high- and low-density EEG. Therefore, low-density EEG may be sufficient for interictal EEG source localisation if high numbers of spikes are available.
Topics: Brain Mapping; Electroencephalography; Epilepsies, Partial; Humans; Magnetic Resonance Imaging; Retrospective Studies; Seizures
PubMed: 34626920
DOI: 10.1016/j.seizure.2021.09.020 -
Insights Into Imaging Feb 2020Gastrointestinal tract (GIT) perforation is a common medical emergency associated with considerable mortality, ranging from 30 to 50%. Clinical presentation varies:...
Gastrointestinal tract (GIT) perforation is a common medical emergency associated with considerable mortality, ranging from 30 to 50%. Clinical presentation varies: oesophageal perforations can present with acute chest pain, odynophagia and vomiting, gastroduodenal perforations with acute severe abdominal pain, while colonic perforations tend to follow a slower progression course with secondary bacterial peritonitis or localised abscesses. A subset of patients may present with delayed symptoms, abscess mimicking an abdominal mass, or with sepsis.Direct multidetector computed tomography (MDCT) findings support the diagnosis and localise the perforation site while ancillary findings may suggest underlying conditions that need further investigation following primary repair of ruptured bowel. MDCT findings include extraluminal gas, visible bowel wall discontinuity, extraluminal contrast, bowel wall thickening, abnormal mural enhancement, localised fat stranding and/or free fluid, as well as localised phlegmon or abscess in contained perforations.The purpose of this article is to review the spectrum of MDCT findings encountered in GIT perforation and emphasise the MDCT and clinical clues suggestive of the underlying aetiology and localisation of perforation site.
PubMed: 32086627
DOI: 10.1186/s13244-019-0823-6